@article {70284, title = {Astrocyte-induced internal state transitions reshape brainwide sensory, integrative, and motor computations}, journal = {bioRxiv}, year = {2026}, month = {2026 Feb 05}, abstract = {

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

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

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

}, doi = {10.1016/j.bpj.2025.11.2270}, url = {https://doi.org/10.1016/j.bpj.2025.11.2270}, author = {Yserentant, Klaus and Chen, Yuda and Hong, Kibeom and Kuang, Yiming and Bhowmick, Arghya and Charles-Orszag, Arthur and Lord, Samuel J. and Lu, Lei and Hou, Kaipeng and Mann, Samuel I and Grimm, Jonathan B and Lavis, Luke D and Mullins, R. Dyche and DeGrado, William F and Huang, Bo} } @article {70313, title = {BPS2026 {\textendash} Real-time visualization and analysis of fibrin polymerization}, journal = {Biophysical Journal}, volume = {125}, year = {2026}, month = {Jan-02-2026}, pages = {227a - 228a}, abstract = {

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

}, issn = {00063495}, doi = {10.1016/j.bpj.2025.11.1510}, url = {https://doi.org/10.1016/j.bpj.2025.11.1510}, author = {Miller, Dylan M. and Elangovan, Aravind and Belcher, Heather A. and Lee, Rachel M. and Hobson, Chad M. and Crosley, Key and Hart, David M. and Laverty, Brittany Bannish E. and Guthold, Martin and Hudson, Nathan E.} } @article {70309, title = {Brain-wide hierarchical and sexually dimorphic tuning for social vocalizations}, journal = {bioRxiv}, year = {2026}, month = {2026 Mar 04}, abstract = {

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

}, doi = {10.64898/2026.03.04.709502}, url = {https://www.biorxiv.org/content/early/2026/03/04/2026.03.04.709502}, author = {Henninger, Jorg and Hoffmann, Maximilian and Kadobianskyi, Mykola and Veith, Johannes and Berlage, Caroline and Groneberg, Antonia and Markov, Daniil and Schulze, Lisanne and Svanidze, Ana and Maler, Leonard and Judkewitz, Benjamin} } @article {70292, title = {Correlates of head-fixed directional forelimb movements in mouse superior colliculus and substantia nigra pars reticulata.}, journal = {Neuroscience}, year = {2026}, month = {2026 Feb 12}, abstract = {

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

}, issn = {1873-7544}, doi = {10.1016/j.neuroscience.2026.02.010}, url = {https://doi.org/10.1016/j.neuroscience.2026.02.010}, author = {Doykos, Ted K and Yamauchi, Taylor and Buteau, Anna and Hanson, Spencer and Dudman, Joshua T and Felsen, Gidon and Stubblefield, Elizabeth A} } @article {70303, title = {A dual-color miniature endoscope for calcium imaging in behaving mice}, journal = {iScience}, year = {2026}, month = {2026 Mar 28}, abstract = {

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

}, doi = {10.1016/j.isci.2026.115514}, url = {https://doi.org/10.1016/j.isci.2026.115514}, author = {Zhang, Jinyong and Hong, Feiyang and Kim, Jiwon and Bakhurin, Konstantin and Kim, Namsoo and Yin, Henry H.} } @article {70315, title = {Evolutionarily conserved neural dynamics across mice, monkeys, and humans}, journal = {bioRxiv}, year = {2026}, month = {2026 Mar 07}, abstract = {

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

}, doi = {10.64898/2026.03.06.709637}, url = {https://www.biorxiv.org/content/early/2026/03/07/2026.03.06.709637}, author = {Codol, Olivier and Asclipe, Margaux and Sobinov, Anton R. and Chen, Zihao and Park, Junchol and Hatsopoulos, Nicholas G. and Dudman, Joshua T. and Gallego, Juan A. and Lajoie, Guillaume and Perich, Matthew G.} } @article {70244, title = {Fast dendritic excitations primarily mediate back-propagation in CA1 pyramidal neurons during behavior}, journal = {bioRxiv}, year = {2026}, month = {2026 Jan 03}, abstract = {

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

}, doi = {10.64898/2026.01.03.696606}, url = {https://www.biorxiv.org/content/early/2026/01/03/2026.01.03.696606}, author = {Lee, Byung Hun and Park, Pojeong and Wu, Xiang and Wong-Campos, J. David and Xu, Junjie and Xiong, Marley and Qi, Yitong and Huang, Yi-Chieh and Itkis, Daniel G. and Plutkis, Sarah E. and Lavis, Luke D. and Cohen, Adam E.} } @article {70093, title = {iGABASnFR2 is an improved genetically encoded protein sensor of GABA}, journal = {eLife}, year = {2026}, month = {2026 Mar 18}, abstract = {

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

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

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

}, doi = {10.64898/2026.03.11.711125}, url = {https://www.biorxiv.org/content/early/2026/03/14/2026.03.11.711125}, author = {Shtengel, David H. and Shtengel, Gleb and Xu, C. Shan and Hess, Harald F.} } @article {70316, title = {Measuring Amorphous Motion: Application of Optical Flow to Three-Dimensional Fluorescence Microscopy Images}, journal = {bioRxiv}, year = {2026}, month = {2026 Mar 10}, abstract = {

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

}, doi = {10.64898/2026.03.06.710169}, url = {https://www.biorxiv.org/content/early/2026/03/10/2026.03.06.710169}, author = {Lee, Rachel M and Eisenman, Leanna R. and Hobson, Chad and Aaron, Jesse S. and Chew, Teng-Leong} } @article {70333, title = {Midgestation metabolic constraint in purine metabolism drives distinct strategies for placenta and fetal growth}, journal = {bioRxiv}, year = {2026}, month = {2026 Mar 18}, abstract = {

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

}, doi = {10.64898/2026.03.18.712680}, url = {https://www.biorxiv.org/content/early/2026/03/18/2026.03.18.712680}, author = {Xu, Weizhi and De La Cruz, Nancy and Woods, Andrea and Lokshtanov, Dmitry and Gao, Shihong and Khan, Nawal and Wright, Sylvia and Florian-Rodriguez, Maria E. and McIntire, Donald D. and Duryea, Elaine L and Nelson, David B. and Spong, Catherine Y. and Herrera, Christina L. and Hanna, Jacob H. and Srivatsan, Sanjay and Aguilera-Castrejon, Alejandro and Solmonson, Ashley} } @article {70256, title = {Model-agnostic linear-memory online learning in spiking neural networks.}, journal = {Nat Commun}, year = {2026}, month = {2026 Jan 19}, abstract = {

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

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

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

}, doi = {10.64898/2026.01.02.697412}, url = {https://www.biorxiv.org/content/early/2026/01/02/2026.01.02.697412}, author = {Choi, Heejun and Halanych, Coral and Kasberg, William and Testa, Michael D. and Rubin-Elgressy, Sarah and Nguyen, Phuong and Walpita, Deepika and Tsang, Arthur and Cortes, Dan and Song, Erin Yue and Wu, Haodi and Weissman, Irving L and Espinosa-Medina, Isabel and Satou, Chie and Song, Jia L. and Matus, David Q. and Lippincott-Schwartz, Jennifer} } @article {70311, title = {A multi-resolution imaging and analysis pipeline for comparative circuit reconstruction in insects}, journal = {bioRxiv}, year = {2026}, month = {2026 Feb 28}, abstract = {

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

}, doi = {10.64898/2026.02.25.708065}, url = {https://www.biorxiv.org/content/early/2026/02/28/2026.02.25.708065}, author = {Gillet, Valentin and Sayre, Marcel E. and Badalamente, Griffin S. and Schieber, Nicole L. and Tedore, Kevin and Funke, Jan and Heinze, Stanley} } @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 {70340, title = {Rapidly evolving aphid gall effector proteins exhibit saposin-like folds}, journal = {bioRxiv}, year = {2026}, month = {2026 Mar 28}, abstract = {

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

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

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

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

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

}, doi = {10.64898/2026.03.17.710314}, url = {https://www.biorxiv.org/content/early/2026/03/18/2026.03.17.710314}, author = {Lokshtanov, Dmitry and Gao, Shihong Max and Xu, Weizhi and Kosman, Avraham and Roncato, Francesco and De La Cruz, Nancy and Khan, Nawal A. and Woods, Andrea and Campbell, Ian and Woehler, Andrew and Christoforou, Christina and Ding, Lang and Hu, Amy and Copeland, Monique and Wang, Lihua and Yang, Xiushuai and Raley, Castle and Delventhal, Kym M. and Herrera, Antonio and Valente, Alessandro and Wright, Sylvia and Gomez-Cesar, Elidet and Shlomo, Raanan and Golenchenko, Sergey and Oldak, Bernardo and Yilmaz, Alperen and Gurhan-Sebinc, Gulben and Comar, Mehmet-Yunus and Viukov, Sergey and Novershtern, Noa and Zhang, Hua and Duong, Thao and Li, Lingjun and Khatib, Nizar and Kakun, Reli Rachel and Espinosa-Medina, Isabel and Florian-Rodriguez, Maria E. and LaManno, Gioele and Tillberg, Paul W. and Wang, Meng C. and Maza, Itay and Srivatsan, Sanjay and Solmonson, Ashley and Hanna, Jacob H. and Aguilera-Castrejon, Alejandro} } @article {70251, title = {SCREWx: A Screwless, Chronic, Recoverable, and Lightweight Neuropixels fixture for freely-moving rodents}, journal = {bioRxiv}, year = {2026}, month = {2026 Jan 06}, abstract = {

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

}, doi = {10.64898/2026.01.06.697790}, url = {https://www.biorxiv.org/content/early/2026/01/06/2026.01.06.697790}, author = {Cheng, Alexandra and DeWeese, Tate and Zhou, Yueqing and Sueoka, Yotaro and Koukuntla, Sai and Green, Merrill and Cullen, Kathleen and Knierim, James and Graves, Austin and Harris, Timothy} } @article {70310, title = {Structural Basis for C8 methylation of 23S ribosomal RNA by Cfr}, journal = {bioRxiv}, year = {2026}, month = {2026 Mar 02}, abstract = {

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

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

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

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2026.116947}, url = {https://doi.org/10.1016/j.celrep.2026.116947}, author = {Herrera, Kristian J and Zarghani-Shiraz, Arman and Ahrens, Misha B and Engert, Florian and Fishman, Mark C} } @article {70329, title = {Unstructured transcription factor interactions enable emergent specificity.}, journal = {Science}, year = {2026}, month = {2026 Mar 19}, pages = {eaeb6487}, abstract = {

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

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

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

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

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

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

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

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

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

}, doi = {10.1101/2025.05.16.654254}, url = {https://www.biorxiv.org/content/early/2025/05/21/2025.05.16.654254}, author = {Januszewski, Micha{\l} and Templier, Thomas and Hayworth, Kenneth Jeffrey and Peale, David and Hess, Harald} } @article {70129, title = {Alternating angle milling suppresses streaking artifacts in FIB-SEM imaging}, journal = {bioRxiv}, year = {2025}, month = {2025 Sep 26}, abstract = {

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

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

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

}, doi = {10.1200/JCO.2025.43.16_suppl.e13028}, url = {https://ascopubs.org/doi/abs/10.1200/JCO.2025.43.16_suppl.e13028}, author = {Liu, Huiping and Squires, Joshua and Sun, Yuanfei and Hoffmann, Andrew Daniel and Zhang, Youbin and Platanias, Leonidas C. and Gradishar, William John and Cristofanilli, Massimo and Stringer, Carsen} } @article {69848, title = {A Bayesian model to count the number of two-state emitters in a diffraction limited spot.}, journal = {Nano Lett}, year = {2025}, month = {2025 Apr 04}, abstract = {

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

}, issn = {1530-6992}, doi = {10.1021/acs.nanolett.4c06304}, url = {https://doi.org/10.1021/acs.nanolett.4c06304}, author = {Hillsley, Alexander and Stein, Johannes and Tillberg, Paul W and Stern, David L and Funke, Jan} } @article {69744, title = {Bio-inspired 3D-printed phantom: Encoding cellular heterogeneity for characterization of quantitative phase imaging}, journal = {Measurement}, volume = {247}, year = {2025}, month = {2025 Apr 15}, pages = {116765}, abstract = {

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

}, keywords = {Cell phantom, Inter-laboratory comparison, Metrology, Phase calibration target, Quantitative phase imaging, Two-photon polymerization lithography}, issn = {0263-2241}, doi = {10.1016/j.measurement.2025.116765}, url = {https://www.sciencedirect.com/science/article/pii/S0263224125001241}, author = {Sylvia Desissaire and Micha{\l} Ziemczonok and Tigrane Cantat-Moltrecht and Arkadiusz Ku{\'s} and Guillaume Godefroy and Lionel Herv{\'e} and Chiara Paviolo and Wojciech Krauze and C{\'e}dric Allier and Ondrej Mandula and Ma{\l}gorzata Kujawi{\'n}ska} } @article {70185, title = {The CENP-A chaperone complex spatially organizes centromeres}, journal = {bioRxiv}, year = {2025}, month = {2026 Nov 09}, abstract = {

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

}, doi = {10.1101/2025.11.07.687291}, url = {https://www.biorxiv.org/content/early/2025/11/09/2025.11.07.687291}, author = {Gupta, Hindol and Haase, Julian and Wu, Yicong and Chen, Jiji and Karadimov, George and Shroff, Hari and Kelly, Alexander E.} } @article {70184, title = {Chemical modulation of gut bacterial metabolism induces colanic acid and extends the lifespan of nematode and mammalian hosts.}, journal = {PLoS Biol}, volume = {23}, year = {2025}, month = {2025 Nov 11}, pages = {e3002749}, abstract = {

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

}, keywords = {Animals, Caenorhabditis elegans, Escherichia coli, Gastrointestinal Microbiome, Longevity, Mice, Polysaccharides}, issn = {1545-7885}, doi = {10.1371/journal.pbio.3002749}, url = {https://doi.org/10.1371/journal.pbio.3002749}, author = {Hu, Guo and Savini, Marzia and Cooke, Matthew Brandon and Wei, Xin and Deng, Dinghuan and Gao, Shihong M and Xia, Ruyue Alps and Guan, Youchen and Wen, Alice X and Yu, Xin and Wang, Jin and Jiang, Chao and Herman, Christophe and Li, Jiefu and Wang, Meng C} } @article {69902, title = {Chromatix: A differentiable, GPU-accelerated wave-optics library}, journal = {bioRxiv}, year = {2025}, month = {2025 May 2}, abstract = {

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

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

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

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

}, issn = {2160-1836}, doi = {10.1093/g3journal/jkaf232}, url = {https://doi.org/10.1093/g3journal/jkaf232}, author = {Glendening, Adam M and Stephens, Cole and Vuruputoor, Vidya S and Chaganti, Tesko and Myles, Meghan N and Stern, David L and Abdelalim, Muhammad and Juang, Yu-Pu and Hogenhout, Saskia A and Mathers, Thomas C and Pauloski, Nicole and Cernak, Tim A and Wegrzyn, Jill L and Fetter, Karl C} } @article {70130, title = {Combinatorial protein barcodes enable self-correcting neuron tracing with nanoscale molecular context}, journal = {bioRxiv}, year = {2025}, month = {2025 Sep 28}, abstract = {

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

}, doi = {10.1101/2025.09.26.678648}, url = {https://www.biorxiv.org/content/early/2025/09/28/2025.09.26.678648}, author = {Park, Sung Yun and Sheridan, Arlo and An, Bobae and Jarvis, Erin and Lyudchik, Julia and Patton, William and Axup, Jun Y. and Chan, Stephanie W. and Damstra, Hugo G.J. and Leible, Daniel and Leung, Kylie S. and Magno, Clarence A. and Meeran, Aashir and Michalska, Julia M. and Rieger, Franz and Wang, Claire and Wu, Michelle and Church, George M. and Funke, Jan and Huffman, Todd and Leeper, Kathleen G.C. and Truckenbrodt, Sven and Winnubst, Johan and Kornfeld, Joergen M.R. and Boyden, Edward S. and Rodriques, Samuel G. and Payne, Andrew C.} } @article {70118, title = {Composing trajectories for rapid inference of navigational goals}, journal = {bioRxiv}, year = {2025}, month = {2025 Sep 24}, abstract = {

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

}, doi = {10.1101/2025.09.24.678123}, url = {https://www.biorxiv.org/content/early/2025/09/24/2025.09.24.678123}, author = {AbdelRahman, Nada Y and Jiang, Wanchen and Coddington, Luke T and Gong, Sheng and Dudman, Joshua T and Hermundstad, Ann M} } @article {70138, title = {The connectome interpreter toolkit}, journal = {bioRxiv}, year = {2025}, month = {2025 Sep 30}, abstract = {

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

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

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

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

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

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

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

}, keywords = {Adenine, Agammaglobulinaemia Tyrosine Kinase, High-Throughput Screening Assays, Humans, Kinetics, Mass Spectrometry, Piperidines, Protein Binding, Protein Kinase Inhibitors, Proteome, Proteomics, Pyrazoles, Pyrimidines}, issn = {2041-1723}, doi = {10.1038/s41467-025-63491-2}, url = {https://doi.org/10.1038/s41467-025-63491-2}, author = {Lin, Hanfeng and Yang, Bin and Ding, Lang and Yang, Yen-Yu and Holt, Matthew V and Jung, Sung Yun and Zhang, Bing and Wang, Meng C and Wang, Jin} } @article {69985, title = {Cross-species comparative connectomics reveals the evolution of an olfactory circuit}, journal = {bioRxiv}, year = {2025}, month = {2025 Jun 11}, abstract = {

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

}, doi = {10.1101/2025.06.11.659158}, url = {https://www.biorxiv.org/content/early/2025/06/11/2025.06.11.659158}, author = {Roberts, Ruairi and Giez, Christoph and Dhawan, Serene and Pang, Song and Randel, Nadine and Zhiyuan, Lu and Gong, Hui and Dekens, Leonard and DiFrisco, James and Xu, C Shan and Hess, Harald and Zlatic, Marta and Cardona, Albert and Prieto-Godino, Lucia L.} } @article {69722, title = {Days-old zebrafish rapidly learn to recognize threatening agents through noradrenergic and forebrain circuits.}, journal = {Curr Biol}, volume = {35}, year = {2025}, month = {12/2024}, pages = {163-176.e4}, abstract = {

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

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

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

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

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

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

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

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

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

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

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

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

}, doi = {10.1038/s41467-025-55819-9}, url = {https://www.biorxiv.org/content/early/2024/05/18/2023.06.02.543490}, author = {Park, Pojeong and Wong-Campos, David and Itkis, Daniel G. and Lee, Byung Hun and Qi, Yitong and Davis, Hunter and Antin, Benjamin and Pasarkar, Amol and Grimm, Jonathan B. and Plutkis, Sarah E. and Holland, Katie L. and Paninski, Liam and Lavis, Luke D. and Cohen, Adam E.} } @article {70047, title = {Distributed control circuits across a brain-and-cord connectome}, journal = {bioRxiv}, year = {2025}, month = {2025 Aug 02}, abstract = {

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

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

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

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

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

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

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

}, issn = {2692-8205}, doi = {10.1101/2025.09.22.677693}, url = {https://doi.org/10.7554/eLife.109362.1}, author = {Hernandez-Nunez, L and Avrami, J and Shi, S and Markarian, A and Ruetten, Virginia M.S. and Boulanger-Weill, J and Zarghani-Shiraz, A and Ahrens, M and Engert, F and Fishman, M C} } @article {70223, title = {Environmental dynamics impact whether matching is optimal}, journal = {PNAS Nexus}, year = {2025}, month = {2025 Dec 17}, pages = {pgaf392}, abstract = {

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

}, issn = {2752-6542}, doi = {10.1093/pnasnexus/pgaf392}, url = {https://doi.org/10.1093/pnasnexus/pgaf392}, author = {Guo, Yipei and Hermundstad, Ann M} } @article {70083, title = {An expanded palette of bright and photostable organellar Ca2+ sensors}, journal = {eLife}, year = {2025}, month = {2025 Aug 26}, abstract = {

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

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

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

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

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

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

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

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

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

}, doi = {10.1101/2025.04.20.649718}, url = {https://www.biorxiv.org/content/early/2025/04/21/2025.04.20.649718}, author = {Moore, Andrew S. and Krug, Tommy and Hansen, Simon B. and Ludlow, Alexander V. and Grimm, Jonathan B. and Ayala, Anthony X. and Plutkis, Sarah E. and Wang, Nan and Goldman, Robert D. and Medalia, Ohad and Lavis, Luke D. and Weitz, David A. and Lippincott-Schwartz, Jennifer} } @article {69629, title = {The first complete 3D reconstruction and morphofunctional mapping of an insect eye}, journal = {eLife}, year = {2025}, month = {2025 May 1}, abstract = {

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

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

}, doi = {10.7554/elife.103247}, url = {https://doi.org/10.7554/elife.103247}, author = {Makarova, Anastasia A. and Chua, Nicholas J. and Diakova, Anna V. and Desyatirkina, Inna A. and Gunn, Pat and Pang, Song and Xu, C Shan and Hess, Harald F and Chklovskii, Dmitri B. and Polilov, Alexey A.} } @article {69723, title = {The first complete 3D reconstruction and morphofunctional mapping of an insect eye}, year = {2025}, month = {01/2025}, doi = {10.7554/elife.103247.1}, url = {http://dx.doi.org/10.7554/eLife.103247.1}, author = {Makarova, Anastasia A and Chua, Nicholas J and Diakova, Anna V and Desyatirkina, Inna A and Gunn, Pat and Pang, Song and Xu, C Shan and Hess, Harald and Chklovskii, Dmitri B and Polilov, Alexey A} } @article {70031, title = {Fishexplorer: A multimodal cellular atlas platform for neuronal circuit dissection in larval zebrafish}, journal = {bioRxiv}, year = {2025}, month = {2025 Jul 14}, abstract = {

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

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

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

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

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

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

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

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

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

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

}, issn = {1548-7105}, doi = {10.1038/s41592-025-02844-7}, url = {https://doi.org/10.1038/s41592-025-02844-7}, author = {Alshaabi, Thayer and Milkie, Daniel E and Liu, Gaoxiang and Shirazinejad, Cyna and Hong, Jason L and Achour, Kemal and G{\"o}rlitz, Frederik and Milunovic-Jevtic, Ana and Simmons, Cat and Abuzahriyeh, Ibrahim S and Hong, Erin and Williams, Samara Erin and Harrison, Nathanael and Huang, Evan and Bae, Eun Seok and Killilea, Alison N and Swinburne, Ian A and Drubin, David G and Upadhyayula, Srigokul and Betzig, Eric} } @article {70101, title = {Functional synapses between neurons and small cell lung cancer.}, journal = {Nature}, year = {2025}, month = {2025 Sep 10}, abstract = {

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

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

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

}, issn = {1754-8411}, doi = {10.1242/dmm.052329}, url = {https://doi.org/10.1242/dmm.052329}, author = {Banerjee, Animesh and Chatterjee, Moumita and Tan, Kah Junn and Tay, Shermaine and Duan, Kaibo and Andiappan, Anand Kumar and Howland, Shanshan Wu and Aso, Yoshinori and Aw, Sherry Shiying} } @article {69833, title = {Glutamate indicators with increased sensitivity and tailored deactivation rates}, journal = {Nat Methods}, year = {2025}, month = {2025 Dec 23}, abstract = {

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

}, doi = {10.1038/s41592-025-02965-z}, url = {https://doi.org/10.1038/s41592-025-02965-z}, author = {Aggarwal, Abhi and Negrean, Adrian and Chen, Yang and Iyer, Rishyashring and Reep, Daniel and Liu, Anyi and Palutla, Anirudh and Xie, Michael E. and MacLennan, Bryan J. and Hagihara, Kenta M. and Kinsey, Lucas W. and Sun, Julianna L. and Yao, Pantong and Zheng, Jihong and Tsang, Arthur and Tsegaye, Getahun and Zhang, Yonghai and Patel, Ronak H. and Arthur, Benjamin J. and Hiblot, Julien and Leippe, Philipp and Tarnawski, Miroslaw and Marvin, Jonathan S. and Vevea, Jason D. and Turaga, Srinivas C. and Tebo, Alison G. and Carandini, Matteo and Rossi, L. F. and Kleinfeld, David and Konnerth, Arthur and Svoboda, Karel and Turner, Glenn C. and Hasseman, Jeremy and Podgorski, Kaspar} } @article {69856, title = {Glutamate indicators with increased sensitivity and tailored deactivation rates}, journal = {Research Square}, year = {2025}, month = {2025 Apr 8}, abstract = {

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

}, doi = {10.21203/rs.3.rs-6257403/v1}, url = {https://doi.org/10.21203/rs.3.rs-6257403/v1}, author = {Podgorski, Kaspar and Aggarwal, Abhi and Negrean, Adrian and Chen, Yang and Iyer, Rishyashring and Reep, Daniel and Liu, Anyi and Palutla, Anirudh and Xie, Michael and Maclennan, Bryan and Hagihara, Kenta and Kinsey, Lucas and Sun, Julianna and Yao, Pantong and Zheng, Jihong and Tsang, Arthur and Tsegaye, Getahun and Zhang, Yonghai and Patel, Ronak and Hasseman, Jeremy} } @article {69720, title = {HD2Net: A deep learning framework for simultaneous denoising and deaberration in fluorescence microscopy}, journal = {bioRxiv}, year = {2025}, month = {01/2025}, abstract = {

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

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

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

}, doi = {10.1101/2025.01.06.631475}, url = {https://www.biorxiv.org/content/early/2025/01/08/2025.01.06.631475}, author = {Hou, Xuekai and Li, Yue and Hobson, Chad M. and Shroff, Hari and Guo, Min and Liu, Huafeng} } @article {70016, title = {How short peptides disassemble tau fibrils in Alzheimer{\textquoteright}s disease}, journal = {Nature}, year = {2025}, month = {2025 Jul 09}, abstract = {

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

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

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

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

}, doi = {10.1101/2025.03.25.644953}, url = {https://www.biorxiv.org/content/early/2025/03/26/2025.03.25.644953}, author = {Kolb, Ilya and Hasseman, Jeremy P. and Matsumoto, Akihiro and Arthur, Benjamin J. and Zhang, Yan and Tsang, Arthur and Reep, Daniel and Tsegaye, Getahun and Zheng, Jihong and Patel, Ronak and Looger, Loren L. and Marvin, Jonathan S. and Korff, Wyatt L. and Yonehara, Keisuke and Turner, Glenn C.} } @article {70084, title = {Imaging cellular activity simultaneously across all organs of a vertebrate reveals body-wide circuits}, journal = {bioRxiv}, year = {2025}, month = {2025 August 22}, abstract = {

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

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

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

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

}, doi = {10.1038/s41592-025-02692-5}, url = {https://doi.org/10.1038/s41592-025-02692-5}, author = {Tsai-Wen Chen and Xian-Bin Huang and Sarah E. Plutkis and Katie L. Holland and Luke D. Lavis and Bei-Jung Lin} } @article {70139, title = {In-situ glial cell-surface proteomics identifies pro-longevity factors in Drosophila}, journal = {eLife}, year = {2025}, month = {2025 Dec 12}, abstract = {

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

}, doi = {10.7554/eLife.109422.1}, url = {https://doi.org/10.7554/eLife.109422.1}, author = {Marques, Madeline P. and Sun, Bo and Park, Ye-Jin and Jackson, Tyler and Lu, Tzu-Chiao and Qi, Yanyan and Harrison, Erin and Wang, Miranda C. and Venkatachalam, Kartik and Pasha, Omar Moussa and Varanasi, Amogh and Carey, Dominique Kiki and Mani, D.R. and Zirin, Jonathan and Qadiri, Mujeeb and Hu, Yanhui and Perrimon, Norbert and Carr, Steven A. and Udeshi, Namrata D. and Luo, Liqun and Li, Jiefu and Li, Hongjie} } @article {70116, title = {stk32a links sleep homeostasis to suppression of sensory and motor systems}, journal = {bioRxiv}, year = {2025}, month = {2025 Sep 11}, abstract = {

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

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

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

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

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

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

}, issn = {1546-1726}, doi = {10.1038/s41593-025-01976-5}, url = {https://doi.org/10.1038/s41593-025-01976-5}, author = {Trautmann, Eric M and Hesse, Janis K and Stine, Gabriel M and Xia, Ruobing and Zhu, Shude and O{\textquoteright}Shea, Daniel J and Karsh, Bill and Colonell, Jennifer and Lanfranchi, Frank F and Vyas, Saurabh and Zimnik, Andrew and Amematsro, Elom and Steinemann, Natalie A and Wagenaar, Daniel A and Pachitariu, Marius and Andrei, Alexandru and Lopez, Carolina Mora and O{\textquoteright}Callaghan, John and Putzeys, Jan and Raducanu, Bogdan C and Welkenhuysen, Marleen and Churchland, Mark and Moore, Tirin and Shadlen, Michael and Shenoy, Krishna and Tsao, Doris and Dutta, Barundeb and Harris, Timothy} } @article {69656, title = {Leukocytes use endothelial membrane tunnels to extravasate the vasculature}, journal = {Cell Rep}, year = {2025}, month = {2025 Sep 04}, abstract = {

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

}, doi = {10.1016/j.celrep.2025.116242}, url = {https://doi.org/10.1016/j.celrep.2025.116242}, author = {van der Meer, Werner and van Steen, Abraham C.I. and Mahlandt, Eike and Rolas, Loic and Wang, Haitao and Arts, Janine and Kempers, Lanette and Gr{\"o}nloh, Max and Schoon, Rianne M. and Driessen, Amber and van Rijssel, Jos and Klaassen, Ingeborg and Schlingemann, Reinier O. and Manavski, Yosif and Hoogenboezem, Mark and Boon, Reinier A. and Khuon, Satya and Wait, Eric and Heddleston, John and Chew, Teng-Leong and Nolte, Martijn A and Nourshargh, Sussan and Goedhart, Joachim and van Buul, Jaap D} } @article {69423, title = {Live-cell single-molecule fluorescence microscopy for protruding organelles reveals regulatory mechanisms of MYO7A-driven cargo transport in stereocilia of inner ear hair cells}, journal = {Nat Commun}, year = {2025}, month = {2025 Sep 01}, abstract = {

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

}, doi = {10.1038/s41467-025-63102-0}, url = {https://doi.org/10.1038/s41467-025-63102-0}, author = {Takushi Miyoshi and Harshad D Vishwasrao and Inna A Belyantseva and Mrudhula Sajeevadathan and Yasuko Ishibashi and Samuel M Adadey and Narinobu Harada and Hari Shroff and Thomas B Friedman} } @article {69782, title = {Melanocortin 3 receptor regulates hepatic autophagy and systemic adiposity.}, journal = {Nat Commun}, volume = {16}, year = {2025}, month = {2025 Feb 16}, pages = {1690}, abstract = {

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

}, keywords = {Adiposity, Animals, Autophagosomes, Autophagy, Basic Helix-Loop-Helix Leucine Zipper Transcription Factors, Female, Hepatocytes, Humans, Lipid Metabolism, Liver, Male, Mice, Mice, Inbred C57BL, Mice, Knockout, Microtubule-Associated Proteins, Obesity, Receptor, Melanocortin, Type 3, Triglycerides}, issn = {2041-1723}, doi = {10.1038/s41467-025-56936-1}, author = {Patel, Tushar P and Jun, Joo Yun and Seo, Arnold Y and Levi, Noah J and Elizondo, Diana M and Chen, Jocelyn and Wong, Adrian M and Tugarinov, Nicol and Altman, Elizabeth K and Gehle, Daniel B and Jung, Sun Min and Patel, Pooja and Ericson, Mark and Haskell-Luevano, Carrie and Demby, Tamar C and Cougnoux, Antony and Wolska, Anna and Yanovski, Jack A} } @article {70039, title = {MicroSplit: Semantic Unmixing of Fluorescent Microscopy Data}, journal = {bioRxiv}, year = {2025}, month = {2025 Jul 21}, abstract = {

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

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

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

Preprint:\ 10.1101/2025.02.22.639343

}, keywords = {Animals, CRISPR-Cas Systems, Cryoelectron Microscopy, Endoplasmic Reticulum, HEK293 Cells, Hela Cells, Humans, Membrane Proteins, Mitochondria, Mitochondrial Membranes, Proteomics, Tacrolimus Binding Proteins}, issn = {2041-1723}, doi = {10.1038/s41467-025-58538-3}, url = {https://doi.org/10.1038/s41467-025-58538-3}, author = {Nakamura, Koki and Aoyama-Ishiwatari, Saeko and Nagao, Takahiro and Paaran, Mohammadreza and Obara, Christopher J and Sakurai-Saito, Yui and Johnston, Jake and Du, Yudan and Suga, Shogo and Tsuboi, Masafumi and Nakakido, Makoto and Tsumoto, Kouhei and Kishi, Yusuke and Gotoh, Yukiko and Kwak, Chulhwan and Rhee, Hyun-Woo and Seo, Jeong Kon and Kosako, Hidetaka and Potter, Clint and Carragher, Bridget and Lippincott-Schwartz, Jennifer and Polleux, Franck and Hirabayashi, Yusuke} } @article {69746, title = {Multicilia dynamically transduce Sonic Hedgehog signaling to regulate choroid plexus functions}, journal = {Cell Reports}, year = {2025}, month = {2025 Mar 25}, abstract = {

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

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

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

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

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

}, doi = {10.1101/2025.06.02.657494}, url = {https://www.biorxiv.org/content/early/2025/06/13/2025.06.02.657494}, author = {Fu, Tian-Ming and Liu, Gaoxiang and Milkie, Daniel E. and Ruan, Xiongtao and G{\"o}rlitz, Frederik and Shi, Yu and Ferro, Valentina and Divekar, Nikita S. and Wang, Wei and York, Harrison M. and Kilic, Velat and Mueller, Matthew and Liang, Yajie and Daugird, Timothy A. and Gacha-Garay, Maria J. and Larkin, Kathryn A. and Adikes, Rebecca C. and Harrison, Nathaniel and Shirazinejad, Cyna and Williams, Samara and Nourse, Jamison L. and Sheu, Shu-Hsien and Gao, Liang and Li, Tongchao and Mondal, Chandrani and Achour, Kemal and Hercule, Wilmene and Stabley, Daniel and Emmerich, Kevin and Dong, Peng and Drubin, David and Liu, Zhe J. and Clapham, David and Mumm, Jeff S. and Koyama, Minoru and Killilea, Alison and Bravo-Cordero, Jose Javier and Keene, C. Dirk and Luo, Liqun and Kirchhausen, Tom and Pathak, Medha M. and Arumugam, Senthil and Nunez, James K. and Gao, Ruixuan and Matus, David Q. and Martin, Benjamin L. and Swinburne, Ian A. and Betzig, Eric and Legant, Wesley R. and Upadhyayula, Srigokul} } @article {69947, title = {Multiplex Detection of Gene Expression in the Intact Drosophila Brain Using Expansion-Assisted Iterative Fluorescence In Situ Hybridization.}, journal = {J Vis Exp}, year = {2025}, month = {2025 May 02}, abstract = {

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

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

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

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

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

}, issn = {1878-1551}, doi = {10.1016/j.devcel.2025.05.002}, url = {https://doi.org/10.1016/j.devcel.2025.05.002}, author = {Sendra, Miquel and McDole, Katie and de Dios Hourcade, Juan and Temi{\~n}o, Susana and Raiola, Morena and Guignard, Leo and Keller, Philipp J and Dom{\'\i}nguez, Jorge N and Torres, Miguel} } @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 {70243, title = {The organization of visual pathways in the Drosophila brain}, journal = {bioRxiv}, year = {2025}, month = {2025 Dec 26}, abstract = {

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

}, doi = {10.64898/2025.12.22.696097}, url = {https://www.biorxiv.org/content/early/2025/12/26/2025.12.22.696097}, author = {Hoeller, Judith and Zhao, Arthur and Nern, Aljoscha and Rogers, Edward M and Romani, Sandro and Reiser, Michael B} } @article {69756, title = {Periodic ER-plasma membrane junctions support long-range Ca signal integration in dendrites.}, journal = {Cell}, volume = {188}, year = {2025}, month = {01/2025}, pages = {484-500.e22}, abstract = {

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

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

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

}, doi = {10.48550/arXiv.2507.23030}, url = {https://arxiv.org/abs/2507.23030}, author = {John J. Briguglio and Jaesung Lee and Albert K. Lee and Vincent Hakim and Sandro Romani} } @article {69904, title = {Quantitative spatial analysis of chromatin biomolecular condensates using cryoelectron tomography.}, journal = {Proc Natl Acad Sci U S A}, volume = {122}, year = {2025}, month = {2025 May 13}, pages = {e2426449122}, abstract = {

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

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

}, keywords = {Animals, Biomolecular Condensates, Chromatin, Cryoelectron Microscopy, Electron Microscope Tomography, Nucleosomes}, issn = {1091-6490}, doi = {10.1073/pnas.2426449122}, url = {https://doi.org/10.1073/pnas.2426449122}, author = {Zhou, Huabin and Hutchings, Joshua and Shiozaki, Momoko and Zhao, Xiaowei and Doolittle, Lynda K and Yang, Shixin and Yan, Rui and Jean, Nikki and Riggi, Margot and Yu, Zhiheng and Villa, Elizabeth and Rosen, Michael K} } @article {70189, title = {Relative phase of membrane potential theta oscillations between individual hippocampal neurons code space}, journal = {bioRxiv}, year = {2025}, month = {2025 Nov 14}, abstract = {

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

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

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

}, keywords = {Animals, Artifacts, Humans, Microscopy, Microscopy, Fluorescence}, issn = {1477-9137}, doi = {10.1242/jcs.263567}, url = {https://doi.org/10.1242/jcs.263567}, author = {Prakash, Kirti and Baddeley, David and Eggeling, Christian and Fiolka, Reto and Heintzmann, Rainer and Manley, Suliana and Radenovic, Aleksandra and Shroff, Hari and Smith, Carlas and Schermelleh, Lothar} } @article {70100, title = {A roadmap for the widespread adoption of frugal microscopes.}, journal = {Nat Commun}, volume = {16}, year = {2025}, month = {2025 Sep 08}, pages = {8241}, abstract = {

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

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

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

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

}, doi = {10.7554/eLife.108210.1}, url = {https://doi.org/10.7554/eLife.108210.1}, author = {Bushey, Daniel and Shiozaki, Hiroshi and Shuai, Yichun and Zheng, Jihong and Jayaraman, Vivek and Hasseman, Jeremy P. and Kolb, Ilya and GENIE Project Team and Turner, Glenn C.} } @article {70044, title = {A sensitive orange fluorescent calcium ion indicator for imaging neural activity}, journal = {bioRxiv}, year = {2025}, month = {2025 Jul 31}, abstract = {

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

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

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

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

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

}, doi = {10.21203/rs.3.rs-6881911/v1}, url = {https://doi.org/10.21203/rs.3.rs-6881911/v1}, author = {Deutsch, David and Matsliah, Arie and Wang, Kaiyu and Dorkenwald, Sven and Mondal, Arpita and Burke, Austin and Hebditch, James and Gager, Jay and Yu, Szi-Chieh and Sterling, Amy and McKellar, Amy and Schlegel, Philipp and Gerhard, Stephan and Sterne, Gabriella and Costa, Marta and Eichler, Katharina and Yin, Yijie and Jefferis, Gregory and Dickson, Barry and Seung, H Sebastian and Murthy, Mala} } @article {70136, title = {A single residue in the yellow fever virus envelope protein modulates virion architecture and antigenicity.}, journal = {Nat Commun}, volume = {16}, year = {2025}, month = {2025 Sep 26}, pages = {8449}, abstract = {

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

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

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

}, keywords = {Animals, Brain, CRISPR-Cas Systems, Mice, Mice, Inbred C57BL, Neurons, Single-Cell Analysis, Synapses}, issn = {2041-1723}, doi = {10.1038/s41467-025-65813-w}, url = {https://doi.org/10.1038/s41467-025-65813-w}, author = {Uchigashima, Motokazu and Iguchi, Risa and Fujii, Kazuma and Shiku, Kaito and Kumar, Pratik and Liu, Xinyi and Isogai, Mari and Hoshino, Chiaki and Abe, Manabu and Nozumi, Motohiro and Okamura, Yosuke and Igarashi, Michihiro and Sakimura, Kenji and Bise, Ryoma and Lavis, Luke D and Mikuni, Takayasu} } @article {70004, title = {SLAy-ing oversplitting errors in high-density electrophysiology spike sorting}, journal = {bioRxiv}, year = {2025}, month = {2025 Jun 25}, abstract = {

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

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

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

}, keywords = {Animals, Homeostasis, Male, Mice, Mice, Inbred C57BL, Midline Thalamic Nuclei, Neuronal Plasticity, Neurons, Optogenetics, Sleep Deprivation, Sleep, Slow-Wave, Wakefulness}, issn = {1095-9203}, doi = {10.1126/science.adm8203}, url = {https://doi.org/10.1126/science.adm8203}, author = {Lee, Sang Soo and Liu, Qiang and Cheng, Alexandra H R and Kim, Dong Won and Boudreau, Daphne M and Mehta, Anuradha and Keles, Mehmet F and Fejfer, Rafal and Palmer, Isabelle and Park, Kristen H and M{\"u}nzberg, Heike and Harris, Timothy D and Graves, Austin R and Blackshaw, Seth and Wu, Mark N} } @article {69984, title = {Spatial reasoning via recurrent neural dynamics in mouse retrosplenial cortex}, journal = {Nat Neurosci}, volume = {28}, year = {2025}, month = {2025 Jun 06}, pages = {1293-1299}, abstract = {

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

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

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

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

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

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

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

}, doi = {10.64898/2025.12.15.693918}, url = {https://www.biorxiv.org/content/early/2025/12/18/2025.12.15.693918}, author = {Smeets, Kasper and Hesselink, Luuk W and Marquez-Legorreta, Emmanuel and Fleishman, Greg M and Eddison, Mark and Tillberg, Paul W and Ahrens, Misha B and Englitz, Bernhard} } @article {69975, title = {Statistical signature of subtle behavioral changes in large-scale assays.}, journal = {PLoS Comput Biol}, volume = {21}, year = {2025}, month = {2025 Apr 21}, pages = {e1012990}, abstract = {

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

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

}, keywords = {Animals, Behavior, Animal, Computational Biology, Drosophila melanogaster, Larva, Machine Learning, Models, Neurological, Models, Statistical, Neurons}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1012990}, url = {https://doi.org/10.1371/journal.pcbi.1012990}, author = {Blanc, Alexandre and Laurent, Francois and Barbier-Chebbah, Alex and Van Assel, Hugues and Cocanougher, Benjamin T and Jones, Benjamin M W and Hague, Peter and Zlatic, Marta and Chikhi, Rayan and Vestergaard, Christian L and Jovanic, Tihana and Masson, Jean-Baptiste and Barre, Chloe} } @article {69771, title = {Symposia report of The Annual Biological Sciences Section Meeting of the Gerontological Society of America 2023, Tampa, Florida.}, journal = {J Gerontol A Biol Sci Med Sci}, year = {2025}, month = {2025 Feb 11}, abstract = {

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

}, issn = {1758-535X}, doi = {10.1093/gerona/glaf026}, url = {https://doi.org/10.1093/gerona/glaf026}, author = {Rogina, Blanka and Anderson, Rozalyn and Lebrasseur, Nathan and Curan, Sean and Yousefzadeh, Matthew J and Ghosh, Bhaswati and Duque, Gustavo and Howlett, Susan and Austad, Steven and Demuth, Ilja and Gerstorf, Denis and Korfhage, Justin and Lombard, David B and Abadir, Peter and Christensen, Kaare and Carey, James R and Alberts, Susan C and Campos, Fernando and Palavicini, Juan Pablo and Palmer, Allyson and Bell, Justice and Basisty, Nathan and de Cabo, Rafael and Gomes, Ana and Dixit, Vishwa Deep and Sen, Payel and Baur, Joseph A and Imai, Shin-Ichiro and Li, Xiaoling and Valdez, Gregorio and Orr, Miranda E and Pletcher, Scott and Andersen, Julie and Jones, Leanne and Castillo-Azofeida, David and Bonaguidi, Michael and Suh, Yousin and Duncan, Francesca E and Murray, Anna and Burkewitz, Kristopher and Henne, Mike and Zhou, Kai and Bouhrara, Mustapha and Benjamini, Dan and Kolind, Shannon and Walker, Keenan A and Reiter, David A and Dean Iii, Doug and Gorbunova, Vera and Gladyshev, Vadim N and Palovics, Robert and Niedernhofer, Laura J and Fan, Rong and Bueckle, Andreas D and Hurley, Jennifer and Esser, Karyn A and Kapahi, Pankaj and Sato, Shogo and Jiang, Nisi and Ashiqueali, Sarah A and Diaz, Jose and Mishra, Sidharth Prasad and Ralmundo, Nuno and Banarjee, Reema and Allsopp, Richard and Reynolds, Lindsay M and Zhang, Bohan and Sebastiani, Paola and Monti, Stefano and Schork, Nicholas and Rappaport, Noa} } @article {69803, title = {TEMI: Tissue Expansion Mass Spectrometry Imaging}, journal = {Nat Methods}, year = {2025}, month = {2025 Apr 22}, abstract = {

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

Preprint:\ 10.1101/2025.02.22.639343

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

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

}, doi = {10.1101/2024.08.26.609738}, url = {https://www.biorxiv.org/content/early/2025/03/03/2024.08.26.609738}, author = {Hermundstad, Ann M. and M{\l}ynarski, Wiktor F.} } @article {70220, title = {Time or distance encoding by hippocampal neurons via heterogeneous ramping rates.}, journal = {Nat Commun}, volume = {16}, year = {2025}, month = {2025 Dec 17}, pages = {11083}, abstract = {

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

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

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

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

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

}, issn = {1471-0080}, doi = {10.1038/s41580-025-00899-0}, url = {https://doi.org/10.1038/s41580-025-00899-0}, author = {Farhan, Hesso and Raote, Ishier and Campelo, Felix and Ge, Liang and Hirschberg, Koret and Forrester, Alison and Zanetti, Giulia and Lippincott-Schwartz, Jennifer and Pastor-Pareja, Jos{\'e} Carlos and Perez, Franck and Saito, Kota and Malhotra, Vivek} } @article {70053, title = {Transgene-free generation of mouse post-gastrulation whole embryo models solely from naive ESCs and iPSCs.}, journal = {Cell Stem Cell}, year = {2025}, month = {2025 Aug 06}, abstract = {

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

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

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

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

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

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

bioRxiv preprint: doi.org/10.1101/2023.08.23.554527

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2025.08.030}, url = {https://doi.org/10.1016/j.neuron.2025.08.030}, author = {Ye, Zhiwen and Shelton, Andrew M and Shaker, Jordan R and Boussard, Julien and Colonell, Jennifer and Birman, Daniel and Manavi, Sahar and Chen, Susu and Windolf, Charlie and Hurwitz, Cole and Yu, Han and Namima, Tomoyuki and Pedraja, Federico and Weiss, Shahaf and Raducanu, Bogdan C and Ness, Torbj{\o}rn V and Jia, Xiaoxuan and Mastroberardino, Giulia and Rossi, L Federico and Carandini, Matteo and H{\"a}usser, Michael and Einevoll, Gaute T and Laurent, Gilles and Sawtell, Nathaniel B and Bair, Wyeth and Pasupathy, Anitha and Mora Lopez, Carolina and Dutta, Barundeb and Paninski, Liam and Siegle, Joshua H and Koch, Christof and Olsen, Shawn R and Harris, Timothy D and Steinmetz, Nicholas A} } @article {69812, title = {Vimentin filament transport and organization revealed by single-particle tracking and 3D FIB-SEM}, journal = {Journal of Cell Biology}, volume = {224}, year = {2025}, month = {2025 Apr 03}, pages = {e202406054}, abstract = {

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

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

}, issn = {0021-9525}, doi = {10.1083/jcb.202406054}, url = {https://doi.org/10.1083/jcb.202406054}, author = {Renganathan, Bhuvanasundar and Moore, Andrew S. and Yeo, Wei-Hong and Petruncio, Alyson and Ackerman, David and Weigel, Aubrey V. and Team, The CellMap and Pasolli, H. Amalia and Xu, C. Shan and Shtengel, Gleb and Hess, Harald F. and Serpinskaya, Anna S. and Zhang, Hao F. and Lippincott-Schwartz, Jennifer and Gelfand, Vladimir I.} } @article {69614, title = {Voltage imaging reveals circuit computations in the raphe underlying serotonin-mediated motor vigor learning}, journal = {Neuron}, year = {2025}, month = {2025 Jun 06}, abstract = {

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

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

}, doi = {10.1016/j.neuron.2025.05.017}, url = {https://doi.org/10.1016/j.neuron.2025.05.017}, author = {Kawashima, Takashi and Wei, Ziqiang and Haruvi, Ravid and Shainer, Inbal and Narayan, Sujatha and Baier, Herwig and Ahrens, Misha B} } @article {69601, title = {3D nanoscale architecture of the respiratory epithelium reveals motile cilia-rootlets-mitochondria axis of communication}, journal = {bioRxiv}, year = {2024}, month = {2024 Sep 08}, abstract = {

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

}, doi = {10.1101/2024.09.08.611854}, url = {https://www.doi.org/10.1101/2024.09.08.611854}, author = {Vijayakumaran, Aaran and Godbehere, Christopher and Abuammar, Analle and Breusegem, Sophia Y. and Hurst, Leah R. and Morone, Nobuhiro and Llodra, Jaime and Dalbay, Melis T. and Tanvir, Niaj M. and MacLellan-Gibson, K. and O{\textquoteright}Callaghan, Chris and Lorentzen, Esben and , and , and Murray, Andrew J. and Narayan, Kedar and Mennella, Vito} } @article {69657, title = {Anti-seizure effects of norepinephrine-induced free fatty acid release.}, journal = {Cell Metab}, year = {2024}, month = {2024 Oct 29}, abstract = {

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

}, issn = {1932-7420}, doi = {10.1016/j.cmet.2024.10.011}, url = {https://doi.org/10.1016/j.cmet.2024.10.011}, author = {Li, Baoman and Sun, Qian and Ding, Fengfei and Xu, Qiwu and Kang, Ning and Xue, Yang and Ladron-de-Guevara, Antonio and Hirase, Hajime and Weikop, Pia and Gong, Sheng and Nathan, Smith and Nedergaard, Maiken} } @article {69385, title = {A Bayesian Solution to Count the Number of Molecules within a Diffraction Limited Spot}, journal = {bioRxiv}, year = {2024}, month = {2024 Apr 22}, abstract = {

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

}, doi = {10.1101/2024.04.18.590066}, url = {https://www.biorxiv.org/content/early/2024/04/22/2024.04.18.590066}, author = {Alexander Hillsley and Johannes Stein and Paul W. Tillberg and David L. Stern and Jan Funke} } @article {69185, title = {Brain-wide neural activity underlying memory-guided movement.}, journal = {Cell}, volume = {187}, year = {2024}, month = {2024 Feb 01}, pages = {676-691.e16}, abstract = {

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

}, keywords = {Brain, Memory, Movement, Neurons, Thalamus}, issn = {1097-4172}, doi = {10.1016/j.cell.2023.12.035}, author = {Chen, Susu and Liu, Yi and Wang, Ziyue Aiden and Colonell, Jennifer and Liu, Liu D and Hou, Han and Tien, Nai-Wen and Wang, Tim and Harris, Timothy and Druckmann, Shaul and Li, Nuo and Svoboda, Karel} } @article {69557, title = {Bridging tuning and invariance with equivariant neuronal representations}, journal = {bioRxiv}, year = {2024}, month = {2024 Aug 02}, abstract = {

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

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

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

}, keywords = {bioimaging networks, BioImaging North America, community-building, imaging scientists, Latin America Bioimaging}, doi = {https://doi.org/10.1111/jmi.13318}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jmi.13318}, author = {De Niz, Mariana and Escobedo Garc{\'\i}a, Rodrigo and Ter{\'a}n Ramirez, Celina and Pakowski, Ysa and Abonza, Yuriney and Bialy, Nikki and Orr, Vanessa L. and Olivera, Andres and Abonza, Victor and Alleva, Karina and Allodi, Silvana and Almeida, Michael F. and Becerril Cuevas, Alexis Ricardo and Bonnet, Frederic and Burgos Solorio, Armando and Chew, Teng-Leong and Chiabrando, Gustavo and Cimini, Beth and Cleret-Buhot, Aur{\'e}lie and Contreras Jim{\'e}nez, Gast{\'o}n and Daza, Laura and De S{\'a}, Vanessa and De Val, Natalia and Delgado-{\'A}lvarez, Diego L. and Eliceiri, Kevin and Fiolka, Reto and Grecco, Hernan and Hanein, Dorit and Hern{\'a}ndez Herrera, Pa{\'u}l and Hockberger, Phil and Hernandez, Haydee O. and Hernandez Guadarrama, Yael and Itano, Michelle and Jacobs, Caron A. and Jim{\'e}nez-Garc{\'\i}a, Luis F. and Jim{\'e}nez Sabinina, Vilma and Kamaid, Andres and Keppler, Antje and Kumar, Abhishek and Lacoste, Judith and Lovy, Alenka and Luby-Phelps, Kate and Mahadevan-Jansen, Anita and Malacrida, Leonel and Mehta, Shalin B. and Miller, Caroline and Miranda, Kildare and Moore, Joshua A. and North, Alison and O{\textquoteright}Toole, Peter and Olivares Urbano, Mariana and Pietrasanta, L{\'\i}a I. and Portugal, Rodrigo V. and Rossi, Andr{\'e}s H. and Sanchez Contreras, Jonathan and Strambio-De-Castilla, Caterina and Soldevila, Gloria and Vale, Bruno and Vazquez, Diana and Wood, Chris and Brown, Claire M. and Guerrero, Adan} } @article {69546, title = {Chemical Induction of Longevity-Promoting Colanic Acid in the Host{\textquoteright}s Microbiota}, journal = {bioRxiv}, year = {2024}, month = {2024 Jul 23}, abstract = {

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

}, doi = {10.1101/2024.07.23.604802}, url = {https://www.doi.org/10.1101/2024.07.23.604802}, author = {Hu, Guo and Cooke, Matthew Brandon and Wen, Alice X and Yu, Xin and Wang, Jin and Herman, Christophe and Wang, Meng Carla} } @article {69373, title = {Connectome-driven neural inventory of a complete visual system}, journal = {Nature}, year = {2024}, month = {2025 Mar 26}, abstract = {

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

}, doi = {10.1038/s41586-025-08746-0}, url = {https://doi.org/10.1038/s41586-025-08746-0}, author = {Aljoscha Nern and Frank Loesche and Shin-ya Takemura and Laura E Burnett and Marisa Dreher and Eyal Gruntman and Judith Hoeller and Gary B Huang and Michal Januszewski and Nathan C Klapoetke and Sanna Koskela and Kit D Longden and Zhiyuan Lu and Stephan Preibisch and Wei Qiu and Edward M Rogers and Pavithraa Seenivasan and Arthur Zhao and John Bogovic and Brandon S Canino and Jody Clements and Michael Cook and Samantha Finley-May and Miriam A Flynn and Imran Hameed and Kenneth J Hayworth and Gary Patrick Hopkins and Philip M Hubbard and William T Katz and Julie Kovalyak and Shirley A Lauchie and Meghan Leonard and Alanna Lohff and Charli A Maldonado and Caroline Mooney and Nneoma Okeoma and Donald J Olbris and Christopher Ordish and Tyler Paterson and Emily M Phillips and Tobias Pietzsch and Jennifer Rivas Salinas and Patricia K Rivlin and Ashley L Scott and Louis A Scuderi and Satoko Takemura and Iris Talebi and Alexander Thomson and Eric T Trautman and Lowell Umayam and Claire Walsh and John J Walsh and C Shan Xu and Emily A Yakal and Tansy Yang and Ting Zhao and Jan Funke and Reed George and Harald F Hess and Gregory S X E Jefferis and Christopher Knecht and Wyatt Korff and Stephen M Plaza and Sandro Romani and Stephan Saalfeld and Louis K Scheffer and Stuart Berg and Gerald M Rubin and Michael B Reiser} } @article {69138, title = {Connectomic reconstruction predicts visual features used for navigation.}, journal = {Nature}, volume = {634}, year = {2024}, month = {2024 Oct 02}, pages = {181-190}, abstract = {

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

}, doi = {10.1038/s41586-024-07967-z}, url = {https://doi.org/10.1038/s41586-024-07967-z}, author = {Garner, Dustin and Kind, Emil and Yuet Ha Lai, Jennifer and Nern, Aljoscha and Zhao, Arthur and Houghton, Lucy and Sancer, Gizem and Wolff, Tanya and Rubin, Gerald M and Wernet, Mathias F and Kim, Sung Soo} } @article {69588, title = {Coordinated cross-brain activity during accumulation of sensory evidence and decision commitment}, journal = {bioRxiv}, year = {2024}, month = {2024 Aug 25}, abstract = {

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

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

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

}, keywords = {Animals, Anterior Thalamic Nuclei, Cerebral Cortex, Cues, Gyrus Cinguli, Mammals, Mice, Rotation}, issn = {2050-084X}, doi = {10.7554/eLife.82952}, author = {van der Goes, Marie-Sophie H and Voigts, Jakob and Newman, Jonathan P and Toloza, Enrique H S and Brown, Norma J and Murugan, Pranav and Harnett, Mark T} } @article {69089, title = {Correlative single molecule lattice light sheet imaging reveals the dynamic relationship between nucleosomes and the local chromatin environment.}, journal = {Nat. Commun.}, year = {2024}, month = {2024 May 16}, abstract = {

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

}, doi = {10.1038/s41467-024-48562-0}, author = {Daugird, Timothy A and Shi, Yu and Holland, Katie L and Rostamian, Hosein and Liu, Zhe and Lavis, Luke D and Rodriguez, Joseph and Strahl, Brian D and Legant, Wesley R} } @article {69527, title = {CRISPR-array-mediated imaging of non-repetitive and multiplex genomic loci in living cells.}, journal = {Nat Methods}, year = {2024}, month = {2024 Jul 04}, abstract = {

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

}, issn = {1548-7105}, doi = {10.1038/s41592-024-02333-3}, url = {https://www.doi.org/10.1038/s41592-024-02333-3}, author = {Yang, Liang-Zhong and Min, Yi-Hui and Liu, Yu-Xin and Gao, Bao-Qing and Liu, Xiao-Qi and Huang, Youkui and Wang, Haifeng and Yang, Li and Liu, Zhe J and Chen, Ling-Ling} } @article {69224, title = {CSPP1 stabilizes microtubules by capping both plus and minus ends.}, journal = {Journal of Molecular Cell Biology}, year = {2024}, month = {2024 Feb 22}, abstract = {

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

}, issn = {1759-4685}, doi = {10.1093/jmcb/mjae007}, author = {Wang, Zhikai and Wang, Wenwen and Liu, Shuaiyu and Yang, Fengrui and Liu, Xu and Hua, Shasha and Zhu, Lijuan and Xu, Aoqing and Hill, Donald L and Wang, Dongmei and Jiang, Kai and Lippincott-Schwartz, Jennifer and Liu, Xing and Yao, Xuebiao} } @article {69568, title = {DaCapo: a modular deep learning framework for scalable 3D image segmentation}, journal = {arXiv}, year = {2024}, month = {2024 Aug 05}, abstract = {

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

}, doi = {10.48550/arXiv.2408.02834}, url = {https://doi.org/10.48550/arXiv.2408.02834}, author = {Patton, William and Jeff L Rhoades and Zouinkhi, Marwan and Ackerman, David G and Malin-Mayor, Caroline and Adjavon, Diane and Heinrich, Larissa and Bennett, Davis and Zubov, Yurii and Team, CellMap Project and Weigel, Aubrey and Funke, Jan} } @article {69706, title = {Days-old zebrafish rapidly learn to recognize threatening agents through noradrenergic and forebrain circuits.}, journal = {Curr Biol}, year = {2024}, month = {2024 Dec 19}, abstract = {

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

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

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

}, doi = {10.48550/arXiv.2407.19160}, url = {https://doi.org/10.48550/arXiv.2407.19160}, author = {Allier, C{\'e}dric and Schneider, Magdalena C and Innerberger, Michael and Heinrich, Larissa and Bogovic, John A and Saalfeld, Stephan} } @article {69327, title = {Development of a First-in-Class RIPK1 Degrader to Enhance Antitumor Immunity}, journal = {Nat Commun}, volume = {15}, year = {2024}, month = {2024 Dec 16}, pages = {10683}, abstract = {

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

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

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

}, keywords = {COVID-19, Humans, Public Opinion, SARS-CoV-2, Science, Surveys and Questionnaires}, issn = {1932-6203}, doi = {10.1371/journal.pone.0313541}, author = {Vickers, Peter and Adamo, Ludovica and Alfano, Mark and Clark, Cory and Cresto, Eleonora and Cui, He and Dang, Haixin and Dells{\'e}n, Finnur and Dupin, Nathalie and Gradowski, Laura and Graf, Simon and Guevara, Aline and Hallap, Mark and Hamilton, Jesse and Hardey, Mariann and Helm, Paula and Landrum, Asheley and Levy, Neil and Machery, Edouard and Mills, Sarah and Muller, Se{\'a}n and Sheppard, Joanne and N K, Shinod and Slater, Matthew and Stegenga, Jacob and Strandin, Henning and Stuart, Michael T and Sweet, David and Tasdan, Ufuk and Taylor, Henry and Towler, Owen and Tulodziecki, Dana and Tworek, Heidi and Wallbank, Rebecca and Wiltsche, Harald and Mitchell Finnigan, Samantha} } @article {69633, title = {A Drosophila computational brain model reveals sensorimotor processing.}, journal = {Nature}, volume = {634}, year = {2024}, month = {2024 Oct 02}, pages = {210-219}, abstract = {

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

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

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

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

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

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2024.05.015}, author = {Huang, Yi-Chieh and Chen, Hui-Ching and Lin, Yu-Ting and Lin, Szu-Ting and Zheng, Qinsi and Abdelfattah, Ahmed S and Lavis, Luke D and Schreiter, Eric R and Lin, Bei-Jung and Chen, Tsai-Wen} } @article {69145, title = {Epigenetic priming of embryonic lineages in the mammalian epiblast}, journal = {bioRxiv}, year = {2024}, month = {2024 Jan 11}, abstract = {

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

}, doi = {10.1101/2024.01.11.575188}, url = {https://doi.org/10.1101/2024.01.11.575188}, author = {Miquel Sendra and Katie McDole and Daniel Jimenez-Carretero and Juan de Dios Hourcade and Susana Temi{\~n}o and L{\'e}o Guignard and Philipp J Keller and F{\'a}tima S{\'a}nchez-Cabo and Jorge N. Dom{\'\i}nguez and Miguel Torres} } @article {69154, title = {Failure to mate enhances investment in behaviors that may promote mating reward and impairs the ability to cope with stressors via a subpopulation of Neuropeptide F receptor neurons.}, journal = {PLoS Genetics}, volume = {20}, year = {2024}, month = {2024 Jan 18}, pages = {e1011054}, abstract = {

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

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

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

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

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

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

}, issn = {2212-8778}, doi = {10.1016/j.molmet.2024.102048}, url = {https://doi.org/10.1016/j.molmet.2024.102048}, author = {Wang, Haizhen and Nikain, Cyrus and Fortounas, Konstantinos I and Amengual, Jaime and Tufanli, Ozlem and La Forest, Maxwell and Yu, Yong and Wang, Meng C and Watts, Russell and Lehner, Richard and Qiu, Yunping and Cai, Min and Kurland, Irwin J and Goldberg, Ira J and Rajan, Sujith and Hussain, M Mahmood and Brodsky, Jeffrey L and Fisher, Edward A} } @article {69252, title = {Four-dimensional quantitative analysis of cell plate development using lattice light sheet microscopy identifies robust transition points between growth phases.}, journal = {Journal of Experimental Botany}, year = {2024}, month = {2024 Mar 4}, abstract = {

Cell plate formation during cytokinesis entails multiple stages occurring concurrently and requiring orchestrated vesicle delivery, membrane remodeling, and timely polysaccharide deposition, such as callose. Understanding such a dynamic process requires dissection in time and space; this has been a major hurdle in studying cytokinesis. Using lattice light sheet microscopy (LLSM) we studied cell plate development in four dimensions, through the behavior of the cytokinesis specific GTPase YFP-RABA2a vesicles. We monitored the entire length of cell plate development, from its first emergence, with the aid of YFP-RABA2a, both in the presence and absence of cytokinetic callose. By developing a robust cytokinetic vesicle volume analysis pipeline, we identified distinct behavioral patterns, allowing the identification of three easily trackable, cell plate developmental phases. Notably, the phase transition between phase I and phase II is striking, indicating a switch from membrane accumulation to the recycling of excess membrane material. We interrogated the role of callose using pharmacological inhibition with LLSM and electron microscopy. Loss of callose inhibited the phase transitions, establishing the critical role and timing of the polysaccharide deposition in cell plate expansion and maturation. This study exemplifies the power of combining LLSM with quantitative analysis to decode and untangle such a complex process.

}, issn = {1460-2431}, doi = {10.1093/jxb/erae091}, author = {Sinclair, Rosalie and Wang, Minmin and Jawaid, Muhammad Zaki and Longkumer, Toshisangba and Aaron, Jesse and Rossetti, Blair and Wait, Eric and McDonald, Kent and Cox, Daniel and Heddleston, John and Wilkop, Thomas and Drakakaki, Georgia} } @article {69461, title = {Four-dimensional quantitative analysis of cell plate development in Arabidopsis using lattice light sheet microscopy identifies robust transition points between growth phases}, journal = {J Exp Bot}, volume = {75}, year = {2024}, month = {2024 May 20}, pages = {2829-2847}, abstract = {

Cell plate formation during cytokinesis entails multiple stages occurring concurrently and requiring orchestrated vesicle delivery, membrane remodelling, and timely deposition of polysaccharides, such as callose. Understanding such a dynamic process requires dissection in time and space; this has been a major hurdle in studying cytokinesis. Using lattice light sheet microscopy (LLSM), we studied cell plate development in four dimensions, through the behavior of yellow fluorescent protein (YFP)-tagged cytokinesis-specific GTPase RABA2a vesicles. We monitored the entire duration of cell plate development, from its first emergence, with the aid of YFP-RABA2a, in both the presence and absence of cytokinetic callose. By developing a robust cytokinetic vesicle volume analysis pipeline, we identified distinct behavioral patterns, allowing the identification of three easily trackable cell plate developmental phases. Notably, the phase transition between phase I and phase II is striking, indicating a switch from membrane accumulation to the recycling of excess membrane material. We interrogated the role of callose using pharmacological inhibition with LLSM and electron microscopy. Loss of callose inhibited the phase transitions, establishing the critical role and timing of the polysaccharide deposition in cell plate expansion and maturation. This study exemplifies the power of combining LLSM with quantitative analysis to decode and untangle such a complex process.

}, keywords = {Arabidopsis, Cytokinesis, Glucans, Microscopy}, issn = {1460-2431}, doi = {10.1093/jxb/erae091}, author = {Sinclair, Rosalie and Wang, Minmin and Jawaid, Muhammad Zaki and Longkumer, Toshisangba and Aaron, Jesse and Rossetti, Blair and Wait, Eric and McDonald, Kent and Cox, Daniel and Heddleston, John and Wilkop, Thomas and Drakakaki, Georgia} } @article {69678, title = {Genomes of two invasive Adelges species (hemlock woolly adelgid and pineapple gall adelgid) enable characterization of nicotinic acetylcholine receptors}, journal = {bioRxiv}, year = {2024}, month = {2024 Nov 26}, abstract = {

Two invasive hemipteran adelgids cause widespread damage to North American conifers. Adelges tsugae (the hemlock woolly adelgid) has decimated Tsuga canadensis and Tsuga caroliniana (the Eastern and Carolina hemlocks, respectively). A. tsugae was introduced from East Asia and reproduces parthenogenetically in North America, where it can kill trees rapidly. A. abietis, introduced from Europe, makes pineapple galls on several North American spruce species, and weakens trees, increasing their susceptibility to other stresses. Broad-spectrum insecticides that are often used to control adelgid populations can have off-target impacts on beneficial insects and the development of more selective chemical treatments could improve control methods and minimize ecological damage. Whole genome sequencing was performed on both species to aid in development of targeted pest control solutions and improve species conservation. The assembled A. tsugae and A. abietis genomes are 231.71 Mbp and 290.39 Mbp, respectively, each consisting of nine chromosomes and both genomes are over 96\% complete based on BUSCO assessment. Genome annotation identified 11,424 and 14,118 protein-coding genes in A. tsugae and A. abietis, respectively. Comparative analysis across 29 Hemipteran species and 14 arthropod outgroups identified 31,666 putative gene families. Gene family expansions in A. abietis included ABC transporters and carboxypeptidases involved in carbohydrate metabolism, while both species showed contractions in core histone families and oxidoreductase pathways. Gene family expansions in A. tsugae highlighted families associated with the regulation of cell differentiation and development (survival motor protein, SMN; juvenile hormone acid methyltransferase JHAMT) as well as those that may be involved in the suppression of plant immunity (clip domain serine protease-D, CLIPD; Endoplasmic reticulum aminopeptidase 1, ERAP1). Among the analyzed gene families, Nicotinic acetylcholine receptors (nAChRs) maintained consistent copy numbers and structural features across species, a finding particularly relevant given their role as targets for current forestry management insecticides. Detailed phylogenetic analysis of nAChR subunits across adelgids and other ecologically important insects revealed remarkable conservation in both sequence composition and predicted structural features, providing crucial insights for the development of more selective pest control strategies.

}, doi = {10.1101/2024.11.21.624573}, url = {https://doi.org/10.1101/2024.11.21.624573}, author = {Glendening, A M and Stephens, Cole and Vuruputoor, Vidya S and Stern, David L and Hogenhout, Saskia A and Mathers, Thomas C and Chaganti, Tesko and Pauloski, Nicole and Cernak, Tim A and Wegrzyn, Jill L and Fetter, Karl C} } @article {69659, title = {A global dopaminergic learning rate enables adaptive foraging across many options}, journal = {bioRxiv}, year = {2024}, month = {2024 Nov 05}, abstract = {

In natural environments, animals must efficiently allocate their choices across multiple concurrently available resources when foraging, a complex decision-making process not fully captured by existing models. To understand how rodents learn to navigate this challenge we developed a novel paradigm in which untrained, water-restricted mice were free to sample from six options rewarded at a range of deterministic intervals and positioned around the walls of a large ( 2m) arena. Mice exhibited rapid learning, matching their choices to integrated reward ratios across six options within the first session. A reinforcement learning model with separate states for staying or leaving an option and a dynamic, global learning rate was able to accurately reproduce mouse learning and decision-making. Fiber photometry recordings revealed that dopamine in the nucleus accumbens core (NAcC), but not dorsomedial striatum (DMS), more closely reflected the global learning rate than local error-based updating. Altogether, our results provide insight into the neural substrate of a learning algorithm that allows mice to rapidly exploit multiple options when foraging in large spatial environments.

}, doi = {10.1101/2024.11.04.621923}, url = {https://doi.org/10.1101/2024.11.04.621923}, author = {Grima, Laura L and Guo, Yipei and Narayan, Lakshmi and Hermundstad, Ann M and Dudman, Joshua T} } @article {69250, title = {High-Performance Genetically Encoded Green Fluorescent Biosensors for Intracellular l-Lactate.}, journal = {ACS Central Science}, volume = {10}, year = {2024}, month = {2024 Feb 28}, pages = {402-416}, abstract = {

l-Lactate is a monocarboxylate produced during the process of cellular glycolysis and has long generally been considered a waste product. However, studies in recent decades have provided new perspectives on the physiological roles of l-lactate as a major energy substrate and a signaling molecule. To enable further investigations of the physiological roles of l-lactate, we have developed a series of high-performance (Δ/ = 15 to 30 ), intensiometric, genetically encoded green fluorescent protein (GFP)-based intracellular l-lactate biosensors with a range of affinities. We evaluated these biosensors in cultured cells and demonstrated their application in an preparation of brain tissue. Using these biosensors, we were able to detect glycolytic oscillations, which we analyzed and mathematically modeled.

}, issn = {2374-7943}, doi = {10.1021/acscentsci.3c01250}, author = {Hario, Saaya and Le, Giang N T and Sugimoto, Hikaru and Takahashi-Yamashiro, Kei and Nishinami, Suguru and Toda, Hirofumi and Li, Selene and Marvin, Jonathan S and Kuroda, Shinya and Drobizhev, Mikhail and Terai, Takuya and Nasu, Yusuke and Campbell, Robert E} } @article {69578, title = {A high-throughput microfabricated platform for rapid quantification of metastatic potential.}, journal = {Sci Adv}, volume = {10}, year = {2024}, month = {2024 Aug 16}, pages = {eadk0015}, abstract = {

Assays that measure morphology, proliferation, motility, deformability, and migration are used to study the invasiveness of cancer cells. However, native invasive potential of cells may be hidden from these contextual metrics because they depend on culture conditions. We created a micropatterned chip that mimics the native environmental conditions, quantifies the invasive potential of tumor cells, and improves our understanding of the malignancy signatures. Unlike conventional assays, which rely on indirect measurements of metastatic potential, our method uses three-dimensional microchannels to measure the basal native invasiveness without chemoattractants or microfluidics. No change in cell death or proliferation is observed on our chips. Using six cancer cell lines, we show that our system is more sensitive than other motility-based assays, measures of nuclear deformability, or cell morphometrics. In addition to quantifying metastatic potential, our platform can distinguish between motility and invasiveness, help study molecular mechanisms of invasion, and screen for targeted therapeutics.

}, keywords = {Cell Line, Tumor, Cell Movement, Cell Proliferation, High-Throughput Screening Assays, Humans, Lab-On-A-Chip Devices, Microtechnology, Neoplasm Invasiveness, Neoplasm Metastasis, Neoplasms}, issn = {2375-2548}, doi = {10.1126/sciadv.adk0015}, url = {https://doi.org/10.1126/sciadv.adk0015}, author = {Bhattacharya, Smiti and Ettela, Abora and Haydak, Jonathan and Hobson, Chad M and Stern, Alan and Yoo, Miran and Chew, Teng-Leong and Gusella, G Luca and Gallagher, Emily J and Hone, James C and Azeloglu, Evren U} } @article {69730, title = {How short peptides can disassemble ultra-stable tau fibrils extracted from Alzheimer{\textquoteright}s disease brain by a strain-relief mechanism}, journal = {Alzheimer{\textquoteright}s \& Dementia}, volume = {20}, year = {2024}, month = {01/2025}, abstract = {

Background

Reducing fibrous aggregates of protein tau is a possible strategy for halting progression of Alzheimer{\textquoteright}s disease (AD). Previously we found that in vitro the D-peptide D-TLKIVWC fragments tau fibrils from AD brains (AD-tau) into benign segments, whereas its six-residue analog D-TLKIVW cannot. However, the underlying fragmentation mechanism remains unknown, preventing the further development of this type of drug candidate for AD.

Method

To understand the necessity of the cysteine residue of D-TLKIVWC in fragmenting AD-tau, we designed a series of peptides of sequence D-TLKIVWX varying only at the seventh residue, X. To better understand the fragmentation process of AD-tau, we conducted a time-course dot blot and EM experiment. We determined the structures of D-TLKIVWX amyloid-like fibrils by atomic force microscopy and cryo-electron microscopy. We studied the complexes of D-TLKIVWX (X = I, S, R) with AD-tau by cryo-electron microscopy and confirmed the binding site between D-TLKIVWX and Tau through NMR.

Result

These D-TLKIVWX candidates showed various efficacies in fragmenting AD-tau in vitro, in which X = Ile was the best performer. From electron microscopy, we discovered that D-TLKIVWX peptides form amyloid-like fibrils themselves, and from atomic force microscopy we learned that these fibrils have a right-handed helical twist, in contrast to the left-handed helical twist of AD-tau. From cryo-EM we learned that D-TLKIVWX protofilaments bind to tau fibrils of opposing twist.

Conclusion

We find that the amyloid-like, fibril-forming property of D-TLKIVWX contributes to the fragmentation of AD-tau fibrils. We propose the strain-relief mechanism of fragmentation and believe the fragmentation of AD-tau fibrils is driven by the release of torsion in D-TLKIVWX protofilaments.

}, issn = {1552-5260}, doi = {10.1002/alz.085001}, url = {https://alz-journals.onlinelibrary.wiley.com/toc/15525279/20/S6}, author = {Hou, Ke and Ge, Peng and Sawaya, Michael R and Dolinsky, Joshua L. and Yang, Yuan and Jiang, Yi Xiao and Lutter, Liisa and Boyer, David and Cheng, Xinyi and Pi, Justin and Zhang, Jeffrey and Lu, Jiahui and Yang, Shixin and Yu, Zhiheng and Feigon, Juli and Eisenberg, David S.} } @article {69456, title = {Hue selectivity from recurrent circuitry in Drosophila}, journal = {Nat Neurosci}, year = {2024}, month = {2024 May 16}, abstract = {

In the perception of color, wavelengths of light reflected off objects are transformed into the derived quantities of brightness, saturation and hue. Neurons responding selectively to hue have been reported in primate cortex, but it is unknown how their narrow tuning in color space is produced by upstream circuit mechanisms. We report the discovery of neurons in the Drosophila optic lobe with hue-selective properties, which enables circuit-level analysis of color processing. From our analysis of an electron microscopy volume of a whole Drosophila brain, we construct a connectomics-constrained circuit model that accounts for this hue selectivity. Our model predicts that recurrent connections in the circuit are critical for generating hue selectivity. Experiments using genetic manipulations to perturb recurrence in adult flies confirm this prediction. Our findings reveal a circuit basis for hue selectivity in color vision.

}, issn = {1546-1726}, doi = {10.1038/s41593-024-01640-4}, author = {Christenson, Matthias P and Sanz Diez, Alvaro and Heath, Sarah L and Saavedra-Weisenhaus, Maia and Adachi, Atsuko and Nern, Aljoscha and Abbott, L F and Behnia, Rudy} } @article {69609, title = {Integration of estimated regional gene expression with neuroimaging and clinical phenotypes at biobank scale.}, journal = {PLoS Biol}, volume = {22}, year = {2024}, month = {2024 Sep 13}, pages = {e3002782}, abstract = {

An understanding of human brain individuality requires the integration of data on brain organization across people and brain regions, molecular and systems scales, as well as healthy and clinical states. Here, we help advance this understanding by leveraging methods from computational genomics to integrate large-scale genomic, transcriptomic, neuroimaging, and electronic-health record data sets. We estimated genetically regulated gene expression (gr-expression) of 18,647 genes, across 10 cortical and subcortical regions of 45,549 people from the UK Biobank. First, we showed that patterns of estimated gr-expression reflect known genetic-ancestry relationships, regional identities, as well as inter-regional correlation structure of directly assayed gene expression. Second, we performed transcriptome-wide association studies (TWAS) to discover 1,065 associations between individual variation in gr-expression and gray-matter volumes across people and brain regions. We benchmarked these associations against results from genome-wide association studies (GWAS) of the same sample and found hundreds of novel associations relative to these GWAS. Third, we integrated our results with clinical associations of gr-expression from the Vanderbilt Biobank. This integration allowed us to link genes, via gr-expression, to neuroimaging and clinical phenotypes. Fourth, we identified associations of polygenic gr-expression with structural and functional MRI phenotypes in the Human Connectome Project (HCP), a small neuroimaging-genomic data set with high-quality functional imaging data. Finally, we showed that estimates of gr-expression and magnitudes of TWAS were generally replicable and that the p-values of TWAS were replicable in large samples. Collectively, our results provide a powerful new resource for integrating gr-expression with population genetics of brain organization and disease.

}, issn = {1545-7885}, doi = {10.1371/journal.pbio.3002782}, url = {https://doi.org/10.1371/journal.pbio.3002782}, author = {Hoang, Nhung and Sardaripour, Neda and Ramey, Grace D and Schilling, Kurt and Liao, Emily and Chen, Yiting and Park, Jee Hyun and Bledsoe, Xavier and Landman, Bennett A and Gamazon, Eric R and Benton, Mary Lauren and Capra, John A and Rubinov, Mikail} } @article {69141, title = {Interactive simulation and visualization of point spread functions in single molecule imaging.}, journal = {Optics Communications}, year = {2024}, month = {2024 Mar 20}, abstract = {

The point spread function (PSF) is fundamental to any type of microscopy, most importantly so for single-molecule localization techniques, where the exact PSF shape is crucial for precise molecule localization at the nanoscale. Optical aberrations and fixed fluorophore dipoles often result in non-isotropic and distorted PSFs, impairing and biasing conventional fitting approaches. Further, PSF shapes are deliberately modified in PSF engineering approaches for providing improved sensitivity, e.g., for 3D localization or determination of dipole orientation. As this can lead to highly complex PSF shapes, a tool for visualizing expected PSFs would facilitate the interpretation of obtained data and the design of experimental approaches. To this end, we introduce a comprehensive and accessible computer application that allows for the simulation of realistic PSFs based on the full vectorial PSF model. Our tool incorporates a wide range of microscope and fluorophore parameters, including orientationally constrained fluorophores, as well as custom aberrations, transmission and phase masks, thus enabling an accurate representation of various imaging conditions. An additional feature is the simulation of crowded molecular environments with overlapping PSFs. Further, our app directly provides the Cram{\'e}r{\textendash}Rao bound for assessing the best achievable localization precision under given conditions. Finally, our software allows for the fitting of custom aberrations directly from experimental data, as well as the generation of a large dataset with randomized simulation parameters, effectively bridging the gap between simulated and experimental scenarios, and enhancing experimental design and result validation.

}, doi = {10.1016/j.optcom.2024.130463}, url = {https://www.sciencedirect.com/science/article/pii/S0030401824002001?via\%3Dihub}, author = {Magdalena C. Schneider and Fabian Hinterer and Alexander Jesacher and Gerhard J. Sch{\"u}tz} } @article {69420, title = {An interphase actin wave promotes mitochondrial content mixing and organelle homeostasis.}, journal = {Nat Commun}, volume = {15}, year = {2024}, month = {2024 May 07}, pages = {3793}, abstract = {

Across the cell cycle, mitochondrial dynamics are regulated by a cycling wave of actin polymerization/depolymerization. In metaphase, this wave induces actin comet tails on mitochondria that propel these organelles to drive spatial mixing, resulting in their equitable inheritance by daughter cells. In contrast, during interphase the cycling actin wave promotes localized mitochondrial fission. Here, we identify the F-actin nucleator/elongator FMNL1 as a positive regulator of the wave. FMNL1-depleted cells exhibit decreased mitochondrial polarization, decreased mitochondrial oxygen consumption, and increased production of reactive oxygen species. Accompanying these changes is a loss of hetero-fusion of wave-fragmented mitochondria. Thus, we propose that the interphase actin wave maintains mitochondrial homeostasis by promoting mitochondrial content mixing. Finally, we investigate the mechanistic basis for the observation that the wave drives mitochondrial motility in metaphase but mitochondrial fission in interphase. Our data indicate that when the force of actin polymerization is resisted by mitochondrial tethering to microtubules, as in interphase, fission results.

}, keywords = {Actins, Animals, Formins, Hela Cells, Homeostasis, Humans, Interphase, Microtubules, Mitochondria, Mitochondrial Dynamics, Mitochondrial Proteins, Reactive Oxygen Species}, issn = {2041-1723}, doi = {10.1038/s41467-024-48189-1}, author = {Coscia, Stephen M and Moore, Andrew S and Thompson, Cameron P and Tirrito, Christian F and Ostap, E Michael and Holzbaur, Erika L F} } @article {69643, title = {IRE1α silences dsRNA to prevent taxane-induced pyroptosis in triple-negative breast cancer.}, journal = {Cell}, year = {2024}, month = {2024 Oct 14}, abstract = {

Chemotherapy is often combined with immune checkpoint inhibitor (ICIs) to enhance immunotherapy responses. Despite the approval of chemo-immunotherapy in multiple human cancers, many immunologically cold tumors remain unresponsive. The mechanisms determining the immunogenicity of chemotherapy are elusive. Here, we identify the ER stress sensor IRE1α as a critical checkpoint that restricts the immunostimulatory effects of taxane chemotherapy and prevents the innate immune recognition of immunologically cold triple-negative breast cancer (TNBC). IRE1α RNase silences taxane-induced double-stranded RNA (dsRNA) through regulated IRE1-dependent decay (RIDD) to prevent NLRP3 inflammasome-dependent pyroptosis. Inhibition of IRE1α in Trp53 TNBC allows taxane to induce extensive dsRNAs that are sensed by ZBP1, which in turn activates NLRP3-GSDMD-mediated pyroptosis. Consequently, IRE1α RNase inhibitor plus taxane converts PD-L1-negative, ICI-unresponsive TNBC tumors into PD-L1 immunogenic tumors that are hyper-sensitive to ICI. We reveal IRE1α as a cancer cell defense mechanism that prevents taxane-induced danger signal accumulation and pyroptotic cell death.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2024.09.032}, url = {https://doi.org/10.1016/j.cell.2024.09.032}, author = {Xu, Longyong and Peng, Fanglue and Luo, Qin and Ding, Yao and Yuan, Fei and Zheng, Liting and He, Wei and Zhang, Sophie S and Fu, Xin and Liu, Jin and Mutlu, Ayse Sena and Wang, Shuyue and Nehring, Ralf Bernd and Li, Xingyu and Tang, Qianzi and Li, Catherine and Lv, Xiangdong and Dobrolecki, Lacey E and Zhang, Weijie and Han, Dong and Zhao, Na and Jaehnig, Eric and Wang, Jingyi and Wu, Weiche and Graham, Davis A and Li, Yumei and Chen, Rui and Peng, Weiyi and Chen, Yiwen and Catic, Andre and Zhang, Zhibin and Zhang, Bing and Mustoe, Anthony M and Koong, Albert C and Miles, George and Lewis, Michael T and Wang, Meng C and Rosenberg, Susan M and O{\textquoteright}Malley, Bert W and Westbrook, Thomas F and Xu, Han and Zhang, Xiang H-F and Osborne, C Kent and Li, Jin Billy and Ellis, Matthew J and Rimawi, Mothaffar F and Rosen, Jeffrey M and Chen, Xi} } @article {69483, title = {It only takes seconds for a human monoclonal autoantibody to inhibit N-methyl-D-aspartate receptors}, journal = {bioRxiv}, year = {2024}, month = {2024 Jun 01}, abstract = {

Transfer of autoantibodies targeting ionotropic N-methyl-D-aspartate receptors in autoimmune encephalitis patients into mice leads to typical disease signs. Long-term effects of the pathogenic antibodies consist of immunoglobulin G-induced crosslinking and receptor internalization. We focused on the direct and immediate impact of a specific pathogenic patient-derived monoclonal autoantibody (immunoglobulin G $\#$003-102) on receptor function.We performed cell-attached recordings in cells transfected with the GluN1 and GluN2A subunit of the N-methyl-D-aspartate receptor. Immunoglobulin G $\#$003-102 binds to the amino-terminal domain of the glycine-binding GluN1 subunit. It reduced simultaneous receptor openings significantly compared to controls at both low and high glutamate and glycine concentrations. Closer examination of our data in 50-second to 2-second intervals revealed, that Immunoglobulin G $\#$003-102 rapidly decreases the number of open receptors. However, antigen-binding fragments of immunoglobulin G $\#$003-102 did not reduce the receptor openings.In conclusion, patient-derived immunoglobulin G $\#$003-102 inhibits N-methyl-D-aspartate receptors rapidly and directly before receptor internalization occurs and the entire immunoglobulin G is necessary for this acute inhibitory effect. This suggests an application of the antigen-binding fragment-like constructs of $\#$003-102 as a potential new treatment strategy for shielding the pathogenic epitopes on the N-methyl-D-aspartate receptors.

}, doi = {10.1101/2024.05.28.595700}, url = {https://www.biorxiv.org/content/early/2024/06/01/2024.05.28.595700}, author = {Yang, Shang and Heckmann, Johanna and Taha, Abdulla and Gao, Shiqiang and Steinke, Stephan and Hust, Michael and Pr{\"u}{\ss}, Harald and Furukawa, Hiro and Geis, Christian and Heckmann, Manfred and Yu-Strzelczyk, Jing} } @article {69525, title = {iTome Volumetric Serial Sectioning Apparatus for TEM}, journal = {bioRxiv}, year = {2024}, month = {2024 Jul 07}, abstract = {

An automated ultra-microtome capable of sectioning thousands of ultrathin sections onto standard TEM slot grids was developed and used to section: a complete Drosophila melanogaster first-instar larva, three sections per grid, into 4,866 34-nm-thick sections with a cutting and pickup success rate of 99.74\%; 30 microns of mouse cortex measuring roughly 400 um x 2000 um at 40 nm per slice; and a full adult Drosophila brain and ventral nerve column into 9,300 sections with a pickup success rate of 99.95\%. The apparatus uses optical interferometers to monitor a reference distance between the cutting knife and multiple sample blocks. Cut sections are picked up from the knife-boat water surface while they are still anchored to the cutting knife. Blocks without embedded tissue are used to displace tissue-containing sections away from the knife edge so that the tissue regions end up in the grid slot instead of on the grid rim.

}, doi = {10.1101/2024.07.02.601671}, url = {https://doi.org/10.1101/2024.07.02.601671 }, author = {Peale, David R. and Hess, Harald and Lee, P. R. and Cardona, Albert and Bock, Davi D. and Schneider-Mizell, Casey and Fetter, Richard D. and Lee, Wei-Ping and Robinson, Camenzind G. and Iyer, Nirmala and Managan, Claire} } @article {69703, title = {Ketamine induces plasticity in a norepinephrine-astroglial circuit to promote behavioral perseverance.}, journal = {Neuron}, year = {2024}, month = {2024 Dec 16}, pages = {1-15}, abstract = {

Transient exposure to ketamine can trigger lasting changes in behavior and mood. We found that brief ketamine exposure causes long-term suppression of futility-induced passivity in larval zebrafish, reversing the "giving-up" response that normally occurs when swimming fails to cause forward movement. Whole-brain imaging revealed that ketamine hyperactivates the norepinephrine-astroglia circuit responsible for passivity. After ketamine washout, this circuit exhibits hyposensitivity to futility, leading to long-term increased perseverance. Pharmacological, chemogenetic, and optogenetic manipulations show that norepinephrine and astrocytes are necessary and sufficient for ketamine{\textquoteright}s long-term perseverance-enhancing aftereffects. In\ vivo calcium imaging revealed that astrocytes in adult mouse cortex are similarly activated during futility in the tail suspension test and that acute ketamine exposure also induces astrocyte hyperactivation. The cross-species conservation of ketamine{\textquoteright}s modulation of noradrenergic-astroglial circuits and evidence that plasticity in this pathway can alter the behavioral response to futility hold promise for identifying new strategies to treat affective disorders.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2024.11.011}, url = {https://doi.org/10.1016/j.neuron.2024.11.011}, author = {Duque, Marc and Chen, Alex B and Hsu, Eric and Narayan, Sujatha and Rymbek, Altyn and Begum, Shahinoor and Saher, Gesine and Cohen, Adam E and Olson, David E and Li, Yulong and Prober, David A and Bergles, Dwight E and Fishman, Mark C and Engert, Florian and Ahrens, Misha B} } @article {69526, title = {LarvaTagger: Manual and automatic tagging of drosophila larval behaviour.}, journal = {Bioinformatics}, year = {2024}, month = {2024 Jul 05}, abstract = {

MOTIVATION: As more behavioural assays are carried out in large-scale experiments on Drosophila larvae, the definitions of the archetypal actions of a larva are regularly refined. In addition, video recording and tracking technologies constantly evolve. Consequently, automatic tagging tools for Drosophila larval behaviour must be retrained to learn new representations from new data. However, existing tools cannot transfer knowledge from large amounts of previously accumulated data.We introduce LarvaTagger, a piece of software that combines a pre-trained deep neural network, providing a continuous latent representation of larva actions for stereotypical behaviour identification, with a graphical user interface to manually tag the behaviour and train new automatic taggers with the updated ground truth.

RESULTS: We reproduced results from an automatic tagger with high accuracy, and we demonstrated that pre-training on large databases accelerates the training of a new tagger, achieving similar prediction accuracy using less data.

AVAILABILITY: All the code is free and open source. Docker images are also available. See gitlab.pasteur.fr/nyx/LarvaTagger.jl.

SUPPLEMENTARY INFORMATION: Supplementary material is available at Bioinformatics online.

}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btae441}, author = {Laurent, Francois and Blanc, Alexandre and May, Lilly and G{\'a}ndara, Lautaro and Cocanougher, Benjamin T and Jones, Benjamin M W and Hague, Peter and Barre, Chloe and Vestergaard, Christian L and Crocker, Justin and Zlatic, Marta and Jovanic, Tihana and Masson, Jean-Baptiste} } @article {69528, title = {Lattice light sheet microscopy reveals 4D force propagation dynamics and leading-edge behaviors in an embryonic epithelium in Drosophila.}, journal = {Curr Biol}, year = {2024}, month = {2024 Jun 27}, abstract = {

How pulsed contractile dynamics drive the remodeling of cell and tissue topologies in epithelial sheets has been a key question in development and disease. Due to constraints in imaging and analysis technologies, studies that have described the in\ vivo mechanisms underlying changes in cell and neighbor relationships have largely been confined to analyses of planar apical regions. Thus, how the volumetric nature of epithelial cells affects force propagation and remodeling of the cell surface in three dimensions, including especially the apical-basal axis, is unclear. Here, we perform lattice light sheet microscopy (LLSM)-based analysis to determine how far and fast forces propagate across different apical-basal layers, as well as where topological changes initiate from in a columnar epithelium. These datasets are highly time- and depth-resolved and reveal that topology-changing forces are spatially entangled, with contractile force generation occurring across the observed apical-basal axis in a pulsed fashion, while the conservation of cell volumes constrains instantaneous cell deformations. Leading layer behaviors occur opportunistically in response to favorable phasic conditions, with lagging layers "zippering" to catch up as new contractile pulses propel further changes in cell topologies. These results argue against specific zones of topological initiation and demonstrate the importance of systematic 4D-based analysis in understanding how forces and deformations in cell dimensions propagate in a three-dimensional environment.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2024.06.017}, url = {https://www.doi.org/10.1016/j.cub.2024.06.017}, author = {Vanderleest, Timothy E and Xie, Yi and Budhathoki, Rashmi and Linvill, Katie and Hobson, Chad and Heddleston, John and Loerke, Dinah and Blankenship, J Todd} } @article {69372, title = {Leptin Activated Hypothalamic BNC2 Neurons Acutely Suppress Food Intake}, journal = {bioRxiv}, year = {2024}, month = {12 Apr 2024}, abstract = {

Leptin is an adipose tissue hormone that maintains homeostatic control of adipose tissue mass by regulating the activity of specific neural populations controlling appetite and metabolism1. Leptin regulates food intake by inhibiting orexigenic agouti-related protein (AGRP) neurons and activating anorexigenic pro-opiomelanocortin (POMC) neurons2. However, while AGRP neurons regulate food intake on a rapid time scale, acute activation of POMC neurons has only a minimal effect3{\textendash}5. This has raised the possibility that there is a heretofore unidentified leptin-regulated neural population that suppresses appetite on a rapid time scale. Here, we report the discovery of a novel population of leptin-target neurons expressing basonuclin 2 (Bnc2) that acutely suppress appetite by directly inhibiting AGRP neurons. Opposite to the effect of AGRP activation, BNC2 neuronal activation elicited a place preference indicative of positive valence in hungry but not fed mice. The activity of BNC2 neurons is finely tuned by leptin, sensory food cues, and nutritional status. Finally, deleting leptin receptors in BNC2 neurons caused marked hyperphagia and obesity, similar to that observed in a leptin receptor knockout in AGRP neurons. These data indicate that BNC2-expressing neurons are a key component of the neural circuit that maintains energy balance, thus filling an important gap in our understanding of the regulation of food intake and leptin action.

}, doi = {10.1101/2024.01.25.577315}, url = {https://www.biorxiv.org/content/early/2024/04/12/2024.01.25.577315}, author = {Han L. Tan and Luping Yin and Yuqi Tan and Jessica Ivanov and Kaja Plucinska and Anoj Ilanges and Brian R. Herb and Putianqi Wang and Christin Kosse and Paul Cohen and Dayu Lin and Jeffrey M. Friedman} } @article {69632, title = {Maintaining and updating accurate internal representations of continuous variables with a handful of neurons.}, journal = {Nat Neurosci}, year = {2024}, month = {2024 Oct 03}, abstract = {

Many animals rely on persistent internal representations of continuous variables for working memory, navigation, and motor control. Existing theories typically assume that large networks of neurons are required to maintain such representations accurately; networks with few neurons are thought to generate discrete representations. However, analysis of two-photon calcium imaging data from tethered flies walking in darkness suggests that their small head-direction system can maintain a surprisingly continuous and accurate representation. We thus ask whether it is possible for a small network to generate a continuous, rather than discrete, representation of such a variable. We show analytically that even very small networks can be tuned to maintain continuous internal representations, but this comes at the cost of sensitivity to noise and variations in tuning. This work expands the computational repertoire of small networks, and raises the possibility that larger networks could represent more and higher-dimensional variables than previously thought.

}, issn = {1546-1726}, doi = {10.1038/s41593-024-01766-5}, url = {https://10.1038/s41593-024-01766-5}, author = {Noorman, Marcella and Hulse, Brad K and Jayaraman, Vivek and Romani, Sandro and Hermundstad, Ann M} } @article {69247, title = {MarShie: a clearing protocol for 3D analysis of single cells throughout the bone marrow at subcellular resolution.}, journal = {Nature Communincations}, volume = {15}, year = {2024}, month = {2024 Feb 26}, pages = {1764}, abstract = {

Analyzing immune cell interactions in the bone marrow is vital for understanding hematopoiesis and bone homeostasis. Three-dimensional analysis of the complete, intact bone marrow within the cortex of whole long bones remains a challenge, especially at subcellular resolution. We present a method that stabilizes the marrow and provides subcellular resolution of fluorescent signals throughout the murine femur, enabling identification and spatial characterization of hematopoietic and stromal cell subsets. By combining a pre-processing algorithm for stripe artifact removal with a machine-learning approach, we demonstrate reliable cell segmentation down to the deepest bone marrow regions. This reveals age-related changes in the marrow. It highlights the interaction between CXCR1 cells and the vascular system in homeostasis, in contrast to other myeloid cell types, and reveals their spatial characteristics after injury. The broad applicability of this method will contribute to a better understanding of bone marrow biology.

}, keywords = {Animals, Bone Marrow, Bone Marrow Cells, Hematopoiesis, Hematopoietic Stem Cells, Mice, Stromal Cells}, issn = {2041-1723}, doi = {10.1038/s41467-024-45827-6}, author = {Mertens, Till Fabian and Liebheit, Alina Tabea and Ehl, Johanna and K{\"o}hler, Ralf and Rakhymzhan, Asylkhan and Woehler, Andrew and Katth{\"a}n, Lukas and Ebel, Gernot and Liublin, Wjatscheslaw and Kasapi, Ana and Triantafyllopoulou, Antigoni and Schulz, Tim Julius and Niesner, Raluca Aura and Hauser, Anja Erika} } @article {69170, title = {Mechanical stretch regulates macropinocytosis in Hydra vulgaris.}, journal = {Molecular Biology of the Cell}, year = {2024}, month = {2024 Jan 24}, pages = {mbcE22020065}, abstract = {

Cells rely on a diverse array of engulfment processes to sense, exploit, and adapt to their environments. Among these, macropinocytosis enables indiscriminate and rapid uptake of large volumes of fluid and membrane, rendering it a highly versatile engulfment strategy. Much of the molecular machinery required for macropinocytosis has been well established, yet how this process is regulated in the context of organs and organisms remains poorly understood. Here, we report the discovery of extensive macropinocytosis in the outer epithelium of the cnidarian . Exploiting {\textquoteright}s relatively simple body plan, we developed approaches to visualize macropinocytosis over extended periods of time, revealing constitutive engulfment across the entire body axis. We show that the direct application of planar stretch leads to calcium influx and the inhibition of macropinocytosis. Finally, we establish a role for stretch-activated channels in inhibiting this process. Together, our approaches provide a platform for the mechanistic dissection of constitutive macropinocytosis in physiological contexts and highlight a potential role for macropinocytosis in responding to cell surface tension. [Media: see text] [Media: see text] [Media: see text] [Media: see text].

}, issn = {1939-4586}, doi = {10.1091/mbc.E22-02-0065}, author = {Skokan, Taylor D and Hobmayer, Bert and McKinley, Kara L and Vale, Ronald D} } @article {69400, title = {Mitochondrially-associated actin waves maintain organelle homeostasis and equitable inheritance.}, journal = {Curr Opin Cell Biol}, volume = {88}, year = {2024}, month = {2024 Apr 30}, pages = {102364}, abstract = {

First identified in dividing cells as revolving clusters of actin filaments, these are now understood as mitochondrially-associated actin waves that are active throughout the cell cycle. These waves are formed from the polymerization of actin onto a subset of mitochondria. Within minutes, this F-actin depolymerizes while newly formed actin filaments assemble onto neighboring mitochondria. In interphase, actin waves locally fragment the mitochondrial network, enhancing mitochondrial content mixing to maintain organelle homeostasis. In dividing cells actin waves spatially mix mitochondria in the mother cell to ensure equitable partitioning of these organelles between daughter cells. Progress has been made in understanding the consequences of actin cycling as well as the underlying molecular mechanisms, but many questions remain, and here we review these elements. Also, we draw parallels between mitochondrially-associated actin cycling and cortical actin waves. These dynamic systems highlight the remarkable plasticity of the actin cytoskeleton.

}, issn = {1879-0410}, doi = {10.1016/j.ceb.2024.102364}, author = {Coscia, Stephen M and Moore, Andrew S and Wong, Yvette C and Holzbaur, Erika L F} } @article {69622, title = {A modular chemigenetic calcium indicator for multiplexed in vivo functional imaging.}, journal = {Nat Methods}, year = {2024}, month = {2024 Sep 20}, abstract = {

Genetically encoded fluorescent calcium indicators allow cellular-resolution recording of physiology. However, bright, genetically targetable indicators that can be multiplexed with existing tools in vivo are needed for simultaneous imaging of multiple signals. Here we describe WHaloCaMP, a modular chemigenetic calcium indicator built from bright dye-ligands and protein sensor domains. Fluorescence change in WHaloCaMP results from reversible quenching of the bound dye via a strategically placed tryptophan. WHaloCaMP is compatible with rhodamine dye-ligands that fluoresce from green to near-infrared, including several that efficiently label the brain in animals. When bound to a near-infrared dye-ligand, WHaloCaMP shows a 7{\texttimes} increase in fluorescence intensity and a 2.1-ns increase in fluorescence lifetime upon calcium binding. We use WHaloCaMP1a to image Ca responses in vivo in flies and mice, to perform three-color multiplexed functional imaging of hundreds of neurons and astrocytes in zebrafish larvae and to quantify Ca concentration using fluorescence lifetime imaging microscopy (FLIM).

}, issn = {1548-7105}, doi = {10.1038/s41592-024-02411-6}, url = {https://doi.org/10.1038/s41592-024-02411-6}, author = {Farrants, Helen and Shuai, Yichun and Lemon, William C and Monroy Hernandez, Christian and Zhang, Deng and Yang, Shang and Patel, Ronak and Qiao, Guanda and Frei, Michelle S and Plutkis, Sarah E and Grimm, Jonathan B and Hanson, Timothy L and Tomaska, Filip and Turner, Glenn C and Stringer, Carsen and Keller, Philipp J and Beyene, Abraham G and Chen, Yao and Liang, Yajie and Lavis, Luke D and Schreiter, Eric R} } @article {69534, title = {Molecular and cellular mechanisms of teneurin signaling in synaptic partner matching.}, journal = {Cell}, year = {2024}, month = {2024 Jul 03}, abstract = {

In developing brains, axons exhibit remarkable precision in selecting synaptic partners among many non-partner cells. Evolutionarily conserved teneurins are transmembrane proteins that instruct synaptic partner matching. However, how intracellular signaling pathways execute teneurins{\textquoteright} functions is unclear. Here, we use in situ proximity labeling to obtain the intracellular interactome of a teneurin (Ten-m) in the Drosophila brain. Genetic interaction studies using quantitative partner matching assays in both olfactory receptor neurons (ORNs) and projection neurons (PNs) reveal a common pathway: Ten-m binds to and negatively regulates a RhoGAP, thus activating the Rac1 small GTPases to promote synaptic partner matching. Developmental analyses with single-axon resolution identify the cellular mechanism of synaptic partner matching: Ten-m signaling promotes local F-actin levels and stabilizes ORN axon branches that contact partner PN dendrites. Combining spatial proteomics and high-resolution phenotypic analyses, this study advanced our understanding of both cellular and molecular mechanisms of synaptic partner matching.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2024.06.022}, author = {Xu, Chuanyun and Li, Zhuoran and Lyu, Cheng and Hu, Yixin and McLaughlin, Colleen N and Wong, Kenneth Kin Lam and Xie, Qijing and Luginbuhl, David J and Li, Hongjie and Udeshi, Namrata D and Svinkina, Tanya and Mani, D R and Han, Shuo and Li, Tongchao and Li, Yang and Guajardo, Ricardo and Ting, Alice Y and Carr, Steven A and Li, Jiefu and Luo, Liqun} } @article {69219, title = {More than just {\textquoteright}added value{\textquoteright}: The perils of not establishing shared core facilities in resource-constrained communities.}, journal = {Journal of Microscopy}, year = {2024}, month = {2024 Feb 20}, abstract = {

The accelerating pace of technological advancements necessitates specialised expertise and cutting-edge instruments to maintain competitive research in life sciences. Core facilities - collaborative laboratories equipped with state-of-the-art tools and staffed by expert personnel - are vital resources that support diverse scientific endeavours. However, their adoption in lower-income communities has been comparatively stagnant due to both financial and cultural challenges. This paper explores the perils of not supporting core facilities on national research enterprises, underscoring the need for balanced investments in discovery science and crucial infrastructure support. We explore the implications from the perspectives of funders, university leaders and lab heads. We advocate for a paradigm shift to recognise these facilities as essential components of national research efforts. Core facilities are positioned not as optional but as strategic investments that can catalyse breakthroughs, particularly in environments with limited resources.

}, issn = {1365-2818}, doi = {10.1111/jmi.13277}, author = {Rahmoon, Mai A and Hobson, Chad M and Aaron, Jesse S and Balasubramanian, Harikrushnan and Chew, Teng-Leong} } @article {69321, title = {More than just {\textquoteright}added value{\textquoteright}: The perils of not establishing shared core facilities in resource-constrained communities.}, journal = {J Microsc}, year = {2024}, month = {2024 Feb 20}, abstract = {

The accelerating pace of technological advancements necessitates specialised expertise and cutting-edge instruments to maintain competitive research in life sciences. Core facilities - collaborative laboratories equipped with state-of-the-art tools and staffed by expert personnel - are vital resources that support diverse scientific endeavours. However, their adoption in lower-income communities has been comparatively stagnant due to both financial and cultural challenges. This paper explores the perils of not supporting core facilities on national research enterprises, underscoring the need for balanced investments in discovery science and crucial infrastructure support. We explore the implications from the perspectives of funders, university leaders and lab heads. We advocate for a paradigm shift to recognise these facilities as essential components of national research efforts. Core facilities are positioned not as optional but as strategic investments that can catalyse breakthroughs, particularly in environments with limited resources.

}, issn = {1365-2818}, doi = {10.1111/jmi.13277}, author = {Rahmoon, Mai A and Hobson, Chad M and Aaron, Jesse S and Balasubramanian, Harikrushnan and Chew, Teng-Leong} } @article {69169, title = {Motion of VAPB molecules reveals ER-mitochondria contact site subdomains.}, journal = {Nature}, volume = {626}, year = {2024}, month = {2024 Jan 24}, pages = {169-176}, abstract = {

To coordinate cellular physiology, eukaryotic cells rely on the rapid exchange of molecules at specialized organelle-organelle contact sites. Endoplasmic reticulum-mitochondrial contact sites (ERMCSs) are particularly vital communication hubs, playing key roles in the exchange of signalling molecules, lipids and metabolites. ERMCSs are maintained by interactions between complementary tethering molecules on the surface of each organelle. However, due to the extreme sensitivity of these membrane interfaces to experimental perturbation, a clear understanding of their nanoscale organization and regulation is still lacking. Here we combine three-dimensional electron microscopy with high-speed molecular tracking of a model organelle tether, Vesicle-associated membrane protein (VAMP)-associated protein B (VAPB), to map the structure and diffusion landscape of ERMCSs. We uncovered dynamic subdomains within VAPB contact sites that correlate with ER membrane curvature and undergo rapid remodelling. We show that VAPB molecules enter and leave ERMCSs within seconds, despite the contact site itself remaining stable over much longer time scales. This metastability allows ERMCSs to remodel with changes in the physiological environment to accommodate metabolic needs of the cell. An amyotrophic lateral sclerosis-associated mutation in VAPB perturbs these subdomains, likely impairing their remodelling capacity and resulting in impaired interorganelle communication. These results establish high-speed single-molecule imaging as a new tool for mapping the structure of contact site interfaces and reveal that the diffusion landscape of VAPB at contact sites is a crucial component of ERMCS homeostasis.

}, keywords = {Amyotrophic Lateral Sclerosis, Endoplasmic Reticulum, Humans, Mitochondria, Mitochondrial Membranes, Signal Transduction, Vesicular Transport Proteins}, issn = {1476-4687}, doi = {10.1038/s41586-023-06956-y}, author = {Obara, Christopher J and Nixon-Abell, Jonathon and Moore, Andrew S and Riccio, Federica and Hoffman, David P and Shtengel, Gleb and Xu, C Shan and Schaefer, Kathy and Pasolli, H Amalia and Masson, Jean-Baptiste and Hess, Harald F and Calderon, Christopher P and Blackstone, Craig and Lippincott-Schwartz, Jennifer} } @article {69301, title = {Motor neurons generate pose-targeted movements via proprioceptive sculpting.}, journal = {Nature}, year = {2024}, month = {2024 Mar 20}, abstract = {

Motor neurons are the final common pathway through which the brain controls movement of the body, forming the basic elements from which all movement is composed. Yet how a single motor neuron contributes to control during natural movement remains unclear. Here we anatomically and functionally characterize the individual roles of the motor neurons that control head movement in the fly, Drosophila melanogaster. Counterintuitively, we find that activity in a single motor neuron rotates the head in different directions, depending on the starting posture of the head, such that the head converges towards a pose determined by the identity of the stimulated motor neuron. A feedback model predicts that this convergent behaviour results from motor neuron drive interacting with proprioceptive feedback. We identify and genetically suppress a single class of proprioceptive neuron that changes the motor neuron-induced convergence as predicted by the feedback model. These data suggest a framework for how the brain controls movements: instead of directly generating movement in a given direction by activating a fixed set of motor neurons, the brain controls movements by adding bias to a continuing proprioceptive-motor loop.

}, issn = {1476-4687}, doi = {10.1038/s41586-024-07222-5}, author = {Gorko, Benjamin and Siwanowicz, Igor and Close, Kari and Christoforou, Christina and Hibbard, Karen L and Kabra, Mayank and Lee, Allen and Park, Jin-Yong and Li, Si Ying and Chen, Alex B and Namiki, Shigehiro and Chen, Chenghao and Tuthill, John C and Bock, Davi D and Rouault, Herv{\'e} and Branson, Kristin and Ihrke, Gudrun and Huston, Stephen J} } @article {68936, title = {Multi-day neuron tracking in high-density electrophysiology recordings using earth mover{\textquoteright}s distance}, journal = {eLife}, year = {2024}, month = {2024-07-10}, abstract = {

Accurate tracking of the same neurons across multiple days is crucial for studying changes in neuronal activity during learning and adaptation. Advances in high-density extracellular electrophysiology recording probes, such as Neuropixels, provide a promising avenue to accomplish this goal. Identifying the same neurons in multiple recordings is, however, complicated by non-rigid movement of the tissue relative to the recording sites (drift) and loss of signal from some neurons. Here, we propose a neuron tracking method that can identify the same cells independent of firing statistics, that are used by most existing methods. Our method is based on between-day non-rigid alignment of spike-sorted clusters. We verified the same cell identity in mice using measured visual receptive fields. This method succeeds on datasets separated from 1 to 47 days, with an 84\% average recovery rate.

}, doi = {10.7554/eLife.92495.3}, url = {https://doi.org/10.7554/eLife.92495.3}, author = {Augustine Xiaoran Yuan and Jennifer Colonell and Anna Lebedeva and Adam Charles and Timothy Harris} } @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 {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 {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 {69669, title = {ONIX: a unified open-source platform for multimodal neural recording and perturbation during naturalistic behavior.}, journal = {Nat Methods}, year = {2024}, month = {2024 Nov 11}, abstract = {

Behavioral neuroscience faces two conflicting demands: long-duration recordings from large neural populations and unimpeded animal behavior. To meet this challenge we developed ONIX, an open-source data acquisition system with high data throughput (2 GB s) and low closed-loop latencies (\<1 ms) that uses a 0.3-mm thin tether to minimize behavioral impact. Head position and rotation are tracked in three dimensions and used to drive active commutation without torque measurements. ONIX can acquire data from combinations of passive electrodes, Neuropixels probes, head-mounted microscopes, cameras, three-dimensional trackers and other data sources. We performed uninterrupted, long (~7 h) neural recordings in mice as they traversed complex three-dimensional terrain, and multiday sleep-tracking recordings (~55 h). ONIX enabled exploration with similar mobility as nonimplanted animals, in contrast to conventional tethered systems, which have restricted movement. By combining long recordings with full mobility, our technology will enable progress on questions that require high-quality neural recordings during ethologically grounded behaviors.

}, issn = {1548-7105}, doi = {10.1038/s41592-024-02521-1}, url = {https://doi.org/10.1038/s41592-024-02521-1}, author = {Newman, Jonathan P and Zhang, Jie and Cuevas-L{\'o}pez, Aar{\'o}n and Miller, Nicholas J and Honda, Takato and van der Goes, Marie-Sophie H and Leighton, Alexandra H and Carvalho, Filipe and Lopes, Gon{\c c}alo and Lakunina, Anna and Siegle, Joshua H and Harnett, Mark T and Wilson, Matthew A and Voigts, Jakob} } @article {68531, title = {Organelle proteomic profiling reveals lysosomal heterogeneity in association with longevity}, journal = {eLife}, year = {2024}, month = {2024 Jan 19}, abstract = {

Lysosomes are active sites to integrate cellular metabolism and signal transduction. A collection of proteins enriched at lysosomes mediate these metabolic and signaling functions. Both lysosomal metabolism and lysosomal signaling have been linked with longevity regulation; however, how lysosomes adjust their protein composition to accommodate this regulation remains unclear. Using large-scale proteomic profiling, we systemically profiled lysosome- enriched proteomes in association with different longevity mechanisms. We further discovered the lysosomal recruitment of AMPK and nucleoporin proteins and their requirements for longevity in response to increased lysosomal lipolysis. Through comparative proteomic analyses of lysosomes from different tissues and labeled with different markers, we discovered lysosomal heterogeneity across tissues as well as the specific enrichment of the Ragulator complex on Cystinosin positive lysosomes. Together, this work uncovers lysosomal proteome heterogeneity at different levels and provides resources for understanding the contribution of lysosomal proteome dynamics in modulating signal transduction, organelle crosstalk and organism longevity.

}, doi = {10.7554/eLife.85214}, url = {https://doi.org/10.7554/eLife.85214}, author = {Yong Yu and Shihong M. Gao and Youchen Guan and Pei-Wen Hu and Qinghao Zhang and Jiaming Liu and Bentian Jing and Qian Zhao and David M Sabatini and Monther Abu-Remaileh and Sung Yun Jung and Meng C. Wang} } @article {69229, title = {Organization of an ascending circuit that conveys flight motor state in Drosophila.}, journal = {Current Biology}, year = {2024}, month = {2024 Feb 13}, abstract = {

Natural behaviors are a coordinated symphony of motor acts that drive reafferent (self-induced) sensory activation. Individual sensors cannot disambiguate exafferent (externally induced) from reafferent sources. Nevertheless, animals readily differentiate between these sources of sensory signals to carry out adaptive behaviors through corollary discharge circuits (CDCs), which provide predictive motor signals from motor pathways to sensory processing and other motor pathways. Yet, how CDCs comprehensively integrate into the nervous system remains unexplored. Here, we use connectomics, neuroanatomical, physiological, and behavioral approaches to resolve the network architecture of two pairs of ascending histaminergic neurons (AHNs) in Drosophila, which function as a predictive CDC in other insects. Both AHN pairs receive input primarily from a partially overlapping population of descending neurons, especially from DNg02, which controls wing motor output. Using Ca imaging and behavioral recordings, we show that AHN activation is correlated to flight behavior and precedes wing motion. Optogenetic activation of DNg02 is sufficient to activate AHNs, indicating that AHNs are activated by descending commands in advance of behavior and not as a consequence of sensory input. Downstream, each AHN pair targets predominantly non-overlapping networks, including those that process visual, auditory, and mechanosensory information, as well as networks controlling wing, haltere, and leg sensorimotor control. These results support the conclusion that the AHNs provide a predictive motor signal about wing motor state to mostly non-overlapping sensory and motor networks. Future work will determine how AHN signaling is driven by other descending neurons and interpreted by AHN downstream targets to maintain adaptive sensorimotor performance.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2024.01.071}, author = {Cheong, Han S J and Boone, Kaitlyn N and Bennett, Marryn M and Salman, Farzaan and Ralston, Jacob D and Hatch, Kaleb and Allen, Raven F and Phelps, Alec M and Cook, Andrew P and Phelps, Jasper S and Erginkaya, Mert and Lee, Wei-Chung A and Card, Gwyneth M and Daly, Kevin C and Dacks, Andrew M} } @article {69707, title = {Pearling Drives Mitochondrial DNA Nucleoid Distribution}, journal = {bioRxiv}, year = {2024}, month = {12/2024}, abstract = {

The regular distribution of mitochondrial DNA-containing nucleoids is essential for mitochondrial function and genome inheritance; however, the underlying mechanisms remain unknown. Our data reveal that mitochondria frequently undergo spontaneous and reversible pearling - a biophysical instability in which tubules undulate into regularly spaced beads. We discovered that pearling imposes a characteristic length scale, simultaneously mediating nucleoid disaggregation and establishing inter-nucleoid distancing with near-maximally achievable precision. Cristae invaginations play a dual role: lamellar cristae density determines pearling frequency and duration, and preserves the resulting nucleoid spacing after recovery. The distribution of mitochondrial genomes is thus fundamentally governed by the interplay between spontaneous pearling and cristae ultrastructure.

}, doi = {10.1101/2024.12.21.629917}, url = {https://www.biorxiv.org/content/early/2024/12/22/2024.12.21.629917}, author = {Landoni, Juan C. and Lycas, Matthew D. and Macuada, Josefa and Jaccard, Romeo and Obara, Christopher J. and Moore, Andrew S. and Ben Nejma, Sheda and Hoffman, David and Lippincott-Schwartz, Jennifer and Marshall, Wallace and Sturm, Gabriel and Manley, Suliana} } @article {69704, title = {Periodic ER-plasma membrane junctions support long-range Ca signal integration in dendrites.}, journal = {Cell}, year = {2024}, month = {2024 Dec 18}, abstract = {

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

}, issn = {1097-4172}, doi = {10.1016/j.cell.2024.11.029}, author = {Benedetti, Lorena and Fan, Ruolin and Weigel, Aubrey V and Moore, Andrew S and Houlihan, Patrick R and Kittisopikul, Mark and Park, Grace and Petruncio, Alyson and Hubbard, Philip M and Pang, Song and Xu, C Shan and Hess, Harald F and Saalfeld, Stephan and Rangaraju, Vidhya and Clapham, David E and De Camilli, Pietro and Ryan, Timothy A and Lippincott-Schwartz, Jennifer} } @article {69472, title = {The physical and cellular mechanism of structural color change in zebrafish.}, journal = {Proc Natl Acad Sci U S A}, volume = {121}, year = {2024}, month = {2024 Jun 04}, pages = {e2308531121}, abstract = {

Many animals exhibit remarkable colors that are produced by the constructive interference of light reflected from arrays of intracellular guanine crystals. These animals can fine-tune their crystal-based structural colors to communicate with each other, regulate body temperature, and create camouflage. While it is known that these changes in color are caused by changes in the angle of the crystal arrays relative to incident light, the cellular machinery that drives color change is not understood. Here, using a combination of 3D focused ion beam scanning electron microscopy (FIB-SEM), micro-focused X-ray diffraction, superresolution fluorescence light microscopy, and pharmacological perturbations, we characterized the dynamics and 3D cellular reorganization of crystal arrays within zebrafish iridophores during norepinephrine (NE)-induced color change. We found that color change results from a coordinated 20{\textdegree} tilting of the intracellular crystals, which alters both crystal packing and the angle at which impinging light hits the crystals. Importantly, addition of the dynein inhibitor dynapyrazole-a completely blocked this NE-induced red shift by hindering crystal dynamics upon NE addition. FIB-SEM and microtubule organizing center (MTOC) mapping showed that microtubules arise from two MTOCs located near the poles of the iridophore and run parallel to, and in between, individual crystals. This suggests that dynein drives crystal angle change in response to NE by binding to the limiting membrane surrounding individual crystals and walking toward microtubule minus ends. Finally, we found that intracellular cAMP regulates the color change process. Together, our results provide mechanistic insight into the cellular machinery that drives structural color change.

}, keywords = {Animals, Color, Microscopy, Electron, Scanning, Norepinephrine, Pigmentation, Zebrafish, Zebrafish Proteins}, issn = {1091-6490}, doi = {10.1073/pnas.2308531121}, author = {Gur, Dvir and Moore, Andrew S and Deis, Rachael and Song, Pang and Wu, Xufeng and Pinkas, Iddo and Deo, Claire and Iyer, Nirmala and Hess, Harald F and Hammer, John A and Lippincott-Schwartz, Jennifer} } @article {69579, title = {Plasticity-induced actin polymerization in the dendritic shaft regulates intracellular AMPA receptor trafficking.}, journal = {Elife}, volume = {13}, year = {2024}, month = {2024 Aug 15}, abstract = {

AMPA-type receptors (AMPARs) are rapidly inserted into synapses undergoing plasticity to increase synaptic transmission, but it is not fully understood if and how AMPAR-containing vesicles are selectively trafficked to these synapses. Here, we developed a strategy to label AMPAR GluA1 subunits expressed from their endogenous loci in cultured rat hippocampal neurons and characterized the motion of GluA1-containing vesicles using single-particle tracking and mathematical modeling. We find that GluA1-containing vesicles are confined and concentrated near sites of stimulation-induced structural plasticity. We show that confinement is mediated by actin polymerization, which hinders the active transport of GluA1-containing vesicles along the length of the dendritic shaft by modulating the rheological properties of the cytoplasm. Actin polymerization also facilitates myosin-mediated transport of GluA1-containing vesicles to exocytic sites. We conclude that neurons utilize F-actin to increase vesicular GluA1 reservoirs and promote exocytosis proximal to the sites of synaptic activity.

}, keywords = {Actins, Animals, Cells, Cultured, Dendrites, Exocytosis, Hippocampus, Neuronal Plasticity, Neurons, Polymerization, Protein Transport, Rats, Receptors, AMPA}, issn = {2050-084X}, doi = {10.7554/eLife.80622}, url = {https://doi.org/10.7554/eLife.80622}, author = {Wong, Victor C and Houlihan, Patrick R and Liu, Hui and Walpita, Deepika and DeSantis, Michael C and Liu, Zhe and O{\textquoteright}Shea, Erin K} } @article {69688, title = {Quantitative Spatial Analysis of Chromatin Biomolecular Condensates using Cryo-Electron Tomography}, journal = {bioRxiv}, year = {2024}, month = {2024 Dec 02}, abstract = {

Phase separation is an important mechanism to generate certain biomolecular condensates and organize the cell interior. Condensate formation and function remain incompletely understood due to difficulties in visualizing the condensate interior at high resolution. Here we analyzed the structure of biochemically reconstituted chromatin condensates through cryo-electron tomography. We found that traditional blotting methods of sample preparation were inadequate, and high-pressure freezing plus focused ion beam milling was essential to maintain condensate integrity. To identify densely packed molecules within the condensate, we integrated deep learning-based segmentation with novel context-aware template matching. Our approaches were developed on chromatin condensates, and were also effective on condensed regions of in situ native chromatin. Using these methods, we determined the average structure of nucleosomes to 6.1 and 12 {\r A} resolution in reconstituted and native systems, respectively, and found that nucleosomes have a nearly random orientation distribution in both cases. Our methods should be applicable to diverse biochemically reconstituted biomolecular condensates and to some condensates in cells.

}, doi = {10.1101/2024.12.01.626131}, url = {https://doi.org/10.1101/2024.12.01.626131}, author = {Zhou, Huabin and Hutchings, Joshua and Shiozaki, Momoko and Zhao, Xiaowei and Doolittle, Lynda K. and Yang, Shixin and Yan, Rui and Jean, Nikki and Riggi, Margot and Yu, Zhiheng and Villa, Elizabeth and Rosen, Michael K.} } @article {69655, title = {Rapid Whole-Organ Characterization via Quantitative Light-Sheet Microscopy}, journal = {Laser \& Photonics Reviews}, year = {2024}, month = {2024 Oct 22}, pages = {2401177}, abstract = {

Whole-organ imaging and characterization at a submicron level provide abundant information on development and diseases while remaining a big challenge, especially in the context of time load. Herein, a quantitative light-sheet microscopy platform that enabled highly time-efficient assessments of fibrous structures within the intact cleared tissue is developed. Dual-view inverted selective plane illumination microscopy (diSPIM), followed by improved registration and deconvolution, led to submicron isotropic imaging of mouse upper genital tract with one hundred-fold speed-ups than previous efforts. Further, optical metrics quantifying 3D local density and structural complexity of targets based on parallel and vectorized convolution in both spatial and frequency domains are developed. Collectively, ≈400{\textendash}2000 fold increases in time efficiency counting for imaging, postprocessing, and quantitative characterization compared to the traditional method is gained. Using this platform, automatic identification of medulla and cortex within the mouse ovary at over 90\% overlap with manual selection by anatomy experts is achieved. Additionally, heterogeneous distributions of immune cells in the mouse ovary and fallopian tube, offering a unique perspective for understanding the immune microenvironment are discovered. This work paves the way for future whole-organ study, and exhibits potential with promise for offering mechanistic insights into physiological and pathological alterations of biological tissues.

}, keywords = {immune microenvironment, light-sheet microscopy, quantitative characterization, whole-organ imaging}, doi = {10.1002/lpor.202401177}, url = {https://doi.org/10.1002/lpor.202401177}, author = {Chen, Lingmei and Su, Yijun and Qian, Shuhao and Zhou, Lingxi and Han, Tao and Wang, Chuncheng and Jiang, Rushan and Ding, Zhihua and Guo, Min and Liu, Zhiyi} } @article {69217, title = {A ratiometric ER calcium sensor for quantitative comparisons across cell types and subcellular regions.}, journal = {bioRxiv}, year = {2024}, month = {2024 Feb 16}, abstract = {

The endoplasmic reticulum (ER) is an important regulator of Ca2+\ in cells and dysregulation of ER calcium homeostasis can lead to numerous pathologies. Understanding how various pharmacological and genetic perturbations of ER Ca2+\ homeostasis impacts cellular physiology would likely be facilitated by more quantitative measurements of ER Ca2+\ levels that allow easier comparisons across conditions. Here, we developed a ratiometric version of our original ER-GCaMP probe that allows for more quantitative comparisons of the concentration of Ca2+\ in the ER across cell types and sub-cellular compartments. Using this approach we show that the resting concentration of ER Ca2+ in primary dissociated neurons is substantially lower than that in measured in embryonic fibroblasts.

}, doi = {10.1101/2024.02.15.580492}, url = {https://doi.org/10.1101/2024.02.15.580492}, author = {Ryan J. Farrell and Kirsten G. Bredvik and Michael B. Hoppa and S. Thomas Hennigan and Timothy A. Brown and Timothy A. Ryan} } @article {69404, title = {Recognising the importance and impact of Imaging Scientists: Global guidelines for establishing career paths within core facilities}, journal = {J Microsc}, year = {2024}, month = {2024 May 01}, abstract = {

In the dynamic landscape of scientific research, imaging core facilities are vital hubs propelling collaboration and innovation at the technology development and dissemination frontier. Here, we present a collaborative effort led by Global BioImaging (GBI), introducing international recommendations geared towards elevating the careers of Imaging Scientists in core facilities. Despite the critical role of Imaging Scientists in modern research ecosystems, challenges persist in recognising their value, aligning performance metrics and providing avenues for career progression and job security. The challenges encompass a mismatch between classic academic career paths and service-oriented roles, resulting in a lack of understanding regarding the value and impact of Imaging Scientists and core facilities and how to evaluate them properly. They further include challenges around sustainability, dedicated training opportunities and the recruitment and retention of talent. Structured across these interrelated sections, the recommendations within this publication aim to propose globally applicable solutions to navigate these challenges. These recommendations apply equally to colleagues working in other core facilities and research institutions through which access to technologies is facilitated and supported. This publication emphasises the pivotal role of Imaging Scientists in advancing research programs and presents a blueprint for fostering their career progression within institutions all around the world.

}, issn = {1365-2818}, doi = {10.1111/jmi.13307}, author = {Wright, Graham D and Thompson, Kerry A and Reis, Yara and Bischof, Johanna and Hockberger, Philip Edward and Itano, Michelle S and Yen, Lisa and Adelodun, Stephen Taiye and Bialy, Nikki and Brown, Claire M and Chaabane, Linda and Chew, Teng-Leong and Chitty, Andrew I and Cordeli{\`e}res, Fabrice P and De Niz, Mariana and Ellenberg, Jan and Engelbrecht, Lize and Fabian-Morales, Eunice and Fazeli, Elnaz and Fernandez-Rodriguez, Julia and Ferrando-May, Elisa and Fletcher, Georgina and Galloway, Graham John and Guerrero, Adan and Guimar{\~a}es, Jander Matos and Jacobs, Caron A and Jayasinghe, Sachintha and Kable, Eleanor and Kitten, Gregory T and Komoto, Shinya and Ma, Xiaoxiao and Marques, J{\'e}ssica Ara{\'u}jo and Millis, Bryan A and Miranda, Kildare and JohnO{\textquoteright}Toole, Peter and Olatunji, Sunday Yinka and Paina, Federica and Pollak, Cora Noemi and Prats, Clara and Pylv{\"a}n{\"a}inen, Joanna W and Rahmoon, Mai Atef and Reiche, Michael A and Riches, James Douglas and Rossi, Andres Hugo and Salamero, Jean and Thiriet, Caroline and Terjung, Stefan and Vasconcelos, Aldenora Dos Santos and Keppler, Antje} } @article {69248, title = {Recommendations for accelerating open preprint peer review to improve the culture of science}, journal = {PLOS Biology}, volume = {22}, year = {2024}, month = {2024 Feb 29}, pages = {e3002502}, abstract = {

Peer review is an important part of the scientific process, but traditional peer review at journals is coming under increased scrutiny for its inefficiency and lack of transparency. As preprints become more widely used and accepted, they raise the possibility of rethinking the peer-review process. Preprints are enabling new forms of peer review that have the potential to be more thorough, inclusive, and collegial than traditional journal peer review, and to thus fundamentally shift the culture of peer review toward constructive collaboration. In this Consensus View, we make a call to action to stakeholders in the community to accelerate the growing momentum of preprint sharing and provide recommendations to empower researchers to provide open and constructive peer review for preprints.

}, doi = {10.1371/journal.pbio.300250210.1371/journal.pbio.3002502.g001}, url = {https://dx.plos.org/10.1371/journal.pbio.3002502https://dx.plos.org/10.1371/journal.pbio.3002502https://dx.plos.org/10.1371/journal.pbio.3002502.g001}, author = {Avissar-Whiting, Michele and Belliard, Fr{\'e}d{\'e}rique and Bertozzi, Stefano M. and Brand, Amy and Brown, Katherine and Cl{\'e}ment-Stoneham, G{\'e}raldine and Dawson, Stephanie and Dey, Gautam and Ecer, Daniel and Edmunds, Scott C. and Farley, Ashley and Fischer, Tara D. and Franko, Maryrose and Fraser, James S. and Funk, Kathryn and Ganier, Clarisse and Harrison, Melissa and Hatch, Anna and Hazlett, Haley and Hindle, Samantha and Hook, Daniel W. and Hurst, Phil and Kamoun, Sophien and Kiley, Robert and Lacy, Michael M. and LaFlamme, Marcel and Lawrence, Rebecca and Lemberger, Thomas and Leptin, Maria and Lumb, Elliott and MacCallum, Catriona J. and Marcum, Christopher Steven and Marinello, Gabriele and Mendon{\c c}a, Alex and Monaco, Sara and Neves, Kleber and Pattinson, Damian and Polka, Jessica K. and Puebla, Iratxe and Rittman, Martyn and Royle, Stephen J. and Saderi, Daniela and Sever, Richard and Shearer, Kathleen and Spiro, John E. and Stern, Bodo and Taraborelli, Dario and Vale, Ron and Vasquez, Claudia G. and Waltman, Ludo and Watt, Fiona M. and Weinberg, Zara Y. and Williams, Mark} } @article {69231, title = {Recording physiological history of cells with chemical labeling.}, journal = {Science}, volume = {383}, year = {2024}, month = {2024 Feb 23}, pages = {890-897}, abstract = {

Recordings of the physiological history of cells provide insights into biological processes, yet obtaining such recordings is a challenge. To address this, we introduce a method to record transient cellular events for later analysis. We designed proteins that become labeled in the presence of both a specific cellular activity and a fluorescent substrate. The recording period is set by the presence of the substrate, whereas the cellular activity controls the degree of the labeling. The use of distinguishable substrates enabled the recording of successive periods of activity. We recorded protein-protein interactions, G protein-coupled receptor activation, and increases in intracellular calcium. Recordings of elevated calcium levels allowed selections of cells from heterogeneous populations for transcriptomic analysis and tracking of neuronal activities in flies and zebrafish.

}, keywords = {Animals, Calcium, Cell Physiological Phenomena, Cells, Coloring Agents, Gene Expression Profiling, Protein Interaction Domains and Motifs, Staining and Labeling, Zebrafish}, issn = {1095-9203}, doi = {10.1126/science.adg0812}, author = {Huppertz, Magnus-Carsten and Wilhelm, Jonas and Grenier, Vincent and Schneider, Martin W and Falt, Tjalda and Porzberg, Nicola and Hausmann, David and Hoffmann, Dirk C and Hai, Ling and Tarnawski, Miroslaw and Pino, Gabriela and Slanchev, Krasimir and Kolb, Ilya and Acuna, Claudio and Fenk, Lisa M and Baier, Herwig and Hiblot, Julien and Johnsson, Kai} } @article {69517, title = {Resolution in super-resolution microscopy - definition, trade-offs and perspectives.}, journal = {Nat Rev Mol Cell Biol}, year = {2024}, month = {2024 Jul 01}, abstract = {

Super-resolution microscopy (SRM) is gaining popularity in biosciences; however, claims about optical resolution are contested and often misleading. In this Viewpoint, experts share their views on resolution and common trade-offs, such as labelling and post-processing, aiming to clarify them for biologists and facilitate deeper understanding and best use of SRM.

}, issn = {1471-0080}, doi = {10.1038/s41580-024-00755-7}, author = {Prakash, Kirti and Baddeley, David and Eggeling, Christian and Fiolka, Reto and Heintzmann, Rainer and Manley, Suliana and Radenovic, Aleksandra and Smith, Carlas and Shroff, Hari and Schermelleh, Lothar} } @article {69473, title = {SciJava Ops: An Improved Algorithms Framework for Fiji and Beyond}, journal = {Front. Bioinform.}, volume = {4}, year = {2024}, month = {2024 Sep 26}, abstract = {

Decades of iteration on scientific imaging hardware and software has yielded an explosion in not only the size, complexity, and heterogeneity of image datasets but also in the tooling used to analyze this data. This wealth of image analysis tools, spanning different programming languages, frameworks, and data structures, is itself a problem for data analysts who must adapt to new technologies and integrate established routines to solve increasingly complex problems. While many {\textquotedblleft}bridge{\textquotedblright} layers exist to unify pairs of popular tools, there exists a need for a general solution to unify new and existing toolkits. The SciJava Ops library presented here addresses this need through two novel principles. Algorithm implementations are declared as plugins called Ops, providing a uniform interface regardless of the toolkit they came from. Users express their needs declaratively to the Op environment, which can then find and adapt available Ops on demand. By using these principles instead of direct function calls, users can write streamlined workflows while avoiding the translation boilerplate of bridge layers. Developers can easily extend SciJava Ops to introduce new libraries and more efficient, specialized algorithm implementations, even immediately benefitting existing workflows. We provide several use cases showing both user and developer benefits, as well as benchmarking data to quantify the negligible impact on overall analysis performance. We have initially deployed SciJava Ops on the Fiji platform, however it would be suitable for integration with additional analysis platforms in the future.

}, doi = {10.3389/fbinf.2024.1435733}, url = {https://doi.org/10.3389/fbinf.2024.1435733 }, author = {Gabriel J. Selzer and Curtis T. Rueden and Mark C. Hiner and Edward L. Evans III and David Kolb and Marcel Wiedenmann and Christian Birkhold and Tim-Oliver Buchholz and Stefan Helfrich and Brian Northan and Alison Walter and Johannes Schindelin and Tobias Pietzsch and Stephan Saalfeld and Michael R. Berthold and Kevin W. Eliceiri} } @article {69227, title = {A series of spontaneously blinking dyes for super-resolution microscopy}, journal = {bioRxiv}, year = {2024}, month = {2024 Feb 24}, abstract = {

Spontaneously blinking fluorophores permit the detection and localization of individual molecules without reducing buffers or caging groups, thus simplifying single-molecule localization microscopy (SMLM). The intrinsic blinking properties of such dyes are dictated by molecular structure and modulated by environment, which can limit utility. We report a series of tuned spontaneously blinking dyes with duty cycles that span two orders of magnitude, allowing facile SMLM in cells and dense biomolecular structures.

}, doi = {10.1101/2024.02.23.581625}, url = {https://www.biorxiv.org/content/early/2024/02/24/2024.02.23.581625}, author = {Katie L. Holland and Sarah E. Plutkis and Timothy A. Daugird and Abhishek Sau and Jonathan B. Grimm and Brian P. English and Qinsi Zheng and Sandeep Dave and Fariha Rahman and Liangqi Xie and Peng Dong and Ariana N. Tkachuk and Timothy A. Brown and Robert H. Singer and Zhe Liu and Catherine G. Galbraith and Siegfried M. Musser and Wesley R. Legant and Luke D. Lavis} } @article {69443, title = {Spatial mapping of hepatic ER and mitochondria architecture reveals zonated remodeling in fasting and obesity}, journal = {Nat Commun}, volume = {15}, year = {2024}, month = {2024 May 10}, pages = {3982}, abstract = {

The hepatocytes within the liver present an immense capacity to adapt to changes in nutrient availability. Here, by using high resolution volume electron microscopy, we map how hepatic subcellular spatial organization is regulated during nutritional fluctuations and as a function of liver zonation. We identify that fasting leads to remodeling of endoplasmic reticulum (ER) architecture in hepatocytes, characterized by the induction of single rough ER sheet around the mitochondria, which becomes larger and flatter. These alterations are enriched in periportal and mid-lobular hepatocytes but not in pericentral hepatocytes. Gain- and loss-of-function in vivo models demonstrate that the Ribosome receptor binding protein1 (RRBP1) is required to enable fasting-induced ER sheet-mitochondria interactions and to regulate hepatic fatty acid oxidation. Endogenous RRBP1 is enriched around periportal and mid-lobular regions of the liver. In obesity, ER-mitochondria interactions are distinct and fasting fails to induce rough ER sheet-mitochondrion interactions. These findings illustrate the importance of a regulated molecular architecture for hepatocyte metabolic flexibility.

}, keywords = {Animals, Endoplasmic Reticulum, Fasting, Fatty Acids, Hepatocytes, Humans, Liver, Male, Mice, Mice, Inbred C57BL, Mitochondria, Mitochondria, Liver, Obesity, Oxidation-Reduction, Ribosomal Proteins}, issn = {2041-1723}, doi = {10.1038/s41467-024-48272-7}, author = {Parlakg{\"u}l, G{\"u}ne{\c s} and Pang, Song and Artico, Leonardo L and Min, Nina and Cagampan, Erika and Villa, Reyna and Goncalves, Renata L S and Lee, Grace Yankun and Xu, C Shan and Hotam{\i}{\c s}l{\i}gil, G{\"o}khan S and Arruda, Ana Paula} } @article {69694, title = {Spatial single-cell Organellomics reveals nutrient dependent hepatocyte heterogeneity and predicts pathophysiological status in vivo}, journal = {bioRxiv}, year = {2024}, month = {2024 Dec 08}, abstract = {

Cellular heterogeneity within complex tissues and organs is essential to coordinate biological processes across biological scales. The effect of local cues and tissue microenvironments on cell heterogeneity has been mainly studied at the transcriptional level. However, it is within the subcellular scale - the organelles - that lays the machinery to conduct most metabolic reactions and maintain cells alive, ensuring proper tissue function. How changes in subcellular organization under different microenvironments define the functional diversity of cells within organs remains largely unexplored. Here we determine how organelles adapt to different microenvironments using the mouse liver as model system, in combination with computational approaches and machine-learning. To understand organelle adaptation in response to changing nutritional conditions, we analyzed 3D fluorescent microscopy volumes of liver samples labeled to simultaneously visualize mitochondria, peroxisomes, and lipid droplets from mice subjected to different diets: a control diet, a high-fat diet, and a control diet plus fasting. A Cellpose based pipeline was implemented for cell and organelle segmentation, which allowed us to measure 100 different organelle metrics and helped us define subcellular architectures in liver samples at the single cell level. Our results showed that hepatocytes display distinct subcellular architectures within different regions of the liver-close to the central vein, in the middle region, and near the portal vein- and across the various diet groups, thus reflecting their adaptation to specific nutritional inputs. Principal component analysis and clustering of hepatocytes based on organelle signatures revealed 12 different hepatocyte categories within the different experimental groups, highlighting a reduction in hepatocyte heterogeneity under nutritional perturbations. Finally, using single cell organelle signatures exclusively, we generated machine learning models that were able to predict with high accuracy different hepatocyte categories, diet groups, and the stages of MASLD. Our results demonstrate how organelle signatures can be used as hallmarks to define hepatocyte heterogeneity and their adaptation to different nutritional conditions. In the future, our strategy, which combines subcellular resolution imaging of liver volumes and machine learning, could help establish protocols to better define and predict liver disease progression.

}, doi = {10.1101/2024.12.06.627285}, url = {https://doi.org/10.1101/2024.12.06.627285}, author = {Hillsley, Alexander and Adhikari, Raghabendra and Johnson, Alana Dowdell and Espinosa-Medina, Isabel and Funke, Jan and Feliciano, Daniel} } @article {69329, title = {A split-GAL4 driver line resource for Drosophila CNS cell types}, journal = {bioRxiv}, year = {2024}, month = {2024 Jan 10}, abstract = {

Techniques that enable precise manipulations of subsets of neurons in the fly central nervous system have greatly facilitated our understanding of the neural basis of behavior. Split-GAL4 driver lines allow specific targeting of cell types in Drosophila melanogaster and other species. We describe here a collection of 3060 lines targeting a range of cell types in the adult Drosophila central nervous system and 1373 lines characterized in third-instar larvae. These tools enable functional, transcriptomic, and proteomic studies based on precise anatomical targeting. NeuronBridge and other search tools relate light microscopy images of these split-GAL4 lines to connectomes reconstructed from electron microscopy images. The collections are the result of screening over 77,000 split hemidriver combinations. In addition to images and fly stocks for these well-characterized lines, we make available 300,000 new 3D images of other split-GAL4 lines.

}, doi = {10.1101/2024.01.09.574419}, url = {https://www.biorxiv.org/content/early/2024/04/01/2024.01.09.574419}, author = {Geoffrey W Meissner and Allison Vannan and Jennifer Jeter and Kari Close and Gina M DePasquale and Zachary Dorman and Kaitlyn Forster and Jaye Anne Beringer and Theresa V Gibney and Joanna H Hausenfluck and Yisheng He and Kristin Henderson and Lauren Johnson and Rebecca M Johnston and Gudrun Ihrke and Nirmala Iyer and Rachel Lazarus and Kelley Lee and Hsing-Hsi Li and Hua-Peng Liaw and Brian Melton and Scott Miller and Reeham Motaher and Alexandra Novak and Omotara Ogundeyi and Alyson Petruncio and Jacquelyn Price and Sophia Protopapas and Susana Tae and Jennifer Taylor and Rebecca Vorimo and Brianna Yarbrough and Kevin Xiankun Zeng and Christopher T Zugates and Heather Dionne and Claire Angstadt and Kelly Ashley and Amanda Cavallaro and Tam Dang and Guillermo A Gonzalez III and Karen L Hibbard and Cuizhen Huang and Jui-Chun Kao and Todd Laverty and Monti Mercer and Brenda Perez and Scarlett Pitts and Danielle Ruiz and Viruthika Vallanadu and Grace Zhiyu Zheng and Cristian Goina and Hideo Otsuna and Konrad Rokicki and Robert R Svirskas and Han SJ Cheong and Michael-John Dolan and Erica Ehrhardt and Kai Feng and Basel El Galfi and Jens Goldammer and Stephen J Huston and Nan Hu and Masayoshi Ito and Claire McKellar and Ryo Minegishi and Shigehiro Namiki and Aljoscha Nern and Catherine E Schretter and Gabriella R Sterne and Lalanti Venkatasubramanian and Kaiyu Wang and Tanya Wolff and Ming Wu and Reed George and Oz Malkesman and Yoshinori Aso and Gwyneth M Card and Barry J Dickson and Wyatt Korff and Kei Ito and James W Truman and Marta Zlatic and Gerald M Rubin and FlyLight Project Team} } @article {69287, title = {Spot Spine, a freely available ImageJ plugin for 3D detection and morphological analysis of dendritic spines}, journal = {F1000Research}, volume = {13}, year = {2024}, month = {2024 Mar 11}, abstract = {

Background

Dendritic spines are tiny protrusions found along the dendrites of neurons, and their number is a measure of the density of synaptic connections. Altered density and morphology is observed in several pathologies, and spine formation as well as morphological changes correlate with learning and memory. The detection of spines in microscopy images and the analysis of their morphology is therefore a prerequisite for many studies. We have developed a new open-source, freely available, plugin for ImageJ/FIJI, called Spot Spine, that allows detection and morphological measurements of spines in three dimensional images.

Method

Local maxima are detected in spine heads, and the intensity distribution around the local maximum is computed to perform the segmentation of each spine head. Spine necks are then traced from the spine head to the dendrite. Several parameters can be set to optimize detection and segmentation, and manual correction gives further control over the result of the process.

Results

The plugin allows the analysis of images of dendrites obtained with various labeling and imaging methods. Quantitative measurements are retrieved including spine head volume and surface, and neck length.

Conclusion

The plugin and instructions for use are available at https://imagej.net/plugins/spot-spine.

}, doi = {10.12688/f1000research.146327.1}, author = {Gilles, JF and Mailly, P and Ferreira, T and Boudier, T and Heck, N} } @article {69419, title = {Statistical signature of subtle behavioural changes in large-scale behavioural assays}, journal = {bioRxiv}, year = {2024}, month = {2024 May 5}, abstract = {

The central nervous system can generate various behaviours, including motor responses, which we can observe through video recordings. Recent advancements in genetics, automated behavioural acquisition at scale, and machine learning enable us to link behaviours to their underlying neural mechanisms causally. Moreover, in some animals, such as the Drosophila larva, this mapping is possible at unprecedented scales of millions of animals and single neurons, allowing us to identify the neural circuits generating particular behaviours.These high-throughput screening efforts are invaluable, linking the activation or suppression of specific neurons to behavioural patterns in millions of animals. This provides a rich dataset to explore how diverse nervous system responses can be to the same stimuli. However, challenges remain in identifying subtle behaviours from these large datasets, including immediate and delayed responses to neural activation or suppression, and understanding these behaviours on a large scale. We introduce several statistically robust methods for analyzing behavioural data in response to these challenges: 1) A generative physical model that regularizes the inference of larval shapes across the entire dataset. 2) An unsupervised kernel-based method for statistical testing in learned behavioural spaces aimed at detecting subtle deviations in behaviour. 3) A generative model for larval behavioural sequences, providing a benchmark for identifying complex behavioural changes. 4) A comprehensive analysis technique using suffix trees to categorize genetic lines into clusters based on common action sequences. We showcase these methodologies through a behavioural screen focused on responses to an air puff, analyzing data from 280,716 larvae across 568 genetic lines.Author Summary There is a significant gap in understanding between the architecture of neural circuits and the mechanisms of action selection and behaviour generation.Drosophila larvae have emerged as an ideal platform for simultaneously probing behaviour and the underlying neuronal computation [1]. Modern genetic tools allow efficient activation or silencing of individual and small groups of neurons. Combining these techniques with standardized stimuli over thousands of individuals makes it possible to relate neurons to behaviour causally. However, extracting these relationships from massive and noisy recordings requires the development of new statistically robust approaches. We introduce a suite of statistical methods that utilize individual behavioural data and the overarching structure of the behavioural screen to deduce subtle behavioural changes from raw data. Given our study{\textquoteright}s extensive number of larvae, addressing and preempting potential challenges in body shape recognition is critical for enhancing behaviour detection. To this end, we have adopted a physics-informed inference model. Our first group of techniques enables robust statistical analysis within a learned continuous behaviour latent space, facilitating the detection of subtle behavioural shifts relative to reference genetic lines. A second array of methods probes for subtle variations in action sequences by comparing them to a bespoke generative model. Together, these strategies have enabled us to construct representations of behavioural patterns specific to a lineage and identify a roster of {\textquotedblright}hit{\textquotedblright} neurons with the potential to influence behaviour subtly.

}, doi = {10.1101/2024.05.03.591825}, url = {https://www.biorxiv.org/content/early/2024/05/05/2024.05.03.591825}, author = {Alexandre Blanc and Fran{\c c}ois Laurent and Alex Barbier{\textendash}Chebbah and Benjamin T. Cocanougher and Benjamin M.W. Jones and Peter Hague and Marta Zlatic and Rayan Chikhi and Christian L. Vestergaard and Tihana Jovanic and Jean-Baptiste Masson and Chlo{\'e} Barr{\'e}} } @article {69502, title = {Steering From the Rear: Coordination of Central Pattern Generators Underlying Navigation by Ascending Interneurons}, journal = {bioRxiv}, year = {2024}, month = {2024 Jun 17}, abstract = {

Understanding how animals coordinate movements to achieve goals is a fundamental pursuit in neuroscience. Here we explore how neurons that reside in posterior lower-order regions of a locomotor system and project to anterior higher-order regions influence steering and navigation. We characterized the anatomy and functional role of a population of ascending interneurons in the ventral nerve cord of Drosophila larvae. Through electron microscopy reconstructions and light microscopy, we determined that the cholinergic 19f cells receive input primarily from premotor interneurons and synapse upon a diverse array of postsynaptic targets within the anterior segments including other 19f cells. Calcium imaging of 19f activity in isolated CNS preparations in relation to motor neurons revealed that 19f neurons are recruited into most larval motor programmes. 19f activity lags behind motor neuron activity and as a population, the cells encode spatio-temporal patterns of locomotor activity in the larval CNS. Optogenetic manipulations of 19f cell activity in isolated CNS preparations revealed that they coordinate the activity of central pattern generators underlying exploratory headsweeps and forward locomotion in a context and location specific manner. In behaving animals, activating 19f cells suppressed exploratory headsweeps and slowed forward locomotion, while inhibition of 19f activity potentiated headsweeps, slowing forward movement. Inhibiting activity in 19f cells ultimately affected the ability of larvae to remain in the vicinity of an odor source during an olfactory navigation task. Overall, our findings provide insights into how ascending interneurons monitor motor activity and shape interactions amongst rhythm generators underlying complex navigational tasks.

}, doi = {10.1101/2024.06.17.598162}, url = {https://www.biorxiv.org/content/early/2024/06/17/2024.06.17.598162}, author = {Jonaitis, Julius and Hibbard, Karen L and Layte, Kaity McCafferty and Hiramoto, Atsuki and Cardona, Albert and Truman, James W and Nose, Akinao and Zwart, Maarten F and Pulver, Stefan R} } @article {69109, title = {Structure, interaction, and nervous connectivity of beta cell primary cilia}, journal = {Nat Commun}, volume = {15}, year = {2024}, month = {2024 Oct 24}, pages = {9168}, abstract = {

Primary cilia are sensory organelles present in many cell types, partaking in various signaling processes. Primary cilia of pancreatic beta cells play pivotal roles in paracrine signaling and their dysfunction is linked to diabetes. Yet, the structural basis for their functions is unclear. We present three-dimensional reconstructions of beta cell primary cilia by electron and expansion microscopy. These cilia are spatially confined within deep ciliary pockets or narrow spaces between cells, lack motility components and display an unstructured axoneme organization. Furthermore, we observe a plethora of beta cell cilia-cilia and cilia-cell interactions with other islet and non-islet cells. Most remarkably, we have identified and characterized axo-ciliary synapses between beta cell cilia and the cholinergic islet innervation. These findings highlight the beta cell cilia{\textquoteright}s role in islet connectivity, pointing at their function in integrating islet intrinsic and extrinsic signals and contribute to understanding their significance in health and diabetes.

}, doi = {10.1038/s41467-024-53348-5}, url = {https://doi.org/10.1038/s41467-024-53348-5}, author = {Andreas M{\"u}ller and Nikolai Klena and Song Pang and Leticia Elizabeth Galicia Garcia and Davud Sulaymankhil and Oleksandra Topcheva and Monika Seliskar and Hassan Mziaut and Eyke Sch{\"o}niger and Daniela Friedland and Nicole Kipke and Susanne Kretschmar and Carla M{\"u}nster and J{\"u}rgen Weitz and Marius Distler and Thomas Kurth and Deborah Schmidt and Harald F. Hess and C. Shan Xu and Gaia Pigino and Michele Solimena} } @article {69698, title = {Temporal BMP4 effects on mouse embryonic and extraembryonic developmentAbstract}, journal = {Nature}, volume = {634}, year = {2024}, month = {09-2024}, pages = {652 - 661}, abstract = {

The developing placenta, which in mice originates through the extraembryonic ectoderm (ExE), is essential for mammalian embryonic development. Yet unbiased characterization of the differentiation dynamics\ of the ExE and its interactions with the embryo proper remains incomplete. Here we develop a temporal single-cell model of mouse gastrulation that maps continuous and parallel differentiation in embryonic and extraembryonic lineages. This is matched with a three-way perturbation approach to target signalling from the embryo proper, the ExE alone, or both. We show that ExE specification involves early spatial and transcriptional bifurcation of uncommitted ectoplacental cone cells and chorion progenitors. Early BMP4 signalling from chorion progenitors is required for proper differentiation of uncommitted ectoplacental cone cells and later for their specification towards trophoblast giant cells. We also find biphasic regulation by BMP4 in the embryo. The early ExE-originating BMP4 signal is necessary for proper mesoendoderm bifurcation and for\ allantois and primordial germ cell specification. However, commencing at embryonic day 7.5, embryo-derived BMP4 restricts the primordial germ cell pool size by favouring differentiation of their extraembryonic mesoderm precursors towards an allantois fate. ExE and embryonic tissues are therefore entangled in time, space and signalling axes, highlighting the importance of their integrated understanding and modelling in vivo and in vitro.

}, issn = {0028-0836}, doi = {10.1038/s41586-024-07937-5}, url = {https://www.nature.com/articles/s41586-024-07937-5https://www.nature.com/articles/s41586-024-07937-5.pdfhttps://www.nature.com/articles/s41586-024-07937-5.pdfhttps://www.nature.com/articles/s41586-024-07937-5}, author = {Hadas, Ron and Rubinstein, Hernan and Mittnenzweig, Markus and Mayshar, Yoav and Ben-Yair, Raz and Cheng, Saifeng and Aguilera-Castrejon, Alejandro and Reines, Netta and Orenbuch, Ayelet-Hashahar and Lifshitz, Aviezer and Chen, Dong-Yuan and Elowitz, Michael B. and Zernicka-Goetz, Magdalena and Hanna, Jacob H. and Tanay, Amos and Stelzer, Yonatan} } @article {69589, title = {A theory of rapid behavioral inferences under the pressure of time}, journal = {PRX Life}, volume = {4}, year = {2024}, month = {2026 Mar 05}, abstract = {

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

Preprint:\ https://www.doi.org/10.1101/2024.08.26.609738

}, doi = {10.1103/8m59-vf2m}, url = { https://doi.org/10.1103/8m59-vf2m}, author = {Hermundstad, Ann M and M{\l}ynarski, Wiktor F} } @article {69491, title = {Transport and Organization of Individual Vimentin Filaments Within Dense Networks Revealed by Single Particle Tracking and 3D FIB-SEM}, journal = {bioRxiv}, year = {2024}, month = {2024 Jun 10}, abstract = {

Vimentin intermediate filaments (VIFs) form complex, tight-packed networks; due to this density, traditional ensemble labeling and imaging approaches cannot accurately discern single filament behavior. To address this, we introduce a sparse vimentin-SunTag labeling strategy to unambiguously visualize individual filament dynamics. This technique confirmed known long-range dynein and kinesin transport of peripheral VIFs and uncovered extensive bidirectional VIF motion within the perinuclear vimentin network, a region we had thought too densely bundled to permit such motility. To examine the nanoscale organization of perinuclear vimentin, we acquired high-resolution electron microscopy volumes of a vitreously frozen cell and reconstructed VIFs and microtubules within a 50 um3 window. Of 583 VIFs identified, most were integrated into long, semi-coherent bundles that fluctuated in width and filament packing density. Unexpectedly, VIFs displayed minimal local co-alignment with microtubules, save for sporadic cross-over sites that we predict facilitate cytoskeletal crosstalk. Overall, this work demonstrates single VIF dynamics and organization in the cellular milieu for the first time.

}, doi = {10.1101/2024.06.10.598346}, url = {https://www.biorxiv.org/content/early/2024/06/10/2024.06.10.598346}, author = {Renganathan, Bhuvanasundar and Moore, Andrew S. and Yeo, Wei-Hong and Petruncio, Alyson and Ackerman, David and Wiegel, Aubrey and CellMap Team and Pasolli, H. Amalia and Xu, C. Shan and Hess, Harald F and Serpinskaya, Anna S. and Zhang, Hao F. and Lippincott-Schwartz, Jennifer and Gelfand, Vladimir I.} } @article {69662, title = {Type IV pili-associated secretion of a biofilm matrix protein from Clostridium perfringens that forms intermolecular isopeptide bonds}, journal = {bioRxiv}, year = {2024}, month = {2024 Nov 04}, abstract = {

Clostridium perfringens is a Gram-positive anaerobic spore-forming bacterial pathogen of humans and animals. C. perfringens also produces type IV pili (T4P) and has two complete sets of T4P-associated genes, one of which has been shown to produce surface pili needed for cell adherence. One hypothesis about the role of the other set of T4P genes is that they could comprise a system analogous to the type II secretion systems (TTSS) found in Gram-negative bacteria, which is used to export folded proteins from the periplasm through the outer membrane to the extracellular environment. Gram-positive bacteria have a similar secretion barrier in the thick peptidoglycan (PG) layer, which blocks secretion of folded proteins \>25 kD. To determine if the T4P-associated genes comprise a Gram-positive TTSS, the secretome of mutants lacking type IV pilins were examined and a single protein, a von Willebrand A domain containing protein BsaC (CPE0517) was identified as being dependent on PilA3 for secretion. BsaC is in an operon with a signal peptidase and two putative biofilm matrix proteins with homology to Bacillus subtilis TasA. One of these proteins, BsaA, was shown by another group to produce high mol wt oligomers. We analyzed BsaA monomer interactions with de novo modeling, which projected that the monomers formed isopeptide bonds as part of a donor strand exchange process. Mutations in residues predicted to form the isopeptide bonds led to loss of oligomerization, supporting the predicted bond formation process. Phylogenetic analysis showed the BsaA family of proteins are widespread among bacteria and archaea but only a subset are predicted to form isopeptide bonds.

}, doi = {10.1101/2024.11.04.621531}, url = {https://doi.org/10.1101/2024.11.04.621531}, author = {Kivimaki, Sarah E. and Dempsey, Samantha and Tani, Julia M. and Camper, Colette and Hicklin, Ian K. and Blaby-Haas, Crysten E. and Brown, Anne M and Melville, Stephen} } @article {69350, title = {Ultra-high density electrodes improve detection, yield, and cell type identification in neuronal recordings}, journal = {bioRxiv}, year = {2024}, month = {2024 Apr 10}, abstract = {

To understand the neural basis of behavior, it is essential to sensitively and accurately measure neural activity at single neuron and single spike resolution. Extracellular electrophysiology delivers this, but it has biases in the neurons it detects and it imperfectly resolves their action potentials. To minimize these limitations, we developed a silicon probe with much smaller and denser recording sites than previous designs, called Neuropixels Ultra (NP Ultra). This device samples neuronal activity at ultra-high spatial density ( 10 times higher than previous probes) with low noise levels, while trading off recording span. NP Ultra is effectively an implantable voltage-sensing camera that captures a planar image of a neuron{\textquoteright}s electrical field. We use a spike sorting algorithm optimized for these probes to demonstrate that the yield of visually-responsive neurons in recordings from mouse visual cortex improves up to 3-fold. We show that NP Ultra can record from small neuronal structures including axons and dendrites. Recordings across multiple brain regions and four species revealed a subset of extracellular action potentials with unexpectedly small spatial spread and axon-like features. We share a large-scale dataset of these brain-wide recordings in mice as a resource for studies of neuronal biophysics. Finally, using ground-truth identification of three major inhibitory cortical cell types, we found that these cell types were discriminable with approximately 75\% success, a significant improvement over lower-resolution recordings. NP Ultra improves spike sorting performance, detection of subcellular compartments, and cell type classification to enable more powerful dissection of neural circuit activity during behavior.

}, doi = {10.1101/2023.08.23.554527}, url = {https://www.biorxiv.org/content/early/2024/04/10/2023.08.23.554527}, author = {Zhiwen Ye and Andrew M Shelton and Jordan R Shaker and Julien M Boussard and Jennifer Colonell and Daniel Birman and Sahar Manavi and Susu Chen and Charlie Windolf and Cole Hurwitz and Tomoyuki Namima and Frederico Pedraja and Shahaf Weiss and Bogdan Raducanu and Torbj{\o}rn Ness and Xiaoxuan Jia and Giulia Mastroberardino and L. Federico Rossi and Matteo Carandini and Michael Hausser and Gaute T Einevoll and Gilles Laurent and Nathaniel B Sawtell and Wyeth Bair and Anitha Pasupathy and Carolina Mora-Lopez and Barun Dutta and Liam Paninski and Joshua H Siegle and Christof Koch and Shawn R Olsen and Timothy D Harris and Nicholas A Steinmetz} } @article {69421, title = {YAP condensates are highly organized hubs}, journal = {iScience}, year = {2024}, month = {2024 May 07}, pages = {109927}, abstract = {

YAP/TEAD signaling is essential for organismal development, cell proliferation, and cancer progression. As a transcriptional coactivator, how YAP activates its downstream target genes is incompletely understood. YAP forms biomolecular condensates in response to hyperosmotic stress, concentrating transcription-related factors to activate downstream target genes. However, whether YAP forms condensates under other signals, how YAP condensates organize and function, and how YAP condensates activate transcription in general are unknown. Here, we report that endogenous YAP forms sub-micron scale condensates in response to Hippo pathway regulation and actin cytoskeletal tension. YAP condensates are stabilized by the transcription factor TEAD1, and recruit BRD4, a coactivator that is enriched at active enhancers. Using single-particle tracking, we found that YAP condensates slowed YAP diffusion within condensate boundaries, a possible mechanism for promoting YAP target search. These results reveal that YAP condensate formation is a highly regulated process that is critical for YAP/TEAD target gene expression.

}, issn = {2589-0042}, doi = {https://doi.org/10.1016/j.isci.2024.109927}, url = {https://www.sciencedirect.com/science/article/pii/S2589004224011490}, author = {Siyuan Hao and Ye Jin Lee and Nadav Benhamou Goldfajn and Eduardo Flores and Jindayi Liang and Hannah Fuehrer and Justin Demmerle and Jennifer Lippincott-Schwartz and Zhe Liu and Shahar Sukenik and Danfeng Cai} } @article {68807, title = {Architecture and dynamics of a desmosome-endoplasmic reticulum complex.}, journal = {Nature Cell Biology}, volume = {25}, year = {2023}, month = {2023 Jun 16}, pages = {823-835}, abstract = {

The endoplasmic reticulum (ER) forms a dynamic network that contacts other cellular membranes to regulate stress responses, calcium signalling and lipid transfer. Here, using high-resolution volume electron microscopy, we find that the ER forms a previously unknown association with keratin intermediate filaments and desmosomal cell-cell junctions. Peripheral ER assembles into mirror image-like arrangements at desmosomes and exhibits nanometre proximity to keratin filaments and the desmosome cytoplasmic plaque. ER tubules exhibit stable associations with desmosomes, and perturbation of desmosomes or keratin filaments alters ER organization, mobility and expression of ER stress transcripts. These findings indicate that desmosomes and the keratin cytoskeleton regulate the distribution, function and dynamics of the ER network. Overall, this study reveals a previously unknown subcellular architecture defined by the structural integration of ER tubules with an epithelial intercellular junction.

}, keywords = {Cytoskeleton, Desmosomes, Endoplasmic Reticulum, Intermediate Filaments, Keratins}, issn = {1476-4679}, doi = {10.1038/s41556-023-01154-4}, author = {Bharathan, Navaneetha Krishnan and Giang, William and Hoffman, Coryn L and Aaron, Jesse S and Khuon, Satya and Chew, Teng-Leong and Preibisch, Stephan and Trautman, Eric T and Heinrich, Larissa and Bogovic, John and Bennett, Davis and Ackerman, David and Park, Woohyun and Petruncio, Alyson and Weigel, Aubrey V and Saalfeld, Stephan and Wayne Vogl, A and Stahley, Sara N and Kowalczyk, Andrew P} } @article {68587, title = {Automated reconstruction of whole-embryo cell lineages by learning from sparse annotations.}, journal = {Nature Biotechnology}, volume = {41}, year = {2023}, month = {2023 Jan 01}, pages = {44-49}, abstract = {

We present a method to automatically identify and track nuclei in time-lapse microscopy recordings of entire developing embryos. The method combines deep learning and global optimization. On a mouse dataset, it reconstructs 75.8\% of cell lineages spanning 1 h, as compared to 31.8\% for the competing method. Our approach improves understanding of where and when cell fate decisions are made in developing embryos, tissues, and organs.

}, keywords = {Animals, Blastocyst, Cell Lineage, Embryo, Mammalian, Mice, Microscopy}, issn = {1546-1696}, doi = {10.1038/s41587-022-01427-7}, author = {Malin-Mayor, Caroline and Hirsch, Peter and Guignard, Leo and McDole, Katie and Wan, Yinan and Lemon, William C and Kainmueller, Dagmar and Keller, Philipp J and Preibisch, Stephan and Funke, Jan} } @article {68787, title = {Autophagy receptor NDP52 alters DNA conformation to modulate RNA polymerase II transcription.}, journal = {Nature Communications}, volume = {14}, year = {2023}, month = {2023 May 18}, pages = {2855}, abstract = {

NDP52 is an autophagy receptor involved in the recognition and degradation of invading pathogens and damaged organelles. Although NDP52 was first identified in the nucleus and is expressed throughout the cell, to date, there is no clear nuclear functions for NDP52. Here, we use a multidisciplinary approach to characterise the biochemical properties and nuclear roles of NDP52. We find that NDP52 clusters with RNA Polymerase II (RNAPII) at transcription initiation sites and that its overexpression promotes the formation of additional transcriptional clusters. We also show that depletion of NDP52 impacts overall gene expression levels in two model mammalian cells, and that transcription inhibition affects the spatial organisation and molecular dynamics of NDP52 in the nucleus. This directly links NDP52 to a role in RNAPII-dependent transcription. Furthermore, we also show that NDP52 binds specifically and with high affinity to double-stranded DNA (dsDNA) and that this interaction leads to changes in DNA structure in vitro. This, together with our proteomics data indicating enrichment for interactions with nucleosome remodelling proteins and DNA structure regulators, suggests a possible function for NDP52 in chromatin regulation. Overall, here we uncover nuclear roles for NDP52 in gene expression and DNA structure regulation.

}, keywords = {Animals, Autophagy, DNA, Mammals, Nuclear Proteins, Nucleic Acid Conformation, RNA Polymerase II}, issn = {2041-1723}, doi = {10.1038/s41467-023-38572-9}, author = {Dos Santos, {\'A}lia and Rollins, Daniel E and Hari-Gupta, Yukti and McArthur, Hannah and Du, Mingxue and Ru, Sabrina Yong Zi and Pidlisna, Kseniia and Stranger, Ane and Lorgat, Faeeza and Lambert, Danielle and Brown, Ian and Howland, Kevin and Aaron, Jesse and Wang, Lin and Ellis, Peter J I and Chew, Teng-Leong and Martin-Fernandez, Marisa and Pyne, Alice L B and Toseland, Christopher P} } @article {68565, title = {Behavioral state-dependent modulation of insulin-producing cells in Drosophila.}, journal = {Current Biology}, volume = {33}, year = {2023}, month = {2023 Feb 06}, pages = {449}, abstract = {

Insulin signaling plays a pivotal role in metabolic control and aging, and insulin accordingly is a key factor in several human diseases. Despite this importance, the in\ vivo activity dynamics of insulin-producing cells (IPCs) are poorly understood. Here, we characterized the effects of locomotion on the activity of IPCs in Drosophila. Using in\ vivo electrophysiology and calcium imaging, we found that IPCs were strongly inhibited during walking and flight and that their activity rebounded and overshot after cessation of locomotion. Moreover, IPC activity changed rapidly during behavioral transitions, revealing that IPCs are modulated on fast timescales in behaving animals. Optogenetic activation of locomotor networks ex\ vivo, in the absence of actual locomotion or changes in hemolymph sugar levels, was sufficient to inhibit IPCs. This demonstrates that the behavioral state-dependent inhibition of IPCs is actively controlled by neuronal pathways and is independent of changes in glucose concentration. By contrast, the overshoot in IPC activity after locomotion was absent ex\ vivo and after starvation, indicating that it was not purely driven by feedforward signals but additionally required feedback derived from changes in hemolymph sugar concentration. We hypothesize that IPC inhibition during locomotion supports mobilization of fuel stores during metabolically demanding behaviors, while the rebound in IPC activity after locomotion contributes to replenishing muscle glycogen stores. In addition, the rapid dynamics of IPC modulation support a potential role of insulin in the state-dependent modulation of sensorimotor processing.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2022.12.005}, author = {Liessem, Sander and Held, Martina and Bisen, Rituja S and Haberkern, Hannah and Lacin, Haluk and Bockem{\"u}hl, Till and Ache, Jan M} } @article {68709, title = {BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets.}, journal = {Nature Methods}, volume = {20}, year = {2023}, month = {2023 Jun 01}, abstract = {

BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. We observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.

}, issn = {1548-7105}, doi = {10.1038/s41592-023-01848-5}, author = {Manubens-Gil, Linus and Zhou, Zhi and Chen, Hanbo and Ramanathan, Arvind and Liu, Xiaoxiao and Liu, Yufeng and Bria, Alessandro and Gillette, Todd and Ruan, Zongcai and Yang, Jian and Radojevi{\'c}, Miroslav and Zhao, Ting and Cheng, Li and Qu, Lei and Liu, Siqi and Bouchard, Kristofer E and Gu, Lin and Cai, Weidong and Ji, Shuiwang and Roysam, Badrinath and Wang, Ching-Wei and Yu, Hongchuan and Sironi, Amos and Iascone, Daniel Maxim and Zhou, Jie and Bas, Erhan and Conde-Sousa, Eduardo and Aguiar, Paulo and Li, Xiang and Li, Yujie and Nanda, Sumit and Wang, Yuan and Muresan, Leila and Fua, Pascal and Ye, Bing and He, Hai-Yan and Staiger, Jochen F and Peter, Manuel and Cox, Daniel N and Simonneau, Michel and Oberlaender, Marcel and Jefferis, Gregory and Ito, Kei and Gonzalez-Bellido, Paloma and Kim, Jinhyun and Rubel, Edwin and Cline, Hollis T and Zeng, Hongkui and Nern, Aljoscha and Chiang, Ann-Shyn and Yao, Jianhua and Roskams, Jane and Livesey, Rick and Stevens, Janine and Liu, Tianming and Dang, Chinh and Guo, Yike and Zhong, Ning and Tourassi, Georgia and Hill, Sean and Hawrylycz, Michael and Koch, Christof and Meijering, Erik and Ascoli, Giorgio A and Peng, Hanchuan} } @article {68647, title = {Brain-wide neural activity underlying memory-guided movement}, journal = {bioRxiv}, year = {2023}, month = {2023 Mar 02}, abstract = {

Behavior requires neural activity across the brain, but most experiments probe neurons in a single area at a time. Here we used multiple Neuropixels probes to record neural activity simultaneously in brain-wide circuits, in mice performing a memory-guided directional licking task. We targeted brain areas that form multi-regional loops with anterior lateral motor cortex (ALM), a key circuit node mediating the behavior. Neurons encoding sensory stimuli, choice, and actions were distributed across the brain. However, in addition to ALM, coding of choice was concentrated in subcortical areas receiving input from ALM, in an ALM-dependent manner. Choice signals were first detected in ALM and the midbrain, followed by the thalamus, and other brain areas. At the time of movement initiation, choice-selective activity collapsed across the brain, followed by new activity patterns driving specific actions. Our experiments provide the foundation for neural circuit models of decision-making and movement initiation.

}, doi = {10.1101/2023.03.01.530520}, url = {https://doi.org/10.1101/2023.03.01.530520}, author = {Susu Chen and Yi Liu and Ziyue Wang and Jennifer Colonell and Liu D. Liu and Han Hou and Nai-Wen Tien and Tim Wang and Timothy Harris and Shaul Druckmann and Nuo Li and Karel Svoboda} } @article {68931, title = {Cell-type-specific plasticity shapes neocortical dynamics for motor learning}, journal = {bioRxiv}, year = {2023}, month = {2023 Aug 14}, abstract = {

Neocortical spiking dynamics control aspects of behavior, yet how these dynamics emerge during motor learning remains elusive. Activity-dependent synaptic plasticity is likely a key mechanism, as it reconfigures network architectures that govern neural dynamics. Here, we examined how the mouse premotor cortex acquires its well-characterized neural dynamics that control movement timing, specifically lick timing. To probe the role of synaptic plasticity, we have genetically manipulated proteins essential for major forms of synaptic plasticity, Ca2+/calmodulin-dependent protein kinase II (CaMKII) and Cofilin, in a region and cell-type-specific manner. Transient inactivation of CaMKII in the premotor cortex blocked learning of new lick timing without affecting the execution of learned action or ongoing spiking activity. Furthermore, among the major glutamatergic neurons in the premotor cortex, CaMKII and Cofilin activity in pyramidal tract (PT) neurons, but not intratelencephalic (IT) neurons, is necessary for learning. High-density electrophysiology in the premotor cortex uncovered that neural dynamics anticipating licks are progressively shaped during learning, which explains the change in lick timing. Such reconfiguration in behaviorally relevant dynamics is impeded by CaMKII manipulation in PT neurons. Altogether, the activity of plasticity-related proteins in PT neurons plays a central role in sculpting neocortical dynamics to learn new behavior.

}, doi = {10.1101/2023.08.09.552699}, url = {https://doi.org/10.1101/2023.08.09.552699}, author = {Shouvik Majumder and Koichi Hirokawa and Zidan Yang and Ronald Paletzki and Charles R. Gerfen and Lorenzo Fontolan and Sandro Romani and Anant Jain and Ryohei Yasuda and Hidehiko K. Inagaki} } @article {68627, title = {The challenges and opportunities of open-access microscopy facilities.}, journal = {Journal of Microscopy}, year = {2023}, month = {2023 Feb 13}, abstract = {

Microscopy core facilities are increasingly utilized research resources, but they are generally only available to users within the host institution. Such localized access misses an opportunity to facilitate research across a broader user base. Here, we present the model of an open-access microscopy facility, using the Advanced Imaging Center (AIC) at Howard Hughes Medical Institute Janelia Research Campus as an example. The AIC has pioneered a model whereby advanced microscopy technologies and expertise are made accessible to researchers on a global scale. We detail our experiences in addressing the considerable challenges associated with this model for those who may be interested in launching an open-access imaging facility. Importantly, we focus on how this model can empower researchers, particularly those from resource-constrained settings. This article is protected by copyright. All rights reserved.

}, issn = {1365-2818}, doi = {10.1111/jmi.13176}, author = {Cartwright, Heather N and Hobson, Chad M and Chew, Teng-Leong and Reiche, Michael A and Aaron, Jesse S} } @article {68257, title = {Characterization, Comparison, and Optimization of Lattice Light Sheets}, journal = {Science Advances}, year = {2023}, month = {2023 Mar 31}, abstract = {

Lattice light sheet microscopy excels at the non-invasive imaging of three-dimensional (3D) dynamic processes at high spatiotemporal resolution within cells and developing embryos. Recently, several papers have called into question the performance of lattice light sheets relative to the Gaussian sheets most common in light sheet microscopy. Here we undertake a comprehensive theoretical and experimental analysis of various forms of light sheet microscopy which both demonstrates and explains why lattice light sheets provide significant improvements in resolution and photobleaching reduction. The analysis provides a procedure to select the correct light sheet for a desired experiment and specifies the processing that maximizes the use of all fluorescence generated within the light sheet excitation envelope for optimal resolution while minimizing image artifacts and photodamage. Development of a new type of {\textquotedblleft}harmonic balanced{\textquotedblright} lattice light sheet is shown to improve performance at all spatial frequencies within its 3D resolution limits and maintains this performance over lengthened propagation distances allowing for expanded fields of view.

}, doi = {10.1126/sciadv.ade6623}, url = {https://doi.org/10.1126/sciadv.ade6623}, author = {Gaoxiang Liu and Xiongtao Ruan and Daniel E. Milkie and Frederik G{\"o}rlitz and Matthew Mueller and Wilmene Hercule and Alison Kililea and Eric Betzig and Srigokul Upadhyayula} } @article {68805, title = {Comparative connectomics and escape behavior in larvae of closely related Drosophila species.}, journal = {Current Biology}, year = {2023}, month = {2023 May 31}, abstract = {

Evolution has generated an enormous variety of morphological, physiological, and behavioral traits in animals. How do behaviors evolve in different directions in species equipped with similar neurons and molecular components? Here we adopted a comparative approach to investigate the similarities and differences of escape behaviors in response to noxious stimuli and their underlying neural circuits between closely related drosophilid species. Drosophilids show a wide range of escape behaviors in response to noxious cues, including escape crawling, stopping, head casting, and rolling. Here we find that D.\ santomea, compared with its close relative D.\ melanogaster, shows a higher probability of rolling in response to noxious stimulation. To assess whether this behavioral difference could be attributed to differences in neural circuitry, we\ generated focused ion beam-scanning electron microscope volumes of the ventral nerve cord of D.\ santomea to reconstruct the downstream partners of mdIV, a nociceptive sensory neuron in D.\ melanogaster. Along with partner interneurons of mdVI (including Basin-2, a multisensory integration neuron necessary for rolling) previously identified in D.\ melanogaster, we identified two additional partners of mdVI in D.\ santomea. Finally, we showed that joint activation of one of the partners (Basin-1) and a common partner (Basin-2) in D.\ melanogaster increased rolling probability, suggesting that the high rolling probability in D.\ santomea is mediated by the additional activation of Basin-1 by mdIV. These results provide a plausible mechanistic explanation for how closely related species exhibit quantitative differences in the likelihood of expressing the same behavior.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2023.05.043}, author = {Zhu, Jiayi and Boivin, Jean-Christophe and Pang, Song and Xu, C Shan and Lu, Zhiyuan and Saalfeld, Stephan and Hess, Harald F and Ohyama, Tomoko} } @article {69018, title = {Complete human day 14 post-implantation embryo models from na{\"\i}ve ES cells}, journal = {Nature}, year = {2023}, month = {09/2023}, abstract = {

The ability to study human post-implantation development remains limited due to ethical and technical challenges associated with intrauterine development after implantation1. Embryo-like models with spatially organized morphogenesis of all defining embryonic and extra-embryonic tissues of the post-implantation human conceptus (i.e., embryonic disk, bilaminar disk, yolk- and chorionic sacs, surrounding trophoblasts) remain lacking2. Mouse na{\"\i}ve embryonic stem cells (ESCs) have recently been shown to give rise to embryonic and extra-embryonic stem cells capable of self-assembling into post-gastrulation mouse Structured Stem cell-based Embryo Models with spatially organized morphogenesis (SEMs)3. Here, we extend these findings to humans, while using only genetically unmodified human na{\"\i}ve ESCs (in HENSM conditions)4. Such human fully integrated SEMs recapitulate the organization of nearly all known lineages and compartments of post-implantation human embryos including epiblast, hypoblast, extra-embryonic mesoderm, and trophoblast surrounding the latter layers. These human complete SEMs demonstrated developmental growth dynamics that resemble key hallmarks of post-implantation stage embryogenesis up to 13-14 days post-fertilization (dpf) (Carnegie stage 6a). This includes embryonic disk and bilaminar disk formation, epiblast lumenogenesis, polarized amniogenesis, anterior-posterior symmetry breaking, PGC specification, polarized yolk sac with visceral and parietal endoderm, extra-embryonic mesoderm expansion that defines a chorionic cavity and a connecting stalk, a trophoblast surrounding compartment demonstrating syncytium and lacunae formation. This SEM platform may enable the experimental interrogation of previously inaccessible windows of human early post-implantation up to peri-gastrulation development.

}, issn = {0028-0836}, doi = {10.1038/s41586-023-06604-5}, url = {https://www.nature.com/articles/s41586-023-06604-5https://www.nature.com/articles/s41586-023-06604-5.pdfhttps://www.nature.com/articles/s41586-023-06604-5.pdfhttps://www.nature.com/articles/s41586-023-06604-5}, author = {Oldak, Bernardo and Wildschutz, Emilie and Bondarenko, Vladyslav and Comar, Mehmet-Yunus and Zhao, Cheng and Aguilera-Castrejon, Alejandro and Tarazi, Shadi and Viukov, Sergey and Pham, Thi Xuan Ai and Ashouokhi, Shahd and Lokshtanov, Dmitry and Roncato, Francesco and Ariel, Eitan and Rose, Max and Livnat, Nir and Shani, Tom and Joubran, Carine and Cohen, Roni and Addadi, Yoseph and Chemla, Muriel and Kedmi, Merav and Keren-Shaul, Hadas and Pasque, Vincent and Petropoulos, Sophie and Lanner, Fredrik and Novershtern, Noa and Hanna, Jacob H.} } @article {69022, title = {A complete reconstruction of the early visual system of an adult insect.}, journal = {Current Biology}, volume = {33}, year = {2023}, month = {2023 Nov 06}, pages = {4611-4623}, abstract = {

For most model organisms in neuroscience, research into visual processing in the brain is difficult because of a lack of high-resolution maps that capture complex neuronal circuitry. The microinsect Megaphragma viggianii, because of its small size and non-trivial behavior, provides a unique opportunity for tractable whole-organism connectomics. We image its whole head using serial electron microscopy. We reconstruct its compound eye and analyze the optical properties of the ommatidia as well as the connectome of the first visual neuropil-the lamina. Compared with the fruit fly and the honeybee, Megaphragma visual system is highly simplified: it has 29 ommatidia per eye and 6 lamina neuron types. We report features that are both stereotypical among most ommatidia and specialized to some. By identifying the "barebones" circuits critical for flying insects, our results will facilitate constructing computational models of visual processing in insects.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2023.09.021}, author = {Chua, Nicholas J and Makarova, Anastasia A and Gunn, Pat and Villani, Sonia and Cohen, Ben and Thasin, Myisha and Wu, Jingpeng and Shefter, Deena and Pang, Song and Xu, C Shan and Hess, Harald F and Polilov, Alexey A and Chklovskii, Dmitri B} } @article {69039, title = {A comprehensive neuroanatomical survey of the Drosophila Lobula Plate Tangential Neurons with predictions for their optic flow sensitivity.}, journal = {bioRxiv}, year = {2023}, month = {2023 Oct 17}, abstract = {

Flying insects exhibit remarkable navigational abilities controlled by their compact nervous systems. Optic flow, the pattern of changes in the visual scene induced by locomotion, is a crucial sensory cue for robust self-motion estimation, especially during rapid flight. Neurons that respond to specific, large-field optic flow patterns have been studied for decades, primarily in large flies, such as houseflies, blowflies, and hover flies. The best-known optic-flow sensitive neurons are the large tangential cells of the dipteran lobula plate, whose visual-motion responses, and to a lesser extent, their morphology, have been explored using single-neuron neurophysiology. Most of these studies have focused on the large, Horizontal and Vertical System neurons, yet the lobula plate houses a much larger set of {\textquoteright}optic-flow{\textquoteright} sensitive neurons, many of which have been challenging to unambiguously identify or to reliably target for functional studies. Here we report the comprehensive reconstruction and identification of the Lobula Plate Tangential Neurons in an Electron Microscopy (EM) volume of a whole Drosophila brain. This catalog of 58 LPT neurons (per brain hemisphere) contains many neurons that are described here for the first time and provides a basis for systematic investigation of the circuitry linking self-motion to locomotion control. Leveraging computational anatomy methods, we estimated the visual motion receptive fields of these neurons and compared their tuning to the visual consequence of body rotations and translational movements. We also matched these neurons, in most cases on a one-for-one basis, to stochastically labeled cells in genetic driver lines, to the mirror-symmetric neurons in the same EM brain volume, and to neurons in an additional EM data set. Using cell matches across data sets, we analyzed the integration of optic flow patterns by neurons downstream of the LPTs and find that most central brain neurons establish sharper selectivity for global optic flow patterns than their input neurons. Furthermore, we found that self-motion information extracted from optic flow is processed in distinct regions of the central brain, pointing to diverse foci for the generation of visual behaviors.

}, doi = {10.1101/2023.10.16.562634}, url = {https://doi.org/10.1101/2023.10.16.562634}, author = {Arthur Zhao and Aljoscha Nern and Sanna Koskela and Marisa Dreher and Mert Erginkaya and Connor W Laughland and Henrique DF Ludwig and Alex G Thomson and Judith Hoeller and Ruchi Parekh and Sandro Romani and Davi D Bock and Eugenia Chiappe and Michael B Reiser} } @article {68800, title = {A Connectome of the Male Drosophila Ventral Nerve Cord}, journal = {bioRxiv}, year = {2023}, month = {2023 Jun 06}, abstract = {

Animal behavior is principally expressed through neural control of muscles. Therefore understanding how the brain controls behavior requires mapping neuronal circuits all the way to motor neurons. We have previously established technology to collect large-volume electron microscopy data sets of neural tissue and fully reconstruct the morphology of the neurons and their chemical synaptic connections throughout the volume. Using these tools we generated a dense wiring diagram, or connectome, for a large portion of the\ Drosophila\ central brain. However, in most animals, including the fly, the majority of motor neurons are located outside the brain in a neural center closer to the body, i.e. the mammalian spinal cord or insect ventral nerve cord (VNC). In this paper, we extend our effort to map full neural circuits for behavior by generating a connectome of the VNC of a male fly.

}, doi = {10.1101/2023.06.05.543757}, url = {https://doi.org/10.1101/2023.06.05.543757}, author = {Shin-ya Takemura and Kenneth J Hayworth and Gary B Huang and Michal Januszewski and Zhiyuan Lu and Elizabeth C Marin and Stephan Preibisch and C Shan Xu and John Bogovic and Andrew S Champion and Han S J Cheong and Marta Costa and Katharina Eichler and William Katz and Christopher Knecht and Feng Li and Billy J Morris and Christopher Ordish and Patricia K Rivlin and Philipp Schlegel and Kazunori Shinomiya and Tomke Sturner and Ting Zhao and Griffin Badalamente and Dennis Bailey and Paul Brooks and Brandon S Canino and Jody Clements and Michael Cook and Octave Duclos and Christopher R Dunne and Kelli Fairbanks and Siqi Fang and Samantha Finley-May and Audrey Francis and Reed George and Marina Gkantia and Kyle Harrington and Gary Patrick Hopkins and Joseph Hsu and Philip M Hubbard and Alexandre Javier and Dagmar Kainmueller and Wyatt Korff and Julie Kovalyak and Dominik Krzeminski and Shirley A Lauchie and Alanna Lohff and Charli Maldonado and Emily A Manley and Caroline Mooney and Erika Neace and Matthew Nichols and Omotara Ogundeyi and Nneoma Okeoma and Tyler Paterson and Elliott Phillips and Emily M Phillips and Caitlin Ribeiro and Sean M Ryan and Jon Thomson Rymer and Anne K Scott and Ashley L Scott and David Shepherd and Aya Shinomiya and Claire Smith and Alia Suleiman and Satoko Takemura and Iris Talebi and Imaan F M Tamimi and Eric T Trautman and Lowell Umayam and John J Walsh and Tansy Yang and Gerald M Rubin and Louis K Scheffer and Jan Funke and Stephan Saalfeld and Harald F Hess and Stephen M Plaza and Gwyneth M Card and Gregory S X E Jefferis and Stuart Berg} } @article {68835, title = {The contribution of inflammatory astrocytes to BBB impairments in a brain-chip model of Parkinson{\textquoteright}s disease.}, journal = {Nature Communications}, volume = {14}, year = {2023}, month = {2023 Jun 20}, pages = {3651}, abstract = {

Astrocyte dysfunction has previously been linked to multiple neurodegenerative disorders including Parkinson{\textquoteright}s disease (PD). Among their many roles, astrocytes are mediators of the brain immune response, and astrocyte reactivity is a pathological feature of PD. They are also involved in the formation and maintenance of the blood-brain barrier (BBB), but barrier integrity is compromised in people with PD. This study focuses on an unexplored area of PD pathogenesis by characterizing the interplay between astrocytes, inflammation and BBB integrity, and by combining patient-derived induced pluripotent stem cells with microfluidic technologies to generate a 3D human BBB\ chip. Here we report that astrocytes derived from female donors harboring the PD-related LRRK2 G2019S mutation are pro-inflammatory and fail to support the formation of a functional capillary in vitro. We show that inhibition of MEK1/2 signaling attenuates the inflammatory profile of mutant astrocytes and rescues BBB formation, providing insights into mechanisms regulating barrier integrity in PD. Lastly, we confirm that vascular changes are also observed in the human\ postmortem substantia nigra of both males and females with PD.

}, keywords = {Astrocytes, Blood-Brain Barrier, Brain, Female, Humans, Male, Parkinson Disease, Substantia Nigra}, issn = {2041-1723}, doi = {10.1038/s41467-023-39038-8}, author = {de Rus Jacquet, A and Alpaugh, M and Denis, H L and Tancredi, J L and Boutin, M and Decaestecker, J and Beauparlant, C and Herrmann, L and Saint-Pierre, M and Parent, M and Droit, A and Breton, S and Cicchetti, F} } @article {68467, title = {De novo protein identification in mammalian sperm using high-resolution in situ cryo-electron tomography}, journal = {Cell}, volume = {186}, year = {2023}, month = {2023 Nov 09}, pages = {5041-5053.e19}, abstract = {

Understanding molecular mechanisms of cellular pathways requires knowledge of the identities of participating proteins, their cellular localization and their 3D structures. Contemporary workflows typically require multiple techniques to identify target proteins, track their localization using fluorescence microscopy, followed by\ in vitro\ structure determination. To identify mammal-specific sperm proteins and understand their functions, we developed a visual proteomics workflow to directly address these challenges. Our\ in situ\ cryo-electron tomography and subtomogram averaging provided 6.0 {\r A} resolution reconstructions of axonemal microtubules and their associated proteins. The well-resolved secondary and tertiary structures allowed us to computationally match, in an unbiased manner, novel densities in our 3D reconstruction maps with 21,615 AlphaFold2-predicted protein models of the mouse proteome. We identified Tektin 5, CCDC105 and SPACA9 as novel microtubule inner proteins that form an extensive network crosslinking the lumen of microtubule and existing proteins. Additional biochemical and mass spectrometry analyses helped validate potential candidates. The novel axonemal sperm structures identified by this approach form an extensive interaction network within the lumen of microtubules, suggesting they have a role in the mechanical and elastic properties of the microtubule filaments required for the vigorous beating motions of flagella.

}, doi = {10.1016/j.cell.2023.09.017}, url = {https://doi.org/10.1016/j.cell.2023.09.017}, author = {Zhen Chen and Momoko Shiozaki and Kelsey M. Haas and Shumei Zhao and Caiying Guo and Benjamin J. Polacco and Zhiheng Yu and Nevan J. Krogan and Robyn M. Kaake and Ronald D. Vale and David A. Agard} } @article {69093, title = {Decoding life{\textquoteright}s inner workings: advances in quantitative bioimaging.}, journal = {Open Biology}, volume = {13}, year = {2023}, month = {2023 Nov 29}, pages = {230329}, abstract = {

This special feature of , titled {\textquoteright}Advances in Quantitative Bioimaging{\textquoteright}, proposes an overview of the latest advancements in quantitative bioimaging techniques and their wide-ranging applications. The articles cover various topics, including modern imaging methods that enable visualization on a nanoscale, such as super-resolution microscopy and single-particle analysis. These techniques offer unparalleled insights into complex molecular structures and dynamic cellular processes , such as mapping nuclear pore proteins or tracking single histone deposition events throughout the cell cycle. The articles presented in this edition showcase cutting-edge quantitative imaging techniques coupled with advanced computational analysis capable of precisely measuring biological structures and processes. Examples range from correlating calcium release events to underlying protein organization in heart cells to pioneering tools for categorizing changes in microglia morphology under various conditions. This editorial highlights how these advancements are revolutionizing our understanding of living systems, while acknowledging challenges that must be addressed to fully exploit the potential of these emerging technologies, such as improving molecular probes, algorithms and correlation protocols.

}, keywords = {Algorithms, Microscopy, Fluorescence, Molecular Structure}, issn = {2046-2441}, doi = {10.1098/rsob.230329}, author = {Henriques, Ricardo and Leterrier, Christophe and Weigel, Aubrey} } @article {68954, title = {Direct observation of the conformational states of PIEZO1.}, journal = {Nature}, volume = {620}, year = {2023}, month = {2023 Aug 31}, pages = {1117-1125}, abstract = {

PIEZOs are mechanosensitive ion channels that convert force into chemoelectric signals and have essential roles in diverse physiological settings. In vitro studies have proposed that PIEZO channels transduce mechanical force through the deformation of extensive blades of transmembrane domains emanating from a central ion-conducting pore. However, little is known about how these channels interact with their native environment and which molecular movements underlie activation. Here we directly observe the conformational dynamics of the blades of individual PIEZO1 molecules in a cell using nanoscopic fluorescence imaging. Compared with previous structural models of PIEZO1, we show that the blades are significantly expanded at rest by the bending stress exerted by the plasma membrane. The degree of expansion varies dramatically along the length of the blade, where decreased binding strength between subdomains can explain increased flexibility of the distal blade. Using chemical and mechanical modulators of PIEZO1, we show that blade expansion and channel activation are correlated. Our findings begin to uncover how PIEZO1 is activated in a native environment. More generally, as we reliably detect conformational shifts of single nanometres from populations of channels, we expect that this approach will serve as a framework for the structural analysis of membrane proteins through nanoscopic imaging.

}, issn = {1476-4687}, doi = {10.1038/s41586-023-06427-4}, author = {Mulhall, Eric M and Gharpure, Anant and Lee, Rachel M and Dubin, Adrienne E and Aaron, Jesse S and Marshall, Kara L and Spencer, Kathryn R and Reiche, Michael A and Henderson, Scott C and Chew, Teng-Leong and Patapoutian, Ardem} } @article {68959, title = {Dissecting Cell Plate Development During Plant Cytokinesis.}, journal = {Microscopy and Microanalysis}, volume = {29}, year = {2023}, month = {2023 Jul 22}, pages = {865}, keywords = {Cytokinesis}, issn = {1435-8115}, doi = {10.1093/micmic/ozad067.428}, author = {Sinclair, Rosalie and Cox, Daniel and Heddleston, John and Aaron, Jesse and Wait, Eric and Wilkop, Thomas and Drakakaki, Georgia} } @article {68632, title = {DNA-initiated epigenetic cascades driven by C9orf72 hexanucleotide repeat.}, journal = {Neuron}, volume = {111}, year = {2023}, month = {2023 Apr 19}, pages = {1205-21}, abstract = {

The C9orf72 hexanucleotide repeat expansion (HRE) is the most frequent genetic cause of the neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Here, we describe the pathogenic cascades that are initiated by the C9orf72 HRE DNA. The HRE DNA binds to its protein partner DAXX and promotes its liquid-liquid phase separation, which is capable of reorganizing genomic structures. An HRE-dependent nuclear accumulation of DAXX drives chromatin remodeling and epigenetic changes such as histone hypermethylation and hypoacetylation in patient cells. While regulating global gene expression, DAXX plays a key role in the suppression of basal and stress-inducible expression of C9orf72 via chromatin remodeling and epigenetic modifications of the promoter of the major C9orf72 transcript. Downregulation of DAXX or rebalancing the epigenetic modifications mitigates the stress-induced sensitivity of C9orf72-patient-derived motor neurons. These studies reveal a C9orf72 HRE DNA-dependent regulatory mechanism for both local and genomic architectural changes in the relevant diseases.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2023.01.022}, author = {Liu, Yang and Huang, Zhiyuan and Liu, Honghe and Ji, Zhicheng and Arora, Amit and Cai, Danfeng and Wang, Hongjin and Liu, Mingming and Simko, Eric A J and Zhang, Yanjun and Periz, Goran and Liu, Zhe and Wang, Jiou} } @article {69007, title = {Driver lines for studying associative learning in Drosophila}, journal = {bioRxiv}, year = {2023}, month = {2023 Sep 16}, abstract = {

The mushroom body (MB) is the center for associative learning in insects. In Drosophila, intersectional split-GAL4 drivers and electron microscopy (EM) connectomes have laid the foundation for precise interrogation of the MB neural circuits. However, many cell types upstream and downstream of the MB remained to be investigated due to lack of driver lines. Here we describe a new collection of over 800 split-GAL4 and split-LexA drivers that cover approximately 300 cell types, including sugar sensory neurons, putative nociceptive ascending neurons, olfactory and thermo-/hygro-sensory projection neurons, interneurons connected with the MB-extrinsic neurons, and various other cell types. We characterized activation phenotypes for a subset of these lines and identified the sugar sensory neuron line most suitable for reward substitution. Leveraging the thousands of confocal microscopy images associated with the collection, we analyzed neuronal morphological stereotypy and discovered that one set of mushroom body output neurons, MBON08/MBON09, exhibits striking individuality and asymmetry across animals. In conjunction with the EM connectome maps, the driver lines reported here offer a powerful resource for functional dissection of neural circuits for associative learning in adult Drosophila.

}, doi = {https://doi.org/10.7554/elife.94168.4}, url = {https://doi.org/10.7554/elife.94168.4 }, author = {Yichun Shuai and Megan Sammons and Gabriella Sterne and Karen Hibbard and He Yang and Ching-Po Yang and Claire Managan and Igor Siwanowicz and Tzumin Lee and Gerald M. Rubin and Glenn Turner and Yoshinori Aso} } @article {68932, title = {Dynamics of cortical contrast adaptation predict perception of signals in noise.}, journal = {Nature Communications}, volume = {14}, year = {2023}, month = {2023 Aug 09}, pages = {4817}, abstract = {

Neurons throughout the sensory pathway adapt their responses depending on the statistical structure of the sensory environment. Contrast gain control is a form of adaptation in the auditory cortex, but it is unclear whether the dynamics of gain control reflect efficient adaptation, and whether they shape behavioral perception. Here, we trained mice to detect a target presented in background noise shortly after a change in the contrast of the background. The observed changes in cortical gain and behavioral detection followed the dynamics of a normative model of efficient contrast gain control; specifically, target detection and sensitivity improved slowly in low contrast, but degraded rapidly in high contrast. Auditory cortex was required for this task, and cortical responses were not only similarly affected by contrast but predicted variability in behavioral performance. Combined, our results demonstrate that dynamic gain adaptation supports efficient coding in auditory cortex and predicts the perception of sounds in noise.

}, keywords = {Acoustic Stimulation, Adaptation, Physiological, Animals, Auditory Cortex, Auditory Perception, Mice, Noise, Sound}, issn = {2041-1723}, doi = {10.1038/s41467-023-40477-6}, author = {Angeloni, Christopher F and M{\l}ynarski, Wiktor and Piasini, Eugenio and Williams, Aaron M and Wood, Katherine C and Garami, Linda and Hermundstad, Ann M and Geffen, Maria N} } @article {68806, title = {Environmental dynamics shape perceptual decision bias.}, journal = {PLoS Computational Biology}, volume = {19}, year = {2023}, month = {2023 Jun 08}, pages = {e1011104}, abstract = {

To interpret the sensory environment, the brain combines ambiguous sensory measurements with knowledge that reflects context-specific prior experience. But environmental contexts can change abruptly and unpredictably, resulting in uncertainty about the current context. Here we address two questions: how should context-specific prior knowledge optimally guide the interpretation of sensory stimuli in changing environments, and do human decision-making strategies resemble this optimum? We probe these questions with a task in which subjects report the orientation of ambiguous visual stimuli that were drawn from three dynamically switching distributions, representing different environmental contexts. We derive predictions for an ideal Bayesian observer that leverages knowledge about the statistical structure of the task to maximize decision accuracy, including knowledge about the dynamics of the environment. We show that its decisions are biased by the dynamically changing task context. The magnitude of this decision bias depends on the observer{\textquoteright}s continually evolving belief about the current context. The model therefore not only predicts that decision bias will grow as the context is indicated more reliably, but also as the stability of the environment increases, and as the number of trials since the last context switch grows. Analysis of human choice data validates all three predictions, suggesting that the brain leverages knowledge of the statistical structure of environmental change when interpreting ambiguous sensory signals.

}, keywords = {Bayes Theorem, Bias, Brain, Decision Making, Humans, Uncertainty}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1011104}, author = {Charlton, Julie A and M{\l}ynarski, Wiktor F and Bai, Yoon H and Hermundstad, Ann M and Goris, Robbe L T} } @article {69021, title = {Extracellular glutamate and GABA transients at the transition from interictal spiking to seizures.}, journal = {Brain}, year = {2023}, month = {2023 Oct 03}, abstract = {

Focal epilepsy is associated with intermittent brief population discharges (interictal spikes), which resemble sentinel spikes that often occur at the onset of seizures. Why interictal spikes self-terminate whilst seizures persist and propagate is incompletely understood. We used fluorescent glutamate and GABA sensors in an awake rodent model of neocortical seizures to resolve the spatiotemporal evolution of both neurotransmitters in the extracellular space. Interictal spikes were accompanied by brief glutamate transients which were maximal at the initiation site and rapidly propagated centrifugally. GABA transients lasted longer than glutamate transients and were maximal \~{}1.5 mm from the focus where they propagated centripetally. Prior to seizure initiation GABA transients were attenuated, whilst glutamate transients increased, consistent with a progressive failure of local inhibitory restraint. As seizures increased in frequency, there was a gradual increase in the spatial extent of spike-associated glutamate transients associated with interictal spikes. Neurotransmitter imaging thus reveals a progressive collapse of an annulus of feed-forward GABA release, allowing seizures to escape from local inhibitory restraint.

}, issn = {1460-2156}, doi = {10.1093/brain/awad336}, author = {Shimoda, Yoshiteru and Leite, Marco and Graham, Robert T and Marvin, Jonathan S and Hasseman, Jeremy and Kolb, Ilya and Looger, Loren L and Magloire, Vincent and Kullmann, Dimitri M} } @article {68715, title = {Extracellular matrix assembly stress initiates Drosophila central nervous system morphogenesis.}, journal = {Developmental Cell}, year = {2023}, month = {2023 Apr 17}, abstract = {

Forces controlling tissue morphogenesis are attributed to cellular-driven activities, and any role for extracellular matrix (ECM) is assumed to be passive. However, all polymer networks, including ECM, can develop autonomous stresses during their assembly. Here, we examine the morphogenetic function of an ECM before reaching homeostatic equilibrium by analyzing de novo ECM assembly during Drosophila ventral nerve cord (VNC) condensation. Asymmetric VNC shortening and a rapid decrease in surface area correlate with the exponential assembly of collagen IV (Col4) surrounding the tissue. Concomitantly, a transient developmentally induced Col4 gradient leads to coherent long-range flow of ECM, which equilibrates the Col4 network. Finite element analysis and perturbation of Col4 network formation through the generation of dominant Col4 mutations that affect assembly reveal that VNC morphodynamics is partially driven by a sudden increase in ECM-driven surface tension. These data suggest that ECM assembly stress and associated network instabilities can actively participate in tissue morphogenesis.

}, issn = {1878-1551}, doi = {10.1016/j.devcel.2023.03.019}, author = {Serna-Morales, Eduardo and S{\'a}nchez-S{\'a}nchez, Besaiz J and Marcotti, Stefania and Nichols, Angus and Bhargava, Anushka and Dragu, Anca and Hirvonen, Liisa M and Diaz-de-la-Loza, Maria-Del-Carmen and Mink, Matyas and Cox, Susan and Rayfield, Emily and Lee, Rachel M and Hobson, Chad M and Chew, Teng-Leong and Stramer, Brian M} } @article {68784, title = {Extracellular matrix assembly stress initiates Drosophila central nervous system morphogenesis.}, journal = {Developmental Cell}, volume = {58}, year = {2023}, month = {2023 May 22}, pages = {825-835.e6}, abstract = {

Forces controlling tissue morphogenesis are attributed to cellular-driven activities, and any role for extracellular matrix (ECM) is assumed to be passive. However, all polymer networks, including ECM, can develop autonomous stresses during their assembly. Here, we examine the morphogenetic function of an ECM before reaching homeostatic equilibrium by analyzing de novo ECM assembly during Drosophila ventral nerve cord (VNC) condensation. Asymmetric VNC shortening and a rapid decrease in surface area correlate with the exponential assembly of collagen IV (Col4) surrounding the tissue. Concomitantly, a transient developmentally induced Col4 gradient leads to coherent long-range flow of ECM, which equilibrates the Col4 network. Finite element analysis and perturbation of Col4 network formation through the generation of dominant Col4 mutations that affect assembly reveal that VNC morphodynamics is partially driven by a sudden increase in ECM-driven surface tension. These data suggest that ECM assembly stress and associated network instabilities can actively participate in tissue morphogenesis.

}, keywords = {Animals, Central Nervous System, Drosophila, Extracellular Matrix, Morphogenesis}, issn = {1878-1551}, doi = {10.1016/j.devcel.2023.03.019}, author = {Serna-Morales, Eduardo and S{\'a}nchez-S{\'a}nchez, Besaiz J and Marcotti, Stefania and Nichols, Angus and Bhargava, Anushka and Dragu, Anca and Hirvonen, Liisa M and Diaz-de-la-Loza, Maria-Del-Carmen and Mink, Matyas and Cox, Susan and Rayfield, Emily and Lee, Rachel M and Hobson, Chad M and Chew, Teng-Leong and Stramer, Brian M} } @article {68665, title = {Fast and sensitive GCaMP calcium indicators for imaging neural populations.}, journal = {Nature}, year = {2023}, month = {2023 Mar 15}, abstract = {

Calcium imaging with protein-based indicators is widely used to follow neural activity in intact nervous systems, but current protein sensors report neural activity at timescales much slower than electrical signalling and are limited by trade-offs between sensitivity and kinetics. Here we used large-scale screening and structure-guided mutagenesis to develop and optimize several fast and sensitive GCaMP-type indicators. The resulting {\textquoteright}jGCaMP8{\textquoteright} sensors, based on the calcium-binding protein calmodulin and a fragment of endothelial nitric oxide synthase, have ultra-fast kinetics (half-rise times of 2 ms) and the highest sensitivity for neural activity reported for a protein-based calcium sensor. jGCaMP8 sensors will allow tracking of large populations of neurons on timescales relevant to neural computation.

}, issn = {1476-4687}, doi = {10.1038/s41586-023-05828-9}, author = {Zhang, Yan and Rozsa, Marton and Liang, Yajie and Bushey, Daniel and Wei, Ziqiang and Zheng, Jihong and Reep, Daniel and Broussard, Gerard Joey and Tsang, Arthur and Tsegaye, Getahun and Narayan, Sujatha and Obara, Christopher J and Lim, Jing-Xuan and Patel, Ronak and Zhang, Rongwei and Ahrens, Misha B and Turner, Glenn C and Wang, Samuel S-H and Korff, Wyatt L and Schreiter, Eric R and Svoboda, Karel and Hasseman, Jeremy P and Kolb, Ilya and Looger, Loren L} } @article {68521, title = {From primordial clocks to circadian oscillators}, journal = {Nature}, year = {2023}, month = {2023 Apr 01}, abstract = {

Circadian rhythms play an essential role in many biological processes and surprisingly only three prokaryotic proteins are required to constitute a true post-translational circadian oscillator. The evolutionary history of the three Kai proteins indicates that KaiC is the oldest member and central component of the clock, with subsequent additions of KaiB and KaiA to regulate its phosphorylation state for time synchronization. The canonical KaiABC system in cyanobacteria is well understood, but little is known about more ancient systems that possess just KaiBC, except for reports that they might exhibit a basic, hourglass-like timekeeping mechanism. Here, we investigate the primordial circadian clock in\ Rhodobacter sphaeroides\ (RS) that contains only KaiBC to elucidate its inner workings despite the missing KaiA. Using a combination X-ray crystallography and cryo-EM we find a novel dodecameric fold for KaiCRS\ where two hexamers are held together by a coiled-coil bundle of 12 helices. This interaction is formed by the C-terminal extension of KaiCRS\ and serves as an ancient regulatory moiety later superseded by KaiA. A coiled-coil register shift between daytime- and nighttime-conformations is connected to the phosphorylation sites through a long-range allosteric network that spans over 160 {\r A}. Our kinetic data identify the difference in ATP-to-ADP ratio between day and night as the environmental cue that drives the clock and further unravels mechanistic details that shed light on the evolution of self-sustained oscillators.

}, doi = {10.1038/s41586-023-05836-9}, url = {https://doi.org/10.1038/s41586-023-05836-9}, author = {Warintra Pitsawong and Ricardo A. P. P{\'a}dua and Timothy Grant and Marc Hoemberger and Renee Otten and Niels Bradshaw and Nikolaus Grigorieff and Dorothee Kern} } @article {68772, title = {Glutamate indicators with improved activation kinetics and localization for imaging synaptic transmission.}, journal = {Nature Methods}, volume = {20}, year = {2023}, month = {2023 Jun 01}, abstract = {

The fluorescent glutamate indicator iGluSnFR enables imaging of neurotransmission with genetic and molecular specificity. However, existing iGluSnFR variants exhibit low in vivo signal-to-noise ratios, saturating activation kinetics and exclusion from postsynaptic densities. Using a multiassay screen in bacteria, soluble protein and cultured neurons, we generated variants with improved signal-to-noise ratios and kinetics. We developed surface display constructs that improve iGluSnFR{\textquoteright}s nanoscopic localization to postsynapses. The resulting indicator iGluSnFR3 exhibits rapid nonsaturating activation kinetics and reports synaptic glutamate release with decreased saturation and increased specificity versus extrasynaptic signals in cultured neurons. Simultaneous imaging and electrophysiology at individual boutons in mouse visual cortex showed that iGluSnFR3 transients report single action potentials with high specificity. In vibrissal sensory cortex layer 4, we used iGluSnFR3 to characterize distinct patterns of touch-evoked feedforward input from thalamocortical boutons and both feedforward and recurrent input onto L4 cortical neuron dendritic spines.

}, issn = {1548-7105}, doi = {10.1038/s41592-023-01863-6}, author = {Aggarwal, Abhi and Liu, Rui and Chen, Yang and Ralowicz, Amelia J and Bergerson, Samuel J and Tomaska, Filip and Mohar, Boaz and Hanson, Timothy L and Hasseman, Jeremy P and Reep, Daniel and Tsegaye, Getahun and Yao, Pantong and Ji, Xiang and Kloos, Marinus and Walpita, Deepika and Patel, Ronak and Mohr, Manuel A and Tillberg, Paul W and Looger, Loren L and Marvin, Jonathan S and Hoppa, Michael B and Konnerth, Arthur and Kleinfeld, David and Schreiter, Eric R and Podgorski, Kaspar} } @article {68008, title = {Hierarchical architecture of dopaminergic circuits enables second-order conditioning in Drosophila}, journal = {eLife}, year = {2023}, month = {2023 Jan 24}, abstract = {

Dopaminergic neurons with distinct projection patterns and physiological properties compose memory subsystems in a brain. However, it is poorly understood whether or how they interact during complex learning. Here, we identify a feedforward circuit formed between dopamine subsystems and show that it is essential for second-order conditioning, an ethologically important form of higher-order associative learning. The\ Drosophila\ mushroom body comprises a series of dopaminergic compartments, each of which exhibits distinct memory dynamics. We find that a slow and stable memory compartment can serve as an effective {\textquotedblleft}teacher{\textquotedblright} by instructing other faster and transient memory compartments via a single key interneuron, which we identify by connectome analysis and neurotransmitter prediction. This excitatory interneuron acquires enhanced response to reward-predicting odor after first-order conditioning and, upon activation, evokes dopamine release in the {\textquotedblleft}student{\textquotedblright} compartments. These hierarchical connections between dopamine subsystems explain distinct properties of first- and second-order memory long known by behavioral psychologists.

