@article {70297, title = {Nanoscale imaging of expanded cells and proteins with spontaneously blinking dyes}, journal = {bioRxiv}, year = {2026}, month = {2026 Feb 23}, abstract = {

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

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

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

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

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

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

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

}, doi = {10.64898/2026.03.22.713468}, url = {https://www.biorxiv.org/content/early/2026/03/22/2026.03.22.713468}, author = {Payne, Anja and Heinz, Daniel A. and Santiago, Chiaki and Hagopian, Lara L. and Ganasi, Rolando Sceptre and Quirk, Clare and Hartzell, Andrea L. and Leutgeb, Jill K. and Leutgeb, Stefan and Bloodgood, Brenda L.} } @article {70170, title = {NanoBlocks: creating fluorescent biosensors from affinity binders using competitive binding}, journal = {bioRxiv}, year = {2025}, month = {2025 October 28}, abstract = {

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

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

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

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

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

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

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

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

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

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

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

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

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

}, doi = {10.1101/2025.02.04.636286}, url = {https://www.biorxiv.org/content/early/2025/02/06/2025.02.04.636286}, author = {Lakunina, Anna and Socha, Karolina Z and Ladd, Alexander and Bowen, Anna J and Chen, Susu and Colonell, Jennifer and Doshi, Anjal and Karsh, Bill and Krumin, Michael and Kulik, Pavel and Li, Anna and Neutens, Pieter and O{\textquoteright}Callaghan, John and Olsen, Meghan and Putzeys, Jan and Tilmans, Harrie AC and Ye, Zhiwen and Welkenhuysen, Marleen and H{\"a}usser, Michael and Koch, Christof and Ting, Jonathan T. and Neuropixels Opto Consortium and Dutta, Barun and Harris, Timothy D and Steinmetz, Nicholas A and Svoboda, Karel and Siegle, Joshua H and Carandini, Matteo} } @article {69559, title = {Nanoscale volumetric fluorescence imaging via photochemical sectioning}, journal = {bioRxiv}, year = {2024}, month = {2024 Aug 05}, abstract = {

Optical nanoscopy of intact biological specimens has been transformed by recent advancements in hydrogel-based tissue clearing and expansion, enabling the imaging of cellular and subcellular structures with molecular contrast. However, existing high-resolution fluorescence microscopes have limited imaging depth, which prevents the study of whole-mount specimens without physical sectioning. To address this challenge, we developed {\textquotedblleft}photochemical sectioning,{\textquotedblright} a spatially precise, light-based sample sectioning process. By combining photochemical sectioning with volumetric lattice light-sheet imaging and petabyte-scale computation, we imaged and reconstructed axons and myelination sheaths across entire mouse olfactory bulbs at nanoscale resolution. An olfactory-bulb-wide analysis of myelinated and unmyelinated axons revealed distinctive patterns of axon degeneration and de-/dysmyelination in the neurodegenerative mouse, highlighting the potential for peta- to exabyte-scale super-resolution studies using this approach.

}, doi = {10.1101/2024.08.01.605857}, url = {https://doi.org/10.1101/2024.08.01.605857}, author = {Wang, Wei and Ruan, Xiongtao and Liu, Gaoxiang and Milkie, Daniel E. and Li, Wenping and Betzig, Eric and Upadhyayula, Srigokul and Gao, Ruixuan} } @article {69511, title = {Near-infrared nanosensors enable optical imaging of oxytocin with selectivity over vasopressin in acute mouse brain slices.}, journal = {Proc Natl Acad Sci U S A}, volume = {121}, year = {2024}, month = {2024 Jun 25}, pages = {e2314795121}, abstract = {

Oxytocin plays a critical role in regulating social behaviors, yet our understanding of its function in both neurological health and disease remains incomplete. Real-time oxytocin imaging probes with spatiotemporal resolution relevant to its endogenous signaling are required to fully elucidate oxytocin{\textquoteright}s role in the brain. Herein, we describe a near-infrared oxytocin nanosensor (nIROXT), a synthetic probe capable of imaging oxytocin in the brain without interference from its structural analogue, vasopressin. nIROXT leverages the inherent tissue-transparent fluorescence of single-walled carbon nanotubes (SWCNT) and the molecular recognition capacity of an oxytocin receptor peptide fragment to selectively and reversibly image oxytocin. We employ these nanosensors to monitor electrically stimulated oxytocin release in brain tissue, revealing oxytocin release sites with a median size of 3 {\textmu}m in the paraventricular nucleus of C57BL/6 mice, which putatively represents the spatial diffusion of oxytocin from its point of release. These data demonstrate that covalent SWCNT constructs, such as nIROXT, are powerful optical tools that can be leveraged to measure neuropeptide release in brain tissue.

}, keywords = {Animals, Brain, Male, Mice, Mice, Inbred C57BL, Nanotubes, Carbon, Optical Imaging, Oxytocin, Receptors, Oxytocin, Spectroscopy, Near-Infrared, Vasopressins}, issn = {1091-6490}, doi = {10.1073/pnas.2314795121}, author = {Mun, Jaewan and Navarro, Nicole and Jeong, Sanghwa and Ouassil, Nicholas and Leem, Esther and Beyene, Abraham G and Landry, Markita P} } @article {69510, title = {Neocortical inhibitory imbalance predicts successful sensory detection.}, journal = {Cell Rep}, volume = {43}, year = {2024}, month = {2024 Jun 20}, pages = {114233}, abstract = {

Perceptual success depends on fast-spiking, parvalbumin-positive interneurons (FS/PVs). However, competing theories of optimal rate and correlation in pyramidal (PYR) firing make opposing predictions regarding the underlying FS/PV dynamics. We addressed this with population calcium imaging of FS/PVs and putative PYR neurons during threshold detection. In primary somatosensory and visual neocortex, a distinct PYR subset shows increased rate and spike-count correlations on detected trials ("hits"), while most show no rate change and decreased correlations. A larger fraction of FS/PVs predicts hits with either rate increases or decreases. Using computational modeling, we found that inhibitory imbalance, created by excitatory "feedback" and interactions between FS/PV pools, can account for the data. Rate-decreasing FS/PVs increase rate and correlation in a PYR subset, while rate-increasing FS/PVs reduce correlations and offset enhanced excitation in PYR neurons. These findings indicate that selection of informative PYR ensembles, through transient inhibitory imbalance, is a common motif of optimal neocortical processing.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2024.114233}, author = {Deister, Christopher A and Moore, Alexander I and Voigts, Jakob and Bechek, Sophia and Lichtin, Rebecca and Brown, Tyler C and Moore, Christopher I} } @article {69008, title = {Nested neural circuits generate distinct acoustic signals during Drosophila courtship}, journal = {Current Biology}, volume = {34}, year = {2024}, month = {2024 Feb 26}, pages = {808-24}, abstract = {

Many motor control systems generate multiple movements using a common set of muscles. How are premotor circuits able to flexibly generate diverse movement patterns? Here, we characterize the neuronal circuits that drive the distinct courtship songs of\ Drosophila melanogaster. Male flies vibrate their wings towards females to produce two different song modes {\textendash} pulse and sine song {\textendash} which signal species identity and male quality. Using cell-type specific genetic reagents and the connectome, we provide a cellular and synaptic map of the circuits in the male ventral nerve cord that generate these songs and examine how activating or inhibiting each cell type within these circuits affects the song. Our data reveal that the song circuit is organized into two nested feed-forward pathways, with extensive reciprocal and feed-back connections. The larger network produces pulse song, the more complex and ancestral song form. A subset of this network produces sine song, the simpler and more recent form. Such nested organization may be a common feature of motor control circuits in which evolution has layered increasing flexibility on to a basic movement pattern.

}, doi = {10.1016/j.cub.2024.01.015}, url = {https://doi.org/10.1016/j.cub.2024.01.015}, author = {Joshua L. Lillvis and Kaiyu Wang and Hiroshi M. Shiozaki and Min Xu and David L. Stern and Barry J. Dickson} } @article {68921, title = {Network statistics of the whole-brain connectome of Drosophila}, journal = {Nature}, volume = {634}, year = {2024}, month = {2024 Oct 02}, pages = {153{\textendash}165}, abstract = {

Brains comprise complex networks of neurons and connections, similar to the nodes and edges of artificial networks. Network analysis applied to the wiring diagrams of brains can offer insights into how they support computations and regulate the flow of\ information underlying perception and behaviour. The completion of the first whole-brain connectome of an adult fly, containing over 130,000 neurons and millions of synaptic connections, offers an opportunity to analyse the statistical properties and topological features of a complete brain. Here we computed the prevalence of two- and three-node motifs, examined their strengths, related this information to both neurotransmitter composition and cell type annotations, and compared these metrics with wiring diagrams of other animals. We found that the network of the fly brain displays rich-club organization, with a large population (30\% of the connectome) of highly connected neurons. We identified subsets of rich-club neurons that may serve as integrators or broadcasters of signals. Finally, we examined subnetworks based on 78 anatomically defined brain regions or neuropils. These data products are shared within the FlyWire Codex (https://codex.flywire.ai) and should serve as a foundation for models and experiments exploring the relationship between neural activity and anatomical structure.

}, doi = {10.1038/s41586-024-07968-y}, url = {https://doi.org/10.1038/s41586-024-07968-y}, author = {Albert Lin and Runzhe Yang and Sven Dorkenwald and Arie Matsliah and Amy R. Sterling and Philipp Schlegel and Szi-chieh Yu and Claire E. McKellar and Marta Costa and Katharina Eichler and Alexander Shakeel Bates and Nils Eckstein and Jan Funke and Gregory S.X.E. Jefferis and Mala Murthy} } @article {68710, title = {A neural basis of choking under pressure}, journal = {Neuron}, year = {2024}, month = {2024 Sep 07}, abstract = {

Incentives tend to drive improvements in performance. But when incentives get too high, we can "choke under pressure" and underperform right when it matters most. What neural processes might lead to choking under pressure? We studied rhesus monkeys performing a challenging reaching task in which they underperformed when an unusually large "jackpot" reward was at stake, and we sought a neural mechanism that might result in that underperformance. We found that increases in reward drive neural activity during movement preparation into, and then past, a zone of optimal performance. We conclude that neural signals of reward and motor preparation interact in the motor cortex (MC) in a manner that can explain why we choke under pressure.

}, doi = {10.1016/j.neuron.2024.08.012}, url = {https://doi.org/10.1016/j.neuron.2024.08.012}, author = {Adam L. Smoulder and Patrick J. Marino and Emily R. Oby and Sam E. Snyder and Hiroo Miyata and Nick P. Pavlovsky and William E. Bishop and Byron M. Yu and Steven M. Chase and Aaron P. Batista} } @article {69172, title = {A neural circuit architecture for rapid learning in goal-directed navigation}, journal = {Neuron}, volume = {112}, year = {2024}, month = {2024 May 23}, pages = {2581-2599.e23}, abstract = {

Anchoring goals to spatial representations enables flexible navigation but is challenging in novel environments when both representations must be acquired simultaneously. We propose a framework for how Drosophila uses internal representations of head direction (HD) to build goal representations upon selective thermal reinforcement. We show that flies use stochastically generated fixations and directed saccades to express heading preferences in an operant visual learning paradigm and that HD neurons are required to modify these preferences based on reinforcement. We used a symmetric visual setting to expose how flies{\textquoteright} HD and goal representations co-evolve and how the reliability of these interacting representations impacts behavior. Finally, we describe how rapid learning of new goal headings may rest on a behavioral policy whose parameters are flexible but whose form is genetically encoded in circuit architecture. Such evolutionarily structured architectures, which enable rapidly adaptive behavior driven by internal representations, may be relevant across species.

}, doi = {https://doi.org/10.1016/j.neuron.2024.04.036}, url = {https://doi.org/10.1016/j.neuron.2024.04.036}, author = {Chuntao Dan and Brad K. Hulse and Ramya Kappagantula and Vivek Jayaraman and Ann M. Hermundstad} } @article {69542, title = {Neural circuit basis of placebo pain relief.}, journal = {Nature}, year = {2024}, month = {2024 Jul 24}, abstract = {

Placebo effects are striking demonstrations of mind-body interactions . During pain perception, in the absence of any treatment, an expectation of pain relief can reduce the experience of pain, a phenomenon known as placebo analgesia . However, despite the strength of placebo effects and their impact on everyday human experience and failure of clinical trials for new therapeutics , the neural circuit basis of placebo effects has remained elusive. Here, we show that analgesia from the expectation of pain relief is mediated by rostral anterior cingulate cortex (rACC) neurons that project to the pontine nucleus (rACC{\textrightarrow}Pn), a pre-cerebellar nucleus with no established function in pain. We created a behavioral assay that generates placebo-like anticipatory pain relief in mice. In vivo calcium imaging of neural activity and electrophysiological recordings in brain slices showed that expectations of pain relief boost the activity of rACC{\textrightarrow}Pn neurons and potentiate neurotransmission in this pathway. Transcriptomic studies of Pn neurons revealed an abundance of opioid receptors, further suggesting a role in pain modulation. Inhibition of the rACC{\textrightarrow}Pn pathway disrupted placebo analgesia and decreased pain thresholds, whereas activation elicited analgesia in the absence of placebo conditioning. Finally, Purkinje cells exhibited activity patterns resembling those of rACC{\textrightarrow}Pn neurons during pain relief expectation, providing cellular-level evidence of a role for the cerebellum in cognitive pain modulation. These findings open the possibility of targeting this prefrontal cortico-ponto-cerebellar pathway with drugs or neurostimulation to treat pain.

}, issn = {1476-4687}, doi = {10.1038/s41586-024-07816-z}, author = {Chen, Chong and Niehaus, Jesse K and Dinc, Fatih and Huang, Karen L and Barnette, Alexander L and Tassou, Adrien and Shuster, S Andrew and Wang, Lihua and Lemire, Andrew and Menon, Vilas and Ritola, Kimberly and Hantman, Adam and Zeng, Hongkui and Schnitzer, Mark J and Scherrer, Gr{\'e}gory} } @article {69438, title = {Neural Control of Naturalistic Behavior Choices}, journal = {Annu Rev Neurosci}, year = {2024}, month = {2024 May 09}, abstract = {

In the natural world, animals make decisions on an ongoing basis, continuously selecting which action to undertake next. In the lab, however, the neural bases of decision processes have mostly been studied using artificial trial structures. New experimental tools based on the genetic toolkit of model organisms now make it experimentally feasible to monitor and manipulate neural activity in small subsets of neurons during naturalistic behaviors. We thus propose a new approach to investigating decision processes, termed reverse neuroethology. In this approach, experimenters select animal models based on experimental accessibility and then utilize cutting-edge tools such as connectomes and genetically encoded reagents to analyze the flow of information through an animal{\textquoteright}s nervous system during naturalistic choice behaviors. We describe how the reverse neuroethology strategy has been applied to understand the neural underpinnings of innate, rapid decision making, with a focus on defensive behavioral choices in the vinegar fly Drosophila melanogaster.

}, issn = {1545-4126}, doi = {10.1146/annurev-neuro-111020-094019}, author = {Asinof, Samuel K and Card, Gwyneth M} } @article {69045, title = {Neural-circuit basis of song preference learning in fruit flies}, journal = {iScience}, volume = {27}, year = {2024}, month = {2024 Jul 19}, abstract = {

As observed in human language learning and song learning in birds, the fruit fly Drosophila melanogaster changes its auditory behaviors according to prior sound experiences. This phenomenon, known as song preference learning in flies, requires GABAergic input to pC1 neurons in the brain, with these neurons playing a key role in mating behavior. The neural circuit basis of this GABAergic input, however, is not known. Here, we find that GABAergic neurons expressing the sex-determination gene doublesex are necessary for song preference learning. In the brain, only four doublesex-expressing GABAergic neurons exist per hemibrain, identified as pCd-2 neurons. pCd-2 neurons directly, and in many cases mutually, connect with pC1 neurons, suggesting the existence of reciprocal circuits between them. Moreover, GABAergic and dopaminergic inputs to doublesex-expressing GABAergic neurons are necessary for song preference learning. Together, this study provides a neural circuit model that underlies experience-dependent auditory plasticity at a single-cell resolution.

}, doi = {10.1016/j.isci.2024.110266}, url = {https://doi.org/10.1016/j.isci.2024.110266}, author = {Keisuke Imoto and Yuki Ishikawa and Yoshinori Aso and Jan Funke and Ryoya Tanaka and Azusa Kamikouchi} } @article {68889, title = {Neuronal wiring diagram of an adult brain.}, journal = {Nature}, volume = {634}, year = {2024}, month = {2024 Oct 02}, pages = {124-138}, abstract = {

Connections between neurons can be mapped by acquiring and analysing electron microscopic brain images. In recent years, this approach has been applied to chunks of brains to reconstruct local connectivity maps that are highly informative, but nevertheless inadequate for understanding brain function more globally. Here we present a neuronal wiring diagram of a whole brain containing 5 {\texttimes} 107 chemical synapses between 139,255 neurons reconstructed from an adult female Drosophila melanogaster. The resource also incorporates annotations of cell classes and types, nerves, hemilineages and predictions of neurotransmitter identities. Data products are available for download, programmatic access and interactive browsing and have been made interoperable with other fly data resources. We derive a projectome-a map of projections between regions-from the connectome and report on tracing of synaptic pathways and the analysis of information flow from inputs (sensory and ascending neurons) to outputs (motor, endocrine and descending neurons) across both hemispheres and between the central brain and the optic lobes. Tracing from a subset of photoreceptors to descending motor pathways illustrates how structure can uncover putative circuit mechanisms underlying sensorimotor behaviours. The technologies and open ecosystem reported here set the stage for future large-scale connectome projects in other species.

}, doi = {10.1038/s41586-024-07558-y}, url = {https://doi.org/10.1038/s41586-024-07558-y}, author = {Dorkenwald, Sven and Matsliah, Arie and Sterling, Amy R and Schlegel, Philipp and Yu, Szi-Chieh and McKellar, Claire E and Lin, Albert and Costa, Marta and Eichler, Katharina and Yin, Yijie and Silversmith, Will and Schneider-Mizell, Casey and Jordan, Chris S and Brittain, Derrick and Halageri, Akhilesh and Kuehner, Kai and Ogedengbe, Oluwaseun and Morey, Ryan and Gager, Jay and Kruk, Krzysztof and Perlman, Eric and Yang, Runzhe and Deutsch, David and Bland, Doug and Sorek, Marissa and Lu, Ran and Macrina, Thomas and Lee, Kisuk and Bae, J Alexander and Mu, Shang and Nehoran, Barak and Mitchell, Eric and Popovych, Sergiy and Wu, Jingpeng and Jia, Zhen and Castro, Manuel and Kemnitz, Nico and Ih, Dodam and Bates, Alexander Shakeel and Eckstein, Nils and Funke, Jan and Collman, Forrest and Bock, Davi D and Jefferis, Gregory S X E and Seung, H Sebastian and Murthy, Mala} } @article {68258, title = {NeuronBridge: an intuitive web application for neuronal morphology search across large data sets}, journal = {BMC Bioinformatics}, volume = {25}, year = {2024}, month = {2024 Mar 15}, pages = {114}, abstract = {

Background

Neuroscience research in\ Drosophila\ is benefiting from large-scale connectomics efforts using electron microscopy (EM) to reveal all the neurons in a brain and their connections. To exploit this knowledge base, researchers relate a connectome{\textquoteright}s structure to neuronal function, often by studying individual neuron cell types. Vast libraries of fly driver lines expressing fluorescent reporter genes in sets of neurons have been created and imaged using confocal light microscopy (LM), enabling the targeting of neurons for experimentation. However, creating a fly line for driving gene expression within a single neuron found in an EM connectome remains a challenge, as it typically requires identifying a pair of driver lines where only the neuron of interest is expressed in both. This task and other emerging scientific workflows require finding similar neurons across large data sets imaged using different modalities.

Results

Here, we present NeuronBridge, a web application for easily and rapidly finding putative morphological matches between large data sets of neurons imaged using different modalities. We describe the functionality and construction of the NeuronBridge service, including its user-friendly graphical user interface (GUI), extensible data model, serverless cloud architecture, and massively parallel image search engine.

Conclusions

NeuronBridge fills a critical gap in the\ Drosophila\ research workflow and is used by hundreds of neuroscience researchers around the world. We offer our software code, open APIs, and processed data sets for integration and reuse, and provide the application as a service at\ http://neuronbridge.janelia.org.

}, doi = {10.1186/s12859-024-05732-7}, url = {https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-024-05732-7}, author = {Jody Clements and Cristian Goina and Philip M. Hubbard and Takashi Kawase and Donald J. Olbris and Hideo Otsuna and Robert Svirskas and Konrad Rokicki} } @article {69439, title = {Neurotransmitter classification from electron microscopy images at synaptic sites in Drosophila melanogaster}, journal = {Cell}, volume = {187}, year = {2024}, month = {2024 May 09}, pages = {2574-2594.e23}, abstract = {

High-resolution electron microscopy of nervous systems has enabled the reconstruction of synaptic connectomes. However, we do not know the synaptic sign for each connection (i.e., whether a connection is excitatory or inhibitory), which is implied by the released transmitter. We demonstrate that artificial neural networks can predict transmitter types for presynapses from electron micrographs: a network trained to predict six transmitters (acetylcholine, glutamate, GABA, serotonin, dopamine, octopamine) achieves an accuracy of 87\% for individual synapses, 94\% for neurons, and 91\% for known cell types across a D.\ melanogaster whole brain. We visualize the ultrastructural features used for prediction, discovering subtle but significant differences between transmitter phenotypes. We also analyze transmitter distributions across the brain and find that neurons that develop together largely express only one fast-acting transmitter (acetylcholine, glutamate, or GABA). We hope that our publicly available predictions act as an accelerant for neuroscientific hypothesis generation for the fly.

}, keywords = {Animals, Brain, Connectome, Drosophila melanogaster, gamma-Aminobutyric Acid, Microscopy, Electron, Neural Networks, Computer, Neurons, Neurotransmitter Agents, Synapses}, issn = {1097-4172}, doi = {10.1016/j.cell.2024.03.016}, author = {Eckstein, Nils and Bates, Alexander Shakeel and Champion, Andrew and Du, Michelle and Yin, Yijie and Schlegel, Philipp and Lu, Alicia Kun-Yang and Rymer, Thomson and Finley-May, Samantha and Paterson, Tyler and Parekh, Ruchi and Dorkenwald, Sven and Matsliah, Arie and Yu, Szi-Chieh and McKellar, Claire and Sterling, Amy and Eichler, Katharina and Costa, Marta and Seung, Sebastian and Murthy, Mala and Hartenstein, Volker and Jefferis, Gregory S X E and Funke, Jan} } @article {68839, title = {New genetic tools for mushroom body output neurons in~Drosophila}, journal = {eLife}, year = {2024}, month = {2024 Jan 24}, abstract = {

How memories of past events influence behavior is a key question in neuroscience. The major associative learning center in\ Drosophila, the Mushroom Body (MB), communicates to the rest of the brain through Mushroom Body Output Neurons (MBONs). While 21 MBON cell types have their dendrites confined to small compartments of the MB lobes, analysis of EM connectomes revealed the presence of an additional 14 MBON cell types that are atypical in having dendritic input both within the MB lobes and in adjacent brain regions. Genetic reagents for manipulating atypical MBONs and experimental data on their functions has been lacking. In this report we describe new cell-type-specific GAL4 drivers for many MBONs, including the majority of atypical MBONs. Using these genetic reagents, we conducted optogenetic activation screening to examine their ability to drive behaviors and learning. These reagents provide important new tools for the study of complex behaviors in\ Drosophila.

}, doi = {10.7554/eLife.90523}, url = {https://doi.org/10.7554/eLife.90523}, author = {Rubin, Gerald M and Aso, Yoshinori} } @article {69635, title = {New Statistical Metric for Robust Target Detection in Cryo-EM Using 2DTM}, journal = {bioRxiv}, year = {2024}, month = {2024 Oct 03}, abstract = {

2D template matching (2DTM) can be used to detect molecules and their assemblies in cellular cryo-EM images with high positional and orientational accuracy. While 2DTM successfully detects spherical targets such as large ribosomal subunits, challenges remain in detecting smaller and more aspherical targets in various environments. In this work, a novel 2DTM metric, referred to as the 2DTM p-value, is developed to extend the 2DTM framework to more complex applications. The 2DTM p-value combines information from two previously used 2DTM metrics, namely the 2DTM signal-to-noise ratio (SNR) and z-score, which are derived from the cross-correlation coefficient between the target and the template. The 2DTM p-value demonstrates robust detection accuracies under various imaging and sample conditions and outperforms the 2DTM SNR and z-score alone. Specifically, the 2DTM p-value improves the detection of aspherical targets such as a modified artificial tubulin patch particle (500 kDa) and a much smaller clathrin monomer (193 kDa) in simulated data. It also accurately recovers mature 60S ribosomes in yeast lamellae samples, even under conditions of increased Gaussian noise. The new metric will enable the detection of a wider variety of targets in both purified and cellular samples through 2DTM.

}, doi = {10.1101/2024.10.01.616095}, url = {https://doi.org/10.1101/2024.10.01.616095}, author = {Zhang, Kexin and Cossio, Pilar and Rangan, Aaditya and Lucas, Bronwyn and Grigorieff, Nikolaus} } @article {69402, title = {NMDAR-mediated activation of pannexin1 channels contributes to the detonator properties of hippocampal mossy fiber synapses.}, journal = {iScience}, volume = {27}, year = {2024}, month = {2024 Apr 06}, pages = {109681}, abstract = {

Pannexins are large-pore ion channels expressed throughout the mammalian brain that participate in various neuropathologies; however, their physiological roles remain obscure. Here, we report that pannexin1 channels (Panx1) can be synaptically activated under physiological recording conditions in rodent acute hippocampal slices. Specifically, NMDA receptor (NMDAR)-mediated responses at the mossy fiber to CA3 pyramidal cell synapse were followed by a slow postsynaptic inward current that could activate CA3 pyramidal cells but was absent in Panx1 knockout mice. Immunoelectron microscopy revealed that Panx1 was localized near the postsynaptic density. Further, Panx1-mediated currents were potentiated by metabotropic receptors and bidirectionally modulated by burst-timing-dependent plasticity of NMDAR-mediated transmission. Lastly, Panx1 channels were preferentially recruited when NMDAR activation enters a supralinear regime, resulting in temporally delayed burst-firing. Thus, Panx1 can contribute to synaptic amplification and broadening the temporal associativity window for co-activated pyramidal cells, thereby supporting the auto-associative functions of the CA3 region.

}, issn = {2589-0042}, doi = {10.1016/j.isci.2024.109681}, author = {Rangel-Sandoval, Cinthia and Soula, Marisol and Li, Wei-Ping and Castillo, Pablo E and Hunt, David L} } @article {69471, title = {Norepinephrine changes behavioral state via astroglial purinergic signaling}, journal = {Science}, year = {2024}, month = {2025 May 15}, abstract = {

Both neurons and glia communicate through diffusible neuromodulators; however, how neuron-glial interactions in such neuromodulatory networks influence circuit computation and behavior is unclear. During futility-induced behavioral transitions in the larval zebrafish, the neuromodulator norepinephrine (NE) drives fast excitation and delayed inhibition of behavior and circuit activity. We found that astroglial purinergic signaling implements the inhibitory arm of this motif. In larval zebrafish, NE triggers astroglial release of adenosine triphosphate (ATP), extracellular conversion of ATP into adenosine, and behavioral suppression through activation of hindbrain neuronal adenosine receptors. Our results suggest a computational and behavioral role for an evolutionarily conserved astroglial purinergic signaling axis in NE-mediated behavioral and brain state transitions and position astroglia as important effectors in neuromodulatory signaling.

Preprint:\ https://www.biorxiv.org/content/early/2024/05/23/2024.05.23.595576

}, doi = {10.1126/science.adq5233}, url = {https://www.science.org/stoken/author-tokens/ST-2654/full}, author = {Chen, Alex B. and Duque, Marc and Wang, Vickie M. and Dhanasekar, Mahalakshmi and Mi, Xuelong and Rymbek, Altyn and Tocquer, Loeva and Narayan, Sujatha and Prober, David and Yu, Guoqiang and Wyart, Claire and Engert, Florian and Ahrens, Misha B.} } @article {69675, title = {A novel rhodopsin-based voltage indicator for simultaneous two-photon optical recording with GCaMP in vivo}, journal = {bioRxiv}, year = {2024}, month = {2024 Nov 15}, abstract = {

Genetically encoded voltage indicators (GEVIs) allow optical recording of membrane potential from targeted cells in vivo. However, red GEVIs that are compatible with two-photon microscopy and that can be multiplexed in vivo with green reporters like GCaMP, are currently lacking. To address this gap, we explored diverse rhodopsin proteins as GEVIs and engineered a novel GEVI, 2Photron, based on a rhodopsin from the green algae Klebsormidium nitens. 2Photron, combined with two photon ultrafast local volume excitation (ULoVE), enabled multiplexed readout of spiking and subthreshold voltage simultaneously with GCaMP calcium signals in visual cortical neurons of awake, behaving mice. These recordings revealed the cell-specific relationship of spiking and subthreshold voltage dynamics with GCaMP responses, highlighting the challenges of extracting underlying spike trains from calcium imaging.

}, doi = {10.1101/2024.11.15.623698}, url = {https://doi.org/10.1101/2024.11.15.623698}, author = {Villette, Vincent and Yang, Shang and Valenti, Rosario and Macklin, John J. and Bradley, Jonathan and Mathieu, Benjamin and Lombardini, Alberto and Podgorski, Kaspar and Dieudonn{\'e}, St{\'e}phane and Schreiter, Eric R. and Abdelfattah, Ahmed S.} } @article {69058, title = {Nanometer-scale views of visual cortex reveal anatomical features of primary cilia poised to detect synaptic spillover}, journal = {bioRxiv}, year = {2023}, month = {2023 Nov 01}, abstract = {

A primary cilium is a thin membrane-bound extension off a cell surface that contains receptors for perceiving and transmitting signals that modulate cell state and activity. While many cell types have a primary cilium, little is known about primary cilia in the brain, where they are less accessible than cilia on cultured cells or epithelial tissues and protrude from cell bodies into a deep, dense network of glial and neuronal processes. Here, we investigated cilia frequency, internal structure, shape, and position in large, high-resolution transmission electron microscopy volumes of mouse primary visual cortex. Cilia extended from the cell bodies of nearly all excitatory and inhibitory neurons, astrocytes, and oligodendrocyte precursor cells (OPCs), but were absent from oligodendrocytes and microglia. Structural comparisons revealed that the membrane structure at the base of the cilium and the microtubule organization differed between neurons and glia. OPC cilia were distinct in that they were the shortest and contained pervasive internal vesicles only occasionally observed in neuron and astrocyte cilia. Investigating cilia-proximal features revealed that many cilia were directly adjacent to synapses, suggesting cilia are well poised to encounter locally released signaling molecules. The internal anatomy, including microtubule changes and centriole location, defined key structural features including cilium placement and shape. Together, the anatomical insights both within and around neuron and glia cilia provide new insights into cilia formation and function across cell types in the brain.

}, doi = {10.1101/2023.10.31.564838}, url = {https://doi.org/10.1101/2023.10.31.564838}, author = {Carolyn M Ott and Russel Torres and Tung-Sheng Kuan and Aaron T Kuan and JoAnn Buchanan and Leila Elabbady and Sharmishtaa Seshamani and Agnes L Bodor and Forrest C Collman and Davi D Bock and Wei-Chung Allen Lee and Nuno Macarico da Costa and Jennifer Lippincott-Schwartz} } @article {68785, title = {Nanoparticle-based targeting of microglia improves the neural regeneration enhancing effects of immunosuppression in the zebrafish retina.}, journal = {Communications Biology}, volume = {6}, year = {2023}, month = {2023 May 18}, pages = {534}, abstract = {

Retinal M{\"u}ller glia function as injury-induced stem-like cells in zebrafish but not mammals. However, insights gleaned from zebrafish have been applied to stimulate nascent regenerative responses in the mammalian retina. For instance, microglia/macrophages regulate M{\"u}ller glia stem cell activity in the chick, zebrafish, and mouse. We previously showed that post-injury immunosuppression by the glucocorticoid dexamethasone accelerated retinal regeneration kinetics in zebrafish. Similarly, microglia ablation enhances regenerative outcomes in the mouse retina. Targeted immunomodulation of microglia reactivity may therefore enhance the regenerative potential of M{\"u}ller glia for therapeutic purposes. Here, we investigated potential mechanisms by which post-injury dexamethasone accelerates retinal regeneration kinetics, and the effects of dendrimer-based targeting of dexamethasone to reactive microglia. Intravital time-lapse imaging revealed that post-injury dexamethasone inhibited microglia reactivity. The dendrimer-conjugated formulation: (1) decreased dexamethasone-associated systemic toxicity, (2) targeted dexamethasone to reactive microglia, and (3) improved the regeneration enhancing effects of immunosuppression by increasing stem/progenitor proliferation rates. Lastly, we show that the gene rnf2 is required for the enhanced regeneration effect of D-Dex. These data support the use of dendrimer-based targeting of reactive immune cells to reduce toxicity and enhance the regeneration promoting effects of immunosuppressants in the retina.

}, keywords = {Animals, Dendrimers, Dexamethasone, Immunosuppression Therapy, Mammals, Mice, Microglia, Retina, Zebrafish}, issn = {2399-3642}, doi = {10.1038/s42003-023-04898-9}, author = {Emmerich, Kevin and White, David T and Kambhampati, Siva P and Casado, Grace L and Fu, Tian-Ming and Chunawala, Zeeshaan and Sahoo, Arpan and Nimmagadda, Saumya and Krishnan, Nimisha and Saxena, Meera T and Walker, Steven L and Betzig, Eric and Kannan, Rangaramanujam M and Mumm, Jeff S} } @article {69057, title = {Nanoscale imaging reveals the mechanisms of ER-to-Golgi transport via a dynamic tubular-vesicular network}, journal = {bioRxiv}, year = {2023}, month = {2023 Oct 27}, abstract = {

The endoplasmic reticulum (ER) and the Golgi apparatus are the first sorting stations along the secretory pathway of mammalian cells and have a crucial role in protein quality control and cellular homeostasis. While machinery components mediating ER-to-Golgi transport have been mapped, it is unclear how exchange between the two closely juxtaposed organelles is coordinated in living cells. Here, using gene editing to tag machinery components, live-cell confocal and stimulated emission depletion (STED) super-resolution microscopy, we show that ER-to-Golgi transport occurs via a dynamic network of tubules positive for the small GTPase ARF4. swCOPI machinery is tightly associated to this network and moves with tubular-vesicular structures. Strikingly, the ARF4 network appears to be continuous with the ER and ARF4 tubules remodel around static ER exit sites (ERES) defined by COPII machinery. We were further able to dissect the steps of ER-to-Golgi transport with functional trafficking assays. A wave of cargo released from the ER percolates through peripheral and Golgi-tethered ARF4 structures before filling the cis-Golgi. Perturbation via acute degradation of ARF4 shows an active regulatory role for the GTPase and COPI in anterograde transport. Our data supports a model in which anterograde ER-to-Golgi transport occurs via an ARF4 tubular-vesicular network directly connecting the ER and Golgi-associated pre-cisternae.

}, doi = {10.1101/2023.10.27.563951}, url = {https://doi.org/10.1101/2023.10.27.563951}, author = {Luis Wong-Dilworth and Gresy Bregu and Steffen Restel and Carmen Rodilla-Ramirez and Svenja Ebeling and Shelly Harel and Paula Leupold and Jonathan Grimm and Luke D. Lavis and Jessica Angulo-Capel and Felix Campelo and Francesca Bottanelli} } @article {68966, title = {The Neural Basis of Drosophila Courtship Song}, journal = {bioRxiv}, year = {2023}, month = {2023 Sep 01}, abstract = {

Animal sounds are produced by patterned vibrations of specific organs, but the neural circuits that drive these vibrations are not well defined in any animal. Here we provide a functional and synaptic map of most of the neurons in the\ Drosophila\ male ventral nerve cord (the analog of the vertebrate spinal cord) that drive complex, patterned song during courtship. Male\ Drosophila\ vibrate their wings toward females during courtship to produce two distinct song modes {\textendash} pulse and sine song {\textendash} with characteristic features that signal species identity and male quality. We identified song-producing neural circuits by optogenetically activating and inhibiting identified cell types in the ventral nerve cord (VNC) and by tracing their patterns of synaptic connectivity in the male VNC connectome. The core song circuit consists of at least eight cell types organized into overlapping circuits, where all neurons are required for pulse song and a subset are required for sine song. The pulse and sine circuits each include a feed-forward pathway from brain descending neurons to wing motor neurons, with extensive reciprocal and feed-back connections. We also identify specific neurons that shape the individual features of each song mode. These results reveal commonalities amongst diverse animals in the neural mechanisms that generate diverse motor patterns from a single set of muscles.

}, doi = {10.1101/2023.08.30.555537}, url = {https://doi.org/10.1101/2023.08.30.555537}, author = {Joshua L. Lillvis and Kaiyu Wang and Hiroshi M. Shiozaki and Min Xu and David L. Stern and Barry J. Dickson} } @article {68571, title = {Neural circuit mechanisms for transforming learned olfactory valences into wind-oriented movement}, journal = {eLife}, year = {2023}, month = {2023 Sep 18}, abstract = {

How memories are used by the brain to guide future action is poorly understood. In olfactory associative learning in Drosophila, multiple compartments of the mushroom body act in parallel to assign valence to a stimulus. Here, we show that appetitive memories stored in different compartments induce different levels of upwind locomotion. Using a photoactivation screen of a new collection of split-GAL4 drivers and EM connectomics, we identified a cluster of neurons postsynaptic to the mushroom body output neurons (MBONs) that can trigger robust upwind steering. These UpWind Neurons (UpWiNs) integrate inhibitory and excitatory synaptic inputs from MBONs of appetitive and aversive memory compartments, respectively. After training, disinhibition from the appetitive-memory MBONs enhances the response of UpWiNs to reward-predicting odors. Blocking UpWiNs impaired appetitive memory and reduced upwind locomotion during retrieval. Photoactivation of UpWiNs also increased the chance of returning to a location where activation was initiated, suggesting an additional role in olfactory navigation. Thus, our results provide insight into how learned abstract valences are gradually transformed into concrete memory-driven actions through divergent and convergent networks, a neuronal architecture that is commonly found in the vertebrate and invertebrate brains.

}, doi = {10.7554/eLife.85756}, url = {https://doi.org/10.7554/eLife.85756}, author = {Yoshinori Aso and Daichi Yamada and Daniel Bushey and Karen Hibbard and Megan Sammons and Hideo Otsuna and Yichun Shuai and Toshihide Hige} } @article {68918, title = {Nonlinear manifolds underlie neural population activity during behaviour.}, journal = {bioRxiv}, year = {2023}, month = {2023 Jul 21}, abstract = {

There is rich variety in the activity of single neurons recorded during behaviour. Yet, these diverse single neuron responses can be well described by relatively few patterns of neural co-modulation. The study of such low-dimensional structure of neural population activity has provided important insights into how the brain generates behaviour. Virtually all of these studies have used linear dimensionality reduction techniques to estimate these population-wide co-modulation patterns, constraining them to a flat "neural manifold". Here, we hypothesised that since neurons have nonlinear responses and make thousands of distributed and recurrent connections that likely amplify such nonlinearities, neural manifolds should be intrinsically nonlinear. Combining neural population recordings from monkey motor cortex, mouse motor cortex, mouse striatum, and human motor cortex, we show that: 1) neural manifolds are intrinsically nonlinear; 2) the degree of their nonlinearity varies across architecturally distinct brain regions; and 3) manifold nonlinearity becomes more evident during complex tasks that require more varied activity patterns. Simulations using recurrent neural network models confirmed the proposed relationship between circuit connectivity and manifold nonlinearity, including the differences across architecturally distinct regions. Thus, neural manifolds underlying the generation of behaviour are inherently nonlinear, and properly accounting for such nonlinearities will be critical as neuroscientists move towards studying numerous brain regions involved in increasingly complex and naturalistic behaviours.

}, doi = {10.1101/2023.07.18.549575}, url = {https://doi.org/10.1101/2023.07.18.549575}, author = {Fortunato, C{\'a}tia and Bennasar-V{\'a}zquez, Jorge and Park, Junchol and Chang, Joanna C and Miller, Lee E and Dudman, Joshua T and Perich, Matthew G and Gallego, Juan A} } @article {67993, title = {A natural timeless polymorphism allowing circadian clock synchronization in "white nights".}, journal = {Nature Communications}, volume = {13}, year = {2022}, month = {2022 Mar 31}, pages = {1724}, abstract = {

Daily temporal organisation offers a fitness advantage and is determined by an interplay between environmental rhythms and circadian clocks. While light:dark cycles robustly synchronise circadian clocks, it is not clear how animals experiencing only weak environmental cues deal with this problem. Like humans, Drosophila originate in sub-Saharan Africa and spread North up to the polar circle, experiencing long summer days or even constant light (LL). LL disrupts clock function, due to constant activation of CRYPTOCHROME, which induces degradation of the clock protein TIMELESS (TIM), but temperature cycles are able to overcome these deleterious effects of LL. We show here that for this to occur a recently evolved natural timeless allele (ls-tim) is required, encoding the less light-sensitive L-TIM in addition to S-TIM, the only form encoded by the ancient s-tim allele. We show that only ls-tim flies can synchronise their behaviour to semi-natural conditions typical for Northern European summers, suggesting that this functional gain is driving the Northward ls-tim spread.

}, keywords = {Animals, Circadian Clocks, Circadian Rhythm, Drosophila, Drosophila Proteins, Light}, issn = {2041-1723}, doi = {10.1038/s41467-022-29293-6}, author = {Lamaze, Angelique and Chen, Chenghao and Leleux, Solene and Xu, Min and George, Rebekah and Stanewsky, Ralf} } @article {68272, title = {neuPrint: An open access tool for EM connectomics.}, journal = {Frontiers in Neuroinformatics}, volume = {16}, year = {2022}, month = {2022 Jul 20}, pages = {896292}, abstract = {

Due to advances in electron microscopy and deep learning, it is now practical to reconstruct a connectome, a description of neurons and the chemical synapses between them, for significant volumes of neural tissue. Smaller past reconstructions were primarily used by domain experts, could be handled by downloading data, and performance was not a serious problem. But new and much larger reconstructions upend these assumptions. These networks now contain tens of thousands of neurons and tens of millions of connections, with yet larger reconstructions pending, and are of interest to a large community of non-specialists. Allowing other scientists to make use of this data needs more than publication-it requires new tools that are publicly available, easy to use, and efficiently handle large data. We introduce neuPrint to address these data analysis challenges. Neuprint contains two major components-a web interface and programmer APIs. The web interface is designed to allow any scientist worldwide, using only a browser, to quickly ask and answer typical biological queries about a connectome. The neuPrint APIs allow more computer-savvy scientists to make more complex or higher volume queries. NeuPrint also provides features for assessing reconstruction quality. Internally, neuPrint organizes connectome data as a graph stored in a neo4j database. This gives high performance for typical queries, provides access though a public and well documented query language Cypher, and will extend well to future larger connectomics databases. Our experience is also an experiment in open science. We find a significant fraction of the readers of the article proceed to examine the data directly. In our case preprints worked exactly as intended, with data inquiries and PDF downloads starting immediately after pre-print publication, and little affected by formal publication later. From this we deduce that many readers are more interested in our data than in our analysis of our data, suggesting that data-only papers can be well appreciated and that public data release can speed up the propagation of scientific results by many months. We also find that providing, and keeping, the data available for online access imposes substantial additional costs to connectomics research.

}, issn = {1662-5196}, doi = {10.3389/fninf.2022.896292}, author = {Plaza, Stephen M and Clements, Jody and Dolafi, Tom and Umayam, Lowell and Neubarth, Nicole N and Scheffer, Louis K and Berg, Stuart} } @article {67965, title = {Neural Algorithms and Circuits for Motor Planning.}, journal = {Annual Reviews Neuroscience}, year = {2022}, month = {2022 Feb 22}, abstract = {

The brain plans and executes volitional movements. The underlying patterns of neural population activity have been explored in the context of movements of the eyes, limbs, tongue, and head in nonhuman primates and rodents. How do networks of neurons produce the slow neural dynamics that prepare specific movements and the fast dynamics that ultimately initiate these movements? Recent work exploits rapid and calibrated perturbations of neural activity to test specific dynamical systems models that are capable of producing the observed neural activity. These joint experimental and computational studies show that cortical dynamics during motor planning reflect fixed points of neural activity (attractors). Subcortical control signals reshape and move attractors over multiple timescales, causing commitment to specific actions and rapid transitions to movement execution. Experiments in rodents are beginning to reveal how these algorithms are implemented at the level of brain-wide neural circuits. Expected final online publication date for the , Volume 45 is July 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

}, issn = {1545-4126}, doi = {10.1146/annurev-neuro-092021-121730}, author = {Inagaki, Hidehiko K and Chen, Susu and Daie, Kayvon and Finklestein, Arseny and Fontolan, Lorenzo and Romani, Sandro and Svoboda, Karel} } @article {68224, title = {Neural Algorithms and Circuits for Motor Planning.}, journal = {Annual Review Neuroscience}, volume = {45}, year = {2022}, month = {2022 Jul 08}, pages = {249-271}, abstract = {

The brain plans and executes volitional movements. The underlying patterns of neural population activity have been explored in the context of movements of the eyes, limbs, tongue, and head in nonhuman primates and rodents. How do networks of neurons produce the slow neural dynamics that prepare specific movements and the fast dynamics that ultimately initiate these movements? Recent work exploits rapid and calibrated perturbations of neural activity to test specific dynamical systems models that are capable of producing the observed neural activity. These joint experimental and computational studies show that cortical dynamics during motor planning reflect fixed points of neural activity (attractors). Subcortical control signals reshape and move attractors over multiple timescales, causing commitment to specific actions and rapid transitions to movement execution. Experiments in rodents are beginning to reveal how these algorithms are implemented at the level of brain-wide neural circuits.

}, keywords = {Algorithms, Animals, Brain, Motor Cortex, Movement, Neurons}, issn = {1545-4126}, doi = {10.1146/annurev-neuro-092021-121730}, author = {Inagaki, Hidehiko K and Chen, Susu and Daie, Kayvon and Finkelstein, Arseny and Fontolan, Lorenzo and Romani, Sandro and Svoboda, Karel} } @article {67895, title = {A neural circuit linking learning and sleep in Drosophila long-term memory.}, journal = {Nature Communications}, volume = {13}, year = {2022}, month = {2022 Feb 01}, pages = {609}, abstract = {

Animals retain some but not all experiences in long-term memory (LTM). Sleep supports LTM retention across animal species. It is well established that learning experiences enhance post-learning sleep. However, the underlying mechanisms of how learning mediates sleep for memory retention are not clear. Drosophila males display increased amounts of sleep after courtship learning. Courtship learning depends on Mushroom Body (MB) neurons, and post-learning sleep is mediated by the sleep-promoting ventral Fan-Shaped Body neurons (vFBs). We show that post-learning sleep is regulated by two opposing output neurons\ (MBONs) from the MB, which encode a measure of learning. Excitatory MBONs-γ2α{\textquoteright}1 becomes increasingly active upon increasing time of learning, whereas inhibitory MBONs-β{\textquoteright}2mp is activated only by a short learning experience. These MB outputs are integrated by SFS neurons, which excite vFBs to promote sleep after prolonged but not short training. This circuit may ensure that only longer or more intense learning experiences induce sleep and are thereby consolidated into LTM.

}, issn = {2041-1723}, doi = {10.1038/s41467-022-28256-1}, author = {Lei, Zhengchang and Henderson, Kristin and Keleman, Krystyna} } @article {68148, title = {Neural circuit pathology driven by Shank3 mutation disrupts social behaviors.}, journal = {Cell Reports}, volume = {39}, year = {2022}, month = {2022 Jun 07}, pages = {110906}, abstract = {

Dysfunctional sociability is a core symptom in autism spectrum disorder (ASD) that may arise from neural-network dysconnectivity between multiple brain regions. However, pathogenic neural-network mechanisms underlying social dysfunction are largely unknown. Here, we demonstrate that circuit-selective mutation (ctMUT) of ASD-risk Shank3 gene within a unidirectional projection from the prefrontal cortex to the basolateral amygdala alters spine morphology and excitatory-inhibitory balance of the circuit. Shank3 ctMUT mice show reduced sociability as well as elevated neural activity and its amplitude variability, which is consistent with the neuroimaging results from human ASD patients. Moreover, the circuit hyper-activity disrupts the temporal correlation of socially tuned neurons to the events of social interactions. Finally, optogenetic circuit activation in wild-type mice partially recapitulates the reduced sociability of Shank3 ctMUT mice, while circuit inhibition in Shank3 ctMUT mice partially rescues social behavior. Collectively, these results highlight a circuit-level pathogenic mechanism of Shank3 mutation that drives social dysfunction.

}, keywords = {Animals, Autism Spectrum Disorder, Disease Models, Animal, Humans, Mice, Microfilament Proteins, Mutation, Nerve Tissue Proteins, Optogenetics, Prefrontal Cortex, Social Behavior}, issn = {2211-1247}, doi = {10.1016/j.celrep.2022.110906}, author = {Kim, Sunwhi and Kim, Yong-Eun and Song, Inuk and Ujihara, Yusuke and Kim, Namsoo and Jiang, Yong-Hui and Yin, Henry H and Lee, Tae-Ho and Kim, Il Hwan} } @article {68569, title = {Neural coding of distinct motor patterns during Drosophila courtship song}, journal = {bioRxiv}, year = {2022}, month = {2022 Dec 15}, abstract = {

Animals flexibly switch between different actions by changing neural activity patterns for motor control. Courting\ Drosophila melanogaster\ males produce two different acoustic signals, pulse and sine song, each of which can be promoted by artificial activation of distinct neurons. However, how the activity of these neurons implements flexible song production is unknown. Here, we developed an assay to record neuronal calcium signals in the ventral nerve cord, which contains the song motor circuit, in singing flies. We found that sine-promoting neurons, but not pulse-promoting neurons, show strong activation during sine song. In contrast, both pulse- and sine-promoting neurons are active during pulse song. Furthermore, population calcium imaging in the song circuit suggests that sine song involves activation of a subset of neurons that are also active during pulse song. Thus, differential activation of overlapping, rather than distinct, neural populations underlies flexible motor actions during acoustic communication in\ D. melanogaster.

}, doi = {10.1101/2022.12.14.520499}, url = {https://doi.org/10.1101/2022.12.14.520499}, author = {Hiroshi M. Shiozaki and Kaiyu Wang and Joshua L. Lillvis and Min Xu and Barry J. Dickson and David L. Stern} } @article {68273, title = {Neural network organization for courtship-song feature detection in Drosophila.}, journal = {Current Biology}, volume = {32}, year = {2022}, month = {2022 Aug 08}, pages = {3317-3333.e7}, abstract = {

Animals communicate using sounds in a wide range of contexts, and auditory systems must encode behaviorally relevant acoustic features to drive appropriate reactions. How feature detection emerges along auditory pathways has been difficult to solve due to challenges in mapping the underlying circuits and characterizing responses to behaviorally relevant features. Here, we study auditory activity in the Drosophila melanogaster brain and investigate feature selectivity for the two main modes of fly courtship song, sinusoids and pulse trains. We identify 24 new cell types of the intermediate layers of the auditory pathway, and using a new connectomic resource, FlyWire, we map all synaptic connections between these cell types, in addition to connections to known early and higher-order auditory neurons-this represents the first circuit-level map of the auditory pathway. We additionally determine the sign (excitatory or inhibitory) of most synapses in this auditory connectome. We find that auditory neurons display a continuum of preferences for courtship song modes and that neurons with different song-mode preferences and response timescales are highly interconnected in a network that lacks hierarchical structure. Nonetheless, we find that the response properties of individual cell types within the connectome are predictable from their inputs. Our study thus provides new insights into the organization of auditory coding within the Drosophila brain.

}, keywords = {Animals, Auditory Perception, Courtship, Drosophila, Drosophila melanogaster, Neural Networks, Computer, Sexual Behavior, Animal, Vocalization, Animal}, issn = {1879-0445}, doi = {10.1016/j.cub.2022.06.019}, author = {Baker, Christa A and McKellar, Claire and Pang, Rich and Nern, Aljoscha and Dorkenwald, Sven and Pacheco, Diego A and Eckstein, Nils and Funke, Jan and Dickson, Barry J and Murthy, Mala} } @article {68379, title = {The Neurodata Without Borders ecosystem for neurophysiological data science.}, journal = {eLife}, volume = {11}, year = {2022}, month = {2022 Oct 04}, abstract = {

The neurophysiology of cells and tissues are monitored electrophysiologically and optically in diverse experiments and species, ranging from flies to humans. Understanding the brain requires integration of data across this diversity, and thus these data must be findable, accessible, interoperable, and reusable (FAIR). This requires a standard language for data and metadata that can coevolve with neuroscience. We describe design and implementation principles for a language for neurophysiology data. Our open-source software (Neurodata Without Borders, NWB) defines and modularizes the interdependent, yet separable, components of a data language. We demonstrate NWB{\textquoteright}s impact through unified description of neurophysiology data across diverse modalities and species. NWB exists in an ecosystem, which includes data management, analysis, visualization, and archive tools. Thus, the NWB data language enables reproduction, interchange, and reuse of diverse neurophysiology data. More broadly, the design principles of NWB are generally applicable to enhance discovery across biology through data FAIRness.

}, keywords = {Data Science, Ecosystem, Humans, Metadata, Neurophysiology, Software}, issn = {2050-084X}, doi = {10.7554/eLife.78362}, author = {Rubel, Oliver and Tritt, Andrew and Ly, Ryan and Dichter, Benjamin K and Ghosh, Satrajit and Niu, Lawrence and Baker, Pamela and Soltesz, Ivan and Ng, Lydia and Svoboda, Karel and Frank, Loren and Bouchard, Kristofer E} } @article {67914, title = {Neuromuscular embodiment of feedback control elements in Drosophila flight.}, journal = {bioRxiv}, year = {2022}, month = {2022 Feb 24}, abstract = {

While insects like\ Drosophila\ are flying, aerodynamic instabilities require that they make millisecond-timescale adjustments to their wing motion to stay aloft and on course. These stabilization reflexes can be modeled as a proportional-integral (PI) controller; however, it is unclear how such control might be instantiated in insects at the level of muscles and neurons. Here, we show that the b1 and b2 motor units{\textemdash}prominent components of the fly{\textquoteright}s steering muscles system{\textemdash}modulate specific elements of the PI controller: the angular displacement (integral, I) and angular velocity (proportional, P), respectively. Moreover, these effects are observed only during the stabilization of pitch. Our results provide evidence for an organizational principle in which each muscle contributes to a specific functional role in flight control, a finding that highlights the power of using top-down behavioral modeling to guide bottom-up cellular manipulation studies.

}, doi = {10.1101/2022.02.22.481344}, author = {Samuel C Whitehead and Sofia Leone and Theodore Lindsay and Matthew R Meiselman and Noah Cowan and Michael H Dickinson and Nilay Yapici and David Stern and Troy Shirangi and Itai Cohen} } @article {67949, title = {Neuromuscular embodiment of feedback control elements in Drosophila flight}, journal = {bioRxiv}, year = {2022}, month = {2022 Mar 07}, abstract = {

While insects like\ Drosophila\ are flying, aerodynamic instabilities require that they make millisecond-timescale adjustments to their wing motion to stay aloft and on course. These stabilization reflexes can be modeled as a proportional-integral (PI) controller; however, it is unclear how such control might be instantiated in insects at the level of muscles and neurons. Here, we show that the b1 and b2 motor units{\textemdash}prominent components of the fly{\textquoteright}s steering muscles system{\textemdash}modulate specific elements of the PI controller: the angular displacement (integral, I) and angular velocity (proportional, P), respectively. Moreover, these effects are observed only during the stabilization of pitch. Our results provide evidence for an organizational principle in which each muscle contributes to a specific functional role in flight control, a finding that highlights the power of using top-down behavioral modeling to guide bottom-up cellular manipulation studies.

}, doi = {10.1101/2022.02.22.481344}, url = {https://doi.org/10.1101/2022.02.22.481344}, author = {Samuel C. Whitehead and Sofia Leone and Theodore Lindsay and Matthew Meiselman and Noah Cowan and Michael Dickinson and Nilay Yapici and David Stern and Troy Shirangi and Itai Cohen} } @article {68557, title = {Neuromuscular embodiment of feedback control elements in flight.}, journal = {Science Advances}, volume = {8}, year = {2022}, month = {2022 Dec 14}, pages = {eabo7461}, abstract = {

While insects such as are flying, aerodynamic instabilities require that they make millisecond time scale adjustments to their wing motion to stay aloft and on course. These stabilization reflexes can be modeled as a proportional-integral (PI) controller; however, it is unclear how such control might be instantiated in insects at the level of muscles and neurons. Here, we show that the b1 and b2 motor units-prominent components of the fly{\textquoteright}s steering muscle system-modulate specific elements of the PI controller: the angular displacement (integral) and angular velocity (proportional), respectively. Moreover, these effects are observed only during the stabilization of pitch. Our results provide evidence for an organizational principle in which each muscle contributes to a specific functional role in flight control, a finding that highlights the power of using top-down behavioral modeling to guide bottom-up cellular manipulation studies.

}, issn = {2375-2548}, doi = {10.1126/sciadv.abo7461}, author = {Whitehead, Samuel C and Leone, Sofia and Lindsay, Theodore and Meiselman, Matthew R and Cowan, Noah J and Dickinson, Michael H and Yapici, Nilay and Stern, David L and Shirangi, Troy and Cohen, Itai} } @article {68501, title = {Neuronal cell types, projections, and spatial organization of the central amygdala}, journal = {iScience}, volume = {25}, year = {2022}, month = {2022 Dec 22}, pages = {105497}, abstract = {

The central amygdala (CEA) has been richly studied for interpreting function and behavior according to specific cell types and circuits. Such work has typically defined molecular cell types by classical inhibitory marker genes; consequently, whether marker-gene-defined cell types exhaustively cover the CEA and co-vary with connectivity remains unresolved. Here, we combined single-cell RNA sequencing, multiplexed fluorescent\ in situ\ hybridization, immunohistochemistry, and long-range projection mapping to derive a {\textquotedblleft}bottom-up{\textquotedblright} understanding of CEA cell types. In doing so, we identify two major cell types, encompassing one-third of all CEA neurons, that have gone unresolved in previous studies. In spatially mapping these novel types, we identify a non-canonical CEA subdomain associated with\ Nr2f2\ expression and uncover an\ Isl1-expressing medial cell type that accounts for many long-range CEA projections. Our results reveal new CEA organizational principles across cell types and spatial scales and provide a framework for future work examining cell-type-specific behavior and function.

}, issn = {25890042}, doi = {10.1016/j.isci.2022.105497}, url = {https://linkinghub.elsevier.com/retrieve/pii/S2589004222017692}, author = {O{\textquoteright}Leary, Timothy P. and Kendrick, Rennie M. and Bristow, Brianna N. and Sullivan, Kaitlin E. and Wang, Lihua and Clements, Jody and Lemire, Andrew L. and Cembrowski, Mark S.} } @article {68225, title = {Neuronal circuits integrating visual motion information in Drosophila melanogaster.}, journal = {Current Biology}, volume = {32}, year = {2022}, month = {2022 Aug 22}, pages = {3529-3544}, abstract = {

The detection of visual motion enables sophisticated animal navigation, and studies on flies have provided profound insights into the cellular and circuit bases of this neural computation. The fly{\textquoteright}s directionally selective T4 and T5 neurons encode ON and OFF motion, respectively. Their axons terminate in one of the four retinotopic layers in the lobula plate, where each layer encodes one of the four directions of motion. Although the input circuitry of the directionally selective neurons has been studied in detail, the synaptic connectivity of circuits integrating T4/T5 motion signals is largely unknown. Here, we report a 3D electron microscopy reconstruction, wherein we comprehensively identified T4/T5{\textquoteright}s synaptic partners in the lobula plate, revealing a diverse set of new cell types and attributing new connectivity patterns to the known cell types. Our reconstruction explains how the ON- and OFF-motion pathways converge. T4 and T5 cells that project to the same layer connect to common synaptic partners and comprise a core motif together with bilayer interneurons, detailing the circuit basis for computing motion opponency. We discovered pathways that likely encode new directions of motion by integrating vertical and horizontal motion signals from upstream T4/T5 neurons. Finally, we identify substantial projections into the lobula, extending the known motion pathways and suggesting that directionally selective signals shape feature detection there. The circuits we describe enrich the anatomical basis for experimental and computations analyses of motion vision and bring us closer to understanding complete sensory-motor pathways.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2022.06.061}, author = {Shinomiya, Kazunori and Nern, Aljoscha and Meinertzhagen, Ian A and Plaza, Stephen M and Reiser, Michael B} } @article {67801, title = {A neuropeptidergic circuit gates selective escape behavior of Drosophila larvae.}, journal = {Current Biology}, volume = {32}, year = {2022}, month = {2022 Jan 10}, pages = {149-63}, abstract = {

Animals display selective escape behaviors when faced with environmental threats. Selection of the appropriate response by the underlying neuronal network is key to maximizing chances of survival, yet the underlying network mechanisms are so far not fully understood. Using synapse-level reconstruction of the Drosophila larval network paired with physiological and behavioral readouts, we uncovered a circuit that gates selective escape behavior for noxious light through acute and input-specific neuropeptide action. Sensory neurons required for avoidance of noxious light and escape in response to harsh touch, each converge on discrete domains of neuromodulatory hub neurons. We show that acute release of hub neuron-derived insulin-like peptide 7 (Ilp7) and cognate relaxin family receptor (Lgr4) signaling in downstream neurons are required for noxious light avoidance, but not harsh touch responses. Our work highlights a role for compartmentalized circuit organization and neuropeptide release from regulatory hubs, acting as central circuit elements gating escape responses.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2021.10.069}, author = {Imambocus, Bibi Nusreen and Zhou, Fangmin and Formozov, Andrey and Wittich, Annika and Tenedini, Federico M and Hu, Chun and Sauter, Kathrin and Macarenhas Varela, Ednilson and Her{\'e}dia, Fabiana and Casimiro, Andreia P and Macedo, Andr{\'e} and Schlegel, Philipp and Yang, Chung-Hui and Miguel-Aliaga, Irene and Wiegert, J Simon and Pankratz, Michael J and Gontijo, Alisson M and Cardona, Albert and Soba, Peter} } @article {68253, title = {Not so spontaneous: Multi-dimensional representations of behaviors and context in sensory areas.}, journal = {Neuron}, volume = {110}, year = {2022}, month = {2022 Oct 05}, pages = {3064}, abstract = {

Sensory areas are spontaneously active in the absence of sensory stimuli. This spontaneous activity has long been studied; however, its functional role remains largely unknown. Recent advances in technology, allowing large-scale neural recordings in the awake and behaving animal, have transformed our understanding of spontaneous activity. Studies using these recordings have discovered high-dimensional spontaneous activity patterns, correlation between spontaneous activity and behavior, and dissimilarity between spontaneous and sensory-driven activity patterns. These findings are supported by evidence from developing animals, where a transition toward these characteristics is observed as the circuit matures, as well as by evidence from mature animals across species. These newly revealed characteristics call for the formulation of a new role for spontaneous activity in neural sensory computation.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2022.06.019}, author = {Avitan, Lilach and Stringer, Carsen} } @article {68012, title = {Nuclear lamin isoforms differentially contribute to LINC complex-dependent nucleocytoskeletal coupling and whole-cell mechanics.}, journal = {Proceedings of the National Academy of Sciences of the U.S.A.}, volume = {119}, year = {2022}, month = {2022 Apr 19}, pages = {e2121816119}, abstract = {

SignificanceInteractions between the cell nucleus and cytoskeleton regulate cell mechanics and are facilitated by the interplay between the nuclear lamina and linker of nucleoskeleton and cytoskeleton (LINC) complexes. To date, the specific contribution of the four lamin isoforms to nucleocytoskeletal connectivity and whole-cell mechanics remains unknown. We discover that A- and B-type lamins distinctively interact with LINC complexes that bind F-actin and vimentin filaments to differentially modulate cortical stiffness, cytoplasmic stiffness, and contractility of mouse embryonic fibroblasts (MEFs). We propose and experimentally verify an integrated lamin-LINC complex-cytoskeleton model that explains cellular mechanical phenotypes in lamin-deficient MEFs. Our findings uncover potential mechanisms for cellular defects in human laminopathies and many cancers associated with mutations or modifications in lamin isoforms.

}, keywords = {Animals, Cell Nucleus, Cytoskeleton, Fibroblasts, Lamin Type A, Lamin Type B, Mice, Nuclear Lamina, Nuclear Matrix, Protein Isoforms}, issn = {1091-6490}, doi = {10.1073/pnas.2121816119}, author = {Vahabikashi, Amir and Sivagurunathan, Suganya and Nicdao, Fiona Ann Sadsad and Han, Yu Long and Park, Chan Young and Kittisopikul, Mark and Wong, Xianrong and Tran, Joseph R and Gundersen, Gregg G and Reddy, Karen L and Luxton, G W Gant and Guo, Ming and Fredberg, Jeffrey J and Zheng, Yixian and Adam, Stephen A and Goldman, Robert D} } @article {67297, title = {Near-infrared catecholamine nanosensors for high spatiotemporal dopamine imaging.}, journal = {Nature Protocols}, volume = {16}, year = {2021}, month = {2021 May 21}, pages = {3026-3048}, abstract = {

Dopamine neuromodulation of neural synapses is a process implicated in a number of critical brain functions and diseases. Development of protocols to visualize this dynamic neurochemical process is essential to understanding how dopamine modulates brain function. We have developed a non-genetically encoded, near-IR (nIR) catecholamine nanosensor (nIRCat) capable of identifying ~2-{\textmu}m dopamine release hotspots in dorsal striatal brain slices. nIRCat is readily synthesized through sonication of single walled carbon nanotubes with DNA oligos, can be readily introduced into both genetically tractable and intractable organisms and is compatible with a number of dopamine receptor agonists and antagonists. Here we describe the synthesis, characterization and implementation of nIRCat in acute mouse brain slices. We demonstrate how nIRCat can be used to image electrically or optogenetically stimulated dopamine release, and how these procedures can be leveraged to study the effects of dopamine receptor pharmacology. In addition, we provide suggestions for building or adapting wide-field microscopy to be compatible with nIRCat nIR fluorescence imaging. We discuss strategies for analyzing nIR video data to identify dopamine release hotspots and quantify their kinetics. This protocol can be adapted and implemented for imaging other neuromodulators by using probes of this class and can be used in a broad range of species without genetic manipulation. The synthesis and characterization protocols for nIRCat take ~5 h, and the preparation and fluorescence imaging of live brain slices by using nIRCats require ~6 h.

}, issn = {1750-2799}, doi = {10.1038/s41596-021-00530-4}, author = {Yang, Sarah J and Del Bonis-O{\textquoteright}Donnell, Jackson Travis and Beyene, Abraham G and Landry, Markita P} } @article {65859, title = {Neural circuit mechanisms of sexual receptivity in Drosophila females.}, journal = {Nature}, volume = {589}, year = {2021}, month = {2021 Jan 01}, pages = {577-81}, abstract = {

Choosing a mate is one of the most consequential decisions a female will make during her lifetime. A female fly signals her willingness to mate by opening her vaginal plates, allowing a courting male to copulate. Vaginal plate opening (VPO) occurs in response to the male courtship song and is dependent on the mating status\ of the female. How these exteroceptive (song) and interoceptive (mating status) inputs are integrated to regulate VPO remains unknown. Here we characterize the neural circuitry that implements mating decisions in the brain of female Drosophila melanogaster. We show that VPO is controlled by a pair of female-specific descending neurons (vpoDNs). The vpoDNs receive excitatory input from auditory neurons (vpoENs), which are tuned to specific features of the D. melanogaster song, and from pC1 neurons, which encode the mating status\ of the female. The song responses of vpoDNs, but not vpoENs, are attenuated upon mating, accounting for the reduced receptivity of mated females. This modulation is mediated by pC1 neurons. The vpoDNs thus directly integrate the external and internal signals that control the mating decisions of Drosophila females.

}, issn = {1476-4687}, doi = {10.1038/s41586-020-2972-7}, author = {Wang, Kaiyu and Wang, Fei and Forknall, Nora and Yang, Tansy and Patrick, Christopher and Parekh, Ruchi and Dickson, Barry J} } @article {65969, title = {Neuromolecular and behavioral effects of ethanol deprivation in Drosophila}, journal = {bioRxiv}, year = {2021}, month = {2021 Jan 04}, abstract = {

Alcohol use disorder (AUD) is characterized by loss of control in limiting alcohol intake. This may involve intermittent periods of abstinence followed by alcohol seeking and, consequently, relapse. However, little is understood of the molecular mechanisms underlying the impact of alcohol deprivation on behavior. Using a new\ Drosophila melanogaster\ repeated intermittent alcohol exposure model, we sought to identify how ethanol deprivation alters spontaneous behavior, determine the associated neural structures, and reveal correlated changes in brain gene expression. We found that repeated intermittent ethanol-odor exposures followed by ethanol-deprivation dynamically induces behaviors associated with a negative affect state. Although behavioral states broadly mapped to many brain regions, persistent changes in social behaviors mapped to the mushroom body and surrounding neuropil. This occurred concurrently with changes in expression of genes associated with sensory responses, neural plasticity, and immunity. Like social behaviors, immune response genes were upregulated following three-day repeated intermittent ethanol-odor exposures and persisted with one or two days of ethanol-deprivation, suggesting an enduring change in molecular function. Our study provides a framework for identifying how ethanol deprivation alters behavior with correlated underlying circuit and molecular changes.

}, doi = {https://doi.org/10.1101/2021.01.02.425101}, author = {Natalie M. D{\textquoteright}Silva and Katie S. McCullar and Ashley M. Conard and Tyler Blackwater and Reza Azanchi and Ulrike Heberlein and Erica Larschan and Karla R. Kaun} } @article {67232, title = {Neuropixels 2.0: A miniaturized high-density probe for stable, long-term brain recordings.}, journal = {Science}, volume = {372}, year = {2021}, month = {2021 Apr 16}, abstract = {

Measuring the dynamics of neural processing across time scales requires following the spiking of thousands of individual neurons over milliseconds and months. To address this need, we introduce the Neuropixels 2.0 probe together with newly designed analysis algorithms. The probe has more than 5000 sites and is miniaturized to facilitate chronic implants in small mammals and recording during unrestrained behavior. High-quality recordings over long time scales were reliably obtained in mice and rats in six laboratories. Improved site density and arrangement combined with newly created data processing methods enable automatic post hoc correction for brain movements, allowing recording from the same neurons for more than 2 months. These probes and algorithms enable stable recordings from thousands of sites during free behavior, even in small animals such as mice.

}, issn = {1095-9203}, doi = {10.1126/science.abf4588}, author = {Steinmetz, Nicholas A and Ayd{\i}n, {\c C}a{\u g}atay and Lebedeva, Anna and Okun, Michael and Pachitariu, Marius and Bauza, Marius and Beau, Maxime and Bhagat, Jai and B{\"o}hm, Claudia and Broux, Martijn and Chen, Susu and Colonell, Jennifer and Gardner, Richard J and Karsh, Bill and Kloosterman, Fabian and Kostadinov, Dimitar and Mora-Lopez, Carolina and O{\textquoteright}Callaghan, John and Park, Junchol and Putzeys, Jan and Sauerbrei, Britton and van Daal, Rik J J and Vollan, Abraham Z and Wang, Shiwei and Welkenhuysen, Marleen and Ye, Zhiwen and Dudman, Joshua T and Dutta, Barundeb and Hantman, Adam W and Harris, Kenneth D and Lee, Albert K and Moser, Edvard I and O{\textquoteright}Keefe, John and Renart, Alfonso and Svoboda, Karel and H{\"a}usser, Michael and Haesler, Sebastian and Carandini, Matteo and Harris, Timothy D} } @article {67826, title = {Nitrite reductase activity within an antiparallel de novo scaffold.}, journal = {JBIC Journal of Biological Inorganic Chemistry}, volume = {26}, year = {2021}, month = {09/2021}, pages = {855 - 862}, abstract = {

Copper nitrite reductase (CuNiR) is a copper enzyme that converts nitrite to nitric oxide and is an important part of the global nitrogen cycle in bacteria. The relatively simple CuHis3\ binding site of the CuNiR active site has made it an enticing target for small molecule modeling and de novo protein design studies. We have previously reported symmetric CuNiR models within parallel three stranded coiled coil systems, with activities that span a range of three orders of magnitude. In this report, we investigate the same CuHis3\ binding site within an antiparallel three helical bundle scaffold, which allows the design of asymmetric constructs. We determine that a simple CuHis3\ binding site can be designed within this scaffold with enhanced activity relative to the comparable construct in parallel coiled coils. Incorporating more complex designs or repositioning this binding site can decrease this activity as much as 15 times. Comparing these constructs, we reaffirm a previous result in which a blue shift in the 1s to 4p transition energy determined by Cu(I) X-ray absorption spectroscopy is correlated with an enhanced activity within imidazole-based constructs. With this step and recent successful electron transfer site designs within this scaffold, we are one step closer to a fully functional de novo designed nitrite reductase.

}, issn = {0949-8257}, doi = {10.1007/s00775-021-01889-1}, url = {https://link.springer.com/10.1007/s00775-021-01889-1}, author = {Koebke, Karl J. and Tebo, Alison G. and Manickas, Elizabeth C. and Deb, Aniruddha and Penner-Hahn, James E. and Pecoraro, Vincent L.} } @article {67773, title = {Non-preferred contrast responses in the Drosophila motion pathways reveal a receptive field structure that explains a common visual illusion.}, journal = {Current Biology}, volume = {31}, year = {2021}, month = {2021 Dec 06}, pages = {5286}, abstract = {

Diverse sensory systems, from audition to thermosensation, feature a separation of inputs into ON (increments) and OFF (decrements) signals. In the Drosophila visual system, separate ON and OFF pathways compute the direction of motion, yet anatomical and functional studies have identified some crosstalk between these channels. We used this well-studied circuit to ask whether the motion computation depends on ON-OFF pathway crosstalk. Using whole-cell electrophysiology, we recorded visual responses of T4 (ON) and T5 (OFF) cells, mapped their composite ON-OFF receptive fields, and found that they share a similar spatiotemporal structure. We fit a biophysical model to these receptive fields that accurately predicts directionally selective T4 and T5 responses to both ON and OFF moving stimuli. This model also provides a detailed mechanistic explanation for the directional preference inversion in response to the prominent reverse-phi illusion. Finally, we used the steering responses of tethered flying flies to validate the model{\textquoteright}s predicted effects of varying stimulus parameters on the behavioral turning inversion.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2021.09.072}, author = {Gruntman, Eyal and Reimers, Pablo and Romani, Sandro and Reiser, Michael B} } @article {67181, title = {A novel family of secreted insect proteins linked to plant gall development.}, journal = {Current Biology}, volume = {31}, year = {2021}, month = {2021 May 10}, pages = {1836}, abstract = {

In an elaborate form of inter-species exploitation, many insects hijack plant development to induce novel plant organs called galls that provide the insect with a source of nutrition and a temporary home. Galls result from dramatic reprogramming of plant cell biology driven by insect molecules, but the roles of specific insect molecules in gall development have not yet been determined. Here, we study the aphid Hormaphis cornu, which makes distinctive "cone" galls on leaves of witch hazel Hamamelis virginiana. We found that derived genetic variants in the aphid gene determinant of gall color (dgc) are associated with strong downregulation of dgc transcription in aphid salivary glands, upregulation in galls of seven genes involved in anthocyanin synthesis, and deposition of two red anthocyanins in galls. We hypothesize that aphids inject DGC protein into galls and that this results in differential expression of a small number of plant genes. dgc is a member of a large, diverse family of novel predicted secreted proteins characterized by a pair of widely spaced cysteine-tyrosine-cysteine (CYC) residues, which we named BICYCLE proteins. bicycle genes are most strongly expressed in the salivary glands specifically of galling aphid generations, suggesting that they may regulate many aspects of gall development. bicycle genes have experienced unusually frequent diversifying selection, consistent with their potential role controlling gall development in a molecular arms race between aphids and their host plants.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2021.01.104}, author = {Korgaonkar, Aishwarya and Han, Clair and Lemire, Andrew L and Siwanowicz, Igor and Bennouna, Djawed and Kopec, Rachel E and Andolfatto, Peter and Shigenobu, Shuji and Stern, David L} } @article {65262, title = {Nanoscale subcellular architecture revealed by multicolor three-dimensional salvaged fluorescence imaging.}, journal = {Nature Methods}, volume = {17}, year = {2020}, month = {2020 Jan 06}, pages = {225-231}, abstract = {

Combining the molecular specificity of fluorescent probes with three-dimensional imaging at nanoscale resolution is critical for investigating the spatial organization and interactions of cellular organelles and protein complexes. We present a 4Pi single-molecule switching super-resolution microscope that enables ratiometric multicolor imaging of mammalian cells at 5-10-nm localization precision in three dimensions using {\textquoteright}salvaged fluorescence{\textquoteright}. Imaging two or three fluorophores simultaneously, we show fluorescence images that resolve the highly convoluted Golgi apparatus and the close contacts between the endoplasmic reticulum and the plasma membrane, structures that have traditionally been the imaging realm of electron microscopy. The salvaged fluorescence approach is equally applicable in most single-objective microscopes.

}, issn = {1548-7105}, doi = {10.1038/s41592-019-0676-4}, author = {Zhang, Yongdeng and Schroeder, Lena K and Lessard, Mark D and Kidd, Phylicia and Chung, Jeeyun and Song, Yuanbin and Benedetti, Lorena and Li, Yiming and Ries, Jonas and Grimm, Jonathan B and Lavis, Luke D and De Camilli, Pietro and Rothman, James E and Baddeley, David and Bewersdorf, Joerg} } @article {65604, title = {Nanoscopic visualization of restricted nonvolume cholinergic and monoaminergic transmission with genetically encoded sensors.}, journal = {Nano Letters}, volume = {20}, year = {2020}, month = {2020 Jun}, pages = {4073-83}, abstract = {

How neuromodulatory transmitters diffuse into the extracellular space remains an unsolved fundamental biological question, despite wide acceptance of the volume transmission model. Here, we report development of a method combining genetically encoded fluorescent sensors with high-resolution imaging and analysis algorithms which permits the first direct visualization of neuromodulatory transmitter diffusion at various neuronal and non-neuronal cells. Our analysis reveals that acetylcholine and monoamines diffuse at individual release sites with a spread length constant of \~{}0.75 μm. These transmitters employ varied numbers of release sites, and when spatially close-packed release sites coactivate they can spillover into larger subcellular areas. Our data indicate spatially restricted (i.e., nonvolume) neuromodulatory transmission to be a prominent intercellular communication mode, reshaping current thinking of control and precision of neuromodulation crucial for understanding behaviors and diseases.

}, issn = {1530-6992}, doi = {10.1021/acs.nanolett.9b04877}, author = {Zhu, Paula K and Zheng, W Sharon and Zhang, Peng and Jing, Miao and Borden, Philip M and Ali, Farhan and Guo, Kaiming and Feng, Jiesi and Marvin, Jonathan S and Wang, Yali and Wan, Jinxia and Gan, Li and Kwan, Alex C and Lin, Li and Looger, Loren L and Li, Yulong and Zhang, Yajun} } @article {65317, title = {Neural circuitry linking mating and egg laying in Drosophila females.}, journal = {Nature}, volume = {579}, year = {2020}, month = {2020 Mar 02}, pages = {101-105}, abstract = {

Mating and egg laying are tightly cooordinated events in the reproductive life of\ all oviparous females. Oviposition is typically rare in virgin females but is initiated after copulation. Here we identify the neural circuitry that links egg laying to mating status in Drosophila melanogaster. Activation of female-specific oviposition descending neurons (oviDNs) is necessary and sufficient for egg laying, and is equally potent in virgin and mated females. After mating, sex peptide-a protein from the male seminal fluid-triggers many behavioural and physiological changes in the female, including the onset of egg laying. Sex peptide is detected by sensory neurons in the uterus, and silences these neurons and their postsynaptic ascending neurons in the abdominal ganglion. We show that these\ abdominal ganglion neurons directly activate the female-specific pC1 neurons. GABAergic (γ-aminobutyric-acid-releasing) oviposition inhibitory neurons (oviINs) mediate feed-forward inhibition from pC1 neurons to both oviDNs and their major excitatory input, the oviposition excitatory neurons (oviENs). By attenuating the abdominal ganglion inputs to pC1 neurons and oviINs, sex peptide disinhibits oviDNs to enable egg laying after mating. This circuitry thus coordinates the two key events in female reproduction: mating and egg laying.

}, issn = {1476-4687}, doi = {10.1038/s41586-020-2055-9}, author = {Wang, Fei and Wang, Kaiyu and Forknall, Nora and Patrick, Christopher and Yang, Tansy and Parekh, Ruchi and Bock, Davi and Dickson, Barry J} } @article {65598, title = {A neural representation of naturalistic motion-guided behavior in the zebrafish brain.}, journal = {Current Biology}, volume = {30}, year = {2020}, month = {2020 Jun 22}, pages = {2321-33}, abstract = {

All animals must transform ambiguous sensory data into successful behavior. This requires sensory representations that accurately reflect the statistics of natural stimuli and behavior. Multiple studies show that visual motion processing is tuned for accuracy under naturalistic conditions, but the sensorimotor circuits extracting these cues and implementing motion-guided behavior remain unclear. Here we show that the larval zebrafish retina extracts a diversity of naturalistic motion cues, and the retinorecipient pretectum organizes these cues around the elements of behavior. We find that higher-order motion stimuli, gliders, induce optomotor behavior matching expectations from natural scene analyses. We then image activity of retinal ganglion cell terminals and pretectal neurons. The retina exhibits direction-selective responses across glider stimuli, and anatomically clustered pretectal neurons respond with magnitudes matching behavior. Peripheral computations thus reflect natural input statistics, whereas central brain activity precisely codes information needed for behavior. This general principle could organize sensorimotor transformations across animal species.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2020.04.043}, author = {Yildizoglu, Tugce and Riegler, Clemens and Fitzgerald, James E and Portugues, Ruben} } @article {65722, title = {The neuroanatomical ultrastructure and function of a biological ring attractor.}, journal = {Neuron}, volume = {108}, year = {2020}, month = {2020 Oct 14}, pages = {145-63}, abstract = {

Neural representations of head direction (HD) have been discovered in many species. Theoretical work has proposed that the dynamics associated with these representations are generated, maintained, and updated by recurrent network structures called ring attractors. We evaluated this theorized structure-function relationship by performing electron-microscopy-based circuit reconstruction and RNA profiling of identified cell types in the HD system of Drosophila melanogaster. We identified motifs that have been hypothesized to maintain the HD representation in darkness, update it when the animal turns, and tether it to visual cues. Functional studies provided support for the proposed roles of individual excitatory or inhibitory circuit elements in shaping activity. We also discovered recurrent connections between neuronal arbors with mixed pre- and postsynaptic specializations. Our results confirm that the Drosophila HD network contains the core components of a ring attractor while also revealing unpredicted structural features that might enhance the network{\textquoteright}s computational power.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2020.08.006}, author = {Turner-Evans, Daniel B and Jensen, Kristopher T and Ali, Saba and Paterson, Tyler and Sheridan, Arlo and Ray, Robert P and Wolff, Tanya and Lauritzen, J Scott and Rubin, Gerald M and Bock, Davi D and Jayaraman, Vivek} } @article {65374, title = {Neuronal upregulation of Prospero protein is driven by alternative mRNA polyadenylation and Syncrip-mediated mRNA stabilisation.}, journal = {Biology Open}, volume = {9}, year = {2020}, month = {2020 May}, abstract = {

During and vertebrate brain development, the conserved transcription factor Prospero/Prox1 is an important regulator of the transition between proliferation and differentiation. Prospero level is low in neural stem cells and their immediate progeny, but is upregulated in larval neurons and it is unknown how this process is controlled. Here, we use single molecule fluorescent hybridisation to show that larval neurons selectively transcribe a long mRNA isoform containing a 15 kb 3{\textquoteright} untranslated region, which is bound in the brain by the conserved RNA-binding protein Syncrip/hnRNPQ. Syncrip binding increases the mRNA stability of the long isoform, which allows an upregulation of Prospero protein production. Adult flies selectively lacking the long isoform show abnormal behaviour that could result from impaired locomotor or neurological activity. Our findings highlight a regulatory strategy involving alternative polyadenylation followed by differential post-transcriptional regulation.

}, issn = {2046-6390}, doi = {10.1242/bio.049684}, author = {Samuels, Tamsin J and Arava, Yoav and J{\"a}rvelin, Aino I and Robertson, Francesca and Lee, Jeffrey Y and Yang, Lu and Yang, Ching-Po and Lee, Tzumin and Ish-Horowicz, David and Davis, Ilan} } @article {65263, title = {The neuropeptide Drosulfakinin regulates social isolation-induced aggression in Drosophila.}, journal = {Journal of Experimental Biology}, volume = {223}, year = {2020}, month = {2020 Jan 03}, abstract = {

Social isolation strongly modulates behavior across the animal kingdom. We utilized the fruit fly to study social isolation-driven changes in animal behavior and gene expression in the brain. RNA-seq identified several head-expressed genes strongly responding to social isolation or enrichment. Of particular interest, social isolation downregulated expression of the gene encoding the neuropeptide (), the homologue of vertebrate cholecystokinin (CCK), which is critical for many mammalian social behaviors. knockdown significantly increased social isolation-induced aggression. Genetic activation or silencing of neurons each similarly increased isolation-driven aggression. Our results suggest a U-shaped dependence of social isolation-induced aggressive behavior on signaling, similar to the actions of many neuromodulators in other contexts.

}, issn = {1477-9145}, doi = {10.1242/jeb.207407}, author = {Agrawal, Pavan and Kao, Damian and Chung, Phuong and Looger, Loren L} } @article {65318, title = {Nicotine exposure and neuronal activity regulate Golgi membrane dispersal and distribution}, journal = {bioRxiv}, year = {2020}, month = {2020 Feb 26}, abstract = {

How nicotine exposure produces long-lasting changes that remodel neural circuits with addiction is unknown. Here, we report that long-term nicotine exposure alters the trafficking of α4β2-type nicotinic acetylcholine receptors (α4β2Rs) by dispersing and redistributing the Golgi apparatus. In cultured neurons, dispersed Golgi membranes were distributed throughout somata, dendrites and axons. Small, mobile vesicles in dendrites and axons lacked standard Golgi markers and were identified by other Golgi enzymes that modify glycans. Nicotine exposure increased levels of dispersed Golgi membranes, which required α4β2R expression. Similar nicotine-induced changes occurred\ in vivo\ at dopaminergic neurons at mouse nucleus accumbens terminals, consistent with these events contributing to nicotine{\textquoteright}s addictive effects. Characterization\ in vitro\ demonstrated that dispersal was reversible, that dispersed Golgi membranes were functional, and that membranes were heterogenous in size, with smaller vesicles emerging from larger {\textquotedblleft}ministacks{\textquotedblright}, similar to Golgi dispersal induced by nocadazole. Protocols that increased cultured neuronal synaptic excitability also increased Golgi dispersal, without the requirement of α4β2R expression. Our findings reveal novel activity- and nicotine-dependent changes in neuronal intracellular morphology. These changes regulate levels and location of dispersed Golgi membranes at dendrites and axons, which function in local trafficking at subdomains.

}, author = {Govind, Anitha P. and Jeyifous, Okunola and Russell, Theron A. and Vaasjo, Lee O. and Yi, Zola and Weigel, Aubrey V. and Newell, Luke and Koranda, Jessica L. and Singh, Karanveer and Valbuena, Fernando and Glick, Benjamin S. and Mukherjee, Jogeshwar and Lippincott-Schwartz, Jennifer and Zhuang, Xiaoxi and Green, William N.} } @article {65724, title = {Novel fluorescent ligands enable single-molecule localization microscopy of the dopamine transporter.}, journal = {ACS Chemical Neuroscience}, year = {2020}, month = {2020 Sep 14}, abstract = {

The dopamine transporter (DAT) is critical for spatiotemporal control of dopaminergic neurotransmission and the target for therapeutic agents, including ADHD medications, and abused substances, such as cocaine. Here, we develop new fluorescently labeled ligands that bind DAT with high affinity and enable single-molecule detection of the transporter. The cocaine analogue MFZ2-12 (1) was conjugated to novel rhodamine-based Janelia Fluorophores (JF549 and JF646). High affinity binding of the resulting ligands to DAT was demonstrated by potent inhibition of [3H]dopamine uptake in DAT transfected CAD cells and by competition radioligand binding experiments on rat striatal membranes. Visualization of binding was substantiated by confocal or TIRF microscopy revealing selective binding of the analogues to DAT transfected CAD cells. Single particle tracking experiments were performed with JF549-conjugated DG3-80 (3) and JF646-conjugated DG4-91 (4) on DAT transfected CAD cells enabling quantification and categorization of the dynamic behavior of DAT into four distinct motion classes (immobile, confined, Brownian, and directed). Finally, we show that the ligands can be used in direct stochastic optical reconstruction microscopy (dSTORM) experiments permitting further analyses of DAT distribution on the nanoscale. In summary, these novel fluorescent ligands are promising new tools for studying DAT localization and regulation with single-molecule resolution.

}, issn = {1948-7193}, doi = {10.1021/acschemneuro.0c00397}, author = {Guthrie, Daryl and Klein Herenbrink, Carmen and Lycas, Matthew and Ku, Therese and Bonifazi, Alessandro and DeVree, Brian and Mathiasen, Signe and Javitch, Jonathan and Grimm, Jonathan B and Lavis, Luke D and Gether, Ulrik and Newman, Amy Hauck} } @article {65758, title = {Nuclear crowding and nonlinear diffusion during interkinetic nuclear migration in the zebrafish retina.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Oct 06}, abstract = {

An important question in early neural development is the origin of stochastic nuclear movement between apical and basal surfaces of neuroepithelia during interkinetic nuclear migration. Tracking of nuclear subpopulations has shown evidence of diffusion - mean squared displacements growing linearly in time - and suggested crowding from cell division at the apical surface drives basalward motion. Yet, this hypothesis has not yet been tested, and the forces involved not quantified. We employ long-term, rapid light-sheet and two-photon imaging of early zebrafish retinogenesis to track entire populations of nuclei within the tissue. The time-varying concentration profiles show clear evidence of crowding as nuclei reach close-packing and are quantitatively described by a nonlinear diffusion model. Considerations of nuclear motion constrained inside the enveloping cell membrane show that concentration-dependent stochastic forces inside cells, compatible in magnitude to those found in cytoskeletal transport, can explain the observed magnitude of the diffusion constant.

}, issn = {2050-084X}, doi = {10.7554/eLife.58635}, author = {Azizi, Afnan and Herrmann, Anne and Wan, Yinan and Buse, Salvador Jrp and Keller, Philipp J and Goldstein, Raymond E and Harris, William A} } @article {68427, title = {Nurturing Undergraduate Researchers in Biomedical Sciences.}, journal = {Cell}, volume = {182}, year = {2020}, month = {07/2020}, pages = {1-4}, abstract = {

Undergraduate researchers are the next-generation scientists. Here, we call for more attention from our community to the proper training of undergraduates in biomedical research laboratories. By dissecting common pitfalls, we suggest how to better mentor undergraduates and prepare them for flourishing careers.