}, doi = {10.7554/eLife.79042}, url = {https://doi.org/10.7554/eLife.79042}, author = {Daichi Yamada and Daniel Bushey and Li Feng and Karen Hibbard and Megan Sammons and Jan Funke and Ashok Litwin-Kumar and Toshihide Hige and Yoshinori Aso} } @article {69076, title = {High-fidelity 3D live-cell nanoscopy through data-driven enhanced super-resolution radial fluctuation.}, journal = {Nature Methods}, year = {2023}, month = {2023 Nov 13}, abstract = {

Live-cell super-resolution microscopy enables the imaging of biological structure dynamics below the diffraction limit. Here we present enhanced super-resolution radial fluctuations (eSRRF), substantially improving image fidelity and resolution compared to the original SRRF method. eSRRF incorporates automated parameter optimization based on the data itself, giving insight into the trade-off between resolution and fidelity. We demonstrate eSRRF across a range of imaging modalities and biological systems. Notably, we extend eSRRF to three dimensions by combining it with multifocus microscopy. This realizes live-cell volumetric super-resolution imaging with an acquisition speed of ~1 volume per second. eSRRF provides an accessible super-resolution approach, maximizing information extraction across varied experimental conditions while minimizing artifacts. Its optimal parameter prediction strategy is generalizable, moving toward unbiased and optimized analyses in super-resolution microscopy.

}, issn = {1548-7105}, doi = {10.1038/s41592-023-02057-w}, author = {Laine, Romain F and Heil, Hannah S and Coelho, Simao and Nixon-Abell, Jonathon and Jimenez, Ang{\'e}lique and Wiesner, Theresa and Mart{\'\i}nez, Dami{\'a}n and Galgani, Tommaso and R{\'e}gnier, Louise and Stubb, Aki and Follain, Gautier and Webster, Samantha and Goyette, Jesse and Dauphin, Aurelien and Salles, Audrey and Culley, Si{\^a}n and Jacquemet, Guillaume and Hajj, Bassam and Leterrier, Christophe and Henriques, Ricardo} } @article {68957, title = {Hydrophobic interactions dominate the recognition of a KRAS G12V neoantigen.}, journal = {Nature Communications}, volume = {14}, year = {2023}, month = {2023 Aug 21}, pages = {5063}, abstract = {

Specificity remains a major challenge to current therapeutic strategies for cancer. Mutation associated neoantigens (MANAs) are products of genetic alterations, making them highly specific therapeutic targets. MANAs are HLA-presented (pHLA) peptides derived from intracellular mutant proteins that are otherwise inaccessible to antibody-based therapeutics. Here, we describe the cryo-EM structure of an antibody-MANA pHLA complex. Specifically, we determine a TCR mimic (TCRm) antibody bound to its MANA target, the KRAS peptide presented by HLA-A*03:01. Hydrophobic residues appear to account for the specificity of the mutant G12V residue. We also determine the structure of the wild-type G12 peptide bound to HLA-A*03:01, using X-ray crystallography. Based on these structures, we perform screens to validate the key residues required for peptide specificity. These experiments led us to a model for discrimination between the mutant and the wild-type peptides presented on HLA-A*03:01 based exclusively on hydrophobic interactions.

}, keywords = {Antibodies, HLA-A Antigens, Hydrophobic and Hydrophilic Interactions, Proto-Oncogene Proteins p21(ras), Recognition, Psychology}, issn = {2041-1723}, doi = {10.1038/s41467-023-40821-w}, author = {Wright, Katharine M and DiNapoli, Sarah R and Miller, Michelle S and Aitana Azurmendi, P and Zhao, Xiaowei and Yu, Zhiheng and Chakrabarti, Mayukh and Shi, WuXian and Douglass, Jacqueline and Hwang, Michael S and Hsiue, Emily Han-Chung and Mog, Brian J and Pearlman, Alexander H and Paul, Suman and Konig, Maximilian F and Pardoll, Drew M and Bettegowda, Chetan and Papadopoulos, Nickolas and Kinzler, Kenneth W and Vogelstein, Bert and Zhou, Shibin and Gabelli, Sandra B} } @article {69055, title = {Imagining the future of optical microscopy: everything, everywhere, all at once.}, journal = {Communications Biology}, volume = {6}, year = {2023}, month = {2023 Oct 28}, pages = {1096}, abstract = {

The optical microscope has revolutionized biology since at least the 17 Century. Since then, it has progressed from a largely observational tool to a powerful bioanalytical platform. However, realizing its full potential to study live specimens is hindered by a daunting array of technical challenges. Here, we delve into the current state of live imaging to explore the barriers that must be overcome and the possibilities that lie ahead. We venture to envision a future where we can visualize and study everything, everywhere, all at once - from the intricate inner workings of a single cell to the dynamic interplay across entire organisms, and a world where scientists could access the necessary microscopy technologies anywhere.

}, keywords = {Microscopy}, issn = {2399-3642}, doi = {10.1038/s42003-023-05468-9}, author = {Balasubramanian, Harikrushnan and Hobson, Chad M and Chew, Teng-Leong and Aaron, Jesse S} } @article {68934, title = {Investigating the composition and recruitment of the mycobacterial ImuA{\textquoteright}-ImuB-DnaE2 mutasome.}, journal = {eLife}, volume = {12}, year = {2023}, month = {2023 Aug 02}, abstract = {

A DNA damage-inducible mutagenic gene cassette has been implicated in the emergence of drug resistance in during anti-tuberculosis (TB) chemotherapy. However, the molecular composition and operation of the encoded {\textquoteright}mycobacterial mutasome{\textquoteright} - minimally comprising DnaE2 polymerase and ImuA{\textquoteright} and ImuB accessory proteins - remain elusive. Following exposure of mycobacteria to DNA damaging agents, we observe that DnaE2 and ImuB co-localize with the DNA polymerase III β subunit (β clamp) in distinct intracellular foci. Notably, genetic inactivation of the mutasome in an mutant containing a disrupted β clamp-binding motif abolishes ImuB-β clamp focus formation, a phenotype recapitulated pharmacologically by treating bacilli with griselimycin and in biochemical assays in which this β clamp-binding antibiotic collapses pre-formed ImuB-β clamp complexes. These observations establish the essentiality of the ImuB-β clamp interaction for mutagenic DNA repair in mycobacteria, identifying the mutasome as target for adjunctive therapeutics designed to protect anti-TB drugs against emerging resistance.

}, keywords = {Antitubercular Agents, Bacterial Proteins, DNA Repair, Mutagenesis, Mycobacterium tuberculosis}, issn = {2050-084X}, doi = {10.7554/eLife.75628}, author = {Gessner, Sophia and Martin, Zela Alexandria-Mae and Reiche, Michael A and Santos, Joana A and Dinkele, Ryan and Ramudzuli, Atondaho and Dhar, Neeraj and de Wet, Timothy J and Anoosheh, Saber and Lang, Dirk M and Aaron, Jesse and Chew, Teng-Leong and Herrmann, Jennifer and M{\"u}ller, Rolf and McKinney, John D and Woodgate, Roger and Mizrahi, Valerie and Venclovas, {\v C}eslovas and Lamers, Meindert H and Warner, Digby F} } @article {69126, title = {Ketamine modulates a norepinephrine-astroglial circuit to persistently suppress futility-induced passivity.}, journal = {bioRxiv}, year = {2023}, month = {2023 Dec 29}, abstract = {

Mood-altering compounds hold promise for the treatment of many psychiatric disorders, such as depression, but connecting their molecular, circuit, and behavioral effects has been challenging. Here we find that, analogous to effects in rodent learned helplessness models, ketamine pre-exposure persistently suppresses futility-induced passivity in larval zebrafish. While antidepressants are thought to primarily act on neurons, brain-wide imaging in behaving zebrafish showed that ketamine elevates intracellular calcium in astroglia for many minutes, followed by persistent calcium downregulation post-washout. Calcium elevation depends on astroglial α1-adrenergic receptors and is required for suppression of passivity. Chemo-/optogenetic perturbations of noradrenergic neurons and astroglia demonstrate that the aftereffects of glial calcium elevation are sufficient to suppress passivity by inhibiting neuronal-astroglial integration of behavioral futility. Imaging in mouse cortex reveals that ketamine elevates astroglial calcium through conserved pathways, suggesting that ketamine exerts its behavioral effects by persistently modulating evolutionarily ancient neuromodulatory systems spanning neurons and astroglia.

}, doi = {10.1101/2022.12.29.522099}, url = {https://doi.org/10.1101/2022.12.29.522099}, author = {Marc Duque and Alex B. Chen and Eric Hsu and Sujatha Narayan and Altyn Rymbek and Shahinoor Begum and Gesine Saher and Adam E. Cohen and David E. Olson and David A. Prober and Dwight E. Bergles and Mark C. Fishman and Florian Engert and Misha B. Ahrens} } @article {69053, title = {Lactate biosensors for spectrally and spatially multiplexed fluorescence imaging.}, journal = {Nature Communications}, volume = {14}, year = {2023}, month = {2023 Oct 27}, pages = {6598}, abstract = {

L-Lactate is increasingly appreciated as a key metabolite and signaling molecule in mammals. However, investigations of the inter- and intra-cellular dynamics of L-lactate are currently hampered by the limited selection and performance of L-lactate-specific genetically encoded biosensors. Here we now report a spectrally and functionally orthogonal pair of high-performance genetically encoded biosensors: a green fluorescent extracellular L-lactate biosensor, designated eLACCO2.1, and a red fluorescent intracellular L-lactate biosensor, designated R-iLACCO1. eLACCO2.1 exhibits excellent membrane localization and robust fluorescence response. To the best of our knowledge, R-iLACCO1 and its affinity variants exhibit larger fluorescence responses than any previously reported intracellular L-lactate biosensor. We demonstrate spectrally and spatially multiplexed imaging of L-lactate dynamics by coexpression of eLACCO2.1 and R-iLACCO1 in cultured cells, and in vivo imaging of extracellular and intracellular L-lactate dynamics in mice.

}, keywords = {Animals, Biosensing Techniques, Cells, Cultured, Fluorescence Resonance Energy Transfer, Lactic Acid, Mammals, Mice, Optical Imaging}, issn = {2041-1723}, doi = {10.1038/s41467-023-42230-5}, author = {Nasu, Yusuke and Aggarwal, Abhi and Le, Giang N T and Vo, Camilla Trang and Kambe, Yuki and Wang, Xinxing and Beinlich, Felix R M and Lee, Ashley Bomin and Ram, Tina R and Wang, Fangying and Gorzo, Kelsea A and Kamijo, Yuki and Boisvert, Marc and Nishinami, Suguru and Kawamura, Genki and Ozawa, Takeaki and Toda, Hirofumi and Gordon, Grant R and Ge, Shaoyu and Hirase, Hajime and Nedergaard, Maiken and Paquet, Marie-Eve and Drobizhev, Mikhail and Podgorski, Kaspar and Campbell, Robert E} } @article {68607, title = {Large-scale brain-wide neural recording in nonhuman primates}, journal = {bioRxiv}, year = {2023}, month = {2023 Feb 04}, abstract = {

High-density, integrated silicon electrodes have begun to transform systems neuroscience, by enabling large-scale neural population recordings with single cell resolution. Existing technologies, however, have provided limited functionality in nonhuman primate species such as macaques, which offer close models of human cognition and behavior. Here, we report the design, fabrication, and performance of Neuropixels 1.0-NHP, a high channel count linear electrode array designed to enable large-scale simultaneous recording in superficial and deep structures within the macaque or other large animal brain. These devices were fabricated in two versions: 4416 electrodes along a 45 mm shank, and 2496 along a 25 mm shank. For both versions, users can programmably select 384 channels, enabling simultaneous multi-area recording with a single probe. We demonstrate recording from over 3000 single neurons within a session, and simultaneous recordings from over 1000 neurons using multiple probes. This technology represents a significant increase in recording access and scalability relative to existing technologies, and enables new classes of experiments involving fine-grained electrophysiological characterization of brain areas, functional connectivity between cells, and simultaneous brain-wide recording at scale.

}, doi = {10.1101/2023.02.01.526664}, url = {https://doi.org/10.1101/2023.02.01.526664}, author = {Eric M. Trautmann and Janis K. Hesse and Gabriel M. Stine and Ruobing Xia and Shude Zhu and Daniel J. O{\textquoteright}Shea and Bill Karsh and Jennifer Colonell and Frank F. Lanfranchi and Saurabh Vyas and Andrew Zimnik and Natalie A. Steinmann and Daniel A. Wagenaar and Alexandru Andrei and Carolina Mora Lopez and John O{\textquoteright}Callaghan and Jan Putzeys and Bogdan C. Raducanu and Marleen Welkenhuysen and Mark Churchland and Tirin Moore and Michael Shadlen and Krishna Shenoy and Doris Tsao and Barundeb Dutta and Timothy Harris} } @article {68774, title = {A leaky integrate-and-fire computational model based on the connectome of the entire adult Drosophila brain reveals insights into sensorimotor processing}, journal = {bioRxiv}, year = {2023}, month = {2023 May 02}, abstract = {

The forthcoming assembly of the adult\ Drosophila melanogaster\ central brain connectome, containing over 125,000 neurons and 50 million synaptic connections, provides a template for examining sensory processing throughout the brain. Here, we create a leaky integrate-and-fire computational model of the entire\ Drosophila\ brain, based on neural connectivity and neurotransmitter identity, to study circuit properties of feeding and grooming behaviors. We show that activation of sugar-sensing or water-sensing gustatory neurons in the computational model accurately predicts neurons that respond to tastes and are required for feeding initiation. Computational activation of neurons in the feeding region of the\ Drosophila\ brain predicts those that elicit motor neuron firing, a testable hypothesis that we validate by optogenetic activation and behavioral studies. Moreover, computational activation of different classes of gustatory neurons makes accurate predictions of how multiple taste modalities interact, providing circuit-level insight into aversive and appetitive taste processing. Our computational model predicts that the sugar and water pathways form a partially shared appetitive feeding initiation pathway, which our calcium imaging and behavioral experiments confirm. Additionally, we applied this model to mechanosensory circuits and found that computational activation of mechanosensory neurons predicts activation of a small set of neurons comprising the antennal grooming circuit that do not overlap with gustatory circuits, and accurately describes the circuit response upon activation of different mechanosensory subtypes. Our results demonstrate that modeling brain circuits purely from connectivity and predicted neurotransmitter identity generates experimentally testable hypotheses and can accurately describe complete sensorimotor transformations.

}, doi = {10.1101/2023.05.02.539144}, url = {https://doi.org/10.1101/2023.05.02.539144}, author = {Philip K. Shiu and Gabriella R. Sterne and Nico Spiller and Romain Franconville and Andrea Sandoval and Joie Zhou and Neha Simha and Chan Hyuk Kang and Seongbong Yu and Jinseop S. Kim and Sven Dorkenwald and Arie Matsliah and Philipp Schlegel and Szi-chieh Yu and Claire E. McKellar and Amy Sterling and Marta Costa and Katharina Eichler and Gregory S.X.E. Jefferis and Mala Murthy and Alexander Shakeel Bates and Nils Eckstein and Jan Funke and Salil S. Bidaye and Stefanie Hampel and Andrew M. Seeds and Kristin Scott} } @article {68922, title = {Localization of fixed dipoles at high precision by accounting for sample drift during illumination}, journal = {Applied Physics Letters}, volume = {123}, year = {2023}, month = {2023 Jul 13}, abstract = {

Single molecule localization microscopy relies on the precise quantification of the position of single dye emitters in a sample. This precision is improved by the number of photons that can be detected from each molecule. Particularly recording at cryogenic temperatures dramatically reduces photobleaching and would, hence, in principle, allow the user to massively increase the illumination time to several seconds. The downside of long illuminations, however, would be image blur due to inevitable jitter or drift occurring during the illuminations, which deteriorates the localization precision. In this paper, we theoretically demonstrate that a parallel recording of the fiducial marker beads together with a fitting approach accounting for the full drift trajectory allows for largely eliminating drift effects for drift magnitudes of several hundred nanometers per frame. We showcase the method for linear and diffusional drift as well as oscillations, assuming fixed dipole orientations during each illumination.

}, issn = {0003-6951}, doi = {10.1063/5.0137834}, url = {https://doi.org/10.1063/5.0137834}, author = {Hinterer, Fabian and Schneider, Magdalena C. and Hubmer, Simon and L{\'o}pez-Mart{\'\i}nez, Montserrat and Ramlau, Ronny and Sch{\"u}tz, Gerhard J.} } @article {69009, title = {Low-latency extracellular spike assignment for high-density electrodes at single-neuron resolution}, journal = {bioRxiv}, year = {2023}, month = {2023 Sep 15}, abstract = {

Real-time neural signal processing is essential for brain-machine interfaces and closed-loop neuronal perturbations. However, most existing applications sacrifice cell-specific identity and temporal spiking information for speed. We developed a hybrid hardware-software system that utilizes a Field Programmable Gate Array (FPGA) chip to acquire and process data in parallel, enabling individual spikes from many simultaneously recorded neurons to be assigned single-neuron identities with 1-millisecond latency. The FPGA assigns labels, validated with ground-truth data, by comparing multichannel spike waveforms from tetrode or silicon probe recordings to a spike-sorted model generated offline in software. This platform allowed us to rapidly inactivate a region in vivo based on spikes from an upstream neuron before these spikes could excite the downstream region. Furthermore, we could decode animal location within 3 ms using data from a population of individual hippocampal neurons. These results demonstrate our system{\textquoteright}s suitability for a broad spectrum of research and clinical applications.

}, doi = {10.1101/2023.09.14.557854}, url = {https://doi.org/10.1101/2023.09.14.557854}, author = {Chongxi Lai and Dohoung Kim and Brian Lustig and Shinsuke Tanaka and Brian Barbarits and Lakshmi Narayan and Jennifer Colonell and Ole Paulsen and Albert K. Lee and Timothy D. Harris} } @article {68700, title = {Mental navigation and telekinesis with a hippocampal map-based brain-machine interface}, journal = {bioRxiv}, year = {2023}, month = {2023 Apr 10}, abstract = {

The hippocampus is critical for recollecting and imagining experiences. This is believed to involve voluntarily drawing from hippocampal memory representations of people, events, and places, including the hippocampus{\textquoteright} map-like representations of familiar environments. However, whether the representations in such {\textquotedblleft}cognitive maps{\textquotedblright} can be volitionally and selectively accessed is unknown. We developed a brain-machine interface to test if rats could control their hippocampal activity in a flexible, goal-directed, model-based manner. We show that rats can efficiently navigate or direct objects to arbitrary goal locations within a virtual reality arena solely by activating and sustaining appropriate hippocampal representations of remote places. This should provide insight into the mechanisms underlying episodic memory recall, mental simulation/planning, and imagination, and open up possibilities for high-level neural prosthetics utilizing hippocampal representations.

}, doi = {10.1101/2023.04.07.536077}, url = {https://doi.org/10.1101/2023.04.07.536077}, author = {Chongxi Lai and Shinsuke Tanaka and Timothy D. Harris and Albert K. Lee} } @article {68836, title = {Method To Diversify Cyanine Chromophore Functionality Enables Improved Biomolecule Tracking and Intracellular Imaging.}, journal = {Journal of the American Chemical Society}, volume = {145}, year = {2023}, month = {2023 Jun 27}, pages = {14647{\textendash}14659}, abstract = {

Heptamethine indocyanines are invaluable probes for near-infrared (NIR) imaging. Despite broad use, there are only a few synthetic methods to assemble these molecules, and each has significant limitations. Here, we report the use of pyridinium benzoxazole (PyBox) salts as heptamethine indocyanine precursors. This method is high yielding, simple to implement, and provides access to previously unknown chromophore functionality. We applied this method to create molecules to address two outstanding objectives in NIR fluorescence imaging. First, we used an iterative approach to develop molecules for protein-targeted tumor imaging. When compared to common NIR fluorophores, the optimized probe increases the tumor specificity of monoclonal antibody (mAb) and nanobody conjugates. Second, we developed cyclizing heptamethine indocyanines with the goal of improving cellular uptake and fluorogenic properties. By modifying both the electrophilic and nucleophilic components, we demonstrate that the solvent sensitivity of the ring-open/ring-closed equilibrium can be modified over a wide range. We then show that a chloroalkane derivative of a compound with tuned cyclization properties undergoes particularly efficient no-wash live cell imaging using organelle-targeted HaloTag self-labeling proteins. Overall, the chemistry reported here broadens the scope of accessible chromophore functionality, and, in turn, enables the discovery of NIR probes with promising properties for advanced imaging applications.

}, issn = {1520-5126}, doi = {10.1021/jacs.3c01765}, author = {Usama, Syed Muhammad and Marker, Sierra C and Li, Dong-Hao and Caldwell, Donald R and Stroet, Marcus and Patel, Nimit L and Tebo, Alison G and Hernot, Sophie and Kalen, Joseph D and Schnermann, Martin} } @article {68783, title = {Modulation of calcium signaling {\textquotedblleft}on demand{\textquotedblright} to decipher the molecular mechanisms responsible for primary aldosteronism}, journal = {Archives of Cardiovascular Diseases Supplements}, volume = {15}, year = {2023}, month = {2023 May 01}, pages = {188}, abstract = {

Primary aldosteronism\ (PA) is the most frequent form of secondary hypertension. Over the past two decades, major advances have been made in our understanding of the disease with the identification of germline or somatic mutations in ion channels and pumps. These mutations enhance\ calcium signaling, the main trigger of\ aldosterone\ biosynthesis.

}, issn = {18786480}, doi = {10.1016/j.acvdsp.2023.03.021}, url = {https://doi.org/10.1016/j.acvdsp.2023.03.021}, author = {Fedlaoui, Bakhta and Cosentino, Teresa and Al Sayed, Zeina R. and Fernandes-Rosa, Fabio L. and Hulot, Jean-S{\'e}bastien and Magnus, Chris and Sternson, Scott M. and Travers-Allard, Simon and Baron, St{\'e}phanie and Giscos-Douriez, Isabelle and Zennaro, Maria Christina and Boulkroun, Sheerazed} } @article {68469, title = {Multimodal mapping of cell types and projections in the central nucleus of the amygdala}, journal = {eLife}, year = {2023}, month = {2023 Jan 20}, abstract = {

The central nucleus of the amygdala (CEA) is a brain region that integrates external and internal sensory information and executes innate and adaptive behaviors through distinct output pathways. Despite its complex functions, the diversity of molecularly defined neuronal types in the CEA and their contributions to major axonal projection targets have not been examined systematically. Here, we performed single-cell RNA-sequencing (scRNA-Seq) to classify molecularly defined cell types in the CEA and identified marker-genes to map the location of these neuronal types using\ expansion\ assisted iterative fluorescence in\ situ\ hybridization (EASI-FISH). We developed new methods to integrate EASI-FISH with 5-plex retrograde axonal labeling to determine the spatial, morphological, and connectivity properties of \~{}30,000 molecularly defined CEA neurons. Our study revealed spatio-molecular organization of the CEA, with medial and lateral CEA associated with distinct cell families. We also found a long-range axon projection network from the CEA, where target regions receive inputs from multiple molecularly defined cell types. Axon collateralization was found primarily among projections to hindbrain targets, which are distinct from forebrain projections. This resource reports marker-gene combinations for molecularly defined cell types and axon-projection types, which will be useful for selective interrogation of these neuronal populations to study their contributions to the diverse functions of the CEA.

}, doi = {10.7554/eLife.84262}, url = {https://doi.org/10.7554/eLife.84262}, author = {Yuhan Wang and Sabine Krabbe and Mark Eddison and Fredrick E. Henry and Greg Fleishman and Andrew L. Lemire and Lihua Wang and Wyatt Korff and Paul W. Tillberg and Andreas L{\"u}thi and Scott M. Sternson} } @article {68965, title = {Multiscale head anatomy of Megaphragma (Hymenoptera: Trichogrammatidae).}, journal = {Arthropod Structure and Development}, volume = {76}, year = {2023}, month = {2023 Sep 01}, pages = {101299}, abstract = {

Methods of three-dimensional electron microscopy have been actively developed recently and open up great opportunities for morphological work. This approach is especially useful for studying microinsects, since it is possible to obtain complete series of high-resolution sections of a whole insect. Studies on the genus Megaphragma are especially important, since the unique phenomenon of lysis of most of the neuron nuclei was discovered in species of this genus. In this study we reveal the anatomical structure of the head of Megaphragma viggianii at all levels from organs to subcellular structures. Despite the miniature size of the body, most of the organ systems of M.\ viggianii retain the structural plan and complexity of organization at all levels. The set of muscles and the well-developed stomatogastric nervous system of this species correspond to those of larger insects, and there is also a well-developed tracheal system in the head of this species. Reconstructions of the head of M.\ viggianii at the cellular and subcellular levels were obtained, and of volumetric data were analyzed. A total of 689 nucleated cells of the head were reconstructed. The ultrastructure of M.\ viggianii is surprisingly complex, and the evolutionary benefits of such complexity are probably among the factors limiting the further miniaturization of parasitoid wasps.

}, issn = {1873-5495}, doi = {10.1016/j.asd.2023.101299}, author = {Desyatirkina, Inna A and Makarova, Anastasia A and Pang, Song and Xu, C Shan and Hess, Harald and Polilov, Alexey A} } @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 {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 {68635, title = {OME-Zarr: a cloud-optimized bioimaging file format with international community support.}, journal = {Histochemistry and Cell Biology}, volume = {160}, year = {2023}, month = {2023 Feb 25}, pages = {223-251}, abstract = {

A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing these problems have designed a format specification process (OME-NGFF) to address these needs. This paper brings together a wide range of those community members to describe the format itself {\textendash} OME-Zarr {\textendash} along with tools and data resources available today to increase FAIR access and remove barriers in the scientific process. The current momentum offers an opportunity to unify a key component of the bioimaging domain {\textemdash} the file format that underlies so many personal, institutional, and global data management and analysis tasks.

}, doi = {10.1007/s00418-023-02209-1}, url = {https://doi.org/10.1007/s00418-023-02209-1}, author = {Josh Moore and Daniela Basurto-Lozada and S{\'e}bastien Besson and John Bogovic and Eva M. Brown and Jean-Marie Burel and Gustavo de Medeiros and Erin E. Diel and David Gault and Satrajit S. Ghosh and Ilan Gold and Yaroslav O. Halchenko and Matthew Hartley and Dave Horsfall and Mark S. Keller and Mark Kittisopikul and Gabor Kovacs and Ayb{\"u}ke K{\"u}pc{\"u} Yolda{\c s} and Albane le Tournoulx de la Villegeorges and Tong Li and Prisca Liberali and Melissa Linkert and Dominik Lindner and Joel L{\"u}thi and Jeremy Maitin-Shepard and Trevor Manz and Matthew McCormick and Khaled Mohamed and William Moore and Bugra {\"O}zdemir and Constantin Pape and Lucas Pelkmans and Martin Prete and Tobias Pietzsch and Stephan Preibisch and Norman Rzepka and David R. Stirling and Jonathan Striebel and Christian Tischer and Daniel Toloudis and Petr Walczysko and Alan M. Watson and Frances Wong and Kevin A. Yamauchi and Omer Bayraktar and Muzlifah Haniffa and Stephan Saalfeld and Jason R. Swedlow} } @article {69042, title = {Optimized Red-Absorbing Dyes for Imaging and Sensing}, journal = {Journal of the American Chemical Society}, year = {2023}, month = {2023 Oct 16}, abstract = {

Rhodamine dyes are excellent scaffolds for developing a broad range of fluorescent probes. A key property of rhodamines is their equilibrium between a colorless lactone and fluorescent zwitterion. Tuning the lactone{\textendash}zwitterion equilibrium constant (KL{\textendash}Z) can optimize dye properties for specific biological applications. Here, we use known and novel organic chemistry to prepare a comprehensive collection of rhodamine dyes to elucidate the structure{\textendash}activity relationships that govern\ KL{\textendash}Z. We discovered that the auxochrome substituent strongly affects the lactone{\textendash}zwitterion equilibrium, providing a roadmap for the rational design of improved rhodamine dyes. Electron-donating auxochromes, such as julolidine, work in tandem with fluorinated pendant phenyl rings to yield bright, red-shifted fluorophores for live-cell single-particle tracking (SPT) and multicolor imaging. The\ N-aryl auxochrome combined with fluorination yields red-shifted F{\"o}rster resonance energy transfer (FRET) quencher dyes useful for creating a new semisynthetic indicator to sense cAMP using fluorescence lifetime imaging microscopy (FLIM). Together, this work expands the synthetic methods available for rhodamine synthesis, generates new reagents for advanced fluorescence imaging experiments, and describes structure{\textendash}activity relationships that will guide the design of future probes.

}, issn = {0002-7863}, doi = {10.1021/jacs.3c0527310.1021/jacs.3c05273}, url = {https://pubs.acs.org/doi/10.1021/jacs.3c05273}, author = {Grimm, Jonathan B. and Tkachuk, Ariana N. and Patel, Ronak and Hennigan, S. Thomas and Gutu, Alina and Dong, Peng and Gandin, Valentina and Osowski, Anastasia M. and Holland, Katie L. and Liu, Zhe J. and Brown, Timothy A. and Lavis, Luke D.} } @article {68828, title = {Organization of an Ascending Circuit that Conveys Flight Motor State}, journal = {bioRxiv}, year = {2023}, month = {2023 Jun 09}, abstract = {

Natural behaviors are a coordinated symphony of motor acts which drive self-induced or reafferent sensory activation. Single sensors only signal presence and magnitude of a sensory cue; they cannot disambiguate exafferent (externally-induced) from reafferent sources. Nevertheless, animals readily differentiate between these sources of sensory signals to make appropriate decisions and initiate adaptive behavioral outcomes. This is mediated by predictive motor signaling mechanisms, which emanate from motor control pathways to sensory processing pathways, but how predictive motor signaling circuits function at the cellular and synaptic level is poorly understood. We use a variety of techniques, including connectomics from both male and female electron microscopy volumes, transcriptomics, neuroanatomical, physiological and behavioral approaches to resolve the network architecture of two pairs of ascending histaminergic neurons (AHNs), which putatively provide predictive motor signals to several sensory and motor neuropil. Both AHN pairs receive input primarily from an overlapping population of descending neurons, many of which drive wing motor output. The two AHN pairs target almost exclusively non-overlapping downstream neural networks including those that process visual, auditory and mechanosensory information as well as networks coordinating wing, haltere, and leg motor output. These results support the conclusion that the AHN pairs multi-task, integrating a large amount of common input, then tile their output in the brain, providing predictive motor signals to non-overlapping sensory networks affecting motor control both directly and indirectly.

}, doi = {10.1101/2023.06.07.544074}, url = {https://doi.org/10.1101/2023.06.07.544074}, author = {Han S. J. Cheong and Kaitlyn N. Boone and Marryn M. Bennett and Farzaan Salman and Jacob D. Ralston and Kaleb Hatch and Raven F. Allen and Alec M. Phelps and Andrew P. Cook and Jasper S. Phelps and Mert Erginkaya and Wei-Chung A. Lee and Gwyneth M. Card and Kevin C. Daly and Andrew M. Dacks} } @article {68385, title = {Rationalized deep learning super-resolution microscopy for sustained live imaging of rapid subcellular processes.}, journal = {Nature Biotechnology}, volume = {41}, year = {2023}, month = {2023 Mar 01}, pages = {367-77}, abstract = {

The goal when imaging bioprocesses with optical microscopy is to acquire the most spatiotemporal information with the least invasiveness. Deep neural networks have substantially improved optical microscopy, including image super-resolution and restoration, but still have substantial potential for artifacts. In this study, we developed rationalized deep learning (rDL) for structured illumination microscopy and lattice light sheet microscopy (LLSM) by incorporating prior knowledge of illumination patterns and, thereby, rationally guiding the network to denoise raw images. Here we demonstrate that rDL structured illumination microscopy eliminates spectral bias-induced resolution degradation and reduces model uncertainty by five-fold, improving the super-resolution information by more than ten-fold over other computational approaches. Moreover, rDL applied to LLSM enables self-supervised training by using the spatial or temporal continuity of noisy data itself, yielding results similar to those of supervised methods. We demonstrate the utility of rDL by imaging the rapid kinetics of motile cilia, nucleolar protein condensation during light-sensitive mitosis and long-term interactions between membranous and membrane-less organelles.

}, issn = {1546-1696}, doi = {10.1038/s41587-022-01471-3}, author = {Qiao, Chang and Li, Di and Liu, Yong and Zhang, Siwei and Liu, Kan and Liu, Chong and Guo, Yuting and Jiang, Tao and Fang, Chuyu and Li, Nan and Zeng, Yunmin and He, Kangmin and Zhu, Xueliang and Lippincott-Schwartz, Jennifer and Dai, Qionghai and Li, Dong} } @article {68537, title = {Reward expectations direct learning and drive operant matching in Drosophila}, journal = {Proceedings of the National Academy of Sciences of the U.S.A.}, volume = {120}, year = {2023}, month = {2023 Sep 26}, pages = {e2221415120}, abstract = {

Foraging animals must use decision-making strategies that dynamically adapt to the changing availability of rewards in the environment. A wide diversity of animals do this by distributing their choices in proportion to the rewards received from each option, Herrnstein{\textquoteright}s operant matching law. Theoretical work suggests an elegant mechanistic explanation for this ubiquitous behavior, as operant matching follows automatically from simple synaptic plasticity rules acting within behaviorally relevant neural circuits. However, no past work has mapped operant matching onto plasticity mechanisms in the brain, leaving the biological relevance of the theory unclear. Here we discovered operant matching in\ Drosophila\ and showed that it requires synaptic plasticity that acts in the mushroom body and incorporates the expectation of reward. We began by developing a novel behavioral paradigm to measure choices from individual flies as they learn to associate odor cues with probabilistic rewards. We then built a model of the fly mushroom body to explain each fly{\textquoteright}s sequential choice behavior using a family of biologically-realistic synaptic plasticity rules. As predicted by past theoretical work, we found that synaptic plasticity rules could explain fly matching behavior by incorporating stimulus expectations, reward expectations, or both. However, by optogenetically bypassing the representation of reward expectation, we abolished matching behavior and showed that the plasticity rule must specifically incorporate reward expectations. Altogether, these results reveal the first synaptic level mechanisms of operant matching and provide compelling evidence for the role of reward expectation signals in the fly brain.

}, doi = {10.1073/pnas.2221415120}, url = {https://doi.org/10.1073/pnas.2221415120}, author = {Adithya E. Rajagopalan and Ran Darshan and Karen L. Hibbard and James E. Fitzgerald and Glenn C. Turner} } @article {69012, title = {A rotational velocity estimate constructed through visuomotor competition updates the fly{\textquoteright}s neural compass}, journal = {bioRxiv}, year = {2023}, month = {2023 Sep 26}, abstract = {

Navigating animals continuously integrate velocity signals to update internal representations of their directional heading and spatial location in the environment. How neural circuits combine sensory and motor information to construct these velocity estimates and how these self-motion signals, in turn, update internal representations that support navigational computations are not well understood. Recent work in Drosophila has identified a neural circuit that performs angular path integration to compute the fly{\textquoteright}s head direction, but the nature of the velocity signal is unknown. Here we identify a pair of neurons necessary for angular path integration that encode the fly{\textquoteright}s rotational velocity with high accuracy using both visual optic flow and motor information. This estimate of rotational velocity does not rely on a moment-to-moment integration of sensory and motor information. Rather, when visual and motor signals are congruent, these neurons prioritize motor information over visual information, and when the two signals are in conflict, reciprocal inhibition selects either the motor or visual signal. Together, our results suggest that flies update their head direction representation by constructing an estimate of rotational velocity that relies primarily on motor information and only incorporates optic flow signals in specific sensorimotor contexts, such as when the motor signal is absent.

}, doi = {10.1101/2023.09.25.559373}, url = {https://doi.org/10.1101/2023.09.25.559373}, author = {Brad K Hulse and Angel Stanoev and Daniel B Turner-Evans and Johannes Seelig and Vivek Jayaraman} } @article {68316, title = {The SARS-CoV-2 accessory protein Orf3a is not an ion channel, but does interact with trafficking proteins}, journal = {eLife}, year = {2023}, month = {2023 Jan 25}, abstract = {

The severe acute respiratory syndrome associated coronavirus 2 (SARS-CoV-2) and SARS-CoV-1 accessory protein Orf3a colocalizes with markers of the plasma membrane, endocytic pathway, and Golgi apparatus. Some reports have led to annotation of both Orf3a proteins as a viroporin. Here we show that neither SARS-CoV-2 nor SARS-CoV-1 form functional ion conducting pores and that the conductances measured are common contaminants in overexpression and with high levels of protein in reconstitution studies. Cryo-EM structures of both SARS-CoV-2 and SARS-CoV-1 Orf3a display a narrow constriction and the presence of a basic aqueous vestibule, which would not favor cation permeation. We observe enrichment of the late endosomal marker Rab7 upon SARS-CoV-2 Orf3a overexpression, and co-immunoprecipitation with VPS39. Interestingly, SARS-CoV-1 Orf3a does not cause the same cellular phenotype as SARS-CoV-2 Orf3a and does not interact with VPS39. To explain this difference, we find that a divergent, unstructured loop of SARS-CoV-2 Orf3a facilitates its binding with VPS39, a HOPS complex tethering protein involved in late endosome and autophagosome fusion with lysosomes. We suggest that the added loop enhances SARS-CoV-2 Orf3a ability to co-opt host cellular trafficking mechanisms for viral exit or host immune evasion.

}, doi = {10.7554/eLife.84477}, url = {https://doi.org/10.7554/eLife.84477}, author = {Alexandria N. Miller and Patrick R. Houlihan and Ella Matamala and Deny Cabezas-Bratesco and Gi Young Lee and Ben Cristofori-Armstrong and Tanya L. Dilan and Silvia Sanchez-Martinez and Doreen Matthies and Rui Yan and Zhiheng Yu and Dejian Ren and Sebastian E. Brauchi and David E. Clapham} } @article {68629, title = {A searchable image resource of Drosophila GAL4-driver expression patterns with single neuron resolution.}, journal = {eLife}, volume = {12}, year = {2023}, month = {2023 Feb 23}, abstract = {

Precise, repeatable genetic access to specific neurons via GAL4/UAS and related methods is a key advantage of Drosophila neuroscience. Neuronal targeting is typically documented using light microscopy of full GAL4 expression patterns, which generally lack the single-cell resolution required for reliable cell type identification. Here we use stochastic GAL4 labeling with the MultiColor FlpOut approach to generate cellular resolution confocal images at large scale. We are releasing aligned images of 74,000 such adult central nervous systems. An anticipated use of this resource is to bridge the gap between neurons identified by electron or light microscopy. Identifying individual neurons that make up each GAL4 expression pattern improves the prediction of split-GAL4 combinations targeting particular neurons. To this end we have made the images searchable on the NeuronBridge website. We demonstrate the potential of NeuronBridge to rapidly and effectively identify neuron matches based on morphology across imaging modalities and datasets.

}, issn = {2050-084X}, doi = {10.7554/eLife.80660}, author = {Meissner, Geoffrey Wilson and Nern, Aljoscha and Dorman, Zachary and Depasquale, Gina M and Forster, Kaitlyn and Gibney, Theresa and Hausenfluck, Joanna H and He, Yisheng and Iyer, Nirmala A and Jeter, Jennifer and Johnson, Lauren and Johnston, Rebecca M and Lee, Kelley and Melton, Brian and Yarbrough, Brianna and Zugates, Christopher T and Clements, Jody and Goina, Cristian and Otsuna, Hideo and Rokicki, Konrad and Svirskas, Robert R and Aso, Yoshinori and Card, Gwyneth M and Dickson, Barry J and Ehrhardt, Erica and Goldammer, Jens and Ito, Masayoshi and Kainmueller, Dagmar and Korff, Wyatt and Mais, Lisa and minegishi, ryo and Namiki, Shigehiro and Rubin, Gerald M and Sterne, Gabriella R and Wolff, Tanya and Malkesman, Oz} } @article {68646, title = {Selective Serotonin Reuptake Inhibitors within Cells: Temporal Resolution in Cytoplasm, Endoplasmic Reticulum, and Membrane.}, journal = {Journal of Neuroscience}, year = {2023}, month = {2023 Mar 02}, abstract = {

Selective serotonin reuptake inhibitors (SSRIs) are the most prescribed treatment for individuals experiencing major depressive disorder (MDD). The therapeutic mechanisms that take place before, during, or after SSRIs bind the serotonin transporter (SERT) are poorly understood, partially because no studies exist of the cellular and subcellular pharmacokinetic properties of SSRIs in living cells. We studied escitalopram and fluoxetine using new intensity-based drug-sensing fluorescent reporters ("iDrugSnFRs") targeted to the plasma membrane (PM), cytoplasm, or endoplasmic reticulum (ER) of cultured neurons and mammalian cell lines. We also employed chemical detection of drug within cells and phospholipid membranes. The drugs attain equilibrium in neuronal cytoplasm and ER, at approximately the same concentration as the externally applied solution, with time constants of a few s (escitalopram) or 200-300 s (fluoxetine). Simultaneously, the drugs accumulate within lipid membranes by >= 18-fold (escitalopram) or 180-fold (fluoxetine), and possibly by much larger factors. Both drugs leave cytoplasm, lumen, and membranes just as quickly during washout. We synthesized membrane-impermeant quaternary amine derivatives of the two SSRIs. The quaternary derivatives are substantially excluded from membrane, cytoplasm, and ER for \> 2.4 h. They inhibit SERT transport-associated currents 6- or 11-fold less potently than the SSRIs (escitalopram or fluoxetine derivative, respectively), providing useful probes for distinguishing compartmentalized SSRI effects. Although our measurements are orders of magnitude faster than the "therapeutic lag" of SSRIs, these data suggest that SSRI-SERT interactions within organelles or membranes may play roles during either the therapeutic effects or the "antidepressant discontinuation syndrome".Selective serotonin reuptake inhibitors stabilize mood in several disorders. In general, these drugs bind to the serotonin (5-hydroxytryptamine) transporter (SERT), which clears serotonin from CNS and peripheral tissues. SERT ligands are effective and relatively safe; primary care practitioners often prescribe them. However, they have several side effects and require 2 to 6 weeks of continuous administration until they act effectively. How they work remains perplexing, contrasting with earlier assumptions that the therapeutic mechanism involves SERT inhibition followed by increased extracellular serotonin levels. This study establishes that two SERT ligands, fluoxetine and escitalopram, enter neurons within minutes, while simultaneously accumulating in many membranes. Such knowledge will motivate future research, hopefully revealing where and how SERT ligands "engage" their therapeutic target(s).

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.1519-22.2022}, author = {Nichols, Aaron L and Blumenfeld, Zack and Luebbert, Laura and Knox, Hailey J and Muthusamy, Anand K and Marvin, Jonathan S and Kim, Charlene H and Grant, Stephen N and Walton, David P and Cohen, Bruce N and Hammar, Rebekkah and Looger, Loren and Artursson, Per and Dougherty, Dennis A and Lester, Henry A} } @article {68690, title = {Sensitivity optimization of a rhodopsin-based fluorescent voltage indicator}, journal = {Neuron}, volume = {111}, year = {2023}, month = {2023 May 17}, pages = {1547-1563}, abstract = {

The ability to optically image cellular transmembrane voltages at millisecond-timescale resolutions can offer unprecedented insight into the function of living brains in behaving animals. Here, we present a\ point mutation\ that increases the sensitivity of Ace2 opsin-based voltage indicators. We use the mutation to develop Voltron2, an improved chemigeneic voltage indicator that has a 65\% higher sensitivity to single APs and 3-fold higher sensitivity to subthreshold potentials than Voltron. Voltron2 retained the sub-millisecond kinetics and photostability of its predecessor, although with lower baseline fluorescence. In multiple\ in\ vitro\ and\ in\ vivo\ comparisons with its predecessor across multiple species, we found Voltron2 to be more sensitive to APs and subthreshold fluctuations. Finally, we used Voltron2 to study and evaluate the possible mechanisms of\ interneuron\ synchronization in the mouse hippocampus. Overall, we have discovered a generalizable mutation that significantly increases the sensitivity of Ace2 rhodopsin-based sensors, improving their voltage reporting capability.

}, issn = {08966273}, doi = {10.1016/j.neuron.2023.03.009}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0896627323002052}, author = {Abdelfattah, Ahmed S. and Zheng, Jihong and Singh, Amrita and Huang, Yi-Chieh and Reep, Daniel and Tsegaye, Getahun and Tsang, Arthur and Arthur, Benjamin J. and Rehorova, Monika and Olson, Carl V.L. and Shuai, Yichun and Zhang, Lixia and Fu, Tian-Ming and Milkie, Daniel E. and Moya, Maria V. and Weber, Timothy D. and Lemire, Andrew L. and Baker, Christopher A. and Falco, Natalie and Zheng, Qinsi and Grimm, Jonathan B. and Yip, Mighten C. and Walpita, Deepika and Chase, Martin and Campagnola, Luke and Murphy, Gabe J. and Wong, Allan M. and Forest, Craig R. and Mertz, Jerome and Economo, Michael N. and Turner, Glenn C. and Koyama, Minoru and Lin, Bei-Jung and Betzig, Eric and Novak, Ondrej and Lavis, Luke D. and Svoboda, Karel and Korff, Wyatt and Chen, Tsai-Wen and Schreiter, Eric R. and Hasseman, Jeremy P. and Kolb, Ilya} } @article {68695, title = {Sequence and Structural Motifs Controlling the Broad Substrate Specificity of the Mycobacterial Hormone-Sensitive Lipase LipN}, journal = {ACS Omega}, volume = {8}, year = {2023}, month = {2023 Mar 30}, pages = {13252 - 13264}, abstract = {

Mycobacterium tuberculosis\ has a complex life cycle transitioning between active and dormant growth states depending on environmental conditions. LipN (Rv2970c) is a conserved mycobacterial serine hydrolase with regulated catalytic activity at the interface between active and dormant growth conditions. LipN also catalyzes the xenobiotic degradation of a tertiary ester substrate and contains multiple conserved motifs connected with the ability to catalyze the hydrolysis of difficult tertiary ester substrates. Herein, we expanded a library of fluorogenic ester substrates to include more tertiary and constrained esters and screened 33 fluorogenic substrates for activation by LipN, identifying its unique substrate signature. LipN preferred short, unbranched ester substrates, but had its second highest activity against a heteroaromatic five-membered oxazole ester. Oxazole esters are present in multiple mycobacterial serine hydrolase inhibitors but have not been tested widely as ester substrates. Combined structural modeling, kinetic measurements, and substitutional analysis of LipN showcased a fairly rigid binding pocket preorganized for catalysis of short ester substrates. Substitution of diverse amino acids across the binding pocket significantly impacted the folded stability and catalytic activity of LipN with two conserved motifs (HGGGW and GDSAG) playing interconnected, multidimensional roles in regulating its substrate specificity. Together this detailed substrate specificity profile of LipN illustrates the complex interplay between structure and function in mycobacterial hormone-sensitive lipase homologues and indicates oxazole esters as promising inhibitor and substrate scaffolds for mycobacterial hydrolases.

}, issn = {2470-1343}, doi = {10.1021/acsomega.3c0053410.1021/acsomega.3c00534.s001}, url = {https://pubs.acs.org/doi/10.1021/acsomega.3c00534}, author = {Schemenauer, Daniel E. and Pool, Emily H. and Raynor, Stephanie N. and Ruiz, Gabriela P. and Goehring, Leah M. and Koelper, Andrew J. and Wilson, Madeleine A. and Durand, Anthony J. and Kourtoglou, Elexi C. and Larsen, Erik M. and Lavis, Luke D. and Esteb, John J. and Hoops, Geoffrey C. and Johnson, R. Jeremy} } @article {68717, title = {Simultaneous photoactivation and high-speed structural tracking reveal diffusion-dominated motion in the endoplasmic reticulum}, journal = {bioRxiv}, year = {2023}, month = {2023 Apr 25}, abstract = {

The endoplasmic reticulum (ER) is a structurally complex, membrane-enclosed compartment that stretches from the nuclear envelope to the extreme periphery of eukaryotic cells. The organelle is crucial for numerous distinct cellular processes, but how these processes are spatially regulated within the structure is unclear. Traditional imaging-based approaches to understanding protein dynamics within the organelle are limited by the convoluted structure and rapid movement of molecular components. Here, we introduce a combinatorial imaging and machine learning-assisted image analysis approach to track the motion of photoactivated proteins within the ER of live cells. We find that simultaneous knowledge of the underlying ER structure is required to accurately analyze fluorescently-tagged protein redistribution, and after appropriate structural calibration we see all proteins assayed show signatures of Brownian diffusion-dominated motion over micron spatial scales. Remarkably, we find that in some cells the ER structure can be explored in a highly asymmetric manner, likely as a result of uneven connectivity within the organelle. This remains true independently of the size, topology, or folding state of the fluorescently-tagged molecules, suggesting a potential role for ER connectivity in driving spatially regulated biology in eukaryotes.

}, doi = {10.1101/2023.04.23.537908}, url = {https://doi.org/10.1101/2023.04.23.537908}, author = {Matteo Dora and Christopher J. Obara and Tim Abel and Jennifer Lippincott-Schwarz and David Holcman} } @article {68517, title = {Structured cerebellar connectivity supports resilient pattern separation.}, journal = {Nature}, volume = {613}, year = {2023}, month = {2023 Jan 01}, pages = {543-549}, abstract = {

The cerebellum is thought to help\ detect and correct errors between intended and executed commands and is critical for social behaviours, cognition and emotion. Computations for motor control must be performed quickly to correct errors in real time and should be sensitive to small differences between patterns for fine error correction while being resilient to noise. Influential theories of cerebellar information processing have largely assumed random network connectivity, which increases the encoding capacity of the network{\textquoteright}s first layer. However, maximizing encoding capacity reduces the resilience to noise. To understand how neuronal circuits address this fundamental trade-off, we mapped the feedforward connectivity in the mouse cerebellar cortex using automated large-scale transmission electron microscopy and convolutional neural network-based image segmentation. We found that both the input and output layers of the circuit exhibit redundant and selective connectivity motifs, which contrast with prevailing models. Numerical simulations suggest that these redundant, non-random connectivity motifs increase the resilience to noise at a negligible cost to the overall encoding capacity. This work reveals how neuronal network structure can support a trade-off between encoding capacity and redundancy, unveiling principles of biological network architecture with implications for the design of artificial neural networks.

}, issn = {1476-4687}, doi = {10.1038/s41586-022-05471-w}, author = {Nguyen, Tri M and Thomas, Logan A and Jeff L Rhoades and Ricchi, Ilaria and Yuan, Xintong Cindy and Sheridan, Arlo and Hildebrand, David G C and Funke, Jan and Regehr, Wade G and Lee, Wei-Chung Allen} } @article {68667, title = {Three-dimensional reconstructions of mechanosensory end organs suggest a unifying mechanism underlying dynamic, light touch}, journal = {Neuron}, year = {2023}, month = {2023 Oct 18}, abstract = {

Specialized mechanosensory end organs within mammalian skin{\textemdash}hair follicle-associated lanceolate complexes, Meissner corpuscles, and Pacinian corpuscles{\textemdash}enable our perception of light, dynamic touch1. In each of these end organs, fast-conducting mechanically sensitive neurons, called Aβ low-threshold mechanoreceptors (Aβ LTMRs), associate with resident glial cells, known as terminal Schwann cells (TSCs) or lamellar cells, to form complex axon ending structures. Lanceolate-forming and corpuscle-innervating Aβ LTMRs share a low threshold for mechanical activation, a rapidly adapting (RA) response to force indentation, and high sensitivity to dynamic stimuli1{\textendash}6. How mechanical stimuli lead to activation of the requisite mechanotransduction channel Piezo27{\textendash}15\ and Aβ RA-LTMR excitation across the morphologically dissimilar mechanosensory end organ structures is not understood. Here, we report the precise subcellular distribution of Piezo2 and high-resolution, isotropic 3D reconstructions of all three end organs formed by Aβ RA-LTMRs determined by large volume enhanced Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) imaging. We found that within each end organ, Piezo2 is enriched along the sensory axon membrane and is minimally or not expressed in TSCs and lamellar cells. We also observed a large number of small cytoplasmic protrusions enriched along the Aβ RA-LTMR axon terminals associated with hair follicles, Meissner corpuscles, and Pacinian corpuscles. These axon protrusions reside within close proximity to axonal Piezo2, occasionally contain the channel, and often form adherens junctions with nearby non-neuronal cells. Our findings support a unified model for Aβ RA-LTMR activation in which axon protrusions anchor Aβ RA-LTMR axon terminals to specialized end organ cells, enabling mechanical stimuli to stretch the axon in hundreds to thousands of sites across an individual end organ and leading to activation of proximal Piezo2 channels and excitation of the neuron.

}, doi = {10.1016/j.neuron.2023.08.023}, url = {https://doi.org/10.1016/j.neuron.2023.08.023}, author = {Annie Handler and Qiyu Zhang and Song Pang and Tri M. Nguyen and Michael Iskols and Michael Nolan-Tamariz and Stuart Cattel and Rebecca Plumb and Brianna Sanchez and Karyl Ashjian and Aria Shotland and Bartianna Brown and Madiha Kabeer and Josef Turecek and Genelle Rankin and Wangchu Xiang and Elisa C. Pavarino and Nusrat Africawala and Celine Santiago and Wei-Chung Allen Lee and C. Shan Xu and David D. Ginty} } @article {68788, title = {Tissue-specific transcriptome analyses in Drosophila provide novel insights into the mode of action of the insecticide spinosad and the function of its target, nAChRα6.}, journal = {Pest Management Science}, year = {2023}, month = {2023 May 29}, abstract = {

BACKGROUND: The insecticides spinosad and imidacloprid are neurotoxins with distinct modes of action. Both target nicotinic acetylcholine receptors (nAChRs), albeit different subunits. Spinosad is an allosteric modulator, that upon binding initiates endocytosis of its target, nAChRα6. Imidacloprid binding triggers excessive neuronal ion influx. Despite these differences, low-dose effects converge downstream in the precipitation of oxidative stress and neurodegeneration.

RESULTS: Using RNA-Seq, we compared the transcriptional signatures of spinosad and imidacloprid, at low-dose exposures. Both insecticides cause upregulation of Glutathione S-transferase and Cytochrome P450 genes in the brain and downregulation in the fat body, whereas reduced expression of immune-related genes is observed in both tissues. Spinosad shows unique impacts on genes involved in lysosomal function, protein folding, and reproduction. Co-expression analyses revealed little to no correlation between genes affected by spinosad and nAChRα6 expressing neurons, but a positive correlation with glial cell markers. We also detected and experimentally confirmed nAChRα6 expression in fat body cells and male germline cells. This led us to uncover lysosomal dysfunction in the fat body following spinosad exposure, and a fitness cost in spinosad-resistant (nAChRα6 null) males - oxidative stress in testes, and reduced fertility.

CONCLUSION: Spinosad and imidacloprid share transcriptional perturbations in immunity-, energy homeostasis-, and oxidative stress-related genes. Low doses of other neurotoxic insecticides should be investigated for similar impacts. While target-site spinosad resistance mutation has evolved in the field, this may have a fitness cost. Our findings demonstrate the power of tissue-specific transcriptomics approach and the use of single-cell transcriptome data. This article is protected by copyright. All rights reserved.

}, issn = {1526-4998}, doi = {10.1002/ps.7585}, author = {Martelli, Felipe and Ravenscroft, Thomas A and Hutchison, William and Batterham, Philip} } @article {68958, title = {Towards Generalizable Organelle Segmentation in Volume Electron Microscopy.}, journal = {Microscopy and Microanalysis}, volume = {29}, year = {2023}, month = {2023 Jul 22}, pages = {975}, keywords = {Organelles, Volume Electron Microscopy}, issn = {1435-8115}, doi = {10.1093/micmic/ozad067.487}, author = {Heinrich, Larissa and Patton, Will and Bennett, Davis and Ackerman, David and Park, Grace and Bogovic, John A and Eckstein, Nils and Petruncio, Alyson and Clements, Jody and Pang, Song and Shan Xu, C and Funke, Jan and Korff, Wyatt and Hess, Harald and Lippincott-Schwartz, Jennifer and Saalfeld, Stephan and Weigel, Aubrey} } @article {68968, title = {Ultra-high density electrodes improve detection, yield, and cell type specificity of brain recordings.}, journal = {bioRxiv}, year = {2023}, month = {2023 Aug 25}, abstract = {

To study the neural basis of behavior, we require methods to sensitively and accurately measure neural activity at single neuron and single spike resolution. Extracellular electrophysiology is a principal method for achieving this, but it has biases in the neurons it detects and it imperfectly resolves their action potentials. To overcome these limitations, we developed a silicon probe with significantly smaller and denser recording sites than previous designs, called Neuropixels Ultra (NP Ultra). This device measures neuronal activity at ultra-high densities (\>1300 sites per mm, 10 times higher than previous probes), with 6 {\textmu}m center-to-center spacing and low noise. This device effectively comprises an implantable voltage-sensing camera that captures a planar image of a neuron{\textquoteright}s electrical field. We introduce a new spike sorting algorithm optimized for these probes and use it to find that the yield of visually-responsive neurons in recordings from mouse visual cortex improves \~{}3-fold. Recordings across multiple brain regions and four species revealed a subset of unexpectedly small extracellular action potentials not previously reported. Further experiments determined that, in visual cortex, these do not correspond to major subclasses of interneurons and instead likely reflect recordings from axons. Finally, using ground-truth identification of cortical inhibitory cell types with optotagging, we found that cell type was discriminable with approximately 75\% success among three types, a significant improvement over lower-resolution recordings. NP Ultra improves spike sorting performance, sampling bias, and cell type classification.

}, doi = {10.1101/2023.08.23.554527}, author = {Ye, Zhiwen and Shelton, Andrew M and Shaker, Jordan R and Boussard, Julien and Colonell, Jennifer and Manavi, Sahar and Chen, Susu and Windolf, Charlie and Hurwitz, Cole and Namima, Tomoyuki and Pedraja, Federico and Weiss, Shahaf and Raducanu, Bogdan and Ness, Torbj{\o}rn V and Einevoll, Gaute T and Laurent, Gilles and Sawtell, Nathaniel B and Bair, Wyeth and Pasupathy, Anitha and Mora Lopez, Carolina and Dutta, Barun and Paninski, Liam and Siegle, Joshua H and Koch, Christof and Olsen, Shawn R and Harris, Timothy D and Steinmetz, Nicholas A} } @article {69073, title = {Volitional activation of remote place representations with a hippocampal brain-machine interface.}, journal = {Science}, volume = {382}, year = {2023}, month = {2023 Nov 03}, pages = {566-573}, abstract = {

The hippocampus is critical for recollecting and imagining experiences. This is believed to involve voluntarily drawing from hippocampal memory representations of people, events, and places, including maplike representations of familiar environments. However, whether representations in such "cognitive maps" can be volitionally accessed is unknown. We developed a brain-machine interface to test whether rats can do so by controlling their hippocampal activity in a flexible, goal-directed, and model-based manner. We found that rats can efficiently navigate or direct objects to arbitrary goal locations within a virtual reality arena solely by activating and sustaining appropriate hippocampal representations of remote places. This provides insight into the mechanisms underlying episodic memory recall, mental simulation and planning, and imagination and opens up possibilities for high-level neural prosthetics that use hippocampal representations.

}, keywords = {Animals, Brain-Computer Interfaces, Hippocampus, Humans, Imagination, Memory, Episodic, Mental Recall, Rats}, issn = {1095-9203}, doi = {10.1126/science.adh5206}, author = {Lai, Chongxi and Tanaka, Shinsuke and Harris, Timothy D and Lee, Albert K} } @article {68513, title = {The 3D ultrastructure of the chordotonal organs in the antenna of a microwasp remains complex although simplified.}, journal = {Scientific Reports}, volume = {12}, year = {2022}, month = {2022 Nov 23}, pages = {20172}, abstract = {

Insect antennae are astonishingly versatile and have multiple sensory modalities. Audition, detection of airflow, and graviception are combined in the antennal chordotonal organs. The miniaturization of these complex multisensory organs has never been investigated. Here we present a comprehensive study of the structure and scaling of the antennal chordotonal organs of the extremely miniaturized parasitoid wasp Megaphragma viggianii based on 3D electron microscopy. Johnston{\textquoteright}s organ of M. viggianii consists of 19 amphinematic scolopidia (95 cells); the central organ consists of five scolopidia (20 cells). Plesiomorphic composition includes one accessory cell per scolopidium, but in M. viggianii this ratio is only 0.3. Scolopale rods in Johnston{\textquoteright}s organ have a unique structure. Allometric analyses demonstrate the effects of scaling on the antennal chordotonal organs in insects. Our results not only shed light on the universal principles of miniaturization of sense organs, but also provide context for future interpretation of the M. viggianii connectome.

}, keywords = {Animals, Arthropod Antennae, Insecta, Mechanoreceptors, Microscopy, Electron, Sense Organs}, issn = {2045-2322}, doi = {10.1038/s41598-022-24390-4}, author = {Diakova, Anna V and Makarova, Anastasia A and Pang, Song and Xu, C Shan and Hess, Harald and Polilov, Alexey A} } @article {68115, title = {Accurate angular integration with only a handful of neurons.}, journal = {bioRxiv}, year = {2022}, month = {2022 May 25}, abstract = {

To flexibly navigate, many animals rely on internal spatial representations that persist when the animal is standing still in darkness, and update accurately by integrating the animal{\textquoteright}s movements in the absence of localizing sensory cues. Theories of mammalian head direction cells have proposed that these dynamics can be realized in a special class of networks that maintain a localized bump of activity via structured recurrent connectivity, and that shift this bump of activity via angular velocity input. Although there are many different variants of these so-called ring attractor networks, they all rely on large numbers of neurons to generate representations that persist in the absence of input and accurately integrate angular velocity input. Surprisingly, in the fly,\ Drosophila melanogaster, a head direction representation is maintained by a much smaller number of neurons whose dynamics and connectivity resemble those of a ring attractor network. These findings challenge our understanding of ring attractors and their putative implementation in neural circuits. Here, we analyzed failures of angular velocity integration that emerge in small attractor networks with only a few computational units. Motivated by the peak performance of the fly head direction system in darkness, we mathematically derived conditions under which small networks, even with as few as 4 neurons, achieve the performance of much larger networks. The resulting description reveals that by appropriately tuning the network connectivity, the network can maintain persistent representations over the continuum of head directions, and it can accurately integrate angular velocity inputs. We then analytically determined how performance degrades as the connectivity deviates from this optimally-tuned setting, and we find a trade-off between network size and the tuning precision needed to achieve persistence and accurate integration. This work shows how even small networks can accurately track an animal{\textquoteright}s movements to guide navigation, and it informs our understanding of the functional capabilities of discrete systems more broadly.

}, doi = {10.1101/2022.05.23.493052}, url = {https://doi.org/10.1101/2022.05.23.493052}, author = {Marcella Noorman and Brad K Hulse and Vivek Jayaraman and Sandro Romani and Ann M Hermundstad} } @article {68045, title = {Actin nano-architecture of phagocytic podosomes}, journal = {Nature Communications}, volume = {13}, year = {2022}, month = {2022 Jul 27}, pages = {4363}, abstract = {

Podosomes are actin-enriched adhesion structures important for multiple cellular processes, including migration, bone remodeling, and phagocytosis. Here, we characterized the structure and organization of phagocytic podosomes using interferometric photoactivated localization microscopy (iPALM), a super-resolution microscopy technique capable of 15-20 nm resolution, together with structured illumination microscopy (SIM) and localization-based superresolution microscopy. Phagocytic podosomes were observed during frustrated phagocytosis, a model in which cells attempt to engulf micro-patterned IgG antibodies. For circular patterns, this resulted in regular arrays of podosomes with well-defined geometry. Using persistent homology, we developed a pipeline for semi-automatic identification and measurement of podosome features. These studies revealed an "hourglass" shape of the podosome actin core, a protruding "knob" at the bottom of the core, and two actin networks extending from the core. Additionally, the distributions of paxillin, talin, myosin II, α-actinin, cortactin, and microtubules relative to actin were characterized.

}, doi = {10.1101/2022.05.04.490675}, author = {J. Cody Herron and Shiqiong Hu and Takashi Watanabe and Ana T. Nogueira and Bei Liu and Megan Kern and Jesse Aaron and Aaron Taylor and Michael Pablo and Teng-Leong Chew and Timothy C. Elston and Klaus M. Hahn} } @article {68023, title = {Allosteric interactions prime androgen receptor dimerization and activation.}, journal = {Molecular Cell}, volume = {82}, year = {2022}, month = {2022 Jun 02}, pages = {2021-31}, abstract = {

The androgen receptor (AR) is a nuclear receptor that governs gene expression programs required for prostate development and male phenotype maintenance. Advanced prostate cancers display AR hyperactivation and transcriptome expansion, in part, through AR amplification and interaction with oncoprotein cofactors. Despite its biological importance, how AR domains and cofactors cooperate to bind DNA has remained elusive. Using single-particle cryo-electron microscopy, we isolated three conformations of AR bound to DNA, showing that AR forms a non-obligate dimer, with the buried dimer interface utilized by ancestral steroid receptors repurposed to facilitate cooperative DNA binding. We identify novel allosteric surfaces which are compromised in androgen insensitivity syndrome and reinforced by AR{\textquoteright}s oncoprotein cofactor, ERG, and by DNA-binding motifs. Finally, we present evidence that this plastic dimer interface may have been adopted for transactivation at the expense of DNA binding. Our work highlights how fine-tuning AR{\textquoteright}s cooperative interactions translate to consequences in development and disease.

}, issn = {1097-4164}, doi = {10.1016/j.molcel.2022.03.035}, author = {Wasmuth, Elizabeth V and Broeck, Arnaud Vanden and LaClair, Justin R and Hoover, Elizabeth A and Lawrence, Kayla E and Paknejad, Navid and Pappas, Kyrie and Matthies, Doreen and Wang, Biran and Feng, Weiran and Watson, Philip A and Zinder, John C and Karthaus, Wouter R and de la Cruz, M Jason and Hite, Richard K and Manova-Todorova, Katia and Yu, Zhiheng and Weintraub, Susan T and Klinge, Sebastian and Sawyers, Charles L} } @article {68193, title = {Architecture and dynamics of a novel desmosome-endoplasmic reticulum organelle}, journal = {bioRxiv}, year = {2022}, month = {2022 Jul 08}, abstract = {

The endoplasmic reticulum (ER) forms a dynamic network that contacts other cellular membranes to regulate stress responses, calcium signaling, and lipid transfer. Using high-resolution volume electron microscopy, we find that the ER forms a previously unknown association with keratin intermediate filaments and desmosomal cell-cell junctions. Peripheral ER assembles into mirror image-like arrangements at desmosomes and exhibits nanometer proximity to keratin filaments and the desmosome cytoplasmic plaque. ER tubules exhibit stable associations with desmosomes, and perturbation of desmosomes or keratin filaments alters ER organization and mobility. These findings indicate that desmosomes and the keratin cytoskeleton pattern the distribution of the ER network. Overall, this study reveals a previously unknown subcellular architecture defined by the structural integration of ER tubules with an epithelial intercellular junction.

}, doi = {10.1101/2022.07.07.499185}, url = {https://doi.org/10.1101/2022.07.07.499185}, author = {Navaneetha Krishnan Bharathan and William Giang and Jesse S. Aaron and Satya Khuon and Teng-Leong Chew and Stephan Preibisch and Eric T. Trautman and Larissa Heinrich and John Bogovic and Davis Bennett and David Ackerman and Woohyun Park and Alyson Petruncio and Aubrey V. Weigel and Stephan Saalfeld and COSEM Project Team and A. Wayne Vogl and Sara N. Stahley and Andrew P. Kowalczyk} } @article {68313, title = {Automated reconstruction of whole-embryo cell lineages by learning from sparse annotations.}, journal = {Nature Biotechnology}, year = {2022}, month = {2022 Sep 05}, abstract = {

We present a method to automatically identify and track nuclei in time-lapse microscopy recordings of entire developing embryos. The method combines deep learning and global optimization. On a mouse dataset, it reconstructs 75.8\% of cell lineages spanning 1 h, as compared to 31.8\% for the competing method. Our approach improves understanding of where and when cell fate decisions are made in developing embryos, tissues, and organs.

}, issn = {1546-1696}, doi = {10.1038/s41587-022-01427-7}, author = {Malin-Mayor, Caroline and Hirsch, Peter and Guignard, Leo and McDole, Katie and Wan, Yinan and Lemon, William C and Kainmueller, Dagmar and Keller, Philipp J and Preibisch, Stephan and Funke, Jan} } @article {69715, title = {Best practice standards for circular RNA research}, journal = {Nature Methods}, volume = {19}, year = {2022}, month = {05/2022}, pages = {1208 - 1220}, abstract = {

Circular RNAs (circRNAs) are formed in all domains of life and via different mechanisms. There has been an explosion in the number of circRNA papers in recent years; however, as a relatively young field, circRNA biology has an urgent need for common experimental standards for isolating, analyzing, expressing and depleting circRNAs. Here we propose a set of guidelines for circRNA studies based on the authors{\textquoteright} experience. This Perspective will specifically address the major class of circRNAs in Eukarya that are generated by a spliceosome-catalyzed back-splicing event. We hope that the implementation of best practice principles for circRNA research will help move the field forward and allow a better functional understanding of this fascinating group of RNAs.

}, issn = {1548-7091}, doi = {10.1038/s41592-022-01487-2}, url = {https://www.nature.com/articles/s41592-022-01487-2https://www.nature.com/articles/s41592-022-01487-2.pdfhttps://www.nature.com/articles/s41592-022-01487-2.pdfhttps://www.nature.com/articles/s41592-022-01487-2}, author = {Nielsen, Anne F. and Bindereif, Albrecht and Bozzoni, Irene and Hanan, Mor and Hansen, Thomas B. and Irimia, Manuel and Kadener, Sebastian and Kristensen, Lasse S. and Legnini, Ivano and Morlando, Mariangela and Jarlstad Olesen, Morten T. and Pasterkamp, R. Jeroen and Preibisch, Stephan and Rajewsky, Nikolaus and Suenkel, Christin and Kjems, J{\o}rgen} } @article {68165, title = {Binding partners regulate unfolding of myosin VI to activate the molecular motor.}, journal = {The Biochemical Journal}, volume = {479}, year = {2022}, month = {2022 Jul 15}, pages = {1409-1428}, abstract = {

Myosin VI is the only minus-end actin motor and is coupled to various cellular processes ranging from endocytosis to transcription. This multi-potent nature is achieved through alternative isoform splicing and interactions with a network of binding partners. There is a complex interplay between isoforms and binding partners to regulate myosin VI. Here, we have compared the regulation of two myosin VI splice isoforms by two different binding partners. By combining biochemical and single-molecule approaches, we propose that myosin VI regulation follows a generic mechanism, independently of the spliced isoform and the binding partner involved. We describe how myosin VI adopts an autoinhibited backfolded state which is released by binding partners. This unfolding activates the motor, enhances actin binding and can subsequently trigger dimerization. We have further expanded our study by using single molecule imaging to investigate the impact of binding partners upon myosin VI molecular organisation and dynamics.

}, issn = {1470-8728}, doi = {10.1042/BCJ20220025}, author = {Dos Santos, {\'A}lia and Fili, Natalia and Hari-Gupta, Yukti and Gough, Rosemarie E and Wang, Lin and Martin-Fernandez, Marisa and Arron, Jesse and Wait, Eric and Chew, Teng Leong and Toseland, Chris} } @article {68011, title = {BRD2 compartmentalizes the accessible genome.}, journal = {Nature Genetics}, volume = {54}, year = {2022}, month = {2022 Apr 11}, pages = {481-491}, abstract = {

Mammalian chromosomes are organized into megabase-sized compartments that are further subdivided into topologically associating domains (TADs). While the formation of TADs is dependent on cohesin, the mechanism behind compartmentalization remains enigmatic. Here, we show that the bromodomain and extraterminal (BET) family scaffold protein BRD2 promotes spatial mixing and compartmentalization of active chromatin after cohesin loss. This activity is independent of transcription but requires BRD2 to recognize acetylated targets through its double bromodomain and interact with binding partners with its low-complexity domain. Notably, genome compartmentalization mediated by BRD2 is antagonized on the one hand by cohesin and on the other hand by the BET homolog protein BRD4, both of which inhibit BRD2 binding to chromatin. Polymer simulation of our data supports a BRD2-cohesin interplay model of nuclear topology, in which genome compartmentalization results from a competition between loop extrusion and chromatin-state-specific affinity interactions.

}, keywords = {Animals, Cell Cycle Proteins, Chromatin, Chromosomes, Mammals, Nuclear Proteins, Protein Binding, Protein Domains, Transcription Factors}, issn = {1546-1718}, doi = {10.1038/s41588-022-01044-9}, author = {Xie, Liangqi and Dong, Peng and Qi, Yifeng and Hsieh, Tsung-Han S and English, Brian P and Jung, Seolkyoung and Chen, Xingqi and De Marzio, Margherita and Casellas, Rafael and Chang, Howard Y and Zhang, Bin and Tjian, Robert and Liu, Zhe} } @article {67992, title = {Bromodomains regulate dynamic targeting of the PBAF chromatin remodeling complex to chromatin hubs.}, journal = {Biophysical Journal}, volume = {121}, year = {2022}, month = {2022 May 3}, pages = {1738-1752}, abstract = {

Chromatin remodelers actively target arrays of acetylated nucleosomes at select enhancers and promoters to facilitate or shut down the repeated recruitment of RNA Pol II during transcriptional bursting. It is poorly understood how chromatin remodelers such as PBAF dynamically target different chromatin states inside a live cell. Our live-cell single molecule fluorescence microscopy study reveals chromatin hubs throughout the nucleus where PBAF rapidly cycles on and off the genome. Deletion of PBAF{\textquoteright}s bromodomains impairs targeting and stable engagement of chromatin in hubs. Dual color imaging reveals that PBAF targets both euchromatic and heterochromatic hubs with distinct genome binding kinetic profiles that mimic chromatin stability. Removal of PBAF{\textquoteright}s bromodomains stabilizes H3.3 binding within chromatin indicating that bromodomains may play a direct role in remodeling of the nucleosome. Our data suggests that PBAF{\textquoteright}s dynamic bromodomain mediated engagement of a nucleosome may reflect the chromatin remodeling potential of differentially bound chromatin states.

}, issn = {1542-0086}, doi = {10.1016/j.bpj.2022.03.027}, author = {Kenworthy, Charles A and Haque, Nayem and Liou, Shu-Hao and Chandris, Panagiotis and Wong, Vincent and Dziuba, Patrycja and Lavis, Luke D and Liu, Wei-Li and Singer, Robert H and Coleman, Robert A} } @article {68502, title = {Channel-independent function of UNC-9/Innexin in spatial arrangement of GABAergic synapses in .}, journal = {eLife}, volume = {11}, year = {2022}, month = {2022 Nov 15}, abstract = {

Precise synaptic connection of neurons with their targets is essential for the proper functioning of the nervous system. A plethora of signaling pathways act in concert to mediate the precise spatial arrangement of synaptic connections. Here we show a novel role for a gap junction protein in controlling tiled synaptic arrangement in the GABAergic motor neurons in , in which their axons and synapses overlap minimally with their neighboring neurons within the same class. We found that while EGL-20/Wnt controls axonal tiling, their presynaptic tiling is mediated by a gap junction protein UNC-9/Innexin, that is localized at the presynaptic tiling border between neighboring dorsal D-type GABAergic motor neurons. Strikingly, the gap junction channel activity of UNC-9 is dispensable for its function in controlling tiled presynaptic patterning. While gap junctions are crucial for the proper functioning of the nervous system as channels, our finding uncovered the novel channel-independent role of UNC-9 in synapse patterning.

}, keywords = {Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Connexins, Membrane Proteins, Motor Neurons, Synapses}, issn = {2050-084X}, doi = {10.7554/eLife.80555}, author = {Hendi, Ardalan and Niu, Long-Gang and Snow, Andrew William and Ikegami, Richard and Wang, Zhao-Wen and Mizumoto, Kota} } @article {68080, title = {Combining multiple fluorescence imaging techniques in biology: when one microscope is not enough.}, journal = {Molecular Biology of the Cell}, volume = {33}, year = {2022}, month = {2022 May 15}, pages = {tp1}, abstract = {

While fluorescence microscopy has proven to be an exceedingly useful tool in bioscience, it is difficult to offer simultaneous high resolution, fast speed, large volume, and good biocompatibility in a single imaging technique. Thus, when determining the image data required to quantitatively test a complex biological hypothesis, it often becomes evident that multiple imaging techniques are necessary. Recent years have seen an explosion in development of novel fluorescence microscopy techniques, each of which features a unique suite of capabilities. In this Technical Perspective, we highlight recent studies to illustrate the benefits, and often the necessity, of combining multiple fluorescence microscopy modalities. We provide guidance in choosing optimal technique combinations to effectively address a biological question. Ultimately, we aim to promote a more well-rounded approach in designing fluorescence microscopy experiments, leading to more robust quantitative insight.

}, keywords = {Biology, Microscopy, Fluorescence, Optical Imaging}, issn = {1939-4586}, doi = {10.1091/mbc.E21-10-0506}, author = {Hobson, Chad M and Aaron, Jesse S} } @article {67896, title = {The complexin C-terminal amphipathic helix stabilizes the fusion pore open state by sculpting membranes.}, journal = {Nature Structural \& Molecular Biology}, volume = {29}, year = {2022}, month = {2022 Feb 07}, pages = {97-107}, abstract = {

Neurotransmitter release is mediated by proteins that drive synaptic vesicle fusion with the presynaptic plasma membrane. While soluble N-ethylmaleimide sensitive factor attachment protein receptors (SNAREs) form the core of the fusion apparatus, additional proteins play key roles in the fusion pathway. Here, we report that the C-terminal amphipathic helix of the mammalian accessory protein, complexin (Cpx), exerts profound effects on membranes, including the formation of pores and the efficient budding and fission of vesicles. Using nanodisc-black lipid membrane electrophysiology, we demonstrate that the membrane remodeling activity of Cpx modulates the structure and stability of recombinant exocytic fusion pores. Cpx had particularly strong effects on pores formed by small numbers of SNAREs. Under these conditions, Cpx increased the current through individual pores 3.5-fold, and increased the open time fraction from roughly 0.1 to 1.0. We propose that the membrane sculpting activity of Cpx contributes to the phospholipid rearrangements that underlie fusion by stabilizing highly curved membrane fusion intermediates.

}, issn = {1545-9985}, doi = {10.1038/s41594-021-00716-0}, author = {Courtney, Kevin C and Wu, Lanxi and Mandal, Taraknath and Swift, Mark and Zhang, Zhao and Alaghemandi, Mohammad and Wu, Zhenyong and Bradberry, Mazdak M and Deo, Claire and Lavis, Luke D and Volkmann, Niels and Hanein, Dorit and Cui, Qiang and Bao, Huan and Chapman, Edwin R} } @article {68520, title = {The connectome of an insect brain}, journal = {bioRxiv}, year = {2022}, month = {2022 Nov 28}, abstract = {

Brains contain networks of interconnected neurons, so knowing the network architecture is essential for understanding brain function. We therefore mapped the synaptic-resolution connectome of an insect brain (Drosophila\ larva) with rich behavior, including learning, value-computation, and action-selection, comprising 3,013 neurons and 544,000 synapses. We characterized neuron-types, hubs, feedforward and feedback pathways, and cross-hemisphere and brain-nerve cord interactions. We found pervasive multisensory and interhemispheric integration, highly recurrent architecture, abundant feedback from descending neurons, and multiple novel circuit motifs. The brain{\textquoteright}s most recurrent circuits comprised the input and output neurons of the learning center. Some structural features, including multilayer shortcuts and nested recurrent loops, resembled powerful machine learning architectures. The identified brain architecture provides a basis for future experimental and theoretical studies of neural circuits.

}, doi = {10.1101/2022.11.28.516756}, url = {https://doi.org/10.1101/2022.11.28.516756}, author = {Michael Winding and Benjamin D. Pedigo and Christopher L. Barnes and Heather G. Patsolic and Youngser Park and Tom Kazimiers and Akira Fushiki and Ingrid V. Andrade and Avinash Khandelwal and Javier Valdes-Aleman and Feng Li and Nadine Randel and Elizabeth Barsotti and Ana Correia and Richard D. Fetter and Volker Hartenstein and Carey E. Priebe and Joshua T. Vogelstein and Albert Cardona and Marta Zlatic} } @article {68044, title = {Cryo-EM structure of the EBV ribonucleotide reductase BORF2 and mechanism of APOBEC3B inhibition.}, journal = {Science Advances}, volume = {8}, year = {2022}, month = {2022 Apr 29}, pages = {eabm2827}, abstract = {

Viruses use a plethora of mechanisms to evade immune responses. A recent example is neutralization of the nuclear DNA cytosine deaminase APOBEC3B by the Epstein-Barr virus (EBV) ribonucleotide reductase subunit BORF2. Cryo-EM studies of APOBEC3B-BORF2 complexes reveal a large \>1000-{\r A} binding surface composed of multiple structural elements from each protein, which effectively blocks the APOBEC3B active site from accessing single-stranded DNA substrates. Evolutionary optimization is suggested by unique insertions in BORF2 absent from other ribonucleotide reductases and preferential binding to APOBEC3B relative to the highly related APOBEC3A and APOBEC3G enzymes. A molecular understanding of this pathogen-host interaction has potential to inform the development of drugs that block the interaction and liberate the natural antiviral activity of APOBEC3B. In addition, given a role for APOBEC3B in cancer mutagenesis, it may also be possible for information from the interaction to be used to develop DNA deaminase inhibitors.

}, issn = {2375-2548}, doi = {10.1126/sciadv.abm2827}, author = {Shaban, Nadine M and Yan, Rui and Shi, Ke and Moraes, Sofia N and Cheng, Adam Z and Carpenter, Michael A and McLellan, Jason S and Yu, Zhiheng and Harris, Reuben S} } @article {68296, title = {Disorder and the Neural Representation of Complex Odors.}, journal = {Frontiers in Computational Neuroscience}, volume = {16}, year = {2022}, month = {2022 Aug 08}, pages = {917786}, abstract = {

Animals smelling in the real world use a small number of receptors to sense a vast number of natural molecular mixtures, and proceed to learn arbitrary associations between odors and valences. Here, we propose how the architecture of olfactory circuits leverages disorder, diffuse sensing and redundancy in representation to meet these immense complementary challenges. First, the diffuse and disordered binding of receptors to many molecules compresses a vast but sparsely-structured odor space into a small receptor space, yielding an odor code that preserves similarity in a precise sense. Introducing any order/structure in the sensing degrades similarity preservation. Next, lateral interactions further reduce the correlation present in the low-dimensional receptor code. Finally, expansive disordered projections from the periphery to the central brain reconfigure the densely packed information into a high-dimensional representation, which contains multiple redundant subsets from which downstream neurons can learn flexible associations and valences. Moreover, introducing any order in the expansive projections degrades the ability to recall the learned associations in the presence of noise. We test our theory empirically using data from . Our theory suggests that the neural processing of sparse but high-dimensional olfactory information differs from the other senses in its fundamental use of disorder.

}, issn = {1662-5188}, doi = {10.3389/fncom.2022.917786}, author = {Krishnamurthy, Kamesh and Hermundstad, Ann M and Mora, Thierry and Walczak, Aleksandra M and Balasubramanian, Vijay} } @article {68984, title = {Embryo~model completes gastrulation to neurulation and organogenesis.}, journal = {Nature}, volume = {610}, year = {2022}, month = {10/2022}, pages = {143-153}, abstract = {

Embryonic stem (ES) cells can undergo many aspects of mammalian embryogenesis in vitro, but their developmental potential is substantially extended by interactions with extraembryonic stem cells, including trophoblast stem (TS) cells, extraembryonic endoderm stem (XEN) cells and inducible XEN (iXEN) cells. Here we assembled stem cell-derived embryos in vitro from mouse ES cells, TS cells and iXEN cells and showed that they recapitulate the development of whole natural mouse embryo in utero up to day 8.5 post-fertilization. Our embryo model displays headfolds with defined forebrain and midbrain regions and develops a beating heart-like structure, a trunk comprising a neural tube and somites, a tail bud containing neuromesodermal progenitors, a gut tube, and primordial germ cells. This complete embryo model develops within an extraembryonic yolk sac that initiates blood island development. Notably, we demonstrate that the neurulating embryo model assembled from Pax6-knockout ES cells aggregated with wild-type TS cells and iXEN cells recapitulates the ventral domain expansion of the neural tube that occurs in natural, ubiquitous Pax6-knockout embryos. Thus, these complete embryoids are a powerful in vitro model for dissecting the roles of diverse cell lineages and genes in development. Our results demonstrate the self-organization ability of ES cells and two types of extraembryonic stem cells to reconstitute mammalian development through and beyond gastrulation to neurulation and early organogenesis.

}, keywords = {Animals, Cell Lineage, Embryo, Mammalian, Embryonic Stem Cells, Endoderm, Gastrulation, Heart, Mesencephalon, Mice, Models, Biological, Neural Tube, Neurulation, Organogenesis, PAX6 Transcription Factor, Prosencephalon, Somites}, issn = {1476-4687}, doi = {10.1038/s41586-022-05246-3}, author = {Amadei, Gianluca and Handford, Charlotte E and Qiu, Chengxiang and De Jonghe, Joachim and Greenfeld, Hannah and Tran, Martin and Martin, Beth K and Chen, Dong-Yuan and Aguilera-Castrejon, Alejandro and Hanna, Jacob H and Elowitz, Michael B and Hollfelder, Florian and Shendure, Jay and Glover, David M and Zernicka-Goetz, Magdalena} } @article {68020, title = {ESCRT-mediated membrane repair protects tumor-derived cells against T cell attack.}, journal = {Science}, volume = {376}, year = {2022}, month = {2022 Apr 22}, pages = {377-382}, abstract = {

Cytotoxic T lymphocytes (CTLs) and natural killer cells kill virus-infected and tumor cells through the polarized release of perforin and granzymes. Perforin is a pore-forming toxin that creates a lesion in the plasma membrane of the target cell through which granzymes enter the cytosol and initiate apoptosis. Endosomal sorting complexes required for transport (ESCRT) proteins are involved in the repair of small membrane wounds. We found that ESCRT proteins were precisely recruited in target cells to sites of CTL engagement immediately after perforin release. Inhibition of ESCRT machinery in cancer-derived cells enhanced their susceptibility to CTL-mediated killing. Thus, repair of perforin pores by ESCRT machinery limits granzyme entry into the cytosol, potentially enabling target cells to resist cytolytic attack.

}, keywords = {Endosomal Sorting Complexes Required for Transport, Granzymes, Membrane Glycoproteins, Perforin, Pore Forming Cytotoxic Proteins, T-Lymphocytes, Cytotoxic}, issn = {1095-9203}, doi = {10.1126/science.abl3855}, author = {Ritter, Alex T and Shtengel, Gleb and Xu, C Shan and Weigel, Aubrey and Hoffman, David P and Freeman, Melanie and Iyer, Nirmala and Alivodej, Nensi and Ackerman, David and Voskoboinik, Ilia and Trapani, Joseph and Hess, Harald F and Mellman, Ira} } @article {68368, title = {The evolutionary dynamics of extrachromosomal DNA in human cancers.}, journal = {Nature Genetics}, year = {2022}, month = {2022 Sep 19}, abstract = {

Oncogene amplification on extrachromosomal DNA (ecDNA) is a common event, driving aggressive tumor growth, drug resistance and shorter survival. Currently, the impact of nonchromosomal oncogene inheritance-random identity by descent-is poorly understood. Also unclear is the impact of ecDNA on somatic variation and selection. Here integrating theoretical models of random segregation, unbiased image analysis, CRISPR-based ecDNA tagging with live-cell imaging and CRISPR-C, we demonstrate that random ecDNA inheritance results in extensive intratumoral ecDNA copy number heterogeneity and rapid adaptation to metabolic stress and targeted treatment. Observed ecDNAs benefit host cell survival or growth and can change within a single cell cycle. ecDNA inheritance can predict, a priori, some of the aggressive features of ecDNA-containing cancers. These properties are facilitated by the ability of ecDNA to rapidly adapt genomes in a way that is not possible through chromosomal oncogene amplification. These results show how the nonchromosomal random inheritance pattern of ecDNA contributes to poor outcomes for patients with cancer.

}, issn = {1546-1718}, doi = {10.1038/s41588-022-01177-x}, author = {Lange, Joshua T and Rose, John C and Chen, Celine Y and Pichugin, Yuriy and Xie, Liangqi and Tang, Jun and Hung, King L and Yost, Kathryn E and Shi, Quanming and Erb, Marcella L and Rajkumar, Utkrisht and Wu, Sihan and Taschner-Mandl, Sabine and Bernkopf, Marie and Swanton, Charles and Liu, Zhe and Huang, Weini and Chang, Howard Y and Bafna, Vineet and Henssen, Anton G and Werner, Benjamin and Mischel, Paul S} } @article {68275, title = {Flexible control of behavioral variability mediated by an internal representation of head direction}, journal = {bioRxiv}, year = {2022}, month = {2022 Aug 19}, abstract = {

Internal representations are thought to support the generation of flexible, long-timescale behavioral patterns in both animals and artificial agents. Here, we present a novel conceptual framework for how\ Drosophila\ use their internal representation of head direction to maintain preferred headings in their surroundings, and how they learn to modify these preferences in the presence of selective thermal reinforcement. To develop the framework, we analyzed flies{\textquoteright} behavior in a classical operant visual learning paradigm and found that they use stochastically generated fixations and directed turns to express their heading preferences. Symmetries in the visual scene used in the paradigm allowed us to expose how flies{\textquoteright} probabilistic behavior in this setting is tethered to their head direction representation. We describe how flies{\textquoteright} ability to quickly adapt their behavior to the rules of their environment may rest on a behavioral policy whose parameters are flexible but whose form is genetically encoded in the structure of their circuits. Many of the mechanisms we outline may also be relevant for rapidly adaptive behavior driven by internal representations in other animals, including mammals.

}, doi = {10.1101/2021.08.18.456004}, url = {https://doi.org/10.1101/2021.08.18.456004}, author = {Chuntao Dan and Brad K. Hulse and Vivek Jayaraman and Ann M. Hermundstad} } @article {68422, title = {Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly.}, journal = {Science}, volume = {375}, year = {2022}, month = {03/2022}, pages = {eabk2432}, abstract = {

For more than 100 years, the fruit fly has been one of the most studied model organisms. Here, we present a single-cell atlas of the adult fly, Tabula , that includes 580,000 nuclei from 15 individually dissected sexed tissues as well as the entire head and body, annotated to \>250 distinct cell types. We provide an in-depth analysis of cell type-related gene signatures and transcription factor markers, as well as sexual dimorphism, across the whole animal. Analysis of common cell types between tissues, such as blood and muscle cells, reveals rare cell types and tissue-specific subtypes. This atlas provides a valuable resource for the community and serves as a reference to study genetic perturbations and disease models at single-cell resolution.

}, keywords = {Animals, Cell Nucleus, Databases, Genetic, Drosophila melanogaster, Drosophila Proteins, Female, Gene Expression Regulation, Gene Regulatory Networks, Genes, Insect, Male, RNA-Seq, Sex Characteristics, Single-Cell Analysis, Transcription Factors, Transcriptome}, issn = {1095-9203}, doi = {10.1126/science.abk2432}, author = {Li, Hongjie and Janssens, Jasper and De Waegeneer, Maxime and Kolluru, Sai Saroja and Davie, Kristofer and Gardeux, Vincent and Saelens, Wouter and David, Fabrice P A and Brbi{\'c}, Maria and Spanier, Katina and Leskovec, Jure and McLaughlin, Colleen N and Xie, Qijing and Jones, Robert C and Brueckner, Katja and Shim, Jiwon and Tattikota, Sudhir Gopal and Schnorrer, Frank and Rust, Katja and Nystul, Todd G and Carvalho-Santos, Zita and Ribeiro, Carlos and Pal, Soumitra and Mahadevaraju, Sharvani and Przytycka, Teresa M and Allen, Aaron M and Goodwin, Stephen F and Berry, Cameron W and Fuller, Margaret T and White-Cooper, Helen and Matunis, Erika L and DiNardo, Stephen and Galenza, Anthony and O{\textquoteright}Brien, Lucy Erin and Dow, Julian A T and Jasper, Heinrich and Oliver, Brian and Perrimon, Norbert and Deplancke, Bart and Quake, Stephen R and Luo, Liqun and Aerts, Stein and Agarwal, Devika and Ahmed-Braimah, Yasir and Arbeitman, Michelle and Ariss, Majd M and Augsburger, Jordan and Ayush, Kumar and Baker, Catherine C and Banisch, Torsten and Birker, Katja and Bodmer, Rolf and Bolival, Benjamin and Brantley, Susanna E and Brill, Julie A and Brown, Nora C and Buehner, Norene A and Cai, Xiaoyu Tracy and Cardoso-Figueiredo, Rita and Casares, Fernando and Chang, Amy and Clandinin, Thomas R and Crasta, Sheela and Desplan, Claude and Detweiler, Angela M and Dhakan, Darshan B and Don{\`a}, Erika and Engert, Stefanie and Floc{\textquoteright}hlay, Swann and George, Nancy and Gonz{\'a}lez-Segarra, Amanda J and Groves, Andrew K and Gumbin, Samantha and Guo, Yanmeng and Harris, Devon E and Heifetz, Yael and Holtz, Stephen L and Horns, Felix and Hudry, Bruno and Hung, Ruei-Jiun and Jan, Yuh Nung and Jaszczak, Jacob S and Jefferis, Gregory S X E and Karkanias, Jim and Karr, Timothy L and Katheder, Nadja Sandra and Kezos, James and Kim, Anna A and Kim, Seung K and Kockel, Lutz and Konstantinides, Nikolaos and Kornberg, Thomas B and Krause, Henry M and Labott, Andrew Thomas and Laturney, Meghan and Lehmann, Ruth and Leinwand, Sarah and Li, Jiefu and Li, Joshua Shing Shun and Li, Kai and Li, Ke and Li, Liying and Li, Tun and Litovchenko, Maria and Liu, Han-Hsuan and Liu, Yifang and Lu, Tzu-Chiao and Manning, Jonathan and Mase, Anjeli and Matera-Vatnick, Mikaela and Matias, Neuza Reis and McDonough-Goldstein, Caitlin E and McGeever, Aaron and McLachlan, Alex D and Moreno-Roman, Paola and Neff, Norma and Neville, Megan and Ngo, Sang and Nielsen, Tanja and O{\textquoteright}Brien, Caitlin E and Osumi-Sutherland, David and Ozel, Mehmet Neset and Papatheodorou, Irene and Petkovic, Maja and Pilgrim, Clare and Pisco, Angela Oliveira and Reisenman, Carolina and Sanders, Erin Nicole and Dos Santos, Gilberto and Scott, Kristin and Sherlekar, Aparna and Shiu, Philip and Sims, David and Sit, Rene V and Slaidina, Maija and Smith, Harold E and Sterne, Gabriella and Su, Yu-Han and Sutton, Daniel and Tamayo, Marco and Tan, Michelle and Tastekin, Ibrahim and Treiber, Christoph and Vacek, David and Vogler, Georg and Waddell, Scott and Wang, Wanpeng and Wilson, Rachel I and Wolfner, Mariana F and Wong, Yiu-Cheung E and Xie, Anthony and Xu, Jun and Yamamoto, Shinya and Yan, Jia and Yao, Zepeng and Yoda, Kazuki and Zhu, Ruijun and Zinzen, Robert P} } @article {68068, title = {Gene structure-based homology search identifies highly divergent putative effector gene family.}, journal = {Genome Biology and Evolution}, year = {2022}, month = {2022 May 09}, abstract = {

Homology of highly divergent genes often cannot be determined from sequence similarity alone. For example, we recently identified in the aphid Hormaphis cornu a family of rapidly evolving bicycle genes, which encode novel proteins implicated as plant gall effectors, and sequence similarity search methods yielded few putative bicycle homologs in other species. Coding sequence-independent features of genes, such as intron-exon boundaries, often evolve more slowly than coding sequences, however, and can provide complementary evidence for homology. We found that a linear logistic regression classifier using only structural features of bicycle genes identified many putative bicycle homologs in other species. Independent evidence from sequence features and intron locations supported homology assignments. To test the potential roles of bicycle genes in other aphids, we sequenced the genome of a second gall-forming aphid, Tetraneura nigriabdominalis, and found that many bicycle genes are strongly expressed in the salivary glands of the gall forming foundress. In addition, bicycle genes are strongly overexpressed in the salivary glands of a non-gall forming aphid, Acyrthosiphon pisum, and in the non-gall forming generations of Hormaphis cornu. These observations suggest that Bicycle proteins may be used by multiple aphid species to manipulate plants in diverse ways. Incorporation of gene structural features into sequence search algorithms may aid identification of deeply divergent homologs, especially of rapidly evolving genes involved in host-parasite interactions.

}, issn = {1759-6653}, doi = {10.1093/gbe/evac069}, author = {Stern, David L and Han, Clair} } @article {68414, title = {High-throughput automated methods for classical and operant conditioning of larvae.}, journal = {eLife}, volume = {11}, year = {2022}, month = {2022 Oct 28}, abstract = {

Learning which stimuli (classical conditioning) or which actions (operant conditioning) predict rewards or punishments can improve chances of survival. However, the circuit mechanisms that underlie distinct types of associative learning are still not fully understood. Automated, high-throughput paradigms for studying different types of associative learning, combined with manipulation of specific neurons in freely behaving animals, can help advance this field. The Drosophila melanogaster larva is a tractable model system for studying the circuit basis of behaviour, but many forms of associative learning have not yet been demonstrated in this animal. Here, we developed a high-throughput (i. e. multi-larva) training system that combines real-time behaviour detection of freely moving larvae with targeted opto- and thermogenetic stimulation of tracked animals. Both stimuli are controlled in either open- or closed-loop, and delivered with high temporal and spatial precision. Using this tracker, we show for the first time that Drosophila larvae can perform classical conditioning with no overlap between sensory stimuli (i. e. trace conditioning). We also demonstrate that larvae are capable of operant conditioning by inducing a bend direction preference through optogenetic activation of reward-encoding serotonergic neurons. Our results extend the known associative learning capacities of Drosophila larvae. Our automated training rig will facilitate the study of many different forms of associative learning and the identification of the neural circuits that underpin them.

}, issn = {2050-084X}, doi = {10.7554/eLife.70015}, author = {Croteau-Chonka, Elise C and Clayton, Michael S and Venkatasubramanian, Lalanti and Harris, Samuel N and Jones, Benjamin M W and Narayan, Lakshmi and Winding, Michael and Masson, Jean-Baptiste and Zlatic, Marta and Klein, Kristina T} } @article {68985, title = {Human primed and na{\"\i}ve PSCs are both able to differentiate into trophoblast stem cells.}, journal = {Stem Cell Reports}, volume = {17}, year = {2022}, month = {11/2022}, pages = {2484-2500}, abstract = {

The recent derivation of human trophoblast stem cells (TSCs) from placental cytotrophoblasts and blastocysts opened opportunities for studying the development and function of the human placenta. Recent reports have suggested that human na{\"\i}ve, but not primed, pluripotent stem cells (PSCs) retain an exclusive potential to generate TSCs. Here we report that, in the absence of WNT stimulation, transforming growth factor β (TGF-β) pathway inhibition leads to direct and robust conversion of primed human PSCs into TSCs. The resulting primed PSC-derived TSC lines exhibit self-renewal, can differentiate into the main trophoblast lineages, and present RNA and epigenetic profiles that are indistinguishable from recently established TSC lines derived from human placenta, blastocysts, or isogenic human na{\"\i}ve PSCs expanded under human enhanced na{\"\i}ve stem cell medium (HENSM) conditions. Activation of nuclear Yes-associated protein (YAP) signaling is sufficient for this conversion and necessary for human TSC maintenance. Our findings underscore a residual plasticity in primed human PSCs that allows their in\ vitro conversion into extra-embryonic trophoblast lineages.

}, keywords = {Blastocyst, Cell Differentiation, Female, Humans, Placenta, Pluripotent Stem Cells, Pregnancy, Trophoblasts}, issn = {2213-6711}, doi = {10.1016/j.stemcr.2022.09.008}, author = {Viukov, Sergey and Shani, Tom and Bayerl, Jonathan and Aguilera-Castrejon, Alejandro and Oldak, Bernardo and Sheban, Daoud and Tarazi, Shadi and Stelzer, Yonatan and Hanna, Jacob H and Novershtern, Noa} } @article {67931, title = {Identifying Inhibitors of -1 Programmed Ribosomal Frameshifting in a Broad Spectrum of Coronaviruses.}, journal = {Viruses}, volume = {14}, year = {2022}, month = {2022 Jan 18}, abstract = {

Recurrent outbreaks of novel zoonotic coronavirus (CoV) diseases in recent years have highlighted the importance of developing therapeutics with broad-spectrum activity against CoVs. Because all CoVs use -1 programmed ribosomal frameshifting (-1 PRF) to control expression of key viral proteins, the frameshift signal in viral mRNA that stimulates -1 PRF provides a promising potential target for such therapeutics. To test the viability of this strategy, we explored whether small-molecule inhibitors of -1 PRF in SARS-CoV-2 also inhibited -1 PRF in a range of bat CoVs-the most likely source of future zoonoses. Six inhibitors identified in new and previous screens against SARS-CoV-2 were evaluated against the frameshift signals from a panel of representative bat CoVs as well as MERS-CoV. Some drugs had strong activity against subsets of these CoV-derived frameshift signals, while having limited to no effect on -1 PRF caused by frameshift signals from other viruses used as negative controls. Notably, the serine protease inhibitor nafamostat suppressed -1 PRF significantly for multiple CoV-derived frameshift signals. These results suggest it is possible to find small-molecule ligands that inhibit -1 PRF specifically in a broad spectrum of CoVs, establishing frameshift signals as a viable target for developing pan-coronaviral therapeutics.

}, issn = {1999-4915}, doi = {10.3390/v14020177}, author = {Munshi, Sneha and Neupane, Krishna and Ileperuma, Sandaru M and Halma, Matthew T J and Kelly, Jamie A and Halpern, Clarissa F and Dinman, Jonathan D and Loerch, Sarah and Woodside, Michael T} } @article {67891, title = {Idiosyncratic learning performance in flies.}, journal = {Biology Letters}, volume = {18}, year = {2022}, month = {2022 Feb 01}, pages = {20210424}, abstract = {

Individuals vary in their innate behaviours, even when they have the same genome and have been reared in the same environment. The extent of individuality in plastic behaviours, like learning, is less well characterized. Also unknown is the extent to which intragenotypic differences in learning generalize: if an individual performs well in one assay, will it perform well in other assays? We investigated this using the fruit fly , an organism long-used to study the mechanistic basis of learning and memory. We found that isogenic flies, reared in identical laboratory conditions, and subject to classical conditioning that associated odorants with electric shock, exhibit clear individuality in their learning responses. Flies that performed well when an odour was paired with shock tended to perform well when the odour was paired with bitter taste or when other odours were paired with shock. Thus, individuality in learning performance appears to be prominent in isogenic animals reared identically, and individual differences in learning performance generalize across some aversive sensory modalities. Establishing these results in flies opens up the possibility of studying the genetic and neural circuit basis of individual differences in learning in a highly suitable model organism.

}, issn = {1744-957X}, doi = {10.1098/rsbl.2021.0424}, author = {Smith, Matthew A-Y and Honegger, Kyle S and Turner, Glenn and de Bivort, Benjamin} } @article {68418, title = {In situ cell-type-specific cell-surface proteomic profiling in mice.}, journal = {Neuron}, year = {2022}, month = {10/2022}, abstract = {

Cell-surface proteins (CSPs) mediate intercellular communication throughout the lives of multicellular organisms. However, there are no generalizable methods for quantitative CSP profiling in specific cell types in vertebrate tissues. Here, we present in situ cell-surface proteome extraction by extracellular labeling (iPEEL), a proximity labeling method in mice that enables spatiotemporally precise labeling of cell-surface proteomes in a cell-type-specific environment in native tissues for discovery proteomics. Applying iPEEL to developing and mature cerebellar Purkinje cells revealed differential enrichment in CSPs with post-translational protein processing and synaptic functions in the developing and mature cell-surface proteomes, respectively. A proteome-instructed in\ vivo loss-of-function screen identified a critical, multifaceted role for Armh4 in Purkinje cell dendrite morphogenesis. Armh4 overexpression also disrupts dendrite morphogenesis; this effect requires its conserved cytoplasmic domain and is augmented by disrupting its endocytosis. Our results highlight the utility of CSP profiling in native mammalian tissues for identifying regulators of cell-surface signaling.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2022.09.025}, author = {Shuster, S Andrew and Li, Jiefu and Chon, URee and Sinantha-Hu, Miley C and Luginbuhl, David J and Udeshi, Namrata D and Carey, Dominique Kiki and Takeo, Yukari H and Xie, Qijing and Xu, Chuanyun and Mani, D R and Han, Shuo and Ting, Alice Y and Carr, Steven A and Luo, Liqun} } @article {68314, title = {In vivo visualization of nitrate dynamics using a genetically encoded biosensor}, journal = {Science Advances}, volume = {8}, year = {2022}, month = {2022 Oct 19}, abstract = {

Nitrate (NO3-) uptake and distribution are critical to plant life. Although the upstream regulation of nitrate uptake and downstream responses to nitrate in a variety of cells have been well-studied, it is still not possible to directly visualize the spatial and temporal distribution of nitrate with high resolution at the cellular level. Here, we report a nuclear-localized, genetically encoded biosensor, nlsNitraMeter3.0, for the quantitative visualization of nitrate distribution in\ Arabidopsis thaliana. The biosensor tracked the spatiotemporal distribution of nitrate along the primary root axis and disruptions by genetic mutation of transport (low nitrate uptake) and assimilation (high nitrate accumulation). The developed biosensor effectively monitors nitrate concentrations at cellular level in real time and spatiotemporal changes during the plant life cycle.

}, doi = {10.1126/sciadv.abq4915}, url = {https://doi.org/10.1126/sciadv.abq4915}, author = {Yen-Ning Chen and Heather Cartwright and Cheng-Hsun Ho} } @article {67814, title = {Internal Models in Control, Bioengineering, and Neuroscience}, journal = {Annual Review of Control, Robotics, and Autonomous Systems}, volume = {5}, year = {2022}, month = {2021 Nov 29}, abstract = {

Internal models are nowadays customarily used in different domains of science and engineering to describe how living organisms or artificial computational units embed their acquired knowledge about recurring events taking place in the surrounding environment. This article reviews the internal model principle in control theory, bioengineering, and neuroscience, illustrating the fundamental concepts and theoretical developments of the few last decades of research.

}, issn = {2573-5144}, doi = {10.1146/control.2022.5.issue-110.1146/annurev-control-042920-102205}, url = {https://www.annualreviews.org/toc/control/5/1https://www.annualreviews.org/doi/10.1146/annurev-control-042920-102205https://www.annualreviews.org/doi/pdf/10.1146/annurev-control-042920-102205}, author = {Bin, Michelangelo and Huang, Jie and Isidori, Alberto and Marconi, Lorenzo and Mischiati, Matteo and Sontag, Eduardo} } @article {68420, title = {KIRCD8 T cells suppress pathogenic T cells and are active in autoimmune diseases and COVID-19.}, journal = {Science}, volume = {376}, year = {2022}, month = {04/2022}, pages = {eabi9591}, abstract = {

In this work, we find that CD8 T cells expressing inhibitory killer cell immunoglobulin-like receptors (KIRs) are the human equivalent of Ly49CD8 regulatory T cells in mice and are increased in the blood and inflamed tissues of patients with a variety of autoimmune diseases. Moreover, these CD8 T cells efficiently eliminated pathogenic gliadin-specific CD4 T cells from the leukocytes of celiac disease patients in vitro. We also find elevated levels of KIRCD8 T cells, but not CD4 regulatory T cells, in COVID-19 patients, correlating with disease severity and vasculitis. Selective ablation of Ly49CD8 T cells in virus-infected mice led to autoimmunity after infection. Our results indicate that in both species, these regulatory CD8 T cells act specifically to suppress pathogenic T cells in autoimmune and infectious diseases.

}, keywords = {Animals, Autoimmune Diseases, CD8-Positive T-Lymphocytes, COVID-19, Humans, Mice, Receptors, KIR, T-Lymphocytes, Regulatory}, issn = {1095-9203}, doi = {10.1126/science.abi9591}, author = {Li, Jing and Zaslavsky, Maxim and Su, Yapeng and Guo, Jing and Sikora, Michael J and van Unen, Vincent and Christophersen, Asbj{\o}rn and Chiou, Shin-Heng and Chen, Liang and Li, Jiefu and Ji, Xuhuai and Wilhelmy, Julie and McSween, Alana M and Palanski, Brad A and Mallajosyula, Venkata Vamsee Aditya and Bracey, Nathan A and Dhondalay, Gopal Krishna R and Bhamidipati, Kartik and Pai, Joy and Kipp, Lucas B and Dunn, Jeffrey E and Hauser, Stephen L and Oksenberg, Jorge R and Satpathy, Ansuman T and Robinson, William H and Dekker, Cornelia L and Steinmetz, Lars M and Khosla, Chaitan and Utz, Paul J and Sollid, Ludvig M and Chien, Yueh-Hsiu and Heath, James R and Fernandez-Becker, Nielsen Q and Nadeau, Kari C and Saligrama, Naresha and Davis, Mark M} } @article {68471, title = {Leveraging the model-experiment loop: Examples from cellular slime mold chemotaxis.}, journal = {Exp Cell Res}, volume = {418}, year = {2022}, month = {09/2022}, pages = {113218}, abstract = {

Interplay between models and experimental data advances discovery and understanding in biology, particularly when models generate predictions that allow well-designed experiments to distinguish between alternative mechanisms. To illustrate how this feedback between models and experiments can lead to key insights into biological mechanisms, we explore three examples from cellular slime mold chemotaxis. These examples include studies that identified chemotaxis as the primary mechanism behind slime mold aggregation, discovered that cells likely measure chemoattractant gradients by sensing concentration differences across cell length, and tested the role of cell-associated chemoattractant degradation in shaping chemotactic fields. Although each study used a different model class appropriate to their hypotheses - qualitative, mathematical, or simulation-based - these examples all highlight the utility of modeling to formalize assumptions and generate testable predictions. A central element of this framework is the iterative use of models and experiments, specifically: matching experimental designs to the models, revising models based on mismatches with experimental data, and validating critical model assumptions and predictions with experiments. We advocate for continued use of this interplay between models and experiments to advance biological discovery.

}, keywords = {Chemotactic Factors, Chemotaxis, Computer Simulation, Dictyosteliida, Dictyostelium, Models, Biological}, issn = {1090-2422}, doi = {10.1016/j.yexcr.2022.113218}, author = {Zhu, Xinwen and Hager, Emily R and Huyan, Chuqiao and Sgro, Allyson E} } @article {68103, title = {Maintaining a stable head direction representation in naturalistic visual environments}, journal = {bioRxiv}, year = {2022}, month = {2022 May 18}, abstract = {

Many animals rely on a representation of head direction for flexible, goal-directed navigation. In insects, a compass-like head direction representation is maintained in a conserved brain region called the central complex. This head direction representation is updated by self-motion information and by tethering to sensory cues in the surroundings through a plasticity mechanism. However, under natural settings, some of these sensory cues may temporarily disappear{\textemdash}for example, when clouds hide the sun{\textemdash}and prominent landmarks at different distances from the insect may move across the animal{\textquoteright}s field of view during translation, creating potential conflicts for a neural compass. We used two-photon calcium imaging in head-fixed Drosophila behaving in virtual reality to monitor the fly{\textquoteright}s compass during navigation in immersive naturalistic environments with approachable local landmarks. We found that the fly{\textquoteright}s compass remains stable even in these settings by tethering to available global cues, likely preserving the animal{\textquoteright}s ability to perform compass-driven behaviors such as maintaining a constant heading.

}, doi = {10.1101/2022.05.17.492284}, url = {https://doi.org/10.1101/2022.05.17.492284}, author = {Hannah Haberkern and Shivam S Chitnis and Philip M Hubbard and Tobias Goulet and Ann M Hermundstad and Vivek Jayaraman} } @article {67951, title = {A midbrain-thalamus-cortex circuit reorganizes cortical dynamics to initiate movement.}, journal = {Cell}, volume = {185}, year = {2022}, month = {2022 Mar 17}, pages = {1065}, abstract = {

Motor behaviors are often planned long before execution but only released after specific sensory events. Planning and execution are each associated with distinct patterns of motor cortex activity. Key questions are how these dynamic activity patterns are generated and how they relate to behavior. Here, we investigate the multi-regional neural circuits that link an auditory "Go cue" and the transition from planning to execution of directional licking. Ascending glutamatergic neurons in the midbrain reticular and pedunculopontine nuclei show short latency and phasic changes in spike rate that are selective for the Go cue. This signal is transmitted via the thalamus to the motor cortex, where it triggers a rapid reorganization of motor cortex state from planning-related activity to a motor command, which in turn drives appropriate movement. Our studies show how midbrain can control cortical dynamics via the thalamus for rapid and precise motor behavior.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2022.02.006}, author = {Inagaki, Hidehiko K and Chen, Susu and Ridder, Margreet C and Sah, Pankaj and Li, Nuo and Yang, Zidan and Hasanbegovic, Hana and Gao, Zhenyu and Gerfen, Charles R and Svoboda, Karel} } @article {68315, title = {Motion of single molecular tethers reveals dynamic subdomains at ER-mitochondria contact sites}, journal = {bioRxiv}, year = {2022}, month = {2022 Sep 03}, abstract = {

To coordinate cellular physiology, eukaryotic cells rely on the inter-organelle transfer of molecules at specialized organelle-organelle contact sites1,2. Endoplasmic reticulum-mitochondria contact sites (ERMCSs) are particularly vital communication hubs, playing key roles in the exchange of signaling molecules, lipids, and metabolites3. ERMCSs are maintained by interactions between complementary tethering molecules on the surface of each organelle4,5. However, due to the extreme sensitivity of these membrane interfaces to experimental perturbation6,7, a clear understanding of their nanoscale structure and regulation is still lacking. Here, we combine 3D electron microscopy with high-speed molecular tracking of a model organelle tether, VAPB, to map the structure and diffusion landscape of ERMCSs. From EM reconstructions, we identified subdomains within the contact site where ER membranes dramatically deform to match local mitochondrial curvature. In parallel live cell experiments, we observed that the VAPB tethers that mediate this interface were not immobile, but rather highly dynamic, entering and leaving the site in seconds. These subdomains enlarged during nutrient stress, indicating ERMCSs can readily remodel under different physiological conditions. An ALS-associated mutation in VAPB altered the normal fluidity of contact sites, likely perturbing effective communication across the contact site and preventing remodeling. These results establish high speed single molecule imaging as a new tool for mapping the structure of contact site interfaces and suggest that the diffusion landscape of VAPB is a crucial component of ERMCS homeostasis.

}, doi = {10.1101/2022.09.03.505525}, url = {https://doi.org/10.1101/2022.09.03.505525}, author = {Christopher J. Obara and Jonathon Nixon-Abell and Andrew S. Moore and Federica Riccio and David P. Hoffman and Gleb Shtengel and C. Shan Xu and Kathy Schaefer and H. Amalia Pasolli and Jean-Baptiste Masson and Harald F. Hess and Christopher P. Calderon and Craig Blackstone and Jennifer Lippincott-Schwartz} } @article {67962, title = {Motor cortical output for skilled forelimb movement is selectively distributed across projection neuron classes.}, journal = {Science Advances}, volume = {8}, year = {2022}, month = {2022 Mar 11}, pages = {eabj5167}, abstract = {

The interaction of descending neocortical outputs and subcortical premotor circuits is critical for shaping skilled movements. Two broad classes of motor cortical output projection neurons provide input to many subcortical motor areas: pyramidal tract (PT) neurons, which project throughout the neuraxis, and intratelencephalic (IT) neurons, which project within the cortex and subcortical striatum. It is unclear whether these classes are functionally in series or whether each class carries distinct components of descending motor control signals. Here, we combine large-scale neural recordings across all layers of motor cortex with cell type-specific perturbations to study cortically dependent mouse motor behaviors: kinematically variable manipulation of a joystick and a kinematically precise reach-to-grasp. We find that striatum-projecting IT neuron activity preferentially represents amplitude, whereas pons-projecting PT neurons preferentially represent the variable direction of forelimb movements. Thus, separable components of descending motor cortical commands are distributed across motor cortical projection cell classes.

}, issn = {2375-2548}, doi = {10.1126/sciadv.abj5167}, author = {Park, Junchol and Phillips, James W and Guo, Jian-Zhong and Martin, Kathleen A and Hantman, Adam W and Dudman, Joshua T} } @article {67963, title = {Myosin VI regulates the spatial organisation of mammalian transcription initiation.}, journal = {Nature Communications}, volume = {13}, year = {2022}, month = {2022 Mar 15}, pages = {1346}, abstract = {

During transcription, RNA Polymerase II (RNAPII) is spatially organised within the nucleus into clusters that correlate with transcription activity. While this is a hallmark of genome regulation in mammalian cells, the mechanisms concerning the assembly, organisation and stability remain unknown. Here, we have used combination of single molecule imaging and genomic approaches to explore the role of nuclear myosin VI (MVI) in the nanoscale organisation of RNAPII. We reveal that MVI in the nucleus acts as the molecular anchor that holds RNAPII in high density clusters. Perturbation of MVI leads to the disruption of RNAPII localisation, chromatin organisation and subsequently a decrease in gene expression. Overall, we uncover the fundamental role of MVI in the spatial regulation of gene expression.

}, issn = {2041-1723}, doi = {10.1038/s41467-022-28962-w}, author = {Hari-Gupta, Yukti and Fili, Natalia and Dos Santos, {\'A}lia and Cook, Alexander W and Gough, Rosemarie E and Reed, Hannah C W and Wang, Lin and Aaron, Jesse and Venit, Tomas and Wait, Eric and Grosse-Berkenbusch, Andreas and Gebhardt, J Christof M and Percipalle, Piergiorgio and Chew, Teng-Leong and Martin-Fernandez, Marisa and Toseland, Christopher P} } @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 {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 {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 {68512, title = {Oligodendrocyte precursor cells ingest axons in the mouse neocortex.}, journal = {Proceedings of the National Academies of Science of the U.S.A.}, volume = {119}, year = {2022}, month = {2022 Nov 29}, pages = {e2202580119}, abstract = {

Neurons in the developing brain undergo extensive structural refinement as nascent circuits adopt their mature form. This physical transformation of neurons is facilitated by the engulfment and degradation of axonal branches and synapses by surrounding glial cells, including microglia and astrocytes. However, the small size of phagocytic organelles and the complex, highly ramified morphology of glia have made it difficult to define the contribution of these and other glial cell types to this crucial process. Here, we used large-scale, serial section transmission\ electron microscopy (TEM) with computational volume segmentation to reconstruct the complete 3D morphologies of distinct glial types in the mouse visual cortex, providing unprecedented resolution of their morphology and composition. Unexpectedly, we discovered that the fine processes of oligodendrocyte precursor cells (OPCs), a population of abundant, highly dynamic glial progenitors, frequently surrounded small branches of axons. Numerous phagosomes and phagolysosomes (PLs) containing fragments of axons and vesicular structures were present inside their processes, suggesting that OPCs engage in axon pruning. Single-nucleus RNA sequencing from the developing mouse cortex revealed that OPCs express key phagocytic genes at this stage, as well as neuronal transcripts, consistent with active axon engulfment. Although microglia are thought to be responsible for the majority of synaptic pruning and structural refinement, PLs were ten times more abundant in OPCs than in microglia at this stage, and these structures were markedly less abundant in newly generated oligodendrocytes, suggesting that OPCs contribute substantially to the refinement of neuronal circuits during cortical development.

}, keywords = {Animals, Axons, Mice, Neocortex, Neurons, Oligodendrocyte Precursor Cells, Oligodendroglia}, issn = {1091-6490}, doi = {10.1073/pnas.2202580119}, author = {Buchanan, JoAnn and Elabbady, Leila and Collman, Forrest and Jorstad, Nikolas L and Bakken, Trygve E and Ott, Carolyn and Glatzer, Jenna and Bleckert, Adam A and Bodor, Agnes L and Brittain, Derrick and Bumbarger, Daniel J and Mahalingam, Gayathri and Seshamani, Sharmishtaa and Schneider-Mizell, Casey and Takeno, Marc M and Torres, Russel and Yin, Wenjing and Hodge, Rebecca D and Castro, Manuel and Dorkenwald, Sven and Ih, Dodam and Jordan, Chris S and Kemnitz, Nico and Lee, Kisuk and Lu, Ran and Macrina, Thomas and Mu, Shang and Popovych, Sergiy and Silversmith, William M and Tartavull, Ignacio and Turner, Nicholas L and Wilson, Alyssa M and Wong, William and Wu, Jingpeng and Zlateski, Aleksandar and Zung, Jonathan and Lippincott-Schwartz, Jennifer and Lein, Ed S and Seung, H Sebastian and Bergles, Dwight E and Reid, R Clay and da Costa, Nuno Ma{\c c}arico} } @article {67930, title = {Online learning for orientation estimation during translation in an insect ring attractor network.}, journal = {Scientific Reports}, volume = {12}, year = {2022}, month = {2022 Feb 25}, pages = {3210}, abstract = {

Insect neural systems are a promising source of inspiration for new navigation algorithms, especially on low size, weight, and power platforms. There have been unprecedented recent neuroscience breakthroughs with Drosophila in behavioral and neural imaging experiments as well as the mapping of detailed connectivity of neural structures. General mechanisms for learning orientation in the central complex (CX) of Drosophila have been investigated previously; however, it is unclear how these underlying mechanisms extend to cases where there is translation through an environment (beyond only rotation), which is critical for navigation in robotic systems. Here, we develop a CX neural connectivity-constrained model that performs sensor fusion, as well as unsupervised learning of visual features for path integration; we demonstrate the viability of this circuit for use in robotic systems in simulated and physical environments. Furthermore, we propose a theoretical understanding of how distributed online unsupervised network weight modification can be leveraged for learning in a trajectory through an environment by minimizing orientation estimation error. Overall, our results may enable a new class of CX-derived low power robotic navigation algorithms and lead to testable predictions to inform future neuroscience experiments.

}, issn = {2045-2322}, doi = {10.1038/s41598-022-05798-4}, author = {Robinson, Brian S and Norman-Tenazas, Raphael and Cervantes, Martha and Symonette, Danilo and Johnson, Erik C and Joyce, Justin and Rivlin, Patricia K and Hwang, Grace and Zhang, Kechen and Gray-Roncal, William} } @article {68102, title = {Perceptual decisions exhibit hallmarks of dynamic Bayesian inference}, journal = {bioRxiv}, year = {2022}, month = {2022 May 24}, abstract = {

To interpret the sensory environment, the brain combines ambiguous sensory measurements with context-specific prior experience. But environmental contexts can change abruptly and unpredictably, resulting in uncertainty about the current context. Here we address two questions: how should context-specific prior knowledge optimally guide the interpretation of sensory stimuli in changing environments, and do human decision-making strategies resemble this optimum? We probe these questions with a task in which subjects report the orientation of ambiguous visual stimuli that were drawn from three dynamically switching distributions, representing different environmental contexts. We derive predictions for an ideal Bayesian observer that leverages the statistical structure of the task to maximize decision accuracy and show that its decisions are biased by task context. The magnitude of this decision bias is not a fixed property of the sensory measurement but depends on the observer{\textquoteright}s belief about the current context. The model therefore predicts that decision bias will grow with the reliability of the context cue, the stability of the environment, and with the number of trials since the last context switch. Analysis of human choice data validates all three predictions, providing evidence that the brain continuously updates probabilistic representations of the environment to best interpret an uncertain, ever-changing world.

}, doi = {10.1101/2022.05.23.493109}, url = {https://doi.org/10.1101/2022.05.23.493109}, author = {Julie A. Charlton and Wiktor F. M{\l}ynarski and Yoon H. Bai and Ann M. Hermundstad and Robbe L. T. Goris} } @article {68116, title = {Plasticity-induced actin polymerization in the dendritic shaft regulates intracellular AMPA receptor trafficking.}, journal = {bioRxiv}, year = {2022}, month = {2022 May 29}, abstract = {

AMPA-type receptors (AMPARs) are rapidly inserted into synapses undergoing long-term potentiation (LTP) to increase synaptic transmission, but how AMPAR-containing vesicles are selectively trafficked to these synapses during LTP is not known. Here we developed a strategy to label AMPAR GluA1 subunits expressed from the endogenous loci of rat hippocampal neurons such that the motion of GluA1-containing vesicles in time-lapse sequences can be characterized using single-particle tracking and mathematical modeling. We find that GluA1-containing vesicles are confined and concentrated near sites of stimulation-induced plasticity. We show that confinement is mediated by actin polymerization, which hinders the active transport of GluA1-containing vesicles along the length of the dendritic shaft by modulating the rheological properties of the cytoplasm. Actin polymerization also facilitates myosin-mediated transport of GluA1-containing vesicles to exocytic sites. We conclude that neurons utilize F-actin to increase vesicular GluA1 reservoirs and promote exocytosis proximal to the sites of neuronal activity.

}, doi = {10.1101/2022.05.29.493906}, url = {https://doi.org/10.1101/2022.05.29.493906}, author = {V. C. Wong and P.R. Houlihan and H. Liu and D. Walpita and M.C. DeSantis and Z. Liu and E. K. O{\textquoteright}Shea} } @article {68983, title = {Post-gastrulation synthetic embryos generated ex utero from mouse naive ESCs}, journal = {Cell}, volume = {185}, year = {2022}, month = {09/2022}, pages = {3290-3306.e25}, abstract = {

Summary In\ vitro cultured stem cells with distinct developmental capacities can contribute to embryonic or extraembryonic tissues after microinjection into pre-implantation mammalian embryos. However, whether cultured stem cells can independently give rise to entire gastrulating embryo-like structures with embryonic and extraembryonic compartments remains unknown. Here, we adapt a recently established platform for prolonged ex utero growth of natural embryos to generate mouse post-gastrulation synthetic whole embryo models (sEmbryos), with both embryonic and extraembryonic compartments, starting solely from naive ESCs. This was achieved by co-aggregating non-transduced ESCs, with naive ESCs transiently expressing Cdx2 or Gata4 to promote their priming toward trophectoderm and primitive endoderm lineages, respectively. sEmbryos adequately accomplish gastrulation, advance through key developmental milestones, and develop organ progenitors within complex extraembryonic compartments similar to E8.5 stage mouse embryos. Our findings highlight the plastic potential of naive pluripotent cells to self-organize and functionally reconstitute and model the entire mammalian embryo beyond gastrulation.

}, keywords = {embryogenesis, embryoids, ESCs, ex utero, extra-embryonic Tissues, iPSCs, naive pluripotency, PGCs, synthetic embryos}, issn = {0092-8674}, doi = {https://doi.org/10.1016/j.cell.2022.07.028}, url = {https://www.sciencedirect.com/science/article/pii/S0092867422009813}, author = {Shadi Tarazi and Alejandro Aguilera-Castrejon and Carine Joubran and Nadir Ghanem and Shahd Ashouokhi and Francesco Roncato and Emilie Wildschutz and Montaser Haddad and Bernardo Oldak and Elidet Gomez-Cesar and Nir Livnat and Sergey Viukov and Dmitry Lokshtanov and Segev Naveh-Tassa and Max Rose and Suhair Hanna and Calanit Raanan and Ori Brenner and Merav Kedmi and Hadas Keren-Shaul and Tsvee Lapidot and Itay Maza and Noa Novershtern and Jacob H. Hanna} } @article {68409, title = {Practical considerations for quantitative light sheet fluorescence microscopy.}, journal = {Nature Methods}, volume = {19}, year = {2022}, month = {2022 Dec 01}, pages = {1538-49}, abstract = {

Fluorescence microscopy has evolved from a purely observational tool to a platform for quantitative, hypothesis-driven research. As such, the demand for faster and less phototoxic imaging modalities has spurred a rapid growth in light sheet fluorescence microscopy (LSFM). By restricting the excitation to a thin plane, LSFM reduces the overall light dose to a specimen while simultaneously improving image contrast. However, the defining characteristics of light sheet microscopes subsequently warrant unique considerations in their use for quantitative experiments. In this Perspective, we outline many of the pitfalls in LSFM that can compromise analysis and confound interpretation. Moreover, we offer guidance in addressing these caveats when possible. In doing so, we hope to provide a useful resource for life scientists seeking to adopt LSFM to quantitatively address complex biological hypotheses.

}, issn = {1548-7105}, doi = {10.1038/s41592-022-01632-x}, author = {Hobson, Chad M and Guo, Min and Vishwasrao, Harshad D and Wu, Yicong and Shroff, Hari and Chew, Teng-Leong} } @article {67989, title = {Quantifying Molecular Dynamics within Complex Cellular Morphologies using LLSM-FRAP.}, journal = {Small Methods}, year = {2022}, month = {2022 Jun 01}, pages = {e2200149}, abstract = {

Quantifying molecular dynamics within the context of complex cellular morphologies is essential toward understanding the inner workings and function of cells. Fluorescence recovery after photobleaching (FRAP) is one of the most broadly applied techniques to measure the reaction diffusion dynamics of molecules in living cells. FRAP measurements typically restrict themselves to single-plane image acquisition within a subcellular-sized region of interest due to the limited temporal resolution and undesirable photobleaching induced by 3D fluorescence confocal or widefield microscopy. Here, an experimental and computational pipeline combining lattice light sheet microscopy, FRAP, and numerical simulations, offering rapid and minimally invasive quantification of molecular dynamics with respect to 3D cell morphology is presented. Having the opportunity to accurately measure and interpret the dynamics of molecules in 3D with respect to cell morphology has the potential to reveal unprecedented insights into the function of living cells.

}, issn = {2366-9608}, doi = {10.1002/smtd.202200149}, author = {Colin-York, Huw and Heddleston, John and Wait, Eric and Karedla, Narain and DeSantis, Michael and Khuon, Satya and Chew, Teng-Leong and Sbalzarini, Ivo F and Fritzsche, Marco} } @article {67849, title = {Rapid reconstruction of neural circuits using tissue expansion and lattice light sheet microscopy}, journal = {eLife}, year = {2022}, month = {2022 Oct 26}, abstract = {

Electron microscopy (EM) allows for the reconstruction of dense neuronal connectomes but suffers from low throughput, limiting its application to small numbers of reference specimens. We developed a protocol and analysis pipeline using tissue expansion and lattice light-sheet microscopy (ExLLSM) to rapidly reconstruct selected circuits across many samples with single synapse resolution and molecular contrast. We validate this approach in\ Drosophila, demonstrating that it yields synaptic counts similar to those obtained by EM, can be used to compare counts across sex and experience, and to correlate structural connectivity with functional connectivity. This approach fills a critical methodological gap in studying variability in the structure and function of neural circuits across individuals within and between species.

}, doi = {10.7554/eLife.81248}, url = {https://doi.org/10.7554/eLife.81248}, author = {Joshua L. Lillvis and Hideo Otsuna and Xiaoyu Ding and Igor Pisarev and Takashi Kawase and Jennifer Colonell and Konrad Rokicki and Cristian Goina and Ruixuan Gao and Amy Hu and Kaiyu Wang and John Bogovic and Daniel E. Milkie and Edward S. Boyden and Stephan Saalfeld and Paul W. Tillberg and Barry J. Dickson} } @article {67847, title = {Rapid synaptic plasticity contributes to a learned conjunctive code of position and choice-related information in the hippocampus.}, journal = {Neuron}, volume = {110}, year = {2022}, month = {2022 Jan 05}, pages = {96-108.e4}, abstract = {

To successfully perform goal-directed navigation, animals must know where they are and what they are doing-e.g., looking for water, bringing food back to the nest, or escaping from a predator. Hippocampal neurons code for these critical variables conjunctively, but little is known about how this "where/what" code is formed or flexibly routed to other brain regions. To address these questions, we performed intracellular whole-cell recordings in mouse CA1 during a cued, two-choice virtual navigation task. We demonstrate that plateau potentials in CA1 pyramidal neurons rapidly strengthen synaptic inputs carrying conjunctive information about position and choice. Plasticity-induced response fields were modulated by cues only in animals previously trained to collect rewards based on available cues. Thus, we reveal that gradual learning is required for the formation of a conjunctive population code, upstream of CA1, while plateau-potential-induced synaptic plasticity in CA1 enables flexible routing of the code to downstream brain regions.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2021.10.003}, author = {Zhao, Xinyu and Hsu, Ching-Lung and Spruston, Nelson} } @article {68986, title = {Recent insights into mammalian natural and synthetic ex utero embryogenesis}, journal = {Current Opinion in Genetics \& Development}, volume = {77}, year = {2022}, month = {12/2022}, pages = {101988}, abstract = {

Research on early postimplantation mammalian development has been limited by the small size and intrauterine confinement of the developing embryos. Owing to the inability to observe and manipulate living embryos at these stages in utero, the establishment of robust ex utero embryo-culture systems that capture prolonged periods of mouse development has been an important research goal. In the last few\ years, these methods have been significantly improved by the optimization and enhancement of in vitro culture systems sustaining embryo development during peri-implantation stages for several species, and more recently, proper growth of natural mouse embryos from pregastrulation to late organogenesis stages and of embryonic stem cell (ES)-derived synthetic embryo models until early organogenesis stages. Here, we discuss the most recent ex utero embryo-culture systems established to date for rodents, nonhuman primates, and humans. We emphasize their technical aspects and developmental timeframe and provide insights into the new opportunities that these methods will contribute to the study of natural and synthetic mammalian embryogenesis and the stem-cell field.

}, issn = {0959-437X}, doi = {https://doi.org/10.1016/j.gde.2022.101988}, url = {https://www.sciencedirect.com/science/article/pii/S0959437X22000971}, author = {Bernardo Oldak and Alejandro Aguilera-Castrejon and Jacob H Hanna} } @article {67961, title = {Regulation of liver subcellular architecture controls metabolic homeostasis.}, journal = {Nature}, volume = {603}, year = {2022}, month = {2022 Mar 09}, pages = {736-742}, abstract = {

Cells display complex intracellular organization by compartmentalization of metabolic processes into organelles, yet the resolution of these structures in the native tissue context and their functional consequences are not well understood. Here we resolved the three-dimensional structural organization of organelles in large (more than 2.8\ {\texttimes}\ 10\ {\textmu}m) volumes of intact liver tissue (15 partial or full hepatocytes per condition) at high resolution (8\ nm isotropic pixel size) using enhanced focused ion beam scanning electron microscopy imaging followed by deep-learning-based automated image segmentation and 3D reconstruction. We also performed a comparative analysis of subcellular structures in liver tissue of lean and obese mice and found substantial alterations, particularly in hepatic endoplasmic reticulum (ER), which undergoes massive structural reorganization characterized by marked disorganization of stacks of ER sheets and predominance of ER tubules. Finally, we demonstrated the functional importance of these structural changes by monitoring the effects of experimental recovery of the subcellular organization on cellular and systemic metabolism. We conclude that the hepatic subcellular organization of\ the ER architecture are highly dynamic, integrated with the metabolic state and critical for adaptive homeostasis and tissue health.

}, issn = {1476-4687}, doi = {10.1038/s41586-022-04488-5}, author = {Parlakg{\"u}l, G{\"u}ne{\c s} and Arruda, Ana Paula and Pang, Song and Cagampan, Erika and Min, Nina and G{\"u}ney, Ekin and Lee, Grace Yankun and Inouye, Karen and Hess, Harald F and Xu, C Shan and Hotam{\i}{\c s}l{\i}gil, G{\"o}khan S} } @article {68079, title = {Rescue of behavioral and electrophysiological phenotypes in a Pitt-Hopkins syndrome mouse model by genetic restoration of expression.}, journal = {eLife}, volume = {11}, year = {2022}, month = {2022 May 10}, abstract = {

Pitt-Hopkins syndrome (PTHS) is a neurodevelopmental disorder caused by monoallelic mutation or deletion in the () gene. Individuals with PTHS typically present in the first year of life with developmental delay and exhibit intellectual disability, lack of speech, and motor incoordination. There are no effective treatments available for PTHS, but the root cause of the disorder, haploinsufficiency, suggests that it could be treated by normalizing gene expression. Here, we performed proof-of-concept viral gene therapy experiments using a conditional mouse model of PTHS and found that postnatally reinstating expression in neurons improved anxiety-like behavior, activity levels, innate behaviors, and memory. Postnatal reinstatement also partially corrected EEG abnormalities, which we characterized here for the first time, and the expression of key TCF4-regulated genes. Our results support a genetic normalization approach as a treatment strategy for PTHS, and possibly other TCF4-linked disorders.

}, keywords = {Animals, Disease Models, Animal, Facies, Hyperventilation, Intellectual Disability, Mice, Phenotype, Transcription Factor 4}, issn = {2050-084X}, doi = {10.7554/eLife.72290}, author = {Kim, Hyojin and Gao, Eric B and Draper, Adam and Berens, Noah C and Vihma, Hanna and Zhang, Xinyuan and Higashi-Howard, Alexandra and Ritola, Kimberly D and Simon, Jeremy M and Kennedy, Andrew J and Philpot, Benjamin D} } @article {65821, title = {Robotic Multi-Probe-Single-Actuator Inchworm Neural Microdrive}, journal = {eLife}, year = {2022}, month = {2022 Nov 10}, abstract = {

Electrophysiology is one of the major experimental techniques used in neuroscience. The favorable spatial and temporal resolution as well as the increasingly larger site counts of brain recording electrodes contribute to the popularity and importance of electrophysiology in neuroscience. Such electrodes are typically mechanically placed in the brain to perform acute or chronic freely moving animal measurements. The micro positioners currently used for such tasks employ a single translator per independent probe being placed into the targeted brain region, leading to significant size and weight restrictions. To overcome this limitation, we have developed a miniature robotic multi-probe neural microdrive that utilizes novel phase-change-material-filled resistive heater micro-grippers. The microscopic dimensions, gentle gripping action, independent electronic actuation control, and high packing density of the grippers allow for micrometer-precision independent positioning of multiple arbitrarily shaped parallel neural electrodes with only a single piezo actuator in an inchworm motor configuration. This multi-probe-single-actuator design allows for significant size and weight reduction, as well as remote control and potential automation of the microdrive. We demonstrate accurate placement of multiple independent recording electrodes into the CA1 region of the rat hippocampus\ in vivo\ in acute and chronic settings. Thus, our robotic neural microdrive technology is applicable towards basic neuroscience and clinical studies, as well as other multi-probe or multi-sensor micro-positioning applications.

}, doi = {10.7554/eLife.71876}, author = {Smith, R.D. and Kolb, Ilya and Tanaka, Shinsuke and Lee, A.K. and Harris, T.D. and Barbic, M.} } @article {67774, title = {RS-FISH: Precise, interactive, fast, and scalable FISH spot detection}, journal = {Nature Methods}, volume = {19}, year = {2022}, month = {2022 Nov 17}, pages = {1563-7}, abstract = {

Fluorescent in-situ hybridization (FISH)-based methods are powerful tools to study molecular processes with subcellular resolution, relying on accurate identification and localization of diffraction-limited spots in microscopy images. We developed the Radial Symmetry-FISH (RS-FISH) software that accurately, robustly, and quickly detects single-molecule spots in two and three dimensions, making it applicable to several key assays, including single-molecule FISH (smFISH), spatial transcriptomics, and spatial genomics. RS-FISH allows interactive parameter tuning and scales to large sets of images as well as tera-byte sized image volumes such as entire brain scans using straight-forward distributed processing on workstations, clusters, and in the cloud.

}, doi = {10.1038/s41592-022-01669-y}, author = {Ella Bahry and Laura Breimann and Marwan Zouinkhi and Leo Epstein and Klim Kolyvanov and Xi Long and Kyle I S Harrington and Timoth{\'e}e Lionnet and Stephan Preibisch} } @article {68278, title = {Selective Serotonin Reuptake Inhibitors Within Cells: Temporal Resolution in Cytoplasm, Endoplasmic Reticulum, and Membrane}, journal = {bioRxiv}, year = {2022}, month = {2022 Aug 12}, abstract = {

Selective serotonin reuptake inhibitors (SSRIs) are the most prescribed treatment for individuals experiencing major depressive disorder (MDD). The therapeutic mechanisms that take place before, during, or after SSRIs bind the serotonin transporter (SERT) are poorly understood, partially because no studies exist of the cellular and subcellular pharmacokinetic properties of SSRIs in living cells. We studied escitalopram and fluoxetine using new intensity- based drug-sensing fluorescent reporters ({\textquotedblleft}iDrugSnFRs{\textquotedblright}) targeted to the plasma membrane (PM), cytoplasm, or endoplasmic reticulum (ER) of cultured neurons and mammalian cell lines. We also employed chemical detection of drug within cells and phospholipid membranes. The drugs attain equilibrium in neuronal cytoplasm and ER, at approximately the same concentration as the externally applied solution, with time constants of a few s (escitalopram) or 200-300 s (fluoxetine). Simultaneously, the drugs accumulate within lipid membranes by >= 18-fold (escitalopram) or 180-fold (fluoxetine), and possibly by much larger factors. Both drugs leave cytoplasm, lumen, and membranes just as quickly during washout. We synthesized membrane-impermeant quaternary amine derivatives of the two SSRIs. The quaternary derivatives are substantially excluded from membrane, cytoplasm, and ER for \> 2.4 h. They inhibit SERT transport-associated currents 6- or 11-fold less potently than the SSRIs (escitalopram or fluoxetine derivative, respectively), providing useful probes for distinguishing compartmentalized SSRI effects. Although our measurements are orders of magnitude faster than the {\textquotedblleft}therapeutic lag{\textquotedblright} of SSRIs, these data suggest that SSRI-SERT interactions within organelles or membranes may play roles during either the therapeutic effects or the {\textquotedblleft}antidepressant discontinuation syndrome{\textquotedblright}.

}, doi = {10.1101/2022.08.09.502705}, url = {https://doi.org/10.1101/2022.08.09.502705}, author = {Aaron L. Nichols and Zack Blumenfeld and Laura Luebbert and Hailey J. Knox and Anand K. Muthusamy and Jonathan S. Marvin and Charlene H. Kim and Stephen N. Grant and David P. Walton and Bruce N. Cohen and Rebekkah Hammar and Loren L. Looger and Per Artursson and Dennis A. Dougherty and Henry A. Lester} } @article {68312, title = {A sensitive and specific genetically encoded potassium ion biosensor for in vivo applications across the tree of life.}, journal = {PLoS Biology}, volume = {20}, year = {2022}, month = {2022 Sep 06}, pages = {e3001772}, abstract = {

Potassium ion (K+) plays a critical role as an essential electrolyte in all biological systems. Genetically encoded fluorescent K+ biosensors are promising tools to further improve our understanding of K+-dependent processes under normal and pathological conditions. Here, we report the crystal structure of a previously reported genetically encoded fluorescent K+ biosensor, GINKO1, in the K+-bound state. Using structure-guided optimization and directed evolution, we have engineered an improved K+ biosensor, designated GINKO2, with higher sensitivity and specificity. We have demonstrated the utility of GINKO2 for in vivo detection and imaging of K+ dynamics in multiple model organisms, including bacteria, plants, and mice.

}, issn = {1545-7885}, doi = {10.1371/journal.pbio.3001772}, author = {Wu, Sheng-Yi and Wen, Yurong and Serre, Nelson B C and Laursen, Cathrine Charlotte Heiede and Dietz, Andrea Grost{\o}l and Taylor, Brian R and Drobizhev, Mikhail and Molina, Rosana S and Abhi Aggarwal and Rancic, Vladimir and Becker, Michael and Ballanyi, Klaus and Podgorski, Kaspar and Hirase, Hajime and Nedergaard, Maiken and Fendrych, Maty{\'a}{\v s} and Lemieux, M Joanne and Eberl, Daniel F and Kay, Alan R and Campbell, Robert E and Shen, Yi} } @article {67810, title = {A serotonergic axon-cilium synapse drives nuclear signaling to maintain chromatin accessibility}, journal = {Cell}, volume = {185}, year = {2022}, month = {2022 Sep 01}, pages = {3390-3407}, abstract = {

Chemical synapses between axons and dendrites mediate much of the brain{\textquoteright}s intercellular communication. Here we describe a new kind of synapse {\textendash} the axo-ciliary synapse - between axons and primary cilia. By employing enhanced focused ion beam {\textendash} scanning electron microscopy on samples with optimally preserved ultrastructure, we discovered synapses between the serotonergic axons arising from the brainstem, and the primary cilia of hippocampal CA1 pyramidal neurons. Functionally, these cilia are enriched in a ciliary-restricted serotonin receptor, 5-hydroxytryptamine receptor 6 (HTR6), whose mutation is associated with learning and memory defects. Using a newly developed cilia-targeted serotonin sensor, we show that optogenetic stimulation of serotonergic axons results in serotonin release onto cilia. Ciliary HTR6 stimulation activates a non-canonical Gαq/11-RhoA pathway. Ablation of this pathway results in nuclear actin and chromatin accessibility changes in CA1 pyramidal neurons. Axo-ciliary synapses serve as a distinct mechanism for neuromodulators to program neuron transcription through privileged access to the nuclear compartment.

}, doi = {10.1016/j.cell.2022.07.026}, author = {Shu-Hsien Sheu and Srigokul Upadhyayula and Vincent Dupuy and Song Pang and Andrew L. Lemire and Deepika Walpita and H. Amalia Pasolli and Fei Deng and Jinxia Wan and Lihua Wang and Justin Houser and Silvia Sanchez-Martinez and Sebastian E. Brauchi and Sambashiva Banala and Melanie Freeman and C. Shan Xu and Tom Kirchhausen and Harald F. Hess and Luke Lavis and Yu-Long Li and S{\'e}verine Chaumont-Dubel and David E. Clapham} } @article {68408, title = {Structure of the OMEGA nickase IsrB in complex with ωRNA and target DNA.}, journal = {Nature}, volume = {610}, year = {2022}, month = {2022 Oct 12}, pages = {575-581}, abstract = {

RNA-guided systems, such as CRISPR-Cas, combine programmable substrate recognition with enzymatic function, a combination that has been used advantageously to develop powerful molecular technologies. Structural studies of these systems have illuminated how the RNA and protein jointly recognize and cleave their substrates, guiding rational engineering for further technology development. Recent work identified a new class of RNA-guided systems, termed OMEGA, which include IscB, the likely ancestor of Cas9, and the nickase IsrB, a homologue of IscB lacking the HNH nuclease domain. IsrB consists of only around 350 amino acids, but its small size is counterbalanced by a relatively large RNA guide (roughly 300-nt ωRNA). Here, we report the cryogenic-electron microscopy structure of Desulfovirgula thermocuniculi IsrB (DtIsrB) in complex with its cognate ωRNA and a target DNA. We find the overall structure of the IsrB protein shares a common scaffold with Cas9. In contrast to Cas9, however, which uses a recognition (REC) lobe to facilitate target selection, IsrB relies on its ωRNA, part of which forms an intricate ternary structure positioned analogously to REC. Structural analyses of IsrB and its ωRNA as well as comparisons to other RNA-guided systems highlight the functional interplay between protein and RNA, advancing our understanding of the biology and evolution of these diverse systems.

}, keywords = {CRISPR-Associated Proteins, CRISPR-Cas Systems, Cryoelectron Microscopy, Deoxyribonuclease I, DNA, RNA, Guide}, issn = {1476-4687}, doi = {10.1038/s41586-022-05324-6}, author = {Hirano, Seiichi and Kappel, Kalli and Altae-Tran, Han and Faure, Guilhem and Wilkinson, Max E and Kannan, Soumya and Demircioglu, F Esra and Yan, Rui and Shiozaki, Momoko and Yu, Zhiheng and Makarova, Kira S and Koonin, Eugene V and Macrae, Rhiannon K and Zhang, Feng} } @article {67908, title = {Structured random receptive fields enable informative sensory encodings}, journal = {bioRxiv}, year = {2022}, month = {2022 Feb 13}, abstract = {

Brains must represent the outside world so that animals survive and thrive. In early sensory systems, neural populations have diverse receptive fields structured to detect important features in inputs, yet significant variability has been ignored in classical models of sensory neurons. We model neuronal receptive fields as random, variable samples from parametrized distributions in two sensory modalities, using data from insect mechanosensors and neurons of mammalian primary visual cortex. We show that these random feature neurons perform a randomized wavelet transform on inputs which removes high frequency noise and boosts the signal. Our result makes a significant theoretical connection between the foundational concepts of receptive fields in neuroscience and random features in artificial neural networks. Further, these random feature neurons enable learning from fewer training samples and with smaller networks in artificial tasks. This structured random model of receptive fields provides a unifying, mathematically tractable framework to understand sensory encodings across both spatial and temporal domains.

}, doi = {10.1101/2021.09.09.459651}, author = {Biraj Pandey and Marius Pachitariu and Bingni W. Brunton and Kameron Decker Harris} } @article {68386, title = {Structured random receptive fields enable informative sensory encodings.}, journal = {PLoS Computational Biology}, volume = {18}, year = {2022}, month = {2022 Oct 10}, pages = {e1010484}, abstract = {

Brains must represent the outside world so that animals survive and thrive. In early sensory systems, neural populations have diverse receptive fields structured to detect important features in inputs, yet significant variability has been ignored in classical models of sensory neurons. We model neuronal receptive fields as random, variable samples from parameterized distributions and demonstrate this model in two sensory modalities using data from insect mechanosensors and mammalian primary visual cortex. Our approach leads to a significant theoretical connection between the foundational concepts of receptive fields and random features, a leading theory for understanding artificial neural networks. The modeled neurons perform a randomized wavelet transform on inputs, which removes high frequency noise and boosts the signal. Further, these random feature neurons enable learning from fewer training samples and with smaller networks in artificial tasks. This structured random model of receptive fields provides a unifying, mathematically tractable framework to understand sensory encodings across both spatial and temporal domains.

}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1010484}, author = {Pandey, Biraj and Pachitariu, Marius and Brunton, Bingni W and Harris, Kameron Decker} } @article {68222, title = {Structured sampling of olfactory input by the fly mushroom body.}, journal = {Current Biology}, volume = {32}, year = {2022}, month = {2022 Aug 08}, pages = {3334-3349.e6}, abstract = {

Associative memory formation and recall in the fruit fly Drosophila melanogaster is subserved by the mushroom body (MB). Upon arrival in the MB, sensory information undergoes a profound transformation from broadly tuned and stereotyped odorant responses in the olfactory projection neuron (PN) layer to narrowly tuned and nonstereotyped responses in the Kenyon cells (KCs). Theory and experiment suggest that this transformation is implemented by random connectivity between KCs and PNs. However, this hypothesis has been challenging to test, given the difficulty of mapping synaptic connections between large numbers of brain-spanning neurons. Here, we used a recent whole-brain electron microscopy volume of the adult fruit fly to map PN-to-KC connectivity at synaptic resolution. The PN-KC connectome revealed unexpected structure, with preponderantly food-responsive PN types converging at above-chance levels on downstream KCs. Axons of the overconvergent PN types tended to arborize near one another in the MB main calyx, making local KC dendrites more likely to receive input from those types. Overconvergent PN types preferentially co-arborize and connect with dendrites of αβ and α{\textquoteright}β{\textquoteright} KC subtypes. Computational simulation of the observed network showed degraded discrimination performance compared with a random network, except when all signal flowed through the overconvergent, primarily food-responsive PN types. Additional theory and experiment will be needed to fully characterize the impact of the observed non-random network structure on associative memory formation and recall.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2022.06.031}, author = {Zheng, Zhihao and Li, Feng and Fisher, Corey and Ali, Iqbal J and Sharifi, Nadiya and Calle-Schuler, Steven and Hsu, Joseph and Masoodpanah, Najla and Kmecova, Lucia and Kazimiers, Tom and Perlman, Eric and Nichols, Matthew and Li, Peter H and Jain, Viren and Bock, Davi D} } @article {68987, title = {SUMOylation of linker histone H1 drives chromatin condensation and restriction of embryonic cell fate identity}, journal = {Molecular Cell}, volume = {82}, year = {2022}, month = {01/2022}, pages = {106-122.e9}, abstract = {

Summary The fidelity of the early embryonic program is underlined by tight regulation of the chromatin. Yet, how the chromatin is organized to prohibit the reversal of the developmental program remains unclear. Specifically, the totipotency-to-pluripotency transition marks one of the most dramatic events to the chromatin, and yet, the nature of histone alterations underlying this process is incompletely characterized. Here, we show that linker histone H1 is post-translationally modulated by SUMO2/3, which facilitates its fixation onto ultra-condensed heterochromatin in embryonic stem cells (ESCs). Upon SUMOylation depletion, the chromatin becomes de-compacted and H1 is evicted, leading to totipotency reactivation. Furthermore, we show that H1 and SUMO2/3 jointly mediate the repression of totipotent elements. Lastly, we demonstrate that preventing SUMOylation on H1 abrogates its ability to repress the totipotency program in ESCs. Collectively, our findings unravel a critical role for SUMOylation of H1 in facilitating chromatin repression and desolation of the totipotent identity.

}, issn = {1097-2765}, doi = {https://doi.org/10.1016/j.molcel.2021.11.011}, url = {https://www.sciencedirect.com/science/article/pii/S1097276521009904}, author = {Daoud Sheban and Tom Shani and Roey Maor and Alejandro Aguilera-Castrejon and Nofar Mor and Bernardo Oldak and Merav D. Shmueli and Avital Eisenberg-Lerner and Jonathan Bayerl and Jakob Hebert and Sergey Viukov and Guoyun Chen and Assaf Kacen and Vladislav Krupalnik and Valeriya Chugaeva and Shadi Tarazi and Alejandra Rodr{\'\i}guez-delaRosa and Mirie Zerbib and Adi Ulman and Solaiman Masarwi and Meital Kupervaser and Yishai Levin and Efrat Shema and Yael David and Noa Novershtern and Jacob H. Hanna and Yifat Merbl} } @article {68167, title = {Super-Resolution Imaging of Fas/CD95 Reorganization Induced by Membrane-Bound Fas Ligand Reveals Nanoscale Clustering Upstream of FADD Recruitment.}, journal = {Cells}, volume = {11}, year = {2022}, month = {2022 Jun 12}, abstract = {

Signaling through the TNF-family receptor Fas/CD95 can trigger apoptosis or non-apoptotic cellular responses and is essential for protection from autoimmunity. Receptor clustering has been observed following interaction with Fas ligand (FasL), but the stoichiometry of Fas, particularly when triggered by membrane-bound FasL, the only form of FasL competent at inducing programmed cell death, is not known. Here we used super-resolution microscopy to study the behavior of single molecules of Fas/CD95 on the plasma membrane after interaction of Fas with FasL on planar lipid bilayers. We observed rapid formation of Fas protein superclusters containing more than 20 receptors after interactions with membrane-bound FasL. Fluorescence correlation imaging demonstrated recruitment of FADD dependent on an intact Fas death domain, with lipid raft association playing a secondary role. Flow-cytometric FRET analysis confirmed these results, and also showed that some Fas clustering can occur in the absence of FADD and caspase-8. Point mutations in the Fas death domain associated with autoimmune lymphoproliferative syndrome (ALPS) completely disrupted Fas reorganization and FADD recruitment, confirming structure-based predictions of the critical role that these residues play in Fas-Fas and Fas-FADD interactions. Finally, we showed that induction of apoptosis correlated with the ability to form superclusters and recruit FADD.

}, keywords = {Apoptosis, Cluster Analysis, Fas Ligand Protein, fas Receptor, Fas-Associated Death Domain Protein, Receptors, Tumor Necrosis Factor}, issn = {2073-4409}, doi = {10.3390/cells11121908}, author = {Frazzette, Nicholas and Cruz, Anthony C and Wu, Xufeng and Hammer, John A and Lippincott-Schwartz, Jennifer and Siegel, Richard M and Sengupta, Prabuddha} } @article {68145, title = {Targeting LIPA independent of its lipase activity is a therapeutic strategy in solid tumors via induction of endoplasmic reticulum stress.}, journal = {Nature Cancer}, volume = {3}, year = {2022}, month = {2022 Jun 02}, pages = {866-884}, abstract = {

Triple-negative breast cancer (TNBC) has a poor clinical outcome, due to a lack of actionable therapeutic targets. Herein we define lysosomal acid lipase A (LIPA) as a viable molecular target in TNBC and identify a stereospecific small molecule (ERX-41) that binds LIPA. ERX-41 induces endoplasmic reticulum (ER) stress resulting in cell death, and this effect is on target as evidenced by specific LIPA mutations providing resistance. Importantly, we demonstrate that ERX-41 activity is independent of LIPA lipase function but dependent on its ER localization. Mechanistically, ERX-41 binding of LIPA decreases expression of multiple ER-resident proteins involved in protein folding. This targeted vulnerability has a large therapeutic window, with no adverse effects either on normal mammary epithelial cells or in mice. Our study implicates a targeted strategy for solid tumors, including breast, brain, pancreatic and ovarian, whereby small, orally bioavailable molecules targeting LIPA block protein folding, induce ER stress and result in tumor cell death.

}, issn = {2662-1347}, doi = {10.1038/s43018-022-00389-8}, author = {Liu, Xihui and Viswanadhapalli, Suryavathi and Kumar, Shourya and Lee, Tae-Kyung and Moore, Andrew and Ma, Shihong and Chen, Liping and Hsieh, Michael and Li, Mengxing and Sareddy, Gangadhara R and Parra, Karla and Blatt, Eliot B and Reese, Tanner C and Zhao, Yuting and Chang, Annabel and Yan, Hui and Xu, Zhenming and Pratap, Uday P and Liu, Zexuan and Roggero, Carlos M and Tan, Zhenqiu and Weintraub, Susan T and Peng, Yan and Tekmal, Rajeshwar R and Arteaga, Carlos L and Lippincott-Schwartz, Jennifer and Vadlamudi, Ratna K and Ahn, Jung-Mo and Raj, Ganesh V} } @article {67859, title = {Toroidal topology of population activity in grid cells.}, journal = {Nature}, volume = {602}, year = {2022}, month = {2022 Jan 12}, pages = {123-128}, abstract = {

The medial entorhinal cortex is part of a neural system for mapping the position of an individual within a physical environment. Grid cells, a key component of this system, fire in a characteristic hexagonal pattern of locations, and are organized in modules that collectively form a population code for the animal{\textquoteright}s allocentric position. The invariance of the correlation structure of this population code across environments and behavioural states, independent of specific sensory inputs, has pointed to intrinsic, recurrently connected continuous attractor networks (CANs) as a possible substrate of the grid pattern. However, whether grid cell networks show continuous attractor dynamics, and how they interface with inputs from the environment, has remained unclear owing to the small samples of cells obtained so far. Here, using simultaneous recordings from many hundreds of grid cells and subsequent topological data analysis, we show that the joint activity of grid cells from an individual module resides on a toroidal manifold, as expected in a two-dimensional CAN. Positions on the torus correspond to positions of the moving animal in the environment. Individual cells are preferentially active at singular positions on the torus. Their positions are maintained between environments and from wakefulness to sleep, as predicted by CAN models for grid cells but not by alternative feedforward models. This demonstration of network dynamics on a toroidal manifold provides a population-level visualization of CAN dynamics in grid cells.

}, issn = {1476-4687}, doi = {10.1038/s41586-021-04268-7}, author = {Gardner, Richard J and Hermansen, Erik and Pachitariu, Marius and Burak, Yoram and Baas, Nils A and Dunn, Benjamin A and Moser, May-Britt and Moser, Edvard I} } @article {68419, title = {Transcription factor Acj6 controls dendrite targeting via a combinatorial cell-surface code.}, journal = {Neuron}, volume = {110}, year = {2022}, month = {07/2022}, pages = {2299-2314.e8}, abstract = {

Transcription factors specify the fate and connectivity of developing neurons. We investigate how a lineage-specific transcription factor, Acj6, controls the precise dendrite targeting of Drosophila olfactory projection neurons (PNs) by regulating the expression of cell-surface proteins. Quantitative cell-surface proteomic profiling of wild-type and acj6 mutant PNs in intact developing brains, and a proteome-informed genetic screen identified PN surface proteins that execute Acj6-regulated wiring decisions. These include canonical cell adhesion molecules and proteins previously not associated with wiring, such as Piezo, whose mechanosensitive ion channel activity is dispensable for its function in PN dendrite targeting. Comprehensive genetic analyses revealed that Acj6 employs unique sets of cell-surface proteins in different PN types for dendrite targeting. Combined expression of Acj6 wiring executors rescued acj6 mutant phenotypes with higher efficacy and breadth than expression of individual executors. Thus, Acj6 controls wiring specificity of different neuron types by specifying distinct combinatorial expression of cell-surface executors.

}, keywords = {Animals, Dendrites, Drosophila, Drosophila Proteins, Ion Channels, Membrane Proteins, Nerve Tissue Proteins, Olfactory Pathways, Olfactory Receptor Neurons, POU Domain Factors, Proteomics, Transcription Factors}, issn = {1097-4199}, doi = {10.1016/j.neuron.2022.04.026}, author = {Xie, Qijing and Li, Jiefu and Li, Hongjie and Udeshi, Namrata D and Svinkina, Tanya and Orlin, Daniel and Kohani, Sayeh and Guajardo, Ricardo and Mani, D R and Xu, Chuanyun and Li, Tongchao and Han, Shuo and Wei, Wei and Shuster, S Andrew and Luginbuhl, David J and Quake, Stephen R and Murthy, Swetha E and Ting, Alice Y and Carr, Steven A and Luo, Liqun} } @article {67988, title = {Transverse endoplasmic reticulum expansion in hereditary spastic paraplegia corticospinal axons.}, journal = {Human Molecular Genetics}, year = {2022}, month = {2022 Mar 26}, abstract = {

Hereditary spastic paraplegias (HSPs) comprise a large group of inherited neurologic disorders affecting the longest corticospinal axons (SPG1-86 plus others), with shared manifestations of lower extremity spasticity and gait impairment. Common autosomal dominant HSPs are caused by mutations in genes encoding the microtubule-severing ATPase spastin (SPAST; SPG4), the membrane-bound GTPase atlastin-1 (ATL1; SPG3A), and the reticulon-like, microtubule-binding protein REEP1 (REEP1; SPG31). These proteins bind one another and function in shaping the tubular endoplasmic reticulum (ER) network. Typically, mouse models of HSPs have mild, later-onset phenotypes, possibly reflecting far shorter lengths of their corticospinal axons relative to humans. Here, we have generated a robust, double mutant mouse model of HSP in which atlastin-1 is genetically modified with a K80A knock-in (KI) missense change that abolishes its GTPase activity, while its binding partner Reep1 is knocked out. Atl1KI/KI/Reep1-/- mice exhibit early-onset and rapidly progressive declines in several motor function tests. Also, ER in mutant corticospinal axons dramatically expands transversely and periodically in a mutation dosage-dependent manner to create a ladder-like appearance, based on reconstructions of focused ion beam-scanning electron microscopy datasets using machine learning-based auto-segmentation. In lockstep with changes in ER morphology, axonal mitochondria are fragmented and proportions of hypophosphorylated neurofilament H and M subunits are dramatically increased in Atl1KI/KI/Reep1-/- spinal cord. Co-occurrence of these findings links ER morphology changes to alterations in mitochondrial morphology and cytoskeletal organization. Atl1KI/KI/Reep1-/- mice represent an early-onset rodent HSP model with robust behavioral and cellular readouts for testing novel therapies.

}, issn = {1460-2083}, doi = {10.1093/hmg/ddac072}, author = {Zhu, Peng-Peng and Hung, Hui-Fang and Batchenkova, Natalia and Nixon-Abell, Jonathon and Henderson, James and Zheng, Pengli and Renvois{\'e}, Benoit and Pang, Song and Xu, C Shan and Saalfeld, Stephan and Funke, Jan and Xie, Yuxiang and Svara, Fabian and Hess, Harald F and Blackstone, Craig} } @article {68298, title = {Transverse endoplasmic reticulum expansion in hereditary spastic paraplegia corticospinal axons.}, journal = {Human Molecular Genetics}, volume = {31}, year = {2022}, month = {2022 Aug 23}, pages = {2779-2795}, abstract = {

Hereditary spastic paraplegias (HSPs) comprise a large group of inherited neurologic disorders affecting the longest corticospinal axons (SPG1-86 plus others), with shared manifestations of lower extremity spasticity and gait impairment. Common autosomal dominant HSPs are caused by mutations in genes encoding the microtubule-severing ATPase spastin (SPAST; SPG4), the membrane-bound GTPase atlastin-1 (ATL1; SPG3A) and the reticulon-like, microtubule-binding protein REEP1 (REEP1; SPG31). These proteins bind one another and function in shaping the tubular endoplasmic reticulum (ER) network. Typically, mouse models of HSPs have mild, later onset phenotypes, possibly reflecting far shorter lengths of their corticospinal axons relative to humans. Here, we have generated a robust, double mutant mouse model of HSP in which atlastin-1 is genetically modified with a K80A knock-in (KI) missense change that abolishes its GTPase activity, whereas its binding partner Reep1 is knocked out. Atl1KI/KI/Reep1-/- mice exhibit early onset and rapidly progressive declines in several motor function tests. Also, ER in mutant corticospinal axons dramatically expands transversely and periodically in a mutation dosage-dependent manner to create a ladder-like appearance, on the basis of reconstructions of focused ion beam-scanning electron microscopy datasets using machine learning-based auto-segmentation. In lockstep with changes in ER morphology, axonal mitochondria are fragmented and proportions of hypophosphorylated neurofilament H and M subunits are dramatically increased in Atl1KI/KI/Reep1-/- spinal cord. Co-occurrence of these findings links ER morphology changes to alterations in mitochondrial morphology and cytoskeletal organization. Atl1KI/KI/Reep1-/- mice represent an early onset rodent HSP model with robust behavioral and cellular readouts for testing novel therapies.

}, keywords = {Animals, Axons, Disease Models, Animal, Endoplasmic Reticulum, GTP Phosphohydrolases, Humans, Membrane Proteins, Membrane Transport Proteins, Mice, Mice, Knockout, Mutation, Spastic Paraplegia, Hereditary, Spastin}, issn = {1460-2083}, doi = {10.1093/hmg/ddac072}, author = {Zhu, Peng-Peng and Hung, Hui-Fang and Batchenkova, Natalia and Nixon-Abell, Jonathon and Henderson, James and Zheng, Pengli and Renvois{\'e}, Benoit and Pang, Song and Xu, C Shan and Saalfeld, Stephan and Funke, Jan and Xie, Yuxiang and Svara, Fabian and Hess, Harald F and Blackstone, Craig} } @article {68276, title = {A vast space of compact strategies for highly efficient decisions}, journal = {Sci. Adv.}, volume = {10}, year = {2022}, month = {2024 Jun 21}, abstract = {

Inference-based decision-making, which underlies a broad range of behavioral tasks, is typically studied using a small number of handcrafted models. We instead enumerate a complete ensemble of strategies that could be used to effectively, but not necessarily optimally, solve a dynamic foraging task. Each strategy is expressed as a behavioral "program" that uses a limited number of internal states to specify actions conditioned on past observations. We show that the ensemble of strategies is enormous-comprising a quarter million programs with up to five internal states-but can nevertheless be understood in terms of algorithmic "mutations" that alter the structure of individual programs. We devise embedding algorithms that reveal how mutations away from a Bayesian-like strategy can diversify behavior while preserving performance, and we construct a compositional description to link low-dimensional changes in algorithmic structure with high-dimensional changes in behavior. Together, this work provides an alternative approach for understanding individual variability in behavior across animals and tasks.

}, doi = {10.1101/2022.08.10.503471}, url = {https://doi.org/10.1101/2022.08.10.503471}, author = {Tzuhsuan Ma and Ann M Hermundstad} } @article {68812, title = {A viral toolbox for conditional and transneuronal gene expression in zebrafish}, journal = {eLife}, volume = {11}, year = {2022}, month = {07/2022}, pages = {e77153}, abstract = {

The zebrafish is an important model in systems neuroscience but viral tools to dissect the structure and function of neuronal circuitry are not established. We developed methods for efficient gene transfer and retrograde tracing in adult and larval zebrafish by herpes simplex viruses (HSV1). HSV1 was combined with the Gal4/UAS system to target cell types with high spatial, temporal, and molecular specificity. We also established methods for efficient transneuronal tracing by modified rabies viruses in zebrafish. We demonstrate that HSV1 and rabies viruses can be used to visualize and manipulate genetically or anatomically identified neurons within and across different brain areas of adult and larval zebrafish. An expandable library of viruses is provided to express fluorescent proteins, calcium indicators, optogenetic probes, toxins and other molecular tools. This toolbox creates new opportunities to interrogate neuronal circuits in zebrafish through combinations of genetic and viral approaches.

}, keywords = {Gene Transfer, Imaging, neuronal circuit, viral vector}, issn = {2050-084X}, doi = {10.7554/eLife.77153}, url = {https://doi.org/10.7554/eLife.77153}, author = {Satou, Chie and Neve, Rachael L and Oyibo, Hassana K and Zmarz, Pawel and Huang, Kuo-Hua and Arn Bouldoires, Estelle and Mori, Takuma and Higashijima, Shin-Ichi and Keller, Georg B and Friedrich, Rainer W}, editor = {Bagnall, Martha W and Stainier, Didier YR and Jin, Lei} } @article {67890, title = {Voltage imaging identifies spinal circuits that modulate locomotor adaptation in zebrafish.}, journal = {Neuron}, year = {2022}, month = {2022 Jan 24}, abstract = {

Motor systems must continuously adapt their output to maintain a desired trajectory. While the spinal circuits underlying rhythmic locomotion are well described, little is known about how the network modulates its output strength. A major challenge has been the difficulty of recording from spinal neurons during behavior. Here, we use voltage imaging to map the membrane potential of large populations of glutamatergic neurons throughout the spinal cord of the larval zebrafish during fictive swimming in a virtual environment. We characterized a previously undescribed subpopulation of tonic-spiking ventral V3 neurons whose spike rate correlated with swimming strength and bout length. Optogenetic activation of V3 neurons led to stronger swimming and longer bouts but did not affect tail beat frequency. Genetic ablation of V3 neurons led to reduced locomotor adaptation. The power of voltage imaging allowed us to identify V3 neurons as a critical driver of locomotor adaptation in zebrafish.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2022.01.001}, author = {B{\"o}hm, Urs L and Kimura, Yukiko and Kawashima, Takashi and Ahrens, Misha B and Higashijima, Shin-Ichi and Engert, Florian and Cohen, Adam E} } @article {67991, title = {Voltage imaging identifies spinal circuits that modulate locomotor adaptation in zebrafish.}, journal = {Neuron}, volume = {110}, year = {2022}, month = {2022 Apr 06}, pages = {1211-1222.e4}, abstract = {

Motor systems must continuously adapt their output to maintain a desired trajectory. While the spinal circuits underlying rhythmic locomotion are well described, little is known about how the network modulates its output strength. A major challenge has been the difficulty of recording from spinal neurons during behavior. Here, we use voltage imaging to map the membrane potential of large populations of glutamatergic neurons throughout the spinal cord of the larval zebrafish during fictive swimming in a virtual environment. We characterized a previously undescribed subpopulation of tonic-spiking ventral V3 neurons whose spike rate correlated with swimming strength and bout length. Optogenetic activation of V3 neurons led to stronger swimming and longer bouts but did not affect tail beat frequency. Genetic ablation of V3 neurons led to reduced locomotor adaptation. The power of voltage imaging allowed us to identify V3 neurons as a critical driver of locomotor adaptation in zebrafish.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2022.01.001}, author = {B{\"o}hm, Urs L and Kimura, Yukiko and Kawashima, Takashi and Ahrens, Misha B and Higashijima, Shin-Ichi and Engert, Florian and Cohen, Adam E} } @article {67987, title = {When light meets biology - how the specimen affects quantitative microscopy.}, journal = {Journal of Cell Science}, volume = {135}, year = {2022}, month = {2022 Mar 15}, abstract = {

Fluorescence microscopy images should not be treated as perfect representations of biology. Many factors within the biospecimen itself can drastically affect quantitative microscopy data. Whereas some sample-specific considerations, such as photobleaching and autofluorescence, are more commonly discussed, a holistic discussion of sample-related issues (which includes less-routine topics such as quenching, scattering and biological anisotropy) is required to appropriately guide life scientists through the subtleties inherent to bioimaging. Here, we consider how the interplay between light and a sample can cause common experimental pitfalls and unanticipated errors when drawing biological conclusions. Although some of these discrepancies can be minimized or controlled for, others require more pragmatic considerations when interpreting image data. Ultimately, the power lies in the hands of the experimenter. The goal of this Review is therefore to survey how biological samples can skew quantification and interpretation of microscopy data. Furthermore, we offer a perspective on how to manage many of these potential pitfalls.

}, issn = {1477-9137}, doi = {10.1242/jcs.259656}, author = {Reiche, Michael A and Aaron, Jesse S and Boehm, Ulrike and DeSantis, Michael C and Hobson, Chad M and Khuon, Satya and Lee, Rachel M and Chew, Teng-Leong} } @article {65905, title = {3D FIB-SEM reconstruction of microtubule-organelle interaction in whole primary mouse β cells.}, journal = {Journal of Cell Biology}, volume = {220}, year = {2021}, month = {2021 Feb 01}, abstract = {

Microtubules play a major role in intracellular trafficking of vesicles in endocrine cells. Detailed knowledge of microtubule organization and their relation to other cell constituents is crucial for understanding cell function. However, their role in insulin transport and secretion is under debate. Here, we use FIB-SEM to image islet β cells in their entirety with unprecedented resolution. We reconstruct mitochondria, Golgi apparati, centrioles, insulin secretory granules, and microtubules of seven β cells, and generate a comprehensive spatial map of microtubule-organelle interactions. We find that microtubules form nonradial networks that are predominantly not connected to either centrioles or endomembranes. Microtubule number and length, but not microtubule polymer density, vary with glucose stimulation. Furthermore, insulin secretory granules are enriched near the plasma membrane, where they associate with microtubules. In summary, we provide the first 3D reconstructions of complete microtubule networks in primary mammalian cells together with evidence regarding their importance for insulin secretory granule positioning and thus their supportive role in insulin secretion.

}, issn = {1540-8140}, doi = {10.1083/jcb.202010039}, author = {M{\"u}ller, Andreas and Schmidt, Deborah and Xu, C Shan and Pang, Song and D{\textquoteright}Costa, Joyson Verner and Kretschmar, Susanne and M{\"u}nster, Carla and Kurth, Thomas and Jug, Florian and Weigert, Martin and Hess, Harald F and Solimena, Michele} } @article {67177, title = {Actin cables and comet tails organize mitochondrial networks in mitosis.}, journal = {Nature}, volume = {591}, year = {2021}, month = {2021 Mar 03}, pages = {659-664}, abstract = {

Symmetric cell division requires the even partitioning of genetic information and cytoplasmic contents between daughter cells. Whereas the mechanisms coordinating the segregation of the genome are well known, the processes that ensure organelle segregation between daughter cells remain less well understood. Here we identify multiple actin assemblies with distinct but complementary roles in mitochondrial organization and inheritance in mitosis. First, we find a dense meshwork of subcortical actin cables assembled throughout the mitotic cytoplasm. This network scaffolds the endoplasmic reticulum and organizes three-dimensional mitochondrial positioning to ensure the equal segregation of mitochondrial mass at cytokinesis. Second, we identify a dynamic wave of actin filaments reversibly assembling on the surface of mitochondria during mitosis. Mitochondria sampled by this wave are enveloped within actin clouds that can spontaneously break symmetry to form elongated comet tails. Mitochondrial comet tails promote randomly directed bursts of movement that shuffle mitochondrial position within the mother cell to randomize inheritance of healthy and damaged mitochondria between daughter cells. Thus, parallel mechanisms mediated by the actin cytoskeleton ensure both equal and random inheritance of mitochondria in symmetrically dividing cells.

}, issn = {1476-4687}, doi = {10.1038/s41586-021-03309-5}, author = {Moore, Andrew S and Coscia, Stephen M and Simpson, Cory L and Ortega, Fabian E and Wait, Eric C and Heddleston, John M and Nirschl, Jeffrey J and Obara, Christopher J and Guedes-Dias, Pedro and Boecker, C Alexander and Chew, Teng-Leong and Theriot, Julie A and Lippincott-Schwartz, Jennifer and Holzbaur, Erika L F} } @article {67298, title = {Adhesion-mediated mechanosignaling forces mitohormesis.}, journal = {Cell Metabolism}, volume = {33}, year = {2021}, month = {2021 July 6}, pages = {1322}, abstract = {

Mitochondria control eukaryotic cell fate by producing the energy needed to support life and the signals required to execute programed cell death. The biochemical milieu is known to affect mitochondrial function and contribute to the dysfunctional mitochondrial phenotypes implicated in cancer and the morbidities of aging. However, the physical characteristics of the extracellular matrix are also altered in cancerous and aging tissues. Here, we demonstrate that cells sense the physical properties of the extracellular matrix and activate a mitochondrial stress response that adaptively tunes mitochondrial function via solute carrier family 9 member A1-dependent ion exchange and heat shock factor 1-dependent transcription. Overall, our data indicate that adhesion-mediated mechanosignaling may play an unappreciated role in the altered mitochondrial functions observed in aging and cancer.

}, issn = {1932-7420}, doi = {10.1016/j.cmet.2021.04.017}, author = {Tharp, Kevin M and Higuchi-Sanabria, Ryo and Timblin, Greg A and Ford, Breanna and Garzon-Coral, Carlos and Schneider, Catherine and Muncie, Jonathon M and Stashko, Connor and Daniele, Joseph R and Moore, Andrew S and Frankino, Phillip A and Homentcovschi, Stefan and Manoli, Sagar S and Shao, Hao and Richards, Alicia L and Chen, Kuei-Ho and Hoeve, Johanna Ten and Ku, Gregory M and Hellerstein, Marc and Nomura, Daniel K and Saijo, Karou and Gestwicki, Jason and Dunn, Alexander R and Krogan, Nevan J and Swaney, Danielle L and Dillin, Andrew and Weaver, Valerie M} } @article {67314, title = {Alpha-1 adrenergic receptor antagonists to prevent hyperinflammation and death from lower respiratory tract infection.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Jun 11}, abstract = {

In severe viral pneumonia, including Coronavirus disease 2019 (COVID-19), the viral replication phase is often followed by hyperinflammation, which can lead to acute respiratory distress syndrome, multi-organ failure, and death. We previously demonstrated that alpha-1 adrenergic receptor (⍺-AR) antagonists can prevent hyperinflammation and death in mice. Here, we conducted retrospective analyses in two cohorts of patients with acute respiratory distress (ARD, n = 18,547) and three cohorts with pneumonia (n = 400,907). Federated across two ARD cohorts, we find that patients exposed to ⍺-AR antagonists, as compared to unexposed patients, had a 34\% relative risk reduction for mechanical ventilation and death (OR = 0.70, p = 0.021). We replicated these methods on three pneumonia cohorts, all with similar effects on both outcomes. All results were robust to sensitivity analyses. These results highlight the urgent need for prospective trials testing whether prophylactic use of ⍺-AR antagonists ameliorates lower respiratory tract infection-associated hyperinflammation and death, as observed in COVID-19.

}, issn = {2050-084X}, doi = {10.7554/eLife.61700}, author = {Koenecke, Allison and Powell, Michael and Xiong, Ruoxuan and Shen, Zhu and Fischer, Nicole and Huq, Sakibul and Khalafallah, Adham M and Trevisan, Marco and Sparen, P{\"a}r and Carrero, Juan J and Nishimura, Akihiko and Caffo, Brian and Stuart, Elizabeth A and Bai, Renyuan and Staedtke, Verena and Thomas, David L and Papadopoulos, Nickolas and Kinzler, Ken W and Vogelstein, Bert and Zhou, Shibin and Bettegowda, Chetan and Konig, Maximilian F and Mensh, Brett D and Vogelstein, Joshua T and Athey, Susan} } @article {65832, title = {Automatic Detection of Synaptic Partners in a Whole-Brain Drosophila EM Dataset}, journal = {Nature Methods}, volume = {18}, year = {2021}, month = {2021 Jul 1}, pages = {771-4}, abstract = {

The study of neural circuits requires the reconstruction of neurons and the identification of synaptic connections between them. To scale the reconstruction to the size of whole-brain datasets, semi-automatic methods are needed to solve those tasks. Here, we present an automatic method for synaptic partner identification in insect brains, which uses convolutional neural networks to identify post-synaptic sites and their pre-synaptic partners. The networks can be trained from human generated point annotations alone and requires only simple post-processing to obtain final predictions. We used our method to extract 244 million putative synaptic partners in the fifty-teravoxel full adult fly brain (FAFB) electron microscopy (EM) dataset and evaluated its accuracy on 146,643 synapses from 702 neurons with a total cable length of 312 mm in four different brain regions. The predicted synaptic connections can be used together with a neuron segmentation to infer a connectivity graph with high accuracy: 96\% of edges between connected neurons are correctly classified as weakly connected (less than five synapses) and strongly connected (at least five synapses). Our synaptic partner predictions for the FAFB dataset are publicly available, together with a query library allowing automatic retrieval of up- and downstream neurons.

}, doi = {10.1038/s41592-021-01183-7}, author = {Buhmann, Julia and Sheridan, Arlo and Gerhard, Stephan and Krause, Renate and Nguyen, Tri and Heinrich, Larissa and Schlegel, Philipp and Lee, Wei-Chung Allen and Wilson, Rachel and Saalfeld, Stephan and Jefferis, Gregory and Bock, Davi and Turaga, Srinivas and Cook, Matthew and Funke, Jan} } @article {67752, title = {Biosensors based on peptide exposure show single molecule conformations in live cells.}, journal = {Cell}, volume = {184}, year = {2021}, month = {2021 Oct 28}, pages = {5670-5685}, abstract = {

We describe an approach to study the conformation of individual proteins during single particle tracking (SPT) in living cells. "Binder/tag" is based on incorporation of a 7-mer peptide (the tag) into a protein where its solvent exposure is controlled by protein conformation. Only upon exposure can the peptide specifically interact with a reporter protein (the binder). Thus, simple fluorescence localization reflects protein conformation. Through direct excitation of bright dyes, the trajectory and conformation of individual proteins can be followed. Simple protein engineering provides highly specific biosensors suitable for SPT and FRET. We describe tagSrc, tagFyn, tagSyk, tagFAK, and an orthogonal binder/tag pair. SPT showed slowly diffusing islands of activated Src within Src clusters and dynamics of activation in adhesions. Quantitative analysis and stochastic modeling revealed in\ vivo Src kinetics. The simplicity of binder/tag can provide access to diverse proteins.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2021.09.026}, author = {Liu, Bei and Stone, Orrin J and Pablo, Michael and Herron, J Cody and Nogueira, Ana T and Dagliyan, Onur and Grimm, Jonathan B and Lavis, Luke D and Elston, Timothy C and Hahn, Klaus M} } @article {67338, title = {A cerebellar-thalamocortical pathway drives behavioral context-dependent movement initiation.}, journal = {Neuron}, volume = {109}, year = {2021}, month = {2021 Jun 15}, pages = {2326-2338}, abstract = {

Executing learned motor behaviors often requires the transformation of sensory cues into patterns of motor commands that generate appropriately timed actions. The cerebellum and thalamus are two key areas involved in shaping cortical output and movement, but the contribution of a cerebellar-thalamocortical pathway to voluntary movement initiation remains poorly understood. Here, we investigated how an auditory "go cue" transforms thalamocortical activity patterns and how these changes relate to movement initiation. Population responses in dentate/interpositus-recipient regions of motor thalamus reflect a time-locked increase in activity immediately prior to movement initiation that is temporally uncoupled from the go cue, indicative of a fixed-latency feedforward motor timing signal. Blocking cerebellar or motor thalamic output suppresses movement initiation, while stimulation triggers movements in a behavioral context-dependent manner. Our findings show how cerebellar output, via the thalamus, shapes cortical activity patterns necessary for learned context-dependent movement initiation.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2021.05.016}, author = {Dacre, Joshua and Colligan, Matt and Clarke, Thomas and Ammer, Julian J and Schiemann, Julia and Chamosa-Pino, Victor and Claudi, Federico and Harston, J Alex and Eleftheriou, Constantinos and Pakan, Janelle M P and Huang, Cheng-Chiu and Hantman, Adam W and Rochefort, Nathalie L and Duguid, Ian} } @article {67762, title = {Coding sequence-independent homology search identifies highly divergent homopteran putative effector gene family}, journal = {bioRxiv}, year = {2021}, month = {2021 Sep 25}, abstract = {

Many genomes contain rapidly evolving and highly divergent genes whose homology to genes of known function often cannot be determined from sequence similarity alone. However, coding sequence-independent features of genes, such as intron-exon boundaries, often evolve more slowly than coding sequences and can provide complementary evidence for homology. We found that a linear logistic regression classifier using only structural features of rapidly evolving\ bicycle\ aphid effector genes identified many putative\ bicycle\ homologs in aphids, phylloxerids, and scale insects, whereas sequence similarity search methods yielded few homologs in most aphids and no homologs in phylloxerids and scale insects. Subsequent examination of sequence features and intron locations supported homology assignments. Differential expression studies of newly-identified\ bicycle\ homologs, together with prior proteomic studies, support the hypothesis that BICYCLE proteins act as plant effector proteins in many aphid species and perhaps also in phylloxerids and scale insects.

}, doi = {https://doi.org/10.1101/2021.09.24.461719}, author = {Stern, David and Han, Claire} } @article {65810, title = {Comparative Connectomics Reveals How Partner Identity, Location, and Activity Specify Synaptic Connectivity in Drosophila.}, journal = {Neuron}, volume = {109}, year = {2021}, month = {2021 Jan 06}, pages = {105-22}, abstract = {

The mechanisms by which synaptic partners recognize each other and establish appropriate numbers of connections during embryonic development to form functional neural circuits are poorly understood. We combined electron microscopy reconstruction, functional imaging of neural activity, and behavioral experiments to elucidate the roles of (1) partner identity, (2) location, and (3) activity in circuit assembly in the embryonic nerve cord of Drosophila. We found that postsynaptic partners are able to find and connect to their presynaptic partners even when these have been shifted to ectopic locations or silenced. However, orderly positioning of axon terminals by positional cues and synaptic activity is required for appropriate numbers of connections between specific partners, for appropriate balance between excitatory and inhibitory connections, and for appropriate functional connectivity and behavior. Our study reveals with unprecedented resolution the fine connectivity effects of multiple factors that work together to control the assembly of neural circuits.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2020.10.004}, author = {Valdes-Aleman, Javier and Fetter, Richard D and Sales, Emily C and Heckman, Emily L and Venkatasubramanian, Lalanti and Doe, Chris Q and Landgraf, Matthias and Cardona, Albert and Zlatic, Marta} } @article {67771, title = {A connectome of the central complex reveals network motifs suitable for flexible navigation and context-dependent action selection.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Oct 26}, abstract = {

Flexible behaviors over long timescales are thought to engage recurrent neural networks in deep brain regions, which are experimentally challenging to study. In insects, recurrent circuit dynamics in a brain region called the central complex (CX) enable directed locomotion, sleep, and context- and experience-dependent spatial navigation. We describe the first complete electron-microscopy-based connectome of the CX, including all its neurons and circuits at synaptic resolution. We identified new CX neuron types, novel sensory and motor pathways, and network motifs that likely enable the CX to extract the fly{\textquoteright}s head-direction, maintain it with attractor dynamics, and combine it with other sensorimotor information to perform vector-based navigational computations. We also identified numerous pathways that may facilitate the selection of CX-driven behavioral patterns by context and internal state. The CX connectome provides a comprehensive blueprint necessary for a detailed understanding of network dynamics underlying sleep, flexible navigation, and state-dependent action selection.

}, issn = {2050-084X}, doi = {10.7554/eLife.66039}, author = {Hulse, Brad K and Haberkern, Hannah and Franconville, Romain and Turner-Evans, Daniel B and Takemura, Shin-ya and Wolff, Tanya and Noorman, Marcella and Dreher, Marisa and Dan, Chuntao and Parekh, Ruchi and Hermundstad, Ann M and Rubin, Gerald M and Jayaraman, Vivek} } @article {67803, title = {De novo endocytic clathrin coats develop curvature at early stages of their formation.}, journal = {Development Cell}, volume = {56}, year = {2021}, month = {2021 Nov 22}, pages = {3146-3159.e5}, abstract = {

Sculpting a flat patch of membrane into an endocytic vesicle requires curvature generation on the cell surface, which is the primary function of the endocytosis machinery. Using super-resolved live cell fluorescence imaging, we demonstrate that curvature generation by individual clathrin-coated pits can be detected in real time within cultured cells and tissues of developing organisms. Our analyses demonstrate that the footprint of clathrin coats increases monotonically during the formation of pits at different levels of plasma membrane tension. These findings are only compatible with models that predict curvature generation at the early stages of endocytic clathrin pit formation. We also found that CALM adaptors associated with clathrin plaques form clusters, whereas AP2 distribution is more homogenous. Considering the curvature sensing and driving roles of CALM, we propose that CALM clusters may increase the strain on clathrin lattices locally, eventually giving rise to rupture and subsequent pit completion at the edges of plaques.

}, issn = {1878-1551}, doi = {10.1016/j.devcel.2021.10.019}, author = {Willy, Nathan M and Ferguson, Joshua P and Akatay, Ata and Huber, Scott and Djakbarova, Umidahan and Silahli, Salih and Cakez, Cemal and Hasan, Farah and Chang, Henry C and Travesset, Alex and Li, Siyu and Zandi, Roya and Li, Dong and Betzig, Eric and Cocucci, Emanuele and Kural, Comert} } @article {67657, title = {Disrupting cortico-cerebellar communication impairs dexterity.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Jul 29}, abstract = {

To control reaching, the nervous system must generate large changes in muscle activation to drive the limb toward the target, and must also make smaller adjustments for precise and accurate behavior. Motor cortex controls the arm through projections to diverse targets across the central nervous system, but it has been challenging to identify the roles of cortical projections to specific targets. Here, we selectively disrupt cortico-cerebellar communication in the mouse by optogenetically stimulating the pontine nuclei in a cued reaching task. This perturbation did not typically block movement initiation, but degraded the precision, accuracy, duration, or success rate of the movement. Correspondingly, cerebellar and cortical activity during movement were largely preserved, but differences in hand velocity between control and stimulation conditions predicted from neural activity were correlated with observed velocity differences. These results suggest that while the total output of motor cortex drives reaching, the cortico-cerebellar loop makes small adjustments that contribute to the successful execution of this dexterous movement.

}, issn = {2050-084X}, doi = {10.7554/eLife.65906}, author = {Guo, Jian-Zhong and Sauerbrei, Britton A and Cohen, Jeremy D and Mischiati, Matteo and Graves, Austin R and Pisanello, Ferruccio and Branson, Kristin M and Hantman, Adam W} } @article {67735, title = {A dominant-negative SOX18 mutant disrupts multiple regulatory layers essential to transcription factor activity.}, journal = {Nucleic Acids Research}, year = {2021}, month = {2021 Sep 27}, abstract = {

Few genetically dominant mutations involved in human disease have been fully explained at the molecular level. In cases where the mutant gene encodes a transcription factor, the dominant-negative mode of action of the mutant protein is particularly poorly understood. Here, we studied the genome-wide mechanism underlying a dominant-negative form of the SOX18 transcription factor (SOX18RaOp) responsible for both the classical mouse mutant Ragged Opossum and the human genetic disorder Hypotrichosis-lymphedema-telangiectasia-renal defect syndrome. Combining three single-molecule imaging assays in living cells together with genomics and proteomics analysis, we found that SOX18RaOp disrupts the system through an accumulation of molecular interferences which impair several functional properties of the wild-type SOX18 protein, including its target gene selection process. The dominant-negative effect is further amplified by poisoning the interactome of its wild-type counterpart, which perturbs regulatory nodes such as SOX7 and MEF2C. Our findings explain in unprecedented detail the multi-layered process that underpins the molecular aetiology of dominant-negative transcription factor function.

}, issn = {1362-4962}, doi = {10.1093/nar/gkab820}, author = {McCann, Alex J and Lou, Jieqiong and Moustaqil, Mehdi and Graus, Matthew S and Blum, Ailisa and Fontaine, Frank and Liu, Hui and Luu, Winnie and Rudolffi-Soto, Paulina and Koopman, Peter and Sierecki, Emma and Gambin, Yann and Meunier, Fr{\'e}d{\'e}ric A and Liu, Zhe and Hinde, Elizabeth and Francois, Mathias} } @article {67746, title = {A dominant-negative SOX18 mutant disrupts multiple regulatory layers essential to transcription factor activity.}, journal = {Nucleic Acids Research}, year = {2021}, month = {2021 Sep 27}, abstract = {

Few genetically dominant mutations involved in human disease have been fully explained at the molecular level. In cases where the mutant gene encodes a transcription factor, the dominant-negative mode of action of the mutant protein is particularly poorly understood. Here, we studied the genome-wide mechanism underlying a dominant-negative form of the SOX18 transcription factor (SOX18RaOp) responsible for both the classical mouse mutant Ragged Opossum and the human genetic disorder Hypotrichosis-lymphedema-telangiectasia-renal defect syndrome. Combining three single-molecule imaging assays in living cells together with genomics and proteomics analysis, we found that SOX18RaOp disrupts the system through an accumulation of molecular interferences which impair several functional properties of the wild-type SOX18 protein, including its target gene selection process. The dominant-negative effect is further amplified by poisoning the interactome of its wild-type counterpart, which perturbs regulatory nodes such as SOX7 and MEF2C. Our findings explain in unprecedented detail the multi-layered process that underpins the molecular aetiology of dominant-negative transcription factor function.

}, issn = {1362-4962}, doi = {10.1093/nar/gkab820}, author = {McCann, Alex J and Lou, Jieqiong and Moustaqil, Mehdi and Graus, Matthew S and Blum, Ailisa and Fontaine, Frank and Liu, Hui and Luu, Winnie and Rudolffi-Soto, Paulina and Koopman, Peter and Sierecki, Emma and Gambin, Yann and Meunier, Fr{\'e}d{\'e}ric A and Liu, Zhe and Hinde, Elizabeth and Francois, Mathias} } @article {67815, title = {EASI-FISH for thick tissue defines lateral hypothalamus spatio-molecular organization.}, journal = {Cell}, volume = {184}, year = {2021}, month = {2021 Dec 01}, pages = {6361}, abstract = {

Determining the spatial organization and morphological characteristics of molecularly defined cell types is a major bottleneck for characterizing the architecture underpinning brain function. We developed Expansion-Assisted Iterative Fluorescence In Situ Hybridization (EASI-FISH) to survey gene expression in brain tissue, as well as a turnkey computational pipeline to rapidly process large EASI-FISH image datasets. EASI-FISH was optimized for thick brain sections (300\ μm) to facilitate reconstruction of spatio-molecular domains that generalize across brains. Using the EASI-FISH pipeline, we investigated the spatial distribution of dozens of molecularly defined cell types in the lateral hypothalamic area (LHA), a brain region with poorly defined anatomical organization. Mapping cell types in the LHA revealed nine spatially and molecularly defined subregions. EASI-FISH also facilitates iterative reanalysis of scRNA-seq datasets to determine marker-genes that further dissociated spatial and morphological heterogeneity. The EASI-FISH pipeline democratizes mapping molecularly defined cell types, enabling discoveries about brain organization.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2021.11.024}, author = {Wang, Yuhan and Eddison, Mark and Fleishman, Greg and Weigert, Martin and Xu, Shengjin and Wang, Tim and Rokicki, Konrad and Goina, Cristian and Henry, Fredrick E and Lemire, Andrew L and Schmidt, Uwe and Yang, Hui and Svoboda, Karel and Myers, Eugene W and Saalfeld, Stephan and Korff, Wyatt and Sternson, Scott M and Tillberg, Paul W} } @article {67806, title = {ecDNA hubs drive cooperative intermolecular oncogene expression.}, journal = {Nature}, volume = {600}, year = {2021}, month = {2021 Dec 01}, pages = {731-6}, abstract = {

Extrachromosomal DNA (ecDNA) is prevalent in human cancers and mediates high expression of oncogenes through gene amplification and altered gene regulation. Gene induction typically involves cis-regulatory elements that contact and activate genes on the same chromosome. Here we show that ecDNA hubs-clusters of around 10-100 ecDNAs within the nucleus-enable intermolecular enhancer-gene interactions to promote oncogene overexpression. ecDNAs that encode multiple distinct oncogenes form hubs in diverse cancer cell types and primary tumours. Each ecDNA is more likely to transcribe the oncogene when spatially clustered with additional ecDNAs. ecDNA hubs are tethered by the bromodomain and extraterminal domain (BET) protein BRD4 in a MYC-amplified colorectal cancer cell line. The BET inhibitor JQ1 disperses ecDNA hubs and preferentially inhibits ecDNA-derived-oncogene transcription. The BRD4-bound PVT1 promoter is ectopically fused to MYC and duplicated in ecDNA, receiving promiscuous enhancer input to drive potent expression of MYC. Furthermore, the PVT1 promoter on an exogenous episome suffices to mediate gene activation in trans by ecDNA hubs in a JQ1-sensitive manner. Systematic silencing of ecDNA enhancers by CRISPR interference reveals intermolecular enhancer-gene activation among multiple oncogene loci that are amplified on distinct ecDNAs. Thus, protein-tethered ecDNA hubs enable intermolecular transcriptional regulation and may serve as units of oncogene function and cooperative evolution and as potential targets for cancer therapy.

}, issn = {1476-4687}, doi = {10.1038/s41586-021-04116-8}, author = {Hung, King L and Yost, Kathryn E and Xie, Liangqi and Shi, Quanming and Helmsauer, Konstantin and Luebeck, Jens and Sch{\"o}pflin, Robert and Lange, Joshua T and Chamorro Gonz{\'a}lez, Roc{\'\i}o and Weiser, Natasha E and Chen, Celine and Valieva, Maria E and Wong, Ivy Tsz-Lo and Wu, Sihan and Dehkordi, Siavash R and Duffy, Connor V and Kraft, Katerina and Tang, Jun and Belk, Julia A and Rose, John C and Corces, M Ryan and Granja, Jeffrey M and Li, Rui and Rajkumar, Utkrisht and Friedlein, Jordan and Bagchi, Anindya and Satpathy, Ansuman T and Tjian, Robert and Mundlos, Stefan and Bafna, Vineet and Henssen, Anton G and Mischel, Paul S and Liu, Zhe and Chang, Howard Y} } @article {67275, title = {Efficient and adaptive sensory codes.}, journal = {Nature Neuroscience}, volume = {24}, year = {2021}, month = {2021 Jul 01}, pages = {998-1009}, abstract = {

The ability to adapt to changes in stimulus statistics is a hallmark of sensory systems. Here, we developed a theoretical framework that can account for the dynamics of adaptation from an information processing perspective. We use this framework to optimize and analyze adaptive sensory codes, and we show that codes optimized for stationary environments can suffer from prolonged periods of poor performance when the environment changes. To mitigate the adversarial effects of these environmental changes, sensory systems must navigate tradeoffs between the ability to accurately encode incoming stimuli and the ability to rapidly detect and adapt to changes in the distribution of these stimuli. We derive families of codes that balance these objectives, and we demonstrate their close match to experimentally observed neural dynamics during mean and variance adaptation. Our results provide a unifying perspective on adaptation across a range of sensory systems, environments, and sensory tasks.

}, issn = {1097-6256}, doi = {10.1038/s41593-021-00846-0}, url = {http://www.nature.com/articles/s41593-021-00846-0}, author = {M{\l}ynarski, Wiktor F. and Hermundstad, Ann M.} } @article {67721, title = {Electrode pooling can boost the yield of extracellular recordings with switchable silicon probes.}, journal = {Nature Communications}, volume = {12}, year = {2021}, month = {2021 Sep 02}, pages = {5245}, abstract = {

State-of-the-art silicon probes for electrical recording from neurons have thousands of recording sites. However, due to volume limitations there are typically many fewer wires carrying signals off the probe, which restricts the number of channels that can be recorded simultaneously. To overcome this fundamental constraint, we propose a method called electrode pooling that uses a single wire to serve many recording sites through a set of controllable switches. Here we present the framework behind this method and an experimental strategy to support it. We then demonstrate its feasibility by implementing electrode pooling on the Neuropixels 1.0 electrode array and characterizing its effect on signal and noise. Finally we use simulations to explore the conditions under which electrode pooling saves wires without compromising the content of the recordings. We make recommendations on the design of future devices to take advantage of this strategy.

}, keywords = {Action Potentials, Animals, Brain, Electrodes, Implanted, Electrophysiology, Equipment Design, Extracellular Space, Mice, Nerve Net, Neurons, Signal Processing, Computer-Assisted, Silicon}, issn = {2041-1723}, doi = {10.1038/s41467-021-25443-4}, author = {Lee, Kyu Hyun and Ni, Yu-Li and Colonell, Jennifer and Karsh, Bill and Putzeys, Jan and Pachitariu, Marius and Harris, Timothy D and Meister, Markus} } @article {66006, title = {Endothelial junctional membrane protrusions serve as hotspots for neutrophil transmigration.}, journal = {bioRxiv}, year = {2021}, month = {2021 Jan 21}, abstract = {

Upon inflammation, leukocytes rapidly transmigrate across the endothelium to enter the inflamed tissue. Evidence accumulates that leukocytes use preferred exit sites, though it is not yet clear how these hotspots in the endothelium are defined and how they are recognized by the leukocyte. Using lattice light sheet microscopy, we discovered that leukocytes prefer endothelial membrane protrusions at cell junctions for transmigration. Phenotypically, these junctional membrane protrusions are present in an asymmetric manner, meaning that one endothelial cell shows the protrusion and the adjacent one does not. Consequently, leukocytes cross the junction by migrating underneath the protruding endothelial cell. These protrusions depend on Rac1 activity and by using a photo-activatable Rac1 probe, we could artificially generate local exit-sites for leukocytes. Overall, we have discovered a new mechanism that uses local induced junctional membrane protrusions to facilitate/steer the leukocyte escape/exit from inflamed vessel walls.

}, doi = {https://doi.org/10.1101/2021.01.18.427135}, author = {Janine J.G. Arts and Eike K. Mahlandt and Max L.B. Gr{\"o}nloh and Lilian Schimmel and Ivar Noordstra and Abraham C.I. van Steen and Simon Tol and Jos van Rijssel and Martijn A. Nolte and Marten Postma and Satya Khuon and John M. Heddleston and Eric Wait and Teng-Leong Chew and Mark Winter and Eloi Montanez and Joachim Goedhart and Jaap D. van Buul} } @article {67710, title = {Endothelial junctional membrane protrusions serve as hotspots for neutrophil transmigration.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Aug 25}, abstract = {

Upon inflammation, leukocytes rapidly transmigrate across the endothelium to enter the inflamed tissue. Evidence accumulates that leukocytes use preferred exit sites, though it is not yet clear how these hotspots in the endothelium are defined and how they are recognized by the leukocyte. Using lattice light sheet microscopy, we discovered that leukocytes prefer endothelial membrane protrusions at cell junctions for transmigration. Phenotypically, these junctional membrane protrusions are present in an asymmetric manner, meaning that one endothelial cell shows the protrusion and the adjacent one does not. Consequently, leukocytes cross the junction by migrating underneath the protruding endothelial cell. These protrusions depend on Rac1 activity and by using a photo-activatable Rac1 probe, we could artificially generate local exit-sites for leukocytes. Overall, we have discovered a new mechanism that uses local induced junctional membrane protrusions to facilitate/steer the leukocyte escape/exit from inflamed vessel walls.

}, issn = {2050-084X}, doi = {10.7554/eLife.66074}, author = {Arts, Janine Jg and Mahlandt, Eike K and Gr{\"o}nloh, Max and Schimmel, Lilian and Noordstra, Ivar and Gordon, Emma and van Steen, Abraham Ci and Tol, Simon and Walzog, Barbara and van Rijssel, Jos and Nolte, Martijn A and Postma, Marten and Khuon, Satya and Heddleston, John M and Wait, Eric and Chew, Teng Leong and Winter, Mark and Montanez, Eloi and Goedhart, Joachim and van Buul, Jaap D} } @article {68473, title = {Erratum: Label-free imaging of fibroblast membrane interfaces and protein signatures with vibrational infrared photothermal and phase signals: publisher{\textquoteright}s note.}, journal = {Biomed Opt Express}, volume = {12}, year = {2021}, month = {09/2021}, pages = {5400}, abstract = {

[This corrects the article on p. 303 in vol. 12, PMID: 33520386.].

}, issn = {2156-7085}, doi = {10.1364/BOE.438946}, author = {Samolis, Panagis D and Langley, Daniel and O{\textquoteright}Reilly, Breanna M and Oo, Zay and Hilzenrat, Geva and Erramilli, Shyamsunder and Sgro, Allyson E and McArthur, Sally and Sander, Michelle Y} } @article {67233, title = {ER-to-Golgi protein delivery through an interwoven, tubular network extending from ER.}, journal = {Cell}, volume = {184}, year = {2021}, month = {2021 Apr 29}, pages = {2412}, abstract = {

Cellular versatility depends on accurate trafficking of diverse proteins to their organellar destinations. For the secretory pathway (followed by approximately 30\% of all proteins), the physical nature of the vessel conducting the first portage (endoplasmic reticulum [ER] to Golgi apparatus) is unclear. We provide a dynamic 3D view of early secretory compartments in mammalian cells with isotropic resolution and precise protein localization using whole-cell, focused ion beam scanning electron microscopy with cryo-structured illumination microscopy and live-cell synchronized cargo release approaches. Rather than vesicles alone, the ER spawns an elaborate, interwoven tubular network of contiguous lipid bilayers (ER exit site) for protein export. This receptacle is capable of extending microns along microtubules while still connected to the ER by a thin neck. COPII localizes to this neck region and dynamically regulates cargo entry from the ER, while COPI acts more distally, escorting the detached, accelerating tubular entity on its way to joining the Golgi apparatus through microtubule-directed movement.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2021.03.035}, author = {Weigel, Aubrey V and Chang, Chi-Lun and Shtengel, Gleb and Xu, C Shan and Hoffman, David P and Freeman, Melanie and Iyer, Nirmala and Aaron, Jesse and Khuon, Satya and Bogovic, John and Qiu, Wei and Hess, Harald F and Lippincott-Schwartz, Jennifer} } @article {66894, title = {Evaluation of multi-color genetically encoded Ca indicators in filamentous fungi.}, journal = {Fungal Genetics and Biology}, year = {2021}, month = {2021 Feb 16}, pages = {103540}, abstract = {

Genetically encoded Ca indicators (GECIs) enable long-term monitoring of cellular and subcellular dynamics of this second messenger in response to environmental and developmental cues without relying on exogenous dyes. Continued development and optimization in GECIs, combined with advances in gene manipulation, offer new opportunities for investigating the mechanism of Ca signaling in fungi, ranging from documenting Ca signatures under diverse conditions and genetic backgrounds to evaluating how changes in Ca signature impact calcium-binding proteins and subsequent cellular changes. Here, we attempted to express multi-color (green, yellow, blue, cyan, and red) circularly permuted fluorescent protein (FP)-based Ca indicators driven by multiple fungal promoters in Fusarium oxysporum, F. graminearum, and Neurospora crassa. Several variants were successfully expressed, with GCaMP5G driven by the Magnaporthe oryzae ribosomal protein 27 (P) and F. verticillioides elongation factor-1α (P) gene promoters being optimal for F. graminearum and F. oxysporum, respectively. Transformants expressing GCaMP5G were compared with those expressing YC3.60, a ratiometric Cameleon Ca indicator. Wild-type and three Ca signaling mutants of F. graminearum expressing GCaMP5G exhibited improved signal-to-noise and increased temporal and spatial resolution and are also more amenable to studies involving multiple FPs compared to strains expressing YC3.60.

}, issn = {1096-0937}, doi = {10.1016/j.fgb.2021.103540}, author = {Kim, Hye-Seon and Kim, Jung-Eun and Hwangbo, Aram and Akerboom, Jasper and Looger, Loren L and Duncan, Randall and Son, Hokyoung and Czymmek, Kirk J and Kang, Seogchan} } @article {68988, title = {Ex Utero Culture of Mouse Embryos from Pregastrulation to Advanced Organogenesis.}, journal = {J Vis Exp}, year = {2021}, month = {10/2021}, abstract = {

Postimplantation mammalian embryo culture methods have been generally inefficient and limited to brief periods after dissection out of the uterus. Platforms have been recently developed for highly robust and prolonged ex utero culture of mouse embryos from egg-cylinder stages until advanced organogenesis. These platforms enable appropriate and faithful development of pregastrulating embryos (E5.5) until the hind limb formation stage (E11). Late gastrulating embryos (E7.5) are grown in rotating bottles in these settings, while extended culture from pregastrulation stages (E5.5 or E6.5) requires a combination of static and rotating bottle cultures. In addition, sensitive regulation of O2 and CO2 concentration, gas pressure, glucose levels, and the use of a specific ex utero culture medium are critical for proper embryo development. Here, a detailed step-by-step protocol for extended ex utero mouse embryo culture is provided. The ability to grow normal mouse embryos ex utero from gastrulation to organogenesis represents a valuable tool for characterizing the effect of different experimental perturbations during embryonic development.

}, keywords = {Animals, Embryo Culture Techniques, Embryo, Mammalian, Embryonic Development, Female, Gastrulation, Mammals, Mice, Organogenesis, Pregnancy}, issn = {1940-087X}, doi = {10.3791/63160}, author = {Aguilera-Castrejon, Alejandro and Hanna, Jacob H} } @article {68989, title = {Ex utero mouse embryogenesis from pre-gastrulation to late organogenesis.}, journal = {Nature}, volume = {593}, year = {2021}, month = {05/2021}, pages = {119-124}, abstract = {

The mammalian body plan is established shortly after the embryo implants into the maternal uterus, and our understanding of post-implantation developmental processes remains limited. Although pre- and peri-implantation mouse embryos are routinely cultured in vitro, approaches for the robust culture of post-implantation embryos from egg cylinder stages until advanced organogenesis remain to be established. Here we present highly effective platforms for the ex utero culture of post-implantation mouse embryos, which enable the appropriate development of embryos from before gastrulation (embryonic day (E) 5.5) until the hindlimb formation stage (E11). Late gastrulating embryos (E7.5) are grown in three-dimensional rotating bottles, whereas extended culture from pre-gastrulation stages (E5.5 or E6.5) requires a combination of static and rotating bottle culture platforms. Histological, molecular and single-cell RNA sequencing analyses confirm that the ex utero cultured embryos recapitulate in utero development precisely. This culture system is amenable to the introduction of a variety of embryonic perturbations and micro-manipulations, the results of which can be followed ex utero for up to six days. The establishment of a system for robustly growing normal mouse embryos ex utero from pre-gastrulation to advanced organogenesis represents a valuable tool for investigating embryogenesis, as it eliminates the uterine barrier and allows researchers to mechanistically interrogate post-implantation morphogenesis and artificial embryogenesis\ in mammals.

}, keywords = {Animals, Embryo Culture Techniques, Embryo, Mammalian, Embryonic Development, Female, Gastrulation, In Vitro Techniques, Male, Mice, Organogenesis, Time Factors, Uterus}, issn = {1476-4687}, doi = {10.1038/s41586-021-03416-3}, author = {Aguilera-Castrejon, Alejandro and Oldak, Bernardo and Shani, Tom and Ghanem, Nadir and Itzkovich, Chen and Slomovich, Sharon and Tarazi, Shadi and Bayerl, Jonathan and Chugaeva, Valeriya and Ayyash, Muneef and Ashouokhi, Shahd and Sheban, Daoud and Livnat, Nir and Lasman, Lior and Viukov, Sergey and Zerbib, Mirie and Addadi, Yoseph and Rais, Yoach and Cheng, Saifeng and Stelzer, Yonatan and Keren-Shaul, Hadas and Shlomo, Raanan and Massarwa, Rada and Novershtern, Noa and Maza, Itay and Hanna, Jacob H} } @article {67243, title = {Expansion-Assisted Iterative-FISH defines lateral hypothalamus spatio-molecular organization}, journal = {bioRxiv}, year = {2021}, month = {2021 Mar 8}, abstract = {

Determining the spatial organization and morphological characteristics of molecularly defined cell types is a major bottleneck for characterizing the architecture underpinning brain function. We developed\ Expansion-Assisted Iterative\ Fluorescence\ In\ Situ\ Hybridization (EASI-FISH) to survey gene expression in brain tissue, as well as a turnkey computational pipeline to rapidly process large EASI-FISH image datasets. EASI-FISH was optimized for thick brain sections (300 {\textmu}m) to facilitate reconstruction of spatio-molecular domains that generalize across brains. Using the EASI-FISH pipeline, we investigated the spatial distribution of dozens of molecularly defined cell types in the lateral hypothalamic area (LHA), a brain region with poorly defined anatomical organization. Mapping cell types in the LHA revealed nine novel spatially and molecularly defined subregions. EASI-FISH also facilitates iterative re-analysis of scRNA-Seq datasets to determine marker-genes that further dissociated spatial and morphological heterogeneity. The EASI-FISH pipeline democratizes mapping molecularly defined cell types, enabling discoveries about brain organization.

}, doi = {10.1101/2021.03.08.434304}, url = {https://doi.org/10.1101/2021.03.08.434304}, author = {Yuhan Wang and Mark Eddison and Greg Fleishman and Martin Weigert and Shengjin Xu and Frederick E. Henry and Tim Wang and Andrew L. Lemire and Uwe Schmidt and Hui Yang and Konrad Rokicki and Cristian Goina and Karel Svoboda and Eugene W. Myers and Stephan Saalfeld and Wyatt Korff and Scott M. Sternson and Paul W. Tillberg} } @article {67715, title = {A framework for studying behavioral evolution by reconstructing ancestral repertoires.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Sep 02}, abstract = {

Although different animal species often exhibit extensive variation in many behaviors, typically scientists examine one or a small number of behaviors in any single study. Here, we propose a new framework to simultaneously study the evolution of many behaviors. We measured the behavioral repertoire of individuals from six species of fruit flies using unsupervised techniques and identified all stereotyped movements exhibited by each species. We then fit a Generalized Linear Mixed Model to estimate the intra- and inter-species behavioral covariances, and, by using the known phylogenetic relationships among species, we estimated the (unobserved) behaviors exhibited by ancestral species. We found that much of intra-specific behavioral variation has a similar covariance structure to previously described long-time scale variation in an individual{\textquoteright}s behavior, suggesting that much of the measured variation between individuals of a single species in our assay reflects differences in the status of neural networks, rather than genetic or developmental differences between individuals. We then propose a method to identify groups of behaviors that appear to have evolved in a correlated manner, illustrating how sets of behaviors, rather than individual behaviors, likely evolved. Our approach provides a new framework for identifying co-evolving behaviors and may provide new opportunities to study the mechanistic basis of behavioral evolution.