}, keywords = {Biomedical Research, Communication, Mentoring, Mentors, Research Personnel}, issn = {1097-4172}, doi = {10.1016/j.cell.2020.05.008}, author = {Li, Jiefu and Luo, Liqun} } @article {64987, title = {NDP52 tunes cortical actin interaction with astral microtubules for accurate spindle orientation.}, journal = {Cell Research}, volume = {29}, year = {2019}, month = {2019 Jun 14}, pages = {666-79}, abstract = {

Oriented cell divisions are controlled by a conserved molecular cascade involving Gαi, LGN, and NuMA. Here, we show that NDP52 regulates spindle orientation via remodeling the polar cortical actin cytoskeleton. siRNA-mediated NDP52 suppression surprisingly revealed a ring-like compact subcortical F-actin architecture surrounding the spindle in prophase/prometaphase cells, which resulted in severe defects of astral microtubule growth and an aberrant spindle orientation. Remarkably, NDP52 recruited the actin assembly factor N-WASP and regulated the dynamics of the subcortical F-actin ring in mitotic cells. Mechanistically, NDP52 was found to bind to phosphatidic acid-containing vesicles, which absorbed cytoplasmic N-WASP to regulate local filamentous actin growth at the polar cortex. Our TIRFM analyses revealed that NDP52-containing vesicles anchored N-WASP and shortened the length of actin filaments in vitro. Based on these results we propose that NDP52-containing vesicles regulate cortical actin dynamics through N-WASP to accomplish a spatiotemporal regulation between astral microtubules and the actin network for proper spindle orientation and precise chromosome segregation. In this way, intracellular vesicles cooperate with microtubules and actin filaments to regulate proper mitotic progression. Since NDP52 is absent from yeast, we reason that metazoans have evolved an elaborate spindle positioning machinery to ensure accurate chromosome segregation in mitosis.

}, issn = {1748-7838}, doi = {10.1038/s41422-019-0189-9}, author = {Yu, Huijuan and Yang, Fengrui and Dong, Peng and Liao, Shanhui and Liu, Wei R and Zhao, Gangyin and Qin, Bo and Dou, Zhen and Liu, Zhe and Liu, Wei and Zang, Jianye and Lippincott-Schwartz, Jennifer and Liu, Xing and Yao, Xuebiao} } @article {64825, title = {Neural basis for looming size and velocity encoding in the Drosophila giant fiber escape pathway.}, journal = {Current Biology : CB}, volume = {29}, year = {2019}, month = {2019 Feb 28}, pages = {1073}, abstract = {

Identified neuron classes in vertebrate cortical [1-4] and subcortical [5-8] areas and invertebrate peripheral [9-11] and central [12-14] brain neuropils encode specific visual features of a panorama. How downstream neurons integrate these features to control vital behaviors, like escape, is unclear [15]. In Drosophila, the timing of a single spike in the giant fiber (GF) descending neuron [16-18] determines whether a fly uses a short or long takeoff when escaping a looming predator [13]. We previously proposed that GF spike timing results from summation of two visual features whose detection is highly conserved across animals [19]: an object{\textquoteright}s subtended angular size and its angular velocity [5-8, 11, 20, 21]. We attributed velocity encoding to input from lobula columnar type 4 (LC4) visual projection neurons, but the size-encoding\ source remained unknown. Here, we show that lobula plate/lobula columnar, type 2 (LPLC2) visual projection neurons anatomically specialized to detect looming [22] provide the entire GF size component. We find LPLC2 neurons to be necessary for GF-mediated escape and show that LPLC2 and LC4 synapse directly onto the GF via reconstruction in a fly brain electron microscopy (EM) volume [23]. LPLC2 silencing eliminates the size component of the GF looming response in patch-clamp recordings, leaving only the velocity component. A model summing a linear function of angular velocity (provided by LC4) and a Gaussian function of angular size (provided by LPLC2) replicates GF looming response dynamics and predicts the peak response time. We thus present an identified circuit in which information from looming feature-detecting neurons is combined by a common post-synaptic target to determine behavioral output.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2019.01.079}, author = {Ache, Jan M and Polsky, Jason and Alghailani, Shada and Parekh, Ruchi and Breads, Patrick and Peek, Martin Y and Bock, Davi D and von Reyn, Catherine R and Card, Gwyneth M} } @article {65141, title = {A neural circuit arbitrates between persistence and withdrawal in hungry drosophila.}, journal = {Neuron}, volume = {104}, year = {2019}, month = {2019 Nov 6}, pages = {544-58}, abstract = {

In pursuit of food, hungry animals mobilize significant energy resources and overcome exhaustion and fear. How need and motivation control the decision to continue or change behavior is not understood. Using a single fly treadmill, we show that hungry flies persistently track a food odor and increase their effort over repeated trials in the absence of reward suggesting that need dominates negative experience. We further show that odor tracking is regulated by two mushroom body output neurons (MBONs) connecting the MB to the lateral horn. These MBONs, together with dopaminergic neurons and Dop1R2 signaling, control behavioral persistence. Conversely, an octopaminergic neuron, VPM4, which directly innervates one of the MBONs, acts as a brake on odor tracking by connecting feeding and olfaction. Together, our data suggest a function for the\ MB in internal state-dependent expression of behavior that can be suppressed by external inputs conveying a competing behavioral drive.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2019.07.028}, author = {Sayin, Sercan and De Backer, Jean-Francois and Siju, K P and Wosniack, Marina E and Lewis, Laurence P and Frisch, Lisa-Marie and Gansen, Benedikt and Schlegel, Philipp and Edmondson-Stait, Amelia and Sharifi, Nadiya and Fisher, Corey B and Calle-Schuler, Steven A and Lauritzen, J Scott and Bock, Davi D and Costa, Marta and Jefferis, Gregory S X E and Gjorgjieva, Julijana and Grunwald Kadow, Ilona C} } @article {65207, title = {A Neural Circuit Arbitrates between Persistence and Withdrawal in Hungry Drosophila.}, journal = {Neuron}, year = {2019}, month = {2019 Aug 09}, abstract = {

In pursuit of food, hungry animals mobilize significant energy resources and overcome exhaustion and fear. How need and motivation control the decision to continue or change behavior is not understood. Using a single fly treadmill, we show that hungry flies persistently track a food odor and increase their effort over repeated trials in the absence of reward suggesting that need dominates negative experience. We further show that odor tracking is regulated by two mushroom body output neurons (MBONs) connecting the MB to the lateral horn. These MBONs, together with dopaminergic neurons and Dop1R2 signaling, control behavioral persistence. Conversely, an octopaminergic neuron, VPM4, which directly innervates one of the MBONs, acts as a brake on odor tracking by connecting feeding and olfaction. Together, our data suggest a function for the\ MB in internal state-dependent expression of behavior that can be suppressed by external inputs conveying a competing behavioral drive.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2019.07.028}, author = {Sayin, Sercan and De Backer, Jean-Francois and Siju, K P and Wosniack, Marina E and Lewis, Laurence P and Frisch, Lisa-Marie and Gansen, Benedikt and Schlegel, Philipp and Edmondson-Stait, Amelia and Sharifi, Nadiya and Fisher, Corey B and Calle-Schuler, Steven A and Lauritzen, J Scott and Bock, Davi D and Costa, Marta and Jefferis, Gregory S X E and Gjorgjieva, Julijana and Grunwald Kadow, Ilona C} } @article {64917, title = {A neural circuit encoding the experience of copulation in female Drosophila.}, journal = {Neuron}, volume = {102}, year = {2019}, month = {2019 Apr 26}, pages = {1025}, abstract = {

Female behavior changes profoundly after mating. In Drosophila, the mechanisms underlying the long-term changes led by seminal products have been extensively studied. However, the effect of the sensory component of copulation on the female{\textquoteright}s internal state and behavior remains elusive. We pursued this question by dissociating the effect of coital sensory inputs from those of male ejaculate. We found that the sensory inputs of copulation cause a reduction of post-coital receptivity in females, referred to as the "copulation effect." We identified three layers of a neural circuit underlying this phenomenon. Abdominal neurons expressing the mechanosensory channel Piezo convey the signal of copulation to female-specific ascending neurons, LSANs, in the ventral nerve cord. LSANs relay this information to neurons expressing myoinhibitory peptides in the brain. We hereby provide a\ neural mechanism by which the experience of\ copulation facilitates females encoding their mating\ status, thus adjusting behavior to optimize reproduction.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2019.04.009}, author = {Shao, Lisha and Chung, Phuong and Wong, Allan and Siwanowicz, Igor and Kent, Clement F and Long, Xi and Heberlein, Ulrike} } @conference {67294, title = {Neural Correlates of Cognition in Primary Visual versus Downstream Posterior Cortices During Evidence Accumulation}, booktitle = {APS March Meeting Abstracts}, year = {2019}, month = {01/2019}, abstract = {

The ability of animals to accumulate sensory information across time is fundamental to decision-making. Using a mouse behavioral paradigm where navigational decisions are based on accumulating pulses of visual cues, I compared neural activity in primary visual (V1) to secondary visual and retrosplenial cortices. Even in V1, only a small fraction of neurons had sensory-like responses to cues. Instead, all areas were grossly similar in how neural populations contained a large variety of task-related information from sensory to cognitive, including cue timings, accumulated counts, place/time, decision and reward outcome. Across-trial influences were prevalent, possibly relevant to how animal behavior incorporates past contexts. Intriguingly, all these variables also modulated the amplitudes of sensory responses. While previous work often modeled the accumulation process as integration, the observed scaling of sensory responses by accumulated counts instead suggests a recursive process where sensory responses are gradually amplified. I show that such a multiplicative feedback-loop algorithm better explains psychophysical data than integration, particularly in how the performance transitions into following Weber-Fechner{\textquoteright}s Law only at high counts.

}, url = {https://ui.adsabs.harvard.edu/abs/2019APS..MARP67013K/abstract}, author = {Koay, Sue Ann and Tank, David and Brody, Carlos} } @article {67287, title = {Neural Correlates of Cognition in Primary Visual versus Neighboring Posterior Cortices during Visual Evidence-Accumulation-based Navigation}, journal = {bioRxiv}, year = {2019}, month = {03/2019}, abstract = {

Studies of perceptual decision-making have often assumed that the main role of sensory cortices is to provide sensory input to downstream processes that accumulate and drive behavioral decisions. We performed a systematic comparison of neural activity in primary visual (V1) to secondary visual and retrosplenial cortices, as mice performed a task where they should accumulate pulsatile visual cues through time to inform a navigational decision. Even in V1, only a small fraction of neurons had sensory-like responses to cues. Instead, in all areas neurons were sequentially active, and contained information ranging from sensory to cognitive, including cue timings, evidence, place/time, decision and reward outcome. Per-cue sensory responses were amplitude-modulated by various cognitive quantities, notably accumulated evidence. This inspired a multiplicative feedback-loop circuit hypothesis that proposes a more intricate role of sensory areas in the accumulation process, and furthermore explains a surprising observation that perceptual discrimination deviates from Weber-Fechner Law.Highlights / eTOC BlurbMice made navigational decisions based on accumulating pulsatile visual cuesThe bulk of neural activity in visual cortices was sequential and beyond-sensoryAccumulated pulse-counts modulated sensory (cue) responses, suggesting feedbackA feedback-loop neural circuit explains behavioral deviations from Weber{\textquoteright}s LawHighlights / eTOC BlurbIn a task where navigation was informed by accumulated pulsatile visual evidence, neural activity in visual cortices predominantly coded for cognitive variables across multiple timescales, including outside of a visual processing context. Even sensory responses to visual pulses were amplitude-modulated by accumulated pulse counts and other variables, inspiring a multiplicative feedback-loop circuit hypothesis that in turn explained behavioral deviations from Weber-Fechner Law.

}, doi = {10.1101/568766}, url = {https://www.biorxiv.org/content/early/2019/03/06/568766}, author = {Koay, Sue Ann and Thiberge, Stephan Y. and Brody, Carlos D. and Tank, David W.} } @article {64841, title = {Neural evolution of context-dependent fly song.}, journal = {Current Biology : CB}, volume = {29}, year = {2019}, month = {2019 Mar 08}, pages = {1089-99}, abstract = {

It is unclear where in the nervous system evolutionary changes tend to occur. To localize the source of neural evolution that has generated divergent behaviors, we developed a new approach to label and functionally manipulate homologous neurons across Drosophila species. We examined homologous descending neurons that drive courtship song in two species that sing divergent song types and localized relevant evolutionary changes in circuit function downstream of the intrinsic physiology of these descending neurons. This evolutionary change causes different species to produce divergent motor patterns in similar social contexts. Artificial stimulation of these descending neurons drives multiple song types, suggesting that multifunctional properties of song circuits may facilitate rapid evolution of song types.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2019.02.019}, author = {Ding, Yun and Lillvis, Joshua L and Cande, Jessica and Berman, Gordon J and Arthur, Benjamin J and Long, Xi and Xu, Min and Dickson, Barry J and Stern, David L} } @article {64785, title = {Neural substrates of Drosophila larval anemotaxis.}, journal = {Current Biology : CB}, volume = {29}, year = {2019}, month = {2019 Jan 29}, pages = {554-66}, abstract = {

Animals use sensory information to move toward more favorable conditions. Drosophila larvae can move up or down gradients of odors (chemotax), light (phototax), and temperature (thermotax) by modulating the probability, direction, and size of turns based on sensory input. Whether larvae can anemotax in gradients of mechanosensory cues is unknown. Further, although many of the sensory neurons that mediate taxis have been described, the central circuits are not well understood. Here, we used high-throughput, quantitative behavioral assays to demonstrate Drosophila larvae anemotax in gradients of wind speeds and to characterize the behavioral strategies involved. We found that larvae modulate the probability, direction, and size of turns to move away from higher wind speeds. This suggests that similar central decision-making mechanisms underlie taxis in somatosensory and other sensory modalities. By silencing the activity of single or very few neuron types in a behavioral screen, we found two sensory (chordotonal and multidendritic class III) and six nerve cord neuron types involved in anemotaxis. We reconstructed the identified neurons in an electron microscopy volume that spans the entire larval nervous system and found they received direct input from the mechanosensory neurons or from each other. In this way, we identified local interneurons and first- and second-order subesophageal zone (SEZ) and brain projection neurons. Finally, silencing a dopaminergic brain neuron type impairs anemotaxis. These findings suggest that anemotaxis involves both nerve cord and brain circuits. The candidate neurons and circuitry identified in our study provide a basis for future detailed mechanistic understanding of the circuit principles of anemotaxis.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2019.01.009}, author = {Jovanic, Tihana and Winding, Michael and Cardona, Albert and Truman, James W and Gershow, Marc and Zlatic, Marta} } @article {64933, title = {Neurogenetic dissection of the lateral horn reveals major outputs, diverse behavioural functions, and interactions with the mushroom body.}, journal = {Elife}, volume = {8}, year = {2019}, month = {2019 May 21}, abstract = {

Animals exhibit innate behaviours to a variety of sensory stimuli including olfactory cues. In , one higher olfactory centre, the lateral horn (LH), is implicated in innate behaviour. However, our structural and functional understanding of the LH is scant, in large part due to a lack of sparse neurogenetic tools for this region. We generate a collection of split-GAL4 driver lines providing genetic access to 82 LH cell types. We use these to create an anatomical and neurotransmitter map of the LH and link this to EM connectomics data. We find ~30\% of LH projections converge with outputs from the mushroom body, site of olfactory learning and memory. Using optogenetic activation, we identify LH cell types that drive changes in valence behavior or specific locomotor programs. In summary, we have generated a resource for manipulating and mapping LH neurons, providing new insights into the circuit basis of innate and learned olfactory behavior.

}, issn = {2050-084X}, doi = {10.7554/eLife.43079}, author = {Dolan, Michael-John and Frechter, Shahar and Bates, Alexander Shakeel and Dan, Chuntao and Huoviala, Paavo and Roberts, Ruair{\'\i} Jv and Schlegel, Philipp and Dhawan, Serene and Tabano, Remy and Dionne, Heather and Christoforou, Christina and Close, Kari and Sutcliffe, Ben and Giuliani, Bianca and Li, Feng and Costa, Marta and Ihrke, Gudrun and Meissner, Geoffrey Wilson and Bock, Davi D and Aso, Yoshinori and Rubin, Gerald M and Jefferis, Gregory Sxe} } @article {67307, title = {Neuronal activity and learning in local cortical networks are modulated by the action-perception state}, journal = {bioRxiv}, year = {2019}, month = {2019 Feb 01}, abstract = {

During sensorimotor learning, neuronal networks change to optimize the associations between action and perception. In this study, we examine how the brain harnesses neuronal patterns that correspond to the current action-perception state during learning. To this end, we recorded activity from motor cortex while monkeys either performed a familiar motor task (movement-state) or learned to control the firing rate of a target neuron using a brain-machine interface (BMI-state). Before learning, monkeys were placed in an observation-state, where no action was required. We found that neuronal patterns during the BMI-state were markedly different from the movement-state patterns. BMI-state patterns were initially similar to those in the observation-state and evolved to produce an increase in the firing rate of the target neuron. The overall activity of the non-target neurons remained similar after learning, suggesting that excitatory-inhibitory balance was maintained. Indeed, a novel neural-level reinforcement-learning network model operating in a chaotic regime of balanced excitation and inhibition predicts our results in detail. We conclude that during BMI learning, the brain can adapt patterns corresponding to the current action-perception state to gain rewards. Moreover, our results show that we can predict activity changes that occur during learning based on the pre-learning activity. This new finding may serve as a key step toward clinical brain-machine interface applications to modify impaired brain activity.

}, doi = {10.1101/537613}, url = {https://doi.org/10.1101/537613}, author = {Ben Engelhard and Ran Darshan and Nofar Ozeri-Engelhard and Zvi Israel and Uri Werner-Reiss and David Hansel and Hagai Bergman and Eilon Vaadia} } @article {69339, title = {Neuronal morphologies built for reliable physiology in a rhythmic motor circuit}, journal = {eLife}, volume = {8}, year = {2019}, month = {2019 Jan 19}, pages = {e41728}, abstract = {

It is often assumed that highly-branched neuronal structures perform compartmentalized computations. However, previously we showed that the Gastric Mill (GM) neuron in the crustacean stomatogastric ganglion (STG) operates like a single electrotonic compartment, despite having thousands of branch points and total cable length \>10 mm (Otopalik et al., 2017a; 2017b). Here we show that compact electrotonic architecture is generalizable to other STG neuron types, and that these neurons present direction-insensitive, linear voltage integration, suggesting they pool synaptic inputs across their neuronal structures. We also show, using simulations of 720 cable models spanning a broad range of geometries and passive properties, that compact electrotonus, linear integration, and directional insensitivity in STG neurons arise from their neurite geometries (diameters tapering from 10-20 {\textmu}m to \uline\< 2 {\textmu}m at their terminal tips). A broad parameter search reveals multiple morphological and biophysical solutions for achieving different degrees of passive electrotonic decrement and computational strategies in the absence of active properties.

}, keywords = {cancer borealis, electrotonus, Stomatogastric ganglion, variability, voltage Integration}, issn = {2050-084X}, doi = {10.7554/eLife.41728}, url = {https://doi.org/10.7554/eLife.41728}, author = {Otopalik, Adriane G and Pipkin, Jason and Marder, Eve}, editor = {Slutsky, Inna and Calabrese, Ronald L} } @article {65107, title = {A neuronal pathway that commands deceleration in Drosophila larval light-avoidance.}, journal = {Neuroscience Bulletin}, volume = {35}, year = {2019}, month = {2019 Dec 1}, abstract = {

When facing a sudden danger or aversive condition while engaged in on-going forward motion, animals transiently slow down and make a turn to escape. The neural mechanisms underlying stimulation-induced deceleration in avoidance behavior are largely unknown. Here, we report that in Drosophila larvae, light-induced deceleration was commanded by a continuous neural pathway that included prothoracicotropic hormone neurons, eclosion hormone neurons, and tyrosine decarboxylase 2 motor neurons (the PET pathway). Inhibiting neurons in the PET pathway led to defects in light-avoidance due to insufficient deceleration and head casting. On the other hand, activation of PET pathway neurons specifically caused immediate deceleration in larval locomotion. Our findings reveal a neural substrate for the emergent deceleration response and provide a new understanding of the relationship between behavioral modules in animal avoidance responses.

}, issn = {1995-8218}, doi = {10.1007/s12264-019-00349-w}, author = {Gong, Caixia and Ouyang, Zhenhuan and Zhao, Weiqiao and Wang, Jie and Li, Kun and Zhou, Peipei and Zhao, Ting and Zheng, Nenggan and Gong, Zhefeng} } @article {64815, title = {Neuronal reactivation during post-learning sleep consolidates long-term memory in .}, journal = {eLife}, volume = {8}, year = {2019}, month = {2019 Feb 25}, abstract = {

Animals consolidate some, but not all, learning experiences into long-term memory. Across the animal kingdom, sleep has been found to have a beneficial effect on the consolidation of recently formed memories into long-term storage. However, the underlying mechanisms of sleep dependent memory consolidation are poorly understood. Here, we show that consolidation of courtship long-term memory in is mediated by reactivation during sleep of dopaminergic neurons that were earlier involved in memory acquisition. We identify specific fan-shaped body neurons that induce sleep after the learning experience and activate dopaminergic neurons for memory consolidation. Thus, we provide a direct link between sleep, neuronal reactivation of dopaminergic neurons, and memory consolidation.

}, issn = {2050-084X}, doi = {10.7554/eLife.42786}, author = {Dag, Ugur and Lei, Zhengchang and Le, Jasmine Q and Wong, Allan and Bushey, Daniel and Keleman, Krystyna} } @article {68992, title = {Neuronal Transdifferentiation Potential of Human Mesenchymal Stem Cells from Neonatal and Adult Sources by a Small Molecule Cocktail.}, journal = {Stem Cells Int}, volume = {2019}, year = {2019}, month = {04/2019}, pages = {7627148}, abstract = {

Human mesenchymal stem cells (MSCs) are good candidates for brain cell replacement strategies and have already been used as adjuvant treatments in neurological disorders. MSCs can be obtained from many different sources, and the present study compares the potential of neuronal transdifferentiation in MSCs from adult and neonatal sources (Wharton{\textquoteright}s jelly (WhJ), dental pulp (DP), periodontal ligament (PDL), gingival tissue (GT), dermis (SK), placenta (PLAC), and umbilical cord blood (UCB)) with a protocol previously tested in bone marrow- (BM-) MSCs consisting of a cocktail of six small molecules: I-BET151, CHIR99021, forskolin, RepSox, Y-27632, and dbcAMP (ICFRYA). Neuronal morphology and the presence of cells positive for neuronal markers (TUJ1 and MAP2) were considered attributes of neuronal induction. The ICFRYA cocktail did not induce neuronal features in WhJ-MSCs, and these features were only partial in the MSCs from dental tissues, SK-MSCs, and PLAC-MSCs. The best response was found in UCB-MSCs, which was comparable to the response of BM-MSCs. The addition of neurotrophic factors to the ICFRYA cocktail significantly increased the number of cells with complex neuron-like morphology and increased the number of cells positive for mature neuronal markers in BM- and UCB-MSCs. The neuronal cells generated from UCB-MSCs and BM-MSCs showed increased reactivity of the neuronal genes TUJ1, MAP2, NF-H, NCAM, ND1, TAU, ENO2, GABA, and NeuN as well as down- and upregulation of MSC and neuronal genes, respectively. The present study showed marked differences between the MSCs from different sources in response to the transdifferentiation protocol used here. These results may contribute to identifying the best source of MSCs for potential cell replacement therapies.

}, issn = {1687-966X}, doi = {10.1155/2019/7627148}, author = {Cort{\'e}s-Medina, Lorena V and Pasantes-Morales, Herminia and Aguilera-Castrejon, Alejandro and Picones, Arturo and Lara-Figueroa, Cesar O and Luis, Enoch and Montesinos, Juan Jose and Cort{\'e}s-Morales, Victor A and De la Rosa Ruiz, M P and Hern{\'a}ndez-Est{\'e}vez, Erika and Bonifaz, Laura C and Alvarez-Perez, Marco Antonio and Ramos-Mandujano, Gerardo} } @article {65067, title = {Neuron-astrocyte metabolic coupling protects against activity-induced fatty acid toxicity.}, journal = {Cell}, volume = {177}, year = {2019}, month = {2019 May 30}, pages = {1522-1535.e14}, abstract = {

Metabolic coordination between neurons and astrocytes is critical for the health of the brain. However, neuron-astrocyte coupling of lipid metabolism, particularly in response to neural activity, remains largely uncharacterized. Here, we demonstrate that toxic fatty acids (FAs) produced in hyperactive neurons are transferred to astrocytic lipid droplets by ApoE-positive lipid particles. Astrocytes consume the FAs stored in lipid droplets via mitochondrial β-oxidation in response to neuronal activity and turn on a detoxification gene expression program. Our findings reveal that FA metabolism is coupled in neurons and astrocytes to protect neurons from FA toxicity during periods of enhanced activity. This coordinated mechanism for metabolizing FAs could underlie both homeostasis and a variety of disease states of the brain.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2019.04.001}, author = {Ioannou, Maria S and Jackson, Jesse and Sheu, Shu-Hsien and Chang, Chi-Lun and Weigel, Aubrey V and Liu, Hui and Pasolli, H Amalia and Xu, C Shan and Pang, Song and Matthies, Doreen and Hess, Harald F and Lippincott-Schwartz, Jennifer and Liu, Zhe} } @article {65139, title = {A neuron-glia Co-culture system for studying intercellular lipid transport.}, journal = {Curr Protoc Cell Biol}, volume = {84}, year = {2019}, month = {2019 Sep 01}, pages = {e95}, abstract = {

Neurons and glia operate in a highly coordinated fashion in the brain. Although glial cells have long been known to supply lipids to neurons via lipoprotein particles, new evidence reveals that lipid transport between neurons and glia is bidirectional. Here, we describe a co-culture system to study transfer of lipids and lipid-associated proteins from neurons to glia. The assay entails culturing neurons and glia on separate coverslips, pulsing the neurons with fluorescently labeled fatty acids, and then incubating the coverslips together. As astrocytes internalize and store neuron-derived fatty acids in lipid droplets, analyzing the number, size, and fluorescence intensity of lipid droplets containing the fluorescent fatty acids provides an easy and quantifiable measure of fatty acid transport. {\textcopyright} 2019 The Authors.

}, issn = {1934-2616}, doi = {10.1002/cpcb.95}, author = {Ioannou, Maria S and Liu, Zhe and Lippincott-Schwartz, Jennifer} } @article {65261, title = {Neuropixels data-acquisition system: A scalable platform for parallel recording of 10 000+ electrophysiological signals.}, journal = {IEEE Transactions on Biomedical Circuits and Systems}, volume = {13}, year = {2019}, month = {2019 Dec 01}, pages = {1635-1644}, abstract = {

Although CMOS fabrication has enabled a quick evolution in the design of high-density neural probes and neural-recording chips, the scaling and miniaturization of the complete data-acquisition systems has happened at a slower pace. This is mainly due to the complexity and the many requirements that change depending on the specific experimental settings. In essence, the fundamental challenge of a neural-recording system is getting the signals describing the largest possible set of neurons out of the brain and down to data storage for analysis. This requires a complete system optimization that considers the physical, electrical, thermal and signal-processing requirements, while accounting for available technology, manufacturing constraints and budget. Here we present a scalable and open-standards-based open-source data-acquisition system capable of recording from over 10,000 channels of raw neural data simultaneously. The components and their interfaces have been optimized to ensure robustness and minimum invasiveness in small-rodent electrophysiology.

}, issn = {1940-9990}, doi = {10.1109/TBCAS.2019.2943077}, author = {Putzeys, Jan and Musa, Silke and Mora Lopez, Carolina and Raducanu, Bogdan C and Carton, Alain and De Ceulaer, Jef and Karsh, Bill and Siegle, Joshua H and Van Helleputte, Nick and Harris, Timothy D and Dutta, Barundeb} } @conference {65315, title = {The Neuropixels probe: A CMOS based integrated microsystems platform for neuroscience and brain-computer interfaces.}, booktitle = {2019 IEEE International Electron Devices Meeting (IEDM)}, year = {2019}, month = {2020 Feb 13}, publisher = {IEEE}, organization = {IEEE}, address = {San Francisco, CA, USA}, abstract = {

We review recent progress in neural probes for brain recording, with a focus on the Neuropixels platform. Historically the number of neurons{\textquoteright} recorded simultaneously, follows a Moore{\textquoteright}s law like behavior, with numbers doubling every 6.7 years. Using traditional techniques of probe fabrication, continuing to scale up electrode densities is very challenging. We describe a custom CMOS process technology that enables electrode counts well beyond 1000 electrodes; with the aim to characterize large neural populations with single neuron spatial precision and millisecond timing resolution. This required integrating analog and digital circuitry with the electrode array, making it a standalone integrated electrophysiology recording system. Input referred noise and power per channel is 7.5{\textmu}V and \<50{\textmu}W respectively to ensure tissue heating \<1{\textdegree}C. This approach enables doubling the number of measured neurons every 12 months.

}, doi = {10.1109/IEDM19573.201910.1109/IEDM19573.2019.8993611}, url = {https://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?punumber=8971803https://ieeexplore.ieee.org/document/8993611/http://xplorestaging.ieee.org/ielx7/8971803/8993428/08993611.pdf?arnumber=8993611}, author = {Dutta, B. and Trautmann, E. M. and Welkenhuysen, M. and Shenoy, K. V. and Andrei, A. and Harris, T. D. and Lopez, C. M. and O{\textquoteright}Callahan, J. and Putzeys, J. and Raducanu, B. C. and Severi, S. and Stavisky, S. D.} } @article {64849, title = {Neurotransmitter identity is acquired in a lineage-restricted manner in the Drosophila CNS.}, journal = {Elife}, volume = {8}, year = {2019}, month = {2019 Mar 26}, abstract = {

The vast majority of the adult fly ventral nerve cord is composed of 34 hemilineages, which are clusters of lineally related neurons. Neurons in these hemilineages use one of the three fast-acting neurotransmitters (acetylcholine, GABA, or glutamate) for communication. We generated a comprehensive neurotransmitter usage map for the entire ventral nerve cord. We did not find any cases of neurons using more than one neurotransmitter, but found that the acetylcholine specific gene ChAT is transcribed in many glutamatergic and GABAergic neurons, but these transcripts typically do not leave the nucleus and are not translated. Importantly, our work uncovered a simple rule: All neurons within a hemilineage use the same neurotransmitter. Thus, neurotransmitter identity is acquired at the stem cell level. Our detailed transmitter- usage/lineage identity map will be a great resource for studying the developmental basis of behavior and deciphering how neuronal circuits function to regulate behavior.

}, issn = {2050-084X}, doi = {10.7554/eLife.43701}, author = {Lacin, Haluk and Chen, Hui-Min and Long, Xi and Singer, Robert H and Lee, Tzumin and Truman, James W} } @article {65227, title = {Nitric oxide acts as a cotransmitter in a subset of dopaminergic neurons to diversify memory dynamics.}, journal = {eLife}, volume = {8}, year = {2019}, month = {2019 Nov 14}, abstract = {

Animals employ diverse learning rules and synaptic plasticity dynamics to record temporal and statistical information about the world. However, the molecular mechanisms underlying this diversity are poorly understood. The anatomically defined compartments of the insect mushroom body function as parallel units of associative learning, with different learning rates, memory decay dynamics and flexibility (Aso \& Rubin 2016). Here we show that nitric oxide (NO) acts as a neurotransmitter in a subset of dopaminergic neurons in . NO{\textquoteright}s effects develop more slowly than those of dopamine and depend on soluble guanylate cyclase in postsynaptic Kenyon cells. NO acts antagonistically to dopamine; it shortens memory retention and facilitates the rapid updating of memories. The interplay of NO and dopamine enables memories stored in local domains along Kenyon cell axons to be specialized for predicting the value of odors based only on recent events. Our results provide key mechanistic insights into how diverse memory dynamics are established in parallel memory systems.

}, issn = {2050-084X}, doi = {10.7554/eLife.49257}, author = {Aso, Yoshinori and Ray, Robert P and Long, Xi and Bushey, Daniel and Cichewicz, Karol and Ngo, Teri-Tb and Sharp, Brandi and Christoforou, Christina and Hu, Amy and Lemire, Andrew L and Tillberg, Paul and Hirsh, Jay and Litwin-Kumar, Ashok and Rubin, Gerald M} } @article {65035, title = {Novel Complex Interactions between Mitochondrial and Nuclear DNA in Schizophrenia and Bipolar Disorder.}, journal = {Mol Neuropsychiatry}, volume = {5}, year = {2019}, month = {2019 Mar 0}, pages = {13-27}, abstract = {

Mitochondrial dysfunction has been associated with schizophrenia (SZ) and bipolar disorder (BD). This review examines recent publications and novel associations between mitochondrial genes and SZ and BD. Associations of nuclear-encoded mitochondrial variants with SZ were found using gene- and pathway-based approaches. Two control region mitochondrial DNA (mtDNA) SNPs, T16519C and T195C, both showed an association with SZ and BD. A review of 4 studies of A15218G located in the cytochrome B oxidase gene (CYTB, SZ = 11,311, control = 35,735) shows a moderate association with SZ ( = 2.15E-03). Another mtDNA allele A12308G was nominally associated with psychosis in BD type I subjects and SZ. The first published study testing the epistatic interaction between nuclear-encoded and mitochondria-encoded genes demonstrated evidence for potential interactions between mtDNA and the nuclear genome for BD. A similar analysis for the risk of SZ revealed significant joint effects (34 nuclear-mitochondria SNP pairs with joint effect <= 5E-07) and significant enrichment of projection neurons. The mitochondria-encoded gene CYTB was found in both the epistatic interactions for SZ and BD and the single SNP association of SZ. Future efforts considering population stratification and polygenic risk scores will test the role of mitochondrial variants in psychiatric disorders.

}, issn = {2296-9209}, doi = {10.1159/000495658}, author = {Schulmann, Anton and Ryu, Euijung and Goncalves, Vanessa and Rollins, Brandi and Christiansen, Michael and Frye, Mark A and Biernacka, Joanna and Vawter, Marquis P} } @article {51253, title = {Nuclear transcriptomes of the seven neuronal cell types that constitute the mushroom bodies.}, journal = {G3 (Bethesda, Md.)}, volume = {9}, year = {2019}, month = {2019 Jan 09}, pages = {81-94}, abstract = {

The insect mushroom body (MB) is a conserved brain structure that plays key roles in a diverse array of behaviors. The MB is the primary invertebrate model of neural circuits related to memory formation and storage, and its development, morphology, wiring, and function has been extensively studied. MBs consist of intrinsic Kenyon Cells that are divided into three major neuron classes (γ, α{\textquoteright}/β{\textquoteright} and α/β) and 7 cell subtypes (γd, γm, α{\textquoteright}/β{\textquoteright}ap, α{\textquoteright}/β{\textquoteright}m, α/βp, α/βs and α/βc) based on their birth order, morphology, and connectivity. These subtypes play distinct roles in memory processing, however the underlying transcriptional differences are unknown. Here, we used RNA sequencing (RNA-seq) to profile the nuclear transcriptomes of each MB neuronal cell subtypes. We identified 350 MB class- or subtype-specific genes, including the widely used α/β class marker and the α{\textquoteright}/β{\textquoteright} class marker Immunostaining corroborates the RNA-seq measurements at the protein level for several cases. Importantly, our data provide a full accounting of the neurotransmitter receptors, transporters, neurotransmitter biosynthetic enzymes, neuropeptides, and neuropeptide receptors expressed within each of these cell types. This high-quality, cell type-level transcriptome catalog for the MB provides a valuable resource for the fly neuroscience community.

}, issn = {2160-1836}, doi = {10.1534/g3.118.200726}, author = {Shih, Meng-Fu Maxwell and Davis, Fred Pejman and Henry, Gilbert Lee and Dubnau, Josh} } @article {59912, title = {NWB:N 2.0: An accessible data standard for neurophysiology.}, journal = {bioRxiv}, year = {2019}, month = {2019 Jan 17}, abstract = {

Neurodata Without Borders: Neurophysiology (NWB:N) is a data standard for neurophysiology, providing neuroscientists with a common standard to share, archive, use, and build common analysis tools for neurophysiology data. With NWB:N version 2.0 (NWB:N 2.0) we made significant advances towards creating a usable standard, software ecosystem, and vibrant community for standardizing neurophysiology data. In this manuscript we focus in particular on the NWB:N data standard schema and present advances towards creating an accessible data standard for neurophysiology.

}, doi = {10.1101/523035}, author = {Rubel, Oliver and Tritt, Andrew and Dichter, Benjamin and Braun, Thomas and Cain, Nicholas and Clack, Nathan G and Davidson, Thomas J and Dougherty, Max and Fillion-Rubin, Jean-Christophe and Graddis, Nile and Grauer, Michael and Kiggins, Justin T and Niu, Lawrence and Ozturk, Doruk and Schroeder, William and Soltesz, Ivan and Sommer, Friedrich T and Svoboda, Karel and Ng, Lydia and et al} } @article {64997, title = {Neural circuit basis of aversive odour processing in drosophila from sensory input to descending output.}, journal = {bioRxiv}, year = {2018}, month = {2018 Aug 26}, abstract = {

Evolution has tuned the nervous system of most animals to produce stereotyped behavioural responses to ethologically relevant stimuli. For example, female\ Drosophila\ avoid laying eggs in the presence of geosmin, an odorant produced by toxic moulds. Using this system, we now identify third order olfactory neurons that are essential for an innate aversive behaviour. Connectomics data place these neurons in the context of a complete synaptic circuit from sensory input to descending output. We find multiple levels of valence-specific convergence, including a novel form of axo-axonic input onto second order neurons conveying another danger signal, the pheromone of parasitoid wasps. However we also observe a massive divergence as geosmin-responsive second order olfactory neurons connect with a diverse array of \~{}75 cell types. Our data suggest a transition from a labelled line organisation in the periphery to one in which olfactory information is mapped onto many different higher order populations with distinct behavioural significance.

}, doi = {10.1101/394403}, author = {Paavo Huoviala and Michael-John Dolan and Fiona M. Love and Shahar Frechter and Ruair{\'\i} J.V. Roberts and Zane Mitrevica and Philipp Schlegel and Alexander Shakeel Bates and Yoshinori Aso and Tiago Rodrigues and Hannah Cornwall and Marcus Stensmyr and Davi Bock and Gerald M. Rubin and Marta Costa and Gregory S.X.E. Jefferis} } @article {49116, title = {A Neural Circuit for the Suppression of Pain by a Competing Need State.}, journal = {Cell}, volume = {173}, year = {2018}, month = {2018 Mar 22}, pages = {140-52}, abstract = {

Hunger and pain are two competing signals that individuals must resolve to ensure survival. However, the neural processes that prioritize conflicting survival needs are poorly understood. We discovered that hunger attenuates behavioral responses and affective properties of inflammatory pain without altering acute\ nociceptive responses. This effect is centrally controlled, as activity in hunger-sensitive agouti-related protein (AgRP)-expressing neurons abrogates\ inflammatory pain. Systematic analysis of AgRP projection subpopulations revealed that the\ neural processing of hunger and inflammatory pain converge in the hindbrain parabrachial nucleus (PBN). Strikingly, activity in AgRP {\textrightarrow} PBN neurons blocked the behavioral response to inflammatory pain as effectively as hunger or analgesics. The anti-nociceptive effect of hunger is mediated by neuropeptide Y (NPY) signaling in the PBN. By investigating the intersection between hunger and pain, we have identified a neural circuit that mediates competing survival needs and uncovered NPY Y1 receptor signaling in the PBN as a target for pain suppression.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2018.02.057}, author = {Alhadeff, Amber L and Su, Zhenwei and Hernandez, Elen and Klima, Michelle L and Phillips, Sophie Z and Holland, Ruby A and Guo, Caiying and Hantman, Adam W and De Jonghe, Bart C and Betley, J Nicholas} } @article {49001, title = {Neural substrates of navigational decision-making in Drosophila larva anemotaxis.}, journal = {bioRxiv}, year = {2018}, month = {2018 Jan 08}, pages = {244608}, abstract = {

Small animals navigate in the environment as a function of varying sensory information in order to reach more favorable environmental conditions. To achieve this Drosophila larvae alternate periods of runs and turns in gradients of light, temperature, odors and CO2. While the sensory neurons that mediate the navigation behaviors in the different sensory gradients have been described, where and how are these navigational strategies are implemented in the central nervous system and controlled by neuronal circuit elements is not well known. Here we characterize for the first time the navigational strategies of Drosophila larvae in gradients of air-current speeds using high-throughput behavioral assays and quantitative behavioral analysis. We find that larvae extend runs when facing favorable conditions and increase turn rate when facing unfavorable direction, a strategy they use in other sensory modalities as well. By silencing the activity of individual neurons and very sparse expression patterns (2 or 3 neuron types), we further identify the sensory neurons and circuit elements in the ventral nerve cord and brain of the larva required for navigational decisions during anemotaxis. The phenotypes of these central neurons are consistent with a mechanism where the increase of the turning rate in unfavorable conditions and decrease in turning rate in favorable conditions are independently controlled.

}, doi = {10.1101/244608}, author = {Jovanic, Tihana and Truman, James W and Gershow, Marc and Zlatic, Marta} } @article {49337, title = {Neuroarchitecture of the Drosophila central complex: A catalog of nodulus and asymmetrical body neurons and a revision of the protocerebral bridge catalog.}, journal = {Journal of Comparative Neurology}, year = {2018}, month = {2018 Aug 7}, abstract = {

The central complex, a set of neuropils in the center of the insect brain, plays a crucial role in spatial aspects of sensory integration and motor control. Stereotyped neurons interconnect these neuropils with one another and with accessory structures. We screened over 5000 Drosophila melanogaster GAL4 lines for expression in two neuropils, the noduli (NO) of the central complex and the asymmetrical body (AB), and used multicolor stochastic labelling to analyze the morphology, polarity and organization of individual cells in a subset of the GAL4 lines that showed expression in these neuropils. We identified nine NO and three AB cell types and describe them here. The morphology of the NO neurons suggests that they receive input primarily in the lateral accessory lobe and send output to each of the six paired noduli. We demonstrate that the AB is a bilateral structure which exhibits asymmetry in size between the left and right bodies. We show that the AB neurons directly connect the AB to the central complex and accessory neuropils, that they target both the left and right ABs, and that one cell type preferentially innervates the right AB. We propose that the AB be considered a central complex neuropil in Drosophila. Finally, we present highly restricted GAL4 lines for most identified protocerebral bridge, NO and AB cell types. These lines, generated using the split-GAL4 method, will facilitate anatomical studies, behavioral assays, and physiological experiments.\ 

}, doi = {10.1002/cne.24512}, author = {Wolff, Tanya and Rubin, Gerald M} } @article {49528, title = {The neuronal basis of an illusory motion percept is explained by decorrelation of parallel motion pathways.}, journal = {Current Biology : CB}, volume = {28}, year = {2018}, month = {2018 Oct 31}, pages = {3748-78}, abstract = {

Both vertebrates and invertebrates perceive illusory motion, known as "reverse-phi," in visual stimuli that contain sequential luminance increments and decrements. However, increment (ON) and decrement (OFF) signals are initially processed by separate visual neurons, and parallel elementary motion detectors downstream respond selectively to the motion of light or dark edges, often termed ON- and OFF-edges. It remains unknown how and where ON and OFF signals combine to generate reverse-phi motion signals. Here, we show that each of Drosophila{\textquoteright}s elementary motion detectors encodes motion by combining both ON and OFF signals. Their pattern of responses reflects combinations of increments and decrements that co-occur in natural motion, serving to decorrelate their outputs. These results suggest that the general principle of signal decorrelation drives the functional specialization of parallel motion detection channels, including their selectivity for moving light or dark edges.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2018.10.007}, author = {Salazar-Gatzimas, Emilio and Agrochao, Margarida and Fitzgerald, James E and Clark, Damon A} } @article {49529, title = {Neuron-subtype-specific expression, interaction affinities, and specificity determinants of DIP/Dpr cell recognition proteins.}, journal = {Neuron}, volume = {100}, year = {2018}, month = {2018 Nov 12}, pages = {1385-1400}, abstract = {

Binding between DIP and Dpr neuronal recognition proteins has been proposed to regulate synaptic connections between lamina and medulla neurons in the Drosophila visual system. Each lamina neuron was previously shown to express many Dprs. Here, we demonstrate, by contrast, that their synaptic partners typically express one or two DIPs, with binding specificities matched to the lamina neuron-expressed Dprs. A deeper understanding of the molecular logic of DIP/Dpr interaction requires quantitative studies on the properties of these proteins. We thus generated a quantitative affinity-based DIP/Dpr interactome for all DIP/Dpr protein family members. This revealed a broad range of affinities and identified homophilic binding for some DIPs and some Dprs. These data, along with full-length ectodomain DIP/Dpr and DIP/DIP crystal structures, led to the identification of molecular determinants of DIP/Dpr specificity. This structural knowledge, along with a comprehensive set of quantitative binding affinities, provides new tools for functional studies in\ vivo.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2018.10.046}, author = {Cosmanescu, Filip and Katsamba, Phinikoula S and Sergeeva, Alina P and Ahlsen, Goran and Patel, Saurabh D and Brewer, Joshua J and Tan, Liming and Xu, Shuwa and Xiao, Qi and Nagarkar-Jaiswal, Sonal and Nern, Aljoscha and Bellen, Hugo J and Zipursky, S Lawrence and Honig, Barry and Shapiro, Lawrence} } @article {49095, title = {NeuroStorm: accelerating brain science discovery in the cloud.}, journal = {arXiv}, year = {2018}, month = {2018 Mar 09}, abstract = {

Neuroscientists are now able to acquire data at staggering rates across spatiotemporal scales. However, our ability to capitalize on existing datasets, tools, and intellectual capacities is hampered by technical challenges. The key barriers to accelerating scientific discovery correspond to the FAIR data principles: findability, global access to data, software interoperability, and reproducibility/re-usability. We conducted a hackathon dedicated to making strides in those steps. This manuscript is a technical report summarizing these achievements, and we hope serves as an example of the effectiveness of focused, deliberate hackathons towards the advancement of our quickly-evolving field.

}, url = {https://arxiv.org/abs/1803.03367}, author = {Kiar, Gregory and Anderson, Robert J and Baden, Alex and Badea, Alexandra and Bridgeford, Eric W and Champion, Andrew and Chandrashekar, Jayaram and Collman, Forrest and Duderstadt, Brandon and Evans, Alan C and Engert, Florian and Falk, Benjamin and Glatard, Tristan and Roncal, William Gray and Kennedy, David N and Maitlin-Shepard and Marren, Ryan A and Nnaemeka, Onyeka and Perlman, Eric and Seshamani, Sharmishtaas} } @article {68994, title = {Neutralizing Gatad2a-Chd4-Mbd3/NuRD Complex Facilitates Deterministic Induction of Naive Pluripotency.}, journal = {Cell Stem Cell}, volume = {23}, year = {2018}, month = {09/2018}, pages = {412-425.e10}, abstract = {

Mbd3, a member of nucleosome remodeling and deacetylase (NuRD) co-repressor complex, was previously identified as an inhibitor for deterministic induced pluripotent stem cell (iPSC) reprogramming, where up to 100\% of donor cells successfully complete the process. NuRD can assume multiple mutually exclusive conformations, and it remains unclear whether this deterministic phenotype can be attributed to a specific Mbd3/NuRD subcomplex. Moreover, since complete ablation of Mbd3 blocks somatic cell proliferation, we aimed to explore functionally relevant alternative ways to neutralize Mbd3-dependent NuRD activity. We identify Gatad2a, a NuRD-specific subunit, whose complete deletion specifically disrupts Mbd3/NuRD repressive activity on the pluripotency circuitry during iPSC differentiation and reprogramming without ablating somatic cell proliferation. Inhibition of Gatad2a facilitates deterministic murine iPSC reprogramming within 8\ days. We validate a distinct molecular axis, Gatad2a-Chd4-Mbd3, within Mbd3/NuRD as being critical for blocking reestablishment of naive pluripotency and further highlight signaling-dependent and post-translational modifications of Mbd3/NuRD that influence its interactions and assembly.

}, keywords = {Animals, Cells, Cultured, DNA Helicases, DNA-Binding Proteins, Female, GATA Transcription Factors, Induced Pluripotent Stem Cells, Male, Mi-2 Nucleosome Remodeling and Deacetylase Complex, Mice, Mice, Inbred C57BL, Mice, Inbred CBA, Mice, Knockout, Mice, Transgenic, Transcription Factors}, issn = {1875-9777}, doi = {10.1016/j.stem.2018.07.004}, author = {Mor, Nofar and Rais, Yoach and Sheban, Daoud and Peles, Shani and Aguilera-Castrejon, Alejandro and Zviran, Asaf and Elinger, Dalia and Viukov, Sergey and Geula, Shay and Krupalnik, Vladislav and Zerbib, Mirie and Chomsky, Elad and Lasman, Lior and Shani, Tom and Bayerl, Jonathan and Gafni, Ohad and Hanna, Suhair and Buenrostro, Jason D and Hagai, Tzachi and Masika, Hagit and Vainorius, Gintautas and Bergman, Yehudit and Greenleaf, William J and Esteban, Miguel A and Elling, Ulrich and Levin, Yishai and Massarwa, Rada and Merbl, Yifat and Novershtern, Noa and Hanna, Jacob H} } @article {49532, title = {NeuTu: Software for Collaborative, Large-Scale, Segmentation-Based Connectome Reconstruction.}, journal = {Frontiers in Neural Circuits}, volume = {12}, year = {2018}, month = {2018}, pages = {101}, abstract = {

Reconstructing a connectome from an EM dataset often requires a large effort of proofreading automatically generated segmentations. While many tools exist to enable tracing or proofreading, recent advances in EM imaging and segmentation quality suggest new strategies and pose unique challenges for tool design to accelerate proofreading. Namely, we now have access to very large multi-TB EM datasets where (1) many segments are largely correct, (2) segments can be very large (several GigaVoxels), and where (3) several proofreaders and scientists are expected to collaborate simultaneously. In this paper, we introduce NeuTu as a solution to efficiently proofread large, high-quality segmentation in a collaborative setting. NeuTu is a client program of our high-performance, scalable image database called DVID so that it can easily be scaled up. Besides common features of typical proofreading software, NeuTu tames unprecedentedly large data with its distinguishing functions, including: (1) low-latency 3D visualization of large mutable segmentations; (2) interactive splitting of very large false merges with highly optimized semi-automatic segmentation; (3) intuitive user operations for investigating or marking interesting points in 3D visualization; (4) visualizing proofreading history of a segmentation; and (5) real-time collaborative proofreading with lock-based concurrency control. These unique features have allowed us to manage the workflow of proofreading a large dataset smoothly without dividing them into subsets as in other segmentation-based tools. Most importantly, NeuTu has enabled some of the largest connectome reconstructions as well as interesting discoveries in the fly brain.

}, issn = {1662-5110}, doi = {10.3389/fncir.2018.00101}, author = {Zhao, Ting and Olbris, Donald J and Yu, Yang and Plaza, Stephen M} } @article {65094, title = {New optical probes bring dopamine to light.}, journal = {Biochemistry}, volume = {57}, year = {2018}, month = {2018 Nov 13}, pages = {6379-6381}, abstract = {

Chemical signaling between neurons in the brain can be divided into two major categories: fast synaptic transmission and neuromodulation. Fast synaptic transmission, mediated by amino acids such as glutamate and GABA, occurs on millisecond time scales and results in the influx of ions through ligand-gated ion channels on postsynaptic neurons (Figure\ 1A). Electrophysiological and optical imaging tools, including genetically encoded voltage indicators, have enabled neuroscientists to link cause (neurotransmitter release) and effect (membrane polarization) of synaptic transmission in time and space. Unlike classical neurotransmitters, neuromodulators do not produce immediate electrical effects that excite or inhibit target neurons. Instead, neuromodulators tune the intrinsic or synaptic properties of neurons, most commonly through interaction with G-protein-coupled receptors (GPCRs) (Figure\ 1B). Neuromodulators can escape the synaptic cleft and diffuse broadly, allowing them to influence the activity of many neurons in a state-dependent manner. Therefore, the spatial component of neuromodulator flux is fundamentally important. However, the temporal and/or spatial limitations of techniques classically used to study neuromodulation, such as microdialysis and fast-scan cyclic voltammetry (FSCV), make it difficult to interpret how neuromodulator release affects the plasticity or function of target neuronal populations on a moment-to-moment basis. Therefore, tools that can detect neuromodulators with high spatiotemporal resolution are critical for understanding their impact on neural computations that control behavior in health and disease.

}, keywords = {Animals, Dopamine, Fluorescent Dyes, Humans, Light, Optical Imaging, Receptors, Dopamine}, issn = {1520-4995}, doi = {10.1021/acs.biochem.8b00883}, author = {Beyene, Abraham G and Delevich, Kristen and Yang, Sarah J and Landry, Markita P} } @article {49244, title = {Nicotinic cholinergic receptors in VTA glutamate neurons modulate excitatory transmission.}, journal = {Cell Reports}, volume = {23}, year = {2018}, month = {2018 May 22}, pages = {2236-2244}, abstract = {

Ventral tegmental area (VTA) glutamate neurons are important components of reward circuitry, but whether they are subject to cholinergic modulation is unknown. To study this, we used molecular, physiological, and photostimulation techniques to examine nicotinic acetylcholine receptors (nAChRs) in VTA glutamate neurons. Cells in the medial VTA, where glutamate neurons are enriched, are responsive to acetylcholine (ACh) released from cholinergic axons. VTA VGLUT2 neurons express mRNA and protein subunits known to comprise heteromeric nAChRs. Electrophysiology, coupled with two-photon microscopy and laser flash photolysis of photoactivatable nicotine, was used to demonstrate nAChR functional activity in the somatodendritic subcellular compartment of VTA VGLUT2 neurons. Finally, optogenetic isolation of intrinsic VTA glutamatergic microcircuits along with gene-editing techniques demonstrated that nicotine potently modulates excitatory transmission within the VTA via heteromeric nAChRs. These results indicate that VTA glutamate neurons are modulated by cholinergic mechanisms and participate in the cascade of physiological responses to nicotine exposure.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2018.04.062}, author = {Yan, Yijin and Peng, Can and Arvin, Matthew C and Jin, Xiao-Tao and Kim, Veronica J and Ramsey, Matthew D and Wang, Yong and Banala, Sambashiva and Wokosin, David L and McIntosh, J Michael and Lavis, Luke D and Drenan, Ryan M} } @article {49086, title = {Nociceptive interneurons control modular motor pathways to promote escape behavior in Drosophila.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Mar 12}, abstract = {

Rapid and efficient escape behaviors in response to noxious sensory stimuli are essential for protection and survival. Yet, how noxious stimuli are transformed to coordinated escape behaviors remains poorly understood. Inlarvae, noxious stimuli trigger sequential body bending and corkscrew-like rolling behavior. We identified a population of interneurons in the nerve cord of, termed Down-and-Back (DnB) neurons, that are activated by noxious heat, promote nociceptive behavior, and are required for robust escape responses to noxious stimuli. Electron microscopic circuit reconstruction shows that DnBs are targets of nociceptive and mechanosensory neurons, are directly presynaptic to pre-motor circuits, and link indirectly to Goro rolling command-like neurons. DnB activation promotes activity in Goro neurons, and coincident inactivation of Goro neurons prevents the rolling sequence but leaves intact body bending motor responses. Thus, activity from nociceptors to DnB interneurons coordinates modular elements of nociceptive escape behavior.

}, issn = {2050-084X}, doi = {10.7554/eLife.26016}, author = {Burgos, Anita and Honjo, Ken and Ohyama, Tomoko and Qian, Cheng Sam and Shin, Grace Ji-Eun and Gohl, Daryl M and Silies, Marion and Tracey, W Daniel and Zlatic, Marta and Cardona, Albert and Grueber, Wesley B} } @article {49457, title = {Noncanonical autophagy at ER exit sites regulates procollagen turnover.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, year = {2018}, month = {2018 Oct 04}, pages = {E10099-108}, abstract = {

Type I collagen is the main component of bone matrix and other connective tissues. Rerouting of its procollagen precursor to a degradative pathway is crucial for osteoblast survival in pathologies involving excessive intracellular buildup of procollagen that is improperly folded and/or trafficked. What cellular mechanisms underlie this rerouting remains unclear. To study these mechanisms, we employed live-cell imaging and correlative light and electron microscopy (CLEM) to examine procollagen trafficking both in wild-type mouse osteoblasts and osteoblasts expressing a bone pathology-causing mutant procollagen. We found that although most procollagen molecules successfully trafficked through the secretory pathway in these cells, a subpopulation did not. The latter molecules appeared in numerous dispersed puncta colocalizing with COPII subunits, autophagy markers and ubiquitin machinery, with more puncta seen in mutant procollagen-expressing cells. Blocking endoplasmic reticulum exit site (ERES) formation suppressed the number of these puncta, suggesting they formed after procollagen entry into ERESs. The punctate structures containing procollagen, COPII, and autophagic markers did not move toward the Golgi but instead were relatively immobile. They appeared to be quickly engulfed by nearby lysosomes through a bafilomycin-insensitive pathway. CLEM and fluorescence recovery after photobleaching experiments suggested engulfment occurred through a noncanonical form of autophagy resembling microautophagy of ERESs. Overall, our findings reveal that a subset of procollagen molecules is directed toward lysosomal degradation through an autophagic pathway originating at ERESs, providing a mechanism to remove excess procollagen from cells.

}, issn = {1091-6490}, doi = {10.1073/pnas.1814552115}, author = {Omari, Shakib and Makareeva, Elena and Roberts-Pilgrim, Anna and Mirigian, Lynn and Jarnik, Michal and Ott, Carolyn and Lippincott-Schwartz, Jennifer and Leikin, Sergey} } @article {49276, title = {A novel pyramidal cell type promotes sharp-wave synchronization in the hippocampus.}, journal = {Nature Neuroscience}, volume = {21}, year = {2018}, month = {2018 Jun 18}, pages = {985-95}, abstract = {

To support cognitive function, the CA3 region of the hippocampus performs computations involving attractor dynamics. Understanding how cellular and ensemble activities of CA3 neurons enable computation is critical for elucidating the neural correlates of cognition. Here we show that CA3 comprises not only classically described pyramid cells with thorny excrescences, but also includes previously unidentified {\textquoteright}athorny{\textquoteright} pyramid cells that lack mossy-fiber input. Moreover, the two neuron types have distinct morphological and physiological phenotypes and are differentially modulated by acetylcholine. To understand the contribution of these athorny pyramid neurons to circuit function, we measured cell-type-specific firing patterns during sharp-wave synchronization events in vivo and recapitulated these dynamics with an attractor network model comprising two principal cell types. Our data and simulations reveal a key role for athorny cell bursting in the initiation of sharp waves: transient network attractor states that signify the execution of pattern completion computations vital to cognitive function.

}, issn = {1546-1726}, doi = {10.1038/s41593-018-0172-7}, author = {Hunt, David L and Linaro, Daniele and Si, Bailu and Romani, Sandro and Spruston, Nelson} } @article {49176, title = {A novel sheet-like virus particle array is a hallmark of Zika virus infection.}, journal = {Emerging Microbes \& Infections}, volume = {7}, year = {2018}, month = {2018 Apr 25}, pages = {69}, abstract = {

Zika virus (ZIKV) is an emerging flavivirus that caused thousands of human infections in recent years. Compared to other human flaviviruses, ZIKV replication is not well understood. Using fluorescent, transmission electron, and focused ion beam-scanning electron microscopy, we examined ZIKV replication dynamics in Vero 76 cells and in the brains of infected laboratory mice. We observed the progressive development of a perinuclear flaviviral replication factory both in vitro and in vivo. In vitro, we illustrated the ZIKV lifecycle from particle cell entry to egress. ZIKV particles assembled and aggregated in an induced convoluted membrane structure and ZIKV strain-specific membranous vesicles. While most mature virus particles egressed via membrane budding, some particles also likely trafficked through late endosomes and egressed through membrane abscission. Interestingly, we consistently observed a novel sheet-like virus particle array consisting of a single layer of ZIKV particles. Our study further defines ZIKV replication and identifies a novel hallmark of ZIKV infection.

}, issn = {2222-1751}, doi = {10.1038/s41426-018-0071-8}, author = {Liu, Jun and Kline, Brandon A and Kenny, Tara A and Smith, Darci R and Soloveva, Veronica and Beitzel, Brett and Pang, Song and Lockett, Stephen and Hess, Harald F and Palacios, Gustavo and Kuhn, Jens H and Sun, Mei G and Zeng, Xiankun} } @article {48866, title = {Nanoscale visualization of biomineral formation in coral proto-polyps.}, journal = {Current Biology : CB}, volume = {27}, year = {2017}, month = {2017 Oct 11}, pages = {3191-6}, abstract = {

Calcium carbonate platforms produced by reef-building stony corals over geologic time are pervasive features around the world [1]; however, the mechanism by which these organisms produce the mineral is poorly understood (see review by [2]). It is generally assumed that stony corals precipitate calcium carbonate extracellularly as aragonite in a calcifying medium between the calicoblastic ectoderm and pre-existing skeleton, separated from the overlying seawater [2]. The calicoblastic ectoderm produces extracellular matrix (ECM) proteins, secreted to the calcifying medium [3-6], which appear to provide the nucleation, alteration, elongation, and inhibition mechanisms of the biomineral [7] and remain occluded and preserved in the skeleton [8-10]. Here we show in cell cultures of the stony coral Stylophora pistillata that calcium is concentrated in intracellular pockets that are subsequently exported from the cell where a nucleation process leads to the formation of extracellular aragonite crystals. Analysis of the growing crystals by lattice light-sheet microscopy suggests that the crystals elongate from the cells{\textquoteright} surfaces outward.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2017.09.012}, author = {Mass, Tali and Drake, Jeana L and Heddleston, John M and Falkowski, Paul G} } @article {48713, title = {Near-atomic resolution cryoelectron microscopy structure of the 30-fold homooligomeric SpoIIIAG channel essential to spore formation in Bacillus subtilis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, year = {2017}, month = {2017 Aug 07}, abstract = {

Bacterial sporulation allows starving cells to differentiate into metabolically dormant spores that can survive extreme conditions. Following asymmetric division, the mother cell engulfs the forespore, surrounding it with two bilayer membranes. During the engulfment process, an essential channel, the so-called feeding tube apparatus, is thought to cross both membranes to create a direct conduit between the mother cell and the forespore. At least nine proteins are required to create this channel, including SpoIIQ and SpoIIIAA-AH. Here, we present the near-atomic resolution structure of one of these proteins, SpoIIIAG, determined by single-particle cryo-EM. A 3D reconstruction revealed that SpoIIIAG assembles into a large and stable 30-fold symmetric complex with a unique mushroom-like architecture. The complex is collectively composed of three distinctive circular structures: a 60-stranded vertical β-barrel that forms a large inner channel encircled by two concentric rings, one β-mediated and the other formed by repeats of a ring-building motif (RBM) common to the architecture of various dual membrane secretion systems of distinct function. Our near-atomic resolution structure clearly shows that SpoIIIAG exhibits a unique and dramatic adaptation of the RBM fold with a unique β-triangle insertion that assembles into the prominent channel, the dimensions of which suggest the potential passage of large macromolecules between the mother cell and forespore during the feeding process. Indeed, mutation of residues located at key interfaces between monomers of this RBM resulted in severe defects both in vivo and in vitro, providing additional support for this unprecedented structure.

}, issn = {1091-6490}, doi = {10.1073/pnas.1704310114}, author = {Zeytuni, Natalie and Hong, Chuan and Flanagan, Kelly A and Worrall, Liam J and Theiltges, Kate A and Vuckovic, Marija and Huang, Rick K and Massoni, Shawn C and Camp, Amy H and Yu, Zhiheng and Strynadka, Natalie C} } @article {48417, title = {Near-infrared fluorescent protein iRFP713 as a reporter protein for optogenetic vectors, a transgenic Cre-reporter rat, and other neuronal studies.}, journal = {Journal of Neuroscience Methods}, volume = {284}, year = {2017}, month = {2017 Apr 02}, pages = {1-14}, abstract = {

BACKGROUND: The use of genetically-encoded fluorescent reporters is essential for the identification and observation of cells that express transgenic modulatory proteins. Near-infrared (NIR) fluorescent proteins have superior light penetration through biological tissue, but are not yet widely adopted.

NEW METHOD: Using the near-infrared fluorescent protein, iRFP713, improves the imaging resolution in thick tissue sections or the intact brain due to the reduced light-scattering at the longer, NIR wavelengths used to image the protein. Additionally, iRFP713 can be used to identify transgenic cells without photobleaching other fluorescent reporters or affecting opsin function. We have generated a set of adeno-associated vectors in which iRFP713 has been fused to optogenetic channels, and can be expressed constitutively or Cre-dependently.

RESULTS: iRFP713 is detectable when expressed in neurons both in vitro and in vivo without exogenously supplied chromophore biliverdin. Neuronally-expressed iRFP713 has similar properties to GFP-like fluorescent proteins, including the ability to be translationally fused to channelrhodopsin or halorhodopsin, however, it shows superior photostability compared to EYFP. Furthermore, electrophysiological recordings from iRFP713-labeled cells compared to cells labeled with mCherry suggest that iRFP713 cells are healthier and therefore more stable and reliable in an ex vivo preparation. Lastly, we have generated a transgenic rat that expresses iRFP713 in a Cre-dependent manner.

CONCLUSIONS: Overall, we have demonstrated that iRFP713 can be used as a reporter in neurons without the use of exogenous biliverdin, with minimal impact on viability and function thereby making it feasible to extend the capabilities for imaging genetically-tagged neurons in slices and in vivo.

}, issn = {1872-678X}, doi = {10.1016/j.jneumeth.2017.03.020}, author = {Richie, Christopher T and Whitaker, Leslie R and Whitaker, Keith W and Necarsulmer, Julie and Baldwin, Heather A and Zhang, Yajun and Fortuno, Lowella and Hinkle, Josh J and Koivula, Pyry and Henderson, Mark J and Sun, Wenzhi and Wang, Kai and Smith, Jeffrey C and Pickel, Jim and Ji, Na and Hope, Bruce T and Harvey, Brandon K} } @article {48919, title = {Network-size independent covering number bounds for deep networks.}, journal = {arXiv}, year = {2017}, month = {2017 Nov 02}, pages = {arXiv:1711.00753 }, abstract = {

We give a covering number bound for deep learning networks that is independent of the size of the network. The key for the simple analysis is that for linear classifiers, rotating the data doesn{\textquoteright}t affect the covering number. Thus, we can ignore the rotation part of each layer{\textquoteright}s linear transformation, and get the covering number bound by concentrating on the scaling part.

}, url = {https://arxiv.org/abs/1711.00753}, author = {Kabra, Mayank and Branson, Kristin M} } @article {48954, title = {Neural mechanisms of movement planning: motor cortex and beyond.}, journal = {Current Opinion in Neurobiology}, volume = {49}, year = {2017}, month = {2017 Nov 20}, pages = {33-41}, abstract = {

Neurons in motor cortex and connected brain regions fire in anticipation of specific movements, long before movement occurs. This neural activity reflects internal processes by which the brain plans and executes volitional movements. The study of motor planning offers an opportunity to understand how the structure and dynamics of neural circuits support persistent internal states and how these states influence behavior. Recent advances in large-scale neural recordings are beginning to decipher the relationship of the dynamics of populations of neurons during motor planning and movements. New behavioral tasks in rodents, together with quantified perturbations, link dynamics in specific nodes of neural circuits to behavior. These studies reveal a neural network distributed across multiple brain regions that collectively supports motor planning. We review recent advances and highlight areas where further work is needed to achieve a deeper understanding of the mechanisms underlying motor planning and related cognitive processes.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2017.10.023}, author = {Svoboda, Karel and Li, Nuo} } @article {48549, title = {Neural signatures of dynamic stimulus selection in Drosophila.}, journal = {Nature Neuroscience}, volume = {20}, year = {2017}, month = {2017 Jun 12}, pages = {1104-13}, abstract = {

Many animals orient using visual cues, but how a single cue is selected from among many is poorly understood. Here we show that Drosophila ring neurons{\textemdash}central brain neurons implicated in navigation{\textemdash}display visual stimulus selection. Using\ in vivo\ two-color two-photon imaging with genetically encoded calcium indicators, we demonstrate that individual ring neurons inherit simple-cell-like receptive fields from their upstream partners. Stimuli in the contralateral visual field suppressed responses to ipsilateral stimuli in both populations. Suppression strength depended on when and where the contralateral stimulus was presented, an effect stronger in ring neurons than in their upstream inputs. This history-dependent effect on the temporal structure of visual responses, which was well modeled by a simple biphasic filter, may determine how visual references are selected for the fly{\textquoteright}s internal compass. Our approach highlights how two-color calcium imaging can help identify and localize the origins of sensory transformations across synaptically connected neural populations.

}, doi = {10.1038/nn.4581}, author = {Sun, Yi and Nern, Aljoscha and Franconville, Romain and Dana, Hod and Schreiter, Eric R and Looger, Loren L and Svoboda, Karel and Kim, Douglas S and Hermundstad, Ann M and Jayaraman, Vivek} } @article {68438, title = {Neurobiology: A bitter-sweet symphony.}, journal = {Nature}, volume = {548}, year = {2017}, month = {08/2017}, pages = {285-287}, abstract = {

No abstract available.

}, keywords = {Humans, Neurobiology, Taste}, issn = {1476-4687}, doi = {10.1038/nature23537}, author = {Li, Jiefu and Luo, Liqun} } @article {48920, title = {Nuclear microenvironments modulate transcription from low-affinity enhancers.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Nov 02}, abstract = {

Transcription factors bind low-affinity DNA sequences for only short durations. It is not clear how brief, low-affinity interactions can drive efficient transcription. Here we report that the transcription factor Ultrabithorax (Ubx) utilizes low-affinity binding sites in the Drosophila melanogastershavenbaby (svb) locus and related enhancers in nuclear microenvironments of high Ubx concentrations. Related enhancers colocalize to the same microenvironments independently of their chromosomal location, suggesting that microenvironments are highly differentiated transcription domains. Manipulating the affinity of svb enhancers revealed an inverse relationship between enhancer affinity and Ubx concentration required for transcriptional activation. The Ubx cofactor, Homothorax (Hth), was co-enriched with Ubx near enhancers that require Hth, even though Ubx and Hth did not co-localize throughout the nucleus. Thus, microenvironments of high local transcription factor and cofactor concentrations could help low-affinity sites overcome their kinetic inefficiency. Mechanisms that generate these microenvironments could be a general feature of eukaryotic transcriptional regulation.

}, issn = {2050-084X}, doi = {10.7554/eLife.28975}, author = {Tsai, Albert and Muthusamy, Anand K and Alves, Mariana Rp and Lavis, Luke D and Singer, Robert H and Stern, David L and Crocker, Justin} } @article {48131, title = {The nanoscale spatial organization of B cell receptors on IgM- and IgG-expressing human B cells.}, journal = {Molecular Biology of the Cell}, volume = {28}, year = {2016}, month = {2016 Dec 14}, pages = {511-23}, abstract = {

B cell activation is initiated by the binding of antigen to the B cell receptor (BCR). Here we used dSTORM super resolution imaging to characterize the nanoscale spatial organization of IgM and IgG BCRs on the surfaces of resting and antigen-activated human peripheral blood B cells. We provide insights into both the fundamental process of antigen-driven BCR clustering as well as differences in the spatial organization of IgM and IgG BCRs that may contribute to the characteristic differences in the responses of na{\"\i}ve and memory B cells to antigen. We provide evidence that although both IgM and IgG BCRs reside in highly heterogeneous protein islands that vary in both size and number of BCR single molecule localizations, both resting and activated B cells intrinsically maintain a high frequency of single isolated BCR localizations, which likely represent BCR monomers. IgG BCRs are more clustered than IgM BCRs on resting cells and form larger protein islands following antigen activation. Small dense BCR clusters likely formed via protein-protein interactions are present on the surface of resting cells and antigen activation induces these to come together to form less dense, larger islands, a process likely governed, at least in part, by protein-lipid interactions.

}, issn = {1939-4586}, doi = {10.1091/mbc.E16-06-0452}, author = {Lee, Jinmin and Sengupta, Prabuddha and Brzostowski, Joseph and Lippincott-Schwartz, Jennifer and Pierce, Susan K} } @article {47766, title = {Natural courtship song variation caused by an intronic retroelement in an ion channel gene.}, journal = {Nature}, year = {2016}, month = {2016 Aug 10}, abstract = {

Animal species display enormous variation for innate behaviours, but little is known about how this diversity arose. Here, using an unbiased genetic approach, we map a courtship song difference between wild isolates of Drosophila simulans and Drosophila mauritiana to a 966 base pair region within the slowpoke (slo) locus, which encodes a calcium-activated potassium channel. Using the reciprocal hemizygosity test, we confirm that slo is the causal locus and resolve the causal mutation to the evolutionarily recent insertion of a retroelement in a slo intron within D. simulans. Targeted deletion of this retroelement reverts the song phenotype and alters slo splicing. Like many ion channel genes, slo is expressed widely in the nervous system and influences a variety of behaviours; slo-null males sing little song with severely disrupted features. By contrast, the natural variant of slo alters a specific component of courtship song, illustrating that regulatory evolution of a highly pleiotropic ion channel gene can cause modular changes in behaviour.

}, issn = {1476-4687}, doi = {10.1038/nature19093}, author = {Ding, Yun and Berrocal, Augusto and Morita, Tomoko and Longden, Kit D and Stern, David L} } @article {48317, title = {A near atomic structure of the active human apoptosome.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Oct 04}, pages = {e17755}, abstract = {

In response to cell death signals, an active apoptosome is assembled from Apaf-1 and procaspase-9 (pc-9). Here we report a near atomic structure of the active human apoptosome determined by cryo-electron microscopy. The resulting model gives insights into cytochrome c binding, nucleotide exchange and conformational changes that drive assembly. During activation an acentric disk is formed on the central hub of the apoptosome. This disk contains four Apaf-1/pc-9 CARD pairs arranged in a shallow spiral with the fourth pc-9 CARD at lower occupancy. On average, Apaf-1 CARDs recruit 3 to 5 pc-9 molecules to the apoptosome and one catalytic domain may be parked on the hub, when an odd number of zymogens are bound. This suggests a stoichiometry of one or at most, two pc-9 dimers per active apoptosome. Thus, our structure provides a molecular framework to understand the role of the apoptosome in programmed cell death and disease.

}, issn = {2050-084X}, doi = {10.7554/eLife.17755}, author = {Cheng, Tat Cheung and Hong, Chuan and Akey, Ildik{\'o} V and Yuan, Shujun and Akey, Christopher W} } @article {48104, title = {A near-atomic structure of the dark apoptosome provides insight into assembly and activation.}, journal = {Structure (London, England : 1993)}, volume = {25}, year = {2016}, month = {2016 Nov 16}, pages = {40-52}, abstract = {

In Drosophila, the Apaf-1-related killer (Dark) forms an apoptosome that activates procaspases. To investigate function, we have determined a near-atomic structure of Dark double rings using cryo-electron microscopy. We then built a nearly complete model of the apoptosome that includes 7- and 8-blade β-propellers. We find that the preference for dATP during Dark assembly may be governed by Ser325, which is in close proximity to the 2{\textquoteright} carbon of the deoxyribose ring. Interestingly, β-propellers in V-shaped domains of the Dark apoptosome are more widely separated, relative to these features in the Apaf-1 apoptosome. This wider spacing may be responsible for the lack of cytochrome c binding to β-propellers in the Dark apoptosome. Our structure also highlights the roles of two loss-of-function mutations that may block Dark assembly. Finally, the improved model provides a framework to understand apical procaspase activation in the intrinsic cell death pathway.

}, issn = {1878-4186}, doi = {10.1016/j.str.2016.11.002}, author = {Cheng, Tat Cheung and Akey, Ildik{\'o} V and Yuan, Shujun and Yu, Zhiheng and Ludtke, Steven J and Akey, Christopher W} } @article {48128, title = {Near-atomic-resolution cryo-EM analysis of the Salmonella T3S injectisome basal body.}, journal = {Nature}, year = {2016}, month = {2016 Dec 14}, abstract = {

The type III secretion (T3S) injectisome is a specialized protein nanomachine that is critical for the pathogenicity of many Gram-negative bacteria, including purveyors of plague, typhoid fever, whooping cough, sexually transmitted infections and major nosocomial infections. This syringe-shaped 3.5-MDa macromolecular assembly spans both bacterial membranes and that of the infected host cell. The internal channel formed by the injectisome allows for the direct delivery of partially unfolded virulence effectors into the host cytoplasm. The structural foundation of the injectisome is the basal body, a molecular lock-nut structure composed predominantly of three proteins that form highly oligomerized concentric rings spanning the inner and outer membranes. Here we present the structure of the prototypical Salmonella enterica serovar Typhimurium pathogenicity island 1 basal body, determined using single-particle cryo-electron microscopy, with the inner-membrane-ring and outer-membrane-ring oligomers defined at 4.3 {\r A} and 3.6 {\r A} resolution, respectively. This work presents the first, to our knowledge, high-resolution structural characterization of the major components of the basal body in the assembled state, including that of the widespread class of outer-membrane portals known as secretins.

}, issn = {1476-4687}, doi = {10.1038/nature20576}, author = {Worrall, L J and Hong, C and Vuckovic, M and Deng, W and Bergeron, J R C and Majewski, D D and Huang, R K and Spreter, T and Finlay, B B and Yu, Z and Strynadka, N C J} } @article {47552, title = {Near-perfect synaptic integration by Nav1.7 in hypothalamic neurons regulates body weight.}, journal = {Cell}, volume = {165}, year = {2016}, month = {2016 Jun 16}, pages = {1749-61}, abstract = {

Neurons are well suited for computations on millisecond timescales, but some neuronal circuits set behavioral states over long time periods, such as those involved in energy homeostasis. We found that multiple types of hypothalamic neurons, including those that oppositely regulate body weight, are specialized as near-perfect synaptic integrators that summate inputs over extended timescales. Excitatory postsynaptic potentials (EPSPs) are greatly prolonged, outlasting the neuronal membrane time-constant up to 10-fold. This is due to the voltage-gated sodium channel Nav1.7 (Scn9a), previously associated with pain-sensation but not synaptic integration.\ Scn9a\ deletion in AGRP, POMC, or paraventricular hypothalamic neurons reduced EPSP duration, synaptic integration, and altered body weight in mice. In\ vivo whole-cell recordings in the hypothalamus confirmed near-perfect synaptic integration. These experiments show that integration of synaptic inputs over time by Nav1.7 is critical for body weight regulation and reveal a mechanism for synaptic control of circuits regulating long term homeostatic functions.

}, doi = {10.1016/j.cell.2016.05.019}, author = {Branco, Tiago and Tozer, Adam and Magnus, Christopher J and Sugino, Ken and Tanaka, Shinsuke and Lee, Albert K and Wood, John N and Sternson, Scott M} } @article {47564, title = {Neural circuits that drive startle behavior, with a focus on the Mauthner cells and spiral fiber neurons of fishes.}, journal = {Journal of Neurogenetics}, volume = {30}, year = {2016}, month = {2016 Jun}, pages = {89-100}, abstract = {

Startle behaviors are rapid, high-performance motor responses to threatening stimuli. Startle responses have been identified in a broad range of species across animal diversity. For investigations of neural circuit structure and function, these behaviors offer a number of benefits, including that they are driven by large and identifiable neurons and their neural control is simple in comparison to other behaviors. Among vertebrates, the best-known startle circuit is the Mauthner cell circuit of fishes. In recent years, genetic approaches in zebrafish have provided key tools for morphological and physiological dissection of circuits and greatly extended understanding of their architecture. Here we discuss the startle circuit of fishes, with a focus on the Mauthner cells and associated interneurons called spiral fiber neurons and we add new observations on hindbrain circuit organization. We also briefly review and compare startle circuits of several other taxa, paying particular attention to how movement direction is controlled.

}, issn = {1563-5260}, doi = {10.1080/01677063.2016.1182526}, author = {Hale, Melina E and Katz, Hilary R and Peek, Martin Y and Fremont, Rachel T} } @article {47283, title = {Neural circuits underlying visually evoked escapes in larval zebrafish.}, journal = {Neuron}, volume = {89}, year = {2016}, month = {2016 Feb 3}, pages = {613-628}, abstract = {

Escape behaviors deliver organisms away from imminent catastrophe. Here, we characterize behavioral responses of freely swimming larval zebrafish to\ looming visual stimuli simulating predators. We report that the visual system alone can recruit lateralized, rapid escape motor programs, similar to those elicited by mechanosensory modalities. Two-photon calcium imaging of retino-recipient midbrain regions isolated the optic tectum as an important center processing looming stimuli, with ensemble activity encoding the critical image size determining escape latency. Furthermore, we describe activity in retinal ganglion cell terminals and superficial inhibitory interneurons in the tectum during looming and propose a model for how temporal dynamics in tectal\ periventricular neurons might arise from computations between these two fundamental constituents. Finally, laser ablations of hindbrain circuitry confirmed that visual and mechanosensory modalities share the same premotor output network. We\ establish a circuit for the processing of aversive stimuli in the context of an innate visual behavior.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.12.021}, author = {Dunn, Timothy W and Gebhardt, Christoph and Naumann, Eva A and Riegler, Clemens and Ahrens, Misha B and Engert, Florian and Del Bene, Filippo} } @article {47965, title = {A new brain dopamine deficient Drosophila and its pharmacological and genetic rescue.}, journal = {Genes, Brain, and Behavior}, volume = {16}, year = {2016}, month = {2017 Mar.01 }, pages = {394-403}, abstract = {

Dopamine (DA) is a neurotransmitter with conserved behavioral roles between invertebrate and vertebrate animals. In addition to its neural functions, in insects DA is a critical substrate for cuticle pigmentation and hardening. Drosophila tyrosine hydroxylase (DTH) is the rate limiting enzyme for DA biosynthesis. Viable brain DA deficient flies were previously generated using tissue selective GAL4-UAS binary expression rescue of a DTH null mutation and these flies show specific behavioral impairments. To circumvent the limitations of rescue via binary expression, here we achieve rescue utilizing genomically integrated mutant DTH. As expected, our DA deficient flies have no detectable DTH or DA in the brain, and show reduced locomotor activity. This deficit can be rescued by L-DOPA/carbidopa feeding, similar to human Parkinson{\textquoteright}s disease treatment. Genetic rescue via GAL4/UAS-DTH was also successful, although this required the generation of a new UAS-DTH1 transgene devoid of most untranslated regions, since existing UAS-DTH transgenes express in the brain without a Gal4 driver via endogenous regulatory elements. A surprising finding of our newly constructed UAS-DTH1m is that it expresses DTH at an undetectable level when regulated by dopaminergic GAL4 drivers even when fully rescuing DA, indicating that DTH immunostaining is not necessarily a valid marker for DA expression. This finding necessitated optimizing DA immunohistochemistry, revealing details of DA innervation to the mushroom body and the central complex. When DA rescue is limited to specific DA neurons, DA does not diffuse beyond the DTH-expressing terminals, such that DA signaling can be limited to very specific brain regions.

}, issn = {1601-183X}, doi = {10.1111/gbb.12353}, author = {Cichewicz, Karol and Garren, Emma J and Adiele, Chika and Aso, Yoshinori and Wang, Zhang and Wu, Martin and Birman, Serge and Rubin, Gerald M and Hirsh, Jay} } @article {68765, title = {Non-centrosomal epidermal microtubules act in parallel to LET-502/ROCK to promote C. elegans elongation}, journal = {Development}, volume = {143}, year = {2016}, month = {01/2016}, pages = {160-173}, abstract = {

C. elegans embryonic elongation is a morphogenetic event driven by actomyosin contractility and muscle-induced tension transmitted through hemidesmosomes. A role for the microtubule cytoskeleton has also been proposed, but its contribution remains poorly characterized. Here, we investigate the organization of the non-centrosomal microtubule arrays present in the epidermis and assess their function in elongation. We show that the microtubule regulators γ-tubulin and NOCA-1 are recruited to hemidesmosomes and adherens junctions early in elongation. Several parallel approaches suggest that microtubule nucleation occurs from these sites. Disrupting the epidermal microtubule array by overexpressing the microtubule-severing protein Spastin or by inhibiting the C. elegans ninein homolog NOCA-1 in the epidermis mildly affected elongation. However, microtubules were essential for elongation when hemidesmosomes or the activity of the Rho kinase LET-502/ROCK were partially compromised. Imaging of junctional components and genetic analyses suggest that epidermal microtubules function together with Rho kinase to promote the transport of E-cadherin to adherens junctions and myotactin to hemidesmosomes. Our results indicate that the role of LET-502 in junctional remodeling is likely to be independent of its established function as a myosin II activator, but requires a microtubule-dependent pathway involving the syntaxin SYX-5. Hence, we propose that non-centrosomal microtubules organized by epidermal junctions contribute to elongation by transporting junction remodeling factors, rather than having a mechanical role.

}, issn = {0950-1991}, doi = {10.1242/dev.126615}, url = {https://doi.org/10.1242/dev.126615}, author = {Quintin, Sophie and Wang, Shahoe and Pontabry, Julien and Bender, Ambre and Robin, Fran{\c c}ois and Hyenne, Vincent and Landmann, Fr{\'e}d{\'e}ric and Gally, Christelle and Oegema, Karen and Labouesse, Michel} } @article {47727, title = {Non-insect crustacean models in developmental genetics including an encomium to Parhyale hawaiensis.}, journal = {Current Opinion in Genetics \& Development}, volume = {39}, year = {2016}, month = {2016 Jul 28}, pages = {149-156}, abstract = {

The impressive diversity of body plans, lifestyles and segmental specializations exhibited by crustaceans (barnacles, copepods, shrimps, crabs, lobsters and their kin) provides great material to address longstanding questions in evolutionary developmental biology. Recent advances in forward and reverse genetics and in imaging approaches applied in the amphipod Parhyale hawaiensis and other emerging crustacean model species have made it possible to probe the molecular and cellular basis of crustacean diversity. A number of biological and technical qualities like the slow tempo and holoblastic cleavage mode, the stereotypy of many cellular processes, the functional and morphological diversity of limbs along the body axis, and the availability of various experimental manipulations, have made Parhyale a powerful system to study normal development and regeneration.

}, issn = {1879-0380}, doi = {10.1016/j.gde.2016.07.004}, author = {Stamataki, Evangelia and Pavlopoulos, Anastasios} } @article {68448, title = {NAD$^{+}$/NADH metabolism and NAD$^{+}$-dependent enzymes in cell death and ischemic brain injury: current advances and therapeutic implications.}, journal = {Curr Med Chem}, volume = {22}, year = {2015}, month = {2015}, pages = {1239-47}, abstract = {

NAD(+) and NADH play crucial roles in a variety of biological processes including energy metabolism, mitochondrial functions, and gene expression. Multiple studies have indicated that NAD(+) administration can profoundly decrease oxidative cell death as well as ischemic and traumatic brain injury, suggesting NAD(+) metabolism as a promising therapeutic target for cerebral ischemia and head injury. Cumulating evidence has suggested that NAD(+) can produce its protective effects by multiple mechanisms, including preventing mitochondrial alterations, enhancing energy metabolism, preventing virtually all forms of cell death including apoptosis, necrosis and autophagy, inhibiting inflammation, directly increasing antioxidation capacity of cells and tissues, and activating SIRT1. Increasing evidence has also suggested that NADH metabolism is a potential therapeutic target for treating several neurological disorders. A number of studies have further indicated that multiple NAD(+)-dependent enzymes such as sirtuins, polymerase(ADP-ribose) polymerases (PARPs) and CD38 mediate cell death and multiple biological processes. In this article, an overview of the recent findings regarding the roles of NAD(+)/NADH and NAD(+)-dependent enzymes in cell death and ischemic brain injury is provided. These findings have collectively indicated that NAD(+)/NADH and NAD(+)-dependent enzymes play fundamental roles in oxidative stress-induced cell death and ischemic brain injury, which may become promising therapeutic targets for brain ischemia and multiple other neurological disorders.

}, keywords = {ADP-ribosyl Cyclase 1, Animals, Brain Injuries, Brain Ischemia, Cell Death, Humans, NAD, Poly(ADP-ribose) Polymerases, Sirtuins}, issn = {1875-533X}, doi = {10.2174/0929867322666150209154420}, author = {Ma, Yingxin and Nie, Hui and Chen, Heyu and Li, Jiefu and Hong, Yunyi and Wang, Ban and Wang, Caixia and Zhang, Jie and Cao, Wei and Zhang, Mingchao and Xu, Yongning and Ding, Xianting and Yin, Shan Kai and Qu, Xinkai and Ying, Weihai} } @article {46894, title = {Neural circuit to integrate opposing motions in the visual field.}, journal = {Cell}, volume = {162}, year = {2015}, month = {2015 Jul 16}, pages = {351-62}, abstract = {

When navigating in their environment, animals use visual motion cues as feedback signals that are elicited by their own motion. Such signals are provided by wide-field neurons sampling motion directions at multiple image points as the animal maneuvers. Each one of these neurons responds selectively to a specific optic flow-field representing the spatial distribution of motion vectors on the retina. Here, we describe the discovery of a group of local, inhibitory interneurons in the fruit fly Drosophila key for filtering these cues. Using anatomy, molecular characterization, activity manipulation, and physiological recordings, we demonstrate that these interneurons convey direction-selective inhibition to wide-field neurons with opposite preferred direction and provide evidence for how their connectivity enables the computation required for integrating opposing motions. Our\ results indicate that, rather than sharpening directional selectivity per se, these circuit elements reduce noise by eliminating non-specific responses to complex visual information.
{\textbullet}Discovery of bi-stratified glutamatergic lobula plate-intrinsic (LPi) interneurons{\textbullet}LPi neurons provide visual null direction inhibition to wide-field tangential cells{\textbullet}Blocking LPi activity leads to target neurons responding to inadequate motion cues{\textbullet}Motion opponency thus increases flow-field selectivity
Newly identified inhibitory neurons are central to an integrative circuit that enables Drosophila to process visual cues with opposite motions generated during flight. The neurons are required to discriminate between distinct complex motion patterns, indicating that neural processing of opposing cues can yield outcomes beyond the simple sum of two inputs.

}, doi = {10.1016/j.cell.2015.06.035}, author = {Mauss, Alex S and Pankova, Katarina and Arenz, Alexander and Nern, Aljoscha and Rubin, Gerald M and Borst, Alexander} } @article {47354, title = {Neural coding in barrel cortex during whisker-guided locomotion.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Dec 23}, abstract = {

Animals seek out relevant information by moving through a dynamic world, but sensory systems are usually studied under highly constrained and passive conditions that may not probe important dimensions of the neural code. Here, we explored neural coding in the barrel cortex of head-fixed mice that tracked walls with their whiskers in tactile virtual reality. Optogenetic manipulations revealed that barrel cortex plays a role in wall-tracking. Closed-loop optogenetic control of layer 4 neurons can substitute for whisker-object contact to guide behavior resembling wall tracking. We measured neural activity using two-photon calcium imaging and extracellular recordings. Neurons were tuned to the distance between the animal snout and the contralateral wall, with monotonic, unimodal, and multimodal tuning curves. This rich representation of object location in the barrel cortex could not be predicted based on simple stimulus-response relationships involving individual whiskers and likely emerges within cortical circuits.

}, issn = {2050-084X}, doi = {10.7554/eLife.12559}, author = {Sofroniew, Nicholas James and Vlasov, Yurii A and Andrew Hires, Samuel and Freeman, Jeremy and Svoboda, Karel} } @article {48312, title = {Neural coding of perceived odor intensity.}, journal = {eNeuro}, volume = {2}, year = {2015}, month = {2015 Nov-Dec}, abstract = {

Stimulus intensity is a fundamental perceptual feature in all sensory systems. In olfaction, perceived odor intensity depends on at least two variables: odor concentration; and duration of the odor exposure or adaptation. To examine how neural activity at early stages of the olfactory system represents features relevant to intensity perception, we studied the responses of mitral/tufted cells (MTCs) while manipulating odor concentration and exposure duration. Temporal profiles of MTC responses to odors changed both as a function of concentration and with adaptation. However, despite the complexity of these responses, adaptation and concentration dependencies behaved similarly. These similarities were visualized by principal component analysis of average population responses and were quantified by discriminant analysis in a trial-by-trial manner. The qualitative functional dependencies of neuronal responses paralleled psychophysics results in humans. We suggest that temporal patterns of MTC responses in the olfactory bulb contribute to an internal perceptual variable: odor intensity.