}, issn = {2050-084X}, doi = {10.7554/eLife.61806}, author = {Hern{\'a}ndez, Dami{\'a}n G and Rivera, Catalina and Cande, Jessica and Zhou, Baohua and Stern, David and Berman, Gordon J} } @article {67821, title = {A genetically defined insula-brainstem circuit selectively controls motivational vigor.}, journal = {Cell}, year = {2021}, month = {2021 Dec 07}, abstract = {

The anterior insular cortex (aIC) plays a critical role in cognitive and motivational control of behavior, but the underlying neural mechanism remains elusive. Here, we show that aIC neurons expressing Fezf2 (aIC), which are the pyramidal tract neurons, signal motivational vigor and invigorate need-seeking behavior through projections to the brainstem nucleus tractus solitarii (NTS). aIC neurons and their postsynaptic NTS neurons acquire anticipatory activity through learning, which encodes the perceived value and the vigor of actions to pursue homeostatic needs. Correspondingly, aIC {\textrightarrow} NTS circuit activity controls vigor, effort, and striatal dopamine release but only if the action is learned and the outcome is needed. Notably, aIC neurons do not represent taste or valence. Moreover, aIC {\textrightarrow} NTS activity neither drives reinforcement nor influences total consumption. These results pinpoint specific functions of aIC {\textrightarrow} NTS circuit for selectively controlling motivational vigor and suggest that motivation is subserved, in part, by aIC{\textquoteright}s top-down regulation of dopamine signaling.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2021.11.019}, author = {Deng, Hanfei and Xiao, Xiong and Yang, Tao and Ritola, Kimberly and Hantman, Adam and Li, Yulong and Huang, Z Josh and Li, Bo} } @article {67816, title = {A genetically encoded fluorescent biosensor for extracellular L-lactate.}, journal = {Nature Communications}, volume = {12}, year = {2021}, month = {2021 Dec 06}, pages = {7058}, abstract = {

L-Lactate, traditionally considered a metabolic waste product, is increasingly recognized as an important intercellular energy currency in mammals. To enable investigations of the emerging roles of intercellular shuttling of L-lactate, we now report an intensiometric green fluorescent genetically encoded biosensor for extracellular L-lactate. This biosensor, designated eLACCO1.1, enables cellular resolution imaging of extracellular L-lactate in cultured mammalian cells and brain tissue.

}, issn = {2041-1723}, doi = {10.1038/s41467-021-27332-2}, author = {Nasu, Yusuke and Murphy-Royal, Ciaran and Wen, Yurong and Haidey, Jordan N and Molina, Rosana S and Abhi Aggarwal and Zhang, Shuce and Kamijo, Yuki and Paquet, Marie-Eve and Podgorski, Kaspar and Drobizhev, Mikhail and Bains, Jaideep S and Lemieux, M Joanne and Gordon, Grant R and Campbell, Robert E} } @article {67765, title = {Genetically identified amygdala-striatal circuits for valence-specific behaviors.}, journal = {Nature Neuroscience}, volume = {24}, year = {2021}, month = {2021 Oct 18}, pages = {1586-1600}, abstract = {

The basolateral amygdala (BLA) plays essential roles in behaviors motivated by stimuli with either positive or negative valence, but how it processes motivationally opposing information and participates in establishing valence-specific behaviors remains unclear. Here, by targeting Fezf2-expressing neurons in the BLA, we identify and characterize two functionally distinct classes in behaving mice, the negative-valence neurons and positive-valence neurons, which innately represent aversive and rewarding stimuli, respectively, and through learning acquire predictive responses that are essential for punishment avoidance or reward seeking. Notably, these two classes of neurons receive inputs from separate sets of sensory and limbic areas, and convey punishment and reward information through projections to the nucleus accumbens and olfactory tubercle, respectively, to drive negative and positive reinforcement. Thus, valence-specific BLA neurons are wired with distinctive input-output structures, forming a circuit framework that supports the roles of the BLA in encoding, learning and executing valence-specific motivated behaviors.

}, issn = {1546-1726}, doi = {10.1038/s41593-021-00927-0}, author = {Zhang, Xian and Guan, Wuqiang and Yang, Tao and Furlan, Alessandro and Xiao, Xiong and Yu, Kai and An, Xu and Galbavy, William and Ramakrishnan, Charu and Deisseroth, Karl and Ritola, Kimberly and Hantman, Adam and He, Miao and Josh Huang, Z and Li, Bo} } @article {66020, title = {Idiosyncratic learning performance in flies generalizes across modalities.}, journal = {bioRxiv}, year = {2021}, month = {2021 Jan 25}, abstract = {

Individuals vary in their innate behaviors, even when they have the same genome and have been reared in the same environment. The extent of individuality in plastic behaviors, like learning, is less well characterized. Also unknown is the extent to which intragenotypic differences in learning generalize: if an individual performs well in one assay, will it perform well in other assays? We investigated this using the fruit fly\ Drosophila melanogaster, an organism long-used to study the mechanistic basis of learning and memory. We found that isogenic flies, reared in identical lab conditions, and subject to classical conditioning that associated odorants with electric shock, exhibit clear individuality in their learning responses. Flies that performed well when an odor was paired with shock tended to perform well when other odors were paired with shock, or when the original odor was paired with bitter taste. Thus, individuality in learning performance appears to be prominent in isogenic animals reared identically, and individual differences in learning performance generalize across stimulus modalities. Establishing these results in flies opens up the possibility of studying the genetic and neural circuit basis of individual differences in learning in a highly suitable model organism.

}, author = {Matthew Smith and Kyle S. Honegger and Glenn Turner and Benjamin de Bivort} } @article {67670, title = {Imaging Africa: a strategic approach to optical microscopy training in Africa.}, journal = {Nature Methods}, volume = {18}, year = {2021}, month = {2021 Aug 20}, pages = {847-855}, issn = {1548-7105}, doi = {10.1038/s41592-021-01227-y}, author = {Reiche, Michael A and Warner, Digby F and Aaron, Jesse and Khuon, Satya and Fletcher, Daniel A and Hahn, Klaus and Rogers, Kelly L and Mhlanga, Musa and Koch, Anastasia and Quaye, Wendye and Chew, Teng-Leong} } @article {67303, title = {Information flow, cell types and stereotypy in a full olfactory connectome.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 May 25}, abstract = {

The connectome provides large scale connectivity and morphology information for the majority of the central brain of . Using this data set, we provide a complete description of the olfactory system, covering all first, second and lateral horn-associated third-order neurons. We develop a generally applicable strategy to extract information flow and layered organisation from connectome graphs, mapping olfactory input to descending interneurons. This identifies a range of motifs including highly lateralised circuits in the antennal lobe and patterns of convergence downstream of the mushroom body and lateral horn. Leveraging a second data set we provide a first quantitative assessment of inter- versus intra-individual stereotypy. Comparing neurons across two brains (three hemispheres) reveals striking similarity in neuronal morphology across brains. Connectivity correlates with morphology and neurons of the same morphological type show similar connection variability within the same brain as across two brains.

}, issn = {2050-084X}, doi = {10.7554/eLife.66018}, author = {Schlegel, Philipp and Bates, Alexander Shakeel and St{\"u}rner, Tomke and Jagannathan, Sridhar R and Drummond, Nikolas and Hsu, Joseph and Serratosa Capdevila, Laia and Javier, Alexandre and Marin, Elizabeth C and Barth-Maron, Asa and Tamimi, Imaan Fm and Li, Feng and Rubin, Gerald M and Plaza, Stephen M and Costa, Marta and Jefferis, Gregory Sxe} } @article {67656, title = {Intercellular Arc Signaling Regulates Vasodilation.}, journal = {Journal of Neuroscience}, year = {2021}, month = {2021 Jul 29}, abstract = {

Injury responses require communication between different cell types in the skin. Sensory neurons contribute to inflammation and can secrete signaling molecules that affect non-neuronal cells. Despite the pervasive role of translational regulation in nociception, the contribution of activity-dependent protein synthesis to inflammation is not well understood. To address this problem, we examined the landscape of nascent translation in murine dorsal root ganglion (DRG) neurons treated with inflammatory mediators using ribosome profiling. We identified the activity-dependent gene, Arc, as a target of translation and Inflammatory cues promote local translation of Arc in the skin. Arc-deficient male mice display exaggerated paw temperatures and vasodilation in response to an inflammatory challenge. Since Arc has recently been shown to be released from neurons in extracellular vesicles (EVs), we hypothesized that intercellular Arc signaling regulates the inflammatory response in skin. We found that the excessive thermal responses and vasodilation observed in Arc defective mice are rescued by injection of Arc-containing EVs into the skin. Our findings suggest that activity-dependent production of Arc in afferent fibers regulates neurogenic inflammation potentially through intercellular signaling.Nociceptors play prominent roles in pain and inflammation. We examined rapid changes in the landscape of nascent translation in cultured dorsal root ganglia (DRGs) treated with a combination of inflammatory mediators using ribosome profiling. We identified several hundred transcripts subject to rapid preferential translation. Among them is the immediate early gene (IEG) Arc. We provide evidence that Arc is translated in afferent fibers in the skin. Arc-deficient mice display several signs of exaggerated inflammation which is normalized on injection of Arc containing extracellular vesicles (EVs). Our work suggests that noxious cues can trigger Arc production by nociceptors which in turn constrains neurogenic inflammation in the skin.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0440-21.2021}, author = {de la Pe{\~n}a, June Bryan and Barragan-Iglesias, Paulino and Lou, Tzu-Fang and Kunder, Nikesh and Loerch, Sarah and Shukla, Tarjani and Basavarajappa, Lokesh and Song, Jane and James, Dominique N and Megat, Salim and Moy, Jamie K and Wanghzou, Andi and Ray, Pradipta R and Hoyt, Kenneth and Steward, Oswald and Price, Theodore J and Shepherd, Jason and Campbell, Zachary T} } @article {66025, title = {Internal state configures olfactory behavior and early sensory processing in larvae.}, journal = {Science Advances}, volume = {7}, year = {2021}, month = {2021 Jan 01}, abstract = {

Animals exhibit different behavioral responses to the same sensory cue depending on their internal state at a given moment. How and where in the brain are sensory inputs combined with state information to select an appropriate behavior? Here, we investigate how food deprivation affects olfactory behavior in larvae. We find that certain odors repel well-fed animals but attract food-deprived animals and that feeding state flexibly alters neural processing in the first olfactory center, the antennal lobe. Hunger differentially modulates two output pathways required for opposing behavioral responses. Upon food deprivation, attraction-mediating uniglomerular projection neurons show elevated odor-evoked activity, whereas an aversion-mediating multiglomerular projection neuron receives odor-evoked inhibition. The switch between these two pathways is regulated by the lone serotonergic neuron in the antennal lobe, CSD. Our findings demonstrate how flexible behaviors can arise from state-dependent circuit dynamics in an early sensory processing center.

}, issn = {2375-2548}, doi = {10.1126/sciadv.abd6900}, author = {Vogt, Katrin and Zimmerman, David M and Schlichting, Matthias and Hernandez-Nunez, Luis and Qin, Shanshan and Malacon, Karen and Rosbash, Michael and Pehlevan, Cengiz and Cardona, Albert and Samuel, Aravinthan D T} } @article {68476, title = {Label-free imaging of fibroblast membrane interfaces and protein signatures with vibrational infrared photothermal and phase signals.}, journal = {Biomed Opt Express}, volume = {12}, year = {2021}, month = {12/2020}, pages = {303-319}, abstract = {

Label-free vibrational imaging of biological samples has attracted significant interest due to its integration of structural and chemical information. Vibrational infrared photothermal amplitude and phase signal (VIPPS) imaging provide label-free chemical identification by targeting the characteristic resonances of biological compounds that are present in the mid-infrared fingerprint region (3 {\textmu}m - 12 {\textmu}m). High contrast imaging of subcellular features and chemical identification of protein secondary structures in unlabeled and labeled fibroblast cells embedded in a collagen-rich extracellular matrix is demonstrated by combining contrast from absorption signatures (amplitude signals) with sensitive detection of different heat properties (lock-in phase signals). We present that the detectability of nano-sized cell membranes is enhanced to well below the optical diffraction limit since the membranes are found to act as thermal barriers. VIPPS offers a novel combination of chemical imaging and thermal diffusion characterization that paves the way towards label-free imaging of cell models and tissues as well as the study of intracellular heat dynamics.

}, issn = {2156-7085}, doi = {10.1364/BOE.411888}, author = {Samolis, Panagis D and Langley, Daniel and O{\textquoteright}Reilly, Breanna M and Oo, Zay and Hilzenrat, Geva and Erramilli, Shyamsunder and Sgro, Allyson E and McArthur, Sally and Sander, Michelle Y} } @article {66021, title = {The level of oncogenic Ras determines the malignant transformation of Lkb1 mutant tissue in vivo.}, journal = {Communications Biology}, volume = {4}, year = {2021}, month = {2021 Jan 29}, pages = {142}, abstract = {

The genetic and metabolic heterogeneity of RAS-driven cancers has confounded therapeutic strategies in the clinic. To address this, rapid and genetically tractable animal models are needed that recapitulate the heterogeneity of RAS-driven cancers in vivo. Here, we generate a Drosophila melanogaster model of Ras/Lkb1 mutant carcinoma. We show that low-level expression of oncogenic Ras (Ras) promotes the survival of Lkb1 mutant tissue, but results in autonomous cell cycle arrest and non-autonomous overgrowth of wild-type tissue. In contrast, high-level expression of oncogenic Ras (Ras) transforms Lkb1 mutant tissue resulting in lethal malignant tumors. Using simultaneous multiview light-sheet microcopy, we have characterized invasion phenotypes of Ras/Lkb1 tumors in living larvae. Our molecular analysis reveals sustained activation of the AMPK pathway in malignant Ras/Lkb1 tumors, and demonstrate the genetic and pharmacologic dependence of these tumors on CaMK-activated Ampk. We further show that LKB1 mutant human lung adenocarcinoma patients with high levels of oncogenic KRAS exhibit worse overall survival and increased AMPK activation. Our results suggest that high levels of oncogenic KRAS is a driving event in the malignant transformation of LKB1 mutant tissue, and uncovers a vulnerability that may be used to target this aggressive genetic subset of RAS-driven tumors.

}, issn = {2399-3642}, doi = {10.1038/s42003-021-01663-8}, author = {Rackley, Briana and Seong, Chang-Soo and Kiely, Evan and Parker, Rebecca E and Rupji, Manali and Dwivedi, Bhakti and Heddleston, John M and Giang, William and Anthony, Neil and Chew, Teng-Leong and Gilbert-Ross, Melissa} } @article {67313, title = {Locating Macromolecular Assemblies in Cells by 2D Template Matching with TEM.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Jun 11}, abstract = {

For a more complete understanding of molecular mechanisms, it is important to study macromolecules and their assemblies in the broader context of the cell. This context can be visualized at nanometer resolution in three dimensions (3D) using electron cryo-tomography, which requires tilt series to be recorded and computationally aligned, currently limiting throughput. Additionally, the high-resolution signal preserved in the raw tomograms is currently limited by a number of technical difficulties, leading to an increased false-positive detection rate when using 3D template matching to find molecular complexes in tomograms. We have recently described a 2D template matching approach that addresses these issues by including high-resolution signal preserved in single-tilt images. A current limitation of this approach is the high computational cost that limits throughput. We describe here a GPU-accelerated implementation of 2D template matching in the image processing software TEM that allows for easy scaling and improves the accessibility of this approach. We apply 2D template matching to identify ribosomes in images of frozen-hydrated cells with high precision and sensitivity, demonstrating that this is a versatile tool for visual proteomics and structure determination. We benchmark the results with 3D template matching of tomograms acquired on identical sample locations and identify strengths and weaknesses of both techniques, which offer complementary information about target localization and identity.

}, issn = {2050-084X}, doi = {10.7554/eLife.68946}, author = {Lucas, Bronwyn A and Himes, Benjamin A and Xue, Liang and Grant, Tim and Mahamid, Julia and Grigorieff, Nikolaus} } @article {67271, title = {Lupus susceptibility region containing CDKN1B rs34330 mechanistically influences expression and function of multiple target genes, also linked to proliferation and apoptosis.}, journal = {Arthritis Rheumatology}, volume = {73}, year = {2021}, month = {2021 Dec 01}, pages = {2303-13}, abstract = {

OBJECTIVE: A recent genome-wide association study (GWAS) reported a significant genetic association between rs34330 of cyclin-dependent kinase inhibitor 1B (CDKN1B) and risk of systemic lupus erythematosus (SLE) in Han Chinese. This study aims to validate the reported association and elucidate the biochemical mechanisms underlying the variant{\textquoteright}s effect.

METHODS: We performed allelic association with SLE followed by meta-analysis across 11 independent cohorts (n=28,872). We applied in silico bioinformatics and experimental validation in SLE-relevant cell lines to determine the functional consequences of rs34330.

RESULTS: We replicated genetic association between SLE and rs34330 (P =5.29x10 , OR (95\% CI)=0.84 (0.81-0.87)). Follow-up bioinformatics and eQTL analysis suggest that rs34330 is located in active chromatin and potentially regulates several target genes. Using luciferase and ChIP-qPCR, we demonstrated substantial allele-specific promoter and enhancer activity, and allele-specific binding of three histone marks (H3K27ac, H3K4me3, H3K4me1), RNA pol II, CTCF, and a critical immune transcription factor (IRF-1). Chromosome conformation capture (3C) detected long-range chromatin interactions between rs34330 and the promoters of neighboring genes APOLD1 and DDX47, and effects on CDKN1B and the other target genes were directly validated by CRISPR-based genome editing. Finally, CRISPR-dCas9-based epigenetic activation/silencing confirmed these results. Gene-edited cell lines also showed higher levels of proliferation and apoptosis.

CONCLUSION: Collectively, these findings suggest a mechanism whereby the rs34330 risk allele (C) influences the presence of histone marks, RNA pol II, and the IRF-1 transcription factor to regulate expression of several target genes linked to proliferation and apoptosis, which potentially underlie the association of rs34330 with SLE.

}, issn = {2326-5205}, doi = {10.1002/art.41799}, author = {Singh, Bhupinder and Maiti, Guru P and Zhou, Xujie and Fazel-Najafabadi, Mehdi and Bae, Sang-Cheol and Sun, Celi and Terao, Chikashi and Okada, Yukinori and Chua, Kek Heng and Kochi, Yuta and Guthridge, Joel M and Zhang, Hong and Weirauch, Matthew and James, Judith A and Harley, John B and Varshney, Gaurav K and Looger, Loren L and Nath, Swapan K} } @article {67305, title = {Micro-Meta App: an interactive software tool to facilitate the collection of microscopy metadata based on community-driven specifications}, journal = {bioRxiv}, year = {2021}, month = {2021 May 31}, abstract = {

For the information content of microscopy images to be appropriately interpreted, reproduced, and meet FAIR (Findable Accessible Interoperable and Reusable) principles, they should be accompanied by detailed descriptions of microscope hardware, image acquisition settings, image pixel and dimensional structure, and instrument performance. Nonetheless, the thorough documentation of imaging experiments is significantly impaired by the lack of community-sanctioned easy-to-use software tools to facilitate the extraction and collection of relevant microscopy metadata. Here we present\ Micro-Meta App, an intuitive open-source software designed to tackle these issues that was developed in the context of nascent global bioimaging community organizations, including\ BioImaging\ North\ America (BINA) and\ QUAlity Assessment and\ REProducibility in\ Light\ Microscopy (QUAREP-LiMi), whose goal is to improve reproducibility, data quality and sharing value for imaging experiments. The App provides a user-friendly interface for building comprehensive descriptions of the conditions utilized to produce individual microscopy datasets as specified by the recently proposed 4DN-BINA-OME tiered-system of Microscopy Metadata model. To achieve this goal the App provides a visual guide for a microscope-user to: 1) interactively build diagrammatic representations of hardware configurations of given microscopes that can be easily reused and shared with colleagues needing to document similar instruments. 2) Automatically extracts relevant metadata from image files and facilitates the collection of missing image acquisition settings and calibration metrics associated with a given experiment. 3) Output all collected Microscopy Metadata to interoperable files that can be used for documenting imaging experiments and shared with the community. In addition to significantly lowering the burden of quality assurance, the visual nature of Micro-Meta App makes it particularly suited for training users that have limited knowledge of the intricacies of light microscopy experiments. To ensure wide-adoption by microscope-users with different needs Micro-Meta App closely interoperates with\ MethodsJ2\ and\ OMERO.mde, two complementary tools described in parallel manuscripts.

}, author = {Alex Rigano and Shannon Ehmsen and Serkan Utku Ozturk and Joel Ryan and Alexander Balashov and Mathias Hammer and Koray Kirli and Karl Bellve and Ulrike Boehm and Claire M. Brown and James J. Chambers and Robert A. Coleman and Andrea Cosolo and Orestis Faklaris and Kevin Fogarty and Thomas Guilbert and Anna B. Hamacher and Michelle S. Itano and Daniel P. Keeley and Susanne Kunis and Judith Lacoste and Alex Laude and Willa Ma and Marco Marcello and Paula Montero-Llopis and Glyn Nelson and Roland Nitschke and Jaime A. Pimentel and Stefanie Weidtkamp-Peters and Peter J. Park and Burak Alver and David Grunwald and Caterina Strambio-De-Castillia} } @article {67811, title = {Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications.}, journal = {Nature Methods}, volume = {18}, year = {2021}, month = {2021 Dec 03}, pages = {1489-1495}, abstract = {

For quality, interpretation, reproducibility and sharing value, microscopy images should be accompanied by detailed descriptions of the conditions that were used to produce them. Micro-Meta App is an intuitive, highly interoperable, open-source software tool that was developed in the context of the 4D Nucleome (4DN) consortium and is designed to facilitate the extraction and collection of relevant microscopy metadata as specified by the recent 4DN-BINA-OME tiered-system of Microscopy Metadata specifications. In addition to substantially lowering the burden of quality assurance, the visual nature of Micro-Meta App makes it particularly suited for training purposes.

}, issn = {1548-7105}, doi = {10.1038/s41592-021-01315-z}, author = {Rigano, Alessandro and Ehmsen, Shannon and {\"O}zt{\"u}rk, Serkan Utku and Ryan, Joel and Balashov, Alexander and Hammer, Mathias and Kirli, Koray and Boehm, Ulrike and Brown, Claire M and Bellve, Karl and Chambers, James J and Cosolo, Andrea and Coleman, Robert A and Faklaris, Orestis and Fogarty, Kevin E and Guilbert, Thomas and Hamacher, Anna B and Itano, Michelle S and Keeley, Daniel P and Kunis, Susanne and Lacoste, Judith and Laude, Alex and Ma, Willa Y and Marcello, Marco and Montero-Llopis, Paula and Nelson, Glyn and Nitschke, Roland and Pimentel, Jaime A and Weidtkamp-Peters, Stefanie and Park, Peter J and Alver, Burak H and Grunwald, David and Strambio-De-Castillia, Caterina} } @article {69336, title = {Molecular profiling of single neurons of known identity in two ganglia from the crab Cancer borealis}, journal = {Proceedings of the National Academy of Sciences}, volume = {116}, year = {2021}, month = {2021 Feb 12}, pages = {26980 - 26990}, abstract = {

Understanding circuit organization depends on identification of cell types. Recent advances in transcriptional profiling methods have enabled classification of cell types by their gene expression. While exceptionally powerful and high throughput, the ground-truth validation of these methods is difficult: If cell type is unknown, how does one assess whether a given analysis accurately captures neuronal identity? To shed light on the capabilities and limitations of solely using transcriptional profiling for cell-type classification, we performed 2 forms of transcriptional profiling{\textemdash}RNA-seq and quantitative RT-PCR, in single, unambiguously identified neurons from 2 small crustacean neuronal networks: The stomatogastric and cardiac ganglia. We then combined our knowledge of cell type with unbiased clustering analyses and supervised machine learning to determine how accurately functionally defined neuron types can be classified by expression profile alone. The results demonstrate that expression profile is able to capture neuronal identity most accurately when combined with multimodal information that allows for post hoc grouping, so analysis can proceed from a supervised perspective. Solely unsupervised clustering can lead to misidentification and an inability to distinguish between 2 or more cell types. Therefore, this study supports the general utility of cell identification by transcriptional profiling, but adds a caution: It is difficult or impossible to know under what conditions transcriptional profiling alone is capable of assigning cell identity. Only by combining multiple modalities of information such as physiology, morphology, or innervation target can neuronal identity be unambiguously determined.

}, issn = {0027-8424}, doi = {10.1073/pnas.1911413116}, url = {https://pnas.org/doi/full/10.1073/pnas.1911413116https://pnas.org/doi/pdf/10.1073/pnas.1911413116http://www.pnas.org/syndication/doi/10.1073/pnas.1911413116}, author = {Northcutt, Adam J. and Kick, Daniel R. and Otopalik, Adriane G. and Goetz, Benjamin M. and Harris, Rayna M. and Santin, Joseph M. and Hofmann, Hans A. and Marder, Eve and Schulz, David 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 {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 {67753, title = {An open-access volume electron microscopy atlas of whole cells and tissues.}, journal = {Nature}, volume = {599}, year = {2021}, month = {2021 Nov 1}, pages = {147-51}, abstract = {

Understanding cellular architecture is essential for understanding biology. Electron microscopy (EM) uniquely visualizes cellular structures with nanometre resolution. However, traditional methods, such as thin-section EM or EM tomography, have limitations in that they visualize only a single slice or a relatively small volume of the cell, respectively. Focused ion beam-scanning electron microscopy (FIB-SEM) has demonstrated the ability to image small volumes of cellular samples with 4-nm isotropic voxels. Owing to advances in the\ precision and stability of FIB milling, together with enhanced signal detection and faster SEM scanning, we have increased the volume that can be imaged with 4-nm\ voxels by two orders of magnitude. Here we present a volume EM atlas at such resolution comprising ten three-dimensional datasets for whole cells and tissues, including cancer cells, immune cells, mouse pancreatic islets and Drosophila neural tissues. These open access data (via OpenOrganelle) represent the foundation of a field of high-resolution whole-cell volume EM and subsequent analyses, and we invite researchers to explore this atlas and\ pose questions.

}, issn = {1476-4687}, doi = {10.1038/s41586-021-03992-4}, author = {Xu, C Shan and Pang, Song and Shtengel, Gleb and M{\"u}ller, Andreas and Ritter, Alex T and Hoffman, Huxley K and Takemura, Shin-ya and Lu, Zhiyuan and Pasolli, H Amalia and Iyer, Nirmala and Chung, Jeeyun and Bennett, Davis and Weigel, Aubrey V and Freeman, Melanie and Van Engelenburg, Schuyler B and Walther, Tobias C and Farese, Robert V and Lippincott-Schwartz, Jennifer and Mellman, Ira and Solimena, Michele and Hess, Harald F} } @article {67274, title = {An open-source semi-automated robotics pipeline for embryo immunohistochemistry.}, journal = {Scientific Reports}, volume = {11}, year = {2021}, month = {2021 May 13}, pages = {10314}, abstract = {

A significant challenge for developmental systems biology is balancing throughput with controlled conditions that minimize experimental artifacts. Large-scale developmental screens such as unbiased mutagenesis surveys have been limited in their applicability to embryonic systems, as the technologies for quantifying precise expression patterns in whole animals has not kept pace with other sequencing-based technologies. Here, we outline an open-source semi-automated pipeline to chemically fixate, stain, and 3D-image Drosophila embryos. Central to this pipeline is a liquid handling robot, Flyspresso, which automates the steps of classical embryo fixation and staining. We provide the schematics and an overview of the technology for an engineer or someone equivalently trained to reproduce and further improve upon Flyspresso, and highlight the Drosophila embryo fixation and colorimetric or antibody staining protocols. Additionally, we provide a detailed overview and stepwise protocol for our adaptive-feedback pipeline for automated embryo imaging on confocal microscopes. We demonstrate the efficiency of this pipeline compared to classical techniques, and how it can be repurposed or scaled to other protocols and biological systems. We hope our pipeline will serve as a platform for future research, allowing a broader community of users to build, execute, and share similar experiments.

}, issn = {2045-2322}, doi = {10.1038/s41598-021-89676-5}, author = {Fuqua, Timothy and Jordan, Jeff and Halavatyi, Aliaksandr and Tischer, Christian and Richter, Kerstin and Crocker, Justin} } @article {67766, title = {A pair of dopamine neurons mediate chronic stress signals to induce learning deficit in Drosophila melanogaster.}, journal = {Proceedings of the National Academy of Sciences of the U. S. A.}, volume = {118}, year = {2021}, month = {2021 Oct 19}, abstract = {

Chronic stress could induce severe cognitive impairments. Despite extensive investigations in mammalian models, the underlying mechanisms remain obscure. Here, we show that chronic stress could induce dramatic learning and memory deficits in The chronic stress-induced learning deficit (CSLD) is long lasting and associated with other depression-like behaviors. We demonstrated that excessive dopaminergic activity provokes susceptibility to CSLD. Remarkably, a pair of PPL1-γ1pedc dopaminergic neurons that project to the mushroom body (MB) γ1pedc compartment play a key role in regulating susceptibility to CSLD so that stress-induced PPL1-γ1pedc hyperactivity facilitates the development of CSLD. Consistently, the mushroom body output neurons (MBON) of the γ1pedc compartment, MBON-γ1pedc\>α/β neurons, are important for modulating susceptibility to CSLD. Imaging studies showed that dopaminergic activity is necessary to provoke the development of chronic stress-induced maladaptations in the MB network. Together, our data support that PPL1-γ1pedc mediates chronic stress signals to drive allostatic maladaptations in the MB network that lead to CSLD.

}, issn = {1091-6490}, doi = {10.1073/pnas.2023674118}, author = {Jia, Jia and He, Lei and Yang, Junfei and Shuai, Yichun and Yang, Jingjing and Wu, Yalan and Liu, Xin and Chen, Tianli and Wang, Guaxiu and Wang, Xingyu and Song, Xiaoxu and Ding, Zhaowen and Zhu, Yan and Ling-Qi Zhang and Chen, Peng and Qin, Hongtao} } @article {67241, title = {A perspective on Microscopy Metadata: data provenance and quality control}, journal = {arXiv}, year = {2021}, month = {2021 Apr 26}, abstract = {

The application of microscopy in biomedical research has come a long way since Antonie van Leeuwenhoek discovered unicellular organisms. Countless innovations have positioned light microscopy as a cornerstone of modern biology and a method of choice for connecting omics datasets to their biological and clinical correlates. Still, regardless of how convincing published imaging data looks, it does not always convey meaningful information about the conditions in which it was acquired, processed, and analyzed. Adequate record-keeping, reporting, and quality control are therefore essential to ensure experimental rigor and data fidelity, allow experiments to be reproducibly repeated, and promote the proper evaluation, interpretation, comparison, and re-use. To this end, microscopy images should be accompanied by complete descriptions detailing experimental procedures, biological samples, microscope hardware specifications, image acquisition parameters, and image analysis procedures, as well as metrics accounting for instrument performance and calibration. However, universal, community-accepted Microscopy Metadata standards and reporting specifications that would result in Findable Accessible Interoperable and Reproducible (FAIR) microscopy data have not yet been established. To understand this shortcoming and to propose a way forward, here we provide an overview of the nature of microscopy metadata and its importance for fostering data quality, reproducibility, scientific rigor, and sharing value in light microscopy. The proposal for tiered Microscopy Metadata Specifications that extend the OME Data Model put forth by the 4D Nucleome Initiative and by Bioimaging North America [1-3] as well as a suite of three complementary and interoperable tools are being developed to facilitate the process of image data documentation and are presented in related manuscripts [4-6].

}, url = {https://arxiv.org/abs/1910.11370}, author = {Maximiliaan Huisman and Mathias Hammer and Alex Rigano and Ulrike Boehm and James J. Chambers and Nathalie Gaudreault and Alison J. North and Jaime A. Pimentel and Damir Sudar and Peter Bajcsy and Claire M. Brown and Alexander D. Corbett and Orestis Faklaris and Judith Lacoste and Alex Laude and Glyn Nelson and Roland Nitschke and David Grunwald and Caterina Strambio-De-Castillia} } @article {68751, title = {Polo-like kinase 1 independently controls microtubule-nucleating capacity and size of the centrosome}, journal = {Journal of Cell Biology}, volume = {220}, year = {2021}, month = {01/2021}, abstract = {

Centrosomes are composed of a centriolar core surrounded by a pericentriolar material (PCM) matrix that docks microtubule-nucleating γ-tubulin complexes. During mitotic entry, the PCM matrix increases in size and nucleating capacity in a process called centrosome maturation. Polo-like kinase 1 (PLK1) is recruited to centrosomes and phosphorylates PCM matrix proteins to drive their self-assembly, which leads to PCM expansion. Here, we show that in addition to controlling PCM expansion, PLK1 independently controls the generation of binding sites for γ-tubulin complexes on the PCM matrix. Selectively preventing the generation of PLK1-dependent γ-tubulin docking sites led to spindle defects and impaired chromosome segregation without affecting PCM expansion, highlighting the importance of phospho-regulated centrosomal γ-tubulin docking sites in spindle assembly. Inhibiting both γ-tubulin docking and PCM expansion by mutating substrate target sites recapitulated the effects of loss of centrosomal PLK1 on the ability of centrosomes to catalyze spindle assembly.

}, issn = {0021-9525}, doi = {10.1083/jcb.202009083}, url = {https://doi.org/10.1083/jcb.202009083}, author = {Ohta, Midori and Zhao, Zhiling and Wu, Di and Wang, Shaohe and Harrison, Jennifer L. and G{\'o}mez-Cavazos, J. Sebasti{\'a}n and Desai, Arshad and Oegema, Karen F.} } @article {68990, title = {Principles of signaling pathway modulation for enhancing human naive pluripotency induction.}, journal = {Cell Stem Cell}, volume = {28}, year = {2021}, month = {09/2021}, pages = {1549-1565.e12}, abstract = {

Isolating human MEK/ERK signaling-independent pluripotent stem cells (PSCs) with naive pluripotency characteristics while maintaining differentiation competence and (epi)genetic integrity remains challenging. Here, we engineer reporter systems that allow the screening for defined conditions that induce molecular and functional features of human naive pluripotency. Synergistic inhibition of WNT/β-CATENIN, protein kinase C (PKC), and SRC signaling consolidates the induction of teratoma-competent naive human PSCs, with the capacity to differentiate into trophoblast stem cells (TSCs) and extraembryonic naive endodermal (nEND) cells in\ vitro. Divergent signaling and transcriptional requirements for boosting naive pluripotency were found between mouse and human. P53 depletion in naive hPSCs increased their contribution to mouse-human cross-species chimeric embryos upon priming and differentiation. Finally, MEK/ERK inhibition can be substituted with the inhibition of NOTCH/RBPj, which induces alternative naive-like hPSCs with a diminished risk for deleterious global DNA hypomethylation. Our findings set a framework for defining the signaling foundations of human naive pluripotency.

}, keywords = {Animals, Cell Differentiation, Embryo, Mammalian, Humans, Mice, Pluripotent Stem Cells, Signal Transduction, Trophoblasts}, issn = {1875-9777}, doi = {10.1016/j.stem.2021.04.001}, author = {Bayerl, Jonathan and Ayyash, Muneef and Shani, Tom and Manor, Yair Shlomo and Gafni, Ohad and Massarwa, Rada and Kalma, Yael and Aguilera-Castrejon, Alejandro and Zerbib, Mirie and Amir, Hadar and Sheban, Daoud and Geula, Shay and Mor, Nofar and Weinberger, Leehee and Naveh Tassa, Segev and Krupalnik, Vladislav and Oldak, Bernardo and Livnat, Nir and Tarazi, Shadi and Tawil, Shadi and Wildschutz, Emilie and Ashouokhi, Shahd and Lasman, Lior and Rotter, Varda and Hanna, Suhair and Ben-Yosef, Dalit and Novershtern, Noa and Viukov, Sergey and Hanna, Jacob H} } @article {66901, title = {Protocol for preparation of heterogeneous biological samples for 3D electron microscopy: a case study for insects.}, journal = {Scientific Reports}, volume = {11}, year = {2021}, month = {2021 Feb 25}, pages = {4717}, abstract = {

Modern morphological and structural studies are coming to a new level by incorporating the latest methods of three-dimensional electron microscopy (3D-EM). One of the key problems for the wide usage of these methods is posed by difficulties with sample preparation, since the methods work poorly with heterogeneous (consisting of tissues different in structure and in chemical composition) samples and require expensive equipment and usually much time. We have developed a simple protocol allows preparing heterogeneous biological samples suitable for 3D-EM in a laboratory that has a standard supply of equipment and reagents for electron microscopy. This protocol, combined with focused ion-beam scanning electron microscopy, makes it possible to study 3D ultrastructure of complex biological samples, e.g., whole insect heads, over their entire volume at the cellular and subcellular levels. The protocol provides new opportunities for many areas of study, including connectomics.

}, issn = {2045-2322}, doi = {10.1038/s41598-021-83936-0}, author = {Polilov, Alexey A and Makarova, Anastasia A and Pang, Song and Shan Xu, C and Hess, Harald} } @article {67295, title = {QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy.}, journal = {Nature Methods}, year = {2021}, month = {2021 May 21}, issn = {1548-7105}, doi = {10.1038/s41592-021-01162-y}, author = {Ulrike Boehm and Nelson, Glyn and Brown, Claire M and Bagley, Steve and Bajcsy, Peter and Bischof, Johanna and Dauphin, Aurelien and Dobbie, Ian M and Eriksson, John E and Faklaris, Orestis and Fernandez-Rodriguez, Julia and Ferrand, Alexia and Gelman, Laurent and Gheisari, Ali and Hartmann, Hella and Kukat, Christian and Laude, Alex and Mitkovski, Miso and Munck, Sebastian and North, Alison J and Rasse, Tobias M and Resch-Genger, Ute and Schuetz, Lucas C and Seitz, Arne and Strambio-De-Castillia, Caterina and Swedlow, Jason R and Nitschke, Roland} } @article {66009, title = {QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy}, journal = {Journal of Microscopy}, volume = {284}, year = {2021}, month = {2021 Oct 01}, pages = {56-73}, abstract = {

In April 2020, the QUality Assessment and REProducibility for Instruments and Images in Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata models, and tools, including detailed protocols, with the ultimate aim of improving reproducible advances in scientific research. This White Paper 1) summarizes the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi initiative; 2) identifies the urgent need to address these obstacles in a grassroots manner, through a community of stakeholders including, researchers, imaging scientists, bioimage analysts, bioimage informatics developers, corporate partners, funding agencies, standards organizations, scientific publishers, and observers of such; 3) outlines the current actions of the QUAREP-LiMi initiative, and 4) proposes future steps that can be taken to improve the dissemination and acceptance of the proposed guidelines to manage QC. To summarize, the principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics.

}, url = {https://arxiv.org/abs/2101.09153}, author = {Glyn Nelson and Ulrike Boehm and Steve Bagley and Peter Bajcsy and Johanna Bischof and Claire M Brown and Aurelien Dauphin and Ian M Dobbie and John E Eriksson and Orestis Faklaris and Julia Fernandez-Rodriguez and Alexia Ferrand and Ali Gheisari and Hella Hartmann and Christian Kukat and Alex Laude and Miso Mitkovski and Sebastian Munck and Alison J North and Tobias M Rasse and Ute Resch-Genger and Lucas C Schuetz and Arne Seitz and Caterina Strambio-De-Castillia and Jason R Swedlow and Ioannis Alexopoulos and Karin Aumayr and Sergiy Avilov and Gert-Jan Bakker and Rodrigo R Bammann and Andrea Bassi and Hannes Beckert and Sebastian Beer and Yury Belyaev and Jakob Bierwagen and Konstantin A Birngruber and Manel Bosch and Juergen Breitlow and Lisa A Cameron and Joe Chalfoun and James J Chambers and Chieh-Li Chen and Eduardo Conde-Sousa and Alexander D Corbett and Fabrice P Cordelieres and Elaine Del Nery and Ralf Dietzel and Frank Eismann and Elnaz Fazeli and Andreas Felscher and Hans Fried and Nathalie Gaudreault and Wah Ing Goh and Thomas Guilbert and Roland Hadleigh and Peter Hemmerich and Gerhard A Holst and Michelle S Itano and Claudia B Jaffe and Helena K Jambor and Stuart C Jarvis and Antje Keppler and David Kirchenbuechler and Marcel Kirchner and Norio Kobayashi and Gabriel Krens and Susanne Kunis and Judith Lacoste and Marco Marcell and Gabriel G Martins and Daniel J Metcalf and Claire A Mitchell and Joshua Moore and Tobias Mueller and Michael S Nelson and Stephen Ogg and Shuichi Onami and Alexandra L Palmer and Perrine Paul-Gilloteaux and Jaime A Pimentel and Laure Plantard and Santosh Podder and Elton Rexhepaj and Arnaud Royon and Markku A Saari and Damien Schapman and Vincent Schoonderwoert and Britta Schroth-Diez and Stanley Schwartz and Michael Shaw and Martin Spitaler and Martin T Stoeckl and Damir Sudar and Jeremie Teillon and Stefan Terjung and Roland Thuenauer and Christian D Wilms and Graham D Wright and Roland Nitschke and Laurent Gelman} } @article {67767, title = {Rapid synaptic plasticity contributes to a learned conjunctive code of position and choice-related information in the hippocampus}, journal = {Neuron}, year = {2021}, month = {2021 Oct 14}, abstract = {

To successfully perform goal-directed navigation, animals must know where they are and what they are doing{\textemdash}e.g., looking for water, bringing food back to the nest, or escaping from a predator. Hippocampal neurons code for these critical variables conjunctively, but little is known about how this where/what code is formed or flexibly routed to other brain regions. To address these questions, we performed intracellular whole-cell recordings in mouse CA1 during a cued, two-choice virtual navigation task. We demonstrate that plateau potentials in CA1 pyramidal neurons rapidly strengthen synaptic inputs carrying conjunctive information about position and choice. Plasticity-induced response fields were modulated by cues only in animals previously trained to collect rewards based on these cues. Thus, we reveal that gradual learning is required for the formation of a conjunctive population code, upstream of CA1, while plateau-potential-induced synaptic plasticity in CA1 enables flexible routing of the code to downstream brain regions.

}, doi = {https://doi.org/10.1101/2021.06.30.450574}, author = {Xinyu Zhao and Ching-Lung Hsu and Nelson Spruston} } @article {65833, title = {Reconstruction of motor control circuits in adult Drosophila using automated transmission electron microscopy}, journal = {Cell}, volume = {184}, year = {2021}, month = {2021 Feb 04}, abstract = {

Many animals use coordinated limb movements to interact with and navigate through the environment. To investigate circuit mechanisms underlying locomotor behavior, we used serial-section electron microscopy (EM) to map synaptic connectivity within a neuronal network that controls limb movements. We present a synapse-resolution EM dataset containing the ventral nerve cord (VNC) of an adult female Drosophila melanogaster. To generate this dataset, we developed GridTape, a technology that combines automated serial-section collection with automated high-throughput transmission EM. Using this dataset, we reconstructed 507 motor neurons, including all those that control the legs and wings. We show that a specific class of leg sensory neurons directly synapse onto the largest-caliber motor neuron axons on both sides of the body, representing a unique feedback pathway for fast limb control. We provide open access to the dataset and reconstructions registered to a standard atlas to permit matching of cells between EM and light microscopy data. We also provide GridTape instrumentation designs and software to make large-scale EM data acquisition more accessible and affordable to the scientific community.

}, doi = {10.1101/2020.01.10.902478}, author = {Maniates-Selvin, Jasper T. and Hildebrand, David Grant Colburn and Graham, Brett J. and Kuan, Aaron T. and Thomas, Logan A. and Nguyen, Tri and Buhmann, Julia and Azevedo, Anthony W. and Shanny, Brendan L. and Funke, Jan and Tuthill, John C. and Lee, Wei-Chung Allen} } @article {67709, title = {Regulated exocytosis: Renal Aquaporin-2 3D Vesicular Network Organization and Association with F-actin.}, journal = {American Journal of Physiology: Cell Physiology}, volume = {321}, year = {2021}, month = {2021 Dec 01}, abstract = {

Regulated vesicle exocytosis is a key response to extracellular stimuli in diverse physiological processes; including hormone regulated short-term urine concentration. In the renal collecting duct, the water channel aquaporin-2 localizes to the apical plasma membrane as well as small, sub-apical vesicles. In response to stimulation with the antidiuretic hormone, arginine vasopressin, aquaporin-2 containing vesicles fuse with the plasma membrane, which increases collecting duct water reabsorption and thus, urine concentration. The nano-scale size of these vesicles has limited analysis of their 3D organization. Using a cell system combined with 3D super resolution microscopy, we provide the first direct analysis of the 3D network of aquaporin-2 containing exocytic vesicles in a cell culture system. We show that aquaporin-2 vesicles are 43 {\textpm} 3nm in diameter, a size similar to synaptic vesicles, and that one fraction of AQP2 vesicles localized with the sub-cortical F-actin layer and the other localized in between the F-actin layer and the plasma membrane. Aquaporin-2 vesicles associated with F-actin and this association was enhanced in a serine 256 phospho-mimic of aquaporin-2, whose phosphorylation is a key event in antidiuretic hormone-mediated aquaporin-2 vesicle exocytosis.

}, issn = {1522-1563}, doi = {10.1152/ajpcell.00255.2021}, author = {Holst, Mikkel R and Gammelgaard, Louis and Aaron, Jesse and Login, Fr{\'e}d{\'e}ric H and Rajkumar, Sampavi and Hahn, Ute and Nejsum, Lene N} } @article {67296, title = {Regulation of coordinated muscular relaxation in Drosophila larvae by a pattern-regulating intersegmental circuit.}, journal = {Nature Communications}, volume = {12}, year = {2021}, month = {2021 May 19}, pages = {2943}, abstract = {

Typical patterned movements in animals are achieved through combinations of contraction and delayed relaxation of groups of muscles. However, how intersegmentally coordinated patterns of muscular relaxation are regulated by the neural circuits remains poorly understood. Here, we identify Canon, a class of higher-order premotor interneurons, that regulates muscular relaxation during backward locomotion of Drosophila larvae. Canon neurons are cholinergic interneurons present in each abdominal neuromere and show wave-like activity during fictive backward locomotion. Optogenetic activation of Canon neurons induces relaxation of body wall muscles, whereas inhibition of these neurons disrupts timely muscle relaxation. Canon neurons provide excitatory outputs to inhibitory premotor interneurons. Canon neurons also connect with each other to form an intersegmental circuit and regulate their own wave-like activities. Thus, our results demonstrate how coordinated muscle relaxation can be realized by an intersegmental circuit that regulates its own patterned activity and sequentially terminates motor activities along the anterior-posterior axis.

}, issn = {2041-1723}, doi = {10.1038/s41467-021-23273-y}, author = {Hiramoto, Atsuki and Jonaitis, Julius and Niki, Sawako and Kohsaka, Hiroshi and Fetter, Richard D and Cardona, Albert and Pulver, Stefan R and Nose, Akinao} } @article {68425, title = {Single-cell transcriptomes of developing and adult olfactory receptor neurons in Drosophila}, journal = {Elife}, volume = {10}, year = {2021}, month = {02/2021}, abstract = {

Recognition of environmental cues is essential for the survival of all organisms. Transcriptional changes occur to enable the generation and function of the neural circuits underlying sensory perception. To gain insight into these changes, we generated single-cell transcriptomes of olfactory- (ORNs), thermo-, and hygro-sensory neurons at an early developmental and adult stage using single-cell and single-nucleus RNA sequencing. We discovered that ORNs maintain expression of the same olfactory receptors across development. Using receptor expression and computational approaches, we matched transcriptomic clusters corresponding to anatomically and physiologically defined neuron types across multiple developmental stages. We found that cell-type-specific transcriptomes partly reflected axon trajectory choices in development and sensory modality in adults. We uncovered stage-specific genes that could regulate the wiring and sensory responses of distinct ORN types. Collectively, our data reveal transcriptomic features of sensory neuron biology and provide a resource for future studies of their development and physiology.

}, keywords = {Animals, Drosophila melanogaster, Drosophila Proteins, Female, Male, Olfactory Receptor Neurons, Sequence Analysis, RNA, Single-Cell Analysis, Smell, Transcriptome}, issn = {2050-084X}, doi = {10.7554/eLife.63856}, author = {McLaughlin, Colleen N and Brbi{\'c}, Maria and Xie, Qijing and Li, Tongchao and Horns, Felix and Kolluru, Sai Saroja and Kebschull, Justus M and Vacek, David and Xie, Anthony and Li, Jiefu and Jones, Robert C and Leskovec, Jure and Quake, Stephen R and Luo, Liqun and Li, Hongjie} } @article {67872, title = {Small-molecule ligands can inhibit -1 programmed ribosomal frameshifting in a broad spectrum of coronaviruses.}, journal = {bioRxiv}, year = {2021}, month = {2021 Aug 06}, abstract = {

Recurrent outbreaks of novel zoonotic coronavirus (CoV) diseases since 2000 have high-lighted the importance of developing therapeutics with broad-spectrum activity against CoVs. Because all CoVs use -1 programmed ribosomal frameshifting (-1 PRF) to control expression of key viral proteins, the frameshift signal in viral mRNA that stimulates -1 PRF provides a promising potential target for such therapeutics. To test the viability of this strategy, we explored a group of 6 small-molecule ligands, evaluating their activity against the frameshift signals from a panel of representative bat CoVs{\textemdash}the most likely source of future zoonoses{\textemdash}as well as SARS-CoV-2 and MERS-CoV. We found that whereas some ligands had notable activity against only a few of the frameshift signals, the serine protease inhibitor nafamostat suppressed -1 PRF significantly in several of them, while having limited to no effect on -1 PRF caused by frameshift signals from other viruses used as negative controls. These results suggest it is possible to find small-molecule ligands that inhibit -1 PRF specifically in a broad spectrum of CoVs, establishing the frameshift signal as a viable target for developing pan-coronaviral therapeutics.

}, doi = {10.1101/2021.08.06.455424}, url = {https://doi.org/10.1101/2021.08.06.455424}, author = {Sneha Munshi and Krishna Neupane and Sandaru M. Ileperuma and Matthew T.J. Halma and Jamie A. Kelly and Clarissa F. Halpern and Jonathan D. Dinman and Sarah Loerch and Michael T. Woodside} } @article {67201, title = {SNT: a unifying toolbox for quantification of neuronal anatomy.}, journal = {Nature Methods}, volume = {18}, year = {2021}, month = {2021 Apr 01}, pages = {374-377}, abstract = {

SNT is an end-to-end framework for neuronal morphometry and whole-brain connectomics that supports tracing, proof-editing, visualization, quantification and modeling of neuroanatomy. With an open architecture, a large user base, community-based documentation, support for complex imagery and several model organisms, SNT is a flexible resource for the broad neuroscience community. SNT is both a desktop application and multi-language scripting library, and it is available through the Fiji distribution of ImageJ.

}, issn = {1548-7105}, doi = {10.1038/s41592-021-01105-7}, author = {Arshadi, Cameron and G{\"u}nther, Ulrik and Eddison, Mark and Harrington, Kyle I S and Ferreira, Tiago A} } @article {67675, title = {Structured patterns of activity in pulse-coupled oscillator networks with varied connectivity.}, journal = {PLoS One}, volume = {16}, year = {2021}, month = {2021 Aug 11}, pages = {e0256034}, abstract = {

Identifying coordinated activity within complex systems is essential to linking their structure and function. We study collective activity in networks of pulse-coupled oscillators that have variable network connectivity and integrate-and-fire dynamics. Starting from random initial conditions, we see the emergence of three broad classes of behaviors that differ in their collective spiking statistics. In the first class ("temporally-irregular"), all nodes have variable inter-spike intervals, and the resulting firing patterns are irregular. In the second ("temporally-regular"), the network generates a coherent, repeating pattern of activity in which all nodes fire with the same constant inter-spike interval. In the third ("chimeric"), subgroups of coherently-firing nodes coexist with temporally-irregular nodes. Chimera states have previously been observed in networks of oscillators; here, we find that the notions of temporally-regular and chimeric states encompass a much richer set of dynamical patterns than has yet been described. We also find that degree heterogeneity and connection density have a strong effect on the resulting state: in binomial random networks, high degree variance and intermediate connection density tend to produce temporally-irregular dynamics, while low degree variance and high connection density tend to produce temporally-regular dynamics. Chimera states arise with more frequency in networks with intermediate degree variance and either high or low connection densities. Finally, we demonstrate that a normalized compression distance, computed via the Lempel-Ziv complexity of nodal spike trains, can be used to distinguish these three classes of behavior even when the phase relationship between nodes is arbitrary.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0256034}, author = {Kadhim, Kyra L and Hermundstad, Ann M and Brown, Kevin S} } @article {66028, title = {Structure-Function Dataset Reveals Environment Effects within a Fluorescent Protein Model System.}, journal = {Angew Chemie (International Edition English)}, year = {2021}, month = {2021 Feb 04}, abstract = {

Anisotropic environments can drastically alter the spectroscopy and photochemistry of molecules, leading to complex structure-function relationships. We examined this using fluorescent proteins as easy-to-modify model systems. Starting from a single scaffold, we have developed a range of 27 photochromic fluorescent proteins that cover a broad range of spectroscopic properties, including the determination of 43 crystal structures. Correlation and principal component analysis confirmed the complex relationship between structure and spectroscopy, but also allowed us to identify consistent trends and to relate these to the spatial organization. We find that changes in spectroscopic properties can come about through multiple underlying mechanisms, of which polarity, hydrogen bonding and presence of water molecules are key modulators. We anticipate that our findings and rich structure/spectroscopy dataset can open opportunities for the development and evaluation of new and existing protein engineering methods.

}, issn = {1521-3773}, doi = {10.1002/anie.202015201}, author = {De Zitter, Elke and Hugelier, Siewert and Duw{\'e}, Sam and Vandenberg, Wim and Tebo, Alison G and Van Meervelt, Luc and Dedecker, Peter} } @article {66008, title = {Survey of spiking in the mouse visual system reveals functional hierarchy.}, journal = {Nature}, volume = {592(7852):86-92}, year = {2021}, month = {2021 Jan 20}, pages = {86-92}, abstract = {

The anatomy of the mammalian visual system, from the retina to the neocortex, is organized hierarchically. However, direct observation of cellular-level functional interactions across this hierarchy is lacking due to the challenge of simultaneously recording activity across numerous regions. Here we describe a large, open dataset-part of the Allen Brain Observatory-that surveys spiking from tens of thousands of units in six cortical and two thalamic regions in the brains of mice responding to a battery of visual stimuli. Using cross-correlation analysis, we reveal that the organization of inter-area functional connectivity during visual stimulation mirrors the anatomical hierarchy from the Allen Mouse Brain Connectivity Atlas. We find that four classical hierarchical measures-response latency, receptive-field size, phase-locking to drifting gratings and response decay timescale-are all correlated with the hierarchy. Moreover, recordings obtained during a visual task reveal that the correlation between neural activity and behavioural choice also increases along the hierarchy. Our study provides a foundation for understanding coding and signal propagation across hierarchically organized cortical and thalamic visual areas.

}, issn = {1476-4687}, doi = {10.1038/s41586-020-03171-x}, author = {Siegle, Joshua H and Jia, Xiaoxuan and Durand, Severine and Gale, Sam and Bennett, Corbett and Graddis, Nile and Heller, Greggory and Ramirez, Tamina K and Choi, Hannah and Luviano, Jennifer A and Groblewski, Peter A and Ahmed, Ruweida and Arkhipov, Anton and Bernard, Amy and Billeh, Yazan N and Brown, Dillan and Buice, Michael A and Cain, Nicolas and Caldejon, Shiella and Casal, Linzy and Cho, Andrew and Chvilicek, Maggie and Cox, Timothy C and Dai, Kael and Denman, Daniel J and de Vries, Saskia E J and Dietzman, Roald and Esposito, Luke and Farrell, Colin and Feng, David and Galbraith, John and Garrett, Marina and Gelfand, Emily C and Hancock, Nicole and Harris, Julie A and Howard, Robert and Hu, Brian and Hytnen, Ross and Iyer, Ramakrishnan and Jessett, Erika and Johnson, Katelyn and Kato, India and Kiggins, Justin and Lambert, Sophie and Lecoq, Jerome and Ledochowitsch, Peter and Lee, Jung Hoon and Leon, Arielle and Li, Yang and Liang, Elizabeth and Long, Fuhui and Mace, Kyla and Melchior, Jose and Millman, Daniel and Mollenkopf, Tyler and Nayan, Chelsea and Ng, Lydia and Ngo, Kiet and Nguyen, Thuyahn and Nicovich, Philip R and North, Kat and Ocker, Gabriel Koch and Ollerenshaw, Doug and Oliver, Michael and Pachitariu, Marius and Perkins, Jed and Reding, Melissa and Reid, David and Robertson, Miranda and Ronellenfitch, Kara and Seid, Sam and Slaughterbeck, Cliff and Stoecklin, Michelle and Sullivan, David and Sutton, Ben and Swapp, Jackie and Thompson, Carol and Turner, Kristen and Wakeman, Wayne and Whitesell, Jennifer D and Williams, Derric and Williford, Ali and Young, Rob and Zeng, Hongkui and Naylor, Sarah and Phillips, John W and Reid, R Clay and Mihalas, Stefan and Olsen, Shawn R and Koch, Christof} } @article {67713, title = {Synchronous and opponent thermosensors use flexible cross-inhibition to orchestrate thermal homeostasis.}, journal = {Science Advances}, volume = {7}, year = {2021}, month = {2021 Aug 27}, abstract = {

Body temperature homeostasis is essential and reliant upon the integration of outputs from multiple classes of cooling- and warming-responsive cells. The computations that integrate these outputs are not understood. Here, we discover a set of warming cells (WCs) and show that the outputs of these WCs combine with previously described cooling cells (CCs) in a cross-inhibition computation to drive thermal homeostasis in larval WCs and CCs detect temperature changes using overlapping combinations of ionotropic receptors: Ir68a, Ir93a, and Ir25a for WCs and Ir21a, Ir93a, and Ir25a for CCs. WCs mediate avoidance to warming while cross-inhibiting avoidance to cooling, and CCs mediate avoidance to cooling while cross-inhibiting avoidance to warming. Ambient temperature-dependent regulation of the strength of WC- and CC-mediated cross-inhibition keeps larvae near their homeostatic set point. Using neurophysiology, quantitative behavioral analysis, and connectomics, we demonstrate how flexible integration between warming and cooling pathways can orchestrate homeostatic thermoregulation.

}, issn = {2375-2548}, doi = {10.1126/sciadv.abg6707}, author = {Hernandez-Nunez, Luis and Chen, Alicia and Budelli, Gonzalo and Berck, Matthew E and Richter, Vincent and Rist, Anna and Thum, Andreas S and Cardona, Albert and Klein, Mason and Garrity, Paul and Samuel, Aravinthan D T} } @article {66001, title = {Systems Neuroscience of Natural Behaviors in Rodents.}, journal = {Journal of Neuroscience}, volume = {41}, year = {2021}, month = {2021 Feb 03}, pages = {911-1}, abstract = {

Animals evolved in complex environments, producing a wide range of behaviors, including navigation, foraging, prey capture, and conspecific interactions, which vary over timescales ranging from milliseconds to days. Historically, these behaviors have been the focus of study for ecology and ethology, while systems neuroscience has largely focused on short timescale behaviors that can be repeated thousands of times and occur in highly artificial environments. Thanks to recent advances in machine learning, miniaturization, and computation, it is newly possible to study freely moving animals in more natural conditions while applying systems techniques: performing temporally specific perturbations, modeling behavioral strategies, and recording from large numbers of neurons while animals are freely moving. The authors of this review are a group of scientists with deep appreciation for the common aims of systems neuroscience, ecology, and ethology. We believe it is an extremely exciting time to be a neuroscientist, as we have an opportunity to grow as a field, to embrace interdisciplinary, open, collaborative research to provide new insights and allow researchers to link knowledge across disciplines, species, and scales. Here we discuss the origins of ethology, ecology, and systems neuroscience in the context of our own work and highlight how combining approaches across these fields has provided fresh insights into our research. We hope this review facilitates some of these interactions and alliances and helps us all do even better science, together.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.1877-20.2020}, author = {Dennis, Emily Jane and El Hady, Ahmed and Michaiel, Angie and Clemens, Ann and Gowan Tervo, Dougal R and Voigts, Jakob and Datta, Sandeep Robert} } @article {67853, title = {Systems Neuroscience of Natural Behaviors in Rodents}, journal = {Journal of Neuroscience}, volume = {41}, year = {2021}, month = {02/2021}, pages = {911{\textendash}919}, abstract = {

Animals evolved in complex environments, producing a wide range of behaviors, including navigation, foraging, prey capture, and conspecific interactions, which vary over timescales ranging from milliseconds to days. Historically, these behaviors have been the focus of study for ecology and ethology, while systems neuroscience has largely focused on short timescale behaviors that can be repeated thousands of times and occur in highly artificial environments. Thanks to recent advances in machine learning, miniaturization, and computation, it is newly possible to study freely moving animals in more natural conditions while applying systems techniques: performing temporally specific perturbations, modeling behavioral strategies, and recording from large numbers of neurons while animals are freely moving. The authors of this review are a group of scientists with deep appreciation for the common aims of systems neuroscience, ecology, and ethology. We believe it is an extremely exciting time to be a neuroscientist, as we have an opportunity to grow as a field, to embrace interdisciplinary, open, collaborative research to provide new insights and allow researchers to link knowledge across disciplines, species, and scales. Here we discuss the origins of ethology, ecology, and systems neuroscience in the context of our own work and highlight how combining approaches across these fields has provided fresh insights into our research. We hope this review facilitates some of these interactions and alliances and helps us all do even better science, together.

}, issn = {0270-6474}, doi = {10.1523/JNEUROSCI.1877-20.2020}, url = {https://www.jneurosci.org/content/41/5/911}, author = {Dennis, Emily Jane and El Hady, Ahmed and Michaiel, Angie and Clemens, Ann and Tervo, Dougal R. Gowan and Voigts, Jakob and Datta, Sandeep Robert} } @article {68426, title = {Temporal evolution of single-cell transcriptomes of olfactory projection neurons.}, journal = {Elife}, volume = {10}, year = {2021}, month = {01/2021}, abstract = {

Neurons undergo substantial morphological and functional changes during development to form precise synaptic connections and acquire specific physiological properties. What are the underlying transcriptomic bases? Here, we obtained the single-cell transcriptomes of olfactory projection neurons (PNs) at four developmental stages. We decoded the identity of 21 transcriptomic clusters corresponding to 20 PN types and developed methods to match transcriptomic clusters representing the same PN type across development. We discovered that PN transcriptomes reflect unique biological processes unfolding at each stage-neurite growth and pruning during metamorphosis at an early pupal stage; peaked transcriptomic diversity during olfactory circuit assembly at mid-pupal stages; and neuronal signaling in adults. At early developmental stages, PN types with adjacent birth order share similar transcriptomes. Together, our work reveals principles of cellular diversity during brain development and provides a resource for future studies of neural development in PNs and other neuronal types.

}, keywords = {Animals, Drosophila melanogaster, Neurites, Olfactory Nerve, Single-Cell Analysis, Time Factors, Transcriptome}, issn = {2050-084X}, doi = {10.7554/eLife.63450}, author = {Xie, Qijing and Brbi{\'c}, Maria and Horns, Felix and Kolluru, Sai Saroja and Jones, Robert C and Li, Jiefu and Reddy, Anay R and Xie, Anthony and Kohani, Sayeh and Li, Zhuoran and McLaughlin, Colleen N and Li, Tongchao and Xu, Chuanyun and Vacek, David and Luginbuhl, David J and Leskovec, Jure and Quake, Stephen R and Luo, Liqun and Li, Hongjie} } @article {67242, title = {Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model.}, journal = {bioRxiv}, year = {2021}, month = {2021 Apr 28}, abstract = {

Digital light microscopy provides powerful tools for quantitatively probing the real-time dynamics of subcellular structures. While the power of modern microscopy techniques is undeniable, rigorous record-keeping and quality control are required to ensure that imaging data may be properly interpreted\ (quality),\ reproduced\ (reproducibility),\ and used to extract reliable information and scientific knowledge which can be shared for further analysis (value). Keeping notes on microscopy experiments and quality control procedures ought to be straightforward, as the microscope is a machine whose components are defined and the performance measurable. Nevertheless, to this date, no universally adopted community-driven specifications exist that delineate the required information about the microscope hardware and acquisition settings (i.e., microscopy {\textquotedblleft}data provenance{\textquotedblright} metadata) and the minimally accepted calibration metrics (i.e., microscopy quality control metadata) that should be automatically recorded by both commercial microscope manufacturers and customized microscope developers. In the absence of agreed guidelines, it is inherently difficult for scientists to create comprehensive records of imaging experiments and ensure the quality of resulting image data or for manufacturers to incorporate standardized reporting and performance metrics. To add to the confusion, microscopy experiments vary greatly in aim and complexity, ranging from purely descriptive work to complex, quantitative and even sub-resolution studies that require more detailed reporting and quality control measures.

}, doi = {10.1101/2021.04.25.441198v1}, url = {https://www.biorxiv.org/content/10.1101/2021.04.25.441198v1}, author = {Mathias Hammer and Maximiliaan Huisman and Alex Rigano and Ulrike Boehm and James J. Chambers and Nathalie Gaudreault and Alison J. North and Jaime A. Pimentel and Damir Sudar and Peter Bajcsy and Claire M. Brown and Alexander D. Corbett and Orestis Faklaris and Judith Lacoste and Alex Laude and Glyn Nelson and Roland Nitschke and Farzin Farzam and Carlas S. Smith and David Grunwald and Caterina Strambio-De-Castillia} } @article {67812, title = {Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model.}, journal = {Nature Methods}, volume = {18}, year = {2021}, month = {2021 Dec 03}, pages = {1427-1440}, issn = {1548-7105}, doi = {10.1038/s41592-021-01327-9}, author = {Hammer, Mathias and Huisman, Maximiliaan and Rigano, Alessandro and Boehm, Ulrike and Chambers, James J and Gaudreault, Nathalie and North, Alison J and Pimentel, Jaime A and Sudar, Damir and Bajcsy, Peter and Brown, Claire M and Corbett, Alexander D and Faklaris, Orestis and Lacoste, Judith and Laude, Alex and Nelson, Glyn and Nitschke, Roland and Farzam, Farzin and Smith, Carlas S and Grunwald, David and Strambio-De-Castillia, Caterina} } @article {67310, title = {Unveiling the sensory and interneuronal pathways of the neuroendocrine connectome in Drosophila.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Jun 04}, abstract = {

Neuroendocrine systems in animals maintain organismal homeostasis and regulate stress response. Although a great deal of work has been done on the neuropeptides and hormones that are released and act on target organs in the periphery, the synaptic inputs onto these neuroendocrine outputs in the brain are less well understood. Here, we use the transmission electron microscopy reconstruction of a whole central nervous system in the larva to elucidate the sensory pathways and the interneurons that provide synaptic input to the neurosecretory cells projecting to the endocrine organs. Predicted by network modeling, we also identify a new carbon dioxide-responsive network that acts on a specific set of neurosecretory cells and that includes those expressing corazonin (Crz) and diuretic hormone 44 (Dh44) neuropeptides. Our analysis reveals a neuronal network architecture for combinatorial action based on sensory and interneuronal pathways that converge onto distinct combinations of neuroendocrine outputs.

}, issn = {2050-084X}, doi = {10.7554/eLife.65745}, author = {H{\"u}ckesfeld, Sebastian and Schlegel, Philipp and Miroschnikow, Anton and Schoofs, Andreas and Zinke, Ingo and Haubrich, Andr{\'e} N and Schneider-Mizell, Casey M and Truman, James W and Fetter, Richard D and Cardona, Albert and Pankratz, Michael J} } @article {67736, title = {Visualizing the Invisible: Advanced Optical Microscopy as a Tool to Measure Biomechanical Forces.}, journal = {Frontiers in Cell and Developmental Biology}, volume = {9}, year = {2021}, month = {2021 Sep 06}, pages = {706126}, abstract = {

The importance of mechanical force in biology is evident across diverse length scales, ranging from tissue morphogenesis during embryo development to mechanotransduction across single adhesion proteins at the cell surface. Consequently, many force measurement techniques rely on optical microscopy to measure forces being applied by cells on their environment, to visualize specimen deformations due to external forces, or even to directly apply a physical perturbation to the sample via photoablation or optogenetic tools. Recent developments in advanced microscopy offer improved approaches to enhance spatiotemporal resolution, imaging depth, and sample viability. These advances can be coupled with already existing force measurement methods to improve sensitivity, duration and speed, amongst other parameters. However, gaining access to advanced microscopy instrumentation and the expertise necessary to extract meaningful insights from these techniques is an unavoidable hurdle. In this Live Cell Imaging special issue Review, we survey common microscopy-based force measurement techniques and examine how they can be bolstered by emerging microscopy methods. We further explore challenges related to the accompanying data analysis in biomechanical studies and discuss the various resources available to tackle the global issue of technology dissemination, an important avenue for biologists to gain access to pre-commercial instruments that can be leveraged for biomechanical studies.

}, issn = {2296-634X}, doi = {10.3389/fcell.2021.706126}, author = {Hobson, Chad M and Aaron, Jesse S and Heddleston, John M and Chew, Teng-Leong} } @article {67750, title = {Whole-cell organelle segmentation in volume electron microscopy.}, journal = {Nature}, volume = {599}, year = {2021}, month = {2021 Nov 01}, pages = {141-46}, abstract = {

Cells contain hundreds of organelles and macromolecular assemblies. Obtaining a complete understanding of their intricate organization requires the nanometre-level, three-dimensional reconstruction of whole cells, which is only feasible with robust and scalable automatic methods. Here, to support the development of such methods, we annotated up to 35 different cellular organelle classes-ranging from endoplasmic reticulum to microtubules to ribosomes-in diverse sample volumes from multiple cell types imaged at a near-isotropic resolution of 4 nm per voxel with focused ion beam scanning electron microscopy (FIB-SEM). We trained deep learning architectures to segment these structures in 4 nm and 8 nm per voxel FIB-SEM volumes, validated their performance and showed that automatic reconstructions can be used to directly quantify previously inaccessible metrics including spatial interactions between cellular components. We also show that such reconstructions can be used to automatically register light and electron microscopy images for correlative studies. We have created an open data and open-source web repository, {\textquoteright}OpenOrganelle{\textquoteright}, to share the data, computer code and trained models, which will enable scientists everywhere to query and further improve automatic reconstruction of these datasets.

}, issn = {1476-4687}, doi = {10.1038/s41586-021-03977-3}, author = {Heinrich, Larissa and Bennett, Davis and Ackerman, David and Park, Woohyun and Bogovic, John and Eckstein, Nils and Petruncio, Alyson and Clements, Jody and Pang, Song and Xu, C Shan and Funke, Jan and Korff, Wyatt and Hess, Harald F and Lippincott-Schwartz, Jennifer and Saalfeld, Stephan and Weigel, Aubrey V} } @article {65368, title = {3D ATAC-PALM: super-resolution imaging of the accessible genome.}, journal = {Nature Methods}, volume = {17}, year = {2020}, month = {2020 Apr 01}, pages = {430-6}, abstract = {

To image the accessible genome at nanometer scale in situ, we developed three-dimensional assay for transposase-accessible chromatin-photoactivated localization microscopy (3D ATAC-PALM) that integrates an assay for transposase-accessible chromatin with visualization, PALM super-resolution imaging and lattice light-sheet microscopy. Multiplexed with oligopaint DNA{\textendash}fluorescence in situ hybridization (FISH), RNA{\textendash}FISH and protein fluorescence, 3D ATAC-PALM connected microscopy and genomic data, revealing spatially segregated accessible chromatin domains (ACDs) that enclose active chromatin and transcribed genes. Using these methods to analyze genetically perturbed cells, we demonstrated that genome architectural protein CTCF prevents excessive clustering of accessible chromatin and decompacts ACDs. These results highlight 3D ATAC-PALM as a useful tool to probe the structure and organizing mechanism of the genome.

}, issn = {1548-7091}, doi = {10.1038/s41592-020-0775-2}, url = {http://www.nature.com/articles/s41592-020-0775-2}, author = {Xie, Liangqi and Dong, Peng and Chen, Xingqi and Hsieh, Tsung-Han S. and Banala, Sambashiva and De Marzio, Margherita and English, Brian P. and Qi, Yifeng and Jung, Seol Kyoung and Kieffer-Kwon, Kyong-Rim and Legant, Wesley R. and Hansen, Anders S. and Schulmann, Anton and Casellas, Rafael and Zhang, Bin and Betzig, Eric and Lavis, Luke D. and Chang, Howard Y. and Tjian, Robert and Liu, Zhe} } @article {68841, title = {Accelerated EM Connectome Reconstruction using 3D Visualization and Segmentation Graphs}, journal = {bioRxiv}, year = {2020}, month = {2020 Jan 17}, abstract = {

Recent advances in automatic image segmentation and synapse prediction in electron microscopy (EM) datasets of the brain enable more efficient reconstruction of neural connectivity. In these datasets, a single neuron can span thousands of images containing complex tree-like arbors with thousands of synapses. While image segmentation algorithms excel within narrow fields of views, the algorithms sometimes struggle to correctly segment large neurons, which require large context given their size and complexity. Conversely, humans are comparatively good at reasoning with large objects. In this paper, we introduce several semi-automated strategies that combine 3D visualization and machine guidance to accelerate connectome reconstruction. In particular, we introduce a strategy to quickly correct a segmentation through merging and\ cleaving, or splitting a segment along supervoxel boundaries, with both operations driven by affinity scores in the underlying segmentation. We deploy these algorithms as streamlined workflows in a tool called\ Neu3\ and demonstrate superior performance compared to prior work, thus enabling efficient reconstruction of much larger datasets. The insights into proofreading from our work clarify the trade-offs to consider when tuning the parameters of image segmentation algorithms.

}, doi = {10.1101/2020.01.17.909572}, url = {https://doi.org/10.1101/2020.01.17.909572}, author = {Philip M. Hubbard and Stuart Berg and Ting Zhao and Donald J. Olbris and Lowell Umayam and Jeremy Maitin-Shepard and Michal Januszewski and William T. Katz and Erika R. Neace and Stephen M. Plaza} } @article {65615, title = {Arousal modulates retinal output.}, journal = {Neuron}, volume = {107}, year = {2020}, month = {2020 Aug 01}, pages = {487}, abstract = {

At various stages of the visual system, visual responses are modulated by arousal. Here, we find that in mice this modulation operates as early as in the first synapse from the retina and even in retinal axons. To measure retinal activity in the awake, intact brain, we imaged the synaptic boutons of retinal axons in the superior colliculus. Their activity depended not only on vision but also on running speed and pupil size, regardless of retinal illumination. Arousal typically reduced their visual responses and selectivity for direction and orientation. Recordings from retinal axons in the optic tract revealed that arousal modulates the firing of some retinal ganglion cells. Arousal had similar effects postsynaptically in colliculus neurons, independent of activity in the other main source of visual inputs to the colliculus, the primary visual cortex. These results indicate that arousal modulates activity at every stage of the mouse visual system.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2020.04.026}, author = {Schr{\"o}der, Sylvia and Steinmetz, Nicholas A and Krumin, Michael and Pachitariu, Marius and Rizzi, Matteo and Lagnado, Leon and Harris, Kenneth D and Carandini, Matteo} } @article {65311, title = {Behavioral features of motivated response to alcohol in Drosophila.}, journal = {bioRxiv}, year = {2020}, month = {2020 Feb 17}, abstract = {

Animals avoid predators and find the best food and mates by learning from the consequences of their behavior. However, reinforcers are not always uniquely appetitive or aversive but can have complex properties. Most intoxicating substances fall within this category; provoking aversive sensory and physiological reactions while simultaneously inducing overwhelming appetitive properties. Here we describe the subtle behavioral features associated with continued seeking for alcohol despite aversive consequences. We developed an automated runway apparatus to measure how Drosophila respond to consecutive exposures of a volatilized substance. Behavior within this Behavioral Expression of Ethanol Reinforcement Runway (BEER Run) demonstrated a defined shift from aversive to appetitive responses to volatilized ethanol. Behavioral metrics attained by combining computer vision and machine learning methods, reveal that a subset of 9 classified behaviors and component behavioral features associate with this shift. We propose this combination of 9 be

}, author = {Catalano, Jamie L. and Mei, Nicholas and Azanchi, Reza and Song, Sophia and Blackwater, Tyler and Heberlein, Ulrike and Kaun, Karla R.} } @article {65798, title = {Behavioral state coding by molecularly defined paraventricular hypothalamic cell type ensembles.}, journal = {Science}, volume = {370}, year = {2020}, month = {2020 Oct 16}, abstract = {

Brains encode behaviors using neurons amenable to systematic classification by gene expression. The contribution of molecular identity to neural coding is not understood because of the challenges involved with measuring neural dynamics and molecular information from the same cells. We developed CaRMA (calcium and RNA multiplexed activity) imaging based on recording in vivo single-neuron calcium dynamics followed by gene expression analysis. We simultaneously monitored activity in hundreds of neurons in mouse paraventricular hypothalamus (PVH). Combinations of cell-type marker genes had predictive power for neuronal responses across 11 behavioral states. The PVH uses combinatorial assemblies of molecularly defined neuron populations for grouped-ensemble coding of survival behaviors. The neuropeptide receptor neuropeptide Y receptor type 1 (Npy1r) amalgamated multiple cell types with similar responses. Our results show that molecularly defined neurons are important processing units for brain function.

}, issn = {1095-9203}, doi = {10.1126/science.abb2494}, author = {Xu, Shengjin and Yang, Hui and Menon, Vilas and Lemire, Andrew L and Wang, Lihua and Henry, Fredrick E and Turaga, Srinivas C and Sternson, Scott M} } @article {65650, title = {Bright and high-performance genetically encoded Ca indicator based on mNeonGreen fluorescent protein.}, journal = {ACS Sensors}, year = {2020}, month = {2020 Jul 08}, abstract = {

Genetically encodable calcium ion (Ca) indicators (GECIs) based on green fluorescent proteins (GFP) are powerful tools for imaging of cell signaling and neural activity in model organisms. Following almost 2 decades of steady improvements in the GFP-based GCaMP series of GECIs, the performance of the most recent generation (i.e., jGCaMP7) may have reached its practical limit due to the inherent properties of GFP. In an effort to sustain the steady progression toward ever-improved GECIs, we undertook the development of a new GECI based on the bright monomeric GFP, mNeonGreen (mNG). The resulting indicator, mNG-GECO1, is 60\% brighter than GCaMP6s in vitro and provides comparable performance as demonstrated by imaging Ca dynamics in cultured cells, primary neurons, and in vivo in larval zebrafish. These results suggest that mNG-GECO1 is a promising next-generation GECI that could inherit the mantle of GCaMP and allow the steady improvement of GECIs to continue for generations to come.

}, issn = {2379-3694}, doi = {10.1021/acssensors.0c00279}, author = {Zarowny, Landon and Abhi Aggarwal and Rutten, Virginia M S and Kolb, Ilya and Patel, Ronak and Huang, Hsin-Yi and Chang, Yu-Fen and Phan, Tiffany and Kanyo, Richard and Ahrens, Misha B and Allison, W Ted and Podgorski, Kaspar and Campbell, Robert E} } @article {65659, title = {Cell types promoting goosebumps form a niche to regulate hair follicle stem cells.}, journal = {Cell}, volume = {182}, year = {2020}, month = {2020 Aug 6}, pages = {578}, abstract = {

Piloerection (goosebumps) requires concerted actions of the hair follicle, the arrector pili muscle (APM), and the sympathetic nerve, providing a model to study interactions across epithelium, mesenchyme, and nerves. Here, we show that APMs and sympathetic nerves form a dual-component niche to modulate hair follicle stem cell (HFSC) activity. Sympathetic nerves form synapse-like structures with HFSCs and regulate HFSCs through norepinephrine, whereas APMs maintain sympathetic innervation to HFSCs. Without norepinephrine signaling, HFSCs enter deep quiescence by down-regulating the cell cycle and metabolism while up-regulating quiescence regulators Foxp1 and Fgf18. During development, HFSC progeny secretes Sonic Hedgehog (SHH) to direct the formation of this APM-sympathetic nerve niche, which in turn controls hair follicle regeneration in adults. Our results reveal a reciprocal interdependence between a regenerative tissue and its niche at different stages and demonstrate sympathetic nerves can modulate stem cells through synapse-like connections and neurotransmitters to couple tissue production with demands.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2020.06.031}, author = {Shwartz, Yulia and Gonzalez-Celeiro, Meryem and Chen, Chih-Lung and Pasolli, H Amalia and Sheu, Shu-Hsien and Fan, Sabrina Mai-Yi and Shamsi, Farnaz and Assaad, Steven and Lin, Edrick Tai-Yu and Zhang, Bing and Tsai, Pai-Chi and He, Megan and Tseng, Yu-Hua and Lin, Sung-Jan and Hsu, Ya-Chieh} } @article {68429, title = {Cell-Surface Proteomic Profiling in the Fly Brain Uncovers Wiring Regulators.}, journal = {Cell}, volume = {180}, year = {2020}, month = {01/2020}, pages = {373-386.e15}, abstract = {

Molecular interactions at the cellular interface mediate organized assembly of single cells into tissues and, thus, govern the development and physiology of multicellular organisms. Here, we developed a cell-type-specific, spatiotemporally resolved approach to profile cell-surface proteomes in intact tissues. Quantitative profiling of cell-surface proteomes of Drosophila olfactory projection neurons (PNs) in pupae and adults revealed global downregulation of wiring molecules and upregulation of synaptic molecules in the transition from developing to mature PNs. A proteome-instructed in\ vivo screen identified 20 cell-surface molecules regulating neural circuit assembly, many of which belong to evolutionarily conserved protein families not previously linked to neural development. Genetic analysis further revealed that the lipoprotein receptor LRP1 cell-autonomously controls PN dendrite targeting, contributing to the formation of a precise olfactory map. These findings highlight the power of temporally resolved in situ cell-surface proteomic profiling in discovering regulators of brain wiring.

}, keywords = {Animals, Axons, Brain, Dendrites, Drosophila melanogaster, Drosophila Proteins, Gene Expression Profiling, Gene Expression Regulation, Developmental, Membrane Proteins, Neurogenesis, Olfactory Nerve, Olfactory Pathways, Olfactory Receptor Neurons, Proteomics, Receptors, Lipoprotein, Smell}, issn = {1097-4172}, doi = {10.1016/j.cell.2019.12.029}, author = {Li, Jiefu and Han, Shuo and Li, Hongjie and Udeshi, Namrata D and Svinkina, Tanya and Mani, D R and Xu, Chuanyun and Guajardo, Ricardo and Xie, Qijing and Li, Tongchao and Luginbuhl, David J and Wu, Bing and McLaughlin, Colleen N and Xie, Anthony and Kaewsapsak, Pornchai and Quake, Stephen R and Carr, Steven A and Ting, Alice Y and Luo, Liqun} } @article {65361, title = {Cell-type specific outcome representation in primary motor cortex.}, journal = {Neuron}, volume = {107}, year = {2020}, month = {2020 Sep 9}, pages = {954-71}, abstract = {

Adaptive movements are critical to animal survival. To guide future actions, the brain monitors different outcomes, including achievement of movement and appetitive goals. The nature of outcome signals and their neuronal and network realization in motor cortex (M1), which commands the performance of skilled movements, is largely unknown. Using a dexterity task, calcium imaging, optogenetic perturbations, and behavioral manipulations, we studied outcome signals in murine M1. We find two populations of layer 2-3 neurons, {\textquotedblleft}success{\textquotedblright}- and {\textquotedblleft}failure{\textquotedblright} related neurons that develop with training and report end-result of trials. In these neurons, prolonged responses were recorded after success or failure trials, independent of reward and kinematics. In contrast, the initial state of layer-5 pyramidal tract neurons contains a memory trace of the previous trial{\textquoteright}s outcome. Inter-trial cortical activity was needed to learn new task requirements. These M1 reflective layer-specific performance outcome signals, can support reinforcement motor learning of skilled behavior.

}, doi = {10.1016/j.neuron.2020.06.006}, author = {Lavzin, Maria and Levy, Shahar and Benisty, Hadas and Dubin, Uri and Brosh, Zohar and Aeed, Fadi and Mensh, Brett D. and Schiller, Yitzhak and Meir, Ron and Barak, Omri and Talmon, Ronen and Hantman, Adam W. and Schiller, Jackie} } @article {65614, title = {Chloroplast Sec14-like 1 (CPSFL1) is essential for normal chloroplast development and affects carotenoid accumulation in Chlamydomonas.}, journal = {Proceedings of the National Academy of Sciences of the U S A}, volume = {117}, year = {2020}, month = {2020 Jun 2}, pages = {1-12}, abstract = {

Plastid isoprenoid-derived carotenoids serve essential roles in chloroplast development and photosynthesis. Although nearly all enzymes that participate in the biosynthesis of carotenoids in plants have been identified, the complement of auxiliary proteins that regulate synthesis, transport, sequestration, and degradation of these molecules and their isoprenoid precursors have not been fully described. To identify such proteins that are necessary for the optimal functioning of oxygenic photosynthesis, we screened a large collection of nonphotosynthetic (acetate-requiring) DNA insertional mutants of and isolated The mutant is extremely light-sensitive and susceptible to photoinhibition and photobleaching. The gene encodes a CRAL-TRIO hydrophobic ligand-binding (Sec14) domain protein. Proteins containing this domain are limited to eukaryotes, but some may have been retargeted to function in organelles of endosymbiotic origin. The mutant showed decreased accumulation of plastidial isoprenoid-derived pigments, especially carotenoids, and whole-cell focused ion-beam scanning-electron microscopy revealed a deficiency of carotenoid-rich chloroplast structures (e.g., eyespot and plastoglobules). The low carotenoid content resulted from impaired biosynthesis at a step prior to phytoene, the committed precursor to carotenoids. The CPSFL1 protein bound phytoene and β-carotene when expressed in and phosphatidic acid in vitro. We suggest that CPSFL1 is involved in the regulation of phytoene synthesis and carotenoid transport and thereby modulates carotenoid accumulation in the chloroplast.

}, issn = {1091-6490}, doi = {10.1073/pnas.1916948117}, author = {Garc{\'\i}a-Cerd{\'a}n, Jos{\'e} G and Schmid, Eva M and Takeuchi, Tomomi and McRae, Ian and McDonald, Kent L and Yordduangjun, Nichakarn and Hassan, Ahmed M and Grob, Patricia and Xu, C Shan and Hess, Harald F and Fletcher, Daniel A and Nogales, Eva and Niyogi, Krishna K} } @article {65757, title = {Chromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin.}, journal = {Science Advances}, volume = {6}, year = {2020}, month = {2020 Sep 23}, abstract = {

Three-dimensional (3D) chromatin organization plays a key role in regulating mammalian genome function; however, many of its physical features at the single-cell level remain underexplored. Here, we use live- and fixed-cell 3D super-resolution and scanning electron microscopy to analyze structural and functional nuclear organization in somatic cells. We identify chains of interlinked ~200- to 300-nm-wide chromatin domains (CDs) composed of aggregated nucleosomes that can overlap with individual topologically associating domains and are distinct from a surrounding RNA-populated interchromatin compartment. High-content mapping uncovers confinement of cohesin and active histone modifications to surfaces and enrichment of repressive modifications toward the core of CDs in both hetero- and euchromatic regions. This nanoscale functional topography is temporarily relaxed in postreplicative chromatin but remarkably persists after ablation of cohesin. Our findings establish CDs as physical and functional modules of mesoscale genome organization.

}, issn = {2375-2548}, doi = {10.1126/sciadv.aba8811}, author = {Miron, Ezequiel and Oldenkamp, Roel and Brown, Jill M and Pinto, David M S and Xu, C Shan and Faria, Ana R and Shaban, Haitham A and Rhodes, James D P and Innocent, Cassandravictoria and de Ornellas, Sara and Hess, Harald F and Buckle, Veronica and Schermelleh, Lothar} } @article {65900, title = {Cis-regulatory variation in the shavenbaby gene underlies intraspecific phenotypic variation, mirroring interspecific divergence in the same trait.}, journal = {Evolution}, year = {2020}, month = {2020 Dec 14}, abstract = {

Despite considerable progress in recent decades in dissecting the genetic causes of natural morphological variation, there is limited understanding of how variation within species ultimately contributes to species differences. We have studied patterning of the non-sensory hairs, commonly known as "trichomes," on the dorsal cuticle of first-instar larvae of Drosophila. Most Drosophila species produce a dense lawn of dorsal trichomes, but a subset of these trichomes were lost in D. sechellia and D. ezoana due entirely to regulatory evolution of the shavenbaby (svb) gene. Here, we describe intraspecific variation in dorsal trichome patterns of first-instar larvae of D. virilis that is similar to the trichome pattern variation identified previously between species. We found that a single large effect QTL, which includes svb, explains most of the trichome number difference between two D. virilis strains and that svb expression correlates with the trichome difference between strains. This QTL does not explain the entire difference between strains, implying that additional loci contribute to variation in trichome numbers. Thus, the genetic architecture of intraspecific variation exhibits similarities and differences with interspecific variation that may reflect differences in long-term and short-term evolutionary processes.

}, issn = {1558-5646}, doi = {10.1111/evo.14142}, author = {Soverna, Ana Faigon and Rodriguez, Nahuel Cabrera and Korgaonkar, Aishwarya and Hasson, Esteban and Stern, David L and Frankel, Nicol{\'a}s} } @article {65646, title = {Comprehensive imaging of sensory-evoked activity of entire neurons within the awake developing brain using ultrafast AOD-based random-access two-photon microscopy.}, journal = {Frontiers in Neural Circuits}, volume = {14}, year = {2020}, month = {2020 Jun 16}, pages = {33}, abstract = {

Determining how neurons transform synaptic input and encode information in action potential (AP) firing output is required for understanding dendritic integration, neural transforms and encoding. Limitations in the speed of imaging 3D volumes of brain encompassing complex dendritic arbors using conventional galvanometer mirror-based laser-scanning microscopy has hampered fully capturing fluorescent sensors of activity throughout an individual neuron{\textquoteright}s entire complement of synaptic inputs and somatic APs. To address this problem, we have developed a two-photon microscope that achieves high-speed scanning by employing inertia-free acousto-optic deflectors (AODs) for laser beam positioning, enabling random-access sampling of hundreds to thousands of points-of-interest restricted to a predetermined neuronal structure, avoiding wasted scanning of surrounding extracellular tissue. This system is capable of comprehensive imaging of the activity of single neurons within the intact and awake vertebrate brain. Here, we demonstrate imaging of tectal neurons within the brains of albino tadpoles labeled using single-cell electroporation for expression of a red space-filling fluorophore to determine dendritic arbor morphology, and either the calcium sensor jGCaMP7s or the glutamate sensor iGluSnFR as indicators of neural activity. Using discrete, point-of-interest scanning we achieve sampling rates of 3 Hz for saturation sampling of entire arbors at 2 μm resolution, 6 Hz for sequentially sampling 3 volumes encompassing the dendritic arbor and soma, and 200-250 Hz for scanning individual planes through the dendritic arbor. This system allows investigations of sensory-evoked information input-output relationships of neurons within the intact and awake brain.

}, issn = {1662-5110}, doi = {10.3389/fncir.2020.00033}, author = {Sakaki, Kelly D R and Podgorski, Kaspar and Dellazizzo Toth, Tristan A and Coleman, Patrick and Haas, Kurt} } @article {68507, title = {A connectome and analysis of the adult Drosophila central brain.}, journal = {Elife}, volume = {9}, year = {2020}, month = {2020 Sep 07}, abstract = {

The neural circuits responsible for animal behavior remain largely unknown. We summarize new methods and present the circuitry of a large fraction of the brain of the fruit fly . Improved methods include new procedures to prepare, image, align, segment, find synapses in, and proofread such large data sets. We define cell types, refine computational compartments, and provide an exhaustive atlas of cell examples and types, many of them novel. We provide detailed circuits consisting of neurons and their chemical synapses for most of the central brain. We make the data public and simplify access, reducing the effort needed to answer circuit questions, and provide procedures linking the neurons defined by our analysis with genetic reagents. Biologically, we examine distributions of connection strengths, neural motifs on different scales, electrical consequences of compartmentalization, and evidence that maximizing packing density is an important criterion in the evolution of the fly{\textquoteright}s brain.

}, keywords = {Animals, Brain, Connectome, Drosophila melanogaster, Female, Male, Neurons, Synapses}, issn = {2050-084X}, doi = {10.7554/eLife.57443}, author = {Scheffer, Louis K and Xu, C Shan and Januszewski, Michal and Lu, Zhiyuan and Takemura, Shin-ya and Hayworth, Kenneth J and Huang, Gary B and Shinomiya, Kazunori and Maitlin-Shepard, Jeremy and Berg, Stuart and Clements, Jody and Hubbard, Philip M and Katz, William T and Umayam, Lowell and Zhao, Ting and Ackerman, David and Blakely, Tim and Bogovic, John and Dolafi, Tom and Kainmueller, Dagmar and Kawase, Takashi and Khairy, Khaled A and Leavitt, Laramie and Li, Peter H and Lindsey, Larry and Neubarth, Nicole and Olbris, Donald J and Otsuna, Hideo and Trautman, Eric T and Ito, Masayoshi and Bates, Alexander S and Goldammer, Jens and Wolff, Tanya and Svirskas, Robert and Schlegel, Philipp and Neace, Erika and Knecht, Christopher J and Alvarado, Chelsea X and Bailey, Dennis A and Ballinger, Samantha and Borycz, Jolanta A and Canino, Brandon S and Cheatham, Natasha and Cook, Michael and Dreher, Marisa and Duclos, Octave and Eubanks, Bryon and Fairbanks, Kelli and Finley, Samantha and Forknall, Nora and Francis, Audrey and Hopkins, Gary Patrick and Joyce, Emily M and Kim, SungJin and Kirk, Nicole A and Kovalyak, Julie and Lauchie, Shirley A and Lohff, Alanna and Maldonado, Charli and Manley, Emily A and McLin, Sari and Mooney, Caroline and Ndama, Miatta and Ogundeyi, Omotara and Okeoma, Nneoma and Ordish, Christopher and Padilla, Nicholas and Patrick, Christopher M and Paterson, Tyler and Phillips, Elliott E and Phillips, Emily M and Rampally, Neha and Ribeiro, Caitlin and Robertson, Madelaine K and Rymer, Jon Thomson and Ryan, Sean M and Sammons, Megan and Scott, Anne K and Scott, Ashley L and Shinomiya, Aya and Smith, Claire and Smith, Kelsey and Smith, Natalie L and Sobeski, Margaret A and Suleiman, Alia and Swift, Jackie and Takemura, Satoko and Talebi, Iris and Tarnogorska, Dorota and Tenshaw, Emily and Tokhi, Temour and Walsh, John J and Yang, Tansy and Horne, Jane Anne and Li, Feng and Parekh, Ruchi and Rivlin, Patricia K and Jayaraman, Vivek and Costa, Marta and Jefferis, Gregory Sxe and Ito, Kei and Saalfeld, Stephan and George, Reed and Meinertzhagen, Ian A and Rubin, Gerald M and Hess, Harald F and Jain, Viren and Plaza, Stephen M} } @article {65382, title = {Conservation and divergence of related neuronal lineages in the central brain.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Apr 07}, abstract = {

Wiring a complex brain requires many neurons with intricate cell specificity, generated by a limited number of neural stem cells. central brain lineages are a predetermined series of neurons, born in a specific order. To understand how lineage identity translates to neuron morphology, we mapped 18 central brain lineages. While we found large aggregate differences between lineages, we also discovered shared patterns of morphological diversification. Lineage identity plus Notch-mediated sister fate govern primary neuron trajectories, whereas temporal fate diversifies terminal elaborations. Further, morphological neuron types may arise repeatedly, interspersed with other types. Despite the complexity, related lineages produce similar neuron types in comparable temporal patterns. Different stem cells even yield two identical series of dopaminergic neuron types, but with unrelated sister neurons. Together, these phenomena suggest that straightforward rules drive incredible neuronal complexity, and that large changes in morphology can result from relatively simple fating mechanisms.

}, issn = {2050-084X}, doi = {10.7554/eLife.53518}, author = {Lee, Ying-Jou and Yang, Ching-Po and Miyares, Rosa L and Huang, Yu-Fen and He, Yisheng and Ren, Qingzhong and Chen, Hui-Min and Kawase, Takashi and Ito, Masayoshi and Otsuna, Hideo and Sugino, Ken and Aso, Yoshi and Ito, Kei and Lee, Tzumin} } @article {68991, title = {Context-dependent functional compensation between Ythdf mA reader proteins.}, journal = {Genes Dev}, volume = {34}, year = {2020}, month = {10/2020}, pages = {1373-1391}, abstract = {

The N6-methyladenosine (mA) modification is the most prevalent post-transcriptional mRNA modification, regulating mRNA decay and splicing. It plays a major role during normal development, differentiation, and disease progression. The modification is regulated by a set of writer, eraser, and reader proteins. The YTH domain family of proteins consists of three homologous mA-binding proteins, Ythdf1, Ythdf2, and Ythdf3, which were suggested to have different cellular functions. However, their sequence similarity and their tendency to bind the same targets suggest that they may have overlapping roles. We systematically knocked out (KO) the Mettl3 writer, each of the Ythdf readers, and the three readers together (triple-KO). We then estimated the effect in vivo in mouse gametogenesis, postnatal viability, and in vitro in mouse embryonic stem cells (mESCs). In gametogenesis, severity is increased as the deletion occurs earlier in the process, and Ythdf2 has a dominant role that cannot be compensated by Ythdf1 or Ythdf3, due to differences in readers{\textquoteright} expression pattern across different cell types, both in quantity and in spatial location. Knocking out the three readers together and systematically testing viable offspring genotypes revealed a redundancy in the readers{\textquoteright} role during early development that is gene dosage-dependent. Finally, in mESCs there is compensation between the three Ythdf reader proteins, since the resistance to differentiate and the significant effect on mRNA decay occur only in the triple-KO cells and not in the single KOs. Thus, we suggest a new model for the Ythdf readers function, in which there is profound dosage-dependent redundancy when all three readers are equivalently coexpressed in the same cell types.

}, keywords = {Animals, Cell Line, Dosage Compensation, Genetic, Embryonic Stem Cells, Fertility, Gametogenesis, Gene Deletion, Gene Expression Profiling, Gene Expression Regulation, Developmental, Methyltransferases, Mice, Mice, Knockout, RNA-Binding Proteins}, issn = {1549-5477}, doi = {10.1101/gad.340695.120}, author = {Lasman, Lior and Krupalnik, Vladislav and Viukov, Sergey and Mor, Nofar and Aguilera-Castrejon, Alejandro and Schneir, Dan and Bayerl, Jonathan and Mizrahi, Orel and Peles, Shani and Tawil, Shadi and Sathe, Shashank and Nachshon, Aharon and Shani, Tom and Zerbib, Mirie and Kilimnik, Itay and Aigner, Stefan and Shankar, Archana and Mueller, Jasmine R and Schwartz, Schraga and Stern-Ginossar, Noam and Yeo, Gene W and Geula, Shay and Novershtern, Noa and Hanna, Jacob H} } @article {65600, title = {The corazonin-PTTH neuronal axis controls systemic body growth by regulating basal ecdysteroid biosynthesis in Drosophila melanogaster.}, journal = {Current Biology}, volume = {30}, year = {2020}, month = {2020 Jun 8}, pages = {2156-65}, abstract = {

Steroid hormones play key roles in development, growth, and reproduction in various animal phyla [1]. The insect steroid hormone, ecdysteroid, coordinates growth and maturation, represented by molting and metamorphosis [2]. In Drosophila melanogaster, the prothoracicotropic hormone (PTTH)-producing neurons stimulate peak levels of ecdysteroid biosynthesis for maturation [3]. Additionally, recent studies on PTTH signaling indicated that basal levels of ecdysteroid negatively affect systemic growth prior to maturation [4-8]. However, it remains unclear how PTTH signaling is regulated for basal ecdysteroid biosynthesis. Here, we report that Corazonin (Crz)-producing neurons regulate basal ecdysteroid biosynthesis by affecting PTTH neurons. Crz belongs to gonadotropin-releasing hormone (GnRH) superfamily, implying an analogous role in growth and maturation [9]. Inhibition of Crz neuronal activity increased pupal size, whereas it hardly affected pupariation timing. This phenotype resulted from enhanced growth rate and a delay in ecdysteroid elevation during the mid-third instar larval (L3) stage. Interestingly, Crz receptor (CrzR) expression in PTTH neurons was higher during the mid- than the late-L3 stage. Silencing of CrzR in PTTH neurons increased pupal size, phenocopying the inhibition of Crz neuronal activity. When Crz neurons were optogenetically activated, a strong calcium response was observed in PTTH neurons during the mid-L3, but not the late-L3, stage. Furthermore, we found that octopamine neurons contact Crz neurons in the subesophageal zone (SEZ), transmitting signals for systemic growth. Together, our results suggest that the Crz-PTTH neuronal axis modulates ecdysteroid biosynthesis in response to octopamine, uncovering a regulatory neuroendocrine system in the developmental transition from growth to maturation.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2020.03.050}, author = {Imura, Eisuke and Shimada-Niwa, Yuko and Nishimura, Takashi and H{\"u}ckesfeld, Sebastian and Schlegel, Philipp and Ohhara, Yuya and Kondo, Shu and Tanimoto, Hiromu and Cardona, Albert and Pankratz, Michael J and Niwa, Ryusuke} } @article {68479, title = {Core Competencies for Undergraduates in Bioengineering and Biomedical Engineering: Findings, Consequences, and Recommendations.}, journal = {Ann Biomed Eng}, volume = {48}, year = {2020}, month = {04/2020}, pages = {905-912}, abstract = {

This paper provides a synopsis of discussions related to biomedical engineering core curricula that occurred at the Fourth BME Education Summit held at Case Western Reserve University in Cleveland, Ohio in May 2019. This summit was organized by the Council of Chairs of Bioengineering and Biomedical Engineering, and participants included over 300 faculty members from 100+ accredited undergraduate programs. This discussion focused on six key questions: QI: Is there a core curriculum, and if so, what are its components? QII: How does our purported core curriculum prepare students for careers, particularly in industry? QIII: How does design distinguish BME/BIOE graduates from other engineers? QIV: What is the state of engineering analysis and systems-level modeling in BME/BIOE curricula? QV: What is the role of data science in BME/BIOE undergraduate education? QVI: What core experimental skills are required for BME/BIOE undergrads?\ s. Indeed, BME/BIOI core curricula exists and has matured to emphasize interdisciplinary topics such as physiology, instrumentation, mechanics, computer programming, and mathematical modeling. Departments demonstrate their own identities by highlighting discipline-specific sub-specialties. In addition to technical competence, Industry partners most highly value our students{\textquoteright} capacity for problem solving and communication. As such, BME/BIOE curricula includes open-ended projects that address unmet patient and clinician needs as primary methods to prepare graduates for careers in industry. Culminating senior design experiences distinguish BME/BIOE graduates through their development of client-centered engineering solutions to healthcare problems. Finally, the overall BME/BIOE curriculum is not stagnant-it is clear that data science will become an ever-important element of our students{\textquoteright} training and that new methods to enhance student engagement will be of pedagogical importance as we embark on the next decade.

}, keywords = {Biomedical Engineering, Curriculum, Data Science, Humans, Students, Universities}, issn = {1573-9686}, doi = {10.1007/s10439-020-02468-2}, author = {White, John A and Gaver, Donald P and Butera, Robert J and Choi, Bernard and Dunlop, Mary J and Grande-Allen, K Jane and Grosberg, Anna and Hitchcock, Robert W and Huang-Saad, Aileen Y and Kotche, Miiri and Kyle, Aaron M and Lerner, Amy L and Linehan, John H and Linsenmeier, Robert A and Miller, Michael I and Papin, Jason A and Setton, Lori and Sgro, Allyson and Smith, Michael L and Zaman, Muhammad and Lee, Abraham P} } @article {65281, title = {Correlative three-dimensional super-resolution and block-face electron microscopy of whole vitreously frozen cells.}, journal = {Science}, volume = {367}, year = {2020}, month = {2020 Jan 17}, abstract = {

Within cells, the spatial compartmentalization of thousands of distinct proteins serves a multitude of diverse biochemical needs. Correlative super-resolution (SR) fluorescence and electron microscopy (EM) can elucidate protein spatial relationships to global ultrastructure, but has suffered from tradeoffs of structure preservation, fluorescence retention, resolution, and field of view. We developed a platform for three-dimensional cryogenic SR and focused ion beam-milled block-face EM across entire vitreously frozen cells. The approach preserves ultrastructure while enabling independent SR and EM workflow optimization. We discovered unexpected protein-ultrastructure relationships in mammalian cells including intranuclear vesicles containing endoplasmic reticulum-associated proteins, web-like adhesions between cultured neurons, and chromatin domains subclassified on the basis of transcriptional activity. Our findings illustrate the value of a comprehensive multimodal view of ultrastructural variability across whole cells.

}, issn = {1095-9203}, doi = {10.1126/science.aaz5357}, author = {Hoffman, David P and Shtengel, Gleb and Xu, C Shan and Campbell, Kirby R and Freeman, Melanie and Wang, Lei and Milkie, Daniel E and Pasolli, H Amalia and Iyer, Nirmala and Bogovic, John A and Stabley, Daniel R and Shirinifard, Abbas and Pang, Song and Peale, David and Schaefer, Kathy and Pomp, Wim and Chang, Chi-Lun and Lippincott-Schwartz, Jennifer and Kirchhausen, Tom and Solecki, David J and Betzig, Eric and Hess, Harald F} } @article {65259, title = {Cortical pattern generation during dexterous movement is input-driven.}, journal = {Nature}, volume = {577}, year = {2020}, month = {2020 Jan 16}, pages = {386-91}, abstract = {

The motor cortex controls skilled arm movement by sending temporal patterns of activity to lower motor centres. Local cortical dynamics are thought to shape these patterns throughout movement execution. External inputs have been implicated in setting the initial state of the motor cortex, but they may also have a pattern-generating role. Here we dissect the contribution of local dynamics and inputs to cortical pattern generation during a prehension task in mice. Perturbing cortex to an aberrant state prevented movement initiation, but after the perturbation was released, cortex either bypassed the normal initial state and immediately generated the pattern that controls reaching or failed to generate this pattern. The difference in these two outcomes was probably a result of external inputs. We directly investigated the role of inputs by inactivating the thalamus; this perturbed cortical activity and disrupted limb kinematics at any stage of the movement. Activation of thalamocortical axon terminals at different frequencies disrupted cortical activity and arm movement in a graded manner. Simultaneous recordings revealed that both thalamic activity and the current state of cortex predicted changes in cortical activity. Thus, the pattern generator for dexterous arm movement is distributed across multiple, strongly interacting brain regions.

}, issn = {1476-4687}, doi = {10.1038/s41586-019-1869-9}, author = {Sauerbrei, Britton A and Guo, Jian-Zhong and Cohen, Jeremy D and Mischiati, Matteo and Guo, Wendy and Kabra, Mayank and Verma, Nakul and Mensh, Brett and Branson, Kristin and Hantman, Adam W} } @article {65799, title = {Dense and pleiotropic regulatory information in a developmental enhancer.}, journal = {Nature}, volume = {587}, year = {2020}, month = {2020 Nov 01}, pages = {235-39}, abstract = {

Changes in gene regulation underlie much of phenotypic evolution. However, our understanding of the potential for regulatory evolution is biased, because most evidence comes from either natural variation or limited experimental perturbations. Using an automated robotics pipeline, we surveyed an unbiased mutation library for a developmental enhancer in Drosophila melanogaster. We found that almost all mutations altered gene expression and that parameters of gene expression-levels, location, and state-were convolved. The widespread pleiotropic effects of most mutations may constrain the evolvability of developmental enhancers. Consistent with these observations, comparisons of diverse Drosophila larvae revealed apparent biases in the phenotypes influenced by the enhancer. Developmental enhancers may encode a higher density of regulatory information than has been appreciated previously, imposing constraints on regulatory evolution.

}, issn = {1476-4687}, doi = {10.1038/s41586-020-2816-5}, author = {Fuqua, Timothy and Jordan, Jeff and van Breugel, Maria Elize and Halavatyi, Aliaksandr and Tischer, Christian and Polidoro, Peter and Abe, Namiko and Tsai, Albert and Mann, Richard S and Stern, David L and Crocker, Justin} } @article {65725, title = {Dense neuronal reconstruction through X-ray holographic nano-tomography.}, journal = {Nature Neuroscience}, volume = {23}, year = {2020}, month = {2020 Dec -1}, pages = {1637-43}, abstract = {

Imaging neuronal networks provides a foundation for understanding the nervous system, but resolving dense nanometer-scale structures over large volumes remains challenging for light microscopy (LM) and electron microscopy (EM). Here we show that X-ray holographic nano-tomography (XNH) can image millimeter-scale volumes with sub-100-nm resolution, enabling reconstruction of dense wiring in Drosophila melanogaster and mouse nervous tissue. We performed correlative XNH and EM to reconstruct hundreds of cortical pyramidal cells and show that more superficial cells receive stronger synaptic inhibition on their apical dendrites. By combining multiple XNH scans, we imaged an adult Drosophila leg with sufficient resolution to comprehensively catalog mechanosensory neurons and trace individual motor axons from muscles to the central nervous system. To accelerate neuronal reconstructions, we trained a convolutional neural network to automatically segment neurons from XNH volumes. Thus, XNH bridges a key gap between LM and EM, providing a new avenue for neural circuit discovery.

}, issn = {1546-1726}, doi = {10.1038/s41593-020-0704-9}, author = {Kuan, Aaron T and Phelps, Jasper S and Thomas, Logan A and Nguyen, Tri M and Han, Julie and Chen, Chiao-Lin and Azevedo, Anthony W and Tuthill, John C and Funke, Jan and Cloetens, Peter and Pacureanu, Alexandra and Lee, Wei-Chung Allen} } @conference {65612, title = {Detecting the Starting Frame of Actions in Video}, booktitle = {2020 IEEE Winter Conference on Applications of Computer Vision (WACV)}, year = {2020}, month = {2020 May 14}, publisher = {IEEE}, organization = {IEEE}, address = {Snowmass Village, CO, USA}, abstract = {

In this work, we address the problem of precisely localizing key frames of an action, for example, the precise time that a pitcher releases a baseball, or the precise time that a crowd begins to applaud. Key frame localization is a largely overlooked and important action-recognition problem, for example in the field of neuroscience, in which we would like to understand the neural activity that produces the start of a bout of an action. To address this problem, we introduce a novel structured loss function that properly weights the types of errors that matter in such applications: it more heavily penalizes extra and missed action start detections over small misalignments. Our structured loss is based on the best matching between predicted and labeled action starts. We train recurrent neural networks (RNNs) to minimize differentiable approximations of this loss. To evaluate these methods, we introduce the Mouse Reach Dataset, a large, annotated video dataset of mice performing a sequence of actions. The dataset was collected and labeled by experts for the purpose of neuroscience research. On this dataset, we demonstrate that our method outperforms related approaches and baseline methods using an unstructured loss.

}, doi = {10.1109/WACV45572.202010.1109/WACV45572.2020.9093405}, url = {https://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?punumber=9087828}, author = {Kwak, Iljung S. and Guo, Jian-Zhong and Hantman, Adam and Branson, Kristin and Kriegman, David} } @article {65902, title = {Directed Evolution of a Selective and Sensitive Serotonin Sensor via Machine Learning.}, journal = {Cell}, volume = {183}, year = {2020}, month = {2020 Dec 23}, pages = {1986-2002.e26}, abstract = {

Serotonin plays a central role in cognition and is the target of most pharmaceuticals for psychiatric disorders. Existing drugs have limited efficacy; creation of improved versions will require better understanding of serotonergic circuitry, which has been hampered by our inability to monitor serotonin release and transport with high spatial and temporal resolution. We developed and applied a binding-pocket redesign strategy, guided by machine learning, to create a high-performance, soluble, fluorescent serotonin sensor (iSeroSnFR), enabling optical detection of millisecond-scale serotonin transients. We demonstrate that iSeroSnFR can be used to detect serotonin release in freely behaving mice during fear conditioning, social interaction, and sleep/wake transitions. We also developed a robust assay of serotonin transporter function and modulation by drugs. We expect that both machine-learning-guided binding-pocket redesign and iSeroSnFR will have broad utility for the development of other sensors and in\ vitro and in\ vivo serotonin detection, respectively.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2020.11.040}, author = {Unger, Elizabeth K and Keller, Jacob P and Altermatt, Michael and Liang, Ruqiang and Matsui, Aya and Dong, Chunyang and Hon, Olivia J and Yao, Zi and Sun, Junqing and Banala, Samba and Flanigan, Meghan E and Jaffe, David A and Hartanto, Samantha and Carlen, Jane and Mizuno, Grace O and Borden, Phillip M and Shivange, Amol V and Cameron, Lindsay P and Sinning, Steffen and Underhill, Suzanne M and Olson, David E and Amara, Susan G and Temple Lang, Duncan and Rudnick, Gary and Marvin, Jonathan S and Lavis, Luke D and Lester, Henry A and Alvarez, Veronica A and Fisher, Andrew J and Prescher, Jennifer A and Kash, Thomas L and Yarov-Yarovoy, Vladimir and Gradinaru, Viviana and Looger, Loren L and Tian, Lin} } @article {65675, title = {Efficient coding of natural scene statistics predicts discrimination thresholds for grayscale textures.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Aug 3}, abstract = {

Previously, in (Hermundstad et al., 2014), we showed that when sampling is limiting, the efficient coding principle leads to a {\textquoteright}variance is salience{\textquoteright} hypothesis, and that this hypothesis accounts for visual sensitivity to binary image statistics. Here, using extensive new psychophysical data and image analysis, we show that this hypothesis accounts for visual sensitivity to a large set of grayscale image statistics at a striking level of detail, and also identify the limits of the prediction. We define a 66-dimensional space of local grayscale light-intensity correlations, and measure the relevance of each direction to natural scenes. The {\textquoteright}variance is salience{\textquoteright} hypothesis predicts that two-point correlations are most salient, and predicts their relative salience. We tested these predictions in a texture-segregation task using un-natural, synthetic textures. As predicted, correlations beyond second order are not salient, and predicted thresholds for over 300 second-order correlations match psychophysical thresholds closely (median fractional error \< 0:13).

}, doi = {10.7554/eLife.54347}, url = {https://elifesciences.org/articles/54347}, author = {Tesileanu, Tiberiu and Conte, Mary M and Briguglio, John J and Hermundstad, Ann M and Victor, Jonathan D and Balasubramanian, Vijay} } @article {65626, title = {Employing NaChBac for cryo-EM analysis of toxin action on voltage-gated Na+ channels in nanodisc}, journal = {Proceedings of the National Academy of Sciences of the U.S.A.}, volume = {117}, year = {2020}, month = {2020 Jun 23}, pages = {14187-93}, abstract = {

NaChBac, the first bacterial voltage-gated Na+\ (Nav) channel to be characterized, has been the prokaryotic prototype for studying the structure{\textendash}function relationship of Nav\ channels. Discovered nearly two decades ago, the structure of NaChBac has not been determined. Here we present the single particle electron cryomicroscopy (cryo-EM) analysis of NaChBac in both detergent micelles and nanodiscs. Under both conditions, the conformation of NaChBac is nearly identical to that of the potentially inactivated NavAb. Determining the structure of NaChBac in nanodiscs enabled us to examine gating modifier toxins (GMTs) of Nav\ channels in lipid bilayers. To study GMTs in mammalian Nav\ channels, we generated a chimera in which the extracellular fragment of the S3 and S4 segments in the second voltage-sensing domain from Nav1.7 replaced the corresponding sequence in NaChBac. Cryo-EM structures of the nanodisc-embedded chimera alone and in complex with HuwenToxin IV (HWTX-IV) were determined to 3.5 and 3.2 {\r A} resolutions, respectively. Compared to the structure of HWTX-IV{\textendash}bound human Nav1.7, which was obtained at an overall resolution of 3.2 {\r A}, the local resolution of the toxin has been improved from \~{}6 to \~{}4 {\r A}. This resolution enabled visualization of toxin docking. NaChBac can thus serve as a convenient surrogate for structural studies of the interactions between GMTs and Nav\ channels in a membrane environment.

}, issn = {0027-8424}, doi = {10.1073/pnas.1922903117}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1922903117https://syndication.highwire.org/content/doi/10.1073/pnas.1922903117}, author = {Gao, Shuai and Valinsky, William C. and On, Nguyen Cam and Houlihan, Patrick R. and Qu, Qian and Liu, Lei and Pan, Xiaojing and Clapham, David E. and Yan, Nieng} } @article {65625, title = {First occurrence of the pest Drosophila suzukii (Diptera: Drosophilidae) in the Comoros Archipelago (Western Indian Ocean)}, journal = {African Entomology}, volume = {28}, year = {2020}, month = {2020 Jun 04}, pages = {78}, abstract = {

Drosophila suzukii\ (Matsumura, 1931) is an Asian pest of grapes and other soft fruits that has invaded North America and Europe during the last decade. Here we report its recent occurrence on two islands of the Comoros archipelago in the Mozambique Channel, namely Mayotte and Ngazidja (Grande Comore), in April 2017 and November 2018, respectively. We also document its absence from other African islands in the Mozambique Channel and the Western Indian Ocean including Mayotte until 2013.\ Drosophila ashburneriTsacas, 1984\ is the only member of the\ suzukii\ species subgroup known from the Comoros, but it is morphologically distinct and likely distantly related to\ D.\ suzukii.\ Drosophila suzukii\ has likely been recently introduced to the Comoros archipelago, perhaps from La R{\'e}union island where it first appeared in November 2013. On all of these tropical islands,\ D.\ suzukii\ was found in high-altitude habitats in agreement with its adaptation to cold environments. These results suggest the high susceptibility of highlands in eastern and southern Africa to be infested by this pest in the near future.

}, doi = {10.4001/003.028.0078}, url = {https://bioone.org/journals/african-entomology/volume-28/issue-1/003.028.0078/First-occurrence-of-the-pest-Drosophila-suzukii-Diptera--Drosophilidae/10.4001/003.028.0078.full}, author = {Hassani, I.M. and Behrman, E.L. and Prigent, S.R. and Gidaszewski, N. and Ravaomanarivo, L.H. Raveloson and Suwalski, A. and Debat, V. and David, J.R. and Yassin, A.} } @article {65602, title = {FMNL2 regulates dynamics of fascin in filopodia.}, journal = {Journal of Cell Biology}, volume = {219}, year = {2020}, month = {2020 May 04}, abstract = {

Filopodia are peripheral F-actin-rich structures that enable cell sensing of the microenvironment. Fascin is an F-actin-bundling protein that plays a key role in stabilizing filopodia to support efficient adhesion and migration. Fascin is also highly up-regulated in human cancers, where it increases invasive cell behavior and correlates with poor patient prognosis. Previous studies have shown that fascin phosphorylation can regulate F-actin bundling, and that this modification can contribute to subcellular fascin localization and function. However, the factors that regulate fascin dynamics within filopodia remain poorly understood. In the current study, we used advanced live-cell imaging techniques and a fascin biosensor to demonstrate that fascin phosphorylation, localization, and binding to F-actin are highly dynamic and dependent on local cytoskeletal architecture in cells in both 2D and 3D environments. Fascin dynamics within filopodia are under the control of formins, and in particular FMNL2, that binds directly to dephosphorylated fascin. Our data provide new insight into control of fascin dynamics at the nanoscale and into the mechanisms governing rapid cytoskeletal adaptation to environmental changes. This filopodia-driven exploration stage may represent an essential regulatory step in the transition from static to migrating cancer cells.

}, issn = {1540-8140}, doi = {10.1083/jcb.201906111}, author = {Pfisterer, Karin and Levitt, James and Lawson, Campbell D and Marsh, Richard J and Heddleston, John M and Wait, Eric and Ameer-Beg, Simon Morris and Cox, Susan and Parsons, Maddy} } @article {64543, title = {Freeze-frame imaging of synaptic activity using SynTagMA.}, journal = {Nature Communications}, volume = {11}, year = {2020}, month = {2020 May 18}, pages = {2464}, abstract = {

Information within the brain travels from neuron to neuron across synapses. At any given moment, only a few synapses within billions will be active and are thought to transmit key information about the environment, a behavior being executed or memory being recalled. Here we present SynTagMA, which marks active synapses within a ~2 s time window. Upon violet illumination, the genetically expressed tag converts from green to red fluorescence if bound to calcium. Targeted to presynaptic terminals, preSynTagMA allows discrimination between active and silent axons. Targeted to excitatory postsynapses, postSynTagMA creates a snapshot of synapses active just before photoconversion. To analyze large datasets, we developed an analysis program that automatically identifies and tracks the fluorescence of thousands of individual synapses in tissue. Together, these tools provide a high throughput method for repeatedly mapping active synapses in vitro and in vivo.

}, doi = {10.1038/s41467-020-16315-4}, author = {Perez-Alvarez, Alberto and Fearey, Brenna C and Schulze, Christian and O{\textquoteright}Toole, Ryan J and Moeyaert, Benjamien and Mohr, Manuel Alexander and Arganda-Carreras, Ignacio and Yang, Wei and Wiegert, J Simon and Schreiter, Eric R and Gee, Christine E and Hoppa, Michael B and Oertner, Thomas G} } @article {65601, title = {Frontline science: dynamic cellular and subcellular features of migrating leukocytes revealed by in vivo lattice lightsheet microscopy.}, journal = {Journal of Leukocyte Biology}, year = {2020}, month = {2020 Apr 23}, abstract = {

Neutrophil and macrophage (Mϕ) migration underpin the inflammatory response. However, the fast velocity, multidirectional instantaneous movement, and plastic, ever-changing shape of phagocytes confound high-resolution intravital imaging. Lattice lightsheet microscopy (LLSM) captures highly dynamic cell morphology at exceptional spatiotemporal resolution. We demonstrate the first extensive application of LLSM to leukocytes in vivo, utilizing optically transparent zebrafish, leukocyte-specific reporter lines that highlighted subcellular structure, and a wounding assay for leukocyte migration. LLSM revealed details of migrating leukocyte morphology, and permitted intricate, volumetric interrogation of highly dynamic activities within their native physiological setting. Very thin, recurrent uropod extensions must now be considered a characteristic feature of migrating neutrophils. LLSM resolved trailing uropod extensions, demonstrating their surprising length, and permitting quantitative assessment of cytoskeletal contributions to their evanescent form. Imaging leukocytes in blood vessel microenvironments at LLSM{\textquoteright}s spatiotemporal resolution displayed blood-flow-induced neutrophil dynamics and demonstrated unexpected leukocyte-endothelial interactions such as leukocyte-induced endothelial deformation against the intravascular pressure. LLSM of phagocytosis and cell death provided subcellular insights and uncovered novel behaviors. Collectively, we provide high-resolution LLSM examples of leukocyte structures (filopodia lamellipodia, uropod extensions, vesicles), and activities (interstitial and intravascular migration, leukocyte rolling, phagocytosis, cell death, and cytoplasmic ballooning). Application of LLSM to intravital leukocyte imaging sets the stage for transformative studies into the cellular and subcellular complexities of phagocyte biology.

}, issn = {1938-3673}, doi = {10.1002/JLB.3HI0120-589R}, author = {Manley, Harriet R and Potter, David L and Heddleston, John M and Chew, Teng-Leong and Keightley, M Cristina and Lieschke, Graham J} } @article {68813, title = {Functional Diversity of Glycinergic Commissural Inhibitory Neurons in Larval Zebrafish}, journal = {Cell Reports}, volume = {30}, year = {2020}, month = {03/2020}, pages = {3036-3050.e4}, abstract = {

Summary Commissural inhibitory neurons in the spinal cord of aquatic vertebrates coordinate left-right body alternation during swimming. Their developmental origin, however, has been elusive. We investigate this by comparing the anatomy and function of two commissural inhibitory neuron types, dI6dmrt3a and V0d, derived from the pd6 and p0 progenitor domains, respectively. We find that both of these commissural neuron types have monosynaptic, inhibitory connections to neuronal populations active during fictive swimming, supporting their role in providing inhibition to the contralateral side. V0d neurons tend to fire during faster and stronger movements, while dI6dmrt3a neurons tend to fire more consistently during normal fictive swimming. Ablation of dI6dmrt3a neurons leads to an impairment of left-right alternating activity through abnormal co-activation of ventral root neurons on both sides of the spinal cord. Our results suggest that dI6dmrt3a and V0d commissural inhibitory neurons synergistically provide inhibition to the opposite side across different swimming behaviors.

}, keywords = {commissural inhibitory neurons, dI6~ neurons, glycinergic interneuons, mid cycle inhibition, spinal cord circuit, V0d neurons, Zebrafish}, issn = {2211-1247}, doi = {https://doi.org/10.1016/j.celrep.2020.02.015}, url = {https://www.sciencedirect.com/science/article/pii/S2211124720301698}, author = {Chie Satou and Takumi Sugioka and Yuto Uemura and Takashi Shimazaki and Pawel Zmarz and Yukiko Kimura and Shin-ichi Higashijima} } @article {65282, title = {A genetic, genomic, and computational resource for exploring neural circuit function.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Jan 15}, abstract = {

The anatomy of many neural circuits is being characterized with increasing resolution, but their molecular properties remain mostly unknown. Here, we characterize gene expression patterns in distinct neural cell types of the visual system using genetic lines to access individual cell types, the TAPIN-seq method to measure their transcriptomes, and a probabilistic method to interpret these measurements. We used these tools to build a resource of high-resolution transcriptomes for 100 driver lines covering 67 cell types, available at http://www.opticlobe.com. Combining these transcriptomes with recently reported connectomes helps characterize how information is transmitted and processed across a range of scales, from individual synapses to circuit pathways. We describe examples that include identifying neurotransmitters, including cases of apparent co-release, generating functional hypotheses based on receptor expression, as well as identifying strong commonalities between different cell types.

}, issn = {2050-084X}, doi = {10.7554/eLife.50901}, author = {Davis, Fred P and Nern, Aljoscha and Picard, Serge and Reiser, Michael B and Rubin, Gerald M and Eddy, Sean R and Henry, Gilbert L} } @article {65739, title = {A genetically defined compartmentalized striatal direct pathway for negative reinforcement.}, journal = {Cell}, volume = {181}, year = {2020}, month = {2020 Oct 1}, pages = {211}, abstract = {

The striosome compartment within the dorsal striatum has been implicated in reinforcement learning and regulation of motivation, but how striosomal neurons contribute to these functions remains elusive. Here, we show that a genetically identified striosomal population, which expresses the Teashirt family zinc finger 1 (Tshz1) and belongs to the direct pathway, drives negative reinforcement and is essential for aversive learning in mice. Contrasting a "conventional" striosomal direct pathway, the Tshz1 neurons cause aversion, movement suppression, and negative reinforcement once activated, and they receive a distinct set of synaptic inputs. These neurons are predominantly excited by punishment rather than reward and represent the anticipation of punishment or the motivation for avoidance. Furthermore, inhibiting these neurons impairs punishment-based learning without affecting reward learning or movement. These results establish a major role of striosomal neurons in behaviors reinforced by punishment and moreover uncover functions of the direct pathway unaccounted for in classic models.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2020.08.032}, author = {Xiao, Xiong and Deng, Hanfei and Furlan, Alessandro and Yang, Tao and Zhang, Xian and Hwang, Ga-Ram and Tucciarone, Jason and Wu, Priscilla and He, Miao and Palaniswamy, Ramesh and Ramakrishnan, Charu and Ritola, Kimberly and Hantman, Adam and Deisseroth, Karl and Osten, Pavel and Huang, Z Josh and Li, Bo} } @article {65636, title = {Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells.}, journal = {Science Advances}, volume = {6}, year = {2020}, month = {2020 Jun 17}, pages = {eaaz6699}, abstract = {

Transcriptional bursting is the stochastic activation and inactivation of promoters, contributing to cell-to-cell heterogeneity in gene expression. However, the mechanism underlying the regulation of transcriptional bursting kinetics (burst size and frequency) in mammalian cells remains elusive. In this study, we performed single-cell RNA sequencing to analyze the intrinsic noise and mRNA levels for elucidating the transcriptional bursting kinetics in mouse embryonic stem cells. Informatics analyses and functional assays revealed that transcriptional bursting kinetics was regulated by a combination of promoter- and gene body-binding proteins, including the polycomb repressive complex 2 and transcription elongation factors. Furthermore, large-scale CRISPR-Cas9-based screening identified that the Akt/MAPK signaling pathway regulated bursting kinetics by modulating transcription elongation efficiency. These results uncovered the key molecular mechanisms underlying transcriptional bursting and cell-to-cell gene expression noise in mammalian cells.

}, issn = {2375-2548}, doi = {10.1126/sciadv.aaz6699}, author = {Ochiai, Hiroshi and Hayashi, Tetsutaro and Umeda, Mana and Yoshimura, Mika and Harada, Akihito and Shimizu, Yukiko and Nakano, Kenta and Saitoh, Noriko and Liu, Zhe and Yamamoto, Takashi and Okamura, Tadashi and Ohkawa, Yasuyuki and Kimura, Hiroshi and Nikaido, Itoshi} } @article {65972, title = {High throughput instrument to screen fluorescent proteins under two-photon excitation.}, journal = {Biomedical Optics Express}, volume = {11}, year = {2020}, month = {2020 Dec 01}, pages = {7192-7203}, abstract = {

Two-photon microscopy together with fluorescent proteins and fluorescent protein-based biosensors are commonly used tools in neuroscience. To enhance their experimental scope, it is important to optimize fluorescent proteins for two-photon excitation. Directed evolution of fluorescent proteins under one-photon excitation is common, but many one-photon properties do not correlate with two-photon properties. A simple system for expressing fluorescent protein mutants is colonies on an agar plate. The small focal volume of two-photon excitation makes creating a high throughput screen in this system a challenge for a conventional point-scanning approach. We present an instrument and accompanying software that solves this challenge by selectively scanning each colony based on a colony map captured under one-photon excitation. This instrument, called the GIZMO, can measure the two-photon excited fluorescence of 10,000 colonies in 7 hours. We show that the GIZMO can be used to evolve a fluorescent protein under two-photon excitation.

}, issn = {2156-7085}, doi = {10.1364/BOE.409353}, author = {Molina, Rosana S and King, Jonathan and Franklin, Jacob and Clack, Nathan and McRaven, Christopher and Goncharov, Vasily and Flickinger, Daniel and Svoboda, Karel and Drobizhev, Mikhail and Hughes, Thomas E} } @article {65696, title = {Hindbrain double-negative feedback mediates palatability-guided food and water consumption.}, journal = {Cell}, volume = {182}, year = {2020}, month = {2020 Sep 17}, pages = {1589-1605}, abstract = {

Hunger and thirst have distinct goals but control similar ingestive behaviors, and little is known about neural processes that are shared between these behavioral states. We identify glutamatergic neurons in the peri-locus coeruleus (periLC neurons) as a polysynaptic convergence node from separate energy-sensitive and hydration-sensitive cell populations. We develop methods for stable hindbrain calcium imaging in free-moving mice, which show that periLC neurons are tuned to ingestive behaviors and respond similarly to food or water consumption. PeriLC neurons are scalably inhibited by palatability and homeostatic need during consumption. Inhibition of periLC neurons is rewarding and increases consumption by enhancing palatability and prolonging ingestion duration. These properties comprise a double-negative feedback relationship that sustains food or water consumption without affecting food- or water-seeking. PeriLC neurons are a hub between hunger and thirst that specifically controls motivation for food and water ingestion, which is a factor that contributes to hedonic overeating and obesity.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2020.07.031}, author = {Gong, Rong and Xu, Shengjin and Hermundstad, Ann and Yu, Yang and Sternson, Scott M} } @article {65637, title = {Identification of dopaminergic neurons that can both establish associative memory and acutely terminate its behavioral expression.}, journal = {Journal of Neuroscience}, volume = {40}, year = {2020}, month = {2020 Jul 29}, pages = {5990-6006}, abstract = {

An adaptive transition from exploring the environment in search of vital resources to exploiting these resources once the search is successful is important to all animals. Here we study the neuronal circuitry that allows larval of either sex to negotiate this exploration-exploitation transition. We do so by combining Pavlovian conditioning with high-resolution behavioral tracking, optogenetic manipulation of individually identified neurons, and EM-data-based analyses of synaptic organization. We find that optogenetic activation of the dopaminergic neuron DAN-i1 can both establish memory during training, and acutely terminate learned search behavior in a subsequent recall test. Its activation leaves innate behavior unaffected, however. Specifically, DAN-i1 activation can establish associative memories of opposite valence upon paired and unpaired training with odor, and its activation during the recall test can terminate the search behavior resulting from either of these memories. Our results further suggest that in its behavioral significance DAN-i1 activation resembles but does not equal sugar reward. Dendrogram analyses of all the synaptic connections between DAN-i1 and its two main targets, the Kenyon cells and the mushroom body output neuron MBON-i1, further suggest that the DAN-i1 signals during training and during the recall test could be delivered to the Kenyon cells and to MBON-i1, respectively, within previously unrecognized, locally confined branching structures. This would provide an elegant circuit motif to terminate search upon its successful completion.In the struggle for survival animals have to explore their environment in search of food. Once food is found, however, it is adaptive to prioritize exploiting it over continuing a search that would now be as pointless as searching for the glasses you are wearing. This exploration-exploitation trade-off is important for animals and humans, as well as for technical search devices. We investigate which of the only 10,000 neurons of a fruit fly larva can tip the balance in this trade-off, and identify a single dopamine neuron called DAN-i1 that can do so. Given the similarities in dopamine neuron function across the animal kingdom, this may reflect a general principle of how search is terminated once it is successful.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0290-20.2020}, author = {Schleyer, Michael and Weiglein, Ali{\'c}e and Thoener, Juliane and Strauch, Martin and Hartenstein, Volker and Kantar Weigelt, Melisa and Schuller, Sarah and Saumweber, Timo and Eichler, Katharina and Rohwedder, Astrid and Merhof, Dorit and Zlatic, Marta and Thum, Andreas S and Gerber, Bertram} } @article {65130, title = {Idiosyncratic neural coding and neuromodulation of olfactory individuality in Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, year = {2020}, month = {2020 Sep 22}, pages = {23292-23297}, abstract = {

Innate behavioral biases and preferences can vary significantly among individuals of the same genotype. Though individuality is a fundamental property of behavior, it is not currently understood how individual differences in brain structure and physiology produce idiosyncratic behaviors. Here we present evidence for idiosyncrasy in olfactory behavior and neural responses in We show that individual female from a highly inbred laboratory strain exhibit idiosyncratic odor preferences that persist for days. We used in vivo calcium imaging of neural responses to compare projection neuron (second-order neurons that convey odor information from the sensory periphery to the central brain) responses to the same odors across animals. We found that, while odor responses appear grossly stereotyped, upon closer inspection, many individual differences are apparent across antennal lobe (AL) glomeruli (compact microcircuits corresponding to different odor channels). Moreover, we show that neuromodulation, environmental stress in the form of altered nutrition, and activity of certain AL local interneurons affect the magnitude of interfly behavioral variability. Taken together, this work demonstrates that individual exhibit idiosyncratic olfactory preferences and idiosyncratic neural responses to odors, and that behavioral idiosyncrasies are subject to neuromodulation and regulation by neurons in the AL.

}, issn = {1091-6490}, doi = {10.1073/pnas.1901623116}, author = {Honegger, Kyle S and Smith, Matthew A-Y and Churgin, Matthew A and Turner, Glenn C and de Bivort, Benjamin L} } @article {65275, title = {Improved HaloTag Ligand Enables BRET Imaging With NanoLuc}, journal = {Frontiers in Chemistry}, volume = {7}, year = {2020}, month = {2020 Jan 14}, doi = {10.3389/fchem.2019.0093810.3389/fchem.2019.00938.s001}, url = {https://www.frontiersin.org/article/10.3389/fchem.2019.00938/fullhttps://www.frontiersin.org/article/10.3389/fchem.2019.00938/fullhttps://www.frontiersin.org/articles/10.3389/fchem.2019.00938/supplementary-material/10.3389/fchem.2019.00938.s001}, author = {Thirukkumaran, Ovia Margaret and Wang, Congrong and Asouzu, Nnamdi Joseph and Fron, Eduard and Rocha, Susana and Hofkens, Johan and Lavis, Luke D. and Mizuno, Hideaki} } @conference {65835, title = {Inpainting Networks Learn to Separate Cells in Microscopy Images}, booktitle = {British Machine Vision Conference}, year = {2020}, month = {2020 Sep}, abstract = {

Deep neural networks trained to inpaint partially occluded images show a deep understanding of image composition and have even been shown to remove objects from images convincingly. In this work, we investigate how this implicit knowledge of image composition can be be used to separate cells in densely populated microscopy images. We propose a measure for the independence of two image regions given a fully self-supervised inpainting network and separate objects by maximizing this independence. We evaluate our method on two cell segmentation datasets and show that cells can be separated completely unsupervised. Furthermore, combined with simple foreground detection, our method yields instance segmentation of similar quality to fully supervised methods.

}, url = {https://www.bmvc2020-conference.com/assets/papers/0528.pdf}, author = {Wolf, Steffen and Hamprecht, Fred A and Funke, Jan} } @article {65314, title = {Input connectivity reveals additional heterogeneity of dopaminergic reinforcement in Drosophila}, journal = {Current Biology}, volume = {30}, year = {2020}, month = {2020 Aug 17}, pages = {3200-11}, abstract = {

Different types of\ Drosophila\ dopaminergic neurons (DANs) reinforce memories of unique valence and provide state-dependent motivational control [1]. Prior studies suggest that the compartment architecture of the mushroom body (MB) is the relevant resolution for distinct DAN functions [2,\ 3]. Here we used a recent electron microscope volume of the fly brain [4] to reconstruct the fine anatomy of individual DANs within three MB compartments. We find the 20 DANs of the γ5 compartment, at least some of which provide reward teaching signals, can be clustered into 5 anatomical subtypes that innervate different regions within γ5. Reconstructing 821 upstream neurons reveals input selectivity, supporting the functional relevance of DAN sub-classification. Only one PAM-γ5 DAN subtype (γ5fb) receives direct recurrent input from γ5β{\textquoteright}2a mushroom body output neurons (MBONs) and behavioral experiments distinguish a role for these DANs in memory revaluation from those reinforcing sugar memory. Other DAN subtypes receive major, and potentially reinforcing, inputs from putative gustatory interneurons or lateral horn neurons, which can also relay indirect feedback from the MB. We similarly reconstructed the single aversively reinforcing PPL1-γ1pedc DAN. The γ1pedc DAN inputs are mostly different to those of γ5 DANs and are clustered onto distinct branches of its dendritic tree, presumably separating its established roles in aversive reinforcement and appetitive motivation [5,\ 6]. Additional tracing identified neurons that provide broad input to γ5, β{\textquoteright}2a and γ1pedc DANs suggesting that distributed DAN populations can be coordinately regulated. These connectomic and behavioral analyses therefore reveal additional complexity of dopaminergic reinforcement circuits between and within MB compartments.

}, author = {Otto, Nils and Pleijzier, Markus W. and Morgan, Isabel C. and Edmondson-Stait, Amelia J and Heinz, Konrad J. and Stark, Ildiko and Dempsey, Georgia and Ito, Masayoshi and Kapoor, Ishaan and Hsu, Joseph and Schlegel, Philipp M. and Bates, Alexander S. and Costa, Marta and Ito, Kei and Bock, Davi D. and Rubin, Gerald M. and Jefferis, Gregory S.X.E. and Waddell, Scott} } @article {65762, title = {Integrated structure-function dataset reveals key mechanisms underlying photochromic fluorescent proteins}, journal = {bioRxiv}, year = {2020}, month = {09/2020}, pages = {2020.09.25.313528}, abstract = {

Photochromic fluorescent proteins have become versatile tools in the life sciences, though our understanding of their structure-function relation is limited. Starting from a single scaffold, we have developed a range of 27 photochromic fluorescent proteins that cover a broad range of spectroscopic properties, yet differ only in one or two mutations. We also determined 43 different crystal structures of these mutants. Correlation and principal component analysis of the spectroscopic and structural properties confirmed the complex relationship between structure and spectroscopy, suggesting that the observed variability does not arise from a limited number of mechanisms, but also allowed us to identify consistent trends and to relate these to the spatial organization around the chromophore. We find that particular changes in spectroscopic properties can come about through multiple different underlying mechanisms, of which the polarity of the chromophore environment and hydrogen bonding of the chromophore are key modulators. Furthermore, some spectroscopic parameters, such as the photochromism, appear to be largely determined by a single or a few structural properties, while other parameters, such as the absorption maximum, do not allow a clear identification of a single cause. We also highlight the role of water molecules close to the chromophore in influencing photochromism. We anticipate that our dataset can open opportunities for the development and evaluation of new and existing protein engineering methods.

}, doi = {10.1101/2020.09.25.313528}, author = {Zitter, Elke De and Hugelier, Siewert and Duw{\'e}, Sam and Vandenberg, Wim and Tebo, Alison G. and Meervelt, Luc Van and Dedecker, Peter} } @article {65322, title = {Kilohertz two-photon fluorescence microscopy imaging of neural activity in vivo.}, journal = {Nature Methods}, volume = {17}, year = {2020}, month = {2020 Mar 02}, pages = {287-290}, abstract = {

Understanding information processing in the brain requires monitoring neuronal activity at high spatiotemporal resolution. Using an ultrafast two-photon fluorescence microscope empowered by all-optical laser scanning, we imaged neuronal activity in vivo at up to 3,000 frames per second and submicrometer spatial resolution. This imaging method enabled monitoring of both supra- and subthreshold electrical activity down to 345 μm below the brain surface in head-fixed awake mice.

}, issn = {1548-7105}, doi = {10.1038/s41592-020-0762-7}, author = {Wu, Jianglai and Liang, Yajie and Chen, Shuo and Hsu, Ching-Lung and Chavarha, Mariya and Evans, Stephen W and Shi, Dongqing and Lin, Michael Z and Tsia, Kevin K and Ji, Na} } @article {68842, title = {Latent Feature Representation via Unsupervised Learning for Pattern Discovery in Massive Electron Microscopy Image Volumes}, journal = {arXiv}, year = {2020}, month = {2020 Dec 22}, abstract = {

We propose a method to facilitate exploration and analysis of new large data sets. In particular, we give an unsupervised deep learning approach to learning a latent representation that captures semantic similarity in the data set. The core idea is to use data augmentations that preserve semantic meaning to generate synthetic examples of elements whose feature representations should be close to one another.
We demonstrate the utility of our method applied to nano-scale electron microscopy data, where even relatively small portions of animal brains can require terabytes of image data. Although supervised methods can be used to predict and identify known patterns of interest, the scale of the data makes it difficult to mine and analyze patterns that are not known a priori. We show the ability of our learned representation to enable query by example, so that if a scientist notices an interesting pattern in the data, they can be presented with other locations with matching patterns. We also demonstrate that clustering of data in the learned space correlates with biologically-meaningful distinctions. Finally, we introduce a visualization tool and software ecosystem to facilitate user-friendly interactive analysis and uncover interesting biological patterns. In short, our work opens possible new avenues in understanding of and discovery in large data sets, arising in domains such as EM analysis.

}, doi = {10.48550/arXiv.2012.12175}, url = {http://doi.org/10.48550/arXiv.2012.12175}, author = {Gary B Huang and Huei-Fang Yang and Shin-ya Takemura and Pat Rivlin and Stephen M Plaza} } @article {65824, title = {Linking axon morphology to gene expression: a strategy for neuronal cell-type classification.}, journal = {Current Opinion in Neurobiology}, volume = {65}, year = {2020}, month = {2020 Dec 01}, pages = {70-76}, abstract = {

To study how the brain drives cognition and behavior we need to understand its cellular composition. Advances in single-cell transcriptomics have revolutionized our ability to characterize neuronal diversity. To arrive at meaningful descriptions of cell types, however, gene expression must be linked to structural and functional properties. Axonal projection patterns are an appropriate measure, as they are diverse, change only gradually over time, and they influence and constrain circuit function. Here, we consider how efforts to map transcriptional and morphological diversity in the mouse brain could be linked to generate a modern taxonomy of the mouse brain.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2020.10.006}, author = {Winnubst, Johan and Spruston, Nelson and Harris, Julie A} } @article {65908, title = {Linking axon morphology to gene expression: a strategy for neuronal cell-type classification.}, journal = {Current Opinion in Neurobiology}, volume = {65}, year = {2020}, month = {2020 Dec 01}, pages = {70-76}, abstract = {

To study how the brain drives cognition and behavior we need to understand its cellular composition. Advances in single-cell transcriptomics have revolutionized our ability to characterize neuronal diversity. To arrive at meaningful descriptions of cell types, however, gene expression must be linked to structural and functional properties. Axonal projection patterns are an appropriate measure, as they are diverse, change only gradually over time, and they influence and constrain circuit function. Here, we consider how efforts to map transcriptional and morphological diversity in the mouse brain could be linked to generate a modern taxonomy of the mouse brain.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2020.10.006}, author = {Winnubst, Johan and Spruston, Nelson and Harris, Julie A} } @article {68359, title = {Meissner corpuscles and their spatially intermingled afferents underlie gentle touch perception}, journal = {Science}, volume = {368}, year = {2020}, month = {06/2020}, pages = {eabb2751}, abstract = {

The Meissner corpuscle, a mechanosensory end organ, was discovered more than 165 years ago and has since been found in the glabrous skin of all mammals, including that on human fingertips. Although prominently featured in textbooks, the function of the Meissner corpuscle is unknown. Neubarth et al. generated adult mice without Meissner corpuscles and used them to show that these corpuscles alone mediate behavioral responses to, and perception of, gentle forces (see the Perspective by Marshall and Patapoutian). Each Meissner corpuscle is innervated by two molecularly distinct, yet physiologically similar, mechanosensory neurons. These two neuronal subtypes are developmentally interdependent and their endings are intertwined within the corpuscle. Both Meissner mechanosensory neuron subtypes are homotypically tiled, ensuring uniform and complete coverage of the skin, yet their receptive fields are overlapping and offset with respect to each other. Science, this issue p. eabb2751; see also p. 1311 Light touch perception and fine sensorimotor control arise from spatially overlapping mechanoreceptors of the Meissner corpuscle. Meissner corpuscles are mechanosensory end organs that densely occupy mammalian glabrous skin. We generated mice that selectively lacked Meissner corpuscles and found them to be deficient in both perceiving the gentlest detectable forces acting on glabrous skin and fine sensorimotor control. We found that Meissner corpuscles are innervated by two mechanoreceptor subtypes that exhibit distinct responses to tactile stimuli. The anatomical receptive fields of these two mechanoreceptor subtypes homotypically tile glabrous skin in a manner that is offset with respect to one another. Electron microscopic analysis of the two Meissner afferents within the corpuscle supports a model in which the extent of lamellar cell wrappings of mechanoreceptor endings determines their force sensitivity thresholds and kinetic properties.

}, doi = {10.1126/science.abb2751}, url = {https://www.science.org/doi/abs/10.1126/science.abb2751}, author = {Nicole L. Neubarth and Alan J. Emanuel and Yin Liu and Mark W. Springel and Annie Handler and Qiyu Zhang and Brendan P. Lehnert and Chong Guo and Lauren L. Orefice and Amira Abdelaziz and Michelle M. DeLisle and Michael Iskols and Julia Rhyins and Soo J. Kim and Stuart J. Cattel and Wade Regehr and Christopher D. Harvey and Jan Drugowitsch and David D. Ginty} } @article {65738, title = {The mind of a mouse.}, journal = {Cell}, volume = {182}, year = {2020}, month = {2020 Sep 17}, pages = {1372-1376}, abstract = {

Large scientific projects in genomics and astronomy are influential not because they answer any single question but because they enable investigation of continuously arising new questions from the same data-rich sources. Advances in automated mapping of the brain{\textquoteright}s synaptic connections (connectomics) suggest that the complicated circuits underlying brain function are ripe for analysis. We discuss benefits of mapping a mouse brain at the level of synapses.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2020.08.010}, author = {Abbott, Larry F and Bock, Davi D and Callaway, Edward M and Denk, Winfried and Dulac, Catherine and Fairhall, Adrienne L and Fiete, Ila and Harris, Kristen M and Helmstaedter, Moritz and Jain, Viren and Kasthuri, Narayanan and LeCun, Yann and Lichtman, Jeff W and Littlewood, Peter B and Luo, Liqun and Maunsell, John H R and Reid, R Clay and Rosen, Bruce R and Rubin, Gerald M and Sejnowski, Terrence J and Seung, H Sebastian and Svoboda, Karel and Tank, David W and Tsao, Doris and Van Essen, David C} } @article {65653, title = {Multifield and inverse-contrast switching of magnetocaloric high contrast ratio MRI labels.}, journal = {Magnetic Resonance in Medicine}, volume = {85}, year = {2020}, month = {2020 Jul 07}, pages = {506-17}, abstract = {

PURPOSE: Demonstrating multifield and inverse contrast switching of magnetocaloric high contrast ratio MRI labels that either have increasing or decreasing moment versus temperature slopes depending on the material at physiological temperatures and different MRI magnetic field strengths.

METHODS: Two iron-rhodium samples of different purity (99\% and 99.9\%) and a lanthanum-iron-silicon sample were obtained from commercial vendors. Temperature and magnetic field-dependent magnetic moment measurements of the samples were performed on a vibrating sample magnetometer. Temperature-dependent MRI of different iron-rhodium and lanthanum-iron-silicon samples were performed on 3 different MRI scanners at 1 Tesla (T), 4.7T, and 7T.

RESULTS: Sharp, first-order magnetic phase transition of each iron-rhodium sample at a physiologically relevant temperature (~37{\textdegree}C) but at different MRI magnetic fields (1T, 4.7T, and 7T, depending on the sample) showed clear image contrast changes in temperature-dependent MRI. Iron-rhodium and lanthanum-iron-silicon samples with sharp, first-order magnetic phase transitions at the same MRI field of 1T and physiological temperature of 37{\textdegree}C, but with positive and negative slope of magnetization versus temperature, respectively, showed clear inverse contrast image changes. Temperature-dependent MRI on individual microparticle samples of lanthanum-iron-silicon also showed sharp image contrast changes.

CONCLUSION: Magnetocaloric materials of different purity and composition were demonstrated to act as diverse high contrast ratio switchable MRI contrast agents. Thus, we show that a range of magnetocaloric materials can be optimized for unique image contrast response under MRI-appropriate conditions at physiological temperatures and be controllably switched in situ.

}, issn = {1522-2594}, doi = {10.1002/mrm.28400}, author = {Barbic, Mladen and Dodd, Stephen J and ElBidweihy, Hatem and Dilley, Neil R and Marcheschi, Barbara and Huston, Alan L and Morris, H Douglas and Koretsky, Alan P} } @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 {65312, title = {Parvalbumin+ and Npas1+ Pallidal neurons have distinct circuit topology and function.}, journal = {Journal of Neuroscience}, year = {2020}, month = {2020 Aug 30}, author = {Pamukcu, Arin and Cui, Qiaoling and Xenias, Harry S. and Berceau, Brianna L. and Augustine, Elizabeth C. and Fan, Isabel and Hantman, Adam W and Lerner, Talia N. and Boca, Simina M. and Chan, C. Savio} } @article {65634, title = {Precision Calcium Imaging of Dense Neural Populations via a Cell-Body-Targeted Calcium Indicator.}, journal = {Neuron}, volume = {107}, year = {2020}, month = {2020 Aug 01}, pages = {470}, abstract = {

Methods for one-photon fluorescent imaging of calcium dynamics can capture the activity of hundreds of neurons across large fields of view at a low equipment complexity and cost. In contrast to two-photon methods, however, one-photon methods suffer from higher levels of crosstalk from neuropil, resulting in a decreased signal-to-noise ratio and artifactual correlations of neural activity. We address this problem by engineering cell-body-targeted variants of the fluorescent calcium indicators GCaMP6f and GCaMP7f. We screened fusions of GCaMP to natural, as well as artificial, peptides and identified fusions that localized GCaMP to within 50\ μm of the cell body of neurons in mice and larval zebrafish. One-photon imaging of soma-targeted GCaMP in dense neural circuits reported fewer artifactual spikes from neuropil, an increased signal-to-noise ratio, and decreased artifactual correlation across neurons. Thus, soma-targeting of fluorescent calcium indicators facilitates usage of simple, powerful, one-photon methods for imaging neural calcium dynamics.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2020.05.029}, author = {Shemesh, Or A and Linghu, Changyang and Piatkevich, Kiryl D and Goodwin, Daniel and Celiker, Orhan Tunc and Gritton, Howard J and Romano, Michael F and Gao, Ruixuan and Yu, Chih-Chieh Jay and Tseng, Hua-An and Bensussen, Seth and Narayan, Sujatha and Yang, Chao-Tsung and Freifeld, Limor and Siciliano, Cody A and Gupta, Ishan and Wang, Joyce and Pak, Nikita and Yoon, Young-Gyu and Ullmann, Jeremy F P and Guner-Ataman, Burcu and Noamany, Habiba and Sheinkopf, Zoe R and Park, Won Min and Asano, Shoh and Keating, Amy E and Trimmer, James S and Reimer, Jacob and Tolias, Andreas S and Bear, Mark F and Tye, Kay M and Han, Xue and Ahrens, Misha B and Boyden, Edward S} } @article {65721, title = {Preventing cytokine storm syndrome in COVID-19 using α-1 adrenergic receptor antagonists.}, journal = {The Journal of Clinical Investigatio}, volume = {130}, year = {2020}, month = {2020 Jul 01}, pages = {3345-47}, keywords = {Adrenergic alpha-1 Receptor Antagonists, Clinical Trials as Topic, Coronavirus Infections, Cytokine Release Syndrome, Humans, Pandemics, Pneumonia, Viral}, issn = {1558-8238}, doi = {10.1172/JCI139642}, author = {Konig, Maximilian F and Powell, Mike and Staedtke, Verena and Bai, Ren-Yuan and Thomas, David L and Fischer, Nicole and Huq, Sakibul and Khalafallah, Adham M and Koenecke, Allison and Xiong, Ruoxuan and Mensh, Brett and Papadopoulos, Nickolas and Kinzler, Kenneth W and Vogelstein, Bert and Vogelstein, Joshua T and Athey, Susan and Zhou, Shibin and Bettegowda, Chetan} } @article {65884, title = {Probabilistic Models of Larval Zebrafish Behavior Reveal Structure on Many Scales}, journal = {Current Biology}, volume = {30}, year = {2020}, month = {01/2020}, pages = {70 - 82.e4}, abstract = {

Nervous systems have evolved to combine environmental information with internal state to select and generate adaptive behavioral sequences. To better understand these computations and their implementation in neural circuits, natural behavior must be carefully measured and quantified. Here, we collect high spatial resolution video of single zebrafish larvae swimming in a naturalistic environment and develop models of their action selection across exploration and hunting. Zebrafish larvae swim in punctuated bouts separated by longer periods of rest called interbout intervals. We take advantage of this structure by categorizing bouts into discrete types and representing their behavior as labeled sequences of bout types emitted over time. We then construct probabilistic models{\textemdash}specifically, marked renewal processes{\textemdash}to evaluate how bout types and interbout intervals are selected by the fish as a function of its internal hunger state, behavioral\ history, and the locations and properties of nearby prey. Finally, we evaluate the models by their predictive likelihood and their ability to generate realistic trajectories of virtual fish swimming through simulated environments. Our simulations capture multiple timescales of structure in larval zebrafish behavior and expose many ways in which hunger state influences their action selection to promote food seeking during hunger and safety during satiety.

}, keywords = {behavioral models, behavioral simulations, exploration, hunger, hunting, natural behavior, Zebrafish}, issn = {0960-9822}, doi = {https://doi.org/10.1016/j.cub.2019.11.026}, url = {http://www.sciencedirect.com/science/article/pii/S0960982219314654}, author = {Robert Evan Johnson and Scott Linderman and Thomas Panier and Caroline Lei Wee and Erin Song and Kristian Joseph Herrera and Andrew Miller and Florian Engert} } @article {68428, title = {Single-Cell Transcriptomes Reveal Diverse Regulatory Strategies for Olfactory Receptor Expression and Axon Targeting.}, journal = {Curr Biol}, volume = {30}, year = {2020}, month = {04/2020}, pages = {1189-1198.e5}, abstract = {

The regulatory mechanisms by which neurons coordinate their physiology and connectivity are not well understood. The Drosophila olfactory receptor neurons (ORNs) provide an excellent system to investigate this question. Each ORN type expresses a unique olfactory receptor, or a combination thereof, and sends their axons to a stereotyped glomerulus. Using single-cell RNA sequencing, we identified 33 transcriptomic clusters for ORNs and mapped 20 to their glomerular types, demonstrating that transcriptomic clusters correspond well with anatomically and physiologically defined ORN types. Each ORN type expresses hundreds of transcription factors. Transcriptome-instructed genetic analyses revealed that (1) one broadly expressed transcription factor (Acj6) only regulates olfactory receptor expression in one ORN type and only wiring specificity in another type, (2) one type-restricted transcription factor (Forkhead) only regulates receptor expression, and (3) another type-restricted transcription factor (Unplugged) regulates both events. Thus, ORNs utilize diverse strategies and complex regulatory networks to coordinate their physiology and connectivity.

}, keywords = {Animals, Axons, Drosophila melanogaster, Drosophila Proteins, Forkhead Transcription Factors, Homeodomain Proteins, Nerve Tissue Proteins, Olfactory Receptor Neurons, POU Domain Factors, Receptors, Odorant, Single-Cell Analysis, Smell, Transcriptome}, issn = {1879-0445}, doi = {10.1016/j.cub.2020.01.049}, author = {Li, Hongjie and Li, Tongchao and Horns, Felix and Li, Jiefu and Xie, Qijing and Xu, Chuanyun and Wu, Bing and Kebschull, Justus M and McLaughlin, Colleen N and Kolluru, Sai Saroja and Jones, Robert C and Vacek, David and Xie, Anthony and Luginbuhl, David J and Quake, Stephen R and Luo, Liqun} } @article {65870, title = {Social hierarchy is established and maintained with distinct acts of aggression in male Drosophila melanogaster.}, journal = {Journal of Experimental Biology}, year = {2020}, month = {2020 Dec 02}, abstract = {

Social interactions pivot on an animal{\textquoteright}s experiences, internal states, and feedback from others. This complexity drives the need for precise descriptions of behavior to dissect the fine detail of its genetic and neural circuit bases. In laboratory assays, male reliably exhibit aggression, and its extent is generally measured by scoring lunges, a feature of aggression in which one male quickly thrusts onto his opponent. Here, we introduce an explicit approach to identify both the onset and reversals in hierarchical status between opponents and observe that distinct aggressive acts reproducibly precede, concur, or follow the establishment of dominance. We find that lunges are insufficient for establishing dominance. Rather, lunges appear to reflect the dominant state of a male and help in maintaining his social status. Lastly, we characterize the recurring and escalating structure of aggression that emerges through subsequent reversals in dominance. Collectively, this work provides a framework for studying the complexity of agonistic interactions in male flies enabling its neurogenetic basis to be understood with precision.

}, issn = {1477-9145}, doi = {10.1242/jeb.232439}, author = {Simon, Jasper C and Heberlein, Ulrike} } @article {65853, title = {The structural basis of Rubisco phase separation in the pyrenoid.}, journal = {Nature Plants}, year = {2020}, month = {2020 Nov 23}, abstract = {

Approximately one-third of global CO fixation occurs in a phase-separated algal organelle called the pyrenoid. The existing data suggest that the pyrenoid forms by the phase separation of the CO-fixing enzyme Rubisco with a linker protein; however, the molecular interactions underlying this phase separation remain unknown. Here we present the structural basis of the interactions between Rubisco and its intrinsically disordered linker protein Essential Pyrenoid Component 1 (EPYC1) in the model alga Chlamydomonas reinhardtii. We find that EPYC1 consists of five evenly spaced Rubisco-binding regions that share sequence similarity. Single-particle cryo-electron microscopy of these regions in complex with Rubisco indicates that each Rubisco holoenzyme has eight binding sites for EPYC1, one on each Rubisco small subunit. Interface mutations disrupt binding, phase separation and pyrenoid formation. Cryo-electron tomography supports a model in which EPYC1 and Rubisco form a codependent multivalent network of specific low-affinity bonds, giving the matrix liquid-like properties. Our results advance the structural and functional understanding of the phase separation underlying the pyrenoid, an organelle that plays a fundamental role in the global carbon cycle.

}, issn = {2055-0278}, doi = {10.1038/s41477-020-00811-y}, author = {He, Shan and Chou, Hui-Ting and Matthies, Doreen and Wunder, Tobias and Meyer, Moritz T and Atkinson, Nicky and Martinez-Sanchez, Antonio and Jeffrey, Philip D and Port, Sarah A and Patena, Weronika and He, Guanhua and Chen, Vivian K and Hughson, Frederick M and McCormick, Alistair J and Mueller-Cajar, Oliver and Engel, Benjamin D and Yu, Zhiheng and Jonikas, Martin C} } @article {65901, title = {The structural basis of Rubisco phase separation in the pyrenoid.}, journal = {Nature Plants}, volume = {6}, year = {2020}, month = {2020 Dec 01}, pages = {1480-1490}, abstract = {

Approximately one-third of global CO fixation occurs in a phase-separated algal organelle called the pyrenoid. The existing data suggest that the pyrenoid forms by the phase separation of the CO-fixing enzyme Rubisco with a linker protein; however, the molecular interactions underlying this phase separation remain unknown. Here we present the structural basis of the interactions between Rubisco and its intrinsically disordered linker protein Essential Pyrenoid Component 1 (EPYC1) in the model alga Chlamydomonas reinhardtii. We find that EPYC1 consists of five evenly spaced Rubisco-binding regions that share sequence similarity. Single-particle cryo-electron microscopy of these regions in complex with Rubisco indicates that each Rubisco holoenzyme has eight binding sites for EPYC1, one on each Rubisco small subunit. Interface mutations disrupt binding, phase separation and pyrenoid formation. Cryo-electron tomography supports a model in which EPYC1 and Rubisco form a codependent multivalent network of specific low-affinity bonds, giving the matrix liquid-like properties. Our results advance the structural and functional understanding of the phase separation underlying the pyrenoid, an organelle that plays a fundamental role in the global carbon cycle.

}, issn = {2055-0278}, doi = {10.1038/s41477-020-00811-y}, author = {He, Shan and Chou, Hui-Ting and Matthies, Doreen and Wunder, Tobias and Meyer, Moritz T and Atkinson, Nicky and Martinez-Sanchez, Antonio and Jeffrey, Philip D and Port, Sarah A and Patena, Weronika and He, Guanhua and Chen, Vivian K and Hughson, Frederick M and McCormick, Alistair J and Mueller-Cajar, Oliver and Engel, Benjamin D and Yu, Zhiheng and Jonikas, Martin C} } @article {65759, title = {Structural insight into the ATP-driven exporter of virulent peptide toxins.}, journal = {Science Advances}, volume = {6}, year = {2020}, month = {2020 Sep 30}, abstract = {

is a major human pathogen that has acquired alarming broad-spectrum antibiotic resistance. One group of secreted toxins with key roles during infection is the phenol-soluble modulins (PSMs). PSMs are amphipathic, membrane-destructive cytolytic peptides that are exported to the host-cell environment by a designated adenosine 5{\textquoteright}-triphosphate (ATP)-binding cassette (ABC) transporter, the PSM transporter (PmtABCD). Here, we demonstrate that the minimal Pmt unit necessary for PSM export is PmtCD and provide its first atomic characterization by single-particle cryo-EM and x-ray crystallography. We have captured the transporter in the ATP-bound state at near atomic resolution, revealing a type II ABC exporter fold, with an additional cytosolic domain. Comparison to a lower-resolution nucleotide-free map displaying an "open" conformation and putative hydrophobic inner chamber of a size able to accommodate the binding of two PSM peptides provides mechanistic insight and sets the foundation for therapeutic design.

}, issn = {2375-2548}, doi = {10.1126/sciadv.abb8219}, author = {Zeytuni, N and Dickey, S W and Hu, J and Chou, H T and Worrall, L J and Alexander, J A N and Carlson, M L and Nosella, M and Duong, F and Yu, Z and Otto, M and Strynadka, N C J} } @article {65635, title = {Structure of human GABA receptor in an inactive state.}, journal = {Nature}, volume = {584}, year = {2020}, month = {2020 Aug 01}, pages = {304-9}, abstract = {

The human GABA receptor-a member of the class C family of G-protein-coupled receptors (GPCRs)-mediates inhibitory neurotransmission and has been implicated in epilepsy, pain and addiction. A unique GPCR that is known to require heterodimerization for function, the GABA receptor has two subunits, GABA and GABA, that are structurally homologous but perform distinct and complementary functions. GABA recognizes orthosteric ligands, while GABA couples with G proteins. Each subunit is characterized by an extracellular Venus flytrap (VFT) module, a descending peptide linker, a seven-helix transmembrane domain and a cytoplasmic tail. Although the VFT heterodimer structure has been resolved, the structure of the full-length receptor and its transmembrane signalling mechanism remain unknown. Here we present a near full-length structure of the GABA receptor at atomic resolution, captured in an inactive state by cryo-electron microscopy. Our structure reveals several ligands that preassociate with the receptor, including two large endogenous phospholipids that are embedded within the transmembrane domains to maintain receptor integrity and modulate receptor function. We also identify a previously unknown heterodimer interface between transmembrane helices 3 and 5 of both subunits, which serves as a signature of the inactive conformation. A unique {\textquoteright}intersubunit latch{\textquoteright} within this transmembrane interface maintains the inactive state, and its disruption leads to constitutive receptor activity.

}, issn = {1476-4687}, doi = {10.1038/s41586-020-2452-0}, author = {Park, Jinseo and Fu, Ziao and Frangaj, Aurel and Liu, Jonathan and Mosyak, Lidia and Shen, Tong and Slavkovich, Vesna N and Ray, Kimberly M and Taura, Jaume and Cao, Baohua and Geng, Yong and Zuo, Hao and Kou, Yongjun and Grassucci, Robert and Chen, Shaoxia and Liu, Zheng and Lin, Xin and Williams, Justin P and Rice, William J and Eng, Edward T and Huang, Rick K and Soni, Rajesh K and Kloss, Brian and Yu, Zhiheng and Javitch, Jonathan A and Hendrickson, Wayne A and Slesinger, Paul A and Quick, Matthias and Graziano, Joseph and Yu, Hongtao and Fiehn, Oliver and Clarke, Oliver B and Frank, Joachim and Fan, Qing R} } @article {65277, title = {Structure of the vesicular stomatitis virus L protein in complex with Its phosphoprotein cofactor.}, journal = {Cell Reports}, volume = {30}, year = {2020}, month = {2020 Jan 07}, pages = {53-60.e5}, abstract = {

The large (L) proteins of non-segmented, negative-strand RNA viruses are multifunctional enzymes that produce capped, methylated, and polyadenylated mRNA and replicate the viral genome. A phosphoprotein (P), required for efficient RNA-dependent RNA polymerization from the viral ribonucleoprotein (RNP) template, regulates the function and conformation of the L protein. We report the structure of vesicular stomatitis virus L in complex with its P cofactor determined by electron cryomicroscopy at 3.0\ {\r A} resolution, enabling us to visualize bound segments of P. The contacts of three P segments with multiple L domains show how P induces a closed, compact, initiation-competent conformation. Binding of P to L positions its N-terminal domain adjacent to a putative RNA exit channel for efficient encapsidation of newly synthesized genomes with the nucleoprotein and orients its C-terminal domain to interact with an RNP template. The model shows that a conserved tryptophan in the priming loop can support the initiating 5{\textquoteright} nucleotide.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2019.12.024}, author = {Jenni, Simon and Bloyet, Louis-Marie and Diaz-Avalos, Ruben and Liang, Bo and Whelan, Sean P J and Grigorieff, Nikolaus and Harrison, Stephen C} } @article {65272, title = {Tiled reconstruction improves structured illumination microscopy.}, journal = {bioRxiv}, year = {2020}, month = {2020 Jan 11}, abstract = {

Structured illumination microscopy (SIM) is widely used for fast, long-term, live-cell super-resolution imaging. However, SIM images can contain substantial artifacts if the sample does not conform to the underlying assumptions of the reconstruction algorithm. Here we describe a simple, easy to implement, process that can be combined with any reconstruction algorithm to alleviate many common SIM reconstruction artifacts and briefly discuss possible extensions.

}, doi = {10.1101/2020.01.06.895318}, author = {Hoffman, David P. and Betzig, Eric} } @article {65660, title = {Towards accurate and unbiased imaging-based differentiation of Parkinson{\textquoteright}s disease, progressive supranuclear palsy and corticobasal syndrome.}, journal = {Brain Communications}, volume = {2}, year = {2020}, month = {2020 Jul 1}, pages = {fcaa051}, abstract = {

The early and accurate differential diagnosis of parkinsonian disorders is still a significant challenge for clinicians. In recent years, a number of studies have used magnetic resonance imaging data combined with machine learning and statistical classifiers to successfully differentiate between different forms of Parkinsonism. However, several questions and methodological issues remain, to minimize bias and artefact-driven classification. In this study, we compared different approaches for feature selection, as well as different magnetic resonance imaging modalities, with well-matched patient groups and tightly controlling for data quality issues related to patient motion. Our sample was drawn from a cohort of 69 healthy controls, and patients with idiopathic Parkinson{\textquoteright}s disease (= 35), progressive supranuclear palsy Richardson{\textquoteright}s syndrome (= 52) and corticobasal syndrome (= 36). Participants underwent standardized T1-weighted and diffusion-weighted magnetic resonance imaging. Strict data quality control and group matching reduced the control and patient numbers to 43, 32, 33 and 26, respectively. We compared two different methods for feature selection and dimensionality reduction: whole-brain principal components analysis, and an anatomical region-of-interest based approach. In both cases, support vector machines were used to construct a statistical model for pairwise classification of healthy controls and patients. The accuracy of each model was estimated using a leave-two-out cross-validation approach, as well as an independent validation using a different set of subjects. Our cross-validation results suggest that using principal components analysis for feature extraction provides higher classification accuracies when compared to a region-of-interest based approach. However, the differences between the two feature extraction methods were significantly reduced when an independent sample was used for validation, suggesting that the principal components analysis approach may be more vulnerable to overfitting with cross-validation. Both T1-weighted and diffusion magnetic resonance imaging data could be used to successfully differentiate between subject groups, with neither modality outperforming the other across all pairwise comparisons in the cross-validation analysis. However, features obtained from diffusion magnetic resonance imaging data resulted in significantly higher classification accuracies when an independent validation cohort was used. Overall, our results support the use of statistical classification approaches for differential diagnosis of parkinsonian disorders. However, classification accuracy can be affected by group size, age, sex and movement artefacts. With appropriate controls and out-of-sample cross validation, diagnostic biomarker evaluation including magnetic resonance imaging based classifiers may be an important adjunct to clinical evaluation.

}, issn = {2632-1297}, doi = {10.1093/braincomms/fcaa051}, author = {Correia, Marta M and Rittman, Timothy and Barnes, Christopher L and Coyle-Gilchrist, Ian T and Ghosh, Boyd and Hughes, Laura E and Rowe, James B} } @article {65320, title = {Transcriptional co-repressor Sin3a regulates hippocampal synaptic plasticity via Homer1/mGluR5.}, journal = {JCI Insight}, year = {2020}, month = {2020 Feb 18}, abstract = {

Long-term memory depends on the control of activity-dependent neuronal gene expression, which is regulated by epigenetic modifications. The epigenetic modification of histones is orchestrated by the opposing activities of two classes of regulatory complexes: permissive co-activators and silencing co-repressors. Much work has focused on co-activator complexes, but little is known about the co-repressor complexes that suppress the expression of plasticity-related genes. Here, we define a critical role for the co-repressor SIN3A in memory and synaptic plasticity, showing that postnatal neuronal deletion of Sin3a enhances hippocampal long-term potentiation and long-term contextual fear memory. SIN3A regulates the expression of genes encoding proteins in the post-synaptic density. Loss of SIN3A increases expression of the synaptic scaffold Homer1, alters the mGluR1α- and mGluR5-dependence of long-term potentiation, and increases activation of extracellular signal regulated kinase (ERK) in the hippocampus after learning. Our studies define a critical role for co-repressors in modulating neural plasticity and memory consolidation and reveal that Homer1/mGluR signaling pathways may be central molecular mechanisms for memory enhancement.

}, issn = {2379-3708}, doi = {10.1172/jci.insight.92385}, author = {Bridi, Morgan S and Schoch, Hannah and Florian, C{\'e}drick and Poplawski, Shane G and Banerjee, Anamika and Hawk, Joshua D and Banks, Giulia S and Lejards, Camille and Hahn, Chang-Gyu and Giese, Karl Peter and Havekes, Robbert and Spruston, Nelson and Abel, Ted} } @article {65256, title = {Trans-endocytosis of intact IL-15Rα-IL-15 complex from presenting cells into NK cells favors signaling for proliferation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, year = {2020}, month = {2020 Jan 07}, pages = {522-531}, abstract = {

Interleukin 15 (IL-15) is an essential cytokine for the survival and proliferation of natural killer (NK) cells. IL-15 activates signaling by the β and common γ (γ) chain heterodimer of the IL-2 receptor through -presentation by cells expressing IL-15 bound to the α chain of the IL-15 receptor (IL-15Rα). We show here that membrane-associated IL-15Rα-IL-15 complexes are transferred from presenting cells to NK cells through -endocytosis and contribute to the phosphorylation of ribosomal protein S6 and NK cell proliferation. NK cell interaction with soluble or surface-bound IL-15Rα-IL-15 complex resulted in Stat5 phosphorylation and NK cell survival at a concentration or density of the complex much lower than required to stimulate S6 phosphorylation. Despite this efficient response, Stat5 phosphorylation was reduced after inhibition of metalloprotease-induced IL-15Rα-IL-15 shedding from -presenting cells, whereas S6 phosphorylation was unaffected. Conversely, inhibition of -endocytosis by silencing of the small GTPase TC21 or expression of a dominant-negative TC21 reduced S6 phosphorylation but not Stat5 phosphorylation. Thus, -endocytosis of membrane-associated IL-15Rα-IL-15 provides a mode of regulating NK cells that is not afforded to IL-2 and is distinct from activation by soluble IL-15. These results may explain the strict IL-15 dependence of NK cells and illustrate how the cellular compartment in which receptor-ligand interaction occurs can influence functional outcome.

}, issn = {1091-6490}, doi = {10.1073/pnas.1911678117}, author = {Anton, Olga M and Peterson, Mary E and Hollander, Michael J and Dorward, David W and Arora, Gunjan and Traba, Javier and Rajagopalan, Sumati and Snapp, Erik L and Garcia, K Christopher and Waldmann, Thomas A and Long, Eric O} } @article {65910, title = {An unbiased template of the Drosophila brain and ventral nerve cord.}, journal = {PLoS One}, volume = {15}, year = {2020}, month = {2020 Dec 31}, pages = {e0236495}, abstract = {

The fruit fly Drosophila melanogaster is an important model organism for neuroscience with a wide array of genetic tools that enable the mapping of individual neurons and neural subtypes. Brain templates are essential for comparative biological studies because they enable analyzing many individuals in a common reference space. Several central brain templates exist for Drosophila, but every one is either biased, uses sub-optimal tissue preparation, is imaged at low resolution, or does not account for artifacts. No publicly available Drosophila ventral nerve cord template currently exists. In this work, we created high-resolution templates of the Drosophila brain and ventral nerve cord using the best-available technologies for imaging, artifact correction, stitching, and template construction using groupwise registration. We evaluated our central brain template against the four most competitive, publicly available brain templates and demonstrate that ours enables more accurate registration with fewer local deformations in shorter time.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0236495}, author = {Bogovic, John A and Otsuna, Hideo and Heinrich, Larissa and Ito, Masayoshi and Jeter, Jennifer and Meissner, Geoffrey and Nern, Aljoscha and Colonell, Jennifer and Malkesman, Oz and Ito, Kei and Saalfeld, Stephan} } @article {65656, title = {The wiring logic of an identified serotonergic neuron that spans sensory networks.}, journal = {Journal of Neuroscience}, volume = {40}, year = {2020}, month = {2020 Aug 12}, pages = {6309-27}, abstract = {

Serotonergic neurons project widely throughout the brain to modulate diverse physiological and behavioral processes. However, a single cell resolution understanding of the connectivity of serotonergic neurons is currently lacking. Using a whole-brain EM dataset of a female , we comprehensively determine the wiring logic of a broadly projecting serotonergic neuron (the "CSDn") that spans several olfactory regions. Within the antennal lobe, the CSDn differentially innervates each glomerulus, yet surprisingly, this variability reflects a diverse set of presynaptic partners, rather than glomerulus-specific differences in synaptic output, which is predominately to local interneurons. Moreover, the CSDn has distinct connectivity relationships with specific local interneuron subtypes, suggesting that the CSDn influences distinct aspects of local network processing. Across olfactory regions, the CSDn has different patterns of connectivity, even having different connectivity with individual projection neurons that also span these regions. Whereas the CSDn targets inhibitory local neurons in the antennal lobe, the CSDn has more distributed connectivity in the LH, preferentially synapsing with principal neuron types based on transmitter content. Lastly, we identify individual novel synaptic partners associated with other sensory domains that provide strong, top-down input to the CSDn. Taken together, our study reveals the complex connectivity of serotonergic neurons which combine the integration of local and extrinsic synaptic input in a nuanced, region-specific manner.All sensory systems receive serotonergic modulatory input. However, a comprehensive understanding of the synaptic connectivity of individual serotonergic neurons is lacking. In this study, we use a whole-brain EM microscopy dataset to comprehensively determine the wiring logic of a broadly projecting serotonergic neuron in the olfactory system of Collectively, our study demonstrates at a single cell level, the complex connectivity of serotonergic neurons within their target networks, identifies specific cell classes heavily targeted for serotonergic modulation in the olfactory system, and reveals novel extrinsic neurons that provide strong input to this serotonergic system outside of the context of olfaction. Elucidating the connectivity logic of individual modulatory neurons provides a ground plan for the seemingly heterogeneous effects of modulatory systems.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0552-20.2020}, author = {Coates, Kaylynn E and Calle-Schuler, Steven A and Helmick, Levi M and Knotts, Victoria L and Martik, Brennah N and Salman, Farzaan and Warner, Lauren T and Valla, Sophia V and Bock, Davi D and Dacks, Andrew M} } @article {65296, title = {Wiring patterns from auditory sensory neurons to the escape and song-relay pathways in fruit flies.}, journal = {Journal of Comparative Neurology}, volume = {528}, year = {2020}, month = {2020 Aug 01}, pages = {2068}, abstract = {

Many animals rely on acoustic cues to decide what action to take next. Unraveling the wiring patterns of the auditory neural pathways is prerequisite for understanding such information processing. Here we reconstructed the first step of the auditory neural pathway in the fruit fly brain, from primary to secondary auditory neurons, at the resolution of transmission electron microscopy. By tracing axons of two major subgroups of auditory sensory neurons in fruit flies, low-frequency tuned Johnston{\textquoteright}s organ (JO)-B neurons and high-frequency tuned JO-A neurons, we observed extensive connections from JO-B neurons to the main second-order neurons in both the song-relay and escape pathways. In contrast, JO-A neurons connected strongly to a neuron in the escape pathway. Our findings suggest that heterogeneous JO neuronal populations could be recruited to modify escape behavior whereas only specific JO neurons contribute to courtship behavior. We also found that all JO neurons have postsynaptic sites at their axons. Presynaptic modulation at the output sites of JO neurons could affect information processing of the auditory neural pathway in flies. This article is protected by copyright. All rights reserved.

}, issn = {1096-9861}, doi = {10.1002/cne.24877}, author = {Kim, Hyunsoo and Horigome, Mihoko and Ishikawa, Yuki and Li, Feng and Lauritzen, J Scott and Card, Gwyneth and Bock, Davi D and Kamikouchi, Azusa} } @article {64784, title = {An actin-based protrusion originating from a podosome-enriched region initiates macrophage fusion.}, journal = {Molecular Biology of the Cell}, volume = {30}, year = {2019}, month = {2019 Aug 1}, pages = {2254-67}, abstract = {

Macrophage fusion resulting in the formation of multinucleated giant cells occurs in a variety of chronic inflammatory diseases, yet the mechanism responsible for initiating macrophage fusion is unknown. Here, we used live cell imaging to show that actin-based protrusions at the leading edge initiate macrophage fusion. Phase contrast video microscopy demonstrated that in the majority of events, short protrusions (3 {\textpm} 1 μm) between two closely apposed cells initiated fusion, but occasionally we observed long protrusions (16 {\textpm} 7 μm). Using macrophages isolated from LifeAct mice and imaging with lattice light sheet microscopy, we further found that fusion-competent actin-based protrusions formed at sites enriched in podosomes. Inducing fusion in mixed populations of GFP- and mRFP-LifeAct macrophages showed rapid spatial overlap between GFP and RFP signal at the site of fusion. Cytochalasin B strongly reduced fusion and when rare fusion events occurred, protrusions were not observed. Fusion of macrophages deficient in Wiskott-Aldrich syndrome protein and Cdc42, key molecules involved in the formation of actin-based protrusions and podosomes, was also impaired both in vitro and in vivo. Finally, inhibiting the activity of the Arp2/3 complex decreased fusion and podosome formation. Together these data indicate that an actin-based protrusion formed at the leading edge macrophage fusion.

}, doi = {10.1101/538314}, author = {Faust, James J and Balabiyev, Arnat and Heddleston, John M and Podolnikova, Nataly P and Baluch, Debra Page and Chew, Teng-Leong and Ugarova, Tatiana P} } @article {64890, title = {Amino acid signatures of HLA Class-I and II molecules are strongly associated with SLE susceptibility and autoantibody production in Eastern Asians.}, journal = {PLoS Genetics}, volume = {15}, year = {2019}, month = {2019 Apr 25}, pages = {e1008092}, abstract = {

Human leukocyte antigen (HLA) is a key genetic factor conferring risk of systemic lupus erythematosus (SLE), but precise independent localization of HLA effects is extremely challenging. As a result, the contribution of specific HLA alleles and amino-acid residues to the overall risk of SLE and to risk of specific autoantibodies are far from completely understood. Here, we dissected (a) overall SLE association signals across HLA, (b) HLA-peptide interaction, and (c) residue-autoantibody association. Classical alleles, SNPs, and amino-acid residues of eight HLA genes were imputed across 4,915 SLE cases and 13,513 controls from Eastern Asia. We performed association followed by conditional analysis across HLA, assessing both overall SLE risk and risk of autoantibody production. DR15 alleles HLA-DRB1*15:01 (P = 1.4x10-27, odds ratio (OR) = 1.57) and HLA-DQB1*06:02 (P = 7.4x10-23, OR = 1.55) formed the most significant haplotype (OR = 2.33). Conditioned protein-residue signals were stronger than allele signals and mapped predominantly to HLA-DRB1 residue 13 (P = 2.2x10-75) and its proxy position 11 (P = 1.1x10-67), followed by HLA-DRB1-37 (P = 4.5x10-24). After conditioning on HLA-DRB1, novel associations at HLA-A-70 (P = 1.4x10-8), HLA-DPB1-35 (P = 9.0x10-16), HLA-DQB1-37 (P = 2.7x10-14), and HLA-B-9 (P = 6.5x10-15) emerged. Together, these seven residues increased the proportion of explained heritability due to HLA to 2.6\%. Risk residues for both overall disease and hallmark autoantibodies (i.e., nRNP: DRB1-11, P = 2.0x10-14; DRB1-13, P = 2.9x10-13; DRB1-30, P = 3.9x10-14) localized to the peptide-binding groove of HLA-DRB1. Enrichment for specific amino-acid characteristics in the peptide-binding groove correlated with overall SLE risk and with autoantibody presence. Risk residues were in primarily negatively charged side-chains, in contrast with rheumatoid arthritis. We identified novel SLE signals in HLA Class I loci (HLA-A, HLA-B), and localized primary Class II signals to five residues in HLA-DRB1, HLA-DPB1, and HLA-DQB1. These findings provide insights about the mechanisms by which the risk residues interact with each other to produce autoantibodies and are involved in SLE pathophysiology.

}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1008092}, author = {Molineros, Julio E and Looger, Loren L and Kim, Kwangwoo and Okada, Yukinori and Terao, Chikashi and Sun, Celi and Zhou, Xu-Jie and Raj, Prithvi and Kochi, Yuta and Suzuki, Akari and Akizuki, Shuji and Nakabo, Shuichiro and Bang, So-Young and Lee, Hye-Soon and Kang, Young Mo and Suh, Chang-Hee and Chung, Won Tae and Park, Yong-Beom and Choe, Jung-Yoon and Shim, Seung-Cheol and Lee, Shin-Seok and Zuo, Xiaoxia and Yamamoto, Kazuhiko and Li, Quan-Zhen and Shen, Nan and Porter, Lauren L and Harley, John B and Chua, Kek Heng and Zhang, Hong and Wakeland, Edward K and Tsao, Betty P and Bae, Sang-Cheol and Nath, Swapan K} } @article {68818, title = {Associative conditioning remaps odor representations and modifies inhibition in a higher olfactory brain area.}, journal = {Nat Neurosci}, volume = {22}, year = {2019}, month = {11/2019}, pages = {1844-1856}, abstract = {

Intelligent behavior involves associations between high-dimensional sensory representations and behaviorally relevant qualities such as valence. Learning of associations involves plasticity of excitatory connectivity, but it remains poorly understood how information flow is reorganized in networks and how inhibition contributes to this process. We trained adult zebrafish in an appetitive odor discrimination task and analyzed odor representations in a specific compartment of the posterior zone of the dorsal telencephalon (Dp), the homolog of mammalian olfactory cortex. Associative conditioning enhanced responses with a preference for the positively conditioned odor. Moreover, conditioning systematically remapped odor representations along an axis in coding space that represented attractiveness (valence). Interindividual variations in this mapping predicted variations in behavioral odor preference. Photoinhibition of interneurons resulted in specific modifications of odor representations that mirrored effects of conditioning and reduced experience-dependent, interindividual variations in odor-valence mapping. These results reveal an individualized odor-to-valence map that is shaped by inhibition and reorganized during learning.

}, keywords = {Animals, Animals, Genetically Modified, Association Learning, Brain Mapping, Discrimination Learning, Female, Individuality, Male, Neural Inhibition, Odorants, Olfactory Cortex, Olfactory Perception, Zebrafish}, issn = {1546-1726}, doi = {10.1038/s41593-019-0495-z}, author = {Frank, Thomas and M{\"o}nig, Nila R and Satou, Chie and Higashijima, Shin-Ichi and Friedrich, Rainer W} } @article {65079, title = {BigStitcher: reconstructing high-resolution image datasets of cleared and expanded samples.}, journal = {Nature Methods}, volume = {16}, year = {2019}, month = {2019 Sep}, pages = {870-74}, abstract = {

Light-sheet imaging of cleared and expanded samples creates terabyte-sized datasets that consist of many unaligned three-dimensional image tiles, which must be reconstructed before analysis. We developed the BigStitcher software to address this challenge. BigStitcher enables interactive visualization, fast and precise alignment, spatially resolved quality estimation, real-time fusion and deconvolution of dual-illumination, multitile, multiview datasets. The software also compensates for optical effects, thereby improving accuracy and enabling subsequent biological analysis.

}, issn = {1548-7091}, doi = {10.1038/s41592-019-0501-0}, url = {http://www.nature.com/articles/s41592-019-0501-0http://www.nature.com/articles/s41592-019-0501-0.pdfhttp://www.nature.com/articles/s41592-019-0501-0.pdfhttp://www.nature.com/articles/s41592-019-0501-0}, author = {H{\"o}rl, David and Rojas Rusak, Fabio and Preusser, Friedrich and Tillberg, Paul and Randel, Nadine and Chhetri, Raghav K. and Cardona, Albert and Keller, Philipp J. and Harz, Hartmann and Leonhardt, Heinrich and Treier, Mathias and Preibisch, Stephan} } @article {65081, title = {Bright and photostable chemigenetic indicators for extended in vivo voltage imaging.}, journal = {Science}, volume = {365}, year = {2019}, month = {2019 Aug 13}, pages = {699-704}, abstract = {

Imaging changes in membrane potential using genetically encoded fluorescent voltage indicators (GEVIs) has great potential for monitoring neuronal activity with high spatial and temporal resolution. Brightness and photostability of fluorescent proteins and rhodopsins have limited the utility of existing GEVIs. We engineered a novel GEVI, "Voltron", that utilizes bright and photostable synthetic dyes instead of protein-based fluorophores, extending the combined duration of imaging and number of neurons imaged simultaneously by more than tenfold relative to existing GEVIs. We used Voltron for in vivo voltage imaging in mice, zebrafish, and fruit flies. In mouse cortex, Voltron allowed single-trial recording of spikes and subthreshold voltage signals from dozens of neurons simultaneously, over 15 min of continuous imaging. In larval zebrafish, Voltron enabled the precise correlation of spike timing with behavior.

}, issn = {1095-9203}, doi = {10.1126/science.aav6416}, author = {Abdelfattah, Ahmed S and Kawashima, Takashi and Singh, Amrita and Novak, Ondrej and Liu, Hui and Shuai, Yichun and Huang, Yi-Chieh and Campagnola, Luke and Seeman, Stephanie C and Yu, Jianing and Zheng, Jihong and Grimm, Jonathan B and Patel, Ronak and Friedrich, Johannes and Mensh, Brett D and Paninski, Liam and Macklin, John J and Murphy, Gabe J and Podgorski, Kaspar and Lin, Bei-Jung and Chen, Tsai-Wen and Turner, Glenn C and Liu, Zhe and Koyama, Minoru and Svoboda, Karel and Ahrens, Misha B and Lavis, Luke D and Schreiter, Eric R} } @article {64937, title = {Busted! A dope ring with activity clocked at dawn and dusk.}, journal = {Neuron}, volume = {102}, year = {2019}, month = {2019 May 22}, pages = {713-5}, abstract = {Clock neurons generate circadian rhythms in behavioral activity, but the relevant pathways remain poorly understood. In this issue of Neuron, Liang et al. (2019) show that distinct clock neurons independently drive movement-promoting {\textquotedblleft}ring neurons{\textquotedblright} in Drosophila through dopaminergic relays to support morning and evening locomotor activity.}, doi = {10.1016/j.neuron.2019.05.004}, author = {Hulse, Brad and Jayaraman, Vivek} } @article {65137, title = {Can one concurrently record electrical spikes from every neuron in a mammalian brain?}, journal = {Neuron}, volume = {103}, year = {2019}, month = {2019 Sep 25}, pages = {1005}, abstract = {

The classic approach to measure the spiking response of neurons involves the use of metal electrodes to record extracellular potentials. Starting over 60 years ago with a single recording site, this technology now extends to ever larger numbers and densities of sites. We argue, based on the mechanical and electrical properties of existing materials, estimates of signal-to-noise ratios, assumptions regarding extracellular space in the brain, and estimates of heat generation by the electronic interface, that it should be possible to fabricate rigid electrodes to concurrently record from essentially every neuron in the cortical mantle. This will involve fabrication with existing yet nontraditional materials and procedures. We further emphasize the need to advance materials for improved flexible electrodes as an essential advance to record from neurons in brainstem and spinal cord in moving animals.

}, issn = {08966273}, doi = {10.1016/j.neuron.2019.08.011}, author = {Kleinfeld, David and Luan, Lan and Mitra, Partha P. and Robinson, Jacob T. and Sarpeshkar, Rahul and Shepard, Kenneth and Xie, Chong and Harris, Timothy D.} } @article {65042, title = {Changes throughout a genetic network mask the contribution of Hox gene evolution.}, journal = {Current Biology}, volume = {29}, year = {2019}, month = {2019 Jul 08}, pages = {2157-66}, abstract = {

Hox genes pattern the anterior-posterior axis of animals and are posited to drive animal body plan evolution, yet their precise role in evolution has been difficult to determine. Here, we identified evolutionary modifications in the Hox gene\ Abd-Bthat dramatically altered its expression along the body plan of\ Drosophila santomea.\ Abd-B\ is required for pigmentation in\ Drosophila yakuba, the sister species of\ D.\ santomea, and changes to Abd-B expression would be predicted to make large contributions to the loss of body pigmentation in\ D.\ santomea. However, manipulating\ Abd-B\ expression in current-day\ D.\ santomea\ does not affect pigmentation. We attribute this epistatic interaction to four other genes within the\ D.\ santomea\ pigmentation network, three of which have evolved expression patterns that do not respond to Abd-B. Our results demonstrate how body plans may evolve through small evolutionary steps distributed throughout Hox-regulated networks. Polygenicity and epistasis may hinder efforts to identify genes and mechanisms underlying macroevolutionary traits.

}, issn = {09609822}, doi = {10.1016/j.cub.2019.05.074}, author = {Liu, Yang and Ramos-Womack, Margarita and Han, Clair and Reilly, Patrick and Brackett, Kelly LaRue and Rogers, William and Williams, Thomas M. and Andolfatto, Peter and Stern, David L. and Rebeiz, Mark} } @article {49582, title = {Characterization of neurite dystrophy after trauma by high speed structured illumination microscopy and lattice light sheet microscopy.}, journal = {Journal of Neuroscience Methods}, volume = {312}, year = {2019}, month = {2019 Jan 15}, pages = {154-61}, abstract = {

BACKGROUND: Unbiased screening studies have repeatedly identified actin-related proteins as one of the families of proteins most influenced by neurotrauma. Nevertheless, the status quo model of cytoskeletal reorganization after neurotrauma excludes actin and incorporates only changes in microtubules and intermediate filaments. Actin is excluded in part because it is difficult to image with conventional techniques. However, recent innovations in fluorescent microscopy provide an opportunity to image the actin cytoskeleton at super-resolution resolution in living cells. This study applied these innovations to an in vitro model of neurotrauma.

NEW METHOD: New methods are introduced for traumatizing neurons before imaging them with high speed structured illumination microscopy or lattice light sheet microscopy. Also, methods for analyzing structured illumination microscopy images to quantify post-traumatic neurite dystrophy are presented.

RESULTS: Human induced pluripotent stem cell-derived neurons exhibited actin organization typical of immature neurons. Neurite dystrophy increased after trauma but was not influenced by jasplakinolide treatment. The F-actin content of dystrophies varied greatly from one dystrophy to another.

COMPARISON WITH EXISTING METHODS: In contrast to fixation dependent methods, these methods capture the evolution of the actin cytoskeleton over time in a living cell. In contrast to prior methods based on counting dystrophies, this quantification scheme parameterizes the severity of a given dystrophy as it evolves from a local swelling to an almost-perfect spheroid that threatens to transect the neurite.

CONCLUSIONS: These methods can be used to investigate genetic factors and therapeutic interventions that modulate the course of neurite dystrophy after trauma.

}, issn = {1872-678X}, doi = {10.1016/j.jneumeth.2018.12.005}, author = {Phillips, Jack K and Sherman, Sydney A and Cotton, Kristen Y and Heddleston, John M and Taylor, Aaron B and Finan, John D} } @article {65058, title = {CHP1 regulates compartmentalized glycerolipid synthesis by activating GPAT4.}, journal = {Molecular Cell}, volume = {74}, year = {2019}, month = {2019 Apr 4}, pages = {45-58.e7}, abstract = {

Cells require a constant supply of fatty acids to survive and proliferate. Fatty acids incorporate into membrane and storage glycerolipids through a series of endoplasmic reticulum (ER) enzymes, but how these enzymes are regulated is not well understood. Here, using a combination of CRISPR-based genetic screens and unbiased lipidomics, we identified calcineurin B homologous protein 1 (CHP1) as a major regulator of ER glycerolipid synthesis. Loss of\ CHP1 severely reduces fatty acid incorporation and storage in mammalian cells and invertebrates. Mechanistically, CHP1 binds and activates GPAT4, which catalyzes the initial rate-limiting step in glycerolipid synthesis. GPAT4 activity requires CHP1 to be N-myristoylated, forming a key molecular interface between the two proteins. Interestingly, upon CHP1 loss, the peroxisomal enzyme, GNPAT, partially compensates for the loss of ER lipid synthesis, enabling cell proliferation. Thus, our work identifies a conserved regulator of glycerolipid metabolism and reveals plasticity in lipid synthesis of proliferating cells.

}, keywords = {3T3 Cells, Acyltransferases, Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Calcium-Binding Proteins, Cell Proliferation, Drosophila melanogaster, Drosophila Proteins, Endoplasmic Reticulum, Enzyme Activation, Gene Expression Regulation, Enzymologic, Glycerides, Glycerol-3-Phosphate O-Acyltransferase, HEK293 Cells, Hela Cells, Hep G2 Cells, Humans, Jurkat Cells, Lipogenesis, Mice, Palmitic Acid, Protein Binding}, issn = {1097-4164}, doi = {10.1016/j.molcel.2019.01.037}, author = {Zhu, Xiphias Ge and Nicholson Puthenveedu, Shirony and Shen, Yihui and La, Konnor and Ozlu, Can and Wang, Tim and Klompstra, Diana and Gultekin, Yetis and Chi, Jingyi and Fidelin, Justine and Peng, Tao and Molina, Henrik and Hang, Howard C and Min, Wei and Birsoy, K{\i}van{\c c}} } @article {51252, title = {Comparisons between the ON- and OFF-edge motion pathways in the brain.}, journal = {eLife}, volume = {8}, year = {2019}, month = {2019 Jan 09}, abstract = {

Understanding the circuit mechanisms behind motion detection is a long-standing question in visual neuroscience. In , recent synapse-level connectomes in the optic lobe, particularly in ON-pathway (T4) receptive-field circuits, in concert with physiological studies, suggest an increasingly intricate motion model compared with the ubiquitous Hassenstein-Reichardt model, while our knowledge of OFF-pathway (T5) has been incomplete. Here we present a conclusive and comprehensive connectome that for the first time integrates detailed connectivity information for inputs to both T4 and T5 pathways in a single EM dataset covering the entire optic lobe. With novel reconstruction methods using automated synapse prediction suited to such a large connectome, we successfully corroborate previous findings in the T4 pathway and comprehensively identify inputs and receptive fields for T5. While the two pathways are likely evolutionarily linked and indeed exhibit many similarities, we uncover interesting differences and interactions that may underlie their distinct functional properties.

}, issn = {2050-084X}, doi = {10.7554/eLife.40025}, author = {Shinomiya, Kazunori and Huang, Gary and Lu, Zhiyuan and Parag, Toufiq and Xu, C Shan and Aniceto, Roxanne and Ansari, Namra and Cheatham, Natasha and Lauchie, Shirley and Neace, Erika and Ogundeyi, Omotara and Ordish, Christopher and Peel, David and Shinomiya, Aya and Smith, Claire and Takemura, Satoko and Talebi, Iris and Rivlin, Patricia K and Nern, Aljoscha and Scheffer, Louis K and Plaza, Stephen M and Meinertzhagen, Ian A} } @article {51795, title = {Cortical column and whole-brain imaging with molecular contrast and nanoscale resolution.}, journal = {Science (New York, N.Y.)}, volume = {363}, year = {2019}, month = {2019 Jan 18}, pages = {eaau8302}, abstract = {

Optical and electron microscopy have made tremendous inroads toward understanding the complexity of the brain. However, optical microscopy offers insufficient resolution to reveal subcellular details, and electron microscopy lacks the throughput and molecular contrast to visualize specific molecular constituents over millimeter-scale or larger dimensions. We combined expansion microscopy and lattice light-sheet microscopy to image the nanoscale spatial relationships between proteins across the thickness of the mouse cortex or the entire\ Drosophila\ brain. These included synaptic proteins at dendritic spines, myelination along axons, and presynaptic densities at dopaminergic neurons in every fly brain region. The technology should enable statistically rich, large-scale studies of neural development, sexual dimorphism, degree of stereotypy, and structural correlations to behavior or neural activity, all with molecular contrast.

}, doi = {10.1126/science.aau8302}, author = {Gao, Ruixuan and Asano, Shoh M and Upadhyayula, Srigokul and Pisarev, Igor and Milkie, Daniel E and Liu, Tsung-Li and Singh, Ved and Graves, Austin R and Huynh, Grace H and Zhao, Yongxin and Bogovic, John A and Colonell, Jennifer and Ott, Carolyn M and Zugates, Christopher T and Tappan, Susan and Rodriguez, Alfredo and Mosaliganti, Kishore R and Sheu, Shu-Hsien and Pasolli, H Amalia and et al} } @article {64833, title = {Cryo-EM fibril structures from systemic AA amyloidosis reveal the species complementarity of pathological amyloids.}, journal = {Nature Communications}, volume = {10}, year = {2019}, month = {2019 Mar 07}, pages = {1104}, abstract = {

Systemic AA amyloidosis is a worldwide occurring protein misfolding disease of humans and animals. It arises from the formation of amyloid fibrils from the acute phase protein serum amyloid A. Here, we report the purification and electron cryo-microscopy analysis of amyloid fibrils from a mouse and a human patient with systemic AA amyloidosis. The obtained resolutions are 3.0 {\r A} and 2.7 {\r A} for the murine and human fibril, respectively. The two fibrils differ in fundamental properties, such as presence of right-hand or left-hand twisted cross-β sheets and overall fold of the fibril proteins. Yet, both proteins adopt highly similar β-arch conformations within the N-terminal ~21 residues. Our data demonstrate the importance of the fibril protein N-terminus for the stability of the analyzed amyloid fibril morphologies and suggest strategies of combating this disease by interfering with specific fibril polymorphs.

}, issn = {2041-1723}, doi = {10.1038/s41467-019-09033-z}, author = {Liberta, Falk and Loerch, Sarah and Rennegarbe, Matthies and Schierhorn, Angelika and Westermark, Per and Westermark, Gunilla T and Hazenberg, Bouke P C and Grigorieff, Nikolaus and F{\"a}ndrich, Marcus and Schmidt, Matthias} } @article {51793, title = {Cryo-EM of retinoschisin branched networks suggests an intercellular adhesive scaffold in the retina.}, journal = {The Journal of Cell Biology}, volume = {218}, year = {2019}, month = {2019 Jan 10}, pages = {1027-38}, abstract = {

Mutations in the retinal protein retinoschisin (RS1) cause progressive loss of vision in young males, a form of macular degeneration called X-linked retinoschisis (XLRS). We previously solved the structure of RS1, a 16-mer composed of paired back-to-back octameric rings. Here, we show by cryo-electron microscopy that RS1 16-mers can assemble into extensive branched networks. We classified the different configurations, finding four types of interaction between the RS1 molecules. The predominant configuration is a linear strand with a wavy appearance. Three less frequent types constitute the branch points of the network. In all cases, the "spikes" around the periphery of the double rings are involved in these interactions. In the linear strand, a loop (usually referred to as spike 1) occurs on both sides of the interface between neighboring molecules. Mutations in this loop suppress secretion, indicating the possibility of intracellular higher-order assembly. These observations suggest that branched networks of RS1 may play a stabilizing role in maintaining the integrity of the retina.

}, issn = {1540-8140}, doi = {10.1083/jcb.201806148}, author = {Heymann, J Bernard and Vijayasarathy, Camasamudram and Huang, Rick K and Dearborn, Altaira D and Sieving, Paul A and Steven, Alasdair C} } @article {64782, title = {Cryo-EM structure of the homohexameric T3SS ATPase-central stalk complex reveals rotary ATPase-like asymmetry.}, journal = {Nature Communications}, volume = {10}, year = {2019}, month = {2019 Feb 07}, pages = {626}, abstract = {

Many Gram-negative bacteria, including causative agents of dysentery, plague, and typhoid fever, rely on a type III secretion system - a multi-membrane spanning syringe-like apparatus - for their pathogenicity. The cytosolic ATPase complex of this injectisome is proposed to play an important role in energizing secretion events and substrate recognition. We present the 3.3 {\r A} resolution cryo-EM structure of the enteropathogenic Escherichia coli ATPase EscN in complex with its central stalk EscO. The structure shows an asymmetric pore with different functional states captured in its six catalytic sites, details directly supporting a rotary catalytic mechanism analogous to that of the heterohexameric F/V-ATPases despite its homohexameric nature. Situated at the C-terminal opening of the EscN pore is one molecule of EscO, with primary interaction mediated through an electrostatic interface. The EscN-EscO structure provides significant atomic insights into how the ATPase contributes to type III secretion, including torque generation and binding of chaperone/substrate complexes.

}, issn = {2041-1723}, doi = {10.1038/s41467-019-08477-7}, author = {Majewski, Dorothy D and Worrall, Liam J and Hong, Chuan and Atkinson, Claire E and Vuckovic, Marija and Watanabe, Nobuhiko and Yu, Zhiheng and Strynadka, Natalie C J} } @article {65211, title = {Cryo-EM structure of the human FLCN-FNIP2-Rag-Ragulator complex.}, journal = {Cell}, volume = {179}, year = {2019}, month = {2019 Nov 27}, pages = {1319-29}, issn = {00928674}, doi = {10.1016/j.cell.2019.10.036}, author = {Shen, Kuang and Rogala, Kacper B. and Chou, Hui-Ting and Huang, Rick K. and Yu, Zhiheng and Sabatini, David M.} } @article {64918, title = {De novo design of tunable, pH-driven conformational changes.}, journal = {Science}, volume = {364}, year = {2019}, month = {2019 May 17}, pages = {658-64}, abstract = {

The ability of naturally occurring proteins to change conformation in response to environmental changes is critical to biological function. Although there have been advances in the de novo design of stable proteins with a single, deep free-energy minimum, the design of conformational switches remains challenging. We present a general strategy to design pH-responsive protein conformational changes by precisely preorganizing histidine residues in buried hydrogen-bond networks. We design homotrimers and heterodimers that are stable above pH 6.5 but undergo cooperative, large-scale conformational changes when the pH is lowered and electrostatic and steric repulsion builds up as the network histidine residues become protonated. The transition pH and cooperativity can be controlled through the number of histidine-containing networks and the strength of the surrounding hydrophobic interactions. Upon disassembly, the designed proteins disrupt lipid membranes both in vitro and after being endocytosed in mammalian cells. Our results demonstrate that environmentally triggered conformational changes can now be programmed by de novo protein design.

}, doi = {10.1126/science.aav7897}, author = {Boyken, Scott E and Benhaim, Mark A and Busch, Florian and Jia, Mengxuan and Back, Matthew J and Choi, Heejun and Klima, Jason C and Chen, Zibo and Walkey, Carl and Mileant, Alexander and Sahasrabuddhe, Aniruddha and Wei, Kathy Y and Hodge, Edgar A and Byron, Sarah and Quijano-Rubio, Alfredo and Sankaran, Banumathi and King, Neil P and Lippincott-Schwartz, Jennifer and Wysocki, Vicki H and et al} } @article {68993, title = {Deterministic Somatic Cell Reprogramming Involves Continuous Transcriptional Changes Governed by Myc and Epigenetic-Driven Modules.}, journal = {Cell Stem Cell}, volume = {24}, year = {2019}, month = {02/2019}, pages = {328-341.e9}, abstract = {

The epigenetic dynamics of induced pluripotent stem cell (iPSC) reprogramming in correctly reprogrammed cells at high resolution and throughout the entire process remain largely undefined. Here, we characterize conversion of mouse fibroblasts into iPSCs using Gatad2a-Mbd3/NuRD-depleted and highly efficient reprogramming systems. Unbiased high-resolution profiling of dynamic changes in levels of gene expression, chromatin engagement, DNA accessibility, and DNA methylation were obtained. We identified two distinct and synergistic transcriptional modules that dominate successful reprogramming, which are associated with cell identity and biosynthetic genes. The pluripotency module is governed by dynamic alterations in epigenetic modifications to promoters and binding by Oct4, Sox2, and Klf4, but not Myc. Early DNA demethylation at certain enhancers prospectively marks cells fated to reprogram. Myc activity drives expression of the essential biosynthetic module and is associated with optimized changes in tRNA codon usage. Our functional validations highlight interweaved epigenetic- and Myc-governed essential reconfigurations that rapidly commission and propel deterministic reprogramming toward naive pluripotency.

}, keywords = {Animals, Cell Lineage, Cellular Reprogramming, Chromatin, Demethylation, Epigenesis, Genetic, Humans, Induced Pluripotent Stem Cells, Kruppel-Like Factor 4, Mice, Protein Binding, Proto-Oncogene Proteins c-myc, RNA, Transfer, Transcription Factors, Transcription, Genetic}, issn = {1875-9777}, doi = {10.1016/j.stem.2018.11.014}, author = {Zviran, Asaf and Mor, Nofar and Rais, Yoach and Gingold, Hila and Peles, Shani and Chomsky, Elad and Viukov, Sergey and Buenrostro, Jason D and Scognamiglio, Roberta and Weinberger, Leehee and Manor, Yair S and Krupalnik, Vladislav and Zerbib, Mirie and Hezroni, Hadas and Jaitin, Diego Adhemar and Larastiaso, David and Gilad, Shlomit and Benjamin, Sima and Gafni, Ohad and Mousa, Awni and Ayyash, Muneef and Sheban, Daoud and Bayerl, Jonathan and Aguilera-Castrejon, Alejandro and Massarwa, Rada and Maza, Itay and Hanna, Suhair and Stelzer, Yonatan and Ulitsky, Igor and Greenleaf, William J and Tanay, Amos and Trumpp, Andreas and Amit, Ido and Pilpel, Yitzhak and Novershtern, Noa and Hanna, Jacob H} } @article {56202, title = {Developmentally arrested precursors of pontine neurons establish an embryonic blueprint of the Drosophila central complex.}, journal = {Current Biology : CB}, volume = {29}, year = {2019}, month = {2019 Jan 15}, pages = {412-25}, abstract = {

Serial electron microscopic analysis shows that the Drosophila brain at hatching possesses a large fraction of developmentally arrested neurons with a small soma, heterochromatin-rich nucleus, and unbranched axon lacking synapses. We digitally reconstructed all 802 "small undifferentiated" (SU) neurons and assigned them to the known brain lineages. By establishing the coordinates and reconstructing trajectories of the SU neuron tracts, we provide a framework of landmarks for the ongoing analyses of the L1 brain circuitry. To address the later fate of SU neurons, we focused on the 54 SU neurons belonging to the DM1-DM4 lineages, which generate all columnar neurons of the central complex. Regarding their topologically ordered projection pattern, these neurons form an embryonic nucleus of the fan-shaped body ("FB pioneers"). Fan-shaped body pioneers survive into the adult stage, where they develop into a specific class of bi-columnar elements, the pontine neurons. Later born, unicolumnar DM1-DM4 neurons fasciculate with the fan-shaped body pioneers. Selective ablation of the fan-shaped body pioneers altered the architecture of the larval fan-shaped body primordium but did not result in gross abnormalities of the trajectories of unicolumnar neurons, indicating that axonal pathfinding of the two systems may be controlled independently. Our comprehensive spatial and developmental analysis of the SU neurons adds to our understanding of the establishment of neuronal circuitry.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2018.12.012}, author = {Andrade, Ingrid V and Riebli, Nadia and Nguyen, Bao-Chau M and Omoto, Jaison J and Cardona, Albert and Hartenstein, Volker} } @article {65203, title = {Drosulfakinin signaling in fruitless circuitry antagonizes P1 neurons to regulate sexual arousal in Drosophila.}, journal = {Nature Communications}, volume = {10}, year = {2019}, month = {2019 Oct 18}, pages = {4770}, abstract = {

Animals perform or terminate particular behaviors by integrating external cues and internal states through neural circuits. Identifying neural substrates and their molecular modulators promoting or inhibiting animal behaviors are key steps to understand how neural circuits control behaviors. Here, we identify the Cholecystokinin-like peptide Drosulfakinin (DSK) that functions at single-neuron resolution to suppress male sexual behavior in Drosophila. We found that Dsk neurons physiologically interact with male-specific P1 neurons, part of a command center for male sexual behaviors, and function oppositely to regulate multiple arousal-related behaviors including sex, sleep and spontaneous walking. We further found that the DSK-2 peptide functions through its receptor CCKLR-17D3 to suppress sexual behaviors in flies. Such a neuropeptide circuit largely overlaps with the fruitless-expressing neural circuit that governs most aspects of male sexual behaviors. Thus DSK/CCKLR signaling in the sex circuitry functions antagonistically with P1 neurons to balance arousal levels and modulate sexual behaviors.

}, issn = {2041-1723}, doi = {10.1038/s41467-019-12758-6}, author = {Wu, Shunfan and Guo, Chao and Zhao, Huan and Sun, Mengshi and Chen, Jie and Han, Caihong and Peng, Qionglin and Qiao, Huanhuan and Peng, Ping and Liu, Yan and Luo, Shengzhan D and Pan, Yufeng} } @article {64875, title = {Enabling cell-type-specific behavioral epigenetics in Drosophila: a modified high-yield INTACT method reveals the impact of social environment on the epigenetic landscape in dopaminergic neurons.}, journal = {BMC Biology}, volume = {17}, year = {2019}, month = {2019 Apr 10}, pages = {30}, abstract = {

BACKGROUND: Epigenetic mechanisms play fundamental roles in brain function and behavior and stressors such as social isolation can alter animal behavior via epigenetic mechanisms. However, due to cellular heterogeneity, identifying cell-type-specific epigenetic changes in the brain is challenging. Here, we report the first use of a modified isolation of nuclei tagged in specific cell type (INTACT) method in behavioral epigenetics of Drosophila melanogaster, a method we call mini-INTACT.