}, keywords = {Adaptation, Physiological, Animals, Mice, Inbred C57BL, Neurons, Odorants, Olfactory Bulb, Perception, Smell}, issn = {2373-2822}, doi = {10.1523/ENEURO.0083-15.2015}, author = {Sirotin, Yevgeniy B and Shusterman, Roman and Rinberg, Dmitry} } @article {47038, title = {A neural command circuit for grooming movement control.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Sep 7}, abstract = {

Animals perform many stereotyped movements, but how nervous systems are organized for controlling specific movements remains unclear. Here we use anatomical, optogenetic, behavioral, and physiological techniques to identify a circuit in Drosophila melanogaster that can elicit stereotyped leg movements that groom the antennae. Mechanosensory chordotonal neurons detect displacements of the antennae and excite three different classes of functionally connected interneurons, which include two classes of brain interneurons and different parallel descending neurons. This multilayered circuit is organized such that neurons within each layer are sufficient to specifically elicit antennal grooming. However, we find differences in the durations of antennal grooming elicited by neurons in the different layers, suggesting that the circuit is organized to both command antennal grooming and control its duration. As similar features underlie stimulus-induced movements in other animals, we infer the possibility of a common circuit organization for movement control that can be dissected in Drosophila.

}, issn = {2050-084X}, doi = {10.7554/eLife.08758}, author = {Hampel, Stefanie and Franconville, Romain and Simpson, Julie H and Seeds, Andrew M} } @article {46694, title = {Neural dynamics for landmark orientation and angular path integration.}, journal = {Nature}, volume = {521}, year = {2015}, month = {2015 May 14}, pages = {186-191}, abstract = {

Many animals navigate using a combination of visual landmarks and path integration. In mammalian brains, head direction cells integrate these two streams of information by representing an animal{\textquoteright}s heading relative to landmarks, yet maintaining their directional tuning in darkness based on self-motion cues. Here we use two-photon calcium imaging in head-fixed Drosophila melanogaster walking on a ball in a virtual reality arena to demonstrate that landmark-based orientation and angular path integration are combined in the population responses of neurons whose dendrites tile the ellipsoid body, a toroidal structure in the centre of the fly brain. The neural population encodes the fly{\textquoteright}s azimuth relative to its environment, tracking visual landmarks when available and relying on self-motion cues in darkness. When both visual and self-motion cues are absent, a representation of the animal{\textquoteright}s orientation is maintained in this network through persistent activity, a potential substrate for short-term memory. Several features of the population dynamics of these neurons and their circular anatomical arrangement are suggestive of ring attractors, network structures that have been proposed to support the function of navigational brain circuits.

}, doi = {10.1038/nature14446}, author = {Seelig, Johannes D and Jayaraman, Vivek} } @article {47134, title = {Neural encoding of odors during active sampling and in turbulent plumes.}, journal = {Neuron}, volume = {88}, year = {2015}, month = {2015 Oct 21}, pages = {403-18}, abstract = {

Sensory inputs are often fluctuating and intermittent, yet animals reliably utilize them to direct behavior. Here we ask how natural stimulus fluctuations influence the dynamic neural encoding of odors. Using the locust olfactory system, we isolated two main causes of odor intermittency: chaotic odor plumes and active sampling behaviors. Despite their irregularity, chaotic odor plumes still drove dynamic neural response features including the synchronization, temporal patterning, and short-term plasticity of spiking in projection neurons, enabling classifier-based stimulus identification and activating downstream decoders (Kenyon cells). Locusts can also impose odor intermittency through active sampling movements with their unrestrained antennae. Odors triggered immediate, spatially targeted antennal scanning that, paradoxically, weakened individual neural responses. However, these frequent but weaker responses were highly informative about stimulus location. Thus, not only are odor-elicited dynamic neural responses compatible with natural stimulus fluctuations and important for stimulus identification, but locusts actively increase intermittency, possibly to improve stimulus localization.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.09.007}, author = {Huston, Stephen J and Stopfer, Mark and Cassenaer, Stijn and Aldworth, Zane N and Laurent, Gilles} } @article {47240, title = {Neural Network Model of Memory Retrieval.}, journal = {Frontiers in Computational Neuroscience}, volume = {9}, year = {2015}, month = {2015 Dec 17}, pages = {149}, abstract = {

Human memory can store large amount of information. Nevertheless, recalling is often a challenging task. In a classical free recall paradigm, where participants are asked to repeat a briefly presented list of words, people make mistakes for lists as short as 5 words. We present a model for memory retrieval based on a Hopfield neural network where transition between items are determined by similarities in their long-term memory representations. Meanfield analysis of the model reveals stable states of the network corresponding (1) to single memory representations and (2) intersection between memory representations. We show that oscillating feedback inhibition in the presence of noise induces transitions between these states triggering the retrieval of different memories. The network dynamics qualitatively predicts the distribution of time intervals required to recall new memory items observed in experiments. It shows that items having larger number of neurons in their representation are statistically easier to recall and reveals possible bottlenecks in our ability of retrieving memories. Overall, we propose a neural network model of information retrieval broadly compatible with experimental observations and is consistent with our recent graphical model (Romani et al., 2013).

}, issn = {1662-5188}, doi = {10.3389/fncom.2015.00149}, author = {Recanatesi, Stefano and Katkov, Mikhail and Romani, Sandro and Tsodyks, Misha} } @article {46189, title = {The neural representation of taste quality at the periphery.}, journal = {Nature}, volume = {517}, year = {2015}, month = {2015 Jan 15}, pages = {373-6}, abstract = {

The mammalian taste system is responsible for sensing and responding to the five basic taste qualities: sweet, sour, bitter, salty and umami. Previously, we showed that each taste is detected by dedicated taste receptor cells (TRCs) on the tongue and palate epithelium. To understand how TRCs transmit information to higher neural centres, we examined the tuning properties of large ensembles of neurons in the first neural station of the gustatory system. Here, we generated and characterized a collection of transgenic mice expressing a genetically encoded calcium indicator in central and peripheral neurons, and used a gradient refractive index microendoscope combined with high-resolution two-photon microscopy to image taste responses from ganglion neurons buried deep at the base of the brain. Our results reveal fine selectivity in the taste preference of ganglion neurons; demonstrate a strong match between TRCs in the tongue and the principal neural afferents relaying taste information to the brain; and expose the highly specific transfer of taste information between taste cells and the central nervous system.

}, keywords = {Animals, Calcium, Geniculate Ganglion, Mice, Mice, Transgenic, Neurons, Taste, Taste Buds, Taste Perception, Tongue}, issn = {1476-4687}, doi = {10.1038/nature13873}, author = {Barretto, Robert P J and Gillis-Smith, Sarah and Chandrashekar, Jayaram and Yarmolinsky, David A and Schnitzer, Mark J and Ryba, Nicholas J P and Zuker, Charles S} } @article {46481, title = {Neuroarchitecture and neuroanatomy of the Drosophila central complex: A GAL4-based dissection of protocerebral bridge neurons and circuits. (Front cover)}, journal = {The Journal of Comparative Neurology}, volume = {523}, year = {2015}, month = {2015 May 1}, pages = {Spc1 (Front Cover)}, abstract = {

Insects exhibit an elaborate repertoire of behaviors in response to environmental stimuli. The central complex plays a key role in combining various modalities of sensory information with an insect{\textquoteright}s internal state and past experience to select appropriate responses. Progress has been made in understanding the broad spectrum of outputs from the central complex neuropils and circuits involved in numerous behaviors. Many resident neurons have also been identified. However, the specific roles of these intricate structures and the functional connections between them remain largely obscure. Significant gains rely on obtaining a comprehensive catalog of the neurons and associated GAL4 lines that arborize within these brain regions, and on mapping neuronal pathways connecting these structures. To this end, small populations of neurons in the Drosophila melanogaster central complex were stochastically labeled using the multicolor flip-out technique and a catalog was created of the neurons, their morphologies, trajectories, relative arrangements, and corresponding GAL4 lines. This report focuses on one structure of the central complex, the protocerebral bridge, and identifies just 17 morphologically distinct cell types that arborize in this structure. This work also provides new insights into the anatomical structure of the four components of the central complex and its accessory neuropils. Most strikingly, we found that the protocerebral bridge contains 18 glomeruli, not 16, as previously believed. Revised wiring diagrams that take into account this updated architectural design are presented. This updated map of the Drosophila central complex will facilitate a deeper behavioral and physiological dissection of this sophisticated set of structures. J. Comp. Neurol. 523:997-1037, 2015. {\textcopyright} 2014 Wiley Periodicals, Inc.

}, issn = {1096-9861}, doi = {10.1002/cne.23773}, author = {Wolff, Tanya and Iyer, Nirmala A and Rubin, Gerald M} } @article {47158, title = {Neurodata without borders: creating a common data format for neurophysiology}, journal = {Neuron}, volume = {88}, year = {2015}, month = {2015 Nov 18}, pages = {629-34}, abstract = {

The Neurodata Without Borders (NWB) initiative promotes data standardization in neuroscience to increase research reproducibility and opportunities. In the first NWB pilot project, neurophysiologists and software developers produced a common data format for recordings and metadata of cellular electrophysiology and optical imaging experiments. The format specification, application programming interfaces, and sample datasets have been released.

}, doi = {10.1016/j.neuron.2015.10.025}, author = {Teeters, Jeffrey L and Godfrey, Keith and Young, Rob and Dang, Chinh and Friedsam, Claudia and Wark, Barry and Asari, Hiroki and Peron, Simon and Li, Nuo and Peyrache, Adrien} } @article {46926, title = {Neuron hemilineages provide the functional ground plan for the Drosophila ventral nervous system.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Jul 20}, abstract = {

Drosophila central neurons arise from neuroblasts that generate neurons in a pair-wise fashion, with the two daughters providing the basis for distinct A and B hemilineage groups. Thirty three postembryonically-born hemilineages contribute over 90\% of the neurons in each thoracic hemisegment. We devised genetic approaches to define the anatomy of most of these hemilineages and to assessed their functional roles using the heat-sensitive channel dTRPA1. The simplest hemilineages contained local interneurons and their activation caused tonic or phasic leg movements lacking interlimb coordination. The next level was hemilineages of similar projection cells that drove intersegmentally coordinated behaviors such as walking. The highest level involved hemilineages whose activation elicited complex behaviors such as takeoff. These activation phenotypes indicate that the hemilineages vary in their behavioral roles with some contributing to local networks for sensorimotor processing and others having higher order functions of coordinating these local networks into complex behavior.

}, issn = {2050-084X}, doi = {10.7554/eLife.04493}, author = {Harris, Robin M and Pfeiffer, Barret D and Rubin, Gerald M and Truman, James W} } @article {46972, title = {Neuronal representation of ultraviolet visual stimuli in mouse primary visual cortex.}, journal = {Scientific Reports}, volume = {5}, year = {2015}, month = {2015 Jul 29}, pages = {12597}, abstract = {

The mouse has become an important model for understanding the neural basis of visual perception. Although it has long been known that mouse lens transmits ultraviolet (UV) light and mouse opsins have absorption in the UV band, little is known about how UV visual information is processed in the mouse brain. Using a custom UV stimulation system and in vivo calcium imaging, we characterized the feature selectivity of layer 2/3 neurons in mouse primary visual cortex (V1). In adult mice, a comparable percentage of the neuronal population responds to UV and visible stimuli, with similar pattern selectivity and receptive field properties. In young mice, the orientation selectivity for UV stimuli increased steadily during development, but not direction selectivity. Our results suggest that, by expanding the spectral window through which the mouse can acquire visual information, UV sensitivity provides an important component for mouse vision.

}, issn = {2045-2322}, doi = {10.1038/srep12597}, author = {Tan, Zhongchao and Sun, Wenzhi and Chen, Tsai-Wen and Kim, Douglas and Ji, Na} } @article {46574, title = {Neurons for hunger and thirst transmit a negative-valence teaching signal.}, journal = {Nature}, volume = {521}, year = {2015}, month = {2015 Apr 27}, pages = {180-5}, abstract = {

Homeostasis is a biological principle for regulation of essential physiological parameters within a set range. Behavioural responses due to deviation from homeostasis are critical for survival, but motivational processes engaged by physiological need states are incompletely understood. We examined motivational characteristics of two separate neuron populations that regulate energy and fluid homeostasis by using cell-type-specific activity manipulations in mice. We found that starvation-sensitive AGRP neurons exhibit properties consistent with a negative-valence teaching signal. Mice avoided activation of AGRP neurons, indicating that AGRP neuron activity has negative valence. AGRP neuron inhibition conditioned preference for flavours and places. Correspondingly, deep-brain calcium imaging revealed that AGRP neuron activity rapidly reduced in response to food-related cues. Complementary experiments activating thirst-promoting neurons also conditioned avoidance. Therefore, these need-sensing neurons condition preference for environmental cues associated with nutrient or water ingestion, which is learned through reduction of negative-valence signals during restoration of homeostasis.

}, doi = {10.1038/nature14416}, author = {Betley, J Nicholas and Xu, Shengjin and Cao, Zhen Fang Huang and Gong, Rong and Magnus, Christopher J and Yu, Yang and Sternson, Scott M} } @article {46479, title = {Neuroscience: hot on the trail of temperature processing.}, journal = {Nature}, volume = {519}, year = {2015}, month = {2015 Mar 19}, pages = {296-7}, issn = {1476-4687}, doi = {10.1038/nature14209}, author = {Florence, T J and Reiser, Michael B} } @article {46799, title = {New insights and system designs for temporally focused multiphoton optogenetics. }, journal = {Proceedings of SPIE}, volume = {9329}, year = {2015}, month = {2015 Mar 5}, pages = {932928}, abstract = {

Temporal focusing (TF) multiphoton systems constitute a powerful solution for cellular resolution optogenetic stimulation and recording in three-dimensional, scattering tissue. Here, we address two fundamental aspects in the design of such systems: first, we examine the design of TF systems with specific optical sectioning by comparatively analyzing previously published results. Next, we develop a solution for obtaining TF in a flexible three-dimensional pattern of cellmatched focal spots. Our solution employs spatio-temporal focusing (SSTF) in a unique optical system design that can be integrated before essentially any multiphoton imaging or stimulation system.

}, doi = {10.1117/12.2078678}, author = {Mayblum, Tom and Schejter, Adi and Dana, Hod and Shoham, Shy} } @article {46504, title = {Next generation multilocus sequence typing (NGMLST) and the analytical software program MLSTEZ enable efficient, cost-effective, high-throughput, multilocus sequencing typing.}, journal = {Fungal Genetics and Biology}, volume = {75}, year = {2015}, month = {2015 Feb}, pages = {64-71}, abstract = {

Multilocus sequence typing (MLST) has become the preferred method for genotyping many biological species, and it is especially useful for analyzing haploid eukaryotes. MLST is rigorous, reproducible, and informative, and MLST genotyping has been shown to identify major phylogenetic clades, molecular groups, or subpopulations of a species, as well as individual strains or clones. MLST molecular types often correlate with important phenotypes. Conventional MLST involves the extraction of genomic DNA and the amplification by PCR of several conserved, unlinked gene sequences from a sample of isolates of the taxon under investigation. In some cases, as few as three loci are sufficient to yield definitive results. The amplicons are sequenced, aligned, and compared by phylogenetic methods to distinguish statistically significant differences among individuals and clades. Although MLST is simpler, faster, and less expensive than whole genome sequencing, it is more costly and time-consuming than less reliable genotyping methods (e.g. amplified fragment length polymorphisms). Here, we describe a new MLST method that uses next-generation sequencing, a multiplexing protocol, and appropriate analytical software to provide accurate, rapid, and economical MLST genotyping of 96 or more isolates in single assay. We demonstrate this methodology by genotyping isolates of the well-characterized, human pathogenic yeast Cryptococcus neoformans.

}, issn = {1096-0937}, doi = {10.1016/j.fgb.2015.01.005}, author = {Chen, Yuan and Frazzitta, Aubrey E and Litvintseva, Anastasia P and Fang, Charles and Mitchell, Thomas G and Springer, Deborah J and Ding, Yun and Yuan, George and Perfect, John R} } @article {68766, title = {NOCA-1 functions with γ-tubulin and in parallel to Patronin to assemble non-centrosomal microtubule arrays in \textitC. elegans}, journal = {eLife}, volume = {4}, year = {2015}, month = {09/2015}, pages = {e08649}, abstract = {

Non-centrosomal microtubule arrays assemble in differentiated tissues to perform mechanical and transport-based functions. In this study, we identify \textitCaenorhabditis elegans NOCA-1 as a protein with homology to vertebrate ninein. NOCA-1 contributes to the assembly of non-centrosomal microtubule arrays in multiple tissues. In the larval epidermis, NOCA-1 functions redundantly with the minus end protection factor Patronin/PTRN-1 to assemble a circumferential microtubule array essential for worm growth and morphogenesis. Controlled degradation of a γ-tubulin complex subunit in this tissue revealed that γ-tubulin acts with NOCA-1 in parallel to Patronin/PTRN-1. In the germline, NOCA-1 and γ-tubulin co-localize at the cell surface, and inhibiting either leads to a microtubule assembly defect. γ-tubulin targets independently of NOCA-1, but NOCA-1 targeting requires γ-tubulin when a non-essential putatively palmitoylated cysteine is mutated. These results show that NOCA-1 acts with γ-tubulin to assemble non-centrosomal arrays in multiple tissues and highlight functional overlap between the ninein and Patronin protein families.

}, keywords = {ninein, NOCA-1, non-centrosomal microtubule array, Patronin, PTRN-1}, issn = {2050-084X}, doi = {10.7554/eLife.08649}, url = {https://doi.org/10.7554/eLife.08649}, author = {Wang, Shaohe and Wu, Di and Quintin, Sophie and Green, Rebecca A and Cheerambathur, Dhanya K and Ochoa, Stacy D and Desai, Arshad and Oegema, Karen}, editor = {Akhmanova, Anna} } @article {48387, title = {Nonlinear circuits for naturalistic visual motion estimation.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Oct 24}, pages = {e09123}, abstract = {

Many animals use visual signals to estimate motion. Canonical models suppose that animals estimate motion by cross-correlating pairs of spatiotemporally separated visual signals, but recent experiments indicate that humans and flies perceive motion from higher-order correlations that signify motion in natural environments. Here we show how biologically plausible processing motifs in neural circuits could be tuned to extract this information. We emphasize how known aspects of Drosophila{\textquoteright}s visual circuitry could embody this tuning and predict fly behavior. We find that segregating motion signals into ON/OFF channels can enhance estimation accuracy by accounting for natural light/dark asymmetries. Furthermore, a diversity of inputs to motion detecting neurons can provide access to more complex higher-order correlations. Collectively, these results illustrate how non-canonical computations improve motion estimation with naturalistic inputs. This argues that the complexity of the fly{\textquoteright}s motion computations, implemented in its elaborate circuits, represents a valuable feature of its visual motion estimator.

}, keywords = {Animals, Drosophila, Locomotion, Models, Neurological, Motion Perception, Neurons, Visual Pathways}, issn = {2050-084X}, doi = {10.7554/eLife.09123}, author = {Fitzgerald, James E and Clark, Damon A} } @article {47016, title = {Novel behavioral paradigm reveals lower temporal limits on mouse olfactory decisions.}, journal = {The Journal of Neuroscience : the Official Journal of the Society for Neuroscience}, volume = {35}, year = {2015}, month = {2015 Aug 19}, pages = {11667-73}, abstract = {

UNLABELLED: Temporal limits on perceptual decisions set strict boundaries on the possible underlying neural computations. How odor information is encoded in the olfactory system is still poorly understood. Here, we sought to define the limit on the speed of olfactory processing. To achieve this, we trained mice to discriminate different odor concentrations in a novel behavioral setup with precise odor delivery synchronized to the sniffing cycle. Mice reported their choice by moving a horizontal treadmill with their front limbs. We found that mice reported discriminations of 75\% accuracy in 70-90 ms after odor inhalation. For a low concentration and nontrigeminal odorant, this time was 90-140 ms, showing that mice process odor information rapidly even in the absence of trigeminal stimulation. These response times establish, after accounting for odor transduction and motor delays, that olfactory processing can take tens of milliseconds. This study puts a strong limit on the underlying neural computations and suggests that the action potentials forming the neural basis for these decisions are fired in a few tens of milliseconds.

SIGNIFICANCE STATEMENT: Understanding how sensory information is processed requires different approaches that span multiple levels of investigation from genes to neurons to behavior. Limits on behavioral performance constrain the possible neural mechanisms responsible for specific computations. Using a novel behavioral paradigm, we established that mice can make decisions about odor intensity surprisingly fast. After accounting for sensory and motor delays, the limit on some olfactory neural computations can be as low as a few tens of milliseconds, which suggests that only the first action potentials across a population of neurons contribute to these computations.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4693-14.2015}, author = {Resulaj, Arbora and Rinberg, Dmitry} } @article {46925, title = {Nuclear accessibility of β-actin mRNA is measured by 3D single-molecule real-time tracking.}, journal = {Journal of Cell Biology}, volume = {209}, year = {2015}, month = {2015 May 25}, pages = {609-19}, abstract = {

Imaging single proteins or RNAs allows direct visualization of the inner workings of the cell. Typically, three-dimensional (3D) images are acquired by sequentially capturing a series of 2D sections. The time required to step through the sample often impedes imaging of large numbers of rapidly moving molecules. Here we applied multifocus microscopy (MFM) to instantaneously capture 3D single-molecule real-time images in live cells, visualizing cell nuclei at 10 volumes per second. We developed image analysis techniques to analyze messenger RNA (mRNA) diffusion in the entire volume of the nucleus. Combining MFM with precise registration between fluorescently labeled mRNA, nuclear pore complexes, and chromatin, we obtained globally optimal image alignment within 80-nm precision using transformation models. We show that β-actin mRNAs freely access the entire nucleus and fewer than 60\% of mRNAs are more than 0.5 {\textmu}m away from a nuclear pore, and we do so for the first time accounting for spatial inhomogeneity of nuclear organization.

}, issn = {1540-8140}, doi = {10.1083/jcb.201411032}, author = {Smith, Carlas S and Preibisch, Stephan and Joseph, Aviva and Abrahamsson, Sara and Rieger, Bernd and Myers, Eugene and Singer, Robert H and Grunwald, David} } @article {46506, title = {Numb is not a critical regulator of Notch-mediated cell fate decisions in the developing chick inner ear.}, journal = {Frontiers in Cellular Neuroscience}, volume = {9}, year = {2015}, month = {2015}, pages = {74}, abstract = {

The Notch signaling pathway controls differentiation of hair cells and supporting cells in the vertebrate inner ear. Here, we have investigated whether Numb, a known regulator of Notch activity in Drosophila, is involved in this process in the embryonic chick. The chicken homolog of Numb is expressed throughout the otocyst at early stages of development and is concentrated at the basal pole of the cells. It is asymmetrically allocated at some cell divisions, as in Drosophila, suggesting that it could act as a determinant inherited by one of the two daughter cells and favoring adoption of a hair-cell fate. To test the implication of Numb in hair cell fate decisions and the regulation of Notch signaling, we used different methods to overexpress Numb at different stages of inner ear development. We found that sustained or late Numb overexpression does not promote hair cell differentiation, and Numb does not prevent the reception of Notch signaling. Surprisingly, none of the Numb-overexpressing cells differentiated into hair cells, suggesting that high levels of Numb protein could interfere with intracellular processes essential for hair cell survival. However, when Numb was overexpressed early and more transiently during ear development, no effect on hair cell formation was seen. These results suggest that in the inner ear at least, Numb does not significantly repress Notch activity and that its asymmetric distribution in dividing precursor cells does not govern the choice between hair cell and supporting cell fates.

}, issn = {1662-5102}, doi = {10.3389/fncel.2015.00074}, author = {Eddison, Mark and Weber, Sara J and Ariza-McNaughton, Linda and Lewis, Julian and Daudet, Nicolas} } @article {46548, title = {Numerical study of multi-conjugate large area wavefront correction for deep tissue microscopy.}, journal = {Optics Express}, volume = {23}, year = {2015}, month = {2015 Mar 23}, pages = {7463-70}, abstract = {

Wavefront distortion fundamentally limits the achievable imaging depth and quality in thick tissue. Wavefront correction can help restore the diffraction limited focus albeit with a small field of view (FOV), which limits its imaging applications. In this work, we numerically investigate whether the multi-conjugate configuration, originally developed for astronomical adaptive optics, may increase the correction FOV in random turbid media. The results show that the multi-conjugate configuration can significantly improve the correction area compared to the widely adopted pupil plane correction. Even in the simple case of single-conjugation, it still outperforms the pupil plane correction. This study provides a guideline for designing the optimal wavefront correction system in deep tissue imaging.

}, issn = {1094-4087}, doi = {10.1364/OE.23.007463}, author = {Wu, Tsai-Wei and Cui, Meng} } @article {46816, title = {The nutrient-responsive hormone CCHamide-2 controls growth by regulating insulin-like peptides in the brain of Drosophila melanogaster.}, journal = {PLoS Genetics}, volume = {11}, year = {2015}, month = {2015 May}, pages = {e1005209}, abstract = {

The coordination of growth with nutritional status is essential for proper development and physiology. Nutritional information is mostly perceived by peripheral organs before being relayed to the brain, which modulates physiological responses. Hormonal signaling ensures this organ-to-organ communication, and the failure of endocrine regulation in humans can cause diseases including obesity and diabetes. In Drosophila melanogaster, the fat body (adipose tissue) has been suggested to play an important role in coupling growth with nutritional status. Here, we show that the peripheral tissue-derived peptide hormone CCHamide-2 (CCHa2) acts as a nutrient-dependent regulator of Drosophila insulin-like peptides (Dilps). A BAC-based transgenic reporter revealed strong expression of CCHa2 receptor (CCHa2-R) in insulin-producing cells (IPCs) in the brain. Calcium imaging of brain explants and IPC-specific CCHa2-R knockdown demonstrated that peripheral-tissue derived CCHa2 directly activates IPCs. Interestingly, genetic disruption of either CCHa2 or CCHa2-R caused almost identical defects in larval growth and developmental timing. Consistent with these phenotypes, the expression of dilp5, and the release of both Dilp2 and Dilp5, were severely reduced. Furthermore, transcription of CCHa2 is altered in response to nutritional levels, particularly of glucose. These findings demonstrate that CCHa2 and CCHa2-R form a direct link between peripheral tissues and the brain, and that this pathway is essential for the coordination of systemic growth with nutritional availability. A mammalian homologue of CCHa2-R, Bombesin receptor subtype-3 (Brs3), is an orphan receptor that is expressed in the islet β-cells; however, the role of Brs3 in insulin regulation remains elusive. Our genetic approach in Drosophila melanogaster provides the first evidence, to our knowledge, that bombesin receptor signaling with its endogenous ligand promotes insulin production.

}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1005209}, author = {Sano, Hiroko and Nakamura, Akira and Texada, Michael J and Truman, James W and Ishimoto, Hiroshi and Kamikouchi, Azusa and Nibu, Yutaka and Kume, Kazuhiko and Ida, Takanori and Kojima, Masayasu} } @article {46426, title = {Nanometer-resolution fluorescence electron microscopy (nano-EM) in cultured cells.}, journal = {Methods in Molecular Biology}, volume = {1117}, year = {2014}, month = {2014}, pages = {503-26}, abstract = {

Nano-resolution fluorescence electron microscopy (nano-fEM) pinpoints the location of individual proteins in electron micrographs. Plastic sections are first imaged using a super-resolution fluorescence microscope and then imaged on an electron microscope. The two images are superimposed to correlate the position of labeled proteins relative to subcellular structures. Here, we describe the method in detail and present five technical advancements: the use of uranyl acetate during the freeze-substitution to enhance the contrast of tissues and reduce the loss of fluorescence, the use of ground-state depletion instead of photoactivation for temporal control of fluorescence, the use of organic fluorophores instead of fluorescent proteins to obtain brighter fluorescence signals, the use of tissue culture cells to broaden the utility of the method, and the use of a transmission electron microscope to achieve sharper images of ultrastructure.

}, keywords = {Animals, Caenorhabditis elegans, Cells, Cultured, Histocytological Preparation Techniques, Image Processing, Computer-Assisted, Mice, Microscopy, Electron, Microscopy, Fluorescence}, issn = {1940-6029}, doi = {10.1007/978-1-62703-776-1_22}, author = {Watanabe, Shigeki and Lehmann, Martin and Hujber, Edward and Fetter, Richard D and Richards, Jackson and S{\"o}hl-Kielczynski, Berit and Felies, Annegret and Rosenmund, Christian and Schmoranzer, Jan and Jorgensen, Erik M} } @article {45062, title = {Natural whisker-guided behavior by head-fixed mice in tactile virtual reality.}, journal = {Journal of Neuroscience}, volume = {34}, year = {2014}, month = {2014 Jul 16}, pages = {9537-50}, abstract = {

During many natural behaviors the relevant sensory stimuli and motor outputs are difficult to quantify. Furthermore, the high dimensionality of the space of possible stimuli and movements compounds the problem of experimental control. Head fixation facilitates stimulus control and movement tracking, and can be combined with techniques for recording and manipulating neural activity. However, head-fixed mouse behaviors are typically trained through extensive instrumental conditioning. Here we present a whisker-based, tactile virtual reality system for head-fixed mice running on a spherical treadmill. Head-fixed mice displayed natural movements, including running and rhythmic whisking at 16 Hz. Whisking was centered on a set point that changed in concert with running so that more protracted whisking was correlated with faster running. During turning, whiskers moved in an asymmetric manner, with more retracted whisker positions in the turn direction and protracted whisker movements on the other side. Under some conditions, whisker movements were phase-coupled to strides. We simulated a virtual reality tactile corridor, consisting of two moveable walls controlled in a closed-loop by running speed and direction. Mice used their whiskers to track the walls of the winding corridor without training. Whisker curvature changes, which cause forces in the sensory follicles at the base of the whiskers, were tightly coupled to distance from the walls. Our behavioral system allows for precise control of sensorimotor variables during natural tactile navigation.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0712-14.2014}, author = {Sofroniew, Nicholas J and Cohen, Jeremy D and Lee, Albert K and Svoboda, Karel} } @article {6824, title = {Neural circuit components of the drosophila OFF motion vision pathway.}, journal = {Current Biology}, volume = {24}, year = {2014}, month = {2014 Feb 17}, pages = {385-92}, abstract = {

BACKGROUND: Detecting the direction of visual motion is an\ essential task of the early visual system. The Reichardt detector has been proven to be a faithful description of the underlying computation in insects. A series of recent studies addressed the neural implementation of the Reichardt detector in Drosophila revealing the overall layout in parallel ON and OFF channels, its input neurons from the lamina (L1{\textrightarrow}ON, and L2{\textrightarrow}OFF), and the respective output neurons to the lobula plate (ON{\textrightarrow}T4, and OFF{\textrightarrow}T5). While anatomical studies showed that T4 cells receive input from L1 via Mi1 and Tm3 cells, the neurons connecting L2 to T5 cells have not been identified so far. It is, however, known that L2 contacts, among others, two neurons, called Tm2 and L4, which show a pronounced directionality in their wiring. RESULTS: We characterized the visual response properties of both Tm2 and L4 neurons via Ca(2+) imaging. We found that Tm2 and L4 cells respond with an increase in activity to moving OFF edges in a direction-unselective manner. To investigate their participation in motion vision, we blocked their output while recording from downstream tangential cells in the lobula plate. Silencing of Tm2 and L4 completely abolishes the response to moving OFF edges. CONCLUSIONS: Our results demonstrate that both cell types are essential components of the Drosophila OFF motion vision pathway, prior to the computation of directionality in the dendrites of T5 cells.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2014.01.006}, author = {Meier, Matthias and Serbe, Etienne and Maisak, Matthew S and Haag, J{\"u}rgen and Dickson, Barry J and Borst, Alexander} } @article {45721, title = {Neural coding for effective rehabilitation.}, journal = {Biomed Research International}, volume = {2014}, year = {2014}, month = {2014}, pages = {286505}, abstract = {

Successful neurological rehabilitation depends on accurate diagnosis, effective treatment, and quantitative evaluation. Neural coding, a technology for interpretation of functional and structural information of the nervous system, has contributed to the advancements in neuroimaging, brain-machine interface (BMI), and design of training devices for rehabilitation purposes. In this review, we summarized the latest breakthroughs in neuroimaging from microscale to macroscale levels with potential diagnostic applications for rehabilitation. We also reviewed the achievements in electrocorticography (ECoG) coding with both animal models and human beings for BMI design, electromyography (EMG) interpretation for interaction with external robotic systems, and robot-assisted quantitative evaluation on the progress of rehabilitation programs. Future rehabilitation would be more home-based, automatic, and self-served by patients. Further investigations and breakthroughs are mainly needed in aspects of improving the computational efficiency in neuroimaging and multichannel ECoG by selection of localized neuroinformatics, validation of the effectiveness in BMI guided rehabilitation programs, and simplification of the system operation in training devices.

}, issn = {2314-6141}, doi = {10.1155/2014/286505}, author = {Hu, Xiaoling and Wang, Yiwen and Zhao, Ting and Gunduz, Aysegul} } @article {46188, title = {Neural computation for rehabilitation.}, journal = {Biomed Research International}, volume = {2014}, year = {2014}, month = {2014}, pages = {603985}, issn = {2314-6141}, doi = {10.1155/2014/603985}, author = {Hu, Xiaoling and Wang, Yiwen and Zhao, Ting and Gunduz, Aysegul} } @article {45147, title = {Neural pathways for the detection and discrimination of conspecific song in D. melanogaster.}, journal = {Current Biology}, volume = {24}, year = {2014}, month = {2014 May 19}, pages = {1039-49}, abstract = {

BACKGROUND: During courtship, male Drosophila melanogaster sing a multipart courtship song to female flies. This song is of particular interest because (1) it is species specific and varies widely within the genus, (2) it is a gating stimulus for females, who are sensitive detectors of conspecific song, and (3) it is the only sexual signal that is under both neural and genetic control. This song is perceived via mechanosensory neurons in the antennal Johnston{\textquoteright}s organ, which innervate the antennal mechanosensory and motor center (AMMC) of the brain. However, AMMC outputs that are responsible for detection and discrimination of conspecific courtship song remain unknown.

RESULTS: Using a large-scale anatomical screen of AMMC interneurons, we identify seven projection neurons (aPNs) and five local interneurons (aLNs) that outline a complex architecture for the ascending mechanosensory pathway. Neuronal inactivation and hyperactivation during behavior reveal that only two classes of interneurons are necessary for song responses--the projection neuron aPN1 and GABAergic interneuron aLN(al). These neurons are necessary in both male and female flies. Physiological recordings in aPN1 reveal the integration of courtship song as a function of pulse rate and outline an intracellular transfer function that likely facilitates the response to conspecific song.

CONCLUSIONS: These results reveal a critical pathway for courtship hearing in male and female flies, in which both aLN(al) and aPN1 mediate the detection of conspecific song. The pathways arising from these neurons likely serve as a critical neural substrate for behavioral reproductive isolation in D. melanogaster.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2014.03.048}, author = {Vaughan, Alexander G and Zhou, Chuan and Manoli, Devanand S and Baker, Bruce S} } @article {45810, title = {The neuronal architecture of the mushroom body provides a logic for associative learning.}, journal = {eLife}, volume = {3}, year = {2014}, month = {2014 Dec 23}, abstract = {

We identified the neurons comprising the Drosophila mushroom body (MB), an associative center in invertebrate brains, and provide a comprehensive map describing their potential connections. Each of the 21 MB output neuron (MBON) types elaborates segregated dendritic arbors along the parallel axons of \~{}2000 Kenyon cells, forming 15 compartments that collectively tile the MB lobes. MBON axons project to five discrete neuropils outside of the MB and three MBON types form a feedforward network in the lobes. Each of the 20 dopaminergic neuron (DAN) types projects axons to one, or at most two, of the MBON compartments. Convergence of DAN axons on compartmentalized Kenyon cell-MBON synapses creates a highly ordered unit that can support learning to impose valence on sensory representations. The elucidation of the complement of neurons of the MB provides a comprehensive anatomical substrate from which one can infer a functional logic of associative olfactory learning and memory.

}, issn = {2050-084X}, doi = {10.7554/eLife.04577}, author = {Aso, Yoshinori and Hattori, Daisuke and Yu, Yang and Johnston, Rebecca M and Iyer, Nirmala A and Ngo, Teri-Tb and Dionne, Heather and Abbott, Lf and Axel, Richard and Tanimoto, Hiromu and Rubin, Gerald M} } @article {46899, title = {The neuronal basis of how sexual experience modulates male aggression.}, journal = {National Science Review}, volume = {1}, year = {2014}, month = {2014 Dec }, pages = {473-4}, doi = {10.1093/nsr/nwu059}, author = {Liang, X H and Rao, Y and Zhou, Chuan} } @article {45974, title = {Neuronal control of Drosophila walking direction.}, journal = {Science}, volume = {344}, year = {2014}, month = {2014 Apr 4}, pages = {97-101}, abstract = {

Most land animals normally walk forward but switch to backward walking upon sensing an obstacle or danger in the path ahead. A change in walking direction is likely to be triggered by descending "command" neurons from the brain that act upon local motor circuits to alter the timing of leg muscle activation. Here we identify descending neurons for backward walking in Drosophila--the MDN neurons. MDN activity is required for flies to walk backward when they encounter an impassable barrier and is sufficient to trigger backward walking under conditions in which flies would otherwise walk forward. We also identify ascending neurons, MAN, that promote persistent backward walking, possibly by inhibiting forward walking. These findings provide an initial glimpse into the circuits and logic that control walking direction in Drosophila.

}, keywords = {Animals, Brain, Drosophila, Extremities, Female, Gait, Ganglia, Invertebrate, Male, Neurons, Walking}, issn = {1095-9203}, doi = {10.1126/science.1249964}, author = {Bidaye, Salil S and Machacek, Christian and Wu, Yang and Dickson, Barry J} } @article {45152, title = {Nonmuscle myosin II isoforms coassemble in living cells.}, journal = {Current Biology}, volume = {24}, year = {2014}, month = {2014 May 19}, pages = {1160-6}, abstract = {

Nonmuscle myosin II (NM II) powers myriad developmental and cellular processes, including embryogenesis, cell migration, and cytokinesis [1]. To exert its functions, monomers of NM II assemble into bipolar filaments that produce a contractile force on the actin cytoskeleton. Mammalian cells express up to three isoforms of NM II (NM IIA, IIB, and IIC), each of which possesses distinct biophysical properties and supports unique as well as redundant cellular functions [2-8]. Despite previous efforts [9-13], it remains unclear whether NM II isoforms assemble in living cells to produce mixed (heterotypic) bipolar filaments or whether filaments consist entirely of a single isoform (homotypic). We addressed this question using fluorescently tagged versions of NM IIA, IIB, and IIC, isoform-specific immunostaining of the endogenous proteins, and two-color total internal reflection fluorescence structured-illumination microscopy, or TIRF-SIM, to visualize individual myosin II bipolar filaments inside cells. We show that NM II isoforms coassemble into heterotypic filaments in a variety of settings, including various types of stress fibers, individual filaments throughout the cell, and the contractile ring. We also show that the differential distribution of NM IIA and NM IIB typically seen in confocal micrographs of well-polarized cells is reflected in the composition of individual bipolar filaments. Interestingly, this differential distribution is less pronounced in freshly spread cells, arguing for the existence of a sorting mechanism acting over time. Together, our work argues that individual NM II isoforms are potentially performing both isoform-specific and isoform-redundant functions while coassembled with other NM II isoforms.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2014.03.071}, author = {Beach, Jordan R and Shao, Lin and Remmert, Kirsten and Li, Dong and Betzig, Eric and Hammer, John A} } @article {46297, title = {Novel cell-based odorant sensor elements based on insect odorant receptors.}, journal = {Biosensors \& Bioelectronics}, volume = {65C}, year = {2014}, month = {2014 Oct 17}, pages = {287-294}, abstract = {

Development of cell-based odorant sensor elements combined not only high degree of sensitivity and selectivity but also long-term stability is crucial for their practical applications. Here we report the development of a novel cell-based odorant sensor element that sensitively and selectively detects odorants and displays increased fluorescent intensities over a long period of time. Our odorant sensor elements, based on Sf21 cell lines expressing insect odorant receptors, are sensitive to the level of several tens of parts per billion in solution, can selectively distinguish between different types of odorants based on the odorant selectivity intrinsic to the expressed receptors, and have response times of approximately 13s. Specifically, with the use of Sf21 cells and insect odorant receptors, we demonstrated that the established cell lines stably expressing insect odorant receptors are able to detect odorants with consistent responsiveness for at least 2 months, thus exceeding the short life-span normally associated with cell-based sensors. We also demonstrated the development of a compact odorant sensor chip by integrating the established insect cell lines into a microfluidic chip. The methodology we established in this study, in conjunction with the large repertoire of insect odorant receptors, will aid in the development of practical cell-based odorant sensors for various applications, including food administration and health management.

}, issn = {1873-4235}, doi = {10.1016/j.bios.2014.10.026}, author = {Mitsuno, Hidefumi and Sakurai, Takeshi and Namiki, Shigehiro and Mitsuhashi, Hiroyuki and Kanzaki, Ryohei} } @article {6384, title = {Nancy E. Beckage 1950-2012: Pioneer in insect host-parasite interactions.}, journal = {Annual Review of Entomology}, volume = {59}, year = {2013}, month = {2013 Oct 9}, pages = {1-12}, abstract = {

Nancy E. Beckage is widely recognized for her pioneering work in the field of insect host-parasitoid interactions beginning with endocrine influences of the tobacco hornworm, Manduca sexta, host and its parasitoid wasp Apanteles congregatus (now Cotesia congregata) on each other{\textquoteright}s development. Moreover, her studies show that the polydnavirus carried by the parasitoid wasp not only protects the parasitoid from the host{\textquoteright}s immune defenses, but also is responsible for some of the developmental effects of parasitism. Nancy was a highly regarded mentor of both undergraduate and graduate students and more widely of women students and colleagues in entomology. Her service both to her particular area and to entomology in general through participation on federal grant review panels and in the governance of the Entomological Society of America, organization of symposia at both national and international meetings, and editorship of several different journal issues and of several books, is legendary. She has left behind a lasting legacy of increased understanding of multilevel endocrine and physiological interactions among insects and other organisms and a strong network of interacting scientists and colleagues in her area of entomology.

}, issn = {1545-4487}, doi = {10.1146/annurev-ento-052913-021246}, author = {Riddiford, L M and Webb, B A} } @article {6130, title = {Nanotools for neuroscience and brain activity mapping.}, journal = {ACS Nano}, volume = {7}, year = {2013}, month = {2013 Mar 26}, pages = {1850-66}, abstract = {

Neuroscience is at a crossroads. Great effort is being invested into deciphering specific neural interactions and circuits. At the same time, there exist few general theories or principles that explain brain function. We attribute this disparity, in part, to limitations in current methodologies. Traditional neurophysiological approaches record the activities of one neuron or a few neurons at a time. Neurochemical approaches focus on single neurotransmitters. Yet, there is an increasing realization that neural circuits operate at emergent levels, where the interactions between hundreds or thousands of neurons, utilizing multiple chemical transmitters, generate functional states. Brains function at the nanoscale, so tools to study brains must ultimately operate at this scale, as well. Nanoscience and nanotechnology are poised to provide a rich toolkit of novel methods to explore brain function by enabling simultaneous measurement and manipulation of activity of thousands or even millions of neurons. We and others refer to this goal as the Brain Activity Mapping Project. In this Nano Focus, we discuss how recent developments in nanoscale analysis tools and in the design and synthesis of nanomaterials have generated optical, electrical, and chemical methods that can readily be adapted for use in neuroscience. These approaches represent exciting areas of technical development and research. Moreover, unique opportunities exist for nanoscientists, nanotechnologists, and other physical scientists and engineers to contribute to tackling the challenging problems involved in understanding the fundamentals of brain function.

}, issn = {1936-086X}, doi = {10.1021/nn4012847}, author = {Alivisatos, A Paul and Andrews, Anne M and Boyden, Edward S and Chun, Miyoung and Church, George M and Deisseroth, Karl and Donoghue, John P and Fraser, Scott E and Lippincott-Schwartz, Jennifer and Looger, Loren L and Masmanidis, Sotiris and McEuen, Paul L and Nurmikko, Arto V and Park, Hongkun and Peterka, Darcy S and Reid, Clay and Roukes, Michael L and Scherer, Axel and Schnitzer, Mark and Sejnowski, Terrence J and Shepard, Kenneth L and Tsao, Doris and Turrigiano, Gina and Weiss, Paul S and Xu, Chris and Yuste, Rafael and Zhuang, Xiaowei} } @article {47641, title = {Nanotools for neuroscience and brain activity mapping.}, journal = {ACS nano}, volume = {7}, year = {2013}, month = {2013 Mar 26}, pages = {1850-66}, abstract = {

Neuroscience is at a crossroads. Great effort is being invested into deciphering specific neural interactions and circuits. At the same time, there exist few general theories or principles that explain brain function. We attribute this disparity, in part, to limitations in current methodologies. Traditional neurophysiological approaches record the activities of one neuron or a few neurons at a time. Neurochemical approaches focus on single neurotransmitters. Yet, there is an increasing realization that neural circuits operate at emergent levels, where the interactions between hundreds or thousands of neurons, utilizing multiple chemical transmitters, generate functional states. Brains function at the nanoscale, so tools to study brains must ultimately operate at this scale, as well. Nanoscience and nanotechnology are poised to provide a rich toolkit of novel methods to explore brain function by enabling simultaneous measurement and manipulation of activity of thousands or even millions of neurons. We and others refer to this goal as the Brain Activity Mapping Project. In this Nano Focus, we discuss how recent developments in nanoscale analysis tools and in the design and synthesis of nanomaterials have generated optical, electrical, and chemical methods that can readily be adapted for use in neuroscience. These approaches represent exciting areas of technical development and research. Moreover, unique opportunities exist for nanoscientists, nanotechnologists, and other physical scientists and engineers to contribute to tackling the challenging problems involved in understanding the fundamentals of brain function.

}, keywords = {Animals, Brain Mapping, Humans, Models, Neurological, Nanomedicine, Nanoparticles, Nanotechnology, Nervous System Physiological Phenomena}, issn = {1936-086X}, doi = {10.1021/nn4012847}, author = {Alivisatos, A Paul and Andrews, Anne M and Boyden, Edward S and Chun, Miyoung and Church, George M and Deisseroth, Karl and Donoghue, John P and Fraser, Scott E and Lippincott-Schwartz, Jennifer and Looger, Loren L and Masmanidis, Sotiris and McEuen, Paul L and Nurmikko, Arto V and Park, Hongkun and Peterka, Darcy S and Reid, Clay and Roukes, Michael L and Scherer, Axel and Schnitzer, Mark and Sejnowski, Terrence J and Shepard, Kenneth L and Tsao, Doris and Turrigiano, Gina and Weiss, Paul S and Xu, Chris and Yuste, Rafael and Zhuang, Xiaowei} } @article {47644, title = {NBR1 acts as an autophagy receptor for peroxisomes.}, journal = {Journal of cell science}, volume = {126}, year = {2013}, month = {2013 Feb 15}, pages = {939-52}, abstract = {

Selective macro-autophagy is an intracellular process by which large cytoplasmic materials are selectively sequestered and degraded in the lysosomes. Substrate selection is mediated by ubiquitylation and recruitment of ubiquitin-binding autophagic receptors such as p62, NBR1, NDP52 and Optineurin. Although it has been shown that these receptors act cooperatively to target some types of substrates to nascent autophagosomes, their precise roles are not well understood. We examined selective autophagic degradation of peroxisomes (pexophagy), and found that NBR1 is necessary and sufficient for pexophagy. Mutagenesis studies of NBR1 showed that the amphipathic α-helical J domain, the ubiquitin-associated (UBA) domain, the LC3-interacting region and the coiled-coil domain are necessary to mediate pexophagy. Strikingly, substrate selectivity is partly achieved by NBR1 itself by coincident binding of the J and UBA domains to peroxisomes. Although p62 is not required when NBR1 is in excess, its binding to NBR1 increases the efficiency of NBR1-mediated pexophagy. Together, these results suggest that NBR1 is the specific autophagy receptor for pexophagy.

}, keywords = {Autophagy, Blotting, Western, Cell Line, Hela Cells, Humans, Microscopy, Confocal, Microscopy, Electron, Peroxisomes, Proteins}, issn = {1477-9137}, doi = {10.1242/jcs.114819}, author = {Deosaran, Elizabeth and Larsen, Kenneth B and Hua, Rong and Sargent, Graeme and Wang, Yuqing and Kim, Sarah and Lamark, Trond and Jauregui, Miluska and Law, Kelsey and Lippincott-Schwartz, Jennifer and Brech, Andreas and Johansen, Terje and Kim, Peter K} } @article {6417, title = {Neural circuits and motivational processes for hunger.}, journal = {Current Opinion in Neurobiology}, volume = {23}, year = {2013}, month = {2013 Jun}, pages = {353-60}, abstract = {

How does an organism{\textquoteright}s internal state direct its actions? At one moment an animal forages for food with acrobatic feats such as tree climbing and jumping between branches. At another time, it travels along the ground to find water or a mate, exposing itself to predators along the way. These behaviors are costly in terms of energy or physical risk, and the likelihood of performing one set of actions relative to another is strongly modulated by internal state. For example, an animal in energy deficit searches for food and a dehydrated animal looks for water. The crosstalk between physiological state and motivational processes influences behavioral intensity and intent, but the underlying neural circuits are poorly understood. Molecular genetics along with optogenetic and pharmacogenetic tools for perturbing neuron function have enabled cell type-selective dissection of circuits that mediate behavioral responses to physiological state changes. Here, we review recent progress into neural circuit analysis of hunger in the mouse by focusing on a starvation-sensitive neuron population in the hypothalamus that is sufficient to promote voracious eating. We also consider research into the motivational processes that are thought to underlie hunger in order to outline considerations for bridging the gap between homeostatic and motivational neural circuits.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2013.04.006}, author = {Sternson, Scott M and Betley, J Nicholas and Cao, Zhen Fang Huang} } @article {6146, title = {Neural coding during active somatosensation revealed using illusory touch.}, journal = {Nature Neuroscience}, volume = {16}, year = {2013}, month = {2013 Jun 2}, pages = {958-65}, abstract = {

Active sensation requires the convergence of external stimuli with representations of body movements. We used mouse behavior, electrophysiology and optogenetics to dissect the temporal interactions among whisker movement, neural activity and sensation of touch. We photostimulated layer 4 activity in single barrels in a closed loop with whisking. Mimicking touch-related neural activity caused illusory perception of an object at a particular location, but scrambling the timing of the spikes over one whisking cycle (tens of milliseconds) did not abolish the illusion, indicating that knowledge of instantaneous whisker position is unnecessary for discriminating object locations. The illusions were induced only during bouts of directed whisking, when mice expected touch, and in the relevant barrel. Reducing activity biased behavior, consistent with a spike count code for object detection at a particular location. Our results show that mice integrate coding of touch with movement over timescales of a whisking bout to produce perception of active touch.

}, issn = {1546-1726}, doi = {10.1038/nn.3419}, author = {O{\textquoteright}Connor, Daniel H and Hires, S Andrew and Guo, Zengcai V and Li, Nuo and Yu, Jianing and Sun, Qian-Quan and Huber, Daniel and Svoboda, Karel} } @article {5539, title = {Neural signals of extinction in the inhibitory microcircuit of the ventral midbrain.}, journal = {Nature Neuroscience}, volume = {16}, year = {2013}, month = {2013 Jan}, pages = {71-8}, abstract = {

Midbrain dopaminergic (DA) neurons are thought to guide learning via phasic elevations of firing in response to reward predicting stimuli. The mechanism for these signals remains unclear. Using extracellular recording during associative learning, we found that inhibitory neurons in the ventral midbrain of mice responded to salient auditory stimuli with a burst of activity that occurred before the onset of the phasic response of DA neurons. This population of inhibitory neurons exhibited enhanced responses during extinction and was anticorrelated with the phasic response of simultaneously recorded DA neurons. Optogenetic stimulation revealed that this population was, in part, derived from inhibitory projection neurons of the substantia nigra that provide a robust monosynaptic inhibition of DA neurons. Thus, our results elaborate on the dynamic upstream circuits that shape the phasic activity of DA neurons and suggest that the inhibitory microcircuit of the midbrain is critical for new learning in extinction.

}, issn = {1546-1726}, doi = {10.1038/nn.3283}, author = {Pan, Wei-Xing and Brown, Jennifer and Dudman, Joshua Tate} } @conference {45640, title = {A neuron as a signal processing device}, booktitle = {2013 Asilomar Conference on Signals, Systems and Computers}, year = {2013}, month = {05/2014}, publisher = {IEEE}, organization = {IEEE}, address = {Pacific Grove, CA}, abstract = {

A neuron is a basic physiological and computational unit of the brain. While much is known about the physiological properties of a neuron, its computational role is poorly understood. Here we propose to view a neuron as a signal processing device that represents the incoming streaming data matrix as a sparse vector of synaptic weights scaled by an outgoing sparse activity vector. Formally, a neuron minimizes a cost function comprising a cumulative squared representation error and regularization terms. We derive an online algorithm that minimizes such cost function by alternating between the minimization with respect to activity and with respect to synaptic weights. The steps of this algorithm reproduce well-known physiological properties of a neuron, such as weighted summation and leaky integration of synaptic inputs, as well as an Oja-like, but parameter-free, synaptic learning rule. Our theoretical framework makes several predictions, some of which can be verified by the existing data, others require further experiments. Such framework should allow modeling the function of neuronal circuits without necessarily measuring all the microscopic biophysical parameters, as well as facilitate the design of neuromorphic electronics.

}, isbn = {9781479923885}, doi = {10.1109/ACSSC.2013.6810296}, author = {Tao Hu and Towfic, Z.J. and Pehlevan, C. and Genkin, A. and Chklovskii, D.B.} } @article {6579, title = {A neuron-based screening platform for optimizing genetically-encoded calcium indicators.}, journal = {PLoS One}, volume = {8}, year = {2013}, month = {2013}, pages = {e77728}, abstract = {

Fluorescent protein-based sensors for detecting neuronal activity have been developed largely based on non-neuronal screening systems. However, the dynamics of neuronal state variables (e.g., voltage, calcium, etc.) are typically very rapid compared to those of non-excitable cells. We developed an electrical stimulation and fluorescence imaging platform based on dissociated rat primary neuronal cultures. We describe its use in testing genetically-encoded calcium indicators (GECIs). Efficient neuronal GECI expression was achieved using lentiviruses containing a neuronal-selective gene promoter. Action potentials (APs) and thus neuronal calcium levels were quantitatively controlled by electrical field stimulation, and fluorescence images were recorded. Images were segmented to extract fluorescence signals corresponding to individual GECI-expressing neurons, which improved sensitivity over full-field measurements. We demonstrate the superiority of screening GECIs in neurons compared with solution measurements. Neuronal screening was useful for efficient identification of variants with both improved response kinetics and high signal amplitudes. This platform can be used to screen many types of sensors with cellular resolution under realistic conditions where neuronal state variables are in relevant ranges with respect to timing and amplitude.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0077728}, author = {Wardill, Trevor J. and Chen, Tsai-Wen and Schreiter, Eric R and Hasseman, Jeremy P and Tsegaye, Getahun and Fosque, Benjamin F and Behnam, Reza and Shields, Brenda C and Ramirez, Melissa and Kimmel, Bruce E and Kerr, Rex A and Jayaraman, Vivek and Looger, Loren L and Svoboda, Karel and Kim, Douglas S.} } @article {5883, title = {New technologies in imaging.}, journal = {Molecular Biology of the Cell}, volume = {24}, year = {2013}, month = {2013 Mar}, pages = {669}, abstract = {

Visualization of cellular and molecular processes is an indispensable tool for cell biologists, and innovations in microscopy methods unfailingly lead to new biological discoveries. Today, light microscopy (LM) provides ever-higher spatial and temporal resolution and visualization of biological process over enormous ranges. Electron microscopy (EM) is moving into the atomic resolution regime and allowing cellular analyses that are more physiological and sophisticated in scope. Importantly, much is being gained by combining multiple approaches, (e.g., LM and EM) to take advantage of their complementary strengths. The advent of high-throughput microscopies has led to a common need for sophisticated computational methods to quantitatively analyze huge amounts of data and translate images into new biological insights.

}, issn = {1939-4586}, doi = {10.1091/mbc.E12-12-0867}, author = {Galbraith, Catherine G and Keller, Philipp J and Nogales, Eva} } @article {65888, title = {NGL-2 Regulates Pathway-Specific Neurite Growth and Lamination, Synapse Formation, and Signal Transmission in the Retina}, journal = {Journal of Neuroscience}, volume = {33}, year = {2013}, month = {May-07-2014}, pages = {11949 - 11959}, abstract = {

Parallel processing is an organizing principle of many neural circuits. In the retina, parallel neuronal pathways process signals from rod and cone photoreceptors and support vision over a wide range of light levels. Toward this end, rods and cones form triad synapses with dendrites of distinct bipolar cell types, and the axons or dendrites, respectively, of horizontal cells (HCs). The molecular cues that promote the formation of specific neuronal pathways remain largely unknown. Here, we discover that developing and mature HCs express the leucine-rich repeat (LRR)-containing protein netrin-G ligand 2 (NGL-2). NGL-2 localizes selectively to the tips of HC axons, which form reciprocal connections with rods. In mice with null mutations in Ngl-2 (Ngl-2$^{-}$/$^{-}$), many branches of HC axons fail to stratify in the outer plexiform layer (OPL) and invade the outer nuclear layer. In addition, HC axons expand lateral territories and increase coverage of the OPL, but establish fewer synapses with rods. NGL-2 can form transsynaptic adhesion complexes with netrin-G2, which we show to be expressed by photoreceptors. In Ngl-2$^{-}$/$^{-}$ mice, we find specific defects in the assembly of presynaptic ribbons in rods, indicating that reverse signaling of complexes involving NGL-2 regulates presynaptic maturation. The development of HC dendrites and triad synapses of cone photoreceptors proceeds normally in the absence of NGL-2 and in vivo electrophysiology reveals selective defects in rod-mediated signal transmission in Ngl-2$^{-}$/$^{-}$ mice. Thus, our results identify NGL-2 as a central component of pathway-specific development in the outer retina.

}, issn = {0270-6474}, doi = {10.1523/JNEUROSCI.1521-13.2013}, url = {http://www.jneurosci.org/cgi/doi/10.1523/JNEUROSCI.1521-13.2013}, author = {Soto, F. and Watkins, K. L. and Johnson, R. E. and Schottler, F. and Kerschensteiner, D.} } @article {6435, title = {nhmmer: DNA homology search with profile HMMs.}, journal = {Bioinformatics}, volume = {29}, year = {2013}, month = {2013 Oct 1}, pages = {2487-9}, abstract = {

SUMMARY: Sequence database searches are an essential part of molecular biology, providing information about the function and evolutionary history of proteins, RNA molecules and DNA sequence elements. We present a tool for DNA/DNA sequence comparison that is built on the HMMER framework, which applies probabilistic inference methods based on hidden Markov models to the problem of homology search. This tool, called nhmmer, enables improved detection of remote DNA homologs, and has been used in combination with Dfam and RepeatMasker to improve annotation of transposable elements in the human genome. AVAILABILITY: nhmmer is a part of the new HMMER3.1 release. Source code and documentation can be downloaded from http://hmmer.org. HMMER3.1 is freely licensed under the GNU GPLv3 and should be portable to any POSIX-compliant operating system, including Linux and Mac OS/X. CONTACT: wheelert@janelia.hhmi.org.

}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btt403}, author = {Wheeler, Travis J and Eddy, Sean R.} } @article {6580, title = {Nonlinear dynamics support a linear population code in a retinal target-tracking circuit.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {33}, year = {2013}, month = {2013 Oct 23}, pages = {16971-82}, abstract = {

A basic task faced by the visual system of many organisms is to accurately track the position of moving prey. The retina is the first stage in the processing of such stimuli; the nature of the transformation here, from photons to spike trains, constrains not only the ultimate fidelity of the tracking signal but also the ease with which it can be extracted by other brain regions. Here we demonstrate that a population of fast-OFF ganglion cells in the salamander retina, whose dynamics are governed by a nonlinear circuit, serve to compute the future position of the target over hundreds of milliseconds. The extrapolated position of the target is not found by stimulus reconstruction but is instead computed by a weighted sum of ganglion cell outputs, the population vector average (PVA). The magnitude of PVA extrapolation varies systematically with target size, speed, and acceleration, such that large targets are tracked most accurately at high speeds, and small targets at low speeds, just as is seen in the motion of real prey. Tracking precision reaches the resolution of single photoreceptors, and the PVA algorithm performs more robustly than several alternative algorithms. If the salamander brain uses the fast-OFF cell circuit for target extrapolation as we suggest, the circuit dynamics should leave a microstructure on the behavior that may be measured in future experiments. Our analysis highlights the utility of simple computations that, while not globally optimal, are efficiently implemented and have close to optimal performance over a limited but ethologically relevant range of stimuli.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.2257-13.2013}, author = {Leonardo, Anthony and Meister, Markus} } @article {6927, title = {Non-redundant coding of aversive odours in the main olfactory pathway.}, journal = {Nature}, volume = {497}, year = {2013}, month = {2013 May 23}, pages = {486-9}, abstract = {

Many species are critically dependent on olfaction for survival. In the main olfactory system of mammals, odours are detected by sensory neurons that express a large repertoire of canonical odorant receptors and a much smaller repertoire of trace amine-associated receptors (TAARs). Odours are encoded in a combinatorial fashion across glomeruli in the main olfactory bulb, with each glomerulus corresponding to a specific receptor. The degree to which individual receptor genes contribute to odour perception is unclear. Here we show that genetic deletion of the olfactory Taar gene family, or even a single Taar gene (Taar4), eliminates the aversion that mice display to low concentrations of volatile amines and to the odour of predator urine. Our findings identify a role for the TAARs in olfaction, namely, in the high-sensitivity detection of innately aversive odours. In addition, our data reveal that aversive amines are represented in a non-redundant fashion, and that individual main olfactory receptor genes can contribute substantially to odour perception.

}, keywords = {Amines, Animals, Avoidance Learning, Female, G-Protein-Coupled, Male, Mice, Models, Neurological, Odorant, Odors, Olfactory Bulb, Olfactory Pathways, Olfactory Receptor Neurons, Predatory Behavior, Receptors, Smell, Urine}, issn = {1476-4687}, doi = {10.1038/nature12114}, author = {Dewan, Adam and Pacifico, Rodrigo and Zhan, Ross and Rinberg, Dmitry and Bozza, Thomas} } @article {46597, title = {The novel gene tank, a tumor suppressor homolog, regulates ethanol sensitivity in Drosophila.}, journal = {The Journal of Neuroscience}, volume = {33}, year = {2013}, month = {2013 May 8}, pages = {8134-43}, abstract = {

In both mammalian and insect models of ethanol intoxication, high doses of ethanol induce motor impairment and eventually sedation. Sensitivity to the sedative effects of ethanol is inversely correlated with risk for alcoholism. However, the genes regulating ethanol sensitivity are largely unknown. Based on a previous genetic screen in Drosophila for ethanol sedation mutants, we identified a novel gene, tank (CG15626), the homolog of the mammalian tumor suppressor EI24/PIG8, which has a strong role in regulating ethanol sedation sensitivity. Genetic and behavioral analyses revealed that tank acts in the adult nervous system to promote ethanol sensitivity. We localized the function of tank in regulating ethanol sensitivity to neurons within the pars intercerebralis that have not been implicated previously in ethanol responses. We show that acutely manipulating the activity of all tank-expressing neurons, or of pars intercerebralis neurons in particular, alters ethanol sensitivity in a sexually dimorphic manner, since neuronal activation enhanced ethanol sedation in males, but not females. Finally, we provide anatomical evidence that tank-expressing neurons form likely synaptic connections with neurons expressing the neural sex determination factor fruitless (fru), which have been implicated recently in the regulation of ethanol sensitivity. We suggest that a functional interaction with fru neurons, many of which are sexually dimorphic, may account for the sex-specific effect induced by activating tank neurons. Overall, we have characterized a novel gene and corresponding set of neurons that regulate ethanol sensitivity in Drosophila.

}, keywords = {Adaptor Proteins, Signal Transducing, Analysis of Variance, Animals, Animals, Genetically Modified, Apoptosis Regulatory Proteins, Behavior, Animal, Central Nervous System Depressants, Dose-Response Relationship, Drug, Drosophila, Drosophila Proteins, Ethanol, Gene Expression Regulation, Green Fluorescent Proteins, Humans, Molecular Biology, Mutation, Nuclear Proteins, RNA Interference, TRPC Cation Channels, Tumor Suppressor Proteins}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3695-12.2013}, author = {Devineni, Anita V and Eddison, Mark and Heberlein, Ulrike} } @article {6412, title = {Nucleosome-free region dominates histone acetylation in targeting SWR1 to promoters for H2A.Z replacement.}, journal = {Cell}, volume = {154}, year = {2013}, month = {2013 Sep 12}, pages = {1232-45}, abstract = {

The histone variant H2A.Z is a genome-wide signature of nucleosomes proximal to eukaryotic regulatory DNA. Whereas the multisubunit chromatin remodeler SWR1 is known to catalyze ATP-dependent deposition of H2A.Z, the mechanism of SWR1 recruitment to S.\ cerevisiae promoters has been unclear. A sensitive assay for competitive binding of dinucleosome substrates revealed that SWR1 preferentially binds long nucleosome-free DNA and the adjoining nucleosome core particle, allowing discrimination of gene promoters over gene bodies. Analysis of mutants indicates that the conserved Swc2/YL1 subunit and the adenosine triphosphatase domain of Swr1 are mainly responsible for binding to substrate. SWR1 binding is enhanced on nucleosomes acetylated by the NuA4 histone acetyltransferase, but recognition of nucleosome-free and nucleosomal DNA is dominant over interaction with acetylated histones. Such hierarchical cooperation between DNA and histone signals expands the dynamic range of genetic switches, unifying classical gene regulation by DNA-binding factors with ATP-dependent nucleosome remodeling and posttranslational histone modifications.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2013.08.005}, author = {Ranjan, Anand and Mizuguchi, Gaku and Fitzgerald, Peter C and Wei, Debbie and Wang, Feng and Huang, Yingzi and Luk, Ed and Woodcock, Christopher L and Wu, Carl} } @article {5153, title = {The Ndc80 kinetochore complex directly modulates microtubule dynamics.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, year = {2012}, month = {2012 Aug 20}, pages = {16113-8}, abstract = {

The conserved Ndc80 complex is an essential microtubule-binding component of the kinetochore. Recent findings suggest that the Ndc80 complex influences microtubule dynamics at kinetochores in vivo. However, it was unclear if the Ndc80 complex mediates these effects directly, or by affecting other factors localized at the kinetochore. Using a reconstituted system in vitro, we show that the human Ndc80 complex directly stabilizes the tips of disassembling microtubules and promotes rescue (the transition from microtubule shortening to growth). In vivo, an N-terminal domain in the Ndc80 complex is phosphorylated by the Aurora B kinase. Mutations that mimic phosphorylation of the Ndc80 complex prevent stable kinetochore-microtubule attachment, and mutations that block phosphorylation damp kinetochore oscillations. We find that the Ndc80 complex with Aurora B phosphomimetic mutations is defective at promoting microtubule rescue, even when robustly coupled to disassembling microtubule tips. This impaired ability to affect dynamics is not simply because of weakened microtubule binding, as an N-terminally truncated complex with similar binding affinity is able to promote rescue. Taken together, these results suggest that in addition to regulating attachment stability, Aurora B controls microtubule dynamics through phosphorylation of the Ndc80 complex.

}, issn = {1091-6490}, doi = {10.1073/pnas.1209615109}, author = {Umbreit, Neil T and Gestaut, Daniel R and Tien, Jerry F and Vollmar, Breanna S and Gonen, Tamir and Asbury, Charles L and Davis, Trisha N} } @article {6220, title = {A network of spiking neurons for computing sparse representations in an energy-efficient way.}, journal = {Neural computation}, volume = {24}, year = {2012}, month = {2012 Nov}, pages = {2852-72}, abstract = {Computing sparse redundant representations is an important problem in both applied mathematics and neuroscience. In many applications, this problem must be solved in an energy-efficient way. Here, we propose a hybrid distributed algorithm (HDA), which solves this problem on a network of simple nodes communicating by low-bandwidth channels. HDA nodes perform both gradient-descent-like steps on analog internal variables and coordinate-descent-like steps via quantized external variables communicated to each other. Interestingly, the operation is equivalent to a network of integrate-and-fire neurons, suggesting that HDA may serve as a model of neural computation. We show that the numerical performance of HDA is on par with existing algorithms. In the asymptotic regime, the representation error of HDA decays with time, t, as 1/t. HDA is stable against time-varying noise; specifically, the representation error decays as 1/√t for gaussian white noise.}, keywords = {Action Potentials, Algorithms, Models, Neural Networks (Computer), Neurological, Neurons}, issn = {1530-888X}, doi = {10.1162/NECO_a_00353}, author = {Hu, Tao and Genkin, Alexander and Chklovskii, Dmitri B} } @article {5710, title = {Network resets in medial prefrontal cortex mark the onset of behavioral uncertainty.}, journal = {Science}, volume = {338}, year = {2012}, month = {2012 Oct 5}, pages = {135-9}, abstract = {

Regions within the prefrontal cortex are thought to process beliefs about the world, but little is known about the circuit dynamics underlying the formation and modification of these beliefs. Using a task that permits dissociation between the activity encoding an animal{\textquoteright}s internal state and that encoding aspects of behavior, we found that transient increases in the volatility of activity in the rat medial prefrontal cortex accompany periods when an animal{\textquoteright}s belief is modified after an environmental change. Activity across the majority of sampled neurons underwent marked, abrupt, and coordinated changes when prior belief was abandoned in favor of exploration of alternative strategies. These dynamics reflect network switches to a state of instability, which diminishes over the period of exploration as new stable representations are formed.

}, keywords = {Animal, Animals, Behavior, Long-Evans, Male, Nerve Net, Neurons, Prefrontal Cortex, Rats, Rejection (Psychology), Reward, Uncertainty}, issn = {1095-9203}, doi = {10.1126/science.1226518}, author = {Karlsson, Mattias P and Tervo, Dougal G R and Karpova, Alla Y} } @article {5161, title = {Neural activity imaging with genetically encoded calcium indicators.}, journal = {Progress in Brain Research}, volume = {196}, year = {2012}, month = {2012}, pages = {79-94}, abstract = {

Genetically encoded calcium indicators (GECIs), together with modern microscopy, allow repeated activity measurement, in real time and with cellular resolution, of defined cellular populations. Recent efforts in protein engineering have yielded several high-quality GECIs that facilitate new applications in neuroscience. Here, we summarize recent progress in GECI design, optimization, and characterization, and provide guidelines for selecting the appropriate GECI for a given biological application. We focus on the unique challenges associated with imaging in behaving animals.

}, keywords = {Animals, Calcium, Calcium Signaling, Molecular Imaging, Neurons}, issn = {1875-7855}, doi = {10.1016/B978-0-444-59426-6.00005-7}, author = {Tian, Lin and Akerboom, Jasper and Schreiter, Eric R and Looger, Loren L} } @article {4600, title = {Neuron transplantation partially reverses an obesity disorder in mice.}, journal = {Cell Metabolism}, volume = {15}, year = {2012}, month = {2012 Feb 8}, pages = {133-4}, abstract = {

Mice lacking leptin receptors are grossly obese and diabetic, in part due to dysfunction in brain circuits important for energy homeostasis. Transplantation of leptin receptor-expressing hypothalamic progenitor neurons into the brains of leptin receptor deficient mice led to integration into neural circuits, reduced obesity, and normalized circulating glucose levels.

}, issn = {1932-7420}, doi = {10.1016/j.cmet.2012.01.011}, author = {Sternson, Scott M} } @article {5658, title = {Neuronal circuits underlying persistent representations despite time varying activity.}, journal = {Current Biology}, volume = {22}, year = {2012}, month = {2012 Nov 20}, pages = {2095-103}, abstract = {

Our brains are capable of remarkably stable stimulus representations despite time-varying neural activity. For instance, during delay periods in working memory tasks, while stimuli are represented in working memory, neurons in the prefrontal cortex, thought to support the memory representation, exhibit time-varying neuronal activity. Since neuronal activity encodes the stimulus, its time-varying dynamics appears to be paradoxical and incompatible with stable network stimulus representations. Indeed, this finding raises a fundamental question: can stable representations only be encoded with stable neural activity, or, its corollary, is every change in activity a sign of change in stimulus representation?

}, issn = {1879-0445}, doi = {10.1016/j.cub.2012.08.058}, author = {Druckmann, S and Chklovskii, Dmitri B} } @article {5435, title = {Neuronal spike generation mechanism as an oversampling, noise-shaping A-to-D converter.}, journal = {Advances in Neural Information Processing Systems}, volume = {24}, year = {2012}, month = {2012}, pages = {503-11}, abstract = {

We explore the hypothesis that the neuronal spike generation mechanism is an analog-to-digital converter, which rectifies low-pass filtered summed synaptic currents and encodes them into spike trains linearly decodable in post-synaptic neurons. To digitally encode an analog current waveform, the sampling rate of the spike generation mechanism must exceed its Nyquist rate. Such oversampling is consistent with the experimental observation that the precision of the spike-generation mechanism is an order of magnitude greater than the cut-off frequency of dendritic low-pass filtering. To achieve additional reduction in the error of analog-to-digital conversion, electrical engineers rely on noise-shaping. If noise-shaping were used in neurons, it would introduce correlations in spike timing to reduce low-frequency (up to Nyquist) transmission error at the cost of high-frequency one (from Nyquist to sampling rate). Using experimental data from three different classes of neurons, we demonstrate that biological neurons utilize noise-shaping. We also argue that rectification by the spike-generation mechanism may improve energy efficiency and carry out de-noising. Finally, the zoo of ion channels in neurons may be viewed as a set of predictors, various subsets of which are activated depending on the statistics of the input current.

}, author = {Chklovskii, Dmitri B and Soudry, Daniel} } @article {5205, title = {Neuroscience. The mind of a male?}, journal = {Science}, volume = {337}, year = {2012}, month = {2012 Jul 27}, pages = {416-7}, keywords = {Animal, Animals, Caenorhabditis elegans, Male, Nerve Net, Neurons, Sexual Behavior, Synapses}, issn = {1095-9203}, doi = {10.1126/science.1225853}, author = {Chklovskii, Dmitri B and Bargmann, Cornelia I} } @article {6293, title = {Noninvasive imaging beyond the diffraction limit of 3D dynamics in thickly fluorescent specimens.}, journal = {Cell}, volume = {151}, year = {2012}, month = {2012 Dec 7}, pages = {1370-85}, abstract = {

Optical imaging of the dynamics of living specimens involves tradeoffs between spatial resolution, temporal resolution, and phototoxicity, made more difficult in three dimensions. Here, however, we report that rapid three-dimensional (3D) dynamics can be studied beyond the diffraction limit in thick or densely fluorescent living specimens over many time points by combining ultrathin planar illumination\ produced by scanned Bessel beams with super-resolution structured illumination microscopy. We demonstrate in\ vivo karyotyping of chromosomes during mitosis and identify different dynamics for the actin cytoskeleton at the dorsal and ventral surfaces of fibroblasts. Compared to spinning disk confocal microscopy, we\ demonstrate substantially reduced photodamage when imaging rapid morphological changes in D.\ discoideum cells, as well as improved contrast and resolution at depth within developing C.\ elegans embryos. Bessel beam structured plane illumination thus promises new insights into complex biological phenomena that require 4D subcellular spatiotemporal detail in either a single or multicellular context.

}, keywords = {Animals, Brain, Caenorhabditis elegans, Cell Line, Dermatitis, Dictyostelium, Drosophila melanogaster, Fibroblasts, Fluorescence, Humans, Imaging, Karyotyping, Larva, Microscopy, Mitosis, Optical Imaging, Phototoxic, Three-Dimensional, Tumor}, issn = {1097-4172}, doi = {10.1016/j.cell.2012.10.008}, author = {Gao, Liang and Shao, Lin and Higgins, Christopher D and Poulton, John S and Peifer, Mark and Davidson, Michael W and Wu, Xufeng and Goldstein, Bob and Betzig, Eric} } @article {6294, title = {Nonlinear dendritic integration of sensory and motor input during an active sensing task.}, journal = {Nature}, volume = {492}, year = {2012}, month = {2012 Dec 13}, pages = {247-51}, abstract = {

Active dendrites provide neurons with powerful processing capabilities. However, little is known about the role of neuronal dendrites in behaviourally related circuit computations. Here we report that a novel global dendritic nonlinearity is involved in the integration of sensory and motor information within layer 5 pyramidal neurons during an active sensing behaviour. Layer 5 pyramidal neurons possess elaborate dendritic arborizations that receive functionally distinct inputs, each targeted to spatially separate regions. At the cellular level, coincident input from these segregated pathways initiates regenerative dendritic electrical events that produce bursts of action potential output and circuits featuring this powerful dendritic nonlinearity can implement computations based on input correlation. To examine this in vivo we recorded dendritic activity in layer 5 pyramidal neurons in the barrel cortex using two-photon calcium imaging in mice performing an object-localization task. Large-amplitude, global calcium signals were observed throughout the apical tuft dendrites when active touch occurred at particular object locations or whisker angles. Such global calcium signals are produced by dendritic plateau potentials that require both vibrissal sensory input and primary motor cortex activity. These data provide direct evidence of nonlinear dendritic processing of correlated sensory and motor information in the mammalian neocortex during active sensation.

}, keywords = {Animal, Animals, Behavior, Calcium, Dendrites, Inbred C57BL, Male, Mice, Motor Activity, Patch-Clamp Techniques, Pyramidal Cells, Sensation, Signal Transduction}, issn = {1476-4687}, doi = {10.1038/nature11601}, author = {Xu, Ning-long and Harnett, Mark T and Williams, Stephen R and Huber, Daniel and O{\textquoteright}Connor, Daniel H and Svoboda, Karel and Magee, Jeffrey C} } @article {4489, title = {Nonlinear structured-illumination microscopy with a photoswitchable protein reveals cellular structures at 50-nm resolution.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, year = {2012}, month = {2012 Jan 17}, pages = {E135-43}, abstract = {

Using ultralow light intensities that are well suited for investigating biological samples, we demonstrate whole-cell superresolution imaging by nonlinear structured-illumination microscopy. Structured-illumination microscopy can increase the spatial resolution of a wide-field light microscope by a factor of two, with greater resolution extension possible if the emission rate of the sample responds nonlinearly to the illumination intensity. Saturating the fluorophore excited state is one such nonlinear response, and a realization of this idea, saturated structured-illumination microscopy, has achieved approximately 50-nm resolution on dye-filled polystyrene beads. Unfortunately, because saturation requires extremely high light intensities that are likely to accelerate photobleaching and damage even fixed tissue, this implementation is of limited use for studying biological samples. Here, reversible photoswitching of a fluorescent protein provides the required nonlinearity at light intensities six orders of magnitude lower than those needed for saturation. We experimentally demonstrate approximately 40-nm resolution on purified microtubules labeled with the fluorescent photoswitchable protein Dronpa, and we visualize cellular structures by imaging the mammalian nuclear pore and actin cytoskeleton. As a result, nonlinear structured-illumination microscopy is now a biologically compatible superresolution imaging method.

}, issn = {1091-6490}, doi = {10.1073/pnas.1107547108}, author = {Rego, E Hesper and Shao, Lin and Macklin, John J and Winoto, Lukman and Johansson, G{\"o}ran A and Kamps-Hughes, Nicholas and Davidson, Michael W and Gustafsson, Mats G L} } @article {46719, title = {Nuclear pore component Nup98 is a potential tumor suppressor and regulates posttranscriptional expression of select p53 target genes.}, journal = {Molecular Cell}, volume = {48}, year = {2012}, month = {2012 Dec 14}, pages = {799-810}, abstract = {

The p53 tumor suppressor utilizes multiple mechanisms to selectively regulate its myriad target genes, which in turn mediate diverse cellular processes. Here, using conventional and single-molecule mRNA analyses, we demonstrate that the nucleoporin Nup98 is required for full expression of p21, a key effector of the p53 pathway, but not several other p53 target genes. Nup98 regulates p21 mRNA levels by a posttranscriptional mechanism in which a complex containing Nup98 and the p21 mRNA 3{\textquoteright}UTR protects p21 mRNA from degradation by the exosome. An in silico approach revealed another p53 target (14-3-3σ) to be similarly regulated by Nup98. The expression of Nup98 is reduced in murine and human hepatocellular carcinomas (HCCs) and correlates with p21 expression in HCC patients. Our study elucidates a previously unrecognized function of wild-type Nup98 in regulating select p53 target genes that is distinct from the well-characterized oncogenic properties of Nup98 fusion proteins.

}, keywords = {14-3-3 Proteins, 3{\textquoteright} Untranslated Regions, Animals, Antineoplastic Agents, Phytogenic, Apoptosis, Binding Sites, Camptothecin, Carcinoma, Hepatocellular, Cell Aging, Cyclin-Dependent Kinase Inhibitor p21, Exosomes, Gene Expression Regulation, Neoplastic, Hep G2 Cells, Humans, Liver Neoplasms, Male, Mice, Mice, Knockout, Nuclear Pore Complex Proteins, P-Glycoproteins, RNA Interference, RNA Processing, Post-Transcriptional, RNA Stability, RNA, Messenger, Time Factors, Transfection, Tumor Suppressor Protein p53}, issn = {1097-4164}, doi = {10.1016/j.molcel.2012.09.020}, author = {Singer, Stephan and Zhao, Ruiying and Barsotti, Anthony M and Ouwehand, Anette and Fazollahi, Mina and Coutavas, Elias and Breuhahn, Kai and Neumann, Olaf and Longerich, Thomas and Pusterla, Tobias and Powers, Maureen A and Giles, Keith M and Leedman, Peter J and Hess, Jochen and Grunwald, David and Bussemaker, Harmen J and Singer, Robert H and Schirmacher, Peter and Prives, Carol} } @article {6329, title = {Nucleotide excision repair (NER) machinery recruitment by the transcription-repair coupling factor involves unmasking of a conserved intramolecular interface.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, year = {2012}, month = {2012 Feb 28}, pages = {3353-8}, abstract = {

Transcription-coupled DNA repair targets DNA lesions that block progression of elongating RNA polymerases. In bacteria, the transcription-repair coupling factor (TRCF; also known as Mfd) SF2 ATPase recognizes RNA polymerase stalled at a site of DNA damage, removes the enzyme from the DNA, and recruits the Uvr(A)BC nucleotide excision repair machinery via UvrA binding. Previous studies of TRCF revealed a molecular architecture incompatible with UvrA binding, leaving its recruitment mechanism unclear. Here, we examine the UvrA recognition determinants of TRCF using X-ray crystallography of a core TRCF-UvrA complex and probe the conformational flexibility of TRCF in the absence and presence of nucleotides using small-angle X-ray scattering. We demonstrate that the C-terminal domain of TRCF is inhibitory for UvrA binding, but not RNA polymerase release, and show that nucleotide binding induces concerted multidomain motions. Our studies suggest that autoinhibition of UvrA binding in TRCF may be relieved only upon engaging the DNA damage.

}, keywords = {Adenosine Triphosphatases, Adenosine Triphosphate, Amino Acid Sequence, Bacterial, Bacterial Proteins, Crystallography, DNA, DNA Damage, DNA Helicases, DNA Repair, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Hydrolysis, Models, Molecular, Molecular Sequence Data, Protein Binding, Protein Conformation, Protein Interaction Mapping, Protein Structure, RNA Polymerase I, Tertiary, Transcription Factors, X-Ray}, issn = {1091-6490}, doi = {10.1073/pnas.1115105109}, author = {Deaconescu, Alexandra M and Sevostyanova, Anastasia and Artsimovitch, Irina and Grigorieff, Nikolaus} } @article {6321, title = {Near-atomic resolution reconstructions of icosahedral viruses from electron cryo-microscopy.}, journal = {Current Opinion in Structural Biology}, volume = {21}, year = {2011}, month = {2011 Apr}, pages = {265-73}, abstract = {

Nine different near-atomic resolution structures of icosahedral viruses, determined by electron cryo-microscopy and published between early 2008 and late 2010, fulfil predictions made 15 years ago that single-particle cryo-EM techniques could visualize molecular detail at 3-4A resolution. This review summarizes technical developments, both in instrumentation and in computation, that have led to the new structures, which advance our understanding of virus assembly and cell entry.

}, keywords = {Computer Simulation, Computer-Assisted, Cryoelectron Microscopy, Image Processing, Models, Molecular, Virus Assembly, Viruses}, issn = {1879-033X}, doi = {10.1016/j.sbi.2011.01.008}, author = {Grigorieff, Nikolaus and Harrison, Stephen C} } @article {2164, title = {Network anatomy and in vivo physiology of visual cortical neurons.}, journal = {Nature}, volume = {471}, year = {2011}, month = {2011 Mar 10}, pages = {177-82}, abstract = {

In the cerebral cortex, local circuits consist of tens of thousands of neurons, each of which makes thousands of synaptic connections. Perhaps the biggest impediment to understanding these networks is that we have no wiring diagrams of their interconnections. Even if we had a partial or complete wiring diagram, however, understanding the network would also require information about each neuron{\textquoteright}s function. Here we show that the relationship between structure and function can be studied in the cortex with a combination of in vivo physiology and network anatomy. We used two-photon calcium imaging to characterize a functional property{\textendash}the preferred stimulus orientation{\textendash}of a group of neurons in the mouse primary visual cortex. Large-scale electron microscopy of serial thin sections was then used to trace a portion of these neurons{\textquoteright} local network. Consistent with a prediction from recent physiological experiments, inhibitory interneurons received convergent anatomical input from nearby excitatory neurons with a broad range of preferred orientations, although weak biases could not be rejected.

}, keywords = {Animals, Calcium Signaling, Electron, Fluorescence, Interneurons, Male, Mice, Microscopy, Microtomy, Nerve Net, Neural Inhibition, Neurons, Pyramidal Cells, Synapses, Transmission, Visual Cortex}, issn = {1476-4687}, doi = {10.1038/nature09802}, author = {Bock, Davi D and Lee, Wei-Chung Allen and Kerlin, Aaron M and Andermann, Mark L and Hood, Greg and Wetzel, Arthur W and Yurgenson, Sergey and Soucy, Edward R and Kim, Hyon Suk and Reid, R Clay} } @article {3867, title = {Neural correlates of illusory motion perception in Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, year = {2011}, month = {2011 Jun 7}, pages = {9685-90}, abstract = {

When the contrast of an image flickers as it moves, humans perceive an illusory reversal in the direction of motion. This classic illusion, called reverse-phi motion, has been well-characterized using psychophysics, and several models have been proposed to account for its effects. Here, we show that Drosophila melanogaster also respond behaviorally to the reverse-phi illusion and that the illusion is present in dendritic calcium signals of motion-sensitive neurons in the fly lobula plate. These results closely match the predictions of the predominant model of fly motion detection. However, high flicker rates cause an inversion of the reverse-phi behavioral response that is also present in calcium signals of lobula plate tangential cell dendrites but not predicted by the model. The fly{\textquoteright}s behavioral and neural responses to the reverse-phi illusion reveal unexpected interactions between motion and flicker signals in the fly visual system and suggest that a similar correlation-based mechanism underlies visual motion detection across the animal kingdom.

}, keywords = {Algorithms, Animals, Dendrites, Drosophila melanogaster, Female, Humans, Male, Models, Motion, Motion Perception, Neural Pathways, Neurological, Neurons, Time Factors}, issn = {1091-6490}, doi = {10.1073/pnas.1100062108}, author = {Tuthill, John C and Chiappe, M Eugenia and Reiser, Michael B} } @article {6860, title = {Neuronal control of Drosophila courtship song.}, journal = {Neuron}, volume = {69}, year = {2011}, month = {2011 Feb 10}, pages = {509-22}, abstract = {

The courtship song of the Drosophila male serves as a genetically tractable model for the investigation of the neural mechanisms of decision-making, action selection, and motor pattern generation. Singing has been causally linked to the activity of the set of neurons that express the sex-specific fru transcripts, but the specific neurons involved have not been identified. Here we identify five distinct classes of fru neuron that trigger or compose the song. Our data suggest that P1 and pIP10 neurons in the brain mediate the decision to sing, and to act upon this decision, while the thoracic neurons dPR1, vPR6, and vMS11 are components of a central pattern generator that times and shapes the song{\textquoteright}s pulses. These neurons are potentially connected in a functional circuit, with the descending pIP10 neuron linking the brain and thoracic song centers. Sexual dimorphisms in each of these neurons may explain why only males sing.

}, keywords = {Animal, Animals, Courtship, Drosophila, Drosophila Proteins, Female, Genetically Modified, Male, Nerve Net, Nerve Tissue Proteins, Neurons, Sex Characteristics, Sexual Behavior, Transcription Factors, Vocalization}, issn = {1097-4199}, doi = {10.1016/j.neuron.2011.01.011}, author = {von Philipsborn, Anne C and Liu, Tianxiao and Yu, Jai Y and Masser, Christopher and Bidaye, Salil S and Dickson, Barry J} } @article {4301, title = {New tools for the analysis of glial cell biology in Drosophila.}, journal = {Glia}, volume = {59}, year = {2011}, month = {2011 Sep}, pages = {1377-86}, abstract = {

Because of its genetic, molecular, and behavioral tractability, Drosophila has emerged as a powerful model system for studying molecular and cellular mechanisms underlying the development and function of nervous systems. The Drosophila nervous system has fewer neurons and exhibits a lower glia:neuron ratio than is seen in vertebrate nervous systems. Despite the simplicity of the Drosophila nervous system, glial organization in flies is as sophisticated as it is in vertebrates. Furthermore, fly glial cells play vital roles in neural development and behavior. In addition, powerful genetic tools are continuously being created to explore cell function in vivo. In taking advantage of these features, the fly nervous system serves as an excellent model system to study general aspects of glial cell development and function in vivo. In this article, we review and discuss advanced genetic tools that are potentially useful for understanding glial cell biology in Drosophila.

}, keywords = {Animals, Cell Biology, Drosophila, Drosophila Proteins, Gene Expression, Genes, Molecular Biology, Mutation, Neuroglia, Reporter, Transcription Factors, Transgenes, Upstream Stimulatory Factors}, issn = {1098-1136}, doi = {10.1002/glia.21133}, author = {Awasaki, Takeshi and Lee, Tzumin} } @article {3629, title = {N-terminal domain of alphaB-crystallin provides a conformational switch for multimerization and structural heterogeneity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, year = {2011}, month = {2011 Apr 19}, pages = {6409-14}, abstract = {

The small heat shock protein (sHSP) αB-crystallin (αB) plays a key role in the cellular protection system against stress. For decades, high-resolution structural studies on heterogeneous sHSPs have been confounded by the polydisperse nature of αB oligomers. We present an atomic-level model of full-length αB as a symmetric 24-subunit multimer based on solid-state NMR, small-angle X-ray scattering (SAXS), and EM data. The model builds on our recently reported structure of the homodimeric α-crystallin domain (ACD) and C-terminal IXI motif in the context of the multimer. A hierarchy of interactions contributes to build multimers of varying sizes: Interactions between two ACDs define a dimer, three dimers connected by their C-terminal regions define a hexameric unit, and variable interactions involving the N-terminal region define higher-order multimers. Within a multimer, N-terminal regions exist in multiple environments, contributing to the heterogeneity observed by NMR. Analysis of SAXS data allows determination of a heterogeneity parameter for this type of system. A mechanism of multimerization into higher-order asymmetric oligomers via the addition of up to six dimeric units to a 24-mer is proposed. The proposed asymmetric multimers explain the homogeneous appearance of αB in negative-stain EM images and the known dynamic exchange of αB subunits. The model of αB provides a structural basis for understanding known disease-associated missense mutations and makes predictions concerning substrate binding and the reported fibrilogenesis of αB.