RESULTS: Using ChIP-seq on mini-INTACT purified dopaminergic nuclei, we identified epigenetic signatures in socially isolated and socially enriched Drosophila males. Social experience altered the epigenetic landscape in clusters of genes involved in transcription and neural function. Some of these alterations could be predicted by expression changes of four transcription factors and the prevalence of their binding sites in several clusters. These transcription factors were previously identified as activity-regulated genes, and their knockdown in dopaminergic neurons reduced the effects of social experience on sleep.

CONCLUSIONS: Our work enables the use of Drosophila as a model for cell-type-specific behavioral epigenetics and establishes that social environment shifts the epigenetic landscape in dopaminergic neurons. Four activity-related transcription factors are required in dopaminergic neurons for the effects of social environment on sleep.

}, issn = {1741-7007}, doi = {10.1186/s12915-019-0646-4}, author = {Agrawal, Pavan and Chung, Phuong and Heberlein, Ulrike and Kent, Clement} } @article {65114, title = {Evolution of embryonic cis-regulatory landscapes between divergent Phallusia and Ciona ascidians.}, journal = {Developmental Biology}, volume = {448}, year = {2019}, month = {2019 Apr 15}, pages = {71-87}, abstract = {

Ascidian species of the Phallusia and Ciona genera are distantly related, their last common ancestor dating several hundred million years ago. Although their genome sequences have extensively diverged since this radiation, Phallusia and Ciona species share almost identical early morphogenesis and stereotyped cell lineages. Here, we explored the evolution of transcriptional control between P. mammillata and C. robusta. We combined genome-wide mapping of open chromatin regions in both species with a comparative analysis of the regulatory sequences of a test set of 10 pairs of orthologous early regulatory genes with conserved expression patterns. We find that ascidian chromatin accessibility landscapes obey similar rules as in other metazoa. Open-chromatin regions are short, highly conserved within each genus and cluster around regulatory genes. The dynamics of chromatin accessibility and closest-gene expression are strongly correlated during early embryogenesis. Open-chromatin regions are highly enriched in cis-regulatory elements: 73\% of 49 open chromatin regions around our test genes behaved as either distal enhancers or proximal enhancer/promoters following electroporation in Phallusia eggs. Analysis of this datasets suggests a pervasive use in ascidians of "shadow" enhancers with partially overlapping activities. Cross-species electroporations point to a deep conservation of both the trans-regulatory logic between these distantly-related ascidians and the cis-regulatory activities of individual enhancers. Finally, we found that the relative order and approximate distance to the transcription start site of open chromatin regions can be conserved between Ciona and Phallusia species despite extensive sequence divergence, a property that can be used to identify orthologous enhancers, whose regulatory activity can partially diverge.

}, issn = {1095-564X}, doi = {10.1016/j.ydbio.2019.01.003}, author = {Madgwick, Alicia and Magri, Marta Silvia and Dantec, Christelle and Gailly, Damien and Fiuza, Ulla-Maj and Guignard, Leo and Hettinger, Sabrina and Gomez-Skarmeta, Jose Luis and Lemaire, Patrick} } @article {68431, title = {Functional divergence of Plexin B structural motifs in distinct steps of olfactory circuit assembly.}, journal = {Elife}, volume = {8}, year = {2019}, month = {06/2019}, abstract = {

Plexins exhibit multitudinous, evolutionarily conserved functions in neural development. How Plexins employ their diverse structural motifs in vivo to perform distinct roles is unclear. We previously reported that Plexin B (PlexB) controls multiple steps during the assembly of the olfactory circuit (Li et al., 2018b). Here, we systematically mutagenized structural motifs of PlexB and examined the function of these variants in these multiple steps: axon fasciculation, trajectory choice, and synaptic partner selection. We found that the extracellular Sema domain is essential for all three steps, the catalytic site of the intracellular RapGAP is engaged in none, and the intracellular GTPase-binding motifs are essential for trajectory choice and synaptic partner selection, but are dispensable for fasciculation. Moreover, extracellular PlexB cleavage serves as a regulatory mechanism of PlexB signaling. Thus, the divergent roles of PlexB motifs in distinct steps of neural development contribute to its functional versatility in neural circuit assembly.

}, keywords = {Animals, Animals, Genetically Modified, Axons, Drosophila melanogaster, Drosophila Proteins, Nerve Tissue Proteins, Neurogenesis, Olfactory Bulb, Receptors, Cell Surface, Semaphorins, Signal Transduction, Smell}, issn = {2050-084X}, doi = {10.7554/eLife.48594}, author = {Guajardo, Ricardo and Luginbuhl, David J and Han, Shuo and Luo, Liqun and Li, Jiefu} } @article {65224, title = {Gas cluster ion beam SEM for imaging of large tissue samples with 10 nm isotropic resolution.}, journal = {Nature Methods}, volume = {17}, year = {2019}, month = {2020 Jan 01}, pages = {68-71}, abstract = {

We demonstrate gas cluster ion beam scanning electron microscopy (SEM), in which wide-area ion milling is performed on a series of thick tissue sections. This three-dimensional electron microscopy technique acquires datasets with \<10 nm isotropic resolution of each section, and these can then be stitched together to span the sectioned volume. Incorporating gas cluster ion beam SEM into existing single-beam and multibeam SEM workflows should be straightforward, increasing reliability while improving z resolution by a factor of three or more.

}, issn = {1548-7105}, doi = {10.1038/s41592-019-0641-2}, author = {Hayworth, Kenneth J and Peale, David and Januszewski, Micha{\l} and Knott, Graham W and Lu, Zhiyuan and Xu, C Shan and Hess, Harald F} } @article {64823, title = {GCIB-SEM: A path to 10 nm isotropic imaging of cubic millimeter volumes.}, journal = {bioRxiv}, year = {2019}, month = {2019 Feb 28}, abstract = {Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) generates 3D datasets optimally suited for segmentation of cell ultrastructure and automated connectome tracing but is limited to small fields of view and is therefore incompatible with the new generation of ultrafast multibeam SEMs. In contrast, section-based techniques are multibeam-compatible but are limited in z-resolution making automatic segmentation of cellular ultrastructure difficult. Here we demonstrate a novel 3D electron microscopy technique, Gas Cluster Ion Beam SEM (GCIB-SEM), in which top-down, wide-area ion milling is performed on a series of thick sections, acquiring < 10 nm isotropic datasets of each which are then stitched together to span the full sectioned volume. Based on our results, incorporating GCIB-SEM into existing single beam and multibeam SEM workflows should be straightforward and should dramatically increase reliability while simultaneously improving z-resolution by a factor of 3 or more.}, doi = {10.1101/563239}, author = {Hayworth, Kenneth J and Peale, David R and Januszewski, Michal and Knott, Graham and Lu, Zhiyuan and Xu, C. Shan and Hess, Harald F} } @article {65234, title = {Generation of stable heading representations in diverse visual scenes.}, journal = {Nature}, volume = {576}, year = {2019}, month = {2019 Nov 20}, pages = {126-31}, abstract = {

Many animals rely on an internal heading representation when navigating in varied environments. How this representation is linked to the sensory cues that define different surroundings is unclear. In the fly brain, heading is represented by {\textquoteright}compass{\textquoteright} neurons that innervate a ring-shaped structure known as the ellipsoid body. Each compass neuron receives inputs from {\textquoteright}ring{\textquoteright} neurons that are selective for particular visual features; this combination provides an ideal substrate for the extraction of directional information from a visual scene. Here we combine two-photon calcium imaging and optogenetics in tethered flying flies with circuit modelling, and show how the correlated activity of compass and visual neurons drives plasticity, which flexibly transforms two-dimensional visual cues into a stable heading representation. We also describe how this plasticity enables the fly to convert a partial heading representation, established from orienting within part of a novel setting, into a complete heading representation. Our results provide mechanistic insight into the memory-related computations that are essential for flexible navigation in varied surroundings.

}, issn = {1476-4687}, doi = {10.1038/s41586-019-1767-1}, author = {Kim, Sung Soo and Hermundstad, Ann M and Romani, Sandro and Abbott, L F and Jayaraman, Vivek} } @article {65157, title = {Genetic dissection of active forgetting in labile and consolidated memories in Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, year = {2019}, month = {2019 Oct 01}, pages = {21191-97}, abstract = {

Different memory components are forgotten through distinct molecular mechanisms. In , the activation of 2 Rho GTPases (Rac1 and Cdc42), respectively, underlies the forgetting of an early labile memory (anesthesia-sensitive memory, ASM) and a form of consolidated memory (anesthesia-resistant memory, ARM). Here, we dissected the molecular mechanisms that tie Rac1 and Cdc42 to the different types of memory forgetting. We found that 2 WASP family proteins, SCAR/WAVE and WASp, act downstream of Rac1 and Cdc42 separately to regulate ASM and ARM forgetting in mushroom body neurons. Arp2/3 complex, which organizes branched actin polymerization, is a canonical downstream effector of WASP family proteins. However, we found that Arp2/3 complex is required in Cdc42/WASp-mediated ARM forgetting but not in Rac1/SCAR-mediated ASM forgetting. Instead, we identified that Rac1/SCAR may function with formin Diaphanous (Dia), a nucleator that facilitates linear actin polymerization, in ASM forgetting. The present study, complementing the previously identified Rac1/cofilin pathway that regulates actin depolymerization, suggests that Rho GTPases regulate forgetting by recruiting both actin polymerization and depolymerization pathways. Moreover, Rac1 and Cdc42 may regulate different types of memory forgetting by tapping into different actin polymerization mechanisms.

}, issn = {1091-6490}, doi = {10.1073/pnas.1903763116}, author = {Gao, Yang and Shuai, Yichun and Zhang, Xuchen and Peng, Yuwei and Wang, Lianzhang and He, Jing and Zhong, Yi and Li, Qian} } @article {68360, title = {Genetic Identification of Vagal Sensory Neurons That Control Feeding}, journal = {Cell}, volume = {179}, year = {2019}, month = {11/2019}, pages = {1129-1143.e23}, abstract = {

Summary Energy homeostasis requires precise measurement of the quantity and quality of ingested food. The vagus nerve innervates the gut and can detect diverse interoceptive cues, but the identity of the key sensory neurons and corresponding signals that regulate food intake remains unknown. Here, we use an approach for target-specific, single-cell RNA sequencing to generate a map of the vagal cell types that innervate the gastrointestinal tract. We show that unique molecular markers identify vagal neurons with distinct innervation patterns, sensory endings, and function. Surprisingly, we find that food intake is most sensitive to stimulation of mechanoreceptors in the intestine, whereas nutrient-activated mucosal afferents have no effect. Peripheral manipulations combined with central recordings reveal that intestinal mechanoreceptors, but not other cell types, potently and durably inhibit hunger-promoting AgRP neurons in the hypothalamus. These findings identify a key role for intestinal mechanoreceptors in the regulation of feeding.

}, keywords = {AgRP Neurons, chemogenetics, fiber photometry, Hypothalamus, Optogenetics, RNA sequencing, Satiation, stretch, vagal afferents, vagus nerve}, issn = {0092-8674}, doi = {https://doi.org/10.1016/j.cell.2019.10.031}, url = {https://www.sciencedirect.com/science/article/pii/S009286741931181X}, author = {Ling Bai and Sheyda Mesgarzadeh and Karthik S. Ramesh and Erica L. Huey and Yin Liu and Lindsay A. Gray and Tara J. Aitken and Yiming Chen and Lisa R. Beutler and Jamie S. Ahn and Linda Madisen and Hongkui Zeng and Mark A. Krasnow and Zachary A. Knight} } @article {56204, title = {A genetically encoded near-infrared fluorescent calcium ion indicator.}, journal = {Nature Methods}, volume = {16}, year = {2019}, month = {2019 Jan 21}, pages = {171-4}, abstract = {

We report an intensiometric, near-infrared fluorescent, genetically encoded calcium ion (Ca) indicator (GECI) with excitation and emission maxima at 678 and 704 nm, respectively. This GECI, designated NIR-GECO1, enables imaging of Ca transients in cultured mammalian cells and brain tissue with sensitivity comparable to that of currently available visible-wavelength GECIs. We demonstrate that NIR-GECO1 opens up new vistas for multicolor Ca imaging in combination with other optogenetic indicators and actuators.

}, issn = {1548-7105}, doi = {10.1038/s41592-018-0294-6}, author = {Qian, Yong and Piatkevich, Kiryl D and Mc Larney, Benedict and Abdelfattah, Ahmed S and Mehta, Sohum and Murdock, Mitchell H and Gottschalk, Sven and Molina, Rosana S and Zhang, Wei and Chen, Yingche and Wu, Jiahui and Drobizhev, Mikhail and Hughes, Thomas E and Zhang, Jin and Schreiter, Eric R and Shoham, Shy and Razansky, Daniel and Boyden, Edward S and Campbell, Robert E} } @article {65020, title = {Genetics of intellectual disability in consanguineous families.}, journal = {Mol Psychiatry}, volume = {24}, year = {2019}, month = {2018 Jan 04}, pages = {1027-1039}, abstract = {

Autosomal recessive (AR) gene defects are the leading genetic cause of intellectual disability (ID) in countries with frequent parental consanguinity, which account for about 1/7th of the world population. Yet, compared to autosomal dominant de novo mutations, which are the predominant cause of ID in Western countries, the identification of AR-ID genes has lagged behind. Here, we report on whole exome and whole genome sequencing in 404 consanguineous predominantly Iranian families with two or more affected offspring. In 219 of these, we found likely causative variants, involving 77 known and 77 novel AR-ID (candidate) genes, 21 X-linked genes, as well as 9 genes previously implicated in diseases other than ID. This study, the largest of its kind published to date, illustrates that high-throughput DNA sequencing in consanguineous families is a superior strategy for elucidating the thousands of hitherto unknown gene defects underlying AR-ID, and it sheds light on their prevalence.

}, issn = {1476-5578}, doi = {10.1038/s41380-017-0012-2}, author = {Hu, Hao and Kahrizi, Kimia and Musante, Luciana and Fattahi, Zohreh and Herwig, Ralf and Hosseini, Masoumeh and Oppitz, Cornelia and Abedini, Seyedeh Sedigheh and Suckow, Vanessa and Larti, Farzaneh and Beheshtian, Maryam and Lipkowitz, Bettina and Akhtarkhavari, Tara and Mehvari, Sepideh and Otto, Sabine and Mohseni, Marzieh and Arzhangi, Sanaz and Jamali, Payman and Mojahedi, Faezeh and Taghdiri, Maryam and Papari, Elaheh and Soltani Banavandi, Mohammad Javad and Akbari, Saeide and Tonekaboni, Seyed Hassan and Dehghani, Hossein and Ebrahimpour, Mohammad Reza and Bader, Ingrid and Davarnia, Behzad and Cohen, Monika and Khodaei, Hossein and Albrecht, Beate and Azimi, Sarah and Zirn, Birgit and Bastami, Milad and Wieczorek, Dagmar and Bahrami, Gholamreza and Keleman, Krystyna and Vahid, Leila Nouri and Tzschach, Andreas and G{\"a}rtner, Jutta and Gillessen-Kaesbach, Gabriele and Varaghchi, Jamileh Rezazadeh and Timmermann, Bernd and Pourfatemi, Fatemeh and Jankhah, Aria and Chen, Wei and Nikuei, Pooneh and Kalscheuer, Vera M and Oladnabi, Morteza and Wienker, Thomas F and Ropers, Hans-Hilger and Najmabadi, Hossein} } @article {64904, title = {The glutamine transporter Slc38a1 regulates GABAergic neurotransmission and synaptic plasticity.}, journal = {Cerebal Cortex}, year = {2019}, month = {2019 May 03}, abstract = {

GABA signaling sustains fundamental brain functions, from nervous system development to the synchronization of population activity and synaptic plasticity. Despite these pivotal features, molecular determinants underscoring the rapid and cell-autonomous replenishment of the vesicular neurotransmitter GABA and its impact on synaptic plasticity remain elusive. Here, we show that genetic disruption of the glutamine transporter Slc38a1 in mice hampers GABA synthesis, modifies synaptic vesicle morphology in GABAergic presynapses and impairs critical period plasticity. We demonstrate that Slc38a1-mediated glutamine transport regulates vesicular GABA content, induces high-frequency membrane oscillations and shapes cortical processing and plasticity. Taken together, this work shows that Slc38a1 is not merely a transporter accumulating glutamine for metabolic purposes, but a key component regulating several neuronal functions.

}, issn = {1460-2199}, doi = {10.1093/cercor/bhz055}, author = {Qureshi, Tayyaba and S{\o}rensen, Christina and Berghuis, Paul and Jensen, Vidar and Dobszay, Marton B and Farkas, Tam{\'a}s and Dalen, Knut Tomas and Guo, Caiying and Hassel, Bj{\o}rnar and Utheim, Tor Paaske and Hvalby, {\O}ivind and Hafting, Torkel and Harkany, Tibor and Fyhn, Marianne and Chaudhry, Farrukh Abbas} } @article {68757, title = {A high-content imaging approach to profile C. elegans embryonic development}, journal = {Development}, volume = {146}, year = {2019}, month = {04-2019}, abstract = {

The Caenorhabditis elegans embryo is an important model for analyzing mechanisms of cell fate specification and tissue morphogenesis. Sophisticated lineage-tracing approaches for analyzing embryogenesis have been developed but are labor intensive and do not naturally integrate morphogenetic readouts. To enable the rapid classification of developmental phenotypes, we developed a high-content method that employs two custom strains: a Germ Layer strain that expresses nuclear markers in the ectoderm, mesoderm and endoderm/pharynx; and a Morphogenesis strain that expresses markers labeling epidermal cell junctions and the neuronal cell surface. We describe a procedure that allows simultaneous live imaging of development in 80-100 embryos and provide a custom program that generates cropped, oriented image stacks of individual embryos to facilitate analysis. We demonstrate the utility of our method by perturbing 40 previously characterized developmental genes in variants of the two strains containing RNAi-sensitizing mutations. The resulting datasets yielded distinct, reproducible signature phenotypes for a broad spectrum of genes that are involved in cell fate specification and morphogenesis. In addition, our analysis provides new in vivo evidence for MBK-2 function in mesoderm fate specification and LET-381 function in elongation.

}, issn = {0950-1991}, doi = {10.1242/dev.174029}, url = {https://doi.org/10.1242/dev.174029}, author = {Wang, Shaohe and Ochoa, Stacy D. and Khaliullin, Renat N. and Gerson-Gurwitz, Adina and Hendel, Jeffrey M. and Zhao, Zhiling and Biggs, Ronald and Chisholm, Andrew D. and Desai, Arshad and Oegema, Karen and Green, Rebecca A.} } @article {49534, title = {High-dimensional geometry of population responses in visual cortex.}, journal = {Nature}, volume = {571}, year = {2019}, month = {2019 Jun 26}, pages = {361-65}, abstract = {

A neuronal population encodes information most efficiently when its activity is uncorrelated and high-dimensional, and most robustly when its activity is correlated and lower-dimensional. Here, we analyzed the correlation structure of natural image coding, in large visual cortical populations recorded from awake mice. Evoked population activity was high dimensional, with correlations obeying an unexpected power-law: the n-th principal component variance scaled as 1/n. This was not inherited from the 1/f spectrum of natural images, because it persisted after stimulus whitening. We proved mathematically that the variance spectrum must decay at least this fast if a population code is smooth, i.e. if small changes in input cannot dominate population activity. The theory also predicts larger power-law exponents for lower-dimensional stimulus ensembles, which we validated experimentally. These results suggest that coding smoothness represents a fundamental constraint governing correlations in neural population codes.

}, doi = {10.1038/s41586-019-1346-5}, author = {Stringer, Carsen and Pachitariu, Marius and Steinmetz, Nicholas A and Carandini, Matteo and Harris, Kenneth D} } @article {64986, title = {High-performance calcium sensors for imaging activity in neuronal populations and microcompartments.}, journal = {Nature Methods}, volume = {16}, year = {2019}, month = {2019 Jun 17}, pages = {649-57}, abstract = {

Calcium imaging with genetically encoded calcium indicators (GECIs) is routinely used to measure neural activity in intact nervous systems. GECIs are frequently used in one of two different modes: to track activity in large populations of neuronal cell bodies, or to follow dynamics in subcellular compartments such as axons, dendrites and individual synaptic compartments. Despite major advances, calcium imaging is still limited by the biophysical properties of existing GECIs, including affinity, signal-to-noise ratio, rise and decay kinetics and dynamic range. Using structure-guided mutagenesis and neuron-based screening, we optimized the green fluorescent protein-based GECI GCaMP6 for different modes of in vivo imaging. The resulting jGCaMP7 sensors provide improved detection of individual spikes (jGCaMP7s,f), imaging in neurites and neuropil (jGCaMP7b), and may allow tracking larger populations of neurons using two-photon (jGCaMP7s,f) or wide-field (jGCaMP7c) imaging.

}, issn = {1548-7105}, doi = {10.1038/s41592-019-0435-6}, author = {Dana, Hod and Sun, Yi and Mohar, Boaz and Hulse, Brad K and Kerlin, Aaron M and Hasseman, Jeremy P and Tsegaye, Getahun and Tsang, Arthur and Wong, Allan and Patel, Ronak and Macklin, John J and Chen, Yang and Konnerth, Arthur and Jayaraman, Vivek and Looger, Loren L and Schreiter, Eric R and Svoboda, Karel and Kim, Douglas S} } @article {65204, title = {High-yield, automated intracellular electrophysiology in retinal pigment epithelia.}, journal = {Journal of Neuroscience Methods}, volume = {328}, year = {2019}, month = {2019 Dec 01}, pages = {108442}, abstract = {

BACKGROUND: Recent advancements with induced pluripotent stem cell-derived (iPSC) retinal pigment epithelium (RPE) have made disease modeling and cell therapy for macular degeneration feasible. However, current techniques for intracellular electrophysiology - used to validate epithelial function - are painstaking and require manual skill; limiting experimental throughput.

NEW METHOD: A five-stage algorithm, leveraging advances in automated patch clamping, systematically derived and optimized, improves yield and reduces skill when compared to conventional, manual techniques.

RESULTS: The automated algorithm improves yield per attempt from 17\% (manually, n = 23) to 22\% (automated, n = 120) (chi-squared, p = 0.004). Specifically for RPE, depressing the local cell membrane by 6 μm and electroporating (buzzing) just prior to this depth (5 μm) maximized yield.

COMPARISON WITH EXISTING METHOD: Conventionally, intracellular epithelial electrophysiology is performed by manually lowering a pipette with a micromanipulator, blindly, towards a monolayer of cells and spontaneously stopping when the magnitude of the instantaneous measured membrane potential decreased below a predetermined threshold. The new method automatically measures the pipette tip resistance during the descent, detects the cell surface, indents the cell membrane, and briefly buzzes to electroporate the membrane while descending, overall achieving a higher yield than conventional methods.

CONCLUSIONS: This paper presents an algorithm for high-yield, automated intracellular electrophysiology in epithelia; optimized for human RPE. Automation reduces required user skill and training while, simultaneously, improving yield. This algorithm could enable large-scale exploration of drug toxicity and physiological function verification for numerous kinds of epithelia.

}, issn = {1872-678X}, doi = {10.1016/j.jneumeth.2019.108442}, author = {Lewallen, Colby F and Wan, Qin and Maminishkis, Arvydas and Stoy, William and Kolb, Ilya and Hotaling, Nathan and Bharti, Kapil and Forest, Craig R} } @article {65175, title = {Histone H3K27 acetylation precedes active transcription during zebrafish zygotic genome activation as revealed by live-cell analysis.}, journal = {Development}, volume = {146}, year = {2019}, month = {2019 Sep 30}, abstract = {

Histone post-translational modifications are key gene expression regulators, but their rapid dynamics during development remain difficult to capture. We applied a Fab-based live endogenous modification labeling technique to monitor the changes in histone modification levels during zygotic genome activation (ZGA) in living zebrafish embryos. Among various histone modifications, H3 Lys27 acetylation (H3K27ac) exhibited most drastic changes, accumulating in two nuclear foci in the 64- to 1k-cell-stage embryos. The elongating form of RNA polymerase II, which is phosphorylated at Ser2 in heptad repeats within the C-terminal domain (RNAP2 Ser2ph), and miR-430 transcripts were also concentrated in foci closely associated with H3K27ac. When treated with α-amanitin to inhibit transcription or JQ-1 to inhibit binding of acetyl-reader proteins, H3K27ac foci still appeared but RNAP2 Ser2ph and miR-430 morpholino were not concentrated in foci, suggesting that H3K27ac precedes active transcription during ZGA. We anticipate that the method presented here could be applied to a variety of developmental processes in any model and non-model organisms.

}, issn = {1477-9129}, doi = {10.1242/dev.179127}, author = {Sato, Yuko and Hilbert, Lennart and Oda, Haruka and Wan, Yinan and Heddleston, John M and Chew, Teng-Leong and Zaburdaev, Vasily and Keller, Philipp and Lionnet, Timoth{\'e}e and Vastenhouw, Nadine and Kimura, Hiroshi} } @article {49449, title = {Idiosyncratic choice bias in decision tasks naturally emerges from neuronal network dynamics.}, journal = {Nature Human Behavior}, volume = {3}, year = {2019}, month = {2019 Sep 02}, pages = {1190-1202}, abstract = {

Idiosyncratic tendency to choose one alternative over others in the absence of an identified reason, is a common observation in two-alternative forced-choice experiments. It is tempting to account for it as resulting from the (unknown) participant-specific history and thus treat it as a measurement noise. Indeed, idiosyncratic choice biases are typically considered as nuisance. Care is taken to account for them by adding an ad-hoc bias parameter or by counterbalancing the choices to average them out. Here we quantify idiosyncratic choice biases in a perceptual discrimination task and a motor task. We report substantial and significant biases in both cases. Then, we present theoretical evidence that even in idealized experiments, in which the settings are symmetric, idiosyncratic choice bias is expected to emerge from the dynamics of competing neuronal networks. We thus argue that idiosyncratic choice bias reflects the microscopic dynamics of choice and therefore is virtually inevitable in any comparison or decision task.

}, doi = {10.1101/284877}, author = {Lebovich, Lior and Darshan, Ran and Lavi, Yoni and Hansel, David and Loewenstein, Yonatan} } @article {65178, title = {ilastik: interactive machine learning for (bio)image analysis.}, journal = {Nature Methods}, volume = {16}, year = {2019}, month = {2019 Sep 30}, pages = {1226-32}, abstract = {

We present ilastik, an easy-to-use interactive tool that brings machine-learning-based (bio)image analysis to end users without substantial computational expertise. It contains pre-defined workflows for image segmentation, object classification, counting and tracking. Users adapt the workflows to the problem at hand by interactively providing sparse training annotations for a nonlinear classifier. ilastik can process data in up to five dimensions (3D, time and number of channels). Its computational back end runs operations on-demand wherever possible, allowing for interactive prediction on data larger than RAM. Once the classifiers are trained, ilastik workflows can be applied to new data from the command line without further user interaction. We describe all ilastik workflows in detail, including three case studies and a discussion on the expected performance.

}, issn = {1548-7105}, doi = {10.1038/s41592-019-0582-9}, author = {Berg, Stuart and Kutra, Dominik and Kroeger, Thorben and Straehle, Christoph N and Kausler, Bernhard X and Haubold, Carsten and Schiegg, Martin and Ales, Janez and Beier, Thorsten and Rudy, Markus and Eren, Kemal and Cervantes, Jaime I and Xu, Buote and Beuttenmueller, Fynn and Wolny, Adrian and Zhang, Chong and Koethe, Ullrich and Hamprecht, Fred A and Kreshuk, Anna} } @article {65024, title = {In situ structure of rotavirus VP1 RNA-dependent RNA polymerase.}, journal = {Journal of Molecular Biology}, volume = {431}, year = {2019}, month = {2019 Jun 21}, pages = {3124-38}, abstract = {

Rotaviruses, like other non-enveloped, double-strand RNA (dsRNA) viruses, package an RNA-dependent RNA polymerase (RdRp) with each duplex of their segmented genomes. Rotavirus cell entry results in loss of an outer protein layer and delivery into the cytosol of an intact, inner capsid particle (the {\textquotedblleft}double-layer particle{\textquotedblright} or DLP). The RdRp, designated VP1, is active inside the DLP; each VP1 achieves many rounds of mRNA transcription from its associated genome segment. Previous work has shown that one VP1 molecule lies close to each fivefold axis of the icosahedrally symmetric DLP, just beneath the inner surface of its protein shell, embedded in tightly packed RNA. We have determined a high-resolution structure for the rotavirus VP1 RdRp\ in situ, by local reconstruction of density around individual fivefold positions. We have analyzed intact virions ({\textquotedblleft}triple-layer particles{\textquotedblright} or TLPs), non-transcribing DLPs and transcribing DLPs. Outer layer dissociation enables the DLP to synthesize RNA,\ in vitro\ as well as\ in vivo, but appears not to induce any detectable structural change in the RdRp. Addition of NTPs, Mg2+, and S-adenosyl methionine, which allows active transcription, results in conformational rearrangements, in both VP1 and the DLP capsid shell protein, that allow a transcript to exit the polymerase and the particle. The position of VP1 (among the five symmetrically related alternatives) at one vertex does not correlate with its position at other vertices. This stochastic distribution of site occupancies limits long-range order in the 11-segment, dsRNA genome.

}, doi = {10.1016/j.jmb.2019.06.016}, author = {Jenni, Simon and Salgado, Eric N. and Herrmann, Tobias and Li, Zongli and Grant, Timothy and Grigorieff, Nikolaus and Trapani, Stefano and Estrozi, Leandro F. and Harrison, Stephen C.} } @article {64851, title = {Interfacial actin protrusions mechanically enhance killing by cytotoxic T cells.}, journal = {Science Immunology}, volume = {4}, year = {2019}, month = {2019 Mar 22}, abstract = {

Cytotoxic T lymphocytes (CTLs) kill by forming immunological synapses with target cells and secreting toxic proteases and the pore-forming protein perforin into the intercellular space. Immunological synapses are highly dynamic structures that boost perforin activity by applying mechanical force against the target cell. Here, we used high-resolution imaging and microfabrication to investigate how CTLs exert synaptic forces and coordinate their mechanical output with perforin secretion. Using micropatterned stimulatory substrates that enable synapse growth in three dimensions, we found that perforin release occurs at the base of actin-rich protrusions that extend from central and intermediate locations within the synapse. These protrusions, which depended on the cytoskeletal regulator WASP and the Arp2/3 actin nucleation complex, were required for synaptic force exertion and efficient killing. They also mediated physical deformation of the target cell surface during CTL-target cell interactions. Our results reveal the mechanical basis of cellular cytotoxicity and highlight the functional importance of dynamic, three-dimensional architecture in immune cell-cell interfaces.

}, issn = {2470-9468}, doi = {10.1126/sciimmunol.aav5445}, author = {Tamzalit, Fella and Wang, Mitchell S and Jin, Weiyang and Tello-Lafoz, Maria and Boyko, Vitaly and Heddleston, John M and Black, Charles T and Kam, Lance C and Huse, Morgan} } @conference {56205, title = {Internal models in control, biology and neuroscience.}, booktitle = {2018 IEEE Conference on Decision and Control (CDC)}, year = {2019}, month = {2019 Jan 21}, abstract = {

This tutorial paper deals with the Internal Model Principle (IMP) from different perspectives. The goal is to start from the principle as introduced and commonly used in the control theory and then enlarge the vision to other fields where {\textquotedblleft}internal models{\textquotedblright} play a role. The biology and neuroscience fields are specifically targeted in the paper. The paper ends by presenting an {\textquotedblleft}abstract{\textquotedblright} theory of IMP applicable to a large class of systems.

}, doi = {10.1109/CDC.2018.8619624}, author = {Huang, J and Isidori, A and Marconi, L and Mischiati, Matteo and Sontag, E and Wonham, W M} } @article {65033, title = {Kilohertz in vivo imaging of neural activity.}, journal = {bioRxiv}, year = {2019}, month = {2019 Feb 06}, abstract = {

Understanding information processing in the brain requires us to monitor neural activity in vivo at high spatiotemporal resolution. Using an ultrafast two-photon fluorescence microscope (2PFM) empowered by all-optical laser scanning, we imaged neural activity in vivo at 1,000 frames per second and submicron spatial resolution. This ultrafast imaging method enabled monitoring of electrical activity down to 300 μm below the brain surface in head fixed awake mice.

}, doi = {10.1101/543058}, author = {Jianglai Wu and Yajie liang and Ching-Lung Hsu and Mariya Chavarha and Stephen Evans and Dongqing Shi and Michael Lin and Kevin Tsia and Na Ji} } @article {68758, title = {The Kinetochore-Microtubule Coupling Machinery Is Repurposed in Sensory Nervous System Morphogenesis}, journal = {Developmental Cell}, volume = {48}, year = {2019}, month = {03/2019}, pages = {864-872.e7}, abstract = {

Summary Dynamic coupling of microtubule ends to kinetochores, built on the centromeres of chromosomes, directs chromosome segregation during cell division. Here, we report that the evolutionarily ancient kinetochore-microtubule\ coupling machine, the KMN (Knl1/Mis12/Ndc80-complex) network, plays a critical role in neuronal morphogenesis. We show that the KMN network concentrates in microtubule-rich dendrites of developing sensory neurons that collectively extend in a multicellular morphogenetic event that occurs during C.\ elegans embryogenesis. Post-mitotic degradation of KMN components in sensory neurons disrupts dendritic extension, leading to patterning and functional defects in the sensory nervous system. Structure-guided mutations revealed that the molecular interface that couples kinetochores to spindle microtubules also functions in neuronal development. These results identify a cell-division-independent function for the chromosome-segregation machinery and define a microtubule-coupling-dependent event in sensory nervous system morphogenesis.

}, keywords = {Chromosome Segregation, dendrite, kinetochore, KMN network, Knl1, microtubule, Mis12 complex, Mitosis, Morphogenesis, Ndc80 complex, Nervous System, sensory neuron}, issn = {1534-5807}, doi = {https://doi.org/10.1016/j.devcel.2019.02.002}, url = {https://www.sciencedirect.com/science/article/pii/S1534580719300577}, author = {Dhanya K. Cheerambathur and Bram Prevo and Tiffany-Lynn Chow and Neil Hattersley and Shaohe Wang and Zhiling Zhao and Taekyung Kim and Adina Gerson-Gurwitz and Karen Oegema and Rebecca Green and Arshad Desai} } @article {64874, title = {Mapping the transcriptional diversity of genetically and anatomically defined cell populations in the mouse brain.}, journal = {Elife}, volume = {8}, year = {2019}, month = {2019 Apr 12}, abstract = {

Understanding the principles governing neuronal diversity is a fundamental goal for neuroscience. Here we provide an anatomical and transcriptomic database of nearly 200 genetically identified cell populations. By separately analyzing the robustness and pattern of expression differences across these cell populations, we identify two gene classes contributing distinctly to neuronal diversity. Short homeobox transcription factors distinguish neuronal populations combinatorially, and exhibit extremely low transcriptional noise, enabling highly robust expression differences. Long neuronal effector genes, such as channels and cell adhesion molecules, contribute disproportionately to neuronal diversity, based on their patterns rather than robustness of expression differences. By linking transcriptional identity to genetic strains and anatomical atlases we provide an extensive resource for further investigation of mouse neuronal cell types.

}, issn = {2050-084X}, doi = {10.7554/eLife.38619}, author = {Sugino, Ken and Clark, Erin and Schulmann, Anton and Shima, Yasuyuki and Wang, Lihua and Hunt, David L and Hooks, Bryan M and Traenkner, Dimitri and Chandrashekar, Jayaram and Picard, Serge and Lemire, Andrew L and Spruston, Nelson and Hantman, Adam W and Nelson, Sacha B} } @article {65255, title = {Mechanisms underlying the neural computation of head direction.}, journal = {Annual Review of Neuroscience}, volume = {43}, year = {2019}, month = {2020 Jul 8}, pages = {31-54}, abstract = {

Many animals use an internal sense of direction to guide their movements through the world. Neurons selective to head direction are thought to support this directional sense and have been found in a diverse range of species, from insects to primates, highlighting their evolutionary importance. Across species, most head-direction networks share four key properties: a unique representation of direction at all times, persistent activity in the absence of movement, integration of angular velocity to update the representation, and the use of directional cues to correct drift. The dynamics of theorized network structures called ring attractors elegantly account for these properties, but their relationship to brain circuits is unclear. Here, we review experiments in rodents and flies that offer insights into potential neural implementations of ring attractor networks. We suggest that a theory-guided search across model systems for biological mechanisms that enable such dynamics would uncover general principles underlying head-direction circuit function. Expected final online publication date for the , Volume 43 is July 8, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

}, issn = {1545-4126}, doi = {10.1146/annurev-neuro-072116-031516}, author = {Hulse, Brad K and Jayaraman, Vivek} } @article {65257, title = {MeCP2 nuclear dynamics in live neurons results from low and high affinity chromatin interactions.}, journal = {eLife}, volume = {8}, year = {2019}, month = {2019 Dec 23}, abstract = {

Methyl-CpG-binding-Protein 2 (MeCP2) is an abundant nuclear protein highly enriched in neurons. Here we report live-cell single-molecule imaging studies of the kinetic features of mouse MeCP2 at high spatial-temporal resolution. MeCP2 displays dynamic features that are distinct from both highly mobile transcription factors and immobile histones. Stable binding of MeCP2 in living neurons requires its methyl-binding domain and is sensitive to DNA modification levels. Diffusion of unbound MeCP2 is strongly constrained by weak, transient interactions mediated primarily by its AT-hook domains, and varies with the level of chromatin compaction and cell type. These findings extend previous studies of the role of the MeCP2 MBD in high affinity DNA binding to living neurons, and identify a new role for its AT-hooks domains as critical determinants of its kinetic behavior. They suggest that limited nuclear diffusion of MeCP2 in live neurons contributes to its local impact on chromatin structure and gene expression.

}, issn = {2050-084X}, doi = {10.7554/eLife.51449}, author = {Piccolo, Francesco M and Liu, Zhe and Dong, Peng and Hsu, Ching-Lung and Stoyanova, Elitsa I and Rao, Anjana and Tjian, Robert and Heintz, Nathaniel} } @article {64853, title = {Membrane-cytoskeletal crosstalk mediated by myosin-I regulates adhesion turnover during phagocytosis.}, journal = {Nature Communications}, volume = {10}, year = {2019}, month = {2019 03 19}, pages = {1249}, abstract = {

Phagocytosis of invading pathogens or cellular debris requires a dramatic change in cell shape driven by actin polymerization. For antibody-covered targets, phagocytosis is thought to proceed through the sequential engagement of Fc-receptors on the phagocyte with antibodies on the target surface, leading to the extension and closure of the phagocytic cup around the target. We find that two actin-dependent molecular motors, class 1 myosins myosin 1e and myosin 1f, are specifically localized to Fc-receptor adhesions and required for efficient phagocytosis of antibody-opsonized targets. Using primary macrophages lacking both myosin 1e and myosin 1f, we find that without the actin-membrane linkage mediated by these myosins, the organization of individual adhesions is compromised, leading to excessive actin polymerization, slower adhesion turnover, and deficient phagocytic internalization. This work identifies a role for class 1 myosins in coordinated adhesion turnover during phagocytosis and supports a mechanism involving membrane-cytoskeletal crosstalk for phagocytic cup closure.

}, issn = {2041-1723}, doi = {10.1038/s41467-019-09104-1}, author = {Barger, Sarah R and Reilly, Nicholas S and Shutova, Maria S and Li, Qingsen and Maiuri, Paolo and Heddleston, John M and Mooseker, Mark S and Flavell, Richard A and Svitkina, Tatyana and Oakes, Patrick W and Krendel, Mira and Gauthier, Nils C} } @article {64873, title = {MicroED data collection with SerialEM.}, journal = {Ultramicroscopy}, volume = {201}, year = {2019}, month = {2019 Mar 19}, pages = {77-80}, abstract = {

The cryoEM method Microcrystal Electron Diffraction (MicroED) involves transmission electron microscope (TEM) and electron detector working in synchrony to collect electron diffraction data by continuous rotation. We previously reported several protein, peptide, and small molecule structures by MicroED using manual control of the microscope and detector to collect data. Here we present a procedure to automate this process using a script developed for the popular open-source software package SerialEM. With this approach, SerialEM coordinates stage rotation, microscope operation, and camera functions for automated continuous-rotation MicroED data collection. Depending on crystal and substrate geometry, more than 300 datasets can be collected overnight in this way, facilitating high-throughput MicroED data collection for large-scale data analyses.

}, issn = {1879-2723}, doi = {10.1016/j.ultramic.2019.03.009}, author = {de la Cruz, M Jason and Martynowycz, Michael W and Hattne, Johan and Gonen, Tamir} } @article {59911, title = {Molecular logic of spinocerebellar tract neuron diversity and connectivity.}, journal = {Cell Reports}, volume = {27}, year = {2019}, month = {2019 May 27}, pages = {2620-35}, abstract = {

Coordinated motor behaviors depend on feedback communication between peripheral sensory systems and central circuits in the brain and spinal cord. Relay of muscle and tendon-derived sensory information to the CNS is facilitated by functionally and anatomically diverse groups of spinocerebellar tract neurons (SCTNs), but the molecular logic by which SCTN diversity and connectivity is achieved is poorly understood. We used single cell RNA sequencing and genetic manipulations to define the mechanisms governing the molecular profile and organization of SCTN subtypes. We found that SCTNs relaying proprioceptive sensory information from limb and axial muscles are generated through segmentally-restricted actions of specific Hox genes. Loss of Hox function disrupts SCTN subtype-specific transcriptional programs, leading to defects in the connections between proprioceptive sensory neurons, SCTNs, and the cerebellum. These results indicate that Hox-dependent genetic programs play essential roles in the assembly of the neural circuits required for proprioception.

}, doi = {10.1016/j.celrep.2019.04.113}, author = {Baek, Myungin and Menon, Vilas and Jessell, Thomas M and Hantman, Adam W and Dasen, Jeremy} } @article {69337, title = {Molecular Profiling to Infer Neuronal Cell Identity: Lessons from small ganglia of the Crab Cancer borealis}, journal = {bioRxiv}, year = {2019}, month = {2019 Jul 2}, abstract = {

Understanding circuit organization depends on identification of cell types. Recent advances in transcriptional profiling methods have enabled classification of cell types by their gene expression. While exceptionally powerful and high throughput, the ground-truth validation of these methods is difficult: if cell type is unknown, how does one assess whether a given analysis accurately captures neuronal identity? To shed light on the capabilities and limitations of solely using transcriptional profiling for cell type classification, we performed two forms of transcriptional profiling {\textendash} RNA-seq and quantitative RT-PCR, in single, unambiguously identified neurons from two small crustacean networks: the stomatogastric and cardiac ganglia. We then combined our knowledge of cell type with unbiased clustering analyses and supervised machine learning to determine how accurately functionally-defined neuron types can be classified by expression profile alone. Our results demonstrate that expression profile is able to capture neuronal identity most accurately when combined with multimodal information that allows for post-hoc grouping so analysis can proceed from a supervised perspective. Solely unsupervised clustering can lead to misidentification and an inability to distinguish between two or more cell types. Therefore, our study supports the general utility of cell identification by transcriptional profiling, but adds a caution: it is difficult or impossible to know under what conditions transcriptional profiling alone is capable of assigning cell identity. Only by combining multiple modalities of information such as physiology, morphology or innervation target can neuronal identity be unambiguously determined.SIGNIFICANCE STATEMENT Single cell transcriptional profiling has become a widespread tool in cell identification, particularly in the nervous system, based on the notion that genomic information determines cell identity. However, many cell type classification studies are unconstrained by other cellular attributes (e.g., morphology, physiology). Here, we systematically test how accurately transcriptional profiling can assign cell identity to well-studied anatomically- and functionally-identified neurons in two small neuronal networks. While these neurons clearly possess distinct patterns of gene expression across cell types, their expression profiles are not sufficient to unambiguously confirm their identity. We suggest that true cell identity can only be determined by combining gene expression data with other cellular attributes such as innervation pattern, morphology, or physiology.

}, doi = {10.1101/690388}, url = {https://www.biorxiv.org/content/early/2019/07/02/690388}, author = {Adam J. Northcutt and Daniel R. Kick and Adriane G. Otopalik and Benjamin M. Goetz and Rayna M. Harris and Joseph M. Santin and Hans A. Hofmann and Eve Marder and David J. Schulz} } @article {64864, title = {Multimodal in vivo brain electrophysiology with integrated glass microelectrodes.}, journal = {Nature Biomedical Engineering}, volume = {3}, year = {2019}, month = {2019 Apr 01}, pages = {741-53}, abstract = {

Electrophysiology is the most used approach for the collection of functional data in basic and translational neuroscience, but it is typically limited to either intracellular or extracellular recordings. The integration of multiple physiological modalities for the routine acquisition of multimodal data with microelectrodes could be useful for biomedical applications, yet this has been challenging owing to incompatibilities of fabrication methods. Here, we present a suite of glass pipettes with integrated microelectrodes for the simultaneous acquisition of multimodal intracellular and extracellular information in vivo, electrochemistry assessments, and optogenetic perturbations of neural activity. We used the integrated devices to acquire multimodal signals from the CA1 region of the hippocampus in mice and rats, and show that these data can serve as ground-truth validation for the performance of spike-sorting algorithms. The microdevices are applicable for basic and translational neurobiology, and for the development of next-generation brain-machine interfaces.

}, issn = {2157-846X}, doi = {10.1038/s41551-019-0373-8}, author = {Hunt, David L and Lai, Chongxi and Smith, Richard D and Lee, Albert K and Harris, Timothy D and Barbic, Mladen} } @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} } @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 {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 {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 {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 {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 {65206, title = {The organization of the second optic chiasm of the optic lobe.}, journal = {Frontiers in Neural Circuits}, volume = {13}, year = {2019}, month = {2019 Oct 11}, pages = {65}, abstract = {

Visual pathways from the compound eye of an insect relay to four neuropils, successively the lamina, medulla, lobula, and lobula plate in the underlying optic lobe. Among these neuropils, the medulla, lobula, and lobula plate are interconnected by the complex second optic chiasm, through which the anteroposterior axis undergoes an inversion between the medulla and lobula. Given their complex structure, the projection patterns through the second optic chiasm have so far lacked critical analysis. By densely reconstructing axon trajectories using a volumetric scanning electron microscopy (SEM) technique, we reveal the three-dimensional structure of the second optic chiasm of , which comprises interleaving bundles and sheets of axons insulated from each other by glial sheaths. These axon bundles invert their horizontal sequence in passing between the medulla and lobula. Axons connecting the medulla and lobula plate are also bundled together with them but do not decussate the sequence of their horizontal positions. They interleave with sheets of projection neuron axons between the lobula and lobula plate, which also lack decussations. We estimate that approximately 19,500 cells per hemisphere, about two thirds of the optic lobe neurons, contribute to the second chiasm, most being Tm cells, with an estimated additional 2,780 T4 and T5 cells each. The chiasm mostly comprises axons and cell body fibers, but also a few synaptic elements. Based on our anatomical findings, we propose that a chiasmal structure between the neuropils is potentially advantageous for processing complex visual information in parallel. The EM reconstruction shows not only the structure of the chiasm in the adult brain, the previously unreported main topic of our study, but also suggest that the projection patterns of the neurons comprising the chiasm may be determined by the proliferation centers from which the neurons develop. Such a complex wiring pattern could, we suggest, only have arisen in several evolutionary steps.

}, issn = {1662-5110}, doi = {10.3389/fncir.2019.00065}, author = {Shinomiya, Kazunori and Horne, Jane Anne and McLin, Sari and Wiederman, Meagan and Nern, Aljoscha and Plaza, Stephen M and Meinertzhagen, Ian A} } @article {66014, title = {Physical Principles of Membrane Shape Regulation by the Glycocalyx}, journal = {Cell}, volume = {177}, year = {2019}, month = {Jan-06-2019}, pages = {1757 - 1770.e21}, abstract = {

Cells bend their plasma membranes into highly curved forms to interact with the local environment, but how shape generation is regulated is not fully resolved. Here, we report a synergy between shape-generating processes in the cell interior and the external organization and composition of the cell-surface\ glycocalyx.\ Mucinbiopolymers\ and long-chain\ polysaccharides\ within the glycocalyx can generate entropic forces that favor or disfavor the projection of spherical and finger-like extensions from the cell surface. A polymer brush model of the glycocalyx successfully predicts the effects of polymer size and cell-surface density on membrane morphologies. Specific glycocalyx compositions can also induce plasma membrane instabilities to generate more exotic undulating and pearled\ membrane structures\ and drive secretion of extracellular vesicles. Together, our results suggest a fundamental role for the glycocalyx in regulating curved membrane features that serve in communication between cells and with the\ extracellular matrix.

}, issn = {00928674}, doi = {10.1016/j.cell.2019.04.017}, url = {https://www.sciencedirect.com/science/article/pii/S0092867419304039?via\%3Dihub}, author = {Shurer, Carolyn R. and Kuo, Joe Chin-Hun and Roberts, LaDeidra Mon{\'e}t and Gandhi, Jay G. and Colville, Marshall J. and Enoki, Thais A. and Pan, Hao and Su, Jin and Noble, Jade M. and Hollander, Michael J. and O{\textquoteright}Donnell, John P. and Yin, Rose and Pedram, Kayvon and M{\"o}ckl, Leonhard and Kourkoutis, Lena F. and Moerner, W.E. and Bertozzi, Carolyn R. and Feigenson, Gerald W. and Reesink, Heidi L. and Paszek, Matthew J.} } @article {64832, title = {Prediction of choice from competing mechanosensory and choice-memory cues during active tactile decision making.}, journal = {The Journal of Neuroscience : the official journal of the Society for Neuroscience}, volume = {39}, year = {2019}, month = {2019 May 15}, pages = {3921-33}, abstract = {

Perceptual decision making is an active process where animals move their sense organs to extract task-relevant information. To investigate how the brain translates sensory input into decisions during active sensation, we developed a mouse active touch task where the mechanosensory input can be precisely measured and that challenges animals to use multiple mechanosensory cues. Male mice were trained to localise a pole using a single whisker and to report their decision by selecting one of three choices. Using high-speed imaging and machine vision we estimated whisker-object mechanical forces at millisecond resolution. Mice solved the task by a sensory-motor strategy where both the strength and direction of whisker bending were informative cues to pole location. We found competing influences of immediate sensory input and choice memory on mouse choice. On correct trials, choice could be predicted from the direction and strength of whisker bending, but not from previous choice. In contrast, on error trials, choice could be predicted from previous choice but not from whisker bending. This study shows that animal choices during active tactile decision making can be predicted from mechanosenory and choice-memory signals; and provides a new task, well-suited for future study of the neural basis of active perceptual decisions.Due to the difficulty of measuring the sensory input to moving sense organs, active perceptual decision making remains poorly understood. The whisker system provides a way forward since it is now possible to measure the mechanical forces due to whisker-object contact during behaviour. Here we train mice in a novel behavioural task that challenges them to use rich mechanosensory cues, but can be performed using one whisker and enables task-relevant mechanical forces to be precisely estimated. This approach enables rigorous study of how sensory cues translate into action during active, perceptual decision making. Our findings provide new insight into active touch and how sensory/internal signals interact to determine behavioural choices.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.2217-18.2019}, author = {Campagner, Dario and Evans, Mathew H and Chlebikova, Katarina and Colins-Rodriguez, Andrea and Loft, Michaela S E and Fox, Sarah and Pettifer, David and Humphries, Mark D and Svoboda, Karel and Petersen, Rasmus S} } @article {64813, title = {Principles governing the dynamics of GABAergic interneurons in the barrel cortex.}, journal = {bioRxiv}, year = {2019}, month = {2019 Feb 21}, abstract = {

Information processing in the neocortex is performed by GABAergic interneurons that are integrated with excitatory neurons into precisely structured circuits. To reveal how each neuron type shapes sensory representations, we measured spikes and membrane potential of specific types of neurons in the barrel cortex while mice performed an active, whisker-dependent object localization task. Whiskers were tracked with millisecond precision. Fast-spiking (FS) neurons were activated by touch with short latency and by whisking. FS neurons track thalamic input and provide feedforward inhibition. Somatostatin (SOM)-expressing neurons were also excited by touch, but with a delay (5 ms) compared to excitatory (E) and FS neurons. SOM neurons monitor local excitation and provide feedback inhibition. Vasoactive intestinal polypeptide (VIP)-expressing neurons were not driven by touch but elevated their spike rate during whisking, disinhibiting E and FS neurons. Our data reveal rules of recruitment for specific interneuron types, providing foundations for understanding cortical computations.

}, doi = {10.1101/554949}, author = {Yu, Jianing and Hu, Hang and Agmon, Ariel and Svoboda, Karel} } @article {65138, title = {Reconstruction of 1,000 projection neurons reveals new cell types and organization of long-range connectivity in the mouse brain.}, journal = {Cell}, volume = {179}, year = {2019}, month = {2019 Sep 19}, pages = {268-81}, abstract = {

Neuronal\ cell\ types\ are the nodes of neural circuits that determine the flow of information within the\ brain. Neuronal morphology, especially the shape of the axonal arbor, provides an essential descriptor of\ cell\ type and\ reveals\ how individual\ neurons\ route their output across the\ brain. Despite the importance of morphology, few\ projection\ neurons\ in the\ mouse\ brain\ have been reconstructed in their entirety. Here we present a robust and efficient platform for imaging and reconstructing complete neuronal morphologies, including axonal arbors that span substantial portions of the\ brain. We used this platform to reconstruct more than\ 1,000\ projection\ neurons\ in the motor cortex, thalamus, subiculum, and hypothalamus. Together, the reconstructed\ neurons\ constitute more than 85\ meters of axonal length and are available in a searchable online database. Axonal shapes revealed previously unknown subtypes of\ projection\ neurons\ and suggest organizational principles of\ long-range\ connectivity.

}, issn = {00928674}, doi = {10.1016/j.cell.2019.07.042}, author = {Winnubst, Johan and Bas, Erhan and Ferreira, Tiago A. and Wu, Zhuhao and Economo, Michael N. and Edson, Patrick and Arthur, Ben J. and Bruns, Christopher and Rokicki, Konrad and Schauder, David and Olbris, Donald J. and Murphy, Sean D. and Ackerman, David G. and Arshadi, Cameron and Baldwin, Perry and Blake, Regina and Elsayed, Ahmad and Hasan, Mashtura and Ramirez, Daniel and Dos Santos, Bruno and Weldon, Monet and Zafar, Amina and Dudman, Joshua T. and Gerfen, Charles R. and Hantman, Adam W. and Korff, Wyatt and Sternson, Scott M. and Spruston, Nelson and Svoboda, Karel and Chandrashekar, Jayaram} } @article {65129, title = {Recruitment of GABAergic interneurons in the barrel cortex during active tactile behavior.}, journal = {Neuron}, volume = {104}, year = {2019}, month = {2019 Oct 23}, pages = {412-27}, abstract = {

Neural computation involves diverse types of GABAergic inhibitory interneurons that are integrated with excitatory (E) neurons into precisely structured circuits. To understand how each neuron type shapes sensory representations, we measured firing patterns of defined types of neurons in the barrel cortex while mice performed an active, whisker-dependent object localization task. Touch excited fast-spiking (FS) interneurons at short latency, followed by activation of E neurons and somatostatin-expressing (SST) interneurons. Touch only weakly modulated vasoactive intestinal polypeptide-expressing (VIP) interneurons. Voluntary whisker movement activated FS neurons in the ventral posteromedial nucleus (VPM) target layers, a subset of SST neurons and a majority of VIP neurons. Together, FS neurons track thalamic input, mediating feedforward inhibition. SST neurons monitor local excitation, providing feedback inhibition. VIP neurons are activated by non-sensory inputs, disinhibiting E and FS neurons. Our data reveal rules of recruitment for interneuron types during behavior, providing foundations for understanding computation in cortical microcircuits.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2019.07.027}, author = {Yu, Jianing and Hu, Hang and Agmon, Ariel and Svoboda, Karel} } @article {65025, title = {Regulation of plasma membrane nanodomains of the water channel aquaporin-3 revealed by fixed and live photoactivated localization microscopy.}, journal = {Nano Letters}, volume = {19}, year = {2019}, month = {2019 Feb 13}, pages = {699-707}, abstract = {

Several aquaporin (AQP) water channels are short-term regulated by the messenger cyclic adenosine monophosphate (cAMP), including AQP3. Bulk measurements show that cAMP can change diffusive properties of AQP3; however, it remains unknown how elevated cAMP affects AQP3 organization at the nanoscale. Here we analyzed AQP3 nano-organization following cAMP stimulation using photoactivated localization microscopy (PALM) of fixed cells combined with pair correlation analysis. Moreover, in live cells, we combined PALM acquisitions of single fluorophores with single-particle tracking (spt-PALM). These analyses revealed that AQP3 tends to cluster and that the diffusive mobility is confined to nanodomains with radii of \~{}150 nm. This domain size increases by \~{}30\% upon elevation of cAMP, which, however, is not accompanied by a significant increase in the confined diffusion coefficient. This regulation of AQP3 organization at the nanoscale may be important for understanding the mechanisms of water AQP3-mediated water transport across plasma membranes.

}, keywords = {Animals, Aquaporin 3, Cell Membrane, Cyclic AMP, Diffusion, Dogs, Epithelial Cells, Madin Darby Canine Kidney Cells, Microscopy, Fluorescence, Photochemical Processes}, issn = {1530-6992}, doi = {10.1021/acs.nanolett.8b03721}, author = {Arnspang, Eva C and Sengupta, Prabuddha and Mortensen, Kim I and Jensen, Helene H and Hahn, Ute and Jensen, Eva B V and Lippincott-Schwartz, Jennifer and Nejsum, Lene N} } @article {65159, title = {A repeated molecular architecture across thalamic pathways.}, journal = {Nature Neuroscience}, volume = {22}, year = {2019}, month = {2019 Sep 16}, pages = {1925-35}, abstract = {

The thalamus is the central communication hub of the forebrain and provides the cerebral cortex with inputs from sensory organs, subcortical systems and the cortex itself. Multiple thalamic regions send convergent information to each cortical region, but the organizational logic of thalamic projections has remained elusive. Through comprehensive transcriptional analyses of retrogradely labeled thalamic neurons in adult mice, we identify three major profiles of thalamic pathways. These profiles exist along a continuum that is repeated across all major projection systems, such as those for vision, motor control and cognition. The largest component of gene expression variation in the mouse thalamus is topographically organized, with features conserved in humans. Transcriptional differences between these thalamic neuronal identities are tied to cellular features that are critical for function, such as axonal morphology and membrane properties. Molecular profiling therefore reveals covariation in the properties of thalamic pathways serving all major input modalities and output targets, thus establishing a molecular framework for understanding the thalamus.

}, issn = {1546-1726}, doi = {10.1038/s41593-019-0483-3}, author = {Phillips, James W and Schulmann, Anton and Hara, Erina and Winnubst, Johan and Liu, Chenghao and Valakh, Vera and Wang, Lihua and Shields, Brenda C and Korff, Wyatt and Chandrashekar, Jayaram and Lemire, Andrew L and Mensh, Brett and Dudman, Joshua T and Nelson, Sacha B and Hantman, Adam W} } @article {65108, title = {Revealing the synaptic hodology of mammalian neural circuits with multiscale neurocartography.}, journal = {Frontiers in Neuroinformatics}, volume = {13}, year = {2019}, month = {2019 Jul 30}, abstract = {

The functional features of neural circuits are determined by a combination of properties that range in scale from projections systems across the whole brain to molecular interactions at the synapse. The burgeoning field of neurocartography seeks to map these relevant features of brain structure{\textemdash}spanning a volume \~{}20 orders of magnitude{\textemdash}to determine how neural circuits perform computations supporting cognitive function and complex behavior. Recent technological breakthroughs in tissue sample preparation, high-throughput electron microscopy imaging, and automated image analyses have produced the first visualizations of all synaptic connections between neurons of invertebrate model systems. However, the sheer size of the central nervous system in mammals implies that reconstruction of the first full brain maps at synaptic scale may not be feasible for decades. In this review, we outline existing and emerging technologies for neurocartography that complement electron microscopy-based strategies and are beginning to derive some basic organizing principles of circuit hodology at the mesoscale, microscale, and nanoscale. Specifically, we discuss how a host of light microscopy techniques including array tomography have been utilized to determine both long-range and subcellular organizing principles of synaptic connectivity. In addition, we discuss how new techniques, such as two-photon serial tomography of the entire mouse brain, have become attractive approaches to dissect the potential connectivity of defined cell types. Ultimately, principles derived from these techniques promise to facilitate a conceptual understanding of how connectomes, and neurocartography in general, can be effectively utilized toward reaching a mechanistic understanding of circuit function.

}, doi = {10.3389/fninf.2019.00052}, url = {https://www.frontiersin.org/article/10.3389/fninf.2019.00052/fullhttps://www.frontiersin.org/article/10.3389/fninf.2019.00052/full}, author = {Bloss, Erik B. and Hunt, David L.} } @article {65156, title = {RNA granules hitchhike on lysosomes for long-distance transport, Using annexin A11 as a molecular tether.}, journal = {Cell}, volume = {179}, year = {2019}, month = {2019 Sep 19}, pages = {147-164.e20}, abstract = {

Long-distance RNA transport enables local protein synthesis at metabolically-active sites distant from the nucleus. This process ensures an appropriate spatial organization of proteins, vital to polarized cells such as neurons. Here, we present a mechanism for RNA transport in which RNA granules "hitchhike" on moving lysosomes. In\ vitro biophysical modeling, live-cell microscopy, and unbiased proximity labeling proteomics reveal that annexin A11 (ANXA11), an RNA granule-associated phosphoinositide-binding protein, acts as a molecular tether between RNA granules and lysosomes. ANXA11 possesses an N-terminal low complexity domain, facilitating its phase separation into membraneless RNA granules, and a C-terminal membrane binding domain, enabling interactions with lysosomes. RNA granule transport requires ANXA11, and amyotrophic lateral sclerosis (ALS)-associated mutations in ANXA11 impair RNA granule transport by disrupting their interactions with lysosomes. Thus, ANXA11 mediates neuronal RNA transport by tethering RNA granules to actively-transported lysosomes, performing a critical cellular function that is disrupted in ALS.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2019.08.050}, author = {Liao, Ya-Cheng and Fernandopulle, Michael S and Wang, Guozhen and Choi, Heejun and Hao, Ling and Drerup, Catherine M and Patel, Rajan and Qamar, Seema and Nixon-Abell, Jonathon and Shen, Yi and Meadows, William and Vendruscolo, Michele and Knowles, Tuomas P J and Nelson, Matthew and Czekalska, Magdalena A and Musteikyte, Greta and Gachechiladze, Mariam A and Stephens, Christina A and Pasolli, H Amalia and Forrest, Lucy R and St George-Hyslop, Peter and Lippincott-Schwartz, Jennifer and Ward, Michael E} } @article {68754, title = {A Semi-high-throughput Imaging Method and Data Visualization Toolkit to Analyze C. elegans Embryonic Development}, journal = {Journal of Visualized Experiments}, year = {2019}, month = {10/2019}, abstract = {

C. elegans\ is the premier system for the systematic analysis of cell fate specification and morphogenetic events during embryonic development. One challenge is that embryogenesis dynamically unfolds over a period of about 13 h; this half day-long timescale has constrained the scope of experiments by limiting the number of embryos that can be imaged. Here, we describe a semi-high-throughput protocol that allows for the simultaneous 3D time-lapse imaging of development in 80{\textendash}100 embryos at moderate time resolution, from up to 14 different conditions, in a single overnight run. The protocol is straightforward and can be implemented by any laboratory with access to a microscope with point visiting capacity. The utility of this protocol is demonstrated by using it to image two custom-built strains expressing fluorescent markers optimized to visualize key aspects of germ-layer specification and morphogenesis. To analyze the data, a custom program that crops individual embryos out of a broader field of view in all channels, z-steps, and timepoints and saves the sequences for each embryo into a separate tiff stack was built. The program, which includes a user-friendly graphical user interface (GUI), streamlines data processing by isolating, pre-processing, and uniformly orienting individual embryos in preparation for visualization or automated analysis. Also supplied is an ImageJ macro that compiles individual embryo data into a multi-panel file that displays maximum intensity fluorescence projection and brightfield images for each embryo at each time point. The protocols and tools described herein were validated by using them to characterize embryonic development following knock-down of 40 previously described developmental genes; this analysis visualized previously annotated developmental phenotypes and revealed new ones. In summary, this work details a semi-high-throughput imaging method coupled with a cropping program and ImageJ visualization tool that, when combined with strains expressing informative fluorescent markers, greatly accelerates experiments to analyze embryonic development.

}, doi = {10.3791/60362}, url = {https://www.jove.com/t/60362/a-semi-high-throughput-imaging-method-data-visualization-toolkit-tohttps://www.jove.com/t/60362/a-semi-high-throughput-imaging-method-data-visualization-toolkit-to}, author = {Khaliullin, Renat N. and Hendel, Jeffrey M. and Gerson-Gurwitz, Adina and Wang, Shaohe and Ochoa, Stacy D. and Zhao, Zhiling and Desai, Arshad and Oegema, Karen and Green, Rebecca A.} } @article {65225, title = {ShuTu: Open-source software for efficient and accurate reconstruction of dendritic morphology.}, journal = {Frontiers in Neuroinformatics}, volume = {13}, year = {2019}, month = {2019 Oct 31}, pages = {68}, abstract = {

Neurons perform computations by integrating inputs from thousands of synapses-mostly in the dendritic tree-to drive action potential firing in the axon. One fruitful approach to studying this process is to record from neurons using patch-clamp electrodes, fill the recorded neurons with a substance that allows subsequent staining, reconstruct the three-dimensional architectures of the dendrites, and use the resulting functional and structural data to develop computer models of dendritic integration. Accurately producing quantitative reconstructions of dendrites is typically a tedious process taking many hours of manual inspection and measurement. Here we present ShuTu, a new software package that facilitates accurate and efficient reconstruction of dendrites imaged using bright-field microscopy. The program operates in two steps: (1) automated identification of dendritic processes, and (2) manual correction of errors in the automated reconstruction. This approach allows neurons with complex dendritic morphologies to be reconstructed rapidly and efficiently, thus facilitating the use of computer models to study dendritic structure-function relationships and the computations performed by single neurons.

}, issn = {1662-5196}, doi = {10.3389/fninf.2019.00068}, author = {Jin, Dezhe Z and Zhao, Ting and Hunt, David L and Tillage, Rachel P and Hsu, Ching-Lung and Spruston, Nelson} } @article {65113, title = {Software for lattice light-sheet imaging of FRET biosensors, illustrated with a new Rap1 biosensor.}, journal = {The Journal of Cell Biology}, volume = {218}, year = {2019}, month = {2019 Sep 2}, pages = {3153-3160}, abstract = {

Lattice light-sheet microscopy (LLSM) is valuable for its combination of reduced photobleaching and outstanding spatiotemporal resolution in 3D. Using LLSM to image biosensors in living cells could provide unprecedented visualization of rapid, localized changes in protein conformation or posttranslational modification. However, computational manipulations required for biosensor imaging with LLSM are challenging for many software packages. The calculations require processing large amounts of data even for simple changes such as reorientation of cell renderings or testing the effects of user-selectable settings, and lattice imaging poses unique challenges in thresholding and ratio imaging. We describe here a new software package, named ImageTank, that is specifically designed for practical imaging of biosensors using LLSM. To demonstrate its capabilities, we use a new biosensor to study the rapid 3D dynamics of the small GTPase Rap1 in vesicles and cell protrusions.

}, issn = {0021-9525}, doi = {10.1083/jcb.201903019}, url = {http://www.jcb.org/lookup/doi/10.1083/jcb.201903019}, author = {O{\textquoteright}Shaughnessy, Ellen C. and Stone, Orrin J. and LaFosse, Paul K. and Azoitei, Mihai L. and Tsygankov, Denis and Heddleston, John M. and Legant, Wesley R. and Wittchen, Erika S. and Burridge, Keith and Elston, Timothy C. and Betzig, Eric and Chew, Teng-Leong and Adalsteinsson, David and Hahn, Klaus M.} } @article {64795, title = {Spastin tethers lipid droplets to peroxisomes and directs fatty acid trafficking through ESCRT-III.}, journal = {Journal of Cell Biology}, volume = {218}, year = {2019}, month = {2019 Jun 21}, pages = {2583-99}, abstract = {

Lipid droplets (LDs) are neutral lipid storage organelles that transfer lipids to various organelles including peroxisomes. Here, we show that the hereditary spastic paraplegia protein M1 Spastin, a membrane-bound AAA ATPase found on LDs, coordinates fatty acid (FA) trafficking from LDs to peroxisomes through two inter-related mechanisms. First, M1 Spastin forms a tethering complex with peroxisomal ABCD1 to promote LD-peroxisome contact formation. Second, M1 Spastin recruits the membrane-shaping ESCRT-III proteins IST1 and CHMP1B to LDs via its MIT domain to facilitate LD-to-peroxisome FA trafficking, possibly through IST1 and CHMP1B modifying LD membrane morphology. Furthermore, M1 Spastin, IST1 and CHMP1B are all required to relieve LDs of lipid peroxidation. The roles of M1 Spastin in tethering LDs to peroxisomes and in recruiting ESCRT-III components to LD-peroxisome contact sites for FA trafficking may help explain the pathogenesis of diseases associated with defective FA metabolism in LDs and peroxisomes.

}, doi = {10.1101/544023}, author = {Chang, Chi-Lun and Weigel, Aubrey V and Ioannou, Maria S and Pasolli, H Amalia and Xu, C Shan and Peale, David R and Shtengel, Gleb and Freeman, Melanie and Hess, Harald F and Blackstone, Craig and Lippincott-Schwartz, Jennifer} } @article {65226, title = {Spatiotemporal constraints on optogenetic inactivation in cortical circuits.}, journal = {eLife}, volume = {8}, year = {2019}, month = {2019 Nov 18}, abstract = {

Optogenetics allows manipulations of genetically and spatially defined neuronal populations with excellent temporal control. However, neurons are coupled with other neurons over multiple length scales, and the effects of localized manipulations thus spread beyond the targeted neurons. We benchmarked several optogenetic methods to inactivate small regions of neocortex. Optogenetic excitation of GABAergic neurons produced more effective inactivation than light-gated ion pumps. Transgenic mice expressing the light-dependent chloride channel GtACR1 produced the most potent inactivation. Generally, inactivation spread substantially beyond the photostimulation light, caused by strong coupling between cortical neurons. Over some range of light intensity, optogenetic excitation of inhibitory neurons reduced activity in these neurons, together with pyramidal neurons, a signature of inhibition-stabilized neural networks ({\textquoteright}paradoxical effect{\textquoteright}). The offset of optogenetic inactivation was followed by rebound excitation in a light dose-dependent manner, limiting temporal resolution. Our data offer guidance for the design of optogenetics experiments.

}, issn = {2050-084X}, doi = {10.7554/eLife.48622}, author = {Li, Nuo and Chen, Susu and Guo, Zengcai V and Chen, Han and Huo, Yan and Inagaki, Hidehiko K and Chen, Guang and Davis, Courtney and Hansel, David and Guo, Caiying and Svoboda, Karel} } @article {49187, title = {Spontaneous behaviors drive multidimensional, brain-wide population activity.}, journal = {Science}, volume = {364}, year = {2019}, month = {2019 Apr 18}, pages = {255}, abstract = {

Sensory cortices are active in the absence of external sensory stimuli. To understand the nature of this ongoing activity, we used two-photon calcium imaging to record from over 10,000 neurons in the visual cortex of mice awake in darkness while monitoring their behavior videographically. Ongoing population activity was multidimensional, exhibiting at least 100 significant dimensions, some of which were related to the spontaneous behaviors of the mice. The largest single dimension was correlated with the running speed and pupil area, while a 16-dimensional summary of orofacial behaviors could predict ~45\% of the explainable neural variance. Electrophysiological recordings with 8 simultaneous Neuropixels probes revealed a similar encoding of high-dimensional orofacial behaviors across multiple forebrain regions. Representation of motor variables continued uninterrupted during visual stimulus presentation, occupying dimensions nearly orthogonal to the stimulus responses. Our results show that a multidimensional representation of motor state is encoded across the forebrain, and is integrated with visual input by neuronal populations in primary visual cortex.

}, doi = {10.1101/306019}, author = {Stringer, Carsen and Pachitariu, Marius and Steinmetz, Nicholas A and Reddy, Charu Bai and Carandini, Matteo and Harris, Kenneth D} } @article {56203, title = {Structural basis for substrate binding and specificity of a sodium-alanine symporter AgcS.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, year = {2019}, month = {2019 Jan 18}, pages = {2086-90}, abstract = {

The amino acid, polyamine, and organocation (APC) superfamily is the second largest superfamily of membrane proteins forming secondary transporters that move a range of organic molecules across the cell membrane. Each transporter in the APC superfamily is specific for a unique subset of substrates, even if they possess a similar structural fold. The mechanism of substrate selectivity remains, by and large, elusive. Here, we report two crystal structures of an APC member from , the alanine or glycine:cation symporter (AgcS), with l- or d-alanine bound. Structural analysis combined with site-directed mutagenesis and functional studies inform on substrate binding, specificity, and modulation of the AgcS family and reveal key structural features that allow this transporter to accommodate glycine and alanine while excluding all other amino acids. Mutation of key residues in the substrate binding site expand the selectivity to include valine and leucine. These studies provide initial insights into substrate selectivity in AgcS symporters.

}, issn = {1091-6490}, doi = {10.1073/pnas.1806206116}, author = {Ma, Jinming and Lei, Hsiang-Ting and Reyes, Francis E and Sanchez-Martinez, Silvia and Sarhan, Maen F and Hattne, Johan and Gonen, Tamir} } @article {65260, title = {Structure of an endosomal signaling GPCR-G protein-β-arrestin megacomplex.}, journal = {Nature Structural and Molecular Biology}, volume = {26}, year = {2019}, month = {2019 Dec 26}, pages = {1123-1131}, abstract = {

Classically, G-protein-coupled receptors (GPCRs) are thought to activate G protein from the plasma membrane and are subsequently desensitized by β-arrestin (β-arr). However, some GPCRs continue to signal through G protein from internalized compartments, mediated by a GPCR-G protein-β-arr {\textquoteright}megaplex{\textquoteright}. Nevertheless, the molecular architecture of the megaplex remains unknown. Here, we present its cryo-electron microscopy structure, which shows simultaneous engagement of human G protein and bovine β-arr to the core and phosphorylated tail, respectively, of a single active human chimeric β-adrenergic receptor with the C-terminal tail of the arginine vasopressin type 2 receptor (βVR). All three components adopt their canonical active conformations, suggesting that a single megaplex GPCR is capable of simultaneously activating G protein and β-arr. Our findings provide a structural basis for GPCR-mediated sustained internalized G protein signaling.

}, issn = {1545-9985}, doi = {10.1038/s41594-019-0330-y}, author = {Nguyen, Anthony H and Thomsen, Alex R B and Cahill, Thomas J and Huang, Rick and Huang, Li-Yin and Marcink, Tara and Clarke, Oliver B and Heissel, S{\o}ren and Masoudi, Ali and Ben-Hail, Danya and Samaan, Fadi and Dandey, Venkata P and Tan, Yong Zi and Hong, Chuan and Mahoney, Jacob P and Triest, Sarah and Little, John and Chen, Xin and Sunahara, Roger and Steyaert, Jan and Molina, Henrik and Yu, Zhiheng and des Georges, Amedee and Lefkowitz, Robert J} } @article {65109, title = {T3S injectisome needle complex structures in four distinct states reveal the basis of membrane coupling and assembly.}, journal = {Nature Microbiology}, volume = {4}, year = {2019}, month = {2019 Aug}, pages = {2010-19}, abstract = {

The bacterial injectisome is a syringe-shaped macromolecular nanomachine utilized by many pathogenic Gram-negative bacteria, including the causative agents of plague, typhoid fever, whooping cough, sexually transmitted infections and major nosocomial infections. Bacterial proteins destined for self-assembly and host-cell targeting are translocated by the injectisome in a process known as type III secretion (T3S). The core structure is the ~4 MDa needle complex (NC), built on a foundation of three highly oligomerized ring-forming proteins that create a hollow scaffold spanning the bacterial inner membrane (IM) (24-mer ring-forming proteins PrgH and PrgK in the\ Salmonella entericaserovar Typhimurium\ Salmonella\ pathogenicity island 1 (SPI-1) type III secretion system (T3SS)) and outer membrane (OM) (15-mer InvG, a member of the broadly conserved secretin pore family). An internalized helical needle projects from the NC and bacterium, ultimately forming a continuous passage to the host, for delivery of virulence effectors. Here, we have captured snapshots of the entire prototypical SPI-1 NC in four distinct needle assembly states, including near-atomic resolution, and local reconstructions in the absence and presence of the needle. These structures reveal the precise localization and molecular interactions of the internalized SpaPQR {\textquoteleft}export apparatus{\textquoteright} complex, which is intimately encapsulated and stabilized within the IM rings in the manner of a nanodisc, and to which the PrgJ rod directly binds and functions as an initiator and anchor of needle polymerization. We also describe the molecular details of the extensive and continuous coupling interface between the OM secretin and IM rings, which is remarkably facilitated by a localized 16-mer stoichiometry in the periplasmic-most coupling domain of the otherwise 15-mer InvG oligomer.

}, doi = {10.1038/s41564-019-0545-z}, url = {http://www.nature.com/articles/s41564-019-0545-zhttp://www.nature.com/articles/s41564-019-0545-z.pdfhttp://www.nature.com/articles/s41564-019-0545-z.pdfhttp://www.nature.com/articles/s41564-019-0545-z}, author = {Hu, Jinhong and Worrall, Liam J. and Vuckovic, Marija and Hong, Chuan and Deng, Wanyin and Atkinson, Claire E. and Brett Finlay, B. and Yu, Zhiheng and Strynadka, Natalie C. J.} } @article {64943, title = {Time-variant SRC kinase activation determines endothelial permeability response.}, journal = {Cell Chemical Biology}, volume = {26}, year = {2019}, month = {2019 Aug 15}, pages = {1081-94}, abstract = {

In the current model of endothelial barrier regulation, the tyrosine kinase SRC is purported to induce disassembly of endothelial adherens junctions (AJs) via\ phosphorylation of VE cadherin, and thereby increase\ junctional permeability. Here, using a chemical biology approach to temporally control SRC activation,\ we show that SRC exerts distinct time-variant effects on the endothelial barrier. We discovered that the immediate effect of SRC activation was to transiently enhance endothelial barrier function as the result of accumulation of VE cadherin at AJs and formation of morphologically distinct reticular AJs. Endothelial barrier enhancement via SRC required phosphorylation of VE cadherin at Y731. In contrast, prolonged SRC activation induced VE cadherin phosphorylation at Y685, resulting in increased endothelial permeability. Thus, time-variant SRC activation differentially phosphorylates VE cadherin and shapes AJs to fine-tune endothelial barrier function. Our work demonstrates important advantages of synthetic biology tools in dissecting complex signaling systems.

}, issn = {2451-9448}, doi = {10.1016/j.chembiol.2019.04.007}, author = {Klomp, Jennifer E and Shaaya, Mark and Matsche, Jacob and Rebiai, Rima and Aaron, Jesse S and Collins, Kerrie B and Huyot, Vincent and Gonzalez, Annette M and Muller, William A and Chew, Teng-Leong and Malik, Asrar B and Karginov, Andrei V} } @article {64840, title = {Ultrapotent chemogenetics for research and potential clinical applications.}, journal = {Science}, volume = {364}, year = {2019}, month = {2019 Mar 14}, pages = {eaav5282}, abstract = {

Chemogenetics enables non-invasive chemical control over cell populations in behaving animals. However, existing small molecule agonists show insufficient potency or selectivity. There is also need for chemogenetic systems compatible with both research and human therapeutic applications. We developed a new ion channel-based platform for cell activation and silencing that is controlled by low doses of the anti-smoking drug varenicline. We then synthesized novel sub-nanomolar potency agonists, called uPSEMs, with high selectivity for the chemogenetic receptors. uPSEMs and their receptors were characterized in brains of mice and a rhesus monkey by in vivo electrophysiology, calcium imaging, positron emission tomography, behavioral efficacy testing, and receptor counterscreening. This platform of receptors and selective ultrapotent agonists enables potential research and clinical applications of chemogenetics.

}, issn = {1095-9203}, doi = {10.1126/science.aav5282}, author = {Magnus, Christopher J and Lee, Peter H and Bonaventura, Jordi and Zemla, Roland and Gomez, Juan L and Ramirez, Melissa H and Hu, Xing and Galvan, Adriana and Basu, Jayeeta and Michaelides, Michael and Sternson, Scott M} } @article {64905, title = {Visually guided behavior and optogenetically induced learning in head-fixed flies exploring a virtual landscape.}, journal = {Current Biology : CB}, year = {2019}, month = {2019 Apr 29}, abstract = {

Studying the intertwined roles of sensation, experience, and directed action in navigation has been facilitated by the development of virtual reality (VR) environments for head-fixed animals, allowing for quantitative measurements of behavior in well-controlled conditions. VR has long featured in studies of Drosophila melanogaster, but these experiments have typically allowed the fly to change only its heading in a visual scene and not its position. Here we explore how flies move in two dimensions (2D) using a visual VR environment that more closely captures an animal{\textquoteright}s experience during free behavior. We show that flies{\textquoteright} 2D interaction with landmarks cannot be automatically derived from their orienting behavior under simpler one-dimensional (1D) conditions. Using novel paradigms, we then demonstrate that flies in 2D VR adapt their behavior in response to optogenetically delivered appetitive and aversive stimuli. Much like free-walking flies after encounters with food, head-fixed flies exploring a 2D VR respond to optogenetic activation of sugar-sensing neurons by initiating a local search, which appears not to rely on visual landmarks. Visual landmarks can, however, help flies to avoid areas in VR where they experience an aversive, optogenetically generated heat stimulus. By coupling aversive virtual heat to the flies{\textquoteright} presence near visual landmarks of specific shapes, we elicit selective learned avoidance of those landmarks. Thus, we demonstrate that head-fixed flies adaptively navigate in 2D virtual environments, but their reliance on visual landmarks is context dependent. These behavioral paradigms set the stage for interrogation of the fly brain circuitry underlying flexible navigation in complex multisensory environments.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2019.04.033}, author = {Haberkern, Hannah and Basnak, Melanie A and Ahanonu, Biafra and Schauder, David and Cohen, Jeremy D and Bolstad, Mark and Bruns, Christopher and Jayaraman, Vivek} } @article {49416, title = {4D cell biology: big data image analytics and lattice light-sheet imaging reveal dynamics of clathrin-mediated endocytosis in stem cell derived intestinal organoids.}, journal = {Molecular Biology of the Cell}, year = {2018}, month = {2018 Sep 06}, pages = {mbcE18060375}, abstract = {

New methods in stem cell 3D organoid tissue culture, advanced imaging and big data image analytics now allow tissue scale 4D cell biology, but currently available analytical pipelines are inadequate for handing and analyzing the resulting gigabytes and terabytes of high-content imaging data. We expressed fluorescent protein fusions of clathrin and dynamin2 at endogenous levels in genome-edited human embryonic stem cells, which were differentiated into hESC-derived intestinal epithelial organoids. Lattice Light-Sheet Imaging with adaptive optics (AO-LLSM) allowed us to image large volumes of these organoids (70{\textmu}m x 60{\textmu}m x 40{\textmu}m xyz) at 5.7s/frame. We developed an open source data analysis package termed pyLattice to process the resulting large (\~{}60Gb) movie datasets and to track clathrin-mediated endocytosis (CME) events. CME tracks could be recorded from \~{}35 cells at a time, resulting in \~{}4000 processed tracks per movie. Based on their localization in the organoid, we classified CME tracks into apical, lateral and basal events and found that CME dynamics are similar for all three classes, despite reported differences in membrane tension. pyLattice coupled with AO-LLSM makes possible quantitative, high temporal and spatial resolution analysis of subcellular events within tissues. Movie S1 Movie S1 Thresholded 3D AO-LLSM data of an intestinal epithelial organoid showing clathrin (red) and dynamin2 (green) puncta in surface depiction. The movie zooms out from a single clathrin mediated endocytosis event that shows both clathrin and dynamin2 at the same location to eventually show the whole AO-LLSM field of view. Nuclear envelopes and the outer membranes of the tissue are depicted in transparent white. Movie S2 Movie S2 Thresholded 3D AO-LLSM data of an intestinal epithelial organoid showing clathrin (red) and dynamin2 (green) puncta in surface depiction. The movie rotates the AO-LLSM field of view. Nuclear envelopes and the outer membranes of the tissue are depicted in transparent white. Movie S3 Movie S3 Thresholded 3D AO-LLSM data of an intestinal epithelial organoid. The curved surface is of the spherical organoid is visible as the movie rotates. Clathrin puncta are visible throughout the tissue (white). Movie S4 Movie S4 The detection step in the data processing pipeline retrieves all clathrin puncta in the volume. Detected puncta are marked with a cube (blue). Movie S5 Movie S5 Zoom on one clathrin puncta in the thresholded 3D dataset. The punctum of interest is marked with a blue cube. Other puncta are also visible. Movie S6 Movie S6 Zoom on the same clathrin puncta as in M3 in non-thresholded 3D data. The surrounding fluorescence is visible as a transparent cloud.

}, issn = {1939-4586}, doi = {10.1091/mbc.E18-06-0375}, author = {Sch{\"o}neberg, Johannes and Dambournet, Daphne and Liu, Tsung-Li and Forster, Ryan and Hockemeyer, Dirk and Betzig, Eric and Drubin, David G} } @article {49341, title = {The actin cytoskeletal architecture of estrogen receptor positive breast cancer cells suppresses invasion.}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {2018 Jul 30}, pages = {2980}, abstract = {

Estrogen promotes growth of estrogen receptor-positive (ER+) breast tumors. However, epidemiological studies examining the prognostic characteristics of breast cancer in postmenopausal women receiving hormone replacement therapy reveal a significant decrease in tumor dissemination, suggesting that estrogen has potential protective effects against cancer cell invasion. Here, we show that estrogen suppresses invasion of ER+ breast cancer cells by increasing transcription of the Ena/VASP protein, EVL, which promotes the generation of suppressive cortical actin bundles that inhibit motility dynamics, and is crucial for the ER-mediated suppression of invasion in vitro and in vivo. Interestingly, despite its benefits in suppressing tumor growth, anti-estrogenic endocrine therapy decreases EVL expression and increases local invasion in patients. Our results highlight the dichotomous effects of estrogen on tumor progression and suggest that, in contrast to its established role in promoting growth of ER+ tumors, estrogen has a significant role in suppressing invasion through actin cytoskeletal remodeling.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-05367-2}, author = {Padilla-Rodriguez, Marco and Parker, Sara S and Adams, Deanna G and Westerling, Thomas and Puleo, Julieann I and Watson, Adam W and Hill, Samantha M and Noon, Muhammad and Gaudin, Rapha{\"e}l and Aaron, Jesse and Tong, Daoqin and Roe, Denise J and Knudsen, Beatrice and Mouneimne, Ghassan} } @article {49477, title = {Active dendritic integration and mixed neocortical network representations during an adaptive sensing behavior.}, journal = {Nature Neuroscience}, volume = {21}, year = {2018}, month = {2018 Oct 22}, pages = {1583-90}, abstract = {

Animals strategically scan the environment to form an accurate perception of their surroundings. Here we investigated the neuronal representations that mediate this behavior. Ca imaging and selective optogenetic manipulation during an active sensing task reveals that layer 5 pyramidal neurons in the vibrissae cortex produce a diverse and distributed representation that is required for mice to adapt their whisking motor strategy to changing sensory cues. The optogenetic perturbation degraded single-neuron selectivity and network population encoding through a selective inhibition of active dendritic integration. Together the data indicate that active dendritic integration in pyramidal neurons produces a nonlinearly mixed network representation of joint sensorimotor parameters that is used to transform sensory information into motor commands during adaptive behavior. The prevalence of the layer 5 cortical circuit motif suggests that this is a general circuit computation.

}, issn = {1546-1726}, doi = {10.1038/s41593-018-0254-6}, author = {Ranganathan, Gayathri N and Apostolides, Pierre F and Harnett, Mark T and Xu, Ning-long and Druckmann, Shaul and Magee, Jeffrey C} } @article {49311, title = {Adaptive coding for dynamic sensory inference.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Jul 10}, abstract = {

Behavior relies on the ability of sensory systems to infer properties of the environment from incoming stimuli. The accuracy of inference depends on the fidelity with which behaviorally relevant properties of stimuli are encoded in neural responses. High-fidelity encodings can be metabolically costly, but low-fidelity encodings can cause errors in inference. Here, we discuss general principles that underlie the tradeoff between encoding cost and inference error. We then derive adaptive encoding schemes that dynamically navigate this tradeoff. These optimal encodings tend to increase the fidelity of the neural representation following a change in the stimulus distribution, and reduce fidelity for stimuli that originate from a known distribution. We predict dynamical signatures of such encoding schemes and demonstrate how known phenomena, such as burst coding and firing rate adaptation, can be understood as hallmarks of optimal coding for accurate inference.

}, issn = {2050-084X}, doi = {10.7554/eLife.32055}, author = {M{\l}ynarski, Wiktor F and Hermundstad, Ann M} } @article {49180, title = {Analysis of global and site-specific radiation damage in cryo-EM.}, journal = {Structure (London, England : 1993)}, volume = {26}, year = {2018}, month = {2018 Apr 18}, pages = {759-66}, abstract = {

Micro-crystal electron diffraction (MicroED) combines the efficiency of electron scattering with diffraction to allow structure determination from nano-sized crystalline samples in cryoelectron microscopy (cryo-EM). It has been used to solve structures of a diverse set of biomolecules and materials, in some cases to sub-atomic resolution. However, little is known about the damaging effects of the electron beam on samples during such measurements. We assess global and site-specific damage from electron radiation on nanocrystals of proteinase K and of a prion hepta-peptide and find that the dynamics of electron-induced damage follow well-established trends observed in X-ray crystallography. Metal ions are perturbed, disulfide bonds are broken, and acidic side chains are decarboxylated while the\ diffracted intensities decay exponentially with increasing exposure. A better understanding of radiation damage in MicroED improves our assessment and processing of all types of cryo-EM data.

}, issn = {1878-4186}, doi = {10.1016/j.str.2018.03.021}, author = {Hattne, Johan and Shi, Dan and Glynn, Calina and Zee, Chih-Te and Gallagher-Jones, Marcus and Martynowycz, Michael W and Rodriguez, Jose A and Gonen, Tamir} } @article {49316, title = {Apical and basal matrix remodeling control epithelial morphogenesis.}, journal = {Developmental Cell}, volume = {46}, year = {2018}, month = {2018 Jul 02}, pages = {23-39.e5}, abstract = {

Epithelial tissues can elongate in two dimensions by polarized cell intercalation, oriented cell division, or cell shape change, owing to local or global actomyosin contractile forces acting in the plane of the tissue. In addition, epithelia can undergo morphogenetic change in three dimensions. We show that elongation of the wings and legs of Drosophila involves a columnar-to-cuboidal cell shape change that reduces cell height and expands cell width. Remodeling of the apical extracellular matrix by the Stubble protease and basal matrix by MMP1/2 proteases induces wing and leg elongation. Matrix remodeling does not occur in the haltere, a limb that fails to elongate. Limb elongation is made anisotropic by planar polarized Myosin-II, which drives convergent extension along the proximal-distal axis. Subsequently, Myosin-II relocalizes to lateral membranes to accelerate columnar-to-cuboidal transition and isotropic tissue expansion. Thus, matrix remodeling induces dynamic changes in actomyosin contractility\ to drive epithelial morphogenesis in three dimensions.

}, issn = {1878-1551}, doi = {10.1016/j.devcel.2018.06.006}, author = {Diaz-de-la-Loza, Maria-Del-Carmen and Ray, Robert P and Ganguly, Poulami S and Alt, Silvanus and Davis, John R and Hoppe, Andreas and Tapon, Nic and Salbreux, Guillaume and Thompson, Barry J} } @article {49123, title = {Architecture of the human GATOR1 and GATOR1-Rag GTPases complexes.}, journal = {Nature}, volume = {556}, year = {2018}, month = {2018 Mar 28}, pages = {64-9}, abstract = {

Nutrients, such as amino acids and glucose, signal through the Rag GTPases to activate mTORC1. The GATOR1 protein complex-comprising DEPDC5, NPRL2 and NPRL3-regulates the Rag GTPases as a GTPase-activating protein (GAP) for RAGA; loss of GATOR1 desensitizes mTORC1 signalling to nutrient starvation. GATOR1 components have no sequence homology to other proteins, so the function of GATOR1 at the molecular level is currently unknown. Here we used cryo-electron microscopy to solve structures of GATOR1 and GATOR1-Rag GTPases complexes. GATOR1 adopts an extended architecture with a cavity in the middle; NPRL2 links DEPDC5 and NPRL3, and DEPDC5 contacts the Rag GTPase heterodimer. Biochemical analyses reveal that our GATOR1-Rag GTPases structure is inhibitory, and that at least two binding modes must exist between the Rag GTPases and GATOR1. Direct interaction of DEPDC5 with RAGA inhibits GATOR1-mediated stimulation of GTP hydrolysis by RAGA, whereas weaker interactions between the NPRL2-NPRL3 heterodimer and RAGA execute GAP activity. These data reveal the structure of a component of the nutrient-sensing mTORC1 pathway and a non-canonical interaction between a GAP and its substrate GTPase.

}, issn = {1476-4687}, doi = {10.1038/nature26158}, author = {Shen, Kuang and Huang, Rick K and Brignole, Edward J and Condon, Kendall J and Valenstein, Max L and Chantranupong, Lynne and Bomaliyamu, Aimaiti and Choe, Abigail and Hong, Chuan and Yu, Zhiheng and Sabatini, David M} } @article {49056, title = {BAK/BAX macropores facilitate mitochondrial herniation and mtDNA efflux during apoptosis.}, journal = {Science (New York, N.Y.)}, volume = {359}, year = {2018}, month = {2018 02 23}, abstract = {

Mitochondrial apoptosis is mediated by BAK and BAX, two proteins that induce mitochondrial outer membrane permeabilization, leading to cytochrome c release and activation of apoptotic caspases. In the absence of active caspases, mitochondrial DNA (mtDNA) triggers the innate immune cGAS/STING pathway, causing dying cells to secrete type I interferon. How cGAS gains access to mtDNA remains unclear. We used live-cell lattice light-sheet microscopy to examine the mitochondrial network in mouse embryonic fibroblasts. We found that after BAK/BAX activation and cytochrome c loss, the mitochondrial network broke down and large BAK/BAX pores appeared in the outer membrane. These BAK/BAX macropores allowed the inner mitochondrial membrane to herniate into the cytosol, carrying with it mitochondrial matrix components, including the mitochondrial genome. Apoptotic caspases did not prevent herniation but dismantled the dying cell to suppress mtDNA-induced innate immune signaling.

}, issn = {1095-9203}, doi = {10.1126/science.aao6047}, author = {McArthur, Kate and Whitehead, Lachlan W and Heddleston, John M and Li, Lucy and Padman, Benjamin S and Oorschot, Viola and Geoghegan, Niall D and Chappaz, Stephane and Davidson, Sophia and San Chin, Hui and Lane, Rachael M and Dramicanin, Marija and Saunders, Tahnee L and Sugiana, Canny and Lessene, Romina and Osellame, Laura D and Chew, Teng-Leong and Dewson, Grant and Lazarou, Michael and Ramm, Georg and Lessene, Guillaume and Ryan, Michael T and Rogers, Kelly L and van Delft, Mark F and Kile, Benjamin T} } @article {49535, title = {Brain-wide circuit interrogation at the cellular level guided by online analysis of neuronal function.}, journal = {Nature Methods}, volume = {15}, year = {2018}, month = {2018 Nov 30}, pages = {1117-1125}, abstract = {

Whole-brain imaging allows for comprehensive functional mapping of distributed neural pathways, but neuronal perturbation experiments are usually limited to targeting predefined regions or genetically identifiable cell types. To complement whole-brain measures of activity with brain-wide manipulations for testing causal interactions, we introduce a system that uses measuredactivity patterns to guide optical perturbations of any subset of neurons in the same fictively behaving larval zebrafish. First, a light-sheet microscope collects whole-brain data that are rapidly analyzed by a distributed computing system to generate functional brain maps. On the basis of these maps, the experimenter can then optically ablate neurons and image activity changes across the brain. We applied this method to characterize contributions of behaviorally tuned populations to the optomotor response. We extended the system to optogenetically stimulate arbitrary subsets of neurons during whole-brain imaging. These open-source methods enable delineating the contributions of neurons to brain-wide circuit dynamics and behavior in individual animals.

}, doi = {10.1038/s41592-018-0221-x}, author = {Vladimirov, Nikita and Wang, Chen and H{\"o}ckendorf, Burkhard and Pujala, Avinash and Tanimoto, Masashi and Mu, Yu and Yang, Chao-Tsung and Wittenbach, Jason and Freeman, Jeremy and Preibisch, Stephan and Koyama, Minoru and Keller, Philipp J and Ahrens, Misha B} } @article {49520, title = {Brain-wide organization of neuronal activity and convergent sensorimotor transformations in larval zebrafish.}, journal = {Neuron}, volume = {100}, year = {2018}, month = {2018 Nov 21}, pages = {876-890.e5}, abstract = {

Simultaneous recordings of large populations of neurons in behaving animals allow detailed observation of high-dimensional, complex brain activity. However, experimental approaches often focus on singular behavioral paradigms or brain areas. Here, we recorded whole-brain neuronal activity of larval zebrafish presented with a battery of visual stimuli while recording fictive motor output. We identified neurons tuned to each stimulus type and motor output and discovered groups of neurons in the anterior hindbrain that respond to different stimuli eliciting similar behavioral responses. These convergent sensorimotor representations were only weakly correlated to instantaneous motor activity, suggesting that they critically inform, but do not directly generate, behavioral choices. To catalog brain-wide activity beyond explicit sensorimotor processing, we developed an unsupervised clustering technique that organizes neurons into functional groups. These analyses enabled a broad overview of the functional organization of the brain and revealed numerous brain nuclei whose neurons exhibit concerted activity patterns.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2018.09.042}, author = {Chen, Xiuye and Mu, Yu and Hu, Yu and Kuan, Aaron T and Nikitchenko, Maxim and Randlett, Owen and Chen, Alex B and Gavornik, Jeffery P and Sompolinsky, Haim and Engert, Florian and Ahrens, Misha B} } @article {49061, title = {Cell type-specific variation of somatotopic precision across corticostriatal projections. }, journal = {bioRxiv}, year = {2018}, month = {2018 Feb 7}, abstract = {

The striatum shows general topographic organization and regional differences in behavioral functions. How corticostriatal topography differs across cortical areas and cell types to support these distinct functions is unclear. This study contrasted corticostriatal projections from two layer 5 cell types, intratelencephalic (IT-type) and pyramidal tract (PT-type) neurons, using viral vectors expressing fluorescent reporters in Cre-driver mice. Long-range corticostriatal projections from sensory and motor cortex are somatotopic, with a decreasing somatotopic specificity as injections move from sensory to motor and frontal areas. Somatotopic organization differs between IT-type and PT-type neurons, including injections in the same site, with IT-type neurons having higher somatotopic stereotypy than PT-type neurons. Furthermore, IT-type projections from interconnected cortical areas have stronger correlations in corticostriatal targeting than PT-type projections do. Thus, as predicted by a long-standing basal ganglia model, corticostriatal projections of interconnected cortical areas form parallel circuits in basal ganglia-thalamus-cortex loops.

}, doi = {10.1101/261446}, author = {Hooks, Bryan M and Papale, Andrew E and Paletzki, Ronald and Feroze, Muhammad and Eastwood, Brian S and Couey, Jonathan J and Winnubst, Johan and Chandrashekar, Jayaram and Gerfen, Charles R} } @article {65772, title = {Circularly Permuted Fluorogenic Proteins for the Design of Modular Biosensors.}, journal = {ACS Chemical Biology}, volume = {13}, year = {2018}, month = {09/2018}, pages = {2392 {\textendash} 2397}, abstract = {

Fluorescent reporters are essential components for the design of optical biosensors that are able to image intracellular analytes in living cells. Herein, we describe the development of circularly permuted variants of Fluorescence-Activating and absorption-Shifting Tag (FAST) and demonstrate their potential as reporting module in biosensors. Circularly permutated FAST (cpFAST) variants allow one to condition the binding and activation of a fluorogenic ligand (and thus fluorescence) to analyte recognition by coupling them with analyte-binding domains. We demonstrated their use for biosensor design by generating multicolor plug-and-play fluorogenic biosensors for imaging the intracellular levels of Ca2+ in living mammalian cells in real time.

}, doi = {10.1021/acschembio.8b00417}, author = {Tebo, Alison G and Pimenta, Frederico M and Zoumpoulaki, Martha and Kikuti, Carlos and Sirkia, Helena and Plamont, Marie-Aude and Houdusse, Anne and Gautier, Arnaud} } @article {49434, title = {Communication from learned to innate olfactory processing centers is required for memory retrieval in Drosophila.}, journal = {Neuron}, volume = {100}, year = {2018}, month = {2018 Sep 19}, pages = {651-68}, abstract = {

The behavioral response to a sensory stimulus may depend on both learned and innate neuronal representations. How these circuits interact to produce appropriate behavior is unknown. In Drosophila, the lateral horn (LH) and mushroom body (MB) are thought to mediate innate and learned olfactory behavior, respectively, although LH function has not been tested directly. Here we identify two LH cell types (PD2a1 and PD2b1) that receive input from an MB output neuron required for recall of aversive olfactory memories. These neurons are required for aversive memory retrieval and modulated by training. Connectomics data demonstrate that PD2a1 and PD2b1 neurons also receive direct input from food odor-encoding neurons. Consistent with this, PD2a1 and PD2b1 are also necessary for unlearned attraction to some odors, indicating that these neurons have a dual behavioral role. This provides a circuit mechanism by which learned and innate olfactory information can interact in identified neurons to produce appropriate behavior.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2018.08.037}, author = {Dolan, Michael-John and Belliart-Gu{\'e}rin, Ghislain and Bates, Alexander Shakeel and Frechter, Shahar and Lampin-Saint-Amaux, Aur{\'e}lie and Aso, Yoshinori and Roberts, Ruair{\'\i} J V and Schlegel, Philipp and Wong, Allan and Hammad, Adnan and Bock, Davi and Rubin, Gerald M and Preat, Thomas and Placais, Pierre-Yves and Jefferis, Gregory S X E} } @article {67219, title = {Community-based benchmarking improves spike rate inference from two-photon calcium imaging data}, journal = {PLOS Computational Biology}, volume = {14}, year = {2018}, month = {Sep-05-2019}, pages = {e1006157}, abstract = {

In recent years, two-photon calcium imaging has become a standard tool to probe the function of neural circuits and to study computations in neuronal populations. However, the acquired signal is only an indirect measurement of neural activity due to the comparatively slow dynamics of fluorescent calcium indicators. Different algorithms for estimating spike rates from noisy calcium measurements have been proposed in the past, but it is an open question how far performance can be improved. Here, we report the results of the\ spikefinder\ challenge, launched to catalyze the development of new spike rate inference algorithms through crowd-sourcing. We present ten of the submitted algorithms which show improved performance compared to previously evaluated methods. Interestingly, the top-performing algorithms are based on a wide range of principles from deep neural networks to generative models, yet provide highly correlated estimates of the neural activity. The competition shows that benchmark challenges can drive algorithmic developments in neuroscience.

}, doi = {10.1371/journal.pcbi.1006157}, url = {https://journals.plos.org/ploscompbiol/article?rev=2\&id=10.1371/journal.pcbi.1006157}, author = {Berens, Philipp and Freeman, Jeremy and Deneux, Thomas and Chenkov, Nikolay and McColgan, Thomas and Speiser, Artur and Macke, Jakob H. and Turaga, Srinivas C. and Mineault, Patrick and Rupprecht, Peter and Gerhard, Stephan and Friedrich, Rainer W. and Friedrich, Johannes and Paninski, Liam and Pachitariu, Marius and Harris, Kenneth D. and Bolte, Ben and Machado, Timothy A. and Ringach, Dario and Stone, Jasmine and Rogerson, Luke E. and Sofroniew, Nicolas J. and Reimer, Jacob and Froudarakis, Emmanouil and Euler, Thomas and Rom{\'a}n Ros{\'o}n, Miroslav and Theis, Lucas and Tolias, Andreas S. and Bethge, Matthias}, editor = {Bush, Daniel} } @article {48620, title = {A complete electron microscopy volume of the brain of adult Drosophila melanogaster.}, journal = {Cell}, volume = {174}, year = {2018}, month = {2018 Jul 12}, pages = {730-43}, abstract = {

Drosophila melanogaster has a rich repertoire of innate and learned behaviors. Its 100,000-neuron brain is a large but tractable target for comprehensive neural circuit mapping. Only electron microscopy (EM) enables complete, unbiased mapping of synaptic connectivity; however, the fly brain is too large for conventional EM. We developed a custom high-throughput EM platform and imaged the entire brain of an adult female fly at synaptic resolution. To validate the dataset, we traced brain-spanning circuitry involving the mushroom body (MB), which has been extensively studied for its role in learning. All inputs to Kenyon cells (KCs), the intrinsic neurons of the MB, were mapped, revealing a previously unknown cell type, postsynaptic partners of KC dendrites, and unexpected clustering of olfactory projection neurons. These reconstructions show that this freely available EM volume supports mapping of brain-spanning circuits, which will significantly accelerate Drosophila neuroscience..

}, doi = {10.1016/j.cell.2018.06.019}, author = {Zheng, Zhihao and Lauritzen, J Scott and Perlman, Eric and Robinson, Camenzind G and Nichols, Matthew and Milkie, Daniel E and Torrens, Omar and Price, John and Fisher, Corey B and Sharifi, Nadiya and Calle-Schuler, Steven A and Kmecova, Lucia and Ali, Iqbal J and Karsh, Bill and Trautman, Eric T and Bogovic, John A and Hanslovsky, Philipp and Jefferis, Gregory S X E and Kazhdan, Michael and Khairy, Khaled} } @article {49583, title = {Convergence of monosynaptic and polysynaptic sensory paths onto common motor outputs in a feeding connectome.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Dec 11}, abstract = {

We reconstructed, from a whole CNS EM volume, the synaptic map of input and output neurons that underlie food intake behavior of larvae. Input neurons originate from enteric, pharyngeal and external sensory organs and converge onto seven distinct sensory synaptic compartments within the CNS. Output neurons consist of feeding motor, serotonergic modulatory and neuroendocrine neurons. Monosynaptic connections from a set of sensory synaptic compartments cover the motor, modulatory and neuroendocrine targets in overlapping domains. Polysynaptic routes are superimposed on top of monosynaptic connections, resulting in divergent sensory paths that converge on common outputs. A completely different set of sensory compartments is connected to the mushroom body calyx. The mushroom body output neurons are connected to interneurons that directly target the feeding output neurons. Our results illustrate a circuit architecture in which monosynaptic and multisynaptic connections from sensory inputs traverse onto output neurons via a series of converging paths.

}, issn = {2050-084X}, doi = {10.7554/eLife.40247}, author = {Miroschnikow, Anton and Schlegel, Philipp and Schoofs, Andreas and Hueckesfeld, Sebastian and Li, Feng and Schneider-Mizell, Casey M and Fetter, Richard D and Truman, James W and Cardona, Albert and Pankratz, Michael J} } @article {49433, title = {Cryo-EM analysis of the T3S injectisome reveals the structure of the needle and open secretin.}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {2018 Sep 21}, pages = {3840}, abstract = {

The bacterial type III secretion system, or injectisome, is a syringe shaped nanomachine essential for the virulence of many disease causing Gram-negative bacteria. At the core of the injectisome structure is the needle complex, a continuous channel formed by the highly oligomerized inner and outer membrane hollow rings and a polymerized helical needle filament which spans through and projects into the infected host cell. Here we present the near-atomic resolution structure of a needle complex from the prototypical Salmonella Typhimurium SPI-1 type III secretion system, with local masking protocols allowing for model building and refinement of the major membrane spanning components of the needle complex\ base in addition to an isolated needle filament. This work provides significant insight into injectisome structure and assembly and importantly captures the molecular basis for substrate induced gating in the giant outer membrane secretin portal family.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-06298-8}, author = {Hu, J and Worrall, L J and Hong, C and Vuckovic, M and Atkinson, C E and Caveney, N and Yu, Z and Strynadka, N C J} } @article {49315, title = {Cryo-EM structure of an essential Plasmodium vivax invasion complex.}, journal = {Nature}, volume = {559}, year = {2018}, month = {2018 Jul}, pages = {135-139}, abstract = {

Plasmodium vivax is the most widely distributed malaria parasite that infects humans. P. vivax invades reticulocytes exclusively, and successful entry depends on specific interactions between the P. vivax reticulocyte-binding protein 2b (PvRBP2b) and transferrin receptor 1 (TfR1). TfR1-deficient erythroid cells are refractory to invasion by P. vivax, and anti-PvRBP2b monoclonal antibodies inhibit reticulocyte binding and block P. vivax invasion in field isolates. Here we report a high-resolution cryo-electron microscopy structure of a ternary complex of PvRBP2b bound to human TfR1 and transferrin, at 3.7 {\r A} resolution. Mutational analyses show that PvRBP2b residues involved in complex formation are conserved; this suggests that antigens could be designed that act across P. vivax strains. Functional analyses of TfR1 highlight how P. vivax hijacks TfR1, an essential housekeeping protein, by binding to sites that govern host specificity, without affecting its cellular function of transporting iron. Crystal and solution structures of PvRBP2b in complex with antibody fragments characterize the inhibitory epitopes. Our results establish a structural framework for understanding how P. vivax reticulocyte-binding protein engages its receptor and the molecular mechanism of inhibitory monoclonal antibodies, providing important information for the design of novel vaccine candidates.

}, issn = {1476-4687}, doi = {10.1038/s41586-018-0249-1}, author = {Gruszczyk, Jakub and Huang, Rick K and Chan, Li-Jin and Menant, S{\'e}bastien and Hong, Chuan and Murphy, James M and Mok, Yee-Foong and Griffin, Michael D W and Pearson, Richard D and Wong, Wilson and Cowman, Alan F and Yu, Zhiheng and Tham, Wai-Hong} } @article {49325, title = {Cryo-EM structure of the polycystin 2-l1 ion channel.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Jul 13}, abstract = {

We report the near atomic resolution (3.3 {\r A}) of the human polycystic kidney disease 2-like 1 (polycystin 2-l1) ion channel. Encoded by PKD2L1, polycystin 2-l1 is a calcium and monovalent cation-permeant ion channel in primary cilia and plasma membranes. The related primary cilium-specific polycystin-2 protein, encoded by PKD2, shares a high degree of sequence similarity, yet has distinct permeability characteristics. Here we show that these differences are reflected in the architecture of polycystin 2-l1.

}, issn = {2050-084X}, doi = {10.7554/eLife.36931}, author = {Hulse, Raymond E and Li, Zongli and Huang, Rick K and Zhang, Jin and Clapham, David E} } @article {49125, title = {Dedicated photoreceptor pathways in Drosophila larvae mediate navigation by processing either spatial or temporal cues.}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {2018 Mar 28}, pages = {1260}, abstract = {

To integrate changing environmental cues with high spatial and temporal resolution is critical for animals to orient themselves. Drosophila larvae show an effective motor program to navigate away from light sources. How the larval visual circuit processes light stimuli to control navigational decision remains unknown. The larval visual system is composed of two sensory input channels, Rhodopsin5 (Rh5) and Rhodopsin6 (Rh6) expressing photoreceptors (PRs). We here characterize how spatial and temporal information are used to control navigation. Rh6-PRs are required to perceive temporal changes of light intensity during head casts, while Rh5-PRs are required to control behaviors that allow navigation in response to spatial cues. We characterize how distinct behaviors are modulated and identify parallel acting and converging features of the visual circuit. Functional features of the larval visual circuit highlight the principle of how early in a sensory circuit distinct behaviors may be computed by partly overlapping sensory pathways.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-03520-5}, author = {Humberg, Tim-Henning and Bruegger, Pascal and Afonso, Bruno and Zlatic, Marta and Truman, James W and Gershow, Marc and Samuel, Aravinthan and Sprecher, Simon G} } @article {49415, title = {Defective cortex glia plasma membrane structure underlies light-induced epilepsy in mutants.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, year = {2018}, month = {2018 Sep 05}, pages = {E8919-28}, abstract = {

Seizures induced by visual stimulation (photosensitive epilepsy; PSE) represent a common type of epilepsy in humans, but the molecular mechanisms and genetic drivers underlying PSE remain unknown, and no good genetic animal models have been identified as yet. Here, we show an animal model of PSE, in , owing to defective cortex glia. The cortex glial membranes are severely compromised in ceramide phosphoethanolamine synthase ()-null mutants and fail to encapsulate the neuronal cell bodies in the neuronal cortex. Expression of human sphingomyelin synthase 1, which synthesizes the closely related ceramide phosphocholine (sphingomyelin), rescues the cortex glial abnormalities and PSE, underscoring the evolutionarily conserved role of these lipids in glial membranes. Further, we show the compromise in plasma membrane structure that underlies the glial cell membrane collapse in mutants and leads to the PSE phenotype.

}, issn = {1091-6490}, doi = {10.1073/pnas.1808463115}, author = {Kunduri, Govind and Turner-Evans, Daniel and Konya, Yutaka and Izumi, Yoshihiro and Nagashima, Kunio and Lockett, Stephen and Holthuis, Joost and Bamba, Takeshi and Acharya, Usha and Acharya, Jairaj K} } @article {49546, title = {Developmental pattern and structural factors of dendritic survival in cerebellar granule cells in vivo.}, journal = {Scientific Reports}, volume = {8}, year = {2018}, month = {2018 Dec 03}, pages = {17561}, abstract = {

Granule cells (GCs) in the cerebellar cortex are important for sparse encoding of afferent sensorimotor information. Modeling studies show that GCs can perform their function most effectively when they have four dendrites. Indeed, mature GCs have four short dendrites on average, each terminating in a claw-like ending that receives both excitatory and inhibitory inputs. Immature GCs, however, have significantly more dendrites-all without claws. How these redundant dendrites are refined during development is largely unclear. Here, we used in vivo time-lapse imaging and immunohistochemistry to study developmental refinement of GC dendritic arbors and its relation to synapse formation. We found that while the formation of dendritic claws stabilized the dendrites, the selection of surviving dendrites was made before claw formation, and longer immature dendrites had a significantly higher chance of survival than shorter dendrites. Using immunohistochemistry, we show that glutamatergic and GABAergic synapses are transiently formed on immature GC dendrites, and the number of GABAergic, but not glutamatergic, synapses correlates with the length of immature dendrites. Together, these results suggest a potential role of transient GABAergic synapses on dendritic selection and show that preselected dendrites are stabilized by the formation of dendritic claws-the site of mature synapses.

}, issn = {2045-2322}, doi = {10.1038/s41598-018-35829-y}, author = {Dhar, Matasha and Hantman, Adam W and Nishiyama, Hiroshi} } @article {49119, title = {Dynamic cues for whisker-based object localization: An analytical solution to vibration during active whisker touch.}, journal = {PLoS Computational Biology}, volume = {14}, year = {2018}, month = {2018 Mar 27}, pages = {e1006032}, abstract = {

Vibrations are important cues for tactile perception across species. Whisker-based sensation in mice is a powerful model system for investigating mechanisms of tactile perception. However, the role vibration plays in whisker-based sensation remains unsettled, in part due to difficulties in modeling the vibration of whiskers. Here, we develop an analytical approach to calculate the vibrations of whiskers striking objects. We use this approach to quantify vibration forces during active whisker touch at a range of locations along the whisker. The frequency and amplitude of vibrations evoked by contact are strongly dependent on the position of contact along the whisker. The magnitude of vibrational shear force and bending moment is comparable to quasi-static forces. The fundamental vibration frequencies are in a detectable range for mechanoreceptor properties and below the maximum spike rates of primary sensory afferents. These results suggest two dynamic cues exist that rodents can use for object localization: vibration frequency and comparison of vibrational to quasi-static force magnitude. These complement the use of quasi-static force angle as a distance cue, particularly for touches close to the follicle, where whiskers are stiff and force angles hardly change during touch. Our approach also provides a general solution to calculation of whisker vibrations in other sensing tasks.

}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1006032}, author = {Vaxenburg, Roman and Wyche, Isis and Svoboda, Karel and Efros, Alexander L and Hires, Samuel Andrew} } @article {49342, title = {The ESCRT-III protein CHMP1A mediates secretion of sonic hedgehog on a distinctive subtype of extracellular vesicles.}, journal = {Cell Reports}, volume = {24}, year = {2018}, month = {2018 Jul 24}, pages = {973-986.e8}, abstract = {

Endosomal sorting complex required for transport (ESCRT) complex proteins regulate biogenesis and release of extracellular vesicles (EVs), which enable cell-to-cell communication in the nervous system essential for development and adult function. We recently showed human loss-of-function (LOF) mutations in ESCRT-III member CHMP1A cause autosomal recessive microcephaly with pontocerebellar hypoplasia, but its mechanism was unclear. Here, we show Chmp1a is required for progenitor proliferation in mouse cortex and cerebellum and progenitor maintenance in human cerebral organoids. In Chmp1a null mice, this defect is associated with impaired sonic hedgehog (Shh) secretion and intraluminal vesicle (ILV) formation in multivesicular bodies (MVBs). Furthermore, we show CHMP1A is important for release of an EV subtype that contains AXL, RAB18, and TMED10 (ART) and SHH. Our findings show CHMP1A loss impairs secretion of SHH on ART-EVs, providing molecular mechanistic insights into the role of ESCRT proteins and EVs in the brain.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2018.06.100}, author = {Coulter, Michael E and Dorobantu, Cristina M and Lodewijk, Gerrald A and Delalande, Fran{\c c}ois and Cianferani, Sarah and Ganesh, Vijay S and Smith, Richard S and Lim, Elaine T and Xu, C Shan and Pang, Song and Wong, Eric T and Lidov, Hart G W and Calicchio, Monica L and Yang, Edward and Gonzalez, Dilenny M and Schlaeger, Thorsten M and Mochida, Ganeshwaran H and Hess, Harald and Lee, Wei-Chung Allen and Lehtinen, Maria K and Kirchhausen, Tomas and Haussler, David and Jacobs, Frank M J and Gaudin, Rapha{\"e}l and Walsh, Christopher A} } @article {49150, title = {Evaluating the potential of using quantum dots for monitoring electrical signals in neurons.}, journal = {Nature Nanotechnology}, volume = {13}, year = {2018}, month = {2018 Apr}, pages = {278-288}, abstract = {

Success in the projects aimed at providing an advanced understanding of the brain is directly predicated on making critical advances in nanotechnology. This Perspective addresses the unique interface of neuroscience and nanomaterials by considering the foundational problem of sensing neuron membrane voltage and offers a potential solution that may be facilitated by a prototypical nanomaterial. Despite substantial improvements, the visualization of instantaneous voltage changes within individual neurons, whether in cell culture or in vivo, at both the single-cell and network level at high speed remains complex and problematic. The unique properties of semiconductor quantum dots (QDs) have made them powerful fluorophores for bioimaging. What is not widely appreciated, however, is that QD photoluminescence is exquisitely sensitive to proximal electric fields. This property should be suitable for sensing voltage changes that occur in the active neuronal membrane. Here, we examine the potential role of QDs in addressing the important challenge of real-time optical voltage imaging.

}, issn = {1748-3395}, doi = {10.1038/s41565-018-0107-1}, author = {Efros, Alexander L and Delehanty, James B and Huston, Alan L and Medintz, Igor L and Barbic, Mladen and Harris, Timothy D} } @article {49129, title = {Fabricating optical-quality glass surfaces to study macrophage fusion.}, journal = {Journal of Visualized Experiments : JoVE}, year = {2018}, month = {2018 Mar 14}, abstract = {

Visualizing the formation of multinucleated giant cells (MGCs) from living specimens has been challenging due to the fact that most live imaging techniques require propagation of light through glass, but on glass macrophage fusion is a rare event. This protocol presents the fabrication of several optical-quality glass surfaces where adsorption of compounds containing long-chain hydrocarbons transforms glass into a fusogenic surface. First, preparation of clean glass surfaces as starting material for surface modification is described. Second, a method is provided for the adsorption of compounds containing long-chain hydrocarbons to convert non-fusogenic glass into a fusogenic substrate. Third, this protocol describes fabrication of surface micropatterns that promote a high degree of spatiotemporal control over MGC formation. Finally, fabricating glass bottom dishes is described. Examples of use of this in vitro cell system as a model to study macrophage fusion and MGC formation are shown.

}, issn = {1940-087X}, doi = {10.3791/56866}, author = {Faust, James J and Christenson, Wayne and Doudrick, Kyle and Heddleston, John and Chew, Teng-Leong and Lampe, Marko and Balabiyev, Arnat and Ros, Robert and Ugarova, Tatiana P} } @article {49324, title = {Fluorogenic structure activity library pinpoints molecular variations in substrate specificity of structurally homologous esterases.}, journal = {The Journal of Biological Chemistry}, volume = {293}, year = {2018}, month = {2018 Jul 13}, pages = {13851-62}, abstract = {

Cellular esterases catalyze many essential biological functions by performing hydrolysis reactions on diverse substrates. The promiscuity of esterases complicates assignment of their substrate preferences and biological functions. To identify universal factors controlling esterase substrate recognition, we designed a 32-member structure-activity relationship (SAR) library of fluorogenic ester substrates and used this library to systematically interrogate esterase preference for chain length, branching patterns, and polarity to differentiate common classes of esterase substrates. Two structurally homologous bacterial esterases were screened against this library, refining their previously broad overlapping substrate specificity. esterase ybfF displayed a preference for γ-position thioethers and ethers, whereas Rv0045c from displayed a preference for branched substrates with and without thioethers. We determined that this substrate differentiation was partially controlled by individual substrate selectivity residues Tyr119 in ybfF and His187 in Rv0045c; reciprocal substitution of these residues shifted each esterase{\textquoteright}s substrate preference. This work demonstrates that the selectivity of esterases is tuned based on transition state stabilization, identifies thioethers as an underutilized functional group for esterase substrates, and provides a rapid method for differentiating structural isozymes. This SAR library could have multi-faceted future applications including in vivo imaging, biocatalyst screening, molecular fingerprinting, and inhibitor design.

}, issn = {1083-351X}, doi = {10.1074/jbc.RA118.003972}, author = {White, Alex and Koelper, Andrew and Russell, Arielle and Larsen, Erik M and Kim, Charles and Lavis, Luke D and Hoops, Geoffrey C and Johnson, R Jeremy} } @article {49010, title = {A genetically encoded Ca2+ indicator based on circularly permutated sea anemone red fluorescent protein eqFP578.}, journal = {BMC Biology}, volume = {16}, year = {2018}, month = {2018 Jan 16}, pages = {9}, abstract = {

BACKGROUND: Genetically encoded calcium ion (Ca2+) indicators (GECIs) are indispensable tools for measuring Ca2+ dynamics and neuronal activities in vitro and in vivo. Red fluorescent protein (RFP)-based GECIs have inherent advantages relative to green fluorescent protein-based GECIs due to the longer wavelength light used for excitation. Longer wavelength light is associated with decreased phototoxicity and deeper penetration through tissue. Red GECI can also enable multicolor visualization with blue- or cyan-excitable fluorophores.

RESULTS: Here we report the development, structure, and validation of a new RFP-based GECI, K-GECO1, based on a circularly permutated RFP derived from the sea anemone Entacmaea quadricolor. We have characterized the performance of K-GECO1 in cultured HeLa cells, dissociated neurons, stem-cell-derived cardiomyocytes, organotypic brain slices, zebrafish spinal cord in vivo, and mouse brain in vivo.

CONCLUSION: K-GECO1 is the archetype of a new lineage of GECIs based on the RFP eqFP578 scaffold. It offers high sensitivity and fast kinetics, similar or better than those of current state-of-the-art indicators, with diminished lysosomal accumulation and minimal blue-light photoactivation. Further refinements of the K-GECO1 lineage could lead to further improved variants with overall performance that exceeds that of the most highly optimized red GECIs.

}, issn = {1741-7007}, doi = {10.1186/s12915-018-0480-0}, author = {Shen, Yi and Dana, Hod and Abdelfattah, Ahmed S and Patel, Ronak and Shea, Jamien and Molina, Rosana S and Rawal, Bijal and Rancic, Vladimir and Chang, Yu-Fen and Wu, Lanshi and Chen, Yingche and Qian, Yong and Wiens, Matthew D and Hambleton, Nathan and Ballanyi, Klaus and Hughes, Thomas E and Drobizhev, Mikhail and Kim, Douglas S and Koyama, Minoru and Schreiter, Eric R and Campbell, Robert E} } @article {49813, title = {High-performance GFP-based calcium indicators for imaging activity in neuronal populations and microcompartments.}, journal = {bioRxiv}, year = {2018}, month = {2018 Oct 3}, abstract = {

Calcium imaging with genetically encoded calcium indicators (GECIs) is routinely used to measure neural activity in intact nervous systems. GECIs are frequently used in one of two different modes: to track activity in large populations of neuronal cell bodies, or to follow dynamics in subcellular compartments such as axons, dendrites and individual synaptic compartments. Despite major advances, calcium imaging is still limited by the biophysical properties of existing GECIs, including affinity, signal-to-noise ratio, rise and decay kinetics, and dynamic range. Using structure-guided mutagenesis and neuron-based screening, we optimized the green fluorescent protein-based GECI GCaMP6 for different modes of in vivo imaging. The jGCaMP7 sensors provide improved detection of individual spikes (jGCaMP7s,f), imaging in neurites and neuropil (jGCaMP7b), and tracking large populations of neurons using 2-photon (jGCaMP7s,f) or wide-field (jGCaMP7c) imaging.

}, doi = {10.1101/434589}, author = {Dana, Hod and Sun, Yi and Mohar, Boaz and Hulse, Brad and Hasseman, Jeremy P and Tsegaye, Getahun and Tsang, Arthur and Wong, Allan and Patel, Ronak and Macklin, John J and Chen, Yang and Konnerth, Arthur and Jayaraman, Vivek and Looger, Loren L and Schreiter, Eric R and Svoboda, Karel and Kim, Douglas S} } @article {49222, title = {Identification of a transporter complex responsible for the cytosolic entry of nitrogen-containing-bisphosphonates.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 May 10}, abstract = {

Nitrogen-containing-bisphosphonates (N-BPs) are a class of drugs widely prescribed to treat osteoporosis and other bone-related diseases. Although previous studies have established that N-BPs function by inhibiting the mevalonate pathway in osteoclasts, the mechanism by which N-BPs enter the cytosol from the extracellular space to reach their molecular target is not understood. Here we implemented a CRISPRi-mediated genome-wide screen and identified (solute carrier family 37 member A3) as a gene required for the action of N-BPs in mammalian cells. We observed that SLC37A3 forms a complex with ATRAID (all-trans retinoic acid-induced differentiation factor), a previously identified genetic target of N-BPs. SLC37A3 and ATRAID localize to lysosomes and are required for releasing N-BP molecules that have trafficked to lysosomes through fluid-phase endocytosis into the cytosol. Our results elucidate the route by which N-BPs are delivered to their molecular target, addressing a key aspect of the mechanism of action of N-BPs that may have significant clinical relevance.

}, issn = {2050-084X}, doi = {10.7554/eLife.36620}, author = {Yu, Zhou and Surface, Lauren E and Park, Chong Yon and Horlbeck, Max A and Wyant, Gregory A and Abu-Remaileh, Monther and Peterson, Timothy R and Sabatini, David M and Weissman, Jonathan S and O{\textquoteright}Shea, Erin K} } @article {49293, title = {Imaging dynamic and selective low-complexity domain interactions that control gene transcription.}, journal = {Science (New York, N.Y.)}, volume = {361}, year = {2018}, month = {2018 Jun 21}, pages = {eaar2555}, abstract = {

Many eukaryotic transcription factors (TFs) contain intrinsically disordered low-complexity domains (LCDs), but how they drive transactivation remains unclear. Here, live-cell single-molecule imaging reveals that TF-LCDs form local high-concentration interaction hubs at synthetic and endogenous genomic loci. TF-LCD hubs stabilize DNA binding, recruit RNA polymerase II (Pol II), and activate transcription. LCD-LCD interactions within hubs are highly dynamic, display selectivity with binding partners, and are differentially sensitive to disruption by hexanediols. Under physiological conditions, rapid and reversible LCD-LCD interactions occur between TFs and the Pol II machinery without detectable phase separation. Our findings reveal fundamental mechanisms underpinning transcriptional control and suggest a framework for developing single-molecule imaging screens for novel drugs targeting gene regulatory interactions implicated in disease.

}, issn = {1095-9203}, doi = {10.1126/science.aar2555}, author = {Chong, Shasha and Dugast-Darzacq, Claire and Liu, Zhe and Dong, Peng and Dailey, Gina M and Cattoglio, Claudia and Heckert, Alec and Banala, Sambashiva and Lavis, Luke and Darzacq, Xavier and Tjian, Robert} } @article {49494, title = {Improved methods for marking active neuron populations.}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {2018 Oct 25}, pages = {4440}, abstract = {

Marking functionally distinct neuronal ensembles with high spatiotemporal resolution is a key challenge in systems neuroscience. We recently introduced CaMPARI, an engineered fluorescent protein whose green-to-red photoconversion depends on simultaneous light exposure and elevated calcium, which enabled marking active neuronal populations with single-cell and subsecond resolution. However, CaMPARI (CaMPARI1) has several drawbacks, including background photoconversion in low calcium, slow kinetics and reduced fluorescence after chemical fixation. In this work, we develop CaMPARI2, an improved sensor with brighter green and red fluorescence, faster calcium unbinding kinetics and decreased photoconversion in low calcium conditions. We demonstrate the improved performance of CaMPARI2 in mammalian neurons and in vivo in larval zebrafish brain and mouse visual cortex. Additionally, we herein develop an immunohistochemical detection method for specific labeling of the photoconverted red form of CaMPARI. The anti-CaMPARI-red antibody provides strong labeling that is selective for photoconverted CaMPARI in activated neurons in rodent brain tissue.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-06935-2}, author = {Moeyaert, Benjamien and Holt, Graham and Madangopal, Rajtarun and Perez-Alvarez, Alberto and Fearey, Brenna C and Trojanowski, Nicholas F and Ledderose, Julia and Zolnik, Timothy A and Das, Aniruddha and Patel, Davina and Brown, Timothy A and Sachdev, Robert N S and Eickholt, Britta J and Larkum, Matthew E and Turrigiano, Gina G and Dana, Hod and Gee, Christine E and Oertner, Thomas G and Hope, Bruce T and Schreiter, Eric R} } @article {49094, title = {Integrative structure and functional anatomy of a nuclear pore complex.}, journal = {Nature}, volume = {555}, year = {2018}, month = {2018 Mar 14}, pages = {475-82}, abstract = {

Nuclear pore complexes play central roles as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm. However, their large size and dynamic nature have impeded a full structural and functional elucidation. Here we determined the structure of the entire 552-protein nuclear pore complex of the yeast Saccharomyces cerevisiae at sub-nanometre precision by satisfying a wide range of data relating to the molecular arrangement of its constituents. The nuclear pore complex incorporates sturdy diagonal columns and connector cables attached to these columns, imbuing the structure with strength and flexibility. These cables also tie together all other elements of the nuclear pore complex, including membrane-interacting regions, outer rings and RNA-processing platforms. Inwardly directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized into distinct functional units. This integrative structure enables us to rationalize the architecture, transport mechanism and evolutionary origins of the nuclear pore complex.

}, issn = {1476-4687}, doi = {10.1038/nature26003}, author = {Kim, Seung Joong and Fernandez-Martinez, Javier and Nudelman, Ilona and Shi, Yi and Zhang, Wenzhu and Raveh, Barak and Herricks, Thurston and Slaughter, Brian D and Hogan, Joanna A and Upla, Paula and Chemmama, Ilan E and Pellarin, Riccardo and Echeverria, Ignacia and Shivaraju, Manjunatha and Chaudhury, Azraa S and Wang, Junjie and Williams, Rosemary and Unruh, Jay R and Greenberg, Charles H and Jacobs, Erica Y and Yu, Zhiheng and de la Cruz, M Jason and Mironska, Roxana and Stokes, David L and Aitchison, John D and Jarrold, Martin F and Gerton, Jennifer L and Ludtke, Steven J and Akey, Christopher W and Chait, Brian T and Sali, Andrej and Rout, Michael P} } @article {49343, title = {Inverse-response Ca2+ indicators for optogenetic visualization of neuronal inhibition.}, journal = {Scientific Reports}, volume = {8}, year = {2018}, month = {2018 Aug 06}, pages = {11758}, abstract = {

We have developed a series of yellow genetically encoded Ca indicators for optical imaging (Y-GECOs) with inverted responses to Ca and apparent dissociation constants (K{\textquoteright}) ranging from 25 to 2400 nM. To demonstrate the utility of this affinity series of Ca indicators, we expressed the four highest affinity variants (K{\textquoteright}s = 25, 63, 121, and 190 nM) in the Drosophila medulla intrinsic neuron Mi1. Hyperpolarization of Mi1 by optogenetic stimulation of the laminar monopolar neuron L1 produced a decrease in intracellular Ca in layers 8-10, and a corresponding increase in Y-GECO fluorescence. These experiments revealed that lower K{\textquoteright} was associated with greater increases in fluorescence, but longer delays to reach the maximum signal change due to slower off-rate kinetics.

}, issn = {2045-2322}, doi = {10.1038/s41598-018-30080-x}, author = {Zhao, Yufeng and Bushey, Daniel and Zhao, Yongxin and Schreiter, Eric R and Harrison, D Jed and Wong, Allan M and Campbell, Robert E} } @article {64996, title = {Knock-in rats expressing Cre and Flp recombinases at the Parvalbumin locus.}, journal = {bioRxiv}, year = {2018}, month = {2018 Aug 07}, abstract = {

Rats have the ability to learn and perform sophisticated behavioral tasks, making them very useful for investigating neural circuit functions. In contrast to the extensive mouse genetic toolkit, the paucity of recombinase-expressing rat models has limited the ability to monitor and manipulate molecularly-defined neural populations in this species. Here we report the generation and validation of two knock-in rat strains expressing either\ Cre\ or\ Flp\ recombinase under the control of\ Parvalbumin (Pvalb), a gene expressed in the critical {\textquotedblleft}fast-spiking{\textquotedblright} subset of inhibitory interneurons (FSIs). These strains were generated with CRISPR-Cas9 gene editing and show highly specific and penetrant labeling of\ Pvalb-expressing neurons, as demonstrated by\ in situ\ hybridization and immunohistochemistry. We validated these models in both prefrontal cortex and striatum using both\ ex vivo\ and\ in vivo\ approaches, including whole-cell recording, optogenetics, extracellular physiology and photometry. Our results demonstrate the utility of these new transgenic models for a wide range of neuroscience experiments.

}, doi = {10.1101/386474}, author = {Jai Y. Yu and Jeffrey R. Pettibone and Caiying Guo and Shuqin Zhang and Thomas L. Saunders and Elizabeth D. Hughes and Wanda E. Filipiak and Michael G. Zeidler and Kevin J. Bender and Frederic Hopf and Clay N. Smyth and Viktor Kharazia and Anna Kiseleva and Thomas J. Davidson and Loren M. Frank and Joshua D. Berke} } @article {64995, title = {Lamellar junctions in the endolymphatic sac act as a relief valve to regulate inner ear pressure.}, journal = {eLife}, year = {2018}, month = {2018 Jun 19}, doi = {10.7554/eLife.37131}, author = {Ian A. Swinburne and Kishore R. Mosaliganti and Srigokul Upadhyayula and Tsung-Li Liu and David G. C. Hildebrand and Tony Y.-C. Tsai and Anzhi Chen and Ebaa Al-Obeidi and Anna K. Fass and Samir Malhotra and Florian Engert and Jeff W. Lichtman and Tom Kirchhausen and Sean G. Megason and Eric Betzig} } @article {49275, title = {Lamellar projections in the endolymphatic sac act as a relief valve to regulate inner ear pressure.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Jun 19}, abstract = {

The inner ear is a fluid-filled closed-epithelial structure whose function requires maintenance of an internal hydrostatic pressure and fluid composition. The endolymphatic sac (ES) is a dead-end epithelial tube connected to the inner ear whose function is unclear. ES defects can cause distended ear tissue, a pathology often seen in hearing and balance disorders. Using live imaging of zebrafish larvae, we reveal that the ES undergoes cycles of slow pressure-driven inflation followed by rapid deflation. Absence of these cycles in mutants leads to distended ear tissue. Using serial-section electron microscopy and adaptive optics lattice light-sheet microscopy, we find a pressure relief valve in the ES comprised of partially separated apical junctions and dynamic overlapping basal lamellae that separate under pressure to release fluid. We propose that this lmx1-dependent pressure relief valve is required to maintain fluid homeostasis in the inner ear and other fluid-filled cavities.

}, issn = {2050-084X}, doi = {10.7554/eLife.37131}, author = {Swinburne, Ian A and Mosaliganti, Kishore R and Upadhyayula, Srigokul and Liu, Tsung-Li and Hildebrand, David G C and Tsai, Tony Y-C and Chen, Anzhi and Al-Obeidi, Ebaa and Fass, Anna K and Malhotra, Samir and Engert, Florian and Lichtman, Jeff W and Kirchausen, Tomas and Betzig, Eric and Megason, Sean G} } @article {49232, title = {Lineage-guided Notch-dependent gliogenesis by multi-potent progenitors.}, journal = {Development (Cambridge, England)}, year = {2018}, month = {2018 May 15}, abstract = {

Macroglial cells in the central nervous system exhibit regional specialization and carry out region-specific functions. Diverse glial cells arise from specific progenitors in specific spatiotemporal patterns. This raises an interesting possibility that there exist glial precursors with distinct developmental fates, which govern region-specific gliogenesis. Here we mapped the glial progeny produced by the type II neuroblasts, which, like vertebrate radial glia cells, yield both neurons and glia via intermediate neural progenitors (INPs). Distinct type II neuroblasts produce different characteristic sets of glia. A single INP can make both astrocyte-like and ensheathing glia, which co-occupy a relatively restrictive subdomain. Blocking apoptosis uncovers further lineage distinctions in the specification, proliferation, and survival of glial precursors. Both the switch from neurogenesis to gliogenesis and the subsequent glial expansion depend on Notch signaling. Taken together, lineage origins preconfigure the development of individual glial precursors with involvement of serial Notch actions in promoting gliogenesis.

}, issn = {1477-9129}, doi = {10.1242/dev.160127}, author = {Ren, Qingzhong and Awasaki, Takeshi and Wang, Yu-Chun and Huang, Yu-Fen and Lee, Tzumin} } @article {49382, title = {Macropinosome formation by tent pole ruffling in macrophages.}, journal = {The Journal of Cell Biology}, volume = {217}, year = {2018}, month = {2018 Aug 27}, pages = {3873-85}, abstract = {

Pathogen-mediated activation of macrophages arms innate immune responses that include enhanced surface ruffling and macropinocytosis for environmental sampling and receptor internalization and signaling. Activation of macrophages with bacterial lipopolysaccharide (LPS) generates prominent dorsal ruffles, which are precursors for macropinosomes. Very rapid, high-resolution imaging of live macrophages with lattice light sheet microscopy (LLSM) reveals new features and actions of dorsal ruffles, which redefine the process of macropinosome formation and closure. We offer a new model in which ruffles are erected and supported by F-actin tent poles that cross over and twist to constrict the forming macropinosomes. This process allows for formation of large macropinosomes induced by LPS. We further describe the enrichment of active Rab13 on tent pole ruffles and show that CRISPR deletion of Rab13 results in aberrant tent pole ruffles and blocks the formation of large LPS-induced macropinosomes. Based on the exquisite temporal and spatial resolution of LLSM, we can redefine the ruffling and macropinosome processes that underpin innate immune responses.

}, issn = {1540-8140}, doi = {10.1083/jcb.201804137}, author = {Condon, Nicholas D and Heddleston, John M and Chew, Teng-Leong and Luo, Lin and McPherson, Peter S and Ioannou, Maria S and Hodgson, Louis and Stow, Jennifer L and Wall, Adam A} } @article {49526, title = {Magnetocaloric materials as switchable high contrast ratio MRI labels.}, journal = {Magnetic Resonance in Medicine}, volume = {81}, year = {2018}, month = {2018 Nov 25}, pages = {2238-46}, abstract = {

PURPOSE: To develop switchable and tunable labels with high contrast ratio for MRI using magnetocaloric materials that have sharp first-order magnetic phase transitions at physiological temperatures and typical MRI magnetic field strengths.

METHODS: A prototypical magnetocaloric material iron-rhodium (FeRh) was prepared by melt mixing, high-temperature annealing, and ice-water quenching. Temperature- and magnetic field-dependent magnetization measurements of wire-cut FeRh samples were performed on a vibrating sample magnetometer. Temperature-dependent MRI of FeRh samples was performed on a 4.7T MRI.

RESULTS: Temperature-dependent MRI clearly demonstrated image contrast changes due to the sharp magnetic state transition of the FeRh samples in the MRI magnetic field (4.7T) and at a physiologically relevant temperature (~37{\textdegree}C).

CONCLUSION: A magnetocaloric material, FeRh, was demonstrated to act as a high contrast ratio switchable MRI contrast agent due to its sharp first-order magnetic phase transition in the DC magnetic field of MRI and at physiologically relevant temperatures. A wide range of magnetocaloric materials are available that can be tuned by materials science techniques to optimize their response under MRI-appropriate conditions and be controllably switched in situ with temperature, magnetic field, or a combination of both.

}, issn = {1522-2594}, doi = {10.1002/mrm.27615}, author = {Barbic, Mladen and Dodd, Stephen J and Morris, H Douglas and Dilley, Neil and Marcheschi, Barbara and Huston, Alan and Harris, Tim D and Koretsky, Alan P} } @article {49153, title = {Measuring the global substrate specificity of mycobacterial serine hydrolases using a library of fluorogenic ester substrates.}, journal = {ACS Infectious Diseases}, volume = {4}, year = {2018}, month = {2018 Jun 8}, pages = {904-11}, abstract = {

Among the proteins required for lipid metabolism in Mycobacterium tuberculosis are a significant number of uncharacterized serine hydrolases, especially lipases and esterases. Using a streamlined synthetic method, a library of immolative fluorogenic ester substrates was expanded to better represent the natural lipidomic diversity of Mycobacterium. This expanded fluorogenic library was then used to rapidly characterize the global structure activity relationship (SAR) of mycobacterial serine hydrolases in M.\ smegmatis under different growth conditions. Confirmation of fluorogenic substrate activation by mycobacterial serine hydrolases was performed using nonspecific serine hydrolase inhibitors and reinforced the biological significance of the SAR. The hydrolases responsible for the global SAR were then assigned using gel-resolved activity measurements, and these assignments were used to rapidly identify the relative substrate specificity of previously uncharacterized mycobacterial hydrolases. These measurements provide a global SAR of mycobacterial hydrolase activity, a picture of cycling hydrolase activity, and a detailed substrate specificity profile for previously uncharacterized hydrolases.

}, issn = {2373-8227}, doi = {10.1021/acsinfecdis.7b00263}, author = {Bassett, Braden and Waibel, Brent and White, Alex and Hansen, Heather and Stephens, Dominique and Koelper, Andrew and Larsen, Erik M and Kim, Charles and Glanzer, Adam and Lavis, Luke D and Hoops, Geoffrey C and Johnson, R Jeremy} } @article {49581, title = {MicroED structures of HIV-1 Gag CTD-SP1 reveal binding interactions with the maturation inhibitor bevirimat.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, year = {2018}, month = {2018 Dec 26}, pages = {13258-63}, abstract = {

HIV-1 protease (PR) cleavage of the Gag polyprotein triggers the assembly of mature, infectious particles. Final cleavage of Gag occurs at the junction helix between the capsid protein CA and the SP1 spacer peptide. Here we used MicroED to delineate the binding interactions of the maturation inhibitor bevirimat (BVM) using very thin frozen-hydrated, 3D microcrystals of a CTD-SP1 Gag construct with and without bound BVM. The 2.9-{\r A} MicroED structure revealed that a single BVM molecule stabilizes the six-helix bundle via both electrostatic interactions with the dimethylsuccinyl moiety and hydrophobic interactions with the pentacyclic triterpenoid ring. These results provide insight into the mechanism of action of BVM and related maturation inhibitors that will inform further drug discovery efforts. This study also demonstrates the capabilities of MicroED for structure-based drug design.

}, issn = {1091-6490}, doi = {10.1073/pnas.1806806115}, author = {Purdy, Michael D and Shi, Dan and Chrustowicz, Jakub and Hattne, Johan and Gonen, Tamir and Yeager, Mark} } @article {49585, title = {Motor cortex is an input-driven dynamical system controlling dexterous movement.}, journal = {bioRxiv}, year = {2018}, month = {2018-12-14}, pages = {266320}, abstract = {

Skillful control of movement is central to our ability to sense and manipulate the world. A large body of work in nonhuman primates has demonstrated that motor cortex provides flexible, time-varying activity patterns that control the arm during reaching and grasping. Previous studies have suggested that these patterns are generated by strong local recurrent dynamics operating autonomously from inputs during movement execution. An alternative possibility is that motor cortex requires coordination with upstream brain regions throughout the entire movement in order to yield these patterns. Here, we developed an experimental preparation in the mouse to directly test these possibilities using optogenetics and electrophysiology during a skilled reach-to-grab-to-eat task. To validate this preparation, we first established that a specific, time-varying pattern of motor cortical activity was required to produce coordinated movement. Next, in order to disentangle the contribution of local recurrent motor cortical dynamics from external input, we optogenetically held the recurrent contribution constant, then observed how motor cortical activity recovered following the end of this perturbation. Both the neural responses and hand trajectory varied from trial to trial, and this variability reflected variability in external inputs. To directly probe the role of these inputs, we used optogenetics to perturb activity in the thalamus. Thalamic perturbation at the start of the trial prevented movement initiation, and perturbation at any stage of the movement prevented progression of the hand to the target; this demonstrates that input is required throughout the movement. By comparing motor cortical activity with and without thalamic perturbation, we were able to estimate the effects of external inputs on motor cortical population activity. Thus, unlike pattern-generating circuits that are local and autonomous, such as those in the spinal cord that generate left-right alternation during locomotion, the pattern generator for reaching and grasping is distributed across multiple, strongly-interacting brain regions.

}, doi = {10.1101/266320}, author = {Sauerbrei, Britton and Guo, Jian-Zhong and Mischiati, Matteo and Guo, Wendy and Kabra, Mayank and Verma, Nakul and Branson, Kristin M and Hantman, Adam W} } @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 {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 {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 {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 {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 {49173, title = {Observing the cell in its native state: Imaging subcellular dynamics in multicellular organisms.}, journal = {Science (New York, N.Y.)}, volume = {360}, year = {2018}, month = {2018 Apr 20}, abstract = {

True physiological imaging of subcellular dynamics requires studying cells within their parent organisms, where all the environmental cues that drive gene expression, and hence the phenotypes that we actually observe, are present. A complete understanding also requires volumetric imaging of the cell and its surroundings at high spatiotemporal resolution, without inducing undue stress on either. We combined lattice light-sheet microscopy with adaptive optics to achieve, across large multicellular volumes, noninvasive aberration-free imaging of subcellular processes, including endocytosis, organelle remodeling during mitosis, and the migration of axons, immune cells, and metastatic cancer cells in vivo. The technology reveals the phenotypic diversity within cells across different organisms and developmental stages and may offer insights into how cells harness their intrinsic variability to adapt to different physiological environments.

}, issn = {1095-9203}, doi = {10.1126/science.aaq1392}, author = {Liu, Tsung-Li and Upadhyayula, Srigokul and Milkie, Daniel E and Singh, Ved and Wang, Kai and Swinburne, Ian A and Mosaliganti, Kishore R and Collins, Zach M and Hiscock, Tom W and Shea, Jamien and Kohrman, Abraham Q and Medwig, Taylor N and Dambournet, Daphne and Forster, Ryan and Cunniff, Brian and Ruan, Yuan and Yashiro, Hanako and Scholpp, Steffen and Meyerowitz, Elliot M and Hockemeyer, Dirk and Drubin, David G and Martin, Benjamin L and Matus, David Q and Koyama, Minoru and Megason, Sean G and Kirchhausen, Tom and Betzig, Eric} } @article {49115, title = {Opportunities and obstacles for deep learning in biology and medicine.}, journal = {Journal of The Royal Society Interface}, year = {2018}, month = {2018 Apr 4}, abstract = {

Deep learning describes a class of machine learning algorithms that are capable of combining raw inputs into layers of intermediate features. These algorithms have recently shown impressive results across a variety of domains. Biology and medicine are data-rich disciplines, but the data are complex and often ill-understood. Hence, deep learning techniques may be particularly well suited to solve problems of these fields. We examine applications of deep learning to a variety of biomedical problems{\textemdash}patient classification, fundamental biological processes and treatment of patients{\textemdash}and discuss whether deep learning will be able to transform these tasks or if the biomedical sphere poses unique challenges. Following from an extensive literature review, we find that deep learning has yet to revolutionize biomedicine or definitively resolve any of the most pressing challenges in the field, but promising advances have been made on the prior state of the art. Even though improvements over previous baselines have been modest in general, the recent progress indicates that deep learning methods will provide valuable means for speeding up or aiding human investigation. Though progress has been made linking a specific neural network{\textquoteright}s prediction to input features, understanding how users should interpret these models to make testable hypotheses about the system under study remains an open challenge. Furthermore, the limited amount of labelled data for training presents problems in some domains, as do legal and privacy constraints on work with sensitive health records. Nonetheless, we foresee deep learning enabling changes at both bench and bedside with the potential to transform several areas of biology and medicine.

}, doi = {10.1098/rsif.2017.0387}, author = {Ching, Travers and Himmelstein, Daniel S and Beaulieu-Jones, Brett K and Kalinin, Alexandr A and Do, Brian T and Way, Gregory P and Ferrero, Enrico and Agapow, Paul-Michael and Zietz, Michael and Hoffman, Michael M and Xie, Wei and Rosen, Gail L and Lengerich, Benjamin J and Israeli, Johnny and Lanchantin, Jack and Woloszynek, Stephen and Carpenter, Anne E and Shrikumar, Avanti and Xu, Jinbo and Cofer, Evan M} } @article {49381, title = {Optical alignment device for two-photon microscopy.}, journal = {Biomedical Optics Express}, volume = {9}, year = {2018}, month = {2018 Aug 1}, pages = {3624-9}, abstract = {

Two-photon excitation fluorescence microscopy has revolutionized our understanding of brain structure and function through the high resolution and large penetration depth it offers. Investigating neural structures\ in vivo\ requires gaining optical access to the brain, which is typically achieved by replacing a part of the skull with one or several layers of cover glass windows. To compensate for the spherical aberrations caused by the presence of these layers of glass, collar-correction objectives are typically used. However, the efficiency of this correction has been shown to depend significantly on the tilt angle between the glass window surface and the optical axis of the imaging system. Here, we first expand these observations and characterize the effect of the tilt angle on the collected fluorescence signal with thicker windows (double cover slide) and compare these results with an objective devoid of collar-correction. Second, we present a simple optical alignment device designed to rapidly minimize the tilt angle\ in vivo\ and align the optical axis of the microscope perpendicularly to the glass window to an angle below 0.25{\textdegree}, thereby significantly improving the imaging quality. Finally, we describe a tilt-correction procedure for users in an\ in vivo\ setting, enabling the accurate alignment with a resolution of \<0.2{\textdegree} in only few iterations.

}, doi = {10.1364/BOE.9.003624}, author = {Gali{\~n}anes, Gregorio L and Marchand, Paul J and Turcotte, Raphael and Pellat, Sebastien and Ji, Na and Huber, Daniel} } @article {49274, title = {Persistent sodium current mediates the steep voltage dependence of spatial coding in hippocampal pyramidal neurons.}, journal = {Neuron}, year = {2018}, month = {2018 Jun 05}, abstract = {

The mammalian hippocampus forms a cognitive map using neurons that fire according to an animal{\textquoteright}s position ("place cells") and many other behavioral and cognitive variables. The responses of these neurons are shaped by their presynaptic inputs and the nature of their postsynaptic integration. In CA1 pyramidal neurons, spatial responses in\ vivo exhibit a strikingly supralinear dependence on baseline membrane potential. The biophysical mechanisms underlying this nonlinear cellular computation are unknown. Here, through a combination of in\ vitro, in\ vivo, and in silico approaches, we show that persistent sodium current mediates the strong membrane potential dependence of place cell activity. This current operates at membrane potentials below the action potential threshold and over seconds-long timescales, mediating a powerful and rapidly reversible amplification of synaptic responses, which drives place cell firing. Thus, we identify a biophysical mechanism that shapes the coding properties of neurons composing the hippocampal cognitive map.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2018.05.025}, author = {Hsu, Ching-Lung and Zhao, Xinyu and Milstein, Aaron D and Spruston, Nelson} } @article {49049, title = {Physical basis of amyloid fibril polymorphism.}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {2018 Feb 16}, pages = {699}, abstract = {

Polymorphism is a key feature of amyloid fibril structures but it remains challenging to explain these variations for a particular sample. Here, we report electron cryomicroscopy-based reconstructions from different fibril morphologies formed by a peptide fragment from an amyloidogenic immunoglobulin light chain. The observed fibril morphologies vary in the number and cross-sectional arrangement of a structurally conserved building block. A comparison with the theoretically possible constellations reveals the experimentally observed spectrum of fibril morphologies to be governed by opposing sets of forces that primarily arise from the β-sheet twist, as well as peptide-peptide interactions within the fibril cross-section. Our results provide a framework for rationalizing and predicting the structure and polymorphism of cross-β fibrils, and suggest that a small number of physical parameters control the observed fibril architectures.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-03164-5}, author = {Close, William and Neumann, Matthias and Schmidt, Andreas and Hora, Manuel and Annamalai, Karthikeyan and Schmidt, Matthias and Reif, Bernd and Schmidt, Volker and Grigorieff, Nikolaus and F{\"a}ndrich, Marcus} } @article {49414, title = {Probing synaptic transmission and behavior in Drosophila with optogenetics: a laboratory exercise}, journal = {Journal of Undergraduate Neuroscience Education}, volume = {16}, year = {2018}, month = {2018 Summer}, pages = {A289-95}, abstract = {

Optogenetics is possibly the most revolutionary advance in neuroscience research techniques within the last decade. Here, we describe lab modules, presented at a workshop for undergraduate neuroscience educators, using optogenetic control of neurons in the fruit fly Drosophila melanogaster. Drosophila is a genetically accessible model system that combines behavioral and neurophysiological complexity, ease of use, and high research relevance. One lab module utilized two transgenic Drosophila strains, each activating specific circuits underlying startle behavior and backwards locomotion, respectively. The red-shifted channelrhodopsin, CsChrimson, was expressed in neurons sharing a common transcriptional profile, with the expression pattern further refined by the use of a Split GAL4 intersectional activation system. Another set of strains was used to investigate\ synaptic transmission at the larval neuromuscular junction. These expressed Channelrhodopsin 2 (ChR2) in glutamatergic neurons, including the motor neurons. The first strain expressed ChR2 in a wild type background, while the second contained the SNAP-25ts mutant allele, which confers heightened evoked potential amplitude and greatly increased spontaneous vesicle release frequency at the larval neuromuscular junction. These modules introduced educators and students to the use of optogenetic stimulation to control behavior and evoked release at a model synapse, and establish a basis for students to explore neurophysiology using this technique, through recapitulating classic experiments and conducting independent research.\ 

}, url = {http://www.funjournal.org/wp-content/uploads/2018/09/june-16-289.pdf?x91298}, author = {Vilinksy, Ilya and Hibbard, Karen L and Johnson Bruce R and Deitcher, David L} } @article {68434, title = {Proximity labeling: spatially resolved proteomic mapping for neurobiology.}, journal = {Curr Opin Neurobiol}, volume = {50}, year = {2018}, month = {06/2018}, pages = {17-23}, abstract = {

Understanding signaling pathways in neuroscience requires high-resolution maps of the underlying protein networks. Proximity-dependent biotinylation with engineered enzymes, in combination with mass spectrometry-based quantitative proteomics, has emerged as a powerful method to dissect molecular interactions and the localizations of endogenous proteins. Recent applications to neuroscience have provided insights into the composition of sub-synaptic structures, including the synaptic cleft and inhibitory post-synaptic density. Here we compare the different enzymes and small-molecule probes for proximity labeling in the context of cultured neurons and tissue, review existing studies, and provide technical suggestions for the in vivo application of proximity labeling.

}, keywords = {Animals, Biotinylation, Humans, Neurobiology, Neuroimaging, Proteome, Proteomics}, issn = {1873-6882}, doi = {10.1016/j.conb.2017.10.015}, author = {Han, Shuo and Li, Jiefu and Ting, Alice Y} } @article {49013, title = {Repetitive aggressive encounters generate a long-lasting internal state in Drosophila melanogaster males.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, year = {2018}, month = {2018 Jan 16}, pages = {1099-104}, abstract = {

Multiple studies have investigated the mechanisms of aggressive behavior in Drosophila; however, little is known about the effects of chronic fighting experience. Here, we investigated if repeated fighting encounters would induce an internal state that could affect the expression of subsequent behavior. We trained wild-type males to become winners or losers by repeatedly pairing them with hypoaggressive or hyperaggressive opponents, respectively. As described previously, we observed that chronic losers tend to lose subsequent fights, while chronic winners tend to win them. Olfactory conditioning experiments showed that winning is perceived as rewarding, while losing is perceived as aversive. Moreover, the effect of chronic fighting experience generalized to other behaviors, such as gap-crossing and courtship. We propose that in response to repeatedly winning or losing aggressive encounters, male flies form an internal state that displays persistence and generalization; fight outcomes can also have positive or negative valence. Furthermore, we show that the activities of the PPL1-γ1pedc dopaminergic neuron and the MBON-γ1pedc\>α/β mushroom body output neuron are required for aversion to an olfactory cue associated with losing fights.

}, issn = {1091-6490}, doi = {10.1073/pnas.1716612115}, author = {Kim, Yong-Kyu and Saver, Mathias and Simon, Jasper and Kent, Clement F and Shao, Lisha and Eddison, Mark and Agrawal, Pavan and Texada, Michael and Truman, James W and Heberlein, Ulrike} } @article {49497, title = {A resource for the antennal lobe provided by the connectome of glomerulus VA1v.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Nov 01}, abstract = {

Using FIB-SEM we report the entire synaptic connectome of glomerulus VA1v of the right antennal lobe in . Within the glomerulus we densely reconstructed all neurons, including hitherto elusive local interneurons. The -positive, sexually dimorphic VA1v included \>11,140 presynaptic sites with ~38,050 postsynaptic dendrites. These connected input olfactory receptor neurons (ORNs, 51 ipsilateral, 56 contralateral), output projection neurons (18 PNs), and local interneurons (56 of \>150 previously reported LNs). ORNs are predominantly presynaptic and PNs predominantly postsynaptic; newly reported LN circuits are largely an equal mixture and confer extensive synaptic reciprocity, except the newly reported LN2V with input from ORNs and outputs mostly to monoglomerular PNs, however. PNs were more numerous than previously reported from genetic screens, suggesting that the latter failed to reach saturation. We report a matrix of 192 bodies each having 50 connections; these form 88\% of the glomerulus{\textquoteright} pre/postsynaptic sites.

}, issn = {2050-084X}, doi = {10.7554/eLife.37550}, author = {Horne, Jane Anne and Langille, Carlie and McLin, Sari and Wiederman, Meagan and Lu, Zhiyuan and Xu, C Shan and Plaza, Stephen M and Scheffer, Louis K and Hess, Harald F and Meinertzhagen, Ian A} } @article {49060, title = {A robotic multidimensional directed evolution approach applied to fluorescent voltage reporters.}, journal = {Nature Chemical Biology}, year = {2018}, month = {2018 Feb 26}, abstract = {

We developed a new way to engineer complex proteins toward multidimensional specifications using a simple, yet scalable, directed evolution strategy. By robotically picking mammalian cells that were identified, under a microscope, as expressing proteins that simultaneously exhibit several specific properties, we can screen hundreds of thousands of proteins in a library in just a few hours, evaluating each along multiple performance axes. To demonstrate the power of this approach, we created\ a genetically encoded fluorescent voltage indicator, simultaneously optimizing its\ brightness and membrane localization using our microscopy-guided cell-picking strategy. We produced the high-performance opsin-based fluorescent voltage reporter Archon1 and demonstrated its utility by imaging spiking and millivolt-scale subthreshold and synaptic activity in acute mouse brain slices and in larval zebrafish in vivo. We also measured postsynaptic responses downstream of optogenetically controlled neurons in C. elegans.

}, issn = {1552-4469}, doi = {10.1038/s41589-018-0004-9}, author = {Piatkevich, Kiryl D and Jung, Erica E and Straub, Christoph and Linghu, Changyang and Park, Demian and Suk, Ho-Jun and Hochbaum, Daniel R and Goodwin, Daniel and Pnevmatikakis, Eftychios and Pak, Nikita and Kawashima, Takashi and Yang, Chao-Tsung and Jeff L Rhoades and Shemesh, Or and Asano, Shoh and Yoon, Young-Gyu and Freifeld, Limor and Saulnier, Jessica L and Riegler, Clemens and Engert, Florian and Hughes, Thom and Drobizhev, Mikhail and Szabo, Balint and Ahrens, Misha B and Flavell, Steven W and Sabatini, Bernardo L and Boyden, Edward S} } @article {48997, title = {Robust model-based analysis of single-particle tracking experiments with Spot-On.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Jan 04}, abstract = {

Single-particle tracking (SPT) has become an important method to bridge biochemistry and cell biology since it allows direct observation of protein binding and diffusion dynamics in live cells. However, accurately inferring information from SPT studies is challenging due to biases in both data analysis and experimental design. To address analysis bias, we introduce {\textquoteright}Spot-On{\textquoteright}, an intuitive web-interface. Spot-On implements a kinetic modeling framework that accounts for known biases, including molecules moving out-of-focus, and robustly infers diffusion constants and subpopulations from pooled single-molecule trajectories. To minimize inherent experimental biases, we implement and validate stroboscopic photo-activation SPT (spaSPT), which minimizes motion-blur bias and tracking errors. We validate Spot-On using experimentally realistic simulations and show that Spot-On outperforms other methods. We then apply Spot-On to spaSPT data from live mammalian cells spanning a wide range of nuclear dynamics and demonstrate that Spot-On consistently and robustly infers subpopulation fractions and diffusion constants.

}, issn = {2050-084X}, doi = {10.7554/eLife.33125}, author = {Hansen, Anders S and Woringer, Maxime and Grimm, Jonathan B and Lavis, Luke D and Tjian, Robert and Darzacq, Xavier} } @article {49345, title = {Robustness of spike deconvolution for neuronal calcium imaging.}, journal = {The Journal of Neuroscience : the official journal of the Society for Neuroscience}, volume = {38}, year = {2018}, month = {2018 Aug 06}, pages = {7976-85}, abstract = {

Calcium imaging is a powerful method to record the activity of neural populations in many species, but inferring spike times from calcium signals is a challenging problem. We compared multiple approaches using multiple datasets with ground truth electrophysiology, and found that simple non-negative deconvolution (NND) outperformed all other algorithms on out-of-sample test data. We introduce a novel benchmark applicable to recordings without electrophysiological ground truth, based on the correlation of responses to two stimulus repeats, and used this to show that unconstrained NND also outperformed the other algorithms when run on "zoomed out" datasets of \~{}10,000 cell recordings from the visual cortex of mice of either sex. Finally, we show that NND-based methods match the performance of a supervised method based on convolutional neural networks, while avoiding some of the biases of such methods, and at much faster running times. We therefore recommend that spikes be inferred from calcium traces using simple NND, due to its simplicity, efficiency and accuracy.The experimental method that currently allows for recordings of the largest numbers of cells simultaneously is two-photon calcium imaging. However, use of this powerful method requires that neuronal firing times be inferred correctly from the large resulting datasets. Previous studies have claimed that complex supervised learning algorithms outperform simple deconvolution methods at this task. Unfortunately, these studies suffered from several problems and biases. When we repeated the analysis, using the same data and correcting these problems, we found that simpler spike inference methods perform better. Even more importantly, we found that supervised learning methods can introduce artifactual structure into spike trains, that can in turn lead to erroneous scientific conclusions. Of the algorithms we evaluated, we found that an extremely simple method performed best in all circumstances tested, was much faster to run, and was insensitive to parameter choices, making incorrect scientific conclusions much less likely.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3339-17.2018}, author = {Pachitariu, Marius and Stringer, Carsen and Harris, Kenneth D} } @article {49495, title = {Shared and distinct transcriptomic cell types across neocortical areas.}, journal = {Nature}, volume = {563}, year = {2018}, month = {2018 Nov}, pages = {72-78}, abstract = {

The neocortex contains a multitude of cell types that are segregated into layers and functionally distinct areas. To investigate the diversity of cell types across the mouse neocortex, here we analysed 23,822 cells from two areas at distant poles of the mouse neocortex: the primary visual cortex and the anterior lateral motor cortex. We define 133 transcriptomic cell types by deep, single-cell RNA sequencing. Nearly all types of GABA (γ-aminobutyric acid)-containing neurons are shared across both areas, whereas most types of glutamatergic neurons were found in one of the two areas. By combining single-cell RNA sequencing and retrograde labelling, we match transcriptomic types of glutamatergic neurons to their long-range projection specificity. Our study establishes a combined transcriptomic and projectional taxonomy of cortical cell types from functionally distinct areas of the adult mouse cortex.

}, issn = {1476-4687}, doi = {10.1038/s41586-018-0654-5}, author = {Tasic, Bosiljka and Yao, Zizhen and Graybuck, Lucas T and Smith, Kimberly A and Nguyen, Thuc Nghi and Bertagnolli, Darren and Goldy, Jeff and Garren, Emma and Economo, Michael N and Viswanathan, Sarada and Penn, Osnat and Bakken, Trygve and Menon, Vilas and Miller, Jeremy and Fong, Olivia and Hirokawa, Karla E and Lathia, Kanan and Rimorin, Christine and Tieu, Michael and Larsen, Rachael and Casper, Tamara and Barkan, Eliza and Kroll, Matthew and Parry, Sheana and Shapovalova, Nadiya V and Hirschstein, Daniel and Pendergraft, Julie and Sullivan, Heather A and Kim, Tae Kyung and Szafer, Aaron and Dee, Nick and Groblewski, Peter and Wickersham, Ian and Cetin, Ali and Harris, Julie A and Levi, Boaz P and Sunkin, Susan M and Madisen, Linda and Daigle, Tanya L and Looger, Loren and Bernard, Amy and Phillips, John and Lein, Ed and Hawrylycz, Michael and Svoboda, Karel and Jones, Allan R and Koch, Christof and Zeng, Hongkui} } @article {49485, title = {Social isolation-induced epigenetic and transcriptional changes in Drosophila dopaminergic neurons.}, journal = {bioRxiv}, year = {2018}, month = {2018 Oct 14}, abstract = {Epigenetic mechanisms play fundamental roles in brain function and behavior and stressors such as social isolation can alter animal behavior via epigenetic mechanisms. However, due to cellular heterogeneity, identifying cell-type-specific epigenetic changes in the brain is challenging. Here we report first use of a modified INTACT method in behavioral epigenetics of Drosophila: a method we call mini-INTACT. Using ChIP-seq on mini-INTACT purified dopaminergic nuclei, we identified epigenetic signatures in socially-isolated and socially-enriched Drosophila males. Social experience altered the epigenetic landscape in clusters of genes involved in transcription and neural function. Some of these alterations were predicted by expression changes of four transcription factors and the prevalence of their binding sites in several clusters. These transcription factors were previously identified as activity-regulated genes and their knockdown in dopaminergic neurons reduced the effects of social experience on sleep. Our work enables the use of Drosophila as a model for cell-type-specific behavioral epigenetics. }, doi = {10.1101/443226}, author = {Agrawal, Pavan and Chung, Phuong and Heberlein, Ulrike and Kent, Clement F} } @article {48984, title = {Stability, affinity and chromatic variants of the glutamate sensor iGluSnFR.}, journal = {Nature Methods}, volume = {15}, year = {2018}, month = {2018 Nov}, pages = {9386-9}, abstract = {

Single-wavelength fluorescent reporters allow visualization of specific neurotransmitters with high spatial and temporal resolution. We report variants of intensity-based glutamate-sensing fluorescent reporter (iGluSnFR) that are functionally brighter; detect submicromolar to millimolar amounts of glutamate; and have blue, cyan, green, or yellow emission profiles. These variants could be imaged in vivo in cases where original iGluSnFR was too dim, resolved glutamate transients in dendritic spines and axonal boutons, and allowed imaging at kilohertz rates.

}, doi = {10.1038/s41592-018-0171-3}, author = {Marvin, Jonathan S and Scholl, Benjamin and Wilson, Daniel E and Podgorski, Kaspar and Kazemipour, Abbas and Mueller, Johannes Alexander and Schoch-McGovern, Susanne and Wang, Samuel S-H and Quiroz, Francisco Jose Urra and Rebola, Nelson and Bao, Huan and Little, Justin P and Tkachuk, Ariana N and Hantman, Adam W and Chapman, Edwin R and Dietrich, Dirk and DiGregorio, David A and Fitzpatrick, David and Looger, Loren L} } @article {49584, title = {Stem cells repurpose proliferation to contain a breach in their niche barrier.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Dec 06}, abstract = {

Adult stem cells are responsible for life-long tissue maintenance. They reside in and interact with specialized tissue microenvironments (niches). Using murine hair follicle as a model, we show that when junctional perturbations in the niche disrupt barrier function, adjacent stem cells dramatically change their transcriptome independent of bacterial invasion and become capable of directly signaling to and recruiting immune cells. Additionally, these stem cells elevate cell cycle transcripts which reduce their quiescence threshold, enabling them to selectively proliferate within this microenvironment of immune distress cues. However, rather than mobilizing to fuel new tissue regeneration, these ectopically proliferative stem cells remain within their niche to contain the breach. Together, our findings expose a potential communication relay system that operates from the niche to the stem cells to the immune system and back. The repurposing of proliferation by these stem cells patch the breached barrier, stoke the immune response and restore niche integrity.

}, issn = {2050-084X}, doi = {10.7554/eLife.41661}, author = {Lay, Kenneth and Yuan, Shaopeng and Gur-Cohen, Shiri and Miao, Yuxuan and Han, Tianxiao and Naik, Shruti and Pasolli, H Amalia and Larsen, Samantha B and Fuchs, Elaine} } @article {49448, title = {Strength of correlations in strongly recurrent neuronal networks.}, journal = {Physical Review X}, year = {2018}, month = {2018 Sep 17}, pages = {031072}, abstract = {

Spatiotemporal correlations in brain activity are functionally important and have been implicated in perception, learning and plasticity, exploratory behavior, and various aspects of cognition. Neurons in the cerebral cortex are strongly interacting. Their activity is temporally irregular and can exhibit substantial correlations. However, how the collective dynamics of highly recurrent and strongly interacting neurons can evolve into a state in which the activity of individual cells is highly irregular yet macroscopically correlated is an open question. Here, we develop a general theory that relates the strength of pairwise correlations to the anatomical features of networks of strongly coupled neurons. To this end, we investigate networks of binary units. When interactions are strong, the activity is irregular in a large region of parameter space. We find that despite the strong interactions, the correlations are generally very weak. Nevertheless, we identify architectural features, which if present, give rise to strong correlations without destroying the irregularity of the activity. For networks with such features, we determine how correlations scale with the network size and the number of connections. Our work shows the mechanism by which strong correlations can be consistent with highly irregular activity, two hallmarks of neuronal dynamics in the central nervous system.

}, doi = {10.1103/PhysRevX.8.031072}, author = {Darshan, Ran and van Vreeswijk, Carl and Hansel, David} } @article {49574, title = {Structure of Plasmodium falciparum Rh5-CyRPA-Ripr invasion complex.}, journal = {Nature}, volume = {565}, year = {2018}, month = {2018 Dec 12}, pages = {118-21}, abstract = {

Plasmodium falciparum causes the severe form of malaria that has high levels of mortality in humans. Blood-stage merozoites of P. falciparum invade erythrocytes, and this requires interactions between multiple ligands from the parasite and receptors in hosts. These interactions include the binding of the Rh5-CyRPA-Ripr complex with the erythrocyte receptor basigin, which is an essential step for entry into human erythrocytes. Here we show that the Rh5-CyRPA-Ripr complex binds the erythrocyte cell line JK-1 significantly better than does Rh5 alone, and that this binding occurs through the insertion of Rh5 and Ripr into host membranes as a complex with high molecular weight. We report a cryo-electron microscopy structure of the Rh5-CyRPA-Ripr complex at subnanometre resolution, which reveals the organization of this essential invasion complex and the mode of interactions between members of the complex, and shows that CyRPA is a critical mediator of complex assembly. Our structure identifies blades 4-6 of the β-propeller of CyRPA as contact sites for Rh5 and Ripr. The limited contacts between Rh5-CyRPA and CyRPA-Ripr are consistent with the dissociation of Rh5 and Ripr from CyRPA for membrane insertion. A comparision of the crystal structure of Rh5-basigin with the cryo-electron microscopy structure of Rh5-CyRPA-Ripr suggests that Rh5 and Ripr are positioned parallel to the erythrocyte membrane before membrane insertion. This provides information on the function of this complex, and thereby provides insights into invasion by P. falciparum.

}, issn = {1476-4687}, doi = {10.1038/s41586-018-0779-6}, author = {Wong, Wilson and Huang, Rick and Menant, S{\'e}bastien and Hong, Chuan and Sandow, Jarrod J and Birkinshaw, Richard W and Healer, Julie and Hodder, Anthony N and Kanjee, Usheer and Tonkin, Christopher J and Heckmann, Denise and Soroka, Vladislav and S{\o}gaard, Teit Max Moscote and J{\o}rgensen, Thomas and Duraisingh, Manoj T and Czabotar, Peter E and de Jongh, Willem A and Tham, Wai-Hong and Webb, Andrew I and Yu, Zhiheng and Cowman, Alan F} } @article {49371, title = {Structure of the mammalian TRPM7, a magnesium channel required during embryonic development.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, year = {2018}, month = {2018 Aug 14}, pages = {E8201-10}, abstract = {

The transient receptor potential ion channel subfamily M, member 7 (TRPM7), is a ubiquitously expressed protein that is required for mouse embryonic development. TRPM7 contains both an ion channel and an α-kinase. The channel domain comprises a nonselective cation channel with notable permeability to Mg and Zn Here, we report the closed state structures of the mouse TRPM7 channel domain in three different ionic conditions to overall resolutions of 3.3, 3.7, and 4.1 {\r A}. The structures reveal key residues for an ion binding site in the selectivity filter, with proposed partially hydrated Mg ions occupying the center of the conduction pore. In high [Mg], a prominent external disulfide bond is found in the pore helix, which is essential for ion channel function. Our results provide a structural framework for understanding the TRPM1/3/6/7 subfamily and extend the knowledge base upon which to study the diversity and evolution of TRP channels.

}, issn = {1091-6490}, doi = {10.1073/pnas.1810719115}, author = {Duan, Jingjing and Li, Zongli and Li, Jian and Hulse, Raymond E and Santa-Cruz, Ana and Valinsky, William C and Abiria, Sunday A and Krapivinsky, Grigory and Zhang, Jin and Clapham, David E} } @article {49006, title = {Sub-{\r a}ngstr{\"o}m cryo-EM structure of a prion protofibril reveals a polar clasp.}, journal = {Nature Structural \& Molecular Biology}, year = {2018}, month = {2018 Jan 15}, abstract = {

The atomic structure of the infectious, protease-resistant, β-sheet-rich and fibrillar mammalian prion remains unknown. Through the cryo-EM method MicroED, we reveal the sub-{\r a}ngstr{\"o}m-resolution structure of a protofibril formed by a wild-type segment from the β2-α2 loop of the bank vole prion protein. The structure of this protofibril reveals a stabilizing network of hydrogen bonds that link polar zippers within a sheet, producing motifs we have named {\textquoteright}polar clasps{\textquoteright}.

}, issn = {1545-9985}, doi = {10.1038/s41594-017-0018-0}, author = {Gallagher-Jones, Marcus and Glynn, Calina and Boyer, David R and Martynowycz, Michael W and Hernandez, Evelyn and Miao, Jennifer and Zee, Chih-Te and Novikova, Irina V and Goldschmidt, Lukasz and McFarlane, Heather T and Helguera, Gustavo F and Evans, James E and Sawaya, Michael R and Cascio, Duilio and Eisenberg, David S and Gonen, Tamir and Rodriguez, Jose A} } @article {49220, title = {Synaptic cleft segmentation in non-isotropic volume electron microscopy of the complete Drosophila brain.}, journal = {Medical Image Computing and Computer Assisted Intervention {\textendash} MICCAI 2018}, year = {2018}, month = {2018 Sep 26}, pages = {317-25}, abstract = {

Neural circuit reconstruction at single synapse resolution is increasingly recognized as crucially important to decipher the function of biological nervous systems. Volume electron microscopy in serial transmission or scanning mode has been demonstrated to provide the necessary resolution to segment or trace all neurites and to annotate all synaptic connections.\ 
Automatic annotation of synaptic connections has been done successfully in near isotropic electron microscopy of vertebrate model organisms. Results on non-isotropic data in insect models, however, are not yet on par with human annotation.\ 
We designed a new 3D-U-Net architecture to optimally represent isotropic fields of view in non-isotropic data. We used regression on a signed distance transform of manually annotated synaptic clefts of the CREMI challenge dataset to train this model and observed significant improvement over the state of the art.\ 
We developed open source software for optimized parallel prediction on very large volumetric datasets and applied our model to predict synaptic clefts in a 50 tera-voxels dataset of the complete Drosophila brain. Our model generalizes well to areas far away from where training data was available.

}, doi = {10.1007/978-3-030-00934-2_36}, author = {Heinrich, Larissa and Funke, Jan and Pape, Constantin and Nunez-Iglesias, Juan and Saalfeld, Stephan} } @article {49470, title = {Thy1 transgenic mice expressing the red fluorescent calcium indicator jRGECO1a for neuronal population imaging in vivo.}, journal = {PloS One}, volume = {13}, year = {2018}, month = {2018}, pages = {e0205444}, abstract = {

Calcium imaging is commonly used to measure the neural activity of large groups of neurons in mice. Genetically encoded calcium indicators (GECIs) can be delivered for this purpose using non-invasive genetic methods. Compared to viral gene transfer, transgenic targeting of GECIs provides stable long-term expression and obviates the need for invasive viral injections. Transgenic mice expressing the green GECI GCaMP6 are already widely used. Here we present the generation and characterization of transgenic mice expressing the sensitive red GECI jRGECO1a, driven by the Thy1 promoter. Four transgenic lines with different expression patterns showed sufficiently high expression for cellular in vivo imaging. We used two-photon microscopy to characterize visual responses of individual neurons in the visual cortex in vivo. The signal-to-noise ratio in transgenic mice was comparable to, or better than, mice transduced with adeno-associated virus. In addition, we show that Thy1-jRGECO1a transgenic mice are useful for transcranial population imaging and functional mapping using widefield fluorescence microscopy. We also demonstrate imaging of visual responses in retinal ganglion cells in vitro. Thy1-jRGECO1a transgenic mice are therefore a useful addition to the toolbox for imaging activity in intact neural networks.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0205444}, author = {Dana, Hod and Novak, Ondrej and Guardado-Montesino, Michael and Fransen, James W and Hu, Amy and Borghuis, Bart G and Guo, Caiying and Kim, Douglas S and Svoboda, Karel} } @article {49456, title = {A toolbox for multiplexed super-resolution imaging of the E. coli nucleoid and membrane using novel PAINT labels.}, journal = {Scientific Reports}, volume = {8}, year = {2018}, month = {2018 Oct 03}, pages = {14768}, abstract = {

Maintenance of the bacterial homeostasis initially emanates from interactions between proteins and the bacterial nucleoid. Investigating their spatial correlation requires high spatial resolution, especially in tiny, highly confined and crowded bacterial cells. Here, we present super-resolution microscopy using a palette of fluorescent labels that bind transiently to either the membrane or the nucleoid of fixed E. coli cells. The presented labels are easily applicable, versatile and allow long-term single-molecule super-resolution imaging independent of photobleaching. The different spectral properties allow for multiplexed imaging in combination with other localisation-based super-resolution imaging techniques. As examples for applications, we demonstrate correlated super-resolution imaging of the bacterial nucleoid with the position of genetic loci, of nascent DNA in correlation to the entire nucleoid, and of the nucleoid of metabolically arrested cells. We furthermore show that DNA- and membrane-targeting labels can be combined with photoactivatable fluorescent proteins and visualise the nano-scale distribution of RNA polymerase relative to the nucleoid in drug-treated E. coli cells.

}, issn = {2045-2322}, doi = {10.1038/s41598-018-33052-3}, author = {Spahn, Christoph K and Glaesmann, Mathilda and Grimm, Jonathan B and Ayala, Anthony X and Lavis, Luke D and Heilemann, Mike} } @article {49413, title = {Topographic precision in sensory and motor corticostriatal projections varies across cell type and cortical area.}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {2018 Sep 03}, pages = {3549}, abstract = {

The striatum shows general topographic organization and regional differences in behavioral functions. How corticostriatal topography differs across cortical areas and cell types to support these distinct functions is unclear. This study contrasted corticostriatal projections from two layer 5 cell types, intratelencephalic (IT-type) and pyramidal tract (PT-type) neurons, using viral vectors expressing fluorescent reporters in Cre-driver mice. Corticostriatal projections from sensory and motor cortex are somatotopic, with a decreasing topographic specificity as injection sites move from sensory to motor and frontal areas. Topographic organization differs between IT-type and PT-type neurons, including injections in the same site, with IT-type neurons having higher topographic stereotypy than PT-type neurons. Furthermore, IT-type projections from interconnected cortical areas have stronger correlations in corticostriatal targeting than PT-type projections do. As predicted by a longstanding model, corticostriatal projections of interconnected cortical areas form parallel circuits in the basal ganglia.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-05780-7}, author = {Hooks, Bryan M and Papale, Andrew E and Paletzki, Ronald F and Feroze, Muhammad W and Eastwood, Brian S and Couey, Jonathan J and Winnubst, Johan and Chandrashekar, Jayaram and Gerfen, Charles R} } @article {49386, title = {An unbiased template of the Drosophila brain and ventral nerve cord.}, journal = {bioRxiv}, year = {2018}, month = {2018 Jul 25}, abstract = {

The fruit fly Drosophila melanogaster is an important model organism for neuroscience with a wide array of genetic tools that enable the mapping of individuals neurons and neural subtypes. Brain templates are essential for comparative biological studies because they enable analyzing many individuals in a common reference space. Several central brain templates exist for Drosophila, but every one is either biased, uses sub-optimal tissue preparation, is imaged at low resolution, or does not account for artifacts. No publicly available Drosophila ventral nerve cord template currently exists. In this work, we created high-resolution templates of the Drosophila brain and ventral nerve cord using the best-available technologies for imaging, artifact correction, stitching, and template construction using groupwise registration. We evaluated our central brain template against the four most competitive, publicly available brain templates and demonstrate that ours enables more accurate registration with fewer local deformations in shorter time.

}, doi = {10.1101/376384}, author = {Bogovic, John A and Otsuna, Hideo and Heinrich, Larissa and Ito, Masayoshi and Jeter, Jennifer and Meissner, Geoffrey W and Nern, Aljoscha and Colonell, Jennifer and Malkesman, Oz and Saalfeld, Stephan} } @article {48839, title = {Vision and locomotion shape the interactions between neuron types in mouse visual cortex.}, journal = {Neuron}, volume = {98}, year = {2018}, month = {2018 May 2}, pages = {602-15}, abstract = {

Cortical computation arises from the interaction of multiple neuronal\ types, including pyramidal (Pyr) cells and interneurons expressing Sst, Vip, or Pvalb. To study the circuit underlying such\ interactions, we imaged these four\ types\ of cells in\ mouse\ primary\ visual\ cortex(V1). Our recordings in darkness were consistent with a "disinhibitory" model in which\ locomotion\ activates Vip cells, thus inhibiting Sst cells and disinhibiting Pyr cells. However, the disinhibitory model failed when\ visual\ stimuli were present:\ locomotion\ increased Sst cell responses to large stimuli and Vip cell responses to small stimuli. A recurrent network model successfully predicted each cell type{\textquoteright}s activity from the measured activity of other\ types. Capturing the effects of\ locomotion, however, required allowing it to increase feedforward synaptic weights and modulate recurrent weights. This network model summarizes interneuron\ interactions\ and suggests that\ locomotion\ may alter cortical computation by changing effective synaptic connectivity.

}, doi = {https://doi.org/10.1101/058396}, author = {Dipoppa, Mario and Ranson, Adam and Krumin, Michael and Pachitariu, Marius and Carandini, Matteo and Harris, Kenneth D} } @article {49512, title = {Visualizing intracellular organelle and cytoskeletal interactions at nanoscale resolution on millisecond timescales. }, journal = {Cell}, volume = {175}, year = {2018}, month = {2018 Nov 15}, pages = {1430-42}, abstract = {In eukaryotic cells, organelles and the cytoskeleton undergo highly dynamic yet organized interactions capable of orchestrating complex cellular functions. Visualizing these interactions requires noninvasive, long-duration imaging of the intracellular environment at high spatiotemporal resolution and low background. To achieve these normally opposing goals, we developed grazing incidence structured illumination microscopy (GI-SIM) that is capable of imaging dynamic events near the basal cell cortex at 97-nm resolution and 266 frames/s over thousands of time points. We employed multi-color GI-SIM to characterize the fast dynamic interactions of diverse organelles and the cytoskeleton, shedding new light on the complex behaviors of these structures. Precise measurements of microtubule growth or shrinkage events helped distinguish among models of microtubule dynamic instability. Analysis of endoplasmic reticulum (ER) interactions with other organelles or microtubules uncovered new ER remodeling mechanisms, such as hitchhiking of the ER on motile organelles. Finally, ER-mitochondria contact sites were found to promote both mitochondrial fission and fusion.}, doi = {10.1016/j.cell.2018.09.057}, author = {Guo, Yuting and Li, Di and Zhang, Siwei and Yang, Yanrui and Liu, Jia-Jia and Wang, Xinyu and Liu, Chong and Milkie, Daniel E and Moore, Regan P and Tulu, U Serdar and Kiehart, Daniel P and Hu, Junjie and Lippincott-Schwartz, Jennifer and Betzig, Eric and Li, Dong} } @article {49576, title = {Whole-cell, 3D and multi-color STED imaging with exchangeable fluorophores.}, journal = {Nano Letters}, volume = {19}, year = {2018}, month = {2018 Dec 10}, pages = {500-5}, abstract = {

We demonstrate STED microscopy of whole bacterial and eukaryotic cells using fluorogenic labels that reversibly bind to their target structure. A constant exchange of labels guarantees the removal of photobleached fluorophores and their replacement by intact fluorophores, thereby circumventing bleaching-related limitations of STED super-resolution imaging. We achieve a constant labeling density and demonstrate a fluorescence signal for long and theoretically unlimited acquisition times. Using this concept, we demonstrate whole-cell, 3D, multi-color and live cell STED microscopy.

}, issn = {1530-6992}, doi = {10.1021/acs.nanolett.8b04385}, author = {Spahn, Christoph and Grimm, Jonathan B and Lavis, Luke D and Lampe, Marko and Heilemann, Mike} } @article {48218, title = {Actin dynamics and competition for myosin monomer govern the sequential amplification of myosin filaments.}, journal = {Nature Cell Biology}, volume = {19}, year = {2017}, month = {2017 Jan 23}, pages = {85-93}, abstract = {

The cellular mechanisms governing non-muscle myosin II (NM2) filament assembly are largely unknown. Using EGFP-NM2A knock-in fibroblasts and multiple super-resolution imaging modalities, we characterized and quantified the sequential amplification of NM2 filaments within lamellae, wherein filaments emanating from single nucleation events continuously partition, forming filament clusters that populate large-scale actomyosin structures deeper in the cell. Individual partitioning events coincide spatially and temporally with the movements of diverging actin fibres, suppression of which inhibits partitioning. These and other data indicate that NM2A filaments are partitioned by the dynamic movements of actin fibres to which they are bound. Finally, we showed that partition frequency and filament growth rate in the lamella depend on MLCK, and that MLCK is competing with centrally active ROCK for a limiting pool of monomer with which to drive lamellar filament assembly. Together, our results provide new insights into the mechanism and spatio-temporal regulation of NM2 filament assembly in cells.

}, issn = {1476-4679}, doi = {10.1038/ncb3463}, author = {Beach, Jordan R and Bruun, Kyle S and Shao, Lin and Li, Dong and Swider, Zac and Remmert, Kirsten and Zhang, Yingfan and Conti, Mary A and Adelstein, Robert S and Rusan, Nasser M and Betzig, Eric and Hammer, John A} } @article {48843, title = {Actin-based protrusions of migrating neutrophils are intrinsically lamellar and facilitate direction changes.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Sep 26}, abstract = {

Leukocytes and other amoeboid cells change shape as they move, forming highly dynamic, actin-filled pseudopods. Although we understand much about the architecture and dynamics of thin lamellipodia made by slow-moving cells on flat surfaces, conventional light microscopy lacks the spatial and temporal resolution required to track complex pseudopods of cells moving in three dimensions. We therefore employed lattice light sheet microscopy to perform three-dimensional, time-lapse imaging of neutrophil-like HL-60 cells crawling through collagen matrices. To analyze three-dimensional pseudopods we: (i) developed fluorescent probe combinations that distinguish cortical actin from dynamic, pseudopod-forming actin networks, and (ii) adapted molecular visualization tools from structural biology to render and analyze complex cell surfaces. Surprisingly, three-dimensional pseudopods turn out to be composed of thin (\<0.75 {\textmu}m), flat sheets that sometimes interleave to form rosettes. Their laminar nature is not templated by an external surface, but likely reflects a linear arrangement of regulatory molecules. Although we find that Arp2/3-dependent pseudopods are dispensable for three-dimensional locomotion, their elimination dramatically decreases the frequency of cell turning, and pseudopod dynamics increase when cells change direction, highlighting the important role pseudopods play in pathfinding.

}, issn = {2050-084X}, doi = {10.7554/eLife.26990}, author = {Fritz-Laylin, Lillian K and Riel-Mehan, Megan and Chen, Bi-Chang and Lord, Samuel J and Goddard, Thomas D and Ferrin, Thomas E and Nicholson-Dykstra, Susan M and Higgs, Henry and Johnson, Graham T and Betzig, Eric and Mullins, R Dyche} } @article {49082, title = {Advances in neural engineering for rehabilitation.}, journal = {Behavioural Neurology}, volume = {2017}, year = {2017}, month = {2017}, pages = {9240921}, issn = {1875-8584}, doi = {10.1155/2017/9240921}, author = {Hu, Xiaoling and Zhao, Ting and Yao, Jun and Kuang, Yu and Yang, Yuan} } @article {48534, title = {Applying systems-level spectral imaging and analysis to reveal the organelle interactome.}, journal = {Nature}, year = {2017}, month = {2017 May 24}, abstract = {

The organization of the eukaryotic cell into discrete membrane-bound organelles allows for the separation of incompatible biochemical processes, but the activities of these organelles must be coordinated. For example, lipid metabolism is distributed between the endoplasmic reticulum for lipid synthesis, lipid droplets for storage and transport, mitochondria and peroxisomes for β-oxidation, and lysosomes for lipid hydrolysis and recycling. It is increasingly recognized that organelle contacts have a vital role in diverse cellular functions. However, the spatial and temporal organization of organelles within the cell remains poorly characterized, as fluorescence imaging approaches are limited in the number of different labels that can be distinguished in a single image. Here we present a systems-level analysis of the organelle interactome using a multispectral image acquisition method that overcomes the challenge of spectral overlap in the fluorescent protein palette. We used confocal and lattice light sheet instrumentation and an imaging informatics pipeline of five steps to achieve mapping of organelle numbers, volumes, speeds, positions and dynamic inter-organelle contacts in live cells from a monkey fibroblast cell line. We describe the frequency and locality of two-, three-, four- and five-way interactions among six different membrane-bound organelles (endoplasmic reticulum, Golgi, lysosome, peroxisome, mitochondria and lipid droplet) and show how these relationships change over time. We demonstrate that each organelle has a characteristic distribution and dispersion pattern in three-dimensional space and that there is a reproducible pattern of contacts among the six organelles, that is affected by microtubule and cell nutrient status. These live-cell confocal and lattice light sheet spectral imaging approaches are applicable to any cell system expressing multiple fluorescent probes, whether in normal conditions or when cells are exposed to disturbances such as drugs, pathogens or stress. This methodology thus offers a powerful descriptive tool and can be used to develop hypotheses about cellular organization and dynamics.

}, issn = {1476-4687}, doi = {10.1038/nature22369}, author = {Valm, Alex M and Cohen, Sarah and Legant, Wesley R and Melunis, Justin and Hershberg, Uri and Wait, Eric and Cohen, Andrew R and Davidson, Michael W and Betzig, Eric and Lippincott-Schwartz, Jennifer} } @article {48156, title = {Atomic structures of fibrillar segments of hIAPP suggest tightly mated β-sheets are important for cytotoxicity.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Jan 03}, abstract = {

hIAPP fibrils are associated with Type-II Diabetes, but the link of hIAPP structure to islet cell death remains elusive. Here we observe that hIAPP fibrils are cytotoxic to cultured pancreatic β-cells, leading us to determine the structure and cytotoxicity of protein segments composing the amyloid spine of hIAPP. Using the cryoEM method MicroED, we discover that one segment, 19-29 S20G, forms pairs of β-sheets mated by a dry interface that share structural features with and are similarly cytotoxic to full-length hIAPP fibrils. In contrast, a second segment, 15-25 WT, forms non-toxic labile β-sheets. These segments possess different structures and cytotoxic effects, however, both can seed full-length hIAPP, and cause hIAPP to take on the cytotoxic and structural features of that segment. These results suggest that protein segment structures represent polymorphs of their parent protein and that segment 19-29 S20G may serve as a model for the toxic spine of hIAPP.

}, issn = {2050-084X}, doi = {10.7554/eLife.19273}, author = {Krotee, Pascal and Rodriguez, Jose A and Sawaya, Michael R and Cascio, Duilio and Reyes, Francis E and Shi, Dan and Hattne, Johan and Nannenga, Brent L and Oskarsson, Marie E and Philipp, Stephan and Griner, Sarah and Jiang, Lin and Glabe, Charles G and Westermark, Gunilla T and Gonen, Tamir and Eisenberg, David S} } @article {48265, title = {Atomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED.}, journal = {Nature Methods}, volume = {14}, year = {2017}, month = {2017 Feb 13}, pages = {399-402}, abstract = {

Traditionally, crystallographic analysis of macromolecules has depended on large, well-ordered crystals, which often require significant effort to obtain. Even sizable crystals sometimes suffer from pathologies that render them inappropriate for high-resolution structure determination. Here we show that fragmentation of large, imperfect crystals into microcrystals or nanocrystals can provide a simple path for high-resolution structure determination by the cryoEM method MicroED and potentially by serial femtosecond crystallography.

}, issn = {1548-7105}, doi = {10.1038/nmeth.4178}, author = {de la Cruz, M Jason and Hattne, Johan and Shi, Dan and Seidler, Paul and Rodriguez, Jose and Reyes, Francis E and Sawaya, Michael R and Cascio, Duilio and Weiss, Simon C and Kim, Sun Kyung and Hinck, Cynthia S and Hinck, Andrew P and Calero, Guillermo and Eisenberg, David and Gonen, Tamir} } @article {48266, title = {Axonal Endoplasmic Reticulum Ca(2+) Content Controls Release Probability in CNS Nerve Terminals.}, journal = {Neuron}, volume = {93}, year = {2017}, month = {2017 Jan 30}, pages = {867-81}, abstract = {

Although the endoplasmic reticulum (ER) extends throughout axons and axonal ER dysfunction is implicated in numerous neurological diseases, its role at nerve terminals is poorly understood. We developed novel genetically encoded ER-targeted low-affinity Ca(2+) indicators optimized for examining axonal ER Ca(2+). Our experiments revealed that presynaptic function is tightly controlled by ER Ca(2+) content. We found that neuronal activity drives net Ca(2+) uptake into presynaptic ER although this activity does not contribute significantly to shaping cytosolic Ca(2+) except during prolonged repetitive firing. In contrast, we found that axonal ER acts as an actuator of plasma membrane (PM) function: [Ca(2+)]ER controls STIM1 activation in presynaptic terminals, which results in the local modulation of presynaptic function, impacting activity-driven Ca(2+) entry and release probability. These experiments reveal a critical role of presynaptic ER in the control of neurotransmitter release and will help frame future investigations into the molecular basis of ER-driven neuronal disease states.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2017.01.010}, author = {de Juan-Sanz, Jaime and Holt, Graham T and Schreiter, Eric R and de Juan, Fernando and Kim, Douglas S and Ryan, Timothy A} } @article {48715, title = {Best practices for managing large CryoEM facilities.}, journal = {Journal of Structural Biology}, volume = {199}, year = {2017}, month = {2017-08-04}, pages = {225-36}, abstract = {

This paper provides an overview of the discussion and presentations from the Workshop on the Management of Large CryoEM Facilities held at the New York Structural Biology Center, New York, NY on February 6{\textendash}7, 2017. A major objective of the workshop was to discuss best practices for managing cryoEM facilities. The discussions were largely focused on supporting single-particle methods for cryoEM and topics included: user access, assessing projects, workflow, sample handling, microscopy, data management and processing, and user training.

}, doi = {10.1016/j.jsb.2017.07.011}, author = {Alewijnse, Bart and Ashton, Alun W and Chambers, Melissa G and Chen, Songye and Cheng, Anchi and Ebrahim, Mark and Eng, Edward T and Hagen, Wim JH and Koster, Abraham J and Lopez, Claudia S and Lukoyanova, Natalya and Ortega, Joaquin and Renault, Ludovic and Reyntjens, Steve and Rice, William J and Scapin, Giovanna and Schrijver, Raymond and Siebert, Alistair and Stagg, Scott M and et al} } @article {48267, title = {A brainstem-spinal cord inhibitory circuit for mechanical pain modulation by GABA and Enkephalins.}, journal = {Neuron}, volume = {93}, year = {2017}, month = {2017 Jan 31}, pages = {822-39}, abstract = {

Pain thresholds are, in part, set as a function of emotional and internal states by descending modulation of nociceptive transmission in the spinal cord. Neurons of the rostral ventromedial medulla (RVM) are thought to critically contribute to this process; however, the neural circuits and synaptic mechanisms by which distinct populations of RVM neurons facilitate or diminish pain remain elusive. Here we used in\ vivo opto/chemogenetic manipulations and trans-synaptic tracing of genetically identified dorsal horn and RVM neurons to uncover an RVM-spinal cord-primary afferent circuit controlling pain thresholds. Unexpectedly, we found that RVM GABAergic neurons facilitate mechanical pain by inhibiting dorsal horn enkephalinergic/GABAergic interneurons. We further demonstrate that these interneurons gate sensory inputs and control pain through temporally coordinated enkephalin- and GABA-mediated presynaptic inhibition of somatosensory neurons. Our results uncover a descending disynaptic inhibitory circuit that facilitates mechanical pain, is engaged during stress, and could be targeted to establish higher pain thresholds.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2017.01.008}, author = {Fran{\c c}ois, Amaury and Low, Sarah A and Sypek, Elizabeth I and Christensen, Amelia J and Sotoudeh, Chaudy and Beier, Kevin T and Ramakrishnan, Charu and Ritola, Kimberly D and Sharif-Naeini, Reza and Deisseroth, Karl and Delp, Scott L and Malenka, Robert C and Luo, Liqun and Hantman, Adam W and Scherrer, Gr{\'e}gory} } @article {48645, title = {Building bridges between cellular and molecular structural biology.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Jul 06}, abstract = {

The integration of cellular and molecular structural data is key to understanding the function of macromolecular assemblies and complexes in their in vivo context. Here we report on the outcomes of a workshop that discussed how to integrate structural data from a range of public archives. The workshop identified two main priorities: the development of tools and file formats to support segmentation (that is, the decomposition of a three-dimensional volume into regions that can be associated with defined objects), and the development of tools to support the annotation of biological structures.

}, issn = {2050-084X}, doi = {10.7554/eLife.25835}, author = {Patwardhan, Ardan and Brandt, Robert and Butcher, Sarah J and Collinson, Lucy and Gault, David and Gr{\"u}newald, Kay and Hecksel, Corey and Huiskonen, Juha T and Iudin, Andrii and Jones, Martin L and Korir, Paul K and Koster, Abraham J and Lagerstedt, Ingvar and Lawson, Catherine L and Mastronarde, David and McCormick, Matthew and Parkinson, Helen and Rosenthal, Peter B and Saalfeld, Stephan and Saibil, Helen R and Sarntivijai, Sirarat and Solanes Valero, Irene and Subramaniam, Sriram and Swedlow, Jason R and Tudose, Ilinca and Winn, Martyn and Kleywegt, Gerard J} } @article {65894, title = {A bulky glycocalyx fosters metastasis formation by promoting G1 cell cycle progression}, journal = {eLife}, volume = {6}, year = {2017}, month = {Sep-12-2018}, abstract = {

Metastasis depends upon cancer cell growth and survival within the metastatic niche. Tumors which remodel their glycocalyces, by overexpressing bulky glycoproteins like mucins, exhibit a higher predisposition to metastasize, but the role of mucins in oncogenesis remains poorly understood. Here we report that a bulky glycocalyx promotes the expansion of disseminated tumor cells in vivo by fostering integrin adhesion assembly to permit G1 cell cycle progression. We engineered tumor cells to display glycocalyces of various thicknesses by coating them with synthetic mucin-mimetic glycopolymers. Cells adorned with longer glycopolymers showed increased metastatic potential, enhanced cell cycle progression, and greater levels of integrin-FAK mechanosignaling and Akt signaling in a syngeneic mouse model of metastasis. These effects were mirrored by expression of the ectodomain of cancer-associated mucin MUC1. These findings functionally link mucinous proteins with tumor aggression, and offer a new view of the cancer glycocalyx as a major driver of disease progression.

}, doi = {https://doi.org/10.7554/eLife.25752}, url = {https://elifesciences.org/articles/25752}, author = {Woods, Elliot C and Kai, FuiBoon and Barnes, J Matthew and Pedram, Kayvon and Pickup, Michael W and Hollander, Michael J and Weaver, Valerie M and Bertozzi, Carolyn R} } @article {49003, title = {A canonical neural mechanism for behavioral variability.}, journal = {Nature Communications}, volume = {8}, year = {2017}, month = {2017 May 22}, pages = {15415}, abstract = {

The ability to generate variable movements is essential for learning and adjusting complex behaviours. This variability has been linked to the temporal irregularity of neuronal activity in the central nervous system. However, how neuronal irregularity actually translates into behavioural variability is unclear. Here we combine modelling, electrophysiological and behavioural studies to address this issue. We demonstrate that a model circuit comprising topographically organized and strongly recurrent neural networks can autonomously generate irregular motor behaviours. Simultaneous recordings of neurons in singing finches reveal that neural correlations increase across the circuit driving song variability, in agreement with the model predictions. Analysing behavioural data, we find remarkable similarities in the babbling statistics of 5-6-month-old human infants and juveniles from three songbird species and show that our model naturally accounts for these {\textquoteright}universal{\textquoteright} statistics.

}, issn = {2041-1723}, doi = {10.1038/ncomms15415}, author = {Darshan, Ran and Wood, William E and Peters, Susan and Leblois, Arthur and Hansel, David} } @article {48858, title = {Cell volume change through water efflux impacts cell stiffness and stem cell fate.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, year = {2017}, month = {2017 Sep 25}, pages = {E8618-27}, abstract = {

Cells alter their mechanical properties in response to their local microenvironment; this plays a role in determining cell function and can even influence stem cell fate. Here, we identify a robust and unified relationship between cell stiffness and cell volume. As a cell spreads on a substrate, its volume decreases, while its stiffness concomitantly increases. We find that both cortical and cytoplasmic cell stiffness scale with volume for numerous perturbations, including varying substrate stiffness, cell spread area, and external osmotic pressure. The reduction of cell volume is a result of water efflux, which leads to a corresponding increase in intracellular molecular crowding. Furthermore, we find that changes in cell volume, and hence stiffness, alter stem-cell differentiation, regardless of the method by which these are induced. These observations reveal a surprising, previously unidentified relationship between cell stiffness and cell volume that strongly influences cell biology.

}, issn = {1091-6490}, doi = {10.1073/pnas.1705179114}, author = {Guo, Ming and Pegoraro, Adrian F and Mao, Angelo and Zhou, Enhua H and Arany, Praveen R and Han, Yulong and Burnette, Dylan T and Jensen, Mikkel H and Kasza, Karen E and Moore, Jeffrey R and Mackintosh, Frederick C and Fredberg, Jeffrey J and Mooney, David J and Lippincott-Schwartz, Jennifer and Weitz, David A} } @article {48268, title = {Cilia-mediated Hedgehog signaling controls form and function in the mammalian larynx.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Feb 08}, abstract = {

Acoustic communication is fundamental to social interactions among animals, including humans. In fact, deficits in voice impair the quality of life for a large and diverse population of patients. Understanding the molecular genetic mechanisms of development and function in the vocal apparatus is thus an important challenge with relevance both to the basic biology of animal communication and to biomedicine. However, surprisingly little is known about the developmental biology of the mammalian larynx. Here, we used genetic fate mapping to chart the embryological origins of the tissues in the mouse larynx, and we describe the developmental etiology of laryngeal defects in mice with disruptions in cilia-mediated Hedgehog signaling. In addition, we show that mild laryngeal defects correlate with changes in the acoustic structure of vocalizations. Together, these data provide key new insights in the molecular genetics of form and function in the mammalian vocal apparatus.

}, issn = {2050-084X}, doi = {10.7554/eLife.19153}, author = {Tabler, Jacqueline M and Rigney, Maggie M and Berman, Gordon J and Gopalakrishnan, Swetha and Heude, Eglantine and Al-Lami, Hadeel Adel and Yannakoudakis, Basil Z and Fitch, Rebecca D and Carter, Christopher M and Vokes, Steven A and Liu, Karen J and Tajbakhsh, Shahragim and Egnor, Se Roian and Wallingford, John B} } @article {48764, title = {A circuit node that integrates convergent input from neuromodulatory and social behavior-promoting neurons to control aggression in Drosophila.}, journal = {Neuron}, volume = {95}, year = {2017}, month = {2017 Aug 30}, pages = {1112-1128.e7}, abstract = {

Diffuse neuromodulatory systems such as norepinephrine (NE) control brain-wide states such as arousal, but whether they control complex social behaviors more specifically is not clear. Octopamine (OA), the insect homolog of NE, is known to promote both arousal and aggression. We have performed a\ systematic, unbiased screen to identify OA receptor-expressing neurons (OARNs) that control aggression in Drosophila. Our results uncover a tiny population of male-specific aSP2 neurons that mediate a specific influence of OA on aggression, independent of any effect on arousal. Unexpectedly, these neurons receive convergent input from OA neurons and P1 neurons, a population of FruM(+) neurons that promotes male courtship behavior. Behavioral epistasis experiments suggest that aSP2 neurons may constitute an integration node at which OAergic neuromodulation can bias the output of P1 neurons to favor aggression over inter-male courtship. These results have potential implications for thinking about\ the role of related neuromodulatory systems in mammals.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2017.08.017}, author = {Watanabe, Kiichi and Chiu, Hui and Pfeiffer, Barret D and Wong, Allan M and Hoopfer, Eric D and Rubin, Gerald M and Anderson, David J} } @article {68437, title = {Classifying Drosophila Olfactory Projection Neuron Subtypes by Single-Cell RNA Sequencing.}, journal = {Cell}, volume = {171}, year = {2017}, month = {11/2017}, pages = {1206-1220.e22}, abstract = {

The definition of neuronal type and how it relates to the transcriptome are open questions. Drosophila olfactory projection neurons (PNs) are among the best-characterized neuronal types: different PN classes target dendrites to distinct olfactory glomeruli, while PNs of the same class exhibit indistinguishable anatomical and physiological properties. Using single-cell RNA sequencing, we comprehensively characterized the transcriptomes of most PN classes and unequivocally mapped transcriptomes to specific olfactory function for six classes. Transcriptomes of\ closely related PN classes exhibit the largest differences during circuit assembly but become indistinguishable in adults, suggesting that neuronal subtype diversity peaks during development. Transcription factors and cell-surface molecules are the most differentially expressed genes between classes and are highly informative in encoding cell identity, enabling us to identify a new lineage-specific transcription factor that instructs PN dendrite targeting. These findings establish that neuronal transcriptomic identity corresponds with anatomical and physiological identity defined by connectivity and function.

}, keywords = {Animals, Brain, Cluster Analysis, Dendrites, Drosophila melanogaster, Gene Expression Profiling, Neurons, Olfactory Bulb, Organ Specificity, Pupa, Sequence Analysis, RNA, Single-Cell Analysis, Transcription Factors}, issn = {1097-4172}, doi = {10.1016/j.cell.2017.10.019}, author = {Li, Hongjie and Horns, Felix and Wu, Bing and Xie, Qijing and Li, Jiefu and Li, Tongchao and Luginbuhl, David J and Quake, Stephen R and Luo, Liqun} } @article {48809, title = {Cohesin can remain associated with chromosomes during DNA replication.}, journal = {Cell Reports}, volume = {20}, year = {2017}, month = {2017 Sep 19}, pages = {2749-55}, abstract = {

To ensure disjunction to opposite poles during anaphase, sister chromatids must be held together following DNA replication. This is mediated by cohesin, which is thought to entrap sister DNAs inside a tripartite ring composed of its Smc and kleisin (Scc1) subunits. How such structures are created during S phase is poorly understood, in particular whether they are derived from complexes that had entrapped DNAs prior to replication. To address this, we used selective photobleaching to determine whether cohesin associated with chromatin in G1 persists in\ situ after replication. We developed a non-fluorescent HaloTag ligand to discriminate the fluorescence recovery signal from labeling of newly synthesized Halo-tagged Scc1 protein (pulse-chase or pcFRAP). In cells where cohesin turnover is inactivated by deletion of WAPL, Scc1 can remain associated with chromatin throughout S phase. These findings suggest that cohesion might be generated by cohesin that is already bound to un-replicated DNA.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2017.08.092}, author = {Rhodes, James D P and Haarhuis, Judith H I and Grimm, Jonathan B and Rowland, Benjamin D and Lavis, Luke D and Nasmyth, Kim A} } @article {48836, title = {Community-based benchmarking improves spike inference from two-photon calcium imaging data.}, journal = {PLoS Computational Biology}, volume = {14}, year = {2017}, month = {2018 May 21}, pages = {e1006157}, abstract = {

In recent years, two-photon calcium imaging has become a standard tool to probe the function of neural circuits and to study computations in neuronal populations. However, the acquired signal is only an indirect measurement of neural activity due to the comparatively slow dynamics of fluorescent calcium indicators. Different algorithms for estimating spike rates from noisy calcium measurements have been proposed in the past, but it is an open question how far performance can be improved. Here, we report the results of the spikefinder challenge, launched to catalyze the development of new spike rate inference algorithms through crowd-sourcing. We present ten of the submitted algorithms which show improved performance compared to previously evaluated methods. Interestingly, the top-performing algorithms are based on a wide range of principles from deep neural networks to generative models, yet provide highly correlated estimates of the neural activity. The competition shows that benchmark challenges can drive algorithmic developments in neuroscience.

}, doi = {10.1371/journal.pcbi.1006157}, author = {Berens, Philipp and Freeman, Jeremy and Deneux, Thomas and Chenkov, Nicolay and McColgan, Thomas and Speiser, Artur and Macke, Jakob H and Turaga, Srinivas C and Mineault, Patrick and Rupprecht, Peter and Gerhard, Stephan and Friedrich, Rainer W and Friedrich, Johannes and Paninski, Liam and Pachitariu, Marius and Harris, Kenneth D and Bolte, Ben and Machado, Timothy A and Ringach, Dario and etal} } @article {48720, title = {The complete connectome of a learning and memory centre in an insect brain.}, journal = {Nature}, volume = {548}, year = {2017}, month = {2017 Aug 09}, pages = {175-182}, abstract = {

Associating stimuli with positive or negative reinforcement is essential for survival, but a complete wiring diagram of a higher-order circuit supporting associative memory has not been previously available. Here we reconstruct one such circuit at synaptic resolution, the Drosophila larval mushroom body. We find that most Kenyon cells integrate random combinations of inputs but that a subset receives stereotyped inputs from single projection neurons. This organization maximizes performance of a model output neuron on a stimulus discrimination task. We also report a novel canonical circuit in each mushroom body compartment with previously unidentified connections: reciprocal Kenyon cell to modulatory neuron connections, modulatory neuron to output neuron connections, and a surprisingly high number of recurrent connections between Kenyon cells. Stereotyped connections found between output neurons could enhance the selection of learned behaviours. The complete circuit map of the mushroom body should guide future functional studies of this learning and memory centre.

}, issn = {1476-4687}, doi = {10.1038/nature23455}, author = {Eichler, Katharina and Li, Feng and Litwin-Kumar, Ashok and Park, Youngser and Andrade, Ingrid and Schneider-Mizell, Casey M and Saumweber, Timo and Huser, Annina and Eschbach, Claire and Gerber, Bertram and Fetter, Richard D and Truman, James W and Priebe, Carey E and Abbott, L F and Thum, Andreas S and Zlatic, Marta and Cardona, Albert} } @article {48302, title = {Conformational states of a soluble, uncleaved HIV-1 envelope trimer.}, journal = {Journal of Virology}, volume = {91}, year = {2017}, month = {2017 Mar 01}, pages = {e00175-17}, abstract = {

HIV-1 envelope spike [Env; trimeric (gp160)3, cleaved to (gp120/gp41)3] induces membrane fusion, leading to viral entry. It is also the viral component targeted by neutralizing antibodies. Vaccine development requires production, in quantities suitable for clinical studies, of a recombinant form that resembles functional Env. HIV-1 gp140 trimers - the uncleaved ectodomains of (gp160)3 - from a few selected viral isolates adopt a compact conformation with many antigenic properties of native Env spikes. One is currently being evaluated in a clinical trial. We report here low-resolution (20{\r A}) cryoEM (electron cryomicroscopy) structures of this gp140 trimer, which adopts two principal conformations, one closed and the other slightly open. The former is indistinguishable at this resolution from those adopted by a stabilized, cleaved trimer (SOSIP) or by a membrane-bound Env trimer with truncated cytoplasmic tail (EnvΔCT). The latter conformation is closer to a partially open Env trimer than to the fully open conformation induced by CD4. These results show that a stable, uncleaved HIV-1 gp140 trimer has a compact structure close to that of native Env.IMPORTANCE Development of any HIV vaccine with a protein component (either prime or boost) requires production of a recombinant form to mimic the trimeric, functional HIV-1 envelope spike, in quantities suitable for clinical studies. Our understanding of the envelope structure has depended in part on a cleaved, soluble trimer, known as SOSIP.664, stabilized by several modifications including an engineered disulfide. This construct, difficult to produce in large quantities, has yet to induce better antibody responses than other envelope-based immunogens, even in animal models. The uncleaved ectodomain of the envelope protein, called gp140, has also been made as a soluble form to mimic the native Env present on the virion surface. Most HIV-1 gp140 preparations are not stable, however, and of inhomogeneous conformation. The results presented here show that gp140 preparations from suitable isolates can adopt a compact, native-like structure, supporting its use as a vaccine candidate.

}, issn = {1098-5514}, doi = {10.1128/JVI.00175-17}, author = {Liu, Yuhang and Pan, Junhua and Cai, Yongfei and Grigorieff, Nikolaus and Harrison, Stephen C and Chen, Bing} } @article {48658, title = {A connectome of a learning and memory center in the adult Drosophila brain.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Jul 18}, pages = {e26975}, abstract = {

Understanding memory formation, storage and retrieval requires knowledge of the underlying neuronal circuits. In\ Drosophila, the mushroom body (MB) is the major site of associative learning. We reconstructed the morphologies and synaptic connections of all 983 neurons within the three functional units, or compartments, that compose the adult MB{\textquoteright}s α lobe, using a dataset of isotropic 8-nm voxels collected by focused ion-beam milling scanning electron microscopy. We found that Kenyon cells (KCs), whose sparse activity encodes sensory information, each make multiple\ en passant\ synapses to MB output neurons (MBONs) in each compartment. Some MBONs have inputs from all KCs, while others differentially sample sensory modalities. Only six percent of KC\>MBON synapses receive a direct synapse from a dopaminergic neuron (DAN). We identified two unanticipated classes of synapses, KC\>DAN and DAN\>MBON. DAN activation produces a slow depolarization of the MBON in these DAN\>MBON synapses and can weaken memory recall.

}, doi = {10.7554/eLife.26975}, author = {Takemura, Shin-ya and Aso, Yoshinori and Hige, Toshihide and Wong, Allan M and Lu, Zhiyuan and Xu, C Shan and Rivlin, Patricia K and Hess, Harald F and Zhao, Ting and Parag, Toufiq and Berg, Stuart and Huang, Gary and Katz, William T and Olbris, Donald J and Plaza, Stephen M and Umayam, Lowell A and Aniceto, Roxanne and Chang, Lei-Ann and Lauchie, Shirley and et al} } @article {48547, title = {Contacts between the endoplasmic reticulum and other membranes in neurons.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, year = {2017}, month = {2017 May 30}, pages = {E4859-67}, abstract = {

Close appositions between the membrane of the endoplasmic reticulum (ER) and other intracellular membranes have important functions in cell physiology. These include lipid homeostasis, regulation of Ca(2+) dynamics, and control of organelle biogenesis and dynamics. Although these membrane contacts have previously been observed in neurons, their distribution and abundance have not been systematically analyzed. Here, we have used focused ion beam-scanning electron microscopy to generate 3D reconstructions of intracellular organelles and their membrane appositions involving the ER (distance <=30 nm) in different neuronal compartments. ER-plasma membrane (PM) contacts were particularly abundant in cell bodies, with large, flat ER cisternae apposed to the PM, sometimes with a notably narrow lumen (thin ER). Smaller ER-PM contacts occurred throughout dendrites, axons, and in axon terminals. ER contacts with mitochondria were abundant in all compartments, with the ER often forming a network that embraced mitochondria. Small focal contacts were also observed with tubulovesicular structures, likely to be endosomes, and with sparse multivesicular bodies and lysosomes found in our reconstructions. Our study provides an anatomical reference for interpreting information about interorganelle communication in neurons emerging from functional and biochemical studies.

}, issn = {1091-6490}, doi = {10.1073/pnas.1701078114}, author = {Wu, Yumei and Whiteus, Christina and Xu, C Shan and Hayworth, Kenneth J and Weinberg, Richard J and Hess, Harald F and De Camilli, Pietro} } @article {48750, title = {Contractile actomyosin arcs promote the activation of primary mouse T cells in a ligand-dependent manner.}, journal = {PLoS One}, volume = {12}, year = {2017}, month = {2017}, pages = {e0183174}, abstract = {

Mechano-transduction is an emerging but still poorly understood component of T cell activation. Here we investigated the ligand-dependent contribution made by contractile actomyosin arcs populating the peripheral supramolecular activation cluster (pSMAC) region of the immunological synapse (IS) to T cell receptor (TCR) microcluster transport and proximal signaling in primary mouse T cells. Using super resolution microscopy, OT1-CD8+ mouse T cells, and two ovalbumin (OVA) peptides with different affinities for the TCR, we show that the generation of organized actomyosin arcs depends on ligand potency and the ability of myosin 2 to contract actin filaments. While weak ligands induce disorganized actomyosin arcs, strong ligands result in organized actomyosin arcs that correlate well with tension-sensitive CasL phosphorylation and the accumulation of ligands at the IS center. Blocking myosin 2 contractility greatly reduces the difference in the extent of Src and LAT phosphorylation observed between the strong and the weak ligand, arguing that myosin 2-dependent force generation within actin arcs contributes to ligand discrimination. Together, our data are consistent with the idea that actomyosin arcs in the pSMAC region of the IS promote a mechano-chemical feedback mechanism that amplifies the accumulation of critical signaling molecules at the IS.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0183174}, author = {Hong, Jinsung and Murugesan, Sricharan and Betzig, Eric and Hammer, John A} } @article {48622, title = {Cryo-electron tomography reveals novel features of a viral RNA replication compartment.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Jun 27}, abstract = {

Positive-strand RNA viruses, the largest genetic class of viruses, include numerous important pathogens such as Zika virus. These viruses replicate their RNA genomes in novel, membrane-bounded mini-organelles, but the organization of viral proteins and RNAs in these compartments is largely unknown. We used cryo-electron tomography to reveal many previously unrecognized features of Flock house nodavirus (FHV) RNA replication compartments. These spherular invaginations of outer mitochondrial membranes are packed with electron-dense RNA fibrils and their volumes are closely correlated with RNA replication template length. Each spherule{\textquoteright}s necked aperture is crowned by a striking cupped ring structure containing multifunctional FHV RNA replication protein A. Subtomogram averaging of these crowns revealed twelve-fold symmetry, concentric flanking protrusions, and a central electron density. Many crowns were associated with long cytoplasmic fibrils, likely to be exported progeny RNA. These results provide new mechanistic insights into positive-strand RNA virus replication compartment structure, assembly, function and control.

}, issn = {2050-084X}, doi = {10.7554/eLife.25940}, author = {Ertel, Kenneth J and Benefield, Desir{\'e}e and Casta{\~n}o-Diez, Daniel and Pennington, Janice and Horswill, Mark and den Boon, Johan A and Otegui, Marisa and Ahlquist, Paul} } @article {48489, title = {CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface.}, journal = {Journal of Molecular Biology}, volume = {429}, year = {2017}, month = {2017 May 12}, pages = {1829-39}, abstract = {

Structure-based vaccine design depends on extensive structural analyses of antigen-antibody complexes. Single-particle electron cryomicroscopy (cryoEM) can circumvent some of the problems of x-ray crystallography as a pipeline for obtaining the required structures. We have examined the potential of single-particle cryoEM for determining the structure of influenza-virus hemagglutinin (HA):single-chain Fv (scFv) complexes, by studying a complex we failed to crystallize in pursuing an extended project of the human immune response to influenza vaccines. The result shows that a combination of cryoEM and molecular modeling can yield details of the antigen:antibody interface, although small variation in the twist of the rod-like HA trimer limited the overall resolution to about 4.5{\r A}. Comparison of principal 3D classes suggests ways to modify the HA trimer to overcome this limitation. A closely related antibody from the same donor did yield crystals when bound with the same HA, giving us an independent validation of the cryoEM results The two structures also augment our understanding of receptor-binding site recognition by antibodies that neutralize a wide range of influenza-virus variants.

}, issn = {1089-8638}, doi = {10.1016/j.jmb.2017.05.011}, author = {Liu, Yuhang and Pan, Junhua and Jenni, Simon and Raymond, Donald D and Caradonna, Tim and Do, Khoi T and Schmidt, Aaron G and Harrison, Stephen C and Grigorieff, Nikolaus} } @article {48607, title = {Cytoskeletal actin dynamics shape a ramifying actin network underpinning immunological synapse formation.}, journal = {Science Advances}, volume = {3}, year = {2017}, month = {2017 Jun 21}, pages = {e1603032}, abstract = {

T cell activation and especially trafficking of T cell receptor microclusters during immunological synapse formation are widely thought to rely on cytoskeletal remodeling. However, important details on the involvement of actin in the latter transport processes are missing. Using a suite of advanced optical microscopes to analyze resting and activated T cells, we show that, following contact formation with activating surfaces, these cells sequentially rearrange their cortical actin across the entire cell, creating a previously unreported ramifying actin network above the immunological synapse. This network shows all the characteristics of an inward-growing transportation network and its dynamics correlating with T cell receptor rearrangements. This actin reorganization is accompanied by an increase in the nanoscale actin meshwork size and the dynamic adjustment of the turnover times and filament lengths of two differently sized filamentous actin populations, wherein formin-mediated long actin filaments support a very flat and stiff contact at the immunological synapse interface. The initiation of immunological synapse formation, as highlighted by calcium release, requires markedly little contact with activating surfaces and no cytoskeletal rearrangements. Our work suggests that incipient signaling in T cells initiates global cytoskeletal rearrangements across the whole cell, including a stiffening process for possibly mechanically supporting contact formation at the immunological synapse interface as well as a central ramified transportation network apparently directed at the consolidation of the contact and the delivery of effector functions.

}, doi = {10.1126/sciadv.1603032}, author = {Fritzsche, Marco and Fernandes, Ricardo A and Chang, Veronica T and Colin-York, Huw and Clausen, Mathias P and Felce, James H and Galiani, Silvia and Erlenk{\"a}mper, Christoph and Santos, Ana M and Heddleston, John M and Pedroza-Pacheco, Isabela and Waithe, Dominic and de la Serna, Jorge Bernadino and Lagerholm, B Christoffer and Liu, Tsung-Li and Chew, Teng-Leong and Betzig, Eric and Davis, Simon J and Eggeling, Christian} } @article {48602, title = {Deep learning for isotropic super-resolution from non-isotropic 3D electron microscopy.}, journal = {International Conference on Medical Image Computing and Computer-Assisted Intervention - MICCAI 2017. MICCAI 2017. Lecture Notes in Computer Science}, volume = {10434}, year = {2017}, month = {2017 Sept 4}, pages = {arXiv:1706.03142}, abstract = {

The most sophisticated existing methods to generate 3D isotropic super-resolution (SR) from non-isotropic electron microscopy (EM) are based on learned dictionaries. Unfortunately, none of the existing methods generate practically satisfying results. For 2D natural images, recently developed super-resolution methods that use deep learning have been shown to significantly outperform the previous state of the art. We have adapted one of the most successful architectures (FSRCNN) for 3D super-resolution, and compared its performance to a 3D U-Net architecture that has not been used previously to generate super-resolution. We trained both architectures on artificially downscaled isotropic ground truth from focused ion beam milling scanning EM (FIB-SEM) and tested the performance for various hyperparameter settings.

Our results indicate that both architectures can successfully generate 3D isotropic super-resolution from non-isotropic EM, with the U-Net performing consistently better. We propose several promising directions for practical application.

}, doi = {10.1007/978-3-319-66185-8_16}, author = {Heinrich, Larissa and Bogovic, John A and Saalfeld, Stephan} } @article {48419, title = {Defects in ER-endosome contacts impact lysosome function in hereditary spastic paraplegia.}, journal = {The Journal of Cell Biology}, volume = {216}, year = {2017}, month = {2017 Apr 07}, pages = {1337-55}, abstract = {

Contacts between endosomes and the endoplasmic reticulum (ER) promote endosomal tubule fission, but the mechanisms involved and consequences of tubule fission failure are incompletely understood. We found that interaction between the microtubule-severing enzyme spastin and the ESCRT protein IST1 at ER-endosome contacts drives endosomal tubule fission. Failure of fission caused defective sorting of mannose 6-phosphate receptor, with consequently disrupted lysosomal enzyme trafficking and abnormal lysosomal morphology, including in mouse primary neurons and human stem cell-derived neurons. Consistent with a role for ER-mediated endosomal tubule fission in lysosome function, similar lysosomal abnormalities were seen in cellular models lacking the WASH complex component strumpellin or the ER morphogen REEP1. Mutations in spastin, strumpellin, or REEP1 cause hereditary spastic paraplegia (HSP), a disease characterized by axonal degeneration. Our results implicate failure of the ER-endosome contact process in axonopathy and suggest that coupling of ER-mediated endosomal tubule fission to lysosome function links different classes of HSP proteins, previously considered functionally distinct, into a unifying pathway for axonal degeneration.

}, issn = {1540-8140}, doi = {10.1083/jcb.201609033}, author = {Allison, Rachel and Edgar, James R and Pearson, Guy and Rizo, Tania and Newton, Timothy and G{\"u}nther, Sven and Berner, Fiamma and Hague, Jennifer and Connell, James W and Winkler, J{\"u}rgen and Lippincott-Schwartz, Jennifer and Beetz, Christian and Winner, Beate and Reid, Evan} } @article {48463, title = {Detachable glass microelectrodes for recording action potentials in active moving organs.}, journal = {American Journal of Physiology. Heart and Circulatory Physiology}, volume = {312}, year = {2017}, month = {2017 May 05}, pages = {H1248-59}, abstract = {

We describe new detachable floating glass micropipette electrode devices that provide targeted action potential recordings in active moving organs without requiring constant mechanical constraint or pharmacological inhibition of tissue motion. The technology is based on the concept of a glass micropipette electrode that is held firmly during cell targeting and intracellular insertion, after which a 100{\textmu}g glass microelectrode, a "microdevice", is gently released to remain within the moving organ. The microdevices provide long-term recordings of action potentials, even during millimeter-scale movement of tissue in which the device is embedded. We demonstrate two different glass micropipette electrode holding and detachment designs appropriate for the heart (sharp glass microdevices for cardiac myocytes in rats, guinea pigs and humans) and the brain (patch glass microdevices for neurons in rats). We explain how microdevices enable measurements of multiple cells within a moving organ that are typically difficult with other technologies. Using sharp microdevices, action potential duration (APD) was monitored continuously for 15 minutes in unconstrained perfused hearts during global ischemia-reperfusion, providing beat-to-beat measurements of changes in APD. Action potentials from neurons in the hippocampus of anaesthetized rats were measured with patch microdevices, which provided stable base potentials during long-term recordings. Our results demonstrate that detachable microdevices are an elegant and robust tool to record electrical activity with high temporal resolution and cellular level localization without disturbing the physiological working conditions of the organ.

}, issn = {1522-1539}, doi = {10.1152/ajpheart.00741.2016}, author = {Barbic, Mladen and Moreno, Angel and Harris, Timothy D and Kay, Matthew W} } @article {65780, title = {Discovery of chemoautotrophic symbiosis in the giant shipworm Kuphus polythalamia (Bivalvia: Teredinidae) extends wooden-steps theory}, journal = {Proceedings of the National Academy of Sciences}, volume = {114}, year = {2017}, month = {05/2017}, pages = {E3652{\textendash}E3658}, abstract = {

Certain marine invertebrates harbor chemosynthetic bacterial symbionts, giving them the remarkable ability to consume inorganic chemicals such as hydrogen sulfide (H2S) rather than organic matter as food. These chemosynthetic animals are found near geochemical (e.g., hydrothermal vents) or biological (e.g., decaying wood or large animal carcasses) sources of H2S on the seafloor. Although many such symbioses have been discovered, little is known about how or where they originated. Here, we demonstrate a new chemosynthetic symbiosis in the giant teredinid bivalve (shipworm) Kuphus polythalamia and show that this symbiosis arose in a wood-eating ancestor via the displacement of ancestral cellulolytic symbionts by sulfur-oxidizing invaders. Here, wood served as an evolutionary stepping stone for a dramatic transition from heterotrophy to chemoautotrophy.The {\textquotedblleft}wooden-steps{\textquotedblright} hypothesis [Distel DL, et al. (2000) Nature 403:725{\textendash}726] proposed that large chemosynthetic mussels found at deep-sea hydrothermal vents descend from much smaller species associated with sunken wood and other organic deposits, and that the endosymbionts of these progenitors made use of hydrogen sulfide from biogenic sources (e.g., decaying wood) rather than from vent fluids. Here, we show that wood has served not only as a stepping stone between habitats but also as a bridge between heterotrophic and chemoautotrophic symbiosis for the giant mud-boring bivalve Kuphus polythalamia. This rare and enigmatic species, which achieves the greatest length of any extant bivalve, is the only described member of the wood-boring bivalve family Teredinidae (shipworms) that burrows in marine sediments rather than wood. We show that K. polythalamia harbors sulfur-oxidizing chemoautotrophic (thioautotrophic) bacteria instead of the cellulolytic symbionts that allow other shipworm species to consume wood as food. The characteristics of its symbionts, its phylogenetic position within Teredinidae, the reduction of its digestive system by comparison with other family members, and the loss of morphological features associated with wood digestion indicate that K. polythalamia is a chemoautotrophic bivalve descended from wood-feeding (xylotrophic) ancestors. This is an example in which a chemoautotrophic endosymbiosis arose by displacement of an ancestral heterotrophic symbiosis and a report of pure culture of a thioautotrophic endosymbiont.

}, issn = {0027-8424}, doi = {10.1073/pnas.1620470114}, url = {https://www.pnas.org/content/114/18/E3652}, author = {Distel, Daniel L. and Altamia, Marvin A. and Lin, Zhenjian and Shipway, J. Reuben and Han, Andrew and Forteza, Imelda and Antemano, Rowena and Limbaco, Ma. Gwen J. Pe{\~n}aflor and Tebo, Alison G. and Dechavez, Rande and Albano, Julie and Rosenberg, Gary and Concepcion, Gisela P. and Schmidt, Eric W. and Haygood, Margo G.} } @article {48786, title = {Dissection of the Drosophila neuropeptide F circuit using a high-throughput two-choice assay.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, year = {2017}, month = {2017 Sep 05}, pages = {e8091-9}, abstract = {

In their classic experiments, Olds and Milner showed that rats learn to lever press to receive an electric stimulus in specific brain regions. This led to the identification of mammalian reward centers. Our interest in defining the neuronal substrates of reward perception in the fruit fly Drosophila melanogaster prompted us to develop a simpler experimental approach wherein flies could implement behavior that induces self-stimulation of specific neurons in their brains. The high-throughput assay employs optogenetic activation of neurons when the fly occupies a specific area of a behavioral chamber, and the flies{\textquoteright} preferential occupation of this area reflects their choosing to experience optogenetic stimulation. Flies in which neuropeptide F (NPF) neurons are activated display preference for the illuminated side of the chamber. We show that optogenetic activation of NPF neuron is rewarding in olfactory conditioning experiments and that the preference for NPF neuron activation is dependent on NPF signaling. Finally, we identify a small subset of NPF-expressing neurons located in the dorsomedial posterior brain that are sufficient to elicit preference in our assay. This assay provides the means for carrying out unbiased screens to map reward neurons in flies.

}, issn = {1091-6490}, doi = {10.1073/pnas.1710552114}, author = {Shao, Lisha and Saver, Mathias and Chung, Phuong and Ren, Qingzhong and Lee, Tzumin and Kent, Clement F and Heberlein, Ulrike} } @article {48416, title = {Diverse protocols for correlative super-resolution fluorescence imaging and electron microscopy of chemically fixed samples.}, journal = {Nature Protocols}, volume = {12}, year = {2017}, month = {2017 May}, pages = {916-946}, abstract = {

Our groups have recently developed related approaches for sample preparation for super-resolution imaging within endogenous cellular environments using correlative light and electron microscopy (CLEM). Four distinct techniques for preparing and acquiring super-resolution CLEM data sets for aldehyde-fixed specimens are provided, including Tokuyasu cryosectioning, whole-cell mount, cell unroofing and platinum replication, and resin embedding and sectioning. The choice of the best protocol for a given application depends on a number of criteria that are discussed in detail. Tokuyasu cryosectioning is relatively rapid but is limited to small, delicate specimens. Whole-cell mount has the simplest sample preparation but is restricted to surface structures. Cell unroofing and platinum replication creates high-contrast, 3D images of the cytoplasmic surface of the plasma membrane but is more challenging than whole-cell mount. Resin embedding permits serial sectioning of large samples but is limited to osmium-resistant probes, and is technically difficult. Expected results from these protocols include super-resolution localization (\~{}10-50 nm) of fluorescent targets within the context of electron microscopy ultrastructure, which can help address cell biological questions. These protocols can be completed in 2-7 d, are compatible with a number of super-resolution imaging protocols, and are broadly applicable across biology.

}, issn = {1750-2799}, doi = {10.1038/nprot.2017.017}, author = {Kopek, Benjamin G and Paez-Segala, Maria G and Shtengel, Gleb and Sochacki, Kem A and Sun, Mei G and Wang, Yalin and Xu, C Shan and Van Engelenburg, Schuyler B and Taraska, Justin W and Looger, Loren L and Hess, Harald F} } @article {48961, title = {Editorial overview: Making evolutionary sense of everything.}, journal = {Current Opinion in Genetics \& Development}, volume = {47}, year = {2017}, month = {2017 Dec}, pages = {iv-vi}, issn = {1879-0380}, doi = {10.1016/j.gde.2017.11.005}, author = {Stern, David L and Haag, Eric} } @article {48192, title = {Electrophoresis of polar fluorescent tracers through the nerve sheath labels neuronal populations for anatomical and functional imaging.}, journal = {Scientific Reports}, volume = {7}, year = {2017}, month = {2017 Jan 13}, pages = {40433}, abstract = {

The delivery of tracers into populations of neurons is essential to visualize their anatomy and analyze their function. In some model systems genetically-targeted expression of fluorescent proteins is the method of choice; however, these genetic tools are not available for most organisms and alternative labeling methods are very limited. Here we describe a new method for neuronal labelling by electrophoretic dye delivery from a suction electrode directly through the neuronal sheath of nerves and ganglia in insects. Polar tracer molecules were delivered into the locust auditory nerve without destroying its function, simultaneously staining peripheral sensory structures and central axonal projections. Local neuron populations could be labelled directly through the surface of the brain, and in-vivo optical imaging of sound-evoked activity was achieved through the electrophoretic delivery of calcium indicators. The method provides a new tool for studying how stimuli are processed in peripheral and central sensory pathways and is a significant advance for the study of nervous systems in non-model organisms.

}, issn = {2045-2322}, doi = {10.1038/srep40433}, author = {Isaacson, Matthew D and Hedwig, Berthold} } @article {48490, title = {Enhanced FIB-SEM systems for large-volume 3D imaging.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 May 13}, abstract = {

Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) can automatically generate 3D images with superior z-axis resolution, yielding data that needs minimal image registration and related post-processing. Obstacles blocking wider adoption of FIB-SEM include slow imaging speed and lack of long-term system stability, which caps the maximum possible acquisition volume. Here we present techniques that accelerate image acquisition while greatly improving FIB-SEM reliability, allowing the system to operate for months and generating continuously imaged volumes \> 10(6) {\textmu}m(3). These volumes are large enough for connectomics, where the excellent z resolution can help in tracing of small neuronal processes and accelerate the tedious and time-consuming human proofreading effort. Even higher resolution can be achieved on smaller volumes. We present example data sets from mammalian neural tissue, Drosophila brain, and Chlamydomonas reinhardtii to illustrate the power of this novel high-resolution technique to address questions in both connectomics and cell biology.

}, issn = {2050-084X}, doi = {10.7554/eLife.25916}, author = {Xu, C Shan and Hayworth, Kenneth J and Lu, Zhiyuan and Grob, Patricia and Hassan, Ahmed M and Garc{\'\i}a-Cerd{\'a}n, Jos{\'e} G and Niyogi, Krishna K and Nogales, Eva and Weinberg, Richard J and Hess, Harald F} } @article {48765, title = {Experimental and statistical reevaluation provides no evidence for Drosophila courtship song rhythms.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, year = {2017}, month = {2017 Aug 29}, pages = {9978-83}, abstract = {

From 1980 to 1992, a series of influential papers reported on the discovery, genetics, and evolution of a periodic cycling of the interval between Drosophila male courtship song pulses. The molecular mechanisms underlying this periodicity were never described. To reinitiate investigation of this phenomenon, we previously performed automated segmentation of songs but failed to detect the proposed rhythm [Arthur BJ, et al. (2013) BMC Biol 11:11; Stern DL (2014) BMC Biol 12:38]. Kyriacou et al. [Kyriacou CP, et al. (2017) Proc Natl Acad Sci USA 114:1970-1975] report that we failed to detect song rhythms because (i) our flies did not sing enough and (ii) our segmenter did not identify many of the song pulses. Kyriacou et al. manually annotated a subset of our recordings and reported that two strains displayed rhythms with genotype-specific periodicity, in agreement with their original reports. We cannot replicate this finding and show that the manually annotated data, the original automatically segmented data, and a new dataset provide no evidence for either the existence of song rhythms or song periodicity differences between genotypes. Furthermore, we have reexamined our methods and analysis and find that our automated segmentation method was not biased to prevent detection of putative song periodicity. We conclude that there is no evidence for the existence of Drosophila courtship song rhythms.

}, issn = {1091-6490}, doi = {10.1073/pnas.1707471114}, author = {Stern, David L and Clemens, Jan and Coen, Philip and Calhoun, Adam J and Hogenesch, John B and Arthur, Ben J and Murthy, Mala} } @article {48204, title = {A fluorescent Hsp90 probe demonstrates the unique association between extracellular Hsp90 and malignancy in vivo.}, journal = {ACS chemical biology}, year = {2017}, month = {2017 Jan 19}, abstract = {

Extracellular expression of heat shock protein 90 (eHsp90) by tumor cells is correlated with malignancy. Development of small molecule probes that can detect eHsp90 in vivo may therefore have utility in the early detection of malignancy. We synthesized a cell impermeable far-red fluorophore-tagged Hsp90 inhibitor to target eHsp90 in vivo. High resolution confocal and lattice light sheet microscopy show that probe-bound eHsp90 accumulates in punctate structures on the plasma membrane of breast tumor cells and is actively internalized. The extent of internalization correlates with tumor cell aggressiveness, and this process can be induced in benign cells by over-expressing p110HER2. Whole body cryoslicing, imaging and histology of flank and spontaneous tumor-bearing mice strongly suggests that eHsp90 expression and internalization is a phenomenon unique to tumor cells in vivo and may provide an {\textquoteright}Achilles heel{\textquoteright} for the early diagnosis of metastatic disease and targeted drug delivery.

}, issn = {1554-8937}, doi = {10.1021/acschembio.7b00006}, author = {Crowe, Lauren B and Hughes, Philip F and Alcorta, David A and Osada, Takuya and Smith, Aaron P and Totzke, Juliane and Loiselle, David R and Lutz, Isaac D and Gargesha, Madhusudhana and Roy, Debasish and Roques, Jose and Darr, David and Lyerly, H Kim and Spector, Neil L and Haystead, Timothy Aj} } @article {48935, title = {Fully integrated silicon probes for high-density recording of neural activity.}, journal = {Nature}, volume = {551}, year = {2017}, month = {2017 Nov 08}, pages = {232-236}, abstract = {

Sensory, motor and cognitive operations involve the coordinated action of large neuronal populations across multiple brain regions in both superficial and deep structures. Existing extracellular probes record neural activity with excellent spatial and temporal (sub-millisecond) resolution, but from only a few dozen neurons per shank. Optical Ca(2+) imaging offers more coverage but lacks the temporal resolution needed to distinguish individual spikes reliably and does not measure local field potentials. Until now, no technology compatible with use in unrestrained animals has combined high spatiotemporal resolution with large volume coverage. Here we design, fabricate and test a new silicon probe known as Neuropixels to meet this need. Each probe has 384 recording channels that can programmably address 960 complementary metal-oxide-semiconductor (CMOS) processing-compatible low-impedance TiN sites that tile a single 10-mm long, 70 {\texttimes} 20-μm cross-section shank. The 6 {\texttimes} 9-mm probe base is fabricated with the shank on a single chip. Voltage signals are filtered, amplified, multiplexed and digitized on the base, allowing the direct transmission of noise-free digital data from the probe. The combination of dense recording sites and high channel count yielded well-isolated spiking activity from hundreds of neurons per probe implanted in mice and rats. Using two probes, more than 700 well-isolated single neurons were recorded simultaneously from five brain structures in an awake mouse. The fully integrated functionality and small size of Neuropixels probes allowed large populations of neurons from several brain structures to be recorded in freely moving animals. This combination of high-performance electrode technology and scalable chip fabrication methods opens a path towards recording of brain-wide neural activity during behaviour.

}, issn = {1476-4687}, doi = {10.1038/nature24636}, author = {Jun, James J and Steinmetz, Nicholas A and Siegle, Joshua H and Denman, Daniel J and Bauza, Marius and Barbarits, Brian and Lee, Albert K and Anastassiou, Costas A and Andrei, Alexandru and Ayd{\i}n, {\c C}a{\u g}atay and Barbic, Mladen and Blanche, Timothy J and Bonin, Vincent and Couto, Jo{\~a}o and Dutta, Barundeb and Gratiy, Sergey L and Gutnisky, Diego A and H{\"a}usser, Michael and Karsh, Bill and Ledochowitsch, Peter and Lopez, Carolina Mora and Mitelut, Catalin and Musa, Silke and Okun, Michael and Pachitariu, Marius and Putzeys, Jan and Rich, P Dylan and Rossant, Cyrille and Sun, Wei-Lung and Svoboda, Karel and Carandini, Matteo and Harris, Kenneth D and Koch, Christof and O{\textquoteright}Keefe, John and Harris, Timothy D} } @article {48698, title = {Genetic and neuronal mechanisms governing the sex-specific interaction between sleep and sexual behaviors in Drosophila.}, journal = {Nature Communications}, volume = {8}, year = {2017}, month = {2017 Jul 28}, pages = {154}, abstract = {

Animals execute one particular behavior among many others in a context-dependent manner, yet the mechanisms underlying such behavioral choice remain poorly understood. Here we studied how two fundamental behaviors, sex and sleep, interact at genetic and neuronal levels in Drosophila. We show that an increased need for sleep inhibits male sexual behavior by decreasing the activity of the male-specific P1 neurons that coexpress the sex determination genes fru (M) and dsx, but does not affect female sexual behavior. Further, we delineate a sex-specific neuronal circuit wherein the P1 neurons encoding increased courtship drive suppressed male sleep by forming mutually excitatory connections with the fru (M) -positive sleep-controlling DN1 neurons. In addition, we find that FRU(M) regulates male courtship and sleep through distinct neural substrates. These studies reveal the genetic and neuronal basis underlying the sex-specific interaction between sleep and sexual behaviors in Drosophila, and provide insights into how competing behaviors are co-regulated.Genes and circuits involved in sleep and sexual arousal have been extensively studied in Drosophila. Here the authors identify the sex determination genes fruitless and doublesex, and a sex-specific P1-DN1 neuronal feedback that governs the interaction between these competing behaviors.

}, issn = {2041-1723}, doi = {10.1038/s41467-017-00087-5}, author = {Chen, Dandan and Sitaraman, Divya and Chen, Nan and Jin, Xin and Han, Caihong and Chen, Jie and Sun, Mengshi and Baker, Bruce S and Nitabach, Michael N and Pan, Yufeng} } @article {48845, title = {Genetic reagents for making split-GAL4 lines in Drosophila.}, journal = {Genetics }, volume = {209}, year = {2017}, month = {2018 March}, pages = {31-5}, abstract = {

The ability to reproducibly target expression of transgenes to small, defined subsets of cells is a key experimental tool for understanding many biological processes. The Drosophila nervous system contains thousands of distinct cell types and it has generally not been possible to limit expression to one or a few cell types when using a single segment of genomic DNA as an enhancer to drive expression. Intersectional methods, in which expression of the transgene only occurs where two different enhancers overlap in their expression patterns, can be used to achieve the desired specificity. This report describes a set of over 2,800 transgenic lines for use with the split-GAL4 intersectional method.

}, doi = {10.1101/197509}, author = {Dionne, Heather and Hibbard, Karen L and Cavallaro, Amanda and Kao, Jui-Chun and Rubin, Gerald M} } @article {48766, title = {Imp and Syp RNA-binding proteins govern decommissioning of Drosophila neural stem cells.}, journal = {Development (Cambridge, England)}, volume = {144}, year = {2017}, month = {2017 Aug 29}, pages = {3454-64}, abstract = {

The termination of the proliferation of Drosophila neural stem cells, also known as neuroblasts (NBs), requires a "decommissioning" phase that is controlled in a lineage-specific manner. Most NBs, with the exception of those of the Mushroom body (MB), are decommissioned by the ecdysone receptor and mediator complex causing them to shrink during metamorphosis, followed by nuclear accumulation of Prospero and cell cycle exit. Here, we demonstrate that the levels of Imp and Syp RNA-binding proteins regulate NB decommissioning. Descending Imp and ascending Syp expression have been shown to regulate neuronal temporal fate. We show that Imp levels decline slower in the MB than other central brain NBs. MB NBs continue to express Imp into pupation, and the presence of Imp prevents decommissioning partly by inhibiting the mediator complex. Late-larval induction of transgenic Imp prevents many non-MB NBs from decommissioning in early pupae. Moreover, the presence of abundant Syp in aged NBs permits Prospero accumulation that, in turn, promotes cell cycle exit. Together our results reveal that progeny temporal fate and progenitor decommissioning are co-regulated in protracted neuronal lineages.

}, issn = {1477-9129}, doi = {10.1242/dev.149500}, author = {Yang, Ching-Po and Samuels, Tamsin J and Huang, Yaling and Yang, Lu and Ish-Horowicz, David and Davis, Ilan and Lee, Tzumin} } @article {48907, title = {Intercellular mRNA trafficking via membrane nanotube-like extensions in mammalian cells.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, year = {2017}, month = {2017 Oct 24}, pages = {E9873-E9882}, abstract = {

RNAs have been shown to undergo transfer between mammalian cells, although the mechanism behind this phenomenon and its overall importance to cell physiology is not well understood. Numerous publications have suggested that RNAs (microRNAs and incomplete mRNAs) undergo transfer via extracellular vesicles (e.g., exosomes). However, in contrast to a diffusion-based transfer mechanism, we find that full-length mRNAs undergo direct cell-cell transfer via cytoplasmic extensions characteristic of membrane nanotubes (mNTs), which connect donor and acceptor cells. By employing a simple coculture experimental model and using single-molecule imaging, we provide quantitative data showing that mRNAs are transferred between cells in contact. Examples of mRNAs that undergo transfer include those encoding GFP, mouse β-actin, and human Cyclin D1, BRCA1, MT2A, and HER2. We show that intercellular mRNA transfer occurs in all coculture models tested (e.g., between primary cells, immortalized cells, and in cocultures of immortalized human and murine cells). Rapid mRNA transfer is dependent upon actin but is independent of de novo protein synthesis and is modulated by stress conditions and gene-expression levels. Hence, this work supports the hypothesis that full-length mRNAs undergo transfer between cells through a refined structural connection. Importantly, unlike the transfer of miRNA or RNA fragments, this process of communication transfers genetic information that could potentially alter the acceptor cell proteome. This phenomenon may prove important for the proper development and functioning of tissues as well as for host-parasite or symbiotic interactions.

}, issn = {1091-6490}, doi = {10.1073/pnas.1706365114}, author = {Haimovich, Gal and Ecker, Christopher M and Dunagin, Margaret C and Eggan, Elliott and Raj, Arjun and Gerst, Jeffrey E and Singer, Robert H} } @article {65773, title = {Intramolecular Photogeneration of a Tyrosine Radical in a Designed Protein}, journal = {ChemPhotoChem}, volume = {1}, year = {2017}, month = {02/2017}, pages = {89 {\textendash} 92}, abstract = {

Long-distance biological electron transfer occurs through a hopping mechanism and often involves tyrosine as a high potential intermediate, for example in the early charge separation steps during photosynthesis. Protein design allows for the development of minimal systems to study the underlying principles of complex systems. Herein, we report the development of the first ruthenium-linked designed protein for the photogeneration of a tyrosine radical by intramolecular electron transfer.

}, doi = {10.1002/cptc.201600044}, url = {https://chemistry-europe.onlinelibrary.wiley.com/doi/abs/10.1002/cptc.201600044}, author = {Tebo, Alison G and Quaranta, Annamaria and Herrero, Christian and Pecoraro, Vincent L and Aukauloo, Ally} } @article {48434, title = {Live-cell super-resolution reveals F-Actin and plasma membrane dynamics at the T Cell synapse.}, journal = {Biophysical Journal}, volume = {112}, year = {2017}, month = {2017 Apr 25}, pages = {1703-13}, abstract = {

The cortical actin cytoskeleton has been shown to be critical for the reorganization and heterogeneity of plasma membrane components of many cells, including T\ cells. Building on previous studies at the T\ cell immunological synapse, we quantitatively assess the structure and dynamics of this meshwork using live-cell superresolution fluorescence microscopy and spatio-temporal image correlation spectroscopy. We show for the first time, to our knowledge, that not only does the dense actin cortex flow in a retrograde fashion toward the synapse center, but the plasma membrane itself shows similar behavior. Furthermore, using two-color, live-cell superresolution cross-correlation spectroscopy, we demonstrate that the two flows are correlated and, in addition, we show that coupling may extend to the outer leaflet of the plasma membrane by examining the flow of GPI-anchored proteins. Finally, we demonstrate that the actin flow is correlated with a third component,\ α-actinin, which upon CRISPR knockout led to reduced plasma membrane flow directionality despite increased actin flow velocity. We hypothesize that this apparent cytoskeletal-membrane coupling could provide a mechanism for driving the observed retrograde flow of signaling molecules such as the TCR, Lck, ZAP70, LAT, and SLP76.

}, doi = {10.1016/j.bpj.2017.01.038}, author = {Ashdown, George W and Burn, Garth L and Williamson, David J and Pandzic, Elvis and Peters, Ruby and Holden, Michael and Ewers, Helge and Shao, Lin and Wiseman, Paul W and Owen, Dylan M} } @article {48219, title = {Long-range self-organization of cytoskeletal myosin II filament stacks.}, journal = {Nature Cell Biology}, volume = {19}, year = {2017}, month = {2017 Jan 23}, pages = {133-41}, abstract = {

Although myosin II filaments are known to exist in non-muscle cells, their dynamics and organization are incompletely understood. Here, we combined structured illumination microscopy with pharmacological and genetic perturbations, to study the process of actomyosin cytoskeleton self-organization into arcs and stress fibres. A striking feature of the myosin II filament organization was their {\textquoteright}registered{\textquoteright} alignment into stacks, spanning up to several micrometres in the direction orthogonal to the parallel actin bundles. While turnover of individual myosin II filaments was fast (characteristic half-life time 60 s) and independent of actin filament turnover, the process of stack formation lasted a longer time (in the range of several minutes) and required myosin II contractility, as well as actin filament assembly/disassembly and crosslinking (dependent on formin Fmnl3, cofilin1 and α-actinin-4). Furthermore, myosin filament stack formation involved long-range movements of individual myosin filaments towards each other suggesting the existence of attractive forces between myosin II filaments. These forces, possibly transmitted via mechanical deformations of the intervening actin filament network, may in turn remodel the actomyosin cytoskeleton and drive its self-organization.

}, issn = {1476-4679}, doi = {10.1038/ncb3466}, author = {Hu, Shiqiong and Dasbiswas, Kinjal and Guo, Zhenhuan and Tee, Yee-Han and Thiagarajan, Visalatchi and Hersen, Pascal and Chew, Teng-Leong and Safran, Samuel A and Zaidel-Bar, Ronen and Bershadsky, Alexander D} } @article {48605, title = {Low-complexity domains adhere by reversible amyloid-like interactions between kinked β-sheets.}, journal = {bioRxiv}, year = {2017}, month = {2017 Jun 22}, abstract = {

Control of metabolism by compartmentation is a widespread feature of higher cells. Recent studies have focused on dynamic intracellular bodies such as stress granules, P-bodies, nucleoli, and metabolic puncta. These bodies appear as separate phases, some containing reversible, amyloid-like fibrils formed by interactions of low-complexity protein domains. Here we report five atomic structures of segments of low-complexity domains from granule-forming proteins, one determined to 1.1 {\r A} resolution by micro-electron diffraction. Four of these interacting protein segments show common characteristics, all in contrast to pathogenic amyloid: kinked peptide backbones, small surface areas of interaction, and predominate attractions between aromatic side-chains. By computationally threading the human proteome on three of our kinked structures, we identified hundreds of low-complexity segments potentially capable of forming such reversible interactions. These segments are found in proteins as diverse as RNA binders, nuclear pore proteins, keratins, and cornified envelope proteins, consistent with the capacity of cells to form a wide variety of dynamic intracellular bodies.

}, doi = {10.1101/153817}, author = {Hughes, Michael P and Sawaya, Michael R and Goldschmidt, Lukasz and Rodriguez, Jose A and Cascio, Duilio and Gonen, Tamir and Eisenberg, David S} } @article {48646, title = {Mapping the neural substrates of behavior.}, journal = {Cell}, volume = {170}, year = {2017}, month = {2017-07-13}, pages = {393-406}, abstract = {

Assigning behavioral functions to neural structures has long been a central goal in neuroscience and is a necessary first step toward a circuit-level understanding of how the brain generates behavior. Here, we map the neural substrates of locomotion and social behaviors for Drosophila melanogaster using automated machine-vision and machine-learning techniques. From videos of 400,000 flies, we quantified the behavioral effects of activating 2,204 genetically targeted populations of neurons. We combined a novel quantification of anatomy with our behavioral analysis to create brain-behavior correlation maps, which are shared as browsable web pages and interactive software. Based on these maps, we generated hypotheses of regions of the brain causally related to sensory processing, locomotor control, courtship, aggression, and sleep. Our maps directly specify genetic tools to target these regions, which we used to identify a small population of neurons with a role in the control of walking.

{\textbullet}We developed machine-vision methods to broadly and precisely quantify fly behavior{\textbullet}We measured effects of activating 2,204 genetically targeted neuronal populations{\textbullet}We created whole-brain maps of neural substrates of locomotor and social behaviors{\textbullet}We created resources for exploring our results and enabling further investigation

Machine-vision analyses of large behavior and neuroanatomy data reveal whole-brain maps of regions associated with numerous complex behaviors.

}, doi = {10.1016/j.cell.2017.06.032}, url = {http://dx.doi.org/10.1016/j.cell.2017.06.032}, author = {Robie, Alice A and Hirokawa, Jonathan and Edwards, Austin W and Umayam, Lowell A and Lee, Allen and Phillips, Mary L and Card, Gwyneth M and Korff, Wyatt and Rubin, Gerald M and Simpson, Julie H and Reiser, Michael B and Branson, Kristin M} } @article {48560, title = {Mechanisms underlying a thalamocortical transformation during active tactile sensation.}, journal = {PLoS Computational Biology}, volume = {13}, year = {2017}, month = {2017 Jun 07}, pages = {e1005576}, abstract = {

During active somatosensation, neural signals expected from movement of the sensors are suppressed in the cortex, whereas information related to touch is enhanced. This tactile suppression underlies low-noise encoding of relevant tactile features and the brain{\textquoteright}s ability to make fine tactile discriminations. Layer (L) 4 excitatory neurons in the barrel cortex, the major target of the somatosensory thalamus (VPM), respond to touch, but have low spike rates and low sensitivity to the movement of whiskers. Most neurons in VPM respond to touch and also show an increase in spike rate with whisker movement. Therefore, signals related to self-movement are suppressed in L4. Fast-spiking (FS) interneurons in L4 show similar dynamics to VPM neurons. Stimulation of halorhodopsin in FS interneurons causes a reduction in FS neuron activity and an increase in L4 excitatory neuron activity. This decrease of activity of L4 FS neurons contradicts the "paradoxical effect" predicted in networks stabilized by inhibition and in strongly-coupled networks. To explain these observations, we constructed a model of the L4 circuit, with connectivity constrained by in vitro measurements. The model explores the various synaptic conductance strengths for which L4 FS neurons actively suppress baseline and movement-related activity in layer 4 excitatory neurons. Feedforward inhibition, in concert with recurrent intracortical circuitry, produces tactile suppression. Synaptic delays in feedforward inhibition allow transmission of temporally brief volleys of activity associated with touch. Our model provides a mechanistic explanation of a behavior-related computation implemented by the thalamocortical circuit.

}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1005576}, author = {Gutnisky, Diego Adrian and Yu, Jianing and Hires, Samuel Andrew and To, Minh-Son and Bale, Michael and Svoboda, Karel and Golomb, David} } @article {48604, title = {A method to minimize condenser lens-induced hysteresis effects in a JEOL JEM-3200FSC microscope to enable stable cryoEM low-dose operations.}, journal = {bioRxiv}, year = {2017}, month = {2017 Jun 21}, abstract = {

Low dose imaging procedures are key for a successful cryoEM experiment (whether by electron cryotomography, single particle analysis, electron crystallography, or MicroED). We present a method to minimize magnetic hysteresis of the condenser lens system in the JEOL JEM-3200FSC transmission electron microscope (TEM) in order to maintain a stable optical axis for the beam path of low-dose imaging. The simple procedure involves independent voltage ramping of the CL1 and CL2 lenses immediately before switching to the focusing and exposure beam settings for data collection.

}, doi = {10.1101/153395}, author = {de la Cruz, Michael Jason and Martynowycz, Michael and Hattne, Johan and Shi, Dan and Gonen, Tamir} } @article {48603, title = {MicroED structures from micrometer thick protein crystals.}, journal = {bioRxiv}, year = {2017}, month = {2017 Jun 20}, abstract = {

Theoretical calculations suggest that crystals exceeding 100 nm thickness are excluded by dynamical scattering from successful structure determination using microcrystal electron diffraction (MicroED). These calculations are at odds with experimental results where MicroED structures have been determined from significantly thicker crystals. Here we systematically evaluate the influence of thickness on the accuracy of MicroED intensities and the ability to determine structures from protein crystals one micrometer thick. To do so, we compare ab initio structures of a human prion protein segment determined from thin crystals to those determined from crystals up to one micrometer thick. We also compare molecular replacement solutions from crystals of varying thickness for a larger globular protein, proteinase K. Our results indicate that structures can be reliably determined from crystals at least an order of magnitude thicker than previously suggested by simulation, opening the possibility for an even broader range of MicroED experiments.

}, doi = {10.1101/152504}, author = {Martynowycz, Michael and Glynn, Calina and Miao, Jennifer and de la Cruz, Michael Jason and Hattne, Johan and Shi, Dan and Cascio, Duilio and Rodriguez, Jose and Gonen, Tamir} } @proceedings {48942, title = {Model-based Bayesian inference of neural activity and connectivity from all-optical interrogation of a neural circuit.}, year = {2017}, month = {2017 Dec 04}, abstract = {

Population activity measurement by calcium imaging can be combined with cellular resolution optogenetic activity perturbations to enable the mapping of neural connectivity in vivo. This requires accurate inference of perturbed and unperturbed neural activity from calcium imaging measurements, which are noisy and indirect, and can also be contaminated by photostimulation artifacts. We have developed a new fully Bayesian approach to jointly inferring spiking activity and neural connectivity from in vivo all-optical perturbation experiments. In contrast to standard approaches that perform spike inference and analysis in two separate maximum-likelihood phases, our joint model is able to propagate uncertainty in spike inference to the inference of connectivity and vice versa. We use the framework of variational autoencoders to model spiking activity using discrete latent variables, low-dimensional latent common input, and sparse spike-and-slab generalized linear coupling between neurons. Additionally, we model two properties of the optogenetic perturbation: off-target photostimulation and photostimulation transients. Our joint model includes at least two sets of discrete random variables; to avoid the dramatic slowdown typically caused by being unable to differentiate such variables, we introduce two strategies that have not, to our knowledge, been used with variational autoencoders. Using this model, we were able to fit models on 30 minutes of data in just 10 minutes. We performed an all-optical circuit mapping experiment in primary visual cortex of the awake mouse, and use our approach to predict neural connectivity between excitatory neurons in layer 2/3. Predicted connectivity is sparse and consistent with known correlations with stimulus tuning, spontaneous correlation and distance.

}, url = {https://papers.nips.cc/paper/6940-model-based-bayesian-inference-of-neural-activity-and-connectivity-from-all-optical-interrogation-of-a-neural-circuit}, author = {Aitchison, Laurence and Russell, Lloyd and Packer, Adam M and Yan, Jinyao and Castonguaye, Philippe and H{\"a}usser, Michael and Turaga, Srinivas C} } @conference {67221, title = {Model-based Bayesian inference of neural activity and connectivity from all-optical interrogation of a neural circuit}, booktitle = {Advances in Neural Information Processing Systems}, year = {2017}, publisher = {Curran Associates, Inc.}, organization = {Curran Associates, Inc.}, abstract = {

Population activity measurement by calcium imaging can be combined with cellular resolution optogenetic activity perturbations to enable the mapping of neural connectivity in vivo. This requires accurate inference of perturbed and unperturbed neural activity from calcium imaging measurements, which are noisy and indirect, and can also be contaminated by photostimulation artifacts. We have developed a new fully Bayesian approach to jointly inferring spiking activity and neural connectivity from in vivo all-optical perturbation experiments. In contrast to standard approaches that perform spike inference and analysis in two separate maximum-likelihood phases, our joint model is able to propagate uncertainty in spike inference to the inference of connectivity and vice versa. We use the framework of variational autoencoders to model spiking activity using discrete latent variables, low-dimensional latent common input, and sparse spike-and-slab generalized linear coupling between neurons. Additionally, we model two properties of the optogenetic perturbation: off-target photostimulation and photostimulation transients. Using this model, we were able to fit models on 30 minutes of data in just 10 minutes. We performed an all-optical circuit mapping experiment in primary visual cortex of the awake mouse, and use our approach to predict neural connectivity between excitatory neurons in layer 2/3. Predicted connectivity is sparse and consistent with known correlations with stimulus tuning, spontaneous correlation and distance.

}, url = {https://discovery.ucl.ac.uk/id/eprint/10072143/}, author = {Aitchison, Laurence and Russell, Lloyd and Packer, Adam M and Yan, Jinyao and Castonguay, Philippe and H{\"a}usser, Michael and Turaga, Srinivas C}, editor = {I. Guyon and U. V. Luxburg and S. Bengio and H. Wallach and R. Fergus and S. Vishwanathan and R. Garnett} } @article {48908, title = {Molecular basis of CENP-C association with the CENP-A nucleosome at yeast centromeres.}, journal = {Genes \& Development}, volume = {31}, year = {2017}, month = {2017 Oct 01}, pages = {1958-1972}, abstract = {

Histone CENP-A-containing nucleosomes play an important role in nucleating kinetochores at centromeres for chromosome segregation. However, the molecular mechanisms by which CENP-A nucleosomes engage with kinetochore proteins are not well understood. Here, we report the finding of a new function for the budding yeast Cse4/CENP-A histone-fold domain interacting with inner kinetochore protein Mif2/CENP-C. Strikingly, we also discovered that AT-rich centromere DNA has an important role for Mif2 recruitment. Mif2 contacts one side of the nucleosome dyad, engaging with both Cse4 residues and AT-rich nucleosomal DNA. Both interactions are directed by a contiguous DNA- and histone-binding domain (DHBD) harboring the conserved CENP-C motif, an AT hook, and RK clusters (clusters enriched for arginine-lysine residues). Human CENP-C has two related DHBDs that bind preferentially to DNA sequences of higher AT content. Our findings suggest that a DNA composition-based mechanism together with residues characteristic for the CENP-A histone variant contribute to the specification of centromere identity.

}, issn = {1549-5477}, doi = {10.1101/gad.304782.117}, author = {Xiao, Hua and Wang, Feng and Wisniewski, Jan and Shaytan, Alexey K and Ghirlando, Rodolfo and Fitzgerald, Peter C and Huang, Yingzi and Wei, Debbie and Li, Shipeng and Landsman, David and Panchenko, Anna R and Wu, Carl} } @article {48936, title = {A moving source of matrix components is essential for de novo basement membrane formation.}, journal = {Current Biology : CB}, volume = {27}, year = {2017}, month = {2017 Nov 02}, pages = {3526-34}, abstract = {

The basement membrane (BM) is a thin layer of extracellular matrix (ECM) beneath nearly all epithelial cell types that is critical for cellular and tissue function. It is composed of numerous components conserved among all bilaterians [1]; however, it is unknown how all of these components are generated and subsequently constructed to form a fully mature BM in the living animal. Although BM formation is thought to simply involve a process of self-assembly [2], this concept suffers from a number of logistical issues when considering its construction in\ vivo. First, incorporation of BM components appears to be hierarchical [3-5], yet it is unclear whether their production during embryogenesis must also be regulated in a temporal fashion. Second, many BM proteins are produced not only by the cells residing on the BM but also by surrounding cell types [6-9], and it is unclear how large, possibly insoluble protein complexes [10] are delivered into the matrix. Here we exploit our ability to live image and genetically dissect de novo BM formation during Drosophila development. This reveals that there is a temporal hierarchy of BM protein production that is essential for proper component incorporation. Furthermore, we show that BM components require secretion by migrating macrophages (hemocytes) during their developmental dispersal, which is critical for embryogenesis. Indeed, hemocyte migration is essential to deliver a subset of ECM components evenly throughout the embryo. This reveals that de novo BM construction requires a combination of both production and distribution logistics allowing for the timely delivery of core components.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2017.10.001}, author = {Matsubayashi, Yutaka and Louani, Adam and Dragu, Anca and S{\'a}nchez-S{\'a}nchez, Besaiz J and Serna-Morales, Eduardo and Yolland, Lawrence and Gyoergy, Attila and Vizcay, Gema and Fleck, Roland A and Heddleston, John M and Chew, Teng-Leong and Siekhaus, Daria E and Stramer, Brian M} } @article {48254, title = {Multicut brings automated neurite segmentation closer to human performance.}, journal = {Nature Methods}, volume = {14}, year = {2017}, month = {2017 Jan 31}, pages = {101-102}, issn = {1548-7105}, doi = {10.1038/nmeth.4151}, author = {Beier, Thorsten and Pape, Constantin and Rahaman, Nasim and Prange, Timo and Berg, Stuart and Bock, Davi D and Cardona, Albert and Knott, Graham W and Plaza, Stephen M and Scheffer, Louis K and Koethe, Ullrich and Kreshuk, Anna and Hamprecht, Fred A} } @article {48278, title = {Multi-view light-sheet imaging and tracking with the MaMuT software reveals the cell lineage of a direct developing arthropod limb.}, journal = {eLife}, volume = {7}, year = {2017}, month = {2018 Mar 29}, pages = {e34410}, abstract = {

During development, coordinated cell behaviors orchestrate tissue and organ morphogenesis. Detailed descriptions of cell lineages and behaviors provide a powerful framework to elucidate the mechanisms of morphogenesis. To study the cellular basis of limb development, we imaged transgenic fluorescently-labeled embryos from the crustacean Parhyale hawaiensis with multi-view light-sheet microscopy at high spatiotemporal resolution over several days of embryogenesis. The cell lineage of outgrowing thoracic limbs was reconstructed at single-cell resolution with new software called Massive Multi-view Tracker (MaMuT). In silico clonal analyses suggested that the early limb primordium becomes subdivided into anterior-posterior and dorsal-ventral compartments whose boundaries intersect at the distal tip of the growing limb. Limb-bud formation is associated with spatial modulation of cell proliferation, while limb elongation is also driven by preferential orientation of cell divisions along the proximal-distal growth axis. Cellular reconstructions were predictive of the expression patterns of limb development genes including the BMP morphogen Decapentaplegic.

}, doi = {10.7554/eLife.34410}, author = {Wolff, Carsten and Tinevez, Jean-Yves and Pietzsch, Tobias and Stamataki, Evangelia and Harich, Benjamin and Guignard, Leo and Preibisch, Stephan and Shorte, Spencer and Keller, Philipp J and Tomancak, Pavel and Pavlopoulos, Anastasios} } @article {48731, title = {Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation.}, journal = {Molecular Cell}, volume = {67}, year = {2017}, month = {2017 Jul 28}, pages = {566-78}, abstract = {

50 years ago, Vincent Allfrey and colleagues discovered that lymphocyte activation triggers massive acetylation of chromatin. However, the molecular mechanisms driving epigenetic accessibility are still unknown. We here show that stimulated lymphocytes decondense chromatin by three differentially regulated steps. First, chromatin is repositioned away from the nuclear periphery in response to global acetylation. Second, histone nanodomain clusters decompact into mononucleosome fibers through a mechanism that requires Myc and continual energy input. Single-molecule imaging shows that this step lowers transcription factor residence time and non-specific collisions during sampling for DNA targets. Third, chromatin interactions shift from long range to predominantly short range, and CTCF-mediated loops and contact domains double in numbers. This architectural change facilitates cognate promoter-enhancer contacts and also requires Myc and continual ATP production. Our results thus define the nature and transcriptional impact of chromatin decondensation and reveal an unexpected role for Myc in the establishment of nuclear topology in mammalian cells.

}, issn = {1097-4164}, doi = {10.1016/j.molcel.2017.07.013}, author = {Kieffer-Kwon, Kyong-Rim and Nimura, Keisuke and Rao, Suhas S P and Xu, Jianliang and Jung, Seolkyoung and Pekowska, Aleksandra and Dose, Marei and Stevens, Evan and Mathe, Ewy and Dong, Peng and Huang, Su-Chen and Ricci, Maria Aurelia and Baranello, Laura and Zheng, Ying and Ardori, Francesco Tomassoni and Resch, Wolfgang and Stavreva, Diana and Nelson, Steevenson and McAndrew, Michael and Casellas, Adriel and Finn, Elizabeth and Gregory, Charles and St Hilaire, Brian Glenn and Johnson, Steven M and Dubois, Wendy and Cosma, Maria Pia and Batchelor, Eric and Levens, David and Phair, Robert D and Misteli, Tom and Tessarollo, Lino and Hager, Gordon and Lakadamyali, Melike and Liu, Zhe and Floer, Monique and Shroff, Hari and Aiden, Erez Lieberman and Casellas, Rafael} } @article {49352, title = {Myosin VI facilitates connexin 43 gap junction accretion.}, journal = {Journal of Cell Science}, volume = {130}, year = {2017}, month = {2017 03 01}, pages = {827-840}, abstract = {

In this study, we demonstrate myosin VI enrichment at Cx43 (also known as GJA1)-containing gap junctions (GJs) in heart tissue, primary cardiomyocytes and cell culture models. In primary cardiac tissue and in fibroblasts from the myosin VI-null mouse as well as in tissue culture cells transfected with siRNA against myosin VI, we observe reduced GJ plaque size with a concomitant reduction in intercellular communication, as shown by fluorescence recovery after photobleaching (FRAP) and a new method of selective calcein administration. Analysis of the molecular role of myosin VI in Cx43 trafficking indicates that myosin VI is dispensable for the delivery of Cx43 to the cell surface and connexon movement in the plasma membrane. Furthermore, we cannot corroborate clathrin or Dab2 localization at gap junctions and we do not observe a function for the myosin-VI-Dab2 complex in clathrin-dependent endocytosis of annular gap junctions. Instead, we found that myosin VI was localized at the edge of Cx43 plaques by using total internal reflection fluorescence (TIRF) microscopy and use FRAP to identify a plaque accretion defect as the primary manifestation of myosin VI loss in Cx43 homeostasis. A fuller understanding of this derangement may explain the cardiomyopathy or gliosis associated with the loss of myosin VI.

}, keywords = {Amino Acid Motifs, Animals, Cell Communication, Cell Membrane, Cells, Cultured, Connexin 43, Embryo, Mammalian, Fibroblasts, Gap Junctions, Golgi Apparatus, Hela Cells, Humans, Mice, Models, Biological, Myocardium, Myocytes, Cardiac, Myosin Heavy Chains, Protein Domains, Protein Transport, Rats}, issn = {1477-9137}, doi = {10.1242/jcs.199083}, author = {Waxse, Bennett J and Sengupta, Prabuddha and Hesketh, Geoffrey G and Lippincott-Schwartz, Jennifer and Buss, Folma} } @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 {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 {48642, title = {The Ol1mpiad: concordance of behavioural faculties of stage 1 and stage 3 Drosophila larvae.}, journal = {The Journal of Experimental Biology}, volume = {220}, year = {2017}, month = {2017 Jul 01}, pages = {2452-2475}, abstract = {

Mapping brain function to brain structure is a fundamental task for neuroscience. For such an endeavour, the Drosophila larva is simple enough to be tractable, yet complex enough to be interesting. It features about 10,000 neurons and is capable of various taxes, kineses and Pavlovian conditioning. All its neurons are currently being mapped into a light-microscopical atlas, and Gal4 strains are being generated to experimentally access neurons one at a time. In addition, an electron microscopic reconstruction of its nervous system seems within reach. Notably, this electron microscope-based connectome is being drafted for a stage 1 larva - because stage 1 larvae are much smaller than stage 3 larvae. However, most behaviour analyses have been performed for stage 3 larvae because their larger size makes them easier to handle and observe. It is therefore warranted to either redo the electron microscopic reconstruction for a stage 3 larva or to survey the behavioural faculties of stage 1 larvae. We provide the latter. In a community-based approach we called the Ol1mpiad, we probed stage 1 Drosophila larvae for free locomotion, feeding, responsiveness to substrate vibration, gentle and nociceptive touch, burrowing, olfactory preference and thermotaxis, light avoidance, gustatory choice of various tastants plus odour-taste associative learning, as well as light/dark-electric shock associative learning. Quantitatively, stage 1 larvae show lower scores in most tasks, arguably because of their smaller size and lower speed. Qualitatively, however, stage 1 larvae perform strikingly similar to stage 3 larvae in almost all cases. These results bolster confidence in mapping brain structure and behaviour across developmental stages.

}, issn = {1477-9145}, doi = {10.1242/jeb.156646}, author = {Almeida-Carvalho, Maria J and Berh, Dimitri and Braun, Andreas and Chen, Yi-chun and Eichler, Katharina and Eschbach, Claire and Fritsch, Pauline M J and Gerber, Bertram and Hoyer, Nina and Jiang, Xiaoyi and Kleber, J{\"o}rg and Kl{\"a}mbt, Christian and K{\"o}nig, Christian and Louis, Matthieu and Michels, Birgit and Miroschnikow, Anton and Mirth, Christen and Miura, Daisuke and Niewalda, Thomas and Otto, Nils and Paisios, Emmanouil and Pankratz, Michael J and Petersen, Meike and Ramsperger, Noel and Randel, Nadine and Risse, Benjamin and Saumweber, Timo and Schlegel, Philipp and Schleyer, Michael and Soba, Peter and Sprecher, Simon G and Tanimura, Teiichi and Thum, Andreas S and Toshima, Naoko and Truman, Jim W and Yarali, Ayse and Zlatic, Marta} } @article {48799, title = {Optogenetic control with a photocleavable protein, PhoCl.}, journal = {Nature Methods}, volume = {14}, year = {2017}, month = {2017 Apr}, pages = {391-394}, abstract = {

To expand the range of experiments that are accessible with optogenetics, we developed a photocleavable protein (PhoCl) that spontaneously dissociates into two fragments after violet-light-induced cleavage of a specific bond in the protein backbone. We demonstrated that PhoCl can be used to engineer light-activatable Cre recombinase, Gal4 transcription factor, and a viral protease that in turn was used to activate opening of the large-pore ion channel Pannexin-1.

}, keywords = {Connexins, Directed Molecular Evolution, Green Fluorescent Proteins, HEK293 Cells, HSP90 Heat-Shock Proteins, Humans, Luminescent Proteins, Nerve Tissue Proteins, Nuclear Localization Signals, Optogenetics, Patch-Clamp Techniques, Photochemistry, Protein Engineering, Recombinant Proteins, Viral Nonstructural Proteins}, issn = {1548-7105}, doi = {10.1038/nmeth.4222}, author = {Zhang, Wei and Lohman, Alexander W and Zhuravlova, Yevgeniya and Lu, Xiaocen and Wiens, Matthew D and Hoi, Hiofan and Yaganoglu, Sine and Mohr, Manuel A and Kitova, Elena N and Klassen, John S and Pantazis, Periklis and Thompson, Roger J and Campbell, Robert E} } @article {48535, title = {Perceptually accurate display of two greyscale images as a single colour image.}, journal = {Journal of Microscopy}, year = {2017}, month = {2017 May 30}, abstract = {

Life scientists often desire to display the signal from two different molecular probes as a single colour image, so as to convey information about the probes{\textquoteright} relative concentrations as well as their spatial corelationship. Traditionally, such colour images are created through a merge display, where each greyscale signal is assigned to different channels of an RGB colour image. However, human perception of colour and greyscale intensity is not equivalent. Thus, a merged image display conveys to the typical viewer only a subset of the absolute and relative intensity information present in and between two greyscale images. The Commission Internationale de l{\textquoteright}Eclairage L*a*b* colour space (CIELAB) has been designed to specify colours according to the perceptually defined quantities of hue (perceived colour) and luminosity (perceived brightness). Here, we use the CIELAB colour space to encode two dimensions of information about two greyscale images within these two perceptual dimensions of a single colour image. We term our method a Perceptually Uniform Projection display and show using biological image examples how these displays convey more information about two greyscale signals than comparable RGB colour space-based techniques.

}, issn = {1365-2818}, doi = {10.1111/jmi.12588}, author = {Taylor, A B and Ioannou, M S and Watanabe, T and Hahn, K and Chew, T-L} } @article {67286, title = {Predictive Coding of Novel versus Familiar Stimuli in the Primary Visual Cortex}, journal = {bioRxiv}, year = {2017}, month = {10/2017}, abstract = {

To explore theories of predictive coding, we presented mice with repeated sequences of images with novel images sparsely substituted. Under these conditions, mice could be rapidly trained to lick in response to a novel image, demonstrating a high level of performance on the first day of testing. Using 2-photon calcium imaging to record from layer 2/3 neurons in the primary visual cortex, we found that novel images evoked excess activity in the majority of neurons. When a new stimulus sequence was repeatedly presented, a majority of neurons had similarly elevated activity for the first few presentations, which then decayed to almost zero activity. The decay time of these transient responses was not fixed, but instead scaled with the length of the stimulus sequence. However, at the same time, we also found a small fraction of the neurons within the population (\~2\%) that continued to respond strongly and periodically to the repeated stimulus. Decoding analysis demonstrated that both the transient and sustained responses encoded information about stimulus identity. We conclude that the layer 2/3 population uses a two-channel predictive code: a dense transient code for novel stimuli and a sparse sustained code for familiar stimuli. These results extend and unify existing theories about the nature of predictive neural codes.

}, doi = {10.1101/197608}, url = {https://www.biorxiv.org/content/early/2017/10/03/197608}, author = {Homann, Jan and Koay, Sue Ann and Glidden, Alistair M. and Tank, David W. and Berry, Michael J.} } @article {48992, title = {Protein-templated gold nanoparticle synthesis: protein organization, controlled gold sequestration, and unexpected reaction products.}, journal = {Dalton Transactions (Cambridge, England : 2003)}, volume = {46}, year = {2017}, month = {2017 Dec 21}, pages = {16465-16473}, abstract = {

Emerging applications that exploit the properties of nanoparticles for biotechnology require that the nanoparticles be biocompatible or support biological recognition. These types of particles can be produced through syntheses that involve biologically relevant molecules (proteins or natural extracts, for example). Many of the protocols that rely on these molecules are performed without a clear understanding of the mechanism by which the materials are produced. We have investigated a previously described reaction in which gold nanoparticles are produced from the reaction of chloroauric acid and proteins in solution. We find that modifications to the starting conditions can alter the product from the expected solution-suspended colloids to a product where colloids are formed within a solid, fibrous protein structure. We have interrogated this synthesis, exploiting the change in products to better understand this reaction. We have evaluated the kinetics and products for 7 different proteins over a range of concentrations and temperatures. The key factor that controls the synthetic outcome (colloid or fiber) is the concentration of the protein relative to the gold concentration. We find that the observed fibrous structures are more likely to form at low protein concentrations and when hydrophilic proteins are used. An analysis of the reaction kinetics shows that AuNP formation occurs faster at lower protein (fiber-forming) concentrations than at higher protein (colloid-forming) concentrations. These results contradict traditional expectations for reaction kinetics and protein-fiber formation and are instructive of the manner in which proteins template gold nanoparticle production.

}, issn = {1477-9234}, doi = {10.1039/c7dt03275g}, author = {Hart, Cassidy and Abuladel, Nouf and Bee, Madeleine and Kreider, Megan C and CVitan, Alexander C and Esson, Moira M and Farag, Andrew and Ibeh, Trisha and Kalivas, Eleni N and Larco, Daniel-Mario and Walker Long, Andrew and Lymperopoulos, Loukas and Mendel, Zachary and Miles, Nancy and Zareba, Carly M and Schwabacher, James C and Slucher, Helen and Vinals, Javier and Heddleston, John M and Li, Wenyue and Fox, Douglas M and Hartings, Matthew R} } @article {48343, title = {Quantifying transcription factor binding dynamics at the single-molecule level in live cells.}, journal = {Methods (San Diego, Calif.)}, year = {2017}, month = {2017 Mar 15}, abstract = {

Progressive, technological achievements in the quantitative fluorescence microscopy field are allowing researches from many different areas to start unraveling the dynamic intricacies of biological processes inside living cells. From super-resolution microscopy techniques to tracking of individual proteins, fluorescence microscopy is changing our perspective on how the cell works. Fortunately, a growing number of research groups are exploring single-molecule studies in living cells. However, no clear consensus exists on several key aspects of the technique such as image acquisition conditions, or analysis of the obtained data. Here, we describe a detailed approach to perform single-molecule tracking (SMT) of transcription factors in living cells to obtain key binding characteristics, namely their residence time and bound fractions. We discuss different types of fluorophores, labeling density, microscope, cameras, data acquisition, and data analysis. Using the glucocorticoid receptor as a model transcription factor, we compared alternate tags (GFP, mEOS, HaloTag, SNAP-tag, CLIP-tag) for potential multicolor applications. We also examine different methods to extract the dissociation rates and compare them with simulated data. Finally, we discuss several challenges that this exciting technique still faces.

}, issn = {1095-9130}, doi = {10.1016/j.ymeth.2017.03.014}, author = {Presman, Diego M and Ball, David A and Paakinaho, Ville and Grimm, Jonathan B and Lavis, Luke D and Karpova, Tatiana S and Hager, Gordon L} } @article {48220, title = {Real-time spike sorting platform for high-density extracellular probes with ground-truth validation and drift correction.}, journal = {bioRxiv}, year = {2017}, month = {2017 Jan 19}, abstract = {

Electrical recordings from a large array of electrodes give us access to neural population activity with single-cell, single-spike resolution. These recordings contain extracellular spikes which must be correctly detected and assigned to individual neurons. Despite numerous spike-sorting techniques developed in the past, a lack of high-quality ground-truth datasets hinders the validation of spike-sorting approaches. Furthermore, existing approaches requiring manual corrections are not scalable for hours of recordings exceeding 100 channels. To address these issues, we built a comprehensive spike-sorting pipeline that performs reliably under noise and probe drift by incorporating a channel-covariance feature and a clustering based on fast density-peak finding. We validated performance of our workflow using multiple ground-truth datasets that recently became available. Our software scales linearly and processes a 1000-channel recording in real-time using a single workstation. Accurate, real-time spike sorting from large recording arrays will enable more precise control of closed-loop feedback experiments and brain-computer interfaces.

}, doi = {10.1101/101030}, author = {Jun, James Jaeyoon and Mitelut, Catalin and Lai, Chongxi and Gratiy, Sergey and Anastassiou, Costas and Harris, Timothy D} } @article {48494, title = {Representations of Novelty and Familiarity in a Mushroom Body Compartment.}, journal = {Cell}, volume = {169}, year = {2017}, month = {2017 May 09}, pages = {956-69}, abstract = {

Animals exhibit a behavioral response to novel sensory stimuli about which they have no prior knowledge. We have examined the neural and behavioral correlates of novelty and familiarity in the olfactory system of Drosophila. Novel odors elicit strong activity in output neurons (MBONs) of the α{\textquoteright}3 compartment of the mushroom body that is rapidly suppressed upon repeated exposure to the same odor. This transition in neural activity upon familiarization requires odor-evoked activity in the dopaminergic neuron innervating this compartment. Moreover, exposure of a fly to novel odors evokes an alerting response that can also be elicited by optogenetic activation of α{\textquoteright}3 MBONs. Silencing these MBONs eliminates the alerting behavior. These data suggest that the α{\textquoteright}3 compartment plays a causal role in the behavioral response to novel and familiar stimuli as a consequence of dopamine-mediated plasticity at the Kenyon cell-MBONα{\textquoteright}3 synapse.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2017.04.028}, author = {Hattori, Daisuke and Aso, Yoshinori and Swartz, Kurtis J and Rubin, Gerald M and Abbott, L F and Axel, Richard} } @article {48837, title = {Robustness of spike deconvolution for calcium imaging of neural spiking.}, journal = {bioRxiv}, year = {2017}, month = {2017 Jun 27}, pages = {156786}, abstract = {

Calcium imaging is a powerful method to record the activity of neural populations, but inferring spike times from calcium signals is a challenging problem. We compared multiple approaches using multiple datasets with ground truth electrophysiology, and found that simple non-negative deconvolution (NND) outperformed all other algorithms. We introduce a novel benchmark applicable to recordings without electrophysiological ground truth, based on the correlation of responses to two stimulus repeats, and used this to show that unconstrained NND also outperformed the other algorithms when run on {\textquoteright}zoomed out{\textquoteright} datasets of ~10,000 cell recordings. Finally, we show that NND-based methods match the performance of a supervised method based on convolutional neural networks, while avoiding some of the biases of such methods, and at much faster running times. We therefore recommend that spikes be inferred from calcium traces using simple NND, due to its simplicity, efficiency and accuracy.

}, doi = {https://doi.org/10.1101/156786}, author = {Pachitariu, Marius and Stringer, Carsen and Harris, Kenneth D} } @article {48787, title = {The role of disulfide bond replacements in analogues of the tarantula toxin ProTx-II and their effects on inhibition of the voltage-gated sodium ion channel Nav1.7.}, journal = {Journal of the American Chemical Society}, volume = {139}, year = {2017}, month = {2017 Sep 07}, pages = {13063-75}, abstract = {

Spider venom toxins, such as Protoxin-II (ProTx-II), have recently received much attention as selective Nav1.7 channel blockers, with potential to be developed as leads for the treatment of chronic nocioceptive pain. ProTx-II is a 30-amino acid peptide with three disulfide bonds that has been reported to adopt a well-defined inhibitory cystine knot (ICK) scaffold structure. Potential drawbacks with such peptides include poor pharmacodynamics and potential scrambling of the disulfide bonds in vivo. In order to address these issues, in the present study we report the solid-phase synthesis of lanthionine-bridged analogues of ProTx-II, in which one of the three disulfide bridges is replaced with a thioether linkage, and evaluate the biological properties of these analogues. We have also investigated the folding and disulfide bridging patterns arising from different methods of oxidation of the linear peptide precursor. Finally, we report the X-ray crystal structure of ProTx-II to atomic resolution; to our knowledge this is the first crystal structure of an ICK spider venom peptide not bound to a substrate.

}, issn = {1520-5126}, doi = {10.1021/jacs.7b06506}, author = {Wright, Zo{\"e} V F and McCarthy, Stephen and Dickman, Rachael and Reyes, Francis E and Sanchez-Martinez, Silvia and Cryar, Adam and Kilford, Ian and Hall, Adrian and Takle, Andrew K and Topf, Maya and Gonen, Tamir and Thalassinos, Konstantinos and Tabor, Alethea B} } @article {48372, title = {Sensorimotor neuroscience: motor precision meets vision.}, journal = {Current Biology : CB}, volume = {27}, year = {2017}, month = {2017 Apr 03}, pages = {R261-R263}, abstract = {

Visual motion sensing neurons in the fly also encode a range of behavior-related signals. These nonvisual inputs appear to be used to correct some of the challenges of visually guided locomotion.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2017.02.047}, author = {Longden, Kit D and Huston, Stephen J and Reiser, Michael B} } @article {48788, title = {Simultaneous activation of parallel sensory pathways promotes a grooming sequence in Drosophila.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Sep 09}, abstract = {

A central model that describes how behavioral sequences are produced features a neural architecture that readies different movements simultaneously, and a mechanism where prioritized suppression between the movements determines their sequential performance. We previously described a model whereby suppression drives a Drosophila grooming sequence that is induced by simultaneous activation of different sensory pathways that each elicit a distinct movement (Seeds et al. 2014). Here, we confirm this model using transgenic expression to identify and optogenetically activate sensory neurons that elicit specific grooming movements. Simultaneous activation of different sensory pathways elicits a grooming sequence that resembles the naturally induced sequence. Moreover, the sequence proceeds after the sensory excitation is terminated, indicating that a persistent trace of this excitation induces the next grooming movement once the previous one is performed. This reveals a mechanism whereby parallel sensory inputs can be integrated and stored to elicit a delayed and sequential grooming response.

}, issn = {2050-084X}, doi = {10.7554/eLife.28804}, author = {Hampel, Stefanie and McKellar, Claire E and Simpson, Julie H and Seeds, Andrew M} } @article {69340, title = {Single-Neuron Gene Expression Analysis Using the Maxwell{\textregistered} 16 LEV System in the Neural Systems and Behavior Course}, journal = {bioRxiv}, year = {2017}, month = {2017 Feb 10}, abstract = {

Gene expression analysis from single cells has become increasingly prominent across biological disciplines; thus, it is important to train students in these approaches. Here, we present an experimental and analysis pipeline that we developed for the Neural Systems \& Behavior (NS\&B) course at Marine Biological Laboratory. Our approach used the Maxwell{\textregistered} 16 LEV simplyRNA Tissue Kit and GoTaq{\textregistered} 2-Step RT-qPCR System for gene expression analysis from single neurons of the crustacean stomatogastric ganglion, a model system to study the generation of rhythmic motor patterns. We used double-stranded RNA to knockdown expression of a putative neuromodulator-activated sodium channel. We then examined the electrophysiological responses to known neuromodulators and confirmed that the response was reduced. Finally, we measured how mRNA levels of several ion channel genes changed in response. Our results provide new insights into the neural mechanisms underlying the generation and modulation of rhythmic motor patterns.

}, doi = {10.1101/107342}, url = {https://www.biorxiv.org/content/early/2017/02/10/107342}, author = {Rayna M. Harris and Adriane G. Otopalik and Colin J. Smith and Dirk Bucher and Jorge Golowasch and Hans A. Hofmann} } @article {48435, title = {Stem cell-intrinsic, seven-up-triggered temporal factor gradients diversify intermediate neural progenitors.}, journal = {Current Biology : CB}, volume = {27}, year = {2017}, month = {2017 Apr 10}, pages = {1303-13}, abstract = {

Building a sizable, complex brain requires both cellular expansion and diversification. One mechanism to achieve these goals is production of multiple transiently amplifying intermediate neural progenitors (INPs) from a single neural stem cell. Like mammalian neural stem cells, Drosophila type II neuroblasts utilize INPs to produce neurons and glia. Within a given lineage, the consecutively born INPs produce morphologically distinct progeny, presumably due to differential inheritance of temporal factors. To uncover the underlying temporal fating mechanisms, we profiled type II neuroblasts{\textquoteright} transcriptome across time. Our results reveal opposing temporal gradients of Imp and Syp RNA-binding proteins (descending and ascending, respectively). Maintaining high Imp throughout serial INP production expands the number of neurons and glia with early temporal fate at the expense of cells with late fate. Conversely, precocious upregulation of Syp reduces the number of cells with early fate. Furthermore, we reveal that the transcription factor Seven-up initiates progression of the Imp/Syp gradients. Interestingly, neuroblasts that maintain initial Imp/Syp levels can still yield progeny with a small range of early fates. We therefore propose that the Seven-up-initiated Imp/Syp gradients create coarse temporal windows within type II neuroblasts to pattern INPs, which subsequently undergo fine-tuned subtemporal patterning.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2017.03.047}, author = {Ren, Qingzhong and Yang, Ching-Po and Liu, Zhiyong and Sugino, Ken and Mok, Kent and He, Yisheng and Ito, Masayoshi and Nern, Aljoscha and Otsuna, Hideo and Lee, Tzumin} } @article {48945, title = {Structural basis of bacterial transcription activation.}, journal = {Science (New York, N.Y.)}, volume = {358}, year = {2017}, month = {2017 Nov 17}, pages = {947-951}, abstract = {

In bacteria, the activation of gene transcription at many promoters is simple and only involves a single activator. The cyclic adenosine 3{\textquoteright},5{\textquoteright}-monophosphate receptor protein (CAP), a classic activator, is able to activate transcription independently through two different mechanisms. Understanding the class I mechanism requires an intact transcription activation complex (TAC) structure at a high resolution. Here we report a high-resolution cryo-electron microscopy structure of an intact Escherichia coli class I TAC containing a CAP dimer, a σ(70)-RNA polymerase (RNAP) holoenzyme, a complete class I CAP-dependent promoter DNA, and a de novo synthesized RNA oligonucleotide. The structure shows how CAP wraps the upstream DNA and how the interactions recruit RNAP. Our study provides a structural basis for understanding how activators activate transcription through the class I recruitment mechanism.

}, issn = {1095-9203}, doi = {10.1126/science.aao1923}, author = {Liu, Bin and Hong, Chuan and Huang, Rick K and Yu, Zhiheng and Steitz, Thomas A} } @article {48840, title = {Suite2p: beyond 10,000 neurons with standard two-photon microscopy.}, journal = {bioRxiv}, year = {2017}, month = {2017 Jul 20}, pages = {061507}, abstract = {

Two-photon microscopy of calcium-dependent sensors has enabled unprecedented recordings from vast populations of neurons. While the sensors and microscopes have matured over several generations of development, computational methods to process the resulting movies remain inefficient and can give results that are hard to interpret. Here we introduce Suite2p: a fast, accurate and complete pipeline that registers raw movies, detects active cells, extracts their calcium traces and infers their spike times. Suite2p runs on standard workstations, operates faster than real time, and recovers ~2 times more cells than the previous state-of-the-art method. Its low computational load allows routine detection of ~10,000 cells simultaneously with standard two-photon resonant-scanning microscopes. Recordings at this scale promise to reveal the fine structure of activity in large populations of neurons or large populations of subcellular structures such as synaptic boutons.

}, doi = {https://doi.org/10.1101/061507}, author = {Pachitariu, Marius and Stringer, Carsen and Dipoppa, Mario and Schr{\"o}der, Sylvia and Rossi, L Federico and Dalgleish, Henry and Carandini, Matteo and Harris, Kenneth D} } @inbook {47793, title = {Targeted manipulation of neuronal activity in behaving adult flies.}, booktitle = {Decoding Neural Circuit Structure and Function}, year = {2017}, month = {2016 Aug 15}, pages = {191-222}, abstract = {

The ability to control the activity of specific neurons in freely behaving animals provides an effective way to probe the contributions of neural circuits to behavior. Wide interest in studying principles of neural circuit function using the fruit fly\ Drosophila melanogaster\ has fueled the construction of an extensive transgenic toolkit for performing such neural manipulations. Here we describe approaches for using these tools to manipulate the activity of specific neurons and assess how those manipulations impact the behavior of flies. We also describe methods for examining connectivity among multiple neurons that together form a neural circuit controlling a specific behavior. This work provides a resource for researchers interested in examining how neurons and neural circuits contribute to the rich repertoire of behaviors performed by flies.

}, doi = {10.1007/978-3-319-57363-2_7}, author = {Hampel, Stefanie and Seeds, Andrew M} } @article {48985, title = {A topographic axis of transcriptional identity in thalamus.}, journal = {bioRxiv}, year = {2017}, month = {2017 Dec 31}, pages = {241315}, abstract = {

A fundamental goal in neuroscience is to uncover common principles by which different modalities of information are processed. In the mammalian brain, thalamus acts as the essential hub for forebrain circuits handling inputs from sensory, motor, limbic, and cognitive pathways. Whether thalamus imposes common transformations on each of these modalities is unknown. Molecular characterization offers a principled approach to revealing the organization of thalamus. Using near-comprehensive and projection-specific transcriptomic sequencing, we found that almost all thalamic nuclei fit into one of three profiles. These profiles lie on a single axis of genetic variance which is aligned with the mediolateral spatial axis of thalamus. Genes defining this axis of variance include receptors and ion channels, providing a systematic diversification of input/output transformations across the topography of thalamus. Single cell transcriptional profiling revealed graded heterogeneity within individual thalamic nuclei, demonstrating that a spectrum of cell types and potentially diverse input/output transforms exist within a given thalamic nucleus. Together, our data argue for an archetypal organization of pathways serving diverse input modalities, and provides a comprehensive organizational scheme for thalamus.

}, doi = {10.1101/241315}, author = {Phillips, James W and Schulman, Anton and Hara, Erina and Liu, Chenghao and Shields, Brenda C and Korff, Wyatt and Lemire, Andrew and Dudman, Joshua T and Nelson, Sacha B and Hantman, Adam W} } @article {48461, title = {What can tiny mushrooms in fruit flies tell us about learning and memory?}, journal = {Neuroscience Research}, volume = {129}, year = {2017}, month = {2017 May 05}, pages = {8-16}, abstract = {

Nervous systems have evolved to translate external stimuli into appropriate behavioral responses. In an ever-changing environment, flexible adjustment of behavioral choice by experience-dependent learning is essential for the animal{\textquoteright}s survival. Associative learning is a simple form of learning that is widely observed from worms to humans. To understand the whole process of learning, we need to know how sensory information is represented and transformed in the brain, how it is changed by experience, and how the changes are reflected on motor output. To tackle these questions, studying numerically simple invertebrate nervous systems has a great advantage. In this review, I will feature the Pavlovian olfactory learning in the fruit fly, Drosophila melanogaster. The mushroom body is a key brain area for the olfactory learning in this organism. Recently, comprehensive anatomical information and the genetic tool sets were made available for the mushroom body circuit. This greatly accelerated the physiological understanding of the learning process. One of the key findings was dopamine-induced long-term synaptic plasticity that can alter the representations of stimulus valence. I will mostly focus on the new studies within these few years and discuss what we can possibly learn about the vertebrate systems from this model organism.

}, issn = {1872-8111}, doi = {10.1016/j.neures.2017.05.002}, author = {Hige, Toshihide} } @article {48497, title = {Whole-brain serial-section electron microscopy in larval zebrafish.}, journal = {Nature}, volume = {545}, year = {2017}, month = {2017 May 18}, pages = {345-349}, abstract = {

High-resolution serial-section electron microscopy (ssEM) makes it possible to investigate the dense meshwork of axons, dendrites, and synapses that form neuronal circuits. However, the imaging scale required to comprehensively reconstruct these structures is more than ten orders of magnitude smaller than the spatial extents occupied by networks of interconnected neurons, some of which span nearly the entire brain. Difficulties in generating and handling data for large volumes at nanoscale resolution have thus restricted vertebrate studies to fragments of circuits. These efforts were recently transformed by advances in computing, sample handling, and imaging techniques, but high-resolution examination of entire brains remains a challenge. Here, we present ssEM data for the complete brain of a larval zebrafish (Danio rerio) at 5.5 days post-fertilization. Our approach utilizes multiple rounds of targeted imaging at different scales to reduce acquisition time and data management requirements. The resulting dataset can be analysed to reconstruct neuronal processes, permitting us to survey all myelinated axons (the projectome). These reconstructions enable precise investigations of neuronal morphology, which reveal remarkable bilateral symmetry in myelinated reticulospinal and lateral line afferent axons. We further set the stage for whole-brain structure-function comparisons by co-registering functional reference atlases and in vivo two-photon fluorescence microscopy data from the same specimen. All obtained images and reconstructions are provided as an open-access resource.

}, issn = {1476-4687}, doi = {10.1038/nature22356}, author = {Hildebrand, David Grant Colburn and Cicconet, Marcelo and Torres, Russel Miguel and Choi, Woohyuk and Quan, Tran Minh and Moon, Jungmin and Wetzel, Arthur Willis and Scott Champion, Andrew and Graham, Brett Jesse and Randlett, Owen and Plummer, George Scott and Portugues, Ruben and Bianco, Isaac Henry and Saalfeld, Stephan and Baden, Alexander David and Lillaney, Kunal and Burns, Randal and Vogelstein, Joshua Tzvi and Schier, Alexander Franz and Lee, Wei-Chung Allen and Jeong, Won-Ki and Lichtman, Jeff William and Engert, Florian} } @article {48305, title = {Zyxin regulates endothelial von Willebrand factor secretion by reorganizing actin filaments around exocytic granules.}, journal = {Nature Communications}, volume = {8}, year = {2017}, month = {2017 Mar 03}, pages = {14639}, abstract = {

Endothelial exocytosis of Weibel-Palade body (WPB) is one of the first lines of defence against vascular injury. However, the mechanisms that control WPB exocytosis in the final stages (including the docking, priming and fusion of granules) are poorly understood. Here we show that the focal adhesion protein zyxin is crucial in this process. Zyxin downregulation inhibits the secretion of von Willebrand factor (VWF), the most abundant cargo in WPBs, from human primary endothelial cells (ECs) induced by cAMP agonists. Zyxin-deficient mice exhibit impaired epinephrine-stimulated VWF release, prolonged bleeding time and thrombosis, largely due to defective endothelial secretion of VWF. Using live-cell super-resolution microscopy, we visualize previously unappreciated reorganization of pre-existing actin filaments around WPBs before fusion, dependent on zyxin and an interaction with the actin crosslinker α-actinin. Our findings identify zyxin as a physiological regulator of endothelial exocytosis through reorganizing local actin network in the final stage of exocytosis.

}, issn = {2041-1723}, doi = {10.1038/ncomms14639}, author = {Han, Xiaofan and Li, Pin and Yang, Zhenghao and Huang, Xiaoshuai and Wei, Guoqin and Sun, Yujie and Kang, Xuya and Hu, Xueting and Deng, Qiuping and Chen, Liangyi and He, Aibin and Huo, Yingqing and Li, Dong and Betzig, Eric and Luo, Jincai} } @article {47875, title = {Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, year = {2016}, month = {2016 Oct 04}, pages = {11232-6}, abstract = {

Electrons, because of their strong interaction with matter, produce high-resolution diffraction patterns from tiny 3D crystals only a few hundred nanometers thick in a frozen-hydrated state. This discovery offers the prospect of facile structure determination of complex biological macromolecules, which cannot be coaxed to form crystals large enough for conventional crystallography or cannot easily be produced in sufficient quantities. Two potential obstacles stand in the way. The first is a phenomenon known as dynamical scattering, in which multiple scattering events scramble the recorded electron diffraction intensities so that they are no longer informative of the crystallized molecule. The second obstacle is the lack of a proven means of de novo phase determination, as is required if the molecule crystallized is insufficiently similar to one that has been previously determined. We show with four structures of the amyloid core of the Sup35 prion protein that, if the diffraction resolution is high enough, sufficiently accurate phases can be obtained by direct methods with the cryo-EM method microelectron diffraction (MicroED), just as in X-ray diffraction. The success of these four experiments dispels the concern that dynamical scattering is an obstacle to ab initio phasing by MicroED and suggests that structures of novel macromolecules can also be determined by direct methods.

}, issn = {1091-6490}, doi = {10.1073/pnas.1606287113}, author = {Sawaya, Michael R and Rodriguez, Jose and Cascio, Duilio and Collazo, Michael J and Shi, Dan and Reyes, Francis E and Hattne, Johan and Gonen, Tamir and Eisenberg, David S} } @article {47894, title = {Adult mouse cortical cell taxonomy revealed by single cell transcriptomics.}, journal = {Nature neuroscience}, volume = {19}, year = {2016}, month = {2016 Feb}, pages = {335-46}, abstract = {

Nervous systems are composed of various cell types, but the extent of cell type diversity is poorly understood. We constructed a cellular taxonomy of one cortical region, primary visual cortex, in adult mice on the basis of single-cell RNA sequencing. We identified 49 transcriptomic cell types, including 23 GABAergic, 19 glutamatergic and 7 non-neuronal types. We also analyzed cell type-specific mRNA processing and characterized genetic access to these transcriptomic types by many transgenic Cre lines. Finally, we found that some of our transcriptomic cell types displayed specific and differential electrophysiological and axon projection properties, thereby confirming that the single-cell transcriptomic signatures can be associated with specific cellular properties.

}, keywords = {Animals, Cell Line, Cerebral Cortex, Classification, gamma-Aminobutyric Acid, Gene Library, Genetic Markers, Glutamic Acid, Interneurons, Male, Mice, Mice, Inbred C57BL, Mice, Transgenic, Neurons, RNA, Sequence Analysis, RNA, Transcriptome, Visual Cortex}, issn = {1546-1726}, doi = {10.1038/nn.4216}, author = {Tasic, Bosiljka and Menon, Vilas and Nguyen, Thuc Nghi and Kim, Tae Kyung and Jarsky, Tim and Yao, Zizhen and Levi, Boaz and Gray, Lucas T and Sorensen, Staci A and Dolbeare, Tim and Bertagnolli, Darren and Goldy, Jeff and Shapovalova, Nadiya and Parry, Sheana and Lee, Changkyu and Smith, Kimberly and Bernard, Amy and Madisen, Linda and Sunkin, Susan M and Hawrylycz, Michael and Koch, Christof and Zeng, Hongkui} } @article {47994, title = {AMPK activation prevents and reverses drug-induced mitochondrial and hepatocyte injury by promoting mitochondrial fusion and function.}, journal = {PLoS One}, volume = {11}, year = {2016}, month = {2016 Oct 31}, pages = {e0165638}, abstract = {

Mitochondrial damage is the major factor underlying drug-induced liver disease but whether conditions that thwart mitochondrial injury can prevent or reverse drug-induced liver damage is unclear. A key molecule regulating mitochondria quality control is AMP activated kinase (AMPK). When activated, AMPK causes mitochondria to elongate/fuse and proliferate, with mitochondria now producing more ATP and less reactive oxygen species. Autophagy is also triggered, a process capable of removing damaged/defective mitochondria. To explore whether AMPK activation could potentially prevent or reverse the effects of drug-induced mitochondrial and hepatocellular damage, we added an AMPK activator to collagen sandwich cultures of rat and human hepatocytes exposed to the hepatotoxic drugs, acetaminophen or diclofenac. In the absence of AMPK activation, the drugs caused hepatocytes to lose polarized morphology and have significantly decreased ATP levels and viability. At the subcellular level, mitochondria underwent fragmentation and had decreased membrane potential due to decreased expression of the mitochondrial fusion proteins Mfn1, 2 and/or Opa1. Adding AICAR, a specific AMPK activator, at the time of drug exposure prevented and reversed these effects. The mitochondria became highly fused and ATP production increased, and hepatocytes maintained polarized morphology. In exploring the mechanism responsible for this preventive and reversal effect, we found that AMPK activation prevented drug-mediated decreases in Mfn1, 2 and Opa1. AMPK activation also stimulated autophagy/mitophagy, most significantly in acetaminophen-treated cells. These results suggest that activation of AMPK prevents/reverses drug-induced mitochondrial and hepatocellular damage through regulation of mitochondrial fusion and autophagy, making it a potentially valuable approach for treatment of drug-induced liver injury.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0165638}, author = {Kang, Sun Woo Sophie and Haydar, Ghada and Taniane, Caitlin and Farrell, Geoffrey and Arias, Irwin M and Lippincott-Schwartz, Jennifer and Fu, Dong} } @article {47730, title = {Atomic resolution structure determination by the cryo-EM method MicroED.}, journal = {Protein Science : a Publication of the Protein Society}, volume = {26}, year = {2016}, month = {2016 Jul 25}, pages = {8-15}, abstract = {

The electron cryo-microscopy (cryoEM) method MicroED has been rapidly developing. In this review we highlight some of the key steps in MicroED from crystal analysis to structure determination. We compare and contrast MicroED and the latest X-ray based diffraction method the X-ray free electron laser (XFEL). Strengths and shortcomings of both MicroED and XFEL are discussed. Finally, all current MicroED structures are tabulated with a view to the future. This article is protected by copyright. All rights reserved.

}, issn = {1469-896X}, doi = {10.1002/pro.2989}, author = {Liu, Shian and Hattne, Johan and Reyes, Francis E and Sanchez-Martinez, Silvia and de la Cruz, M Jason and Shi, D and Gonen, T} } @article {47850, title = {Behavioural integration of auditory and antennal stimulation during phonotaxis in the field cricket Gryllus bimaculatus (DeGeer).}, journal = {The Journal of Experimental Biology}, volume = {219}, year = {2016}, month = {2016 Sep 8}, pages = {3575-86}, abstract = {

Animals need to flexibly respond to stimuli from their environment without compromising behavioural consistency. For example, female crickets orienting toward a conspecific male{\textquoteright}s calling song in search of a mating partner need to stay responsive to other signals that provide information about obstacles and predators. Here, we investigate how spontaneously walking crickets and crickets engaging in acoustically guided goal-directed navigation, i.e. phonotaxis, respond to mechanosensory stimuli detected by their long antennae. We monitored walking behaviour of female crickets on a trackball during lateral antennal stimulation, which was achieved by moving a wire mesh transiently into reach of one antenna. During antennal stimulation alone, females reduced their walking speed, oriented toward the object and actively explored it with antennal movements. Additionally, some crickets initially turned away from the approaching object. Females responded in a similar way when the antennal stimulus was presented during ongoing phonotaxis: forward velocity was reduced and phonotactic steering was suppressed while the females turned toward and explored the object. Further, rapid steering bouts to individual chirps, typical for female phonotaxis, no longer occurred.Our data reveals that in this experimental situation antennal stimulation overrides phonotaxis for extended time periods. Phonotaxis in natural environments, which require the integration of multiple sensory cues, may therefore be more variable than phonotaxis measured under ideal laboratory conditions. Combining this new behavioural paradigm with neurophysiological methods will show where the sensory-motor integration of antennal and acoustic stimulation occurs and how this is achieved on a mechanistic level.

}, issn = {1477-9145}, doi = {10.1242/jeb.141606}, author = {Haberkern, Hannah and Hedwig, Berthold} } @article {47527, title = {A bright cyan-excitable orange fluorescent protein facilitates dual-emission microscopy and enhances bioluminescence imaging in vivo.}, journal = {Nature Biotechnology}, volume = {34}, year = {2016}, month = {2016 May 30}, pages = {760-7}, abstract = {

Orange-red fluorescent proteins (FPs) are widely used in biomedical research for multiplexed epifluorescence microscopy with GFP-based probes, but their different excitation requirements make multiplexing with new advanced microscopy methods difficult. Separately, orange-red FPs are useful for deep-tissue imaging in mammals owing to the relative tissue transmissibility of orange-red light, but their dependence on illumination limits their sensitivity as reporters in deep tissues. Here we describe CyOFP1, a bright, engineered, orange-red FP that is excitable by cyan light. We show that CyOFP1 enables single-excitation multiplexed imaging with GFP-based probes in single-photon and two-photon microscopy, including time-lapse imaging in light-sheet systems. CyOFP1 also serves as an efficient acceptor for resonance energy transfer from the highly catalytic blue-emitting luciferase NanoLuc. An optimized fusion of CyOFP1 and NanoLuc, called Antares, functions as a highly sensitive bioluminescent reporter in vivo, producing substantially brighter signals from deep tissues than firefly luciferase and other bioluminescent proteins.

}, issn = {1546-1696}, doi = {10.1038/nbt.3550}, author = {Chu, Jun and Oh, Younghee and Sens, Alex and Ataie, Niloufar and Dana, Hod and Macklin, John J and Laviv, Tal and Welf, Erik S and Dean, Kevin M and Zhang, Feijie and Kim, Benjamin B and Tang, Clement Tran and Hu, Michelle and Baird, Michelle A and Davidson, Michael W and Kay, Mark A and Fiolka, Reto and Yasuda, Ryohei and Kim, Douglas S and Ng, Ho-Leung and Lin, Michael Z} } @article {47849, title = {Cell class-lineage analysis reveals sexually dimorphic lineage compositions in the Drosophila brain.}, journal = {Current Biology : CB}, volume = {26}, year = {2016}, month = {2016 Sep 08}, pages = {2583-93}, abstract = {

The morphology and physiology of neurons are directed by developmental decisions made within their lines of descent from single stem cells. Distinct stem cells may produce neurons having shared properties that define their cell class, such as the type of secreted neurotransmitter. The relationship between cell class and lineage is complex. Here we developed the transgenic cell class-lineage intersection (CLIn) system to assign cells of a particular class to specific lineages within the Drosophila brain. CLIn also enables birth-order analysis and genetic manipulation of particular cell classes arising from particular lineages. We demonstrated the power of CLIn in the context of the eight central brain type II lineages, which produce highly diverse progeny through intermediate neural progenitors. We mapped 18 dopaminergic neurons from three distinct clusters to six type\ II lineages that show lineage-characteristic neurite trajectories. In addition, morphologically distinct dopaminergic neurons are produced within a given lineage, and they arise in an invariant sequence. We also identified type II lineages that produce doublesex- and fruitless-expressing neurons and examined whether female-specific apoptosis in these lineages accounts for the lower number of these neurons in the female brain. Blocking apoptosis in these lineages resulted in more cells in both sexes with males still carrying more cells than females. This argues that sex-specific stem cell fate together with differential progeny apoptosis contribute to the final sexual dimorphism.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2016.07.086}, author = {Ren, Qingzhong and Awasaki, Takeshi and Huang, Yu-Fen and Liu, Zhiyong and Lee, Tzumin} } @article {48297, title = {The ciliary marginal zone of the zebrafish retina: clonal and time-lapse analysis of a continuously growing tissue.}, journal = {Development (Cambridge, England)}, volume = {143}, year = {2016}, month = {2016 Apr 01}, pages = {1099-107}, abstract = {

Clonal analysis is helping us understand the dynamics of cell replacement in homeostatic adult tissues (Simons and Clevers, 2011). Such an analysis, however, has not yet been achieved for continuously growing adult tissues, but is essential if we wish to understand the architecture of adult organs. The retinas of lower vertebrates grow throughout life from retinal stem cells (RSCs) and retinal progenitor cells (RPCs) at the rim of the retina, called the ciliary marginal zone (CMZ). Here, we show that RSCs reside in a niche at the extreme periphery of the CMZ and divide asymmetrically along a radial (peripheral to central) axis, leaving one daughter in the peripheral RSC niche and the other more central where it becomes an RPC. We also show that RPCs of the CMZ have clonal sizes and compositions that are statistically similar to progenitor cells of the embryonic retina and fit the same stochastic model of proliferation. These results link embryonic and postembryonic cell behaviour, and help to explain the constancy of tissue architecture that has been generated over a lifetime.

}, keywords = {Animals, Animals, Genetically Modified, Cell Differentiation, Cell Division, Cell Proliferation, Gene Expression Regulation, Developmental, Retina, Stem Cells, Zebrafish}, issn = {1477-9129}, doi = {10.1242/dev.133314}, author = {Wan, Yinan and Almeida, Alexandra D and Rulands, Steffen and Chalour, Naima and Muresan, Leila and Wu, Yunmin and Simons, Benjamin D and He, Jie and Harris, William A} } @article {47422, title = {The collection of MicroED data for macromolecular crystallography.}, journal = {Nature Protocols}, volume = {11}, year = {2016}, month = {2016 May}, pages = {895-904}, abstract = {

The formation of large, well-ordered crystals for crystallographic experiments remains a crucial bottleneck to the structural understanding of many important biological systems. To help alleviate this problem in crystallography, we have developed the MicroED method for the collection of electron diffraction data from 3D microcrystals and nanocrystals of radiation-sensitive biological material. In this approach, liquid solutions containing protein microcrystals are deposited on carbon-coated electron microscopy grids and are vitrified by plunging them into liquid ethane. MicroED data are collected for each selected crystal using cryo-electron microscopy, in which the crystal is diffracted using very few electrons as the stage is continuously rotated. This protocol gives advice on how to identify microcrystals by light microscopy or by negative-stain electron microscopy in samples obtained from standard protein crystallization experiments. The protocol also includes information about custom-designed equipment for controlling crystal rotation and software for recording experimental parameters in diffraction image metadata. Identifying microcrystals, preparing samples and setting up the microscope for diffraction data collection take approximately half an hour for each step. Screening microcrystals for quality diffraction takes roughly an hour, and the collection of a single data set is \~{}10 min in duration. Complete data sets and resulting high-resolution structures can be obtained from a single crystal or by merging data from multiple crystals.

}, issn = {1750-2799}, doi = {10.1038/nprot.2016.046}, author = {Shi, Dan and Nannenga, Brent L and de la Cruz, M Jason and Liu, Jinyang and Sawtelle, Steven and Calero, Guillermo and Reyes, Francis E and Hattne, Johan and Gonen, Tamir} } @article {47353, title = {Data publication with the structural biology data grid supports live analysis.}, journal = {Nature Communications}, volume = {7}, year = {2016}, month = {2016 Mar 07}, pages = {10882}, abstract = {

Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. It is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis.

}, issn = {2041-1723}, doi = {10.1038/ncomms10882}, author = {Meyer, Peter A and Socias, Stephanie and Key, Jason and Ransey, Elizabeth and Tjon, Emily C and Buschiazzo, Alejandro and Lei, Ming and Botka, Chris and Withrow, James and Neau, David and Rajashankar, Kanagalaghatta and Anderson, Karen S and Baxter, Richard H and Blacklow, Stephen C and Boggon, Titus J and Bonvin, Alexandre M J J and Borek, Dominika and Brett, Tom J and Caflisch, Amedeo and Chang, Chung-I and Chazin, Walter J and Corbett, Kevin D and Cosgrove, Michael S and Crosson, Sean and Dhe-Paganon, Sirano and Di Cera, Enrico and Drennan, Catherine L and Eck, Michael J and Eichman, Brandt F and Fan, Qing R and Ferr{\'e}-D{\textquoteright}Amar{\'e}, Adrian R and Christopher Fromme, J and Garcia, K Christopher and Gaudet, Rachelle and Gong, Peng and Harrison, Stephen C and Heldwein, Ekaterina E and Jia, Zongchao and Keenan, Robert J and Kruse, Andrew C and Kvansakul, Marc and McLellan, Jason S and Modis, Yorgo and Nam, Yunsun and Otwinowski, Zbyszek and Pai, Emil F and Pereira, Pedro Jos{\'e} Barbosa and Petosa, Carlo and Raman, C S and Rapoport, Tom A and Roll-Mecak, Antonina and Rosen, Michael K and Rudenko, Gabby and Schlessinger, Joseph and Schwartz, Thomas U and Shamoo, Yousif and Sondermann, Holger and Tao, Yizhi J and Tolia, Niraj H and Tsodikov, Oleg V and Westover, Kenneth D and Wu, Hao and Foster, Ian and Fraser, James S and Maia, Filipe R N C and Gonen, Tamir and Kirchhausen, Tom and Diederichs, Kay and Crosas, Merc{\`e} and Sliz, Piotr} } @article {47508, title = {Design and synthesis of a calcium-sensitive photocage.}, journal = {Angewandte Chemie (International ed. in English)}, year = {2016}, month = {2016 May 24}, abstract = {

Photolabile protecting groups (or "photocages") enable precise spatiotemporal control of chemical functionality and facilitate advanced biological experiments. Extant photocages exhibit a simple input-output relationship, however, where application of light elicits a photochemical reaction irrespective of the environment. Herein, we refine and extend the concept of photolabile groups, synthesizing the first Ca(2+) -sensitive photocage. This system functions as a chemical coincidence detector, releasing small molecules only in the presence of both light and elevated [Ca(2+) ]. Caging a fluorophore with this ion-sensitive moiety yields an "ion integrator" that permanently marks cells undergoing high Ca(2+) flux during an illumination-defined time period. Our general design concept demonstrates a new class of light-sensitive material for cellular imaging, sensing, and targeted molecular delivery.

}, issn = {1521-3773}, doi = {10.1002/anie.201602941}, author = {Heckman, Laurel M and Grimm, Jonathan B and Schreiter, Eric R and Kim, Charles and Verdecia, Mark A and Shields, Brenda C and Lavis, Luke D} } @article {47562, title = {Design of a hyperstable 60-subunit protein icosahedron.}, journal = {Nature}, year = {2016}, month = {2016 Jun 15}, abstract = {

The icosahedron is the largest of the Platonic solids, and icosahedral protein structures are widely used in biological systems for packaging and transport. There has been considerable interest in repurposing such structures for applications ranging from targeted delivery to multivalent immunogen presentation. The ability to design proteins that self-assemble into precisely specified, highly ordered icosahedral structures would open the door to a new generation of protein containers with properties custom-tailored to specific applications. Here we describe the computational design of a 25-nanometre icosahedral nanocage that self-assembles from trimeric protein building blocks. The designed protein was produced in Escherichia coli, and found by electron microscopy to assemble into a homogenous population of icosahedral particles nearly identical to the design model. The particles are stable in 6.7 molar guanidine hydrochloride at up to 80 degrees Celsius, and undergo extremely abrupt, but reversible, disassembly between 2 molar and 2.25 molar guanidinium thiocyanate. The icosahedron is robust to genetic fusions: one or two copies of green fluorescent protein (GFP) can be fused to each of the 60 subunits to create highly fluorescent {\textquoteright}standard candles{\textquoteright} for use in light microscopy, and a designed protein pentamer can be placed in the centre of each of the 20 pentameric faces to modulate the size of the entrance/exit channels of the cage. Such robust and customizable nanocages should have considerable utility in targeted drug delivery, vaccine design and synthetic biology.

}, issn = {1476-4687}, doi = {10.1038/nature18010}, author = {Hsia, Yang and Bale, Jacob B and Gonen, Shane and Shi, Dan and Sheffler, William and Fong, Kimberly K and Nattermann, Una and Xu, Chunfu and Huang, Po-Ssu and Ravichandran, Rashmi and Yi, Sue and Davis, Trisha N and Gonen, Tamir and King, Neil P and Baker, David} } @article {47934, title = {A designer AAV variant permits efficient retrograde access to projection neurons.}, journal = {Neuron}, volume = {92}, year = {2016}, month = {2016 Oct 19}, pages = {372-82}, abstract = {

Efficient retrograde access to projection neurons for the delivery of sensors and effectors constitutes an important and enabling capability for neural circuit dissection. Such an approach would also be useful for gene therapy, including the treatment of neurodegenerative disorders characterized by pathological spread through functionally connected and highly distributed networks. Viral vectors, in particular, are powerful gene delivery vehicles for the nervous system, but all available tools suffer from inefficient retrograde transport or limited clinical potential. To address this need, we applied in\ vivo directed evolution to engineer potent retrograde functionality into the capsid of adeno-associated virus (AAV), a vector that has shown promise in neuroscience research and the clinic. A newly evolved variant, rAAV2-retro, permits robust retrograde access to projection neurons with efficiency comparable to classical synthetic retrograde tracers and enables sufficient sensor/effector expression for functional circuit interrogation and in\ vivo genome editing in targeted neuronal populations. VIDEO ABSTRACT.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2016.09.021}, author = {Tervo, D Gowanlock R and Hwang, Bum-Yeol and Viswanathan, Sarada and Gaj, Thomas and Lavzin, Maria and Ritola, Kimberly D and Lindo, Sarah and Michael, Susan and Kuleshova, Elena and Ojala, David and Huang, Cheng-Chiu and Gerfen, Charles R and Schiller, Jackie and Dudman, Joshua T and Hantman, Adam W and Looger, Loren L and Schaffer, David V and Karpova, Alla Y} } @article {48206, title = {Developmentally programmed germ cell remodelling by endodermal cell cannibalism.}, journal = {Nature Cell Biology}, volume = {18}, year = {2016}, month = {2016 Dec}, pages = {1302-10}, abstract = {

Primordial germ cells (PGCs) in many species associate intimately with endodermal cells, but the significance of such interactions is largely unexplored. Here, we show that Caenorhabditis elegans PGCs form lobes that are removed and digested by endodermal cells, dramatically altering PGC size and mitochondrial content. We demonstrate that endodermal cells do not scavenge lobes PGCs shed, but rather, actively remove lobes from the cell body. CED-10 (Rac)-induced actin, DYN-1 (dynamin) and LST-4 (SNX9) transiently surround lobe necks and are required within endodermal cells for lobe scission, suggesting that scission occurs through a mechanism resembling vesicle endocytosis. These findings reveal an unexpected role for endoderm in altering the contents of embryonic PGCs, and define a form of developmentally programmed cell remodelling involving intercellular cannibalism. Active roles for engulfing cells have been proposed in several neuronal remodelling events, suggesting that intercellular cannibalism may be a more widespread method used to shape cells than previously thought.

}, issn = {1476-4679}, doi = {10.1038/ncb3439}, author = {Abdu, Yusuff and Maniscalco, Chelsea and Heddleston, John M and Chew, Teng-Leong and Nance, Jeremy} } @article {47397, title = {The Dfam database of repetitive DNA families.}, journal = {Nucleic Acids Research}, volume = {44}, year = {2016}, month = {2016 Jan 4}, pages = {D81-9}, abstract = {

Repetitive DNA, especially that due to transposable elements (TEs), makes up a large fraction of many genomes. Dfam is an open access database of families of repetitive DNA elements, in which each family is represented by a multiple sequence alignment and a profile hidden Markov model (HMM). The initial release of Dfam, featured in the 2013 NAR Database Issue, contained 1143 families of repetitive elements found in humans, and was used to produce more than 100 Mb of additional annotation of TE-derived regions in the human genome, with improved speed. Here, we describe recent advances, most notably expansion to 4150 total families including a comprehensive set of known repeat families from four new organisms (mouse, zebrafish, fly and nematode). We describe improvements to coverage, and to our methods for identifying and reducing false annotation. We also describe updates to the website interface. The Dfam website has moved to http://dfam.org. Seed alignments, profile HMMs, hit lists and other underlying data are available for download.

}, issn = {1362-4962}, doi = {10.1093/nar/gkv1272}, author = {Hubley, Robert and Finn, Robert D and Clements, Jody and Eddy, Sean R and Jones, Thomas A and Bao, Weidong and Smit, Arian F A and Wheeler, Travis J} } @article {47434, title = {Direct neural pathways convey distinct visual information to Drosophila mushroom bodies.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Apr 15}, pages = {e14009}, abstract = {

Previously, we identified that visual and olfactory associative memories of Drosophila share the mushroom body (MB) circuits (Vogt et al. 2014). Despite well-characterized odor representations in the Drosophila MB, the MB circuit for visual information is totally unknown. Here we show that a small subset of MB Kenyon cells (KCs) selectively responds to visual but not olfactory stimulation. The dendrites of these atypical KCs form a ventral accessory calyx (vAC), distinct from the main calyx that receives olfactory input. We identified two types of visual projection neurons (VPNs) directly connecting the optic lobes and the vAC. Strikingly, these VPNs are differentially required for visual memories of color and brightness. The segregation of visual and olfactory domains in the MB allows independent processing of distinct sensory memories and may be a conserved form of sensory representations among insects.

}, issn = {2050-084X}, doi = {10.7554/eLife.14009}, author = {Vogt, Katrin and Aso, Yoshinori and Hige, Toshihide and Knapek, Stephan and Ichinose, Toshiharu and Friedrich, Anja B and Turner, Glenn C and Rubin, Gerald M and Tanimoto, Hiromu} } @booklet {67218, title = {Discovering Neuronal Cell Types and Their Gene Expression Profiles Using a Spatial Point Process Mixture Model}, year = {2016}, abstract = {

Cataloging the neuronal cell types that comprise circuitry of individual brain regions is a major goal of modern neuroscience and the BRAIN initiative. Single-cell RNA sequencing can now be used to measure the gene expression profiles of individual neurons and to categorize neurons based on their gene expression profiles. While the single-cell techniques are extremely powerful and hold great promise, they are currently still labor intensive, have a high cost per cell, and, most importantly, do not provide information on spatial distribution of cell types in specific regions of the brain. We propose a complementary approach that uses computational methods to infer the cell types and their gene expression profiles through analysis of brain-wide single-cell resolution in situ hybridization (ISH) imagery contained in the Allen Brain Atlas (ABA). We measure the spatial distribution of neurons labeled in the ISH image for each gene and model it as a spatial point process mixture, whose mixture weights are given by the cell types which express that gene. By fitting a point process mixture model jointly to the ISH images, we infer both the spatial point process distribution for each cell type and their gene expression profile. We validate our predictions of cell type-specific gene expression profiles using single cell RNA sequencing data, recently published for the mouse somatosensory cortex. Jointly with the gene expression profiles, cell features such as cell size, orientation, intensity and local density level are inferred per cell type.

}, author = {Furong Huang and Animashree Anandkumar and Christian Borgs and Jennifer Chayes and Ernest Fraenkel and Michael Hawrylycz and Ed Lein and Alessandro Ingrosso and Srinivas Turaga} } @article {48300, title = {Distinct subpopulations of FOXD1 stroma-derived cells regulate renal erythropoietin.}, journal = {The Journal of Clinical Investigation}, volume = {126}, year = {2016}, month = {2016 May 02}, pages = {1926-38}, abstract = {

Renal peritubular interstitial fibroblast-like cells are critical for adult erythropoiesis, as they are the main source of erythropoietin (EPO). Hypoxia-inducible factor 2 (HIF-2) controls EPO synthesis in the kidney and liver and is regulated by prolyl-4-hydroxylase domain (PHD) dioxygenases PHD1, PHD2, and PHD3, which function as cellular oxygen sensors. Renal interstitial cells with EPO-producing capacity are poorly characterized, and the role of the PHD/HIF-2 axis in renal EPO-producing cell (REPC) plasticity is unclear. Here we targeted the PHD/HIF-2/EPO axis in FOXD1 stroma-derived renal interstitial cells and examined the role of individual PHDs in REPC pool size regulation and renal EPO output. Renal interstitial cells with EPO-producing capacity were entirely derived from FOXD1-expressing stroma, and Phd2 inactivation alone induced renal Epo in a limited number of renal interstitial cells. EPO induction was submaximal, as hypoxia or pharmacologic PHD inhibition further increased the REPC fraction among Phd2-/- renal interstitial cells. Moreover, Phd1 and Phd3 were differentially expressed in renal interstitium, and heterozygous deficiency for Phd1 and Phd3 increased REPC numbers in Phd2-/- mice. We propose that FOXD1 lineage renal interstitial cells consist of distinct subpopulations that differ in their responsiveness to Phd2 inactivation and thus regulation of HIF-2 activity and EPO production under hypoxia or conditions of pharmacologic or genetic PHD inactivation.

}, issn = {1558-8238}, doi = {10.1172/JCI83551}, author = {Kobayashi, Hanako and Liu, Qingdu and Binns, Thomas C and Urrutia, Andres A and Davidoff, Olena and Kapitsinou, Pinelopi P and Pfaff, Andrew S and Olauson, Hannes and Wernerson, Annika and Fogo, Agnes B and Fong, Guo-Hua and Gross, Kenneth W and Haase, Volker H} } @article {47749, title = {Drosophila larval to pupal switch under nutrient stress requires IP3R/Ca(2+) signalling in glutamatergic interneurons.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Aug 5}, abstract = {

Neuronal circuits are known to integrate nutritional information, but the identity of the circuit components is not completely understood. Amino acids are a class of nutrients that are vital for the growth and function of an organism. Here, we report a neuronal circuit that allows Drosophila larvae to overcome amino acid deprivation and pupariate. We find that nutrient stress is sensed by the class IV multidendritic cholinergic neurons. Through live calcium imaging experiments, we show that these cholinergic stimuli are conveyed to glutamatergic neurons in the ventral ganglion through mAChR. We further show that IP3R-dependent calcium transients in the glutamatergic neurons convey this signal to downstream medial neurosecretory cells (mNSCs). The circuit ultimately converges at the ring gland and regulates expression of ecdysteroid biosynthetic genes. Activity in this circuit is thus likely to be an adaptation that provides a layer of regulation to help surpass nutritional stress during development.

}, issn = {2050-084X}, doi = {10.7554/eLife.17495}, author = {Jayakumar, Siddharth and Richhariya, Shlesha and Reddy, O Venkateswara and Texada, Michael J and Hasan, Gaiti} } @article {48042, title = {Engulfed cadherin fingers are polarized junctional structures between collectively migrating endothelial~cells.}, journal = {Nature Cell Biology}, volume = {18}, year = {2016}, month = {2016 Nov 14}, pages = {1311-23}, abstract = {

The development and maintenance of tissues requires collective cell movement, during which neighbouring cells coordinate the polarity of their migration machineries. Here, we ask how polarity signals are transmitted from one cell to another across symmetrical cadherin junctions, during collective migration. We demonstrate that collectively migrating endothelial cells have polarized VE-cadherin-rich membrane protrusions, {\textquoteleft}cadherin fingers{\textquoteright}, which leading cells extend from their rear and follower cells engulf at their front, thereby generating opposite membrane curvatures and asymmetric recruitment of curvature-sensing proteins. In follower cells, engulfment of cadherin fingers occurs along with the formation of a lamellipodia-like zone with low actomyosin contractility, and requires VE-cadherin/catenin complexes and Arp2/3-driven actin polymerization. Lateral accumulation of cadherin fingers in follower cells precedes turning, and increased actomyosin contractility can initiate cadherin finger extension as well as engulfment by a neighbouring cell, to promote follower behaviour. We propose that cadherin fingers serve as guidance cues that direct collective cell migration.

}, doi = {10.1038/ncb3438}, author = {Hayer, Arnold and Shao, Lin and Chung, Mingyu and Joubert, Lydia-Marie and Yang, Hee Won and Tsai, Feng-Chiao and Bisaria, Anjali and Betzig, Eric and Meyer, Tobias} } @article {47412, title = {Epigenomic landscapes of retinal rods and cones.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Mar 07}, abstract = {

Rod and cone photoreceptors are highly similar in many respects but they have important functional and molecular differences. Here, we investigate genome-wide patterns of DNA methylation and chromatin accessibility in mouse rods and cones and correlate differences in these features with gene expression, histone marks, transcription factor binding, and DNA sequence motifs. Loss of NR2E3 in rods shifts their epigenomes to a more cone-like state. The data further reveal wide differences in DNA methylation between retinal photoreceptors and brain neurons. Surprisingly, we also find a substantial fraction of DNA hypo-methylated regions in adult rods that are not in active chromatin. Many of these regions exhibit hallmarks of regulatory regions that were active earlier in neuronal development, suggesting that these regions could remain undermethylated due to the highly compact chromatin in mature rods. This work defines the epigenomic landscapes of rods and cones, revealing features relevant to photoreceptor development and function.

}, issn = {2050-084X}, doi = {10.7554/eLife.11613}, author = {Mo, Alisa and Luo, Chongyuan and Davis, Fred P and Mukamel, Eran A and Henry, Gilbert L and Nery, Joseph R and Urich, Mark A and Picard, Serge and Lister, Ryan and Eddy, Sean R and Beer, Michael A and Ecker, Joseph R and Nathans, Jeremy} } @article {47688, title = {Evaluation of the Ser-His dipeptide, a putative catalyst of amide and ester hydrolysis.}, journal = {Organic Letters}, year = {2016}, month = {2016 Jul 11}, abstract = {

Efficient hydrolysis of amide bonds has long been a reaction of interest for organic chemists. The rate constants of proteases are unmatched by those of any synthetic catalyst. It has been proposed that a dipeptide containing serine and histidine is an effective catalyst of amide hydrolysis, based on an apparent ability to degrade a protein. The capacity of the Ser-His dipeptide to catalyze the hydrolysis of several discrete ester and amide substrates is investigated using previously described conditions. This dipeptide does not catalyze the hydrolysis of amide or unactivated ester groups in any of the substrates under the conditions evaluated.

}, issn = {1523-7052}, doi = {10.1021/acs.orglett.6b01279}, author = {MacDonald, Melissa J and Lavis, Luke D and Hilvert, Donald and Gellman, Samuel H} } @conference {48832, title = {Fast and accurate spike sorting of high-channel count probes with KiloSort.}, booktitle = {Neural Information Processing Systems (NIPS 2016)}, year = {2016}, month = {2016 Dec 05}, address = {Barcelona, Spain}, abstract = {

New silicon technology is enabling large-scale electrophysiological recordings in vivo from hundreds to thousands of channels. Interpreting these recordings requires scalable and accurate automated methods for spike sorting, which should minimize the time required for manual curation of the results. Here we introduce KiloSort, a new integrated spike sorting framework that uses template matching both during spike detection and during spike clustering. KiloSort models the electrical voltage as a sum of template waveforms triggered on the spike times, which allows overlapping spikes to be identified and resolved. Unlike previous algorithms that compress the data with PCA, KiloSort operates on the raw data which allows it to construct a more accurate model of the waveforms. Processing times are faster than in previous algorithms thanks to batch-based optimization on GPUs. We compare KiloSort to an established algorithm and show favorable performance, at much reduced processing times. A novel post-clustering merging step based on the continuity of the templates further reduced substantially the number of manual operations required on this data, for the neurons with near-zero error rates, paving the way for fully automated spike sorting of multichannel electrode recordings.

}, url = {http://papers.nips.cc/paper/6326-fast-and-accurate-spike-sorting-of-high-channel-count-probes-with-kilosort}, author = {Pachitariu, Marius and Steinmetz, Nicholas A and Kadir, Shabnam N and Carandini, Matteo and Harris, Kenneth D} } @article {47485, title = {Flagellar membrane fusion and protein exchange in trypanosomes; a new form of cell-cell communication?}, journal = {F1000 Research}, volume = {5}, year = {2016}, month = {2016 Apr 14}, pages = {682}, abstract = {

Diverse structures facilitate direct exchange of proteins between cells, including plasmadesmata in plants and tunnelling nanotubes in bacteria and higher eukaryotes.\  Here we describe a new mechanism of protein transfer, flagellar membrane fusion, in the unicellular parasite\ Trypanosoma brucei. When fluorescently tagged trypanosomes were co-cultured, a small proportion of double-positive cells were observed. The formation of double-positive cells was dependent on the presence of extracellular calcium and was enhanced by placing cells in medium supplemented with fresh bovine serum. Time-lapse microscopy revealed that double-positive cells arose by bidirectional protein exchange in the absence of nuclear transfer.\  Furthermore, super-resolution microscopy showed that this process occurred in <=1 minute, the limit of temporal resolution in these experiments. Both cytoplasmic and membrane proteins could be transferred provided they gained access to the flagellum. Intriguingly, a component of the RNAi machinery (Argonaute) was able to move between cells, raising the possibility that small interfering RNAs are transported as cargo. Transmission electron microscopy showed that shared flagella contained two axonemes and two paraflagellar rods bounded by a single membrane. In some cases flagellar fusion was partial and interactions between cells were transient. In other cases fusion occurred along the entire length of the flagellum, was stable for several hours and might be irreversible. Fusion did not appear to be deleterious for cell function: paired cells were motile and could give rise to progeny while fused. The motile flagella of unicellular organisms are related to the sensory cilia of higher eukaryotes, raising the possibility that protein transfer between cells via cilia or flagella occurs more widely in nature.

}, doi = { 10.12688/f1000research.8249.1}, author = {Imhof, Simon and Fragoso, Cristina and Hemphill, Andrew and von Schubert, Conrad and Li, Dong and Legant, Wesley and Betzig, Eric} } @article {47768, title = {Flight of the dragonflies and damselflies.}, journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences}, volume = {371}, year = {2016}, month = {2016 Sep 26}, abstract = {

This work is a synthesis of our current understanding of the mechanics, aerodynamics and visually mediated control of dragonfly and damselfly flight, with the addition of new experimental and computational data in several key areas. These are: the diversity of dragonfly wing morphologies, the aerodynamics of gliding flight, force generation in flapping flight, aerodynamic efficiency, comparative flight performance and pursuit strategies during predatory and territorial flights. New data are set in context by brief reviews covering anatomy at several scales, insect aerodynamics, neuromechanics and behaviour. We achieve a new perspective by means of a diverse range of techniques, including laser-line mapping of wing topographies, computational fluid dynamics simulations of finely detailed wing geometries, quantitative imaging using particle image velocimetry of on-wing and wake flow patterns, classical aerodynamic theory, photography in the field, infrared motion capture and multi-camera optical tracking of free flight trajectories in laboratory environments. Our comprehensive approach enables a novel synthesis of datasets and subfields that integrates many aspects of flight from the neurobiology of the compound eye, through the aeromechanical interface with the surrounding fluid, to flight performance under cruising and higher-energy behavioural modes.This article is part of the themed issue {\textquoteright}Moving in a moving medium: new perspectives on flight{\textquoteright}.

}, issn = {1471-2970}, doi = {10.1098/rstb.2015.0389}, author = {Bomphrey, Richard J and Nakata, Toshiyuki and Henningsson, Per and Lin, Huai-Ti} } @article {47993, title = {Formin-generated actomyosin arcs propel T cell receptor microcluster movement at the immune synapse.}, journal = {The Journal of Cell Biology}, volume = {215}, year = {2016}, month = {2016 Oct 31}, pages = {383-99}, abstract = {

Actin assembly and inward flow in the plane of the immunological synapse (IS) drives the centralization of T cell receptor microclusters (TCR MCs) and the integrin leukocyte functional antigen 1 (LFA-1). Using structured-illumination microscopy (SIM), we show that actin arcs populating the medial, lamella-like region of the IS arise from linear actin filaments generated by one or more formins present at the IS distal edge. After traversing the outer, Arp2/3-generated, lamellipodia-like region of the IS, these linear filaments are organized by myosin II into antiparallel concentric arcs. Three-dimensional SIM shows that active LFA-1 often aligns with arcs, whereas TCR MCs commonly reside between arcs, and total internal reflection fluorescence SIM shows TCR MCs being swept inward by arcs. Consistently, disrupting actin arc formation via formin inhibition results in less centralized TCR MCs, missegregated integrin clusters, decreased T-B cell adhesion, and diminished TCR signaling. Together, our results define the origin, organization, and functional significance of a major actomyosin contractile structure at the IS that directly propels TCR MC transport.

}, issn = {1540-8140}, doi = {10.1083/jcb.201603080}, author = {Murugesan, Sricharan and Hong, Jinsung and Yi, Jason and Li, Dong and Beach, Jordan R and Shao, Lin and Meinhardt, John and Madison, Grey and Wu, Xufeng and Betzig, Eric and Hammer, John A} } @article {47303, title = {Four individually identified paired dopamine neurons signal reward in larval Drosophila.}, journal = {Current Biology : CB}, year = {2016}, month = {2016 Feb 10}, abstract = {

Dopaminergic neurons serve multiple functions, including reinforcement processing during associative learning [1-12]. It is thus warranted to understand which dopaminergic neurons mediate which function. We study larval Drosophila, in which only approximately 120 of a total of 10,000 neurons are dopaminergic, as judged by the expression of tyrosine hydroxylase (TH), the rate-limiting enzyme of dopamine biosynthesis [5, 13]. Dopaminergic neurons mediating reinforcement in insect olfactory learning target the mushroom bodies, a higher-order "cortical" brain region [1-5, 11, 12, 14, 15]. We discover four previously undescribed paired neurons, the primary protocerebral anterior medial (pPAM) neurons. These neurons are TH positive and subdivide the medial lobe of the mushroom body into four distinct subunits. These pPAM neurons are acutely necessary for odor-sugar reward learning and require intact TH function in this process. However, they are dispensable for aversive learning and innate behavior toward the odors and sugars employed. Optogenetical activation of pPAM neurons is sufficient as a reward. Thus, the pPAM neurons convey a likely dopaminergic reward signal. In contrast, DL1 cluster neurons convey a corresponding punishment signal [5], suggesting a cellular division of labor to convey dopaminergic reward and punishment signals. On the level of individually identified neurons, this uncovers an organizational principle shared with adult Drosophila and mammals [1-4, 7, 9, 10] (but see [6]). The numerical simplicity and connectomic tractability of the larval nervous system [16-19] now offers a prospect for studying circuit principles of dopamine function at unprecedented resolution.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2016.01.012}, author = {Rohwedder, Astrid and Wenz, Nana L and Stehle, Bernhard and Huser, Annina and Yamagata, Nobuhiro and Zlatic, Marta and Truman, James W and Tanimoto, Hiromu and Saumweber, Timo and Gerber, Bertram and Thum, Andreas S} } @article {47924, title = {Fully-automatic synapse prediction and validation on a large data set.}, journal = {Frontiers in Neural Circuits}, volume = {12}, year = {2016}, month = {2018 Oct 29}, pages = {87}, abstract = {

Extracting a connectome from an electron microscopy (EM) data set requires identification of neurons and determination of synapses between neurons. As manual extraction of this information is very time-consuming, there has been extensive research effort to automatically segment the neurons to help guide and eventually replace manual tracing. Until recently, there has been comparatively less research on automatically detecting the actual synapses between neurons. This discrepancy can, in part, be attributed to several factors: obtaining neuronal shapes is a prerequisite first step in extracting a connectome, manual tracing is much more time-consuming than annotating synapses, and neuronal contact area can be used as a proxy for synapses in determining connections.
However, recent research has demonstrated that contact area alone is not a sufficient predictor of synaptic connection. Moreover, as segmentation has improved, we have observed that synapse annotation is consuming a more significant fraction of overall reconstruction time. This ratio will only get worse as segmentation improves, gating overall possible speed-up. Therefore, we address this problem by developing algorithms that automatically detect pre-synaptic neurons and their post-synaptic partners. In particular, pre-synaptic structures are detected using a Deep and Wide Multiscale Recursive Network, and post-synaptic partners are detected using a MLP with features conditioned on the local segmentation.
This work is novel because it requires minimal amount of training, leverages advances in image segmentation directly, and provides a complete solution for polyadic synapse detection. We further introduce novel metrics to evaluate our algorithm on connectomes of meaningful size. These metrics demonstrate that complete automatic prediction can be used to effectively characterize most connectivity correctly.

}, author = {Huang, Gary B. and Scheffer, Louis K and Plaza, Stephen M.} } @article {47348, title = {High-density genotyping of immune-related loci identifies new SLE risk variants in individuals with Asian ancestry.}, journal = {Nature Genetics}, volume = {48}, year = {2016}, month = {2016 Mar}, pages = {323-30}, abstract = {

Systemic lupus erythematosus (SLE) has a strong but incompletely understood genetic architecture. We conducted an association study with replication in 4,478 SLE cases and 12,656 controls from six East Asian cohorts to identify new SLE susceptibility loci and better localize known loci. We identified ten new loci and confirmed 20 known loci with genome-wide significance. Among the new loci, the most significant locus was GTF2IRD1-GTF2I at 7q11.23 (rs73366469, Pmeta = 3.75 {\texttimes} 10(-117), odds ratio (OR) = 2.38), followed by DEF6, IL12B, TCF7, TERT, CD226, PCNXL3, RASGRP1, SYNGR1 and SIGLEC6. We identified the most likely functional variants at each locus by analyzing epigenetic marks and gene expression data. Ten candidate variants are known to alter gene expression in cis or in trans. Enrichment analysis highlights the importance of these loci in B cell and T cell biology. The new loci, together with previously known loci, increase the explained heritability of SLE to 24\%. The new loci share functional and ontological characteristics with previously reported loci and are possible drug targets for SLE therapeutics.

}, issn = {1546-1718}, doi = {10.1038/ng.3496}, author = {Sun, Celi and Molineros, Julio E and Looger, Loren L and Zhou, Xu-Jie and Kim, Kwangwoo and Okada, Yukinori and Ma, Jianyang and Qi, Yuan-Yuan and Kim-Howard, Xana and Motghare, Prasenjeet and Bhattarai, Krishna and Adler, Adam and Bang, So-Young and Lee, Hye-Soon and Kim, Tae-Hwan and Kang, Young Mo and Suh, Chang-Hee and Chung, Won Tae and Park, Yong-Beom and Choe, Jung-Yoon and Shim, Seung Cheol and Kochi, Yuta and Suzuki, Akari and Kubo, Michiaki and Sumida, Takayuki and Yamamoto, Kazuhiko and Lee, Shin-Seok and Kim, Young Jin and Han, Bok-Ghee and Dozmorov, Mikhail and Kaufman, Kenneth M and Wren, Jonathan D and Harley, John B and Shen, Nan and Chua, Kek Heng and Zhang, Hong and Bae, Sang-Cheol and Nath, Swapan K} } @article {47811, title = {Highly photostable, reversibly photoswitchable fluorescent protein with high contrast ratio for live-cell superresolution microscopy.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, year = {2016}, month = {2016 Aug 25}, pages = {10364-9}, abstract = {

Two long-standing problems for superresolution (SR) fluorescence microscopy are high illumination intensity and long acquisition time, which significantly hamper its application for live-cell imaging. Reversibly photoswitchable fluorescent proteins (RSFPs) have made it possible to dramatically lower the illumination intensities in saturated depletion-based SR techniques, such as saturated depletion nonlinear structured illumination microscopy (NL-SIM) and reversible saturable optical fluorescence transition microscopy. The characteristics of RSFPs most critical for SR live-cell imaging include, first, the integrated fluorescence signal across each switching cycle, which depends upon the absorption cross-section, effective quantum yield, and characteristic switching time from the fluorescent "on" to "off" state; second, the fluorescence contrast ratio of on/off states; and third, the photostability under excitation and depletion. Up to now, the RSFPs of the Dronpa and rsEGFP (reversibly switchable EGFP) families have been exploited for SR imaging. However, their limited number of switching cycles, relatively low fluorescence signal, and poor contrast ratio under physiological conditions ultimately restrict their utility in time-lapse live-cell imaging and their ability to reach the desired resolution at a reasonable signal-to-noise ratio. Here, we present a truly monomeric RSFP, Skylan-NS, whose properties are optimized for the recently developed patterned activation NL-SIM, which enables low-intensity (\~{}100 W/cm(2)) live-cell SR imaging at \~{}60-nm resolution at subsecond acquisition times for tens of time points over broad field of view.

}, issn = {1091-6490}, doi = {10.1073/pnas.1611038113}, author = {Zhang, Xi and Zhang, Mingshu and Li, Dong and He, Wenting and Peng, Jianxin and Betzig, Eric and Xu, Pingyong} } @article {47728, title = {Identification of excitatory premotor interneurons which regulate local muscle contraction during Drosophila larval locomotion.}, journal = {Scientific Reports}, volume = {6}, year = {2016}, month = {2016}, pages = {30806}, abstract = {

We use Drosophila larval locomotion as a model to elucidate the working principles of motor circuits. Larval locomotion is generated by rhythmic and sequential contractions of body-wall muscles from the posterior to anterior segments, which in turn are regulated by motor neurons present in the corresponding neuromeres. Motor neurons are known to receive both excitatory and inhibitory inputs, combined action of which likely regulates patterned motor activity during locomotion. Although recent studies identified candidate inhibitory premotor interneurons, the identity of premotor interneurons that provide excitatory drive to motor neurons during locomotion remains unknown. In this study, we searched for and identified two putative excitatory premotor interneurons in this system, termed CLI1 and CLI2 (cholinergic lateral interneuron 1 and 2). These neurons were segmentally arrayed and activated sequentially from the posterior to anterior segments during peristalsis. Consistent with their being excitatory premotor interneurons, the CLIs formed GRASP- and ChAT-positive putative synapses with motoneurons and were active just prior to motoneuronal firing in each segment. Moreover, local activation of CLI1s induced contraction of muscles in the corresponding body segments. Taken together, our results suggest that the CLIs directly activate motoneurons sequentially along the segments during larval locomotion.

}, issn = {2045-2322}, doi = {10.1038/srep30806}, author = {Hasegawa, Eri and Truman, James W and Nose, Akinao} } @article {48296, title = {Image-based correction of continuous and discontinuous non-planar axial distortion in serial section microscopy.}, journal = {Bioinformatics (Oxford, England)}, year = {2016}, month = {2016 Dec 23}, abstract = {

MOTIVATION: Serial section microscopy is an established method for detailed anatomy reconstruction of biological specimen. During the last decade, high resolution electron microscopy (EM) of serial sections has become the de-facto standard for reconstruction of neural connectivity at ever increasing scales (EM connectomics). In serial section microscopy, the axial dimension of the volume is sampled by physically removing thin sections from the embedded specimen and subsequently imaging either the block-face or the section series. This process has limited precision leading to inhomogeneous non-planar sampling of the axial dimension of the volume which, in turn, results in distorted image volumes. This includes that section series may be collected and imaged in unknown order.

RESULTS: We developed methods to identify and correct these distortions through image-based signal analysis without any additional physical apparatus or measurements. We demonstrate the efficacy of our methods in proof of principle experiments and application to real world problems.

AVAILABILITY AND IMPLEMENTATION: We made our work available as libraries for the ImageJ distribution Fiji and for deployment in a high performance parallel computing environment. Our sources are open and available at http://github.com/saalfeldlab/section-sort, http://github.com/saalfeldlab/z-spacing and http://github.com/saalfeldlab/z-spacing-spark CONTACT: : saalfelds@janelia.hhmi.orgSupplementary information: Supplementary data are available at Bioinformatics online.

}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btw794}, author = {Hanslovsky, Philipp and Bogovic, John A and Saalfeld, Stephan} } @article {47812, title = {Improving data quality in neuronal population recordings.}, journal = {Nature Neuroscience}, volume = {19}, year = {2016}, month = {2016 Aug 26}, pages = {1165-74}, abstract = {

Understanding how the brain operates requires understanding how large sets of neurons function together. Modern recording technology makes it possible to simultaneously record the activity of hundreds of neurons, and technological developments will soon allow recording of thousands or tens of thousands. As with all experimental techniques, these methods are subject to confounds that complicate the interpretation of such recordings, and could lead to erroneous scientific conclusions. Here we discuss methods for assessing and improving the quality of data from these techniques and outline likely future directions in this field.

}, issn = {1546-1726}, doi = {10.1038/nn.4365}, author = {Harris, Kenneth D and Quiroga, Rodrigo Quian and Freeman, Jeremy and Smith, Spencer L} } @article {47969, title = {Increased spatiotemporal resolution reveals highly dynamic dense tubular matrices in the peripheral ER.}, journal = {Science (New York, N.Y.)}, volume = {354}, year = {2016}, month = {2016 Oct 28}, pages = {433-46}, abstract = {

The endoplasmic reticulum (ER) is an expansive, membrane-enclosed organelle that plays crucial roles in numerous cellular functions. We used emerging superresolution imaging technologies to clarify the morphology and dynamics of the peripheral ER, which contacts and modulates most other intracellular organelles. Peripheral components of the ER have classically been described as comprising both tubules and flat sheets. We show that this system consists almost exclusively of tubules at varying densities, including structures that we term ER matrices. Conventional optical imaging technologies had led to misidentification of these structures as sheets because of the dense clustering of tubular junctions and a previously uncharacterized rapid form of ER motion. The existence of ER matrices explains previous confounding evidence that had indicated the occurrence of ER {\textquotedblleft}sheet{\textquotedblright} proliferation after overexpression of tubular junction{\textendash}forming proteins.

}, doi = {10.1126/science.aaf3928}, author = {Nixon-Abell, Jonathon and Obara, Christopher J and Weigel, Aubrey V and Li, Dong and Legant, Wesley R and Xu, CShan and Pasolli, H Amalia and Harvey, Kirsten and Hess, Harald F and Betzig, Eric and Blackstone, Craig and Lippincott-Schwartz, Jennifer} } @article {48842, title = {Inhibitory control of correlated intrinsic variability in cortical networks.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Dec 07}, abstract = {

Cortical networks exhibit intrinsic dynamics that drive coordinated, large-scale fluctuations across neuronal populations and create noise correlations that impact sensory coding. To investigate the network-level mechanisms that underlie these dynamics, we developed novel computational techniques to fit a deterministic spiking network model directly to multi-neuron recordings from different rodent species, sensory modalities, and behavioral states. The model generated correlated variability without external noise and accurately reproduced the diverse activity patterns in our recordings. Analysis of the model parameters suggested that differences in noise correlations across recordings were due primarily to differences in the strength of feedback inhibition. Further analysis of our recordings confirmed that putative inhibitory neurons were indeed more active during desynchronized cortical states with weak noise correlations. Our results demonstrate that network models with intrinsically-generated variability can accurately reproduce the activity patterns observed in multi-neuron recordings and suggest that inhibition modulates the interactions between intrinsic dynamics and sensory inputs to control the strength of noise correlations.

}, issn = {2050-084X}, doi = {10.7554/eLife.19695}, author = {Stringer, Carsen and Pachitariu, Marius and Steinmetz, Nicholas A and Okun, Michael and Bartho, Peter and Harris, Kenneth D and Sahani, Maneesh and Lesica, Nicholas A} } @article {65751, title = {Inhibitory control of correlated intrinsic variability in cortical networks}, journal = {Elife}, volume = {5}, year = {2016}, month = {12/2016}, pages = {e19695}, abstract = {

Cortical networks exhibit intrinsic dynamics that drive coordinated, large-scale fluctuations across neuronal populations and create noise correlations that impact sensory coding. To investigate the network-level mechanisms that underlie these dynamics, we developed novel computational techniques to fit a deterministic spiking network model directly to multi-neuron recordings from different rodent species, sensory modalities, and behavioral states. The model generated correlated variability without external noise and accurately reproduced the diverse activity patterns in our recordings. Analysis of the model parameters suggested that differences in noise correlations across recordings were due primarily to differences in the strength of feedback inhibition. Further analysis of our recordings confirmed that putative inhibitory neurons were indeed more active during desynchronized cortical states with weak noise correlations. Our results demonstrate that network models with intrinsically-generated variability can accurately reproduce the activity patterns observed in multi-neuron recordings and suggest that inhibition modulates the interactions between intrinsic dynamics and sensory inputs to control the strength of noise correlations.

}, doi = {https://doi.org/10.7554/eLife.19695}, author = {Stringer, Carsen and Pachitariu, Marius and Steinmetz, Nicholas A and Okun, Michael and Bartho, Peter and Harris, Kenneth D and Sahani, Maneesh and Lesica, Nicholas A} } @article {47974, title = {Layer 4 fast-spiking interneurons filter thalamocortical signals during active somatosensation.}, journal = {Nature Neuroscience}, volume = {19}, year = {2016}, month = {2016 Oct 17}, pages = {1647-57}, abstract = {

We rely on movement to explore the environment, for example, by palpating an object. In somatosensory cortex, activity related to movement of digits or whiskers is suppressed, which could facilitate detection of touch. Movement-related suppression is generally assumed to involve corollary discharges. Here we uncovered a thalamocortical mechanism in which cortical fast-spiking interneurons, driven by sensory input, suppress movement-related activity in layer 4 (L4) excitatory neurons. In mice locating objects with their whiskers, neurons in the ventral posteromedial nucleus (VPM) fired in response to touch and whisker movement. Cortical L4 fast-spiking interneurons inherited these responses from VPM. In contrast, L4 excitatory neurons responded mainly to touch. Optogenetic experiments revealed that fast-spiking interneurons reduced movement-related spiking in excitatory neurons, enhancing selectivity for touch-related information during active tactile sensation. These observations suggest a fundamental computation performed by the thalamocortical circuit to accentuate salient tactile information.

}, issn = {1546-1726}, doi = {10.1038/nn.4412}, author = {Yu, Jianing and Gutnisky, Diego A and Hires, S Andrew and Svoboda, Karel} } @article {47937, title = {Light sheet microscopes: Novel imaging toolbox for visualizing life{\textquoteright}s processes.}, journal = {The International Journal of Biochemistry \& Cell Biology}, year = {2016}, month = {2016 Oct 7}, abstract = {

Capturing dynamic processes in live samples is a nontrivial task in biological imaging. Although fluorescence provides high specificity and contrast compared to other light microscopy techniques, the photophysical principles of this method can have a harmful effect on the sample. Current advances in light sheet microscopy have created a novel imaging toolbox that allows for rapid acquisition of high-resolution fluorescent images with minimal perturbation of the processes of interest. Each unique design has its own advantages and limitations. In this review, we describe several cutting edge light sheet microscopes and their optimal applications.

}, issn = {1878-5875}, doi = {10.1016/j.biocel.2016.10.002}, author = {Heddleston, John M and Chew, Teng-Leong} } @article {48135, title = {Live cell single molecule-guided Bayesian localization super resolution microscopy.}, journal = {Cell Research}, year = {2016}, month = {2016 Dec 30}, issn = {1748-7838}, doi = {10.1038/cr.2015.160}, author = {Xu, Fan and Zhang, Mingshu and He, Wenting and Han, Renmin and Xue, Fudong and Liu, Zhiyong and Zhang, Fa and Lippincott-Schwartz, Jennifer and Xu, Pingyong} } @article {47933, title = {Live-cell single-molecule tracking reveals co-recognition of H3K27me3 and DNA targets polycomb Cbx7-PRC1 to chromatin.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Oct 10}, abstract = {

The Polycomb PRC1 plays essential roles in development and disease pathogenesis. Targeting of PRC1 to chromatin is thought to be mediated by the Cbx family proteins (Cbx2/4/6/7/8) binding to histone H3 with a K27me3 modification (H3K27me3). Despite this prevailing view, the molecular mechanisms of targeting remain poorly understood. Here, by combining live-cell single-molecule tracking (SMT) and genetic engineering, we reveal that H3K27me3 contributes significantly to the targeting of Cbx7 and Cbx8 to chromatin, but less to Cbx2, Cbx4, and Cbx6. Genetic disruption of the complex formation of PRC1 facilitates the targeting of Cbx7 to chromatin. Biochemical analyses uncover that the CD and AT-hook-like (ATL) motif of Cbx7 constitute a functional DNA-binding unit. Live-cell SMT of Cbx7 mutants demonstrates that Cbx7 is targeted to chromatin by co-recognizing of H3K27me3 and DNA. Our data suggest a novel hierarchical cooperation mechanism by which histone modifications and DNA coordinate to target chromatin regulatory complexes.

}, issn = {2050-084X}, doi = {10.7554/eLife.17667}, author = {Zhen, Chao Yu and Tatavosian, Roubina and Huynh, Thao Ngoc and Duc, Huy Nguyen and Das, Raibatak and Kokotovic, Marko and Grimm, Jonathan B and Lavis, Luke D and Lee, Jun and Mejia, Frances J and Li, Yang and Yao, Tingting and Ren, Xiaojun} } @article {47565, title = {Macular telangiectasia type 1 managed with long-term aflibercept therapy.}, journal = {Ophthalmic Surgery, Lasers and Imaging Retina}, volume = {47}, year = {2016}, month = {2016 Jun}, pages = {593-5}, abstract = {

A 60-year-old man diagnosed with macular telangiectasia type 1 (MacTel 1) was treated for 3 years with monthly aflibercept (Eylea; Regeneron, Tarrytown, NY) and serially imaged with spectral-domain optical coherence tomography. When administered monthly, aflibercept appeared to have a beneficial effect on macular edema secondary to MacTel 1. Visual acuity preservation despite minimal chronic macular edema could be attributed to the lack of significant photoreceptor disruption.

}, doi = {10.3928/23258160-20160601-14}, author = {Kovach, Jaclyn L and Hess, Harald F and Rosenfeld, Philip J} } @article {47383, title = {A mammalian enhancer trap resource for discovering and manipulating neuronal cell types.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Mar 21}, abstract = {

There is a continuing need for driver strains to enable cell type-specific manipulation in the nervous system. Each cell type expresses a unique set of genes, and recapitulating expression of marker genes by BAC transgenesis or knock-in has generated useful transgenic mouse lines. However since genes are often expressed in many cell types, many of these lines have relatively broad expression patterns. We report an alternative transgenic approach capturing distal enhancers for more focused expression. We identified an enhancer trap probe often producing restricted reporter expression and developed efficient enhancer trap screening with the PiggyBac transposon. We established more than 200 lines and found many lines that label small subsets of neurons in brain substructures, including known and novel cell types. Images and other information about each line are available online (enhancertrap.bio.brandeis.edu).

}, issn = {2050-084X}, doi = {10.7554/eLife.13503}, author = {Shima, Yasuyuki and Sugino, Ken and Hempel, Chris and Shima, Masami and Taneja, Praveen and Bullis, James B and Mehta, Sonam and Lois, Carlos and Nelson, Sacha B} } @article {47790, title = {Membrane dynamics of dividing cells imaged by lattice light-sheet microscopy.}, journal = {Molecular Biology of the Cell}, volume = {27}, year = {2016}, month = {2016 Aug 17}, pages = {3418-35}, abstract = {

Membrane remodeling is an essential part for transfer of components to and from the cell surface and membrane-bound organelles, and for changes in cell shape, particularly critical during cell division. Earlier analyses, based on classical optical live-cell imaging, mostly restricted by technical necessity to the attached bottom surface, showed persistent formation of endocytic clathrin pits and vesicles during mitosis. Taking advantage of the resolution, speed, and non-invasive illumination of the newly developed lattice light sheet fluorescence microscope, we reexamined their assembly dynamics over the entire cell surface and showed that clathrin pits form at a lower rate during late mitosis. Full-cell imaging measurements of cell surface area and volume throughout the cell cycle of single cells in culture and in zebrafish embryos showed that the total surface increased rapidly during the transition from telophase to cytokinesis, whereas cell volume increased slightly in metaphase and remained relatively constant during cytokinesis. These applications demonstrate the advantage of lattice light sheet microscopy and enable a new standard for imaging membrane dynamics in single cells and in multicellular assemblies.

}, issn = {1939-4586}, doi = {10.1091/mbc.E16-03-0164}, author = {Aguet, Fran{\c c}ois and Upadhyayula, Srigokul and Gaudin, Rapha{\"e}l and Chou, Yi-ying and Cocucci, Emanuele and He, Kangmin and Chen, Bi-Chang and Mosaliganti, Kishore and Pasham, Mithun and Skillern, Wesley and Legant, Wesley R and Liu, Tsung-Li and Findlay, Greg and Marino, Eric and Danuser, Gaudenz and Megason, Sean and Betzig, Eric and Kirchhausen, Tom} } @article {47484, title = {Modeling truncated pixel values of faint reflections in MicroED images.}, journal = {Journal of Applied Crystallography}, volume = {49}, year = {2016}, month = {2016 May 11}, abstract = {

The weak pixel counts surrounding the Bragg spots in a diffraction image are important for establishing a model of the background underneath the peak and estimating the reliability of the integrated intensities. Under certain circumstances, particularly with equipment not optimized for low-intensity measurements, these pixel values may be corrupted by corrections applied to the raw image. This can lead to truncation of low pixel counts, resulting in anomalies in the integrated Bragg intensities, such as systematically higher signal-to-noise ratios. A correction for this effect can be approximated by a three-parameter lognormal distribution fitted to the weakly positive-valued pixels at similar scattering angles. The procedure is validated by the improved\ refinement\ of an atomic model against\ structure factor\ amplitudes derived from corrected micro-electron diffraction (MicroED) images.

}, doi = {10.1107/S1600576716007196}, author = {Hattne, Johan and Shi, Dan and de la Cruz, M Jason and Reyes, Francis E and Gonen, Tamir} } @article {47418, title = {Multifocus microscopy with precise color multi-phase diffractive optics applied in functional neuronal imaging.}, journal = {Biomedical Optics Express}, volume = {7}, year = {2016}, month = {2016 Feb 16}, pages = {855-69}, abstract = {

Multifocus microscopy (MFM) allows high-resolution instantaneous three-dimensional (3D) imaging and has been applied to study biological specimens ranging from single molecules inside cells nuclei to entire embryos. We here describe pattern designs and nanofabrication methods for diffractive optics that optimize the light-efficiency of the central optical component of MFM: the diffractive multifocus grating (MFG). We also implement a {\textquotedblleft}precise color{\textquotedblright} MFM layout with MFGs tailored to individual fluorophores in separate optical arms. The reported advancements enable faster and brighter volumetric time-lapse imaging of biological samples. In live microscopy applications, photon budget is a critical parameter and light-efficiency must be optimized to obtain the fastest possible frame rate while minimizing photodamage. We provide comprehensive descriptions and code for designing diffractive optical devices, and a detailed methods description for nanofabrication of devices. Theoretical efficiencies of reported designs is ≈90\% and we have obtained efficiencies of \> 80\% in MFGs of our own manufacture. We demonstrate the performance of a multi-phase MFG in 3D functional neuronal imaging in living\ C. elegans.

Additional authors include:

Xin Jin, Joan Pulupa, Christine Cho, Mustafa Mir, Mohamed El Beheiry, Xavier Darzacq, Marcelo Nollmann, Maxime Dahan, Carl Wu, Timoth{\'e}e Lionnet, J. Alexander Liddle, and Cornelia I. Bargmann

}, doi = {10.1364/BOE.7.000855}, author = {Abrahamsson, Sara and Ilic, Rob and Wisniewski, Jan and Mehl, Brian and Yu, Liya and Chen, Lei and Davanco, Marcelo and Oujedi, Laura and Fiche, Jean-Bernard and Hajj, Bassam} } @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 {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 {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 {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 {47305, title = {Postembryonic lineages of the Drosophila ventral nervous system: Neuroglian expression reveals the adult hemilineage associated fiber tracts in the adult thoracic neuromeres.}, journal = {The Journal of Comparative Neurology}, volume = {524}, year = {2016}, month = {2016 Feb 15}, pages = {2677-95}, abstract = {

During larval life most of the thoracic neuroblasts (NBs) in Drosophila undergo a second phase of neurogenesis to generate adult-specific neurons that remain in an immature, developmentally stalled state until pupation. Using a combination of MARCM and immunostaining with a neurotactin antibody Truman et al. (2004) identified 24 adult specific NB lineages within each thoracic hemineuromere of the larval ventral nervous system (VNS) but because the neurotactin labeling of lineage tracts disappearing early in metamorphosis they were unable extend the identification of the these lineages into the adult. Here we show that immunostaining with an antibody against the cell adhesion molecule Neuroglian reveals the same larval secondary lineage projections through metamorphosis and by identifying each neuroglian positive tract at selected stages we have traced the larval hemilineage tracts for all three thoracic neuromeres through metamorphosis into the adult. To validate tract identifications we used the genetic toolkit developed by Harris et al. (2015) to preserve hemilineage specific GAL4 expression patterns from larval into the adult stage. The immortalized expression proved a powerful confirmation of the analysis of the neuroglian scaffold. This work has enabled us to directly link the secondary, larval NB lineages to their adult counterparts. The data provide an anatomical framework that 1) makes it possible to assign most neurons to their parent lineage and 2) allows more precise definitions of the neuronal organization of the adult VNS based in developmental units/rules. This article is protected by copyright. All rights reserved.

}, issn = {1096-9861}, doi = {10.1002/cne.23988}, author = {Shepherd, David and Harris, Robin and Williams, Darren and Truman, James W} } @article {47419, title = {PSF engineering in multifocus microscopy for increased depth volumetric imaging.}, journal = {Biomedical Optics Express}, volume = {7}, year = {2016}, month = {2016 Feb 16}, pages = {726-31}, abstract = {

Imaging and localizing single molecules with high accuracy in a 3D volume is a challenging task. Here we combine multifocal microscopy, a recently developed volumetric imaging technique, with point spread function engineering to achieve an increased depth for single molecule imaging. Applications in 3D single molecule localization-based super-resolution imaging is shown over an axial depth of 4 {\textmu}m as well as for the tracking of diffusing beads in a fluid environment over 8 {\textmu}m.

}, doi = {10.1364/BOE.7.000726}, author = {Hajj, Bassam and El Beheiry, Mohamed and Dahan, Maxime} } @article {47537, title = {Rapid and semi-automated extraction of neuronal cell bodies and nuclei from electron microscopy image stacks.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1427}, year = {2016}, month = {2016}, pages = {277-90}, abstract = {

Connectomics-the study of how neurons wire together in the brain-is at the forefront of modern neuroscience research. However, many connectomics studies are limited by the time and precision needed to correctly segment large volumes of electron microscopy (EM) image data. We present here a semi-automated segmentation pipeline using freely available software that can significantly decrease segmentation time for extracting both nuclei and cell bodies from EM image volumes.

}, issn = {1940-6029}, doi = {10.1007/978-1-4939-3615-1_16}, author = {Holcomb, Paul S and Morehead, Michael and Doretto, Gianfranco and Chen, Peter and Berg, Stuart and Plaza, Stephen and Spirou, George} } @article {47938, title = {Rapid dynamics of general transcription factor TFIIB binding during preinitiation complex assembly revealed by single-molecule analysis.}, journal = {Genes and Development}, volume = {30}, year = {2016}, month = {2016 Sep 15}, pages = {2106-18}, abstract = {

Transcription of protein-encoding genes in eukaryotic cells requires the coordinated action of multiple general transcription factors (GTFs) and RNA polymerase II (Pol II). A {\textquotedblleft}step-wise{\textquotedblright} preinitiation complex (PIC) assembly model has been suggested based on conventional ensemble biochemical measurements, in which protein factors bind stably to the promoter DNA sequentially to build a functional PIC. However, recent dynamic measurements in live cells suggest that transcription factors mostly interact with chromatin DNA rather transiently. To gain a clearer dynamic picture of PIC assembly, we established an integrated in vitro single-molecule transcription platform reconstituted from highly purified human transcription factors and complemented it by live-cell imaging. Here we performed real-time measurements of the hierarchal promoter-specific binding of TFIID, TFIIA, and TFIIB. Surprisingly, we found that while promoter binding of TFIID and TFIIA is stable, promoter binding by TFIIB is highly transient and dynamic (with an average residence time of 1.5 sec). Stable TFIIB{\textendash}promoter association and progression beyond this apparent PIC assembly checkpoint control occurs only in the presence of Pol II{\textendash}TFIIF. This transient-to-stable transition of TFIIB-binding dynamics has gone undetected previously and underscores the advantages of single-molecule assays for revealing the dynamic nature of complex biological reactions.

}, doi = {10.1101/gad.285395.116}, author = {Zhang, Zhengjian and English, Brian P and Grimm, Jonathan B and Kazane, Stephanie A and Hu, Wenxin and Tsai, Albert and Inouye, Carla and You, Changjiang and Piehler, Jacob and Schultz, Peter G and Lavis, Luke D and Revyakin, Andrey and Tjian, Robert} } @article {47440, title = {Repulsive cues combined with physical barriers and cell{\textendash}cell adhesion determine progenitor cell positioning during organogenesis}, journal = {Nature Communications}, volume = {7}, year = {2016}, month = {2016 Apr 18}, pages = {11288}, abstract = {

The precise positioning of organ progenitor cells constitutes an essential, yet poorly understood step during organogenesis. Using primordial germ cells that participate in gonad formation, we present the developmental mechanisms maintaining a motile progenitor cell population at the site where the organ develops. Employing high-resolution live-cell microscopy, we find that repulsive cues coupled with physical barriers confine the cells to the correct bilateral positions. This analysis revealed that cell polarity changes on interaction with the physical barrier and that the establishment of compact clusters involves increased cell-cell interaction time. Using particle-based simulations, we demonstrate the role of reflecting barriers, from which cells turn away on contact, and the importance of proper cell-cell adhesion level for maintaining the tight cell clusters and their correct positioning at the target region. The combination of these developmental and cellular mechanisms prevents organ fusion, controls organ positioning and is thus critical for its proper function.

}, doi = {10.1038/ncomms11288}, author = {Paksa, Azadeh and Bandemer, Jan and H{\"o}ckendorf, Burkhard and Razin, Nitzan and Tarbashevich, Katsiaryna and Minina, Sofia and Meyen, Dana and Gov, Nir S and Keller, Philipp J and Raz, Erez} } @conference {47735, title = {Robust registration of calcium images by learned contrast synthesis.}, booktitle = {IEEE 13th International Symposium on Biomedical Imaging: From Nano to Macro}, year = {2016}, month = {2016 Jun 15}, address = {Clarion Congress Hotel in Prague Prague; Czech Republic}, abstract = {

Multi-modal image registration is a challenging task that is vital to fuse complementary signals for subsequent analyses. Despite much research into cost functions addressing this challenge, there exist cases in which these are ineffective. In this work, we show that (1) this is true for the registration of in-vivo Drosophila brain volumes visualizing genetically encoded calcium indicators to an nc82 atlas and (2) that machine learning based contrast synthesis can yield improvements. More specifically, the number of subjects for which the registration outright failed was greatly reduced (from 40\% to 15\%) by using a synthesized image.

}, isbn = {978-147992350-2}, doi = {10.1109/ISBI.2016.7493463}, author = {Bogovic, John A and Hanslovsky, Philipp and Wong, Allen M and Saalfeld, Stephan} } @article {47767, title = {Satb2 stations neurons along reflex arcs.}, journal = {Neuron}, volume = {91}, year = {2016}, month = {2016 Aug 17}, pages = {711-3}, abstract = {

The nociceptive flexor withdrawal reflex has an august place in the history of neuroscience. In this issue of\ Neuron, Hilde et\ al. (2016) advance our understanding of this reflex by characterizing the molecular identity and circuit connectivity of component interneurons. They assess how a DNA-binding factor Satb2 controls\ cell position, molecular identity, pre-and postsynaptic targeting, and function of a population of inhibitory sensory relay interneurons that serve to integrate both proprioceptive and nociceptive afferent information.

The nociceptive flexor withdrawal reflex has an august place in the history of neuroscience. In this issue of\ Neuron, Hilde et\ al. (2016) advance our understanding of this reflex by characterizing the molecular identity and circuit connectivity of component interneurons. They assess how a DNA-binding factor Satb2 controls cell position, molecular identity, pre-and postsynaptic targeting, and function of a population of inhibitory sensory relay interneurons that serve to integrate both proprioceptive and nociceptive afferent information.

}, doi = {10.1016/j.neuron.2016.08.005}, author = {Hantman, Adam W and Kaltschmidt, Julia A} } @article {47511, title = {Segmenting and Tracking Multiple Dividing Targets Using ilastik.}, journal = {Advances in anatomy, embryology, and cell biology}, volume = {219}, year = {2016}, month = {2016 May 21}, pages = {199-229}, abstract = {

Tracking crowded cells or other targets in biology is often a challenging task due to poor signal-to-noise ratio, mutual occlusion, large displacements, little discernibility, and the ability of cells to divide. We here present an open source implementation of conservation tracking (Schiegg et\ al., IEEE international conference on computer vision (ICCV). IEEE, New York, pp\ 2928-2935, 2013) in the ilastik software framework. This robust tracking-by-assignment algorithm explicitly makes allowance for false positive detections, undersegmentation, and cell division. We give an overview over the underlying algorithm and parameters, and explain the use for a light sheet microscopy sequence of a Drosophila embryo. Equipped with this knowledge, users will be able to track targets of interest in their own data.

}, issn = {0301-5556}, doi = {10.1007/978-3-319-28549-8_8}, author = {Haubold, Carsten and Schiegg, Martin and Kreshuk, Anna and Berg, Stuart and Koethe, Ullrich and Hamprecht, Fred A} } @article {47396, title = {Sensitive red protein calcium indicators for imaging neural activity.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Mar 24}, abstract = {

Genetically encoded calcium indicators (GECIs) allow measurement of activity in large populations of neurons and in small neuronal compartments, over times of milliseconds to months. Although GFP-based GECIs are widely used for in vivo neurophysiology, GECIs with red-shifted excitation and emission spectra have advantages for in vivo imaging because of reduced scattering and absorption in tissue, and a consequent reduction in phototoxicity. However, current red GECIs are inferior to the state-of-the-art GFP-based GCaMP6 indicators for detecting and quantifying neural activity. Here we present improved red GECIs based on mRuby (jRCaMP1a, b) and mApple (jRGECO1a), with sensitivity comparable to GCaMP6. We characterized the performance of the new red GECIs in cultured neurons and in mouse, Drosophila, zebrafish and C. elegans in vivo. Red GECIs facilitate deep-tissue imaging, dual-color imaging together with GFP-based reporters, and the use of optogenetics in combination with calcium imaging.

}, issn = {2050-084X}, doi = {10.7554/eLife.12727}, author = {Dana, Hod and Mohar, Boaz and Sun, Yi and Narayan, Sujatha and Gordus, Andrew and Hasseman, Jeremy P and Tsegaye, Getahun and Holt, Graham T and Hu, Amy and Walpita, Deepika and Patel, Ronak and Macklin, John J and Bargmann, Cornelia I and Ahrens, Misha B and Schreiter, Eric R and Jayaraman, Vivek and Looger, Loren L and Svoboda, Karel and Kim, Douglas S} } @article {65891, title = {Spatially resolved proteomic mapping in living cells with the engineered peroxidase APEX2}, journal = {Nature Protocols}, volume = {11}, year = {2016}, month = {Jan-03-2016}, pages = {456 - 475}, abstract = {

This protocol describes a method to obtain spatially resolved proteomic maps of specific compartments within living mammalian cells. An engineered peroxidase, APEX2, is genetically targeted to a cellular region of interest. Upon the addition of hydrogen peroxide for 1 min to cells preloaded with a biotin-phenol substrate, APEX2 generates biotin-phenoxyl radicals that covalently tag proximal endogenous proteins. Cells are then lysed, and biotinylated proteins are enriched with streptavidin beads and identified by mass spectrometry. We describe the generation of an appropriate APEX2 fusion construct, proteomic sample preparation, and mass spectrometric data acquisition and analysis. A two-state stable isotope labeling by amino acids in cell culture (SILAC) protocol is used for proteomic mapping of membrane-enclosed cellular compartments from which APEX2-generated biotin-phenoxyl radicals cannot escape. For mapping of open cellular regions, we instead use a {\textquoteright}ratiometric{\textquoteright} three-state SILAC protocol for high spatial specificity. Isotopic labeling of proteins takes 5{\textendash}7 cell doublings. Generation of the biotinylated proteomic sample takes 1 d, acquiring the mass spectrometric data takes 2{\textendash}5 d and analysis of the data to obtain the final proteomic list takes 1 week.

}, issn = {1754-2189}, doi = {10.1038/nprot.2016.018}, url = {http://www.nature.com/articles/nprot.2016.018http://www.nature.com/articles/nprot.2016.018.pdfhttp://www.nature.com/articles/nprot.2016.018.pdfhttp://www.nature.com/articles/nprot.2016.018}, author = {Hung, Victoria and Udeshi, Namrata D and Lam, Stephanie S and Loh, Ken H and Cox, Kurt J and Pedram, Kayvon and Carr, Steven A and Ting, Alice Y} } @article {47420, title = {Steroid receptors reprogram FoxA1 occupancy through dynamic chromatin transitions.}, journal = {Cell}, year = {2016}, month = {2016 Apr 6}, abstract = {

The estrogen receptor (ER), glucocorticoid receptor (GR), and forkhead box protein 1 (FoxA1) are significant factors in breast cancer progression. FoxA1 has been implicated in establishing ER-binding patterns though its unique ability to serve as a pioneer factor. However, the molecular interplay between ER, GR, and FoxA1 requires further investigation. Here we show that ER and GR both have the ability to alter the genomic distribution of the FoxA1 pioneer factor. Single-molecule tracking experiments in live cells reveal a highly dynamic interaction of FoxA1 with chromatin in\ vivo. Furthermore, the FoxA1 factor is not associated with detectable footprints at its binding sites throughout the genome. These findings support a model wherein interactions between transcription factors and pioneer factors are highly dynamic. Moreover, at a subset of genomic sites, the role of pioneer can be reversed, with the steroid receptors serving to enhance binding of FoxA1.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2016.02.067}, author = {Swinstead, Erin E and Miranda, Tina B and Paakinaho, Ville and Baek, Songjoon and Goldstein, Ido and Hawkins, Mary and Karpova, Tatiana S and Ball, David and Mazza, Davide and Lavis, Luke D and Grimm, Jonathan B and Morisaki, Tatsuya and Gr{\o}ntved, Lars and Presman, Diego M and Hager, Gordon L} } @article {47292, title = {Studying small brains to understand the building blocks of cognition.}, journal = {Current Opinion in Neurobiology}, volume = {37}, year = {2016}, month = {2016 Jan 28}, pages = {59-65}, abstract = {

Cognition encompasses a range of higher-order mental processes, such as attention, working memory, and model-based decision-making. These processes are thought to involve the dynamic interaction of multiple central brain regions. A mechanistic understanding of such computations requires not only monitoring and manipulating specific neural populations during behavior, but also knowing the connectivity of the underlying circuitry. These goals are experimentally challenging in mammals, but are feasible in numerically simpler insect brains. In Drosophila melanogaster in particular, genetic tools enable precisely targeted physiology and optogenetics in actively behaving animals. In this article we discuss how these advantages are increasingly being leveraged to study abstract neural representations and sensorimotor computations that may be relevant for cognition in both insects and mammals.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2016.01.007}, author = {Haberkern, Hannah and Jayaraman, Vivek} } @article {48045, title = {Synaptic transmission parallels neuromodulation in a central food-intake circuit.}, journal = {eLife}, year = {2016}, month = {2016 Nov 15}, abstract = {

NeuromedinU is a potent regulator of food intake and activity in mammals. In\ Drosophila, neurons producing the homologous neuropeptide hugin regulate feeding and locomotion in a similar manner. Here, we use EM-based reconstruction to generate the entire connectome of hugin-producing neurons in the\ Drosophila\ larval CNS. We demonstrate that hugin neurons use synaptic transmission in addition to peptidergic neuromodulation and identify acetylcholine as a key transmitter. Hugin neuropeptide and acetylcholine are both necessary for the regulatory effect on feeding. We further show that subtypes of hugin neurons connect chemosensory to endocrine system by combinations of synaptic and peptide-receptor connections. Targets include endocrine neurons producing DH44, a CRH-like peptide, and insulin-like peptides. Homologs of these peptides are likewise downstream of neuromedinU, revealing striking parallels in flies and mammals. We propose that hugin neurons are part of an ancient physiological control system that has been conserved at functional and molecular level.

}, doi = {10.7554/eLife.16799}, author = {Schlegel, Philipp and Texada, Michael J and Miroschnikow, Anton and Schoofs, Andreas and H{\"u}ckesfeld, Sebastian and Peters, Marc and Schneider-Mizell, Casey M and Lacin, Haluk and Li, Feng and Fetter, Richard D and Truman, James W and Cardona, Albert and Pankratz, Michael J} } @article {47525, title = {TRICK: A single-molecule method for imaging the first round of translation in living cells and animals.}, journal = {Methods in Enzymology}, volume = {572}, year = {2016}, month = {2016}, pages = {123-57}, abstract = {

The life of an mRNA is dynamic within a cell. The development of quantitative fluorescent microscopy techniques to image single molecules of RNA has allowed many aspects of the mRNA lifecycle to be directly observed in living cells. Recent advances in live-cell multicolor RNA imaging, however, have now made it possible to investigate RNA metabolism in greater detail. In this chapter, we present an overview of the design and implementation of the translating RNA imaging by coat protein knockoff RNA biosensor, which allows untranslated mRNAs to be distinguished from ones that have undergone a round of translation. The methods required for establishing this system in mammalian cell lines and Drosophila melanogaster oocytes are described here, but the principles may be applied to any experimental system.

}, issn = {1557-7988}, doi = {10.1016/bs.mie.2016.02.027}, author = {Halstead, J M and Wilbertz, J H and Wippich, F and Lionnet, T and Ephrussi, A and Chao, J A} } @article {47971, title = {V-1 regulates capping protein activity in vivo.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, year = {2016}, month = {2016 Oct 25}, pages = {E6610-9}, abstract = {

Capping Protein (CP) plays a central role in the creation of the Arp2/3-generated branched actin networks comprising lamellipodia and pseudopodia by virtue of its ability to cap the actin filament barbed end, which promotes Arp2/3-dependent filament nucleation and optimal branching. The highly conserved protein V-1/Myotrophin binds CP tightly in vitro to render it incapable of binding the barbed end. Here we addressed the physiological significance of this CP antagonist in Dictyostelium, which expresses a V-1 homolog that we show is very similar biochemically to mouse V-1. Consistent with previous studies of CP knockdown, overexpression of V-1 in Dictyostelium reduced the size of pseudopodia and the cortical content of Arp2/3 and induced the formation of filopodia. Importantly, these effects scaled positively with the degree of V-1 overexpression and were not seen with a V-1 mutant that cannot bind CP. V-1 is present in molar excess over CP, suggesting that it suppresses CP activity in the cytoplasm at steady state. Consistently, cells devoid of V-1, like cells overexpressing CP described previously, exhibited a significant decrease in cellular F-actin content. Moreover, V-1-null cells exhibited pronounced defects in macropinocytosis and chemotactic aggregation that were rescued by V-1, but not by the V-1 mutant. Together, these observations demonstrate that V-1 exerts significant influence in vivo on major actin-based processes via its ability to sequester CP. Finally, we present evidence that V-1{\textquoteright}s ability to sequester CP is regulated by phosphorylation, suggesting that cells may manipulate the level of active CP to tune their "actin phenotype."

}, issn = {1091-6490}, doi = {10.1073/pnas.1605350113}, author = {Jung, Goeh and Alexander, Christopher J and Wu, Xufeng S and Piszczek, Grzegorz and Chen, Bi-Chang and Betzig, Eric and Hammer, John A} } @article {47814, title = {Whole-animal imaging with high spatio-temporal resolution.}, journal = {Proceedings of SPIE}, volume = {9720}, year = {2016}, month = {2016 Jul 18}, pages = {97200R}, abstract = {

We developed isotropic multiview (IsoView) light-sheet microscopy in order to image fast cellular dynamics, such as cell movements in an entire developing embryo or neuronal activity throughput an entire brain or nervous system, with high resolution in all dimensions, high imaging speeds, good physical coverage and low photo-damage. To achieve high temporal resolution and high spatial resolution at the same time, IsoView microscopy rapidly images large specimens via simultaneous light-sheet illumination and fluorescence detection along four orthogonal directions. In a post-processing step, these four views are then combined by means of high-throughput multiview deconvolution to yield images with a system resolution of <= 450 nm in all three dimensions. Using IsoView microscopy, we performed whole-animal functional imaging of Drosophila embryos and larvae at a spatial resolution of 1.1-2.5 μm and at a temporal resolution of 2 Hz for up to 9 hours. We also performed whole-brain functional imaging in larval zebrafish and multicolor imaging of fast cellular dynamics across entire, gastrulating Drosophila embryos with isotropic, sub-cellular resolution. Compared with conventional (spatially anisotropic) light-sheet microscopy, IsoView microscopy improves spatial resolution at least sevenfold and decreases resolution anisotropy at least threefold. Compared with existing high-resolution light-sheet techniques, such as lattice lightsheet microscopy or diSPIM, IsoView microscopy effectively doubles the penetration depth and provides subsecond temporal resolution for specimens 400-fold larger than could previously be imaged.

}, isbn = {978-162841954-2}, issn = { 0277786X}, doi = {10.1117/12.2212564}, author = {Chhetri, Raghav and Amat, Fernando and Wan, Yinan and H{\"o}ckendorf, Burkhard and Lemon, William C and Keller, Philipp J} } @article {47486, title = {The wiring diagram of a glomerular olfactory system.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 May 13}, abstract = {

The sense of smell enables animals to react to long-distance cues according to learned and innate valences. Here, we have mapped with electron microscopy the complete wiring diagram of the Drosophila larval antennal lobe, an olfactory neuropil similar to the vertebrate olfactory bulb. We found a canonical circuit with uniglomerular projection neurons (uPNs) relaying gain-controlled ORN activity to the mushroom body and the lateral horn. A second, parallel circuit with multiglomerular projection neurons (mPNs) and hierarchically connected local neurons (LNs) selectively integrates multiple ORN signals already at the first synapse. LN-LN synaptic connections putatively implement a bistable gain control mechanism that either computes odor saliency through panglomerular inhibition, or allows some glomeruli to respond to faint aversive odors in the presence of strong appetitive odors. This complete wiring diagram will support experimental and theoretical studies towards bridging the gap between circuits and behavior.

}, issn = {2050-084X}, doi = {10.7554/eLife.14859}, author = {Berck, Matthew E and Khandelwal, Avinash and Claus, Lindsey and Hernandez-Nunez, Luis and Si, Guangwei and Tabone, Christopher J and Li, Feng and Truman, James W and Fetter, Richard D and Louis, Matthieu and Samuel, Aravinthan Dt and Cardona, Albert} } @article {47162, title = {The 2015 super-resolution microscopy roadmap.}, journal = {Journal of Physics D: Applied Physics}, volume = {48}, year = {2015}, month = {2015 Oct 14}, pages = {443001}, abstract = {

Far-field optical microscopy using focused light is an important tool in a number of scientific disciplines including chemical, (bio)physical and biomedical research, particularly with respect to the study of living cells and organisms. Unfortunately, the applicability of the optical microscope is limited, since the diffraction of light imposes limitations on the spatial resolution of the image. Consequently the details of, for example, cellular protein distributions, can be visualized only to a certain extent. Fortunately, recent years have witnessed the development of {\textquoteright}super-resolution{\textquoteright} far-field optical microscopy (nanoscopy) techniques such as stimulated emission depletion (STED), ground state depletion (GSD), reversible saturated optical (fluorescence) transitions (RESOLFT), photoactivation localization microscopy (PALM), stochastic optical reconstruction microscopy (STORM), structured illumination microscopy (SIM) or saturated structured illumination microscopy (SSIM), all in one way or another addressing the problem of the limited spatial resolution of far-field optical microscopy. While SIM achieves a two-fold improvement in spatial resolution compared to conventional optical microscopy, STED, RESOLFT, PALM/STORM, or SSIM have all gone beyond, pushing the limits of optical image resolution to the nanometer scale. Consequently, all super-resolution techniques open new avenues of biomedical research. Because the field is so young, the potential capabilities of different super-resolution microscopy approaches have yet to be fully explored, and uncertainties remain when considering the best choice of methodology. Thus, even for experts, the road to the future is sometimes shrouded in mist. The super-resolution optical microscopy roadmap of\ Journal of Physics D: Applied Physicsaddresses this need for clarity. It provides guidance to the outstanding questions through a collection of short review articles from experts in the field, giving a thorough discussion on the concepts underlying super-resolution optical microscopy, the potential of different approaches, the importance of label optimization (such as reversible photoswitchable proteins) and applications in which these methods will have a significant impact.

}, doi = {10.1088/0022-3727/48/44/443001}, author = {Hell, Stefan W and Sahl, Steffen J and Bates, Mark and Zhuang, Xiaowei and Heintzmann, Rainer and Booth, Martin J and Bewersdorf, Joerg and Shtengel, Gleb and Hess, Harald F and Tinnefeld, Philip} } @article {46901, title = {BigNeuron: Large-scale 3D neuron reconstruction from optical microscopy images.}, journal = {Neuron}, volume = {87}, year = {2015}, month = {2015 Jul 15}, pages = {252-6}, abstract = {

Understanding the structure of single neurons is critical for understanding how they function within neural circuits. BigNeuron is a new community effort that combines modern bioimaging informatics, recent leaps in labeling and microscopy, and the widely recognized need for openness and standardization to provide a community resource for automated reconstruction of dendritic and axonal morphology of single neurons.

Understanding the structure of single neurons is critical for understanding how they function within neural circuits. BigNeuron is a new community effort that combines modern bioimaging informatics, recent leaps in labeling and microscopy, and the widely recognized need for openness and standardization to provide a community resource for automated reconstruction of dendritic and axonal morphology of single neurons.

}, doi = {10.1016/j.neuron.2015.06.036}, author = {Peng, Hanchuan and Hawrylycz, Michael and Roskams, Jane and Hill, Sean and Spruston, Nelson and Meijering, Erik and Ascoli, Giorgio A} } @article {46813, title = {BlastNeuron for automated comparison, retrieval and clustering of 3D neuron morphologies.}, journal = {Neuroinformatics}, volume = {13}, year = {2015}, month = {2015 Jun 3}, pages = {487-99}, abstract = {

Characterizing the identity and types of neurons in the brain, as well as their associated function, requires a means of quantifying and comparing 3D neuron morphology. Presently, neuron comparison methods are based on statistics from neuronal morphology such as size and number of branches, which are not fully suitable for detecting local similarities and differences in the detailed structure. We developed BlastNeuron to compare neurons in terms of their global appearance, detailed arborization patterns, and topological similarity. BlastNeuron first compares and clusters 3D neuron reconstructions based on global morphology features and moment invariants, independent of their orientations, sizes, level of reconstruction and other variations. Subsequently, BlastNeuron performs local alignment between any pair of retrieved neurons via a tree-topology driven dynamic programming method. A 3D correspondence map can thus be generated at the resolution of single reconstruction nodes. We applied BlastNeuron to three datasets: (1) 10,000+ neuron reconstructions from a public morphology database, (2) 681 newly and manually reconstructed neurons, and (3) neurons reconstructions produced using several independent reconstruction methods. Our approach was able to accurately and efficiently retrieve morphologically and functionally similar neuron structures from large morphology database, identify the local common structures, and find clusters of neurons that share similarities in both morphology and molecular profiles.

}, issn = {1559-0089}, doi = {10.1007/s12021-015-9272-7}, author = {Wan, Yinan and Long, Fuhui and Qu, Lei and Xiao, Hang and Hawrylycz, Michael and Myers, Eugene W and Peng, Hanchuan} } @article {47895, title = {Canonical genetic signatures of the adult human brain.}, journal = {Nature neuroscience}, volume = {18}, year = {2015}, month = {2015 Dec}, pages = {1832-44}, abstract = {

The structure and function of the human brain are highly stereotyped, implying a conserved molecular program responsible for its development, cellular structure and function. We applied a correlation-based metric called differential stability to assess reproducibility of gene expression patterning across 132 structures in six individual brains, revealing mesoscale genetic organization. The genes with the highest differential stability are highly biologically relevant, with enrichment for brain-related annotations, disease associations, drug targets and literature citations. Using genes with high differential stability, we identified 32 anatomically diverse and reproducible gene expression signatures, which represent distinct cell types, intracellular components and/or associations with neurodevelopmental and neurodegenerative disorders. Genes in neuron-associated compared to non-neuronal networks showed higher preservation between human and mouse; however, many diversely patterned genes displayed marked shifts in regulation between species. Finally, highly consistent transcriptional architecture in neocortex is correlated with resting state functional connectivity, suggesting a link between conserved gene expression and functionally relevant circuitry.

}, keywords = {Adult, Animals, Brain, Gene Regulatory Networks, Humans, Mice, Nerve Net, Transcriptome}, issn = {1546-1726}, doi = {10.1038/nn.4171}, author = {Hawrylycz, Michael and Miller, Jeremy A and Menon, Vilas and Feng, David and Dolbeare, Tim and Guillozet-Bongaarts, Angela L and Jegga, Anil G and Aronow, Bruce J and Lee, Chang-Kyu and Bernard, Amy and Glasser, Matthew F and Dierker, Donna L and Menche, J{\"o}rg and Szafer, Aaron and Collman, Forrest and Grange, Pascal and Berman, Kenneth A and Mihalas, Stefan and Yao, Zizhen and Stewart, Lance and Barab{\'a}si, Albert-L{\'a}szl{\'o} and Schulkin, Jay and Phillips, John and Ng, Lydia and Dang, Chinh and Haynor, David R and Jones, Allan and Van Essen, David C and Koch, Christof and Lein, Ed} } @article {47033, title = {Cell type-specific transcriptomics of hypothalamic energy-sensing neuron responses to weight-loss.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Sep 2}, abstract = {

Molecular and cellular processes in neurons are critical for sensing and responding to energy deficit states, such as during weight-loss. AGRP neurons are a key hypothalamic population that is activated during energy deficit and increases appetite and weight-gain. Cell type-specific transcriptomics can be used to identify pathways that counteract weight-loss, and here we report high-quality gene expression profiles of AGRP neurons from well-fed and food-deprived young adult mice. For comparison, we also analyzed POMC neurons, an intermingled population that suppresses appetite and body weight. We find that AGRP neurons are considerably more sensitive to energy deficit than POMC neurons. Furthermore, we identify cell type-specific pathways involving endoplasmic reticulum-stress, circadian signaling, ion channels, neuropeptides, and receptors. Combined with methods to validate and manipulate these pathways, this resource greatly expands molecular insight into neuronal regulation of body weight, and may be useful for devising therapeutic strategies for obesity and eating disorders.

}, issn = {2050-084X}, doi = {10.7554/eLife.09800}, author = {Henry, Fredrick E and Sugino, Ken and Tozer, Adam and Branco, Tiago and Sternson, Scott M} } @article {47034, title = {Chemical perturbation of an intrinsically disordered region of TFIID distinguishes two modes of transcription initiation.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Aug 28}, abstract = {

Intrinsically disordered protein regions (IDRs) are peptide segments that fail to form stable 3-dimensional structures in the absence of partner proteins. They are abundant in eukaryotic proteomes and are often associated with human diseases, but their biological functions have been elusive to study. Here we report the identification of a tin(IV) oxochloride-derived cluster that binds an evolutionarily conserved IDR within the metazoan TFIID transcription complex. Binding arrests an isomerization of promoter-bound TFIID that is required for the engagement of Pol II during the first (de novo) round of transcription initiation. However, the specific chemical probe does not affect reinitiation, which requires the re-entry of Pol II, thus, mechanistically distinguishing these two modes of transcription initiation. This work also suggests a new avenue for targeting the elusive IDRs by harnessing certain features of metal-based complexes for mechanistic studies, and for the development of novel pharmaceutical interventions.

}, issn = {2050-084X}, doi = {10.7554/eLife.07777}, author = {Zhang, Zhengjian and Boskovic, Zarko and Hussain, Mahmud M and Hu, Wenxin and Inouye, Carla and Kim, Han-Je and Abole, A Katherine and Doud, Mary K and Lewis, Timothy A and Koehler, Angela N and Schreiber, Stuart L and Tjian, Robert} } @article {47901, title = {Correlated gene expression and target specificity demonstrate excitatory projection neuron diversity.}, journal = {Cerebral Cortex (New York, N.Y. : 1991)}, volume = {25}, year = {2015}, month = {2015 Feb}, pages = {433-49}, abstract = {

The neocortex contains diverse populations of excitatory neurons segregated by layer and further definable by their specific cortical and subcortical projection targets. The current study describes a systematic approach to identify molecular correlates of specific projection neuron classes in mouse primary somatosensory cortex (S1), using a combination of in situ hybridization (ISH) data mining, marker gene colocalization, and combined retrograde labeling with ISH for layer-specific marker genes. First, we identified a large set of genes with specificity for each cortical layer, and that display heterogeneous patterns within those layers. Using these genes as markers, we find extensive evidence for the covariation of gene expression and projection target specificity in layer 2/3, 5, and 6, with individual genes labeling neurons projecting to specific subsets of target structures. The combination of gene expression and target specificity imply a great diversity of projection neuron classes that is similar to or greater than that of GABAergic interneurons. The covariance of these 2 phenotypic modalities suggests that these classes are both discrete and genetically specified.

}, keywords = {Animals, Atlases as Topic, Data Mining, Gene Expression, In Situ Hybridization, Fluorescence, Male, Mice, Mice, Inbred C57BL, Neural Pathways, Neuronal Tract-Tracers, Neurons, Somatosensory Cortex}, issn = {1460-2199}, doi = {10.1093/cercor/bht243}, author = {Sorensen, Staci A and Bernard, Amy and Menon, Vilas and Royall, Joshua J and Glattfelder, Katie J and Desta, Tsega and Hirokawa, Karla and Mortrud, Marty and Miller, Jeremy A and Zeng, Hongkui and Hohmann, John G and Jones, Allan R and Lein, Ed S} } @article {47277, title = {Cortex commands the performance of skilled movement.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Dec 3}, abstract = {

Mammalian cerebral cortex is accepted as being critical for voluntary motor control, but what functions depend on cortex is still unclear. Here we used rapid, reversible optogenetic inhibition to test the role of cortex during a head-fixed task in which mice reach, grab, and eat a food pellet. Sudden cortical inhibition blocked initiation or froze execution of this skilled prehension behavior, but left untrained forelimb movements unaffected. Unexpectedly, kinematically normal prehension occurred immediately after cortical inhibition even during rest periods lacking cue and pellet. This {\textquoteright}rebound{\textquoteright} prehension was only evoked in trained and food-deprived animals, suggesting that a motivation-gated motor engram sufficient to evoke prehension is activated at inhibition{\textquoteright}s end. These results demonstrate the necessity and sufficiency of cortical activity for enacting a learned skill.

}, issn = {2050-084X}, doi = {10.7554/eLife.10774}, author = {Guo, Jian-Zhong and Graves, Austin R and Guo, Wendy W and Zheng, Jihong and Lee, Allen and Rodr{\'\i}guez-Gonz{\'a}lez, Juan and Li, Nuo and Macklin, John J and Phillips, James W and Mensh, Brett D and Branson, Kristin and Hantman, Adam W} } @article {46380, title = {Data Exploration Toolkit for serial diffraction experiments.}, journal = {Acta Crystallographica Section D: Biological Crystallography}, volume = {71}, year = {2015}, month = {2015 Feb}, pages = {352-6}, abstract = {

Ultrafast diffraction at X-ray free-electron lasers (XFELs) has the potential to yield new insights into important biological systems that produce radiation-sensitive crystals. An unavoidable feature of the {\textquoteleft}diffraction before destruction{\textquoteright} nature of these experiments is that images are obtained from many distinct crystals and/or different regions of the same crystal. Combined with other sources of XFEL shot-to-shot variation, this introduces significant heterogeneity into the diffraction data, complicating processing and interpretation. To enable researchers to get the most from their collected data, a toolkit is presented that provides insights into the quality of, and the variation present in, serial crystallography data sets. These tools operate on the unmerged, partial intensity integration results from many individual crystals, and can be used on two levels: firstly to guide the experimental strategy during data collection, and secondly to help users make informed choices during data processing.

}, issn = {1399-0047}, doi = {10.1107/S1399004714025875}, author = {Zeldin, Oliver B and Brewster, Aaron S and Hattne, Johan and Uervirojnangkoorn, Monarin and Lyubimov, Artem Y and Zhou, Qiangjun and Zhao, Minglei and Weis, William I and Sauter, Nicholas K and Brunger, Axel T} } @article {47620, title = {Deacetylation of nuclear LC3 drives autophagy initiation under starvation.}, journal = {Molecular cell}, volume = {57}, year = {2015}, month = {2015 Feb 5}, pages = {456-66}, abstract = {

Shuttling of macromolecules between different cellular compartments helps regulate the timing and extent of different cellular activities. Here, we report that LC3, a key initiator of autophagy that cycles between the nucleus and cytoplasm, becomes selectively activated in the nucleus during starvation through deacetylation by the nuclear deacetylase Sirt1. Deacetylation of LC3 at K49 and K51 by Sirt1 allows LC3 to interact with the nuclear protein DOR and return to the cytoplasm with DOR, where it is able to bind Atg7 and other autophagy factors and undergo phosphatidylethanolamine conjugation to preautophagic membranes. The association of deacetylated LC3 with autophagic factors shifts LC3{\textquoteright}s distribution from the nucleus toward the cytoplasm. Thus, an acetylation-deacetylation cycle ensures that LC3 effectively redistributes in an activated form from nucleus to cytoplasm, where it plays a central role in autophagy to enable the cell to cope with the lack of external nutrients.

}, keywords = {Acetylation, Autophagy, Cell Nucleus, Cytoplasm, HEK293 Cells, Hela Cells, Humans, Lysine, Microscopy, Confocal, Microtubule-Associated Proteins, Sirtuin 1, Ubiquitin-Activating Enzymes}, issn = {1097-4164}, doi = {10.1016/j.molcel.2014.12.013}, author = {Huang, Rui and Xu, Yinfeng and Wan, Wei and Shou, Xin and Qian, Jiali and You, Zhiyuan and Liu, Bo and Chang, Chunmei and Zhou, Tianhua and Lippincott-Schwartz, Jennifer and Liu, Wei} } @article {47201, title = {Dendritic sodium spikes are required for long-term potentiation at distal synapses on hippocampal pyramidal neurons.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Aug 06}, abstract = {

Dendritic integration of synaptic inputs mediates rapid neural computation as well as longer-lasting plasticity. Several channel types can mediate dendritically initiated spikes (dSpikes), which may impact information processing and storage across multiple timescales; however, the roles of different channels in the rapid vs long-term effects of dSpikes are unknown. We show here that dSpikes mediated by Nav channels (blocked by a low concentration of TTX) are required for long-term potentiation (LTP) in the distal apical dendrites of hippocampal pyramidal neurons. Furthermore, imaging, simulations, and buffering experiments all support a model whereby fast Nav channel-mediated dSpikes (Na-dSpikes) contribute to LTP induction by promoting large, transient, localized increases in intracellular calcium concentration near the calcium-conducting pores of NMDAR and L-type Cav channels. Thus, in addition to contributing to rapid neural processing, Na-dSpikes are likely to contribute to memory formation via their role in long-lasting synaptic plasticity.

}, issn = {2050-084X}, doi = {10.7554/eLife.06414}, author = {Kim, Yujin and Hsu, Ching-Lung and Cembrowski, Mark S and Mensh, Brett D and Spruston, Nelson} } @article {46849, title = {Direct wavefront sensing for high-resolution in vivo imaging in scattering tissue.}, journal = {Nature Communications}, volume = {6}, year = {2015}, month = {2015-Jun-15}, pages = {7276}, abstract = {

Adaptive optics by direct imaging of the wavefront distortions of a laser-induced guide star has long been used in astronomy, and more recently in microscopy to compensate for aberrations in transparent specimens. Here we extend this approach to tissues that strongly scatter visible light by exploiting the reduced scattering of near-infrared guide stars. The method enables in vivo two-photon morphological and functional imaging down to 700 μm inside the mouse brain.

}, issn = {2041-1723}, doi = {10.1038/ncomms8276}, author = {Wang, Kai and Sun, Wenzhi and Richie, Christopher T and Harvey, Brandon K and Betzig, Eric and Ji, Na} } @article {46184, title = {Distribution and function of HCN channels in the apical dendritic tuft of neocortical pyramidal neurons.}, journal = {Journal of Neuroscience}, volume = {35}, year = {2015}, month = {2015 Jan 21}, pages = {1024-37}, abstract = {

The apical tuft is the most remote area of the dendritic tree of neocortical pyramidal neurons. Despite its distal location, the apical dendritic tuft of layer 5 pyramidal neurons receives substantial excitatory synaptic drive and actively processes corticocortical input during behavior. The properties of the voltage-activated ion channels that regulate synaptic integration in tuft dendrites have, however, not been thoroughly investigated. Here, we use electrophysiological and optical approaches to examine the subcellular distribution and function of hyperpolarization-activated cyclic nucleotide-gated nonselective cation (HCN) channels in rat layer 5B pyramidal neurons. Outside-out patch recordings demonstrated that the amplitude and properties of ensemble HCN channel activity were uniform in patches excised from distal apical dendritic trunk and tuft sites. Simultaneous apical dendritic tuft and trunk whole-cell current-clamp recordings revealed that the pharmacological blockade of HCN channels decreased voltage compartmentalization and enhanced the generation and spread of apical dendritic tuft and trunk regenerative activity. Furthermore, multisite two-photon glutamate uncaging demonstrated that HCN channels control the amplitude and duration of synaptically evoked regenerative activity in the distal apical dendritic tuft. In contrast, at proximal apical dendritic trunk and somatic recording sites, the blockade of HCN channels decreased excitability. Dynamic-clamp experiments revealed that these compartment-specific actions of HCN channels were heavily influenced by the local and distributed impact of the high density of HCN channels in the distal apical dendritic arbor. The properties and subcellular distribution pattern of HCN channels are therefore tuned to regulate the interaction between integration compartments in layer 5B pyramidal neurons.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.2813-14.2015}, author = {Harnett, Mark T and Magee, Jeffrey C and Williams, Stephen R} } @article {46524, title = {Dual-channel circuit mapping reveals sensorimotor convergence in the primary motor cortex.}, journal = {The Journal of Neuroscience}, volume = {35}, year = {2015}, month = {2015 Mar 11}, pages = {4418-26}, abstract = {

Cortical cells integrate synaptic input from multiple sources, but how these different inputs are distributed across individual neurons is largely unknown. Differences in input might account for diverse responses in neighboring neurons during behavior. We present a strategy for comparing the strengths of multiple types of input onto the same neuron. We developed methods for independent dual-channel photostimulation of synaptic inputs using ChR2 together with ReaChR, a red-shifted channelrhodopsin. We used dual-channel photostimulation to probe convergence of sensory information in the mouse primary motor cortex. Input from somatosensory cortex and thalamus converges in individual neurons. Similarly, inputs from distinct somatotopic regions of the somatosensory cortex are integrated at the level of single motor cortex neurons. We next developed a ReaChR transgenic mouse under the control of both Flp- and Cre-recombinases that is an effective tool for circuit mapping. Our approach to dual-channel photostimulation enables quantitative comparison of the strengths of multiple pathways across all length scales of the brain.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3741-14.2015}, author = {Hooks, Bryan M and Lin, John Y and Guo, Caiying and Svoboda, Karel} } @article {46528, title = {Dynamics of ionic shifts in cortical spreading depression.}, journal = {Cerebral Cortex}, volume = {25}, year = {2015}, month = {2015 Apr 2}, pages = {4469-76}, abstract = {

Cortical spreading depression is a slowly propagating wave of near-complete depolarization of brain cells followed by temporary suppression of neuronal activity. Accumulating evidence indicates that cortical spreading depression underlies the migraine aura and that similar waves promote tissue damage in stroke, trauma, and hemorrhage. Cortical spreading depression is characterized by neuronal swelling, profound elevation of extracellular potassium and glutamate, multiphasic blood flow changes, and drop in tissue oxygen tension. The slow speed of the cortical spreading depression wave implies that it is mediated by diffusion of a chemical substance, yet the identity of this substance and the pathway it follows are unknown. Intercellular spread between gap junction-coupled neurons or glial cells and interstitial diffusion of K(+) or glutamate have been proposed. Here we use extracellular direct current potential recordings, K(+)-sensitive microelectrodes, and 2-photon imaging with ultrasensitive Ca(2+) and glutamate fluorescent probes to elucidate the spatiotemporal dynamics of ionic shifts associated with the propagation of cortical spreading depression in the visual cortex of adult living mice. Our data argue against intercellular spread of Ca(2+) carrying the cortical spreading depression wavefront and are in favor of interstitial K(+) diffusion, rather than glutamate diffusion, as the leading event in cortical spreading depression.

}, issn = {1460-2199}, doi = {10.1093/cercor/bhv054}, author = {Enger, Rune and Tang, Wannan and Vindedal, Gry Fluge and Jensen, Vidar and Johannes Helm, P and Sprengel, Rolf and Looger, Loren L and Nagelhus, Erlend A} } @article {47467, title = {Early steps in primary cilium assembly require EHD1/EHD3-dependent ciliary vesicle formation.}, journal = {Nature Cell Biology}, volume = {17}, year = {2015}, month = {2015 Feb 16}, pages = {228-40}, abstract = {

Membrane association with mother centriole (M-centriole) distal appendages is critical for ciliogenesis initiation. How the Rab GTPase Rab11{\textendash}​Rab8\ cascade functions in early ciliary membrane assembly is unknown. Here, we show that the membrane shaping proteins ​EHD1\ and ​EHD3, in association with the Rab11{\textendash}​Rab8\ cascade, function in early ciliogenesis. ​EHD1\ and ​EHD3\ localize to preciliary membranes and the ciliary pocket. EHD-dependent membrane tubulation is essential for ciliary vesicle formation from smaller distal appendage vesicles (DAVs). Importantly, this step functions in M-centriole to basal body transformation and recruitment of transition zone proteins and ​IFT20. ​SNAP29, a SNARE membrane fusion regulator and ​EHD1-binding protein, is also required for DAV-mediated ciliary vesicle assembly. Interestingly, only after ciliary vesicle assembly is ​Rab8\ activated for ciliary growth. Our studies uncover molecular mechanisms informing a previously uncharacterized ciliogenesis step, whereby ​EHD1\ and ​EHD3\ reorganize the M-centriole and associated DAVs before coordinated ciliary membrane and axoneme growth.

}, issn = {1476-4679}, doi = {10.1038/ncb3109}, author = {Lu, Quanlong and Insinna, Christine and Ott, Carolyn and Stauffer, Jimmy and Pintado, Petra A and Rahajeng, Juliati and Baxa, Ulrich and Walia, Vijay and Cuenca, Adrian and Hwang, Yoo-Seok and Daar, Ira O and Lopes, Susana and Lippincott-Schwartz, Jennifer and Jackson, Peter K and Caplan, Steve and Westlake, Christopher J} } @article {47082, title = {Efficient processing and analysis of large-scale light-sheet microscopy data.}, journal = {Nature Protocols}, volume = {10}, year = {2015}, month = {2015 Oct 2}, pages = {1679-96}, abstract = {

Light-sheet microscopy is a powerful method for imaging the development and function of complex biological systems at high spatiotemporal resolution and over long time scales. Such experiments typically generate terabytes of multidimensional image data, and thus they demand efficient computational solutions for data management, processing and analysis. We present protocols and software to tackle these steps, focusing on the imaging-based study of animal development. Our protocols facilitate (i) high-speed lossless data compression and content-based multiview image fusion optimized for multicore CPU architectures, reducing image data size 30{\textendash}500-fold; (ii) automated large-scale cell tracking and segmentation; and (iii) visualization, editing and annotation of multiterabyte image data and cell-lineage reconstructions with tens of millions of data points. These software modules are open source. They provide high data throughput using a single computer workstation and are readily applicable to a wide spectrum of biological model systems.

}, doi = {10.1038/nprot.2015.111}, author = {Amat, Fernando and H{\"o}ckendorf, Burkhard and Wan, Yinan and Lemon, William C and McDole, Katie and Keller, Philipp J} } @article {47263, title = {An emerging technology framework for the neurobiology of appetite.}, journal = {Cell Metabolism}, volume = {23}, year = {2015}, month = {2015 Dec 24}, pages = {234-53}, abstract = {

Advances in neuro-technology for mapping, manipulating, and monitoring molecularly defined cell types are rapidly advancing insight into neural circuits that regulate appetite. Here, we review these important tools and their applications in circuits that control food seeking and consumption. Technical capabilities provided by these tools establish a rigorous experimental framework for research into the neurobiology of hunger.

}, doi = {10.1016/j.cmet.2015.12.002}, author = {Sternson, Scott M and Atasoy, Deniz and Betley, J Nicholas and Henry, Fredrick E and Xu, Sheng-jin} } @article {46526, title = {Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Mar 17}, abstract = {

There is considerable potential for X-ray free electron lasers (XFELs) to enable determination of macromolecular crystal structures that are difficult to solve using current synchrotron sources. Prior XFEL studies often involved the collection of thousands to millions of diffraction images, in part due to limitations of data processing methods. We implemented a data processing system based on classical post-refinement techniques, adapted to specific properties of XFEL diffraction data. When applied to XFEL data from three different proteins collected using various sample delivery systems and XFEL beam parameters, our method improved the quality of the diffraction data as well as the resulting refined atomic models and electron density maps. Moreover, the number of observations for a reflection necessary to assemble an accurate data set could be reduced to a few observations. These developments will help expand the applicability of XFEL crystallography to challenging biological systems, including cases where sample is limited.

}, issn = {2050-084X}, doi = {10.7554/eLife.05421}, author = {Uervirojnangkoorn, Monarin and Zeldin, Oliver B and Lyubimov, Artem Y and Hattne, Johan and Brewster, Aaron S and Sauter, Nicholas K and Brunger, Axel T and Weis, William I} } @article {46471, title = {An enhanced gene targeting toolkit for Drosophila: golic+.}, journal = {Genetics}, volume = {199}, year = {2015}, month = {2015 Mar}, pages = {683-94}, abstract = {

Ends-out gene targeting allows seamless replacement of endogenous genes with engineered DNA fragments by homologous recombination, thus creating designer "genes" in the endogenous locus. Conventional gene targeting in Drosophila involves targeting with the preintegrated donor DNA in the larval primordial germ cells. Here we report G: ene targeting during O: ogenesis with L: ethality I: nhibitor and C: RISPR/Cas (Golic+), which improves on all major steps in such transgene-based gene targeting systems. First, donor DNA is integrated into precharacterized attP sites for efficient flip-out. Second, FLP, I-SceI, and Cas9 are specifically expressed in cystoblasts, which arise continuously from female germline stem cells, thereby providing a continual source of independent targeting events in each offspring. Third, a repressor-based lethality selection is implemented to facilitate screening for correct targeting events. Altogether, Golic+ realizes high-efficiency ends-out gene targeting in ovarian cystoblasts, which can be readily scaled up to achieve high-throughput genome editing.

}, issn = {1943-2631}, doi = {10.1534/genetics.114.173716}, author = {Chen, Hui-Min and Huang, Yaling and Pfeiffer, Barret D and Yao, Xiaohao and Lee, Tzumin} } @article {46852, title = {Epigenomic signatures of neuronal diversity in the mammalian brain.}, journal = {Neuron}, volume = {86}, year = {2015}, month = {2015 Jun 17}, pages = {1369-1384}, abstract = {

Neuronal diversity is essential for mammalian brain function but poses a challenge to molecular profiling. To address the need for tools that facilitate cell-type-specific epigenomic studies, we developed the first\ affinity purification approach to isolate nuclei from genetically defined cell types in a mammal. We\ combine this technique with next-generation sequencing to show that three subtypes of neocortical neurons have highly distinctive epigenomic landscapes. Over 200,000 regions differ in chromatin accessibility and DNA methylation signatures characteristic of gene regulatory regions. By footprinting and motif analyses, these regions are predicted to bind distinct cohorts of neuron subtype-specific transcription factors. Neuronal epigenomes reflect both past and present gene expression, with DNA hyper-methylation at developmentally critical genes appearing as a novel epigenomic signature in mature neurons. Taken together, our findings link the functional and transcriptional complexity of neurons to their underlying epigenomic diversity.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.05.018}, author = {Mo, Alisa and Mukamel, Eran A and Davis, Fred P and Luo, Chongyuan and Henry, Gilbert L and Picard, Serge and Urich, Mark A and Nery, Joseph R and Sejnowski, Terrence J and Lister, Ryan and Eddy, Sean R and Ecker, Joseph R and Nathans, Jeremy} } @article {47135, title = {Even-Skipped(+) interneurons are core components of a sensorimotor circuit that maintains left-right symmetric muscle contraction amplitude.}, journal = {Neuron}, volume = {88}, year = {2015}, month = {2015 Oct 21}, pages = {314-29}, abstract = {

Bilaterally symmetric motor patterns-those in which left-right pairs of muscles contract synchronously and with equal amplitude (such as breathing, smiling,\ whisking, and locomotion)-are widespread throughout the animal kingdom. Yet, surprisingly little is known about the underlying neural circuits. We performed a thermogenetic screen to identify neurons required for bilaterally symmetric locomotion in Drosophila larvae and identified the evolutionarily conserved Even-skipped(+) interneurons (Eve/Evx). Activation or ablation of Eve(+) interneurons disrupted bilaterally symmetric muscle contraction amplitude, without affecting the timing of motor output. Eve(+) interneurons are not rhythmically active and thus function independently of the locomotor CPG. GCaMP6 calcium imaging of Eve(+) interneurons in freely moving larvae showed left-right asymmetric activation that correlated with larval behavior. TEM reconstruction of Eve(+) interneuron inputs and outputs showed that the Eve(+) interneurons are at the core of a sensorimotor circuit capable of detecting and modifying body wall muscle contraction.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.09.009}, author = {Heckscher, Ellie S and Zarin, Aref Arzan and Faumont, Serge and Clark, Matthew Q and Manning, Laurina and Fushiki, Akira and Schneider-Mizell, Casey M and Fetter, Richard D and Truman, James W and Zwart, Maarten F and Landgraf, Matthias and Cardona, Albert and Lockery, Shawn R and Doe, Chris Q} } @article {47020, title = {Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics.}, journal = {Science (New York, N.Y.)}, volume = {349}, year = {2015}, month = {2015 Aug 28}, abstract = {

Super-resolution fluorescence microscopy is distinct among nanoscale imaging tools in its ability to image protein dynamics in living cells. Structured illumination microscopy (SIM) stands out in this regard because of its high speed and low illumination intensities, but typically offers only a twofold resolution gain. We extended the resolution of live-cell SIM through two approaches: ultrahigh numerical aperture SIM at 84-nanometer lateral resolution for more than 100 multicolor frames, and nonlinear SIM with patterned activation at 45- to 62-nanometer resolution for approximately 20 to 40 frames. We applied these approaches to image dynamics near the plasma membrane of spatially resolved assemblies of clathrin and caveolin, Rab5a in early endosomes, and α-actinin, often in relationship to cortical actin. In addition, we examined mitochondria, actin, and the Golgi apparatus dynamics in three dimensions.