}, keywords = {alpha-Crystallin B Chain, Animals, Biomolecular, Humans, Missense, Models, Molecular, Mutation, Nuclear Magnetic Resonance, Protein Multimerization, Protein Structure, Quaternary, Tertiary}, issn = {1091-6490}, doi = {10.1073/pnas.1014656108}, author = {Jehle, Stefan and Vollmar, Breanna S and Bardiaux, Benjamin and Dove, Katja K and Rajagopal, Ponni and Gonen, Tamir and Oschkinat, Hartmut and Klevit, Rachel E} } @article {46741, title = {A nucleoporin, Nup60p, affects the nuclear and cytoplasmic localization of ASH1 mRNA in S. cerevisiae.}, journal = {RNA}, volume = {17}, year = {2011}, month = {2011 Jan}, pages = {134-44}, abstract = {

The biogenesis of a localization-competent mRNP begins in the nucleus. It is thought that the coordinated action of nuclear and cytoplasmic components of the localization machinery is required for the efficient export and subsequent subcellular localization of these mRNAs in the cytoplasm. Using quantitative poly(A)(+) and transcript-specific fluorescent in situ hybridization, we analyzed different nonessential nucleoporins and nuclear pore-associated proteins for their potential role in mRNA export and localization. We found that Nup60p, a nuclear pore protein located on the nucleoplasmic side of the nuclear pore complex, was required for the mRNA localization pathway. In a Δnup60 background, localized mRNAs were preferentially retained within the nucleus compared to nonlocalized transcripts. However, the export block was only partial and some transcripts could still reach the cytoplasm. Importantly, downstream processes were also affected. Localization of ASH1 and IST2 mRNAs to the bud was impaired in the Δnup60 background, suggesting that the assembly of a localization competent mRNP ("locasome") was inhibited when NUP60 was deleted. These results demonstrate transcript specificity of a nuclear mRNA retention defect and identify a specific nucleoporin as a functional component of the localization pathway in budding yeast.

}, keywords = {Cell Nucleus, Cytoplasm, Gene Deletion, In Situ Hybridization, Fluorescence, Nuclear Pore Complex Proteins, Poly A, Repressor Proteins, RNA Transport, RNA, Fungal, RNA, Messenger, RNA-Binding Proteins, Saccharomyces cerevisiae Proteins, Transcription, Genetic}, issn = {1469-9001}, doi = {10.1261/rna.1210411}, author = {Powrie, Erin A and Zenklusen, Daniel and Singer, Robert H} } @article {2908, title = {N-WASp is required for Schwann cell cytoskeletal dynamics, normal myelin gene expression and peripheral nerve myelination.}, journal = {Development}, volume = {138}, year = {2011}, month = {2011 Apr}, pages = {1329-37}, abstract = {

Schwann cells elaborate myelin sheaths around axons by spirally wrapping and compacting their plasma membranes. Although actin remodeling plays a crucial role in this process, the effectors that modulate the Schwann cell cytoskeleton are poorly defined. Here, we show that the actin cytoskeletal regulator, neural Wiskott-Aldrich syndrome protein (N-WASp), is upregulated in myelinating Schwann cells coincident with myelin elaboration. When N-WASp is conditionally deleted in Schwann cells at the onset of myelination, the cells continue to ensheath axons but fail to extend processes circumferentially to elaborate myelin. Myelin-related gene expression is also severely reduced in the N-WASp-deficient cells and in vitro process and lamellipodia formation are disrupted. Although affected mice demonstrate obvious motor deficits these do not appear to progress, the mutant animals achieving normal body weights and living to advanced age. Our observations demonstrate that N-WASp plays an essential role in Schwann cell maturation and myelin formation.

}, keywords = {Animals, Axons, Blotting, Cells, Cultured, Cytoskeleton, Fluorescent Antibody Technique, Gait, Gene Expression, Knockout, Mice, Myelin Sheath, Neuronal, Peripheral Nerves, Reverse Transcriptase Polymerase Chain Reaction, Schwann Cells, Western, Wiskott-Aldrich Syndrome Protein}, issn = {1477-9129}, doi = {10.1242/dev.058677}, author = {Jin, Fuzi and Dong, Baoxia and Georgiou, John and Jiang, Qiuhong and Zhang, Jinyi and Bharioke, Arjun and Qiu, Frank and Lommel, Silvia and Feltri, M Laura and Wrabetz, Lawrence and Roder, John C and Eyer, Joel and Chen, Xiequn and Peterson, Alan C and Siminovitch, Katherine A} } @article {926, title = {Nanoscale architecture of integrin-based cell adhesions.}, journal = {Nature}, volume = {468}, year = {2010}, month = {2010 Nov 25}, pages = {580-4}, abstract = {

Cell adhesions to the extracellular matrix (ECM) are necessary for morphogenesis, immunity, and wound healing. Focal adhesions are multifunctional organelles that mediate cell-ECM adhesion, force transmission, cytoskeletal regulation and signaling. Focal adhesions consist of a complex network of trans-plasma-membrane integrins and cytoplasmic proteins that form a \<200-nm plaque linking the ECM to the actin cytoskeleton. The complexity of focal adhesion composition and dynamics implicate an intricate molecular machine. However, focal adhesion molecular architecture remains unknown. Here we used three-dimensional super-resolution fluorescence microscopy (interferometric photoactivated localization microscopy) to map nanoscale protein organization in focal adhesions. Our results reveal that integrins and actin are vertically separated by a \~{}40-nm focal adhesion core region consisting of multiple protein-specific strata: a membrane-apposed integrin signaling layer containing integrin cytoplasmic tails, focal adhesion kinase, and paxillin; an intermediate force-transduction layer containing talin and vinculin; and an uppermost actin-regulatory layer containing zyxin, vasodilator-stimulated phosphoprotein and α-actinin. By localizing amino- and carboxy-terminally tagged talins, we reveal talin{\textquoteright}s polarized orientation, indicative of a role in organizing the focal adhesion strata. The composite multilaminar protein architecture provides a molecular blueprint for understanding focal adhesion functions.

}, keywords = {Actins, Animals, Biological, Cell Adhesion, Cell Line, Cell Membrane, Extracellular Matrix, Humans, Integrins, Mice, Models, Tumor}, issn = {1476-4687}, doi = {10.1038/nature09621}, author = {Kanchanawong, Pakorn and Shtengel, Gleb and Pasapera, Ana M and Ramko, Ericka B and Davidson, Michael W and Hess, Harald F and Waterman, Clare M} } @article {6339, title = {Nanoscale flexibility parameters of Alzheimer amyloid fibrils determined by electron cryo-microscopy.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {49}, year = {2010}, month = {2010 Feb 8}, pages = {1321-3}, abstract = {

Versatile nanomaterial: Unusually high nanoscale flexibility was displayed by amyloid fibils in electron microscopy studies (see picture). This finding is relevant for understanding amyloid pathogenicity and for potential biotechnological applications.

}, keywords = {Alzheimer Disease, Amyloid, Cryoelectron Microscopy, Humans, Nanotechnology, Protein Folding}, issn = {1521-3773}, doi = {10.1002/anie.200904781}, author = {Sachse, Carsten and Grigorieff, Nikolaus and F{\"a}ndrich, Marcus} } @article {6322, title = {The Ndc80 kinetochore complex forms oligomeric arrays along microtubules.}, journal = {Nature}, volume = {467}, year = {2010}, month = {2010 Oct 14}, pages = {805-10}, abstract = {

The Ndc80 complex is a key site of regulated kinetochore-microtubule attachment (a process required for cell division), but the molecular mechanism underlying its function remains unknown. Here we present a subnanometre-resolution cryo-electron microscopy reconstruction of the human Ndc80 complex bound to microtubules, sufficient for precise docking of crystal structures of the component proteins. We find that the Ndc80 complex binds the microtubule with a tubulin monomer repeat, recognizing α- and β-tubulin at both intra- and inter-tubulin dimer interfaces in a manner that is sensitive to tubulin conformation. Furthermore, Ndc80 complexes self-associate along protofilaments through interactions mediated by the amino-terminal tail of the NDC80 protein, which is the site of phospho-regulation by Aurora B kinase. The complex{\textquoteright}s mode of interaction with the microtubule and its oligomerization suggest a mechanism by which Aurora B could regulate the stability of load-bearing kinetochore-microtubule attachments.

}, keywords = {Binding Sites, Biological, Cryoelectron Microscopy, Humans, Kinetochores, Microtubules, Mitosis, Models, Molecular, Nuclear Proteins, Protein Conformation, Tubulin}, issn = {1476-4687}, doi = {10.1038/nature09423}, author = {Alushin, Gregory M and Ramey, Vincent H and Pasqualato, Sebastiano and Ball, David A and Grigorieff, Nikolaus and Musacchio, Andrea and Nogales, Eva} } @article {1575, title = {Near-isotropic 3D optical nanoscopy with photon-limited chromophores.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, year = {2010}, month = {2010 Jun 1}, pages = {10068-73}, abstract = {

Imaging approaches based on single molecule localization break the diffraction barrier of conventional fluorescence microscopy, allowing for bioimaging with nanometer resolution. It remains a challenge, however, to precisely localize photon-limited single molecules in 3D. We have developed a new localization-based imaging technique achieving almost isotropic subdiffraction resolution in 3D. A tilted mirror is used to generate a side view in addition to the front view of activated single emitters, allowing their 3D localization to be precisely determined for superresolution imaging. Because both front and side views are in focus, this method is able to efficiently collect emitted photons. The technique is simple to implement on a commercial fluorescence microscope, and especially suitable for biological samples with photon-limited chromophores such as endogenously expressed photoactivatable fluorescent proteins. Moreover, this method is relatively resistant to optical aberration, as it requires only centroid determination for localization analysis. Here we demonstrate the application of this method to 3D imaging of bacterial protein distribution and neuron dendritic morphology with subdiffraction resolution.

}, keywords = {Animals, Base Sequence, Dendrites, DNA Primers, Escherichia coli K12, Escherichia coli Proteins, Fluorescence, Imaging, Luminescent Proteins, Microscopy, Nanotechnology, Optical Devices, Photons, Rats, Recombinant Fusion Proteins, Sprague-Dawley, Three-Dimensional}, issn = {1091-6490}, doi = {10.1073/pnas.1004899107}, author = {Tang, Jianyong and Akerboom, Jasper and Vaziri, Alipasha and Looger, Loren L and Shank, Charles V} } @article {3911, title = {Network mechanisms of theta related neuronal activity in hippocampal CA1 pyramidal neurons.}, journal = {Nature Neuroscience}, volume = {13}, year = {2010}, month = {2010 Aug}, pages = {967-72}, abstract = {

Although hippocampal theta oscillations represent a prime example of temporal coding in the mammalian brain, little is known about the specific biophysical mechanisms. Intracellular recordings support a particular abstract oscillatory interference model of hippocampal theta activity, the soma-dendrite interference model. To gain insight into the cellular and circuit level mechanisms of theta activity, we implemented a similar form of interference using the actual hippocampal network in mice in vitro. We found that pairing increasing levels of phasic dendritic excitation with phasic stimulation of perisomatic projecting inhibitory interneurons induced a somatic polarization and action potential timing profile that reproduced most common features. Alterations in the temporal profile of inhibition were required to fully capture all features. These data suggest that theta-related place cell activity is generated through an interaction between a phasic dendritic excitation and a phasic perisomatic shunting inhibition delivered by interneurons, a subset of which undergo activity-dependent presynaptic modulation.

}, keywords = {Animals, Gene Knock-In Techniques, Hippocampus, Inbred C57BL, Inhibitory Postsynaptic Potentials, Mice, Nerve Net, Organ Culture Techniques, Patch-Clamp Techniques, Pyramidal Cells, Theta Rhythm}, issn = {1546-1726}, doi = {10.1038/nn.2597}, author = {Losonczy, Attila and Zemelman, Boris V and Vaziri, Alipasha and Magee, Jeffrey C} } @article {4289, title = {Neural activity in barrel cortex underlying vibrissa-based object localization in mice.}, journal = {Neuron}, volume = {67}, year = {2010}, month = {2010 Sep 23}, pages = {1048-61}, abstract = {

Classical studies have related the spiking of selected neocortical neurons to behavior, but little is known about activity sampled from the entire neural population. We recorded from neurons selected independent of spiking, using cell-attached recordings and two-photon calcium imaging, in the barrel cortex of mice performing an object localization task. Spike rates varied across neurons, from silence to \>60 Hz. Responses were diverse, with some neurons showing large increases in spike rate when whiskers contacted the object. Nearly half the neurons discriminated object location; a small fraction of neurons discriminated perfectly. More active neurons were more discriminative. Layer (L) 4 and L5 contained the highest fractions of discriminating neurons (\~{}63\% and 79\%, respectively), but a few L2/3 neurons were also highly discriminating. Approximately 13,000 spikes per activated barrel column were available to mice for decision making. Coding of object location in the barrel cortex is therefore highly redundant.

}, keywords = {Action Potentials, Afferent Pathways, Animal, Animals, Behavior, Biological, Brain Mapping, Calcium, Discrimination (Psychology), Inbred C57BL, Male, Mice, Models, Neurons, Physical Stimulation, ROC Curve, Somatosensory Cortex, Vibrissae}, issn = {1097-4199}, doi = {10.1016/j.neuron.2010.08.026}, author = {O{\textquoteright}Connor, Daniel H and Peron, Simon P and Huber, Daniel and Svoboda, Karel} } @article {2386, title = {A new focus on plant sciences.}, journal = {Science}, volume = {330}, year = {2010}, month = {2010 Nov 19}, pages = {1021}, keywords = {Agriculture, Botany, Financing, Government, Plants, Research Support as Topic, United States}, issn = {1095-9203}, doi = {10.1073/pnas.1100640108}, author = {McCormick, Steven J and Tjian, Robert} } @article {1681, title = {Nlcam modulates midline convergence during anterior neural plate morphogenesis.}, journal = {Developmental Biology}, volume = {339}, year = {2010}, month = {2010 Mar 1}, pages = {14-25}, abstract = {

During development, different cell types must undergo distinct morphogenetic programs so that tissues develop the right dimensions in the appropriate place. In early eye morphogenesis, retinal progenitor cells (RPCs) move first towards the midline, before turning around to migrate out into the evaginating optic vesicles. Neighbouring forebrain cells, however, converge rapidly and then remain at the midline. These differential behaviours are regulated by the transcription factor Rx3. Here, we identify a downstream target of Rx3, the Ig-domain protein Nlcam, and characterise its role in regulating cell migration during the initial phase of optic vesicle morphogenesis. Through sophisticated live imaging and comprehensive cell tracking experiments in zebrafish, we show that ectopic expression of Nlcam in RPCs, as is observed in Rx3 mutants, causes enhanced convergence of these cells. Expression levels of Nlcam therefore regulate the migratory properties of RPCs. Our results provide evidence that the two phases of optic vesicle morphogenesis: slowed convergence and outward-directed migration, are under different genetic control. We propose that Nlcam forms part of the guidance machinery directing rapid midline migration of forebrain precursors, where it is normally expressed, and that its ectopic expression upon loss of Rx3 imparts these migratory characteristics upon RPCs.

}, keywords = {Animals, Base Sequence, Body Patterning, Cell Adhesion Molecules, Chick Embryo, DNA Primers, Electrophoretic Mobility Shift Assay, Homeodomain Proteins, Morphogenesis, Neural Plate, Protein Binding, Zebrafish}, issn = {1095-564X}, doi = {10.1016/j.ydbio.2009.12.003}, author = {Brown, Katherine E and Keller, Philipp J and Ramialison, Mirana and Rembold, Martina and Stelzer, Ernst H K and Loosli, Felix and Wittbrodt, Joachim} } @article {1541, title = {Nodavirus-induced membrane rearrangement in replication complex assembly requires replicase protein a, RNA templates, and polymerase activity.}, journal = {Journal of Virology}, volume = {84}, year = {2010}, month = {2010 Dec}, pages = {12492-503}, abstract = {

Positive-strand RNA [(+)RNA] viruses invariably replicate their RNA genomes on modified intracellular membranes. In infected Drosophila cells, Flock House nodavirus (FHV) RNA replication complexes form on outer mitochondrial membranes inside \~{}50-nm, virus-induced spherular invaginations similar to RNA replication-linked spherules induced by many (+)RNA viruses at various membranes. To better understand replication complex assembly, we studied the mechanisms of FHV spherule formation. FHV has two genomic RNAs; RNA1 encodes multifunctional RNA replication protein A and RNA interference suppressor protein B2, while RNA2 encodes the capsid proteins. Expressing genomic RNA1 without RNA2 induced mitochondrial spherules indistinguishable from those in FHV infection. RNA1 mutation showed that protein B2 was dispensable and that protein A was the only FHV protein required for spherule formation. However, expressing protein A alone only "zippered" together the surfaces of adjacent mitochondria, without inducing spherules. Thus, protein A is necessary but not sufficient for spherule formation. Coexpressing protein A plus a replication-competent FHV RNA template induced RNA replication in trans and membrane spherules. Moreover, spherules were not formed when replicatable FHV RNA templates were expressed with protein A bearing a single, polymerase-inactivating amino acid change or when wild-type protein A was expressed with a nonreplicatable FHV RNA template. Thus, unlike many (+)RNA viruses, the membrane-bounded compartments in which FHV RNA replication occurs are not induced solely by viral protein(s) but require viral RNA synthesis. In addition to replication complex assembly, the results have implications for nodavirus interaction with cell RNA silencing pathways and other aspects of virus control.

}, keywords = {Animals, Blotting, Capsid Proteins, DNA-Directed RNA Polymerases, Drosophila melanogaster, Genome, Intracellular Membranes, Mitochondria, Nodaviridae, Northern, Plasmids, RNA, RNA Replicase, RNA Virus Infections, Small Interfering, Viral, Virus Replication, Western}, issn = {1098-5514}, doi = {10.1128/JVI.01495-10}, url = {http://jvi.asm.org/content/84/24/12492.short}, author = {Kopek, Benjamin G and Settles, Erik W and Friesen, Paul D and Ahlquist, Paul} } @article {6597, title = {Nuclear physics: quantitative single-cell approaches to nuclear organization and gene expression.}, journal = {Cold Spring Harbor Symposia on Quantitative Biology}, volume = {75}, year = {2010}, month = {2010}, pages = {113-26}, abstract = {

The internal workings of the nucleus remain a mystery. A list of component parts exists, and in many cases their functional roles are known for events such as transcription, RNA processing, or nuclear export. Some of these components exhibit structural features in the nucleus, regions of concentration or bodies that have given rise to the concept of functional compartmentalization{\textendash}that there are underlying organizational principles to be described. In contrast, a picture is emerging in which transcription appears to drive the assembly of the functional components required for gene expression, drawing from pools of excess factors. Unifying this seemingly dual nature requires a more rigorous approach, one in which components are tracked in time and space and correlated with onset of specific nuclear functions. In this chapter, we anticipate tools that will address these questions and provide the missing kinetics of nuclear function. These tools are based on analyzing the fluctuations inherent in the weak signals of endogenous nuclear processes and determining values for them. In this way, it will be possible eventually to provide a computational model describing the functional relationships of essential components.

}, keywords = {Biological, Biophysical Phenomena, Biophysics, Cell Nucleus, Fluorescence, Fluorescence Recovery After Photobleaching, Gene Dosage, Gene Expression Regulation, Kinetics, Models, Saccharomyces cerevisiae, Spectrometry}, issn = {1943-4456}, doi = {10.1101/sqb.2010.75.057}, author = {Lionnet, T and Wu, B and Gr{\"u}nwald, D and Singer, R H and Larson, D R} } @article {46422, title = {Negative regulation of active zone assembly by a newly identified SR protein kinase.}, journal = {PLoS Biology}, volume = {7}, year = {2009}, month = {2009 Sep}, pages = {e1000193}, abstract = {

Presynaptic, electron-dense, cytoplasmic protrusions such as the T-bar (Drosophila) or ribbon (vertebrates) are believed to facilitate vesicle movement to the active zone (AZ) of synapses throughout the nervous system. The molecular composition of these structures including the T-bar and ribbon are largely unknown, as are the mechanisms that specify their synapse-specific assembly and distribution. In a large-scale, forward genetic screen, we have identified a mutation termed air traffic controller (atc) that causes T-bar-like protein aggregates to form abnormally in motoneuron axons. This mutation disrupts a gene that encodes for a serine-arginine protein kinase (SRPK79D). This mutant phenotype is specific to SRPK79D and is not secondary to impaired kinesin-dependent axonal transport. The srpk79D gene is neuronally expressed, and transgenic rescue experiments are consistent with SRPK79D kinase activity being necessary in neurons. The SRPK79D protein colocalizes with the T-bar-associated protein Bruchpilot (Brp) in both the axon and synapse. We propose that SRPK79D is a novel T-bar-associated protein kinase that represses T-bar assembly in peripheral axons, and that SRPK79D-dependent repression must be relieved to facilitate site-specific AZ assembly. Consistent with this model, overexpression of SRPK79D disrupts AZ-specific Brp organization and significantly impairs presynaptic neurotransmitter release. These data identify a novel AZ-associated protein kinase and reveal a new mechanism of negative regulation involved in AZ assembly. This mechanism could contribute to the speed and specificity with which AZs are assembled throughout the nervous system.

}, keywords = {Animals, Drosophila melanogaster, Drosophila Proteins, Immunohistochemistry, Microscopy, Electron, Transmission, Motor Neurons, Presynaptic Terminals, Protein-Serine-Threonine Kinases, Synaptic Transmission}, issn = {1545-7885}, doi = {10.1371/journal.pbio.1000193}, author = {Johnson, Ervin L and Fetter, Richard D and Davis, Graeme W} } @article {5693, title = {Neuronal fiber tracts connecting the brain and ventral nerve cord of the early Drosophila larva.}, journal = {The Journal of Comparative Neurology}, volume = {515}, year = {2009}, month = {2009 Aug 1}, pages = {427-40}, abstract = {

By using a combination of dye injections, clonal labeling, and molecular markers, we have reconstructed the axonal connections between brain and ventral nerve cord of the first-instar Drosophila larva. Out of the approximately 1,400 neurons that form the early larval brain hemisphere, less than 50 cells have axons descending into the ventral nerve cord. Descending neurons fall into four topologically defined clusters located in the anteromedial, anterolateral, dorsal, and basoposterior brain, respectively. The anterolateral cluster represents a lineage derived from a single neuroblast. Terminations of descending neurons are almost exclusively found in the anterior part of the ventral nerve cord, represented by the gnathal and thoracic neuromeres. This region also contains small numbers of neurons with axons ascending into the brain. Terminals of the ascending axons are found in the same basal brain regions that also contain descending neurons. We have mapped ascending and descending axons to the previously described scaffold of longitudinal fiber tracts that interconnect different neuromeres of the ventral nerve cord and the brain. This work provides a structural framework for functional and genetic studies addressing the control of Drosophila larval behavior by brain circuits.

}, keywords = {Animals, Brain, Cell Count, Drosophila, Drosophila Proteins, Ganglia, Genetically Modified, Green Fluorescent Proteins, Imaging, Invertebrate, Larva, Models, Neural Pathways, Neurological, Neurons, Spinal Cord, Three-Dimensional}, issn = {1096-9861}, doi = {10.1002/cne.22086}, author = {Cardona, Albert and Larsen, Camilla and Hartenstein, Volker.} } @article {2687, title = {Neurotoxic effects induced by the Drosophila amyloid-beta peptide suggest a conserved toxic function.}, journal = {Neurobiology of Disease}, volume = {33}, year = {2009}, month = {2009 Feb}, pages = {274-81}, abstract = {

The accumulation of amyloid-beta (Abeta) into plaques is a hallmark feature of Alzheimer{\textquoteright}s disease (AD). While amyloid precursor protein (APP)-related proteins are found in most organisms, only Abeta fragments from human APP have been shown to induce amyloid deposits and progressive neurodegeneration. Therefore, it was suggested that neurotoxic effects are a specific property of human Abeta. Here we show that Abeta fragments derived from the Drosophila orthologue APPL aggregate into intracellular fibrils, amyloid deposits, and cause age-dependent behavioral deficits and neurodegeneration. We also show that APPL can be cleaved by a novel fly beta-secretase-like enzyme. This suggests that Abeta-induced neurotoxicity is a conserved function of APP proteins whereby the lack of conservation in the primary sequence indicates that secondary structural aspects determine their pathogenesis. In addition, we found that the behavioral phenotypes precede extracellular amyloid deposit formation, supporting results that intracellular Abeta plays a key role in AD.

}, keywords = {Aging, Amino Acid Sequence, Amyloid, Amyloid beta-Protein Precursor, Amyloid Precursor Protein Secretases, Animal, Animals, Apoptosis, Behavior, Blotting, Brain, Cell Surface, Drosophila melanogaster, Drosophila Proteins, Electron, Gene Expression, Immunohistochemistry, Light, Membrane Proteins, Microscopy, Molecular Sequence Data, Nerve Degeneration, Nerve Tissue Proteins, Neurons, Peptide Fragments, Protease Nexins, Receptors, Western}, issn = {1095-953X}, doi = {10.1016/j.nbd.2008.10.014}, author = {Carmine-Simmen, Katia and Proctor, Thomas and Tsch{\"a}pe, Jakob and Poeck, Burkhard and Triphan, Tilman and Strauss, Roland and Kretzschmar, Doris} } @article {4265, title = {A new generation of homology search tools based on probabilistic inference.}, journal = {Genome Informatics. International Conference on Genome Informatics}, volume = {23}, year = {2009}, month = {2009 Oct}, pages = {205-11}, abstract = {

Many theoretical advances have been made in applying probabilistic inference methods to improve the power of sequence homology searches, yet the BLAST suite of programs is still the workhorse for most of the field. The main reason for this is practical: BLAST{\textquoteright}s programs are about 100-fold faster than the fastest competing implementations of probabilistic inference methods. I describe recent work on the HMMER software suite for protein sequence analysis, which implements probabilistic inference using profile hidden Markov models. Our aim in HMMER3 is to achieve BLAST{\textquoteright}s speed while further improving the power of probabilistic inference based methods. HMMER3 implements a new probabilistic model of local sequence alignment and a new heuristic acceleration algorithm. Combined with efficient vector-parallel implementations on modern processors, these improvements synergize. HMMER3 uses more powerful log-odds likelihood scores (scores summed over alignment uncertainty, rather than scoring a single optimal alignment); it calculates accurate expectation values (E-values) for those scores without simulation using a generalization of Karlin/Altschul theory; it computes posterior distributions over the ensemble of possible alignments and returns posterior probabilities (confidences) in each aligned residue; and it does all this at an overall speed comparable to BLAST. The HMMER project aims to usher in a new generation of more powerful homology search tools based on probabilistic inference methods.

}, keywords = {Markov Chains, Probability, Sequence Alignment}, issn = {0919-9454}, author = {Eddy, Sean R.} } @article {4272, title = {New genetic tools for cell lineage analysis in Drosophila.}, journal = {Nature Methods}, volume = {6}, year = {2009}, month = {2009 Aug}, pages = {566-8}, abstract = {

Real-time lineage tracing in flies gets a boost with three techniques to specifically label a progenitor{\textquoteright}s daughter cells.

}, keywords = {Animals, Cell Lineage, Drosophila melanogaster, Genetic Techniques, Recombinant Proteins, Stem Cells, Transgenes}, issn = {1548-7105}, doi = {10.1038/nmeth0809-566}, author = {Lee, Tzumin} } @article {4430, title = {Nonlinear integration of visual and haltere inputs in fly neck motor neurons.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {29}, year = {2009}, month = {2009 Oct 21}, pages = {13097-105}, abstract = {

Animals use information from multiple sensory organs to generate appropriate behavior. Exactly how these different sensory inputs are fused at the motor system is not well understood. Here we study how fly neck motor neurons integrate information from two well characterized sensory systems: visual information from the compound eye and gyroscopic information from the mechanosensory halteres. Extracellular recordings reveal that a subpopulation of neck motor neurons display "gating-like" behavior: they do not fire action potentials in response to visual stimuli alone but will do so if the halteres are coactivated. Intracellular recordings show that these motor neurons receive small, sustained subthreshold visual inputs in addition to larger inputs that are phase locked to haltere movements. Our results suggest that the nonlinear gating-like effect results from summation of these two inputs with the action potential threshold providing the nonlinearity. As a result of this summation, the sustained visual depolarization is transformed into a temporally structured train of action potentials synchronized to the haltere beating movements. This simple mechanism efficiently fuses two different sensory signals and may also explain the context-dependent effects of visual inputs on fly behavior.

}, keywords = {Action Potentials, Age Factors, Animals, Diptera, Female, Functional Laterality, Motor Neurons, Neck, Nonlinear Dynamics, Patch-Clamp Techniques, Photic Stimulation, Sense Organs, Sensory Gating, Touch, Visual Pathways}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.2915-09.2009}, author = {Huston, Stephen J and Krapp, Holger G} } @article {2849, title = {A novel mechanism of antagonism between ATP-dependent chromatin remodeling complexes regulates RNR3 expression.}, journal = {Molecular and Cellular Biology}, volume = {29}, year = {2009}, month = {2009 Jun}, pages = {3255-65}, abstract = {

Gene expression depends upon the antagonistic actions of chromatin remodeling complexes. While this has been studied extensively for the enzymes that covalently modify the tails of histones, the mechanism of how ATP-dependent remodeling complexes antagonize each other to maintain the proper level of gene activity is not known. The gene encoding a large subunit of ribonucleotide reductase, RNR3, is regulated by ISW2 and SWI/SNF, complexes that repress and activate transcription, respectively. Here, we studied the functional interactions of these two complexes at RNR3. Deletion of ISW2 causes constitutive recruitment of SWI/SNF, and conditional reexpression of ISW2 causes the repositioning of nucleosomes and reduced SWI/SNF occupancy at RNR3. Thus, ISW2 is required for restriction of access of SWI/SNF to the RNR3 promoter under the uninduced condition. Interestingly, the binding of sequence-specific DNA binding factors and the general transcription machinery are unaffected by the status of ISW2, suggesting that disruption of nucleosome positioning does not cause a nonspecific increase in cross-linking of all factors to RNR3. We provide evidence that ISW2 does not act on SWI/SNF directly but excludes its occupancy by positioning nucleosomes over the promoter. Genetic disruption of nucleosome positioning by other means led to a similar phenotype, linking repressed chromatin structure to SWI/SNF exclusion. Thus, incorporation of promoters into a repressive chromatin structure is essential for prevention of the opportunistic actions of nucleosome-disrupting activities in vivo, providing a novel mechanism for maintaining tight control of gene expression.

}, keywords = {Adenosine Triphosphatases, Adenosine Triphosphate, Base Sequence, Chromatin, Chromatin Assembly and Disassembly, DNA, Fungal, Gene Expression, Genes, Genetic, Multiprotein Complexes, Mutation, Nucleosomes, Promoter Regions, Ribonucleoside Diphosphate Reductase, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Transcription Factors}, issn = {1098-5549}, doi = {10.1128/MCB.01741-08}, author = {Tomar, Raghuvir S and Psathas, James N and Zhang, Hesheng and Zhang, Zhengjian and Reese, Joseph C} } @article {2501, title = {The nuclear receptor E75A has a novel pair-rule-like function in patterning the milkweed bug, Oncopeltus fasciatus.}, journal = {Developmental Biology}, volume = {334}, year = {2009}, month = {2009 Oct 1}, pages = {300-10}, abstract = {

Genetic studies of the fruit fly Drosophila have revealed a hierarchy of segmentation genes (maternal, gap, pair-rule and HOX) that subdivide the syncytial blastoderm into sequentially finer-scale coordinates. Within this hierarchy, the pair-rule genes translate gradients of information into periodic stripes of expression. How pair-rule genes function during the progressive mode of segmentation seen in short and intermediate-germ insects is an ongoing question. Here we report that the nuclear receptor Of{\textquoteright}E75A is expressed with double segment periodicity in the head and thorax. In the abdomen, Of{\textquoteright}E75A is expressed in a unique pattern during posterior elongation, and briefly resembles a sequence that is typical of pair-rule genes. Depletion of Of{\textquoteright}E75A mRNA caused loss of a subset of odd-numbered parasegments, as well as parasegment 6. Because these parasegments straddle segment boundaries, we observe fusions between adjacent segments. Finally, expression of Of{\textquoteright}E75A in the blastoderm requires even-skipped, which is a gap gene in Oncopeltus. These data show that the function of Of{\textquoteright}E75A during embryogenesis shares many properties with canonical pair-rule genes in other insects. They further suggest that parasegment specification may occur through irregular and episodic pair-rule-like activity.

}, keywords = {Animals, Blastoderm, Body Patterning, Cytoplasmic and Nuclear, Embryo, Hemiptera, Insect Proteins, Nonmammalian, Receptors, RNA Interference}, issn = {1095-564X}, doi = {10.1016/j.ydbio.2009.06.038}, author = {Erezyilmaz, Deniz F and Kelstrup, Hans C and Riddiford, Lynn M} } @article {4274, title = {Nuclear receptor unfulfilled regulates axonal guidance and cell identity of Drosophila mushroom body neurons.}, journal = {PLoS One}, volume = {4}, year = {2009}, month = {2009 Dec 22}, pages = {e8392}, abstract = {

Nuclear receptors (NRs) comprise a family of ligand-regulated transcription factors that control diverse critical biological processes including various aspects of brain development. Eighteen NR genes exist in the Drosophila genome. To explore their roles in brain development, we knocked down individual NRs through the development of the mushroom bodies (MBs) by targeted RNAi. Besides recapitulating the known MB phenotypes for three NRs, we found that unfulfilled (unf), an ortholog of human photoreceptor specific nuclear receptor (PNR), regulates axonal morphogenesis and neuronal subtype identity. The adult MBs develop through remodeling of gamma neurons plus de-novo elaboration of both alpha{\textquoteright}/beta{\textquoteright} and alpha/beta neurons. Notably, unf is largely dispensable for the initial elaboration of gamma neurons, but plays an essential role in their re-extension of axons after pruning during early metamorphosis. The subsequently derived MB neuron types also require unf for extension of axons beyond the terminus of the pruned bundle. Tracing single axons revealed misrouting rather than simple truncation. Further, silencing unf in single-cell clones elicited misguidance of axons in otherwise unperturbed MBs. Such axon guidance defects may occur as MB neurons partially lose their subtype identity, as evidenced by suppression of various MB subtype markers in unf knockdown MBs. In sum, unf governs axonal morphogenesis of multiple MB neuron types, possibly through regulating neuronal subtype identity.

}, keywords = {Aging, Animals, Axons, Biological Markers, Cytoplasmic and Nuclear, Drosophila melanogaster, Drosophila Proteins, Gene Knockdown Techniques, Gene Silencing, MicroRNAs, Morphogenesis, Mushroom Bodies, Phenotype, Receptors}, issn = {1932-6203}, doi = {10.1371/journal.pone.0008392}, author = {Lin, Suewei and Huang, Yaling and Lee, Tzumin} } @article {1161, title = {Native R-loops persist throughout the mouse mitochondrial DNA genome.}, journal = {The Journal of Biological Chemistry}, volume = {283}, year = {2008}, month = {2008 Dec 26}, pages = {36743-51}, abstract = {

Mammalian mtDNA has been found here to harbor RNA-DNA hybrids at a variety of locations throughout the genome. The R-loop, previously characterized in vitro at the leading strand replication origin (OH), is isolated as a native RNA-DNA hybrid copurifying with mtDNA. Surprisingly, other mitochondrial transcripts also form stable partial R-loops. These are abundant and affect mtDNA conformation. Current models regarding the mechanism of mammalian mtDNA replication have been expanded by recent data and discordant hypotheses. The presence of stable, nonreplicative, and partially hybridized RNA on the mtDNA template is significant for the reevaluation of replication models based on two-dimensional agarose gel analyses. In addition, the close association of a subpopulation of mtRNA with the DNA template has further implications regarding the structure, maintenance, and expression of the mitochondrial genome. These results demonstrate that variously processed and targeted mtRNAs within mammalian mitochondria likely have multiple functions in addition to their conventional roles.

}, keywords = {Alleles, Animals, Atomic Force, Blotting, DNA, DNA Primers, Electrophoresis, Gel, Genetic, Genome, Mice, Microscopy, Mitochondrial, Models, Northern, Nucleic Acid Conformation, Protein Conformation, RNA, RNA Probes, Two-Dimensional}, issn = {0021-9258}, doi = {10.1016/j.ymeth.2010.01.001}, author = {Brown, Timothy A and Tkachuk, Ariana N and Clayton, David A} } @proceedings {4527, title = {Natural image denoising with convolutional networks.}, year = {2008}, month = {2008 }, address = {Vancouver, B.C., Canada}, author = {Jain, Viren and Seung, H Sebastian} } @article {45967, title = {Noncanonical binding of calmodulin to aquaporin-0: implications for channel regulation.}, journal = {Structure}, volume = {16}, year = {2008}, month = {2008 Sep 10}, pages = {1389-98}, abstract = {

Aquaporins (AQPs) are a family of ubiquitous membrane channels that conduct water across cell membranes. AQPs form homotetramers containing four functional and independent water pores. Aquaporin-0 (AQP0) is expressed in the eye lens, where its water permeability is regulated by calmodulin (CaM). Here we use a combination of biochemical methods and NMR spectroscopy to probe the interaction between AQP0 and CaM. We show that CaM binds the AQP0 C-terminal domain in a calcium-dependent manner. We demonstrate that only two CaM molecules bind a single AQP0 tetramer in a noncanonical fashion, suggesting a form of cooperativity between AQP0 monomers. Based on these results, we derive a structural model of the AQP0/CaM complex, which suggests CaM may be inhibitory to channel permeability by capping the vestibules of two monomers within the AQP0 tetramer. Finally, phosphorylation within AQP0{\textquoteright}s CaM binding domain inhibits the AQP0/CaM interaction, suggesting a temporal regulatory mechanism for complex formation.

}, keywords = {Amino Acid Sequence, Animals, Aquaporins, Calcium, Calmodulin, Crystallins, Eye Proteins, Ion Channels, Models, Molecular, Molecular Sequence Data, Phosphorylation, Protein Binding, Protein Structure, Quaternary, Protein Structure, Secondary, Protein Structure, Tertiary, Protein-Serine-Threonine Kinases, Sequence Homology, Amino Acid, Sheep}, issn = {0969-2126}, doi = {10.1016/j.str.2008.06.011}, author = {Reichow, Steve L and Gonen, Tamir} } @article {5505, title = {Nonlinearities and contextual influences in auditory cortical responses modeled with multilinear spectrotemporal methods.}, journal = {The Journal of Neuroscience}, volume = {28}, year = {2008}, month = {2008 Feb 20}, pages = {1929-42}, abstract = {

The relationship between a sound and its neural representation in the auditory cortex remains elusive. Simple measures such as the frequency response area or frequency tuning curve provide little insight into the function of the auditory cortex in complex sound environments. Spectrotemporal receptive field (STRF) models, despite their descriptive potential, perform poorly when used to predict auditory cortical responses, showing that nonlinear features of cortical response functions, which are not captured by STRFs, are functionally important. We introduce a new approach to the description of auditory cortical responses, using multilinear modeling methods. These descriptions simultaneously account for several nonlinearities in the stimulus-response functions of auditory cortical neurons, including adaptation, spectral interactions, and nonlinear sensitivity to sound level. The models reveal multiple inseparabilities in cortical processing of time lag, frequency, and sound level, and suggest functional mechanisms by which auditory cortical neurons are sensitive to stimulus context. By explicitly modeling these contextual influences, the models are able to predict auditory cortical responses more accurately than are STRF models. In addition, they can explain some forms of stimulus dependence in STRFs that were previously poorly understood.

}, keywords = {Acoustic Stimulation, Animals, Auditory Cortex, Biological, Mice, Models, Nonlinear Dynamics, Rats, Time Factors}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3377-07.2008}, author = {Ahrens, Misha B and Linden, Jennifer F and Sahani, Maneesh} } @article {1413, title = {A novel basal ganglia pathway forms a loop linking a vocal learning circuit with its dopaminergic input.}, journal = {The Journal of Comparative Neurology}, volume = {508}, year = {2008}, month = {2008 Jun 10}, pages = {824-39}, abstract = {

Dopamine has been implicated in mediating contextual modulation of motor behaviors and learning in many species. In songbirds, dopamine may act on the basal ganglia nucleus Area X to influence the neural activity that contributes to vocal learning and contextual changes in song variability. Neurons in midbrain dopamine centers, the substantia nigra pars compacta (SNc) and ventral tegmental area (VTA), densely innervate Area X and show singing-related changes in firing rate. In addition, dopamine levels in Area X change during singing. It is unknown, however, how song-related information could reach dopaminergic neurons. Here we report an anatomical pathway that could provide song-related information to the SNc and VTA. By using injections of bidirectionally transported fluorescent tracers in adult male zebra finches, we show that Area X and other song control nuclei do not project directly to the SNc or VTA. Instead, we describe an indirect pathway from Area X to midbrain dopaminergic neurons via a connection in the ventral pallidum (VP). Specifically, Area X projects to the VP via axon collaterals of Area X output neurons that also project to the thalamus. Dual injections revealed that the area of VP receiving input from Area X projects to the SNc and VTA. Furthermore, VP terminals in the SNc and VTA overlap with cells that project back to Area X. A portion of the arcopallium also projects to the SNc and VTA and could carry auditory information. These data demonstrate an anatomical loop through which Area X activity could influence its dopaminergic input.

}, keywords = {Animal, Animals, Basal Ganglia, Dopamine, Finches, Learning, Male, Nerve Net, Neural Pathways, Vocalization}, issn = {1096-9861}, doi = {10.1002/cne.21700}, author = {Gale, Samuel D and Person, Abigail L and Perkel, David J} } @article {2397, title = {The nucleosome remodeling factor (NURF) regulates genes involved in Drosophila innate immunity.}, journal = {Developmental Biology}, volume = {316}, year = {2008}, month = {2008 Apr 15}, pages = {538-47}, abstract = {

The Drosophila nucleosome remodeling factor (NURF) is an ISWI-containing chromatin remodeling complex that catalyzes ATP-dependent nucleosome sliding. By sliding nucleosomes, NURF has the ability to alter chromatin structure and regulate transcription. Previous studies have shown that mutation of Drosophila NURF induces melanotic tumors, implicating NURF in innate immune function. Here, we show that NURF mutants exhibit identical innate immune responses to gain-of-function mutants in the Drosophila JAK/STAT pathway. Using microarrays, we identify a common set of target genes that are activated in both mutants. In silico analysis of promoter sequences of these defines a consensus regulatory element comprising a STAT-binding sequence overlapped by a binding-site for the transcriptional repressor Ken. NURF interacts physically and genetically with Ken. Chromatin immunoprecipitation (ChIP) localizes NURF to Ken-binding sites in hemocytes, suggesting that Ken recruits NURF to repress STAT responders. Loss of NURF leads to precocious activation of STAT target genes.

}, keywords = {Animals, Chromosomal Proteins, DNA-Binding Proteins, Drosophila, Drosophila Proteins, Gene Expression Profiling, Gene Expression Regulation, Genetic, Genome, Immunity, Innate, Non-Histone, Oligonucleotide Array Sequence Analysis, Phenotype, Recombinant Proteins, Reverse Transcriptase Polymerase Chain Reaction, RNA, Signal Transduction, Transcription}, issn = {1095-564X}, doi = {10.1073/pnas.1100640108}, author = {Kwon, So Yeon and Xiao, Hua and Glover, Bradley P and Tjian, Robert and Wu, Carl and Badenhorst, Paul} } @article {5819, title = {Neurobiology of the basal platyhelminth Macrostomum lignano: map and digital 3D model of the juvenile brain neuropile.}, journal = {Development Genes \& Evolution}, volume = {217}, year = {2007}, month = {2007 Aug}, pages = {569-84}, abstract = {

We have analyzed brain structure in Macrostomum lignano, a representative of the basal platyhelminth taxon Macrostomida. Using confocal microscopy and digital 3D modeling software on specimens labeled with general markers for neurons (tyrTub), muscles (phalloidin), and nuclei (Sytox), an atlas and digital model of the juvenile Macrostomum brain was generated. The brain forms a ganglion with a central neuropile surrounded by a cortex of neuronal cell bodies. The neuropile contains a stereotypical array of compact axon bundles, as well as branched terminal axons and dendrites. Muscle fibers penetrate the flatworm brain horizontally and vertically at invariant positions. Beside the invariant pattern of neurite bundles, these "cerebral muscles" represent a convenient system of landmarks that help define discrete compartments in the juvenile brain. Commissural axon bundles define a dorsal and ventro-medial neuropile compartment, respectively. Longitudinal axons that enter the neuropile through an invariant set of anterior and posterior nerve roots define a ventro-basal and a central medial compartment in the neuropile. Flanking these "fibrous" compartments are neuropile domains that lack thick axon bundles and are composed of short collaterals and terminal arborizations of neurites. Two populations of neurons, visualized by antibodies against FMRFamide and serotonin, respectively, were mapped relative to compartment boundaries. This study will aid in the documentation and interpretation of patterns of gene expression, as well as functional studies, in the developing Macrostomum brain.