}, issn = {1095-9203}, doi = {10.1126/science.aab3500}, author = {Li, Dong and Shao, Lin and Chen, Bi-Chang and Zhang, Xi and Zhang, Mingshu and Moses, Brian and Milkie, Daniel E and Beach, Jordan R and Hammer, John A and Pasham, Mithun and Kirchhausen, Tomas and Baird, Michelle A and Davidson, Michael W and Xu, Pingyong and Betzig, Eric} } @article {45844, title = {Fixation-resistant photoactivatable fluorescent proteins for CLEM.}, journal = {Nature Methods}, volume = {12}, year = {2015}, month = {2015 Mar}, pages = {215-8}, abstract = {

Fluorescent proteins facilitate a variety of imaging paradigms in live and fixed samples. However, they lose their fluorescence after heavy fixation, hindering applications such as correlative light and electron microscopy (CLEM). Here we report engineered variants of the photoconvertible Eos fluorescent protein that fluoresce and photoconvert normally in heavily fixed (0.5-1\% OsO4), plastic resin-embedded samples, enabling correlative super-resolution fluorescence imaging and high-quality electron microscopy.

}, issn = {1548-7105}, doi = {10.1038/nmeth.3225}, author = {Paez-Segala, Maria G and Sun, Mei G and Shtengel, Gleb and Viswanathan, Sarada and Baird, Michelle A and Macklin, John J and Patel, Ronak and Allen, John R and Howe, Elizabeth S and Piszczek, Grzegorz and Hess, Harald F and Davidson, Michael W and Wang, Yalin and Looger, Loren L} } @article {46535, title = {Genetic architecture and functional characterization of genes underlying the rapid diversification of male external genitalia between Drosophila simulans and Drosophila mauritiana.}, journal = {Genetics}, year = {2015}, month = {2015 Mar 16}, abstract = {

Male sexual characters are often among the first traits to diverge between closely related species and identifying the genetic basis of such changes can contribute to our understanding of their evolutionary history. However, little is known about the genetic architecture or the specific genes underlying the evolution of male genitalia. The morphology of the claspers, posterior lobes and anal plates exhibit striking differences between Drosophila mauritiana and Drosophila simulans. Using QTL and introgression-based high-resolution mapping, we identified several small regions on chromosome arms 3L and 3R that contribute to differences in these traits. However, we found that the loci underlying the evolution of clasper differences between these two species are independent from those that contribute to posterior lobe and anal plate divergence. Furthermore, while most of the loci affect each trait in the same direction and act additively, we also found evidence for epistasis between loci for clasper bristle number. In addition, we conducted an RNAi screen in D. melanogaster to investigate if positional and expression candidate genes located on chromosome 3L, are also involved in genital development. We found that six of these genes, including components of Wnt signaling and male-specific lethal 3 (msl3), regulate the development of genital traits consistent with the effects of the introgressed regions where they are located and that thus represent promising candidate genes for the evolution these traits.

}, issn = {1943-2631}, doi = {10.1534/genetics.114.174045}, author = {Tanaka, Kentaro M and Hopfen, Corinna and Herbert, Matthew R and Schl{\"o}tterer, Christian and Stern, David L and Masly, John P and McGregor, Alistair P and Nunes, Maria D S} } @article {46756, title = {Genomic signatures of evolutionary transitions from solitary to group living.}, journal = {Science}, year = {2015}, month = {2015 May 14}, abstract = {

The evolution of eusociality is one of the major transitions in evolution, but the underlying genomic changes are unknown. We compared the genomes of ten bee species that vary in social complexity, representing multiple independent transitions in social evolution, and report three major findings. First, many important genes show evidence of neutral evolution as a consequence of relaxed selection with increasing social complexity. Second, there is no single road map to eusociality; independent evolutionary transitions in sociality have independent genetic underpinnings. Third, though clearly independent in detail, these transitions do have similar general features, including an increase in constrained protein evolution accompanied by increases in the potential for gene regulation and decreases in diversity and abundance of transposable elements. Eusociality may arise through different mechanisms each time, but would likely always involve an increase in the complexity of gene networks.

}, issn = {1095-9203}, doi = {10.1126/science.aaa4788}, author = {Kapheim, Karen M and Pan, Hailin and Li, Cai and Salzberg, Steven L and Puiu, Daniela and Magoc, Tanja and Robertson, Hugh M and Hudson, Matthew E and Venkat, Aarti and Fischman, Brielle J and Hernandez, Alvaro and Yandell, Mark and Ence, Daniel and Holt, Carson and Yocum, George D and Kemp, William P and Bosch, Jordi and Waterhouse, Robert M and Zdobnov, Evgeny M and Stolle, Eckart and Kraus, F Bernhard and Helbing, Sophie and Moritz, Robin F A and Glastad, Karl M and Hunt, Brendan G and Goodisman, Michael A D and Hauser, Frank and Grimmelikhuijzen, Cornelis J P and Pinheiro, Daniel Guariz and Nunes, Francis Morais Franco and Soares, Michelle Prioli Miranda and Tanaka, {\'E}rica Donato and Sim{\~o}es, Zil{\'a} Luz Paulino and Hartfelder, Klaus and Evans, Jay D and Barribeau, Seth M and Johnson, Reed M and Massey, Jonathan H and Southey, Bruce R and Hasselmann, Martin and Hamacher, Daniel and Biewer, Matthias and Kent, Clement F and Zayed, Amro and Blatti, Charles and Sinha, Saurabh and Johnston, J Spencer and Hanrahan, Shawn J and Kocher, Sarah D and Wang, Jun and Robinson, Gene E and Zhang, Guojie} } @article {46973, title = {H2A histone-fold and DNA elements in nucleosome activate SWR1-mediated H2A.Z replacement in budding yeast.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Jun 27}, abstract = {

The histone variant H2A.Z is a universal mark of gene promoters, enhancers, and regulatory elements in eukaryotic chromatin. The chromatin remodeler SWR1 mediates site-specific incorporation of H2A.Z by a multi-step histone replacement reaction, evicting histone H2A-H2B from the canonical nucleosome and depositing the H2A.Z-H2B dimer. Binding of both substrates, the canonical nucleosome and the H2A.Z-H2B dimer, is essential for activation of SWR1. We found that SWR1 primarily recognizes key residues within the α2 helix in the histone-fold of nucleosomal histone H2A, a region not previously known to influence remodeler activity. Moreover, SWR1 interacts preferentially with nucleosomal DNA at superhelix location 2 on the nucleosome face distal to its linker-binding site. Our findings provide new molecular insights on recognition of the canonical nucleosome by a chromatin remodeler and have implications for ATP-driven mechanisms of histone eviction and deposition.

}, issn = {2050-084X}, doi = {10.7554/eLife.06845}, author = {Ranjan, Anand and Wang, Feng and Mizuguchi, Gaku and Wei, Debbie and Huang, Yingzi and Wu, Carl} } @article {47180, title = {Heterosynaptic plasticity underlies aversive olfactory learning in Drosophila}, journal = {Neuron}, volume = {88}, year = {2015}, month = {2015 Dec 2}, pages = {985-98}, abstract = {

Although associative learning has been localized to specific brain areas in many animals, identifying the underlying synaptic processes in vivo has been difficult. Here, we provide the first demonstration of long-term synaptic plasticity at the output site of the Drosophila mushroom body. Pairing an odor with activation of specific dopamine neurons induces both learning and odor-specific synaptic depression. The plasticity induction strictly depends on the temporal order of the two stimuli, replicating the logical requirement for associative learning. Furthermore, we reveal that dopamine action is confined to and distinct across different anatomical compartments of the mushroom body lobes. Finally, we find that overlap between sparse representations of different odors defines both stimulus specificity of the plasticity and generalizability of associative memories across odors. Thus, the plasticity we find here not only manifests important features of associative learning but also provides general insights into how a sparse sensory code is read out.

}, doi = {10.1016/j.neuron.2015.11.003}, author = {Hige, Toshihide and Aso, Yoshinori and Modi, Mehrab and Rubin, Gerald M and Turner, Glenn C} } @article {46576, title = {High-performance probes for light and electron microscopy.}, journal = {Nature Methods}, volume = {12}, year = {2015}, month = {2015 Apr 27}, pages = {568-76}, abstract = {

We describe an engineered family of highly antigenic molecules based on GFP-like fluorescent proteins. These molecules contain numerous copies of peptide epitopes and simultaneously bind IgG antibodies at each location. These {\textquoteright}spaghetti monster{\textquoteright} fluorescent proteins (smFPs) distributed well in neurons, notably into small dendrites, spines and axons. smFP immunolabeling localized weakly expressed proteins not well resolved with traditional epitope tags. By varying epitope and scaffold, we generated a diverse family of mutually orthogonal antigens. In cultured neurons and mouse and fly brains, smFP probes allowed robust, orthogonal multicolor visualization of proteins, cell populations and neuropil. smFP variants complement existing tracers and greatly increase the number of simultaneous imaging channels, and they performed well in advanced preparations such as array tomography, super-resolution fluorescence imaging and electron microscopy. In living cells, the probes improved single-molecule image tracking and increased yield for RNA-seq. These probes facilitate new experiments in connectomics, transcriptomics and protein localization.

}, issn = {1548-7105}, doi = {10.1038/nmeth.3365}, author = {Viswanathan, Sarada and Williams, Megan E. and Bloss, Erik B. and Stasevich, Timothy J. and Speer, Colenso M. and Nern, Aljoscha and Pfeiffer, Barret D. and Hooks, Bryan M. and Li, Wei-Ping and English, Brian P. and Tian, Teresa and Henry, Gilbert L. and Macklin, John J. and Patel, Ronak and Gerfen, Charles R and Zhuang, Xiaowei and Wang, Yalin and Rubin, Gerald M and Looger, Loren L} } @article {46819, title = {High-resolution live imaging reveals axon-glia interactions during peripheral nerve injury and repair in zebrafish.}, journal = {Disease Models \& Mechanisms}, volume = {8}, year = {2015}, month = {2015 Jun 1}, pages = {553-64}, abstract = {

Neural damage is a devastating outcome of physical trauma. The glia are one of the main effectors of neuronal repair in the nervous system, but the dynamic interactions between peripheral neurons and Schwann cells during injury and regeneration remain incompletely characterized. Here, we combine laser microsurgery, genetic analysis, high-resolution intravital imaging and lattice light-sheet microscopy to study the interaction between Schwann cells and sensory neurons in a zebrafish model of neurotrauma. We found that chronic denervation by neuronal ablation leads to Schwann-cell death, whereas acute denervation by axonal severing does not affect the overall complexity and architecture of the glia. Neuronal-circuit regeneration begins when Schwann cells extend bridging processes to close the injury gap. Regenerating axons grow faster and directionally after the physiological clearing of distal debris by the Schwann cells. This might facilitate circuit repair by ensuring that axons are guided through unoccupied spaces within bands of B{\"u}ngner towards their original peripheral target. Accordingly, in the absence of Schwann cells, regenerating axons are misrouted, impairing the re-innervation of sensory organs. Our results indicate that regenerating axons use haptotaxis as a directional cue during the reconstitution of a neural circuit. These findings have implications for therapies aimed at neurorepair, which will benefit from preserving the architecture of the peripheral glia during periods of denervation.

}, issn = {1754-8411}, doi = {10.1242/dmm.018184}, author = {Xiao, Yan and Faucherre, Ad{\`e}le and Pola-Morell, Laura and Heddleston, John M and Liu, Tsung-Li and Chew, Teng-Leong and Sato, Fuminori and Sehara-Fujisawa, Atsuko and Kawakami, Koichi and L{\'o}pez-Schier, Hern{\'a}n} } @article {47161, title = {Imaging fictive locomotor patterns in larval Drosophila.}, journal = {Journal of Neurophysiology}, volume = {114}, year = {2015}, month = {2015 Nov 06}, pages = {2564-77}, abstract = {

We have established a preparation in larval Drosophila to monitor fictive locomotion simultaneously across abdominal and thoracic segments of the isolated CNS with genetically encoded Ca(2+) indicators. The Ca(2+) signals closely followed spiking activity measured electrophysiologically in nerve roots. Three motor patterns are analyzed. Two comprise waves of Ca(2+) signals that progress along the longitudinal body axis in a posterior-to-anterior or anterior-to-posterior direction. These waves had statistically indistinguishable intersegmental phase delays compared with segmental contractions during forward and backward crawling behavior, despite being \~{}10 times slower. During these waves, motor neurons of the dorsal longitudinal and transverse muscles were active in the same order as the muscle groups are recruited during crawling behavior. A third fictive motor pattern exhibits a left-right asymmetry across segments and bears similarities with turning behavior in intact larvae, occurring equally frequently and involving asymmetry in the same segments. Ablation of the segments in which forward and backward waves of Ca(2+) signals were normally initiated did not eliminate production of Ca(2+) waves. When the brain and subesophageal ganglion (SOG) were removed, the remaining ganglia retained the ability to produce both forward and backward waves of motor activity, although the speed and frequency of waves changed. Bilateral asymmetry of activity was reduced when the brain was removed and abolished when the SOG was removed. This work paves the way to studying the neural and genetic underpinnings of segmentally coordinated motor pattern generation in Drosophila with imaging techniques.

}, issn = {1522-1598}, doi = {10.1152/jn.00731.2015}, author = {Pulver, Stefan R and Bayley, Timothy G and Taylor, Adam L and Berni, Jimena and Bate, Michael and Hedwig, Berthold} } @article {46701, title = {In the right place at the right time: visualizing and understanding mRNA localization.}, journal = {Nature Reviews Molecular Cell Biology}, volume = {16}, year = {2015}, month = {2015 Feb}, pages = {95-109}, abstract = {

The spatial regulation of protein translation is an efficient way to create functional and structural asymmetries in cells. Recent research has furthered our understanding of how individual cells spatially organize protein synthesis, by applying innovative technology to characterize the relationship between mRNAs and their regulatory proteins, single-mRNA trafficking dynamics, physiological effects of abrogating mRNA localization in vivo and for endogenous mRNA labelling. The implementation of new imaging technologies has yielded valuable information on mRNA localization, for example, by observing single molecules in tissues. The emerging movements and localization patterns of mRNAs in morphologically distinct unicellular organisms and in neurons have illuminated shared and specialized mechanisms of mRNA localization, and this information is complemented by transgenic and biochemical techniques that reveal the biological consequences of mRNA mislocalization.

}, keywords = {Animals, Biological Transport, Humans, Neurons, Protein Biosynthesis, Protein Transport, RNA, Messenger}, issn = {1471-0080}, doi = {10.1038/nrm3918}, author = {Buxbaum, Adina R and Haimovich, Gal and Singer, Robert H} } @article {47284, title = {The innate immune receptor PGRP-LC controls presynaptic homeostatic plasticity.}, journal = {Neuron}, volume = {88}, year = {2015}, month = {2015 Dec 16}, pages = {1157-64}, abstract = {

It is now appreciated that the brain is immunologically active. Highly conserved innate immune signaling responds to pathogen invasion and injury and promotes structural refinement of neural circuitry. However, it remains generally unknown whether innate immune signaling has a function during the day-to-day regulation of neural function in the absence of pathogens and irrespective of cellular damage or developmental change. Here we show that an innate immune receptor, a member of the peptidoglycan pattern recognition receptor family (PGRP-LC), is required for the induction and sustained expression of homeostatic synaptic plasticity. This receptor functions presynaptically, controlling the homeostatic modulation of the readily releasable pool of synaptic vesicles following inhibition of postsynaptic glutamate receptor function. Thus, PGRP-LC is a candidate receptor for retrograde, trans-synaptic signaling, a novel activity for innate immune signaling and the first known function of a PGRP-type receptor in the nervous system of any organism.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.10.049}, author = {Harris, Nathan and Braiser, Daniel J and Dickman, Dion K and Fetter, Richard D and Tong, Amy and Davis, Graeme W} } @article {48830, title = {Learning enhances sensory and multiple non-sensory representations in primary visual cortex.}, journal = {Neuron}, volume = {86}, year = {2015}, month = {2015 Jun 17}, pages = {1478-90}, abstract = {

We determined how learning modifies neural representations in primary visual cortex (V1) during acquisition of a visually guided behavioral task. We imaged the activity of the same layer 2/3 neuronal populations as mice learned to discriminate two visual patterns while running through a virtual corridor, where one pattern was rewarded. Improvements in behavioral performance were closely associated with increasingly distinguishable population-level representations of task-relevant stimuli, as a result of stabilization of existing and recruitment of new neurons selective for these stimuli. These effects correlated with the appearance of multiple task-dependent signals during learning: those that increased neuronal selectivity across the population when expert animals engaged in the task, and those reflecting anticipation or behavioral choices specifically in neuronal subsets preferring the rewarded stimulus. Therefore, learning engages diverse mechanisms that modify sensory and non-sensory representations in V1 to adjust its processing to task requirements and the behavioral relevance of visual stimuli.

}, keywords = {Animals, Calcium, Discrimination (Psychology), Female, Learning, Luminescent Proteins, Male, Mice, Mice, Inbred C57BL, Mice, Transgenic, Models, Neurological, Neurons, Nonlinear Dynamics, Optogenetics, Photic Stimulation, Sensory Receptor Cells, User-Computer Interface, Vision, Ocular, Visual Cortex}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.05.037}, author = {Poort, Jasper and Khan, Adil G and Pachitariu, Marius and Nemri, Abdellatif and Orsolic, Ivana and Krupic, Julija and Bauza, Marius and Sahani, Maneesh and Keller, Georg B and Mrsic-Flogel, Thomas D and Hofer, Sonja B} } @article {47744, title = {Learning: the good, the bad, and the fly.}, journal = {Neuron}, volume = {86}, year = {2015}, month = {2015 Apr 22}, pages = {343-5}, abstract = {

Olfactory memories can be very good-your mother{\textquoteright}s baking-or very bad-your father{\textquoteright}s cooking. We go through life forming these different associations with the smells we encounter. But what makes one association pleasant and another repulsive? Work in deep areas of the Drosophila brain has revealed the beginnings of an answer, as reported in this issue of Neuron by Owald et al. (2015).

}, keywords = {Animals, Appetitive Behavior, Dopaminergic Neurons, Drosophila, Mushroom Bodies, Smell}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.04.012}, author = {Hige, Toshihide and Turner, Glenn} } @article {47144, title = {A Low Affinity GCaMP3 Variant (GCaMPer) for Imaging the Endoplasmic Reticulum Calcium Store.}, journal = {PloS one}, volume = {10}, year = {2015}, month = {2015 Oct 09}, pages = {e0139273}, abstract = {

Endoplasmic reticulum calcium homeostasis is critical for cellular functions and is disrupted in diverse pathologies including neurodegeneration and cardiovascular disease. Owing to the high concentration of calcium within the ER, studying this subcellular compartment requires tools that are optimized for these conditions. To develop a single-fluorophore genetically encoded calcium indicator for this organelle, we targeted a low affinity variant of GCaMP3 to the ER lumen (GCaMPer (10.19)). A set of viral vectors was constructed to express GCaMPer in human neuroblastoma cells, rat primary cortical neurons, and human induced pluripotent stem cell-derived cardiomyocytes. We observed dynamic changes in GCaMPer (10.19) fluorescence in response to pharmacologic manipulations of the ER calcium store. Additionally, periodic calcium efflux from the ER was observed during spontaneous beating of cardiomyocytes. GCaMPer (10.19) has utility in imaging ER calcium in living cells and providing insight into luminal calcium dynamics under physiologic and pathologic states.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0139273}, author = {Henderson, Mark J and Baldwin, Heather A and Werley, Christopher A and Boccardo, Stefano and Whitaker, Leslie R and Yan, Xiaokang and Holt, Graham T and Schreiter, Eric R and Looger, Loren L and Cohen, Adam E and Kim, Douglas S and Harvey, Brandon K} } @article {46987, title = {Low-noise encoding of active touch by layer 4 in the somatosensory cortex.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Aug 6}, abstract = {

Cortical spike trains often appear noisy, with the timing and number of spikes varying across repetitions of stimuli. Spiking variability can arise from internal (behavioral state, unreliable neurons, or chaotic dynamics in neural circuits) and external (uncontrolled behavior or sensory stimuli) sources. The amount of irreducible internal noise in spike trains, an important constraint on models of cortical networks, has been difficult to estimate, since behavior and brain state must be precisely controlled or tracked. We recorded from excitatory barrel cortex neurons in layer 4 during active behavior, where mice control tactile input through learned whisker movements. Touch was the dominant sensorimotor feature, with \>70\% spikes occurring in millisecond timescale epochs after touch onset. The variance of touch responses was smaller than expected from Poisson processes, often reaching the theoretical minimum. Layer 4 spike trains thus reflect the millisecond-timescale structure of tactile input with little noise.

}, issn = {2050-084X}, doi = {10.7554/eLife.06619}, author = {Andrew Hires, Samuel and Gutnisky, Diego A and Yu, Jianing and O{\textquoteright}Connor, Daniel H and Svoboda, Karel} } @article {46326, title = {Mapping social behavior-induced brain activation at cellular resolution in the mouse.}, journal = {Cell Reports}, volume = {10}, year = {2015}, month = {2015 Jan 13}, pages = {292-305}, abstract = {

Understanding how brain activation mediates behaviors is a central goal of systems neuroscience. Here, we apply an automated method for mapping brain activation in the mouse in order to probe how sex-specific social behaviors are represented in the male brain. Our method uses the immediate-early-gene c-fos, a marker of neuronal activation, visualized by serial two-photon tomography: the c-fos-GFP+ neurons are computationally detected, their distribution is registered to a reference brain and a brain atlas, and their numbers are analyzed by statistical tests. Our results reveal distinct and shared female and male interaction-evoked patterns of male brain activation representing sex discrimination and social recognition. We also identify brain regions whose degree of activity correlates to specific features of social behaviors and estimate the total numbers and the densities of activated neurons per brain areas. Our study opens the door to automated screening of behavior-evoked brain activation in the mouse.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2014.12.014}, author = {Kim, Yongsoo and Venkataraju, Kannan Umadevi and Pradhan, Kith and Mende, Carolin and Taranda, Julian and Turaga, Srinivas C and Arganda-Carreras, Ignacio and Ng, Lydia and Hawrylycz, Michael J and Rockland, Kathleen S and Seung, H Sebastian and Osten, Pavel} } @article {46881, title = {MicroED data collection and processing.}, journal = {Acta Crystallographica Section A: Foundations \& Advances}, volume = {71}, year = {2015}, month = {2015 Jul 01}, pages = {353-60}, abstract = {

MicroED, a method at the intersection of X-ray crystallography and electron cryo-microscopy, has rapidly progressed by exploiting advances in both fields and has already been successfully employed to determine the atomic structures of several proteins from sub-micron-sized, three-dimensional crystals. A major limiting factor in X-ray crystallography is the requirement for large and well ordered crystals. By permitting electron diffraction patterns to be collected from much smaller crystals, or even single well ordered domains of large crystals composed of several small mosaic blocks, MicroED has the potential to overcome the limiting size requirement and enable structural studies on difficult-to-crystallize samples. This communication details the steps for sample preparation, data collection and reduction necessary to obtain refined, high-resolution, three-dimensional models by MicroED, and presents some of its unique challenges.

}, issn = {2053-2733}, doi = {10.1107/S2053273315010669}, author = {Hattne, Johan and Reyes, Francis E and Nannenga, Brent L and Shi, Dan and de la Cruz, M Jason and Leslie, Andrew G W and Gonen, Tamir} } @article {48205, title = {Microtubule-dependent transport and dynamics of vimentin intermediate filaments.}, journal = {Molecular Biology of the Cell}, volume = {26}, year = {2015}, month = {2015 May 01}, pages = {1675-86}, abstract = {

We studied two aspects of vimentin intermediate filament dynamics-transport of filaments and subunit exchange. We observed transport of long filaments in the periphery of cells using live-cell structured illumination microscopy. We studied filament transport elsewhere in cells using a photoconvertible-vimentin probe and total internal reflection microscopy. We found that filaments were rapidly transported along linear tracks in both anterograde and retrograde directions. Filament transport was microtubule dependent but independent of microtubule polymerization and/or an interaction with the plus end-binding protein APC. We also studied subunit exchange in filaments by long-term imaging after photoconversion. We found that converted vimentin remained in small clusters along the length of filaments rather than redistributing uniformly throughout the network, even in cells that divided after photoconversion. These data show that vimentin filaments do not depolymerize into individual subunits; they recompose by severing and reannealing. Together these results show that vimentin filaments are very dynamic and that their transport is required for network maintenance.

}, keywords = {HEK293 Cells, Histone Deacetylase Inhibitors, Humans, Intermediate Filaments, Microtubules, Protein Multimerization, Protein Transport, Vimentin}, issn = {1939-4586}, doi = {10.1091/mbc.E14-09-1398}, author = {Hookway, Caroline and Ding, Liya and Davidson, Michael W and Rappoport, Joshua Z and Danuser, Gaudenz and Gelfand, Vladimir I} } @article {46823, title = {Molecular mechanism of vinculin activation and nanoscale spatial organization in focal adhesions.}, journal = {Nature Cell Biology}, volume = {17}, year = {2015}, month = {2015 Jun 8}, pages = {880-92}, abstract = {

Focal adhesions (FAs) link the extracellular matrix to the actin cytoskeleton to mediate cell adhesion, migration, mechanosensing and signalling. FAs have conserved nanoscale protein organization, suggesting that the position of proteins within FAs regulates their activity and function. Vinculin binds different FA proteins to mediate distinct cellular functions, but how vinculin{\textquoteright}s interactions are spatiotemporally organized within FAs is unknown. Using interferometric photoactivation localization super-resolution microscopy to assay vinculin nanoscale localization and a FRET biosensor to assay vinculin conformation, we found that upward repositioning within the FA during FA maturation facilitates vinculin activation and mechanical reinforcement of FAs. Inactive vinculin localizes to the lower integrin signalling layer in FAs by binding to phospho-paxillin. Talin binding activates vinculin and targets active vinculin higher in FAs where vinculin can engage retrograde actin flow. Thus, specific protein interactions are spatially segregated within FAs at the nanoscale to regulate vinculin activation and function.

}, issn = {1476-4679}, doi = {10.1038/ncb3180}, author = {Case, Lindsay B and Baird, Michelle A and Shtengel, Gleb and Campbell, Sharon L and Hess, Harald F and Davidson, Michael W and Waterman, Clare M} } @article {46531, title = {A multi-layered protein network stabilizes the Escherichia coli FtsZ-ring and modulates constriction dynamics.}, journal = {PLoS Genetics}, volume = {11}, year = {2015}, month = {2015 Apr 07}, pages = {e1005128}, abstract = {

The prokaryotic tubulin homolog, FtsZ, forms a ring-like structure (FtsZ-ring) at midcell. The FtsZ-ring establishes the division plane and enables the assembly of the macromolecular division machinery (divisome). Although many molecular components of the divisome have been identified and their interactions extensively characterized, the spatial organization of these proteins within the divisome is unclear. Consequently, the physical mechanisms that drive divisome assembly, maintenance, and constriction remain elusive. Here we applied single-molecule based superresolution imaging, combined with genetic and biophysical investigations, to reveal the spatial organization of cellular structures formed by four important divisome proteins in E. coli: FtsZ, ZapA, ZapB and MatP. We show that these interacting proteins are arranged into a multi-layered protein network extending from the cell membrane to the chromosome, each with unique structural and dynamic properties. Further, we find that this protein network stabilizes the FtsZ-ring, and unexpectedly, slows down cell constriction, suggesting a new, unrecognized role for this network in bacterial cell division. Our results provide new insight into the structure and function of the divisome, and highlight the importance of coordinated cell constriction and chromosome segregation.

}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1005128}, author = {Buss, Jackson and Coltharp, Carla and Shtengel, Gleb and Yang, Xinxing and Hess, Harald and Xiao, Jie} } @article {46527, title = {Myosin 18A coassembles with nonmuscle myosin 2 to form mixed bipolar filaments.}, journal = {Current Biology}, volume = {25}, year = {2015}, month = {2015 Mar 30}, pages = {942-8}, abstract = {

Class-18 myosins are most closely related to conventional class-2 nonmuscle myosins (NM2). Surprisingly, the purified head domains of Drosophila, mouse, and human myosin 18A (M18A) lack actin-activated ATPase activity and the ability to translocate actin filaments, suggesting that the functions of M18A in\ vivo do not depend on intrinsic motor activity. M18A has the longest coiled coil of any myosin outside of the class-2 myosins, suggesting that it might form bipolar filaments similar to conventional myosins. To address this possibility, we expressed and purified full-length mouse M18A using the baculovirus/Sf9 system. M18A did not form large bipolar filaments under any of the conditions tested. Instead, M18A formed an \~{}65-nm-long bipolar structure with two heads at each end. Importantly, when NM2 was polymerized in the presence of M18A, the two myosins formed mixed bipolar filaments, as evidenced by cosedimentation, electron microscopy, and single-molecule imaging. Moreover, super-resolution imaging of NM2 and M18A using fluorescently tagged proteins and immunostaining of endogenous proteins showed that NM2 and M18A are present together within individual filaments inside living cells. Together, our in\ vitro and live-cell imaging data argue strongly that M18A coassembles with NM2 into mixed bipolar filaments. M18A could regulate the biophysical properties of these filaments and, by virtue of its extra N- and C-terminal domains, determine the localization and/or molecular interactions of the filaments. Given the numerous, fundamental cellular and developmental roles attributed to NM2, our results have far-reaching biological implications.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2015.02.012}, author = {Billington, Neil and Beach, Jordan R and Heissler, Sarah M and Remmert, Kirsten and Guzik-Lendrum, Stephanie and Nagy, Attila and Takagi, Yasuharu and Shao, Lin and Li, Dong and Yang, Yi and Zhang, Yingfan and Barzik, Melanie and Betzig, Eric and Hammer, John A and Sellers, James R} } @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 {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 {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 {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 {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 {47017, title = {Optogenetics: 10 years after ChR2 in neurons-views from the community.}, journal = {Nature Neuroscience}, volume = {18}, year = {2015}, month = {2015 Aug 26}, pages = {1202-12}, issn = {1546-1726}, doi = {10.1038/nn.4106}, author = {Adamantidis, Antoine and Arber, Silvia and Bains, Jaideep S and Bamberg, Ernst and Bonci, Antonello and Buzs{\'a}ki, Gy{\"o}rgy and Cardin, Jessica A and Costa, Rui M and Dan, Yang and Goda, Yukiko and Graybiel, Ann M and H{\"a}usser, Michael and Hegemann, Peter and Huguenard, John R and Insel, Thomas R and Janak, Patricia H and Johnston, Daniel and Josselyn, Sheena A and Koch, Christof and Kreitzer, Anatol C and L{\"u}scher, Christian and Malenka, Robert C and Miesenb{\"o}ck, Gero and Nagel, Georg and Roska, Botond and Schnitzer, Mark J and Shenoy, Krishna V and Soltesz, Ivan and Sternson, Scott M and Tsien, Richard W and Tsien, Roger Y and Turrigiano, Gina G and Tye, Kay M and Wilson, Rachel I} } @article {47304, title = {P1 interneurons promote a persistent internal state that enhances inter-male aggression in Drosophila.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Dec 29}, abstract = {

How brains are hardwired to produce aggressive behavior, and how aggression circuits are related to those that mediate courtship, is not well understood. A large-scale screen for aggression-promoting neurons in Drosophila identified several independent hits that enhanced both inter-male aggression and courtship. Genetic intersections revealed that 8-10 P1 interneurons, previously thought to exclusively control male courtship, were sufficient to promote fighting. Optogenetic experiments indicated that P1 activation could promote aggression at a threshold below that required for wing extension. P1 activation in the absence of wing extension triggered persistent aggression via an internal state that could endure for minutes. High-frequency P1 activation promoted wing extension and suppressed aggression during photostimulation, whereas aggression resumed and wing extension was inhibited following photostimulation offset. Thus, P1 neuron activation promotes a latent, internal state that facilitates aggression and courtship, and controls the overt expression of these social behaviors in a threshold-dependent, inverse manner.

}, issn = {2050-084X}, doi = {10.7554/eLife.11346}, author = {Hoopfer, Eric D and Jung, Yonil and Inagaki, Hidehiko K and Rubin, Gerald M and Anderson, David J} } @article {47409, title = {Plasticity-driven individualization of olfactory coding in mushroom body output neurons.}, journal = {Nature}, volume = {526}, year = {2015}, month = {2015 Oct 8}, pages = {258-62}, abstract = {

Although all sensory circuits ascend to higher brain areas where stimuli are represented in sparse, stimulus-specific activity patterns, relatively little is known about sensory coding on the descending side of neural circuits, as a network converges. In insects, mushroom bodies have been an important model system for studying sparse coding in the olfactory system, where this format is important for accurate memory formation. In Drosophila, it has recently been shown that the 2,000 Kenyon cells of the mushroom body converge onto a population of only 34 mushroom body output neurons (MBONs), which fall into 21 anatomically distinct cell types. Here we provide the first, to our knowledge, comprehensive view of olfactory representations at the fourth layer of the circuit, where we find a clear transition in the principles of sensory coding. We show that MBON tuning curves are highly correlated with one another. This is in sharp contrast to the process of progressive decorrelation of tuning in the earlier layers of the circuit. Instead, at the population level, odour representations are reformatted so that positive and negative correlations arise between representations of different odours. At the single-cell level, we show that uniquely identifiable MBONs display profoundly different tuning across different animals, but that tuning of the same neuron across the two hemispheres of an individual fly was nearly identical. Thus, individualized coordination of tuning arises at this level of the olfactory circuit. Furthermore, we find that this individualization is an active process that requires a learning-related gene, rutabaga. Ultimately, neural circuits have to flexibly map highly stimulus-specific information in sparse layers onto a limited number of different motor outputs. The reformatting of sensory representations we observe here may mark the beginning of this sensory-motor transition in the olfactory system.

}, keywords = {Adenylyl Cyclases, Animals, Drosophila melanogaster, Drosophila Proteins, Female, Learning, Male, Mushroom Bodies, Mutation, Neuronal Plasticity, Neurons, Olfactory Pathways, Olfactory Perception, Psychomotor Performance}, issn = {1476-4687}, doi = {10.1038/nature15396}, author = {Hige, Toshihide and Aso, Yoshinori and Rubin, Gerald M and Turner, Glenn C} } @article {46788, title = {Post-acquisition image based compensation for thickness variation in microscopy section series.}, journal = {IEEE International Symposium on Biomedical Imaging}, year = {2015}, month = {2014 Nov 25}, pages = {507-11}, abstract = {

Serial section Microscopy is an established method for volumetric anatomy reconstruction. Section series imaged with Electron Microscopy are currently vital for the reconstruction of the synaptic connectivity of entire animal brains such as that of Drosophila melanogaster. The process of removing ultrathin layers from a solid block containing the specimen, however, is a fragile procedure and has limited precision with respect to section thickness. We have developed a method to estimate the relative z-position of each individual section as a function of signal change across the section series. First experiments show promising results on both serial section Transmission Electron Microscopy (ssTEM) data and Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) series. We made our solution available as Open Source plugins for the TrakEM2 software and the ImageJ distribution Fiji.

}, url = {http://arxiv.org/abs/1411.6970}, author = {Hanslovsky, Philpp and Bogovic, John A and Saalfeld, Stephan} } @conference {47129, title = {Post-acquisition image based compensation for thickness variation in microscopy section series.}, booktitle = {IEEE 12th International Symposium on Biomedical Imaging (ISBI)}, year = {2015}, month = {2015 Jul 01}, abstract = {

Serial section Microscopy is an established method for volumetric anatomy reconstruction. Section series imaged with Electron Microscopy are currently vital for the reconstruction of the synaptic connectivity of entire animal brains such as that of Drosophila melanogaster. The process of removing ultrathin layers from a solid block containing the specimen, however, is a fragile procedure and has limited precision with respect to section thickness. We have developed a method to estimate the relative z-position of each individual section as a function of signal change across the section series. First experiments show promising results on both serial section Transmission Electron Microscopy (ssTEM) data and Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) series. We made our solution available as Open Source plugins for the TrakEM2 software and the ImageJ distribution Fiji.

}, doi = {10.1109/ISBI.2015.7163922}, author = {Hanslovsky, Philipp and Bogovic, John and Saalfeld, Stephan} } @article {69344, title = {Quantitative Reevaluation of the Effects of Short- and Long-Term Removal of Descending Modulatory Inputs on the Pyloric Rhythm of the Crab, Cancer borealis }, journal = {eneuro}, volume = {2}, year = {2015}, month = {2015 Jan 14}, pages = {ENEURO.0058-14.2015}, abstract = {

The crustacean stomatogastric ganglion (STG) receives descending neuromodulatory inputs from three anterior ganglia: the paired commissural ganglia (CoGs), and the single esophageal ganglion (OG). In this paper, we provide the first detailed and quantitative analyses of the short- and long-term effects of removal of these descending inputs (decentralization) on the pyloric rhythm of the STG. Thirty minutes after decentralization, the mean frequency of the pyloric rhythm dropped from 1.20 Hz in control to 0.52 Hz. Whereas the relative phase of pyloric neuron activity was approximately constant across frequency in the controls, after decentralization this changed markedly. Nine control preparations kept for 5{\textendash}6 d\ in vitro\ maintained pyloric rhythm frequencies close to their initial values. Nineteen decentralized preparations kept for 5{\textendash}6 d dropped slightly in frequency from those seen at 30 min following decentralization, but then displayed stable activity over 6 d. Bouts of higher frequency activity were intermittently seen in both control and decentralized preparations, but the bouts began earlier and were more frequent in the decentralized preparations. Although the bouts may indicate that the removal of the modulatory inputs triggered changes in neuronal excitability, these changes did not produce obvious long-lasting changes in the frequency of the decentralized preparations.

}, doi = {10.1523/ENEURO.0058-14.2015}, url = {https://www.eneuro.org/lookup/doi/10.1523/ENEURO.0058-14.2015https://syndication.highwire.org/content/doi/10.1523/ENEURO.0058-14.2015}, author = {Hamood, Albert W. and Haddad, Sara A. and Otopalik, Adriane G. and Rosenbaum, Philipp and Marder, Eve} } @article {46499, title = {The Release 6 reference sequence of the Drosophila melanogaster genome.}, journal = {Genome Research}, volume = {25}, year = {2015}, month = {2015 Mar}, pages = {445-58}, abstract = {

Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and completeness of this sequence continues to be important to further progress. We previously described improvement of the 117-Mb sequence in the euchromatic portion of the genome and 21 Mb in the heterochromatic portion, using a whole-genome shotgun assembly, BAC physical mapping, and clone-based finishing. Here, we report an improved reference sequence of the single-copy and middle-repetitive regions of the genome, produced using cytogenetic mapping to mitotic and polytene chromosomes, clone-based finishing and BAC fingerprint verification, ordering of scaffolds by alignment to cDNA sequences, incorporation of other map and sequence data, and validation by whole-genome optical restriction mapping. These data substantially improve the accuracy and completeness of the reference sequence and the order and orientation of sequence scaffolds into chromosome arm assemblies. Representation of the Y chromosome and other heterochromatic regions is particularly improved. The new 143.9-Mb reference sequence, designated Release 6, effectively exhausts clone-based technologies for mapping and sequencing. Highly repeat-rich regions, including large satellite blocks and functional elements such as the ribosomal RNA genes and the centromeres, are largely inaccessible to current sequencing and assembly methods and remain poorly represented. Further significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads.

}, issn = {1549-5469}, doi = {10.1101/gr.185579.114}, author = {Hoskins, Roger A and Carlson, Joseph W and Wan, Kenneth H and Park, Soo and Mendez, Ivonne and Galle, Samuel E and Booth, Benjamin W and Pfeiffer, Barret D and George, Reed A and Svirskas, Robert and Krzywinski, Martin and Schein, Jacqueline and Accardo, Maria Carmela and Damia, Elisabetta and Messina, Giovanni and Mendez-Lago, Maria and de Pablos, Beatriz and Demakova, Olga V and Andreyeva, Evgeniya N and Boldyreva, Lidiya V and Marra, Marco and Carvalho, A Bernardo and Dimitri, Patrizio and Villasante, Alfredo and Zhimulev, Igor F and Rubin, Gerald M and Karpen, Gary H and Celniker, Susan E} } @article {46454, title = {A sensitive and robust enzyme kinetic experiment using microplates and fluorogenic ester substrates}, journal = {Journal of Chemical Education}, volume = {92}, year = {2015}, month = {2015 Feb}, pages = {385-8}, abstract = {

Enzyme kinetics measurements are a standard component of undergraduate biochemistry laboratories. The combination of serine hydrolases and fluorogenic enzyme substrates provides a rapid, sensitive, and general method for measuring enzyme kinetics in an undergraduate biochemistry laboratory. In this method, the kinetic activity of multiple protein variants is determined in parallel using a microplate reader, multichannel pipets, serial dilutions, and fluorogenic ester substrates. The utility of this methodology is illustrated by the measurement of differential enzyme activity in microplate volumes in triplicate with small protein samples and low activity enzyme variants. Enzyme kinetic measurements using fluorogenic substrates are, thus, adaptable for use with student-purified enzyme variants and for comparative enzyme kinetics studies. The rapid setup and analysis of these kinetic experiments not only provides advanced undergraduates with experience in a fundamental biochemical technique, but also provides the adaptability for use in inquiry-based laboratories.

}, issn = {0021-9584}, doi = {10.1021/ed500452f}, author = {Johnson, R. Jeremy and Hoops, Geoffrey C. and Savas, Christopher J. and Kartje, Zachary and Lavis, Luke D} } @article {46187, title = {Sensory determinants of behavioral dynamics in Drosophila thermotaxis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, year = {2015}, month = {2015 Jan 13}, pages = {E220-9}, abstract = {

Complex animal behaviors are built from dynamical relationships between sensory inputs, neuronal activity, and motor outputs in patterns with strategic value. Connecting these patterns illuminates how nervous systems compute behavior. Here, we study Drosophila larva navigation up temperature gradients toward preferred temperatures (positive thermotaxis). By tracking the movements of animals responding to fixed spatial temperature gradients or random temperature fluctuations, we calculate the sensitivity and dynamics of the conversion of thermosensory inputs into motor responses. We discover three thermosensory neurons in each dorsal organ ganglion (DOG) that are required for positive thermotaxis. Random optogenetic stimulation of the DOG thermosensory neurons evokes behavioral patterns that mimic the response to temperature variations. In vivo calcium and voltage imaging reveals that the DOG thermosensory neurons exhibit activity patterns with sensitivity and dynamics matched to the behavioral response. Temporal processing of temperature variations carried out by the DOG thermosensory neurons emerges in distinct motor responses during thermotaxis.

}, issn = {1091-6490}, doi = {10.1073/pnas.1416212112}, author = {Klein, Mason and Afonso, Bruno and Vonner, Ashley J and Hernandez-Nunez, Luis and Berck, Matthew and Tabone, Christopher J and Kane, Elizabeth A and Pieribone, Vincent A and Nitabach, Michael N and Cardona, Albert and Zlatic, Marta and Sprecher, Simon G and Gershow, Marc and Garrity, Paul A and Samuel, Aravinthan D T} } @article {47085, title = {A specific E3 ligase/deubiquitinase pair modulates TBP protein levels during muscle differentiation.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015}, abstract = {

TFIID-a complex of TATA-binding protein (TBP) and TBP-associated factors (TAFs)-is a central component of the Pol II promoter recognition apparatus. Recent studies have revealed significant downregulation of TFIID subunits in terminally differentiated myocytes, hepatocytes and adipocytes. Here, we report that TBP protein levels are tightly regulated by the ubiquitin-proteasome system. Using an in vitro ubiquitination assay coupled with biochemical fractionation, we identified Huwe1 as an E3 ligase targeting TBP for K48-linked ubiquitination and proteasome-mediated degradation. Upregulation of Huwe1 expression during myogenesis induces TBP degradation and myotube differentiation. We found that Huwe1 activity on TBP is antagonized by the deubiquitinase USP10, which protects TBP from degradation. Thus, modulating the levels of both Huwe1 and USP10 appears to fine-tune the requisite degradation of TBP during myogenesis. Together, our study unmasks a previously unknown interplay between an E3 ligase and a deubiquitinating enzyme regulating TBP levels during cellular differentiation.

}, issn = {2050-084X}, doi = {10.7554/eLife.08536}, author = {Li, Li and Martinez, Silvia Sanchez and Hu, Wenxin and Liu, Zhe and Tjian, Robert} } @article {46379, title = {Stimulation-evoked Ca2+ signals in astrocytic processes at hippocampal CA3-CA1 synapses of adult mice are modulated by glutamate and ATP.}, journal = {The Journal of Neuroscience}, volume = {35}, year = {2015}, month = {2015 Feb 18}, pages = {3016-21}, abstract = {

To date, it has been difficult to reveal physiological Ca(2+) events occurring within the fine astrocytic processes of mature animals. The objective of the study was to explore whether neuronal activity evokes astrocytic Ca(2+) signals at glutamatergic synapses of adult mice. We stimulated the Schaffer collateral/commissural fibers in acute hippocampal slices from adult mice transduced with the genetically encoded Ca(2+) indicator GCaMP5E driven by the glial fibrillary acidic protein promoter. Two-photon imaging revealed global stimulation-evoked astrocytic Ca(2+) signals with distinct latencies, rise rates, and amplitudes in fine processes and somata. Specifically, the Ca(2+) signals in the processes were faster and of higher amplitude than those in the somata. A combination of P2 purinergic and group I/II metabotropic glutamate receptor (mGluR) antagonists reduced the amplitude of the Ca(2+) transients by 30-40\% in both astrocytic compartments. Blockage of the mGluRs alone only modestly reduced the magnitude of the stimulation-evoked Ca(2+) signals in processes and failed to affect the somatic Ca(2+) response. Local application of group I or I/II mGluR agonists or adenosine triphosphate (ATP) elicited global astrocytic Ca(2+) signals that mimicked the stimulation-evoked astrocytic Ca(2+) responses. We conclude that stimulation-evoked Ca(2+) signals in astrocytic processes at CA3-CA1 synapses of adult mice (1) differ from those in astrocytic somata and (2) are modulated by glutamate and ATP.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3319-14.2015}, author = {Tang, Wannan and Szokol, Karolina and Jensen, Vidar and Enger, Rune and Trivedi, Chintan A and Hvalby, {\O}ivind and Helm, P Johannes and Looger, Loren L and Sprengel, Rolf and Nagelhus, Erlend A} } @article {47133, title = {Stochastic electrotransport selectively enhances the transport of highly electromobile molecules.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, year = {2015}, month = {2015 Nov 2}, pages = {E6274-83}, abstract = {

Nondestructive chemical processing of porous samples such as fixed biological tissues typically relies on molecular diffusion. Diffusion into a porous structure is a slow process that significantly delays completion of chemical processing. Here, we present a novel electrokinetic method termed stochastic electrotransport for rapid nondestructive processing of porous samples. This method uses a rotational electric field to selectively disperse highly electromobile molecules throughout a porous sample without displacing the low-electromobility molecules that constitute the sample. Using computational models, we show that stochastic electrotransport can rapidly disperse electromobile molecules in a porous medium. We apply this method to completely clear mouse organs within 1{\textendash}3 days and to stain them with nuclear dyes, proteins, and antibodies within 1 day. Our results demonstrate the potential of stochastic electrotransport to process large and dense tissue samples that were previously infeasible in time when relying on diffusion.

}, doi = {10.1073/pnas.1510133112}, author = {Kim, Sung-Yon and Cho, Jae Hun and Murray, Evan and Bakh, Naveed and Choi, Heejin and Ohn, Kimberly and Ruelas, Luzdary and Hubbert, Austin and McCue, Meg and Vassallo, Sara L and Keller, Philipp J and Chung, Kwanghun} } @article {48316, title = {Structure of the L protein of vesicular stomatitis virus from electron cryomicroscopy.}, journal = {Cell}, volume = {162}, year = {2015}, month = {2015 Jul 16}, pages = {314-27}, abstract = {

The large (L) proteins of non-segmented, negative-strand RNA viruses, a group that includes Ebola and rabies viruses, catalyze RNA-dependent RNA polymerization with viral ribonucleoprotein as template, a non-canonical sequence of capping and methylation reactions, and polyadenylation of viral messages. We have determined by electron cryomicroscopy the structure of the vesicular stomatitis virus (VSV) L protein. The density map, at a resolution of 3.8 {\r A}, has led to an atomic model for nearly all of the 2109-residue polypeptide chain, which comprises three enzymatic domains (RNA-dependent RNA polymerase [RdRp], polyribonucleotidyl transferase [PRNTase], and methyltransferase) and two structural domains. The RdRp resembles the corresponding enzymatic regions of dsRNA virus polymerases and influenza virus polymerase. A loop from the PRNTase (capping) domain projects into the catalytic site of the RdRp, where it appears to have the role of a priming loop and to couple product elongation to large-scale conformational changes in L.

}, keywords = {Cryoelectron Microscopy, DNA-Directed RNA Polymerases, Models, Molecular, Protein Structure, Tertiary, Sequence Homology, Amino Acid, Transcription, Genetic, Vesicular stomatitis Indiana virus, Viral Proteins}, issn = {1097-4172}, doi = {10.1016/j.cell.2015.06.018}, author = {Liang, Bo and Li, Zongli and Jenni, Simon and Rahmeh, Amal A and Morin, Benjamin M and Grant, Timothy and Grigorieff, Nikolaus and Harrison, Stephen C and Whelan, Sean P J} } @article {47031, title = {Structure of the toxic core of α-synuclein from invisible crystals.}, journal = {Nature}, volume = {525}, year = {2015}, month = {2015 Sep 9}, pages = {486-90}, abstract = {

The protein α-synuclein is the main component of Lewy bodies, the neuron-associated aggregates seen in Parkinson disease and other neurodegenerative pathologies. An 11-residue segment, which we term NACore, appears to be responsible for amyloid formation and cytotoxicity of human α-synuclein. Here we describe crystals of NACore that have dimensions smaller than the wavelength of visible light and thus are invisible by optical microscopy. As the crystals are thousands of times too small for structure determination by synchrotron X-ray diffraction, we use micro-electron diffraction to determine the structure at atomic resolution. The 1.4 {\r A} resolution structure demonstrates that this method can determine previously unknown protein structures and here yields, to our knowledge, the highest resolution achieved by any cryo-electron microscopy method to date. The structure exhibits protofibrils built of pairs of face-to-face β-sheets. X-ray fibre diffraction patterns show the similarity of NACore to toxic fibrils of full-length α-synuclein. The NACore structure, together with that of a second segment, inspires a model for most of the ordered portion of the toxic, full-length α-synuclein fibril, presenting opportunities for the design of inhibitors of α-synuclein fibrils.

}, issn = {1476-4687}, doi = {10.1038/nature15368}, author = {Rodriguez, Jose A and Ivanova, Magdalena I and Sawaya, Michael R and Cascio, Duilio and Reyes, Francis E and Shi, Dan and Sangwan, Smriti and Guenther, Elizabeth L and Johnson, Lisa M and Zhang, Meng and Jiang, Lin and Arbing, Mark A and Nannenga, Brent L and Hattne, Johan and Whitelegge, Julian and Brewster, Aaron S and Messerschmidt, Marc and Boutet, S{\'e}bastien and Sauter, Nicholas K and Gonen, Tamir and Eisenberg, David S} } @article {47039, title = {A subset of serotonergic neurons evokes hunger in adult Drosophila.}, journal = {Current Biology : CB}, volume = {25}, year = {2015}, month = {2015 Sep 2}, pages = {2435-40}, abstract = {

Hunger is a complex motivational state that drives multiple behaviors. The sensation of hunger is caused by an imbalance between energy intake and expenditure. One immediate response to hunger is increased food consumption. Hunger also modulates behaviors related to food seeking such as increased locomotion and enhanced sensory sensitivity in both insects [1-5] and vertebrates [6, 7]. In addition, hunger can promote the expression of food-associated memory [8, 9]. Although progress is being made [10], how hunger is represented in the brain and how it coordinates these behavioral responses is not fully understood in any system. Here, we use Drosophila melanogaster to identify neurons encoding hunger. We found a small group of neurons that, when activated, induced a fed fly to eat as though it were starved, suggesting that these neurons are downstream of the metabolic regulation of hunger. Artificially activating these neurons also promotes appetitive memory performance in sated flies, indicating that these neurons are not simply feeding command neurons but likely play a more general role in encoding hunger. We determined that the neurons relevant for the feeding effect are serotonergic and project broadly within the brain, suggesting a possible mechanism for how various responses to hunger are coordinated. These findings extend our\ understanding of the neural circuitry that drives feeding and enable future exploration of how state influences neural activity within this circuit.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2015.08.005}, author = {Albin, Stephanie D and Kaun, Karla R and Knapp, Jon-Michael and Chung, Phuong and Heberlein, Ulrike and Simpson, Julie H} } @article {47152, title = {Synaptic circuits and their variations within different columns in the visual system of Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, year = {2015}, month = {2015 Nov 3}, pages = {13711-6}, abstract = {

We reconstructed the synaptic circuits of seven columns in the second neuropil or medulla behind the fly{\textquoteright}s compound eye. These neurons embody some of the most stereotyped circuits in one of the most miniaturized of animal brains. The reconstructions allow us, for the first time to our knowledge, to study variations between circuits in the medulla{\textquoteright}s neighboring columns. This variation in the number of synapses and the types of their synaptic partners has previously been little addressed because methods that visualize multiple circuits have not resolved detailed connections, and existing connectomic studies, which can see such connections, have not so far examined multiple reconstructions of the same circuit. Here, we address the omission by comparing the circuits common to all seven columns to assess variation in their connection strengths and the resultant rates of several different and distinct types of connection error. Error rates reveal that, overall, \<1\% of contacts are not part of a consensus circuit, and we classify those contacts that supplement (E+) or are missing from it (E-). Autapses, in which the same cell is both presynaptic and postsynaptic at the same synapse, are occasionally seen; two cells in particular, Dm9 and Mi1, form >=20-fold more autapses than do other neurons. These results delimit the accuracy of developmental events that establish and normally maintain synaptic circuits with such precision, and thereby address the operation of such circuits. They also establish a precedent for error rates that will be required in the new science of connectomics.

}, issn = {1091-6490}, doi = {10.1073/pnas.1509820112}, author = {Takemura, Shin-ya and Xu, C Shan and Lu, Zhiyuan and Rivlin, Patricia K and Parag, Toufiq and Olbris, Donald J and Plaza, Stephen and Zhao, Ting and Katz, William T and Umayam, Lowell and Weaver, Charlotte and Hess, Harald F and Horne, Jane Anne and Nunez-Iglesias, Juan and Aniceto, Roxanne and Chang, Lei-Ann and Lauchie, Shirley and Nasca, Ashley and Ogundeyi, Omotara and Sigmund, Christopher and Takemura, Satoko and Tran, Julie and Langille, Carlie and Le Lacheur, Kelsey and McLin, Sari and Shinomiya, Aya and Chklovskii, Dmitri B and Meinertzhagen, Ian A and Scheffer, Louis K} } @article {46697, title = {Synonymous modification results in high-fidelity gene expression of repetitive protein and nucleotide sequences.}, journal = {Genes \& Development}, volume = {29}, year = {2015}, month = {2015 Apr 15}, pages = {876-86}, abstract = {

Repetitive nucleotide or amino acid sequences are often engineered into probes and biosensors to achieve functional readouts and robust signal amplification. However, these repeated sequences are notoriously prone to aberrant deletion and degradation, impacting the ability to correctly detect and interpret biological functions. Here, we introduce a facile and generalizable approach to solve this often unappreciated problem by modifying the nucleotide sequences of the target mRNA to make them nonrepetitive but still functional ("synonymous"). We first demonstrated the procedure by designing a cassette of synonymous MS2 RNA motifs and tandem coat proteins for RNA imaging and showed a dramatic improvement in signal and reproducibility in single-RNA detection in live cells. The same approach was extended to enhancing the stability of engineered fluorescent biosensors containing a fluorescent resonance energy transfer (FRET) pair of fluorescent proteins on which a great majority of systems thus far in the field are based. Using the synonymous modification to FRET biosensors, we achieved correct expression of full-length sensors, eliminating the aberrant truncation products that often were assumed to be due to nonspecific proteolytic cleavages. Importantly, the biological interpretations of the sensor are significantly different when a correct, full-length biosensor is expressed. Thus, we show here a useful and generally applicable method to maintain the integrity of expressed genes, critical for the correct interpretation of probe readouts.

}, issn = {1549-5477}, doi = {10.1101/gad.259358.115}, author = {Wu, Bin and Miskolci, Veronika and Sato, Hanae and Tutucci, Evelina and Kenworthy, Charles A and Donnelly, Sara K and Yoon, Young J and Cox, Dianne and Singer, Robert H and Hodgson, Louis} } @article {47242, title = {Synthesis of a far-red photoactivatable silicon-containing rhodamine for super-resolution microscopy.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {55}, year = {2015}, month = {2015 Dec 11}, pages = {1723-7}, abstract = {

The rhodamine system is a flexible framework for building small-molecule fluorescent probes. Changing N-substitution patterns and replacing the xanthene oxygen with a dimethylsilicon moiety can shift the absorption and fluorescence emission maxima of rhodamine dyes to longer wavelengths. Acylation of the rhodamine nitrogen atoms forces the molecule to adopt a nonfluorescent lactone form, providing a convenient method to make fluorogenic compounds. Herein, we take advantage of all of these structural manipulations and describe a novel photoactivatable fluorophore based on a Si-containing analogue of Q-rhodamine. This probe is the first example of a "caged" Si-rhodamine, exhibits higher photon counts compared to established localization microscopy dyes, and is sufficiently red-shifted to allow multicolor imaging. The dye is a useful label for super-resolution imaging and constitutes a new scaffold for far-red fluorogenic molecules.

}, issn = {1521-3773}, doi = {10.1002/anie.201509649}, author = {Grimm, Jonathan B and Klein, Teresa and Kopek, Benjamin G and Shtengel, Gleb and Hess, Harald F and Sauer, Markus and Lavis, Luke D} } @article {46369, title = {Tracking surface glycans on live cancer cells with single-molecule sensitivity.}, journal = {Angewandte Chemie International Edition English}, volume = {54}, year = {2015}, month = {2015 Feb 2}, pages = {1765-9}, abstract = {

Using a combination of metabolically labeled glycans, a bioorthogonal copper(I)-catalyzed azide-alkyne cycloaddition, and the controlled bleaching of fluorescent probes conjugated to azide- or alkyne-tagged glycans, a sufficiently low spatial density of dye-labeled glycans was achieved, enabling dynamic single-molecule tracking and super-resolution imaging of N-linked sialic acids and O-linked N-acetyl galactosamine (GalNAc) on the membrane of live cells. Analysis of the trajectories of these dye-labeled glycans in mammary cancer cells revealed constrained diffusion of both N- and O-linked glycans, which was interpreted as reflecting the mobility of the glycan rather than to be caused by transient immobilization owing to spatial inhomogeneities on the plasma membrane. Stochastic optical reconstruction microscopy (STORM) imaging revealed the structure of dynamic membrane nanotubes.

}, issn = {1521-3773}, doi = {10.1002/anie.201407976}, author = {Jiang, Hao and English, Brian P and Hazan, Rachel B and Wu, Peng and Ovryn, Ben} } @article {47025, title = {The transgenic RNAi project at Harvard Medical School: resources and validation.}, journal = {Genetics}, volume = {201}, year = {2015}, month = {2015 Aug 28}, pages = {843-52}, abstract = {

To facilitate large scale functional studies in Drosophila, the Drosophila Transgenic RNAi Project (TRiP) at Harvard Medical School (HMS) was established along with several goals: developing efficient vectors for RNAi that work in all tissues, generating a genome scale collection of RNAi stocks with input from the community, distributing the lines as they are generated through existing stock centers, validating as many lines as possible using RT-qPCR and phenotypic analyses, and developing tools and web resources for identifying RNAi lines and retrieving existing information on their quality. With these goals in mind, here we describe in detail the various tools we developed and the status of the collection, which is currently comprised of 11,491 lines and covering 71\% of Drosophila genes. Data on the characterization of the lines either by RT-qPCR or phenotype is available on a dedicated web site, the RNAi Stock Validation and Phenotypes Project (RSVP; www.flyrnai.org/RSVP.html), and stocks are available from three stock centers, the Bloomington Drosophila Stock Center (USA), National Institute of Genetics (Japan), and TsingHua Fly Center (China).

}, issn = {1943-2631}, doi = {10.1534/genetics.115.180208}, author = {Perkins, L A and Holderbaum, L and Tao, R and Hu, Y and Sopko, R and McCall, K and Yang-Zhou, D and Flockhart, I and Binari, R and Shim, H-S and Miller, A and Housden, A and Foos, M and Randkelv, S and Kelley, C and Namgyal, P and Villalta, C and Liu, L-P and Jiang, X and Huan-Huan, Q and Xia, W and Fujiyama, A and Toyoda, A and Ayers, K and Blum, A and Czech, B and Neumuller, R and Yan, D and Cavallaro, A and Hibbard, K and Hall, D and Cooley, L and Hannon, G J and Lehmann, R and Parks, A and Mohr, S E and Ueda, R and Kondo, S and Ni, J-Q and Perrimon, Norbert} } @article {46533, title = {Translation. An RNA biosensor for imaging the first round of translation from single cells to living animals.}, journal = {Science}, volume = {347}, year = {2015}, month = {2015 Mar 20}, pages = {1367-671}, abstract = {

Analysis of single molecules in living cells has provided quantitative insights into the kinetics of fundamental biological processes; however, the dynamics of messenger RNA (mRNA) translation have yet to be addressed. We have developed a fluorescence microscopy technique that reports on the first translation events of individual mRNA molecules. This allowed us to examine the spatiotemporal regulation of translation during normal growth and stress and during Drosophila oocyte development. We have shown that mRNAs are not translated in the nucleus but translate within minutes after export, that sequestration within P-bodies regulates translation, and that oskar mRNA is not translated until it reaches the posterior pole of the oocyte. This methodology provides a framework for studying initiation of protein synthesis on single mRNAs in living cells.

}, issn = {1095-9203}, doi = {10.1126/science.aaa3380}, author = {Halstead, James M and Lionnet, Timoth{\'e}e and Wilbertz, Johannes H and Wippich, Frank and Ephrussi, Anne and Singer, Robert H and Chao, Jeffrey A} } @article {46325, title = {Ultrastructurally smooth thick partitioning and volume stitching for large-scale connectomics.}, journal = {Nature Methods}, volume = {12}, year = {2015}, month = {2015 Feb 16}, pages = {319-22}, abstract = {

Focused-ion-beam scanning electron microscopy (FIB-SEM) has become an essential tool for studying neural tissue at resolutions below 10 nm {\texttimes} 10 nm {\texttimes} 10 nm, producing data sets optimized for automatic connectome tracing. We present a technical advance, ultrathick sectioning, which reliably subdivides embedded tissue samples into chunks (20 μm thick) optimally sized and mounted for efficient, parallel FIB-SEM imaging. These chunks are imaged separately and then {\textquoteright}volume stitched{\textquoteright} back together, producing a final three-dimensional data set suitable for connectome tracing.

}, issn = {1548-7105}, doi = {10.1038/nmeth.3292}, author = {Hayworth, Kenneth J and Xu, C Shan and Lu, Zhiyuan and Knott, Graham W and Fetter, Richard D and Tapia, Juan Carlos and Lichtman, Jeff W and Hess, Harald F} } @article {65781, title = {Variable primary coordination environments of Cd(II) binding to three helix bundles provide a pathway for rapid metal exchange.}, journal = {Metallomics}, volume = {7}, year = {2015}, month = {10/2015}, pages = {1555 {\textendash} 1561}, abstract = {

Members of the ArsR/SmtB family of transcriptional repressors, such as CadC, regulate the intracellular levels of heavy metals like Cd(II), Hg(II), and Pb(II). These metal sensing proteins bind their target metals with high specificity and affinity, however, a lack of structural information about these proteins makes defining the coordination sphere of the target metal difficult. Lingering questions as to the identity of Cd(II) coordination in CadC are addressed via protein design techniques. Two designed peptides with tetrathiolate metal binding sites were prepared and characterized, revealing fast exchange between CdS3O and CdS4 coordination spheres. Correlation of (111m)Cd PAC spectroscopy and (113)Cd NMR spectroscopy suggests that Cd(II) coordinated to CadC is in fast exchange between CdS3O and CdS4 forms, which may provide a mechanism for rapid sensing of heavy metal contaminants by this regulatory protein.

}, doi = {10.1039/c5mt00228a}, author = {Tebo, Alison G and Hemmingsen, Lars and Pecoraro, Vincent L} } @article {46744, title = {Visualization and neuronal cell targeting during electrophysiological recordings facilitated by quantum dots.}, journal = {Proceedings of SPIE}, volume = {9305}, year = {2015}, month = {2015 Mar 10}, pages = {9305Y}, abstract = {

The simultaneous visualization, identification and targeting of neurons during patch clamp-mediated electrophysiological recordings is a basic technique in neuroscience, yet it is often complicated by the inability to visualize the pipette tip, particularly in deep brain tissue. Here we demonstrate a novel approach in which fluorescent quantum dot probes are used to coat pipettes prior to their use. The strong two-photon absorption cross sections of the quantum dots afford robust contrast at significantly deeper penetration depths than current methods allow. We demonstrate the utility of this technique in multiple recording formats both in vitro and in vivo where imaging of the pipettes is achieved at remarkable depths (up to 800 microns). Notably, minimal perturbation of cellular physiology is observed over the hours-long time course of neuronal recordings. We discuss our results within the context of the role that quantum dot nanoprobes may play in understanding neuronal cell physiology.

}, doi = {10.1117/12.2076934}, author = {Field, Lauren D and Andrasfalvy, Bertalan K and Gali{\~n}anes, Gregorio L and Huber, Daniel and Barbic, Mladen and Macklin, John J and Susumu, Kimihiro and Delehanty, James B and Huston, Alan L and Makara, Judit K and Medintz, Igor L} } @inbook {47184, title = {Who is talking to whom: Synaptic partner detection in anisotropic volumes of insect brain.}, booktitle = {Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2015}, number = {9349}, year = {2015}, pages = {661-8}, abstract = {

Automated reconstruction of neural connectivity graphs from electron microscopy image stacks is an essential step towards large-scale neural circuit mapping. While significant progress has recently been made in automated segmentation of neurons and detection of synapses, the problem of synaptic partner assignment for polyadic (one-to-many) synapses, prevalent in the\ Drosophila\ brain, remains unsolved. In this contribution, we propose a method which automatically assigns pre- and postsynaptic roles to neurites adjacent to a synaptic site. The method constructs a probabilistic graphical model over potential synaptic partner pairs which includes factors to account for a high rate of one-to-many connections, as well as the possibility of the same neuron to be pre-synaptic in one synapse and post-synaptic in another. The algorithm has been validated on a publicly available stack of ssTEM images of\ Drosophila\ neural tissue and has been shown to reconstruct most of the synaptic relations correctly.

}, doi = {10.1007/978-3-319-24553-9_81}, author = {Kreshuk, Anna and Funke, Jan and Cardona, Albert and Hamprecht, Fred A} } @article {47116, title = {Whole-animal functional and developmental imaging with isotropic spatial resolution}, journal = {Nature Methods}, volume = {12}, year = {2015}, month = {2015 Oct 26}, pages = {1171-8}, abstract = {

Imaging fast cellular dynamics across large specimens requires high resolution in all dimensions, high imaging speeds, good physical coverage and low photo-damage. To meet these requirements, we developed isotropic multiview (IsoView) light-sheet microscopy, which rapidly images large specimens via simultaneous light-sheet illumination and fluorescence detection along four orthogonal directions. Combining these four views by means of high-throughput multiview deconvolution yields images with high resolution in all three dimensions. We demonstrate whole-animal functional imaging of Drosophila larvae at a spatial resolution of 1.1-2.5 μm and temporal resolution of 2 Hz for several hours. We also present spatially isotropic whole-brain functional imaging in Danio rerio larvae and spatially isotropic multicolor imaging of fast cellular dynamics across gastrulating Drosophila embryos. Compared with conventional light-sheet microscopy, IsoView microscopy improves spatial resolution at least sevenfold and decreases resolution anisotropy at least threefold. Compared with existing high-resolution light-sheet techniques, IsoView microscopy effectively doubles the penetration depth and provides subsecond temporal resolution for specimens 400-fold larger than could previously be imaged.

}, doi = {10.1038/nmeth.3632}, author = {Chhetri, Raghav K and Amat, Fernando and Wan, Yinan and H{\"o}ckendorf, Burkhard and Lemon, William C and Keller, Philipp J} } @article {46984, title = {Whole-central nervous system functional imaging in larval Drosophila.}, journal = {Nature Communications}, volume = {6}, year = {2015}, month = {2015 Aug 11}, pages = {7924}, abstract = {

Understanding how the brain works in tight concert with the rest of the central nervous system (CNS) hinges upon knowledge of coordinated activity patterns across the whole CNS. We present a method for measuring activity in an entire, non-transparent CNS with high spatiotemporal resolution. We combine a light-sheet microscope capable of simultaneous multi-view imaging at volumetric speeds 25-fold faster than the state-of-the-art, a whole-CNS imaging assay for the isolated Drosophila larval CNS and a computational framework for analysing multi-view, whole-CNS calcium imaging data. We image both brain and ventral nerve cord, covering the entire CNS at 2 or 5 Hz with two- or one-photon excitation, respectively. By mapping network activity during fictive behaviours and quantitatively comparing high-resolution whole-CNS activity maps across individuals, we predict functional connections between CNS regions and reveal neurons in the brain that identify type and temporal state of motor programs executed in the ventral nerve cord.

}, doi = {10.1038/ncomms8924}, author = {Lemon, William C and Pulver, Stefan R and H{\"o}ckendorf, Burkhard and McDole, Katie and Branson, Kristin M and Freeman, Jeremy and Keller, Philipp J} } @article {45102, title = {Accessing the third dimension in localization-based super-resolution microscopy.}, journal = {Physical Chemistry Chemical Physics}, volume = {16}, year = {2014}, month = {2014 Jul 16}, pages = {16340-8}, abstract = {

Only a few years after its inception, localization-based super-resolution microscopy has become widely employed in biological studies. Yet, it is primarily used in two-dimensional imaging and accessing the organization of cellular structures at the nanoscale in three dimensions (3D) still poses important challenges. Here, we review optical and computational techniques that enable the 3D localization of individual emitters and the reconstruction of 3D super-resolution images. These techniques are grouped into three main categories: PSF engineering, multiple plane imaging and interferometric approaches. We provide an overview of their technical implementation as well as commentary on their applicability. Finally, we discuss future trends in 3D localization-based super-resolution microscopy.

}, issn = {1463-9084}, doi = {10.1039/c4cp01380h}, author = {Hajj, Bassam and El Beheiry, Mohamed and Izeddin, Ignacio and Darzacq, Xavier and Dahan, Maxime} } @article {6935, title = {Allelic heterogeneity in NCF2 associated with systemic lupus erythematosus (SLE) susceptibility across four ethnic populations.}, journal = {Human Molecular Genetics}, volume = {23}, year = {2014}, month = {2014 Mar 15}, pages = {1656-68}, abstract = {

Recent reports have associated NCF2, encoding a core component of the multi-protein NADPH oxidase (NADPHO), with systemic lupus erythematosus (SLE) susceptibility in individuals of European ancestry. To identify ethnicity-specific and -robust variants within NCF2, we assessed 145 SNPs in and around the NCF2 gene in 5325 cases and 21 866 controls of European-American (EA), African-American (AA), Hispanic (HS) and Korean (KR) ancestry. Subsequent imputation, conditional, haplotype and bioinformatic analyses identified seven potentially functional SLE-predisposing variants. Association with non-synonymous rs17849502, previously reported in EA, was detected in EA, HS and AA (P(EA) = 1.01 {\texttimes} 10(-54), PHS = 3.68 {\texttimes} 10(-10), P(AA) = 0.03); synonymous rs17849501 was similarly significant. These SNPs were monomorphic in KR. Novel associations were detected with coding variants at rs35937854 in AA (PAA = 1.49 {\texttimes} 10(-9)), and rs13306575 in HS and KR (P(HS) = 7.04 {\texttimes} 10(-7), P(KR) = 3.30 {\texttimes} 10(-3)). In KR, a 3-SNP haplotype was significantly associated (P = 4.20 {\texttimes} 10(-7)), implying that SLE predisposing variants were tagged. Significant SNP-SNP interaction (P = 0.02) was detected between rs13306575 and rs17849502 in HS, and a dramatically increased risk (OR = 6.55) with a risk allele at each locus. Molecular modeling predicts that these non-synonymous mutations could disrupt NADPHO complex assembly. The risk allele of rs17849501, located in a conserved transcriptional regulatory region, increased reporter gene activity, suggesting in vivo enhancer function. Our results not only establish allelic heterogeneity within NCF2 associated with SLE, but also emphasize the utility of multi-ethnic cohorts to identify predisposing variants explaining additional phenotypic variance ({\textquoteright}missing heritability{\textquoteright}) of complex diseases like SLE.

}, issn = {1460-2083}, doi = {10.1093/hmg/ddt532}, author = {Kim-Howard, Xana and Sun, Celi and Molineros, Julio E and Maiti, Amit K and Chandru, Hema and Adler, Adam and Wiley, Graham B and Kaufman, Kenneth M and Kottyan, Leah and Guthridge, Joel M and Rasmussen, Astrid and Kelly, Jennifer and S{\'a}nchez, Elena and Raj, Prithvi and Li, Quan-Zhen and Bang, So-Young and Lee, Hye-Soon and Kim, Tae-Hwan and Kang, Young Mo and Suh, Chang-Hee and Chung, Won Tae and Park, Yong-Beom and Choe, Jung-Yoon and Shim, Seung Cheol and Lee, Shin-Seok and Han, Bok-Ghee and Olsen, Nancy J and Karp, David R and Moser, Kathy and Pons-Estel, Bernardo A and Wakeland, Edward K and James, Judith A and Harley, John B and Bae, Sang-Cheol and Gaffney, Patrick M and Alarc{\'o}n-Riquelme, Marta and Looger, Loren L and Nath, Swapan K} } @article {6932, title = {Amphotericin forms an extramembranous and fungicidal sterol sponge.}, journal = {Nature Chemical Biology}, volume = {10}, year = {2014}, month = {2014 Mar 30}, pages = {400-6}, abstract = {

For over 50 years, amphotericin has remained the powerful but highly toxic last line of defense in treating life-threatening fungal infections in humans with minimal development of microbial resistance. Understanding how this small molecule kills yeast is thus critical for guiding development of derivatives with an improved therapeutic index and other resistance-refractory antimicrobial agents. In the widely accepted ion channel model for its mechanism of cytocidal action, amphotericin forms aggregates inside lipid bilayers that permeabilize and kill cells. In contrast, we report that amphotericin exists primarily in the form of large, extramembranous aggregates that kill yeast by extracting ergosterol from lipid bilayers. These findings reveal that extraction of a polyfunctional lipid underlies the resistance-refractory antimicrobial action of amphotericin and suggests a roadmap for separating its cytocidal and membrane-permeabilizing activities. This new mechanistic understanding is also guiding development of what are to our knowledge the first derivatives of amphotericin that kill yeast but not human cells.

}, issn = {1552-4469}, doi = {10.1038/nchembio.1496}, author = {Anderson, Thomas M and Clay, Mary C and Cioffi, Alexander G and Diaz, Katrina A and Hisao, Grant S and Tuttle, Marcus D and Nieuwkoop, Andrew J and Comellas, Gemma and Maryum, Nashrah and Wang, Shu and Uno, Brice E and Wildeman, Erin L and Gonen, Tamir and Rienstra, Chad M and Burke, Martin D} } @article {46226, title = {Annotating synapses in large EM datasets.}, journal = {arXiv}, year = {2014}, month = {2014 Sep 5}, pages = {arXiv:1409.1801 [q-bio.QM]}, abstract = {

Reconstructing neuronal circuits at the level of synapses is a central problem in neuroscience and becoming a focus of the emerging field of connectomics. To date, electron microscopy (EM) is the most proven technique for identifying and quantifying synaptic connections. As advances in EM make acquiring larger datasets possible, subsequent manual synapse identification ({\em i.e.}, proofreading) for deciphering a connectome becomes a major time bottleneck. Here we introduce a large-scale, high-throughput, and semi-automated methodology to efficiently identify synapses. We successfully applied our methodology to the Drosophila medulla optic lobe, annotating many more synapses than previous connectome efforts. Our approaches are extensible and will make the often complicated process of synapse identification accessible to a wider-community of potential proofreaders.

}, url = {http://arxiv.org/abs/1409.1801}, author = {Plaza, Stephen M and Parag, Toufiq and Huang, Gary and Olbris, Donald J. and Saunders, Mathew A. and Rivlin, Patricia K.} } @article {45048, title = {Ascending SAG neurons control sexual receptivity of Drosophila females.}, journal = {Neuron}, volume = {83}, year = {2014}, month = {2014 Jul 2}, pages = {135-48}, abstract = {

Mating induces pronounced changes in female reproductive behavior, typically including a dramatic reduction in sexual receptivity. In Drosophila, postmating behavioral changes are triggered by sex peptide (SP), a male seminal fluid peptide that acts via a\ receptor (SPR) expressed in sensory neurons (SPSNs) of the female reproductive tract. Here, we identify second-order neurons that mediate the behavioral changes induced by SP. These SAG neurons receive synaptic input from SPSNs in the abdominal ganglion and project to the dorsal protocerebrum. Silencing SAG neurons renders virgin females unreceptive, whereas activating them increases the receptivity of females that have already mated. Physiological experiments demonstrate that SP downregulates the excitability of the SPSNs, and hence their input onto SAG neurons. These data thus provide a physiological correlate of mating status in the female central nervous system and a key entry point into the brain circuits that control sexual receptivity.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2014.05.017}, author = {Feng, Kai and Palfreyman, Mark T and H{\"a}semeyer, Martin and Talsma, Aaron and Dickson, Barry J} } @article {45418, title = {Atlas-builder software and the eNeuro atlas: resources for developmental biology and neuroscience.}, journal = {Development}, volume = {141}, year = {2014}, month = {2014 Jun}, pages = {2524-32}, abstract = {

A major limitation in understanding embryonic development is the lack of cell type-specific markers. Existing gene expression and marker atlases provide valuable tools, but they typically have one or more limitations: a lack of single-cell resolution; an inability to register multiple expression patterns to determine their precise relationship; an inability to be upgraded by users; an inability to compare novel patterns with the database patterns; and a lack of three-dimensional images. Here, we develop new {\textquoteright}atlas-builder{\textquoteright} software that overcomes each of these limitations. A newly generated atlas is three-dimensional, allows the precise registration of an infinite number of cell type-specific markers, is searchable and is open-ended. Our software can be used to create an atlas of any tissue in any organism that contains stereotyped cell positions. We used the software to generate an {\textquoteright}eNeuro{\textquoteright} atlas of the Drosophila embryonic CNS containing eight transcription factors that mark the major CNS cell types (motor neurons, glia, neurosecretory cells and interneurons). We found neuronal, but not glial, nuclei occupied stereotyped locations. We added 75 new Gal4 markers to the atlas to identify over 50\% of all interneurons in the ventral CNS, and these lines allowed functional access to those interneurons for the first time. We expect the atlas-builder software to benefit a large proportion of the developmental biology community, and the eNeuro atlas to serve as a publicly accessible hub for integrating neuronal attributes - cell lineage, gene expression patterns, axon/dendrite projections, neurotransmitters--and linking them to individual neurons.

}, keywords = {Animals, Axons, Cell Lineage, Central Nervous System, Computational Biology, Databases, Genetic, Dendrites, Drosophila melanogaster, Drosophila Proteins, Gene Expression Profiling, Gene Expression Regulation, Developmental, Genetic Markers, Interneurons, Mice, Neurons, Neurotransmitter Agents, Rats, Software}, issn = {1477-9129}, doi = {10.1242/dev.108720}, author = {Heckscher, Ellie S and Long, Fuhui and Layden, Michael J and Chuang, Chein-Hui and Manning, Laurina and Richart, Jourdain and Pearson, Joseph C and Crews, Stephen T and Peng, Hanchuan and Myers, Eugene and Doe, Chris Q} } @article {6880, title = {Automated detection of synapses in serial section transmission electron microscopy image stacks.}, journal = {PloS one}, volume = {9}, year = {2014}, month = {2014}, pages = {e87351}, abstract = {We describe a method for fully automated detection of chemical synapses in serial electron microscopy images with highly anisotropic axial and lateral resolution, such as images taken on transmission electron microscopes. Our pipeline starts from classification of the pixels based on 3D pixel features, which is followed by segmentation with an Ising model MRF and another classification step, based on object-level features. Classifiers are learned on sparse user labels; a fully annotated data subvolume is not required for training. The algorithm was validated on a set of 238 synapses in 20 serial 7197{\texttimes}7351 pixel images (4.5{\texttimes}4.5{\texttimes}45 nm resolution) of mouse visual cortex, manually labeled by three independent human annotators and additionally re-verified by an expert neuroscientist. The error rate of the algorithm (12\% false negative, 7\% false positive detections) is better than state-of-the-art, even though, unlike the state-of-the-art method, our algorithm does not require a prior segmentation of the image volume into cells. The software is based on the ilastik learning and segmentation toolkit and the vigra image processing library and is freely available on our website, along with the test data and gold standard annotations (http://www.ilastik.org/synapse-detection/sstem).}, issn = {1932-6203}, doi = {10.1371/journal.pone.0087351}, author = {Kreshuk, Anna and Koethe, Ullrich and Pax, Elizabeth and Bock, Davi D and Hamprecht, Fred A} } @article {6910, title = {The catalytic subunit of the SWR1 remodeler is a histone chaperone for the H2A.Z-H2B dimer.}, journal = {Molecular Cell}, volume = {53}, year = {2014}, month = {2014 Feb 6}, pages = {498-505}, abstract = {

Histone variant H2A.Z-containing nucleosomes exist at most eukaryotic promoters and play important roles in gene transcription and genome stability. The multisubunit nucleosome-remodeling enzyme complex SWR1, conserved from yeast to mammals, catalyzes the ATP-dependent replacement of histone H2A in canonical nucleosomes with H2A.Z. How SWR1 catalyzes the replacement reaction is largely unknown. Here, we determined the crystal structure of the N-terminal region (599-627) of the catalytic subunit Swr1, termed Swr1-Z domain, in complex with the H2A.Z-H2B dimer at 1.78 {\r A} resolution. The Swr1-Z domain forms a 310 helix and an irregular chain. A conserved LxxLF motif in the Swr1-Z 310 helix specifically recognizes the αC helix of H2A.Z. Our results show that the Swr1-Z domain can deliver the H2A.Z-H2B dimer to the DNA-(H3-H4)2 tetrasome to form the nucleosome by a histone chaperone mechanism.

}, issn = {1097-4164}, doi = {10.1016/j.molcel.2014.01.010}, author = {Hong, Jingjun and Feng, Hanqiao and Wang, Feng and Ranjan, Anand and Chen, Jianhong and Jiang, Jiansheng and Ghirlando, Rodolfo and Xiao, T Sam and Wu, Carl and Bai, Yawen} } @article {6952, title = {Cell-type-based model explaining coexpression patterns of genes in the brain.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, year = {2014}, month = {2014 Apr 8}, pages = {5397-402}, abstract = {

Spatial patterns of gene expression in the vertebrate brain are not independent, as pairs of genes can exhibit complex patterns of coexpression. Two genes may be similarly expressed in one region, but differentially expressed in other regions. These correlations have been studied quantitatively, particularly for the Allen Atlas of the adult mouse brain, but their biological meaning remains obscure. We propose a simple model of the coexpression patterns in terms of spatial distributions of underlying cell types and establish its plausibility using independently measured cell-type-specific transcriptomes. The model allows us to predict the spatial distribution of cell types in the mouse brain.

}, issn = {1091-6490}, doi = {10.1073/pnas.1312098111}, author = {Grange, Pascal and Bohland, Jason W and Okaty, Benjamin W and Sugino, Ken and Bokil, Hemant and Nelson, Sacha B and Ng, Lydia and Hawrylycz, Michael and Mitra, Partha P} } @article {45638, title = {Cell-type-specific repression by methyl-CpG-binding protein 2 is biased toward long genes.}, journal = {Journal of Neuroscience}, volume = {34}, year = {2014}, month = {2014 Sep 17}, pages = {12877-83}, abstract = {

Mutations in methyl-CpG-binding protein 2 (MeCP2) cause Rett syndrome and related autism spectrum disorders (Amir et al., 1999). MeCP2 is believed to be required for proper regulation of brain gene expression, but prior microarray studies in Mecp2 knock-out mice using brain tissue homogenates have revealed only subtle changes in gene expression (Tudor et al., 2002; Nuber et al., 2005; Jordan et al., 2007; Chahrour et al., 2008). Here, by profiling discrete subtypes of neurons we uncovered more dramatic effects of MeCP2 on gene expression, overcoming the "dilution problem" associated with assaying homogenates of complex tissues. The results reveal misregulation of genes involved in neuronal connectivity and communication. Importantly, genes upregulated following loss of MeCP2 are biased toward longer genes but this is not true for downregulated genes, suggesting MeCP2 may selectively repress long genes. Because genes involved in neuronal connectivity and communication, such as cell adhesion and cell-cell signaling genes, are enriched among longer genes, their misregulation following loss of MeCP2 suggests a possible etiology for altered circuit function in Rett syndrome.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.2674-14.2014}, author = {Sugino, Ken and Hempel, Chris M and Okaty, Benjamin W and Arnson, Hannah A and Kato, Saori and Dani, Vardhan S and Nelson, Sacha B} } @article {45181, title = {Combined protein- and nucleic acid-level effects of rs1143679 (R77H), a lupus-predisposing variant within ITGAM.}, journal = {Human Molecular Genetics}, volume = {23}, year = {2014}, month = {2014 Aug 1}, pages = {4161-76}, abstract = {

Integrin alpha M (ITGAM; CD11b) is a component of the macrophage-1 antigen complex, which mediates leukocyte adhesion, migration and phagocytosis as part of the immune system. We previously identified a missense polymorphism, rs1143679 (R77H), strongly associated with systemic lupus erythematosus (SLE). However, the molecular mechanisms of this variant are incompletely understood. A meta-analysis of published and novel data on 28 439 individuals with European, African, Hispanic and Asian ancestries reinforces genetic association between rs1143679 and SLE [Pmeta = 3.60 {\texttimes} 10(-90), odds ratio (OR) = 1.76]. Since rs1143679 is in the most active region of chromatin regulation and transcription factor binding in ITGAM, we quantitated ITGAM RNA and surface protein levels in monocytes from patients with each rs1143679 genotype. We observed that transcript levels significantly decreased for the risk allele ({\textquoteright}A{\textquoteright}) relative to the non-risk allele ({\textquoteright}G{\textquoteright}), in a dose-dependent fashion: ({\textquoteright}AA{\textquoteright} \< {\textquoteright}AG{\textquoteright} \< {\textquoteright}GG{\textquoteright}). CD11b protein levels in patients{\textquoteright} monocytes were directly correlated with RNA levels. Strikingly, heterozygous individuals express much lower (average 10- to 15-fold reduction) amounts of the {\textquoteright}A{\textquoteright} transcript than {\textquoteright}G{\textquoteright} transcript. We found that the non-risk sequence surrounding rs1143679 exhibits transcriptional enhancer activity in vivo and binds to Ku70/80, NFKB1 and EBF1 in vitro, functions that are significantly reduced with the risk allele. Mutant CD11b protein shows significantly reduced binding to fibrinogen and vitronectin, relative to non-risk, both in purified protein and in cellular models. This two-pronged contribution (nucleic acid- and protein-level) of the rs1143679 risk allele to decreasing ITGAM activity provides insight into the molecular mechanisms of its potent association with SLE.

}, issn = {1460-2083}, doi = {10.1093/hmg/ddu106}, author = {Maiti, Amit K and Kim-Howard, Xana and Motghare, Prasenjeet and Pradhan, Vandana and Chua, Kek Heng and Sun, Celi and Arango-Guerrero, Mar{\'\i}a Teresa and Ghosh, Kanjaksha and Niewold, Timothy B and Harley, John B and Anaya, Juan-Manual and Looger, Loren L and Nath, Swapan K} } @article {6960, title = {Conditions and constraints for astrocyte calcium signaling in the hippocampal mossy fiber pathway.}, journal = {Neuron}, volume = {82}, year = {2014}, month = {2014 Apr 16}, pages = {413-29}, abstract = {

The spatiotemporal activities of astrocyte Ca(2+) signaling in mature neuronal circuits remain unclear. We used genetically encoded Ca(2+) and glutamate indicators as well as pharmacogenetic and electrical control of neurotransmitter release to explore astrocyte activity in the hippocampal mossy fiber pathway. Our data revealed numerous localized, spontaneous Ca(2+) signals in astrocyte branches and territories, but these were not driven by neuronal activity or glutamate. Moreover, evoked astrocyte Ca(2+) signaling changed linearly with the number of mossy fiber action potentials. Under these settings, astrocyte responses were global, suppressed by neurotransmitter clearance, and mediated by glutamate and GABA. Thus, astrocyte engagement in the fully developed mossy fiber pathway was slow and territorial, contrary to that frequently proposed for astrocytes within microcircuits. We show that astrocyte Ca(2+) signaling functionally segregates large volumes of neuropil and that these transients are not suited for responding to, or regulating, single synapses in the mossy fiber pathway.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2014.02.041}, author = {Haustein, Martin D and Kracun, Sebastian and Lu, Xiao-Hong and Shih, Tiffany and Jackson-Weaver, Olan and Tong, Xiaoping and Xu, Ji and Yang, X William and O{\textquoteright}Dell, Thomas J and Marvin, Jonathan S and Ellisman, Mark H and Bushong, Eric A and Looger, Loren L and Khakh, Baljit S.} } @article {6711, title = {Correlative super-resolution fluorescence and metal-replica transmission electron microscopy.}, journal = {Nature Methods}, volume = {11}, year = {2014}, month = {2014 Jan 26}, pages = {305-8}, abstract = {

We combine super-resolution localization fluorescence microscopy with transmission electron microscopy of metal replicas to locate proteins on the landscape of the cellular plasma membrane at the nanoscale. We validate robust correlation on the scale of 20 nm by imaging endogenous clathrin (in two and three dimensions) and apply the method to find the previously unknown three-dimensional position of the endocytic protein epsin on clathrin-coated structures at the plasma membrane.

}, issn = {1548-7105}, doi = {10.1038/nmeth.2816}, author = {Sochacki, Kem A and Shtengel, Gleb and Van Engelenburg, Schuyler B and Hess, Harald F and Taraska, Justin W} } @article {68450, title = {Cytoplasmic tyrosine phosphatase Shp2 coordinates hepatic regulation of bile acid and FGF15/19 signaling to repress bile acid synthesis.}, journal = {Cell Metab}, volume = {20}, year = {2014}, month = {08/2014}, pages = {320-32}, abstract = {

Bile acid (BA) biosynthesis is tightly controlled by intrahepatic negative feedback signaling elicited by BA binding to farnesoid X receptor (FXR) and also by enterohepatic communication involving ileal BA reabsorption and FGF15/19 secretion. However, how these pathways are coordinated is poorly understood. We show here that nonreceptor tyrosine phosphatase Shp2 is a critical player that couples and regulates the intrahepatic and enterohepatic signals for repression of BA synthesis. Ablating Shp2 in hepatocytes suppressed signal relay from FGFR4, receptor for FGF15/19, and attenuated BA activation of FXR signaling, resulting in elevation of systemic BA levels and chronic hepatobiliary disorders in mice. Acting immediately downstream of FGFR4, Shp2 associates with FRS2α and promotes the receptor activation and signal relay to several pathways. These results elucidate a molecular mechanism for the control of BA homeostasis by Shp2 through the orchestration of multiple signals in hepatocytes.

}, keywords = {Animals, Bile Acids and Salts, Bile Ducts, Cell Line, Cholesterol 7-alpha-Hydroxylase, Fibroblast Growth Factors, Liver, Membrane Proteins, Mice, Mice, Knockout, Protein Tyrosine Phosphatase, Non-Receptor Type 11, Receptor, Fibroblast Growth Factor, Type 4, Signal Transduction, Up-Regulation}, issn = {1932-7420}, doi = {10.1016/j.cmet.2014.05.020}, author = {Li, Shuangwei and Hsu, Diane D F and Li, Bing and Luo, Xiaolin and Alderson, Nazilla and Qiao, Liping and Ma, Lina and Zhu, Helen H and He, Zhao and Suino-Powell, Kelly and Ji, Kaihong and Li, Jiefu and Shao, Jianhua and Xu, H Eric and Li, Tiangang and Feng, Gen-Sheng} } @article {45419, title = {Development of the annelid axochord: insights into notochord evolution.}, journal = {Science}, volume = {345}, year = {2014}, month = {2014 Sep 12}, pages = {1365-8}, abstract = {

The origin of chordates has been debated for more than a century, with one key issue being the emergence of the notochord. In vertebrates, the notochord develops by convergence and extension of the chordamesoderm, a population of midline cells of unique molecular identity. We identify a population of mesodermal cells in a developing invertebrate, the marine annelid Platynereis dumerilii, that converges and extends toward the midline and expresses a notochord-specific combination of genes. These cells differentiate into a longitudinal muscle, the axochord, that is positioned between central nervous system and axial blood vessel and secretes a strong collagenous extracellular matrix. Ancestral state reconstruction suggests that contractile mesodermal midline cells existed in bilaterian ancestors. We propose that these cells, via vacuolization and stiffening, gave rise to the chordate notochord.

}, issn = {1095-9203}, doi = {10.1126/science.1253396}, author = {Lauri, Antonella and Brunet, Thibaut and Handberg-Thorsager, Mette and Fischer, Antje H L and Simakov, Oleg and Steinmetz, Patrick R H and Tomer, Raju and Keller, Philipp J and Arendt, Detlev} } @article {45779, title = {Distinct substrate selectivity of a metabolic hydrolase from Mycobacterium tuberculosis.}, journal = {Biochemistry}, volume = {53}, year = {2014}, month = {2014 Oct 29}, pages = {7386-95}, abstract = {

The transition between dormant and active Mycobacterium tuberculosis infection requires reorganization of its lipid metabolism and activation of a battery of serine hydrolase enzymes. Among these serine hydrolases, Rv0045c is a mycobacterial-specific serine hydrolase with limited sequence homology outside mycobacteria but structural homology to divergent bacterial hydrolase families. Herein, we determined the global substrate specificity of Rv0045c against a library of fluorogenic hydrolase substrates, constructed a combined experimental and computational model for its binding pocket, and performed comprehensive substitutional analysis to develop a structural map of its binding pocket. Rv0045c showed strong substrate selectivity toward short, straight chain alkyl esters with the highest activity toward four atom chains. This strong substrate preference was maintained through the combined action of residues in a flexible loop connecting the cap and α/β hydrolase domains and in residues close to the catalytic triad. Two residues bracketing the substrate-binding pocket (Gly90 and His187) were essential to maintaining the narrow substrate selectivity of Rv0045c toward various acyl ester substituents, as independent conversion of these residues significantly increased its catalytic activity and broadened its substrate specificity. Focused saturation mutagenesis of position 187 implicated this residue, as the differentiation point between the substrate specificity of Rv0045c and the structurally homologous ybfF hydrolase family. Insertion of the analogous tyrosine residue from ybfF hydrolases into Rv0045c increased the catalytic activity of Rv0045 by over 20-fold toward diverse ester substrates. The unique binding pocket structure and selectivity of Rv0045c provide molecular indications of its biological role and evidence for expanded substrate diversity in serine hydrolases from M. tuberculosis.

}, issn = {1520-4995}, doi = {10.1021/bi501108u}, author = {Lukowski, Jessica K and Savas, Christopher P and Gehring, Alexandra M and McKary, Magy G and Adkins, Chinessa T and Lavis, Luke D and Hoops, Geoffrey C and Johnson, R Jeremy} } @article {6710, title = {Distribution of ESCRT machinery at HIV assembly sites reveals virus scaffolding of ESCRT subunits.}, journal = {Science}, volume = {343}, year = {2014}, month = {2014 Jan 16}, pages = {653-6}, abstract = {

The human immunodeficiency virus (HIV) hijacks the endosomal sorting complexes required for transport (ESCRT) to mediate virus release from infected cells. The nanoscale organization of ESCRT machinery necessary for mediating viral abscission is unclear. Here, we applied three-dimensional superresolution microscopy and correlative electron microscopy to delineate the organization of ESCRT components at HIV assembly sites. We observed ESCRT subunits localized within the head of budding virions and released particles, with head-localized levels of CHMP2A decreasing relative to Tsg101 and CHMP4B upon virus abscission. Thus, the driving force for HIV release may derive from initial scaffolding of ESCRT subunits within the viral bud interior followed by plasma membrane association and selective remodeling of ESCRT subunits.

}, issn = {1095-9203}, doi = {10.1126/science.1247786}, author = {Van Engelenburg, Schuyler B and Shtengel, Gleb and Sengupta, Prabuddha and Waki, Kayoko and Jarnik, Michal and Ablan, Sherimay D and Freed, Eric O and Hess, Harald F and Lippincott-Schwartz, Jennifer} } @article {47631, title = {Distribution of ESCRT machinery at HIV assembly sites reveals virus scaffolding of ESCRT subunits.}, journal = {Science (New York, N.Y.)}, volume = {343}, year = {2014}, month = {2014 Feb 7}, pages = {653-6}, abstract = {

The human immunodeficiency virus (HIV) hijacks the endosomal sorting complexes required for transport (ESCRT) to mediate virus release from infected cells. The nanoscale organization of ESCRT machinery necessary for mediating viral abscission is unclear. Here, we applied three-dimensional superresolution microscopy and correlative electron microscopy to delineate the organization of ESCRT components at HIV assembly sites. We observed ESCRT subunits localized within the head of budding virions and released particles, with head-localized levels of CHMP2A decreasing relative to Tsg101 and CHMP4B upon virus abscission. Thus, the driving force for HIV release may derive from initial scaffolding of ESCRT subunits within the viral bud interior followed by plasma membrane association and selective remodeling of ESCRT subunits.

}, keywords = {Endosomal Sorting Complexes Required for Transport, gag Gene Products, Human Immunodeficiency Virus, HIV Infections, HIV-1, Humans, Imaging, Three-Dimensional, Microscopy, Protein Subunits, Virion, Virus Assembly, Virus Release}, issn = {1095-9203}, doi = {10.1126/science.1247786}, author = {Van Engelenburg, Schuyler B and Shtengel, Gleb and Sengupta, Prabuddha and Waki, Kayoko and Jarnik, Michal and Ablan, Sherimay D and Freed, Eric O and Hess, Harald F and Lippincott-Schwartz, Jennifer} } @article {45842, title = {The Drosophila surface glia transcriptome: evolutionary conserved blood-brain barrier processes.}, journal = {Frontiers in Neuroscience}, volume = {8}, year = {2014}, month = {2014 Nov 7}, pages = {346}, abstract = {

Central nervous system (CNS) function is dependent on the stringent regulation of metabolites, drugs, cells, and pathogens exposed to the CNS space. Cellular blood-brain barrier (BBB) structures are highly specific checkpoints governing entry and exit of all small molecules to and from the brain interstitial space, but the precise mechanisms that regulate the BBB are not well understood. In addition, the BBB has long been a challenging obstacle to the pharmacologic treatment of CNS diseases; thus model systems that can parse the functions of the BBB are highly desirable. In this study, we sought to define the transcriptome of the adult Drosophila melanogaster BBB by isolating the BBB surface glia with fluorescence activated cell sorting (FACS) and profiling their gene expression with microarrays. By comparing the transcriptome of these surface glia to that of all brain glia, brain neurons, and whole brains, we present a catalog of transcripts that are selectively enriched at the Drosophila BBB. We found that the fly surface glia show high expression of many ATP-binding cassette (ABC) and solute carrier (SLC) transporters, cell adhesion molecules, metabolic enzymes, signaling molecules, and components of xenobiotic metabolism pathways. Using gene sequence-based alignments, we compare the Drosophila and Murine BBB transcriptomes and discover many shared chemoprotective and small molecule control pathways, thus affirming the relevance of invertebrate models for studying evolutionary conserved BBB properties. The Drosophila BBB transcriptome is valuable to vertebrate and insect biologists alike as a resource for studying proteins underlying diffusion barrier development and maintenance, glial biology, and regulation of drug transport at tissue barriers.

}, issn = {1662-4548}, doi = {10.3389/fnins.2014.00346}, author = {DeSalvo, Michael K and Hindle, Samantha J and Rusan, Zeid M and Orng, Souvinh and Eddison, Mark and Halliwill, Kyle and Bainton, Roland J} } @article {46595, title = {EGFR and FGFR pathways have distinct roles in Drosophila mushroom body development and ethanol-induced behavior.}, journal = {PLoS One}, volume = {9}, year = {2014}, month = {2014 Jan 31}, pages = {e87714}, abstract = {

Epidermal Growth Factor Receptor (EGFR) signaling has a conserved role in ethanol-induced behavior in flies and mice, affecting ethanol-induced sedation in both species. However it is not known what other effects EGFR signaling may have on ethanol-induced behavior, or what roles other Receptor Tyrosine Kinase (RTK) pathways may play in ethanol induced behaviors. We examined the effects of both the EGFR and Fibroblast Growth Factor Receptor (FGFR) RTK signaling pathways on ethanol-induced enhancement of locomotion, a behavior distinct from sedation that may be associated with the rewarding effects of ethanol. We find that both EGFR and FGFR genes influence ethanol-induced locomotion, though their effects are opposite - EGFR signaling suppresses this behavior, while FGFR signaling promotes it. EGFR signaling affects development of the Drosophila mushroom bodies in conjunction with the JNK MAP kinase basket (bsk), and with the Ste20 kinase tao, and we hypothesize that the EGFR pathway affects ethanol-induced locomotion through its effects on neuronal development. We find, however, that FGFR signaling most likely affects ethanol-induced behavior through a different mechanism, possibly through acute action in adult neurons.

}, keywords = {Animals, Behavior, Animal, Central Nervous System Depressants, Drosophila melanogaster, Drosophila Proteins, Ethanol, Locomotion, Mice, Mushroom Bodies, Receptor, Epidermal Growth Factor, Receptors, Invertebrate Peptide, Signal Transduction}, issn = {1932-6203}, doi = {10.1371/journal.pone.0087714}, author = {King, Ian F G and Eddison, Mark and Kaun, Karla R and Heberlein, Ulrike} } @article {47626, title = {ER stress-induced clearance of misfolded GPI-anchored proteins via the secretory pathway.}, journal = {Cell}, volume = {158}, year = {2014}, month = {2014 Jul 31}, pages = {522-33}, abstract = {

Proteins destined for the cell surface are first assessed in the endoplasmic reticulum (ER) for proper folding before release into the secretory pathway. This ensures that defective proteins are normally prevented from entering the extracellular environment, where they could be disruptive. Here, we report that, when ER folding capacity is saturated during stress, misfolded glycosylphosphatidylinositol-anchored proteins dissociate from resident ER chaperones, engage export receptors, and quantitatively leave the ER via vesicular transport to the Golgi. Clearance from the ER commences within minutes of acute ER stress, before the transcriptional component of the unfolded protein response is activated. These aberrant proteins then access the cell surface transiently before destruction in lysosomes. Inhibiting this stress-induced pathway by depleting the ER-export receptors leads to aggregation of the ER-retained misfolded protein. Thus, this rapid response alleviates the elevated burden of misfolded proteins in the ER at the onset of ER stress, promoting protein homeostasis in the ER.

}, keywords = {Animals, Cell Line, Endoplasmic Reticulum Stress, Humans, Lysosomes, Mice, Prions, Protein Folding, Rats, Secretory Pathway, Unfolded Protein Response}, issn = {1097-4172}, doi = {10.1016/j.cell.2014.06.026}, author = {Satpute-Krishnan, Prasanna and Ajinkya, Monica and Bhat, Savithri and Itakura, Eisuke and Hegde, Ramanujan S and Lippincott-Schwartz, Jennifer} } @article {6879, title = {Flow of cortical activity underlying a tactile decision in mice.}, journal = {Neuron}, volume = {81}, year = {2014}, month = {2014 Jan 8}, pages = {179-94}, abstract = {

Perceptual decisions involve distributed cortical activity. Does information flow sequentially from one cortical area to another, or do networks of interconnected areas contribute at the same time? Here we delineate when and how activity in specific areas drives a whisker-based decision in mice. A short-term memory component temporally separated tactile "sensation" and "action" (licking). Using optogenetic inhibition (spatial resolution, 2 mm; temporal resolution, 100 ms), we surveyed the neocortex for regions driving behavior during specific behavioral epochs. Barrel cortex was critical for sensation. During the short-term memory, unilateral inhibition of anterior lateral motor cortex biased responses to the ipsilateral side. Consistently, barrel cortex showed stimulus-specific activity during sensation, whereas motor cortex showed choice-specific preparatory activity and movement-related activity, consistent with roles in motor planning and movement. These results suggest serial information flow from sensory to motor areas during perceptual decision making.

}, keywords = {Action Potentials, Afferent Pathways, Animals, Cerebral Cortex, Conditioning, Decision Making, Discrimination (Psychology), Female, Green Fluorescent Proteins, Male, Mice, Motion Perception, Nerve Net, Neurons, Operant, Photic Stimulation, Rhodopsin, Touch, Transgenic, Vesicular Inhibitory Amino Acid Transport Proteins, Vibrissae}, issn = {1097-4199}, doi = {10.1016/j.neuron.2013.10.020}, author = {Guo, Zengcai V and Li, Nuo and Huber, Daniel and Ophir, Eran and Gutnisky, Diego and Ting, Jonathan T and Feng, Guoping and Svoboda, Karel} } @article {45059, title = {FlyMAD: rapid thermogenetic control of neuronal activity in freely walking Drosophila.}, journal = {Nature Methods}, volume = {11}, year = {2014}, month = {2014 Jul 11}, pages = {756-62}, abstract = {

Rapidly and selectively modulating the activity of defined neurons in unrestrained animals is a powerful approach in investigating the circuit mechanisms that shape behavior. In Drosophila melanogaster, temperature-sensitive silencers and activators are widely used to control the activities of genetically defined neuronal cell types. A limitation of these thermogenetic approaches, however, has been their poor temporal resolution. Here we introduce FlyMAD (the fly mind-altering device), which allows thermogenetic silencing or activation within seconds or even fractions of a second. Using computer vision, FlyMAD targets an infrared laser to freely walking flies. As a proof of principle, we demonstrated the rapid silencing and activation of neurons involved in locomotion, vision and courtship. The spatial resolution of the focused beam enabled preferential targeting of neurons in the brain or ventral nerve cord. Moreover, the high temporal resolution of FlyMAD allowed us to discover distinct timing relationships for two neuronal cell types previously linked to courtship song.

}, issn = {1548-7105}, doi = {10.1038/nmeth.2973}, author = {Bath, Daniel E and Stowers, John R and H{\"o}rmann, Dorothea and Poehlmann, Andreas and Dickson, Barry J and Straw, Andrew D} } @article {45637, title = {High thermodynamic stability of parametrically designed helical bundles.}, journal = {Science}, volume = {346}, year = {2014}, month = {2014 Oct 24}, pages = {481-5}, abstract = {

We describe a procedure for designing proteins with backbones produced by varying the parameters in the Crick coiled coil-generating equations. Combinatorial design calculations identify low-energy sequences for alternative helix supercoil arrangements, and the helices in the lowest-energy arrangements are connected by loop building. We design an antiparallel monomeric untwisted three-helix bundle with 80-residue helices, an antiparallel monomeric right-handed four-helix bundle, and a pentameric parallel left-handed five-helix bundle. The designed proteins are extremely stable (extrapolated ΔGfold \> 60 kilocalories per mole), and their crystal structures are close to those of the design models with nearly identical core packing between the helices. The approach enables the custom design of hyperstable proteins with fine-tuned geometries for a wide range of applications.

}, issn = {1095-9203}, doi = {10.1126/science.1257481}, author = {Huang, Po-Ssu and Oberdorfer, Gustav and Xu, Chunfu and Pei, Xue Y and Nannenga, Brent L and Rogers, Joseph M and DiMaio, Frank and Gonen, Tamir and Luisi, Ben and Baker, David} } @article {47897, title = {A high-resolution spatiotemporal atlas of gene expression of the developing mouse brain.}, journal = {Neuron}, volume = {83}, year = {2014}, month = {2014 Jul 16}, pages = {309-23}, abstract = {

To provide a temporal framework for the genoarchitecture of brain development, we generated in situ hybridization data for embryonic and postnatal mouse brain at seven developmental stages for \~{}2,100 genes, which were processed with an automated informatics pipeline and manually annotated. This resource comprises 434,946 images, seven reference atlases, an ontogenetic ontology, and tools to explore coexpression of genes across neurodevelopment. Gene sets coinciding with developmental phenomena were identified. A temporal shift in the principles governing the molecular organization of the brain was detected, with transient neuromeric, plate-based organization of the brain present at E11.5 and E13.5. Finally, these data provided a transcription factor code that discriminates brain structures and identifies the developmental age of a tissue, providing a foundation for eventual genetic manipulation or tracking of specific brain structures over development. The resource is available as the Allen Developing Mouse Brain Atlas (http://developingmouse.brain-map.org).

}, keywords = {Animals, Brain, Brain Mapping, Gene Expression, Gene Expression Profiling, Gene Expression Regulation, Developmental, Mice}, issn = {1097-4199}, doi = {10.1016/j.neuron.2014.05.033}, author = {Thompson, Carol L and Ng, Lydia and Menon, Vilas and Martinez, Salvador and Lee, Chang-Kyu and Glattfelder, Katie and Sunkin, Susan M and Henry, Alex and Lau, Christopher and Dang, Chinh and Garcia-Lopez, Raquel and Martinez-Ferre, Almudena and Pombero, Ana and Rubenstein, John L R and Wakeman, Wayne B and Hohmann, John and Dee, Nick and Sodt, Andrew J and Young, Rob and Smith, Kimberly and Nguyen, Thuc-Nghi and Kidney, Jolene and Kuan, Leonard and Jeromin, Andreas and Kaykas, Ajamete and Miller, Jeremy and Page, Damon and Orta, Geri and Bernard, Amy and Riley, Zackery and Smith, Simon and Wohnoutka, Paul and Hawrylycz, Michael J and Puelles, Luis and Jones, Allan R} } @article {46231, title = {Identifying synapses using deep and wide multiscale recursive networks.}, journal = {arXiv}, year = {2014}, month = {2014 Sep 5}, pages = {arXiv:1409.1789 [cs.CV]}, abstract = {

In this work, we propose a learning framework for identifying synapses using a deep and wide multi-scale recursive (DAWMR) network, previously considered in image segmentation applications. We apply this approach on electron microscopy data from invertebrate fly brain tissue. By learning features directly from the data, we are able to achieve considerable improvements over existing techniques that rely on a small set of hand-designed features. We show that this system can reduce the amount of manual annotation required, in both acquisition of training data as well as verification of inferred detections.

}, url = {http://arxiv.org/abs/1409.1789}, author = {Huang, Gary and Plaza, Stephen M} } @article {45032, title = {Imaging ATUM ultrathin section libraries with WaferMapper: a multi-scale approach to EM reconstruction of neural circuits.}, journal = {Frontiers in Neural Circuits}, volume = {8}, year = {2014}, month = {2014 Jun 27}, pages = {68}, abstract = {

The automated tape-collecting ultramicrotome (ATUM) makes it possible to collect large numbers of ultrathin sections quickly-the equivalent of a petabyte of high resolution images each day. However, even high throughput image acquisition strategies generate images far more slowly (at present ~1 terabyte per day). We therefore developed WaferMapper, a software package that takes a multi-resolution approach to mapping and imaging select regions within a library of ultrathin sections. This automated method selects and directs imaging of corresponding regions within each section of an ultrathin section library (UTSL) that may contain many thousands of sections. Using WaferMapper, it is possible to map thousands of tissue sections at low resolution and target multiple points of interest for high resolution imaging based on anatomical landmarks. The program can also be used to expand previously imaged regions, acquire data under different imaging conditions, or re-image after additional tissue treatments.

}, issn = {1662-5110}, doi = {10.3389/fncir.2014.00068}, author = {Hayworth, Kenneth J and Morgan, Josh L and Schalek, Richard and Berger, Daniel R and Hildebrand, David G C and Lichtman, Jeff W} } @article {45060, title = {Imaging cellular ultrastructure by PALM, iPALM, and correlative iPALM-EM.}, journal = {Methods in Cell Biology}, volume = {123}, year = {2014}, month = {2014}, pages = {273-94}, abstract = {

Many biomolecules in cells can be visualized with high sensitivity and specificity by fluorescence microscopy. However, the resolution of conventional light microscopy is limited by diffraction to ~200-250nm laterally and \>500nm axially. Here, we describe superresolution methods based on single-molecule localization analysis of photoswitchable fluorophores (PALM: photoactivated localization microscopy) as well as our recent three-dimensional (3D) method (iPALM: interferometric PALM) that allows imaging with a resolution better than 20nm in all three dimensions. Considerations for their implementations, applications to multicolor imaging, and a recent development that extend the imaging depth of iPALM to ~750nm are discussed. As the spatial resolution of superresolution fluorescence microscopy converges with that of electron microscopy (EM), direct imaging of the same specimen using both approaches becomes feasible. This could be particularly useful for cross validation of experiments, and thus, we also describe recent methods that were developed for correlative superresolution fluorescence and EM.

}, issn = {0091-679X}, doi = {10.1016/B978-0-12-420138-5.00015-X}, author = {Shtengel, Gleb and Wang, Yilin and Zhang, Zhen and Goh, Wah Ing and Hess, Harald F and Kanchanawong, Pakorn} } @article {45166, title = {Imaging the fate of histone Cse4 reveals de novo replacement in S phase and subsequent stable residence at centromeres.}, journal = {eLife}, volume = {3}, year = {2014}, month = {2014 May 20}, pages = {e02203}, abstract = {

The budding yeast centromere contains Cse4, a specialized histone H3 variant. Fluorescence pulse-chase analysis of an internally tagged Cse4 reveals that it is replaced with newly synthesized molecules in S phase, remaining stably associated with centromeres thereafter. In contrast, C-terminally-tagged Cse4 is functionally impaired, showing slow cell growth, cell lethality at elevated temperatures, and extra-centromeric nuclear accumulation. Recent studies using such strains gave conflicting findings regarding the centromeric abundance and cell cycle dynamics of Cse4. Our findings indicate that internally tagged Cse4 is a better reporter of the biology of this histone variant. Furthermore, the size of centromeric Cse4 clusters was precisely mapped with a new 3D-PALM method, revealing substantial compaction during anaphase. Cse4-specific chaperone Scm3 displays steady-state, stoichiometric co-localization with Cse4 at centromeres throughout the cell cycle, while undergoing exchange with a nuclear pool. These findings suggest that a stable Cse4 nucleosome is maintained by dynamic chaperone-in-residence Scm3.DOI: http://dx.doi.org/10.7554/eLife.02203.001.

}, issn = {2050-084X}, doi = {10.7554/eLife.02203}, author = {Wisniewski, Jan and Hajj, Bassam and Chen, Jiji and Mizuguchi, Gaku and Xiao, Hua and Wei, Debbie and Dahan, Maxime and Wu, Carl} } @article {47898, title = {Improving reliability and absolute quantification of human brain microarray data by filtering and scaling probes using RNA-Seq.}, journal = {BMC genomics}, volume = {15}, year = {2014}, month = {2014}, pages = {154}, abstract = {

BACKGROUND: High-throughput sequencing is gradually replacing microarrays as the preferred method for studying mRNA expression levels, providing nucleotide resolution and accurately measuring absolute expression levels of almost any transcript, known or novel. However, existing microarray data from clinical, pharmaceutical, and academic settings represent valuable and often underappreciated resources, and methods for assessing and improving the quality of these data are lacking.

RESULTS: To quantitatively assess the quality of microarray probes, we directly compare RNA-Seq to Agilent microarrays by processing 231 unique samples from the Allen Human Brain Atlas using RNA-Seq. Both techniques provide highly consistent, highly reproducible gene expression measurements in adult human brain, with RNA-Seq slightly outperforming microarray results overall. We show that RNA-Seq can be used as ground truth to assess the reliability of most microarray probes, remove probes with off-target effects, and scale probe intensities to match the expression levels identified by RNA-Seq. These sequencing scaled microarray intensities (SSMIs) provide more reliable, quantitative estimates of absolute expression levels for many genes when compared with unscaled intensities. Finally, we validate this result in two human cell lines, showing that linear scaling factors can be applied across experiments using the same microarray platform.

CONCLUSIONS: Microarrays provide consistent, reproducible gene expression measurements, which are improved using RNA-Seq as ground truth. We expect that our strategy could be used to improve probe quality for many data sets from major existing repositories.

}, keywords = {Brain, Cluster Analysis, Computational Biology, Gene Expression, Gene Expression Profiling, High-Throughput Nucleotide Sequencing, Humans, Neocortex, Oligonucleotide Array Sequence Analysis, Reproducibility of Results, Sequence Analysis, RNA, Transcriptome}, issn = {1471-2164}, doi = {10.1186/1471-2164-15-154}, author = {Miller, Jeremy A and Menon, Vilas and Goldy, Jeff and Kaykas, Ajamete and Lee, Chang-Kyu and Smith, Kimberly A and Shen, Elaine H and Phillips, John W and Lein, Ed S and Hawrylycz, Mike J} } @article {45371, title = {Integrated action of pheromone signals in promoting courtship behavior in male mice.}, journal = {eLife}, volume = {3}, year = {2014}, month = {2014 Jul 29}, pages = {e03025}, abstract = {

The mammalian vomeronasal organ encodes pheromone information about gender, reproductive status, genetic background and individual differences. It remains unknown how pheromone information interacts to trigger innate behaviors. In this study, we identify vomeronasal receptors responsible for detecting female pheromones. A sub-group of V1re clade members recognizes gender-identifying cues in female urine. Multiple members of the V1rj clade are cognate receptors for urinary estrus signals, as well as for sulfated estrogen (SE) compounds. In both cases, the same cue activates multiple homologous receptors, suggesting redundancy in encoding female pheromone cues. Neither gender-specific cues nor SEs alone are sufficient to promote courtship behavior in male mice, whereas robust courtship behavior can be induced when the two cues are applied together. Thus, integrated action of different female cues is required in pheromone-triggered mating behavior. These results suggest a gating mechanism in the vomeronasal circuit in promoting specific innate behavior.DOI: http://dx.doi.org/10.7554/eLife.03025.001.

}, issn = {2050-084X}, doi = {10.7554/eLife.03025}, author = {Haga-Yamanaka, Sachiko and Ma, Limei and He, Jie and Qiu, Qiang and Lavis, Luke D and Looger, Loren L and Yu, C Ron} } @article {49004, title = {Interference and shaping in sensorimotor adaptations with rewards.}, journal = {PLoS Computational B2014-01-09iology}, volume = {10}, year = {2014}, month = {2014 Jan}, pages = {e1003377}, abstract = {

When a perturbation is applied in a sensorimotor transformation task, subjects can adapt and maintain performance by either relying on sensory feedback, or, in the absence of such feedback, on information provided by rewards. For example, in a classical rotation task where movement endpoints must be rotated to reach a fixed target, human subjects can successfully adapt their reaching movements solely on the basis of binary rewards, although this proves much more difficult than with visual feedback. Here, we investigate such a reward-driven sensorimotor adaptation process in a minimal computational model of the task. The key assumption of the model is that synaptic plasticity is gated by the reward. We study how the learning dynamics depend on the target size, the movement variability, the rotation angle and the number of targets. We show that when the movement is perturbed for multiple targets, the adaptation process for the different targets can interfere destructively or constructively depending on the similarities between the sensory stimuli (the targets) and the overlap in their neuronal representations. Destructive interferences can result in a drastic slowdown of the adaptation. As a result of interference, the time to adapt varies non-linearly with the number of targets. Our analysis shows that these interferences are weaker if the reward varies smoothly with the subject{\textquoteright}s performance instead of being binary. We demonstrate how shaping the reward or shaping the task can accelerate the adaptation dramatically by reducing the destructive interferences. We argue that experimentally investigating the dynamics of reward-driven sensorimotor adaptation for more than one sensory stimulus can shed light on the underlying learning rules.

}, keywords = {Adaptation, Physiological, Algorithms, Biomechanical Phenomena, Brain, Computational Biology, Computer Simulation, Feedback, Sensory, Humans, Learning, Models, Neurological, Movement, Neuronal Plasticity, Neurons, Psychomotor Performance, Reproducibility of Results, Reward, Rotation, Synapses}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1003377}, author = {Darshan, Ran and Leblois, Arthur and Hansel, David} } @article {45720, title = {Internal models direct dragonfly interception steering.}, journal = {Nature}, year = {2014}, month = {2014 Dec 10}, abstract = {

Sensorimotor control in vertebrates relies on internal models. When extending an arm to reach for an object, the brain uses predictive models of both limb dynamics and target properties. Whether invertebrates use such models remains unclear. Here we examine to what extent prey interception by dragonflies (Plathemis lydia), a behaviour analogous to targeted reaching, requires internal models. By simultaneously tracking the position and orientation of a dragonfly{\textquoteright}s head and body during flight, we provide evidence that interception steering is driven by forward and inverse models of dragonfly body dynamics and by models of prey motion. Predictive rotations of the dragonfly{\textquoteright}s head continuously track the prey{\textquoteright}s angular position. The head-body angles established by prey tracking appear to guide systematic rotations of the dragonfly{\textquoteright}s body to align it with the prey{\textquoteright}s flight path. Model-driven control thus underlies the bulk of interception steering manoeuvres, while vision is used for reactions to unexpected prey movements. These findings illuminate the computational sophistication with which insects construct behaviour.

}, issn = {1476-4687}, doi = {10.1038/nature14045}, author = {Mischiati, Matteo and Lin, Huai-Ti and Herold, Paul and Imler, Elliot and Olberg, Robert and Leonardo, Anthony} } @article {45186, title = {Large-scale, high-density (up to 512 channels) recording of local circuits in behaving animals.}, journal = {Journal of Neurophysiology}, volume = {111}, year = {2014}, month = {2014 Mar}, pages = {1132-49}, abstract = {

Monitoring representative fractions of neurons from multiple brain circuits in behaving animals is necessary for understanding neuronal computation. Here, we describe a system that allows high-channel-count recordings from a small volume of neuronal tissue using a lightweight signal multiplexing headstage that permits free behavior of small rodents. The system integrates multishank, high-density recording silicon probes, ultraflexible interconnects, and a miniaturized microdrive. These improvements allowed for simultaneous recordings of local field potentials and unit activity from hundreds of sites without confining free movements of the animal. The advantages of large-scale recordings are illustrated by determining the electroanatomic boundaries of layers and regions in the hippocampus and neocortex and constructing a circuit diagram of functional connections among neurons in real anatomic space. These methods will allow the investigation of circuit operations and behavior-dependent interregional interactions for testing hypotheses of neural networks and brain function.

}, issn = {1522-1598}, doi = {10.1152/jn.00785.2013}, author = {Berenyi, Antal and Somogyv{\'a}ri, Zolt{\'a}n and Nagy, Anett J and Roux, Lisa and Long, John D and Fujisawa, Shigeyoshi and Stark, Eran and Leonardo, Anthony and Harris, Timothy D and Buzs{\'a}ki, Gy{\"o}rgy} } @article {45617, title = {Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution.}, journal = {Science}, volume = {346}, year = {2014}, month = {2014 Oct 24}, pages = {1257998}, abstract = {

Although fluorescence microscopy provides a crucial window into the physiology of living specimens, many biological processes are too fragile, are too small, or occur too rapidly to see clearly with existing tools. We crafted ultrathin light sheets from two-dimensional optical lattices that allowed us to image three-dimensional (3D) dynamics for hundreds of volumes, often at subsecond intervals, at the diffraction limit and beyond. We applied this to systems spanning four orders of magnitude in space and time, including the diffusion of single transcription factor molecules in stem cell spheroids, the dynamic instability of mitotic microtubules, the immunological synapse, neutrophil motility in a 3D matrix, and embryogenesis in Caenorhabditis elegans and Drosophila melanogaster. The results provide a visceral reminder of the beauty and the complexity of living systems.

}, issn = {1095-9203}, doi = {10.1126/science.1257998}, author = {Chen, Bi-Chang and Legant, Wesley R and Wang, Kai and Shao, Lin and Milkie, Daniel E and Davidson, Michael W and Janetopoulos, Chris and Wu, Xufeng S and Hammer, John A and Liu, Zhe and English, Brian P and Mimori-Kiyosue, Yuko and Romero, Daniel P and Ritter, Alex T and Lippincott-Schwartz, Jennifer and Fritz-Laylin, Lillian and Mullins, R Dyche and Mitchell, Diana M and Bembenek, Joshua N and Reymann, Anne-Cecile and B{\"o}hme, Ralph and Grill, Stephan W and Wang, Jennifer T and Seydoux, Geraldine and Tulu, U Serdar and Kiehart, Daniel P and Betzig, Eric} } @article {45841, title = {Leptin mediates the increase in blood pressure associated with obesity.}, journal = {Cell}, volume = {159}, year = {2014}, month = {2014 Dec 4}, pages = {1404-16}, abstract = {

Obesity is associated with increased blood pressure (BP), which in turn increases the risk of cardiovascular diseases. We found that the increase in leptin levels seen in diet-induced obesity (DIO) drives an increase in BP in rodents, an effect that was not seen in animals deficient in leptin or leptin receptors (LepR). Furthermore, humans with loss-of-function mutations in leptin and the LepR have low BP despite severe obesity. Leptin{\textquoteright}s effects on BP are mediated by neuronal circuits in the dorsomedial hypothalamus (DMH), as blocking leptin with a specific antibody, antagonist, or inhibition of the activity of LepR-expressing neurons in the DMH caused a rapid reduction of BP in DIO mice, independent of changes in weight. Re-expression of LepRs in the DMH of DIO LepR-deficient mice caused an increase in BP. These studies demonstrate that leptin couples changes in weight to changes in BP in mammalian species.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2014.10.058}, author = {Simonds, Stephanie E and Pryor, Jack T and Ravussin, Eric and Greenway, Frank L and Dileone, Ralph and Allen, Andrew M and Bassi, Jaspreet and Elmquist, Joel K and Keogh, Julia M and Henning, Elana and Myers, Martin G and Licinio, Julio and Brown, Russell D and Enriori, Pablo J and O{\textquoteright}Rahilly, Stephen and Sternson, Scott M and Grove, Kevin L and Spanswick, David C and Farooqi, I Sadaf and Cowley, Michael A} } @article {47630, title = {LKB1/AMPK and PKA control ABCB11 trafficking and polarization in hepatocytes.}, journal = {PloS one}, volume = {9}, year = {2014}, month = {2014}, pages = {e91921}, abstract = {

Polarization of hepatocytes is manifested by bile canalicular network formation and activation of LKB1 and AMPK, which control cellular energy metabolism. The bile acid, taurocholate, also regulates development of the canalicular network through activation of AMPK. In the present study, we used collagen sandwich hepatocyte cultures from control and liver-specific LKB1 knockout mice to examine the role of LKB1 in trafficking of ABCB11, the canalicular bile acid transporter. In polarized hepatocytes, ABCB11 traffics from Golgi to the apical plasma membrane and endogenously cycles through the rab 11a-myosin Vb recycling endosomal system. LKB1 knockout mice were jaundiced, lost weight and manifested impaired bile canalicular formation and intracellular trafficking of ABCB11, and died within three weeks. Using live cell imaging, fluorescence recovery after photobleaching (FRAP), particle tracking, and biochemistry, we found that LKB1 activity is required for microtubule-dependent trafficking of ABCB11 to the canalicular membrane. In control hepatocytes, ABCB11 trafficking was accelerated by taurocholate and cAMP; however, in LKB1 knockout hepatocytes, ABCB11 trafficking to the apical membrane was greatly reduced and restored only by cAMP, but not taurocholate. cAMP acted through a PKA-mediated pathway which did not activate AMPK. Our studies establish a regulatory role for LKB1 in ABCB11 trafficking to the canalicular membrane, hepatocyte polarization, and canalicular network formation.

}, keywords = {AMP-Activated Protein Kinases, Animals, ATP-Binding Cassette Transporters, Bile Acids and Salts, Cell Membrane, Cell Polarity, Cyclic AMP, Cyclic AMP-Dependent Protein Kinases, Endosomes, Gene Expression Regulation, Golgi Apparatus, Hepatocytes, Mice, Mice, Knockout, Myosin Type V, Primary Cell Culture, Protein Transport, Protein-Serine-Threonine Kinases, rab GTP-Binding Proteins, Signal Transduction, Taurocholic Acid}, issn = {1932-6203}, doi = {10.1371/journal.pone.0091921}, author = {Homolya, L{\'a}szl{\'o} and Fu, Dong and Sengupta, Prabuddha and Jarnik, Michal and Gillet, Jean-Pierre and Vitale-Cross, Lynn and Gutkind, J Silvio and Lippincott-Schwartz, Jennifer and Arias, Irwin M} } @article {45718, title = {Making biology transparent.}, journal = {Nature Biotechnology}, volume = {32}, year = {2014}, month = {2014 Nov 7}, pages = {1104-5}, abstract = {

The molecular and cellular architecture of the organs in a whole mouse is revealed through optical clearing.

}, issn = {1546-1696}, doi = {10.1038/nbt.3061}, author = {H{\"o}ckendorf, Burkhard and Lavis, Luke D and Keller, Philipp J} } @article {6898, title = {Making Drosophila lineage-restricted drivers via patterned recombination in neuroblasts.}, journal = {Nature Neuroscience}, volume = {17}, year = {2014}, month = {2014 Apr}, pages = {631-7}, abstract = {

The Drosophila cerebrum originates from about 100 neuroblasts per hemisphere, with each neuroblast producing a characteristic set of neurons. Neurons from a neuroblast are often so diverse that many neuron types remain unexplored. We developed new genetic tools that target neuroblasts and their diverse descendants, increasing our ability to study fly brain structure and development. Common enhancer-based drivers label neurons on the basis of terminal identities rather than origins, which provides limited labeling in the heterogeneous neuronal lineages. We successfully converted conventional drivers that are temporarily expressed in neuroblasts, into drivers expressed in all subsequent neuroblast progeny. One technique involves immortalizing GAL4 expression in neuroblasts and their descendants. Another depends on loss of the GAL4 repressor, GAL80, from neuroblasts during early neurogenesis. Furthermore, we expanded the diversity of MARCM-based reagents and established another site-specific mitotic recombination system. Our transgenic tools can be combined to map individual neurons in specific lineages of various genotypes.

}, issn = {1546-1726}, doi = {10.1038/nn.3654}, author = {Awasaki, Takeshi and Kao, Chih-Fei and Lee, Ying-Jou and Yang, Ching-Po and Huang, Yaling and Pfeiffer, Barret D and Luan, Haojiang and Jing, Xiaotang and Huang, Yu-Fen and He, Yisheng and Schroeder, Mark David and Kuzin, Alexander and Brody, Thomas and Zugates, Christopher T and Odenwald, Ward F and Lee, Tzumin} } @article {45811, title = {Mushroom body output neurons encode valence and guide memory-based action selection in Drosophila.}, journal = {eLife}, volume = {4}, year = {2014}, month = {12/2014}, abstract = {

Animals discriminate stimuli, learn their predictive value and use this knowledge to modify their behavior. In Drosophila, the mushroom body (MB) plays a key role in these processes. Sensory stimuli are sparsely represented by \~{}2000 Kenyon cells, which converge onto 34 output neurons (MBONs) of 21 types. We studied the role of MBONs in several associative learning tasks and in sleep regulation, revealing the extent to which information flow is segregated into distinct channels and suggesting possible roles for the multi-layered MBON network. We also show that optogenetic activation of MBONs can, depending on cell type, induce repulsion or attraction in flies. The behavioral effects of MBON perturbation are combinatorial, suggesting that the MBON ensemble collectively represents valence. We propose that local, stimulus-specific dopaminergic modulation selectively alters the balance within the MBON network for those stimuli. Our results suggest that valence encoded by the MBON ensemble biases memory-based action selection.

}, issn = {2050-084X}, doi = {10.7554/eLife.04580}, author = {Aso, Yoshinori and Sitaraman, Divya and Ichinose, Toshiharu and Kaun, Karla R and Vogt, Katrin and Belliart-Gu{\'e}rin, Ghislain and Placais, Pierre-Yves and Robie, Alice A and Yamagata, Nobuhiro and Schnaitmann, Christopher and Rowell, William J and Johnston, Rebecca M and Ngo, Teri-T B and Chen, Nan and Korff, Wyatt and Nitabach, Michael N and Heberlein, Ulrike and Preat, Thomas and Branson, Kristin M and Tanimoto, Hiromu and Rubin, Gerald M} } @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 {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 {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 {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 {45698, title = {Oscillatory activity in the medial prefrontal cortex and nucleus accumbens correlates with impulsivity and reward outcome.}, journal = {PLoS One}, volume = {9}, year = {2014}, month = {2014 Oct 21}, pages = {e111300}, abstract = {

Actions expressed prematurely without regard for their consequences are considered impulsive. Such behaviour is governed by a network of brain regions including the prefrontal cortex (PFC) and nucleus accumbens (NAcb) and is prevalent in disorders including attention deficit hyperactivity disorder (ADHD) and drug addiction. However, little is known of the relationship between neural activity in these regions and specific forms of impulsive behaviour. In the present study we investigated local field potential (LFP) oscillations in distinct sub-regions of the PFC and NAcb on a 5-choice serial reaction time task (5-CSRTT), which measures sustained, spatially-divided visual attention and action restraint. The main findings show that power in gamma frequency (50-60 Hz) LFP oscillations transiently increases in the PFC and NAcb during both the anticipation of a cue signalling the spatial location of a nose-poke response and again following correct responses. Gamma oscillations were coupled to low-frequency delta oscillations in both regions; this coupling strengthened specifically when an error response was made. Theta (7-9 Hz) LFP power in the PFC and NAcb increased during the waiting period and was also related to response outcome. Additionally, both gamma and theta power were significantly affected by upcoming premature responses as rats waited for the visual cue to respond. In a subgroup of rats showing persistently high levels of impulsivity we found that impulsivity was associated with increased error signals following a nose-poke response, as well as reduced signals of previous trial outcome during the waiting period. Collectively, these in-vivo neurophysiological findings further implicate the PFC and NAcb in anticipatory impulsive responses and provide evidence that abnormalities in the encoding of rewarding outcomes may underlie trait-like impulsive behaviour.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0111300}, author = {Donnelly, Nicholas A and Holtzman, Tahl and Rich, P Dylan and Nevado-Holgado, Alejo J and Fernando, Anushka B P and Van Dijck, Gert and Holzhammer, Tobias and Paul, Oliver and Ruther, Patrick and Paulsen, Ole and Robbins, Trevor W and Dalley, Jeffrey W} } @article {6886, title = {Pfam: the protein families database.}, journal = {Nucleic acids research}, volume = {42}, year = {2014}, month = {2014 Jan}, pages = {D222-30}, abstract = {Pfam, available via servers in the UK (http://pfam.sanger.ac.uk/) and the USA (http://pfam.janelia.org/), is a widely used database of protein families, containing 14 831 manually curated entries in the current release, version 27.0. Since the last update article 2 years ago, we have generated 1182 new families and maintained sequence coverage of the UniProt Knowledgebase (UniProtKB) at nearly 80\%, despite a 50\% increase in the size of the underlying sequence database. Since our 2012 article describing Pfam, we have also undertaken a comprehensive review of the features that are provided by Pfam over and above the basic family data. For each feature, we determined the relevance, computational burden, usage statistics and the functionality of the feature in a website context. As a consequence of this review, we have removed some features, enhanced others and developed new ones to meet the changing demands of computational biology. Here, we describe the changes to Pfam content. Notably, we now provide family alignments based on four different representative proteome sequence data sets and a new interactive DNA search interface. We also discuss the mapping between Pfam and known 3D structures.}, keywords = {Databases, DNA, Internet, Intrinsically Disordered Proteins, Protein, Protein Conformation, Proteins, Proteome, Sequence Alignment, Sequence Analysis}, issn = {1362-4962}, doi = {10.1093/nar/gkt1223}, author = {Finn, Robert D and Bateman, Alex and Clements, Jody and Coggill, Penelope and Eberhardt, Ruth Y and Sean R. Eddy and Heger, Andreas and Hetherington, Kirstie and Holm, Liisa and Mistry, Jaina and Sonnhammer, Erik L L and Tate, John and Punta, Marco} } @article {45053, title = {Phase shifts in binaural stimuli provide directional cues for sound localisation in the field cricket Gryllus bimaculatus.}, journal = {Journal of Experimental Biology}, volume = {217}, year = {2014}, month = {2014 Jul 1}, pages = {2390-8}, abstract = {

The cricket{\textquoteright}s auditory system is a highly directional pressure difference receiver whose function is hypothesised to depend on phase relationships between the sound waves propagating through the auditory trachea that connects the left and right hearing organs. We tested this hypothesis by measuring the effect of experimentally constructed phase shifts in acoustic stimuli on phonotactic behavior of Gryllus bimaculatus, the oscillatory response patterns of the tympanic membrane, and the activity of the auditory afferents. The same artificial calling song was played simultaneously at the left and right sides of the cricket, but one sound pattern was shifted in phase by 90 deg (carrier frequencies between 3.6 and 5.4 kHz). All three levels of auditory processing are sensitive to experimentally induced acoustic phase shifts, and the response characteristics are dependent on the carrier frequency of the sound stimulus. At lower frequencies, crickets steered away from the sound leading in phase, while tympanic membrane vibrations and auditory afferent responses were smaller when the ipsilateral sound was leading. In contrast, opposite responses were observed at higher frequencies in all three levels of auditory processing. Minimal responses occurred near the carrier frequency of the cricket{\textquoteright}s calling song, suggesting a stability at this frequency. Our results indicate that crickets may use directional cues arising from phase shifts in acoustic signals for sound localisation, and that the response properties of pressure difference receivers may be analysed with phase-shifted sound stimuli to further our understanding of how insect auditory systems are adapted for directional processing.

}, issn = {1477-9145}, doi = {10.1242/jeb.101402}, author = {Seagraves, Kelly M and Hedwig, Berthold} } @article {6717, title = {Population genomics of the honey bee reveals strong signatures of positive selection on worker traits.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, year = {2014}, month = {2014 Jan 31}, pages = {2614-19}, abstract = {

Most theories used to explain the evolution of eusociality rest upon two key assumptions: mutations affecting the phenotype of sterile workers evolve by positive selection if the resulting traits benefit fertile kin, and that worker traits provide the primary mechanism allowing social insects to adapt to their environment. Despite the common view that positive selection drives phenotypic evolution of workers, we know very little about the prevalence of positive selection acting on the genomes of eusocial insects. We mapped the footprints of positive selection in Apis mellifera through analysis of 40 individual genomes, allowing us to identify thousands of genes and regulatory sequences with signatures of adaptive evolution over multiple timescales. We found Apoidea- and Apis-specific genes to be enriched for signatures of positive selection, indicating that novel genes play a disproportionately large role in adaptive evolution of eusocial insects. Worker-biased proteins have higher signatures of adaptive evolution relative to queen-biased proteins, supporting the view that worker traits are key to adaptation. We also found genes regulating worker division of labor to be enriched for signs of positive selection. Finally, genes associated with worker behavior based on analysis of brain gene expression were highly enriched for adaptive protein and cis-regulatory evolution. Our study highlights the significant contribution of worker phenotypes to adaptive evolution in social insects, and provides a wealth of knowledge on the loci that influence fitness in honey bees.

}, issn = {1091-6490}, doi = {10.1073/pnas.1315506111}, author = {Harpur, Brock A and Kent, Clement F and Molodtsova, Daria and Lebon, Jonathan M D and Alqarni, Abdulaziz S and Owayss, Ayman A and Zayed, Amro} } @article {45336, title = {Population of sensory neurons essential for asthmatic hyperreactivity of inflamed airways.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, year = {2014}, month = {2014 Aug 5}, pages = {11515-20}, abstract = {

Asthma is a common debilitating inflammatory lung disease affecting over 200 million people worldwide. Here, we investigated neurogenic components involved in asthmatic-like attacks using the ovalbumin-sensitized murine model of the disease, and identified a specific population of neurons that are required for airway hyperreactivity. We show that ablating or genetically silencing these neurons abolished the hyperreactive broncho-constrictions, even in the presence of a fully developed lung inflammatory immune response. These neurons are found in the vagal ganglia and are characterized by the expression of the transient receptor potential vanilloid 1 (TRPV1) ion channel. However, the TRPV1 channel itself is not required for the asthmatic-like hyperreactive airway response. We also demonstrate that optogenetic stimulation of this population of TRP-expressing cells with channelrhodopsin dramatically exacerbates airway hyperreactivity of inflamed airways. Notably, these cells express the sphingosine-1-phosphate receptor 3 (S1PR3), and stimulation with a S1PR3 agonist efficiently induced broncho-constrictions, even in the absence of ovalbumin sensitization and inflammation. Our results show that the airway hyperreactivity phenotype can be physiologically dissociated from the immune component, and provide a platform for devising therapeutic approaches to asthma that target these pathways separately.

}, issn = {1091-6490}, doi = {10.1073/pnas.1411032111}, author = {Tr{\"a}nkner, Dimitri and Hahne, Nadeau and Sugino, Ken and Hoon, Mark A and Zuker, Charles} } @inbook {65784, title = {Porphyrins and Metalloporphyrins at Components in Artificial Photosynthesis Research}, booktitle = {Handbook of Porphyrin Science}, volume = {34}, year = {2014}, pages = {196 {\textendash} 233}, publisher = {World Scientific Pulishing}, organization = {World Scientific Pulishing}, isbn = {978-981-4425-10-0}, doi = {10.1142/9789814417297_0016}, author = {Tebo, Alison G. and Herrero, C and Aukauloo, A}, editor = {Kadish, Karl M and Smith, Kevin M and undefined, and Guilard, Roger} } @article {6897, title = {Procedures for behavioral experiments in head-fixed mice.}, journal = {PLoS One}, volume = {9}, year = {2014}, month = {2014}, pages = {e88678}, abstract = {

The mouse is an increasingly prominent model for the analysis of mammalian neuronal circuits. Neural circuits ultimately have to be probed during behaviors that engage the circuits. Linking circuit dynamics to behavior requires precise control of sensory stimuli and measurement of body movements. Head-fixation has been used for behavioral research, particularly in non-human primates, to facilitate precise stimulus control, behavioral monitoring and neural recording. However, choice-based, perceptual decision tasks by head-fixed mice have only recently been introduced. Training mice relies on motivating mice using water restriction. Here we describe procedures for head-fixation, water restriction and behavioral training for head-fixed mice, with a focus on active, whisker-based tactile behaviors. In these experiments mice had restricted access to water (typically 1 ml/day). After ten days of water restriction, body weight stabilized at approximately 80\% of initial weight. At that point mice were trained to discriminate sensory stimuli using operant conditioning. Head-fixed mice reported stimuli by licking in go/no-go tasks and also using a forced choice paradigm using a dual lickport. In some cases mice learned to discriminate sensory stimuli in a few trials within the first behavioral session. Delay epochs lasting a second or more were used to separate sensation (e.g. tactile exploration) and action (i.e. licking). Mice performed a variety of perceptual decision tasks with high performance for hundreds of trials per behavioral session. Up to four months of continuous water restriction showed no adverse health effects. Behavioral performance correlated with the degree of water restriction, supporting the importance of controlling access to water. These behavioral paradigms can be combined with cellular resolution imaging, random access photostimulation, and whole cell recordings.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0088678}, author = {Guo, Zengcai V and Hires, S Andrew and Li, Nuo and O{\textquoteright}Connor, Daniel H and Komiyama, Takaki and Ophir, Eran and Huber, Daniel and Bonardi, Claudia and Morandell, Karin and Gutnisky, Diego and Peron, Simon and Xu, Ning-long and Cox, James and Svoboda, Karel} } @article {6936, title = {Proteome analysis and conditional deletion of the EAAT2 glutamate transporter provide evidence against a role of EAAT2 in pancreatic insulin secretion in mice.}, journal = {The Journal of Biological Chemistry}, volume = {289}, year = {2014}, month = {2014 Jan 17}, pages = {1329-44}, abstract = {

Islet function is incompletely understood in part because key steps in glutamate handling remain undetermined. The glutamate (excitatory amino acid) transporter 2 (EAAT2; Slc1a2) has been hypothesized to (a) provide islet cells with glutamate, (b) protect islet cells against high extracellular glutamate concentrations, (c) mediate glutamate release, or (d) control the pH inside insulin secretory granules. Here we floxed the EAAT2 gene to produce the first conditional EAAT2 knock-out mice. Crossing with Nestin-cyclization recombinase (Cre) eliminated EAAT2 from the brain, resulting in epilepsy and premature death, confirming the importance of EAAT2 for brain function and validating the genetic construction. Crossing with insulin-Cre lines (RIP-Cre and IPF1-Cre) to obtain pancreas-selective deletion did not appear to affect survival, growth, glucose tolerance, or β-cell number. We found (using TaqMan RT-PCR, immunoblotting, immunocytochemistry, and proteome analysis) that the EAAT2 levels were too low to support any of the four hypothesized functions. The proteome analysis detected more than 7,000 islet proteins of which more than 100 were transporters. Although mitochondrial glutamate transporters and transporters for neutral amino acids were present at high levels, all other transporters with known ability to transport glutamate were strikingly absent. Glutamate-metabolizing enzymes were abundant. The level of glutamine synthetase was 2 orders of magnitude higher than that of glutaminase. Taken together this suggests that the uptake of glutamate by islets from the extracellular fluid is insignificant and that glutamate is intracellularly produced. Glutamine synthetase may be more important for islets than assumed previously.

}, keywords = {Animals, Crosses, Excitatory Amino Acid Transporter 2, Gene Deletion, Genetic, Glutamic Acid, Insulin, Insulin-Secreting Cells, Knockout, Mice, Proteome}, issn = {1083-351X}, doi = {10.1074/jbc.M113.529065}, author = {Zhou, Yun and Waanders, Leonie F and Holmseth, Silvia and Guo, Caiying and Berger, Urs V and Li, Yuchuan and Lehre, Anne-Catherine and Lehre, Knut P and Danbolt, Niels C} } @article {45812, title = {Quantum dot-based multiphoton fluorescent pipettes for targeted neuronal electrophysiology.}, journal = {Nature Methods}, volume = {11}, year = {2014}, month = {2014 Dec}, pages = {1237-41}, abstract = {

Targeting visually identified neurons for electrophysiological recording is a fundamental neuroscience technique; however, its potential is hampered by poor visualization of pipette tips in deep brain tissue. We describe quantum dot-coated glass pipettes that provide strong two-photon contrast at deeper penetration depths than those achievable with current methods. We demonstrated the pipettes{\textquoteright} utility in targeted patch-clamp recording experiments and single-cell electroporation of identified rat and mouse neurons in vitro and in vivo.

}, issn = {1548-7105}, doi = {10.1038/nmeth.3146}, author = {Andrasfalvy, Bertalan K and Gali{\~n}anes, Gregorio L and Huber, Daniel and Barbic, Mladen and Macklin, John J and Susumu, Kimihiro and Delehanty, James B and Huston, Alan L and Makara, Judit K and Medintz, Igor L} } @article {45866, title = {Regulation of branching dynamics by axon-intrinsic asymmetries in Tyrosine Kinase Receptor signaling.}, journal = {eLife}, volume = {3}, year = {2014}, month = {2014 Apr 22}, pages = {e01699}, abstract = {

Axonal branching allows a neuron to connect to several targets, increasing neuronal circuit complexity. While axonal branching is well described, the mechanisms that control it remain largely unknown. We find that in the Drosophila CNS branches develop through a process of excessive growth followed by pruning. In vivo high-resolution live imaging of developing brains as well as loss and gain of function experiments show that activation of Epidermal Growth Factor Receptor (EGFR) is necessary for branch dynamics and the final branching pattern. Live imaging also reveals that intrinsic asymmetry in EGFR localization regulates the balance between dynamic and static filopodia. Elimination of signaling asymmetry by either loss or gain of EGFR function results in reduced dynamics leading to excessive branch formation. In summary, we propose that the dynamic process of axon branch development is mediated by differential local distribution of signaling receptors. DOI: http://dx.doi.org/10.7554/eLife.01699.001.

}, issn = {2050-084X}, doi = {10.7554/eLife.01699}, author = {Zsch{\"a}tzsch, Marlen and Oliva, Carlos and Langen, Marion and De Geest, Natalie and Ozel, Mehmet Neset and Williamson, W Ryan and Lemon, William C and Soldano, Alessia and Munck, Sebastian and Hiesinger, P Robin and Sanchez-Soriano, Natalia and Hassan, Bassem A} } @article {45843, title = {Regulation of RNA polymerase II activation by histone acetylation in single living cells.}, journal = {Nature}, volume = {516}, year = {2014}, month = {2014 Dec 11}, pages = {272-5}, abstract = {

In eukaryotic cells, post-translational histone modifications have an important role in gene regulation. Starting with early work on histone acetylation, a variety of residue-specific modifications have now been linked to RNA polymerase II (RNAP2) activity, but it remains unclear if these markers are active regulators of transcription or just passive byproducts. This is because studies have traditionally relied on fixed cell populations, meaning temporal resolution is limited to minutes at best, and correlated factors may not actually be present in the same cell at the same time. Complementary approaches are therefore needed to probe the dynamic interplay of histone modifications and RNAP2 with higher temporal resolution in single living cells. Here we address this problem by developing a system to track residue-specific histone modifications and RNAP2 phosphorylation in living cells by fluorescence microscopy. This increases temporal resolution to the tens-of-seconds range. Our single-cell analysis reveals histone H3 lysine-27 acetylation at a gene locus can alter downstream transcription kinetics by as much as 50\%, affecting two temporally separate events. First acetylation enhances the search kinetics of transcriptional activators, and later the acetylation accelerates the transition of RNAP2 from initiation to elongation. Signatures of the latter can be found genome-wide using chromatin immunoprecipitation followed by sequencing. We argue that this regulation leads to a robust and potentially tunable transcriptional response.

}, issn = {1476-4687}, doi = {10.1038/nature13714}, author = {Stasevich, Timothy J and Hayashi-Takanaka, Yoko and Sato, Yuko and Maehara, Kazumitsu and Ohkawa, Yasuyuki and Sakata-Sogawa, Kumiko and Tokunaga, Makio and Nagase, Takahiro and Nozaki, Naohito and McNally, James G and Kimura, Hiroshi} } @article {6961, title = {Reproductive status, endocrine physiology and chemical signaling in the Neotropical, swarm-founding eusocial wasp, Polybia micans Ducke (Vespidae: Epiponini).}, journal = {The Journal of Experimental Biology}, volume = {217}, year = {2014}, month = {2014 Apr 17}, pages = {2399-410}, abstract = {

In the evolution of caste-based societies in Hymenoptera, the classical insect hormones, juvenile hormone (JH) and ecdysteroids, were co-opted into new functions. Social wasps, which show all levels of sociality and lifestyles, are an ideal group to study such functional changes. Virtually all studies on the physiological mechanisms underlying reproductive division of labor and caste functions in wasps have been done on independent-founding paper wasps, and the majority of these studies have focused on species specially adapted for overwintering. The relatively little studied tropical swarming-founding wasps of the Epiponini (Vespidae) are a diverse group of permanently social wasps, with some species maintaining caste flexibility well into the adult phase. We investigated the behavior, reproductive status, JH and ecdysteroid titers in hemolymph, ecdysteroid content of the ovary and cuticular hydrocarbon (CHC) profiles in the caste-monomorphic, epiponine wasp Polybia micans Ducke. We found that the JH titer was not elevated in competing queens from established multiple-queen nests, but increased in lone queens that lack direct competition. In queenless colonies, JH titers rose transiently in young potential reproductives upon challenge by nestmates, suggesting that JH may prime the ovaries for further development. Ovarian ecdysteroids were very low in workers but higher and correlated with the number of vitellogenic oocytes in the queens. Hemolymph ecdysteroid levels were low and variable in both. Profiles of P. micans CHCs reflected caste, age and reproductive status, but were not tightly linked to either hormone. These findings show a significant divergence in hormone function in swarm-founding wasps compared to independent-founding ones.

}, issn = {1477-9145}, doi = {10.1242/jeb.096750}, author = {Kelstrup, Hans C and Hartfelder, Klaus and Nascimento, Fabio S and Riddiford, Lynn M} } @article {45785, title = {The role of juvenile hormone in dominance behavior, reproduction and cuticular pheromone signaling in the caste-flexible epiponine wasp, Synoeca surinama.}, journal = {Frontiers in Zoology}, volume = {11}, year = {2014}, month = {2014}, pages = {78}, abstract = {

BACKGROUND: The popular view on insect sociality is that of a harmonious division of labor among two morphologically distinct and functionally non-overlapping castes. But this is a highly derived state and not a prerequisite for a functional society. Rather, caste-flexibility is a central feature in many eusocial wasps, where adult females have the potential to become queens or workers, depending on the social environment. In non-swarming paper wasps (e.g., Polistes), prospective queens fight one another to assert their dominance, with losers becoming workers if they remain on the nest. This aggression is fueled by juvenile hormone (JH) and ecdysteroids, major factors involved in caste differentiation in most eusocial insects. We tested whether these hormones have conserved aggression-promoting functions in Synoeca surinama, a caste-flexible swarm-founding wasp (Epiponini) where reproductive competition is high and aggressive displays are common.

RESULTS: We observed the behavioral interactions of S. surinama females in field nests before and after we had removed the egg-laying queen(s). We measured the ovarian reproductive status, hemolymph JH and ecdysteroid titers, ovarian ecdysteroid content, and analyzed the cuticular hydrocarbon (CHC) composition of females engaged in competitive interactions in both queenright and queenless contexts. These data, in combination with hormone manipulation experiments, revealed that neither JH nor ecdysteroids are necessary for the expression of dominance behaviors in S. surinama. Instead, we show that JH likely functions as a gonadotropin and directly modifies the cuticular hydrocarbon blend of young workers to match that of a reproductive. Hemolymph ecdysteroids, in contrast, are not different between queens and workers despite great differences in ovarian ecdysteroid content.

CONCLUSIONS: The endocrine profile of S. surinama shows surprising differences from those of other caste-flexible wasps, although a rise in JH titers in replacement queens is a common theme. Extensive remodeling of hormone functions is also evident in the highly eusocial bees, which has been attributed to the evolution of morphologically defined castes. Our results show that hormones which regulate caste-plasticity can lose these roles even while caste-plasticity is preserved.

}, issn = {1742-9994}, doi = {10.1186/s12983-014-0078-5}, author = {Kelstrup, Hans C and Hartfelder, Klaus and Nascimento, Fabio S and Riddiford, Lynn M} } @article {45337, title = {A self-adaptive method for creating high efficiency communication channels through random scattering media.}, journal = {Science Reports}, volume = {4}, year = {2014}, month = {2014 Jul 29}, pages = {5874}, abstract = {

Controlling the propagation of electromagnetic waves is important to a broad range of applications. Recent advances in controlling wave propagation in random scattering media have enabled optical focusing and imaging inside random scattering media. In this work, we propose and demonstrate a new method to deliver optical power more efficiently through scattering media. Drastically different from the random matrix characterization approach, our method can rapidly establish high efficiency communication channels using just a few measurements, regardless of the number of optical modes, and provides a practical and robust solution to boost the signal levels in optical or short wave communications. We experimentally demonstrated analog and digital signal transmission through highly scattering media with greatly improved performance. Besides scattering, our method can also reduce the loss of signal due to absorption. Experimentally, we observed that our method forced light to go around absorbers, leading to even higher signal improvement than in the case of purely scattering media. Interestingly, the resulting signal improvement is highly directional, which provides a new means against eavesdropping.

}, issn = {2045-2322}, doi = {10.1038/srep05874}, author = {Hao, Xiang and Martin-Rouault, Laure and Cui, Meng} } @article {6919, title = {Single-molecule dynamics of enhanceosome assembly in embryonic stem cells.}, journal = {Cell}, volume = {156}, year = {2014}, month = {2014 Mar 13}, pages = {1274-85}, abstract = {

Enhancer-binding pluripotency regulators (Sox2 and Oct4) play a seminal role in embryonic stem (ES) cell-specific gene regulation. Here, we combine in\ vivo and in\ vitro single-molecule imaging, transcription factor (TF) mutagenesis, and ChIP-exo mapping to\ determine how TFs dynamically search for and assemble on their cognate DNA target sites. We find that enhanceosome assembly is hierarchically ordered with kinetically favored Sox2 engaging the target DNA first, followed by assisted binding of Oct4. Sox2/Oct4 follow a trial-and-error sampling mechanism involving 84-97 events of 3D diffusion (3.3-3.7 s) interspersed with brief nonspecific collisions (0.75-0.9 s) before acquiring and dwelling at specific target DNA (12.0-14.6 s). Sox2 employs a 3D diffusion-dominated search mode facilitated by 1D sliding along open DNA to efficiently locate targets. Our findings also reveal fundamental aspects of gene and developmental regulation by fine-tuning TF dynamics and influence of the epigenome on target search parameters.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2014.01.062}, author = {Chen, Jiji and Zhang, Zhengjian and Li Li and Chen, Bi-Chang and Revyakin, Andrey and Hajj, Bassam and Legant, Wesley and Dahan, Maxime and Lionnet, Timoth{\'e}e and Betzig, Eric and Tjian, Robert and Liu, Zhe} } @conference {65048, title = {Sparse LMS via online linearized Bregman iteration.}, booktitle = {ICASSP 2014 - 2014 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)2014 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)}, year = {2014}, month = {2014 Jul 14}, publisher = {IEEE}, organization = {IEEE}, address = {Florence, Italy}, abstract = {

We propose a version of least-mean-square (LMS) algorithm for sparse system identification. Our algorithm called online linearized Bregman iteration (OLBI) is derived from minimizing the cumulative prediction error squared along with an l\ 1\ -l\ 2\ norm regularizer. By systematically treating the non-differentiable regularizer we arrive at a simple two-step iteration. We demonstrate that OLBI is bias free and compare its operation with existing sparse LMS algorithms by rederiving them in the online convex optimization framework. We perform convergence analysis of OLBI for white input signals and derive theoretical expressions for the steady state mean square deviations (MSD). We demonstrate numerically that OLBI improves the performance of LMS type algorithms for signals generated from sparse tap weights.

}, doi = {10.1109/ICASSP.2014.6855000}, url = {http://ieeexplore.ieee.org/document/6855000/http://xplorestaging.ieee.org/ielx7/6844297/6853544/06855000.pdf?arnumber=6855000}, author = {Hu, Tao and Chklovskii, Dmitri B.} } @article {6956, title = {Structural basis for the prion-like MAVS filaments in antiviral innate immunity.}, journal = {eLife}, volume = {3}, year = {2014}, month = {2014 Jan 1}, pages = {e01489}, abstract = {

Mitochondrial antiviral signaling (MAVS) protein is required for innate immune responses against RNA viruses. In virus-infected cells MAVS forms prion-like aggregates to activate antiviral signaling cascades, but the underlying structural mechanism is unknown. Here we report cryo-electron microscopic structures of the helical filaments formed by both the N-terminal caspase activation and recruitment domain (CARD) of MAVS and a truncated MAVS lacking part of the proline-rich region and the C-terminal transmembrane domain. Both structures are left-handed three-stranded helical filaments, revealing specific interfaces between individual CARD subunits that are dictated by electrostatic interactions between neighboring strands and hydrophobic interactions within each strand. Point mutations at multiple locations of these two interfaces impaired filament formation and antiviral signaling. Super-resolution imaging of virus-infected cells revealed rod-shaped MAVS clusters on mitochondria. These results elucidate the structural mechanism of MAVS polymerization, and explain how an α-helical domain uses distinct chemical interactions to form self-perpetuating filaments. DOI: http://dx.doi.org/10.7554/eLife.01489.001.

}, issn = {2050-084X}, doi = {10.7554/eLife.01489}, author = {Xu, Hui and He, Xiaojing and Zheng, Hui and Huang, Lily J and Hou, Fajian and Yu, Zhiheng and de la Cruz, Michael Jason and Borkowski, Brian and Zhang, Xuewu and Chen, Zhijian J and Jiang, Qiu-Xing} } @article {47704, title = {Structurally-constrained relationships between cognitive states in the human brain.}, journal = {PLoS computational biology}, volume = {10}, year = {2014}, month = {2014 May}, pages = {e1003591}, abstract = {

The anatomical connectivity of the human brain supports diverse patterns of correlated neural activity that are thought to underlie cognitive function. In a manner sensitive to underlying structural brain architecture, we examine the extent to which such patterns of correlated activity systematically vary across cognitive states. Anatomical white matter connectivity is compared with functional correlations in neural activity measured via blood oxygen level dependent (BOLD) signals. Functional connectivity is separately measured at rest, during an attention task, and during a memory task. We assess these structural and functional measures within previously-identified resting-state functional networks, denoted task-positive and task-negative networks, that have been independently shown to be strongly anticorrelated at rest but also involve regions of the brain that routinely increase and decrease in activity during task-driven processes. We find that the density of anatomical connections within and between task-positive and task-negative networks is differentially related to strong, task-dependent correlations in neural activity. The space mapped out by the observed structure-function relationships is used to define a quantitative measure of separation between resting, attention, and memory states. We find that the degree of separation between states is related to both general measures of behavioral performance and relative differences in task-specific measures of attention versus memory performance. These findings suggest that the observed separation between cognitive states reflects underlying organizational principles of human brain structure and function.

}, keywords = {Attention, Brain, Cognition, Computer Simulation, Connectome, Humans, Memory, Models, Anatomic, Models, Neurological, Nerve Net, White Matter}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1003591}, author = {Hermundstad, Ann M and Brown, Kevin S and Bassett, Danielle S and Aminoff, Elissa M and Frithsen, Amy and Johnson, Arianne and Tipper, Christine M and Miller, Michael B and Grafton, Scott T and Carlson, Jean M} } @article {45552, title = {Structure of catalase determined by MicroED.}, journal = {eLife}, volume = {3}, year = {2014}, month = {2014 Oct 17}, pages = {e03600}, abstract = {

MicroED is a recently developed method that uses electron diffraction for structure determination from very small three-dimensional crystals of biological material. Previously we used a series of still diffraction patterns to determine the structure of lysozyme at 2.9 {\r A} resolution with MicroED (Shi et al., 2013). Here we present the structure of bovine liver catalase determined from a single crystal at 3.2 {\r A} resolution by MicroED. The data were collected by continuous rotation of the sample under constant exposure and were processed and refined using standard programs for X-ray crystallography. The ability of MicroED to determine the structure of bovine liver catalase, a protein that has long resisted atomic analysis by traditional electron crystallography, demonstrates the potential of this method for structure determination.

}, issn = {2050-084X}, doi = {10.7554/eLife.03600}, author = {Nannenga, Brent L and Shi, Dan and Hattne, Johan and Reyes, Francis E and Gonen, Tamir} } @article {45417, title = {A suppression hierarchy among competing motor programs drives sequential grooming in Drosophila.}, journal = {eLife}, volume = {3}, year = {2014}, month = {2014 Aug 19}, pages = {e02951}, abstract = {

Motor sequences are formed through the serial execution of different movements, but how nervous systems implement this process remains largely unknown. We determined the organizational principles governing how dirty fruit flies groom their bodies with sequential movements. Using genetically targeted activation of neural subsets, we drove distinct motor programs that clean individual body parts. This enabled competition experiments revealing that the motor programs are organized into a suppression hierarchy; motor programs that occur first suppress those that occur later. Cleaning one body part reduces the sensory drive to its motor program, which relieves suppression of the next movement, allowing the grooming sequence to progress down the hierarchy. A model featuring independently evoked cleaning movements activated in parallel, but selected serially through hierarchical suppression, was successful in reproducing the grooming sequence. This provides the first example of an innate motor sequence implemented by the prevailing model for generating human action sequences.

}, issn = {2050-084X}, doi = {10.7554/eLife.02951}, author = {Seeds, Andrew M and Ravbar, Primoz and Chung, Phuong and Hampel, Stefanie and Midgley, Frank M and Mensh, Brett D and Simpson, Julie H} } @article {6884, title = {A systematic nomenclature for the insect brain.}, journal = {Neuron}, volume = {81}, year = {2014}, month = {2014 Feb 19}, pages = {755-65}, abstract = {

Despite the importance of the insect nervous system for functional and developmental neuroscience, descriptions of insect brains have suffered from a lack of uniform nomenclature. Ambiguous definitions of brain regions and fiber bundles have contributed to the variation of names used to describe the same structure. The lack of clearly determined neuropil boundaries has made it difficult to document precise locations of neuronal projections for connectomics study. To address such issues, a consortium of\ neurobiologists studying arthropod brains, the Insect Brain Name Working Group, has established the present hierarchical nomenclature system, using the brain of Drosophila melanogaster as the reference framework, while taking the brains of other taxa into careful consideration for maximum consistency and expandability. The following summarizes the consortium{\textquoteright}s nomenclature system and highlights examples of existing ambiguities and remedies for them. This nomenclature is intended to serve as a\ standard of reference for the study of the brain of Drosophila and other insects.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2013.12.017}, author = {Ito, Kei and Shinomiya, Kazunori and Ito, Masayoshi and Armstrong, J Douglas and Boyan, George and Hartenstein, Volker and Harzsch, Steffen and Heisenberg, Martin and Homberg, Uwe and Jenett, Arnim and Keshishian, Haig and Restifo, Linda L and R{\"o}ssler, Wolfgang and Simpson, Julie H and Strausfeld, Nicholas J and Strauss, Roland and Vosshall, Leslie B} } @article {45591, title = {Thorough GABAergic innervation of the entire axon initial segment revealed by an optogenetic {\textquoteright}laserspritzer{\textquoteright}.}, journal = {Journal of Physiology - London}, volume = {592}, year = {2014}, month = {2014 Oct 1}, pages = {4257-76}, abstract = {

GABAergic terminals of chandelier cells exclusively innervate the axon initial segment (AIS) of excitatory neurons. Although the anatomy of these synapses has been well-studied in several brain areas, relatively little is known about their physiological properties. Using vesicular γ-aminobutyric acid transporter-channelrhodopsin\ 2-enhanced yellow fluorescence protein (VGAT-ChR2-YFP)-expressing mice and a novel fibreoptic {\textquoteright}laserspritzer{\textquoteright} approach that we developed, we investigated the physiological properties of axo-axonic synapses (AASs) in brain slices from the piriform cortex (PC) of mice. AASs were in close proximity to voltage-gated Na(+) (NaV) channels located at the AIS. AASs were selectively activated by a 5\ μm laserspritzer placed in close proximity to the AIS. Under a minimal laser stimulation condition and using whole-cell somatic voltage-clamp recordings, the amplitudes and kinetics of IPSCs mediated by AASs were similar to those mediated by perisomatic inhibitions. Results were further validated with channelrhodopsin\ 2-assisted circuit mapping (CRACM) of the entire inhibitory inputs map. For the first time, we revealed that the laserspritzer-induced AAS-IPSCs persisted in the presence of TTX and TEA but not 4-AP. Next, using gramicidin-based perforated patch recordings, we found that the GABA reversal potential (EGABA) was -73.6\ {\textpm}\ 1.2\ mV when induced at the AIS and -72.8\ {\textpm}\ 1.1\ mV when induced at the perisomatic site. Our anatomical and physiological results lead to the novel conclusions that: (1) AASs innervate the entire length of the AIS, as opposed to forming a highly concentrated cartridge, (2) AAS inhibition suppresses action potentials and epileptiform activity more robustly than perisomatic inhibitions, and (3) AAS activation alone can be sufficient to inhibit action potential generation and epileptiform activities in vitro.

}, issn = {1469-7793}, doi = {10.1113/jphysiol.2014.275719}, author = {Wang, Xinjun and Hooks, Bryan M and Sun, Qian-Quan} } @article {45353, title = {Thy1 - GCaMP6 transgenic mice for neuronal population imaging in vivo.}, journal = {PLoS One}, volume = {9}, year = {2014}, month = {2014}, pages = {e108697}, chapter = {e108697}, abstract = {

Genetically-encoded calcium indicators (GECIs) facilitate imaging activity of genetically defined neuronal populations in vivo. The high intracellular GECI concentrations required for in vivo imaging are usually achieved by viral gene transfer using adeno-associated viruses. Transgenic expression of GECIs promises important advantages, including homogeneous, repeatable, and stable expression without the need for invasive virus injections. Here we present the generation and characterization of transgenic mice expressing the GECIs GCaMP6s or GCaMP6f under the Thy1 promoter. We quantified GCaMP6 expression across brain regions and neurons and compared to other transgenic mice and AAV-mediated expression. We tested three mouse lines for imaging in the visual cortex in vivo and compared their performance to mice injected with AAV expressing GCaMP6. Furthermore, we show that GCaMP6 Thy1 transgenic mice are useful for long-term, high-sensitivity imaging in behaving mice.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0108697}, author = {Dana, Hod and Chen, Tsai-Wen and Hu, Amy and Shields, Brenda C and Cui, Guohong and Looger, Loren and Kim, Douglas S. and Svoboda, Karel} } @article {45372, title = {A type VI secretion-related pathway in bacteroidetes mediates interbacterial antagonism.}, journal = {Cell Host Microbe}, volume = {16}, year = {2014}, month = {2014 Aug 13}, pages = {227-36}, abstract = {

Bacteroidetes are a phylum of Gram-negative bacteria abundant in mammalian-associated polymicrobial communities, where they impact digestion, immunity, and resistance to infection. Despite the extensive competition at high cell density that occurs in these settings, cell contact-dependent mechanisms of interbacterial antagonism, such as the type VI secretion system (T6SS), have not been defined in this group of organisms. Herein we report the bioinformatic and functional characterization of a T6SS-like pathway in diverse Bacteroidetes. Using prominent human gut commensal and soil-associated species, we demonstrate that these systems localize dynamically within the cell, export antibacterial proteins, and target competitor bacteria. The Bacteroidetes system is a distinct pathway with marked differences in gene content and high evolutionary divergence from the canonical T6S pathway. Our findings offer a potential molecular explanation for the abundance of Bacteroidetes in polymicrobial environments, the observed stability of Bacteroidetes in healthy humans, and the barrier presented by the microbiota against pathogens.

}, issn = {1934-6069}, doi = {10.1016/j.chom.2014.07.007}, author = {Russell, Alistair B and Wexler, Aaron G and Harding, Brittany N and Whitney, John C and Bohn, Alan J and Goo, Young Ah and Tran, Bao Q and Barry, Natasha A and Zheng, Hongjin and Peterson, S Brook and Chou, Seemay and Gonen, Tamir and Goodlett, David R and Goodman, Andrew L and Mougous, Joseph D} } @article {47703, title = {Variance predicts salience in central sensory processing.}, journal = {eLife}, volume = {3}, year = {2014}, month = {2014}, abstract = {

Information processing in the sensory periphery is shaped by natural stimulus statistics. In the periphery, a transmission bottleneck constrains performance; thus efficient coding implies that natural signal components with a predictably wider range should be compressed. In a different regime--when sampling limitations constrain performance--efficient coding implies that more resources should be allocated to informative features that are more variable. We propose that this regime is relevant for sensory cortex when it extracts complex features from limited numbers of sensory samples. To test this prediction, we use central visual processing as a model: we show that visual sensitivity for local multi-point spatial correlations, described by dozens of independently-measured parameters, can be quantitatively predicted from the structure of natural images. This suggests that efficient coding applies centrally, where it extends to higher-order sensory features and operates in a regime in which sensitivity increases with feature variability.

}, keywords = {Humans, Sensory Receptor Cells, Visual Cortex, Visual Perception}, issn = {2050-084X}, doi = {10.7554/eLife.03722}, author = {Hermundstad, Ann M and Briguglio, John J and Conte, Mary M and Victor, Jonathan D and Balasubramanian, Vijay and Tka{\v c}ik, Ga{\v s}per} } @article {45064, title = {Virtual finger boosts three-dimensional imaging and microsurgery as well as terabyte volume image visualization and analysis.}, journal = {Nature Communications}, volume = {5}, year = {2014}, month = {2014 Jul 11}, pages = {4342}, abstract = {

Three-dimensional (3D) bioimaging, visualization and data analysis are in strong need of powerful 3D exploration techniques. We develop virtual finger (VF) to generate 3D curves, points and regions-of-interest in the 3D space of a volumetric image with a single finger operation, such as a computer mouse stroke, or click or zoom from the 2D-projection plane of an image as visualized with a computer. VF provides efficient methods for acquisition, visualization and analysis of 3D images for roundworm, fruitfly, dragonfly, mouse, rat and human. Specifically, VF enables instant 3D optical zoom-in imaging, 3D free-form optical microsurgery, and 3D visualization and annotation of terabytes of whole-brain image volumes. VF also leads to orders of magnitude better efficiency of automated 3D reconstruction of neurons and similar biostructures over our previous systems. We use VF to generate from images of 1,107 Drosophila GAL4 lines a projectome of a Drosophila brain.

}, issn = {2041-1723}, doi = {10.1038/ncomms5342}, author = {Peng, Hanchuan and Tang, Jianyong and Xiao, Hang and Bria, Alessandro and Zhou, Jianlong and Butler, Victoria and Zhou, Zhi and Gonzalez-Bellido, Paloma T and Oh, Seung W and Chen, Jichao and Mitra, Ananya and Tsien, Richard W and Zeng, Hongkui and Ascoli, Giorgio A and Iannello, Giulio and Hawrylycz, Michael and Myers, Eugene and Long, Fuhui} } @article {45778, title = {Whole-cell, multicolor superresolution imaging using volumetric multifocus microscopy.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, year = {2014}, month = {2014 Dec 9}, pages = {17480-5}, abstract = {

Single molecule-based superresolution imaging has become an essential tool in modern cell biology. Because of the limited depth of field of optical imaging systems, one of the major challenges in superresolution imaging resides in capturing the 3D nanoscale morphology of the whole cell. Despite many previous attempts to extend the application of photo-activated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM) techniques into three dimensions, effective localization depths do not typically exceed 1.2 {\textmu}m. Thus, 3D imaging of whole cells (or even large organelles) still demands sequential acquisition at different axial positions and, therefore, suffers from the combined effects of out-of-focus molecule activation (increased background) and bleaching (loss of detections). Here, we present the use of multifocus microscopy for volumetric multicolor superresolution imaging. By simultaneously imaging nine different focal planes, the multifocus microscope instantaneously captures the distribution of single molecules (either fluorescent proteins or synthetic dyes) throughout an \~{}4-{\textmu}m-deep volume, with lateral and axial localization precisions of \~{}20 and 50 nm, respectively. The capabilities of multifocus microscopy to rapidly image the 3D organization of intracellular structures are illustrated by superresolution imaging of the mammalian mitochondrial network and yeast microtubules during cell division.

}, issn = {1091-6490}, doi = {10.1073/pnas.1412396111}, author = {Hajj, Bassam and Wisniewski, Jan and El Beheiry, Mohamed and Chen, Jiji and Revyakin, Andrey and Wu, Carl and Dahan, Maxime} } @article {47642, title = {Accelerating 3B single-molecule super-resolution microscopy with cloud computing.}, journal = {Nature methods}, volume = {10}, year = {2013}, month = {2013 Feb}, pages = {96-7}, keywords = {Computational Biology, Computers, Fluorescent Dyes, Microscopy, Fluorescence, Nanotechnology}, issn = {1548-7105}, doi = {10.1038/nmeth.2335}, author = {Hu, Ying S and Nan, Xiaolin and Sengupta, Prabuddha and Lippincott-Schwartz, Jennifer and Cang, Hu} } @article {6534, title = {Addiction.}, journal = {Current Opinion in Neurobiology}, volume = {23}, year = {2013}, month = {2013 Aug}, pages = {463-6}, abstract = {

Drug addiction and obesity share the core feature that those afflicted by the disorders express a desire to limit drug or food consumption yet persist despite negative consequences. Emerging evidence suggests that the compulsivity that defines these disorders may arise, to some degree at least, from common underlying neurobiological mechanisms. In particular, both disorders are associated with diminished striatal dopamine D2 receptor (D2R) availability, likely reflecting their decreased maturation and surface expression. In striatum, D2Rs are expressed by approximately half of the principal medium spiny projection neurons (MSNs), the striatopallidal neurons of the so-called {\textquoteright}indirect{\textquoteright} pathway. D2Rs are also expressed presynaptically on dopamine terminals and on cholinergic interneurons. This heterogeneity of D2R expression has hindered attempts, largely using traditional pharmacological approaches, to understand their contribution to compulsive drug or food intake. The emergence of genetic technologies to target discrete populations of neurons, coupled to optogenetic and chemicogenetic tools to manipulate their activity, have provided a means to dissect striatopallidal and cholinergic contributions to compulsivity. Here, we review recent evidence supporting an important role for striatal D2R signaling in compulsive drug use and food intake. We pay particular attention to striatopallidal projection neurons and their role in compulsive responding for food and drugs. Finally, we identify opportunities for future obesity research using known mechanisms of addiction as a heuristic, and leveraging new tools to manipulate activity of specific populations of striatal neurons to understand their contributions to addiction and obesity.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2013.07.003}, author = {Everitt, Barry J and Heberlein, Ulrike} } @article {6127, title = {Admixture mapping in lupus identifies multiple functional variants within IFIH1 associated with apoptosis, inflammation, and autoantibody production.}, journal = {PLoS Genetics}, volume = {9}, year = {2013}, month = {2013 Feb 18}, pages = {e1003222}, abstract = {

Systemic lupus erythematosus (SLE) is an inflammatory autoimmune disease with a strong genetic component. African-Americans (AA) are at increased risk of SLE, but the genetic basis of this risk is largely unknown. To identify causal variants in SLE loci in AA, we performed admixture mapping followed by fine mapping in AA and European-Americans (EA). Through genome-wide admixture mapping in AA, we identified a strong SLE susceptibility locus at 2q22-24 (LOD=6.28), and the admixture signal is associated with the European ancestry (ancestry risk ratio \ 1.5). Large-scale genotypic analysis on 19,726 individuals of African and European ancestry revealed three independently associated variants in the IFIH1 gene: an intronic variant, rs13023380 [P(meta) = 5.20{\texttimes}10(-14); odds ratio, 95\% confidence interval = 0.82 (0.78-0.87)], and two missense variants, rs1990760 (Ala946Thr) [P(meta) = 3.08{\texttimes}10(-7); 0.88 (0.84-0.93)] and rs10930046 (Arg460His) [P(dom) = 1.16{\texttimes}10(-8); 0.70 (0.62-0.79)]. Both missense variants produced dramatic phenotypic changes in apoptosis and inflammation-related gene expression. We experimentally validated function of the intronic SNP by DNA electrophoresis, protein identification, and in vitro protein binding assays. DNA carrying the intronic risk allele rs13023380 showed reduced binding efficiency to a cellular protein complex including nucleolin and lupus autoantigen Ku70/80, and showed reduced transcriptional activity in vivo. Thus, in SLE patients, genetic susceptibility could create a biochemical imbalance that dysregulates nucleolin, Ku70/80, or other nucleic acid regulatory proteins. This could promote antibody hypermutation and auto-antibody generation, further destabilizing the cellular network. Together with molecular modeling, our results establish a distinct role for IFIH1 in apoptosis, inflammation, and autoantibody production, and explain the molecular basis of these three risk alleles for SLE pathogenesis.

}, keywords = {African Americans, Alleles, Antigens, Apoptosis, Autoantibodies, Chromosome Mapping, DEAD-box RNA Helicases, DNA-Binding Proteins, European Continental Ancestry Group, Genetic Predisposition to Disease, Genome, Haplotypes, Human, Humans, Inflammation, Lupus Erythematosus, Nuclear, Polymorphism, Protein Binding, Single Nucleotide, Systemic}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1003222}, author = {Molineros, Julio E and Maiti, Amit K and Sun, Celi and Looger, Loren L and Han, Shizhong and Kim-Howard, Xana and Glenn, Stuart and Adler, Adam and Kelly, Jennifer A and Niewold, Timothy B and Gilkeson, Gary S and Brown, Elizabeth E and Alarc{\'o}n, Graciela S and Edberg, Jeffrey C and Petri, Michelle and Ramsey-Goldman, Rosalind and Reveille, John D and Vil{\'a}, Luis M and Freedman, Barry I and Tsao, Betty P and Criswell, Lindsey A and Jacob, Chaim O and Moore, Jason H and Vyse, Timothy J and Langefeld, Carl L and Guthridge, Joel M and Gaffney, Patrick M and Moser, Kathy L and Scofield, R Hal and Alarc{\'o}n-Riquelme, Marta E and Williams, Scott M and Merrill, Joan T and James, Judith A and Kaufman, Kenneth M and Kimberly, Robert P and Harley, John B and Nath, Swapan K} } @article {6252, title = {Allosteric mechanism of water-channel gating by Ca(2+)-calmodulin.}, journal = {Nature Structural \& Molecular Biology}, volume = {20}, year = {2013}, month = {2013 Jul 28}, pages = {1085-92}, abstract = {

Calmodulin (CaM) is a universal regulatory protein that communicates the presence of calcium to its molecular targets and correspondingly modulates their function. This key signaling protein is important for controlling the activity of hundreds of membrane channels and transporters. However, understanding of the structural mechanisms driving CaM regulation of full-length membrane proteins has remained elusive. In this study, we determined the pseudoatomic structure of full-length mammalian aquaporin-0 (AQP0, Bos taurus) in complex with CaM, using EM to elucidate how this signaling protein modulates water-channel function. Molecular dynamics and functional mutation studies reveal how CaM binding inhibits AQP0 water permeability by allosterically closing the cytoplasmic gate of AQP0. Our mechanistic model provides new insight, only possible in the context of the fully assembled channel, into how CaM regulates multimeric channels by facilitating cooperativity between adjacent subunits.

}, issn = {1545-9985}, doi = {10.1038/nsmb.2630}, author = {Reichow, Steve L and Clemens, Daniel M and Freites, J Alfredo and N{\'e}meth-Cahalan, Karin L and Heyden, Matthias and Tobias, Douglas J and Hall, James E and Gonen, Tamir} } @article {45850, title = {Automated long-term tracking and social behavioural phenotyping of animal colonies within a semi-natural environment.}, journal = {Nature Communications}, volume = {4}, year = {2013}, month = {2013}, pages = {2018}, abstract = {

Social behaviour has a key role in animal survival across species, ranging from insects to primates and humans. However, the biological mechanisms driving natural interactions between multiple animals, over long-term periods, are poorly studied and remain elusive. Rigorous and objective quantification of behavioural parameters within a group poses a major challenge as it requires simultaneous monitoring of the positions of several individuals and comprehensive consideration of many complex factors. Automatic tracking and phenotyping of interacting animals could thus overcome the limitations of manual tracking methods. Here we report a broadly applicable system that automatically tracks the locations of multiple, uniquely identified animals, such as mice, within a semi-natural setting. The system combines video and radio frequency identified tracking data to obtain detailed behavioural profiles of both individuals and groups. We demonstrate the usefulness of these data in characterizing individual phenotypes, interactions between pairs and the collective social organization of groups.

}, keywords = {Animals, Automation, Behavior, Animal, Crosses, Genetic, Data Collection, Environment, Female, Hierarchy, Social, Locomotion, Male, Mice, Mice, Inbred C57BL, Phenotype, Radio Frequency Identification Device, Social Behavior, Time Factors, Video Recording}, issn = {2041-1723}, doi = {10.1038/ncomms3018}, author = {Weissbrod, Aharon and Shapiro, Alexander and Vasserman, Genadiy and Edry, Liat and Dayan, Molly and Yitzhaky, Assif and Hertzberg, Libi and Feinerman, Ofer and Kimchi, Tali} } @article {6268, title = {Aβ induces astrocytic glutamate release, extrasynaptic NMDA receptor activation, and synaptic loss.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, year = {2013}, month = {2013 Jul 2}, pages = {E2518-27}, abstract = {

Synaptic loss is the cardinal feature linking neuropathology to cognitive decline in Alzheimer{\textquoteright}s disease (AD). However, the mechanism of synaptic damage remains incompletely understood. Here, using FRET-based glutamate sensor imaging, we show that amyloid-β peptide (Aβ) engages α7 nicotinic acetylcholine receptors to induce release of astrocytic glutamate, which in turn activates extrasynaptic NMDA receptors (eNMDARs) on neurons. In hippocampal autapses, this eNMDAR activity is followed by reduction in evoked and miniature excitatory postsynaptic currents (mEPSCs). Decreased mEPSC frequency may reflect early synaptic injury because of concurrent eNMDAR-mediated NO production, tau phosphorylation, and caspase-3 activation, each of which is implicated in spine loss. In hippocampal slices, oligomeric Aβ induces eNMDAR-mediated synaptic depression. In AD-transgenic mice compared with wild type, whole-cell recordings revealed excessive tonic eNMDAR activity accompanied by eNMDAR-sensitive loss of mEPSCs. Importantly, the improved NMDAR antagonist NitroMemantine, which selectively inhibits extrasynaptic over physiological synaptic NMDAR activity, protects synapses from Aβ-induced damage both in vitro and in vivo.

}, issn = {1091-6490}, doi = {10.1073/pnas.1306832110}, author = {Talantova, Maria and Sanz-Blasco, Sara and Zhang, Xiaofei and Xia, Peng and Akhtar, Mohd Waseem and Okamoto, Shu-ichi and Dziewczapolski, Gustavo and Nakamura, Tomohiro and Cao, Gang and Pratt, Alexander E and Kang, Yeon-Joo and Tu, Shichun and Molokanova, Elena and McKercher, Scott R and Hires, Samuel Andrew and Sason, Hagit and Stouffer, David G and Buczynski, Matthew W and Solomon, James P and Michael, Sarah and Powers, Evan T and Kelly, Jeffery W and Roberts, Amanda and Tong, Gary and Fang-Newmeyer, Traci and Parker, James and Holland, Emily A and Zhang, Dongxian and Nakanishi, Nobuki and Chen, H-S Vincent and Wolosker, Herman and Wang, Yuqiang and Parsons, Loren H and Ambasudhan, Rajesh and Masliah, Eliezer and Heinemann, Stephen F and Pi{\~n}a-Crespo, Juan C and Lipton, Stuart A} } @article {46052, title = {Bidirectional NMDA receptor plasticity controls CA3 output and heterosynaptic metaplasticity.}, journal = {Nature Neuroscience}, volume = {16}, year = {2013}, month = {2013 Aug}, pages = {1049-59}, abstract = {

NMDA receptors (NMDARs) are classically known as coincidence detectors for the induction of long-term synaptic plasticity and have been implicated in hippocampal CA3 cell-dependent spatial memory functions that likely rely on dynamic cellular ensemble encoding of space. The unique functional properties of both NMDARs and mossy fiber projections to CA3 pyramidal cells place mossy fiber NMDARs in a prime position to influence CA3 ensemble dynamics. By mimicking presynaptic and postsynaptic activity patterns observed in vivo, we found a burst timing-dependent pattern of activity that triggered bidirectional long-term NMDAR plasticity at mossy fiber-CA3 synapses in rat hippocampal slices. This form of plasticity imparts bimodal control of mossy fiber-driven CA3 burst firing and spike temporal fidelity. Moreover, we found that mossy fiber NMDARs mediate heterosynaptic metaplasticity between mossy fiber and associational-commissural synapses. Thus, bidirectional NMDAR plasticity at mossy fiber-CA3 synapses could substantially contribute to the formation, storage and recall of CA3 cell assembly patterns.

}, keywords = {2-Amino-5-phosphonovalerate, Action Potentials, Animals, CA3 Region, Hippocampal, Dentate Gyrus, Dynamins, Egtazic Acid, Endocytosis, Female, Indoles, Long-Term Potentiation, Long-Term Synaptic Depression, Male, Mossy Fibers, Hippocampal, Nerve Tissue Proteins, Nifedipine, Okadaic Acid, Patch-Clamp Techniques, Phosphoric Monoester Hydrolases, Pyramidal Cells, Rats, Rats, Long-Evans, Rats, Wistar, Receptor, Metabotropic Glutamate 5, Receptors, Metabotropic Glutamate, Receptors, N-Methyl-D-Aspartate, Synaptic Transmission}, issn = {1546-1726}, doi = {10.1038/nn.3461}, author = {Hunt, David L and Puente, Nagore and Grandes, Pedro and Castillo, Pablo E} } @article {6273, title = {Carbofluoresceins and carborhodamines as scaffolds for high-contrast fluorogenic probes.}, journal = {ACS Chemical Biology}, volume = {8}, year = {2013}, month = {2013 Apr 24}, pages = {1303-10}, abstract = {

Fluorogenic molecules are important tools for advanced biochemical and biological experiments. The extant collection of fluorogenic probes is incomplete, however, leaving regions of the electromagnetic spectrum unutilized. Here, we synthesize green-excited fluorescent and fluorogenic analogues of the classic fluorescein and rhodamine 110 fluorophores by replacement of the xanthene oxygen with a quaternary carbon. These anthracenyl "carbofluorescein" and "carborhodamine 110" fluorophores exhibit excellent fluorescent properties and can be masked with enzyme- and photolabile groups to prepare high-contrast fluorogenic molecules useful for live cell imaging experiments and super-resolution microscopy. Our divergent approach to these red-shifted dye scaffolds will enable the preparation of numerous novel fluorogenic probes with high biological utility.

}, issn = {1554-8937}, doi = {10.1021/cb4000822}, author = {Grimm, Jonathan B and Sung, Andrew J and Legant, Wesley R and Hulamm, Phuson and Matlosz, Sylwia M and Betzig, Eric and Lavis, Luke D} } @inbook {6304, title = {The chemistry of small-molecule fluorogenic probes.}, booktitle = {Progress in Molecular Biology and Translational Science}, volume = {113}, year = {2013}, pages = {1-34}, abstract = {

Chemical fluorophores find wide use in biology to detect and visualize different phenomena. A key advantage of small-molecule dyes is the ability to construct compounds where fluorescence is activated by chemical or biochemical processes. Fluorogenic molecules, in which fluorescence is activated by enzymatic activity, light, or environmental changes, enable advanced bioassays and sophisticated imaging experiments. Here, we detail the collection of fluorophores and highlight both general strategies and unique approaches that are employed to control fluorescence using chemistry.

}, issn = {1878-0814}, doi = {10.1016/B978-0-12-386932-6.00001-6}, author = {Grimm, Jonathan B and Heckman, Laurel M and Lavis, Luke D} } @article {6284, title = {Clonal development and organization of the adult Drosophila central brain.}, journal = {Current biology : CB}, volume = {23}, year = {2013}, month = {2013 Apr 22}, pages = {633-43}, abstract = {BACKGROUND: The insect brain can be divided into neuropils that are formed by neurites of both local and remote origin. The complexity of the interconnections obscures how these neuropils are established and interconnected through development. The Drosophila central brain develops from a fixed number of neuroblasts (NBs) that deposit neurons in regional clusters. RESULTS: By determining individual NB clones and pursuing their projections into specific neuropils, we unravel the regional development of the brain neural network. Exhaustive clonal analysis revealed 95 stereotyped neuronal lineages with characteristic cell-body locations and neurite trajectories. Most clones show complex projection patterns, but despite the complexity, neighboring clones often coinnervate the same local neuropil or neuropils and further target a restricted set of distant neuropils. CONCLUSIONS: These observations argue for regional clonal development of both neuropils and neuropil connectivity throughout the Drosophila central brain.}, issn = {1879-0445}, doi = {10.1016/j.cub.2013.02.057}, author = {Yu, Hung-Hsiang and Awasaki, Takeshi and Schroeder, Mark David and Long, Fuhui and Yang, Jacob S and He, Yisheng and Ding, Peng and Kao, Jui-Chun and Wu, Gloria Yueh-Yi and Peng, Hanchuan and Myers, Gene and Lee, Tzumin} } @article {46712, title = {Colocalization of different influenza viral RNA segments in the cytoplasm before viral budding as shown by single-molecule sensitivity FISH analysis.}, journal = {PLoS Pathogens}, volume = {9}, year = {2013}, month = {2013}, pages = {e1003358}, abstract = {

The Influenza A virus genome consists of eight negative sense, single-stranded RNA segments. Although it has been established that most virus particles contain a single copy of each of the eight viral RNAs, the packaging selection mechanism remains poorly understood. Influenza viral RNAs are synthesized in the nucleus, exported into the cytoplasm and travel to the plasma membrane where viral budding and genome packaging occurs. Due to the difficulties in analyzing associated vRNPs while preserving information about their positions within the cell, it has remained unclear how and where during cellular trafficking the viral RNAs of different segments encounter each other. Using a multicolor single-molecule sensitivity fluorescence in situ hybridization (smFISH) approach, we have quantitatively monitored the colocalization of pairs of influenza viral RNAs in infected cells. We found that upon infection, the viral RNAs from the incoming particles travel together until they reach the nucleus. The viral RNAs were then detected in distinct locations in the nucleus; they are then exported individually and initially remain separated in the cytoplasm. At later time points, the different viral RNA segments gather together in the cytoplasm in a microtubule independent manner. Viral RNAs of different identities colocalize at a high frequency when they are associated with Rab11 positive vesicles, suggesting that Rab11 positive organelles may facilitate the association of different viral RNAs. Using engineered influenza viruses lacking the expression of HA or M2 protein, we showed that these viral proteins are not essential for the colocalization of two different viral RNAs in the cytoplasm. In sum, our smFISH results reveal that the viral RNAs travel together in the cytoplasm before their arrival at the plasma membrane budding sites. This newly characterized step of the genome packaging process demonstrates the precise spatiotemporal regulation of the infection cycle.

}, keywords = {Active Transport, Cell Nucleus, Animals, Cell Nucleus, Dogs, Hemagglutinin Glycoproteins, Influenza Virus, Humans, In Situ Hybridization, Fluorescence, Influenza A virus, Madin Darby Canine Kidney Cells, rab GTP-Binding Proteins, RNA, Viral, Viral Matrix Proteins, Virus Assembly}, issn = {1553-7374}, doi = {10.1371/journal.ppat.1003358}, author = {Chou, Yi-ying and Heaton, Nicholas S and Gao, Qinshan and Palese, Peter and Singer, Robert H and Singer, Robert and Lionnet, Timoth{\'e}e} } @article {46414, title = {Common genetic variation at the IL1RL1 locus regulates IL-33/ST2 signaling.}, journal = {The Journal of Clinical Investigation}, volume = {123}, year = {2013}, month = {2013 Oct}, pages = {4208-18}, abstract = {

The suppression of tumorigenicity 2/IL-33 (ST2/IL-33) pathway has been implicated in several immune and inflammatory diseases. ST2 is produced as 2 isoforms. The membrane-bound isoform (ST2L) induces an immune response when bound to its ligand, IL-33. The other isoform is a soluble protein (sST2) that is thought to be a decoy receptor for IL-33 signaling. Elevated sST2 levels in serum are associated with an increased risk for cardiovascular disease. We investigated the determinants of sST2 plasma concentrations in 2,991 Framingham Offspring Cohort participants. While clinical and environmental factors explained some variation in sST2 levels, much of the variation in sST2 production was driven by genetic factors. In a genome-wide association study (GWAS), multiple SNPs within IL1RL1 (the gene encoding ST2) demonstrated associations with sST2 concentrations. Five missense variants of IL1RL1 correlated with higher sST2 levels in the GWAS and mapped to the intracellular domain of ST2, which is absent in sST2. In a cell culture model, IL1RL1 missense variants increased sST2 expression by inducing IL-33 expression and enhancing IL-33 responsiveness (via ST2L). Our data suggest that genetic variation in IL1RL1 can result in increased levels of sST2 and alter immune and inflammatory signaling through the ST2/IL-33 pathway.

}, keywords = {Amino Acid Substitution, Female, Gene Expression, Gene Expression Regulation, Genetic Association Studies, HEK293 Cells, Humans, Interleukins, Male, Middle Aged, Models, Molecular, Myelin and Lymphocyte-Associated Proteolipid Proteins, Myeloid Differentiation Factor 88, NF-kappa B, Polymorphism, Single Nucleotide, Promoter Regions, Genetic, Prospective Studies, Protein Structure, Tertiary, Receptors, Cell Surface, Signal Transduction, Transcription Factor AP-1}, issn = {1558-8238}, doi = {10.1172/JCI67119}, author = {Ho, Jennifer E and Chen, Wei-Yu and Chen, Ming-Huei and Larson, Martin G and McCabe, Elizabeth L and Cheng, Susan and Ghorbani, Anahita and Coglianese, Erin and Emilsson, Valur and Johnson, Andrew D and Walter, Stefan and Franceschini, Nora and O{\textquoteright}Donnell, Christopher J and Dehghan, Abbas and Lu, Chen and Levy, Daniel and Newton-Cheh, Christopher and Lin, Honghuang and Felix, Janine F and Schreiter, Eric R and Vasan, Ramachandran S and Januzzi, James L and Lee, Richard T and Wang, Thomas J} } @article {46596, title = {Competing dopamine neurons drive oviposition choice for ethanol in Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, year = {2013}, month = {2013 Dec 24}, pages = {21153-8}, abstract = {

The neural circuits that mediate behavioral choice evaluate and integrate information from the environment with internal demands and then initiate a behavioral response. Even circuits that support simple decisions remain poorly understood. In Drosophila melanogaster, oviposition on a substrate containing ethanol enhances fitness; however, little is known about the neural mechanisms mediating this important choice behavior. Here, we characterize the neural modulation of this simple choice and show that distinct subsets of dopaminergic neurons compete to either enhance or inhibit egg-laying preference for ethanol-containing food. Moreover, activity in α{\textquoteright}β{\textquoteright} neurons of the mushroom body and a subset of ellipsoid body ring neurons (R2) is required for this choice. We propose a model where competing dopaminergic systems modulate oviposition preference to adjust to changes in natural oviposition substrates.

}, keywords = {Analysis of Variance, Animals, Choice Behavior, Dopaminergic Neurons, Drosophila melanogaster, Ethanol, Female, Fermentation, Fruit, Mushroom Bodies, Oviposition}, issn = {1091-6490}, doi = {10.1073/pnas.1320208110}, author = {Azanchi, Reza and Kaun, Karla R and Heberlein, Ulrike} } @article {6828, title = {A comprehensive wiring diagram of the protocerebral bridge for visual information processing in the Drosophila brain.}, journal = {Cell Reports}, volume = {3}, year = {2013}, month = {2013 May 30}, pages = {1739-53}, abstract = {

How the brain perceives sensory information and generates meaningful behavior depends critically on its underlying circuitry. The protocerebral bridge (PB) is a major part of the insect central complex (CX), a premotor center that may be analogous to the human basal ganglia. Here, by deconstructing hundreds of PB single neurons and reconstructing them into a common three-dimensional framework, we have constructed a comprehensive map of PB circuits with labeled polarity and predicted directions of information flow. Our analysis reveals a highly ordered information processing system that involves directed information flow among CX subunits through 194 distinct PB neuron types. Circuitry properties such as mirroring, convergence, divergence, tiling, reverberation, and parallel signal propagation were observed; their functional and evolutional significance is discussed. This layout of PB neuronal circuitry may provide guidelines for further investigations on transformation of sensory (e.g., visual) input into locomotor commands in fly brains.

}, keywords = {Animals, Biological, Brain, Drosophila, Models, Neurons}, issn = {2211-1247}, doi = {10.1016/j.celrep.2013.04.022}, author = {Lin, Chih-Yung and Chuang, Chao-Chun and Hua, Tzu-En and Chen, Chun-Chao and Dickson, Barry J and Greenspan, Ralph J and Chiang, Ann-Shyn} } @article {6261, title = {Connectomic reconstruction of the inner plexiform layer in the mouse retina.}, journal = {Nature}, volume = {500}, year = {2013}, month = {2013 Aug 8}, pages = {168-74}, abstract = {

Comprehensive high-resolution structural maps are central to functional exploration and understanding in biology. For the nervous system, in which high resolution and large spatial extent are both needed, such maps are scarce as they challenge data acquisition and analysis capabilities. Here we present for the mouse inner plexiform layer{\textendash}the main computational neuropil region in the mammalian retina{\textendash}the dense reconstruction of 950 neurons and their mutual contacts. This was achieved by applying a combination of crowd-sourced manual annotation and machine-learning-based volume segmentation to serial block-face electron microscopy data. We characterize a new type of retinal bipolar interneuron and show that we can subdivide a known type based on connectivity. Circuit motifs that emerge from our data indicate a functional mechanism for a known cellular response in a ganglion cell that detects localized motion, and predict that another ganglion cell is motion sensitive.

}, keywords = {Amacrine Cells, Animals, Biological, Cell Communication, Computer-Assisted, Connectome, Electron, Image Processing, Inbred C57BL, Mice, Microscopy, Models, Neuropil, Retina, Retinal Ganglion Cells}, issn = {1476-4687}, doi = {10.1038/nature12346}, author = {Helmstaedter, Moritz and Briggman, Kevin L and Turaga, Srinivas C and Jain, Viren and Seung, H Sebastian and Denk, Winfried} } @article {6091, title = {Contributions of the 12 neuron classes in the fly lamina to motion vision.}, journal = {Neuron}, volume = {79}, year = {2013}, month = {07/2013}, pages = {128-140}, abstract = {

Motion detection is a fundamental neural computation performed by many sensory systems. In the fly, local motion computation is thought to occur within the first two layers of the visual system, the lamina and medulla. We constructed specific genetic driver lines for each of the 12 neuron classes in the lamina. We then depolarized and hyperpolarized each neuron type and quantified fly behavioral responses to a diverse set of motion stimuli. We found that only a small number of lamina output neurons are essential for motion detection, while most neurons serve to sculpt and enhance these feedforward pathways. Two classes of feedback neurons (C2 and C3), and lamina output neurons (L2 and L4), are required for normal detection of directional motion stimuli. Our results reveal a prominent role for feedback and lateral interactions in motion processing and demonstrate that motion-dependent behaviors rely on contributions from nearly all lamina neuron classes.

}, doi = {http://dx.doi.org/10.1016/j.neuron.2013.05.024}, author = {Tuthill, John C and Nern, Aljoscha and Stephen L. Holtz and Rubin, Gerald M and Reiser, Michael B} } @article {5893, title = {Convergence of pontine and proprioceptive streams onto multimodal cerebellar granule cells.}, journal = {eLife}, volume = {2}, year = {2013}, month = {2013 Feb 26}, pages = {e00400}, abstract = {

Cerebellar granule cells constitute the majority of neurons in the brain and are the primary conveyors of sensory and motor-related mossy fiber information to Purkinje cells. The functional capability of the cerebellum hinges on whether individual granule cells receive mossy fiber inputs from multiple precerebellar nuclei or are instead unimodal; this distinction is unresolved. Using cell-type-specific projection mapping with synaptic resolution, we observed the convergence of separate sensory (upper body proprioceptive) and basilar pontine pathways onto individual granule cells and mapped this convergence across cerebellar cortex. These findings inform the long-standing debate about the multimodality of mammalian granule cells and substantiate their associative capacity predicted in the Marr-Albus theory of cerebellar function. We also provide evidence that the convergent basilar pontine pathways carry corollary discharges from upper body motor cortical areas. Such merging of related corollary and sensory streams is a critical component of circuit models of predictive motor control. DOI:http://dx.doi.org/10.7554/eLife.00400.001.

}, issn = {2050-084X}, doi = {10.7554/eLife.00400}, author = {Huang, Cheng-Chiu and Sugino, Ken and Shima, Yasuyuki and Guo, Caiying and Bai, Suxia and Mensh, Brett D and Nelson, Sacha B and Hantman, Adam W} } @article {6712, title = {Correlative photoactivated localization and scanning electron microscopy.}, journal = {PLoS One}, volume = {8}, year = {2013}, month = {2013 Oct 25}, pages = {e77209}, abstract = {

The ability to localize proteins precisely within subcellular space is crucial to understanding the functioning of biological systems. Recently, we described a protocol that correlates a precise map of fluorescent fusion proteins localized using three-dimensional super-resolution optical microscopy with the fine ultrastructural context of three-dimensional electron micrographs. While it achieved the difficult simultaneous objectives of high photoactivated fluorophore preservation and ultrastructure preservation, it required a super-resolution optical and specialized electron microscope that is not available to many researchers. We present here a faster and more practical protocol with the advantage of a simpler two-dimensional optical (Photoactivated Localization Microscopy (PALM)) and scanning electron microscope (SEM) system that retains the often mutually exclusive attributes of fluorophore preservation and ultrastructure preservation. As before, cryosections were prepared using the Tokuyasu protocol, but the staining protocol was modified to be amenable for use in a standard SEM without the need for focused ion beam ablation. We show the versatility of this technique by labeling different cellular compartments and structures including mitochondrial nucleoids, peroxisomes, and the nuclear lamina. We also demonstrate simultaneous two-color PALM imaging with correlated electron micrographs. Lastly, this technique can be used with small-molecule dyes as demonstrated with actin labeling using phalloidin conjugated to a caged dye. By retaining the dense protein labeling expected for super-resolution microscopy combined with ultrastructural preservation, simplifying the tools required for correlative microscopy, and expanding the number of useful labels we expect this method to be accessible and valuable to a wide variety of researchers.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0077209}, author = {Kopek, Benjamin G and Shtengel, Gleb and Grimm, Jonathan B and Clayton, David A and Hess, Harald F} } @article {6285, title = {Dfam: a database of repetitive DNA based on profile hidden Markov models.}, journal = {Nucleic Acids Research}, volume = {41}, year = {2013}, month = {2013 Jan}, pages = {D70-82}, abstract = {

We present a database of repetitive DNA elements, called Dfam (http://dfam.janelia.org). Many genomes contain a large fraction of repetitive DNA, much of which is made up of remnants of transposable elements (TEs). Accurate annotation of TEs enables research into their biology and can shed light on the evolutionary processes that shape genomes. Identification and masking of TEs can also greatly simplify many downstream genome annotation and sequence analysis tasks. The commonly used TE annotation tools RepeatMasker and Censor depend on sequence homology search tools such as cross_match and BLAST variants, as well as Repbase, a collection of known TE families each represented by a single consensus sequence. Dfam contains entries corresponding to all Repbase TE entries for which instances have been found in the human genome. Each Dfam entry is represented by a profile hidden Markov model, built from alignments generated using RepeatMasker and Repbase. When used in conjunction with the hidden Markov model search tool nhmmer, Dfam produces a 2.9\% increase in coverage over consensus sequence search methods on a large human benchmark, while maintaining low false discovery rates, and coverage of the full human genome is 54.5\%. The website provides a collection of tools and data views to support improved TE curation and annotation efforts. Dfam is also available for download in flat file format or in the form of MySQL table dumps.

}, keywords = {Databases, DNA Transposable Elements, Genome, Human, Humans, Internet, Markov Chains, Models, Molecular Sequence Annotation, Nucleic Acid, Statistical}, issn = {1362-4962}, doi = {10.1093/nar/gks1265}, author = {Wheeler, Travis J and Clements, Jody and Eddy, Sean R. and Hubley, Robert and Jones, Thomas A and Jurka, Jerzy and Smit, Arian F A and Finn, Robert D} } @article {6275, title = {A directional tuning map of Drosophila elementary motion detectors.}, journal = {Nature}, volume = {500}, year = {2013}, month = {2013 Aug 8}, pages = {212-6}, abstract = {

The extraction of directional motion information from changing retinal images is one of the earliest and most important processing steps in any visual system. In the fly optic lobe, two parallel processing streams have been anatomically described, leading from two first-order interneurons, L1 and L2, via T4 and T5 cells onto large, wide-field motion-sensitive interneurons of the lobula plate. Therefore, T4 and T5 cells are thought to have a pivotal role in motion processing; however, owing to their small size, it is difficult to obtain electrical recordings of T4 and T5 cells, leaving their visual response properties largely unknown. We circumvent this problem by means of optical recording from these cells in Drosophila, using the genetically encoded calcium indicator GCaMP5 (ref. 2). Here we find that specific subpopulations of T4 and T5 cells are directionally tuned to one of the four cardinal directions; that is, front-to-back, back-to-front, upwards and downwards. Depending on their preferred direction, T4 and T5 cells terminate in specific sublayers of the lobula plate. T4 and T5 functionally segregate with respect to contrast polarity: whereas T4 cells selectively respond to moving brightness increments (ON edges), T5 cells only respond to moving brightness decrements (OFF edges). When the output from T4 or T5 cells is blocked, the responses of postsynaptic lobula plate neurons to moving ON (T4 block) or OFF edges (T5 block) are selectively compromised. The same effects are seen in turning responses of tethered walking flies. Thus, starting with L1 and L2, the visual input is split into separate ON and OFF pathways, and motion along all four cardinal directions is computed separately within each pathway. The output of these eight different motion detectors is then sorted such that ON (T4) and OFF (T5) motion detectors with the same directional tuning converge in the same layer of the lobula plate, jointly providing the input to downstream circuits and motion-driven behaviours.

}, keywords = {Animal, Animals, Behavior, Drosophila, Interneurons, Locomotion, Motion Perception, Neurons, Signal Transduction, Visual Pathways}, issn = {1476-4687}, doi = {10.1038/nature12320}, author = {Maisak, Matthew S and Haag, Juergen and Ammer, Georg and Serbe, Etienne and Meier, Matthias and Leonhardt, Aljoscha and Schilling, Tabea and Bahl, Armin and Rubin, Gerald M and Nern, Aljoscha and Dickson, Barry J and Reiff, Dierk F and Hopp, Elisabeth and Borst, Alexander} } @article {6588, title = {Distinct balance of excitation and inhibition in an interareal feedforward and feedback circuit of mouse visual cortex.}, journal = {The Journal of Neuroscience}, volume = {33}, year = {2013}, month = {2013 Oct 30}, pages = {17373-84}, abstract = {

Mouse visual cortex is subdivided into multiple distinct, hierarchically organized areas that are interconnected through feedforward (FF) and feedback (FB) pathways. The principal synaptic targets of FF and FB axons that reciprocally interconnect primary visual cortex (V1) with the higher lateromedial extrastriate area (LM) are pyramidal cells (Pyr) and parvalbumin (PV)-expressing GABAergic interneurons. Recordings in slices of mouse visual cortex have shown that layer 2/3 Pyr cells receive excitatory monosynaptic FF and FB inputs, which are opposed by disynaptic inhibition. Most notably, inhibition is stronger in the FF than FB pathway, suggesting pathway-specific organization of feedforward inhibition (FFI). To explore the hypothesis that this difference is due to diverse pathway-specific strengths of the inputs to PV neurons we have performed subcellular Channelrhodopsin-2-assisted circuit mapping in slices of mouse visual cortex. Whole-cell patch-clamp recordings were obtained from retrobead-labeled FFV1{\textrightarrow}LM- and FBLM{\textrightarrow}V1-projecting Pyr cells, as well as from tdTomato-expressing PV neurons. The results show that the FFV1{\textrightarrow}LM pathway provides on average 3.7-fold stronger depolarizing input to layer 2/3 inhibitory PV neurons than to neighboring excitatory Pyr cells. In the FBLM{\textrightarrow}V1 pathway, depolarizing inputs to layer 2/3 PV neurons and Pyr cells were balanced. Balanced inputs were also found in the FFV1{\textrightarrow}LM pathway to layer 5 PV neurons and Pyr cells, whereas FBLM{\textrightarrow}V1 inputs to layer 5 were biased toward Pyr cells. The findings indicate that FFI in FFV1{\textrightarrow}LM and FBLM{\textrightarrow}V1 circuits are organized in a pathway- and lamina-specific fashion.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.2515-13.2013}, author = {Yang, Weiguo and Carrasquillo, Yarimar and Hooks, Bryan M and Nerbonne, Jeanne M and Burkhalter, Andreas} } @article {6277, title = {Diverse neuronal lineages make stereotyped contributions to the Drosophila locomotor control center, the central complex.}, journal = {The Journal of Comparative Neurology}, volume = {521}, year = {2013}, month = {2013 Aug 15}, pages = {2645-62, Spc1}, abstract = {

The Drosophila central brain develops from a fixed number of neuroblasts. Each neuroblast makes a clone of neurons that exhibit common trajectories. Here we identified 15 distinct clones that carry larval-born neurons innervating the Drosophila central complex (CX), which consists of four midline structures including the protocerebral bridge (PB), fan-shaped body (FB), ellipsoid body (EB), and noduli (NO). Clonal analysis revealed that the small-field CX neurons, which establish intricate projections across different CX substructures, exist in four isomorphic groups that respectively derive from four complex posterior asense-negative lineages. In terms of the region-characteristic large-field CX neurons, we found that two lineages make PB neurons, 10 lineages produce FB neurons, three lineages generate EB neurons, and two lineages yield NO neurons. The diverse FB developmental origins reflect the discrete input pathways for different FB subcompartments. Clonal analysis enlightens both development and anatomy of the insect locomotor control center.

}, issn = {1096-9861}, doi = {10.1002/cne.23339}, author = {Yang, Jacob S and Awasaki, Takeshi and Yu, Hung-Hsiang and He, Yisheng and Ding, Peng and Kao, Jui-Chun and Lee, Tzumin} } @article {47900, title = {Dynamic Bayesian clustering.}, journal = {Journal of bioinformatics and computational biology}, volume = {11}, year = {2013}, month = {2013 Oct}, pages = {1342001}, abstract = {

Clusters of time series data may change location and memberships over time; in gene expression data, this occurs as groups of genes or samples respond differently to stimuli or experimental conditions at different times. In order to uncover this underlying temporal structure, we consider dynamic clusters with time-dependent parameters which split and merge over time, enabling cluster memberships to change. These interesting time-dependent structures are useful in understanding the development of organisms or complex organs, and could not be identified using traditional clustering methods. In cell cycle data, these time-dependent structure may provide links between genes and stages of the cell cycle, whilst in developmental data sets they may highlight key developmental transitions.

}, keywords = {Algorithms, Animals, Bayes Theorem, Brain, Cell Cycle, Cluster Analysis, Computational Biology, Databases, Genetic, Gene Expression Regulation, Developmental, Markov Chains, Mice, Models, Statistical, Monte Carlo Method}, issn = {1757-6334}, doi = {10.1142/S0219720013420018}, author = {Fowler, Anna and Menon, Vilas and Heard, Nicholas A} } @article {6676, title = {Electron microscopy reconstruction of brain structure using sparse representations over learned dictionaries.}, journal = {IEEE Transactions on Medical Imaging}, volume = {32}, year = {2013}, month = {2013 Aug 2}, pages = {2179-88}, abstract = {

A central problem in neuroscience is reconstructing neuronal circuits on the synapse level. Due to a wide range of scales in brain architecture such reconstruction requires imaging that is both high-resolution and high-throughput. Existing electron microscopy (EM) techniques possess required resolution in the lateral plane and either high-throughput or high depth resolution but not both. Here, we exploit recent advances in unsupervised learning and signal processing to obtain high depth-resolution EM images computationally without sacrificing throughput. First, we show that the brain tissue can be represented as a sparse linear combination of localized basis functions that are learned using high-resolution datasets. We then develop compressive sensing-inspired techniques that can reconstruct the brain tissue from very few (typically 5) tomographic views of each section. This enables tracing of neuronal processes and, hence, high throughput reconstruction of neural circuits on the level of individual synapses.