}, keywords = {Animals, Brain, Brain Mapping, Cells, Computer Simulation, Cultured, Imaging, Models, Muscle Fibers, Neurological, Neuropil, Platyhelminths, Skeletal, Three-Dimensional}, issn = {0949-944X}, doi = {10.1007/s00427-007-0166-z}, author = {Morris, Joshua and Cardona, Albert and De Miguel-Bonet, Maria Del Mar and Hartenstein, Volker} } @article {1112, title = {A new strategy for the synthesis of benzylic sulfonamides: palladium-catalyzed arylation and sulfonamide metathesis.}, journal = {The Journal of Organic Chemistry}, volume = {72}, year = {2007}, month = {2007 Oct 12}, pages = {8135-8}, abstract = {

An efficient two-step strategy has been developed to access diversely functionalized benzylic sulfonamides. Execution of this strategy required the development of two reaction methods: the palladium-catalyzed cross-coupling of aryl halides with CH-acidic methanesulfonamides and a metathesis reaction between the resulting alpha-arylated sulfonamides and diverse amines. The broad scope of the cross-coupling process combined with a versatile sulfonamide metathesis constitutes an efficient strategy for the synthesis of various benzylic sulfonamides.

}, keywords = {Benzyl Compounds, Catalysis, Molecular Structure, Palladium, Sulfonamides}, issn = {0022-3263}, doi = {10.1021/jo701431j}, author = {Grimm, Jonathan B and Katcher, Matthew H and Witter, David J and Northrup, Alan B} } @article {46427, title = {NF-κB, IκB, and IRAK control glutamate receptor density at the Drosophila NMJ.}, journal = {Neuron}, volume = {55}, year = {2007}, month = {2007 Sep 20}, pages = {859-73}, abstract = {

NF-κB signaling has been implicated in neurodegenerative disease, epilepsy, and neuronal plasticity. However, the cellular and molecular activity of NF-κB signaling within the nervous system remains to be clearly defined. Here,\ we show that the NF-κB and IκB homologs Dorsal and Cactus surround postsynaptic glutamate receptor (GluR) clusters at the Drosophila\ NMJ. We then show that mutations in dorsal, cactus, and IRAK/pelle kinase specifically impair GluR levels, assayed immunohistochemically and electrophysiologically, without affecting NMJ growth, the size of the postsynaptic density, or homeostatic plasticity. Additional genetic experiments support the conclusion that cactus functions in concert with, rather than in opposition to, dorsal and pelle in this process. Finally, we provide evidence that Dorsal and Cactus act\ posttranscriptionally, outside the nucleus, to control GluR density. Based upon our data we speculate that Dorsal, Cactus, and Pelle could function together, locally at the postsynaptic density, to specify GluR levels.

}, keywords = {Developmental Biology, molecular neurology, signaling}, doi = {10.1016/j.neuron.2007.08.005}, author = {Heckscher, Elizabeth S and Fetter, Richard D and Marek, Kurt W and Albin, Stephanie D and Davis, Graeme W} } @article {5828, title = {A novel multiple objective optimization framework for constraining conductance-based neuron models by experimental data.}, journal = {Frontiers in Neuroscience}, volume = {1}, year = {2007}, month = {2007 Nov}, pages = {7-18}, abstract = {

We present a novel framework for automatically constraining parameters of compartmental models of neurons, given a large set of experimentally measured responses of these neurons. In experiments, intrinsic noise gives rise to a large variability (e.g., in firing pattern) in the voltage responses to repetitions of the exact same input. Thus, the common approach of fitting models by attempting to perfectly replicate, point by point, a single chosen trace out of the spectrum of variable responses does not seem to do justice to the data. In addition, finding a single error function that faithfully characterizes the distance between two spiking traces is not a trivial pursuit. To address these issues, one can adopt a multiple objective optimization approach that allows the use of several error functions jointly. When more than one error function is available, the comparison between experimental voltage traces and model response can be performed on the basis of individual features of interest (e.g., spike rate, spike width). Each feature can be compared between model and experimental mean, in units of its experimental variability, thereby incorporating into the fitting this variability. We demonstrate the success of this approach, when used in conjunction with genetic algorithm optimization, in generating an excellent fit between model behavior and the firing pattern of two distinct electrical classes of cortical interneurons, accommodating and fast-spiking. We argue that the multiple, diverse models generated by this method could serve as the building blocks for the realistic simulation of large neuronal networks.

}, issn = {1662-453X}, doi = {10.3389/neuro.01.1.1.001.2007}, author = {Druckmann, Shaul and Banitt, Yoav and Gidon, Albert and Sch{\"u}rmann, Felix and Markram, Henry and Segev, Idan} } @article {2405, title = {Novel TRF1/BRF target genes revealed by genome-wide analysis of Drosophila Pol III transcription.}, journal = {The EMBO Journal}, volume = {26}, year = {2007}, month = {2007 Jan 10}, pages = {79-89}, abstract = {

Metazoans have evolved multiple paralogues of the TATA binding protein (TBP), adding another tunable level of gene control at core promoters. While TBP-related factor 1 (TRF1) shares extensive homology with TBP and can direct both Pol II and Pol III transcription in vitro, TRF1 target sites in vivo have remained elusive. Here, we report the genome-wide identification of TRF1-binding sites using high-resolution genome tiling microarrays. We found 354 TRF1-binding sites genome-wide with approximately 78\% of these sites displaying colocalization with BRF. Strikingly, the majority of TRF1 target genes are Pol III-dependent small noncoding RNAs such as tRNAs and small nonmessenger RNAs. We provide direct evidence that the TRF1/BRF complex is functionally required for the activity of two novel TRF1 targets (7SL RNA and small nucleolar RNAs). Our studies suggest that unlike most other eukaryotic organisms that rely on TBP for Pol III transcription, in Drosophila and possibly other insects the alternative TRF1/BRF complex appears responsible for the initiation of all known classes of Pol III transcription.

}, keywords = {Animals, Base Sequence, Binding Sites, Chromatin Immunoprecipitation, Deoxyribonuclease I, DNA Polymerase III, Drosophila melanogaster, Genetic, Genome, Molecular Sequence Data, Oligonucleotide Probes, Protein Binding, RNA, Small Nucleolar, Telomeric Repeat Binding Protein 1, Transcription, Transcription Factor TFIIIB}, issn = {0261-4189}, doi = {10.1073/pnas.1100640108}, author = {Isogai, Yoh and Takada, Shinako and Tjian, Robert and Kele\c s, S{\"u}nd{\"u}z} } @article {1980, title = {Network variability limits stimulus-evoked spike timing precision in retinal ganglion cells.}, journal = {Neuron}, volume = {52}, year = {2006}, month = {2006 Nov 9}, pages = {511-24}, abstract = {

Visual, auditory, somatosensory, and olfactory stimuli generate temporally precise patterns of action potentials (spikes). It is unclear, however, how the precision of spike generation relates to the pattern and variability of synaptic input elicited by physiological stimuli. We determined how synaptic conductances evoked by light stimuli that activate the rod bipolar pathway control spike generation in three identified types of mouse retinal ganglion cells (RGCs). The relative amplitude, timing, and impact of excitatory and inhibitory input differed dramatically between On and Off RGCs. Spikes evoked by repeated somatic injection of identical light-evoked synaptic conductances were more temporally precise than those evoked by light. However, the precision of spikes evoked by conductances that varied from trial to trial was similar to that of light-evoked spikes. Thus, the rod bipolar pathway modulates different RGCs via unique combinations of synaptic input, and RGC temporal variability reflects variability in the input this circuit provides.

}, keywords = {Action Potentials, Animals, Dose-Response Relationship, Electric Stimulation, Inbred C57BL, Mice, Models, Neurological, Patch-Clamp Techniques, Photic Stimulation, Radiation, Retinal Ganglion Cells, Synapses, Synaptic Transmission, Visual Pathways}, issn = {0896-6273}, doi = {10.1016/j.neuron.2006.09.014}, author = {Murphy, Gabe J and Rieke, Fred} } @article {1289, title = {A new role for microRNA pathways: modulation of degeneration induced by pathogenic human disease proteins.}, journal = {Cell Cycle }, volume = {5}, year = {2006}, month = {2006 Dec}, pages = {2835-8}, abstract = {

MicroRNAs (miRNAs) are small noncoding RNAs that regulate the expression of target transcript mRNAs. Many miRNAs have been defined, however their roles and the processes influenced by miRNA pathways are still being elucidated. A role for miRNAs in development and cancer has been described. We recently isolated the miRNA bantam (ban) in a genetic screen for modulators of pathogenicity of a human neurodegenerative disease model in Drosophila. These studies showed that upregulation of ban mitigates degeneration induced by the pathogenic polyglutamine (polyQ) protein Ataxin-3, which is mutated in the human polyglutamine disease spinocerebellar ataxia type 3 (SCA3). To address the broader role for miRNAs in neuroprotection, we also showed that loss of all miRNAs, by dicer mutation, dramatically enhances pathogenic polyQ protein toxicity in flies and in human HeLa cells. These studies suggest that miRNAs may be important for neuronal survival in the context of human neurodegenerative disease. These studies provide the foundation to define the miRNAs involved in neurodegenerative disease, and the biological pathways affected.

}, keywords = {Animal, Animals, Cyclins, Disease Models, Drosophila, Drosophila Proteins, Eye, Hela Cells, Humans, MicroRNAs, Nerve Degeneration, Neurodegenerative Diseases, Peptides, Trinucleotide Repeat Expansion}, issn = {1551-4005}, author = {Bilen, Julide and Liu, Nan and Bonini, Nancy M} } @article {46401, title = {NikR-operator complex structure and the mechanism of repressor activation by metal ions.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, year = {2006}, month = {2006 Sep 12}, pages = {13676-81}, abstract = {

Metal ion homeostasis is critical to the survival of all cells. Regulation of nickel concentrations in Escherichia coli is mediated by the NikR repressor via nickel-induced transcriptional repression of the nickel ABC-type transporter, NikABCDE. Here, we report two crystal structures of nickel-activated E. coli NikR, the isolated repressor at 2.1 A resolution and in a complex with its operator DNA sequence from the nik promoter at 3.1 A resolution. Along with the previously published structure of apo-NikR, these structures allow us to evaluate functional proposals for how metal ions activate NikR, delineate the drastic conformational changes required for operator recognition, and describe the formation of a second metal-binding site in the presence of DNA. They also provide a rare set of structural views of a ligand-responsive transcription factor in the unbound, ligand-induced, and DNA-bound states, establishing a model system for the study of ligand-mediated effects on transcription factor function.

}, keywords = {Amino Acid Sequence, Base Sequence, Binding Sites, Crystallography, Escherichia coli Proteins, Molecular Sequence Data, Nickel, Operator Regions, Genetic, Protein Conformation, Repressor Proteins}, issn = {0027-8424}, doi = {10.1073/pnas.0606247103}, author = {Schreiter, Eric R and Wang, Sheila C and Zamble, Deborah B and Drennan, Catherine L} } @article {4006, title = {Noise-induced vocal modulation in cotton-top tamarins (Saguinus oedipus).}, journal = {American Journal of Primatology}, volume = {68}, year = {2006}, month = {2006 Dec}, pages = {1183-90}, abstract = {

The Lombard effect-an increase in vocalization amplitude in response to an increase in background noise-is observed in a wide variety of animals. We investigated this basic form of vocal control in the cotton-top tamarin (Saguinus oedipus) by measuring the amplitude of a contact call, the combination long call (CLC), while simultaneously varying the background noise level. All subjects showed a significant increase in call amplitude and syllable duration in response to an increase in background noise amplitude. Together with prior results, this study shows that tamarins have greater vocal control in the context of auditory feedback perturbation than previously suspected.

}, keywords = {Animal, Animals, Female, Head, Male, Noise, Saguinus, Speech Acoustics, Vocalization}, issn = {0275-2565}, doi = {10.1002/ajp.20317}, author = {Egnor, S E Roian and Hauser, Marc D} } @article {1736, title = {A novel spectroscopic probe for molecular chirality.}, journal = {Chirality}, volume = {18}, year = {2006}, month = {2006 Feb}, pages = {146-58}, abstract = {

Recent advances in developing sum frequency generation (SFG) as a novel spectroscopic probe for molecular chirality are reviewed. The basic principle underlying the technique is briefly described, in comparison with circular dichroism (CD). The significantly better sensitivity of the technique than CD is pointed out, and the reason is discussed. Bi-naphthol (BN) and amino acids are used as representatives for two different types of chiral molecules; the measured chirality in their electronic transitions can be understood by two different molecular models, respectively, that are extensions of models developed earlier for CD. Optically active or chiral SFG from vibrational transitions are weaker, but with the help of electronic-vibrational double resonance, the vibrational spectrum of a monolayer of BN has been obtained. Generally, optically active SFG is sufficiently sensitive to be employed to probe in-situ chirality of chiral monolayers and thin films.

}, keywords = {Algorithms, Chemistry, Molecular Conformation, Physical, Physicochemical Phenomena, Stereoisomerism}, issn = {0899-0042}, doi = {10.1002/chir.20238}, author = {Ji, Na and Shen, Yuen-Ron} } @article {1691, title = {Nud1p, the yeast homolog of Centriolin, regulates spindle pole body inheritance in meiosis.}, journal = {The EMBO Journal}, volume = {25}, year = {2006}, month = {2006 Aug 23}, pages = {3856-68}, abstract = {

Nud1p, a protein homologous to the mammalian centrosome and midbody component Centriolin, is a component of the budding yeast spindle pole body (SPB), with roles in anchorage of microtubules and regulation of the mitotic exit network during vegetative growth. Here we analyze the function of Nud1p during yeast meiosis. We find that a nud1-2 temperature-sensitive mutant has two meiosis-related defects that reflect genetically distinct functions of Nud1p. First, the mutation affects spore formation due to its late function during spore maturation. Second, and most important, the mutant loses its ability to distinguish between the ages of the four spindle pole bodies, which normally determine which SPB would be preferentially included in the mature spores. This affects the regulation of genome inheritance in starved meiotic cells and leads to the formation of random dyads instead of non-sister dyads under these conditions. Both functions of Nud1p are connected to the ability of Spc72p to bind to the outer plaque and half-bridge (via Kar1p) of the SPB.

}, keywords = {Cell Cycle Proteins, Deoxyribonucleases, Fungal, Genome, Humans, Meiosis, Microtubule-Associated Proteins, Mitotic Spindle Apparatus, Mutation, Nuclear Proteins, Protein Binding, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Spores, tRNA Methyltransferases}, issn = {0261-4189}, doi = {10.1038/sj.emboj.7601254}, author = {Gordon, Oren and Taxis, Christof and Keller, Philipp J and Benjak, Aleksander and Stelzer, Ernst H K and Simchen, Giora and Knop, Michael} } @article {2409, title = {Nutrient availability and growth: regulation of insulin signaling by dFOXO/FOXO1.}, journal = {Cell Cycle}, volume = {5}, year = {2006}, month = {2006 Mar}, pages = {503-5}, abstract = {

Organisms adjust their rate of growth depending on the availability of nutrients. Thus, when environmental conditions limit nutrients, growth is slowed and is only restored after food again becomes abundant. Many aspects of the molecular mechanisms that govern this complex control system remain unknown. However, it has been shown that the insulin/IGF-1 (insulin-like growth factor 1) receptor pathway, together with the FOXO family of transcription factors, play an important role in this process. Recent studies with the fruit fly Drosophila melanogaster have provided new insights into the regulatory circuitry that controls both growth and gene expression in response to nutrient availability.

}, keywords = {Animal Nutritional Physiological Phenomena, Animals, Drosophila melanogaster, Drosophila Proteins, Forkhead Transcription Factors, Insulin, Receptor, Signal Transduction}, issn = {1551-4005}, doi = {10.1073/pnas.1100640108}, author = {Puig, Oscar and Tjian, Robert} } @article {45757, title = {Natural selection and developmental constraints in the evolution of allometries.}, journal = {Science}, volume = {307}, year = {2005}, month = {2005 Feb 4}, pages = {718-20}, abstract = {

In animals, scaling relationships between appendages and body size exhibit high interspecific variation but low intraspecific variation. This pattern could result from natural selection for specific allometries or from developmental constraints on patterns of differential growth. We performed artificial selection on the allometry between forewing area and body size in a butterfly to test for developmental constraints, and then used the resultant increased range of phenotypic variation to quantify natural selection on the scaling relationship. Our results show that the short-term evolution of allometries is not limited by developmental constraints. Instead, scaling relationships are shaped by strong natural selection.

}, keywords = {Alleles, Animals, Biological Evolution, Body Size, Butterflies, Crosses, Genetic, Female, Flight, Animal, Genetic Variation, Male, Phenotype, Reproduction, Selection, Genetic, Wing}, issn = {1095-9203}, doi = {10.1126/science.1105409}, author = {Frankino, W Anthony and Zwaan, Bas J and Stern, David L and Brakefield, Paul M} } @article {1249, title = {Neurogeometry and potential synaptic connectivity.}, journal = {Trends in Neurosciences}, volume = {28}, year = {2005}, month = {2005 Jul}, pages = {387-94}, abstract = {

The advent of high-quality 3D reconstructions of neuronal arbors has revived the hope of inferring synaptic connectivity from the geometric shapes of axons and dendrites, or {\textquoteright}neurogeometry{\textquoteright}. A quantitative description of connectivity must be built on a sound theoretical framework. Here, we review recent developments in neurogeometry that can provide such a framework. We base the geometric description of connectivity on the concept of a {\textquoteright}potential synapse{\textquoteright}{\textendash}the close apposition between axons and dendrites necessary to form an actual synapse. In addition to describing potential synaptic connectivity in neuronal circuits, neurogeometry provides insight into basic features of functional connectivity, such as specificity and plasticity.

}, keywords = {Animals, Axons, Dendrites, Imaging, Models, Neural Pathways, Neurological, Neuronal Plasticity, Neurons, Synapses, Synaptic Transmission, Three-Dimensional}, issn = {0166-2236}, doi = {10.1016/j.tins.2005.05.006}, author = {Stepanyants, Armen and Chklovskii, Dmitri B} } @article {2359, title = {Nitric oxide produced in rat liver mitochondria causes oxidative stress and impairment of respiration after transient hypoxia.}, journal = {The FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology}, volume = {17}, year = {2003}, month = {2003 Dec}, pages = {2194-201}, abstract = {

Nitric oxide (NO) is produced in mammals by different isoforms of NO synthase (NOS), including the constitutive mitochondrial enzyme (mtNOS). Here we demonstrate that the concentration of NO resulting from a mitochondrial NOS activity increases under hypoxic conditions in isolated rat liver mitochondria. We show that mitochondrially derived NO mediates the impairment of active (state 3) respiration as measured in the presence of the substrates glutamate and malate after reoxygenation. Simultaneously, NO induces oxidative stress in mitochondria, characterized by an increase in the amount of protein carbonyls and a decrease in glutathione (GSH). Both the accumulation of oxidative stress markers during and the impaired respiration after reoxygenation were prevented by blocking NO production with the NOS inhibitor L-NAME. These observations suggest that mitochondria are exposed to high amounts of NO generated by a mitochondrial NOS upon hypoxia/reoxygenation. Such increased NO levels, in turn, inhibit mitochondrial respiration and may cause oxidative stress that leads to irreversible impairment of mitochondria.

}, keywords = {Animals, Cell Hypoxia, Cell Respiration, Enzyme Inhibitors, Liver, Mitochondria, NG-Nitroarginine Methyl Ester, Nitric Oxide, Nitric Oxide Synthase, Oxidative Stress, Oxygen Consumption, Rats}, issn = {1530-6860}, doi = {10.1016/j.cub.2010.06.072}, author = {Schild, Lorenz and Reinheckel, Thomas and Reiser, Michael and Horn, Thomas F W and Wolf, Gerald and Augustin, Wolfgang} } @article {2138, title = {Normalization of Ca2+ signals by small oblique dendrites of CA1 pyramidal neurons.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {23}, year = {2003}, month = {2003 Apr 15}, pages = {3243-50}, abstract = {

Oblique dendrites of CA1 pyramidal neurons predominate in stratum radiatum and receive approximately 80\% of the synaptic input from Schaffer collaterals. Despite this fact, most of our understanding of dendritic signal processing in these neurons comes from studies of the main apical dendrite. Using a combination of Ca2+ imaging and whole-cell recording techniques in rat hippocampal slices, we found that the properties of the oblique dendrites differ markedly from those of the main dendrites. These different properties tend to equalize the Ca2+ rise from single action potentials as they backpropagate into the oblique dendrites from the main trunk. Evidence suggests that this normalization of Ca2+ signals results from a higher density of a transient, A-type K+ current [I(K(A))] in the oblique versus the main dendrites. The higher density of I(K(A)) may have important implications for our understanding of synaptic integration and plasticity in these structures.

}, keywords = {4-Aminopyridine, Action Potentials, Animals, Calcium, Calcium Channel Blockers, Calcium Signaling, Dendrites, Electric Stimulation, Fluorescent Dyes, Hippocampus, Patch-Clamp Techniques, Potassium Channel Blockers, Potassium Channels, Pyramidal Cells, Rats, Sodium Channels, Sprague-Dawley, Tetrodotoxin}, issn = {1529-2401}, doi = {10.1002/cbic.201000254}, author = {Frick, Andreas and Magee, Jeffrey and Koester, Helmut J and Migliore, Michele and Johnston, Daniel} } @article {1265, title = {Network motifs: simple building blocks of complex networks.}, journal = {Science}, volume = {298}, year = {2002}, month = {2002 Oct 25}, pages = {824-7}, abstract = {

Complex networks are studied across many fields of science. To uncover their structural design principles, we defined {\textquotedblleft}network motifs,{\textquotedblright} patterns of interconnections occurring in complex networks at numbers that are significantly higher than those in randomized networks. We found such motifs in networks from biochemistry, neurobiology, ecology, and engineering. The motifs shared by ecological food webs were distinct from the motifs shared by the genetic networks of Escherichia coli and Saccharomyces cerevisiae or from those found in the World Wide Web. Similar motifs were found in networks that perform information processing, even though they describe elements as different as biomolecules within a cell and synaptic connections between neurons in Caenorhabditis elegans. Motifs may thus define universal classes of networks. This approach may uncover the basic building blocks of most networks.

}, issn = {1095-9203}, author = {Milo, R. and Shen-Orr, S. and Itzkovitz, S. and Kashtan, N. and Chklovskii, D.B. and Alon, U.} } @article {1779, title = {Neurobiology: a cool ion channel.}, journal = {Nature}, volume = {416}, year = {2002}, month = {2002 Mar 7}, pages = {27-8}, keywords = {Cold Temperature, Drug, Humans, Ion Channels, Menthol, Neoplasm Proteins, Neurons, Receptors, Thermoreceptors, TRPM Cation Channels}, issn = {0028-0836}, doi = {10.1038/416027a}, author = {Zuker, Charles S} } @article {2429, title = {Neurodegeneration. A glutamine-rich trail leads to transcription factors.}, journal = {Science }, volume = {296}, year = {2002}, month = {2002 Jun 21}, pages = {2149-50}, keywords = {Animals, Brain, CREB-Binding Protein, DNA-Binding Proteins, Dopamine D2, Gene Expression Regulation, Genetic, Humans, Huntington Disease, Mice, Models, Nerve Tissue Proteins, Neurodegenerative Diseases, Neurons, Nuclear Proteins, Peptides, Promoter Regions, Protein Binding, Protein Structure, Receptors, Sp1 Transcription Factor, TATA-Binding Protein Associated Factors, Tertiary, Trans-Activators, Transcription, Transcription Factor TFIID, Transcription Factors, Trinucleotide Repeat Expansion}, issn = {1095-9203}, doi = {10.1073/pnas.1100640108}, author = {Freiman, Richard N and Tjian, Robert} } @article {2295, title = {A new NOS2 promoter polymorphism associated with increased nitric oxide production and protection from severe malaria in Tanzanian and Kenyan children.}, journal = {Lancet}, volume = {360}, year = {2002}, month = {2002 Nov 9}, pages = {1468-75}, abstract = {

Nitric oxide (NO) is a mediator of immunity to malaria, and genetic polymorphisms in the promoter of the inducible NO synthase gene (NOS2) could modulate production of NO. We postulated that NOS2 promoter polymorphisms would affect resistance to severe malaria.

}, keywords = {Anemia, Cerebral, Child, DNA, Falciparum, Female, Genetic, Humans, Immunity, Infant, Innate, Kenya, Malaria, Male, Nitric Oxide, Nitric Oxide Synthase, Nitric Oxide Synthase Type II, Parasitemia, Polymorphism, Preschool, Sequence Analysis, Single-Stranded Conformational, Tanzania}, issn = {0140-6736}, doi = {10.1016/S0140-6736(02)11474-7}, author = {Hobbs, Maurine R and Udhayakumar, Venkatachalam and Levesque, Marc C and Booth, Jennifer and Roberts, Jacquelin M and Tkachuk, Ariana N and Pole, Ann and Coon, Hilary and Kariuki, Simon and Nahlen, Bernard L and Mwaikambo, Esther D and Lal, Altaf L and Granger, Donald L and Anstey, Nicholas M and Weinberg, J Brice} } @article {5823, title = {A novel invertebrate trophic factor related to invertebrate neurotrophins is involved in planarian body regional survival and asexual reproduction.}, journal = {Developmental biology}, volume = {252}, year = {2002}, month = {2002 Dec 15}, pages = {188-201}, abstract = {

Trophic factors are a heterogeneous group of molecules that promote cell growth and survival. In freshwater planarians, the small secreted protein TCEN49 is linked to the regional maintenance of the planarian central body region. To investigate its function in vivo, we performed loss-of-function and gain-of-function experiments by RNA interference and by the implantation of microbeads soaked in TCEN49, respectively. We show that TCEN49 behaves as a trophic factor involved in central body region neuron survival. In planarian tail regenerates, tcen49 expression inhibition by double-stranded RNA interference causes extensive apoptosis in various cell types, including nerve cells. This phenotype is rescued by the implantation of microbeads soaked in TCEN49 after RNA interference. On the other hand, in organisms committed to asexual reproduction, both tcen49 mRNA and its protein are detected not only in the central body region but also in the posterior region, expanding from cells close to the ventral nerve chords. In some cases, the implantation of microbeads soaked in TCEN49 in the posterior body region drives organisms to reproduce asexually, and the inhibition of tcen49 expression obstructs this process, suggesting a link between the central nervous system, TCEN49, regional induction, and asexual reproduction. Finally, the distribution of TCEN49 cysteine and tyrosine residues also points to a common evolutionary origin for TCEN49 and molluscan neurotrophins.

}, keywords = {Amino Acid, Amino Acid Sequence, Animals, Biological Factors, Immunohistochemistry, In Situ Hybridization, In Situ Nick-End Labeling, Molecular Sequence Data, Nerve Growth Factors, Planarians, Reproduction, Sequence Homology}, issn = {0012-1606}, author = {Bueno, David and Fern{\`a}ndez-Rodr{\'\i}guez, Juana and Cardona, Albert and Hern{\`a}ndez-Hern{\`a}ndez, Victor and Romero, Rafael} } @article {2472, title = {Nuclear degradation of p53 occurs during down-regulation of the p53 response after DNA damage.}, journal = {The FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology}, volume = {16}, year = {2002}, month = {2002 Mar}, pages = {420-2}, abstract = {

The principal regulator of p53 stability is HDM2, an E3 ligase that mediates p53 degradation via the ubiquitin-26S proteasome pathway. The current model holds that p53 degradation occurs exclusively on cytoplasmic proteasomes and hence has an absolute requirement for nuclear export of p53 via the CRM-1 pathway. However, proteasomes are abundant in both cytosol and nucleus, and no studies have been done to determine under what physiological circumstances p53 degradation might occur in the nucleus. We analyzed HDM2-mediated degradation of endogenous p53 in the presence of various nuclear export inhibitors of CRM-1, including leptomycin B (LMB), a noncompetitive, specific, and fast-acting inhibitor; and HTLV1-Rex protein, a potent competitive inhibitor. We found that significant HDM2-mediated p53 degradation took place in the presence of LMB or HTLV1-Rex, indicating that endogenous p53 degradation occurs locally in the nucleus, in parallel to cytoplasmic degradation. Moreover, p53 null cells that coexpressed export-defective mutants of p53 and HDM2 retained partial competence for p53 degradation. It is important that nuclear degradation of p53 occurred during the poststress recovery phase of a p53 response, after DNA damage ceased. We propose that the capability of local p53 degradation within the nucleus provides a tighter and faster control during the down-regulatory phase, when an active p53 program needs to be turned off quickly.

}, keywords = {Active Transport, Animals, Biological, Cell Line, Cell Nucleus, Cytoplasm, DNA Damage, Down-Regulation, Gene Products, Kinetics, Models, Mutation, Nuclear Localization Signals, Nuclear Proteins, Proto-Oncogene Proteins, Proto-Oncogene Proteins c-mdm2, rex, Transfection, Tumor Suppressor Protein p53}, issn = {1530-6860}, doi = {10.1096/fj.01-0617fje}, author = {Shirangi, Troy R and Zaika, Alex and Moll, Ute M} } @article {2452, title = {Neural network partitioning by NO and cGMP.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {21}, year = {2001}, month = {2001 Mar 1}, pages = {1610-8}, abstract = {

The stomatogastric ganglion (STG) of the crab Cancer productus contains approximately 30 neurons arrayed into two different networks (gastric mill and pyloric), each of which produces a distinct motor pattern in vitro. Here we show that the functional division of the STG into these two networks requires intact NO-cGMP signaling. Multiple nitric oxide synthase (NOS)-like proteins are expressed in the stomatogastric nervous system, and NO appears to be released as an orthograde transmitter from descending inputs to the STG. The receptor of NO, a soluble guanylate cyclase (sGC), is expressed in a subset of neurons in both motor networks. When NO diffusion or sGC activation are blocked within the ganglion, the two networks combine into a single conjoint circuit. The gastric mill motor rhythm breaks down, and several gastric neurons pattern switch and begin firing in pyloric time. The functional reorganization of the STG is both rapid and reversible, and the gastric mill motor rhythm is restored when the ganglion is returned to normal saline. Finally, pharmacological manipulations of the NO-cGMP pathway are ineffective when descending modulatory inputs to the STG are blocked. This suggests that the NO-cGMP pathway may interact with other biochemical cascades to partition rhythmic motor output from the ganglion.

}, keywords = {Animals, Arginine, Brachyura, Citrulline, Cyclic GMP, Digestive System, Enzyme Inhibitors, Fluorescent Dyes, Ganglia, Guanylate Cyclase, Immunohistochemistry, Invertebrate, Isoquinolines, Male, Nerve Net, Neurons, Neurotransmitter Agents, Nitric Oxide, Nitric Oxide Donors, Periodicity, Signal Transduction}, issn = {1529-2401}, author = {Scholz, N L and de Vente, J and Truman, J W and Graubard, K} } @article {1785, title = {A novel family of mammalian taste receptors.}, journal = {Cell}, volume = {100}, year = {2000}, month = {2000 Mar 17}, pages = {693-702}, abstract = {

In mammals, taste perception is a major mode of sensory input. We have identified a novel family of 40-80 human and rodent G protein-coupled receptors expressed in subsets of taste receptor cells of the tongue and palate epithelia. These candidate taste receptors (T2Rs) are organized in the genome in clusters and are genetically linked to loci that influence bitter perception in mice and humans. Notably, a single taste receptor cell expresses a large repertoire of T2Rs, suggesting that each cell may be capable of recognizing multiple tastants. T2Rs are exclusively expressed in taste receptor cells that contain the G protein alpha subunit gustducin, implying that they function as gustducin-linked receptors. In the accompanying paper, we demonstrate that T2Rs couple to gustducin in vitro, and respond to bitter tastants in a functional expression assay.

}, keywords = {Amino Acid, Animals, Cell Surface, Chemoreceptor Cells, Cloning, Evolution, G-Protein-Coupled, Gene Expression, GTP-Binding Proteins, Humans, Mammals, Membrane Proteins, Messenger, Mice, Molecular, Molecular Sequence Data, Multigene Family, Rats, Receptors, RNA, Sequence Homology, Taste, Taste Buds, Transducin}, issn = {0092-8674}, author = {Adler, E and Hoon, M A and Mueller, K L and Chandrashekar, J and Ryba, N J and Zuker, C S} } @article {2459, title = {Neuropeptide hierarchies and the activation of sequential motor behaviors in the hawkmoth, Manduca sexta.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {17}, year = {1997}, month = {1997 Jun 1}, pages = {4389-97}, abstract = {

In insects, the shedding of the old cuticle at the end of a molt involves a stereotyped sequence of distinct behaviors. Our studies on the isolated nervous system of Manduca sexta show that the peptides ecdysis-triggering hormone (ETH) and crustacean cardioactive peptide (CCAP) elicit the first two motor behaviors, the pre-ecdysis and ecdysis behaviors, respectively. Exposing isolated abdominal ganglia to ETH resulted in the generation of sustained pre-ecdysis bursts. By contrast, exposing the entire isolated CNS to ETH resulted in the sequential appearance of pre-ecdysis and ecdysis motor outputs. Previous research has shown that ETH activates neurons within the brain that then release eclosion hormone within the CNS. The latter elevates cGMP levels within and increases the excitability of a group of neurons containing CCAP. In our experiments, the ETH-induced onset of ecdysis bursts was always associated with a rise in intracellular cGMP within these CCAP neurons. We also found that CCAP immunoreactivity decreases centrally during normal ecdysis. Isolated, desheathed abdominal ganglia responded to CCAP by generating rhythmical ecdysis bursts. These ecdysis motor bursts persisted as long as CCAP was present and could be reinduced by successive application of the peptide. CCAP exposure also actively terminated pre-ecdysis bursts from the abdominal CNS, even in the continued presence of ETH. Thus, the sequential performance of the two behaviors arises from one modulator activating the first behavior and also initiating the release of the second modulator. The second modulator then turns off the first behavior while activating the second.

}, keywords = {Animal, Animals, Antibody Specificity, Behavior, Calcitonin, Cyclic GMP, Electrophysiology, Ganglia, Insect Hormones, Invertebrate, Larva, Manduca, Molting, Motor Activity, Nervous System, Nervous System Physiological Phenomena, Neuropeptides, Peptide Fragments, Peptides, Sensitivity and Specificity}, issn = {0270-6474}, author = {Gammie, S C and Truman, J W} } @article {2460, title = {Nitric oxide-sensitive guanylate cyclase activity is associated with the maturational phase of neuronal development in insects.}, journal = {Development}, volume = {122}, year = {1996}, month = {1996 Dec}, pages = {3949-58}, abstract = {

Many developing insect neurones pass through a phase when they respond to nitric oxide (NO) by producing cyclic GMP. Studies on identified grasshopper motoneurones show that this NO sensitivity appears after the growth cone has arrived at its target but before it has started to send out branches. NO sensitivity typically ends as synaptogenesis is nearing completion. Data from interneurones and sensory neurones are also consistent with the hypothesis that NO sensitivity appears as a developing neurone changes from axonal outgrowth to maturation and synaptogenesis. Cyclic GMP likely constitutes part of a retrograde signalling pathway between a neurone and its synaptic partner. NO sensitivity also appears in some mature neurones at times when they may be undergoing synaptic rearrangement. Comparative studies on other insects indicate that the association between an NO-sensitive guanylate cyclase and synaptogenesis is an ancient one, as evidenced by its presence in both ancient and more recently evolved insect groups.

}, keywords = {Afferent, Animals, Cyclic GMP, Dihydrolipoamide Dehydrogenase, Drosophila melanogaster, Grasshoppers, Guanylate Cyclase, Insects, Interneurons, Motor Neurons, Nervous System, Neurons, Nitric Oxide, Nitroprusside, Phylogeny}, issn = {0950-1991}, author = {Truman, J W and de Vente, J and Ball, E E} } @article {922, title = {Near-field spectroscopy of the quantum constituents of a luminescent system.}, journal = {Science}, volume = {264}, year = {1994}, month = {1994 Jun 17}, pages = {1740-5}, abstract = {

Luminescent centers with sharp (\<0.07 millielectron volt), spectrally distinct emission lines were imaged in a GaAs/AIGaAs quantum well by means of low-temperature near-field scanning optical microscopy. Temperature, magnetic field, and linewidth measurements establish that these centers arise from excitons laterally localized at interface fluctuations. For sufficiently narrow wells, virtually all emission originates from such centers. Near-field microscopy/spectroscopy provides a means to access energies and homogeneous line widths for the individual eigenstates of these centers, and thus opens a rich area of physics involving quantum resolved systems.

}, issn = {0036-8075}, doi = {10.1126/science.264.5166.1740}, author = {Hess, H F and Betzig, E and Harris, T D and Pfeiffer, L N and West, K W} } @article {2084, title = {Near-field spectroscopy of the quantum constituents of a luminescent system. (With commentary)}, journal = {Science}, volume = {264}, year = {1994}, month = {1994 Jun 17}, pages = {1740-5}, abstract = {

Luminescent centers with sharp (\<0.07 millielectron volt), spectrally distinct emission lines were imaged in a GaAs/AIGaAs quantum well by means of low-temperature near-field scanning optical microscopy. Temperature, magnetic field, and linewidth measurements establish that these centers arise from excitons laterally localized at interface fluctuations. For sufficiently narrow wells, virtually all emission originates from such centers. Near-field microscopy/spectroscopy provides a means to access energies and homogeneous line widths for the individual eigenstates of these centers, and thus opens a rich area of physics involving quantum resolved systems.

Commentary: Harald Hess and I joined forces, combining my near-field optical technology with his cryogenic scanned probe microscope to produce the first paper on high resolution spectroscopy beyond the diffraction limit. We discovered that the broad luminescence spectrum traditionally observed from quantum well heterostructures reflects a resolution-limited ensemble average of emission from numerous discrete sites of exciton recombination occurring at atomic-scale corrugations in the confining interfaces. With the combination of high spatial resolution from near-field excitation and high spectral resolution from cryogenic operation, we were able to isolate these emission sites in a multidimensional space of xy position and wavelength, even though their density was too great to isolate them on the basis of spatial resolution alone. This insight was very influential in the genesis of the concept (see above) that would eventually lead to far-field superresolution by PALM.

}, issn = {0036-8075}, doi = {10.1126/science.264.5166.1740}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17839907}, author = {Hess, H F and Betzig, E and Harris, T D and Pfeiffer, L N and West, K W} } @article {2461, title = {Neuropeptide induction of cyclic GMP increases in the insect CNS: resolution at the level of single identifiable neurons.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {14}, year = {1994}, month = {1994 Dec}, pages = {7704-12}, abstract = {

In insects, the neuropeptide eclosion hormone (EH) acts on the CNS to evoke the stereotyped behaviors that cause ecdysis, the shedding of the cuticle at the end of each molt. Concomitantly, EH induces an increase in cyclic GMP (cGMP). Using antibodies against this second messenger, we show that this increase is confined to a network of 50 peptidergic neurons distributed throughout the CNS. Increases appeared 30 min after EH treatment, spread rapidly throughout these neurons, and were extremely long lived. We show that this response is synaptically driven, and does not involve the soluble, nitric oxide (NO)-activated, guanylate cyclase. Stereotyped variations in the duration of the cGMP response among neurons suggest a role in coordinating responses having different latencies and durations.

}, keywords = {Animals, Central Nervous System, Cyclic GMP, Enzyme Activation, Guanylate Cyclase, Immunohistochemistry, Insect Hormones, Manduca, Neurons, Synapses, Time Factors}, issn = {0270-6474}, author = {Ewer, J and de Vente, J and Truman, J W} } @article {2096, title = {Near-field fluorescence imaging of cytoskeletal actin. (With commentary)}, journal = {Bioimaging}, volume = {1}, year = {1993}, month = {1993 Sep}, pages = {129-35}, abstract = {

Near-field scanning optical microscopy (NSOM) has been used to generate high resolution flourescence images of cytoskeletal actin within fixed mouse fibroblast cells. Comparison with other microscopic methods indicates a transverse resolution well beyond that of confocal microscopy, and contrast far more revealing than in force microscopy. Effects unique to the near field are shown to be involved in the excitation of flourescence, yet the resulting images remain readily interpretable. As an initial demonstration of its utility, the technique is used to analyze the actin-based cytoskeletal structure between stress fibers and in cellular protrusions formed in the process of wound healing.

Commentary: The first superresolution fluorescence imaging of a biological system: the actin cytoskeleton in fixed, cultured fibroblast cells. This work strongly influenced me in two ways. First, calculations based on the signal-to-noise-ratio in images of single actin filaments in the paper suggested that single molecule imaging might be feasible. This was soon proven to be the case (see above). Second, the limitations of exogenous labeling for superresolution microscopy were revealed: samples which appeared correctly stained by conventional microscopy often exhibited sketchy, punctuate labeling of actin filaments as well as substantial non-specific background in the corresponding near field images. Indeed, it was the advent of GFP, with its promise of dense labeling and perfect specificity, that lured me back to superresolution microscopy when I first heard of it in 2003.

}, author = {Betzig, E and Chichester, R J and Lanni, F and Taylor, D L} } @article {45776, title = {Nonfloral sources of chemicals that attract male euglossine bees (Apidae: Euglossini).}, journal = {J Chem Ecol}, volume = {19}, year = {1993}, month = {1993 Dec}, pages = {3017-27}, abstract = {

We present chemical analysis of four rotten or fungus-infected logs that attracted fragrance-collecting male euglossine bees. Eight of the 10 volatile compounds detected have never been found in the fragrances of orchids pollinated by male euglossine bees. Nonfloral sources of chemicals such as rotting wood may constitute an important fragrance resource for male bees. Since rotten logs produce large quantities of chemicals over long periods of time, such nonfloral sources might be more important than flowers as a source of certain fragrances for some euglossine bee species. Fragrance collecting in euglossine bees might have evolved originally in relation with rotting wood rather than flowers.

}, issn = {0098-0331}, doi = {10.1007/BF00980599}, author = {Whitten, W M and Young, A M and Stern, D L} } @article {2097, title = {Near-field magneto-optics and high density data storage. (With commentary)}, journal = {Applied Physics Letters.}, volume = {61}, year = {1992}, month = {1992}, abstract = {

Near-field scanning optical microscopy (NSOM) has been used to image and record domains in thin-film magneto-optic (MO) materials. In the imaging mode, resolution of 30-50 nm has been consistently obtained, whereas in the recording mode, domains down to -60 nm have been written reproducibly. Data densities of -45 Gbits/in.{\textquoteright} have been achieved, well in excess\ of current magnetic or MO technologies. A brief analysis of speed and other issues indicates that the technique may represent a viable alternative to density data storage needs.

Commentary: The first demonstration of optical recording and playback beyond the diffraction limit, using magneto-optic multilayer films and polarization contrast near-field microscopy. Bits as small as 60 nm were recorded {\textendash} beyond estimates at the time of the superparamagnetic limit to bit stability. Bit densities of 45 Gbits/in2 were also achieved, well in excess of optical or magnetic recording technologies of the era. In the years following this work, massive resources were spent on the commercialization of near-field data storage, largely for naught.

}, author = {Betzig, E and Trautman, J K and Wolfe, R and Gyorgy, E M and Finn, P L and Kryder, M H and Chang, C H} } @article {2093, title = {Near-field optics: microscopy, spectroscopy, and surface modification beyond the diffraction limit. (With commentary)}, journal = {Science}, volume = {257}, year = {1992}, month = {1992 Jul 10}, pages = {189-95}, abstract = {

The near-field optical interaction between a sharp probe and a sample of interest can be exploited to image, spectroscopically probe, or modify surfaces at a resolution (down to approximately 12 nm) inaccessible by traditional far-field techniques. Many of the attractive features of conventional optics are retained, including noninvasiveness, reliability, and low cost. In addition, most optical contrast mechanisms can be extended to the near-field regime, resulting in a technique of considerable versatility. This versatility is demonstrated by several examples, such as the imaging of nanometric-scale features in mammalian tissue sections and the creation of ultrasmall, magneto-optic domains having implications for highdensity data storage. Although the technique may find uses in many diverse fields, two of the most exciting possibilities are localized optical spectroscopy of semiconductors and the fluorescence imaging of living cells.

Commentary: An overview of our work in near-field optics at the time, after our invention of the adiabatically tapered fiber probe and shear force feedback (see below) led to the first practical near-field scanning optical microscope. In this work, superresolution imaging via absorption, reflectivity, fluorescence, spectroscopy, polarization, and refractive index contrast were all demonstrated. Unlike all far-field superresolution fluorescence methods that were to appear a decade later, near-field microscopy remains the only superresolution technique capable of taking advantage of the full panoply of optical contrast mechanisms.

}, issn = {0036-8075}, doi = {10.1126/science.257.5067.189}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17794749}, author = {Betzig, E and Trautman, J K} } @article {984, title = {The nucleotide sequence of Saccharomyces cerevisiae 5.8 S ribosomal ribonucleic acid.}, journal = {The Journal of Biological Chemistry}, volume = {248}, year = {1973}, month = {1973 Jun 10}, pages = {3860-75}, keywords = {Autoradiography, Base Sequence, Chemical Phenomena, Chemistry, Coliphages, Drug Stability, Electrophoresis, Models, Oligonucleotides, Pancreas, Phosphorus Isotopes, Polyacrylamide Gel, Ribonucleases, Ribonucleotides, Ribosomal, RNA, Saccharomyces cerevisiae, Species Specificity, Structural}, issn = {0021-9258}, doi = {10.1186/gb-2007-8-7-r145}, author = {Rubin, G M} } @article {2467, title = {Neuroendocrine control of ecdysis in silkmoths.}, journal = {Science}, volume = {167}, year = {1970}, month = {1970 Mar 20}, pages = {1624-6}, abstract = {

An adult moth sheds its pupal skin only during a specific period of the day. The brain is necessary for the synchronization of this behavior with the environmental photoperiod. This function is fully preserved when all the brain{\textquoteright}s nervous connections are severed or when a "loose" brain is transplanted into the tip of the abdomen. By appropriate experiments it was possible to show that the entire mechanism is brain-centered. The components include a photoreceptor mechanism, a clock, and a neuroendocrine output. The clock-controlled release of the hormone acts on the central nervous system to trigger a species-specific behavior pattern which culminates in ecdysis.

}, issn = {0036-8075}, doi = {10.1126/science.167.3925.1624}, author = {Truman, J W and Riddiford, L M} }