}, issn = {1558-254X}, doi = {10.1109/TMI.2013.2276018}, author = {Hu, Tao and Nunez-Iglesias, Juan and Vitaladevuni, Shiv and Scheffer, Lou and Xu, Shan and Bolorizadeh, Mehdi and Hess, Harald and Fetter, Richard and Chklovskii, Dmitri} } @article {6270, title = {Essential role of the mushroom body in context-dependent CO2 avoidance in Drosophila.}, journal = {Current Biology}, volume = {23}, year = {2013}, month = {2013 Jul 8}, pages = {1228-34}, abstract = {

Internal state as well as environmental conditions influence choice behavior. The neural circuits underpinning state-dependent behavior remain largely unknown. Carbon dioxide (CO2) is an important olfactory cue for many insects, including mosquitoes, flies, moths, and honeybees [1]. Concentrations of CO2 higher than 0.02\% above atmospheric level trigger a strong innate avoidance in the fly Drosophila melanogaster [2, 3]. Here, we show that the mushroom body (MB), a brain center essential for olfactory associative memories [4-6] but thought to be dispensable for innate odor processing [7], is essential for CO2 avoidance behavior only in the context of starvation or in the context of a food-related odor. Consistent with this, CO2 stimulation elicits Ca(2+) influx into the MB intrinsic cells (Kenyon cells: KCs) in\ vivo. We identify an atypical projection neuron (bilateral ventral projection neuron, biVPN) that connects CO2 sensory input bilaterally to the MB calyx. Blocking synaptic output of the biVPN completely abolishes CO2 avoidance in food-deprived flies, but not in fed flies. These findings show that two alternative neural pathways control innate choice behavior, and they are dependent on the animal{\textquoteright}s internal state. In addition, they suggest that, during innate choice behavior, the MB serves as an integration site for internal state and olfactory input.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2013.05.029}, author = {Br{\"a}cker, Lasse B and Siju, K P and Varela, N{\'e}lia and Aso, Yoshinori and Zhang, Mo and Hein, Irina and Vasconcelos, Maria Lu{\'\i}sa and Grunwald Kadow, Ilona C} } @article {46599, title = {The evolution of Drosophila melanogaster as a model for alcohol research.}, journal = {Annual Reviews of Neuroscience}, volume = {36}, year = {2013}, month = {2013 Jul 8}, pages = {121-38}, abstract = {

Animal models have been widely used to gain insight into the mechanisms underlying the acute and long-term effects of alcohol exposure. The fruit fly Drosophila melanogaster encounters ethanol in its natural habitat and possesses many adaptations that allow it to survive and thrive in ethanol-rich environments. Several assays to study ethanol-related behaviors in flies, ranging from acute intoxication to self-administration and reward, have been developed in the past 20 years. These assays have provided the basis for studying the physiological and behavioral effects of ethanol and for identifying genes mediating these effects. In this review we describe the ecological relationship between flies and ethanol, the effects of ethanol on fly development and behavior, the use of flies as a model for alcohol addiction, and the interaction between ethanol and social behavior. We discuss these advances in the context of their utility to help decipher the mechanisms underlying the diverse effects of ethanol, including those that mediate ethanol dependence and addiction in humans.

}, keywords = {Alcoholism, Animals, Biological Evolution, Disease Models, Animal, Drosophila melanogaster, Ethanol, Humans, Reward, Self Administration}, issn = {1545-4126}, doi = {10.1146/annurev-neuro-062012-170256}, author = {Devineni, Anita V and Heberlein, Ulrike} } @conference {48833, title = {Extracting regions of interest from biological images with convolutional sparse block coding.}, booktitle = {Neural Information Processing Systems (NIPS 2013)}, year = {2013}, month = {2013 Dec 05}, address = {Lake Tahoe}, abstract = {

Biological tissue is often composed of cells with similar morphologies replicated throughout large volumes and many biological applications rely on the accurate identification of these cells and their locations from image data. Here we develop a generative model that captures the regularities present in images composed of repeating elements of a few different types. Formally, the model can be described as convolutional sparse block coding. For inference we use a variant of convolutional matching pursuit adapted to block-based representations. We extend the K-SVD learning algorithm to subspaces by retaining several principal vectors from the SVD decomposition instead of just one. Good models with little cross-talk between subspaces can be obtained by learning the blocks incrementally. We perform extensive experiments on simulated images and the inference algorithm consistently recovers a large proportion of the cells with a small number of false positives. We fit the convolutional model to noisy GCaMP6 two-photon images of spiking neurons and to Nissl-stained slices of cortical tissue and show that it recovers cell body locations without supervision. The flexibility of the block-based representation is reflected in the variability of the recovered cell shapes.

}, url = {http://papers.nips.cc/paper/5167-extracting-regions-of-interest-from-biological-images-with-convolutional-sparse-block-coding}, author = {Pachitariu, Marius and Packer, Adam M and Pettit, Noah and Dalgleish, Henry and H{\"a}usser, Michael and Sahani, Maneesh} } @article {6454, title = {Extremes of lineage plasticity in the Drosophila brain.}, journal = {Current Biology}, volume = {23}, year = {2013}, month = {2013 Sep 19}, pages = {1908-13}, abstract = {

An often-overlooked aspect of neural plasticity is the plasticity of neuronal composition, in which the numbers of neurons of particular classes are altered in response to environment and experience. The Drosophila brain features several well-characterized lineages in which a single neuroblast gives rise to multiple neuronal classes in a stereotyped sequence during development [1]. We find that in the\ intrinsic mushroom body neuron lineage, the numbers for each class are highly plastic, depending on the timing of temporal fate transitions and the rate of neuroblast proliferation. For example, mushroom body neuroblast cycling can continue under starvation conditions, uncoupled from\ temporal fate transitions that depend on extrinsic cues reflecting organismal growth and development. In contrast, the proliferation rates of antennal lobe lineages are closely associated with organismal development, and\ their temporal fate changes appear to be cell cycle-dependent, such that the same numbers and types of uniglomerular projection neurons innervate the antennal lobe following various perturbations. We propose that this surprising difference in plasticity for these brain lineages is adaptive, given their respective roles as parallel\ processors versus discrete carriers of olfactory information.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2013.07.074}, author = {Lin, Suewei and Marin, Elizabeth C and Yang, Ching-Po and Kao, Chih-Fei and Apenteng, Bettye A and Huang, Yaling and O{\textquoteright}Connor, Michael B and Truman, James W and Lee, Tzumin} } @article {5522, title = {Fast multicolor 3D imaging using aberration-corrected multifocus microscopy.}, journal = {Nature Methods}, volume = {10}, year = {2013}, month = {2013}, pages = {60-3}, abstract = {

Conventional acquisition of three-dimensional (3D) microscopy data requires sequential z scanning and is often too slow to capture biological events. We report an aberration-corrected multifocus microscopy method capable of producing an instant focal stack of nine 2D images. Appended to an epifluorescence microscope, the multifocus system enables high-resolution 3D imaging in multiple colors with single-molecule sensitivity, at speeds limited by the camera readout time of a single image.

}, issn = {1548-7105}, doi = {10.1038/nmeth.2277}, author = {Abrahamsson, Sara and Chen, Jiji and Hajj, Bassam and Stallinga, Sjoerd and Katsov, Alexander Y and Wisniewski, Jan and Mizuguchi, Gaku and Soule, Pierre and Mueller, Florian and Darzacq, Claire Dugast and Darzacq, Xavier and Wu, Carl and Bargmann, Cornelia I and Agard, David A and Dahan, Maxime and Gustafsson, Mats G L} } @article {46714, title = {The fate of the messenger is pre-determined: a new model for regulation of gene expression.}, journal = {Biochimica et Biophysica Acta (BBA)}, volume = {1829}, year = {2013}, month = {2013 Jun-Jul}, pages = {643-53}, abstract = {

Recent years have seen a rise in publications demonstrating coupling between transcription and mRNA decay. This coupling most often accompanies cellular processes that involve transitions in gene expression patterns, for example during mitotic division and cellular differentiation and in response to cellular stress. Transcription can affect the mRNA fate by multiple mechanisms. The most novel finding is the process of co-transcriptional imprinting of mRNAs with proteins, which in turn regulate cytoplasmic mRNA stability. Transcription therefore is not only a catalyst of mRNA synthesis but also provides a platform that enables imprinting, which coordinates between transcription and mRNA decay. Here we present an overview of the literature, which provides the evidence of coupling between transcription and decay, review the mechanisms and regulators by which the two processes are coupled, discuss why such coupling is beneficial and present a new model for regulation of gene expression. This article is part of a Special Issue entitled: RNA Decay mechanisms.

}, keywords = {Cytoplasm, Gene Expression Regulation, Fungal, Genomic Imprinting, Humans, Poly(A)-Binding Proteins, Ribonucleases, RNA Polymerase II, RNA Stability, RNA, Messenger, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Transcription, Genetic}, issn = {0006-3002}, doi = {10.1016/j.bbagrm.2013.01.004}, author = {Haimovich, Gal and Choder, Mordechai and Singer, Robert H and Trcek, Tatjana} } @article {6541, title = {Genetically encoded calcium indicators for multi-color neural activity imaging and combination with optogenetics.}, journal = {Frontiers in Molecular Neuroscience}, volume = {6}, year = {2013}, month = {2013 Mar 4}, pages = {2}, abstract = {

Genetically encoded calcium indicators (GECIs) are powerful tools for systems neuroscience. Here we describe red, single-wavelength GECIs, "RCaMPs," engineered from circular permutation of the thermostable red fluorescent protein mRuby. High-resolution crystal structures of mRuby, the red sensor RCaMP, and the recently published red GECI R-GECO1 give insight into the chromophore environments of the Ca(2+)-bound state of the sensors and the engineered protein domain interfaces of the different indicators. We characterized the biophysical properties and performance of RCaMP sensors in vitro and in vivo in Caenorhabditis elegans, Drosophila larvae, and larval zebrafish. Further, we demonstrate 2-color calcium imaging both within the same cell (registering mitochondrial and somatic [Ca(2+)]) and between two populations of cells: neurons and astrocytes. Finally, we perform integrated optogenetics experiments, wherein neural activation via channelrhodopsin-2 (ChR2) or a red-shifted variant, and activity imaging via RCaMP or GCaMP, are conducted simultaneously, with the ChR2/RCaMP pair providing independently addressable spectral channels. Using this paradigm, we measure calcium responses of naturalistic and ChR2-evoked muscle contractions in vivo in crawling C. elegans. We systematically compare the RCaMP sensors to R-GECO1, in terms of action potential-evoked fluorescence increases in neurons, photobleaching, and photoswitching. R-GECO1 displays higher Ca(2+) affinity and larger dynamic range than RCaMP, but exhibits significant photoactivation with blue and green light, suggesting that integrated channelrhodopsin-based optogenetics using R-GECO1 may be subject to artifact. Finally, we create and test blue, cyan, and yellow variants engineered from GCaMP by rational design. This engineered set of chromatic variants facilitates new experiments in functional imaging and optogenetics.

}, issn = {1662-5099}, doi = {10.3389/fnmol.2013.00002}, author = {Akerboom, Jasper and Carreras Calder{\'o}n, Nicole and Tian, Lin and Wabnig, Sebastian and Prigge, Matthias and Tol{\"o}, Johan and Gordus, Andrew and Orger, Michael B. and Severi, Kristen E and Macklin, John J and Patel, Ronak and Pulver, Stefan R and Wardill, Trevor J. and Fischer, Elisabeth and Sch{\"u}ler, Christina and Chen, Tsai-Wen and Sarkisyan, Karen S and Marvin, Jonathan S and Bargmann, Cornelia I and Kim, Douglas S. and K{\"u}gler, Sebastian and Lagnado, Leon and Hegemann, Peter and Gottschalk, Alexander and Schreiter, Eric R and Looger, Loren L} } @article {6262, title = {High-throughput analysis of stimulus-evoked behaviors in Drosophila larva reveals multiple modality-specific escape strategies.}, journal = {PLoS One}, volume = {8}, year = {2013}, month = {2013 Aug 20}, pages = {e71706}, abstract = {

All organisms react to noxious and mechanical stimuli but we still lack a complete understanding of cellular and molecular mechanisms by which somatosensory information is transformed into appropriate motor outputs. The small number of neurons and excellent genetic tools make Drosophila larva an especially tractable model system in which to address this problem. We developed high throughput assays with which we can simultaneously expose more than 1,000 larvae per man-hour to precisely timed noxious heat, vibration, air current, or optogenetic stimuli. Using this hardware in combination with custom software we characterized larval reactions to somatosensory stimuli in far greater detail than possible previously. Each stimulus evoked a distinctive escape strategy that consisted of multiple actions. The escape strategy was context-dependent. Using our system we confirmed that the nociceptive class IV multidendritic neurons were involved in the reactions to noxious heat. Chordotonal (ch) neurons were necessary for normal modulation of head casting, crawling and hunching, in response to mechanical stimuli. Consistent with this we observed increases in calcium transients in response to vibration in ch neurons. Optogenetic activation of ch neurons was sufficient to evoke head casting and crawling. These studies significantly increase our understanding of the functional roles of larval ch neurons. More generally, our system and the detailed description of wild type reactions to somatosensory stimuli provide a basis for systematic identification of neurons and genes underlying these behaviors.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0071706}, author = {Ohyama, Tomoko and Jovanic, Tihana and Denisov, Gennady and Dang, Tam C and Hoffmann, Dominik and Kerr, Rex A and Zlatic, Marta} } @article {68819, title = {Hindbrain V2a Neurons in the Excitation of Spinal Locomotor Circuits during Zebrafish Swimming}, journal = {Current Biology}, volume = {23}, year = {2013}, month = {05/2013}, pages = {843-849}, abstract = {

During locomotion in vertebrates, reticulospinal neurons in the hindbrain play critical roles in providing descending excitation to the spinal cord locomotor systems. However, despite the fact that many genes that are used to classify the neuronal identities of neurons in the hindbrain have been identified, the molecular identity of the reticulospinal neurons that are critically involved in locomotor drive is not well understood. Chx10-expressing neurons (V2a neurons) are ipsilaterally projecting glutamatergic neurons in the spinal cord and the hindbrain. Many of the V2a neurons in the hindbrain are known to project to the spinal cord in zebrafish, making hindbrain V2a neurons a prime candidate in descending locomotor drive. Results We investigated the roles of hindbrain V2a neurons using optogenetic and electrophysiological approaches. The forced activation of hindbrain V2a neurons using channelrhodopsin efficiently evoked swimming, whereas the forced inactivation of them using Archearhodopsin3 or Halorhodpsin reliably stopped ongoing swimming. Electrophysiological recordings of two populations of hindbrain reticulospinal V2a neurons showed that they were active during swimming. One population of neurons, small V2a neurons in the caudal hindbrain, fired with low rhythmicity, whereas the other population of neurons, large reticulospinal V2a neurons, called MiV1 neurons, fired more rhythmically. Conclusions These results indicated that hindbrain reticulospinal V2a neurons play critical roles in providing excitation to the spinal locomotor circuits during swimming by providing both tonic and phasic inputs to the circuits.

}, issn = {0960-9822}, doi = {https://doi.org/10.1016/j.cub.2013.03.066}, url = {https://www.sciencedirect.com/science/article/pii/S0960982213003680}, author = {Yukiko Kimura and Chie Satou and Shunji Fujioka and Wataru Shoji and Keiko Umeda and Toru Ishizuka and Hiromu Yawo and Shin-ichi Higashijima} } @article {47220, title = {Imaging a population code for odor identity in the Drosophila mushroom body.}, journal = {The Journal of Neuroscience : the official journal of the Society for Neuroscience}, volume = {33}, year = {2013}, month = {2013 Jun 19}, pages = {10568-81}, abstract = {

The brain represents sensory information in the coordinated activity of neuronal ensembles. Although the microcircuits underlying olfactory processing are well characterized in Drosophila, no studies to date have examined the encoding of odor identity by populations of neurons and related it to the odor specificity of olfactory behavior. Here we used two-photon Ca(2+) imaging to record odor-evoked responses from \>100 neurons simultaneously in the Drosophila mushroom body (MB). For the first time, we demonstrate quantitatively that MB population responses contain substantial information on odor identity. Using a series of increasingly similar odor blends, we identified conditions in which odor discrimination is difficult behaviorally. We found that MB ensemble responses accounted well for olfactory acuity in this task. Kenyon cell ensembles with as few as 25 cells were sufficient to match behavioral discrimination accuracy. Using a generalization task, we demonstrated that the MB population code could predict the flies{\textquoteright} responses to novel odors. The degree to which flies generalized a learned aversive association to unfamiliar test odors depended upon the relative similarity between the odors{\textquoteright} evoked MB activity patterns. Discrimination and generalization place different demands on the animal, yet the flies{\textquoteright} choices in these tasks were reliably predicted based on the amount of overlap between MB activity patterns. Therefore, these different behaviors can be understood in the context of a single physiological framework.

}, keywords = {Animals, Calcium, Discrimination (Psychology), Drosophila, Generalization (Psychology), Image Processing, Computer-Assisted, Learning, Linear Models, Mushroom Bodies, Neuroimaging, Odors, Olfactory Pathways, Olfactory Perception, Psychomotor Performance, Synaptic Transmission}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0682-12.2013}, author = {Campbell, Robert A A and Honegger, Kyle S and Qin, Hongtao and Li, Wanhe and Demir, Ebru and Turner, Glenn C} } @article {46575, title = {Inferring neural population dynamics from multiple partial recordings of the same neural circuit.}, journal = {Advances in Neural Information Processing Systems (NIPS) }, volume = {26}, year = {2013}, month = {2013}, abstract = {

Simultaneous recordings of the activity of large neural populations are extremely valuable as they can be used to infer the dynamics and interactions of neurons in a local circuit, shedding light on the computations performed. It is now possible to measure the activity of hundreds of neurons using 2-photon calcium imaging. However, many computations are thought to involve circuits consisting of thousands of neurons, such as cortical barrels in rodent somatosensory cortex. Here we contribute a statistical method for stitching" together sequentially imaged sets of neurons into one model by phrasing the problem as fitting a latent dynamical system with missing observations. This method allows us to substantially expand the population-sizes for which population dynamics can be characterized---beyond the number of simultaneously imaged neurons. In particular, we demonstrate using recordings in mouse somatosensory cortex that this method makes it possible to predict noise correlations between non-simultaneously recorded neuron pairs.

}, url = {http://papers.nips.cc/paper/4874-inferring-neural-population-dynamics-from-multiple-partial-recordings-of-the-same-neural-circuit}, author = {Turaga, Srinivas C and Buesing, Lars and Packer, Adam M. and Dalgleish, Henry and Pettit, Noah and H{\"a}usser, Michael and Macke, Jakob H.} } @article {6291, title = {A localized Wnt signal orients asymmetric stem cell division in vitro.}, journal = {Science}, volume = {339}, year = {2013}, month = {2013 Mar 22}, pages = {1445-8}, abstract = {

Developmental signals such as Wnts are often presented to cells in an oriented manner. To examine the consequences of local Wnt signaling, we immobilized Wnt proteins on beads and introduced them to embryonic stem cells in culture. At the single-cell level, the Wnt-bead induced asymmetric distribution of Wnt-β-catenin signaling components, oriented the plane of mitotic division, and directed asymmetric inheritance of centrosomes. Before cytokinesis was completed, the Wnt-proximal daughter cell expressed high levels of nuclear β-catenin and pluripotency genes, whereas the distal daughter cell acquired hallmarks of differentiation. We suggest that a spatially restricted Wnt signal induces an oriented cell division that generates distinct cell fates at predictable positions relative to the Wnt source.

}, keywords = {Animals, Asymmetric Cell Division, beta Catenin, Cell Differentiation, Cells, Centrosome, Cultured, Cytokinesis, Embryonic Stem Cells, Gene Expression, Homeodomain Proteins, Mice, Mitosis, Octamer Transcription Factor-3, Pluripotent Stem Cells, Recombinant Proteins, Single-Cell Analysis, Transcription Factors, Wnt Proteins, Wnt Signaling Pathway, Wnt3A Protein}, issn = {1095-9203}, doi = {10.1126/science.1231077}, author = {Habib, Shukry J and Chen, Bi-Chang and Tsai, Feng-Chiao and Anastassiadis, Konstantinos and Meyer, Tobias and Betzig, Eric and Nusse, Roel} } @article {6324, title = {Location of the dsRNA-dependent polymerase, VP1, in rotavirus particles.}, journal = {Journal of Molecular Biology}, volume = {425}, year = {2013}, month = {2013 Jan 9}, pages = {124-32}, abstract = {

Double-stranded RNA (dsRNA) viruses transcribe and replicate RNA within an assembled, inner capsid particle; only plus-sense mRNA emerges into the intracellular milieu. During infectious entry of a rotavirus particle, the outer layer of its three-layer structure dissociates, delivering the inner double-layered particle (DLP) into the cytosol. DLP structures determined by X-ray crystallography and electron cryomicroscopy (cryoEM) show that the RNA coils uniformly into the particle interior, avoiding a "fivefold hub" of more structured density projecting inward from the VP2 shell of the DLP along each of the twelve 5-fold axes. Analysis of the X-ray crystallographic electron density map suggested that principal contributors to the hub are the N-terminal arms of VP2, but reexamination of the cryoEM map has shown that many features come from a molecule of VP1, randomly occupying five equivalent and partly overlapping positions. We confirm here that the electron density in the X-ray map leads to the same conclusion, and we describe the functional implications of the orientation and position of the polymerase. The exit channel for the nascent transcript directs the nascent transcript toward an opening along the 5-fold axis. The template strand enters from within the particle, and the dsRNA product of the initial replication step exits in a direction tangential to the inner surface of the VP2 shell, allowing it to coil optimally within the DLP. The polymerases of reoviruses appear to have similar positions and functional orientations.

}, keywords = {Capsid, Computer-Assisted, Cryoelectron Microscopy, Crystallography, Double-Stranded, Image Processing, Messenger, Models, Molecular, RNA, Rotavirus, Viral, Viral Core Proteins, Virus Assembly, X-Ray}, issn = {1089-8638}, doi = {10.1016/j.jmb.2012.10.011}, author = {Estrozi, Leandro F and Settembre, Ethan C and Goret, Ga{\"e}l and McClain, Brian and Zhang, Xing and Chen, James Z and Grigorieff, Nikolaus and Harrison, Stephen C} } @article {6144, title = {A low-bandwidth camera sensor platform with applications in smart camera networks.}, journal = {ACM Transactions on Sensor Networks}, volume = {9}, year = {2013}, month = {2013 Mar}, abstract = {

Smart camera networks have recently emerged as a new class of sensor network infrastructure that is capable of supporting high-power in-network signal processing and enabling a wide range of applications. In this article, we provide an exposition of our efforts to build a low-bandwidth wireless camera network platform, called CITRIC, and its applications in smart camera networks. The platform integrates a camera, a microphone, a frequency-scalable (up to 624 MHz) CPU, 16 MB FLASH, and 64 MB RAM onto a single device. The device then connects with a standard sensor network mote to form a wireless camera mote. With reasonably low power consumption and extensive algorithmic libraries running on a decent operating system that is easy to program, CITRIC is ideal for research and applications in distributed image and video processing. Its capabilities of in-network image processing also reduce communication requirements, which has been high in other existing camera networks with centralized processing. Furthermore, the mote easily integrates with other low-bandwidth sensor networks via the IEEE 802.15.4 protocol. To justify the utility of CITRIC, we present several representative applications. In particular, concrete research results will be demonstrated in two areas, namely, distributed coverage hole identification and distributed object recognition.

}, issn = {1550-4859}, url = {http://dl.acm.org/citation.cfm?doid=2422966.2422978}, author = {Phoebus Chen and Kirak Hong and Nikhil Naikal and S. Shankar Sastry and Doug Tygar and Yan, Posu and Yang, Allen and Chang, Lung-Chung and Lin, Leon and Wang, Simon and Lobaton, Edgar and Oh, Songhwai and Ahammad, Parvez} } @article {6158, title = {The mechanical variables underlying object localization along the axis of the whisker.}, journal = {The Journal of Neuroscience}, volume = {33}, year = {2013}, month = {2013 Apr 17}, pages = {6726-41}, abstract = {

Rodents move their whiskers to locate objects in space. Here we used psychophysical methods to show that head-fixed mice can localize objects along the axis of a single whisker, the radial dimension, with one-millimeter precision. High-speed videography allowed us to estimate the forces and bending moments at the base of the whisker, which underlie radial distance measurement. Mice judged radial object location based on multiple touches. Both the number of touches (1-17) and the forces exerted by the pole on the whisker (up to 573 μN; typical peak amplitude, 100 μN) varied greatly across trials. We manipulated the bending moment and lateral force pressing the whisker against the sides of the follicle and the axial force pushing the whisker into the follicle by varying the compliance of the object during behavior. The behavioral responses suggest that mice use multiple variables (bending moment, axial force, lateral force) to extract radial object localization. Characterization of whisker mechanics revealed that whisker bending stiffness decreases gradually with distance from the face over five orders of magnitude. As a result, the relative amplitudes of different stress variables change dramatically with radial object distance. Our data suggest that mice use distance-dependent whisker mechanics to estimate radial object location using an algorithm that does not rely on precise control of whisking, is robust to variability in whisker forces, and is independent of object compliance and object movement. More generally, our data imply that mice can measure the amplitudes of forces in the sensory follicles for tactile sensation.

}, keywords = {Algorithms, Animals, Biological, Computer Simulation, Corneal Topography, Cues, Decision Making, Electron, Exploratory Behavior, Functional Laterality, Inbred C57BL, Male, Mice, Microscopy, Models, Physical Stimulation, Psychophysics, Scanning, Time Factors, Touch, Vibrissae}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4316-12.2013}, author = {Pammer, Lorenz and O{\textquoteright}Connor, Daniel H and Hires, S Andrew and Clack, Nathan G and Huber, Daniel and Myers, Eugene W and Svoboda, Karel} } @article {6486, title = {Mechanisms of retroaxonal barrage firing in hippocampal interneurons.}, journal = {The Journal of Physiology}, volume = {591}, year = {2013}, month = {2013 Oct 1}, pages = {4793-805}, abstract = {

Abstract We recently described a new form of neural integration and firing in a subset of interneurons, in which evoking hundreds of action potentials over tens of seconds to minutes produces a sudden barrage of action potentials lasting about a minute beyond the inciting stimulation. During this persistent firing, action potentials are generated in the distal axon and propagate retrogradely to the soma. To distinguish this from other forms of persistent firing, we refer to it here as {\textquoteright}retroaxonal barrage firing{\textquoteright}, or {\textquoteright}barrage firing{\textquoteright} for short. Its induction is blocked by chemical inhibitors of gap junctions and curiously, stimulation of one interneuron in some cases triggers barrage firing in a nearby, unstimulated interneuron. Beyond these clues, the mechanisms of barrage firing are unknown. Here we report new results related to these mechanisms. Induction of barrage firing was blocked by lowering extracellular calcium, as long as normal action potential threshold was maintained, and it was inhibited by blocking L-type voltage-gated calcium channels. Despite its calcium dependence, barrage firing was not prevented by inhibiting chemical synaptic transmission. Furthermore, loading the stimulated/recorded interneuron with BAPTA did not block barrage firing, suggesting that the required calcium entry occurs in other cells. Finally, barrage firing was normal in mice with deletion of the primary gene for neuronal gap junctions (connexin36), suggesting that non-neuronal gap junctions may be involved. Together, these findings suggest that barrage firing is probably triggered by a multicellular mechanism involving calcium signalling and gap junctions, but operating independently of chemical synaptic transmission.

}, issn = {1469-7793}, doi = {10.1113/jphysiol.2013.258418}, author = {Sheffield, Mark E J and Edgerton, Gabrielle B and Heuermann, Robert J and Deemyad, Tara and Mensh, Brett D and Spruston, Nelson} } @article {6383, title = {A molt timer is involved in the metamorphic molt in Manduca sexta larvae.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, year = {2013}, month = {2013 Jul 30}, pages = {12518-25}, abstract = {

Manduca sexta larvae are a model for growth control in insects, particularly for the demonstration of critical weight, a threshold weight that the larva must surpass before it can enter metamorphosis on a normal schedule, and the inhibitory action of juvenile hormone on this checkpoint. We examined the effects of nutrition on allatectomized (CAX) larvae that lack juvenile hormone to impose the critical weight checkpoint. Normal larvae respond to prolonged starvation at the start of the last larval stage, by extending their subsequent feeding period to ensure that they begin metamorphosis above critical weight. CAX larvae, by contrast, show no homeostatic adjustment to starvation but start metamorphosis 4 d after feeding onset, regardless of larval size or the state of development of their imaginal discs. By feeding starved CAX larvae for various durations, we found that feeding for only 12-24 h was sufficient to result in metamorphosis on day 4, regardless of further feeding or body size. Manipulation of diet composition showed that protein was the critical macronutrient to initiate this timing. This constant period between the start of feeding and the onset of metamorphosis suggests that larvae possess a molt timer that establishes a minimal time to metamorphosis. Ligation experiments indicate that a portion of the timing may occur in the prothoracic glands. This positive system that promotes molting and the negative control via the critical weight checkpoint provide antagonistic pathways that evolution can modify to adapt growth to the ecological needs of different insects.

}, issn = {1091-6490}, doi = {10.1073/pnas.1311405110}, author = {Suzuki, Yuichiro and Koyama, Takashi and Hiruma, Kiyoshi and Riddiford, Lynn M and Truman, James W} } @article {46044, title = {Morphological and molecular changes in aging rat prelimbic prefrontal cortical synapses.}, journal = {Neurobiology of Aging}, volume = {34}, year = {2013}, month = {2013 Jan}, pages = {200-10}, abstract = {

Age-related impairments of executive functions appear to be related to reductions of the number and plasticity of dendritic spine synapses in the prefrontal cortex (PFC). Experimental evidence suggests that synaptic plasticity is mediated by the spine actin cytoskeleton, and a major pathway regulating actin-based plasticity is controlled by phosphorylated LIM kinase (pLIMK). We asked whether aging resulted in altered synaptic density, morphology, and pLIMK expression in the rat prelimbic region of the PFC. Using unbiased electron microscopy, we found an approximate 50\% decrease in the density of small synapses with aging, while the density of large synapses remained unchanged. Postembedding immunogold revealed that pLIMK localized predominantly to the postsynaptic density where it was increased in aging synapses by approximately 50\%. Furthermore, the age-related increase in pLIMK occurred selectively within the largest subset of prelimbic PFC synapses. Because pLIMK is known to inhibit actin filament plasticity, these data support the hypothesis that age-related increases in pLIMK may explain the stability of large synapses at the expense of their plasticity.

}, keywords = {Age Factors, Aging, Analysis of Variance, Animals, Gene Expression Regulation, Lim Kinases, Male, Microscopy, Electron, Transmission, Microscopy, Immunoelectron, Neurons, Post-Synaptic Density, Prefrontal Cortex, Rats, Rats, Sprague-Dawley, Synapses}, issn = {1558-1497}, doi = {10.1016/j.neurobiolaging.2012.05.014}, author = {Bloss, Erik B and Puri, Rishi and Yuk, Frank and Punsoni, Michael and Hara, Yuko and Janssen, William G and McEwen, Bruce S and Morrison, John H} } @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 {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} } @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 {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 {48165, title = {Omnidirectional displacements for deformable surfaces.}, journal = {Medical image analysis}, volume = {17}, year = {2013}, month = {2013 May}, pages = {429-41}, abstract = {

Deformable surface models are often represented as triangular meshes in image segmentation applications. For a fast and easily regularized deformation onto the target object boundary, the vertices of the mesh are commonly moved along line segments (typically surface normals). However, in case of high mesh curvature, these lines may not intersect with the target boundary at all. Consequently, certain deformations cannot be achieved. We propose omnidirectional displacements for deformable surfaces (ODDS) to overcome this limitation. ODDS allow each vertex to move not only along a line segment but within the volumetric inside of a surrounding sphere, and achieve globally optimal deformations subject to local regularization constraints. However, allowing a ball-shaped instead of a linear range of motion per vertex significantly increases runtime and memory. To alleviate this drawback, we propose a hybrid approach, fastODDS, with improved runtime and reduced memory requirements. Furthermore, fastODDS can also cope with simultaneous segmentation of multiple objects. We show the theoretical benefits of ODDS with experiments on synthetic data, and evaluate ODDS and fastODDS quantitatively on clinical image data of the mandible and the hip bones. There, we assess both the global segmentation accuracy as well as local accuracy in high curvature regions, such as the tip-shaped mandibular coronoid processes and the ridge-shaped acetabular rims of the hip bones.

}, keywords = {Algorithms, Computer Simulation, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, Models, Biological, Pattern Recognition, Automated, Reproducibility of Results, Sensitivity and Specificity}, issn = {1361-8423}, doi = {10.1016/j.media.2012.11.006}, author = {Kainmueller, Dagmar and Lamecker, Hans and Heller, Markus O and Weber, Britta and Hege, Hans-Christian and Zachow, Stefan} } @article {6128, title = {An optimized fluorescent probe for visualizing glutamate neurotransmission.}, journal = {Nature Methods}, volume = {10}, year = {2013}, month = {2013 Feb}, pages = {162-70}, abstract = {

We describe an intensity-based glutamate-sensing fluorescent reporter (iGluSnFR) with signal-to-noise ratio and kinetics appropriate for in vivo imaging. We engineered iGluSnFR in vitro to maximize its fluorescence change, and we validated its utility for visualizing glutamate release by neurons and astrocytes in increasingly intact neurological systems. In hippocampal culture, iGluSnFR detected single field stimulus-evoked glutamate release events. In pyramidal neurons in acute brain slices, glutamate uncaging at single spines showed that iGluSnFR responds robustly and specifically to glutamate in situ, and responses correlate with voltage changes. In mouse retina, iGluSnFR-expressing neurons showed intact light-evoked excitatory currents, and the sensor revealed tonic glutamate signaling in response to light stimuli. In worms, glutamate signals preceded and predicted postsynaptic calcium transients. In zebrafish, iGluSnFR revealed spatial organization of direction-selective synaptic activity in the optic tectum. Finally, in mouse forelimb motor cortex, iGluSnFR expression in layer V pyramidal neurons revealed task-dependent single-spine activity during running.

}, keywords = {Animals, Astrocytes, Biosensing Techniques, Caenorhabditis elegans, Calcium Signaling, Escherichia coli Proteins, Excitatory Postsynaptic Potentials, Fluorescent Dyes, Glutamic Acid, Green Fluorescent Proteins, Hippocampus, Mice, Motor Cortex, Neurons, Photic Stimulation, Pyramidal Cells, Recombinant Fusion Proteins, Retina, Signal-To-Noise Ratio, Synaptic Transmission, Zebrafish}, issn = {1548-7105}, doi = {10.1038/nmeth.2333}, author = {Marvin, Jonathan S and Borghuis, Bart G and Tian, Lin and Cichon, Joseph and Harnett, Mark T and Akerboom, Jasper and Gordus, Andrew and Renninger, Sabine L. and Chen, Tsai-Wen and Bargmann, Cornelia I and Orger, Michael B. and Schreiter, Eric R and Demb, Jonathan B and Gan, Wen-Biao and Hires, S Andrew and Looger, Loren L} } @article {6295, title = {Organization of cortical and thalamic input to pyramidal neurons in mouse motor cortex.}, journal = {The Journal of Neuroscience}, volume = {33}, year = {2013}, month = {2013 Jan 9}, pages = {748-60}, abstract = {

Determining how long-range synaptic inputs engage pyramidal neurons in primary motor cortex (M1) is important for understanding circuit mechanisms involved in regulating movement. We used channelrhodopsin-2-assisted circuit mapping to characterize the long-range excitatory synaptic connections made by multiple cortical and thalamic areas onto pyramidal neurons in mouse vibrissal motor cortex (vM1). Each projection innervated vM1 pyramidal neurons with a unique laminar profile. Collectively, the profiles for different sources of input partially overlapped and spanned all cortical layers. Specifically, orbital cortex (OC) inputs primarily targeted neurons in L6. Secondary motor cortex (M2) inputs excited neurons mainly in L5B, including pyramidal tract neurons. In contrast, thalamocortical inputs from anterior motor-related thalamic regions, including VA/VL (ventral anterior thalamic nucleus/ventrolateral thalamic nucleus), targeted neurons in L2/3 through L5B, but avoided L6. Inputs from posterior sensory-related thalamic areas, including POm (posterior thalamic nuclear group), targeted neurons only in the upper layers (L2/3 and L5A), similar to inputs from somatosensory (barrel) cortex. Our results show that long-range excitatory inputs target vM1 pyramidal neurons in a layer-specific manner. Inputs from sensory-related cortical and thalamic areas preferentially target the upper-layer pyramidal neurons in vM1. In contrast, inputs from OC and M2, areas associated with volitional and cognitive aspects of movements, bypass local circuitry and have direct monosynaptic access to neurons projecting to brainstem and thalamus.

}, keywords = {Animals, Cerebral Cortex, Data Interpretation, Efferent Pathways, Electric Stimulation, Electrophysiological Phenomena, Female, Inbred C57BL, Male, Mice, Motor Cortex, Neurons, Patch-Clamp Techniques, Pons, Pyramidal Tracts, Statistical, Thalamus}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4338-12.2013}, author = {Hooks, Bryan M and Mao, Tianyi and Gutnisky, Diego A and Yamawaki, Naoki and Svoboda, Karel and Shepherd, Gordon M G} } @article {6526, title = {The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes.}, journal = {PLoS Biology}, volume = {11}, year = {2013}, month = {2013 Jan}, pages = {e1001473}, abstract = {

The macronuclear genome of the ciliate Oxytricha trifallax displays an extreme and unique eukaryotic genome architecture with extensive genomic variation. During sexual genome development, the expressed, somatic macronuclear genome is whittled down to the genic portion of a small fraction (\~{}5\%) of its precursor "silent" germline micronuclear genome by a process of "unscrambling" and fragmentation. The tiny macronuclear "nanochromosomes" typically encode single, protein-coding genes (a small portion, 10\%, encode 2-8 genes), have minimal noncoding regions, and are differentially amplified to an average of \~{}2,000 copies. We report the high-quality genome assembly of \~{}16,000 complete nanochromosomes (\~{}50 Mb haploid genome size) that vary from 469 bp to 66 kb long (mean \~{}3.2 kb) and encode \~{}18,500 genes. Alternative DNA fragmentation processes \~{}10\% of the nanochromosomes into multiple isoforms that usually encode complete genes. Nucleotide diversity in the macronucleus is very high (SNP heterozygosity is \~{}4.0\%), suggesting that Oxytricha trifallax may have one of the largest known effective population sizes of eukaryotes. Comparison to other ciliates with nonscrambled genomes and long macronuclear chromosomes (on the order of 100 kb) suggests several candidate proteins that could be involved in genome rearrangement, including domesticated MULE and IS1595-like DDE transposases. The assembly of the highly fragmented Oxytricha macronuclear genome is the first completed genome with such an unusual architecture. This genome sequence provides tantalizing glimpses into novel molecular biology and evolution. For example, Oxytricha maintains tens of millions of telomeres per cell and has also evolved an intriguing expansion of telomere end-binding proteins. In conjunction with the micronuclear genome in progress, the O. trifallax macronuclear genome will provide an invaluable resource for investigating programmed genome rearrangements, complementing studies of rearrangements arising during evolution and disease.

}, keywords = {Base Sequence, DNA, DNA Copy Number Variations, DNA Fragmentation, Gene Amplification, Gene Rearrangement, Genes, Genetic Variation, Genome, Macronucleus, Messenger, Molecular Sequence Data, Oxytricha, Protein Binding, Protozoan, RNA, Sequence Analysis, Telomere}, issn = {1545-7885}, doi = {10.1371/journal.pbio.1001473}, author = {Swart, Estienne C and Bracht, John R and Magrini, Vincent and Minx, Patrick and Chen, Xiao and Zhou, Yi and Khurana, Jaspreet S and Goldman, Aaron D and Nowacki, Mariusz and Schotanus, Klaas and Jung, Seolkyoung and Fulton, Robert S and Ly, Amy and McGrath, Sean and Haub, Kevin and Wiggins, Jessica L and Storton, Donna and Matese, John C and Parsons, Lance and Chang, Wei-Jen and Bowen, Michael S and Stover, Nicholas A and Jones, Thomas A and Eddy, Sean R. and Herrick, Glenn A and Doak, Thomas G and Wilson, Richard K and Mardis, Elaine R and Landweber, Laura F} } @article {6267, title = {Potassium channels control the interaction between active dendritic integration compartments in layer 5 cortical pyramidal neurons.}, journal = {Neuron}, volume = {79}, year = {2013}, month = {2013 Aug 7}, pages = {516-29}, abstract = {

Active dendritic synaptic integration enhances the computational power of neurons. Such nonlinear processing generates an object-localization signal in the apical dendritic tuft of layer 5B cortical pyramidal neurons during sensory-motor behavior. Here, we employ electrophysiological and optical approaches in brain slices and behaving animals to investigate how excitatory synaptic input to this distal dendritic compartment influences neuronal output. We find that active dendritic integration throughout the apical dendritic tuft is highly compartmentalized by voltage-gated potassium (KV) channels. A high density of both transient and sustained KV channels was observed in all apical dendritic compartments. These channels potently regulated the interaction between apical dendritic tuft, trunk, and axosomatic integration zones to control neuronal output in\ vitro as well as the engagement of dendritic nonlinear processing in\ vivo during sensory-motor behavior. Thus, KV channels dynamically tune the interaction between active dendritic integration compartments in layer 5B pyramidal neurons to shape behaviorally relevant neuronal computations.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2013.06.005}, author = {Harnett, Mark T and Xu, Ning-long and Magee, Jeffrey C and Williams, Stephen R} } @article {6594, title = {Real-time dynamics of RNA polymerase II clustering in live human cells.}, journal = {Science}, volume = {341}, year = {2013}, month = {2013 Aug 9}, pages = {664-7}, abstract = {

Transcription is reported to be spatially compartmentalized in nuclear transcription factories with clusters of RNA polymerase II (Pol II). However, little is known about when these foci assemble or their relative stability. We developed a quantitative single-cell approach to characterize protein spatiotemporal organization, with single-molecule sensitivity in live eukaryotic cells. We observed that Pol II clusters form transiently, with an average lifetime of 5.1 ({\textpm} 0.4) seconds, which refutes the notion that they are statically assembled substructures. Stimuli affecting transcription yielded orders-of-magnitude changes in the dynamics of Pol II clusters, which implies that clustering is regulated and plays a role in the cell{\textquoteright}s ability to effect rapid response to external signals. Our results suggest that transient crowding of enzymes may aid in rate-limiting steps of gene regulation.

}, keywords = {Cell Line, Flavonoids, Gene Expression Regulation, Genetic, Humans, Piperidines, RNA Polymerase II, Single-Cell Analysis, Time Factors, Transcription, Transcription Elongation, Tumor}, issn = {1095-9203}, doi = {10.1126/science.1239053}, author = {Cisse, Ibrahim I and Izeddin, Ignacio and Causse, Sebastien Z and Boudarene, Lydia and Senecal, Adrien and Muresan, Leila and Dugast-Darzacq, Claire and Hajj, Bassam and Dahan, Maxime and Darzacq, Xavier} } @article {6278, title = {Shortening of the elastic tandem immunoglobulin segment of titin leads to diastolic dysfunction.}, journal = {Circulation}, volume = {128}, year = {2013}, month = {2013 Jul 2}, pages = {19-28}, abstract = {

BACKGROUND: Diastolic dysfunction is a poorly understood but clinically pervasive syndrome that is characterized by increased diastolic stiffness. Titin is the main determinant of cellular passive stiffness. However, the physiological role that the tandem immunoglobulin (Ig) segment of titin plays in stiffness generation and whether shortening this segment is sufficient to cause diastolic dysfunction need to be established. METHODS AND RESULTS: We generated a mouse model in which 9 Ig-like domains (Ig3-Ig11) were deleted from the proximal tandem Ig segment of the spring region of titin (IG KO). Exon microarray analysis revealed no adaptations in titin splicing, whereas novel phospho-specific antibodies did not detect changes in titin phosphorylation. Passive myocyte stiffness was increased in the IG KO, and immunoelectron microscopy revealed increased extension of the remaining titin spring segments as the sole likely underlying mechanism. Diastolic stiffness was increased at the tissue and organ levels, with no consistent changes in extracellular matrix composition or extracellular matrix-based passive stiffness, supporting a titin-based mechanism for in vivo diastolic dysfunction. Additionally, IG KO mice have a reduced exercise tolerance, a phenotype often associated with diastolic dysfunction. CONCLUSIONS: Increased titin-based passive stiffness is sufficient to cause diastolic dysfunction with exercise intolerance.

}, issn = {1524-4539}, doi = {10.1161/CIRCULATIONAHA.112.001268}, author = {Chung, Charles S and Hutchinson, Kirk R and Methawasin, Mei and Saripalli, Chandra and Smith, John E and Hidalgo, Carlos G and Luo, Xiuju and Labeit, Siegfried and Guo, Caiying and Granzier, Henk L} } @article {46716, title = {Single-molecule analysis of gene expression using two-color RNA labeling in live yeast.}, journal = {Nature Methods}, volume = {10}, year = {2013}, month = {2013 Feb}, pages = {119-21}, abstract = {

Live-cell imaging of mRNA yields important insights into gene expression, but it has generally been limited to the labeling of one RNA species and has never been used to count single mRNAs over time in yeast. We demonstrate a two-color imaging system with single-molecule resolution using MS2 and PP7 RNA labeling. We use this methodology to measure intrinsic noise in mRNA levels and RNA polymerase II kinetics at a single gene.

}, keywords = {Adenosine Triphosphatases, Gene Expression, In Situ Hybridization, Fluorescence, Levivirus, RNA Polymerase II, RNA, Fungal, RNA, Messenger, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins}, issn = {1548-7105}, doi = {10.1038/nmeth.2305}, author = {Hocine, Sami and Raymond, Pascal and Zenklusen, Daniel and Chao, Jeffrey A and Singer, Robert H} } @article {46601, title = {A small group of neurosecretory cells expressing the transcriptional regulator apontic and the neuropeptide corazonin mediate ethanol sedation in Drosophila.}, journal = {The Journal of Neuroscience}, volume = {33}, year = {2013}, month = {2013 Feb 27}, pages = {4044-54}, abstract = {

In the fruit fly Drosophila melanogaster, as in mammals, acute exposure to a high dose of ethanol leads to stereotypical behavioral changes beginning with increased activity, followed by incoordination, loss of postural control, and eventually, sedation. The mechanism(s) by which ethanol impacts the CNS leading to ethanol-induced sedation and the genes required for normal sedation sensitivity remain largely unknown. Here we identify the gene apontic (apt), an Myb/SANT-containing transcription factor that is required in the nervous system for normal sensitivity to ethanol sedation. Using genetic and behavioral analyses, we show that apt mediates sensitivity to ethanol sedation by acting in a small set of neurons that express Corazonin (Crz), a neuropeptide likely involved in the physiological response to stress. The activity of Crz neurons regulates the behavioral response to ethanol, as silencing and activating these neurons affects sedation sensitivity in opposite ways. Furthermore, this effect is mediated by Crz, as flies with reduced crz expression show reduced sensitivity to ethanol sedation. Finally, we find that both apt and crz are rapidly upregulated by acute ethanol exposure. Thus, we have identified two genes and a small set of peptidergic neurons that regulate sensitivity to ethanol-induced sedation. We propose that Apt regulates the activity of Crz neurons and/or release of the neuropeptide during ethanol exposure.

}, keywords = {Animals, Animals, Genetically Modified, Behavior, Animal, Brain, DNA-Binding Proteins, Dose-Response Relationship, Drug, Drosophila, Drosophila Proteins, Ethanol, Gene Expression Regulation, Green Fluorescent Proteins, Hypnotics and Sedatives, Metamorphosis, Biological, Mutation, Neurons, Neuropeptides, Neurosecretory Systems, RNA, Messenger, Transcription Factors}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3413-12.2013}, author = {McClure, Kimberly D and Heberlein, Ulrike} } @article {6222, title = {Spinal projection neurons control turning behaviors in zebrafish.}, journal = {Current Biology}, volume = {23}, year = {2013}, month = {2013 Aug 19}, pages = {1566-73}, abstract = {

Discrete populations of brainstem spinal projection neurons (SPNs) have been shown to exhibit behavior-specific responses during locomotion [1-9], suggesting that separate descending pathways, each dedicated to a specific behavior, control locomotion. In an alternative model, a large variety of motor outputs could be generated from different combinations of a small number of basic motor pathways. We examined this possibility by studying the precise role of ventromedially located hindbrain SPNs (vSPNs) in generating turning behaviors. We found that unilateral laser ablation of vSPNs reduces the tail deflection and cycle period specifically during the first undulation cycle of a swim bout, whereas later tail movements are unaffected. This holds true during phototaxic [10], optomotor [11], dark-flash-induced [12], and spontaneous turns [13], suggesting a universal role of these neurons in controlling turning behaviors. Importantly, we found that the ablation not only abolishes turns but also results in a dramatic increase in the number of forward swims, suggesting that these neurons transform forward swims into turns by introducing turning kinematics into a basic motor pattern of symmetric tail undulations. Finally, we show that vSPN activity is direction specific and graded by turning angle. Together, these results provide a clear example of how a specific motor pattern can be transformed into different behavioral events by the graded activation of a small set of SPNs.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2013.06.044}, author = {Huang, Kuo-Hua and Ahrens, Misha B and Dunn, Timothy W. and Engert, Florian} } @article {47705, title = {Structural foundations of resting-state and task-based functional connectivity in the human brain.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, year = {2013}, month = {2013 Apr 9}, pages = {6169-74}, abstract = {

Magnetic resonance imaging enables the noninvasive mapping of both anatomical white matter connectivity and dynamic patterns of neural activity in the human brain. We examine the relationship between the structural properties of white matter streamlines (structural connectivity) and the functional properties of correlations in neural activity (functional connectivity) within 84 healthy human subjects both at rest and during the performance of attention- and memory-demanding tasks. We show that structural properties, including the length, number, and spatial location of white matter streamlines, are indicative of and can be inferred from the strength of resting-state and task-based functional correlations between brain regions. These results, which are both representative of the entire set of subjects and consistently observed within individual subjects, uncover robust links between structural and functional connectivity in the human brain.

}, keywords = {Aging, Attention, Brain, Brain Mapping, Cognition, Computational Biology, Diffusion Magnetic Resonance Imaging, Humans, Magnetic Resonance Imaging, Memory, Models, Statistical, Neural Pathways, Software}, issn = {1091-6490}, doi = {10.1073/pnas.1219562110}, author = {Hermundstad, Ann M and Bassett, Danielle S and Brown, Kevin S and Aminoff, Elissa M and Clewett, David and Freeman, Scott and Frithsen, Amy and Johnson, Arianne and Tipper, Christine M and Miller, Michael B and Grafton, Scott T and Carlson, Jean M} } @article {6582, title = {Structure of fully liganded Hb zeta(2)beta(s)(2) trapped in a tense conformation.}, journal = {Acta Crystallographica Section D:Biological Crystallography}, volume = {69}, year = {2013}, month = {2013 Oct}, pages = {2061-71}, abstract = {

A variant Hb zeta(2)beta(s)(2) that is formed from sickle hemoglobin (Hb S; alpha(2)beta(s)(2)) by exchanging adult alpha-globin with embryonic zeta-globin subunits shows promise as a therapeutic agent for sickle-cell disease (SCD). Hb zeta(2)beta(s)(2) inhibits the polymerization of deoxygenated Hb S in vitro and reverses characteristic features of SCD in vivo in mouse models of the disorder. When compared with either Hb S or with normal human adult Hb A (alpha(2)beta(2)), Hb zeta(2)beta(s)(2) exhibits atypical properties that include a high oxygen affinity, reduced cooperativity, a weak Bohr effect and blunted 2,3-diphosphoglycerate allostery. Here, the 1.95 angstrom resolution crystal structure of human Hb zeta(2)beta(s)(2) that was expressed in complex transgenic knockout mice and purified from their erythrocytes is presented. When fully liganded with carbon monoxide, Hb zeta(2)beta(s)(2) displays a central water cavity, a zeta 1-beta(s)2 (or zeta 2-beta(s)1) interface, intersubunit salt-bridge/hydrogen-bond interactions, C-terminal beta His146 salt-bridge interactions, and a beta-cleft, that are highly unusual for a relaxed hemoglobin structure and are more typical of a tense conformation. These quaternary tense-like features contrast with the tertiary relaxed-like conformations of the zeta 1-beta(s1) dimer and the CD and FG corners, as well as the overall structures of the heme cavities. This crystallographic study provides insights into the altered oxygen-transport properties of Hb zeta(2)beta(s)(2) and, moreover, decouples tertiary- and quaternary-structural events that are critical to Hb ligand binding and allosteric function.

}, issn = {0907-444910.1107/s0907444913019197}, doi = {10.1107/S0907444913019197}, author = {Safo, M. K. and Ko, T. P. and Abdulmalik, O. and He, Z. N. and Wang, A. H. J. and Schreiter, E. R. and Russell, J. E.} } @article {46606, title = {Taok2 controls behavioral response to ethanol in mice.}, journal = {Genes, Brain, and Behavior}, volume = {12}, year = {2013}, month = {2013 Feb}, pages = {87-97}, abstract = {

Despite recent advances in the understanding of ethanol{\textquoteright}s biological action, many of the molecular targets of ethanol and mechanisms behind ethanol{\textquoteright}s effect on behavior remain poorly understood. In an effort to identify novel genes, the products of which regulate behavioral responses to ethanol, we recently identified a mutation in the dtao gene that confers resistance to the locomotor stimulating effect of ethanol in Drosophila. dtao encodes a member of the Ste20 family of serine/threonine kinases implicated in MAP kinase signaling pathways. In this study, we report that conditional ablation of the mouse dtao homolog, Taok2, constitutively and specifically in the nervous system, results in strain-specific and overlapping alterations in ethanol-dependent behaviors. These data suggest a functional conservation of dtao and Taok2 in mediating ethanol{\textquoteright}s biological action and identify Taok2 as a putative candidate gene for ethanol use disorders in humans.

}, keywords = {Alcohol Drinking, Alcoholism, Animals, Behavior, Animal, Conditioning, Classical, Ethanol, Gait Ataxia, Locomotion, MAP Kinase Kinase Kinases, Mice, Mice, Inbred C57BL, Mice, Transgenic, Protein-Serine-Threonine Kinases}, issn = {1601-183X}, doi = {10.1111/j.1601-183X.2012.00834.x}, author = {Kapfhamer, D and Taylor, S and Zou, M E and Lim, J P and Kharazia, V and Heberlein, U} } @article {6889, title = {Tapered whiskers are required for active tactile sensation.}, journal = {eLife}, volume = {2}, year = {2013}, month = {2013 Nov 19}, pages = {e01350}, abstract = {

Many mammals forage and burrow in dark constrained spaces. Touch through facial whiskers is important during these activities, but the close quarters makes whisker deployment challenging. The diverse shapes of facial whiskers reflect distinct ecological niches. Rodent whiskers are conical, often with a remarkably linear taper. Here we use theoretical and experimental methods to analyze interactions of mouse whiskers with objects. When pushed into objects, conical whiskers suddenly slip at a critical angle. In contrast, cylindrical whiskers do not slip for biologically plausible movements. Conical whiskers sweep across objects and textures in characteristic sequences of brief sticks and slips, which provide information about the tactile world. In contrast, cylindrical whiskers stick and remain stuck, even when sweeping across fine textures. Thus the conical whisker structure is adaptive for sensor mobility in constrained environments and in feature extraction during active haptic exploration of objects and surfaces. DOI: http://dx.doi.org/10.7554/eLife.01350.001.

}, issn = {2050-084X}, doi = {10.7554/eLife.01350}, author = {Hires, Samuel Andrew and Pammer, Lorenz and Svoboda, Karel and Golomb, David} } @article {6674, title = {Thalamocortical input onto layer 5 pyramidal neurons measured using quantitative large-scale array tomography.}, journal = {Frontiers in Neural Circuits}, volume = {7}, year = {2013}, month = {2013}, pages = {177}, abstract = {

The subcellular locations of synapses on pyramidal neurons strongly influences dendritic integration and synaptic plasticity. Despite this, there is little quantitative data on spatial distributions of specific types of synaptic input. Here we use array tomography (AT), a high-resolution optical microscopy method, to examine thalamocortical (TC) input onto layer 5 pyramidal neurons. We first verified the ability of AT to identify synapses using parallel electron microscopic analysis of TC synapses in layer 4. We then use large-scale array tomography (LSAT) to measure TC synapse distribution on L5 pyramidal neurons in a 1.00 {\texttimes} 0.83 {\texttimes} 0.21 mm(3) volume of mouse somatosensory cortex. We found that TC synapses primarily target basal dendrites in layer 5, but also make a considerable input to proximal apical dendrites in L4, consistent with previous work. Our analysis further suggests that TC inputs are biased toward certain branches and, within branches, synapses show significant clustering with an excess of TC synapse nearest neighbors within 5-15 μm compared to a random distribution. Thus, we show that AT is a sensitive and quantitative method to map specific types of synaptic input on the dendrites of entire neurons. We anticipate that this technique will be of wide utility for mapping functionally-relevant anatomical connectivity in neural circuits.

}, issn = {1662-5110}, doi = {10.3389/fncir.2013.00177}, author = {Rah, Jong-Cheol and Bas, Erhan and Colonell, Jennifer and Mishchenko, Yuriy and Karsh, Bill and Fetter, Richard D and Myers, Eugene W and Chklovskii, Dmitri B and Svoboda, Karel and Harris, Timothy D and Isaac, John T R} } @article {68814, title = {Transgenic tools to characterize neuronal properties of discrete populations of zebrafish neurons}, journal = {Development}, volume = {140}, year = {2013}, month = {09/2013}, pages = {3927-3931}, abstract = {

The developing nervous system consists of a variety of cell types. Transgenic animals expressing reporter genes in specific classes of neuronal cells are powerful tools for the study of neuronal network formation. We generated a wide variety of transgenic zebrafish that expressed reporter genes in specific classes of neurons or neuronal progenitors. These include lines in which neurons of specific neurotransmitter phenotypes expressed fluorescent proteins or Gal4, and lines in which specific subsets of the dorsal progenitor domain in the spinal cord expressed fluorescent proteins. Using these, we examined domain organization in the developing dorsal spinal cord, and found that there are six progenitor domains in zebrafish, which is similar to the domain organization in mice. We also systematically characterized neurotransmitter properties of the neurons that are produced from each domain. Given that reporter gene expressions occurs in a wide area of the nervous system in the lines generated, these transgenic fish should serve as powerful tools for the investigation of not only the neurons in the dorsal spinal cord but also neuronal structures and functions in many other regions of the nervous system.

}, issn = {0950-1991}, doi = {10.1242/dev.099531}, url = {https://doi.org/10.1242/dev.099531}, author = {Satou, Chie and Kimura, Yukiko and Hirata, Hiromi and Suster, Maximiliano L. and Kawakami, Koichi and Higashijima, Shin-Ichi} } @article {6031, title = {Two-photon calcium imaging during fictive navigation in virtual environments.}, journal = {Frontiers in Neural Circuits}, volume = {7}, year = {2013}, month = {2013 Jun 6}, pages = {104}, abstract = {

A full understanding of nervous system function requires recording from large populations of neurons during naturalistic behaviors. Here we enable paralyzed larval zebrafish to fictively navigate two-dimensional virtual environments while we record optically from many neurons with two-photon imaging. Electrical recordings from motor nerves in the tail are decoded into intended forward swims and turns, which are used to update a virtual environment displayed underneath the fish. Several behavioral features-such as turning responses to whole-field motion and dark avoidance-are well-replicated in this virtual setting. We readily observed neuronal populations in the hindbrain with laterally selective responses that correlated with right or left optomotor behavior. We also observed neurons in the habenula, pallium, and midbrain with response properties specific to environmental features. Beyond single-cell correlations, the classification of network activity in such virtual settings promises to reveal principles of brainwide neural dynamics during behavior.

}, issn = {1662-5110}, doi = {10.3389/fncir.2013.00104 *equal contribution}, author = {Ahrens, Misha B* and Huang, Kuo Hua* and Narayan, Sujatha and Mensh, Brett D and Engert, Florian} } @article {6533, title = {Unclosed HIV-1 capsids suggest a curled sheet model of assembly.}, journal = {Journal of Molecular Biology}, volume = {425}, year = {2013}, month = {2013 Jan 9}, pages = {112-23}, abstract = {

The RNA genome of retroviruses is encased within a protein capsid. To gather insight into the assembly and function of this capsid, we used electron cryotomography to image human immunodeficiency virus (HIV) and equine infectious anemia virus (EIAV) particles. While the majority of viral cores appeared closed, a variety of unclosed structures including rolled sheets, extra flaps, and cores with holes in the tip were also seen. Simulations of nonequilibrium growth of elastic sheets recapitulated each of these aberrations and further predicted the occasional presence of seams, for which tentative evidence was also found within the cryotomograms. To test the integrity of viral capsids in vivo, we observed that \ 25\% of cytoplasmic HIV complexes captured by TRIM5α had holes large enough to allow internal green fluorescent protein (GFP) molecules to escape. Together, these findings suggest that HIV assembly at least sometimes involves the union in space of two edges of a curling sheet and results in a substantial number of unclosed forms.

}, keywords = {Animals, Capsid, Carrier Proteins, Computer Simulation, Cryoelectron Microscopy, Equine, Fluorescence, Green Fluorescent Proteins, HEK293 Cells, HIV-1, Humans, Infectious Anemia Virus, Microscopy, Models, Molecular, Viral Core Proteins, Virus Assembly}, issn = {1089-8638}, doi = {10.1016/j.jmb.2012.10.006}, author = {Yu, Zhiheng and Dobro, Megan J and Woodward, Cora L and Levandovsky, Artem and Danielson, Cindy M and Sandrin, Virginie and Shi, Jiong and Aiken, Christopher and Zandi, Roya and Hope, Thomas J and Jensen, Grant J} } @article {6178, title = {A visual motion detection circuit suggested by Drosophila connectomics.}, journal = {Nature}, volume = {500}, year = {2013}, month = {2013 Aug 7}, pages = {175{\textendash}81}, abstract = {

Animal behaviour arises from computations in neuronal circuits, but our understanding of these computations has been frustrated by the lack of detailed synaptic connection maps, or connectomes. For example, despite intensive investigations over half a century, the neuronal implementation of local motion detection in the insect visual system remains elusive. Here we develop a semi-automated pipeline using electron microscopy to reconstruct a connectome, containing 379 neurons and 8,637 chemical synaptic contacts, within the Drosophila optic medulla. By matching reconstructed neurons to examples from light microscopy, we assigned neurons to cell types and assembled a connectome of the repeating module of the medulla. Within this module, we identified cell types constituting a motion detection circuit, and showed that the connections onto individual motion-sensitive neurons in this circuit were consistent with their direction selectivity. Our results identify cellular targets for future functional investigations, and demonstrate that connectomes can provide key insights into neuronal computations.

}, issn = {1476-4687}, doi = {doi:10.1038/nature12450}, url = {http://www.nature.com/nature/journal/v500/n7461/full/nature12450.html}, author = {Takemura, Shin-ya and Bharioke, Arjun and Lu, Zhiyuan and Nern, Aljoscha and Vitaladevuni, Shiv and Rivlin, Patricia K. and Katz, William T. and Olbris, Donald J. and Plaza, Stephen M and Winston, Philip and Zhao, Ting and Horne, Jane Anne and Fetter, Richard D and Takemura, Satoko and Blazek, Katerina and Chang, Lei-Ann and Ogundeyi, Omotara and Saunders, Mathew A. and Shapiro, Victor and Sigmund, Christopher and Rubin, Gerald M and Scheffer, Louis K and Meinertzhagen, Ian A. and Chklovskii, Dmitri B} } @article {5162, title = {Activity in motor-sensory projections reveals distributed coding in somatosensation.}, journal = {Nature}, volume = {489}, year = {2012}, month = {2012 Sep 13}, pages = {299-303}, abstract = {

Cortical-feedback projections to primary sensory areas terminate most heavily in layer 1 (L1) of the neocortex, where they make synapses with tuft dendrites of pyramidal neurons. L1 input is thought to provide {\textquoteleft}contextual{\textquoteright} information, but the signals transmitted by L1 feedback remain uncharacterized. In the rodent somatosensory system, the spatially diffuse feedback projection from vibrissal motor cortex (vM1) to vibrissal somatosensory cortex (vS1, also known as the barrel cortex) may allow whisker touch to be interpreted in the context of whisker position to compute object location. When mice palpate objects with their whiskers to localize object features, whisker touch excites vS1 and later vM1 in a somatotopic manner. Here we use axonal calcium imaging to track activity in vM1{\textendash}\>vS1 afferents in L1 of the barrel cortex while mice performed whisker-dependent object localization. Spatially intermingled individual axons represent whisker movements, touch and other behavioural features. In a subpopulation of axons, activity depends on object location and persists for seconds after touch. Neurons in the barrel cortex thus have information to integrate movements and touches of multiple whiskers over time, key components of object identification and navigation by active touch.

}, issn = {1476-4687}, doi = {10.1038/nature11321}, author = {Petreanu, Leopoldo and Gutnisky, Diego A and Huber, Daniel and Xu, Ning-long and O{\textquoteright}Connor, Dan H and Tian, Lin and Looger, Loren and Svoboda, Karel} } @article {46604, title = {Acute ethanol responses in Drosophila are sexually dimorphic.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, year = {2012}, month = {2012 Dec 18}, pages = {21087-92}, abstract = {

In mammalian and insect models of ethanol intoxication, low doses of ethanol stimulate locomotor activity whereas high doses induce sedation. Sex differences in acute ethanol responses, which occur in humans, have not been characterized in Drosophila. In this study, we find that male flies show increased ethanol hyperactivity and greater resistance to ethanol sedation compared with females. We show that the sex determination gene transformer (tra) acts in the developing nervous system, likely through regulation of fruitless (fru), to at least partially mediate the sexual dimorphism in ethanol sedation. Although pharmacokinetic differences may contribute to the increased sedation sensitivity of females, neuronal tra expression regulates ethanol sedation independently of ethanol pharmacokinetics. We also show that acute activation of fru-expressing neurons affects ethanol sedation, further supporting a role for fru in regulating this behavior. Thus, we have characterized previously undescribed sex differences in behavioral responses to ethanol, and implicated fru in mediating a subset of these differences.

}, keywords = {Alcoholic Intoxication, Animals, Central Nervous System Stimulants, Crosses, Genetic, Disease Models, Animal, Drosophila melanogaster, Ethanol, Female, Gene Expression Regulation, Male, Models, Statistical, Neurons, Sex Characteristics, Sex Factors}, issn = {1091-6490}, doi = {10.1073/pnas.1218850110}, author = {Devineni, Anita V and Heberlein, Ulrike} } @article {5200, title = {Automated tracking of whiskers in videos of head fixed rodents.}, journal = {PLoS Computational Biology}, volume = {8}, year = {2012}, month = {2012 Jul}, pages = {e1002591}, abstract = {

We have developed software for fully automated tracking of vibrissae (whiskers) in high-speed videos (\>500 Hz) of head-fixed, behaving rodents trimmed to a single row of whiskers. Performance was assessed against a manually curated dataset consisting of 1.32 million video frames comprising 4.5 million whisker traces. The current implementation detects whiskers with a recall of 99.998\% and identifies individual whiskers with 99.997\% accuracy. The average processing rate for these images was 8 Mpx/s/cpu (2.6 GHz Intel Core2, 2 GB RAM). This translates to 35 processed frames per second for a 640 px{\texttimes}352 px video of 4 whiskers. The speed and accuracy achieved enables quantitative behavioral studies where the analysis of millions of video frames is required. We used the software to analyze the evolving whisking strategies as mice learned a whisker-based detection task over the course of 6 days (8148 trials, 25 million frames) and measure the forces at the sensory follicle that most underlie haptic perception.

}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1002591}, author = {Clack, Nathan G and O{\textquoteright}Connor, Daniel H and Huber, Daniel and Petreanu, Leopoldo and Hires, Andrew and Peron, Simon and Svoboda, Karel and Myers, Eugene W} } @article {6527, title = {A battery-free multichannel digital neural/EMG telemetry system for flying insects.}, journal = {IEEE Transactions on Biomedical Circuits and Systems}, volume = {6}, year = {2012}, month = {2012 Oct}, pages = {424-36}, abstract = {

This paper presents a digital neural/EMG telemetry system small enough and lightweight enough to permit recording from insects in flight. It has a measured flight package mass of only 38 mg. This system includes a single-chip telemetry integrated circuit (IC) employing RF power harvesting for battery-free operation, with communication via modulated backscatter in the UHF (902-928 MHz) band. An on-chip 11-bit ADC digitizes 10 neural channels with a sampling rate of 26.1 kSps and 4 EMG channels at 1.63 kSps, and telemeters this data wirelessly to a base station. The companion base station transceiver includes an RF transmitter of +36 dBm (4 W) output power to wirelessly power the telemetry IC, and a digital receiver with a sensitivity of -70 dBm for 10$^{-}$$^{5}$ BER at 5.0 Mbps to receive the data stream from the telemetry IC. The telemetry chip was fabricated in a commercial 0.35 μ m 4M1P (4 metal, 1 poly) CMOS process. The die measures 2.36 {\texttimes} 1.88 mm, is 250 μm thick, and is wire bonded into a flex circuit assembly measuring 4.6 {\texttimes} 6.8 mm.

}, issn = {1940-9990}, doi = {10.1109/TBCAS.2012.2222881}, author = {Thomas, Stewart J and Harrison, Reid R. and Leonardo, Anthony and Reynolds, Matthew S} } @article {47661, title = {Bayesian localization microscopy reveals nanoscale podosome dynamics.}, journal = {Nature methods}, volume = {9}, year = {2012}, month = {2012 Feb}, pages = {195-200}, abstract = {

We describe a localization microscopy analysis method that is able to extract results in live cells using standard fluorescent proteins and xenon arc lamp illumination. Our Bayesian analysis of the blinking and bleaching (3B analysis) method models the entire dataset simultaneously as being generated by a number of fluorophores that may or may not be emitting light at any given time. The resulting technique allows many overlapping fluorophores in each frame and unifies the analysis of the localization from blinking and bleaching events. By modeling the entire dataset, we were able to use each reappearance of a fluorophore to improve the localization accuracy. The high performance of this technique allowed us to reveal the nanoscale dynamics of podosome formation and dissociation throughout an entire cell with a resolution of 50 nm on a 4-s timescale.

}, keywords = {Bayes Theorem, Cell Line, Tumor, Humans, Nanotechnology}, issn = {1548-7105}, doi = {10.1038/nmeth.1812}, author = {Cox, Susan and Rosten, Edward and Monypenny, James and Jovanovic-Talisman, Tijana and Burnette, Dylan T and Lippincott-Schwartz, Jennifer and Jones, Gareth E and Heintzmann, Rainer} } @article {6320, title = {Beam-induced motion of vitrified specimen on holey carbon film.}, journal = {Journal of Structural Biology}, volume = {177}, year = {2012}, month = {2012 Mar}, pages = {630-7}, abstract = {

The contrast observed in images of frozen-hydrated biological specimens prepared for electron cryo-microscopy falls significantly short of theoretical predictions. In addition to limits imposed by the current instrumentation, it is widely acknowledged that motion of the specimen during its exposure to the electron beam leads to significant blurring in the recorded images. We have studied the amount and direction of motion of virus particles suspended in thin vitrified ice layers across holes in perforated carbon films using exposure series. Our data show that the particle motion is correlated within patches of 0.3-0.5 μm, indicating that the whole ice layer is moving in a drum-like motion, with accompanying particle rotations of up to a few degrees. Support films with smaller holes, as well as lower electron dose rates tend to reduce beam-induced specimen motion, consistent with a mechanical effect. Finally, analysis of movies showing changes in the specimen during beam exposure show that the specimen moves significantly more at the start of an exposure than towards its end. We show how alignment and averaging of movie frames can be used to restore high-resolution detail in images affected by beam-induced motion.

}, keywords = {Computer-Assisted, Cryoelectron Microscopy, Image Processing}, issn = {1095-8657}, doi = {10.1016/j.jsb.2012.02.003}, author = {Brilot, Axel F and Chen, James Z and Cheng, Anchi and Pan, Junhua and Harrison, Stephen C and Potter, Clinton S and Carragher, Bridget and Henderson, Richard and Grigorieff, Nikolaus} } @article {6303, title = {The bHLH repressor Deadpan regulates the self-renewal and specification of Drosophila larval neural stem cells independently of Notch.}, journal = {PLoS One}, volume = {7}, year = {2012}, month = {2012 Oct 8}, pages = {e46724}, abstract = {

Neural stem cells (NSCs) are able to self-renew while giving rise to neurons and glia that comprise a functional nervous system. However, how NSC self-renewal is maintained is not well understood. Using the Drosophila larval NSCs called neuroblasts (NBs) as a model, we demonstrate that the Hairy and Enhancer-of-Split (Hes) family protein Deadpan (Dpn) plays important roles in NB self-renewal and specification. The loss of Dpn leads to the premature loss of NBs and truncated NB lineages, a process likely mediated by the homeobox protein Prospero (Pros). Conversely, ectopic/over-expression of Dpn promotes ectopic self-renewing divisions and maintains NB self-renewal into adulthood. In type II NBs, which generate transit amplifying intermediate neural progenitors (INPs) like mammalian NSCs, the loss of Dpn results in ectopic expression of type I NB markers Asense (Ase) and Pros before these type II NBs are lost at early larval stages. Our results also show that knockdown of Notch leads to ectopic Ase expression in type II NBs and the premature loss of type II NBs. Significantly, dpn expression is unchanged in these transformed NBs. Furthermore, the loss of Dpn does not inhibit the over-proliferation of type II NBs and immature INPs caused by over-expression of activated Notch. Our data suggest that Dpn plays important roles in maintaining NB self-renewal and specification of type II NBs in larval brains and that Dpn and Notch function independently in regulating type II NB proliferation and specification.

}, keywords = {Animals, Basic Helix-Loop-Helix Transcription Factors, Drosophila, Drosophila Proteins, Larva, Neural Stem Cells, Notch, Nuclear Proteins, Receptors}, issn = {1932-6203}, doi = {10.1371/journal.pone.0046724}, author = {Zhu, Sijun and Wildonger, Jill and Barshow, Suzanne and Younger, Susan and Huang, Yaling and Lee, Tzumin} } @article {65014, title = {Calcium signaling in dendritic spines.}, journal = {Cold Spring Harb Perspect Biol}, volume = {4}, year = {2012}, month = {2012 Apr 01}, pages = {a005686}, abstract = {

Calcium (Ca(2+)) is a ubiquitous signaling molecule that accumulates in the cytoplasm in response to diverse classes of stimuli and, in turn, regulates many aspects of cell function. In neurons, Ca(2+) influx in response to action potentials or synaptic stimulation triggers neurotransmitter release, modulates ion channels, induces synaptic plasticity, and activates transcription. In this article, we discuss the factors that regulate Ca(2+) signaling in mammalian neurons with a particular focus on Ca(2+) signaling within dendritic spines. This includes consideration of the routes of entry and exit of Ca(2+), the cellular mechanisms that establish the temporal and spatial profile of Ca(2+) signaling, and the biophysical criteria that determine which downstream signals are activated when Ca(2+) accumulates in a spine. Furthermore, we also briefly discuss the technical advances that made possible the quantitative study of Ca(2+) signaling in dendritic spines.

}, keywords = {Action Potentials, Animals, Calcium Signaling, Dendritic Spines, Mammals, Neuronal Plasticity}, issn = {1943-0264}, doi = {10.1101/cshperspect.a005686}, author = {Higley, Michael J and Sabatini, Bernardo L} } @article {6283, title = {Cell type-specific genomics of Drosophila neurons.}, journal = {Nucleic Acids Research}, volume = {40}, year = {2012}, month = {2012 Oct}, pages = {9691-704}, abstract = {

Many tools are available to analyse genomes but are often challenging to use in a cell type-specific context. We have developed a method similar to the isolation of nuclei tagged in a specific cell type (INTACT) technique [Deal,R.B. and Henikoff,S. (2010) A simple method for gene expression and chromatin profiling of individual cell types within a tissue. Dev. Cell, 18, 1030-1040; Steiner,F.A., Talbert,P.B., Kasinathan,S., Deal,R.B. and Henikoff,S. (2012) Cell-type-specific nuclei purification from whole animals for genome-wide expression and chromatin profiling. Genome Res., doi:10.1101/gr.131748.111], first developed in plants, for use in Drosophila neurons. We profile gene expression and histone modifications in Kenyon cells and octopaminergic neurons in the adult brain. In addition to recovering known gene expression differences, we also observe significant cell type-specific chromatin modifications. In particular, a small subset of differentially expressed genes exhibits a striking anti-correlation between repressive and activating histone modifications. These genes are enriched for transcription factors, recovering those known to regulate mushroom body identity and predicting analogous regulators of octopaminergic neurons. Our results suggest that applying INTACT to specific neuronal populations can illuminate the transcriptional regulatory networks that underlie neuronal cell identity.

}, keywords = {Animals, Cell Fractionation, Cell Nucleus, Chromatin, Drosophila, Gene Expression Profiling, Gene Silencing, Genomics, Histones, Luminescent Proteins, Neurons, Transcription Factors}, issn = {1362-4962}, doi = {10.1093/nar/gks671}, author = {Henry, Gilbert L and Davis, Fred P and Picard, Serge and Eddy, Sean R.} } @article {45187, title = {Correlative 3D superresolution fluorescence and electron microscopy reveal the relationship of mitochondrial nucleoids to membranes.}, journal = {Proceedings of the National Academy of Science of the United States of America}, volume = {109}, year = {2012}, month = {2012 Apr 17}, pages = {6136-41}, abstract = {

Microscopic images of specific proteins in their cellular context yield important insights into biological processes and cellular architecture. The advent of superresolution optical microscopy techniques provides the possibility to augment EM with nanometer-resolution fluorescence microscopy to access the precise location of proteins in the context of cellular ultrastructure. Unfortunately, efforts to combine superresolution fluorescence and EM have been stymied by the divergent and incompatible sample preparation protocols of the two methods. Here, we describe a protocol that preserves both the delicate photoactivatable fluorescent protein labels essential for superresolution microscopy and the fine ultrastructural context of EM. This preparation enables direct 3D imaging in 500- to 750-nm sections with interferometric photoactivatable localization microscopy followed by scanning EM images generated by focused ion beam ablation. We use this process to "colorize" detailed EM images of the mitochondrion with the position of labeled proteins. The approach presented here has provided a new level of definition of the in vivo nature of organization of mitochondrial nucleoids, and we expect this straightforward method to be applicable to many other biological questions that can be answered by direct imaging.

}, keywords = {3T3 Cells, Animals, DNA, Mitochondrial, DNA-Binding Proteins, Fibroblasts, High Mobility Group Proteins, Imaging, Three-Dimensional, Luminescent Proteins, Mice, Microscopy, Electron, Microscopy, Fluorescence, Microscopy, Interference, Mitochondria, Mitochondrial Membranes, Mitochondrial Proteins, Reproducibility of Results}, issn = {1091-6490}, doi = {10.1073/pnas.1121558109}, author = {Kopek, Benjamin G and Shtengel, Gleb and Xu, C Shan and Clayton, David A and Hess, Harald F} } @article {4601, title = {A Cre-dependent GCaMP3 reporter mouse for neuronal imaging in vivo.}, journal = {The Journal of Neuroscience}, volume = {32}, year = {2012}, month = {2012 Feb 29}, pages = {3131-41}, abstract = {

Fluorescent calcium indicator proteins, such as GCaMP3, allow imaging of activity in genetically defined neuronal populations. GCaMP3 can be expressed using various gene delivery methods, such as viral infection or electroporation. However, these methods are invasive and provide inhomogeneous and nonstationary expression. Here, we developed a genetic reporter mouse, Ai38, which expresses GCaMP3 in a Cre-dependent manner from the ROSA26 locus, driven by a strong CAG promoter. Crossing Ai38 with appropriate Cre mice produced robust GCaMP3 expression in defined cell populations in the retina, cortex, and cerebellum. In the primary visual cortex, visually evoked GCaMP3 signals showed normal orientation and direction selectivity. GCaMP3 signals were rapid, compared with virally expressed GCaMP3 and synthetic calcium indicators. In the retina, Ai38 allowed imaging spontaneous calcium waves in starburst amacrine cells during development, and light-evoked responses in ganglion cells in adult tissue. Our results show that the Ai38 reporter mouse provides a flexible method for targeted expression of GCaMP3.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4469-11.2012}, author = {Zariwala, Hatim A and Borghuis, Bart G and Hoogland, Tycho M and Madisen, Linda and Tian, Lin and De Zeeuw, Chris I and Zeng, Hongkui and Looger, Loren L and Svoboda, Karel and Chen, Tsai-Wen} } @article {6922, title = {Deletion of the γ-aminobutyric acid transporter 2 (GAT2 and SLC6A13) gene in mice leads to changes in liver and brain taurine contents.}, journal = {The Journal of Biological Chemistry}, volume = {287}, year = {2012}, month = {2012 Oct 12}, pages = {35733-46}, abstract = {

The GABA transporters (GAT1, GAT2, GAT3, and BGT1) have mostly been discussed in relation to their potential roles in controlling the action of transmitter GABA in the nervous system. We have generated the first mice lacking the GAT2 (slc6a13) gene. Deletion of GAT2 (both mRNA and protein) neither affected growth, fertility, nor life span under nonchallenging rearing conditions. Immunocytochemistry showed that the GAT2 protein was predominantly expressed in the plasma membranes of periportal hepatocytes and in the basolateral membranes of proximal tubules in the renal cortex. This was validated by processing tissue from wild-type and knockout mice in parallel. Deletion of GAT2 reduced liver taurine levels by 50\%, without affecting the expression of the taurine transporter TAUT. These results suggest an important role for GAT2 in taurine uptake from portal blood into liver. In support of this notion, GAT2-transfected HEK293 cells transported [(3)H]taurine. Furthermore, most of the uptake of [(3)H]GABA by cultured rat hepatocytes was due to GAT2, and this uptake was inhibited by taurine. GAT2 was not detected in brain parenchyma proper, excluding a role in GABA inactivation. It was, however, expressed in the leptomeninges and in a subpopulation of brain blood vessels. Deletion of GAT2 increased brain taurine levels by 20\%, suggesting a taurine-exporting role for GAT2 in the brain.

}, keywords = {Animals, Brain, Brain Chemistry, GABA Plasma Membrane Transport Proteins, HEK293 Cells, Hepatocytes, Humans, Kidney Cortex, Kidney Tubules, Knockout, Liver, Male, Mice, Proximal, Rabbits, Rats, Taurine, Wistar}, issn = {1083-351X}, doi = {10.1074/jbc.M112.368175}, author = {Zhou, Yun and Holmseth, Silvia and Guo, Caiying and Hassel, Bj{\o}rnar and H{\"o}fner, Georg and Huitfeldt, Henrik S and Wanner, Klaus T and Danbolt, Niels C} } @article {46605, title = {DlgS97/SAP97, a neuronal isoform of discs large, regulates ethanol tolerance.}, journal = {PLoS One}, volume = {7}, year = {2012}, month = {2012 Nov 7}, pages = {e48967}, abstract = {

From a genetic screen for Drosophila melanogaster mutants with altered ethanol tolerance, we identified intolerant (intol), a novel allele of discs large 1 (dlg1). Dlg1 encodes Discs Large 1, a MAGUK (Membrane Associated Guanylate Kinase) family member that is the highly conserved homolog of mammalian PSD-95 and SAP97. The intol mutation disrupted specifically the expression of DlgS97, a SAP97 homolog, and one of two major protein isoforms encoded by dlg1 via alternative splicing. Expression of the major isoform, DlgA, a PSD-95 homolog, appeared unaffected. Ethanol tolerance in the intol mutant could be partially restored by transgenic expression of DlgS97, but not DlgA, in specific neurons of the fly{\textquoteright}s brain. Based on co-immunoprecipitation, DlgS97 forms a complex with N-methyl-D-aspartate (NMDA) receptors, a known target of ethanol. Consistent with these observations, flies expressing reduced levels of the essential NMDA receptor subunit dNR1 also showed reduced ethanol tolerance, as did mutants in the gene calcium/calmodulin-dependent protein kinase (caki), encoding the fly homolog of mammalian CASK, a known binding partner of DlgS97. Lastly, mice in which SAP97, the mammalian homolog of DlgS97, was conditionally deleted in adults failed to develop rapid tolerance to ethanol{\textquoteright}s sedative/hypnotic effects. We propose that DlgS97/SAP97 plays an important and conserved role in the development of tolerance to ethanol via NMDA receptor-mediated synaptic plasticity.

}, keywords = {Alleles, Alternative Splicing, Animals, Drosophila melanogaster, Drosophila Proteins, Ethanol, Female, Guanylate Kinase, Male, Membrane Proteins, Mice, Mice, Inbred C57BL, Mutation, Neurons, Protein Isoforms, Receptors, N-Methyl-D-Aspartate, Repressor Proteins, Tumor Suppressor Proteins}, issn = {1932-6203}, doi = {10.1371/journal.pone.0048967}, author = {Maiya, Rajani and Lee, Seonok and Berger, Karen H and Kong, Eric C and Slawson, Justin B and Griffith, Leslie C and Takamiya, Kogo and Huganir, Richard L and Margolis, Ben and Heberlein, Ulrike} } @article {5319, title = {Dorsorostral snout muscles in the rat subserve coordinated movement for whisking and sniffing.}, journal = {Anatomical Record}, volume = {295}, year = {2012}, month = {2012 Jul}, pages = {1181-91}, abstract = {

Histochemical examination of the dorsorostral quadrant of the rat snout revealed superficial and deep muscles that are involved in whisking, sniffing, and airflow control. The part of M. nasolabialis profundus that acts as an intrinsic (follicular) muscle to facilitate protraction and translation of the vibrissae is described. An intraturbinate and selected rostral-most nasal muscles that can influence major routs of inspiratory airflow and rhinarial touch through their control of nostril configuration, atrioturbinate and rhinarium position, were revealed.

}, issn = {1932-8494}, doi = {10.1002/ar.22501}, author = {Haidarliu, Sebastian and Golomb, David and Kleinfeld, David and Ahissar, Ehud} } @article {4522, title = {Drosophila melanogaster as a model to study drug addiction.}, journal = {Human Genetics}, volume = {131}, year = {2012}, month = {2012 Feb 17}, pages = {959-75}, abstract = {

Animal studies have been instrumental in providing knowledge about the molecular and neural mechanisms underlying drug addiction. Recently, the fruit fly Drosophila melanogaster has become a valuable system to model not only the acute stimulating and sedating effects of drugs but also their more complex rewarding properties. In this review, we describe the advantages of using the fly to study drug-related behavior, provide a brief overview of the behavioral assays used, and review the molecular mechanisms and neural circuits underlying drug-induced behavior in flies. Many of these mechanisms have been validated in mammals, suggesting that the fly is a useful model to understand the mechanisms underlying addiction.

}, issn = {1432-1203}, doi = {10.1007/s00439-012-1146-6}, author = {Kaun, Karla R and Devineni, Anita V and Heberlein, Ulrike} } @conference {5685, title = {Efficient automatic 3D-reconstruction of branching neurons from EM data.}, booktitle = {Computer Vision and Pattern Recognition (CVPR), 2012 IEEE Conference on}, year = {2012}, month = {2012}, abstract = {

We present an approach for the automatic reconstruction of neurons from 3D stacks of electron microscopy sections. The core of our system is a set of possible assignments, each of which proposes with some cost a link between neuron regions in consecutive sections. These can model the continuation, branching, and end of neurons. The costs are trainable on positive assignment samples. An optimal and consistent set of assignments is found for the whole volume at once by solving an integer linear program. This set of assignments determines both the segmentation into neuron regions and the correspondence between such regions in neighboring slices. For each picked assignment, a confidence value helps to prioritize decisions to be reviewed by a human expert. We evaluate the performance of our method on an annotated volume of neural tissue and compare to the current state of the art [26]. Our method is superior in accuracy and can be trained using a small number of samples. The observed inference times are linear with about 2 milliseconds per neuron and section.

}, author = {Funke, Jan and Andres, Bjoern and Hamprecht, Fred and Cardona, Albert and Cook, Matthew} } @article {4596, title = {Excitation spectra and brightness optimization of two-photon excited probes.}, journal = {Biophysical Journal}, volume = {102}, year = {2012}, month = {2012 Feb 22}, pages = {934-44}, abstract = {

Two-photon probe excitation data are commonly presented as absorption cross section or molecular brightness (the detected fluorescence rate per molecule). We report two-photon molecular brightness spectra for a diverse set of organic and genetically encoded probes with an automated spectroscopic system based on fluorescence correlation spectroscopy. The two-photon action cross section can be extracted from molecular brightness measurements at low excitation intensities, while peak molecular brightness (the maximum molecular brightness with increasing excitation intensity) is measured at higher intensities at which probe photophysical effects become significant. The spectral shape of these two parameters was similar across all dye families tested. Peak molecular brightness spectra, which can be obtained rapidly and with reduced experimental complexity, can thus serve as a first-order approximation to cross-section spectra in determining optimal wavelengths for two-photon excitation, while providing additional information pertaining to probe photostability. The data shown should assist in probe choice and experimental design for multiphoton microscopy studies. Further, we show that, by the addition of a passive pulse splitter, nonlinear bleaching can be reduced-resulting in an enhancement of the fluorescence signal in fluorescence correlation spectroscopy by a factor of two. This increase in fluorescence signal, together with the observed resemblance of action cross section and peak brightness spectra, suggests higher-order photobleaching pathways for two-photon excitation.

}, issn = {1542-0086}, doi = {10.1016/j.bpj.2011.12.056}, author = {M{\"u}tze, J{\"o}rg and Iyer, Vijay and Macklin, John J and Colonell, Jennifer and Karsh, Bill and Petr{\'a}\v sek, Zden\v ek and Schwille, Petra and Looger, Loren L and Lavis, Luke D and Harris, Timothy D} } @article {5634, title = {Fiji: an open-source platform for biological-image analysis.}, journal = {Nature Methods}, volume = {9}, year = {2012}, month = {2012 Jul}, pages = {676-82}, abstract = {

Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.

}, keywords = {Algorithms, Animals, Brain, Computational Biology, Computer-Assisted, Drosophila melanogaster, Image Enhancement, Image Processing, Imaging, Information Dissemination, Software, Software Design, Three-Dimensional}, issn = {1548-7105}, doi = {10.1038/nmeth.2019}, author = {Schindelin, Johannes and Arganda-Carreras, Ignacio and Frise, Erwin and Kaynig, Verena and Longair, Mark and Pietzsch, Tobias and Preibisch, Stephan and Rueden, Curtis and Saalfeld, Stephan and Schmid, Benjamin and Tinevez, Jean-Yves and White, Daniel James and Hartenstein, Volker and Eliceiri, Kevin and Tomancak, Pavel and Cardona, Albert} } @article {5423, title = {A GAL4-driver line resource for Drosophila neurobiology.}, journal = {Cell Reports}, volume = {2}, year = {2012}, month = {2012 Oct 25}, pages = {991-1001}, abstract = {

We established a collection of 7,000 transgenic lines of Drosophila melanogaster. Expression of GAL4 in each line is controlled by a different, defined fragment of genomic DNA that serves as a transcriptional enhancer. We used confocal microscopy of dissected nervous systems to determine the expression patterns driven by each fragment in the adult brain and ventral nerve cord. We present image data on 6,650 lines. Using both manual and machine-assisted annotation, we describe the expression patterns in the most useful lines. We illustrate the utility of these data for identifying novel neuronal cell types, revealing brain asymmetry, and describing the nature and extent of neuronal shape stereotypy. The GAL4 lines allow expression of exogenous genes in distinct, small subsets of the adult nervous system. The set of DNA fragments, each driving a documented expression pattern, will facilitate the generation of additional constructs for manipulating neuronal function. synapse was substantially elevated, at the endocytic zone there was no enhanced polymerization activity. We conclude that actin subserves spatially diverse, independently regulated processes throughout spines. Perisynaptic actin forms a uniquely dynamic structure well suited for direct, active regulation of the synapse.

For the overall strategy and methods used to produce the GAL4 lines:
Pfeiffer, B.D., Jenett, A., Hammonds, A.S., Ngo, T.T., Misra, S., Murphy, C., Scully, A., Carlson, J.W., Wan, K.H., Laverty, T.R., Mungall, C., Svirskas, R., Kadonaga, J.T., Doe, C.Q., Eisen, M.B., Celniker, S.E., Rubin, G.M. (2008). Tools for neuroanatomy and neurogenetics in Drosophila. Proc. Natl. Acad. Sci. USA 105, 9715-9720. http://www.pnas.org/content/105/28/9715.full.pdf+html synapse was substantially elevated, at the endocytic zone there was no enhanced polymerization activity. We conclude that actin subserves spatially diverse, independently regulated processes throughout spines. Perisynaptic actin forms a uniquely dynamic structure well suited for direct, active regulation of the synapse.

For data on expression in the embryo:
Manning, L., Purice, M.D., Roberts, J., Pollard, J.L., Bennett, A.L., Kroll, J.R., Dyukareva, A.V., Doan, P.N., Lupton, J.R., Strader, M.E., Tanner, S., Bauer, D., Wilbur, A., Tran, K.D., Laverty, T.R., Pearson, J.C., Crews, S.T., Rubin, G.M., and Doe, C.Q. (2012) Annotated embryonic CNS expression patterns of 5000 GMR GAL4 lines: a resource for manipulating gene expression and analyzing cis-regulatory motifs. Cell Reports (2012) Doi: 10.1016/j.celrep.2012.09.009 http://www.cell.com/cell-reports/fulltext/S2211-1247(12)00290-2 synapse was substantially elevated, at the endocytic zone there was no enhanced polymerization activity. We conclude that actin subserves spatially diverse, independently regulated processes throughout spines. Perisynaptic actin forms a uniquely dynamic structure well suited for direct, active regulation of the synapse.

For data on expression in imaginal discs:
Jory, A., Estella, C., Giorgianni, M.W., Slattery, M., Laverty, T.R., Rubin, G.M., and Mann, R.S. (2012) A survey of 6300 genomic fragments for cis-regulatory activity in the imaginal discs of Drosophila melanogaster. Cell Reports (2012) Doi: 10.1016/j.celrep.2012.09.010 http://www.cell.com/cell-reports/fulltext/S2211-1247(12)00291-4 synapse was substantially elevated, at the endocytic zone there was no enhanced polymerization activity. We conclude that actin subserves spatially diverse, independently regulated processes throughout spines. Perisynaptic actin forms a uniquely dynamic structure well suited for direct, active regulation of the synapse.

For data on expression in the larval nervous system:
Li, H.-H., Kroll, J.R., Lennox, S., Ogundeyi, O., Jeter, J., Depasquale, G., and Truman, J.W. (2013) A GAL4 driver resource for developmental and behavioral studies on the larval CNS of Drosophila. Cell Reports (submitted).

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2012.09.011}, author = {Jenett, Arnim and Rubin, Gerald M and Ngo, Teri-T B and Shepherd, David and Murphy, Christine and Dionne, Heather and Pfeiffer, Barret D and Cavallaro, Amanda and Hall, Donald and Jeter, Jennifer and Iyer, Nirmala and Fetter, Dona and Hausenfluck, Joanna H and Peng, Hanchuan and Trautman, Eric T and Svirskas, Robert R and Myers, Eugene W and Iwinski, Zbigniew R and Aso, Yoshinori and Depasquale, Gina M and Enos, Adrianne and Hulamm, Phuson and Lam, Shing Chun Benny and Li, Hsing-Hsi and Laverty, Todd R and Long, Fuhui and Qu, Lei and Murphy, Sean D and Rokicki, Konrad and Safford, Todd and Shaw, Kshiti and Simpson, Julie H and Sowell, Allison and Tae, Susana and Yu, Yang and Zugates, Christopher T} } @article {68815, title = {Generation of Multiple Classes of V0 Neurons in Zebrafish Spinal Cord: Progenitor Heterogeneity and Temporal Control of Neuronal Diversity}, journal = {Journal of Neuroscience}, volume = {32}, year = {2012}, month = {02/2012}, pages = {1771{\textendash}1783}, abstract = {

The developing spinal cord is subdivided into distinct progenitor domains, each of which gives rise to different types of neurons. However, the developmental mechanisms responsible for generating neuronal diversity within a domain are not well understood. Here, we have studied zebrafish V0 neurons, those that derive from the p0 progenitor domain, to address this question. We find that all V0 neurons have commissural axons, but they can be divided into excitatory and inhibitory classes. V0 excitatory neurons (V0-e) can be further categorized into three groups based on their axonal trajectories; V0-eA (ascending), V0-eB (bifurcating), and V0-eD (descending) neurons. By using time-lapse imaging of p0 progenitors and their progeny, we show that inhibitory and excitatory neurons are produced from different progenitors. We also demonstrate that V0-eA neurons are produced from distinct progenitors, while V0-eB and V0-eD neurons are produced from common progenitors. We then use birth-date analysis to reveal that V0-eA, V0-eB, and V0-eD neurons arise in this order. By perturbing Notch signaling and accelerating neuronal differentiation, we predictably alter the generation of early born V0-e neurons at the expense of later born ones. These results suggest that multiple types of V0 neurons are produced by two distinct mechanisms; from heterogeneous p0 progenitors and from the same p0 progenitor, but in a time-dependent manner.

}, issn = {0270-6474}, doi = {10.1523/JNEUROSCI.5500-11.2012}, url = {https://www.jneurosci.org/content/32/5/1771}, author = {Chie Satou and Yukiko Kimura and Shin-ichi Higashijima} } @article {6288, title = {Genetic architecture and adaptive significance of the selfing syndrome in Capsella.}, journal = {Evolution: International Journal of Organic Evolution}, volume = {66}, year = {2012}, month = {2012 May}, pages = {1360-74}, abstract = {

The transition from outcrossing to predominant self-fertilization is one of the most common evolutionary transitions in flowering plants. This shift is often accompanied by a suite of changes in floral and reproductive characters termed the selfing syndrome. Here, we characterize the genetic architecture and evolutionary forces underlying evolution of the selfing syndrome in Capsella rubella following its recent divergence from the outcrossing ancestor C. grandiflora. We conduct genotyping by multiplexed shotgun sequencing and map floral and reproductive traits in a large (N= 550) F2 population. Our results suggest that in contrast to previous studies of the selfing syndrome, changes at a few loci, some with major effects, have shaped the evolution of the selfing syndrome in Capsella. The directionality of QTL effects, as well as population genetic patterns of polymorphism and divergence at 318 loci, is consistent with a history of directional selection on the selfing syndrome. Our study is an important step toward characterizing the genetic basis and evolutionary forces underlying the evolution of the selfing syndrome in a genetically accessible model system.

}, keywords = {Biological Evolution, Capsella, Chromosome Mapping, DNA, Flowers, Genetic, Genetic Markers, Genotype, Hybridization, Multilocus Sequence Typing, Phenotype, Plant, Pollination, Polymerase Chain Reaction, Quantitative Trait Loci, Reproduction, Selection, Self-Fertilization, Self-Incompatibility in Flowering Plants, Sequence Analysis}, issn = {1558-5646}, doi = {10.1111/j.1558-5646.2011.01540.x}, author = {Slotte, Tanja and Hazzouri, Khaled M and Stern, David and Andolfatto, Peter and Wright, Stephen I} } @article {46602, title = {A genetic screen for olfactory habituation mutations in Drosophila: analysis of novel foraging alleles and an underlying neural circuit.}, journal = {PLoS One}, volume = {7}, year = {2012}, month = {2012 Dec 17}, pages = {e51684}, abstract = {

Habituation is a form of non-associative learning that enables animals to reduce their reaction to repeated harmless stimuli. When exposed to ethanol vapor, Drosophila show an olfactory-mediated startle response characterized by a transient increase in locomotor activity. Upon repeated exposures, this olfactory startle attenuates with the characteristics of habituation. Here we describe the results of a genetic screen to identify olfactory startle habituation (OSH) mutants. One mutation is a transcript specific allele of foraging (for) encoding a cGMP-dependent kinase. We show this allele of for reduces expression of a for-T1 isoform expressed in the head and functions normally to inhibit OSH. We localize for-T1 function to a limited set of neurons that include olfactory receptor neurons (ORNs) and the mushroom body (MB). Overexpression of for-T1 in ORNs inhibits OSH, an effect also seen upon synaptic silencing of the ORNs; for-T1 may therefore function in ORNs to decrease synaptic release upon repeated exposure to ethanol vapor. Overall, this work contributes to our understanding of the genes and neurons underlying olfactory habituation in Drosophila.

}, keywords = {Alleles, Animals, Anti-Infective Agents, Local, Cyclic GMP-Dependent Protein Kinases, Drosophila melanogaster, Drosophila Proteins, Ethanol, Genetic Testing, Habituation, Psychophysiologic, Mushroom Bodies, Mutation, Neurons, Olfactory Receptor Neurons, Reaction Time, Reflex, Startle, Smell}, issn = {1932-6203}, doi = {10.1371/journal.pone.0051684}, author = {Eddison, Mark and Belay, Amsale T and Sokolowski, Marla B and Heberlein, Ulrike} } @article {4590, title = {Hierarchical deployment of factors regulating temporal fate in a diverse neuronal lineage of the Drosophila central brain.}, journal = {Neuron}, volume = {73}, year = {2012}, month = {2012 Feb 23}, pages = {677-84}, abstract = {

The anterodorsal projection neuron lineage of Drosophila melanogaster produces 40 neuronal types in a stereotypic order. Here we take advantage of this complete lineage sequence to examine the role of known temporal fating factors, including Chinmo and the Hb/Kr/Pdm/Cas transcriptional cascade, within this diverse central brain lineage. Kr mutation affects the temporal fate of the neuroblast (NB) itself, causing a single fate to be skipped, whereas Chinmo null only elicits fate transformation of NB progeny without altering cell counts. Notably, Chinmo operates in two separate windows to prevent fate transformation (into the subsequent Chinmo-indenpendent fate) within each window. By contrast, Hb/Pdm/Cas play no detectable role, indicating that Kr either acts outside of the cascade identified in the ventral nerve cord or that redundancy exists at the level of fating factors. Therefore, hierarchical fating mechanisms operate within the lineage to generate neuronal diversity in an unprecedented fashion.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2011.12.018}, author = {Kao, Chih-Fei and Yu, Hung-Hsiang and He, Yisheng and Kao, Jui-Chun and Lee, Tzumin} } @article {5659, title = {A hierarchical structure of cortical interneuron electrical diversity revealed by automated statistical analysis.}, journal = {Cerebral Cortex}, volume = {23}, year = {2012}, month = {2012 Sep 17}, pages = {2994-3006}, abstract = {

Although the diversity of cortical interneuron electrical properties is well recognized, the number of distinct electrical types (e-types) is still a matter of debate. Recently, descriptions of interneuron variability were standardized by multiple laboratories on the basis of a subjective classification scheme as set out by the Petilla convention (Petilla Interneuron Nomenclature Group, PING). Here, we present a quantitative, statistical analysis of a database of nearly five hundred neurons manually annotated according to the PING nomenclature. For each cell, 38 features were extracted from responses to suprathreshold current stimuli and statistically analyzed to examine whether cortical interneurons subdivide into e-types. We showed that the partitioning into different e-types is indeed the major component of data variability. The analysis suggests refining the PING e-type classification to be hierarchical, whereby most variability is first captured within a coarse subpartition, and then subsequently divided into finer subpartitions. The coarse partition matches the well-known partitioning of interneurons into fast spiking and adapting cells. Finer subpartitions match the burst, continuous, and delayed subtypes. Additionally, our analysis enabled the ranking of features according to their ability to differentiate among e-types. We showed that our quantitative e-type assignment is more than 90\% accurate and manages to catch several human errors.

}, issn = {1460-2199}, doi = {10.1093/cercor/bhs290}, author = {Druckmann, S and Hill, Sean and Sch{\"u}rmann, Felix and Markram, Henry and Segev, Idan} } @article {46726, title = {IGF2BP1 promotes cell migration by regulating MK5 and PTEN signaling.}, journal = {Genes \& Development}, volume = {26}, year = {2012}, month = {2012 Jan 15}, pages = {176-89}, abstract = {

In primary neurons, the oncofetal RNA-binding protein IGF2BP1 (IGF2 mRNA-binding protein 1) controls spatially restricted β-actin (ACTB) mRNA translation and modulates growth cone guidance. In cultured tumor-derived cells, IGF2BP1 was shown to regulate the formation of lamellipodia and invadopodia. However, how and via which target mRNAs IGF2BP1 controls the motility of tumor-derived cells has remained elusive. In this study, we reveal that IGF2BP1 promotes the velocity and directionality of tumor-derived cell migration by determining the cytoplasmic fate of two novel target mRNAs: MAPK4 and PTEN. Inhibition of MAPK4 mRNA translation by IGF2BP1 antagonizes MK5 activation and prevents phosphorylation of HSP27, which sequesters actin monomers available for F-actin polymerization. Consequently, HSP27-ACTB association is reduced, mobilizing cellular G-actin for polymerization in order to promote the velocity of cell migration. At the same time, stabilization of the PTEN mRNA by IGF2BP1 enhances PTEN expression and antagonizes PIP(3)-directed signaling. This enforces the directionality of cell migration in a RAC1-dependent manner by preventing additional lamellipodia from forming and sustaining cell polarization intrinsically. IGF2BP1 thus promotes the velocity and persistence of tumor cell migration by controlling the expression of signaling proteins. This fine-tunes and connects intracellular signaling networks in order to enhance actin dynamics and cell polarization.

}, keywords = {Actins, Cell Line, Tumor, Cell Movement, Cell Polarity, Enzyme Activation, Extracellular Signal-Regulated MAP Kinases, HSP27 Heat-Shock Proteins, Humans, Intracellular Signaling Peptides and Proteins, Phosphorylation, Protein-Serine-Threonine Kinases, PTEN Phosphohydrolase, RNA, Messenger, Signal Transduction}, issn = {1549-5477}, doi = {10.1101/gad.177642.111}, author = {St{\"o}hr, Nadine and K{\"o}hn, Marcel and Lederer, Marcell and Glass, Markus and Reinke, Claudia and Singer, Robert H and H{\"u}ttelmaier, Stefan} } @article {3933, title = {Imaging neural activity with genetically encoded calcium indicator.}, journal = {Cold Spring Harbor Protocols}, volume = {2012}, year = {2012}, month = {2012 Jun 1}, pages = {647-56}, abstract = {

Genetically encoded calcium indicators (GECIs), which are based on chimeric fluorescent proteins, can be used to monitor calcium transients in living cells and organisms. Because they are encoded by DNA, GECIs can be delivered to the intact brain noninvasively and targeted to defined populations of neurons and specific subcellular compartments for long-term, repeated measurements in vivo. GECIs have improved iteratively and are becoming useful for imaging neural activity in vivo. Here we summarize extrinsic and intrinsic factors that influence a GECI{\textquoteright}s performance and provides guidelines for selecting the appropriate GECI for a given application. We also review recent progress in GECI design, optimization, and standardized testing protocols.

}, author = {Tian, Lin and Hires, A and Looger, Loren L} } @article {5851, title = {Imaging the post-fusion release and capture of a vesicle membrane protein.}, journal = {Nature Communications}, volume = {3}, year = {2012}, month = {2012}, pages = {1154}, abstract = {

The molecular mechanism responsible for capturing, sorting and retrieving vesicle membrane proteins following triggered exocytosis is not understood. Here we image the post-fusion release and then capture of a vesicle membrane protein, the vesicular acetylcholine transporter, from single vesicles in living neuroendocrine cells. We combine these measurements with super-resolution interferometric photo-activation localization microscopy and electron microscopy, and modelling to map the nanometer-scale topography and architecture of the structures responsible for the transporter{\textquoteright}s capture following exocytosis. We show that after exocytosis, the transporter rapidly diffuses into the plasma membrane, but most travels only a short distance before it is locally captured over a dense network of membrane-resident clathrin-coated structures. We propose that the extreme density of these structures acts as a short-range diffusion trap. They quickly sequester diffusing vesicle material and limit its spread across the membrane. This system could provide a means for clathrin-mediated endocytosis to quickly recycle vesicle proteins in highly excitable cells.

}, issn = {2041-1723}, doi = {10.1038/ncomms2158}, author = {Sochacki, Kem A and Larson, Ben T and Sengupta, Deepali C and Daniels, Mathew P and Shtengel, Gleb and Hess, Harald F and Taraska, Justin W} } @article {4595, title = {An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.}, journal = {The ISME Journal}, volume = {6}, year = {2012}, month = {2012 Mar}, pages = {610-8}, abstract = {

Reference phylogenies are crucial for providing a taxonomic framework for interpretation of marker gene and metagenomic surveys, which continue to reveal novel species at a remarkable rate. Greengenes is a dedicated full-length 16S rRNA gene database that provides users with a curated taxonomy based on de novo tree inference. We developed a {\textquoteright}taxonomy to tree{\textquoteright} approach for transferring group names from an existing taxonomy to a tree topology, and used it to apply the Greengenes, National Center for Biotechnology Information (NCBI) and cyanoDB (Cyanobacteria only) taxonomies to a de novo tree comprising 408 315 sequences. We also incorporated explicit rank information provided by the NCBI taxonomy to group names (by prefixing rank designations) for better user orientation and classification consistency. The resulting merged taxonomy improved the classification of 75\% of the sequences by one or more ranks relative to the original NCBI taxonomy with the most pronounced improvements occurring in under-classified environmental sequences. We also assessed candidate phyla (divisions) currently defined by NCBI and present recommendations for consolidation of 34 redundantly named groups. All intermediate results from the pipeline, which includes tree inference, jackknifing and transfer of a donor taxonomy to a recipient tree (tax2tree) are available for download. The improved Greengenes taxonomy should provide important infrastructure for a wide range of megasequencing projects studying ecosystems on scales ranging from our own bodies (the Human Microbiome Project) to the entire planet (the Earth Microbiome Project). The implementation of the software can be obtained from http://sourceforge.net/projects/tax2tree/.

}, issn = {1751-7370}, doi = {10.1038/ismej.2011.139}, author = {McDonald, Daniel and Price, Morgan N and Goodrich, Julia and Nawrocki, Eric P and Desantis, Todd Z and Probst, Alexander and Andersen, Gary L and Knight, Rob and Hugenholtz, Philip} } @article {65029, title = {An intra-cerebral drug delivery system for freely moving animals.}, journal = {Biomed Microdevices}, volume = {14}, year = {2012}, month = {2012 Oct 01}, pages = {799-809}, abstract = {

Microinfusions of drugs directly into the central nervous system of awake animals represent a widely used means of unravelling brain functions related to behaviour. However, current approaches generally use tethered liquid infusion systems and a syringe pump to deliver drugs into the brain, which often interfere with behaviour. We address this shortfall with a miniaturised electronically-controlled drug delivery system (20 {\texttimes} 17.5 {\texttimes} 5 mm{\textthreesuperior}) designed to be skull-mounted in rats. The device features a micropump connected to two 8-mm-long silicon microprobes with a cross section of 250 {\texttimes} 250 μm{\texttwosuperior} and integrated fluid microchannels. Using an external electronic control unit, the device allows infusion of 16 metered doses (0.25 μL each, 8 per silicon shaft). Each dosage requires 3.375 Ws of electrical power making the device additionally compatible with state-of-the-art wireless headstages. A dosage precision of 0.25 {\textpm} 0.01 μL was determined in vitro before in vivo tests were carried out in awake rats. No passive leakage from the loaded devices into the brain could be detected using methylene blue dye. Finally, the device was used to investigate the effects of the NMDA-receptor antagonist 3-((R)-2-Carboxypiperazin-4-yl)-propyl-1-phosphonic acid, (R)-CPP, administered directly into the prefrontal cortex of rats during performance on a task to assess visual attention and impulsivity. In agreement with previous findings using conventional tethered infusion systems, acute (R)-CPP administration produced a marked increase in impulsivity.

}, keywords = {Animals, Attention, Brain, Drug Delivery Systems, Equipment Design, Impulsive Behavior, Microinjections, Piperazines, Rats, Receptors, N-Methyl-D-Aspartate}, issn = {1572-8781}, doi = {10.1007/s10544-012-9659-2}, author = {Spieth, Sven and Schumacher, Axel and Holtzman, Tahl and Rich, P Dylan and Theobald, David E and Dalley, Jeffrey W and Nouna, Rachid and Messner, Stephan and Zengerle, Roland} } @article {46603, title = {JNK pathway activation is controlled by Tao/TAOK3 to modulate ethanol sensitivity.}, journal = {PLoS One}, volume = {7}, year = {2012}, month = {2012 Dec 5}, pages = {e50594}, abstract = {

Neuronal signal transduction by the JNK MAP kinase pathway is altered by a broad array of stimuli including exposure to the widely abused drug ethanol, but the behavioral relevance and the regulation of JNK signaling is unclear. Here we demonstrate that JNK signaling functions downstream of the Sterile20 kinase family gene tao/Taok3 to regulate the behavioral effects of acute ethanol exposure in both the fruit fly Drosophila and mice. In flies tao is required in neurons to promote sensitivity to the locomotor stimulant effects of acute ethanol exposure and to establish specific brain structures. Reduced expression of key JNK pathway genes substantially rescued the structural and behavioral phenotypes of tao mutants. Decreasing and increasing JNK pathway activity resulted in increased and decreased sensitivity to the locomotor stimulant properties of acute ethanol exposure, respectively. Further, JNK expression in a limited pattern of neurons that included brain regions implicated in ethanol responses was sufficient to restore normal behavior. Mice heterozygous for a disrupted allele of the homologous Taok3 gene (Taok3Gt) were resistant to the acute sedative effects of ethanol. JNK activity was constitutively increased in brains of Taok3Gt/+ mice, and acute induction of phospho-JNK in brain tissue by ethanol was occluded in Taok3Gt/+ mice. Finally, acute administration of a JNK inhibitor conferred resistance to the sedative effects of ethanol in wild-type but not Taok3Gt/+ mice. Taken together, these data support a role of a TAO/TAOK3-JNK neuronal signaling pathway in regulating sensitivity to acute ethanol exposure in flies and in mice.

}, keywords = {Animals, Base Sequence, Behavior, Animal, DNA Primers, Drosophila, Drosophila Proteins, Ethanol, Immunohistochemistry, MAP Kinase Kinase 4, Mice, Mice, Inbred C57BL, Mutation, Protein-Serine-Threonine Kinases, Reverse Transcriptase Polymerase Chain Reaction}, issn = {1932-6203}, doi = {10.1371/journal.pone.0050594}, author = {Kapfhamer, David and King, Ian and Zou, Mimi E and Lim, Jana P and Heberlein, Ulrike and Wolf, Fred W} } @article {6290, title = {Lineage analysis of Drosophila lateral antennal lobe neurons reveals notch-dependent binary temporal fate decisions.}, journal = {PLoS Biology}, volume = {10}, year = {2012}, month = {2012 Nov 20}, pages = {e1001425}, abstract = {

Binary cell fate decisions allow the production of distinct sister neurons from an intermediate precursor. Neurons are further diversified based on the birth order of intermediate precursors. Here we examined the interplay between binary cell fate and birth-order-dependent temporal fate in the Drosophila lateral antennal lobe (lAL) neuronal lineage. Single-cell mapping of the lAL lineage by twin-spot mosaic analysis with repressible cell markers (ts-MARCM) revealed that projection neurons (PNs) and local interneurons (LNs) are made in pairs through binary fate decisions. Forty-five types of PNs innervating distinct brain regions arise in a stereotyped sequence; however, the PNs with similar morphologies are not necessarily born in a contiguous window. The LNs are morphologically less diverse than the PNs, and the sequential morphogenetic changes in the two pairs occur independently. Sanpodo-dependent Notch activity promotes and patterns the LN fates. By contrast, Notch diversifies PN temporal fates in a Sanpodo-dispensable manner. These pleiotropic Notch actions underlie the differential temporal fate specification of twin neurons produced by common precursors within a lineage, possibly by modulating postmitotic neurons{\textquoteright} responses to Notch-independent transcriptional cascades.

}, keywords = {Animals, Biological Markers, Brain, Cell Division, Cell Lineage, Cellular, Developmental, Drosophila, Drosophila Proteins, Embryo, Gene Expression Regulation, Genes, Immunohistochemistry, Insect, Larva, Mechanotransduction, Nerve Tissue Proteins, Neurogenesis, Neurons, Nonmammalian, Notch, Receptors, Single-Cell Analysis}, issn = {1545-7885}, doi = {10.1371/journal.pbio.1001425}, author = {Lin, Suewei and Kao, Chih-Fei and Yu, Hung-Hsiang and Huang, Yaling and Lee, Tzumin} } @article {46607, title = {Lmo4 in the basolateral complex of the amygdala modulates fear learning.}, journal = {PLoS One}, volume = {7}, year = {2012}, month = {2012 Apr 3}, pages = {e34559}, abstract = {

Pavlovian fear conditioning is an associative learning paradigm in which mice learn to associate a neutral conditioned stimulus with an aversive unconditioned stimulus. In this study, we demonstrate a novel role for the transcriptional regulator Lmo4 in fear learning. LMO4 is predominantly expressed in pyramidal projection neurons of the basolateral complex of the amygdala (BLC). Mice heterozygous for a genetrap insertion in the Lmo4 locus (Lmo4gt/+), which express 50\% less Lmo4 than their wild type (WT) counterparts display enhanced freezing to both the context and the cue in which they received the aversive stimulus. Small-hairpin RNA-mediated knockdown of Lmo4 in the BLC, but not the dentate gyrus region of the hippocampus recapitulated this enhanced conditioning phenotype, suggesting an adult- and brain region-specific role for Lmo4 in fear learning. Immunohistochemical analyses revealed an increase in the number of c-Fos positive puncta in the BLC of Lmo4gt/+ mice in comparison to their WT counterparts after fear conditioning. Lastly, we measured anxiety-like behavior in Lmo4gt/+ mice and in mice with BLC-specific downregulation of Lmo4 using the elevated plus maze, open field, and light/dark box tests. Global or BLC-specific knockdown of Lmo4 did not significantly affect anxiety-like behavior. These results suggest a selective role for LMO4 in the BLC in modulating learned but not unlearned fear.

}, keywords = {Adaptor Proteins, Signal Transducing, Amygdala, Animals, Behavior, Animal, Conditioning (Psychology), Cues, Fear, Gene Knockdown Techniques, LIM Domain Proteins, Male, Mice, Mice, Inbred C57BL, Neurons, Protein Transport}, issn = {1932-6203}, doi = {10.1371/journal.pone.0034559}, author = {Maiya, Rajani and Kharazia, Viktor and Lasek, Amy W and Heberlein, Ulrike} } @article {5661, title = {A mechanistic model of early sensory processing based on subtracting sparse representations.}, journal = {Advances in Neural Information Processing Systems}, volume = {25}, year = {2012}, month = {2012}, pages = {1979-87}, abstract = {

Early stages of sensory systems face the challenge of compressing information from numerous receptors onto a much smaller number of projection neurons, a so called communication bottleneck. To make more efficient use of limited bandwidth, compression may be achieved using predictive coding, whereby predictable, or redundant, components of the stimulus are removed. In the case of the retina, Srinivasan et al. (1982) suggested that feedforward inhibitory connections subtracting a linear prediction generated from nearby receptors implement such compression, resulting in biphasic center-surround receptive fields. However, feedback inhibitory circuits are common in early sensory circuits and furthermore their dynamics may be nonlinear. Can such circuits implement predictive coding as well? Here, solving the transient dynamics of nonlinear reciprocal feedback circuits through analogy to a signal-processing algorithm called linearized Bregman iteration we show that nonlinear predictive coding can be implemented in an inhibitory feedback circuit. In response to a step stimulus, interneuron activity in time constructs progressively less sparse but more accurate representations of the stimulus, a temporally evolving prediction. This analysis provides a powerful theoretical framework to interpret and understand the dynamics of early sensory processing in a variety of physiological experiments and yields novel predictions regarding the relation between activity and stimulus statistics.

}, author = {Druckmann, Shaul and Hu, T and Chklovskii, D} } @article {6319, title = {Movies of ice-embedded particles enhance resolution in electron cryo-microscopy.}, journal = {Structure}, volume = {20}, year = {2012}, month = {2012 Nov 7}, pages = {1823-8}, abstract = {

Low-dose images obtained by electron cryo-microscopy (cryo-EM) are often affected by blurring caused by sample motion during electron beam exposure, degrading signal especially at high resolution. We show here that we can align frames of movies, recorded with a direct electron detector during beam exposure of rotavirus double-layered particles, thereby greatly reducing image blurring caused by beam-induced motion and sample stage instabilities. This procedure increases the efficiency of cryo-EM imaging and enhances the resolution obtained in three-dimensional reconstructions of the particle. Using movies in this way is generally applicable to all cryo-EM samples and should also improve the performance of midrange electron microscopes that may have limited mechanical stability and beam coherence.

}, keywords = {Cryoelectron Microscopy, Ice, Rotavirus}, issn = {1878-4186}, doi = {10.1016/j.str.2012.08.026}, author = {Campbell, Melody G and Cheng, Anchi and Brilot, Axel F and Moeller, Arne and Lyumkis, Dmitry and Veesler, David and Pan, Junhua and Harrison, Stephen C and Potter, Clinton S and Carragher, Bridget and Grigorieff, Nikolaus} } @article {4761, title = {Multiple dynamic representations in the motor cortex during sensorimotor learning.}, journal = {Nature}, volume = {484}, year = {2012}, month = {2012 Apr 26}, pages = {473-8}, abstract = {

The mechanisms linking sensation and action during learning are poorly understood. Layer 2/3 neurons in the motor cortex might participate in sensorimotor integration and learning; they receive input from sensory cortex and excite deep layer neurons, which control movement. Here we imaged activity in the same set of layer 2/3 neurons in the motor cortex over weeks, while mice learned to detect objects with their whiskers and report detection with licking. Spatially intermingled neurons represented sensory (touch) and motor behaviours (whisker movements and licking). With learning, the population-level representation of task-related licking strengthened. In trained mice, population-level representations were redundant and stable, despite dynamism of single-neuron representations. The activity of a subpopulation of neurons was consistent with touch driving licking behaviour. Our results suggest that ensembles of motor cortex neurons couple sensory input to multiple, related motor programs during learning.

}, issn = {1476-4687}, doi = {10.1038/nature11039}, author = {Huber, D and Gutnisky, D A and Peron, S and O{\textquoteright}Connor, D H and Wiegert, J S and Tian, L and Oertner, T G and Looger, LL and Svoboda, K} } @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 {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 {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 {5329, title = {Optogenetic analysis of a nociceptor neuron and network reveals ion channels acting downstream of primary sensors.}, journal = {Current Biology}, volume = {22}, year = {2012}, month = {2012 May 8}, pages = {743-52}, abstract = {

Nociception generally evokes rapid withdrawal behavior in order to protect the tissue from harmful insults. Most nociceptive neurons responding to mechanical insults display highly branched dendrites, an anatomy shared by Caenorhabditis elegans FLP and PVD neurons, which mediate harsh touch responses. Although several primary molecular nociceptive sensors have been characterized, less is known about modulation and amplification of noxious signals within nociceptor neurons. First, we analyzed the FLP/PVD network by optogenetics and studied integration of signals from these cells in downstream interneurons. Second, we investigated which genes modulate PVD function, based on prior single-neuron mRNA profiling of PVD.

}, keywords = {Ion Channels, Neurons}, issn = {1879-0445}, doi = {10.1016/j.cub.2012.02.066}, author = {Husson, Steven J and Costa, Wagner Steuer and Wabnig, Sebastian and Stirman, Jeffrey N and Watson, Joseph D and Spencer, W Clay and Akerboom, Jasper and Looger, Loren L and Treinin, Millet and Miller, David M and Lu, Hang and Gottschalk, Alexander} } @article {6330, title = {Outcome of the first electron microscopy validation task force meeting.}, journal = {Structure}, volume = {20}, year = {2012}, month = {2012 Feb 8}, pages = {205-14}, abstract = {

This Meeting Review describes the proceedings and conclusions from the inaugural meeting of the Electron Microscopy Validation Task Force organized by the Unified Data Resource for 3DEM (http://www.emdatabank.org) and held at Rutgers University in New Brunswick, NJ on September 28 and 29, 2010. At the workshop, a group of scientists involved in collecting electron microscopy data, using the data to determine three-dimensional electron microscopy (3DEM) density maps, and building molecular models into the maps explored how to assess maps, models, and other data that are deposited into the Electron Microscopy Data Bank and Protein Data Bank public data archives. The specific recommendations resulting from the workshop aim to increase the impact of 3DEM in biology and medicine.

}, keywords = {Animals, Databases, Electron, Factual, Guidelines as Topic, Humans, Information Storage and Retrieval, Macromolecular Substances, Microscopy, Models, Molecular, Molecular Conformation, Molecular Sequence Annotation}, issn = {1878-4186}, doi = {10.1016/j.str.2011.12.014}, author = {Henderson, Richard and Sali, Andrej and Baker, Matthew L and Carragher, Bridget and Devkota, Batsal and Downing, Kenneth H and Egelman, Edward H and Feng, Zukang and Frank, Joachim and Grigorieff, Nikolaus and Jiang, Wen and Ludtke, Steven J and Medalia, Ohad and Penczek, Pawel A and Rosenthal, Peter B and Rossmann, Michael G and Schmid, Michael F and Schr{\"o}der, Gunnar F and Steven, Alasdair C and Stokes, David L and Westbrook, John D and Wriggers, Willy and Yang, Huanwang and Young, Jasmine and Berman, Helen M and Chiu, Wah and Kleywegt, Gerard J and Lawson, Catherine L} } @article {66011, title = {Pediatric epilepsy surgery: long-term 5-year seizure remission and medication use}, journal = {Neurosurgery}, volume = {71}, year = {2012}, month = {Feb-08-2013}, pages = {985 - 993}, abstract = {

Background:\ It is unclear whether long-term seizure outcomes in children are similar to those in adult epilepsy surgery patients.

Objective:\ To determine 5-year outcomes and antiepilepsy drug (AED) use in pediatric epilepsy surgery patients from a single institution.

Methods:\ The cohort consisted of children younger than 18 years of age whose 5-year outcome data would have been available by 2010. Comparisons were made between patients with and without 5-year data (n = 338), patients with 5-year data for seizure outcome (n = 257), and seizure-free patients on and off AEDs (n = 137).

Results:\ Five-year data were available from 76\% of patients. More seizure-free patients with focal resections for hippocampal sclerosis and tumors lacked 5-year data compared with other cases. Of those with 5-year data, 53\% were continuously seizure free, 18\% had late seizure recurrence, 3\% became seizure free after initial failure, and 25\% were never seizure free. Patients were more likely to be continuously seizure free if their surgery was performed during the period 2001 to 2005 (68\%) compared with surgery performed from 1996 to 2000 (61\%), 1991 to 1995 (36\%), and 1986 to 1990 (46\%). More patients had 1 or fewer seizures per month in the late seizure recurrence (47\%) compared with the not seizure-free group (20\%). Four late deaths occurred in the not seizure-free group compared with 1 in the seizure-free group. Of patients who were continuously seizure free, 55\% were not taking AEDs, and more cortical dysplasia patients (74\%) had stopped taking AEDs compared with hemimegalencephaly patients (18\%).

Conclusion:\ In children, 5-year outcomes improved over 20 years of clinical experience. Our results are similar to those of adult epilepsy surgery patients despite mostly extratemporal and hemispheric operations for diverse developmental etiologies.

}, issn = {0148-396X}, doi = {10.1227/NEU.0b013e31826cdd5a}, url = {https://academic.oup.com/neurosurgery/article/71/5/985/2595469http://academic.oup.com/neurosurgery/article-pdf/71/5/985/32585196/00006123-201211000-00011.pdfhttp://academic.oup.com/neurosurgery/article-pdf/71/5/985/32585196/00006123-201211000-00011.pdf}, author = {Hauptman, Jason S. and Pedram, Kayvon and Sison, Christia Angela and Sankar, Raman and Salamon, Noriko and Vinters, Harry V. and Mathern, Gary W.} } @article {6296, title = {The Pfam protein families database.}, journal = {Nucleic acids research}, volume = {40}, year = {2012}, month = {2012 Jan}, pages = {D290-301}, abstract = {

Pfam is a widely used database of protein families, currently containing more than 13,000 manually curated protein families as of release 26.0. Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/). Here, we report on changes that have occurred since our 2010 NAR paper (release 24.0). Over the last 2 years, we have generated 1840 new families and increased coverage of the UniProt Knowledgebase (UniProtKB) to nearly 80\%. Notably, we have taken the step of opening up the annotation of our families to the Wikipedia community, by linking Pfam families to relevant Wikipedia pages and encouraging the Pfam and Wikipedia communities to improve and expand those pages. We continue to improve the Pfam website and add new visualizations, such as the {\textquoteright}sunburst{\textquoteright} representation of taxonomic distribution of families. In this work we additionally address two topics that will be of particular interest to the Pfam community. First, we explain the definition and use of family-specific, manually curated gathering thresholds. Second, we discuss some of the features of domains of unknown function (also known as DUFs), which constitute a rapidly growing class of families within Pfam.

}, keywords = {Amino Acid, Databases, Encyclopedias as Topic, Internet, Protein, Protein Structure, Proteins, Sequence Homology, Tertiary}, issn = {1362-4962}, doi = {10.1093/nar/gkr1065}, author = {Punta, Marco and Coggill, Penny C and Eberhardt, Ruth Y and Mistry, Jaina and Tate, John and Boursnell, Chris and Pang, Ningze and Forslund, Kristoffer and Ceric, Goran and Clements, Jody and Heger, Andreas and Holm, Liisa and Sonnhammer, Erik L L and Sean R. Eddy and Bateman, Alex and Finn, Robert D} } @article {5460, title = {Proprioceptive coupling within motor neurons drives C. elegans forward locomotion.}, journal = {Neuron}, volume = {76}, year = {2012}, month = {2012 Nov 21}, pages = {750-61}, abstract = {

Locomotion requires coordinated motor activity throughout an animal{\textquoteright}s body. In both vertebrates and invertebrates, chains of coupled central pattern generators (CPGs) are commonly evoked to explain local rhythmic behaviors. In C.\ elegans, we report that proprioception within the motor circuit is responsible for propagating and coordinating rhythmic undulatory waves from head to tail during forward movement. Proprioceptive coupling between adjacent body regions transduces rhythmic movement initiated near the head into bending waves driven along the body by a chain of reflexes. Using optogenetics and calcium imaging to manipulate and monitor motor circuit activity of moving C.\ elegans held in microfluidic devices, we found that the B-type cholinergic motor neurons transduce the proprioceptive signal. In C.\ elegans, a sensorimotor feedback loop operating within a specific type of motor neuron both drives and organizes body movement.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2012.08.039}, author = {Wen, Quan and Po, Michelle D. and Hulme, Elizabeth and Chen, Sway and Liu, Xinyu and Kwok, Sen Wai and Gershow, Marc and Leifer, Andrew M. and Butler, Victoria and Fang-Yen, Christopher and Kawano, Taizo and Schafer, William R and Whitesides, George and Wyart, Matthieu and Chklovskii, Dmitri B and Samuel, Aravinthan D. T.} } @article {47647, title = {Rab10 and myosin-Va mediate insulin-stimulated GLUT4 storage vesicle translocation in adipocytes.}, journal = {The Journal of cell biology}, volume = {198}, year = {2012}, month = {2012 Aug 20}, pages = {545-60}, abstract = {

Rab proteins are important regulators of insulin-stimulated GLUT4 translocation to the plasma membrane (PM), but the precise steps in GLUT4 trafficking modulated by particular Rab proteins remain unclear. Here, we systematically investigate the involvement of Rab proteins in GLUT4 trafficking, focusing on Rab proteins directly mediating GLUT4 storage vesicle (GSV) delivery to the PM. Using dual-color total internal reflection fluorescence (TIRF) microscopy and an insulin-responsive aminopeptidase (IRAP)-pHluorin fusion assay, we demonstrated that Rab10 directly facilitated GSV translocation to and docking at the PM. Rab14 mediated GLUT4 delivery to the PM via endosomal compartments containing transferrin receptor (TfR), whereas Rab4A, Rab4B, and Rab8A recycled GLUT4 through the endosomal system. Myosin-Va associated with GSVs by interacting with Rab10, positioning peripherally recruited GSVs for ultimate fusion. Thus, multiple Rab proteins regulate the trafficking of GLUT4, with Rab10 coordinating with myosin-Va to mediate the final steps of insulin-stimulated GSV translocation to the PM.

}, keywords = {3T3-L1 Cells, Adipocytes, Animals, Cell Membrane, Cytoplasmic Vesicles, Glucose Transporter Type 4, Insulin, Mice, Myosin Heavy Chains, Myosin Type V, Protein Transport, rab GTP-Binding Proteins}, issn = {1540-8140}, doi = {10.1083/jcb.201111091}, author = {Chen, Yu and Wang, Yan and Zhang, Jinzhong and Deng, Yongqiang and Jiang, Li and Song, Eli and Wu, Xufeng S and Hammer, John A and Xu, Tao and Lippincott-Schwartz, Jennifer} } @article {6515, title = {A resource for manipulating gene expression and analyzing cis-regulatory modules in the Drosophila CNS.}, journal = {Cell Reports}, volume = {2}, year = {2012}, month = {2012 Oct 25}, pages = {1002-13}, abstract = {

Here, we describe the embryonic central nervous system expression of 5,000 GAL4 lines made using molecularly defined cis-regulatory DNA inserted into a single attP genomic location. We document and annotate the patterns in early embryos when neurogenesis is at its peak, and in older embryos where there is maximal neuronal diversity and the first neural circuits are established. We note expression in other tissues, such as the lateral body wall (muscle, sensory neurons, and trachea) and viscera. Companion papers report on the adult brain and larval imaginal discs, and the integrated data sets\ are available online (http://www.janelia.org/gal4-gen1). This collection of embryonically expressed GAL4 lines will be valuable for determining neuronal morphology and function. The 1,862 lines expressed in small subsets of neurons (\<20/segment) will be especially valuable for characterizing\ interneuronal diversity and function, because although interneurons comprise the majority of all central nervous system neurons, their gene expression profile and function remain virtually unexplored.

}, keywords = {Animals, Central Nervous System, Databases, Drosophila, Drosophila Proteins, Embryo, Factual, Female, Gene Expression, Genes, Genetically Modified, Internet, Male, Nonmammalian, Regulatory Elements, Reporter, Transcription Factors, Transcriptional}, issn = {2211-1247}, doi = {10.1016/j.celrep.2012.09.009}, author = {Manning, Laurina and Heckscher, Ellie S and Purice, Maria D and Roberts, Jourdain and Bennett, Alysha L and Kroll, Jason R and Pollard, Jill L and Strader, Marie E and Lupton, Josh R and Dyukareva, Anna V and Doan, Phuong Nam and Bauer, David M and Wilbur, Allison N and Tanner, Stephanie and Kelly, Jimmy J and Lai, Sen-Lin and Tran, Khoa D and Kohwi, Minoree and Laverty, Todd R and Pearson, Joseph C and Crews, Stephen T and Rubin, Gerald M and Doe, Chris Q} } @article {5160, title = {Selective esterase-ester pair for targeting small molecules with cellular specificity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, year = {2012}, month = {2012 Mar 27}, pages = {4756-61}, abstract = {

Small molecules are important tools to measure and modulate intracellular signaling pathways. A longstanding limitation for using chemical compounds in complex tissues has been the inability to target bioactive small molecules to a specific cell class. Here, we describe a generalizable esterase-ester pair capable of targeted delivery of small molecules to living cells and tissue with cellular specificity. We used fluorogenic molecules to rapidly identify a small ester masking motif that is stable to endogenous esterases, but is efficiently removed by an exogenous esterase. This strategy allows facile targeting of dyes and drugs in complex biological environments to label specific cell types, illuminate gap junction connectivity, and pharmacologically perturb distinct subsets of cells. We expect this approach to have general utility for the specific delivery of many small molecules to defined cellular populations.

}, keywords = {Animals, Astrocytes, Biocatalysis, Cell Survival, Cells, Coculture Techniques, Esterases, Esters, Fluorescence, Fluorescent Dyes, Gap Junctions, Hela Cells, Hippocampus, Humans, Hydrolysis, Mice, Microscopy, Neurons, Organ Specificity, Permeability, Rats, Small Molecule Libraries}, issn = {1091-6490}, doi = {10.1073/pnas.1111943109}, author = {Tian, Lin and Yang, Yunlei and Wysocki, Laura M and Arnold, Alma C and Hu, Amy and Ravichandran, Balaji and Sternson, Scott M and Looger, Loren L and Lavis, Luke D} } @article {5480, title = {Sexual deprivation increases ethanol intake in Drosophila.}, journal = {Science}, volume = {335}, year = {2012}, month = {2012 Mar 16}, pages = {1351-5}, abstract = {

The brain{\textquoteright}s reward systems reinforce behaviors required for species survival, including sex, food consumption, and social interaction. Drugs of abuse co-opt these neural pathways, which can lead to addiction. Here, we used Drosophila melanogaster to investigate the relationship between natural and drug rewards. In males, mating increased, whereas sexual deprivation reduced, neuropeptide F (NPF) levels. Activation or inhibition of the NPF system in turn reduced or enhanced ethanol preference. These results thus link sexual experience, NPF system activity, and ethanol consumption. Artificial activation of NPF neurons was in itself rewarding and precluded the ability of ethanol to act as a reward. We propose that activity of the NPF-NPF receptor axis represents the state of the fly reward system and modifies behavior accordingly.

}, keywords = {Acetates, Addictive, Alcohol Drinking, Animal, Animals, Behavior, Cohort Studies, Conditioning (Psychology), Cues, Drosophila melanogaster, Drosophila Proteins, Ethanol, Female, Male, Neurons, Neuropeptide, Neuropeptides, Oleic Acids, Pheromones, Receptors, Reward, Sexual Behavior, TRPC Cation Channels}, issn = {1095-9203}, doi = {10.1126/science.1215932}, author = {Shohat-Ophir, G. and Kaun, K.R. and Azanchi, R. and Mohammed, H and Heberlein, U} } @article {4521, title = {Sexual experience affects ethanol intake in Drosophila through Neuropeptide F.}, journal = {Science}, volume = {335}, year = {2012}, month = {03/2012}, pages = {1351-5}, abstract = {

The brain{\textquoteright}s reward systems reinforce behaviors required for species survival, including sex, food consumption, and social interaction. Drugs of abuse co-opt these neural pathways, which can lead to addiction. Here, we used Drosophila melanogaster to investigate the relationship between natural and drug rewards. In males, mating increased, whereas sexual deprivation reduced, neuropeptide F (NPF) levels. Activation or inhibition of the NPF system in turn reduced or enhanced ethanol preference. These results thus link sexual experience, NPF system activity, and ethanol consumption. Artificial activation of NPF neurons was in itself rewarding and precluded the ability of ethanol to act as a reward. We propose that activity of the NPF{\textendash}NPF receptor axis represents the state of the fly reward system and modifies behavior accordingly.

}, doi = {10.1126/science.1215932 }, author = {Shohat-Ophir, G. and Kaun, K.R. and Azanchi, R. and Heberlein, U} } @article {68361, title = {Sexually Dimorphic BDNF Signaling Directs Sensory Innervation of the Mammary Gland}, journal = {Science}, volume = {338}, year = {2012}, month = {12/2012}, pages = {1357-1360}, abstract = {

Male and female mice differ in the neuronal patterns that serve the mammary glands. Yin Liu et al. (p. 1357) now describe how gonadal hormones drive development of distinct male and female sensory innervations. Although both male and female mammary glands develop their sensory innervation similarly in early embryogenesis, once the androgens take effect, the developmental trajectories diverge. By birth, the rich network of sensory neurons present in the female is absent in the male. Androgens cause a switch from expression of the full-length neurotrophin receptor TrkB to its truncated form, TrkB.T1, both of which are expressed on the neurons. In males, truncated TrkB.T1 sequesters brain-derived neurotrophic factor (BDNF) from further activity, whereas in females, full-length TrkB binds BDNF and supports neuronal development. Androgen-driven changes in receptor expression disrupt a neuronal signaling pathway and de-innervation. How neural circuits associated with sexually dimorphic organs are differentially assembled during development is unclear. Here, we report a sexually dimorphic pattern of mouse mammary gland sensory innervation and the mechanism of its formation. Brain-derived neurotrophic factor (BDNF), emanating from mammary mesenchyme and signaling through its receptor TrkB on sensory axons, is required for establishing mammary gland sensory innervation of both sexes at early developmental stages. Subsequently, in males, androgens promote mammary mesenchymal expression of a truncated form of TrkB, which prevents BDNF-TrkB signaling in sensory axons and leads to a rapid loss of mammary gland innervation independent of neuronal apoptosis. Thus, sex hormone regulation of a neurotrophic factor signal directs sexually dimorphic axonal growth and maintenance, resulting in generation of a sex-specific neural circuit.

}, doi = {10.1126/science.1228258}, url = {https://www.science.org/doi/abs/10.1126/science.1228258}, author = {Yin Liu and Michael Rutlin and Siyi Huang and Colleen A. Barrick and Fan Wang and Kevin R. Jones and Lino Tessarollo and David D. Ginty} } @article {67279, title = {Simplified models for LHC new physics searches}, journal = {Journal of Physics G: Nuclear and Particle Physics}, volume = {39}, year = {2012}, month = {Jan-10-2012}, pages = {105005}, abstract = {

This document proposes a collection of simplified models relevant to the design of new-physics searches at the Large Hadron Collider (LHC) and the characterization of their results. Both ATLAS and CMS have already presented some results in terms of simplified models, and we encourage them to continue and expand this effort, which supplements both signature-based results and benchmark model interpretations. A simplified model is defined by an effective Lagrangian describing the interactions of a small number of new particles. Simplified models can equally well be described by a small number of masses and cross-sections. These parameters are directly related to collider physics observables, making simplified models a particularly effective framework for evaluating searches and a useful starting point for characterizing positive signals of new physics. This document serves as an official summary of the results from the {\textquoteright}Topologies for Early LHC Searches{\textquoteright} workshop, held at SLAC in September of 2010, the purpose of which was to develop a set of representative models that can be used to cover all relevant phase space in experimental searches. Particular emphasis is placed on searches relevant for the first ~50{\textendash}500 pb-1\ of data and those motivated by supersymmetric models. This note largely summarizes material posted at\ http://lhcnewphysics.org/, which includes simplified model definitions, Monte Carlo material, and supporting contacts within the theory community. We also comment on future developments that may be useful as more data is gathered and analyzed by the experiments.

}, issn = {0954-3899}, doi = {10.1088/0954-3899/39/10/105005}, url = {https://iopscience.iop.org/article/10.1088/0954-3899/39/10/105005}, author = {Alves, Daniele and Arkani-Hamed, Nima and Arora, Sanjay and Bai, Yang and Baumgart, Matthew and Berger, Joshua and Buckley, Matthew and Butler, Bart and Chang, Spencer and Cheng, Hsin-Chia and Cheung, Clifford and Chivukula, R Sekhar and Cho, Won Sang and Cotta, Randy and D{\textquoteright}Alfonso, Mariarosaria and Hedri, Sonia El and Essig, Rouven and Evans, Jared A and Fitzpatrick, Liam and Fox, Patrick and Franceschini, Roberto and Freitas, Ayres and Gainer, James S and Gershtein, Yuri and Gray, Richard and Gregoire, Thomas and Gripaios, Ben and Gunion, Jack and Han, Tao and Haas, Andy and Hansson, Per and Hewett, JoAnne and Hits, Dmitry and Hubisz, Jay and Izaguirre, Eder and Kaplan, Jared and Katz, Emanuel and Kilic, Can and Kim, Hyung-Do and Kitano, Ryuichiro and Koay, Sue Ann and Ko, Pyungwon and Krohn, David and Kuflik, Eric and Lewis, Ian and Lisanti, Mariangela and Liu, Tao and Liu, Zhen and Lu, Ran and Luty, Markus and Meade, Patrick and Morrissey, David and Mrenna, Stephen and Nojiri, Mihoko and Okui, Takemichi and Padhi, Sanjay and Papucci, Michele and Park, Michael and Park, Myeonghun and Perelstein, Maxim and Peskin, Michael and Phalen, Daniel and Rehermann, Keith and Rentala, Vikram and Roy, Tuhin and Ruderman, Joshua T and Sanz, Veronica and Schmaltz, Martin and Schnetzer, Stephen and Schuster, Philip and Schwaller, Pedro and Schwartz, Matthew D and Schwartzman, Ariel and Shao, Jing and Shelton, Jessie and Shih, David and Shu, Jing and Silverstein, Daniel and Simmons, Elizabeth and Somalwar, Sunil and Spannowsky, Michael and Spethmann, Christian and Strassler, Matthew and Su, Shufang and Tait, Tim and Thomas, Brooks and Thomas, Scott and Toro, Natalia and Volansky, Tomer and Wacker, Jay and Waltenberger, Wolfgang and Yavin, Itay and Yu, Felix and Zhao, Yue and Zurek, Kathryn} } @article {6504, title = {Solitary and gregarious locusts differ in circadian rhythmicity of a visual output neuron.}, journal = {Journal of BiologicalRrhythms}, volume = {27}, year = {2012}, month = {2012 Jun}, pages = {196-205}, abstract = {

Locusts demonstrate remarkable phenotypic plasticity driven by changes in population density. This density dependent phase polyphenism is associated with many physiological, behavioral, and morphological changes, including observations that cryptic solitarious (solitary-reared) individuals start to fly at dusk, whereas gregarious (crowd-reared) individuals are day-active. We have recorded for 24-36 h, from an identified visual output neuron, the descending contralateral movement detector (DCMD) of Schistocerca gregaria in solitarious and gregarious animals. DCMD signals impending collision and participates in flight avoidance maneuvers. The strength of DCMD{\textquoteright}s response to looming stimuli, characterized by the number of evoked spikes and peak firing rate, varies approximately sinusoidally with a period close to 24 h under constant light in solitarious locusts. In gregarious individuals the 24-h pattern is more complex, being modified by secondary ultradian rhythms. DCMD{\textquoteright}s strongest responses occur around expected dusk in solitarious locusts but up to 6 h earlier in gregarious locusts, matching the times of day at which locusts of each type are most active. We thus demonstrate a neuronal correlate of a temporal shift in behavior that is observed in gregarious locusts. Our ability to alter the nature of a circadian rhythm by manipulating the rearing density of locusts under identical light-dark cycles may provide important tools to investigate further the mechanisms underlying diurnal rhythmicity.

}, keywords = {Animal, Animals, Behavior, Biological, Circadian Rhythm, Female, Grasshoppers, Habituation, Male, Models, Neurons, Ocular, Phenotype, Psychophysiologic, Sense Organs, Social Behavior, Time Factors, Vision, Visual Fields}, issn = {1552-4531}, doi = {10.1177/0748730412440860}, author = {Gaten, Edward and Huston, Stephen J and Dowse, Harold B and Matheson, Tom} } @article {46732, title = {Spatial arrangement of an RNA zipcode identifies mRNAs under post-transcriptional control.}, journal = {Genes \& Development}, volume = {26}, year = {2012}, month = {2012 Jan 1}, pages = {43-53}, abstract = {

How RNA-binding proteins recognize specific sets of target mRNAs remains poorly understood because current approaches depend primarily on sequence information. In this study, we demonstrate that specific recognition of messenger RNAs (mRNAs) by RNA-binding proteins requires the correct spatial positioning of these sequences. We characterized both the cis-acting sequence elements and the spatial restraints that define the mode of RNA binding of the zipcode-binding protein 1 (ZBP1/IMP1/IGF2BP1) to the β-actin zipcode. The third and fourth KH (hnRNP K homology) domains of ZBP1 specifically recognize a bipartite RNA element comprised of a 5{\textquoteright} element (CGGAC) followed by a variable 3{\textquoteright} element (C/A-CA-C/U) that must be appropriately spaced. Remarkably, the orientation of these elements is interchangeable within target transcripts bound by ZBP1. The spatial relationship of this consensus binding site identified conserved transcripts that were verified to associate with ZBP1 in vivo. The dendritic localization of one of these transcripts, spinophilin, was found to be dependent on both ZBP1 and the RNA elements recognized by ZBP1 KH34.

}, keywords = {Actins, Animals, Base Sequence, Cells, Cultured, Consensus Sequence, Dendrites, Gene Expression Regulation, Glycoproteins, Humans, Ligands, Mice, Microfilament Proteins, Models, Molecular, Molecular Sequence Data, Nerve Tissue Proteins, Protein Binding, Protein Structure, Tertiary, RNA, Messenger}, issn = {1549-5477}, doi = {10.1101/gad.177428.111}, author = {Patel, Vivek L and Mitra, Somdeb and Harris, Richard and Buxbaum, Adina R and Lionnet, Timoth{\'e}e and Brenowitz, Michael and Girvin, Mark and Levy, Matthew and Almo, Steven C and Singer, Robert H and Chao, Jeffrey A} } @article {6299, title = {The structural basis for the narrow substrate specificity of an acetyl esterase from Thermotoga maritima.}, journal = {Biochimica et Biophysica Acta}, volume = {1824}, year = {2012}, month = {2012 Sep}, pages = {1024-30}, abstract = {

Acetyl esterases from carbohydrate esterase family 7 exhibit unusual substrate specificity. These proteins catalyze the cleavage of disparate acetate esters with high efficiency, but are unreactive to larger acyl groups. The structural basis for this distinct selectivity profile is unknown. Here, we investigate a thermostable acetyl esterase (TM0077) from Thermotoga maritima using evolutionary relationships, structural information, fluorescent kinetic measurements, and site directed mutagenesis. We measured the kinetic and structural determinants for this specificity using a diverse series of small molecule enzyme substrates, including novel fluorogenic esters. These experiments identified two hydrophobic plasticity residues (Pro228, and Ile276) surrounding the nucleophilic serine that impart this specificity of TM0077 for small, straight-chain esters. Substitution of these residues with alanine imparts broader specificity to TM0077 for the hydrolysis of longer and bulkier esters. Our results suggest the specificity of acetyl esterases have been finely tuned by evolution to catalyze the removal of acetate groups from diverse substrates, but can be modified by focused amino acid substitutions to yield enzymes capable of cleaving larger ester functionalities.

}, keywords = {Acetylesterase, Bacterial Proteins, Binding Sites, Catalysis, Esters, Fluoresceins, Fluorescent Dyes, Hydrolysis, Kinetics, Models, Molecular, Mutagenesis, Site-Directed, Substrate Specificity, Thermotoga maritima}, issn = {0006-3002}, doi = {10.1016/j.bbapap.2012.05.009}, author = {Hedge, Matthew K and Gehring, Alexandra M and Adkins, Chinessa T and Weston, Leigh A and Lavis, Luke D and Johnson, R Jeremy} } @article {6175, title = {Super-resolution using sparse representations over learned dictionaries: reconstruction of brain structure using electron microscopy.}, journal = {arXiv.org }, year = {2012}, month = {2012 Oct}, abstract = {

A central problem in neuroscience is reconstructing neuronal circuits on the synapse level. Due to a wide range of scales in brain architecture such reconstruction requires imaging that is both high-resolution and high-throughput. Existing electron microscopy (EM) techniques possess required resolution in the lateral plane and either high-throughput or high depth resolution but not both. Here, we exploit recent advances in unsupervised learning and signal processing to obtain high depth-resolution EM images computationally without sacrificing throughput. First, we show that the brain tissue can be represented as a sparse linear combination of localized basis functions that are learned using high-resolution datasets. We then develop compressive sensing-inspired techniques that can reconstruct the brain tissue from very few (typically 5) tomographic views of each section. This enables tracing of neuronal processes and, hence, high throughput reconstruction of neural circuits on the level of individual synapses.

}, author = {Hu, T and Nunez-Iglesias, J and Vitaladevuni, S. and Scheffer, L. and Xu, S and Bolorizadeh, M and Hess, H and Fetter, R and Chklovskii, D} } @article {5922, title = {Synaptic amplification by dendritic spines enhances input cooperativity.}, journal = {Nature}, volume = {491}, year = {2012}, month = {2012 Nov 22}, pages = {599-602}, abstract = {

Dendritic spines are the nearly ubiquitous site of excitatory synaptic input onto neurons and as such are critically positioned to influence diverse aspects of neuronal signalling. Decades of theoretical studies have proposed that spines may function as highly effective and modifiable chemical and electrical compartments that regulate synaptic efficacy, integration and plasticity. Experimental studies have confirmed activity-dependent structural dynamics and biochemical compartmentalization by spines. However, there is a longstanding debate over the influence of spines on the electrical aspects of synaptic transmission and dendritic operation. Here we measure the amplitude ratio of spine head to parent dendrite voltage across a range of dendritic compartments and calculate the associated spine neck resistance (R(neck)) for spines at apical trunk dendrites in rat hippocampal CA1 pyramidal neurons. We find that R(neck) is large enough (\ 500 MΩ) to amplify substantially the spine head depolarization associated with a unitary synaptic input by \ 1.5- to \ 45-fold, depending on parent dendritic impedance. A morphologically realistic compartmental model capable of reproducing the observed spatial profile of the amplitude ratio indicates that spines provide a consistently high-impedance input structure throughout the dendritic arborization. Finally, we demonstrate that the amplification produced by spines encourages electrical interaction among coactive inputs through an R(neck)-dependent increase in spine head voltage-gated conductance activation. We conclude that the electrical properties of spines promote nonlinear dendritic processing and associated forms of plasticity and storage, thus fundamentally enhancing the computational capabilities of neurons.

}, keywords = {Animals, Dendritic Spines, Electric Impedance, Excitatory Postsynaptic Potentials, Male, Models, Neurological, Pyramidal Cells, Rats, Sprague-Dawley, Synapses, Wistar}, issn = {1476-4687}, doi = {10.1038/nature11554}, author = {Harnett, Mark T and Makara, Judit K and Spruston, Nelson and Kath, William L and Magee, Jeffrey C} } @article {46051, title = {Synaptic plasticity of NMDA receptors: mechanisms and functional implications.}, journal = {Current Opinion in Neurobiology}, volume = {22}, year = {2012}, month = {2012 Jun}, pages = {496-508}, abstract = {

Beyond their well-established role as triggers for LTP and LTD of fast synaptic transmission mediated by AMPA receptors, an expanding body of evidence indicates that NMDA receptors (NMDARs) themselves are also dynamically regulated and subject to activity-dependent long-term plasticity. NMDARs can significantly contribute to information transfer at synapses particularly during periods of repetitive activity. It is also increasingly recognized that NMDARs participate in dendritic synaptic integration and are critical for generating persistent activity of neural assemblies. Here we review recent advances on the mechanisms and functional consequences of NMDAR plasticity. Given the unique biophysical properties of NMDARs, synaptic plasticity of NMDAR-mediated transmission emerges as a particularly powerful mechanism for the fine tuning of information encoding and storage throughout the brain.

}, keywords = {Animals, Biophysics, Neuronal Plasticity, Receptors, N-Methyl-D-Aspartate, Synapses, Synaptic Transmission}, issn = {1873-6882}, doi = {10.1016/j.conb.2012.01.007}, author = {Hunt, David L and Castillo, Pablo E} } @article {43051, title = {Tandem fluorescent protein timers for in vivo analysis of protein dynamics.}, journal = {Nature Biotechnology}, volume = {30}, year = {2012}, month = {2012 Jun 24}, pages = {708-14}, abstract = {

The functional state of a cell is largely determined by the spatiotemporal organization of its proteome. Technologies exist for measuring particular aspects of protein turnover and localization, but comprehensive analysis of protein dynamics across different scales is possible only by combining several methods. Here we describe tandem fluorescent protein timers (tFTs), fusions of two single-color fluorescent proteins that mature with different kinetics, which we use to analyze protein turnover and mobility in living cells. We fuse tFTs to proteins in yeast to study the longevity, segregation and inheritance of cellular components and the mobility of proteins between subcellular compartments; to measure protein degradation kinetics without the need for time-course measurements; and to conduct high-throughput screens for regulators of protein turnover. Our experiments reveal the stable nature and asymmetric inheritance of nuclear pore complexes and identify regulators of N-end rule{\textendash}mediated protein degradation.

}, keywords = {Green Fluorescent Proteins, High-Throughput Screening Assays, Kinetics, Nuclear Pore, Protein Stability, Proteins, Proteolysis, Saccharomyces cerevisiae, Subcellular Fractions}, issn = {1546-1696}, doi = {10.1038/nbt.2281}, author = {Khmelinskii, Anton and Keller, Philipp J and Bartosik, Anna and Meurer, Matthias and Barry, Joseph D and Mardin, Balca R and Kaufmann, Andreas and Trautmann, Susanne and Wachsmuth, Malte and Pereira, Gislene and Huber, Wolfgang and Schiebel, Elmar and Knop, Michael} } @article {5482, title = {Tissue-specific activation of a single gustatory receptor produces opposing behavioral responses in Drosophila.}, journal = {Genetics}, volume = {192}, year = {2012}, month = {2012 Oct}, pages = {521-32}, abstract = {

Understanding sensory systems that perceive environmental inputs and neural circuits that select appropriate motor outputs is essential for studying how organisms modulate behavior and make decisions necessary for survival. Drosophila melanogaster oviposition is one such important behavior, in which females evaluate their environment and choose to lay eggs on substrates they may find aversive in other contexts. We employed neurogenetic techniques to characterize neurons that influence the choice between repulsive positional and attractive egg-laying responses toward the bitter-tasting compound lobeline. Surprisingly, we found that neurons expressing Gr66a, a gustatory receptor normally involved in avoidance behaviors, receive input for both attractive and aversive preferences. We hypothesized that these opposing responses may result from activation of distinct Gr66a-expressing neurons. Using tissue-specific rescue experiments, we found that Gr66a-expressing neurons on the legs mediate positional aversion. In contrast, pharyngeal taste cells mediate the egg-laying attraction to lobeline, as determined by analysis of mosaic flies in which subsets of Gr66a neurons were silenced. Finally, inactivating mushroom body neurons disrupted both aversive and attractive responses, suggesting that this brain structure is a candidate integration center for decision-making during Drosophila oviposition. We thus define sensory and central neurons critical to the process by which flies decide where to lay an egg. Furthermore, our findings provide insights into the complex nature of gustatory perception in Drosophila. We show that tissue-specific activation of bitter-sensing Gr66a neurons provides one mechanism by which the gustatory system differentially encodes aversive and attractive responses, allowing the female fly to modulate her behavior in a context-dependent manner.

}, issn = {1943-2631}, doi = {10.1534/genetics.112.142455}, author = {Joseph, Ryan M and Heberlein, Ulrike} } @article {6301, title = {A toolbox of Cre-dependent optogenetic transgenic mice for light-induced activation and silencing.}, journal = {Nature Neuroscience}, volume = {15}, year = {2012}, month = {2012 May}, pages = {793-802}, abstract = {

Cell type-specific expression of optogenetic molecules allows temporally precise manipulation of targeted neuronal activity. Here we present a toolbox of four knock-in mouse lines engineered for strong, Cre-dependent expression of channelrhodopsins ChR2-tdTomato and ChR2-EYFP, halorhodopsin eNpHR3.0 and archaerhodopsin Arch-ER2. All four transgenes mediated Cre-dependent, robust activation or silencing of cortical pyramidal neurons in vitro and in vivo upon light stimulation, with ChR2-EYFP and Arch-ER2 demonstrating light sensitivity approaching that of in utero or virally transduced neurons. We further show specific photoactivation of parvalbumin-positive interneurons in behaving ChR2-EYFP reporter mice. The robust, consistent and inducible nature of our ChR2 mice represents a significant advance over previous lines, and the Arch-ER2 and eNpHR3.0 mice are to our knowledge the first demonstration of successful conditional transgenic optogenetic silencing. When combined with the hundreds of available Cre driver lines, this optimized toolbox of reporter mice will enable widespread investigations of neural circuit function with unprecedented reliability and accuracy.

}, keywords = {Action Potentials, Animals, Archaeal Proteins, Brain, Electroporation, Halorhodopsins, Integrases, Light, Luminescent Proteins, Mice, Neurogenesis, Neurons, Optics and Photonics, Proteins, Rhodopsin, Transgenic, Wakefulness}, issn = {1546-1726}, doi = {10.1038/nn.3078}, author = {Madisen, Linda and Mao, Tianyi and Koch, Henner and Zhuo, Jia-min and Berenyi, Antal and Fujisawa, Shigeyoshi and Hsu, Yun-Wei A and Garcia, Alfredo J and Gu, Xuan and Zanella, Sebastien and Kidney, Jolene and Gu, Hong and Mao, Yimei and Hooks, Bryan M and Boyden, Edward S and Buzs{\'a}ki, Gy{\"o}rgy and Ramirez, Jan Marino and Jones, Allan R and Svoboda, Karel and Han, Xue and Turner, Eric E and Zeng, Hongkui} } @article {5684, title = {TrakEM2 software for neural circuit reconstruction.}, journal = {PLoS One}, volume = {7}, year = {2012}, month = {2012}, pages = {e38011}, abstract = {

A key challenge in neuroscience is the expeditious reconstruction of neuronal circuits. For model systems such as Drosophila and C. elegans, the limiting step is no longer the acquisition of imagery but the extraction of the circuit from images. For this purpose, we designed a software application, TrakEM2, that addresses the systematic reconstruction of neuronal circuits from large electron microscopical and optical image volumes. We address the challenges of image volume composition from individual, deformed images; of the reconstruction of neuronal arbors and annotation of synapses with fast manual and semi-automatic methods; and the management of large collections of both images and annotations. The output is a neural circuit of 3d arbors and synapses, encoded in NeuroML and other formats, ready for analysis.

}, keywords = {Animals, Models, Nerve Net, Neuroimaging, Neurological, Neurons, Software, Synapses, Synaptic Transmission}, issn = {1932-6203}, doi = {10.1371/journal.pone.0038011}, author = {Cardona, Albert and Saalfeld, Stephan and Schindelin, Johannes and Arganda-Carreras, Ignacio and Preibisch, Stephan and Longair, Mark and Tomancak, Pavel and Hartenstein, Volker and Douglas, Rodney J} } @article {46785, title = {TrakEM2 software for neural circuit reconstruction.}, journal = {PLoS One}, volume = {7}, year = {2012}, month = {2012}, pages = {e38011}, abstract = {

A key challenge in neuroscience is the expeditious reconstruction of neuronal circuits. For model systems such as Drosophila and C. elegans, the limiting step is no longer the acquisition of imagery but the extraction of the circuit from images. For this purpose, we designed a software application, TrakEM2, that addresses the systematic reconstruction of neuronal circuits from large electron microscopical and optical image volumes. We address the challenges of image volume composition from individual, deformed images; of the reconstruction of neuronal arbors and annotation of synapses with fast manual and semi-automatic methods; and the management of large collections of both images and annotations. The output is a neural circuit of 3d arbors and synapses, encoded in NeuroML and other formats, ready for analysis.

}, keywords = {Animals, Models, Neurological, Nerve Net, Neuroimaging, Neurons, Software, Synapses, Synaptic Transmission}, issn = {1932-6203}, doi = {10.1371/journal.pone.0038011}, author = {Cardona, Albert and Saalfeld, Stephan and Schindelin, Johannes and Arganda-Carreras, Ignacio and Preibisch, Stephan and Longair, Mark and Tomancak, Pavel and Hartenstein, Volker and Douglas, Rodney J} } @article {5339, title = {Transcriptional control of cell fate specification: lessons from the fly retina.}, journal = {Current Topics in Developmental Biology}, volume = {98}, year = {2012}, month = {2012}, pages = {259-76}, abstract = {

It is now widely recognized that as cells of developing tissues transition through successive states of decreasing pluripotency into a state of terminal differentiation, they undergo significant changes in their gene expression profiles. Interestingly, these successive states of increasing differentiation are marked by the spatially and temporally restricted expression of sets of transcription factors. Each wave of transcription factors not only signals the arrival of a given stage in cellular differentiation, but it is also necessary for the activation of the next set of transcription factors, creating the appearance of a smooth, directed, and deterministic genetic program of cellular differentiation. Until recently, however, it was largely unknown which genes, besides each other, these transcription factors were activating. Thus, the molecular definition of any given step of differentiation, and how it gave rise to the following step remained unclear. Recent advances in transcriptomics, bioinformatics, and molecular genetics resulted in the identification of numerous transcription factor target genes (TGs). These advances have opened the door to using similar approaches in developmental biology to understand what the transcriptional cascades of cellular differentiation might be. Using the development of the Drosophila eye as a model system, we discuss the role of transcription factors and their TGs in cell fate specification and terminal differentiation.

}, keywords = {Animals, Cell Lineage, Developmental, Drosophila melanogaster, Gene Expression Regulation, Genetic, Humans, Retina, Signal Transduction, Transcription}, issn = {1557-8933}, doi = {10.1016/B978-0-12-386499-4.00010-0}, author = {Quan, Xiao-jiang and Ramaekers, Ariane and Hassan, Bassem A} } @article {68820, title = {Transcriptional signature of accessory cells in the lateral line, using the Tnk1bp1:EGFP transgenic zebrafish line}, journal = {BMC developmental biology}, volume = {12}, year = {2012}, month = {01/2012}, pages = {6}, abstract = {

Background:\ Because of the structural and molecular similarities between the two systems, the lateral line, a fish and amphibian specific sensory organ, has been widely used in zebrafish as a model to study the development/biology of neuroepithelia of the inner ear. Both organs have hair cells, which are the mechanoreceptor cells, and supporting cells providing other functions to the epithelium. In most vertebrates (excluding mammals), supporting cells comprise a pool of progenitors that replace damaged or dead hair cells. However, the lack of regenerative capacity in mammals is the single leading cause for acquired hearing disorders in humans.

Results:\ In an effort to understand the regenerative process of hair cells in fish, we characterized and cloned an egfp transgenic stable fish line that trapped tnks1bp1, a highly conserved gene that has been implicated in the maintenance of telomeres{\textquoteright} length. We then used this Tg(tnks1bp1:EGFP) line in a FACsorting strategy combined with microarrays to identify new molecular markers for supporting cells.

Conclusions:\ We present a Tg(tnks1bp1:EGFP) stable transgenic line, which we used to establish a transcriptional profile of supporting cells in the zebrafish lateral line. Therefore we are providing a new set of markers specific for supporting cells as well as candidates for functional analysis of this important cell type. This will prove to be a valuable tool for the study of regeneration in the lateral line of zebrafish in particular and for regeneration of neuroepithelia in general.

}, doi = {10.1186/1471-213X-12-6}, author = {Behra, Martine and Gallardo, Viviana and Bradsher, John and Torrado, Aranza and Elkahloun, Abdel and Idol, Jennifer and Sheehy, Jessica and Zonies, Seth and Xu, Lisha and Shaw, Kenna and Satou, Chie and Higashijima, Shin-Ichi and Weinstein, Brant and Burgess, Shawn} } @article {46731, title = {Transgenic expression of ZBP1 in neurons suppresses cocaine-associated conditioning.}, journal = {Learning \& Memory}, volume = {19}, year = {2012}, month = {2012 Feb}, pages = {35-42}, abstract = {

To directly address whether regulating mRNA localization can influence animal behavior, we created transgenic mice that conditionally express Zipcode Binding Protein 1 (ZBP1) in a subset of neurons in the brain. ZBP1 is an RNA-binding protein that regulates the localization, as well as translation and stability of target mRNAs in the cytoplasm. We took advantage of the absence of ZBP1 expression in the mature brain to examine the effect of expressing ZBP1 on animal behavior. We constructed a transgene conditionally expressing a GFP-ZBP1 fusion protein in a subset of forebrain neurons and compared cocaine-cued place conditioning in these mice versus noninduced littermates. Transgenic ZBP1 expression resulted in impaired place conditioning relative to nonexpressing littermates, and acutely repressing expression of the transgene restored normal cocaine conditioning. To gain insight into the molecular changes that accounted for this change in behavior, we identified mRNAs that specifically immunoprecipitated with transgenic ZBP1 protein from the brains of these mice. These data suggest that RNA-binding proteins can be used as a tool to identify the post-transcriptional regulation of gene expression in the establishment and function of neural circuits involved in addiction behaviors.

}, keywords = {Animals, Brain, Cocaine, Conditioning (Psychology), Cues, DNA-Binding Proteins, Dopamine Uptake Inhibitors, Doxycycline, Gene Expression Regulation, Green Fluorescent Proteins, Immunoprecipitation, Male, Mice, Mice, Transgenic, Microarray Analysis, Neurons, RNA, Messenger, RNA-Binding Proteins}, issn = {1549-5485}, doi = {10.1101/lm.024471.111}, author = {Lapidus, Kyle A B and Nwokafor, Chiso and Scott, Daniel and Baroni, Timothy E and Tenenbaum, Scott A and Hiroi, Noboru and Singer, Robert H and Czaplinski, Kevin} } @article {4598, title = {Triggering a cell shape change by exploiting preexisting actomyosin contractions.}, journal = {Science}, volume = {335}, year = {2012}, month = {2012 Mar 9}, pages = {1232-5}, abstract = {

Apical constriction changes cell shapes, driving critical morphogenetic events, including gastrulation in diverse organisms and neural tube closure in vertebrates. Apical constriction is thought to be triggered by contraction of apical actomyosin networks. We found that apical actomyosin contractions began before cell shape changes in both Caenorhabitis elegans and Drosophila. In C. elegans, actomyosin networks were initially dynamic, contracting and generating cortical tension without substantial shrinking of apical surfaces. Apical cell-cell contact zones and actomyosin only later moved increasingly in concert, with no detectable change in actomyosin dynamics or cortical tension. Thus, apical constriction appears to be triggered not by a change in cortical tension, but by dynamic linking of apical cell-cell contact zones to an already contractile apical cortex.

}, issn = {1095-9203}, doi = {10.1126/science.1217869}, author = {Roh-Johnson, Minna and Shemer, Gidi and Higgins, Christopher D and McClellan, Joseph H and Werts, Adam D and Tulu, U Serdar and Gao, Liang and Betzig, Eric and Kiehart, Daniel P and Goldstein, Bob} } @article {46614, title = {Abnormal behavior in mice mutant for the Disc1 binding partner, Dixdc1.}, journal = {Translational Psychiatry}, volume = {1}, year = {2011}, month = {2011}, pages = {e43}, abstract = {

Disrupted-in-Schizophrenia-1 (DISC1) is a genetic susceptibility locus for major mental illness, including schizophrenia and depression. The Disc1 protein was recently shown to interact with the Wnt signaling protein, DIX domain containing 1 (Dixdc1). Both proteins participate in neural progenitor proliferation dependent on Wnt signaling, and in neural migration independently of Wnt signaling. Interestingly, their effect on neural progenitor proliferation is additive. By analogy to Disc1, mutations in Dixdc1 may lead to abnormal behavior in mice, and to schizophrenia or depression in humans. To explore this hypothesis further, we generated mice mutant at the Dixdc1 locus and analyzed their behavior. Dixdc1(-/-) mice had normal prepulse inhibition, but displayed decreased spontaneous locomotor activity, abnormal behavior in the elevated plus maze and deficits in startle reactivity. Our results suggest that Dixdc1(-/-) mice will be a useful tool to elucidate molecular pathophysiology involving Disc1 in major mental illnesses.

}, keywords = {Animals, Behavior, Animal, Epistasis, Genetic, Humans, Intracellular Signaling Peptides and Proteins, Male, Mice, Mice, 129 Strain, Mice, Mutant Strains, Mice, Transgenic, Microfilament Proteins, Nerve Tissue Proteins}, issn = {2158-3188}, doi = {10.1038/tp.2011.41}, author = {Kivim{\"a}e, S and Martin, P-M and Kapfhamer, D and Ruan, Y and Heberlein, U and Rubenstein, J L R and Cheyette, B N R} } @article {5483, title = {Alk is a transcriptional target of LMO4 and ERα that promotes cocaine sensitization and reward.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {31}, year = {2011}, month = {2011 Oct 5}, pages = {14134-41}, abstract = {

Previously, we showed that the mouse LIM-domain only 4 (Lmo4) gene, which encodes a protein containing two zinc-finger LIM domains that interact with various DNA-binding transcription factors, attenuates behavioral sensitivity to repeated cocaine administration. Here we show that transcription of anaplastic lymphoma kinase (Alk) is repressed by LMO4 in the striatum and that Alk promotes the development of cocaine sensitization and conditioned place preference, a measure of cocaine reward. Since LMO4 is known to interact with estrogen receptor α (ERα) at the promoters of target genes, we investigated whether Alk expression might be controlled by a similar mechanism. We found that LMO4 and ERα are associated with the Alk promoter by chromatin immunoprecipitation and that Alk is an estrogen-responsive gene in the striatum. Moreover, we show that ERα knock-out mice exhibit enhanced cocaine sensitization and conditioned place preference and an increase in Alk expression in the nucleus accumbens. These data define a novel regulatory network involved in behavioral responses to cocaine. Interestingly, sex differences in several behavioral responses to cocaine in humans and rodents have been described, and estrogen is thought to mediate some of these differences. Our data suggest that estrogen regulation of Alk may be one mechanism responsible for sexually dimorphic responses to cocaine.

}, keywords = {Adaptor Proteins, Animals, Cells, Cocaine, Cultured, Estrogen Receptor alpha, Gene Targeting, Genetic, HEK293 Cells, Humans, Inbred C57BL, Knockout, LIM Domain Proteins, Male, Mice, Motor Activity, Newborn, Receptor Protein-Tyrosine Kinases, Reward, Signal Transducing, Transcription}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3415-11.2011}, author = {Lasek, Amy W and Gesch, Julie and Giorgetti, Francesco and Kharazia, Viktor and Heberlein, Ulrike} } @article {4523, title = {Arouser reveals a role for synapse number in the regulation of ethanol sensitivity.}, journal = {Neuron}, volume = {70}, year = {2011}, month = {2011 Jun 9}, pages = {979-90}, abstract = {

A reduced sensitivity to the sedating effects of alcohol is a characteristic associated with alcohol use disorders (AUDs). A genetic screen for ethanol sedation mutants in Drosophila identified arouser (aru), which functions in developing neurons to reduce ethanol sensitivity. Genetic evidence suggests that aru regulates ethanol sensitivity through its activation by Egfr/Erk signaling and its inhibition by PI3K/Akt signaling. The aru mutant also has an increased number of synaptic terminals in the larva and adult fly. Both the increased ethanol sensitivity and synapse number of the aru mutant are restored upon adult social isolation, suggesting a causal relationship between synapse number and ethanol sensitivity. We thus show that a developmental abnormality affecting synapse number and ethanol sensitivity is not permanent and can be reversed by manipulating the environment of the adult fly.

}, keywords = {Adaptor Proteins, Animal, Animals, Arabidopsis Proteins, Behavior, Brain, Central Nervous System Depressants, Developmental, Drosophila, Drosophila Proteins, Epidermal Growth Factor, Ethanol, Gene Expression Regulation, Genetically Modified, Green Fluorescent Proteins, Invertebrate Peptide, Larva, Mutation, Neuromuscular Junction, Neurons, Phosphatidylinositol 3-Kinases, Receptor, Receptors, Reflex, RNA Interference, Signal Transducing, Signal Transduction, Social Isolation, Synapses}, issn = {1097-4199}, doi = {10.1016/j.neuron.2011.03.030}, author = {Eddison, Mark and Guarnieri, Douglas J and Cheng, Ling and Liu, Che-Hsiung and Moffat, Kevin G and Davis, Graeme and Heberlein, Ulrike} } @article {46345, title = {Associative learning between odorants and mechanosensory punishment in larval Drosophila.}, journal = {Journal of Expiremental Biology}, volume = {214}, year = {2011}, month = {2011 Dec 1}, pages = {3897-905}, abstract = {

We tested whether Drosophila larvae can associate odours with a mechanosensory disturbance as a punishment, using substrate vibration conveyed by a loudspeaker (buzz:). One odour (A) was presented with the buzz, while another odour (B) was presented without the buzz (A/B training). Then, animals were offered the choice between A and B. After reciprocal training (A/B), a second experimental group was tested in the same way. We found that larvae show conditioned escape from the previously punished odour. We further report an increase of associative performance scores with the number of punishments, and an increase according to the number of training cycles. Within the range tested (between 50 and 200 Hz), however, the pitch of the buzz does not apparently impact associative success. Last, but not least, we characterized odour-buzz memories with regard to the conditions under which they are behaviourally expressed--or not. In accordance with what has previously been found for associative learning between odours and bad taste (such as high concentration salt or quinine), we report that conditioned escape after odour-buzz learning is disabled if escape is not warranted, i.e. if no punishment to escape from is present during testing. Together with the already established paradigms for the association of odour and bad taste, the present assay offers the prospect of analysing how a relatively simple brain orchestrates memory and behaviour with regard to different kinds of {\textquoteright}bad{\textquoteright} events.

}, keywords = {Animals, Association Learning, Behavior, Animal, Conditioning (Psychology), Drosophila melanogaster, Larva, Mechanotransduction, Cellular, Memory, Odors, Punishment, Sound}, issn = {1477-9145}, doi = {10.1242/jeb.060533}, author = {Eschbach, Claire and Cano, Carmen and Haberkern, Hannah and Schraut, Karla and Guan, Chonglin and Triphan, Tilman and Gerber, Bertram} } @article {6335, title = {Atomic model of an infectious rotavirus particle.}, journal = {The EMBO Journal}, volume = {30}, year = {2011}, month = {2011 Jan 19}, pages = {408-16}, abstract = {

Non-enveloped viruses of different types have evolved distinct mechanisms for penetrating a cellular membrane during infection. Rotavirus penetration appears to occur by a process resembling enveloped-virus fusion: membrane distortion linked to conformational changes in a viral protein. Evidence for such a mechanism comes from crystallographic analyses of fragments of VP4, the rotavirus-penetration protein, and infectivity analyses of structure-based VP4 mutants. We describe here the structure of an infectious rotavirus particle determined by electron cryomicroscopy (cryoEM) and single-particle analysis at about 4.3 {\r A} resolution. The cryoEM image reconstruction permits a nearly complete trace of the VP4 polypeptide chain, including the positions of most side chains. It shows how the two subfragments of VP4 (VP8(*) and VP5(*)) retain their association after proteolytic cleavage, reveals multiple structural roles for the β-barrel domain of VP5(*), and specifies interactions of VP4 with other capsid proteins. The virion model allows us to integrate structural and functional information into a coherent mechanism for rotavirus entry.

}, keywords = {Capsid Proteins, Cell Membrane, Cryoelectron Microscopy, Crystallography, Models, Molecular, Protein Structure, Rotavirus, Secondary, Virion, Virus Internalization}, issn = {1460-2075}, doi = {10.1038/emboj.2010.322}, author = {Settembre, Ethan C and Chen, James Z and Dormitzer, Philip R and Grigorieff, Nikolaus and Harrison, Stephen C} } @article {4928, title = {The binding of cholera toxin to the periplasmic vestibule of the type II secretion channel.}, journal = {Channels}, volume = {5}, year = {2011}, month = {2011 May-Jun}, pages = {215-8}, abstract = {

The type II secretion system (T2SS) is a large macromolecular complex spanning the inner and outer membranes of many gram-negative bacteria. The T2SS is responsible for the secretion of virulence factors such as cholera toxin (CT) and heat-labile enterotoxin (LT) from Vibrio cholerae and enterotoxigenic Escherichia coli, respectively. CT and LT are closely related AB5 heterohexamers, composed of one A subunit and a B-pentamer. Both CT and LT are translocated, as folded protein complexes, from the periplasm across the outer membrane through the type II secretion channel, the secretin GspD. We recently published the 19 {\r A} structure of the V. cholerae secretin (VcGspD) in its closed state and showed by SPR measurements that the periplasmic domain of GspD interacts with the B-pentamer complex. Here we extend these studies by characterizing the binding of the cholera toxin B-pentamer to VcGspD using electron microscopy of negatively stained preparations. Our studies indicate that the pentamer is captured within the large periplasmic vestibule of VcGspD. These new results agree well with our previously published studies and are in accord with a piston-driven type II secretion mechanism.

}, keywords = {Bacterial Proteins, Bacterial Secretion Systems, Cholera Toxin, Periplasm, Porins, Protein Folding, Protein Structure, Protein Subunits, Protein Transport, Quaternary, Tertiary, Vibrio cholerae}, issn = {1933-6969}, author = {Reichow, Steve L and Korotkov, Konstantin V and Gonen, Melissa and Sun, Ji and Delarosa, Jaclyn R and Hol, Wim G J and Gonen, Tamir} } @article {47221, title = {Cellular-resolution population imaging reveals robust sparse coding in the Drosophila mushroom body.}, journal = {The Journal of Neuroscience : the official journal of the Society for Neuroscience}, volume = {31}, year = {2011}, month = {2011 Aug 17}, pages = {11772-85}, abstract = {

Sensory stimuli are represented in the brain by the activity of populations of neurons. In most biological systems, studying population coding is challenging since only a tiny proportion of cells can be recorded simultaneously. Here we used two-photon imaging to record neural activity in the relatively simple Drosophila mushroom body (MB), an area involved in olfactory learning and memory. Using the highly sensitive calcium indicator GCaMP3, we simultaneously monitored the activity of \>100 MB neurons in vivo (\~{}5\% of the total population). The MB is thought to encode odors in sparse patterns of activity, but the code has yet to be explored either on a population level or with a wide variety of stimuli. We therefore imaged responses to odors chosen to evaluate the robustness of sparse representations. Different odors activated distinct patterns of MB neurons; however, we found no evidence for spatial organization of neurons by either response probability or odor tuning within the cell body layer. The degree of sparseness was consistent across a wide range of stimuli, from monomolecular odors to artificial blends and even complex natural smells. Sparseness was mainly invariant across concentrations, largely because of the influence of recent odor experience. Finally, in contrast to sensory processing in other systems, no response features distinguished natural stimuli from monomolecular odors. Our results indicate that the fundamental feature of odor processing in the MB is to create sparse stimulus representations in a format that facilitates arbitrary associations between odor and punishment or reward.

}, keywords = {Animals, Animals, Genetically Modified, Diagnostic Imaging, Drosophila, Microscopy, Fluorescence, Multiphoton, Mushroom Bodies, Odors, Olfactory Pathways, Olfactory Receptor Neurons, Random Allocation, Smell}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.1099-11.2011}, author = {Honegger, Kyle S and Campbell, Robert A A and Turner, Glenn C} } @article {68821, title = {Compartmentalized Notch signaling sustains epithelial mirror symmetry}, journal = {Development}, volume = {138}, year = {2011}, month = {03/2011}, pages = {1143-1152}, abstract = {

Bilateral symmetric tissues must interpret axial references to maintain their global architecture during growth or repair. The regeneration of hair cells in the zebrafish lateral line, for example, forms a vertical midline that bisects the neuromast epithelium into perfect mirror-symmetric plane-polarized halves. Each half contains hair cells of identical planar orientation but opposite to that of the confronting half. The establishment of bilateral symmetry in this organ is poorly understood. Here, we show that hair-cell regeneration is strongly directional along an axis perpendicular to that of epithelial planar polarity. We demonstrate compartmentalized Notch signaling in neuromasts, and show that directional regeneration depends on the development of hair-cell progenitors in polar compartments that have low Notch activity. High-resolution live cell tracking reveals a novel process of planar cell inversions whereby sibling hair cells invert positions immediately after progenitor cytokinesis, demonstrating that oriented progenitor divisions are dispensable for bilateral symmetry. Notwithstanding the invariably directional regeneration, the planar polarization of the epithelium eventually propagates symmetrically because mature hair cells move away from the midline towards the periphery of the neuromast. We conclude that a strongly anisotropic regeneration process that relies on the dynamic stabilization of progenitor identity in permissive polar compartments sustains bilateral symmetry in the lateral line.

}, issn = {0950-1991}, doi = {10.1242/dev.060566}, url = {https://doi.org/10.1242/dev.060566}, author = {Wibowo, Indra and Pinto-Teixeira, Filipe and Satou, Chie and Higashijima, Shin-Ichi and L{\'o}pez-Schier, Hern{\'a}n} } @article {46735, title = {A date with telomerase: pick you up at S phase.}, journal = {Molecular Cell}, volume = {44}, year = {2011}, month = {2011 Dec 9}, pages = {685-6}, abstract = {

Using the MS2 system for labeling mRNA, in this issue, Gallardo et al. (2011) find that telomere lengthening depends on a stable accumulation of multiple telomerase complexes in late S phase and that this process is temporally regulated by Rif1/2 proteins.

}, issn = {1097-4164}, doi = {10.1016/j.molcel.2011.11.013}, author = {Hocine, S and Singer, R H} } @article {6874, title = {Deletion of the betaine-GABA transporter (BGT1; slc6a12) gene does not affect seizure thresholds of adult mice.}, journal = {Epilepsy Research}, volume = {95}, year = {2011}, month = {2011 Jun}, pages = {70-81}, abstract = {

Gamma-aminobutyric acid (GABA) is the major inhibitory neurotransmitter in the mammalian brain. Once released, it is removed from the extracellular space by cellular uptake catalyzed by GABA transporter proteins. Four GABA transporters (GAT1, GAT2, GAT3 and BGT1) have been identified. Inhibition of the GAT1 by the clinically available anti-epileptic drug tiagabine has been an effective strategy for the treatment of some patients with partial seizures. Recently, the investigational drug EF1502, which inhibits both GAT1 and BGT1, was found to exert an anti-convulsant action synergistic to that of tiagabine, supposedly due to inhibition of BGT1. The present study addresses the role of BGT1 in seizure control and the effect of EF1502 by developing and exploring a new mouse line lacking exons 3-5 of the BGT1 (slc6a12) gene. The deletion of this sequence abolishes the expression of BGT1 mRNA. However, homozygous BGT1-deficient mice have normal development and show seizure susceptibility indistinguishable from that in wild-type mice in a variety of seizure threshold models including: corneal kindling, the minimal clonic and minimal tonic extension seizure threshold tests, the 6Hz seizure threshold test, and the i.v. pentylenetetrazol threshold test. We confirm that BGT1 mRNA is present in the brain, but find that the levels are several hundred times lower than those of GAT1 mRNA; possibly explaining the apparent lack of phenotype. In conclusion, the present results do not support a role for BGT1 in the control of seizure susceptibility and cannot provide a mechanistic understanding of the synergism that has been previously reported with tiagabine and EF1502.

}, keywords = {Animals, Anticonvulsants, Convulsants, Crosses, Dose-Response Relationship, Drug, Electroshock, Exons, Female, GABA Plasma Membrane Transport Proteins, Genetic, Inbred C57BL, Isoxazoles, Kindling, Knockout, Male, Messenger, Mice, Neurologic, Nipecotic Acids, Pentylenetetrazole, RNA, Seizures}, issn = {1872-6844}, doi = {10.1016/j.eplepsyres.2011.02.014}, author = {Lehre, A C and Rowley, N M and Zhou, Y. and Holmseth, S and Guo, C and Holen, T and Hua, R and Laake, P and Olofsson, A M and Poblete-Naredo, I and Rusakov, D A and Madsen, K K and Clausen, R P and Schousboe, A and White, H S and Danbolt, N C} } @article {46050, title = {Distinct functions of kainate receptors in the brain are determined by the auxiliary subunit Neto1.}, journal = {Nature Neuroscience}, volume = {14}, year = {2011}, month = {2011 Jul}, pages = {866-73}, abstract = {

Ionotropic glutamate receptors principally mediate fast excitatory transmission in the brain. Among the three classes of ionotropic glutamate receptors, kainate receptors (KARs) have a unique brain distribution, which has been historically defined by (3)H-radiolabeled kainate binding. Compared with recombinant KARs expressed in heterologous cells, synaptic KARs exhibit characteristically slow rise-time and decay kinetics. However, the mechanisms responsible for these distinct KAR properties remain unclear. We found that both the high-affinity binding pattern in the mouse brain and the channel properties of native KARs are determined by the KAR auxiliary subunit Neto1. Through modulation of agonist binding affinity and off-kinetics of KARs, but not trafficking of KARs, Neto1 determined both the KAR high-affinity binding pattern and the distinctively slow kinetics of postsynaptic KARs. By regulating KAR excitatory postsynaptic current kinetics, Neto1 can control synaptic temporal summation, spike generation and fidelity.

}, keywords = {Animals, Animals, Newborn, Biophysical Phenomena, Biophysics, CA1 Region, Hippocampal, Cell Line, Transformed, Cerebellum, Dizocilpine Maleate, Dose-Response Relationship, Drug, Drug Interactions, Electric Stimulation, Excitatory Amino Acid Agonists, Excitatory Amino Acid Antagonists, Excitatory Postsynaptic Potentials, Gene Expression Regulation, Green Fluorescent Proteins, Guanylate Kinase, Humans, Immunoprecipitation, In Vitro Techniques, Intracellular Signaling Peptides and Proteins, Kainic Acid, Lipoproteins, LDL, Membrane Potentials, Membrane Proteins, Mice, Mice, Knockout, Neurons, Patch-Clamp Techniques, Presynaptic Terminals, Protein Binding, Protein Subunits, Receptors, Kainic Acid, Synaptophysin, Transfection, Tritium}, issn = {1546-1726}, doi = {10.1038/nn.2837}, author = {Straub, Christoph and Hunt, David L and Yamasaki, Miwako and Kim, Kwang S and Watanabe, Masahiko and Castillo, Pablo E and Tomita, Susumu} } @article {1513, title = {Drosophila brainbow: a recombinase-based fluorescence labeling technique to subdivide neural expression patterns.}, journal = {Nature Methods}, volume = {8}, year = {2011}, month = {2011 Mar}, pages = {253-9}, abstract = {

We developed a multicolor neuron labeling technique in Drosophila melanogaster that combines the power to specifically target different neural populations with the label diversity provided by stochastic color choice. This adaptation of vertebrate Brainbow uses recombination to select one of three epitope-tagged proteins detectable by immunofluorescence. Two copies of this construct yield six bright, separable colors. We used Drosophila Brainbow to study the innervation patterns of multiple antennal lobe projection neuron lineages in the same preparation and to observe the relative trajectories of individual aminergic neurons. Nerve bundles, and even individual neurites hundreds of micrometers long, can be followed with definitive color labeling. We traced motor neurons in the subesophageal ganglion and correlated them to neuromuscular junctions to identify their specific proboscis muscle targets. The ability to independently visualize multiple lineage or neuron projections in the same preparation greatly advances the goal of mapping how neurons connect into circuits.

}, issn = {1548-7105}, doi = {10.1038/nmeth.1566}, author = {Hampel, Stefanie and Chung, Phuong and McKellar, Claire E and Hall, Donald and Looger, Loren L and Simpson, Julie H} } @article {5686, title = {The Drosophila larval visual system: high-resolution analysis of a simple visual neuropil.}, journal = {Developmental Biology}, volume = {358}, year = {2011}, month = {2011 Oct 1}, pages = {33-43}, abstract = {

The task of the visual system is to translate light into neuronal encoded information. This translation of photons into neuronal signals is achieved by photoreceptor neurons (PRs), specialized sensory neurons, located in the eye. Upon perception of light the PRs will send a signal to target neurons, which represent a first station of visual processing. Increasing complexity of visual processing stems from the number of distinct PR subtypes and their various types of target neurons that are contacted. The visual system of the fruit fly larva represents a simple visual system (larval optic neuropil, LON) that consists of 12 PRs falling into two classes: blue-senstive PRs expressing Rhodopsin 5 (Rh5) and green-sensitive PRs expressing Rhodopsin 6 (Rh6). These afferents contact a small number of target neurons, including optic lobe pioneers (OLPs) and lateral clock neurons (LNs). We combine the use of genetic markers to label both PR subtypes and the distinct, identifiable sets of target neurons with a serial EM reconstruction to generate a high-resolution map of the larval optic neuropil. We find that the larval optic neuropil shows a clear bipartite organization consisting of one domain innervated by PRs and one devoid of PR axons. The topology of PR projections, in particular the relationship between Rh5 and Rh6 afferents, is maintained from the nerve entering the brain to the axon terminals. The target neurons can be subdivided according to neurotransmitter or neuropeptide they use as well as the location within the brain. We further track the larval optic neuropil through development from first larval instar to its location in the adult brain as the accessory medulla.

}, keywords = {Animals, Confocal, Drosophila, Drosophila Proteins, Electron, Immunohistochemistry, Invertebrate, Larva, Microscopy, Neuropil, Ocular, Photoreceptor Cells, Rhodopsin, Synapses, Transmission, Vision}, issn = {1095-564X}, doi = {10.1016/j.ydbio.2011.07.006}, author = {Sprecher, Simon G and Cardona, Albert and Hartenstein, Volker.} } @article {4524, title = {A Drosophila model for alcohol reward.}, journal = {Nature Neuroscience}, volume = {14}, year = {2011}, month = {2011 May}, pages = {612-9}, abstract = {

The rewarding properties of drugs contribute to the development of abuse and addiction. We developed a new assay for investigating the motivational properties of ethanol in the genetically tractable model Drosophila melanogaster. Flies learned to associate cues with ethanol intoxication and, although transiently aversive, the experience led to a long-lasting attraction for the ethanol-paired cue, implying that intoxication is rewarding. Temporally blocking transmission in dopaminergic neurons revealed that flies require activation of these neurons to express, but not develop, conditioned preference for ethanol-associated cues. Moreover, flies acquired, consolidated and retrieved these rewarding memories using distinct sets of neurons in the mushroom body. Finally, mutations in scabrous, encoding a fibrinogen-related peptide that regulates Notch signaling, disrupted the formation of memories for ethanol reward. Our results thus establish that Drosophila can be useful for understanding the molecular, genetic and neural mechanisms underling the rewarding properties of ethanol.

}, keywords = {Alcohol-Related Disorders, Alcohols, Analysis of Variance, Animal, Animals, Behavior, Chromatography, Conditioning (Psychology), Disease Models, Dopamine, Drosophila, Drosophila Proteins, Electric Stimulation, Ethanol, Food Preferences, Genetically Modified, Green Fluorescent Proteins, High Pressure Liquid, Male, Maze Learning, Mushroom Bodies, Neurons, Odors, Reward, Synaptic Transmission, Time Factors, Tyrosine 3-Monooxygenase}, issn = {1546-1726}, doi = {10.1038/nn.2805}, author = {Kaun, Karla R and Azanchi, Reza and Maung, Zaw and Hirsh, Jay and Heberlein, Ulrike} } @article {5484, title = {A Drosophila model for fetal alcohol syndrome disorders: role for the insulin pathway.}, journal = {Disease Models \& Mechanisms}, volume = {4}, year = {2011}, month = {2011 May}, pages = {335-46}, abstract = {

Prenatal exposure to ethanol in humans results in a wide range of developmental abnormalities, including growth deficiency, developmental delay, reduced brain size, permanent neurobehavioral abnormalities and fetal death. Here we describe the use of Drosophila melanogaster as a model for exploring the effects of ethanol exposure on development and behavior. We show that developmental ethanol exposure causes reduced viability, developmental delay and reduced adult body size. We find that flies reared on ethanol-containing food have smaller brains and imaginal discs, which is due to reduced cell division rather than increased apoptosis. Additionally, we show that, as in mammals, flies reared on ethanol have altered responses to ethanol vapor exposure as adults, including increased locomotor activation, resistance to the sedating effects of the drug and reduced tolerance development upon repeated ethanol exposure. We have found that the developmental and behavioral defects are largely due to the effects of ethanol on insulin signaling; specifically, a reduction in Drosophila insulin-like peptide (Dilp) and insulin receptor expression. Transgenic expression of Dilp proteins in the larval brain suppressed both the developmental and behavioral abnormalities displayed by ethanol-reared adult flies. Our results thus establish Drosophila as a useful model system to uncover the complex etiology of fetal alcohol syndrome.

}, keywords = {Adaptation, Animal, Animals, Apoptosis, Behavior, Brain, Cell Proliferation, Disease Models, Drosophila melanogaster, Drosophila Proteins, Ethanol, Eye, Female, Fetal Alcohol Syndrome, Humans, Insulin, Larva, Physiological, Pregnancy, Receptor, Signal Transduction, Survival Analysis}, issn = {1754-8411}, doi = {10.1242/dmm.006411}, author = {McClure, Kimberly D and French, Rachael L and Heberlein, Ulrike} } @article {4525, title = {Drosophila tao controls mushroom body development and ethanol-stimulated behavior through par-1.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {31}, year = {2011}, month = {2011 Jan 19}, pages = {1139-48}, abstract = {

In both mammalian and insect models of ethanol-induced behavior, low doses of ethanol stimulate locomotion. However, the mechanisms of the stimulant effects of ethanol on the CNS are mostly unknown. We have identified tao, encoding a serine-threonine kinase of the Ste20 family, as a gene necessary for ethanol-induced locomotor hyperactivity in Drosophila. Mutations in tao also affect behavioral responses to cocaine and nicotine, making flies resistant to the effects of both drugs. We show that tao function is required during the development of the adult nervous system and that tao mutations cause defects in the development of central brain structures, including the mushroom body. Silencing of a subset of mushroom body neurons is sufficient to reduce ethanol-induced hyperactivity, revealing the mushroom body as an important locus mediating the stimulant effects of ethanol. We also show that mutations in par-1 suppress both the mushroom body morphology and behavioral phenotypes of tao mutations and that the phosphorylation state of the microtubule-binding protein Tau can be altered by RNA interference knockdown of tao, suggesting that tao and par-1 act in a pathway to control microtubule dynamics during neural development.

}, keywords = {Analysis of Variance, Animal, Animals, Behavior, Biological, Blotting, Drosophila, Drosophila Proteins, Ethanol, Hyperkinesis, Immunohistochemistry, Metamorphosis, Motor Activity, Mushroom Bodies, Neurons, Protein-Serine-Threonine Kinases, Western}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4416-10.2011}, author = {King, Ian and Tsai, Linus T-Y and Pflanz, Ralf and Voigt, Aaron and Lee, Seongsoo and J{\"a}ckle, Herbert and Lu, Bingwei and Heberlein, Ulrike} } @article {47672, title = {Dynamics of endosomal sorting complex required for transport (ESCRT) machinery during cytokinesis and its role in abscission.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, year = {2011}, month = {2011 Mar 22}, pages = {4846-51}, abstract = {

The final stage of cytokinesis is abscission, the cutting of the narrow membrane bridge connecting two daughter cells. The endosomal sorting complex required for transport (ESCRT) machinery is required for cytokinesis, and ESCRT-III has membrane scission activity in vitro, but the role of ESCRTs in abscission has been undefined. Here, we use structured illumination microscopy and time-lapse imaging to dissect the behavior of ESCRTs during abscission. Our data reveal that the ESCRT-I subunit tumor-susceptibility gene 101 (TSG101) and the ESCRT-III subunit charged multivesicular body protein 4b (CHMP4B) are sequentially recruited to the center of the intercellular bridge, forming a series of cortical rings. Late in cytokinesis, however, CHMP4B is acutely recruited to the narrow constriction site where abscission occurs. The ESCRT disassembly factor vacuolar protein sorting 4 (VPS4) follows CHMP4B to this site, and cell separation occurs immediately. That arrival of ESCRT-III and VPS4 correlates both spatially and temporally with the abscission event suggests a direct role for these proteins in cytokinetic membrane abscission.

}, keywords = {Animals, Cell Line, Cytokinesis, DNA-Binding Proteins, Dogs, Endosomal Sorting Complexes Required for Transport, Endosomes, Humans, Transcription Factors}, issn = {1091-6490}, doi = {10.1073/pnas.1102714108}, author = {Elia, Natalie and Sougrat, Rachid and Spurlin, Tighe A and Hurley, James H and Lippincott-Schwartz, Jennifer} } @article {5660, title = {Effective stimuli for constructing reliable neuron models.}, journal = {PLoS Computational Biology}, volume = {7}, year = {2011}, month = {2011 Aug}, pages = {e1002133}, abstract = {

The rich dynamical nature of neurons poses major conceptual and technical challenges for unraveling their nonlinear membrane properties. Traditionally, various current waveforms have been injected at the soma to probe neuron dynamics, but the rationale for selecting specific stimuli has never been rigorously justified. The present experimental and theoretical study proposes a novel framework, inspired by learning theory, for objectively selecting the stimuli that best unravel the neuron{\textquoteright}s dynamics. The efficacy of stimuli is assessed in terms of their ability to constrain the parameter space of biophysically detailed conductance-based models that faithfully replicate the neuron{\textquoteright}s dynamics as attested by their ability to generalize well to the neuron{\textquoteright}s response to novel experimental stimuli. We used this framework to evaluate a variety of stimuli in different types of cortical neurons, ages and animals. Despite their simplicity, a set of stimuli consisting of step and ramp current pulses outperforms synaptic-like noisy stimuli in revealing the dynamics of these neurons. The general framework that we propose paves a new way for defining, evaluating and standardizing effective electrical probing of neurons and will thus lay the foundation for a much deeper understanding of the electrical nature of these highly sophisticated and non-linear devices and of the neuronal networks that they compose.

}, keywords = {Action Potentials, Algorithms, Animals, Computational Biology, Electric Conductivity, Electrophysiology, Interneurons, Mice, Models, Neurological, Neurons, Patch-Clamp Techniques, Pyramidal Cells, Rats, Wistar}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1002133}, author = {Druckmann, Shaul and Berger, Thomas K and Sch{\"u}rmann, Felix and Hill, Sean and Markram, Henry and Segev, Idan} } @article {2906, title = {Electro-optical pockels scattering from a single nanocrystal.}, journal = {Optics Express}, volume = {19}, year = {2011}, month = {2011 May 9}, pages = {9000-7}, abstract = {

The electro-optical Pockels response from a single non-centrosymmetric nanocrystal is reported. High sensitivity to the weak electric-field dependent nonlinear scattering is achieved through a dedicated imaging interferometric microscope and the linear dependence of electro-optical signal upon the applied field is checked. Using different incident light polarization states, a priori random spatial orientation of the crystal can be inferred. The electro-optical response from a nanocrystal provides local subwavelength sensor of quasi-static electric fields with potential applications in physics and biology. It also leads to a new sub-wavelength microscopy towards the nanoscale investigation of interesting phenomena such as nanoferroelectricity.

}, issn = {1094-4087}, doi = {10.1364/OE.19.009000}, author = {Hajj, Bassam and Perruchas, Sandrine and Lautru, Joseph and Dantelle, G{\'e}raldine and Gacoin, Thierry and Zyss, Joseph and Chauvat, Dominique} } @article {46610, title = {An evolutionary conserved role for anaplastic lymphoma kinase in behavioral responses to ethanol.}, journal = {PLoS One}, volume = {6}, year = {2011}, month = {2011 Jul 22}, pages = {e22636}, abstract = {

Anaplastic lymphoma kinase (Alk) is a gene expressed in the nervous system that encodes a receptor tyrosine kinase commonly known for its oncogenic function in various human cancers. We have determined that Alk is associated with altered behavioral responses to ethanol in the fruit fly Drosophila melanogaster, in mice, and in humans. Mutant flies containing transposon insertions in dAlk demonstrate increased resistance to the sedating effect of ethanol. Database analyses revealed that Alk expression levels in the brains of recombinant inbred mice are negatively correlated with ethanol-induced ataxia and ethanol consumption. We therefore tested Alk gene knockout mice and found that they sedate longer in response to high doses of ethanol and consume more ethanol than wild-type mice. Finally, sequencing of human ALK led to the discovery of four polymorphisms associated with a low level of response to ethanol, an intermediate phenotype that is predictive of future alcohol use disorders (AUDs). These results suggest that Alk plays an evolutionary conserved role in ethanol-related behaviors. Moreover, ALK may be a novel candidate gene conferring risk for AUDs as well as a potential target for pharmacological intervention.

}, keywords = {Alcohol Drinking, Alcoholics, Animals, Behavior, Animal, Conscious Sedation, Drosophila melanogaster, Drosophila Proteins, Ethanol, Evolution, Molecular, Female, Gene Expression Regulation, Enzymologic, Homeodomain Proteins, Humans, Male, Mice, Polymorphism, Genetic, Receptor Protein-Tyrosine Kinases}, issn = {1932-6203}, doi = {10.1371/journal.pone.0022636}, author = {Lasek, Amy W and Lim, Jana and Kliethermes, Christopher L and Berger, Karen H and Joslyn, Geoff and Brush, Gerry and Xue, Liquan and Robertson, Margaret and Moore, Monica S and Vranizan, Karen and Morris, Stephan W and Schuckit, Marc A and White, Raymond L and Heberlein, Ulrike} } @article {46611, title = {The genetic relationships between ethanol preference, acute ethanol sensitivity, and ethanol tolerance in Drosophila melanogaster.}, journal = {Fly (Austin)}, volume = {5}, year = {2011}, month = {2011 Jul-Sep}, pages = {191-9}, abstract = {

The relationship between alcohol consumption, sensitivity, and tolerance is an important question that has been addressed in humans and rodent models. Studies have shown that alcohol consumption and risk of abuse may correlate with (1) increased sensitivity to the stimulant effects of alcohol, (2) decreased sensitivity to the depressant effects of alcohol, and (3) increased alcohol tolerance. However, many conflicting results have been observed. To complement these studies, we utilized a different organism and approach to analyze the relationship between ethanol consumption and other ethanol responses. Using a set of 20 Drosophila melanogaster mutants that were isolated for altered ethanol sensitivity, we measured ethanol-induced hyperactivity, ethanol sedation, sedation tolerance, and ethanol consumption preference. Ethanol preference showed a strong positive correlation with ethanol tolerance, consistent with some rodent and human studies, but not with ethanol hyperactivity or sedation. No pairwise correlations were observed between ethanol hyperactivity, sedation, and tolerance. The evolutionary conservation of the relationship between tolerance and ethanol consumption in flies, rodents, and humans indicates that there are fundamental biological mechanisms linking specific ethanol responses.

}, keywords = {Alcohol Drinking, Alcoholic Intoxication, Animals, Central Nervous System Depressants, Drosophila melanogaster, Drosophila Proteins, Ethanol, Food Preferences, Hyperkinesis, Male, Transcription Factors}, issn = {1933-6942}, author = {Devineni, Anita V and McClure, Kimberly D and Guarnieri, Douglas J and Corl, Ammon B and Wolf, Fred W and Eddison, Mark and Heberlein, Ulrike} } @article {46613, title = {Genome-wide association and genetic functional studies identify autism susceptibility candidate 2 gene (AUTS2) in the regulation of alcohol consumption.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, year = {2011}, month = {2011 Apr 26}, pages = {7119-24}, abstract = {

Alcohol consumption is a moderately heritable trait, but the genetic basis in humans is largely unknown, despite its clinical and societal importance. We report a genome-wide association study meta-analysis of \~{}2.5 million directly genotyped or imputed SNPs with alcohol consumption (gram per day per kilogram body weight) among 12 population-based samples of European ancestry, comprising 26,316 individuals, with replication genotyping in an additional 21,185 individuals. SNP rs6943555 in autism susceptibility candidate 2 gene (AUTS2) was associated with alcohol consumption at genome-wide significance (P = 4 {\texttimes} 10(-8) to P = 4 {\texttimes} 10(-9)). We found a genotype-specific expression of AUTS2 in 96 human prefrontal cortex samples (P = 0.026) and significant (P \< 0.017) differences in expression of AUTS2 in whole-brain extracts of mice selected for differences in voluntary alcohol consumption. Down-regulation of an AUTS2 homolog caused reduced alcohol sensitivity in Drosophila (P \< 0.001). Our finding of a regulator of alcohol consumption adds knowledge to our understanding of genetic mechanisms influencing alcohol drinking behavior.

}, keywords = {Alcohol Drinking, Animals, Drosophila melanogaster, European Continental Ancestry Group, Female, Gene Expression Regulation, Genome-Wide Association Study, Genotype, Humans, Male, Mice, Nuclear Proteins, Polymorphism, Single Nucleotide, Proteins, Quantitative Trait, Heritable}, issn = {1091-6490}, doi = {10.1073/pnas.1017288108}, author = {Schumann, Gunter and Coin, Lachlan J and Lourdusamy, Anbarasu and Charoen, Pimphen and Berger, Karen H and Stacey, David and Desrivi{\`e}res, Sylvane and Aliev, Fazil A and Khan, Anokhi A and Amin, Najaf and Aulchenko, Yurii S and Bakalkin, Georgy and Bakker, Stephan J and Balkau, Beverley and Beulens, Joline W and Bilbao, Ainhoa and de Boer, Rudolf A and Beury, Delphine and Bots, Michiel L and Breetvelt, Elemi J and Cauchi, St{\'e}phane and Cavalcanti-Proen{\c c}a, Christine and Chambers, John C and Clarke, Toni-Kim and Dahmen, Norbert and de Geus, Eco J and Dick, Danielle and Ducci, Francesca and Easton, Alanna and Edenberg, Howard J and Esko, T{\~o}nu and Esk, T{\~o}nu and Fern{\'a}ndez-Medarde, Alberto and Foroud, Tatiana and Freimer, Nelson B and Girault, Jean-Antoine and Grobbee, Diederick E and Guarrera, Simonetta and Gudbjartsson, Daniel F and Hartikainen, Anna-Liisa and Heath, Andrew C and Hesselbrock, Victor and Hofman, Albert and Hottenga, Jouke-Jan and Isohanni, Matti K and Kaprio, Jaakko and Khaw, Kay-Tee and Kuehnel, Brigitte and Laitinen, Jaana and Lobbens, St{\'e}phane and Luan, Jian{\textquoteright}an and Mangino, Massimo and Maroteaux, Matthieu and Matullo, Giuseppe and McCarthy, Mark I and Mueller, Christian and Navis, Gerjan and Numans, Mattijs E and N{\'u}{\~n}ez, Alejandro and Nyholt, Dale R and Onland-Moret, Charlotte N and Oostra, Ben A and O{\textquoteright}Reilly, Paul F and Palkovits, Miklos and Penninx, Brenda W and Polidoro, Silvia and Pouta, Anneli and Prokopenko, Inga and Ricceri, Fulvio and Santos, Eugenio and Smit, Johannes H and Soranzo, Nicole and Song, Kijoung and Sovio, Ulla and Stumvoll, Michael and Surakk, Ida and Thorgeirsson, Thorgeir E and Thorsteinsdottir, Unnur and Troakes, Claire and Tyrfingsson, Thorarinn and T{\"o}njes, Anke and Uiterwaal, Cuno S and Uitterlinden, Andre G and van der Harst, Pim and van der Schouw, Yvonne T and Staehlin, Oliver and Vogelzangs, Nicole and Vollenweider, Peter and Waeber, Gerard and Wareham, Nicholas J and Waterworth, Dawn M and Whitfield, John B and Wichmann, Erich H and Willemsen, Gonneke and Witteman, Jacqueline C and Yuan, Xin and Zhai, Guangju and Zhao, Jing H and Zhang, Weihua and Martin, Nicholas G and Metspalu, Andres and Doering, Angela and Scott, James and Spector, Tim D and Loos, Ruth J and Boomsma, Dorret I and Mooser, Vincent and Peltonen, Leena and Stefansson, Kari and van Duijn, Cornelia M and Vineis, Paolo and Sommer, Wolfgang H and Kooner, Jaspal S and Spanagel, Rainer and Heberlein, Ulrike A and Jarvelin, Marjo-Riitta and Elliott, Paul} } @article {4300, title = {Glia instruct developmental neuronal remodeling through TGF-β signaling.}, journal = {Nature Neuroscience}, volume = {14}, year = {2011}, month = {2011 Jun 19}, pages = {821-3}, abstract = {

We found that glia secrete myoglianin, a TGF-β ligand, to instruct developmental neural remodeling in Drosophila. Glial myoglianin upregulated neuronal expression of an ecdysone nuclear receptor that triggered neurite remodeling following the late-larval ecdysone peak. Thus glia orchestrate developmental neural remodeling not only by engulfment of unwanted neurites but also by enabling neuron remodeling.

}, keywords = {Animals, Developmental, Double-Stranded, Drosophila, Drosophila Proteins, Gene Expression Regulation, Genetically Modified, Green Fluorescent Proteins, MicroRNAs, Models, Mushroom Bodies, Mutation, Neurogenesis, Neuroglia, Neurological, RNA, Signal Transduction, Transforming Growth Factor beta}, issn = {1546-1726}, doi = {10.1038/nn.2833}, author = {Awasaki, Takeshi and Huang, Yaling and O{\textquoteright}Connor, Michael B and Lee, Tzumin} } @article {47905, title = {Hallmarks of molecular action of microtubule stabilizing agents: effects of epothilone B, ixabepilone, peloruside A, and laulimalide on microtubule conformation.}, journal = {The Journal of biological chemistry}, volume = {286}, year = {2011}, month = {2011 Apr 1}, pages = {11765-78}, abstract = {

Microtubule stabilizing agents (MSAs) comprise a class of drugs that bind to microtubule (MT) polymers and stabilize them against disassembly. Several of these agents are currently in clinical use as anticancer drugs, whereas others are in various stages of development. Nonetheless, there is insufficient knowledge about the molecular modes of their action. Recent studies from our laboratory utilizing hydrogen-deuterium exchange in combination with mass spectrometry (MS) provide new information on the conformational effects of Taxol and discodermolide on microtubules isolated from chicken erythrocytes (CET). We report here a comprehensive analysis of the effects of epothilone B, ixabepilone (IXEMPRA(TM)), laulimalide, and peloruside A on CET conformation. The results of our comparative hydrogen-deuterium exchange MS studies indicate that all MSAs have significant conformational effects on the C-terminal H12 helix of α-tubulin, which is a likely molecular mechanism for the previously observed modulations of MT interactions with microtubule-associated and motor proteins. More importantly, the major mode of MT stabilization by MSAs is the tightening of the longitudinal interactions between two adjacent αβ-tubulin heterodimers at the interdimer interface. In contrast to previous observations reported with bovine brain tubulin, the lateral interactions between the adjacent protofilaments in CET are particularly strongly stabilized by peloruside A and laulimalide, drugs that bind outside the taxane site. This not only highlights the significance of tubulin isotype composition in modulating drug effects on MT conformation and stability but also provides a potential explanation for the synergy observed when combinations of taxane and alternative site binding drugs are used.

}, keywords = {Animals, Bicyclo Compounds, Heterocyclic, Binding Sites, Brain, Brain Chemistry, Cattle, Epothilones, Lactones, Macrolides, Mass Spectrometry, Microtubules, Nerve Tissue Proteins, Protein Structure, Secondary, Tubulin, Tubulin Modulators}, issn = {1083-351X}, doi = {10.1074/jbc.M110.162214}, author = {Khrapunovich-Baine, Marina and Menon, Vilas and Yang, Chia-Ping Huang and Northcote, Peter T and Miller, John H and Angeletti, Ruth Hogue and Fiser, Andras and Horwitz, Susan Band and Xiao, Hui} } @article {4325, title = {High resolution segmentation of neuronal tissues from low depth-resolution EM imagery.}, journal = {8th International Conference of Energy Minimization Methods in Computer Vision and Pattern Recognition Energy Minimization Methods in Computer Vision and Pattern Recognition}, volume = {6819}, year = {2011}, month = {2011}, pages = {261-72}, abstract = {

The challenge of recovering the topology of massive neuronal circuits can potentially be met by high throughput Electron Microscopy (EM) imagery. Segmenting a 3-dimensional stack of EM images into the individual neurons is difficult, due to the low depth-resolution in existing high-throughput EM technology, such as serial section Transmission EM (ssTEM). In this paper we propose methods for detecting the high resolution locations of membranes from low depth-resolution images. We approach this problem using both a method that learns a discriminative, over-complete dictionary and a kernel SVM. We test this approach on tomographic sections produced in simulations from high resolution Focused Ion Beam (FIB) images and on low depth-resolution images acquired with ssTEM and evaluate our results by comparing it to manual labeling of this data.

}, issn = {978-3-642-23093-6}, author = {Glasner, Daniel and Hu, Tao and Nunez-Iglesias, Juan and Scheffer, Lou and Xu, CS and Hess, Harald and Fetter, Richard and Chklovskii, Dmitri and Basri, Ronen} } @article {46608, title = {Insulin attenuates the acquisition and expression of ethanol-induced locomotor sensitization in DBA/2J mice.}, journal = {Life Sciences}, volume = {89}, year = {2011}, month = {2011 Dec 19}, pages = {968-74}, abstract = {

AIM: Ethanol-induced locomotor sensitization is a behavioral manifestation of physiological responses to repeated ethanol exposures. While ethanol exerts direct effects on multiple neurotransmitter systems in the brain, ethanol-induced changes in metabolic state, including acute hyperglycemia and inhibition of insulin signaling, also have plausible roles in the expression of ethanol-related behaviors through direct and indirect effects on brain function. The current experiments examined whether insulin administration or the resultant hypoglycemia might attenuate the development of sensitization to the locomotor stimulant effect of ethanol.

MAIN METHODS: Male and female DBA/2J mice received daily injections of 5 or 10 IU/kg insulin before or after a stimulating dose of ethanol and subsequent testing in an automated activity monitor. Blood glucose levels were determined upon the completion of the experiments.

KEY FINDINGS: Insulin injected prior to ethanol blunted the acute stimulant response as well as the acquisition and expression of locomotor sensitization, while insulin given after ethanol did not affect the development of the sensitized response. In a separate experiment, mice given glucose concurrently with insulin developed ethanol-induced locomotor sensitization normally.

SIGNIFICANCE: These experiments suggest that insulin attenuates the development of ethanol-induced locomotor sensitization, and that blood glucose levels can largely account for this effect. Further studies of the role of ethanol-induced metabolic states should provide novel information on the expression of ethanol-related behaviors.

}, keywords = {Animals, Behavior, Animal, Blood Glucose, Central Nervous System Depressants, Dose-Response Relationship, Drug, Ethanol, Female, Glucose, Hypoglycemia, Hypoglycemic Agents, Insulin, Male, Mice, Mice, Inbred DBA, Motor Activity}, issn = {1879-0631}, doi = {10.1016/j.lfs.2011.10.011}, author = {Kliethermes, Christopher L and Heberlein, Ulrike} } @article {4303, title = {Laminar analysis of excitatory local circuits in vibrissal motor and sensory cortical areas.}, journal = {PLoS Biology}, volume = {9}, year = {2011}, month = {2011 Jan 4}, pages = {e1000572}, abstract = {

Rodents move their whiskers to locate and identify objects. Cortical areas involved in vibrissal somatosensation and sensorimotor integration include the vibrissal area of the primary motor cortex (vM1), primary somatosensory cortex (vS1; barrel cortex), and secondary somatosensory cortex (S2). We mapped local excitatory pathways in each area across all cortical layers using glutamate uncaging and laser scanning photostimulation. We analyzed these maps to derive laminar connectivity matrices describing the average strengths of pathways between individual neurons in different layers and between entire cortical layers. In vM1, the strongest projection was L2/3{\textrightarrow}L5. In vS1, strong projections were L2/3{\textrightarrow}L5 and L4{\textrightarrow}L3. L6 input and output were weak in both areas. In S2, L2/3{\textrightarrow}L5 exceeded the strength of the ascending L4{\textrightarrow}L3 projection, and local input to L6 was prominent. The most conserved pathways were L2/3{\textrightarrow}L5, and the most variable were L4{\textrightarrow}L2/3 and pathways involving L6. Local excitatory circuits in different cortical areas are organized around a prominent descending pathway from L2/3{\textrightarrow}L5, suggesting that sensory cortices are elaborations on a basic motor cortex-like plan.

}, keywords = {Animals, Brain Mapping, Mice, Motor Cortex, Nerve Net, Presynaptic Terminals, Somatosensory Cortex, Vibrissae}, issn = {1545-7885}, doi = {10.1371/journal.pbio.1000572}, author = {Hooks, B M and Hires, S Andrew and Zhang, Ying-Xin and Huber, Daniel and Petreanu, Leopoldo and Svoboda, Karel and Shepherd, Gordon M G} } @article {4326, title = {Large-scale automated histology in the pursuit of connectomes.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {31}, year = {2011}, month = {2011 Nov 9}, pages = {16125-38}, abstract = {

How does the brain compute? Answering this question necessitates neuronal connectomes, annotated graphs of all synaptic connections within defined brain areas. Further, understanding the energetics of the brain{\textquoteright}s computations requires vascular graphs. The assembly of a connectome requires sensitive hardware tools to measure neuronal and neurovascular features in all three dimensions, as well as software and machine learning for data analysis and visualization. We present the state of the art on the reconstruction of circuits and vasculature that link brain anatomy and function. Analysis at the scale of tens of nanometers yields connections between identified neurons, while analysis at the micrometer scale yields probabilistic rules of connection between neurons and exact vascular connectivity.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4077-11.2011}, author = {Kleinfeld, David and Bharioke, Arjun and Blinder, Pablo and Bock, Davi D and Briggman, Kevin L and Chklovskii, Dmitri B and Denk, Winfried and Helmstaedter, Moritz and Kaufhold, John P and Lee, Wei-Chung Allen and Meyer, Hanno S and Micheva, Kristina D and Oberlaender, Marcel and Prohaska, Steffen and Reid, R Clay and Smith, Stephen J and Takemura, Shinya and Tsai, Philbert S and Sakmann, Bert} } @article {47706, title = {Learning, memory, and the role of neural network architecture.}, journal = {PLoS computational biology}, volume = {7}, year = {2011}, month = {2011 Jun}, pages = {e1002063}, abstract = {

The performance of information processing systems, from artificial neural networks to natural neuronal ensembles, depends heavily on the underlying system architecture. In this study, we compare the performance of parallel and layered network architectures during sequential tasks that require both acquisition and retention of information, thereby identifying tradeoffs between learning and memory processes. During the task of supervised, sequential function approximation, networks produce and adapt representations of external information. Performance is evaluated by statistically analyzing the error in these representations while varying the initial network state, the structure of the external information, and the time given to learn the information. We link performance to complexity in network architecture by characterizing local error landscape curvature. We find that variations in error landscape structure give rise to tradeoffs in performance; these include the ability of the network to maximize accuracy versus minimize inaccuracy and produce specific versus generalizable representations of information. Parallel networks generate smooth error landscapes with deep, narrow minima, enabling them to find highly specific representations given sufficient time. While accurate, however, these representations are difficult to generalize. In contrast, layered networks generate rough error landscapes with a variety of local minima, allowing them to quickly find coarse representations. Although less accurate, these representations are easily adaptable. The presence of measurable performance tradeoffs in both layered and parallel networks has implications for understanding the behavior of a wide variety of natural and artificial learning systems.

}, keywords = {Computational Biology, Humans, Learning, Memory, Models, Neurological, Nerve Net, Neural Networks (Computer)}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1002063}, author = {Hermundstad, Ann M and Brown, Kevin S and Bassett, Danielle S and Carlson, Jean M} } @proceedings {46351, title = {Learning to Agglomerate Superpixel Hierarchies}, volume = {24}, year = {2011}, month = {12/2011}, publisher = {MIT Press}, address = {Granada, Spain}, abstract = {

An agglomerative clustering algorithm merges the most similar pair of clusters at every iteration. The function that evaluates similarity is traditionally hand- designed, but there has been recent interest in supervised or semisupervised settings in which ground-truth clustered data is available for training. Here we show how to train a similarity function by regarding it as the action-value function of a reinforcement learning problem. We apply this general method to segment images by clustering superpixels, an application that we call Learning to Agglomerate Superpixel Hierarchies (LASH). When applied to a challenging dataset of brain images from serial electron microscopy, LASH dramatically improved segmentation accuracy when clustering supervoxels generated by state of the boundary detection algorithms. The naive strategy of directly training only supervoxel similarities and applying single linkage clustering produced less improvement.

}, author = {Viren Jain and Srinivas C. Turaga and K Briggman and Moritz N. Helmstaedter and Winfried Denk and H. S. Seung} } @article {3846, title = {Learning to agglomerate superpixel hierarchies.}, journal = {Neural Information Processing Systems}, volume = {24}, year = {2011}, month = {2011}, pages = {648-56}, abstract = {

An agglomerative clustering algorithm merges the most similar pair of clusters at every iteration. The function that evaluates similarity is traditionally handdesigned, but there has been recent interest in supervised or semisupervised settings in which ground-truth clustered data is available for training. Here we show how to train a similarity function by regarding it as the action-value function of a reinforcement learning problem. We apply this general method to segment images by clustering superpixels, an application that we call Learning to Agglomerate Superpixel Hierarchies (LASH). When applied to a challenging dataset of brain images from serial electron microscopy, LASH dramatically improved segmentation accuracy when clustering supervoxels generated by state of the boundary detection algorithms. The naive strategy of directly training only supervoxel similarities and applying single linkage clustering produced less improvement.

}, author = {Jain, Viren and Turaga, Srinivas and Briggman, Kevin and Helmstaedter, Moritz N. and Denk, Winfried and Seung, Sebastian} } @article {2720, title = {Limiting amounts of centrosome material set centrosome size in C.elegans embryos.}, journal = {Current Biology}, volume = {21}, year = {2011}, month = {2011 Aug 9}, pages = {1259-67}, abstract = {

The ways in which cells set the size of intracellular structures is an important but largely unsolved problem [1]. Early embryonic divisions pose special problems in this regard. Many checkpoints common in somatic cells are missing from these divisions, which are characterized by rapid reductions in cell size and short cell cycles [2]. Embryonic cells must therefore possess simple and robust mechanisms that allow the size of many of their intracellular structures to rapidly scale with cell size.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2011.06.002}, author = {Decker, Markus and Jaensch, Steffen and Pozniakovsky, A and Zinke, A and O{\textquoteright}Connell, K F and Zachariae, W and Myers, Eugene and Hyman, Anthony A} } @article {65011, title = {Lineage-based analysis of the development of the central complex of the Drosophila brain.}, journal = {J Comp Neurol}, volume = {519}, year = {2011}, month = {2011 Mar 01}, pages = {661-89}, abstract = {

Most neurons of the central complex belong to 10 secondary (larvally produced) lineages. In the late larva, undifferentiated axon tracts of these lineages form a primordium in which all of the compartments of the central complex can be recognized as discrete entities. Four posterior lineages (DPMm1, DPMpm1, DPMpm2, and CM4) generate the classes of small-field neurons that interconnect the protocerebral bridge, fan-shaped body, noduli, and ellipsoid body. Three lineages located in the anterior brain, DALv2, BAmv1, and DALcl2, form the large-field neurons of the ellipsoid body and fan-shaped body, respectively. These lineages provide an input channel from the optic tubercle and connect the central complex with adjacent anterior brain compartments. Three lineages in the posterior cortex, CM3, CP2, and DPMpl2, connect the posterior brain neuropil with specific layers of the fan-shaped body. Even though all of the compartments of the central complex are prefigured in the late larval brain by the axon tracts of the above-mentioned lineages, the neuropil differentiates during the first 2 days of the pupal period when terminal branches and synapses of secondary neurons are formed. During this phase the initially straight horizontal layers of the central complex bend in the frontal plane, which produces the characteristic shape of the fan-shaped and ellipsoid body. Our analysis provides a comprehensive picture of the lineages that form the central complex, and will facilitate future studies that address the structure or function of the central complex at the single cell level.

}, keywords = {Animals, Brain, Cell Lineage, Drosophila melanogaster, Drosophila Proteins, Metamorphosis, Biological, Morphogenesis, Neurons}, issn = {1096-9861}, doi = {10.1002/cne.22542}, author = {Pereanu, Wayne and Younossi-Hartenstein, Amelia and Lovick, Jennifer and Spindler, Shana and Hartenstein, Volker} } @article {46612, title = {Lmo genes regulate behavioral responses to ethanol in Drosophila melanogaster and the mouse.}, journal = {Alcoholism, Clinical and Experimental Research}, volume = {35}, year = {2011}, month = {2011 Sep}, pages = {1600-6}, abstract = {

BACKGROUND: Previous work from our laboratory demonstrated a role for the Drosophila Lim-only (dLmo) gene in regulating behavioral responses to cocaine. Herein, we examined whether dLmo influences the flies{\textquoteright} sensitivity to ethanol{\textquoteright}s sedating effects. We also investigated whether 1 of the mammalian homologs of dLmo, Lmo3, is involved in behavioral responses to ethanol in mice.

METHODS: To examine dLmo function in ethanol-induced sedation, mutant flies with reduced or increased dLmo expression were tested using the loss of righting (LOR) assay. To determine whether mouse Lmo3 regulates behavioral responses to ethanol, we generated transgenic mice expressing a short-hairpin RNA targeting Lmo3 for RNA interference-mediated knockdown by lentiviral infection of single cell embryos. Adult founder mice, expressing varying amounts of Lmo3 in the brain, were tested using ethanol loss-of-righting-reflex (LORR) and 2-bottle choice ethanol consumption assays.

RESULTS: We found that in flies, reduced dLmo activity increased sensitivity to ethanol-induced sedation, whereas increased expression of dLmo led to increased resistance to ethanol-induced sedation. In mice, reduced levels of Lmo3 were correlated with increased sedation time in the LORR test and decreased ethanol consumption in the 2-bottle choice protocol.

CONCLUSIONS: These data describe a novel and conserved role for Lmo genes in flies and mice in behavioral responses to ethanol. These studies also demonstrate the feasibility of rapidly translating findings from invertebrate systems to mammalian models of alcohol abuse by combining RNA interference in transgenic mice and behavioral testing.

}, keywords = {Adaptor Proteins, Signal Transducing, Animals, Behavior, Animal, Brain, Central Nervous System Depressants, Disease Models, Animal, Drosophila melanogaster, Drosophila Proteins, Ethanol, Female, Genotype, Green Fluorescent Proteins, Homeodomain Proteins, Hypnotics and Sedatives, LIM Domain Proteins, Male, Mice, Mice, Inbred C57BL, Mice, Transgenic, RNA, Small Interfering}, issn = {1530-0277}, doi = {10.1111/j.1530-0277.2011.01506.x}, author = {Lasek, Amy W and Giorgetti, Francesco and Berger, Karen H and Tayor, Stacy and Heberlein, Ulrike} } @article {5283, title = {Long-range neuronal circuits underlying the interaction between sensory and motor cortex.}, journal = {Neuron}, volume = {72}, year = {2011}, month = {2011 Oct 6}, pages = {111-23}, abstract = {

In the rodent vibrissal system, active sensation and sensorimotor integration are mediated in part by connections between barrel cortex and vibrissal motor cortex. Little is known about how these structures interact at the level of neurons. We used Channelrhodopsin-2 (ChR2) expression, combined with anterograde and retrograde labeling, to map connections between barrel cortex and pyramidal neurons in mouse motor cortex. Barrel cortex axons preferentially targeted upper layer (L2/3, L5A) neurons in motor cortex; input to neurons projecting back to barrel cortex was particularly strong. Barrel cortex input to deeper layers (L5B, L6) of motor cortex, including neurons projecting to the brainstem, was weak, despite pronounced geometric overlap of dendrites with axons from barrel cortex. Neurons in different layers received barrel cortex input within stereotyped dendritic domains. The cortico-cortical neurons in superficial layers of motor cortex thus couple motor and sensory signals and might mediate sensorimotor integration and motor learning.

}, keywords = {Animals, Inbred C57BL, Membrane Potentials, Mice, Molecular Imaging, Motor Cortex, Neural Pathways, Neuroanatomical Tract-Tracing Techniques, Neurons, Somatosensory Cortex, Vibrissae}, issn = {1097-4199}, doi = {10.1016/j.neuron.2011.07.029}, author = {Mao, Tianyi and Kusefoglu, Deniz and Hooks, Bryan M and Huber, Daniel and Petreanu, Leopoldo and Svoboda, Karel} } @article {6445, title = {Mapping a sensory-motor network onto a structural and functional ground plan in the hindbrain.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, year = {2011}, month = {2011 Jan 18}, pages = {1170-5}, abstract = {

The hindbrain of larval zebrafish contains a relatively simple ground plan in which the neurons throughout it are arranged into stripes that represent broad neuronal classes that differ in transmitter identity, morphology, and transcription factor expression. Within the stripes, neurons are stacked continuously according to age as well as structural and functional properties, such as axonal extent, input resistance, and the speed at which they are recruited during movements. Here we address the question of how particular networks among the many different sensory-motor networks in hindbrain arise from such an orderly plan. We use a combination of transgenic lines and pairwise patch recording to identify excitatory and inhibitory interneurons in the hindbrain network for escape behaviors initiated by the Mauthner cell. We map this network onto the ground plan to show that an individual hindbrain network is built by drawing components in predictable ways from the underlying broad patterning of cell types stacked within stripes according to their age and structural and functional properties. Many different specialized hindbrain networks may arise similarly from a simple early patterning.

}, keywords = {Animals, Body Patterning, Brain Mapping, Computer-Assisted, Electrophysiology, Escape Reaction, Genetically Modified, Image Processing, Immunohistochemistry, Interneurons, Larva, Nerve Net, Patch-Clamp Techniques, Psychomotor Performance, Rhombencephalon, Zebrafish}, issn = {1091-6490}, doi = {10.1073/pnas.1012189108}, author = {Koyama, Minoru and Kinkhabwala, Amina and Satou, Chie and Higashijima, Shin-Ichi and Fetcho, Joseph} } @article {6393, title = {Met and gce are functionally redundant in transducing the {\textquotedblleft}status quo{\textquotedblright} action of juvenile hormone in Drosophila.}, journal = {Insect Biochemistry and Molecular Biology}, volume = {41}, year = {2011}, month = {2011 Dec}, pages = {938-45}, abstract = {

The Drosophila Methoprene-tolerant (Met) and Germ cell-expressed (Gce) bHLH-PAS transcription factors are products of two paralogous genes. Both proteins potentially mediate the effect of juvenile hormone (JH) as candidate JH receptors. Here we report that Met and Gce are partially redundant in transducing JH action. Both Met and gce null single mutants are fully viable, but the Met gce double mutant, Met(27) gce(2.5k), dies during the larval-pupal transition. Precocious and enhanced caspase-dependent programmed cell death (PCD) appears in fat body cells of Met(27) gce(2.5k) during the early larval stages. Expression of Kr-h1, a JH response gene that inhibits 20-hydroxyecdysone (20E)-induced broad (br) expression, is abolished in Met(27) gce(2.5k) during larval molts. Consequently, expression of br occurs precociously in Met(27) gce(2.5k), which may cause precocious caspase-dependent PCD during the early larval stages. Defective phenotypes and gene expression changes in Met(27) gce(2.5k) double mutants are similar to those found in JH-deficient animals. Importantly, exogenous application of JH agonists rescued the JH-deficient animals but not the Met(27) gce(2.5k) mutants. Our data suggest a model in which Drosophila Met and Gce redundantly transduce JH action to prevent 20E-induced caspase-dependent PCD during larval molts by induction of Kr-h1 expression and inhibition of br expression.

}, issn = {1879-0240}, doi = {10.1016/j.ibmb.2011.09.003}, author = {Abdou, M and He, Q and Wen, D and Zyaan, O and Wang, J and Xu, J and Baumann, Aaron and Joseph, J and WIlson, TG and Li, S and Wang, J} } @article {5381, title = {Minimum-energy vesicle and cell shapes calculated using spherical harmonics parameterization.}, journal = {Soft Matter}, volume = {7}, year = {2011}, month = {2011 Jan 21}, pages = {2138-43}, abstract = {

An important open question in biophysics is to understand how mechanical forces shape membrane-bounded cells and their organelles. A general solution to this problem is to calculate the bending energy of an arbitrarily shaped membrane surface, which can include both lipids and cytoskeletal proteins, and minimize the energy subject to all mechanical constraints. However, the calculations are difficult to perform, especially for shapes that do not possess axial symmetry. We show that the spherical harmonics parameterization (SHP) provides an analytic description of shape that can be used to quickly and reliably calculate minimum energy shapes of both symmetric and asymmetric surfaces. Using this method, we probe the entire set of shapes predicted by the bilayer couple model, unifying work based on different computational approaches, and providing additional details of the transitions between different shape classes. In addition, we present new minimum-energy morphologies based on non-linear models of membrane skeletal elasticity that closely mimic extreme shapes of red blood cells. The SHP thus provides a versatile shape description that can be used to investigate forces that shape cells.

}, doi = {10.1039/c0sm01193b}, author = {Khairy, Khaled and Howard, Jonathon} } @article {3565, title = {Multiplexed shotgun genotyping for rapid and efficient genetic mapping.}, journal = {Genome Research}, volume = {21}, year = {2011}, month = {2011 Apr}, pages = {610-7}, abstract = {

We present a new approach to genotyping based on multiplexed shotgun sequencing that can identify recombination breakpoints in a large number of individuals simultaneously at a resolution sufficient for most mapping purposes, such as quantitative trait locus (QTL) mapping and mapping of induced mutations. We first describe a simple library construction protocol that uses just 10 ng of genomic DNA per individual and makes the approach accessible to any laboratory with standard molecular biology equipment. Sequencing this library results in a large number of sequence reads widely distributed across the genomes of multiplexed bar-coded individuals. We develop a Hidden Markov Model to estimate ancestry at all genomic locations in all individuals using these data. We demonstrate the utility of the approach by mapping a dominant marker allele in D. simulans to within 105 kb of its true position using 96 F1-backcross individuals genotyped in a single lane on an Illumina Genome Analyzer. We further demonstrate the utility of our method by genetically mapping more than 400 previously unassembled D. simulans contigs to linkage groups and by evaluating the quality of targeted introgression lines. At this level of multiplexing and divergence between strains, our method allows estimation of recombination breakpoints to a median of 38-kb intervals. Our analysis suggests that higher levels of multiplexing and/or use of strains with lower levels of divergence are practicable.

}, keywords = {Animals, Chromosome Breakpoints, Chromosome Mapping, Computational Biology, DNA, Dominant, Drosophila, Female, Genes, Genetic, Genetic Markers, Genotype, Male, Molecular Typing, Phenotype, Quantitative Trait Loci, Recombination, Research Design, Sequence Analysis}, issn = {1549-5469}, doi = {10.1101/gr.115402.110}, author = {Andolfatto, Peter and Davison, Dan and Erezyilmaz, Deniz and Hu, Tina T and Mast, Joshua and Sunayama-Morita, Tomoko and Stern, David L} } @article {47904, title = {Multi-scale correlation structure of gene expression in the brain.}, journal = {Neural networks : the official journal of the International Neural Network Society}, volume = {24}, year = {2011}, month = {2011 Nov}, pages = {933-42}, abstract = {

The mammalian brain is best understood as a multi-scale hierarchical neural system, in the sense that connection and function occur on multiple scales from micro to macro. Modern genomic-scale expression profiling can provide insight into methodologies that elucidate this architecture. We present a methodology for understanding the relationship of gene expression and neuroanatomy based on correlation between gene expression profiles across tissue samples. A resulting tool, NeuroBlast, can identify networks of genes co-expressed within or across neuroanatomic structures. The method applies to any data modality that can be mapped with sufficient spatial resolution, and provides a computation technique to elucidate neuroanatomy via patterns of gene expression on spatial and temporal scales. In addition, from the perspective of spatial location, we discuss a complementary technique that identifies gene classes that contribute to defining anatomic patterns.

}, keywords = {Algorithms, Animals, Atlases as Topic, Brain, Brain Chemistry, Data Mining, Databases, Genetic, Gene Expression, Mice, Mice, Inbred C57BL, Nerve Tissue Proteins, Tryptophan Hydroxylase}, issn = {1879-2782}, doi = {10.1016/j.neunet.2011.06.012}, author = {Hawrylycz, Mike and Ng, Lydia and Page, Damon and Morris, John and Lau, Chris and Faber, Sky and Faber, Vance and Sunkin, Susan and Menon, Vilas and Lein, Ed and Jones, Allan} } @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 {6489, title = {PALM and STORM: unlocking live-cell super-resolution.}, journal = {Biopolymers}, volume = {95}, year = {2011}, month = {2011 May}, pages = {322-31}, abstract = {

Live-cell fluorescence light microscopy has emerged as an important tool in the study of cellular biology. The development of fluorescent markers in parallel with super-resolution imaging systems has pushed light microscopy into the realm of molecular visualization at the nanometer scale. Resolutions previously only attained with electron microscopes are now within the grasp of light microscopes. However, until recently, live-cell imaging approaches have eluded super-resolution microscopy, hampering it from reaching its full potential for revealing the dynamic interactions in biology occurring at the single molecule level. Here we examine recent advances in the super-resolution imaging of living cells by reviewing recent breakthroughs in single molecule localization microscopy methods such as PALM and STORM to achieve this important goal.

}, keywords = {Buffers, Fluorescence, Fluorescent Dyes, Luminescent Proteins, Microscopy, Nanotechnology, Photochemical Processes, Single-Cell Analysis}, issn = {0006-3525}, doi = {10.1002/bip.21586}, author = {Henriques, Ricardo and Griffiths, Caron and Hesper Rego, E and Mhlanga, Musa M} } @article {3602, title = {Phase resolved interferometric spectral modulation (PRISM) for ultrafast pulse measurement and compression.}, journal = {Optics Express}, volume = {19}, year = {2011}, month = {2011 Jul 4}, pages = {12961-8}, abstract = {

We show through experiments and simulations that parallel phase modulation, a technique developed in the field of adaptive optics, can be employed to quickly determine the spectral phase profile of ultrafast laser pulses and to perform phase compensation as well as pulse shaping. Different from many existing ultrafast pulse measurement methods, the technique reported here requires no spectrum measurements of nonlinear signals. Instead, the power of nonlinear signals is used directly to quickly measure the spectral phase, a convenient feature for applications such as two-photon fluorescence microscopy. The method is found to work with both smooth and even completely random distortions. The experimental results are verified with MIIPS measurements.

}, issn = {1094-4087}, doi = {10.1364/OE.19.012961}, author = {Wu, Tsai-Wei and Tang, Jianyong and Hajj, Bassam and Cui, Meng} } @article {5383, title = {Probing tension and dynamics in actomyosin mediated cell shape change.}, journal = {Molecular Biology of the Cell}, volume = {22}, year = {2011}, month = {2011}, author = {Higgins, C. D. and Tulu, U. S. and Gao, L. and Betzig, E and Kiehart, D. P. and Goldstein, B.} } @article {46739, title = {Qualification of a new and precise automatic tool for the assessment of hair diameters in phototrichograms.}, journal = {Skin Research \& Technology}, volume = {17}, year = {2011}, month = {2011 May}, pages = {186-95}, abstract = {

BACKGROUND/PURPOSE: To automatically assess hair growth during cosmetic trials, incorporating parameters such as anagen-to-telogen rate, growth rate, and especially hair diameter.

METHODS: We designed and qualified a new and automatic phototrichogram system based on a high-resolution DSLR camera system (theoretical resolution of 2.557 μm/pixel) and modular macrolens system with fixed focus, combined with a trainable pattern recognition software for automated analysis.

RESULTS: We improved the standard routine for dermatological phototrichogram technique to overcome inaccuracy in thickness measurements due to hair swelling by using an alternative immersion fluid, and increased the effective resolution for hair size and thickness measurement to \<4 μm. After having qualified manual measurements as gold standard for the determination of hair diameters, we established a new trainable automatic picture analysis software able to locate and measure individual hairs in length and thickness even in picture series taken from the same skin area at different time points. Comparisons between manual and automatic measurements of the same hairs showed a \>90\% correlation, and by comparing the automatic results with manual measurements of the same images without individual hair annotation, we could find a correlation of at least 80\%.

CONCLUSION: According to the results and findings generated in this qualification study, we have a reliable tool now that enables us to test cosmetic products for hair treatment in a highly automated way with a sufficient degree of precision and accuracy to detect even small changes in hair diameter during cosmetic trials.

}, keywords = {Alopecia, Dermatology, Equipment Design, Female, Hair, Hair Preparations, Humans, Image Processing, Computer-Assisted, Male, Photography, Software}, issn = {1600-0846}, doi = {10.1111/j.1600-0846.2010.00482.x}, author = {Scheede, Stefan and Herpens, Andreas and Burmeister, Frank and Oltrogge, Bernhard and Saenger, K and Schmidt-Rose, Thomas and Schreiner, Volker and Wenck, Horst and Knieps, Torsten and Berlage, Thomas} } @article {4926, title = {Secretins: dynamic channels for protein transport across membranes.}, journal = {Trends in Biochemical Sciences}, volume = {36}, year = {2011}, month = {2011 Aug}, pages = {433-43}, abstract = {

Secretins form megadalton bacterial-membrane channels in at least four sophisticated multiprotein systems that are crucial for translocation of proteins and assembled fibers across the outer membrane of many species of bacteria. Secretin subunits contain multiple domains, which interact with numerous other proteins, including pilotins, secretion-system partner proteins, and exoproteins. Our understanding of the structure of secretins is rapidly progressing, and it is now recognized that features common to all secretins include a cylindrical arrangement of 12-15 subunits, a large periplasmic vestibule with a wide opening at one end and a periplasmic gate at the other. Secretins might also play a key role in the biogenesis of their cognate secretion systems.

}, keywords = {Bacterial Outer Membrane Proteins, Bacterial Proteins, Carrier Proteins, Gram-Negative Bacteria, Membrane Transport Proteins, Models, Molecular, Protein Binding, Protein Conformation, Protein Structure, Protein Transport, Secondary, Secretin, Tertiary}, issn = {0968-0004}, doi = {10.1016/j.tibs.2011.04.002}, author = {Korotkov, Konstantin V and Gonen, Tamir and Hol, Wim G J} } @article {4304, title = {Serotonin-mushroom body circuit modulating the formation of anesthesia-resistant memory in Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, year = {2011}, month = {2011 Aug 16}, pages = {13794-9}, abstract = {

Pavlovian olfactory learning in Drosophila produces two genetically distinct forms of intermediate-term memories: anesthesia-sensitive memory, which requires the amnesiac gene, and anesthesia-resistant memory (ARM), which requires the radish gene. Here, we report that ARM is specifically enhanced or inhibited in flies with elevated or reduced serotonin (5HT) levels, respectively. The requirement for 5HT was additive with the memory defect of the amnesiac mutation but was occluded by the radish mutation. This result suggests that 5HT and Radish protein act on the same pathway for ARM formation. Three supporting lines of evidence indicate that ARM formation requires 5HT released from only two dorsal paired medial (DPM) neurons onto the mushroom bodies (MBs), the olfactory learning and memory center in Drosophila: (i) DPM neurons were 5HT-antibody immunopositive; (ii) temporal inhibition of 5HT synthesis or release from DPM neurons, but not from other serotonergic neurons, impaired ARM formation; (iii) knocking down the expression of d5HT1A serotonin receptors in α/β MB neurons, which are innervated by DPM neurons, inhibited ARM formation. Thus, in addition to the Amnesiac peptide required for anesthesia-sensitive memory formation, the two DPM neurons also release 5HT acting on MB neurons for ARM formation.

}, issn = {1091-6490}, doi = {10.1073/pnas.1019483108}, author = {Lee, Pei-Tseng and Lin, Hsuan-Wen and Chang, Yu-Hsuan and Fu, Tsai-Feng and Dubnau, Josh and Hirsh, Jay and Lee, Tzumin and Chiang, Ann-Shyn} } @article {6444, title = {A structural and functional ground plan for neurons in the hindbrain of zebrafish.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, year = {2011}, month = {2011 Jan 18}, pages = {1164-9}, abstract = {

The vertebrate hindbrain contains various sensory-motor networks controlling movements of the eyes, jaw, head, and body. Here we show that stripes of neurons with shared neurotransmitter phenotype that extend throughout the hindbrain of young zebrafish reflect a broad underlying structural and functional patterning. The neurotransmitter stripes contain cell types with shared gross morphologies and transcription factor markers. Neurons within a stripe are stacked systematically by extent and location of axonal projections, input resistance, and age, and are recruited along the axis of the stripe during behavior. The implication of this pattern is that the many networks in hindbrain are constructed from a series of neuronal components organized into stripes that are ordered from top to bottom according to a neuron{\textquoteright}s age, structural and functional properties, and behavioral roles. This simple organization probably forms a foundation for the construction of the networks underlying the many behaviors produced by the hindbrain.

}, keywords = {Age Factors, Animals, Body Patterning, Calcium, Confocal, Electrophysiology, Genetically Modified, Interneurons, Microscopy, Models, Nerve Net, Neurological, Neurotransmitter Agents, Rhombencephalon, Zebrafish}, issn = {1091-6490}, doi = {10.1073/pnas.1012185108}, author = {Kinkhabwala, Amina and Riley, Michael and Koyama, Minoru and Monen, Joost and Satou, Chie and Kimura, Yukiko and Higashijima, Shin-Ichi and Fetcho, Joseph} } @article {68822, title = {A structural and functional ground plan for neurons in the hindbrain of zebrafish}, journal = {Proceedings of the National Academy of Sciences}, volume = {108}, year = {2011}, month = {01/2011}, pages = {1164-1169}, abstract = {

The vertebrate hindbrain contains various sensory-motor networks controlling movements of the eyes, jaw, head, and body. Here we show that stripes of neurons with shared neurotransmitter phenotype that extend throughout the hindbrain of young zebrafish reflect a broad underlying structural and functional patterning. The neurotransmitter stripes contain cell types with shared gross morphologies and transcription factor markers. Neurons within a stripe are stacked systematically by extent and location of axonal projections, input resistance, and age, and are recruited along the axis of the stripe during behavior. The implication of this pattern is that the many networks in hindbrain are constructed from a series of neuronal components organized into stripes that are ordered from top to bottom according to a neuron{\textquoteright}s age, structural and functional properties, and behavioral roles. This simple organization probably forms a foundation for the construction of the networks underlying the many behaviors produced by the hindbrain.

}, doi = {10.1073/pnas.1012185108}, url = {https://www.pnas.org/doi/abs/10.1073/pnas.1012185108}, author = {Amina Kinkhabwala and Michael Riley and Minoru Koyama and Joost Monen and Chie Satou and Yukiko Kimura and Shin-ichi Higashijima and Joseph Fetcho} } @article {1233, title = {Structural properties of the Caenorhabditis elegans neuronal network.}, journal = {PLoS Computational Biology}, volume = {7}, year = {2011}, month = {2011 Feb 3}, pages = {e1001066}, abstract = {

Despite recent interest in reconstructing neuronal networks, complete wiring diagrams on the level of individual synapses remain scarce and the insights into function they can provide remain unclear. Even for Caenorhabditis elegans, whose neuronal network is relatively small and stereotypical from animal to animal, published wiring diagrams are neither accurate nor complete and self-consistent. Using materials from White et al. and new electron micrographs we assemble whole, self-consistent gap junction and chemical synapse networks of hermaphrodite C. elegans. We propose a method to visualize the wiring diagram, which reflects network signal flow. We calculate statistical and topological properties of the network, such as degree distributions, synaptic multiplicities, and small-world properties, that help in understanding network signal propagation. We identify neurons that may play central roles in information processing, and network motifs that could serve as functional modules of the network. We explore propagation of neuronal activity in response to sensory or artificial stimulation using linear systems theory and find several activity patterns that could serve as substrates of previously described behaviors. Finally, we analyze the interaction between the gap junction and the chemical synapse networks. Since several statistical properties of the C. elegans network, such as multiplicity and motif distributions are similar to those found in mammalian neocortex, they likely point to general principles of neuronal networks. The wiring diagram reported here can help in understanding the mechanistic basis of behavior by generating predictions about future experiments involving genetic perturbations, laser ablations, or monitoring propagation of neuronal activity in response to stimulation.

}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1001066}, author = {Varshney, Lav R and Chen, Beth L and Paniagua, Eric and Hall, David H and Chklovskii, Dmitri B} } @article {3328, title = {Studying sensorimotor integration in insects.}, journal = {Current Opinion in Neurobiology}, volume = {21}, year = {2011}, month = {2011 Jun 24}, pages = {527-34}, abstract = {

Sensorimotor integration is a field rich in theory backed by a large body of psychophysical evidence. Relating the underlying neural circuitry to these theories has, however, been more challenging. With a wide array of complex behaviors coordinated by their small brains, insects provide powerful model systems to study key features of sensorimotor integration at a mechanistic level. Insect neural circuits perform both hard-wired and learned sensorimotor transformations. They modulate their neural processing based on both internal variables, such as the animal{\textquoteright}s behavioral state, and external ones, such as the time of day. Here we present some studies using insect model systems that have produced insights, at the level of individual neurons, about sensorimotor integration and the various ways in which it can be modified by context.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2011.05.030}, author = {Huston*, Stephen J and Jayaraman, Vivek} } @article {2385, title = {Subnuclear segregation of genes and core promoter factors in myogenesis. (With commentary)}, journal = {Genes \& Development}, volume = {25}, year = {2011}, month = {2011 Mar 15}, pages = {569-80}, abstract = {

Recent findings implicate alternate core promoter recognition complexes in regulating cellular differentiation. Here we report a spatial segregation of the alternative core factor TAF3, but not canonical TFIID subunits, away from the nuclear periphery, where the key myogenic gene MyoD is preferentially localized in myoblasts. This segregation is correlated with the differential occupancy of TAF3 versus TFIID at the MyoD promoter. Loss of this segregation by modulating either the intranuclear location of the MyoD gene or TAF3 protein leads to altered TAF3 occupancy at the MyoD promoter. Intriguingly, in differentiated myotubes, the MyoD gene is repositioned to the nuclear interior, where TAF3 resides. The specific high-affinity recognition of H3K4Me3 by the TAF3 PHD (plant homeodomain) finger appears to be required for the sequestration of TAF3 to the nuclear interior. We suggest that intranuclear sequestration of core transcription components and their target genes provides an additional mechanism for promoter selectivity during differentiation.

Commentary: Jie Yao in Bob Tijan{\textquoteright}s lab used a combination of confocal microscopy and dual label PALM in thin sections cut from resin-embedded cells to show that certain core transcription components and their target genes are spatially segregated in myoblasts, but not in differentiated myotubes, suggesting that such spatial segregation may play a role in guiding cellular differentiation.

}, issn = {1549-5477}, doi = {10.1073/pnas.1100640108}, author = {Yao, Jie and Fetter, Richard D and Hu, Ping and Betzig, Eric and Tjian, Robert} } @article {4469, title = {Superresolution fluorescence imaging of mitochondrial nucleoids reveals their spatial range, limits, and membrane interaction.}, journal = {Molecular and Cellular Biology}, volume = {31}, year = {2011}, month = {2011 Dec}, pages = {4994-5010}, abstract = {

A fundamental objective in molecular biology is to understand how DNA is organized in concert with various proteins, RNA, and biological membranes. Mitochondria maintain and express their own DNA (mtDNA), which is arranged within structures called nucleoids. Their functions, dimensions, composition, and precise locations relative to other mitochondrial structures are poorly defined. Superresolution fluorescence microscopy techniques that exceed the previous limits of imaging within the small and highly compartmentalized mitochondria have been recently developed. We have improved and employed both two- and three-dimensional applications of photoactivated localization microscopy (PALM and iPALM, respectively) to visualize the core dimensions and relative locations of mitochondrial nucleoids at an unprecedented resolution. PALM reveals that nucleoids differ greatly in size and shape. Three-dimensional volumetric analysis indicates that, on average, the mtDNA within ellipsoidal nucleoids is extraordinarily condensed. Two-color PALM shows that the freely diffusible mitochondrial matrix protein is largely excluded from the nucleoid. In contrast, nucleoids are closely associated with the inner membrane and often appear to be wrapped around cristae or crista-like inner membrane invaginations. Determinations revealing high packing density, separation from the matrix, and tight association with the inner membrane underscore the role of mechanisms that regulate access to mtDNA and that remain largely unknown.

}, keywords = {3T3 Cells, Animals, Confocal, DNA, Fluorescence, Mice, Microscopy, Mitochondria, Mitochondrial, Mitochondrial Proteins, Plasmids, Sequence Alignment, Sequence Analysis}, issn = {1098-5549}, doi = {10.1128/MCB.05694-11}, url = {http://mcb.asm.org/content/31/24/4994.short}, author = {Brown, Timothy A and Tkachuk, Ariana N and Shtengel, Gleb and Kopek, Benjamin G and Bogenhagen, Daniel F and Hess, Harald F and Clayton, David A} } @article {46609, title = {Tao kinases as coordinators of actin and microtubule dynamics in developing neurons.}, journal = {Communicative \& Integrative Biology}, volume = {4}, year = {2011}, month = {2011 Sep}, pages = {554-6}, abstract = {

Drosophila tao, encoding a Ste20 family kinase, was identified as a gene involved in ethanol, cocaine and nicotine sensitivity. The behavioral phenotypes appear to be caused by defects in the development of the adult brain. Specifically, Drosophila tao functions to promote axon guidance of mushroom body (MB) neurons. The MB is a large structure in the central brain of the fly whose development and function have been well characterized. tao interacts genetically with mutations in the par-1 gene, also encoding a serine-threonine kinase. Since Par-1 has been implicated in the regulation of microtubule dynamics, this suggests that tao regulates the microtubule cytoskeleton in developing MB neurons. Here we discuss these results in light of previous studies that have proposed that Drosophila tao and its mammalian homologs function as a link between the actin and microtubule cytoskeletons, regulating microtubule stability in response to actin signals.

}, issn = {1942-0889}, doi = {10.4161/cib.4.5.16051}, author = {King, Ian and Heberlein, Ulrike} } @article {6332, title = {Tilt-pair analysis of images from a range of different specimens in single-particle electron cryomicroscopy.}, journal = {Journal of Molecular Biology}, volume = {413}, year = {2011}, month = {2011 Nov 11}, pages = {1028-46}, abstract = {

The comparison of a pair of electron microscope images recorded at different specimen tilt angles provides a powerful approach for evaluating the quality of images, image-processing procedures, or three-dimensional structures. Here, we analyze tilt-pair images recorded from a range of specimens with different symmetries and molecular masses and show how the analysis can produce valuable information not easily obtained otherwise. We show that the accuracy of orientation determination of individual single particles depends on molecular mass, as expected theoretically since the information in each particle image increases with molecular mass. The angular uncertainty is less than 1{\textdegree} for particles of high molecular mass (\ 50 MDa), several degrees for particles in the range 1-5 MDa, and tens of degrees for particles below 1 MDa. Orientational uncertainty may be the major contributor to the effective temperature factor (B-factor) describing contrast loss and therefore the maximum resolution of a structure determination. We also made two unexpected observations. Single particles that are known to be flexible showed a wider spread in orientation accuracy, and the orientations of the largest particles examined changed by several degrees during typical low-dose exposures. Smaller particles presumably also reorient during the exposure; hence, specimen movement is a second major factor that limits resolution. Tilt pairs thus enable assessment of orientation accuracy, map quality, specimen motion, and conformational heterogeneity. A convincing tilt-pair parameter plot, where 60\% of the particles show a single cluster around the expected tilt axis and tilt angle, provides confidence in a structure determined using electron cryomicroscopy.

}, keywords = {Adenosine Triphosphatases, Animals, beta-Galactosidase, Cattle, Computer-Assisted, Cryoelectron Microscopy, Image Processing, Rotavirus, Virion, Yeasts}, issn = {1089-8638}, doi = {10.1016/j.jmb.2011.09.008}, author = {Henderson, Richard and Chen, Shaoxia and Chen, James Z and Grigorieff, Nikolaus and Passmore, Lori A and Ciccarelli, Luciano and Rubinstein, John L and Crowther, R Anthony and Stewart, Phoebe L and Rosenthal, Peter B} } @article {4305, title = {Two-photon calcium imaging of evoked activity from L5 somatosensory neurons in vivo.}, journal = {Nature Neuroscience}, volume = {14}, year = {2011}, month = {2011 Aug}, pages = {1089-93}, abstract = {

Multiphoton imaging (MPI) is widely used for recording activity simultaneously from many neurons in superficial cortical layers in vivo. We combined regenerative amplification multiphoton microscopy (RAMM) with genetically encoded calcium indicators to extend MPI of neuronal population activity into layer 5 (L5) of adult mouse somatosensory cortex. We found that this approach could be used to record and quantify spontaneous and sensory-evoked activity in populations of L5 neuronal somata located as much as 800 μm below the pia. In addition, we found that RAMM could be used to simultaneously image activity from large (80) populations of apical dendrites and follow these dendrites down to their somata of origin.

}, keywords = {Animals, Axons, Calcium, Dendrites, Evoked Potentials, Green Fluorescent Proteins, Inbred C57BL, Mice, Nerve Net, Neurons, Newborn, Photons, Physical Stimulation, Probability, Reaction Time, Somatosensory, Somatosensory Cortex, Statistics as Topic, Transgenic}, issn = {1546-1726}, doi = {10.1038/nn.2879}, author = {Mittmann, Wolfgang and Wallace, Damian J and Czubayko, Uwe and Herb, Jan T and Schaefer, Andreas T and Looger, Loren L and Denk, Winfried and Kerr, Jason N D} } @article {5385, title = {Wireless neural/EMG telemetry systems for small freely moving animals.}, journal = {IEEE Transactions on Biomedical Circuits and Systems}, volume = {5}, year = {2011}, month = {2011 Apr}, pages = {103-11}, abstract = {

We have developed miniature telemetry systems that capture neural, EMG, and acceleration signals from a freely moving insect or other small animal and transmit the data wirelessly to a remote digital receiver. The systems are based on custom low-power integrated circuits (ICs) that amplify, filter, and digitize four biopotential signals using low-noise circuits. One of the chips also digitizes three acceleration signals from an off-chip microelectromechanical-system accelerometer. All information is transmitted over a wireless ~ 900-MHz telemetry link. The first unit, using a custom chip fabricated in a 0.6- μm BiCMOS process, weighs 0.79 g and runs for two hours on two small batteries. We have used this system to monitor neural and EMG signals in jumping and flying locusts as well as transdermal potentials in weakly swimming electric fish. The second unit, using a custom chip fabricated in a 0.35-μ m complementary metal-oxide semiconductor CMOS process, weighs 0.17 g and runs for five hours on a single 1.5-V battery. This system has been used to monitor neural potentials in untethered perching dragonflies.

}, issn = {1932-4545}, doi = {10.1109/TBCAS.2011.2131140}, author = {Harrison, Reid R. and Fotowat, Haleh and Chan, Raymond and Kier, Ryan J and Olberg, Robert and Leonardo, Anthony and Gabbiani, Fabrizio} } @article {48172, title = {3D reconstruction of the human rib cage from 2D projection images using a statistical shape model.}, journal = {International journal of computer assisted radiology and surgery}, volume = {5}, year = {2010}, month = {2010 Mar}, pages = {111-24}, abstract = {

PURPOSE: This paper describes an approach for the three-dimensional (3D) shape and pose reconstruction of the human rib cage from few segmented two-dimensional (2D) projection images. Our work is aimed at supporting temporal subtraction techniques of subsequently acquired radiographs by establishing a method for the assessment of pose differences in sequences of chest radiographs of the same patient.

METHODS: The reconstruction method is based on a 3D statistical shape model (SSM) of the rib cage, which is adapted to binary 2D projection images of an individual rib cage. To drive the adaptation we minimize a distance measure that quantifies the dissimilarities between 2D projections of the 3D SSM and the projection images of the individual rib cage. We propose different silhouette-based distance measures and evaluate their suitability for the adaptation of the SSM to the projection images.

RESULTS: An evaluation was performed on 29 sets of biplanar binary images (posterior-anterior and lateral). Depending on the chosen distance measure, our experiments on the combined reconstruction of shape and pose of the rib cages yield reconstruction errors from 2.2 to 4.7 mm average mean 3D surface distance. Given a geometry of an individual rib cage, the rotational errors for the pose reconstruction range from 0.1 degrees to 0.9 degrees.

CONCLUSIONS: The results show that our method is suitable for the estimation of pose differences of the human rib cage in binary projection images. Thus, it is able to provide crucial 3D information for registration during the generation of 2D subtraction images.

}, keywords = {Humans, Image Interpretation, Computer-Assisted, Image Processing, Computer-Assisted, Imaging, Three-Dimensional, Models, Anatomic, Radiographic Image Enhancement, Ribs, Subtraction Technique}, issn = {1861-6429}, doi = {10.1007/s11548-009-0390-2}, author = {Dworzak, Jalda and Lamecker, Hans and von Berg, Jens and Klinder, Tobias and Lorenz, Cristian and Kainm{\"u}ller, Dagmar and Seim, Heiko and Hege, Hans-Christian and Zachow, Stefan} } @article {1454, title = {3D segmentation of cell boundaries from whole cell cryogenic electron tomography volumes.}, journal = {Journal of Structural Biology}, volume = {170}, year = {2010}, month = {2010 Apr}, pages = {134-45}, abstract = {

Cryogenic electron tomography (cryo-ET) has gained increasing interest in recent years due to its ability to image whole cells and subcellular structures in 3D at nanometer resolution in their native environment. However, due to dose restrictions and the inability to acquire high tilt angle images, the reconstructed volumes are noisy and have missing information. Thus, features are unreliable, and precision extraction of the cell boundary is difficult, manual and time intensive. This paper presents an efficient recursive algorithm called BLASTED (Boundary Localization using Adaptive Shape and Texture Discovery) to automatically extract the cell boundary using a conditional random field (CRF) framework in which boundary points and shape are jointly inferred. The algorithm learns the texture of the boundary region progressively, and uses a global shape model and shape-dependent features to propose candidate boundary points on a slice of the membrane. It then updates the shape of that slice by accepting the appropriate candidate points using local spatial clustering, the global shape model, and trained boosted texture classifiers. The BLASTED algorithm segmented the cell membrane over an average of 93\% of the length of the cell in 19 difficult cryo-ET datasets.

}, keywords = {Algorithms, Cell Membrane, Cryoelectron Microscopy, Electron Microscope Tomography}, issn = {1095-8657}, doi = {10.1016/j.jsb.2009.12.015}, author = {Moussavi, Farshid and Heitz, Geremy and Amat, Fernando and Comolli, Luis R and Koller, Daphne and Horowitz, Mark} } @article {46615, title = {Addiction-like behavior in Drosophila.}, journal = {Communicative \& Integrative Biology}, volume = {3}, year = {2010}, month = {2010 Jul}, pages = {357-9}, abstract = {

Alcohol abuse is a pervasive problem known to be influenced by genetic factors, yet our understanding of the mechanisms underlying alcohol addiction is far from complete. Drosophila melanogaster has been established as a model for studying the molecular mechanisms that mediate the acute and chronic effects of alcohol. However, the Drosophila model has not yet been extended to include more complex alcohol-related behaviors such as self-administration. We recently established a paradigm to characterize ethanol consumption and preference in flies. We demonstrated that flies prefer to consume ethanol-containing food over regular food, and this preference exhibits several features of alcohol addiction: flies increase ethanol consumption over time, they consume ethanol to pharmacologically relevant concentrations, they will overcome an aversive stimulus in order to consume ethanol, and they exhibit relapse after a period of ethanol deprivation. Thus, ethanol preference in flies provides a new model for studying important aspects of addiction and their underlying mechanisms. One mutant that displayed decreased ethanol preference, krasavietz, may represent a first step toward uncovering those mechanisms.

}, issn = {1942-0889}, author = {Devineni, Anita V and Heberlein, Ulrike} } @article {1450, title = {Alignment of cryo-electron tomography datasets.}, journal = {Methods in Enzymology}, volume = {482}, year = {2010}, month = {2010}, pages = {343-67}, abstract = {

Data acquisition of cryo-electron tomography (CET) samples described in previous chapters involves relatively imprecise mechanical motions: the tilt series has shifts, rotations, and several other distortions between projections. Alignment is the procedure of correcting for these effects in each image and requires the estimation of a projection model that describes how points from the sample in three-dimensions are projected to generate two-dimensional images. This estimation is enabled by finding corresponding common features between images. This chapter reviews several software packages that perform alignment and reconstruction tasks completely automatically (or with minimal user intervention) in two main scenarios: using gold fiducial markers as high contrast features or using relevant biological structures present in the image (marker-free). In particular, we emphasize the key decision points in the process that users should focus on in order to obtain high-resolution reconstructions.

}, keywords = {Computer-Assisted, Cryoelectron Microscopy, Electron Microscope Tomography, Image Processing}, issn = {1557-7988}, doi = {10.1016/S0076-6879(10)82014-2}, author = {Amat, Fernando and Casta{\~n}o-Diez, Daniel and Lawrence, Albert and Moussavi, Farshid and Winkler, Hanspeter and Horowitz, Mark} } @article {1452, title = {Analysis of the intact surface layer of Caulobacter crescentus by cryo-electron tomography.}, journal = {Journal of Bacteriology}, volume = {192}, year = {2010}, month = {2010 Nov}, pages = {5855-65}, abstract = {

The surface layers (S layers) of those bacteria and archaea that elaborate these crystalline structures have been studied for 40 years. However, most structural analysis has been based on electron microscopy of negatively stained S-layer fragments separated from cells, which can introduce staining artifacts and allow rearrangement of structures prone to self-assemble. We present a quantitative analysis of the structure and organization of the S layer on intact growing cells of the Gram-negative bacterium Caulobacter crescentus using cryo-electron tomography (CET) and statistical image processing. Instead of the expected long-range order, we observed different regions with hexagonally organized subunits exhibiting short-range order and a broad distribution of periodicities. Also, areas of stacked double layers were found, and these increased in extent when the S-layer protein (RsaA) expression level was elevated by addition of multiple rsaA copies. Finally, we combined high-resolution amino acid residue-specific Nanogold labeling and subtomogram averaging of CET volumes to improve our understanding of the correlation between the linear protein sequence and the structure at the 2-nm level of resolution that is presently available. The results support the view that the U-shaped RsaA monomer predicted from negative-stain tomography proceeds from the N terminus at one vertex, corresponding to the axis of 3-fold symmetry, to the C terminus at the opposite vertex, which forms the prominent 6-fold symmetry axis. Such information will help future efforts to analyze subunit interactions and guide selection of internal sites for display of heterologous protein segments.

}, keywords = {Amino Acids, Bacterial Proteins, Caulobacter crescentus, Computer-Assisted, Cryoelectron Microscopy, Electron Microscope Tomography, Image Processing, Membrane Glycoproteins, Metal Nanoparticles, Staining and Labeling}, issn = {1098-5530}, doi = {10.1128/JB.00747-10}, author = {Amat, Fernando and Comolli, Luis R and Nomellini, John F and Moussavi, Farshid and Downing, Kenneth H and Smit, John and Horowitz, Mark} } @article {5690, title = {As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets.}, journal = {Bioinformatics}, volume = {26}, year = {2010}, month = {2010 Jun 15}, pages = {i57-63}, abstract = {

Tiled serial section Transmission Electron Microscopy (ssTEM) is increasingly used to describe high-resolution anatomy of large biological specimens. In particular in neurobiology, TEM is indispensable for analysis of synaptic connectivity in the brain. Registration of ssTEM image mosaics has to recover the 3D continuity and geometrical properties of the specimen in presence of various distortions that are applied to the tissue during sectioning, staining and imaging. These include staining artifacts, mechanical deformation, missing sections and the fact that structures may appear dissimilar in consecutive sections.

}, keywords = {Animals, Databases, Drosophila, Electron, Factual, Imaging, Microscopy, Three-Dimensional, Transmission}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btq219}, author = {Saalfeld, Stephan and Cardona, Albert and Hartenstein, Volker and Tomancak, Pavel.} } @article {2327, title = {Automated tracking and analysis of centrosomes in early Caenorhabditis elegans embryos.}, journal = {Bioinformatics}, volume = {26}, year = {2010}, month = {2010 Jun 15}, pages = {i13-20}, abstract = {

The centrosome is a dynamic structure in animal cells that serves as a microtubule organizing center during mitosis and also regulates cell-cycle progression and sets polarity cues. Automated and reliable tracking of centrosomes is essential for genetic screens that study the process of centrosome assembly and maturation in the nematode Caenorhabditis elegans.

}, keywords = {Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Cell Division, Cell Lineage, Centrosome, Embryo, Fluorescence, Microscopy, Mitotic Spindle Apparatus, Nonmammalian}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btq190}, author = {Jaensch, Steffen and Decker, Markus and Hyman, Anthony A and Myers, Eugene W} } @conference {3858, title = {Boundary learning by optimization with topological constraints.}, booktitle = {IEEE Conference on Computer Vision and Pattern Recognition}, year = {2010}, month = {2010}, abstract = {

Recent studies have shown that machine learning can improve the accuracy of detecting object boundaries in images. In the standard approach, a boundary detector is trained by minimizing its pixel-level disagreement with human boundary tracings. This naive metric is problematic because it is overly sensitive to boundary locations. This problem is solved by metrics provided with the Berkeley Segmentation Dataset, but these can be insensitive to topological differences, such as gaps in boundaries. Furthermore, the Berkeley metrics have not been useful as cost functions for supervised learning. Using concepts from digital topology, we propose a new metric called the warping error that tolerates disagreements over boundary location, penalizes topological disagreements, and can be used directly as a cost function for learning boundary detection, in a method that we call Boundary Learning by Optimization with Topological Constraints (BLOTC). We trained boundary detectors on electron microscopic images of neurons, using both BLOTC and standard training. BLOTC produced substantially better performance on a 1.2 million pixel test set, as measured by both the warping error and the Rand index evaluated on segmentations generated from the boundary labelings. We also find our approach yields significantly better segmentation performance than either gPb-OWT-UCM or multiscale normalized cut, as well as Boosted Edge Learning trained directly on our data.

}, author = {Jain, Viren and Bollmann, Benjamin and Richardson, Mark and Berger, Daniel R. and Helmstaedter, Moritz N. and Briggman, Kevin L and Denk, Winfried and Bowden, Jared B. and Mendenhall, John M. and Abraham, Wickliffe C. and Harris, Kristen M and Kasthuri, Narayanan and Hayworth, Ken J. and Schalek, Richard and Tapia, Juan Carlos and Lichtman, Jeff W. and Seung, Hyunjune Sebastian} } @article {1767, title = {The cells and peripheral representation of sodium taste in mice.}, journal = {Nature}, volume = {464}, year = {2010}, month = {2010 Mar 11}, pages = {297-301}, abstract = {

Salt taste in mammals can trigger two divergent behavioural responses. In general, concentrated saline solutions elicit robust behavioural aversion, whereas low concentrations of NaCl are typically attractive, particularly after sodium depletion. Notably, the attractive salt pathway is selectively responsive to sodium and inhibited by amiloride, whereas the aversive one functions as a non-selective detector for a wide range of salts. Because amiloride is a potent inhibitor of the epithelial sodium channel (ENaC), ENaC has been proposed to function as a component of the salt-taste-receptor system. Previously, we showed that four of the five basic taste qualities-sweet, sour, bitter and umami-are mediated by separate taste-receptor cells (TRCs) each tuned to a single taste modality, and wired to elicit stereotypical behavioural responses. Here we show that sodium sensing is also mediated by a dedicated population of TRCs. These taste cells express the epithelial sodium channel ENaC, and mediate behavioural attraction to NaCl. We genetically engineered mice lacking ENaCalpha in TRCs, and produced animals exhibiting a complete loss of salt attraction and sodium taste responses. Together, these studies substantiate independent cellular substrates for all five basic taste qualities, and validate the essential role of ENaC for sodium taste in mice.

}, keywords = {Animals, Behavior, Epithelial Sodium Channel, Mice, Sodium, Taste, Taste Buds, Transgenic}, issn = {1476-4687}, doi = {10.1038/nature08783}, author = {Chandrashekar, Jayaram and Kuhn, Christina and Oka, Yuki and Yarmolinsky, David A and Hummler, Edith and Ryba, Nicholas J P and Zuker, Charles S} } @article {5896, title = {Clarke{\textquoteright}s column neurons as the focus of a corticospinal corollary circuit.}, journal = {Nature Neuroscience}, volume = {13}, year = {2010}, month = {2010 Oct}, pages = {1233-9}, abstract = {

Proprioceptive sensory signals inform the CNS of the consequences of motor acts, but effective motor planning involves internal neural systems capable of anticipating actual sensory feedback. Just where and how predictive systems exert their influence remains poorly understood. We explored the possibility that spinocerebellar neurons that convey proprioceptive sensory information also integrate information from cortical command systems. Analysis of the circuitry and physiology of identified dorsal spinocerebellar tract neurons in mouse spinal cord revealed distinct populations of Clarke{\textquoteright}s column neurons that received direct excitatory and/or indirect inhibitory inputs from descending corticospinal axons. The convergence of these descending inhibitory and excitatory inputs to Clarke{\textquoteright}s column neurons established local spinal circuits with the capacity to mark or modulate incoming proprioceptive input. Together, our genetic, anatomical and physiological results indicate that Clarke{\textquoteright}s column spinocerebellar neurons nucleate local spinal corollary circuits that are relevant to motor planning and evaluation.

}, keywords = {3-dione, 6-Cyano-7-nitroquinoxaline-2, Animals, beta-Galactosidase, Bicuculline, Cerebellum, Cholera Toxin, Electric Stimulation, Estrogen Antagonists, Excitatory Amino Acid Antagonists, Feedback, GABA Antagonists, Gene Expression Regulation, Glial Cell Line-Derived Neurotrophic Factor, Glycine Agents, Glycine Plasma Membrane Transport Proteins, Green Fluorescent Proteins, Homeodomain Proteins, Lysine, Membrane Potentials, Messenger, Mice, Models, Nerve Net, Neural Inhibition, Neural Pathways, Neurological, Newborn, Parvalbumins, Patch-Clamp Techniques, Protein Kinase C, RNA, Sensory, Sensory Receptor Cells, Spinal Cord, Stilbamidines, Strychnine, Tamoxifen, tau Proteins, Transcription Factors, Transgenic, Vesicular Glutamate Transport Protein 1}, issn = {1546-1726}, doi = {10.1038/nn.2637}, author = {Hantman, Adam W and Jessell, Thomas M} } @article {783, title = {A complete developmental sequence of a Drosophila neuronal lineage as revealed by twin-spot MARCM.}, journal = {PLoS Biology}, volume = {8}, year = {2010}, month = {2010 Aug 24}, abstract = {

Drosophila brains contain numerous neurons that form complex circuits. These neurons are derived in stereotyped patterns from a fixed number of progenitors, called neuroblasts, and identifying individual neurons made by a neuroblast facilitates the reconstruction of neural circuits. An improved MARCM (mosaic analysis with a repressible cell marker) technique, called twin-spot MARCM, allows one to label the sister clones derived from a common progenitor simultaneously in different colors. It enables identification of every single neuron in an extended neuronal lineage based on the order of neuron birth. Here we report the first example, to our knowledge, of complete lineage analysis among neurons derived from a common neuroblast that relay olfactory information from the antennal lobe (AL) to higher brain centers. By identifying the sequentially derived neurons, we found that the neuroblast serially makes 40 types of AL projection neurons (PNs). During embryogenesis, one PN with multi-glomerular innervation and 18 uniglomerular PNs targeting 17 glomeruli of the adult AL are born. Many more PNs of 22 additional types, including four types of polyglomerular PNs, derive after the neuroblast resumes dividing in early larvae. Although different offspring are generated in a rather arbitrary sequence, the birth order strictly dictates the fate of each post-mitotic neuron, including the fate of programmed cell death. Notably, the embryonic progenitor has an altered temporal identity following each self-renewing asymmetric cell division. After larval hatching, the same progenitor produces multiple neurons for each cell type, but the number of neurons for each type is tightly regulated. These observations substantiate the origin-dependent specification of neuron types. Sequencing neuronal lineages will not only unravel how a complex brain develops but also permit systematic identification of neuron types for detailed structure and function analysis of the brain.

}, keywords = {Animals, Brain, Cell Lineage, Clone Cells, Drosophila, Genetic Techniques, Mosaicism, Neurogenesis, Neurons, Olfactory Pathways}, issn = {1545-7885}, doi = {10.1371/journal.pbio.1000461}, author = {Yu, Hung-Hsiang and Kao, Chih-Fei and He, Yisheng and Ding, Peng and Kao, Jui-Chun and Lee, Tzumin} } @article {3844, title = {Convolutional networks can learn to generate affinity graphs for image segmentation.}, journal = {Neural Computation}, volume = {22}, year = {2010}, month = {2010 Feb}, pages = {511-38}, abstract = {

Many image segmentation algorithms first generate an affinity graph and then partition it. We present a machine learning approach to computing an affinity graph using a convolutional network (CN) trained using ground truth provided by human experts. The CN affinity graph can be paired with any standard partitioning algorithm and improves segmentation accuracy significantly compared to standard hand-designed affinity functions. We apply our algorithm to the challenging 3D segmentation problem of reconstructing neuronal processes from volumetric electron microscopy (EM) and show that we are able to learn a good affinity graph directly from the raw EM images. Further, we show that our affinity graph improves the segmentation accuracy of both simple and sophisticated graph partitioning algorithms. In contrast to previous work, we do not rely on prior knowledge in the form of hand-designed image features or image preprocessing. Thus, we expect our algorithm to generalize effectively to arbitrary image types.

}, keywords = {Algorithms, Artificial Intelligence, Automated, Computer-Assisted, Electron, Image Processing, Mathematical Computing, Mathematical Concepts, Mathematics, Microscopy, Neural Networks (Computer), Pattern Recognition}, issn = {1530-888X}, doi = {10.1162/neco.2009.10-08-881}, author = {Turaga, Srinivas C and Murray, Joseph F and Jain, Viren and Roth, Fabian and Helmstaedter, Moritz and Briggman, Kevin and Denk, Winfried and Seung, Hyunjune Sebastian} } @article {1449, title = {Cortical representations of olfactory input by trans-synaptic tracing.}, journal = {Nature}, volume = {472}, year = {2010}, month = {2010 Dec 22}, pages = {191-6}, abstract = {

In the mouse, each class of olfactory receptor neurons expressing a given odorant receptor has convergent axonal projections to two specific glomeruli in the olfactory bulb, thereby creating an odour map. However, it is unclear how this map is represented in the olfactory cortex. Here we combine rabies-virus-dependent retrograde mono-trans-synaptic labelling with genetics to control the location, number and type of {\textquoteright}starter{\textquoteright} cortical neurons, from which we trace their presynaptic neurons. We find that individual cortical neurons receive input from multiple mitral cells representing broadly distributed glomeruli. Different cortical areas represent the olfactory bulb input differently. For example, the cortical amygdala preferentially receives dorsal olfactory bulb input, whereas the piriform cortex samples the whole olfactory bulb without obvious bias. These differences probably reflect different functions of these cortical areas in mediating innate odour preference or associative memory. The trans-synaptic labelling method described here should be widely applicable to mapping connections throughout the mouse nervous system.

}, issn = {1476-4687}, doi = {10.1038/nature09714}, author = {Miyamichi, Kazunari and Amat, Fernando and Moussavi, Farshid and Wang, Chen and Wickersham, Ian and Wall, Nicholas R and Taniguchi, Hiroki and Tasic, Bosiljka and Huang, Z Josh and He, Zhigang and Callaway, Edward M and Horowitz, Mark A and Luo, Liqun} } @article {68825, title = {Dermal morphogenesis controls lateral line patterning during postembryonic development of teleost fish}, journal = {Developmental Biology}, volume = {340}, year = {2010}, month = {04/2010}, pages = {583-594}, abstract = {

The lateral line system displays highly divergent patterns in adult teleost fish. The mechanisms underlying this variability are poorly understood. Here, we demonstrate that the lateral line mechanoreceptor, the neuromast, gives rise to a series of accessory neuromasts by a serial budding process during postembryonic development in zebrafish. We also show that accessory neuromast formation is highly correlated to the development of underlying dermal structures such as bones and scales. Abnormalities in opercular bone morphogenesis, in endothelin 1-knockdown embryos, are accompanied by stereotypic errors in neuromast budding and positioning, further demonstrating the tight correlation between the patterning of neuromasts and of the underlying dermal bones. In medaka, where scales form between peridermis and opercular bones, the lateral line displays a scale-specific pattern which is never observed in zebrafish. These results strongly suggest a control of postembryonic neuromast patterns by underlying dermal structures. This dermal control may explain some aspects of the evolution of lateral line patterns.

}, keywords = {Dermal bone, Lateral line, Medaka, Neuromast, Opercle, Postembryonic development, Scale, Zebrafish}, issn = {0012-1606}, doi = {https://doi.org/10.1016/j.ydbio.2010.02.017}, url = {https://www.sciencedirect.com/science/article/pii/S0012160610001028}, author = {Hironori Wada and Alain Ghysen and Chie Satou and Shin-ichi Higashijima and Koichi Kawakami and Satoshi Hamaguchi and Mitsuru Sakaizumi} } @article {2493, title = {Developmental expression of mRNAs for epidermal and fat body proteins and hormonally regulated transcription factors in the tobacco hornworm, Manduca sexta.}, journal = {Journal of Insect Physiology}, volume = {56}, year = {2010}, month = {2010 Oct}, pages = {1390-5}, abstract = {

This paper provides a compilation of diagrammatic representations of the expression profiles of epidermal and fat body mRNAs during the last two larval instars and metamorphosis of the tobacco hornworm, Manduca sexta. Included are those encoding insecticyanin, three larval cuticular proteins, dopa decarboxylase, moling, and the juvenile hormone-binding protein JP29 produced by the dorsal abdominal epidermis, and arylphorin and the methionine-rich storage proteins made by the fat body. The mRNA profiles of the ecdysteroid-regulated cascade of transcription factors in the epidermis during the larval molt and the onset of metamorphosis and in the pupal wing during the onset of adult development are also shown. These profiles are accompanied by a brief summary of the current knowledge about the regulation of these mRNAs by ecdysteroids and juvenile hormone based on experimental manipulations, both in vivo and in vitro.

}, keywords = {Animals, Developmental, Epidermis, Fat Body, Gene Expression Regulation, Insect Hormones, Insect Proteins, Manduca, Messenger, RNA, Transcription Factors}, issn = {1879-1611}, doi = {10.1016/j.jinsphys.2010.03.029}, author = {Hiruma, Kiyoshi and Riddiford, Lynn M} } @article {65010, title = {Development-based compartmentalization of the Drosophila central brain.}, journal = {J Comp Neurol}, volume = {518}, year = {2010}, month = {2010 Aug 01}, pages = {2996-3023}, abstract = {

The neuropile of the Drosophila brain is subdivided into anatomically discrete compartments. Compartments are rich in terminal neurite branching and synapses; they are the neuropile domains in which signal processing takes place. Compartment boundaries are defined by more or less dense layers of glial cells as well as long neurite fascicles. These fascicles are formed during the larval period, when the approximately 100 neuronal lineages that constitute the Drosophila central brain differentiate. Each lineage forms an axon tract with a characteristic trajectory in the neuropile; groups of spatially related tracts congregate into the brain fascicles that can be followed from the larva throughout metamorphosis into the adult stage. Here we provide a map of the adult brain compartments and the relevant fascicles defining compartmental boundaries. We have identified the neuronal lineages contributing to each fascicle, which allowed us to compare compartments of the larval and adult brain directly. Most adult compartments can be recognized already in the early larval brain, where they form a "protomap" of the later adult compartments. Our analysis highlights the morphogenetic changes shaping the Drosophila brain; the data will be important for studies that link early-acting genetic mechanisms to the adult neuronal structures and circuits controlled by these mechanisms.

}, keywords = {Animals, Antibodies, Monoclonal, Axons, Brain, Brain Mapping, Cadherins, Chemokine CX3CL1, Drosophila, Image Processing, Computer-Assisted, Immunohistochemistry, Larva, Neural Pathways, Neuroglia, Synapses}, issn = {1096-9861}, doi = {10.1002/cne.22376}, author = {Pereanu, Wayne and Kumar, Abilasha and Jennett, Arnim and Reichert, Heinrich and Hartenstein, Volker} } @article {2784, title = {Direct detection of benzene, toluene, and ethylbenzene at trace levels in ambient air by atmospheric pressure chemical ionization using a handheld mass spectrometer.}, journal = {Journal of the American Society for Mass Spectrometry}, volume = {21}, year = {2010}, month = {2010 Jan}, pages = {132-5}, abstract = {

The capabilities of a portable mass spectrometer for real-time monitoring of trace levels of benzene, toluene, and ethylbenzene in air are illustrated. An atmospheric pressure interface was built to implement atmospheric pressure chemical ionization for direct analysis of gas-phase samples on a previously described miniature mass spectrometer (Gao et al. Anal. Chem.2006, 78, 5994-6002). Linear dynamic ranges, limits of detection and other analytical figures of merit were evaluated: for benzene, a limit of detection of 0.2 parts-per-billion was achieved for air samples without any sample preconcentration. The corresponding limits of detection for toluene and ethylbenzene were 0.5 parts-per-billion and 0.7 parts-per-billion, respectively. These detection limits are well below the compounds{\textquoteright} permissible exposure levels, even in the presence of added complex mixtures of organics at levels exceeding the parts-per-million level. The linear dynamic ranges of benzene, toluene, and ethylbenzene are limited to approximately two orders of magnitude by saturation of the detection electronics.

}, keywords = {Air, Atmospheric Pressure, Benzene, Benzene Derivatives, Equipment Design, Ions, Limit of Detection, Mass Spectrometry, Toluene}, issn = {1879-1123}, doi = {10.1364/AO.50.001792}, author = {Huang, Guangming and Gao, Liang and Duncan, Jason and Harper, Jason D and Sanders, Nathaniel L and Ouyang, Zheng and Cooks, R Graham} } @article {4408, title = {Dynamics of genome evolution in facultative symbionts of aphids.}, journal = {Environmental Microbiology}, volume = {12}, year = {2010}, month = {2010 Aug}, pages = {2060-9}, abstract = {

Aphids are sap-feeding insects that host a range of bacterial endosymbionts including the obligate, nutritional mutualist Buchnera plus several bacteria that are not required for host survival. Among the latter, {\textquoteright}Candidatus Regiella insecticola{\textquoteright} and {\textquoteright}Candidatus Hamiltonella defensa{\textquoteright} are found in pea aphids and other hosts and have been shown to protect aphids from natural enemies. We have sequenced almost the entire genome of R. insecticola (2.07 Mbp) and compared it with the recently published genome of H. defensa (2.11 Mbp). Despite being sister species the two genomes are highly rearranged and the genomes only have \~{}55\% of genes in common. The functions encoded by the shared genes imply that the bacteria have similar metabolic capabilities, including only two essential amino acid biosynthetic pathways and active uptake mechanisms for the remaining eight, and similar capacities for host cell toxicity and invasion (type 3 secretion systems and RTX toxins). These observations, combined with high sequence divergence of orthologues, strongly suggest an ancient divergence after establishment of a symbiotic lifestyle. The divergence in gene sets and in genome architecture implies a history of rampant recombination and gene inactivation and the ongoing integration of mobile DNA (insertion sequence elements, prophage and plasmids).

}, keywords = {Animals, Aphids, Bacterial, Comparative Genomic Hybridization, DNA, Enterobacteriaceae, Evolution, Genome, Genomic Islands, Molecular, Molecular Sequence Data, Phylogeny, Sequence Analysis, Symbiosis}, issn = {1462-2920}, doi = {10.1111/j.1462-2920.2009.02085.x}, author = {Degnan, Patrick H and Leonardo, Teresa E and Cass, Bodil N and Hurwitz, Bonnie and Stern, David and Gibbs, Richard A and Richards, Stephen and Moran, Nancy A} } @article {3634, title = {An engineered DNA-binding protein self-assembles metallic nanostructures.}, journal = {Chembiochem: A European Journal of Chemical Biology}, volume = {11}, year = {2010}, month = {2010 Oct 18}, pages = {2108-12}, abstract = {

The golden age of DNA: We describe a strategy for engineering bifunctional proteins that simultaneously associate with metals and DNA to create self-assembled nanostructures. A DNA binding protein engineered with a gold binding peptide arranges colloidal gold particles along a DNA guide by virtue of its introduced peptide motif. These self-assembled complexes represent a step toward constructing nanoarchitectures with potential in nanoelectronic and photonic devices.

}, keywords = {Amino Acid Sequence, DNA, DNA Helicases, Escherichia coli Proteins, Gold, Nanostructures, Nucleic Acid Conformation, Peptide Library, Peptides, Protein Binding, Protein Engineering, Single-Stranded}, issn = {1439-7633}, doi = {10.1002/cbic.201000407}, author = {Hall Sedlak, Ruth and Hnilova, Marketa and Gachelet, Eliora and Przybyla, Laralynne and Dranow, David and Gonen, Tamir and Sarikaya, Mehmet and Tamerler, Candan and Traxler, Beth} } @article {65007, title = {Ephus: multipurpose data acquisition software for neuroscience experiments.}, journal = {Front Neural Circuits}, volume = {4}, year = {2010}, month = {2010}, pages = {100}, abstract = {

Physiological measurements in neuroscience experiments often involve complex stimulus paradigms and multiple data channels. Ephus (http://www.ephus.org) is an open-source software package designed for general-purpose data acquisition and instrument control. Ephus operates as a collection of modular programs, including an ephys program for standard whole-cell recording with single or multiple electrodes in typical electrophysiological experiments, and a mapper program for synaptic circuit mapping experiments involving laser scanning photostimulation based on glutamate uncaging or channelrhodopsin-2 excitation. Custom user functions allow user-extensibility at multiple levels, including on-line analysis and closed-loop experiments, where experimental parameters can be changed based on recently acquired data, such as during in vivo behavioral experiments. Ephus is compatible with a variety of data acquisition and imaging hardware. This paper describes the main features and modules of Ephus and their use in representative experimental applications.

}, issn = {1662-5110}, doi = {10.3389/fncir.2010.00100}, author = {Suter, Benjamin A and O{\textquoteright}Connor, Timothy and Iyer, Vijay and Petreanu, Leopoldo T and Hooks, Bryan M and Kiritani, Taro and Svoboda, Karel and Shepherd, Gordon M G} } @article {2326, title = {Error tolerant indexing and alignment of short reads with covering template families.}, journal = {Journal of Computational Biology: A Journal of Computational Molecular Cell Biology}, volume = {17}, year = {2010}, month = {2010 Oct}, pages = {1397-1411}, abstract = {

The rapid adoption of high-throughput next generation sequence data in biological research is presenting a major challenge for sequence alignment tools{\textemdash}specifically, the efficient alignment of vast amounts of short reads to large references in the presence of differences arising from sequencing errors and biological sequence variations. To address this challenge, we developed a short read aligner for high-throughput sequencer data that is tolerant of errors or mutations of all types{\textemdash}namely, substitutions, deletions, and insertions. The aligner utilizes a multi-stage approach in which template-based indexing is used to identify candidate regions for alignment with dynamic programming. A template is a pair of gapped seeds, with one used with the read and one used with the reference. In this article, we focus on the development of template families that yield error-tolerant indexing up to a given error-budget. A general algorithm for finding those families is presented, and a recursive construction that creates families with higher error tolerance from ones with a lower error tolerance is developed.

}, keywords = {Algorithms, Base Sequence, DNA, Genetic, Molecular Sequence Data, Sequence Alignment, Sequence Analysis, Software, Templates}, issn = {1557-8666}, doi = {10.1089/cmb.2010.0005}, author = {Giladi, Eldar and Healy, John and Myers, Gene and Hart, Chris and Kapranov, Philipp and Lipson, Doron and Roels, Steve and Thayer, Edward and Letovsky, Stan} } @article {46619, title = {Ethanol-regulated genes that contribute to ethanol sensitivity and rapid tolerance in Drosophila.}, journal = {Alcoholism, Clinical and Experimental Research}, volume = {34}, year = {2010}, month = {2010 Feb}, pages = {302-16}, abstract = {

BACKGROUND: Increased ethanol intake, a major predictor for the development of alcohol use disorders, is facilitated by the development of tolerance to both the aversive and pleasurable effects of the drug. The molecular mechanisms underlying ethanol tolerance development are complex and are not yet well understood.

METHODS: To identify genetic mechanisms that contribute to ethanol tolerance, we examined the time course of gene expression changes elicited by a single sedating dose of ethanol in Drosophila, and completed a behavioral survey of strains harboring mutations in ethanol-regulated genes.

RESULTS: Enrichment for genes in metabolism, nucleic acid binding, olfaction, regulation of signal transduction, and stress suggests that these biological processes are coordinately affected by ethanol exposure. We also detected a coordinate up-regulation of genes in the Toll and Imd innate immunity signal transduction pathways. A multi-study comparison revealed a small set of genes showing similar regulation, including increased expression of 3 genes for serine biosynthesis. A survey of Drosophila strains harboring mutations in ethanol-regulated genes for ethanol sensitivity and tolerance phenotypes revealed roles for serine biosynthesis, olfaction, transcriptional regulation, immunity, and metabolism. Flies harboring deletions of the genes encoding the olfactory co-receptor Or83b or the sirtuin Sir2 showed marked changes in the development of ethanol tolerance.

CONCLUSIONS: Our findings implicate novel roles for these genes in regulating ethanol behavioral responses.

}, keywords = {Animals, Behavior, Animal, Central Nervous System Depressants, Coenzyme A Ligases, Drosophila, Drosophila Proteins, Drug Tolerance, Ethanol, Female, Gene Expression Regulation, Histone Deacetylases, Male, Motor Activity, Mutation, Oligonucleotide Array Sequence Analysis, Receptors, Odorant, Reverse Transcriptase Polymerase Chain Reaction, Serpins, Sirtuins, Species Specificity}, issn = {1530-0277}, doi = {10.1111/j.1530-0277.2009.01093.x}, author = {Kong, Eric C and Allouche, Lorien and Chapot, Paul A and Vranizan, Karen and Moore, Monica S and Heberlein, Ulrike and Wolf, Fred W} } @article {2955, title = {Fast live simultaneous multiwavelength four-dimensional optical microscopy.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, year = {2010}, month = {2010 Sep 14}, pages = {16016-22}, abstract = {

Live fluorescence microscopy has the unique capability to probe dynamic processes, linking molecular components and their localization with function. A key goal of microscopy is to increase spatial and temporal resolution while simultaneously permitting identification of multiple specific components. We demonstrate a new microscope platform, OMX, that enables subsecond, multicolor four-dimensional data acquisition and also provides access to subdiffraction structured illumination imaging. Using this platform to image chromosome movement during a complete yeast cell cycle at one 3D image stack per second reveals an unexpected degree of photosensitivity of fluorophore-containing cells. To avoid perturbation of cell division, excitation levels had to be attenuated between 100 and 10,000{\texttimes} below the level normally used for imaging. We show that an image denoising algorithm that exploits redundancy in the image sequence over space and time allows recovery of biological information from the low light level noisy images while maintaining full cell viability with no fading.

}, keywords = {Algorithms, Animals, Cell Survival, Drosophila melanogaster, Fluorescence, Microscopy, Saccharomyces cerevisiae, Software}, issn = {1091-6490}, doi = {10.1073/pnas.1004037107}, author = {Carlton, Peter M and Boulanger, J{\'e}r{\^o}me and Kervrann, Charles and Sibarita, Jean-Baptiste and Salamero, Jean and Gordon-Messer, Susannah and Bressan, Debra and Haber, James E and Haase, Sebastian and Shao, Lin and Winoto, Lukman and Matsuda, Atsushi and Kner, Peter and Uzawa, Satoru and Gustafsson, Mats and Kam, Zvi and Agard, David A and Sedat, John W} } @article {3931, title = {Functional imaging of hippocampal place cells at cellular resolution during virtual navigation.}, journal = {Nature Neuroscience}, volume = {13}, year = {2010}, month = {2010 Nov}, pages = {1433-40}, abstract = {

Spatial navigation is often used as a behavioral task in studies of the neuronal circuits that underlie cognition, learning and memory in rodents. The combination of in vivo microscopy with genetically encoded indicators has provided an important new tool for studying neuronal circuits, but has been technically difficult to apply during navigation. Here we describe methods for imaging the activity of neurons in the CA1 region of the hippocampus with subcellular resolution in behaving mice. Neurons that expressed the genetically encoded calcium indicator GCaMP3 were imaged through a chronic hippocampal window. Head-restrained mice performed spatial behaviors in a setup combining a virtual reality system and a custom-built two-photon microscope. We optically identified populations of place cells and determined the correlation between the location of their place fields in the virtual environment and their anatomical location in the local circuit. The combination of virtual reality and high-resolution functional imaging should allow a new generation of studies to investigate neuronal circuit dynamics during behavior.

}, keywords = {Action Potentials, Animals, Calcium, Cerebral Cortex, Computer-Assisted, Dendrites, Genetic, Hippocampus, Image Processing, Inbred C57BL, Male, Membrane Potentials, Mice, Neurons, Nonlinear Dynamics, Patch-Clamp Techniques, Space Perception, Spatial Behavior, Synapsins, Transduction, User-Computer Interface}, issn = {1546-1726}, doi = {10.1038/nn.2648}, author = {Dombeck, Daniel A and Harvey, Christopher D and Tian, Lin and Looger, Loren L and Tank, David W} } @article {5691, title = {A high-level 3D visualization API for Java and ImageJ.}, journal = {BMC Bioinformatics}, volume = {11}, year = {2010}, month = {2010}, pages = {274}, abstract = {

Current imaging methods such as Magnetic Resonance Imaging (MRI), Confocal microscopy, Electron Microscopy (EM) or Selective Plane Illumination Microscopy (SPIM) yield three-dimensional (3D) data sets in need of appropriate computational methods for their analysis. The reconstruction, segmentation and registration are best approached from the 3D representation of the data set.

}, keywords = {Automated, Computer Graphics, Computer-Assisted, Confocal, Image Interpretation, Imaging, Microscopy, Pattern Recognition, Programming Languages, Software, Three-Dimensional}, issn = {1471-2105}, doi = {10.1186/1471-2105-11-274}, author = {Schmid, Benjamin and Schindelin, Johannes and Cardona, Albert and Longair, Mark and Heisenberg, Martin.} } @article {5689, title = {Identifying neuronal lineages of Drosophila by sequence analysis of axon tracts.}, journal = {The Journal of Neuroscience}, volume = {30}, year = {2010}, month = {2010 Jun 2}, pages = {7538-53}, abstract = {

The Drosophila brain is formed by an invariant set of lineages, each of which is derived from a unique neural stem cell (neuroblast) and forms a genetic and structural unit of the brain. The task of reconstructing brain circuitry at the level of individual neurons can be made significantly easier by assigning neurons to their respective lineages. In this article we address the automation of neuron and lineage identification. We focused on the Drosophila brain lineages at the larval stage when they form easily recognizable secondary axon tracts (SATs) that were previously partially characterized. We now generated an annotated digital database containing all lineage tracts reconstructed from five registered wild-type brains, at higher resolution and including some that were previously not characterized. We developed a method for SAT structural comparisons based on a dynamic programming approach akin to nucleotide sequence alignment and a machine learning classifier trained on the annotated database of reference SATs. We quantified the stereotypy of SATs by measuring the residual variability of aligned wild-type SATs. Next, we used our method for the identification of SATs within wild-type larval brains, and found it highly accurate (93-99\%). The method proved highly robust for the identification of lineages in mutant brains and in brains that differed in developmental time or labeling. We describe for the first time an algorithm that quantifies neuronal projection stereotypy in the Drosophila brain and use the algorithm for automatic neuron and lineage recognition.

}, keywords = {Algorithms, Animals, Automatic Data Processing, Axons, Brain, Brain Mapping, Caspase 3, Cell Lineage, Computer-Assisted, Confocal, Dendrites, Drosophila, Drosophila Proteins, Embryo, Genetically Modified, Green Fluorescent Proteins, Image Processing, Microscopy, Models, Neurological, Neurons, Nonmammalian, Reproducibility of Results, Software}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0186-10.2010}, author = {Cardona, Albert and Saalfeld, Stephan and Arganda, Ignacio and Pereanu, Wayne and Schindelin, Johannes and Hartenstein, Volker.} } @article {48167, title = {Improving deformable surface meshes through omni-directional displacements and MRFs.}, journal = {Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention}, volume = {13}, year = {2010}, month = {2010}, pages = {227-34}, abstract = {

Deformable surface models are often represented as triangular meshes in image segmentation applications. For a fast and easily regularized deformation onto the target object boundary, the vertices of the mesh are commonly moved along line segments (typically surface normals). However, in case of high mesh curvature, these lines may intersect with the target boundary at "non-corresponding" positions, or even not at all. Consequently, certain deformations cannot be achieved. We propose an approach that allows each vertex to move not only along a line segment, but within a surrounding sphere. We achieve globally regularized deformations via Markov Random Field optimization. We demonstrate the potential of our approach with experiments on synthetic data, as well as an evaluation on 2 x 106 coronoid processes of the mandible in Cone-Beam CTs, and 56 coccyxes (tailbones) in low-resolution CTs.

}, keywords = {Algorithms, Computer Simulation, Cone-Beam Computed Tomography, Finite Element Analysis, Humans, Imaging, Three-Dimensional, Models, Biological, Radiographic Image Enhancement, Radiographic Image Interpretation, Computer-Assisted, Reproducibility of Results, Sensitivity and Specificity}, author = {Kainmueller, D and Lamecker, H and Seim, H and Zachow, S and Hege, H C} } @article {1245, title = {Increasing depth resolution of electron microscopy of neural circuits using sparse tomographic reconstruction.}, journal = {Computer Vision and Pattern Recognition (CVPR)}, year = {2010}, month = {2010}, pages = {1767-74}, issn = {1063-6919}, doi = {10.1109/CVPR.2010.5539846}, author = {Veeraraghavan, Ashok and Genkin, Alex V and Vitaladevuni, Shiv and Scheffer, Lou and Xu, CShan and Hess, Harald and Fetter, Richard and Cantoni, Marco and Knott, Graham and Chklovskii, Dmitri B} } @article {5687, title = {An integrated micro- and macroarchitectural analysis of the Drosophila brain by computer-assisted serial section electron microscopy.}, journal = {PLoS Biology}, volume = {8}, year = {2010}, month = {2010}, abstract = {

The analysis of microcircuitry (the connectivity at the level of individual neuronal processes and synapses), which is indispensable for our understanding of brain function, is based on serial transmission electron microscopy (TEM) or one of its modern variants. Due to technical limitations, most previous studies that used serial TEM recorded relatively small stacks of individual neurons. As a result, our knowledge of microcircuitry in any nervous system is very limited. We applied the software package TrakEM2 to reconstruct neuronal microcircuitry from TEM sections of a small brain, the early larval brain of Drosophila melanogaster. TrakEM2 enables us to embed the analysis of the TEM image volumes at the microcircuit level into a light microscopically derived neuro-anatomical framework, by registering confocal stacks containing sparsely labeled neural structures with the TEM image volume. We imaged two sets of serial TEM sections of the Drosophila first instar larval brain neuropile and one ventral nerve cord segment, and here report our first results pertaining to Drosophila brain microcircuitry. Terminal neurites fall into a small number of generic classes termed globular, varicose, axiform, and dendritiform. Globular and varicose neurites have large diameter segments that carry almost exclusively presynaptic sites. Dendritiform neurites are thin, highly branched processes that are almost exclusively postsynaptic. Due to the high branching density of dendritiform fibers and the fact that synapses are polyadic, neurites are highly interconnected even within small neuropile volumes. We describe the network motifs most frequently encountered in the Drosophila neuropile. Our study introduces an approach towards a comprehensive anatomical reconstruction of neuronal microcircuitry and delivers microcircuitry comparisons between vertebrate and insect neuropile.

}, keywords = {Animals, Brain, Computer-Assisted, Drosophila melanogaster, Electron, Humans, Image Processing, Imaging, Microscopy, Neurons, Neuropil, Software, Synapses, Three-Dimensional, Transmission}, issn = {1545-7885}, doi = {10.1371/journal.pbio.1000502}, author = {Cardona, Albert and Saalfeld, Stephan and Preibisch, Stephan and Schmid, Benjamin and Cheng, Anchi and Pulokas, Jim and Tomancak, Pavel and Hartenstein, Volker.} } @article {6346, title = {IP3 receptor sensitization during in vivo amphetamine experience enhances NMDA receptor plasticity in dopamine neurons of the ventral tegmental area.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {30}, year = {2010}, month = {2010 May 12}, pages = {6689-99}, abstract = {

Synaptic plasticity in the mesolimbic dopamine (DA) system is critically involved in reward-based conditioning and the development of drug addiction. Ca2+ signals triggered by postsynaptic action potentials (APs) drive the induction of synaptic plasticity in the CNS. However, it is not clear how AP-evoked Ca2+ signals and the resulting synaptic plasticity are altered during in vivo exposure to drugs of abuse. We have recently described long-term potentiation (LTP) of NMDA receptor (NMDAR)-mediated transmission onto DA neurons that is induced in a manner dependent on bursts of APs. LTP induction requires amplification of burst-evoked Ca2+ signals by preceding activation of metabotropic glutamate receptors (mGluRs) generating inositol 1,4,5-trisphosphate (IP3). In this study, using brain slices prepared from male rats, we show that repeated in vivo exposure to the psychostimulant amphetamine (5 mg/kg, i.p., 3-7 d) upregulates mGluR-dependent facilitation of burst-evoked Ca2+ signals in DA neurons of the ventral tegmental area (VTA). Protein kinase A (PKA)-induced sensitization of IP3 receptors mediates this upregulation of mGluR action. As a consequence, NMDAR-mediated transmission becomes more susceptible to LTP induction after repeated amphetamine exposure. We have also found that the magnitude of amphetamine-conditioned place preference (CPP) in behaving rats correlates with the magnitude of mGluR-dependent Ca2+ signal facilitation measured in VTA slices prepared from these rats. Furthermore, the development of amphetamine CPP is significantly attenuated by intra-VTA infusion of the PKA inhibitor H89. We propose that enhancement of mGluR-dependent NMDAR plasticity in the VTA may promote the learning of environmental stimuli repeatedly associated with amphetamine experience.

}, keywords = {4, 5-Trisphosphate Receptors, Amphetamine, Animals, Calcium, Central Nervous System Stimulants, Classical, Conditioning, Cyclic AMP-Dependent Protein Kinases, Dopamine, Inositol 1, Isoquinolines, Long-Term Potentiation, Male, N-Methyl-D-Aspartate, Neurons, Protein Kinase Inhibitors, Rats, Receptors, Space Perception, Sprague-Dawley, Sulfonamides, Synaptic Transmission, Ventral Tegmental Area}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4453-09.2010}, author = {Ahn, Kee-Chan and Bernier, Brian E and Harnett, Mark T and Morikawa, Hitoshi} } @article {4288, title = {Learning-related fine-scale specificity imaged in motor cortex circuits of behaving mice.}, journal = {Nature}, volume = {464}, year = {2010}, month = {2010 Apr 22}, pages = {1182-6}, abstract = {

Cortical neurons form specific circuits, but the functional structure of this microarchitecture and its relation to behaviour are poorly understood. Two-photon calcium imaging can monitor activity of spatially defined neuronal ensembles in the mammalian cortex. Here we applied this technique to the motor cortex of mice performing a choice behaviour. Head-fixed mice were trained to lick in response to one of two odours, and to withhold licking for the other odour. Mice routinely showed significant learning within the first behavioural session and across sessions. Microstimulation and trans-synaptic tracing identified two non-overlapping candidate tongue motor cortical areas. Inactivating either area impaired voluntary licking. Imaging in layer 2/3 showed neurons with diverse response types in both areas. Activity in approximately half of the imaged neurons distinguished trial types associated with different actions. Many neurons showed modulation coinciding with or preceding the action, consistent with their involvement in motor control. Neurons with different response types were spatially intermingled. Nearby neurons (within approximately 150 mum) showed pronounced coincident activity. These temporal correlations increased with learning within and across behavioural sessions, specifically for neuron pairs with similar response types. We propose that correlated activity in specific ensembles of functionally related neurons is a signature of learning-related circuit plasticity. Our findings reveal a fine-scale and dynamic organization of the frontal cortex that probably underlies flexible behaviour.

}, keywords = {Animal, Animals, Axonal Transport, Behavior, Chemical, Choice Behavior, Inbred C57BL, Learning, Male, Mice, Motor Cortex, Motor Neurons, Neural Pathways, Odors, Pyramidal Cells, Reward, Stimulation, Time Factors, Tongue}, issn = {1476-4687}, doi = {10.1038/nature08897}, author = {Komiyama, Takaki and Sato, Takashi R and O{\textquoteright}Connor, Daniel H and Zhang, Ying-Xin and Huber, Daniel and Hooks, Bryan M and Gabitto, Mariano and Svoboda, Karel} } @article {5367, title = {Lineage-based connectivity map of the Drosophila brain.}, journal = {Journal of Neurogenetics}, volume = {24}, year = {2010}, month = {2010}, pages = {79}, author = {Hartenstein, Volker and Pereanu, Wayne and Truman, Jim and Cardona, Albert} } @article {46616, title = {Lmo4 in the nucleus accumbens regulates cocaine sensitivity.}, journal = {Genes, Brain, and Behavior}, volume = {9}, year = {2010}, month = {2010 Oct}, pages = {817-24}, abstract = {

An estimated 2 million Americans use cocaine, resulting in large personal and societal costs. Discovery of the genetic factors that contribute to cocaine abuse is important for understanding this complex disease. Previously, mutations in the Drosophila LIM-only (dLmo) gene were identified because of their increased behavioral sensitivity to cocaine. Here we show that the mammalian homolog Lmo4, which is highly expressed in brain regions implicated in drug addiction, plays a similar role in cocaine-induced behaviors. Mice with a global reduction in Lmo4 levels show increased sensitivity to the locomotor stimulatory effects of cocaine upon chronic cocaine administration. This effect is reproduced with downregulation of Lmo4 in the nucleus accumbens by RNA interference. Thus, Lmo genes play conserved roles in regulating the behavioral effects of cocaine in invertebrate and mammalian models of drug addiction.

}, keywords = {Adaptor Proteins, Signal Transducing, Animals, Behavior, Animal, beta-Galactosidase, Cells, Cultured, Cloning, Molecular, Cocaine, Dendritic Spines, Dopamine Uptake Inhibitors, Gene Expression, Homeodomain Proteins, Immunohistochemistry, Lentivirus, LIM Domain Proteins, Male, Mice, Mice, Inbred C57BL, Microdissection, Motor Activity, Mutagenesis, Insertional, Nucleus Accumbens, Reverse Transcriptase Polymerase Chain Reaction, RNA, RNA Interference, Stereotaxic Techniques, Transcription Factors}, issn = {1601-183X}, doi = {10.1111/j.1601-183X.2010.00620.x}, author = {Lasek, A W and Kapfhamer, D and Kharazia, V and Gesch, J and Giorgetti, F and Heberlein, U} } @article {2290, title = {Malaria severity and human nitric oxide synthase type 2 (NOS2) promoter haplotypes.}, journal = {Human Genetics}, volume = {127}, year = {2010}, month = {2010 Feb}, pages = {163-82}, abstract = {

Nitric oxide (NO) mediates host resistance to severe malaria and other infectious diseases. NO production and mononuclear cell expression of the NO producing enzyme-inducible nitric oxide synthase (NOS2) have been associated with protection from severe falciparum malaria. The purpose of this study was to identify single nucleotide polymorphisms (SNPs) and haplotypes in the NOS2 promoter, to identify associations of these haplotypes with malaria severity and to test the effects of these polymorphisms on promoter activity. We identified 34 SNPs in the proximal 7.3 kb region of the NOS2 promoter and inferred NOS2 promoter haplotypes based on genotyping 24 of these SNPs in a population of Tanzanian children with and without cerebral malaria. We identified 71 haplotypes; 24 of these haplotypes comprised 82\% of the alleles. We determined whether NOS2 promoter haplotypes were associated with malaria severity in two groups of subjects from Dar es Salaam (N = 185 and N = 250) and in an inception cohort of children from Muheza-Tanga, Tanzania (N = 883). We did not find consistent associations of NOS2 promoter haplotypes with malaria severity or malarial anemia, although interpretation of these results was potentially limited by the sample size of each group. Furthermore, cytokine-induced NOS2 promoter activity determined using luciferase reporter constructs containing the proximal 7.3 kb region of the NOS2 promoter and the G-954C or C-1173T SNPs did not differ from NOS2 promoter constructs that lacked these polymorphisms. Taken together, these studies suggest that the relationship between NOS2 promoter polymorphisms and malaria severity is more complex than previously described.

}, keywords = {Alleles, Base Sequence, Cell Line, Child, DNA, Gene Frequency, Genetic, Genetic Heterogeneity, Genotype, Haplotypes, Humans, Infant, Kenya, Linkage Disequilibrium, Malaria, Molecular Sequence Data, Mutation, Nitric Oxide Synthase Type II, Nucleic Acid, Polymorphism, Preschool, Promoter Regions, Sequence Analysis, Sequence Homology, Severity of Illness Index, Single Nucleotide, Tanzania, Tumor}, issn = {1432-1203}, doi = {10.1007/s00439-009-0753-3}, author = {Levesque, Marc C and Hobbs, Maurine R and O{\textquoteright}Loughlin, Charles W and Chancellor, Jennifer A and Chen, Youwei and Tkachuk, Ariana N and Booth, Jennifer and Patch, Kistie B and Allgood, Sallie and Pole, Ann R and Fernandez, Carolyn A and Mwaikambo, Esther D and Mutabingwa, Theonest K and Fried, Michal and Sorensen, Bess and Duffy, Patrick E and Granger, Donald L and Anstey, Nicholas M and Weinberg, J Brice} } @article {47681, title = {Mitochondria supply membranes for autophagosome biogenesis during starvation.}, journal = {Cell}, volume = {141}, year = {2010}, month = {2010 May 14}, pages = {656-67}, abstract = {

Starvation-induced autophagosomes engulf cytosol and/or organelles and deliver them to lysosomes for degradation, thereby resupplying depleted nutrients. Despite advances in understanding the molecular basis of this process, the membrane origin of autophagosomes remains unclear. Here, we demonstrate that, in starved cells, the outer membrane of mitochondria participates in autophagosome biogenesis. The early autophagosomal marker, Atg5, transiently localizes to punctae on mitochondria, followed by the late autophagosomal marker, LC3. The tail-anchor of an outer mitochondrial membrane protein also labels autophagosomes and is sufficient to deliver another outer mitochondrial membrane protein, Fis1, to autophagosomes. The fluorescent lipid NBD-PS (converted to NBD-phosphotidylethanolamine in mitochondria) transfers from mitochondria to autophagosomes. Photobleaching reveals membranes of mitochondria and autophagosomes are transiently shared. Disruption of mitochondria/ER connections by mitofusin2 depletion dramatically impairs starvation-induced autophagy. Mitochondria thus play a central role in starvation-induced autophagy, contributing membrane to autophagosomes.

}, keywords = {Animals, Cell Line, Cell Physiological Phenomena, Culture Media, Membrane Proteins, Mitochondria, Mitochondrial Membranes, Mitochondrial Proteins, Phagosomes, Rats}, issn = {1097-4172}, doi = {10.1016/j.cell.2010.04.009}, author = {Hailey, Dale W and Rambold, Angelika S and Satpute-Krishnan, Prasanna and Mitra, Kasturi and Sougrat, Rachid and Kim, Peter K and Lippincott-Schwartz, Jennifer} } @article {2677, title = {Molecular mechanisms of corticosteroid synergy with thyroid hormone during tadpole metamorphosis.}, journal = {General and Comparative Endocrinology}, volume = {168}, year = {2010}, month = {2010 Sep 1}, pages = {209-19}, abstract = {

Corticosteroids (CS) act synergistically with thyroid hormone (TH) to accelerate amphibian metamorphosis. Earlier studies showed that CS increase nuclear 3,5,3{\textquoteright}-triiodothyronine (T(3)) binding capacity in tadpole tail, and 5{\textquoteright} deiodinase activity in tadpole tissues, increasing the generation of T(3) from thyroxine (T(4)). In the present study we investigated CS synergy with TH by analyzing expression of key genes involved in TH and CS signaling using tadpole tail explant cultures, prometamorphic tadpoles, and frog tissue culture cells (XTC-2 and XLT-15). Treatment of tail explants with T(3) at 100 nM, but not at 10 nM caused tail regression. Corticosterone (CORT) at three doses (100, 500 and 3400 nM) had no effect or increased tail size. T(3) at 10 nM plus CORT caused tails to regress similar to 100 nM T(3). Thyroid hormone receptor beta (TRbeta) mRNA was synergistically upregulated by T(3) plus CORT in tail explants, tail and brain in vivo, and tissue culture cells. The activating 5{\textquoteright} deiodinase type 2 (D2) mRNA was induced by T(3) and CORT in tail explants and tail in vivo. Thyroid hormone increased expression of glucocorticoid (GR) and mineralocorticoid receptor (MR) mRNAs. Our findings support that the synergistic actions of TH and CS in metamorphosis occur at the level of expression of genes for TRbeta and D2, enhancing tissue sensitivity to TH. Concurrently, TH enhances tissue sensitivity to CS by upregulating GR and MR. Environmental stressors can modulate the timing of tadpole metamorphosis in part by CS enhancing the response of tadpole tissues to the actions of TH.

}, keywords = {Adrenal Cortex Hormones, Animals, Biological, Cell Line, Drug Synergism, Larva, Metamorphosis, Reverse Transcriptase Polymerase Chain Reaction, Triiodothyronine, Xenopus}, issn = {1095-6840}, doi = {10.1016/j.ygcen.2010.03.014}, author = {Bonett, Ronald M and Hoopfer, Eric D and Denver, Robert J} } @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 {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 {46618, title = {A pair of dopamine neurons target the D1-like dopamine receptor DopR in the central complex to promote ethanol-stimulated locomotion in Drosophila.}, journal = {PLoS One}, volume = {5}, year = {2010}, month = {2010 Apr 1}, pages = {e9954}, abstract = {

Dopamine is a mediator of the stimulant properties of drugs of abuse, including ethanol, in mammals and in the fruit fly Drosophila. The neural substrates for the stimulant actions of ethanol in flies are not known. We show that a subset of dopamine neurons and their targets, through the action of the D1-like dopamine receptor DopR, promote locomotor activation in response to acute ethanol exposure. A bilateral pair of dopaminergic neurons in the fly brain mediates the enhanced locomotor activity induced by ethanol exposure, and promotes locomotion when directly activated. These neurons project to the central complex ellipsoid body, a structure implicated in regulating motor behaviors. Ellipsoid body neurons are required for ethanol-induced locomotor activity and they express DopR. Elimination of DopR blunts the locomotor activating effects of ethanol, and this behavior can be restored by selective expression of DopR in the ellipsoid body. These data tie the activity of defined dopamine neurons to D1-like DopR-expressing neurons to form a neural circuit that governs acute responding to ethanol.

}, keywords = {Animals, Behavior, Animal, Central Nervous System Depressants, Dopamine, Drosophila, Drosophila Proteins, Ethanol, Locomotion, Motor Activity, Neurons, Receptors, Dopamine}, issn = {1932-6203}, doi = {10.1371/journal.pone.0009954}, author = {Kong, Eric C and Woo, Katherine and Li, Haiyan and Lebestky, Tim and Mayer, Nasima and Sniffen, Melissa R and Heberlein, Ulrike and Bainton, Roland J and Hirsh, Jay and Wolf, Fred W} } @article {46041, title = {Persistence of coordinated long-term potentiation and dendritic spine enlargement at mature hippocampal CA1 synapses requires N-cadherin.}, journal = {Journal of Neuroscience}, volume = {30}, year = {2010}, month = {2010 Jul 28}, pages = {9984-9}, abstract = {

Persistent changes in spine shape are coupled to long-lasting synaptic plasticity in hippocampus. The molecules that coordinate such persistent structural and functional plasticity are unknown. Here, we generated mice in which the cell adhesion molecule N-cadherin was conditionally ablated from postnatal, excitatory synapses in hippocampus. We applied to adult mice of either sex a combination of whole-cell recording, two-photon microscopy, and spine morphometric analysis to show that postnatal ablation of N-cadherin has profound effects on the stability of coordinated spine enlargement and long-term potentiation (LTP) at mature CA1 synapses, with no effects on baseline spine density or morphology, baseline properties of synaptic neurotransmission, or long-term depression. Thus, N-cadherin couples persistent spine structural modifications with long-lasting synaptic functional modifications associated selectively with LTP, revealing unexpectedly distinct roles at mature synapses in comparison with earlier, broader functions in synapse and spine development.

}, keywords = {Action Potentials, Animals, Biophysics, CA1 Region, Hippocampal, Cadherins, Dendritic Spines, Electric Stimulation, Excitatory Postsynaptic Potentials, In Vitro Techniques, Long-Term Potentiation, Mice, Mice, Inbred C57BL, Mice, Knockout, Microscopy, Immunoelectron, Patch-Clamp Techniques, Pyramidal Cells, Statistics, Nonparametric, Synapses}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.1223-10.2010}, author = {Bozdagi, Ozlem and Wang, Xiao-bin and Nikitczuk, Jessica S and Anderson, Tonya R and Bloss, Erik B and Radice, Glenn L and Zhou, Qiang and Benson, Deanna L and Huntley, George W} } @article {4253, title = {The Pfam protein families database.}, journal = {Nucleic Acids Research}, volume = {38}, year = {2010}, month = {2010 Jan}, pages = {D211-22}, abstract = {

Pfam is a widely used database of protein families and domains. This article describes a set of major updates that we have implemented in the latest release (version 24.0). The most important change is that we now use HMMER3, the latest version of the popular profile hidden Markov model package. This software is approximately 100 times faster than HMMER2 and is more sensitive due to the routine use of the forward algorithm. The move to HMMER3 has necessitated numerous changes to Pfam that are described in detail. Pfam release 24.0 contains 11,912 families, of which a large number have been significantly updated during the past two years. Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/).

}, keywords = {Amino Acid, Amino Acid Sequence, Animals, Archaeal, Computational Biology, Databases, Fungal, Genome, Humans, Information Storage and Retrieval, Internet, Molecular Sequence Data, Nucleic Acid, Protein, Protein Structure, Sequence Alignment, Sequence Homology, Software, Tertiary}, issn = {1362-4962}, doi = {10.1093/nar/gkp985}, author = {Finn, Robert D and Mistry, Jaina and Tate, John and Coggill, Penny and Heger, Andreas and Pollington, Joanne E and Gavin, O Luke and Gunasekaran, Prasad and Ceric, Goran and Forslund, Kristoffer and Holm, Liisa and Sonnhammer, Erik L L and Eddy, Sean R. and Bateman, Alex} } @article {68824, title = {Proneural gene-linked neurogenesis in zebrafish cerebellum}, journal = {Developmental Biology}, volume = {343}, year = {2010}, month = {07/2010}, pages = {1-17}, abstract = {

In mammals, cerebellar neurons are categorized as glutamatergic or GABAergic, and are derived from progenitors that express the proneural genes atoh1 or ptf1a, respectively. In zebrafish, three atoh1 genes, atoh1a, atoh1b, and atoh1c, are expressed in overlapping but distinct expression domains in the upper rhombic lip (URL): ptf1a is expressed exclusively in the ventricular zone (VZ). Using transgenic lines expressing fluorescent proteins under the control of the regulatory elements of atoh1a and ptf1a, we traced the lineages of the cerebellar neurons. The atoh1+ progenitors gave rise not only to granule cells but also to neurons of the anteroventral rhombencephalon. The ptf1a+ progenitors generated Purkinje cells. The olig2+ eurydendroid cells, which are glutamatergic, were derived mostly from ptf1a+ progenitors in the VZ but some originated from the atoh1+ progenitors in the URL. In the adult cerebellum, atoh1a, atoh1b, and atoh1c are expressed in the molecular layer of the valvula cerebelli and of the medial corpus cerebelli, and ptf1a was detected in the VZ. The proneural gene expression patterns coincided with the sites of proliferating neuronal progenitors in the adult cerebellum. Our data indicate that proneural gene-linked neurogenesis is evolutionarily conserved in the cerebellum among vertebrates, and that the continuously generated neurons help remodel neural circuits in the adult zebrafish cerebellum.

}, keywords = {Adult neurogenesis, Cerebellum, GABAergic neuron, Glutamatergic neuron, Hindbrain, Proneural gene, Zebrafish}, issn = {0012-1606}, doi = {https://doi.org/10.1016/j.ydbio.2010.03.024}, url = {https://www.sciencedirect.com/science/article/pii/S0012160610002071}, author = {Shuichi Kani and Young-Ki Bae and Takashi Shimizu and Koji Tanabe and Chie Satou and Michael J. Parsons and Ethan Scott and Shin-ichi Higashijima and Masahiko Hibi} } @article {46617, title = {Protein Phosphatase 2a and glycogen synthase kinase 3 signaling modulate prepulse inhibition of the acoustic startle response by altering cortical M-Type potassium channel activity.}, journal = {The Journal of Neuroscience}, volume = {30}, year = {2010}, month = {2010 Jun 30}, pages = {8830-40}, abstract = {

There is considerable interest in the regulation of sensorimotor gating, since deficits in this process could play a critical role in the symptoms of schizophrenia and other psychiatric disorders. Sensorimotor gating is often studied in humans and rodents using the prepulse inhibition of the acoustic startle response (PPI) model, in which an acoustic prepulse suppresses behavioral output to a startle-inducing stimulus. However, the molecular and neural mechanisms underlying PPI are poorly understood. Here, we show that a regulatory pathway involving protein phosphatase 2A (PP2A), glycogen synthase kinase 3 beta (GSK3beta), and their downstream target, the M-type potassium channel, regulates PPI. Mice (Mus musculus) carrying a hypomorphic allele of Ppp2r5delta, encoding a regulatory subunit of PP2A, show attenuated PPI. This PPP2R5delta reduction increases the phosphorylation of GSK3beta at serine 9, which inactivates GSK3beta, indicating that PPP2R5delta positively regulates GSK3beta activity in the brain. Consistently, genetic and pharmacological manipulations that reduce GSK3beta function attenuate PPI. The M-type potassium channel subunit, KCNQ2, is a putative GSK3beta substrate. Genetic reduction of Kcnq2 also reduces PPI, as does systemic inhibition of M-channels with linopirdine. Importantly, both the GSK3 inhibitor 3-(2,4-dichlorophenyl)-4-(1-methyl-1H-indol-3-yl)1H-pyrrole-2,5-dione (SB216763) and linopirdine reduce PPI when directly infused into the medial prefrontal cortex (mPFC). Whole-cell electrophysiological recordings of mPFC neurons show that SB216763 and linopirdine have similar effects on firing, and GSK3 inhibition occludes the effects of M-channel inhibition. These data support a previously uncharacterized mechanism by which PP2A/GSK3beta signaling regulates M-type potassium channel activity in the mPFC to modulate sensorimotor gating.

}, keywords = {Amino Acid Sequence, Animals, Auditory Perception, Brain, Glycogen Synthase Kinase 3, Inhibition (Psychology), KCNQ2 Potassium Channel, Mice, Mice, Inbred C57BL, Mice, Transgenic, Models, Neurological, Neurons, Phosphorylation, Potassium Channels, Prefrontal Cortex, Protein Phosphatase 2, Reflex, Startle, Signal Transduction}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.1292-10.2010}, author = {Kapfhamer, David and Berger, Karen H and Hopf, F Woodward and Seif, Taban and Kharazia, Viktor and Bonci, Antonello and Heberlein, Ulrike} } @article {987, title = {Refinement of tools for targeted gene expression in Drosophila.}, journal = {Genetics}, volume = {186}, year = {2010}, month = {2010 Oct}, pages = {735-55}, abstract = {

A wide variety of biological experiments rely on the ability to express an exogenous gene in a transgenic animal at a defined level and in a spatially and temporally controlled pattern. We describe major improvements of the methods available for achieving this objective in Drosophila melanogaster. We have systematically varied core promoters, UTRs, operator sequences, and transcriptional activating domains used to direct gene expression with the GAL4, LexA, and Split GAL4 transcription factors and the GAL80 transcriptional repressor. The use of site-specific integration allowed us to make quantitative comparisons between different constructs inserted at the same genomic location. We also characterized a set of PhiC31 integration sites for their ability to support transgene expression of both drivers and responders in the nervous system. The increased strength and reliability of these optimized reagents overcome many of the previous limitations of these methods and will facilitate genetic manipulations of greater complexity and sophistication.

}, issn = {1943-2631}, doi = {10.1534/genetics.110.119917}, author = {Pfeiffer, Barret D and Ngo, Teri-T B and Hibbard, Karen L and Murphy, Christine and Jenett, Arnim and Truman, James W and Rubin, Gerald M} } @article {2768, title = {Snapshot Image Mapping Spectrometer (IMS) with high sampling density for hyperspectral microscopy.}, journal = {Optics Express}, volume = {18}, year = {2010}, month = {2010 Jul 5}, pages = {14330-44}, abstract = {

A snapshot Image Mapping Spectrometer (IMS) with high sampling density is developed for hyperspectral microscopy, measuring a datacube of dimensions 285 x 285 x 60 (x, y, lambda). The spatial resolution is approximately 0.45 microm with a FOV of 100 x 100 microm(2). The measured spectrum is from 450 nm to 650 nm and is sampled by 60 spectral channels with average sampling interval approximately 3.3 nm. The channel{\textquoteright}s spectral resolution is approximately 8nm. The spectral imaging results demonstrate the potential of the IMS for real-time cellular fluorescence imaging.

}, keywords = {Animals, Cattle, Cell Nucleus, Endothelial Cells, Fluorescence, Imaging, Microscopy, Pulmonary Artery, Spectrum Analysis, Staining and Labeling, Three-Dimensional}, issn = {1094-4087}, doi = {10.1364/AO.50.001792}, author = {Gao, Liang and Kester, Robert T and Hagen, Nathan and Tkaczyk, Tomasz S} } @article {4298, title = {Structural plasticity underlies experience-dependent functional plasticity of cortical circuits.}, journal = {The Journal of Neuroscience}, volume = {30}, year = {2010}, month = {2010 Apr 7}, pages = {4927-32}, abstract = {

The stabilization of new spines in the barrel cortex is enhanced after whisker trimming, but its relationship to experience-dependent plasticity is unclear. Here we show that in wild-type mice, whisker potentiation and spine stabilization are most pronounced for layer 5 neurons at the border between spared and deprived barrel columns. In homozygote alphaCaMKII-T286A mice, which lack experience-dependent potentiation of responses to spared whiskers, there is no increase in new spine stabilization at the border between barrel columns after whisker trimming. Our data provide a causal link between new spine synapses and plasticity of adult cortical circuits and suggest that alphaCaMKII autophosphorylation plays a role in the stabilization but not formation of new spines.

}, keywords = {Animals, Cerebral Cortex, Dendritic Spines, Inbred C57BL, Learning, Male, Mice, Nerve Net, Neuronal Plasticity, Synapses, Transgenic, Vibrissae}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.6403-09.2010}, author = {Wilbrecht, Linda and Holtmaat, Anthony and Wright, Nick and Fox, Kevin and Svoboda, Karel} } @article {6340, title = {Structure of clathrin coat with bound Hsc70 and auxilin: mechanism of Hsc70-facilitated disassembly.}, journal = {The EMBO Journal}, volume = {29}, year = {2010}, month = {2010 Feb 3}, pages = {655-65}, abstract = {

The chaperone Hsc70 drives the clathrin assembly-disassembly cycle forward by stimulating dissociation of a clathrin lattice. A J-domain containing co-chaperone, auxilin, associates with a freshly budded clathrin-coated vesicle, or with an in vitro assembled clathrin coat, and recruits Hsc70 to its specific heavy-chain-binding site. We have determined by electron cryomicroscopy (cryoEM), at about 11 A resolution, the structure of a clathrin coat (in the D6-barrel form) with specifically bound Hsc70 and auxilin. The Hsc70 binds a previously analysed site near the C-terminus of the heavy chain, with a stoichiometry of about one per three-fold vertex. Its binding is accompanied by a distortion of the clathrin lattice, detected by a change in the axial ratio of the D6 barrel. We propose that when Hsc70, recruited to a position close to its target by the auxilin J-domain, splits ATP, it clamps firmly onto its heavy-chain site and locks in place a transient fluctuation. Accumulation of the local strain thus imposed at multiple vertices can then lead to disassembly.

}, keywords = {Animals, Auxilins, Biological, Cattle, Clathrin, Clathrin-Coated Vesicles, Cryoelectron Microscopy, HSC70 Heat-Shock Proteins, Models, Molecular, Multiprotein Complexes, Protein Binding, Protein Multimerization, Protein Structure, Quaternary, Secondary}, issn = {1460-2075}, doi = {10.1038/emboj.2009.383}, author = {Xing, Yi and B{\"o}cking, Till and Wolf, Matthias and Grigorieff, Nikolaus and Kirchhausen, Tomas and Harrison, Stephen C} } @article {5688, title = {Structure of the central nervous system of a juvenile acoel, Symsagittifera roscoffensis.}, journal = {Development Genes \& Evolution}, volume = {220}, year = {2010}, month = {2010 Sep}, pages = {61-76}, abstract = {

The neuroarchitecture of Acoela has been at the center of morphological debates. Some authors, using immunochemical tools, suggest that the nervous system in Acoela is organized as a commissural brain that bears little resemblance to the central, ganglionic type brain of other flatworms, and bilaterians in general. Others, who used histological staining on paraffin sections, conclude that it is a compact structure (an endonal brain; e.g., Raikova 2004; von Graff 1891; Delage Arch Zool Exp G{\'e}n 4:109-144, 1886). To address this question with modern tools, we have obtained images from serial transmission electron microscopic sections of the entire hatchling of Symsagittifera roscoffensis. In addition, we obtained data from wholemounts of hatchlings labeled with markers for serotonin and tyrosinated tubulin. Our data show that the central nervous system of a juvenile S. roscoffensis consists of an anterior compact brain, formed by a dense, bilobed mass of neuronal cell bodies surrounding a central neuropile. The neuropile flanks the median statocyst and contains several types of neurites, classified according to their types of synaptic vesicles. The neuropile issues three pairs of nerve cords that run at different dorso-ventral positions along the whole length of the body. Neuronal cell bodies flank the cords, and neuromuscular synapses are abundant. The TEM analysis also reveals different classes of peripheral sensory neurons and provides valuable information about the spatial relationships between neurites and other cell types within the brain and nerve cords. We conclude that the acoel S. roscoffensis has a central brain that is comparable in size and architecture to the brain of other (rhabditophoran) flatworms.

}, keywords = {Anatomic, Animals, Brain, Central Nervous System, Electron, Imaging, Microscopy, Models, Muscles, Nerve Fibers, Nerve Net, Neurites, Neuropil, Platyhelminths, Sensory Receptor Cells, Synapses, Three-Dimensional, Transmission}, issn = {1432-041X}, doi = {10.1007/s00427-010-0328-2}, author = {Bery, Amandine and Cardona, Albert and Martinez, Pedro and Hartenstein, Volker.} } @article {3632, title = {Structure of the cholera toxin secretion channel in its closed state.}, journal = {Nature Structural \& Molecular Biology}, volume = {17}, year = {2010}, month = {2010 Oct}, pages = {1226-32}, abstract = {

The type II secretion system (T2SS) is a macromolecular complex spanning the inner and outer membranes of Gram-negative bacteria. Remarkably, the T2SS secretes folded proteins, including multimeric assemblies such as cholera toxin and heat-labile enterotoxin from Vibrio cholerae and enterotoxigenic Escherichia coli, respectively. The major outer membrane T2SS protein is the {\textquoteright}secretin{\textquoteright} GspD. Cryo-EM reconstruction of the V. cholerae secretin at 19-{\r A} resolution reveals a dodecameric structure reminiscent of a barrel, with a large channel at its center that contains a closed periplasmic gate. The GspD periplasmic domain forms a vestibule with a conserved constriction, and it binds to a pentameric exoprotein and to the trimeric tip of the T2SS pseudopilus. By combining our results with structures of the cholera toxin and T2SS pseudopilus tip, we provide a structural basis for a possible secretion mechanism of the T2SS.

}, keywords = {Amino Acid, Amino Acid Sequence, Bacterial, Bacterial Outer Membrane Proteins, Cholera Toxin, Computer-Assisted, Conserved Sequence, Cryoelectron Microscopy, Fimbriae, Image Processing, Models, Molecular, Molecular Sequence Data, Periplasm, Protein Conformation, Protein Structure, Recombinant Fusion Proteins, Sequence Alignment, Sequence Homology, Surface Plasmon Resonance, Tertiary, Vibrio cholerae}, issn = {1545-9985}, doi = {10.1038/nsmb.1910}, author = {Reichow, Steve L and Korotkov, Konstantin V and Hol, Wim G J and Gonen, Tamir} } @article {1453, title = {Subtomogram alignment by adaptive Fourier coefficient thresholding.}, journal = {Journal of Structural Biology}, volume = {171}, year = {2010}, month = {2010 Sep}, pages = {332-44}, abstract = {

In the past few years, three-dimensional (3D) subtomogram alignment has become an important tool in cryo-electron tomography (CET). This technique allows one to produce higher resolution images of structures which can not be reconstructed using single-particle methods. Building on previous work, we present a new dissimilarity measure between subtomograms that works well for the noisy images that often occur in CET images. A technique that is more robust to noise provides the ability to analyze macromolecules in thicker samples such as whole cells or lower the defocus in thinner samples to push the first zero of the Contrast Transfer Function (CTF). Our method, Threshold Constrained Cross-Correlation (TCCC), uses statistics of the noise to automatically select only a small percentage of the Fourier coefficients to compute the cross-correlation, which has two main advantages: first, it reduces the influence of the noise by looking at only those peaks dominated by signal; and second, it avoids the missing wedge normalization problem since we consider the same number of coefficients for all possible pairs of subtomograms. We present results with synthetic and real data to compare our approach with other existing methods under different SNR and missing wedge conditions, and show that TCCC improves alignment results for datasets with SNR\<0.1. We have made our source code freely available for the community.

}, keywords = {Algorithms, Electron Microscope Tomography}, issn = {1095-8657}, doi = {10.1016/j.jsb.2010.05.013}, author = {Amat, Fernando and Comolli, Luis R and Moussavi, Farshid and Smit, John and Downing, Kenneth H and Horowitz, Mark} } @article {6336, title = {Subunit interactions in bovine papillomavirus.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, year = {2010}, month = {2010 Apr 6}, pages = {6298-303}, abstract = {

Papillomaviruses, members of a group of dsDNA viruses associated with epithelial growths and tumors, have compact capsids assembled from 72 pentamers of the protein L1. We have determined the structure of bovine papillomavirus by electron cryomicrosopy (cryoEM), at approximately 3.6 A resolution. The density map, obtained from single-particle analysis of approximately 4,000 particle images, shows the trace of the L1 polypeptide chain and reveals how the N- and C-terminal "arms" of a subunit (extensions from its beta-jelly-roll core) associate with a neighboring pentamer. Critical contacts come from the C-terminal arm, which loops out from the core of the subunit, forms contacts (including a disulfide) with two subunits in a neighboring pentamer, and reinserts into the pentamer from which it emanates. This trace corrects one feature of an earlier model. We discuss implications of the structure for virion assembly and for pathways of infectious viral entry. We suggest that it should be possible to obtain image reconstructions of comparable resolution from cryoEM images of asymmetric particles. From the work on papillomavirus described here, we estimate that such a reconstruction will require about 1.5 million images to achieve the same number of averaged asymmetric units; structural variability will increase this number substantially.

}, keywords = {Cryoelectron Microscopy, Models, Molecular, Papillomaviridae, Protein Interaction Domains and Motifs, Protein Structure, Protein Subunits, Quaternary, Tertiary, Viral Envelope Proteins, Virion}, issn = {1091-6490}, doi = {10.1073/pnas.0914604107}, author = {Wolf, Matthias and Garcea, Robert L and Grigorieff, Nikolaus and Harrison, Stephen C} } @article {6487, title = {Tetracycline-controlled transgene activation using the ROSA26-iM2-GFP knock-in mouse strain permits GFP monitoring of DOX-regulated transgene-expression.}, journal = {BMC Developmental Biology}, volume = {10}, year = {2010}, month = {2010}, pages = {95}, abstract = {

BACKGROUND: Conditional gene activation is an efficient strategy for studying gene function in genetically modified animals. Among the presently available gene switches, the tetracycline-regulated system has attracted considerable interest because of its unique potential for reversible and adjustable gene regulation. RESULTS: To investigate whether the ubiquitously expressed Gt(ROSA)26Sor locus enables uniform DOX-controlled gene expression, we inserted the improved tetracycline-regulated transcription activator iM2 together with an iM2 dependent GFP gene into the Gt(ROSA)26Sor locus, using gene targeting to generate ROSA26-iM2-GFP (R26t1Δ) mice. Despite the presence of ROSA26 promoter driven iM2, R26t1Δ mice showed very sparse DOX-activated expression of different iM2-responsive reporter genes in the brain, mosaic expression in peripheral tissues and more prominent expression in erythroid, myeloid and lymphoid lineages, in hematopoietic stem and progenitor cells and in olfactory neurons. CONCLUSIONS: The finding that gene regulation by the DOX-activated transcriptional factor iM2 in the Gt(ROSA)26Sor locus has its limitations is of importance for future experimental strategies involving transgene activation from the endogenous ROSA26 promoter. Furthermore, our ROSA26-iM2 knock-in mouse model (R26t1Δ) represents a useful tool for implementing gene function in vivo especially under circumstances requiring the side-by-side comparison of gene manipulated and wild type cells. Since the ROSA26-iM2 mouse allows mosaic gene activation in peripheral tissues and haematopoietic cells, this model will be very useful for uncovering previously unknown or unsuspected phenotypes.

}, keywords = {Animals, Doxycycline, Gene Knock-In Techniques, Genetic Techniques, Green Fluorescent Proteins, Mice, Tetracycline, Transgenes, Transgenic}, issn = {1471-213X}, doi = {10.1186/1471-213X-10-95}, author = {W{\"o}rtge, Simone and Eshkind, Leonid and Cabezas-Wallscheid, Nina and Lakaye, Bernard and Kim, Jinhyun and Heck, Rosario and Abassi, Yasmin and Diken, Mustafa and Sprengel, Rolf and Bockamp, Ernesto} } @article {1235, title = {Ultrastructural analysis of hippocampal neuropil from the connectomics perspective.}, journal = {Neuron}, volume = {67}, year = {2010}, month = {2010 Sep 23}, pages = {1009-20}, abstract = {

Complete reconstructions of vertebrate neuronal circuits on the synaptic level require new approaches. Here, serial section transmission electron microscopy was automated to densely reconstruct four volumes, totaling 670 μm(3), from the rat hippocampus as proving grounds to determine when axo-dendritic proximities predict synapses. First, in contrast with Peters{\textquoteright} rule, the density of axons within reach of dendritic spines did not predict synaptic density along dendrites because the fraction of axons making synapses was variable. Second, an axo-dendritic touch did not predict a synapse; nevertheless, the density of synapses along a hippocampal dendrite appeared to be a universal fraction, 0.2, of the density of touches. Finally, the largest touch between an axonal bouton and spine indicated the site of actual synapses with about 80\% precision but would miss about half of all synapses. Thus, it will be difficult to predict synaptic connectivity using data sets missing ultrastructural details that distinguish between axo-dendritic touches and bona fide synapses.

}, keywords = {Animals, Automatic Data Processing, Axons, Dendrites, Electron, Hippocampus, Long-Evans, Male, Microscopy, Neuropil, Newborn, Rats, Synapses, Transmission}, issn = {1097-4199}, doi = {10.1371/journal.pcbi.1001066}, author = {Mishchenko, Yuriy and Hu, Tao and Spacek, Josef and Mendenhall, John and Harris, Kristen M and Chklovskii, Dmitri B} } @article {2329, title = {Vibrissa-based object localization in head-fixed mice.}, journal = {The Journal of Neuroscience}, volume = {30}, year = {2010}, month = {2010 Feb 3}, pages = {1947-67}, abstract = {

Linking activity in specific cell types with perception, cognition, and action, requires quantitative behavioral experiments in genetic model systems such as the mouse. In head-fixed primates, the combination of precise stimulus control, monitoring of motor output, and physiological recordings over large numbers of trials are the foundation on which many conceptually rich and quantitative studies have been built. Choice-based, quantitative behavioral paradigms for head-fixed mice have not been described previously. Here, we report a somatosensory absolute object localization task for head-fixed mice. Mice actively used their mystacial vibrissae (whiskers) to sense the location of a vertical pole presented to one side of the head and reported with licking whether the pole was in a target (go) or a distracter (no-go) location. Mice performed hundreds of trials with high performance (\>90\% correct) and localized to \<0.95 mm (\<6 degrees of azimuthal angle). Learning occurred over 1-2 weeks and was observed both within and across sessions. Mice could perform object localization with single whiskers. Silencing barrel cortex abolished performance to chance levels. We measured whisker movement and shape for thousands of trials. Mice moved their whiskers in a highly directed, asymmetric manner, focusing on the target location. Translation of the base of the whiskers along the face contributed substantially to whisker movements. Mice tended to maximize contact with the go (rewarded) stimulus while minimizing contact with the no-go stimulus. We conjecture that this may amplify differences in evoked neural activity between trial types.

}, keywords = {Animals, Exploratory Behavior, Head Movements, Inbred C57BL, Mice, Movement, Physical, Restraint, Somatosensory Cortex, Space Perception, Touch, Vibrissae}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3762-09.2010}, author = {O{\textquoteright}Connor, Daniel H and Clack, Nathan G and Huber, Daniel and Komiyama, Takaki and Myers, Eugene W and Svoboda, Karel} } @proceedings {65006, title = {A wireless neural/EMG telemetry system for freely moving insects.}, year = {2010}, month = {2010 May 30}, abstract = {

We have developed a miniature telemetry system that captures neural, EMG, and acceleration signals from a freely moving insect and transmits the data wirelessly to a remote digital receiver. The system is based on a custom low-power integrated circuit that amplifies and digitizes four biopotential signals as well as three acceleration signals from an off-chip MEMS accelerometer, and transmits this information over a wireless 920-MHz telemetry link. The unit weighs 0.79 g and runs for two hours on two small batteries. We have used this system to monitor neural and EMG signals in jumping and flying locusts.

}, doi = {10.1109/ISCAS.2010.5538034}, author = {Reid R. Harrison and Ryan J. Kier and Anthony Leonardo and Haleh Fotowat and Raymond Chan and Fabrizio Gabbiani} } @article {6343, title = {Abeta(1-40) fibril polymorphism implies diverse interaction patterns in amyloid fibrils.}, journal = {Journal of Molecular Biology}, volume = {386}, year = {2009}, month = {2009 Feb 27}, pages = {869-77}, abstract = {

Amyloid fibrils characterize a diverse group of human diseases that includes Alzheimer{\textquoteright}s disease, Creutzfeldt-Jakob and type II diabetes. Alzheimer{\textquoteright}s amyloid fibrils consist of amyloid-beta (Abeta) peptide and occur in a range of structurally different fibril morphologies. The structural characteristics of 12 single Abeta(1-40) amyloid fibrils, all formed under the same solution conditions, were determined by electron cryo-microscopy and three-dimensional reconstruction. The majority of analyzed fibrils form a range of morphologies that show almost continuously altering structural properties. The observed fibril polymorphism implies that amyloid formation can lead, for the same polypeptide sequence, to many different patterns of inter- or intra-residue interactions. This property differs significantly from native, monomeric protein folding reactions that produce, for one protein sequence, only one ordered conformation and only one set of inter-residue interactions.

}, keywords = {Amyloid beta-Peptides, Cryoelectron Microscopy, Humans, Imaging, Peptide Fragments, Protein Binding, Protein Structure, Quaternary, Three-Dimensional}, issn = {1089-8638}, doi = {10.1016/j.jmb.2008.11.005}, author = {Meinhardt, Jessica and Sachse, Carsten and Hortschansky, Peter and Grigorieff, Nikolaus and F{\"a}ndrich, Marcus} } @article {48169, title = {An articulated statistical shape model for accurate hip joint segmentation.}, journal = {Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference}, volume = {2009}, year = {2009}, month = {2009}, pages = {6345-51}, abstract = {

In this paper we propose a framework for fully automatic, robust and accurate segmentation of the human pelvis and proximal femur in CT data. We propose a composite statistical shape model of femur and pelvis with a flexible hip joint, for which we extend the common definition of statistical shape models as well as the common strategy for their adaptation. We do not analyze the joint flexibility statistically, but model it explicitly by rotational parameters describing the bent in a ball-and-socket joint. A leave-one-out evaluation on 50 CT volumes shows that image driven adaptation of our composite shape model robustly produces accurate segmentations of both proximal femur and pelvis. As a second contribution, we evaluate a fine grain multi-object segmentation method based on graph optimization. It relies on accurate initializations of femur and pelvis, which our composite shape model can generate. Simultaneous optimization of both femur and pelvis yields more accurate results than separate optimizations of each structure. Shape model adaptation and graph based optimization are embedded in a fully automatic framework.

}, keywords = {Algorithms, Artificial Intelligence, Computer Simulation, Hip Joint, Imaging, Three-Dimensional, Models, Anatomic, Models, Statistical, Pattern Recognition, Automated, Radiographic Image Enhancement, Radiographic Image Interpretation, Computer-Assisted, Reproducibility of Results, Sensitivity and Specificity, Tomography, X-Ray Computed}, issn = {1557-170X}, doi = {10.1109/IEMBS.2009.5333269}, author = {Kainmueller, Dagmar and Lamecker, Hans and Zachow, Stefan and Hege, Hans-Christian} } @article {2678, title = {Automated monitoring and analysis of social behavior in Drosophila.}, journal = {Nature Methods}, volume = {6}, year = {2009}, month = {2009 Apr}, pages = {297-303}, abstract = {

We introduce a method based on machine vision for automatically measuring aggression and courtship in Drosophila melanogaster. The genetic and neural circuit bases of these innate social behaviors are poorly understood. High-throughput behavioral screening in this genetically tractable model organism is a potentially powerful approach, but it is currently very laborious. Our system monitors interacting pairs of flies and computes their location, orientation and wing posture. These features are used for detecting behaviors exhibited during aggression and courtship. Among these, wing threat, lunging and tussling are specific to aggression; circling, wing extension (courtship {\textquoteright}song{\textquoteright}) and copulation are specific to courtship; locomotion and chasing are common to both. Ethograms may be constructed automatically from these measurements, saving considerable time and effort. This technology should enable large-scale screens for genes and neural circuits controlling courtship and aggression.

}, keywords = {Animal, Animals, Artificial Intelligence, Automated, Behavior, Computer-Assisted, Drosophila melanogaster, Humans, Image Interpretation, Monitoring, Movement, Pattern Recognition, Physiologic, Posture, Social Behavior}, issn = {1548-7105}, doi = {10.1038/nmeth.1310}, author = {Dankert, Heiko and Wang, Liming and Hoopfer, Eric D and Anderson, David J and Perona, Pietro} } @article {48176, title = {Automatic Extraction of Anatomical Landmarks From Medical Image Data: An Evaluation of Different Methods}, year = {2009}, abstract = {

This work presents three different methods for automatic detection of anatomical landmarks in CT data, namely for the left and right anterior superior iliac spines and the pubic symphysis. The methods exhibit different degrees of generality in terms of portability to other anatomical landmarks and require a different amount of training data. The srst method is problem-specisc and is based on the convex hull of the pelvis. Method two is a more generic approach based on a statistical shape model including the landmarks of interest for every training shape. With our third method we present the most generic approach, where only a small set of training landmarks is required. Those landmarks are transferred to the patient specisc geometry based on Mean Value Coordinates (MVCs). The methods work on surfaces of the pelvis that need to be extracted beforehand. We perform this geometry reconstruction with our previously introduced fully automatic segmentation framework for the pelvic bones. With a focus on the accuracy of our novel MVC-based approach, we evaluate and compare our methods on 100 clinical CT datasets, for which gold standard landmarks were desned manually by multiple observers.

}, author = {Kainmueller, Dagmar and Hans-Christian Hege and Heiko Seim and Markus Heller and Stefan Zachow} } @article {4275, title = {A bright and photostable photoconvertible fluorescent protein.}, journal = {Nature Methods}, volume = {6}, year = {2009}, month = {2009 Feb}, pages = {131-3}, abstract = {

Photoconvertible fluorescent proteins are potential tools for investigating dynamic processes in living cells and for emerging super-resolution microscopy techniques. Unfortunately, most probes in this class are hampered by oligomerization, small photon budgets or poor photostability. Here we report an EosFP variant that functions well in a broad range of protein fusions for dynamic investigations, exhibits high photostability and preserves the approximately 10-nm localization precision of its parent.

}, keywords = {Animals, Fibroblasts, Fluorescence, Fluorescent Dyes, Hela Cells, Humans, Luminescent Proteins, Microscopy, Mutagenesis, Photochemical Processes, Recombinant Fusion Proteins, Site-Directed}, issn = {1548-7105}, doi = {10.1038/nmeth.1296}, author = {McKinney, Sean A and Murphy, Christopher S and Hazelwood, Kristin L and Davidson, Michael W and Looger, Loren L} } @article {6348, title = {Burst-timing-dependent plasticity of NMDA receptor-mediated transmission in midbrain dopamine neurons.}, journal = {Neuron}, volume = {62}, year = {2009}, month = {2009 Jun 25}, pages = {826-38}, abstract = {

Bursts of spikes triggered by sensory stimuli in midbrain dopamine neurons evoke phasic release of dopamine in target brain areas, driving reward-based reinforcement learning and goal-directed behavior. NMDA-type glutamate receptors (NMDARs) play a critical role in the generation of these bursts. Here we report LTP of NMDAR-mediated excitatory transmission onto dopamine neurons in the substantia nigra. Induction of LTP requires burst-evoked Ca2+ signals amplified by preceding metabotropic neurotransmitter inputs in addition to the activation of NMDARs themselves. PKA activity gates LTP induction by regulating the magnitude of Ca2+ signal amplification. This form of plasticity is associative, input specific, reversible, and depends on the relative timing of synaptic input and postsynaptic bursting in a manner analogous to the timing rule for cue-reward learning paradigms in behaving animals. NMDAR plasticity might thus represent a potential neural substrate for conditioned dopamine neuron burst responses to environmental stimuli acquired during reward-based learning.

}, keywords = {2-Amino-5-phosphonovalerate, 4, 5-Trisphosphate, Action Potentials, Animals, Biophysics, Calcium, Dopamine, Dose-Response Relationship, Drug, Electric Stimulation, Enzyme Inhibitors, Excitatory Amino Acid Antagonists, Gene Expression Regulation, Inositol 1, Intracellular Signaling Peptides and Proteins, Long-Term Potentiation, Male, Mesencephalon, Methoxyhydroxyphenylglycol, N-Methyl-D-Aspartate, Neural Pathways, Neuronal Plasticity, Neurons, Peptide Fragments, Rats, Receptors, Sprague-Dawley, Time Factors}, issn = {1097-4199}, doi = {10.1016/j.neuron.2009.05.011}, author = {Harnett, Mark T and Bernier, Brian E and Ahn, Kee-Chan and Morikawa, Hitoshi} } @article {46421, title = {Caenorhabditis elegans innexins regulate active zone differentiation.}, journal = {The Journal of Neuroscience}, volume = {29}, year = {2009}, month = {2009 Apr 22}, pages = {5207-17}, abstract = {

In a genetic screen for active zone defective mutants in Caenorhabditis elegans, we isolated a loss-of-function allele of unc-7, a gene encoding an innexin/pannexin family gap junction protein. Innexin UNC-7 regulates the size and distribution of active zones at C. elegans neuromuscular junctions. Loss-of-function mutations in another innexin, UNC-9, cause similar active zone defects as unc-7 mutants. In addition to presumptive gap junction localizations, both UNC-7 and UNC-9 are also localized perisynaptically throughout development and required in presynaptic neurons to regulate active zone differentiation. Our mosaic analyses, electron microscopy, as well as expression studies suggest a novel and likely nonjunctional role of specific innexins in active zone differentiation in addition to gap junction formations.

}, keywords = {Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Cell Differentiation, Connexins, Gap Junctions, Gene Expression Regulation, Developmental, Male, Membrane Proteins, Organisms, Genetically Modified, Presynaptic Terminals}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0637-09.2009}, author = {Yeh, Edward and Kawano, Taizo and Ng, Sharon and Fetter, Richard and Hung, Wesley and Wang, Ying and Zhen, Mei} } @article {6347, title = {Calcium-sensing receptor: a high-affinity presynaptic target for aminoglycoside-induced weakness.}, journal = {Neuropharmacology}, volume = {57}, year = {2009}, month = {2009 Oct-Nov}, pages = {502-5}, abstract = {

Administration of aminoglycoside antibiotics can precipitate sudden, profound bouts of weakness that have been attributed to block of presynaptic voltage-activated calcium channels (VACCs) and failure of neuromuscular transmission. This serious adverse drug reaction is more likely in neuromuscular diseases such as myasthenia gravis. The relatively low affinity of VACC for aminoglycosides prompted us to explore alternative mechanisms. We hypothesized that the presynaptic Ca(2+)-sensing receptor (CaSR) may contribute to aminoglycoside-induced weakness due to its role in modulating synaptic transmission and its sensitivity to aminoglycosides in heterologous expression systems. We have previously shown that presynaptic CaSR controls a non-selective cation channel (NSCC) that regulates nerve terminal excitability and transmitter release. Using direct, electrophysiological recording, we report that neuronal VACCs are inhibited by neomycin (IC(50) 830 +/- 110 microM) at a much lower affinity than CaSR-modulated NSCC currents recorded from acutely isolated presynaptic terminals (synaptosomes; IC(50) 20 +/- 1 microM). Thus, at clinically relevant concentrations, aminoglycoside-induced weakness is likely precipitated by enhanced CaSR activation and subsequent decrease in terminal excitability rather than through direct inhibition of VACCs themselves.

}, keywords = {Aminoglycosides, Animals, Anti-Bacterial Agents, Calcium-Sensing, Ion Channels, Kinetics, Membrane Potentials, Muscle Weakness, Neomycin, Neurons, Patch-Clamp Techniques, Presynaptic Terminals, Rats, Receptors, Sprague-Dawley, Superior Cervical Ganglion, Synaptosomes}, issn = {1873-7064}, doi = {10.1016/j.neuropharm.2009.07.031}, author = {Harnett, Mark T and Chen, Wenyan and Smith, Stephen M} } @article {5817, title = {CATMAID: collaborative annotation toolkit for massive amounts of image data.}, journal = {Bioinformatics}, volume = {25}, year = {2009}, month = {2009 Aug 1}, pages = {1984-6}, abstract = {

SUMMARY: High-resolution, three-dimensional (3D) imaging of large biological specimens generates massive image datasets that are difficult to navigate, annotate and share effectively. Inspired by online mapping applications like GoogleMaps, we developed a decentralized web interface that allows seamless navigation of arbitrarily large image stacks. Our interface provides means for online, collaborative annotation of the biological image data and seamless sharing of regions of interest by bookmarking. The CATMAID interface enables synchronized navigation through multiple registered datasets even at vastly different scales such as in comparisons between optical and electron microscopy. AVAILABILITY: http://fly.mpi-cbg.de/catmaid.

}, keywords = {Algorithms, Computational Biology, Computer Graphics, Database Management Systems, Databases, Factual, Imaging, Information Storage and Retrieval, Software, Three-Dimensional}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btp266}, author = {Saalfeld, Stephan and Cardona, Albert and Hartenstein, Volker and Tomancak, Pavel} } @article {2197, title = {The challenges of sequencing by synthesis.}, journal = {Nature Biotechnology}, volume = {27}, year = {2009}, month = {2009 Nov}, pages = {1013-23}, abstract = {

DNA sequencing-by-synthesis (SBS) technology, using a polymerase or ligase enzyme as its core biochemistry, has already been incorporated in several second-generation DNA sequencing systems with significant performance. Notwithstanding the substantial success of these SBS platforms, challenges continue to limit the ability to reduce the cost of sequencing a human genome to $100,000 or less. Achieving dramatically reduced cost with enhanced throughput and quality will require the seamless integration of scientific and technological effort across disciplines within biochemistry, chemistry, physics and engineering. The challenges include sample preparation, surface chemistry, fluorescent labels, optimizing the enzyme-substrate system, optics, instrumentation, understanding tradeoffs of throughput versus accuracy, and read-length/phasing limitations. By framing these challenges in a manner accessible to a broad community of scientists and engineers, we hope to solicit input from the broader research community on means of accelerating the advancement of genome sequencing technology.

}, keywords = {Animals, DNA, Fluorescent Dyes, Humans, Optical Phenomena, Sequence Analysis, Substrate Specificity, Surface Properties}, issn = {1546-1696}, doi = {10.1038/nbt0510-426}, author = {Fuller, Carl W and Middendorf, Lyle R and Benner, Steven A and Church, George M and Harris, Timothy and Huang, Xiaohua and Jovanovich, Stevan B and Nelson, John R and Schloss, Jeffery A and Schwartz, David C and Vezenov, Dmitri V} } @article {65013, title = {Cofactor engineering of lactobacillus brevis alcohol dehydrogenase by computational design.}, journal = {Engineering in Life Sciences}, volume = {9}, year = {2009}, month = {2009 Feb 20}, pages = {38-44}, abstract = {

The R-specific alcohol dehydrogenase from\ Lactobacillus brevis\ (Lb-ADH) catalyzes the enantioselective reduction of prochiral ketones to the corresponding secondary alcohols. It is stable and has broad substrate specificity. These features make this enzyme an attractive candidate for biotechnological applications. A drawback is its preference for NADP(H) as a cofactor, which is more expensive and labile than NAD(H). Structure-based computational protein engineering was used to predict mutations to alter the cofactor specificity of Lb-ADH. Mutations were introduced into Lb-ADH and tested against the substrate acetophenone, with either NAD(H) or NADP(H) as cofactor. The mutant Arg38Pro showed fourfold increased activity with acetophenone and NAD(H) relative to the wild type. Both Arg38Pro and wild type exhibit a pH optimum of 5.5 with NAD(H) as cofactor, significantly more acidic than with NADP(H). These and related Lb-ADH mutants may prove useful for the green synthesis of pharmaceutical precursors.

}, doi = {10.1002/elsc.200800046}, author = {Ronnie Machielsen and Loren L. Looger and John Raedts and Sjoerd Dijkhuizen and Werner Hummel and Hans-Georg Hennemann and Thomas Daussmann and John van der Oost} } @article {6498, title = {Comparative endocrinology in the 21st century.}, journal = {Integrative and Comparative Biology}, volume = {49}, year = {2009}, month = {2009 Oct}, pages = {339-48}, abstract = {

Hormones coordinate developmental, physiological, and behavioral processes within and between all living organisms. They orchestrate and shape organogenesis from early in development, regulate the acquisition, assimilation, and utilization of nutrients to support growth and metabolism, control gamete production and sexual behavior, mediate organismal responses to environmental change, and allow for communication of information between organisms. Genes that code for hormones; the enzymes that synthesize, metabolize, and transport hormones; and hormone receptors are important targets for natural selection, and variation in their expression and function is a major driving force for the evolution of morphology and life history. Hormones coordinate physiology and behavior of populations of organisms, and thus play key roles in determining the structure of populations, communities, and ecosystems. The field of endocrinology is concerned with the study of hormones and their actions. This field is rooted in the comparative study of hormones in diverse species, which has provided the foundation for the modern fields of evolutionary, environmental, and biomedical endocrinology. Comparative endocrinologists work at the cutting edge of the life sciences. They identify new hormones, hormone receptors and mechanisms of hormone action applicable to diverse species, including humans; study the impact of habitat destruction, pollution, and climatic change on populations of organisms; establish novel model systems for studying hormones and their functions; and develop new genetic strains and husbandry practices for efficient production of animal protein. While the model system approach has dominated biomedical research in recent years, and has provided extraordinary insight into many basic cellular and molecular processes, this approach is limited to investigating a small minority of organisms. Animals exhibit tremendous diversity in form and function, life-history strategies, and responses to the environment. A major challenge for life scientists in the 21st century is to understand how a changing environment impacts all life on earth. A full understanding of the capabilities of organisms to respond to environmental variation, and the resilience of organisms challenged by environmental changes and extremes, is necessary for understanding the impact of pollution and climatic change on the viability of populations. Comparative endocrinologists have a key role to play in these efforts.

}, issn = {1557-7023}, doi = {10.1093/icb/icp082}, author = {Denver, Robert J and Hopkins, Penny M and McCormick, Stephen D and Propper, Catherine R and Riddiford, Lynn and Sower, Stacia A and Wingfield, John C} } @article {48171, title = {Comparison and evaluation of methods for liver segmentation from CT datasets.}, journal = {IEEE transactions on medical imaging}, volume = {28}, year = {2009}, month = {2009 Aug}, pages = {1251-65}, abstract = {

This paper presents a comparison study between 10 automatic and six interactive methods for liver segmentation from contrast-enhanced CT images. It is based on results from the "MICCAI 2007 Grand Challenge" workshop, where 16 teams evaluated their algorithms on a common database. A collection of 20 clinical images with reference segmentations was provided to train and tune algorithms in advance. Participants were also allowed to use additional proprietary training data for that purpose. All teams then had to apply their methods to 10 test datasets and submit the obtained results. Employed algorithms include statistical shape models, atlas registration, level-sets, graph-cuts and rule-based systems. All results were compared to reference segmentations five error measures that highlight different aspects of segmentation accuracy. All measures were combined according to a specific scoring system relating the obtained values to human expert variability. In general, interactive methods reached higher average scores than automatic approaches and featured a better consistency of segmentation quality. However, the best automatic methods (mainly based on statistical shape models with some additional free deformation) could compete well on the majority of test images. The study provides an insight in performance of different segmentation approaches under real-world conditions and highlights achievements and limitations of current image analysis techniques.

}, keywords = {Algorithms, Bayes Theorem, Databases, Factual, Humans, Image Processing, Computer-Assisted, Liver, Tomography, X-Ray Computed}, issn = {1558-254X}, doi = {10.1109/TMI.2009.2013851}, author = {Heimann, Tobias and van Ginneken, Bram and Styner, Martin A and Arzhaeva, Yulia and Aurich, Volker and Bauer, Christian and Beck, Andreas and Becker, Christoph and Beichel, Reinhard and Bekes, Gy{\"o}rgy and Bello, Fernando and Binnig, Gerd and Bischof, Horst and Bornik, Alexander and Cashman, Peter M M and Chi, Ying and Cordova, Andr{\'e}s and Dawant, Benoit M and Fidrich, M{\'a}rta and Furst, Jacob D and Furukawa, Daisuke and Grenacher, Lars and Hornegger, Joachim and Kainm{\"u}ller, Dagmar and Kitney, Richard I and Kobatake, Hidefumi and Lamecker, Hans and Lange, Thomas and Lee, Jeongjin and Lennon, Brian and Li, Rui and Li, Senhu and Meinzer, Hans-Peter and Nemeth, G{\'a}bor and Raicu, Daniela S and Rau, Anne-Mareike and van Rikxoort, Eva M and Rousson, Mika{\"e}l and Rusko, L{\'a}szl{\'o} and Saddi, Kinda A and Schmidt, G{\"u}nter and Seghers, Dieter and Shimizu, Akinobu and Slagmolen, Pieter and Sorantin, Erich and Soza, Grzegorz and Susomboon, Ruchaneewan and Waite, Jonathan M and Wimmer, Andreas and Wolf, Ivo} } @article {46423, title = {A contiguous compartment functions as endoplasmic reticulum and endosome/lysosome in Giardia lamblia.}, journal = {Eukaryotic Cell}, volume = {8}, year = {2009}, month = {2009 Nov}, pages = {1665-76}, abstract = {

The dynamic evolution of organelle compartmentalization in eukaryotes and how strictly compartmentalization is maintained are matters of ongoing debate. While the endoplasmic reticulum (ER) is classically envisioned as the site of protein cotranslational translocation, it has recently been proposed to have pluripotent functions. Using transfected reporter constructs, organelle-specific markers, and functional enzyme assays, we now show that in an early-diverging protozoan, Giardia lamblia, endocytosis and subsequent degradation of exogenous proteins occur in the ER or in an adjacent and communicating compartment. The Giardia endomembrane system is simple compared to those of typical eukaryotes. It lacks peroxisomes, a classical Golgi apparatus, and canonical lysosomes. Giardia orthologues of mammalian lysosomal proteases function within an ER-like tubulovesicular compartment, which itself can dynamically communicate with clathrin-containing vacuoles at the periphery of the cell to receive endocytosed proteins. These primitive characteristics support Giardia{\textquoteright}s proposed early branching and could serve as a model to study the compartmentalization of endocytic and lysosomal functions into organelles distinct from the ER. This system also may have functional similarity to the retrograde transport of toxins and major histocompatibility complex class I function in the ER of mammals.

}, keywords = {Endoplasmic Reticulum, Endosomes, Giardia lamblia, Lysosomes, Protozoan Proteins}, issn = {1535-9786}, doi = {10.1128/EC.00123-09}, author = {Abodeely, Marla and DuBois, Kelly N and Hehl, Adrian and Stefanic, Sasa and Sajid, Mohammed and DeSouza, Wanderley and Attias, Marcia and Engel, Juan C and Hsieh, Ivy and Fetter, Richard D and McKerrow, James H} } @article {1555, title = {Crystal structures of the GCaMP calcium sensor reveal the mechanism of fluorescence signal change and aid rational design.}, journal = {The Journal of Biological Chemistry}, volume = {284}, year = {2009}, month = {2009 Mar 6}, pages = {6455-64}, abstract = {

The genetically encoded calcium indicator GCaMP2 shows promise for neural network activity imaging, but is currently limited by low signal-to-noise ratio. We describe x-ray crystal structures as well as solution biophysical and spectroscopic characterization of GCaMP2 in the calcium-free dark state, and in two calcium-bound bright states: a monomeric form that dominates at intracellular concentrations observed during imaging experiments and an unexpected domain-swapped dimer with decreased fluorescence. This series of structures provides insight into the mechanism of Ca2+-induced fluorescence change. Upon calcium binding, the calmodulin (CaM) domain wraps around the M13 peptide, creating a new domain interface between CaM and the circularly permuted enhanced green fluorescent protein domain. Residues from CaM alter the chemical environment of the circularly permuted enhanced green fluorescent protein chromophore and, together with flexible inter-domain linkers, block solvent access to the chromophore. Guided by the crystal structures, we engineered a series of GCaMP2 point mutants to probe the mechanism of GCaMP2 function and characterized one mutant with significantly improved signal-to-noise. The mutation is located at a domain interface and its effect on sensor function could not have been predicted in the absence of structural data.

}, keywords = {Animals, Calcium, Calcium-Binding Proteins, Crystallography, Fluorescent Dyes, Green Fluorescent Proteins, Models, Molecular, Peptides, Protein Binding, Protein Structure, Recombinant Fusion Proteins, Structure-Activity Relationship, Tertiary, X-Ray}, issn = {0021-9258}, doi = {10.1074/jbc.M807657200}, author = {Akerboom, Jasper and Rivera, Jonathan D V{\'e}lez and Guilbe, Mar{\'\i}a M Rodr{\'\i}guez and Malav{\'e}, Elisa C Alfaro and Hernandez, Hector H and Tian, Lin and Hires, S Andrew and Marvin, Jonathan S and Looger, Loren L and Schreiter, Eric R} } @article {47906, title = {Distinct pose of discodermolide in taxol binding pocket drives a complementary mode of microtubule stabilization.}, journal = {Biochemistry}, volume = {48}, year = {2009}, month = {2009 Dec 15}, pages = {11664-77}, abstract = {

The microtubule cytoskeleton has proven to be an effective target for cancer therapeutics. One class of drugs, known as microtubule stabilizing agents (MSAs), binds to microtubule polymers and stabilizes them against depolymerization. The prototype of this group of drugs, Taxol, is an effective chemotherapeutic agent used extensively in the treatment of human ovarian, breast, and lung carcinomas. Although electron crystallography and photoaffinity labeling experiments determined that the binding site for Taxol is in a hydrophobic pocket in beta-tubulin, little was known about the effects of this drug on the conformation of the entire microtubule. A recent study from our laboratory utilizing hydrogen-deuterium exchange (HDX) in concert with various mass spectrometry (MS) techniques has provided new information on the structure of microtubules upon Taxol binding. In the current study we apply this technique to determine the binding mode and the conformational effects on chicken erythrocyte tubulin (CET) of another MSA, discodermolide, whose synthetic analogues may have potential use in the clinic. We confirmed that, like Taxol, discodermolide binds to the taxane binding pocket in beta-tubulin. However, as opposed to Taxol, which has major interactions with the M-loop, discodermolide orients itself away from this loop and toward the N-terminal H1-S2 loop. Additionally, discodermolide stabilizes microtubules mainly via its effects on interdimer contacts, specifically on the alpha-tubulin side, and to a lesser extent on interprotofilament contacts between adjacent beta-tubulin subunits. Also, our results indicate complementary stabilizing effects of Taxol and discodermolide on the microtubules, which may explain the synergy observed between the two drugs in vivo.

}, keywords = {Alkanes, Animals, Binding Sites, Carbamates, Cattle, Chickens, Deuterium Exchange Measurement, Dimerization, Drug Synergism, Lactones, Microtubules, Paclitaxel, Peptide Fragments, Protein Binding, Protein Isoforms, Protein Stability, Pyrones, Tubulin, Tubulin Modulators}, issn = {1520-4995}, doi = {10.1021/bi901351q}, author = {Khrapunovich-Baine, Marina and Menon, Vilas and Verdier-Pinard, Pascal and Smith, Amos B and Angeletti, Ruth Hogue and Fiser, Andras and Horwitz, Susan Band and Xiao, Hui} } @article {46623, title = {Drosophila, a genetic model system to study cocaine-related behaviors: a review with focus on LIM-only proteins.}, journal = {Neuropharmacology}, volume = {56 Suppl 1}, year = {2009}, month = {2009}, pages = {97-106}, abstract = {

In the last decade, the fruit fly Drosophila melanogaster, highly accessible to genetic, behavioral and molecular analyses, has been introduced as a novel model organism to help decipher the complex genetic, neurochemical, and neuroanatomical underpinnings of behaviors induced by drugs of abuse. Here we review these data, focusing specifically on cocaine-related behaviors. Several of cocaine{\textquoteright}s most characteristic properties have been recapitulated in Drosophila. First, cocaine induces motor behaviors in flies that are remarkably similar to those observed in mammals. Second, repeated cocaine administration induces behavioral sensitization a form of behavioral plasticity believed to underlie certain aspects of addiction. Third, a key role for dopaminergic systems in mediating cocaine{\textquoteright}s effects has been demonstrated through both pharmacological and genetic methods. Finally, and most importantly, unbiased genetic screens, feasible because of the simplicity and scale with which flies can be manipulated in the laboratory, have identified several novel genes and pathways whose role in cocaine behaviors had not been anticipated. Many of these genes and pathways have been validated in mammalian models of drug addiction. We focus in this review on the role of LIM-only proteins in cocaine-induced behaviors.

}, keywords = {Animals, Animals, Genetically Modified, Behavior, Animal, Cocaine, Cocaine-Related Disorders, Disease Models, Animal, Dopamine Uptake Inhibitors, Drosophila melanogaster, Drosophila Proteins, Homeodomain Proteins, Models, Genetic}, issn = {0028-3908}, doi = {10.1016/j.neuropharm.2008.07.023}, author = {Heberlein, Ulrike and Tsai, Linus T-Y and Kapfhamer, David and Lasek, Amy W} } @article {5692, title = {Drosophila brain development: closing the gap between a macroarchitectural and microarchitectural approach.}, journal = {Cold Spring Harbor Symposia on Quantitative Biology}, volume = {74}, year = {2009}, month = {2009}, pages = {235-48}, abstract = {

Neurobiologists address neural structure, development, and function at the level of "macrocircuits" (how different brain compartments are interconnected; what overall pattern of activity they produce) and at the level of "microcircuits" (how connectivity and physiology of individual neurons and their processes within a compartment determine the functional output of this compartment). Work in our lab aims at reconstructing the developing Drosophila brain at both levels. Macrocircuits can be approached conveniently by reconstructing the pattern of brain lineages, which form groups of neurons whose projections form cohesive fascicles interconnecting the compartments of the larval and adult brain. The reconstruction of microcircuits requires serial section electron microscopy, due to the small size of terminal neuronal processes and their synaptic contacts. Because of the amount of labor that traditionally comes with this approach, very little is known about microcircuitry in brains across the animal kingdom. Many of the problems of serial electron microscopy reconstruction are now solvable with digital image recording and specialized software for both image acquisition and postprocessing. In this chapter, we introduce our efforts to reconstruct the small Drosophila larval brain and discuss our results in light of the published data on neuropile ultrastructure in other animal taxa.

}, keywords = {Animals, Brain, Cell Lineage, Drosophila, Electron, Genetically Modified, Imaging, Larva, Mice, Microscopy, Models, Nerve Net, Neurites, Neurological, Neuropil, Phylogeny, Species Specificity, Synapses, Three-Dimensional, Transmission}, issn = {1943-4456}, doi = {10.1101/sqb.2009.74.037}, author = {Cardona, A and Saalfeld, S and Tomancak, P and Hartenstein, V.} } @article {4278, title = {A Drosophila resource of transgenic RNAi lines for neurogenetics.}, journal = {Genetics}, volume = {182}, year = {2009}, month = {2009 Aug}, pages = {1089-100}, abstract = {

Conditional expression of hairpin constructs in Drosophila is a powerful method to disrupt the activity of single genes with a spatial and temporal resolution that is impossible, or exceedingly difficult, using classical genetic methods. We previously described a method (Ni et al. 2008) whereby RNAi constructs are targeted into the genome by the phiC31-mediated integration approach using Vermilion-AttB-Loxp-Intron-UAS-MCS (VALIUM), a vector that contains vermilion as a selectable marker, an attB sequence to allow for phiC31-targeted integration at genomic attP landing sites, two pentamers of UAS, the hsp70 core promoter, a multiple cloning site, and two introns. As the level of gene activity knockdown associated with transgenic RNAi depends on the level of expression of the hairpin constructs, we generated a number of derivatives of our initial vector, called the "VALIUM" series, to improve the efficiency of the method. Here, we report the results from the systematic analysis of these derivatives and characterize VALIUM10 as the most optimal vector of this series. A critical feature of VALIUM10 is the presence of gypsy insulator sequences that boost dramatically the level of knockdown. We document the efficacy of VALIUM as a vector to analyze the phenotype of genes expressed in the nervous system and have generated a library of 2282 constructs targeting 2043 genes that will be particularly useful for studies of the nervous system as they target, in particular, transcription factors, ion channels, and transporters.

}, keywords = {Animals, Carrier Proteins, Drosophila, Gene Knockdown Techniques, Ion Channels, Methods, Nervous System, RNA, RNA Interference, Small Interfering, Transcription Factors}, issn = {1943-2631}, doi = {10.1534/genetics.109.103630}, author = {Ni, Jian-Quan and Liu, Lu-Ping and Binari, Richard and Hardy, Robert and Shim, Hye-Seok and Cavallaro, Amanda and Booker, Matthew and Pfeiffer, Barret D and Markstein, Michele and Wang, Hui and Villalta, Christians and Laverty, Todd R and Perkins, Lizabeth A and Perrimon, Norbert} } @article {2905, title = {Electro-optical imaging microscopy of dye-doped artificial lipidic membranes.}, journal = {Biophysical Journal}, volume = {97}, year = {2009}, month = {2009 Dec 2}, pages = {2913-21}, abstract = {

Artificial lipidic bilayers are widely used as a model for the lipid matrix in biological cell membranes. We use the Pockels electro-optical effect to investigate the properties of an artificial lipidic membrane doped with nonlinear molecules in the outer layer. We report here what is believed to be the first electro-optical Pockels signal and image from such a membrane. The electro-optical dephasing distribution within the membrane is imaged and the signal is shown to be linear as a function of the applied voltage. A theoretical analysis taking into account the statistical orientation distribution of the inserted dye molecules allows us to estimate the doped membrane nonlinearity. Ongoing extensions of this work to living cell membranes are discussed.

}, keywords = {Artificial, Cell Membrane, Coloring Agents, Lipid Bilayers, Membrane Potentials, Membranes, Microfluidic Analytical Techniques, Microscopy, Molecular Imaging, Optical Processes, Phosphatidylcholines, Potentiometry, Pyridinium Compounds}, issn = {1542-0086}, doi = {10.1016/j.bpj.2009.08.055}, author = {Hajj, Bassam and De Reguardati, Sophie and Hugonin, Lo\"{\i}c and Le Pioufle, Bruno and Osaki, Toshihisa and Suzuki, Hiroaki and Takeuchi, Shoji and Mojzisova, Halina and Chauvat, Dominique and Zyss, Joseph} } @article {796, title = {Endodomain diversity in the Drosophila Dscam and its roles in neuronal morphogenesis.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {29}, year = {2009}, month = {2009 Feb 11}, pages = {1904-14}, abstract = {

Drosophila Down syndrome cell adhesion molecule (Dscam) can be variably spliced to encode 152,064 distinct single-pass transmembrane proteins. In addition to 19,008 possible ectodomains and two alternative transmembrane segments, it may carry endodomains containing or lacking exons 19 and 23. Here, we determine the role of Dscam endodomain diversity in neural development. Dscam with full-length endodomain is largely restricted to embryogenesis. In contrast, most Dscams lack exons 19 and 23 at postembryonic stages. As implicated from the expression patterns, removal of Dscam exon 19-containing variants disrupts wiring of embryonic neurons while silencing of Dscam transcripts lacking exon 19 or exon 23 effectively blocks postembryonic neuronal morphogenesis. Furthermore, compared with exon 19-containing Dscam, transgenic Dscam without exon 19 is more efficiently targeted to neurites and more potently suppresses axon bifurcation in Dscam mutant neurons. In sum, Dscam with or without exon 19 in its endodomain is used to govern different stage-specific neuronal morphogenetic processes, possibly due to differences in protein targeting.

}, keywords = {Amino Acid Motifs, Amino Acid Sequence, Animals, Cell Adhesion Molecules, Drosophila, Drosophila Proteins, Gene Targeting, Genetically Modified, Molecular Sequence Data, Morphogenesis, Neurogenesis, Neurons, Protein Structure, Tertiary}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.5743-08.2009}, author = {Yu, Hung-Hsiang and Yang, Jacob S and Wang, Jian and Huang, Yaling and Lee, Tzumin} } @article {4267, title = {Experience-dependent structural synaptic plasticity in the mammalian brain.}, journal = {Nature Reviews Neuroscience}, volume = {10}, year = {2009}, month = {2009 Sep}, pages = {647-58}, abstract = {

Synaptic plasticity in adult neural circuits may involve the strengthening or weakening of existing synapses as well as structural plasticity, including synapse formation and elimination. Indeed, long-term in vivo imaging studies are beginning to reveal the structural dynamics of neocortical neurons in the normal and injured adult brain. Although the overall cell-specific morphology of axons and dendrites, as well as of a subpopulation of small synaptic structures, are remarkably stable, there is increasing evidence that experience-dependent plasticity of specific circuits in the somatosensory and visual cortex involves cell type-specific structural plasticity: some boutons and dendritic spines appear and disappear, accompanied by synapse formation and elimination, respectively. This Review focuses on recent evidence for such structural forms of synaptic plasticity in the mammalian cortex and outlines open questions.

}, keywords = {Animals, Brain, Humans, Nerve Net, Neurogenesis, Neuronal Plasticity, Synapses}, issn = {1471-0048}, doi = {10.1038/nrn2699}, author = {Holtmaat, Anthony and Svoboda, Karel} } @article {1116, title = {Exploring the pharmacokinetic properties of phosphorus-containing selective HDAC 1 and 2 inhibitors (SHI-1:2).}, journal = {Bioorganic \& Medicinal Chemistry Letters}, volume = {19}, year = {2009}, month = {2009 Apr 1}, pages = {2053-8}, abstract = {

We report the preparation and structure-activity relationships of phosphorus-containing histone deacetylase inhibitors. A strong trend between decreasing phosphorus functional group size and superior mouse pharmacokinetic properties was identified. In addition, optimized candidates showed tumor growth inhibition in xenograft studies.

}, keywords = {Administration, Animals, Antineoplastic Agents, Enzyme Inhibitors, Heterologous, Histone Deacetylase 1, Histone Deacetylase 2, Histone Deacetylase Inhibitors, Histone Deacetylases, Mice, Nude, Oral, Phosphonic Acids, Repressor Proteins, Transplantation}, issn = {1464-3405}, doi = {10.1016/j.bmcl.2009.02.009}, author = {Heidebrecht, Richard W and Chenard, Melissa and Close, Joshua and Dahlberg, William K and Fleming, Judith and Grimm, Jonathan B and Hamill, Julie E and Harsch, Andreas and Haines, Brian B and Hughes, Bethany and Kral, Astrid M and Middleton, Richard E and Mushti, Chandrasekhar and Ozerova, Nicole and Szewczak, Alexander A and Wang, Hongmei and Wilson, Kevin and Witter, David J and Secrist, J Paul and Miller, Thomas A} } @article {3913, title = {Fast synaptic subcortical control of hippocampal circuits.}, journal = {Science}, volume = {326}, year = {2009}, month = {2009 Oct 16}, pages = {449-53}, abstract = {

Cortical information processing is under state-dependent control of subcortical neuromodulatory systems. Although this modulatory effect is thought to be mediated mainly by slow nonsynaptic metabotropic receptors, other mechanisms, such as direct synaptic transmission, are possible. Yet, it is currently unknown if any such form of subcortical control exists. Here, we present direct evidence of a strong, spatiotemporally precise excitatory input from an ascending neuromodulatory center. Selective stimulation of serotonergic median raphe neurons produced a rapid activation of hippocampal interneurons. At the network level, this subcortical drive was manifested as a pattern of effective disynaptic GABAergic inhibition that spread throughout the circuit. This form of subcortical network regulation should be incorporated into current concepts of normal and pathological cortical function.

}, keywords = {Afferent, Animals, Electric Stimulation, Excitatory Postsynaptic Potentials, Glutamic Acid, Hippocampus, Inhibitory Postsynaptic Potentials, Interneurons, Mice, Neural Inhibition, Neural Pathways, Neurons, Patch-Clamp Techniques, Photic Stimulation, Raphe Nuclei, Rats, Serotonin, Sprague-Dawley, Synapses, Synaptic Potentials}, issn = {1095-9203}, doi = {10.1126/science.1178307}, author = {Varga, Viktor and Losonczy, Attila and Zemelman, Boris V and Borhegyi, Zsolt and Nyiri, G{\'a}bor and Domonkos, Andor and Hangya, Bal{\'a}zs and Holderith, No{\'e}mi and Magee, Jeffrey C and Freund, Tam{\'a}s F} } @article {5351, title = {Fast throughput low voltage scanning transmission electron microscope imaging of nano-resolution three dimensional tissue.}, journal = {Microscopy and Microanalysis}, volume = {15}, year = {2009}, month = {2009 Jul 26}, pages = {642-3}, doi = {10.1017/S1431927609092435}, author = {Bolorizadeh, Mehdi and Hess, Harald F} } @article {68816, title = {Functional Role of a Specialized Class of Spinal Commissural Inhibitory Neurons during Fast Escapes in Zebrafish}, journal = {Journal of Neuroscience}, volume = {29}, year = {2009}, month = {05/2009}, pages = {6780{\textendash}6793}, abstract = {

In teleost fish, the Mauthner (M) cell, a large reticulospinal neuron in the brainstem, triggers escape behavior. Spinal commissural inhibitory interneurons that are electrotonically excited by the M-axon have been identified, but the behavioral roles of these neurons have not yet been addressed. Here, we studied these neurons, named CoLo (commissural local), in larval zebrafish using an enhancer-trap line in which the entire population of CoLos was visualized by green fluorescent protein. CoLos were present at one cell per hemi-segment. Electrophysiological recordings showed that an M-spike evoked a spike in CoLos via electrotonic transmission and that CoLos made monosynaptic inhibitory connections onto contralateral primary motoneurons, consistent with the results in adult goldfish. We further showed that CoLos were active only during escapes. We examined the behavioral roles of CoLos by investigating escape behaviors in CoLo-ablated larvae. The results showed that the escape behaviors evoked by sound/vibration stimuli were often impaired with a reduced initial bend of the body, indicating that CoLos play important roles in initiating escapes. We obtained several lines of evidence that strongly suggested that the impaired escapes occurred during bilateral activation of the M-cells: in normal larvae, CoLo-mediated inhibitory circuits enable animals to perform escapes even in these occasions by silencing the output of the slightly delayed firing of the second M-cell. This study illustrates (1) a clear example of the behavioral role of a specialized class of interneurons and (2) the capacity of the spinal circuits to filter descending commands and thereby produce the appropriate behavior.

}, issn = {0270-6474}, doi = {10.1523/JNEUROSCI.0801-09.2009}, url = {https://www.jneurosci.org/content/29/21/6780}, author = {Chie Satou and Yukiko Kimura and Tsunehiko Kohashi and Kazuki Horikawa and Hiroyuki Takeda and Yoichi Oda and Shin-ichi Higashijima} } @article {46621, title = {Genetic aspects of behavioral neurotoxicology.}, journal = {Neurotoxicology}, volume = {30}, year = {2009}, month = {2009 Sep}, pages = {741-53}, abstract = {

Considerable progress has been made over the past couple of decades concerning the molecular bases of neurobehavioral function and dysfunction. The field of neurobehavioral genetics is becoming mature. Genetic factors contributing to neurologic diseases such as Alzheimer{\textquoteright}s disease have been found and evidence for genetic factors contributing to other diseases such as schizophrenia and autism are likely. This genetic approach can also benefit the field of behavioral neurotoxicology. It is clear that there is substantial heterogeneity of response with behavioral impairments resulting from neurotoxicants. Many factors contribute to differential sensitivity, but it is likely that genetic variability plays a prominent role. Important discoveries concerning genetics and behavioral neurotoxicity are being made on a broad front from work with invertebrate and piscine mutant models to classic mouse knockout models and human epidemiologic studies of polymorphisms. Discovering genetic factors of susceptibility to neurobehavioral toxicity not only helps identify those at special risk, it also advances our understanding of the mechanisms by which toxicants impair neurobehavioral function in the larger population. This symposium organized by Edward Levin and Annette Kirshner, brought together researchers from the laboratories of Michael Aschner, Douglas Ruden, Ulrike Heberlein, Edward Levin and Kathleen Welsh-Bohmer conducting studies with Caenorhabditis elegans, Drosophila, fish, rodents and humans studies to determine the role of genetic factors in susceptibility to behavioral impairment from neurotoxic exposure.

}, keywords = {Animals, Behavior, Disease Models, Animal, Genetics, Humans, Neurotoxicity Syndromes, Neurotoxins, Phylogeny, Toxicology}, issn = {1872-9711}, doi = {10.1016/j.neuro.2009.07.014}, author = {Levin, Edward D and Aschner, Michael and Heberlein, Ulrike and Ruden, Douglas and Welsh-Bohmer, Kathleen A and Bartlett, Selena and Berger, Karen and Chen, Lang and Corl, Ammon B and Eddins, Donnie and French, Rachael and Hayden, Kathleen M and Helmcke, Kirsten and Hirsch, Helmut V B and Linney, Elwood and Lnenicka, Greg and Page, Grier P and Possidente, Debra and Possidente, Bernard and Kirshner, Annette} } @article {5485, title = {Glycogen synthase kinase-3/Shaggy mediates ethanol-induced excitotoxic cell death of Drosophila olfactory neurons.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, year = {2009}, month = {2009 Dec 8}, pages = {20924-9}, abstract = {

It has long been known that heavy alcohol consumption leads to neuropathology and neuronal death. While the response of neurons to an ethanol insult is strongly influenced by genetic background, the underlying mechanisms are poorly understood. Here, we show that even a single intoxicating exposure to ethanol causes non-cell-autonomous apoptotic death specifically of Drosophila olfactory neurons, which is accompanied by a loss of a behavioral response to the smell of ethanol and a blackening of the third antennal segment. The Drosophila homolog of glycogen synthase kinase-3 (GSK-3)beta, Shaggy, is required for ethanol-induced apoptosis. Consistent with this requirement, the GSK-3beta inhibitor lithium protects against the neurotoxic effects of ethanol, indicating the possibility for pharmacological intervention in cases of alcohol-induced neurodegeneration. Ethanol-induced death of olfactory neurons requires both their neural activity and functional NMDA receptors. This system will allow the investigation of the genetic and molecular basis of ethanol-induced apoptosis in general and provide an understanding of the molecular role of GSK-3beta in programmed cell death.

}, keywords = {Amino Acid, Animals, Cell Death, Drosophila melanogaster, Drosophila Proteins, Electricity, Ethanol, Gene Silencing, Glycogen Synthase Kinase 3, Lithium, N-Methyl-D-Aspartate, Neurotoxins, Olfactory Receptor Neurons, Receptors, Sequence Homology, Volatilization}, issn = {1091-6490}, doi = {10.1073/pnas.0910813106}, author = {French, Rachael L and Heberlein, Ulrike} } @article {5481, title = {Happyhour, a Ste20 family kinase, implicates EGFR signaling in ethanol-induced behaviors.}, journal = {Cell}, volume = {137}, year = {2009}, month = {2009 May 29}, pages = {949-60}, abstract = {

The consequences of alcohol use disorders (AUDs) are devastating to individuals and society, yet few treatments are currently available. To identify genes regulating the behavioral effects of ethanol, we conducted a genetic screen in Drosophila and identified a mutant, happyhour (hppy), due to its increased resistance to the sedative effects of ethanol. Hppy protein shows strong homology to mammalian Ste20 family kinases of the GCK-1 subfamily. Genetic and biochemical experiments revealed that the epidermal growth factor (EGF)-signaling pathway regulates ethanol sensitivity in Drosophila and that Hppy functions as an inhibitor of the pathway. Acute pharmacological inhibition of the EGF receptor (EGFR) in adult animals altered acute ethanol sensitivity in both flies and mice and reduced ethanol consumption in a preclinical rat model of alcoholism. Inhibitors of the EGFR or components of its signaling pathway are thus potential pharmacotherapies for AUDs.

}, keywords = {Alcohol-Induced Disorders, Animal, Animals, Crosses, Disease Models, Dopamine, Drosophila melanogaster, Drosophila Proteins, Epidermal Growth Factor, Ethanol, Female, Genetic, Insulin, Male, Mice, Mutation, Phosphorylation, Protein-Serine-Threonine Kinases, Receptor, Signal Transduction}, issn = {1097-4172}, doi = {10.1016/j.cell.2009.03.020}, author = {Corl, Ammon B and Berger, Karen H and Ophir-Shohat, Galit and Gesch, Julie and Simms, Jeffrey A and Bartlett, Selena E and Heberlein, Ulrike} } @article {5237, title = {Hydrogen peroxide stimulates activity and alters behavior in Drosophila melanogaster.}, journal = {PLoS One}, volume = {4}, year = {2009}, month = {2009 Oct 28}, pages = {e7580}, abstract = {

Circadian rhythms in animals are regulated at the level of individual cells and by systemic signaling to coordinate the activities of multiple tissues. The circadian pacemakers have several physiological outputs, including daily locomotor rhythms. Several redox-active compounds have been found to function in regulation of circadian rhythms in cells, however, how particular compounds might be involved in regulating specific animal behaviors remains largely unknown. Here the effects of hydrogen peroxide on Drosophila movement were analyzed using a recently developed three-dimensional real-time multiple fly tracking assay. Both hydrogen peroxide feeding and direct injection of hydrogen peroxide caused increased adult fly locomotor activity. Continuous treatment with hydrogen peroxide also suppressed daily locomotor rhythms. Conditional over-expression of the hydrogen peroxide-producing enzyme superoxide dismutase (SOD) also increased fly activity and altered the patterns of locomotor activity across days and weeks. The real-time fly tracking system allowed for detailed analysis of the effects of these manipulations on behavior. For example, both hydrogen peroxide feeding and SOD over-expression increased all fly motion parameters, however, hydrogen peroxide feeding caused relatively more erratic movement, whereas SOD over-expression produced relatively faster-moving flies. Taken together, the data demonstrate that hydrogen peroxide has dramatic effects on fly movement and daily locomotor rhythms, and implicate hydrogen peroxide in the normal control of these processes.

}, keywords = {Animal, Animals, Behavior, Biological, Crosses, Drosophila melanogaster, Flight, Fluorescence, Genetic, Genetically Modified, Hydrogen Peroxide, Microscopy, Models, Movement, Oxidants, Oxidation-Reduction, Seasons, Superoxide Dismutase, Time Factors}, issn = {1932-6203}, doi = {10.1371/journal.pone.0007580}, author = {Grover, Dhruv and Ford, Daniel and Brown, Christopher and Hoe, Nicholas and Erdem, Aysen and Tavar{\'e}, Simon and Tower, John} } @article {1646, title = {Imaging neural activity in worms, flies and mice with improved GCaMP calcium indicators.}, journal = {Nature Methods}, volume = {6}, year = {2009}, month = {2009 Dec}, pages = {875-81}, abstract = {

Genetically encoded calcium indicators (GECIs) can be used to image activity in defined neuronal populations. However, current GECIs produce inferior signals compared to synthetic indicators and recording electrodes, precluding detection of low firing rates. We developed a single-wavelength GCaMP2-based GECI (GCaMP3), with increased baseline fluorescence (3-fold), increased dynamic range (3-fold) and higher affinity for calcium (1.3-fold). We detected GCaMP3 fluorescence changes triggered by single action potentials in pyramidal cell dendrites, with signal-to-noise ratio and photostability substantially better than those of GCaMP2, D3cpVenus and TN-XXL. In Caenorhabditis elegans chemosensory neurons and the Drosophila melanogaster antennal lobe, sensory stimulation-evoked fluorescence responses were significantly enhanced with GCaMP3 (4-6-fold). In somatosensory and motor cortical neurons in the intact mouse, GCaMP3 detected calcium transients with amplitudes linearly dependent on action potential number. Long-term imaging in the motor cortex of behaving mice revealed large fluorescence changes in imaged neurons over months.

}, keywords = {Animals, Brain, Caenorhabditis elegans, Calcium, Cell Line, Drosophila melanogaster, Fluorescence Resonance Energy Transfer, Humans, Mice, Neurons}, issn = {1548-7105}, doi = {10.1038/nmeth.1398}, author = {Tian, Lin and Hires, S Andrew and Mao, Tianyi and Huber, Daniel and Chiappe, M Eugenia and Chalasani, Sreekanth H and Petreanu, Leopoldo and Akerboom, Jasper and McKinney, Sean A and Schreiter, Eric R and Bargmann, Cornelia I and Jayaraman, Vivek and Svoboda, Karel and Looger, Loren L} } @article {927, title = {Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, year = {2009}, month = {2009 Mar 3}, pages = {3125-30}, abstract = {

Understanding molecular-scale architecture of cells requires determination of 3D locations of specific proteins with accuracy matching their nanometer-length scale. Existing electron and light microscopy techniques are limited either in molecular specificity or resolution. Here, we introduce interferometric photoactivated localization microscopy (iPALM), the combination of photoactivated localization microscopy with single-photon, simultaneous multiphase interferometry that provides sub-20-nm 3D protein localization with optimal molecular specificity. We demonstrate measurement of the 25-nm microtubule diameter, resolve the dorsal and ventral plasma membranes, and visualize the arrangement of integrin receptors within endoplasmic reticulum and adhesion complexes, 3D protein organization previously resolved only by electron microscopy. iPALM thus closes the gap between electron tomography and light microscopy, enabling both molecular specification and resolution of cellular nanoarchitecture.

}, keywords = {Animals, Cell Line, Cercopithecus aethiops, Fluorescence, Humans, Imaging, Interference, Microscopy, Microtubules, Three-Dimensional}, issn = {1091-6490}, doi = {10.1073/pnas.0813131106}, author = {Shtengel, Gleb and Galbraith, James A and Galbraith, Catherine G and Lippincott-Schwartz, Jennifer and Gillette, Jennifer M and Manley, Suliana and Sougrat, Rachid and Waterman, Clare M and Kanchanawong, Pakorn and Davidson, Michael W and Fetter, Richard D and Hess, Harald F} } @proceedings {46329, title = {Maximin affinity learning of image segmentation}, volume = {22}, year = {2009}, publisher = {MIT Press}, abstract = {

Images can be segmented by first using a classifier to predict an affinity graph that reflects the degree to which image pixels must be grouped together and then partitioning the graph to yield a segmentation. Machine learning has been applied to the affinity classifier to produce affinity graphs that are good in the sense of minimizing edge misclassification rates. However, this error measure is only indirectly related to the quality of segmentations produced by ultimately partitioning the affinity graph. We present the first machine learning algorithm for training a classifier to produce affinity graphs that are good in the sense of producing segmentations that directly minimize the Rand index, a well known segmentation performance measure. The Rand index measures segmentation performance by quantifying the classification of the connectivity of image pixel pairs after segmentation. By using the simple graph partitioning algorithm of finding the connected components of the thresholded affinity graph, we are able to train an affinity classifier to directly minimize the Rand index of segmentations resulting from the graph partitioning. Our learning algorithm corresponds to the learning of maximin affinities between image pixel pairs, which are predictive of the pixel-pair connectivity.

}, author = {Srinivas C. Turaga and Kevin Briggman and Moritz N. Helmstaedter and Winfried Denk and Sebastian Seung} } @article {6342, title = {Molecular interactions in rotavirus assembly and uncoating seen by high-resolution cryo-EM.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, year = {2009}, month = {2009 Jun 30}, pages = {10644-8}, abstract = {

Rotaviruses, major causes of childhood gastroenteritis, are nonenveloped, icosahedral particles with double-strand RNA genomes. By the use of electron cryomicroscopy and single-particle reconstruction, we have visualized a rotavirus particle comprising the inner capsid coated with the trimeric outer-layer protein, VP7, at a resolution (4 A) comparable with that of X-ray crystallography. We have traced the VP7 polypeptide chain, including parts not seen in its X-ray crystal structure. The 3 well-ordered, 30-residue, N-terminal "arms" of each VP7 trimer grip the underlying trimer of VP6, an inner-capsid protein. Structural differences between free and particle-bound VP7 and between free and VP7-coated inner capsids may regulate mRNA transcription and release. The Ca(2+)-stabilized VP7 intratrimer contact region, which presents important neutralizing epitopes, is unaltered upon capsid binding.

}, keywords = {Antigens, Biological, Calcium, Capsid Proteins, Cryoelectron Microscopy, Crystallography, Models, Molecular, Protein Multimerization, Protein Structure, Quaternary, Rotavirus, Viral, Viral Core Proteins, Virion, X-Ray}, issn = {1091-6490}, doi = {10.1073/pnas.0904024106}, author = {Chen, James Z and Settembre, Ethan C and Aoki, Scott T and Zhang, Xing and Bellamy, A Richard and Dormitzer, Philip R and Harrison, Stephen C and Grigorieff, Nikolaus} } @article {2497, title = {The molecular mechanisms of cuticular melanization: the ecdysone cascade leading to dopa decarboxylase expression in Manduca sexta.}, journal = {Insect Biochemistry and Molecular Biology}, volume = {39}, year = {2009}, month = {2009 Apr}, pages = {245-53}, abstract = {

Many insect developmental color changes are known to be regulated by both ecdysone and juvenile hormone. Yet the molecular mechanisms underlying this regulation have not been well understood. This review highlights the hormonal mechanisms involved in the regulation of two key enzymes [dopa decarboxylase (DDC) and phenoloxidase] necessary for insect cuticular melanization, and the molecular action of 20-hydroxyecdysone on various transcription factors leading to DDC expression at the end of a larval molt in Manduca sexta. In addition, the ecdysone cascade found in M. sexta is compared with that of other organisms.

}, keywords = {Animals, Developmental, Dopa Decarboxylase, Ecdysone, Gene Expression Regulation, Insect Proteins, Manduca, Melanins}, issn = {1879-0240}, doi = {10.1016/j.ibmb.2009.01.008}, author = {Hiruma, Kiyoshi and Riddiford, Lynn M} } @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 {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 {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 {5486, title = {Oviposition preference for and positional avoidance of acetic acid provide a model for competing behavioral drives in Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, year = {2009}, month = {2009 Jul 7}, pages = {11352-7}, abstract = {

Selection of appropriate oviposition sites is essential for progeny survival and fitness in generalist insect species, such as Drosophila melanogaster, yet little is known about the mechanisms regulating how environmental conditions and innate adult preferences are evaluated and balanced to yield the final substrate choice for egg-deposition. Female D. melanogaster are attracted to food containing acetic acid (AA) as an oviposition substrate. However, our observations reveal that this egg-laying preference is a complex process, as it directly opposes an otherwise strong, default behavior of positional avoidance for the same food. We show that 2 distinct sensory modalities detect AA. Attraction to AA-containing food for the purpose of egg-laying relies on the gustatory system, while positional repulsion depends primarily on the olfactory system. Similarly, distinct central brain regions are involved in AA attraction and repulsion. Given this unique situation, in which a single environmental stimulus yields 2 opposing behavioral outputs, we propose that the interaction of egg-laying attraction and positional aversion for AA provides a powerful model for studying how organisms balance competing behavioral drives and integrate signals involved in choice-like processes.

}, keywords = {Acetic Acid, Animal, Animal Feed, Animals, Avoidance Learning, Biological, Brain, Drosophila melanogaster, Female, Hydrogen-Ion Concentration, Models, Neurons, Olfactory Pathways, Oviposition, Sexual Behavior, Taste}, issn = {1091-6490}, doi = {10.1073/pnas.0901419106}, author = {Joseph, Ryan M and Devineni, Anita V and King, Ian F G and Heberlein, Ulrike} } @article {4441, title = {The phase diagram and the pathway of phase transitions for traffic flow in a circular one-lane roadway.}, journal = {Physica A: Statistical Mechanics and its Applications}, volume = {388}, year = {2009}, month = {2009 Apr 15}, pages = {1665-72}, abstract = {

This paper demonstrates that patient driving habits lead to homogenous congested flow while impatient driving habits lead to wide-moving jam flow in the high density region based on the numerical simulation of the intelligent driver model proposed by M.Treiber [M. Treiber, A.Hennecke, D. Helbing, Phys. Rev. E 62 (2) (2000), 1805{\textendash}1824]. In a circular one lane traffic system which includes homogeneous drivers, we obtain the stable condition of homogenous flow and the phase diagram of traffic flow based on the linearization analysis. The phase diagram shows three possible pathways of phase transition along with the increase of global density: from the homogenous free flow to the homogenous congested flow directly, from the homogenous free flow to the synchronized flow then to the homogenous congested flow, or from the homogenous free flow to synchronized flow then to the wide-moving jam flow. The paper also analyzes the traffic flow including heterogenous drivers, and the results indicate that homogenous congested flow will lose its stability when the proportion of impatient drivers reaches a critical value and some new kinds of traffic flow emerge: wide-moving jam flow or a mixture of synchronized flow and wide-moving jam flow.

}, author = {Wei, Ziqiang and Hong, Yiguang and Wang, Dahui} } @article {4526, title = {Preferential ethanol consumption in Drosophila models features of addiction.}, journal = {Current Biology}, volume = {19}, year = {2009}, month = {2009 Dec 29}, pages = {2126-32}, abstract = {

Alcohol addiction is a common affliction with a strong genetic component [1]. Although mammalian studies have provided significant insight into the molecular mechanisms underlying ethanol consumption [2], other organisms such as Drosophila melanogaster are better suited for unbiased, forward genetic approaches to identify novel genes. Behavioral responses to ethanol, such as hyperactivity, sedation, and tolerance, are conserved between flies and mammals [3, 4], as are the underlying molecular pathways [5-9]. However, few studies have investigated ethanol self-administration in flies [10]. Here we characterize ethanol consumption and preference in Drosophila. Flies prefer to consume ethanol-containing food over regular food, and this preference increases over time. Flies are attracted to the smell of ethanol, which partially mediates ethanol preference, but are averse to its taste. Preference for consuming ethanol is not entirely explained by attraction to either its sensory or caloric properties. We demonstrate that flies can exhibit features of alcohol addiction. First, flies self-administer ethanol to pharmacologically relevant concentrations. Second, flies will overcome an aversive stimulus in order to consume ethanol. Third, flies rapidly return to high levels of ethanol consumption after a period of imposed abstinence. Thus, ethanol preference in Drosophila provides a new model for studying aspects of addiction.

}, keywords = {Alcohol Drinking, Alcoholism, Analysis of Variance, Animal, Animals, Disease Models, Drosophila melanogaster, Drosophila Proteins, Ethanol, Eukaryotic Initiation Factor-5, Food Preferences, Smell, Taste}, issn = {1879-0445}, doi = {10.1016/j.cub.2009.10.070}, author = {Devineni, Anita V and Heberlein, Ulrike} } @article {6491, title = {A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale.}, journal = {PLoS Computational Biology}, volume = {5}, year = {2009}, month = {2009 Mar}, pages = {e1000334}, abstract = {

In this era of complete genomes, our knowledge of neuroanatomical circuitry remains surprisingly sparse. Such knowledge is critical, however, for both basic and clinical research into brain function. Here we advocate for a concerted effort to fill this gap, through systematic, experimental mapping of neural circuits at a mesoscopic scale of resolution suitable for comprehensive, brainwide coverage, using injections of tracers or viral vectors. We detail the scientific and medical rationale and briefly review existing knowledge and experimental techniques. We define a set of desiderata, including brainwide coverage; validated and extensible experimental techniques suitable for standardization and automation; centralized, open-access data repository; compatibility with existing resources; and tractability with current informatics technology. We discuss a hypothetical but tractable plan for mouse, additional efforts for the macaque, and technique development for human. We estimate that the mouse connectivity project could be completed within five years with a comparatively modest budget.

}, keywords = {Animals, Brain, Databases, Factual, Humans, Macaca, Mice, Models, Nerve Net, Neuroanatomy, Neurological, Research Design}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1000334}, author = {Bohland, Jason W and Wu, Caizhi and Barbas, Helen and Bokil, Hemant and Bota, Mihail and Breiter, Hans C and Cline, Hollis T and Doyle, John C and Freed, Peter J and Greenspan, Ralph J and Haber, Suzanne N and Hawrylycz, Michael and Herrera, Daniel G and Hilgetag, Claus C and Huang, Z Josh and Jones, Allan and Jones, Edward G and Karten, Harvey J and Kleinfeld, David and K{\"o}tter, Rolf and Lester, Henry A and Lin, John M and Mensh, Brett D and Mikula, Shawn and Panksepp, Jaak and Price, Joseph L and Safdieh, Joseph and Saper, Clifford B and Schiff, Nicholas D and Schmahmann, Jeremy D and Stillman, Bruce W and Svoboda, Karel and Swanson, Larry W and Toga, Arthur W and Van Essen, David C and Watson, James D and Mitra, Partha P} } @article {5253, title = {Rapid functional maturation of nascent dendritic spines.}, journal = {Neuron}, volume = {61}, year = {2009}, month = {2009 Jan 29}, pages = {247-58}, abstract = {

Spine growth and retraction with synapse formation and elimination plays an important role in shaping brain circuits during development and in the adult brain, yet the temporal relationship between spine morphogenesis and the formation of functional synapses remains poorly defined. We imaged hippocampal pyramidal neurons to identify spines of different ages. We then used two-photon glutamate uncaging, whole-cell recording, and Ca(2+) imaging to analyze the properties of nascent spines and their older neighbors. New spines expressed glutamate-sensitive currents that were indistinguishable from mature spines of comparable volumes. Some spines exhibited negligible AMPA receptor-mediated responses, but the occurrence of these "silent" spines was uncorrelated with spine age. In contrast, NMDA receptor-mediated Ca(2+) accumulations were significantly lower in new spines. New spines reconstructed using electron microscopy made synapses. Our data support a model in which outgrowth and enlargement of nascent spines is tightly coupled to formation and maturation of glutamatergic synapses.

}, keywords = {AMPA, Animals, Calcium, Calcium Signaling, Cell Differentiation, Confocal, Dendritic Spines, Electron, Glutamic Acid, Hippocampus, Microscopy, Neuronal Plasticity, Organ Culture Techniques, Patch-Clamp Techniques, Pyramidal Cells, Rats, Receptors, Synapses, Synaptic Membranes, Synaptic Transmission, Time Factors, Transmission}, issn = {1097-4199}, doi = {10.1016/j.neuron.2008.10.054}, author = {Zito, Karen and Scheuss, Volker and Knott, Graham and Hill, Travis and Svoboda, Karel} } @article {2780, title = {Reactive astrocytes in glial scar attract olfactory ensheathing cells migration by secreted TNF-alpha in spinal cord lesion of rat.}, journal = {PLoS One}, volume = {4}, year = {2009}, month = {2009 Dec 3}, pages = {e8141}, abstract = {

After spinal cord injury (SCI), the formation of glial scar contributes to the failure of injured adult axons to regenerate past the lesion. Increasing evidence indicates that olfactory ensheathing cells (OECs) implanted into spinal cord are found to migrate into the lesion site and induce axons regeneration beyond glial scar and resumption of functions. However, little is known about the mechanisms of OECs migrating from injection site to glial scar/lesion site.

}, keywords = {Animals, Astrocytes, Cell Movement, Cicatrix, Conditioned, Culture Media, Enzyme Activation, Mitogen-Activated Protein Kinases, Olfactory Pathways, Rats, Receptors, Spinal Cord, Sprague-Dawley, Tumor Necrosis Factor, Tumor Necrosis Factor-alpha, Type I}, issn = {1932-6203}, doi = {10.1364/AO.50.001792}, author = {Su, Zhida and Yuan, Yimin and Chen, Jingjing and Cao, Li and Zhu, Yanling and Gao, Liang and Qiu, Yang and He, Cheng} } @article {1246, title = {Reconstruction of sparse circuits using multi-neuronal excitation (RESCUME).}, journal = {Neural Information Processing Systems}, volume = {22}, year = {2009}, month = {2009}, pages = {790-8}, abstract = {

One of the central problems in neuroscience is reconstructing synaptic connectivity in neural circuits. Synapses onto a neuron can be probed by sequentially stimulating potentially pre-synaptic neurons while monitoring the membrane voltage of the post-synaptic neuron. Reconstructing a large neural circuit using such a "brute force" approach is rather time-consuming and inefficient because the connectivity in neural circuits is sparse. Instead, we propose to measure a post-synaptic neuron{\textquoteright}s voltage while stimulating sequentially random subsets of multiple potentially pre-synaptic neurons. To reconstruct these synaptic connections from the recorded voltage we apply a decoding algorithm recently developed for compressive sensing. Compared to the brute force approach, our method promises significant time savings that grow with the size of the circuit. We use computer simulations to find optimal stimulation parameters and explore the feasibility of our reconstruction method under realistic experimental conditions including noise and non-linear synaptic integration. Multineuronal stimulation allows reconstructing synaptic connectivity just from the spiking activity of post-synaptic neurons, even when sub-threshold voltage is unavailable. By using calcium indicators, voltage-sensitive dyes, or multi-electrode arrays one could monitor activity of multiple postsynaptic neurons simultaneously, thus mapping their synaptic inputs in parallel, potentially reconstructing a complete neural circuit.

}, author = {Hu, Tao and Chklovskii, Dmitri B} } @article {5249, title = {Reverse engineering the mouse brain.}, journal = {Nature}, volume = {461}, year = {2009}, month = {2009 Oct 15}, pages = {923-9}, abstract = {

Behaviour is governed by activity in highly structured neural circuits. Genetically targeted sensors and switches facilitate measurement and manipulation of activity in vivo, linking activity in defined nodes of neural circuits to behaviour. Because of access to specific cell types, these molecular tools will have the largest impact in genetic model systems such as the mouse. Emerging assays of mouse behaviour are beginning to rival those of behaving monkeys in terms of stimulus and behavioural control. We predict that the confluence of new behavioural and molecular tools in the mouse will reveal the logic of complex mammalian circuits.

}, keywords = {Action Potentials, Animal, Animals, Behavior, Brain, Mice, Neural Pathways, Somatosensory Cortex}, issn = {1476-4687}, doi = {10.1038/nature08539}, author = {O{\textquoteright}Connor, Daniel H and Huber, Daniel and Svoboda, Karel} } @article {46622, title = {Sensory neurons in the Drosophila genital tract regulate female reproductive behavior.}, journal = {Neuron}, volume = {61}, year = {2009}, month = {2009 Feb 26}, pages = {511-8}, abstract = {

Females of many animal species behave very differently before and after mating. In Drosophila melanogaster, changes in female behavior upon mating are triggered by the sex peptide (SP), a small peptide present in the male{\textquoteright}s seminal fluid. SP activates a specific receptor, the sex peptide receptor (SPR), which is broadly expressed in the female reproductive tract and nervous system. Here, we pinpoint the action of SPR to a small subset of internal sensory neurons that innervate the female uterus and oviduct. These neurons express both fruitless (fru), a marker for neurons likely to have sex-specific functions, and pickpocket (ppk), a marker for proprioceptive neurons. We show that SPR expression in these fru+ ppk+ neurons is both necessary and sufficient for behavioral changes induced by mating. These neurons project to regions of the central nervous system that have been implicated in the control of reproductive behaviors in Drosophila and other insects.

}, keywords = {Animals, Drosophila, Drosophila Proteins, Female, Ganglia, Invertebrate, Gene Silencing, Genitalia, Female, Immunohistochemistry, Peptides, Sensory Receptor Cells, Sexual Behavior, Animal, Signal Transduction, Uterus}, issn = {1097-4199}, doi = {10.1016/j.neuron.2009.01.009}, author = {H{\"a}semeyer, Martin and Yapici, Nilay and Heberlein, Ulrike and Dickson, Barry J} } @article {4634, title = {Simplified approach to diffraction tomography in optical microscopy.}, journal = {Optics Express}, volume = {17}, year = {2009}, month = {2009 Jul 20}, pages = {12407-17}, abstract = {

We present a novel microscopy technique to measure the scattered wavefront emitted from an optically transparent microscopic object. The complex amplitude is decoded via phase stepping in a common-path interferometer, enabling high mechanical stability. We demonstrate theoretically and practically that the incoherent summation of multiple illumination directions into a single image increases the resolving power and facilitates image reconstruction in diffraction tomography. We propose a slice-by-slice object-scatter extraction algorithm entirely based in real space in combination with ordinary z-stepping. Thereby the computational complexity affiliated with tomographic methods is significantly reduced. Using the first order Born approximation for weakly scattering objects it is possible to obtain estimates of the scattering density from the exitwaves.

}, keywords = {Algorithms, Cheek, Computer-Assisted, Equipment Design, Fourier Analysis, Green Fluorescent Proteins, Humans, Image Processing, Imaging, Interferometry, Microscopy, Models, Optics and Photonics, Radiation, Scattering, Statistical, Three-Dimensional, Tomography}, issn = {1094-4087}, author = {Fiolka, Reto and Wicker, Kai and Heintzmann, Rainer and Stemmer, Andreas} } @article {46039, title = {Structural and functional alterations to rat medial prefrontal cortex following chronic restraint stress and recovery.}, journal = {Neuroscience}, volume = {164}, year = {2009}, month = {2009 Dec 1}, pages = {798-808}, abstract = {

Chronic stress has been shown in animal models to result in altered dendritic morphology of pyramidal neurons of the medial prefrontal cortex (mPFC). It has been hypothesized that the stress-induced dendritic retractions and spine loss lead to disrupted connectivity that results in stress-induced functional impairment of mPFC. While these alterations were initially viewed as a neurodegenerative event, it has recently been established that stress induced dendritic alterations are reversible if animals are given time to recover from chronic stress. However, whether spine growth accompanies dendritic extension remains to be demonstrated. It is also not known if recovery-phase dendritic extension allows for re-establishment of functional capacity. The goal of this study, therefore, was to characterize the structural and functional effects of chronic stress and recovery on the infralimbic (IL) region of the rat mPFC. We compared neuronal morphology of IL layer V pyramidal neurons from male Sprague-Dawley rats subjected to 21 days of chronic restraint stress (CRS) to those that experienced CRS followed by a 21 day recovery period. Layer V pyramidal cell functional capacity was assessed by intra-IL long-term potentiation (LTP) both in the absence and presence of SKF38393, a dopamine receptor partial agonist and a known PFC LTP modulator. We found that stress-induced IL apical dendritic retraction and spine loss co-occur with receptor-mediated impairments to catecholaminergic facilitation of synaptic plasticity. We also found that while post-stress recovery did not reverse distal dendritic retraction, it did result in over extension of proximal dendritic arbors and spine growth as well as a full reversal of CRS-induced impairments to catecholaminergic-mediated synaptic plasticity. Our results support the hypothesis that disease-related PFC dysfunction is a consequence of network disruption secondary to altered structural and functional plasticity and that circuitry reestablishment may underlie elements of recovery. Accordingly, we believe that pharmacological treatments targeted at preventing dendritic retraction and spine loss or encouraging circuitry re-establishment and stabilization may be advantageous in the prevention and treatment of mood and anxiety disorders.

}, keywords = {2,3,4,5-Tetrahydro-7,8-dihydroxy-1-phenyl-1H-3-benzazepine, Animals, Chronic Disease, Dendrites, Dendritic Spines, Dopamine, Dopamine Agonists, Long-Term Potentiation, Male, Prefrontal Cortex, Pyramidal Cells, Random Allocation, Rats, Rats, Sprague-Dawley, Receptors, Dopamine D1, Restraint, Physical, Stress, Psychological, Time Factors, Weight Gain}, issn = {1873-7544}, doi = {10.1016/j.neuroscience.2009.08.053}, author = {Goldwater, D S and Pavlides, C and Hunter, R G and Bloss, E B and Hof, P R and McEwen, B S and Morrison, J H} } @article {5251, title = {Subcellular dynamics of type II PKA in neurons.}, journal = {Neuron}, volume = {62}, year = {2009}, month = {2009 May 14}, pages = {363-74}, abstract = {

Protein kinase A (PKA) plays multiple roles in neurons. The localization and specificity of PKA are largely controlled by A-kinase anchoring proteins (AKAPs). However, the dynamics of PKA in neurons and the roles of specific AKAPs are poorly understood. We imaged the distribution of type II PKA in hippocampal and cortical layer 2/3 pyramidal neurons in vitro and in vivo. PKA was concentrated in dendritic shafts compared to the soma, axons, and dendritic spines. This spatial distribution was imposed by the microtubule-binding protein MAP2, indicating that MAP2 is the dominant AKAP in neurons. Following cAMP elevation, catalytic subunits dissociated from the MAP2-tethered regulatory subunits and rapidly became enriched in nearby spines. The spatial gradient of type II PKA between dendritic shafts and spines was critical for the regulation of synaptic strength and long-term potentiation. Therefore, the localization and activity-dependent translocation of type II PKA are important determinants of PKA function.

}, keywords = {A Kinase Anchor Proteins, Animals, Cerebral Cortex, Cyclic AMP-Dependent Protein Kinases, Dendritic Spines, Hippocampus, Mice, Microtubule-Associated Proteins, Pyramidal Cells, Rats, Subcellular Fractions, Tissue Distribution, Transgenic}, issn = {1097-4199}, doi = {10.1016/j.neuron.2009.03.013}, author = {Zhong, Haining and Sia, Gek-Ming and Sato, Takashi R and Gray, Noah W and Mao, Tianyi and Khuchua, Zaza and Huganir, Richard L and Svoboda, Karel} } @article {6785, title = {Synaptic depolarization is more effective than back-propagating action potentials during induction of associative long-term potentiation in hippocampal pyramidal neurons.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {29}, year = {2009}, month = {2009 Mar 11}, pages = {3233-41}, abstract = {

Long-term potentiation (LTP) requires postsynaptic depolarization that can result from EPSPs paired with action potentials or larger EPSPs that trigger dendritic spikes. We explored the relative contribution of these sources of depolarization to LTP induction during synaptically driven action potential firing in hippocampal CA1 pyramidal neurons. Pairing of a weak test input with a strong input resulted in large LTP (approximately 75\% increase) when the weak and strong inputs were both located in the apical dendrites. This form of LTP did not require somatic action potentials. When the strong input was located in the basal dendrites, the resulting LTP was smaller (\< or =25\% increase). Pairing the test input with somatically evoked action potentials mimicked this form of LTP. Thus, back-propagating action potentials may contribute to modest LTP, but local synaptic depolarization and/or dendritic spikes mediate a stronger form of LTP that requires spatial proximity of the associated synaptic inputs.

}, keywords = {Action Potentials, Animals, Ganglia, Hippocampus, Long-Term Potentiation, Neuronal Plasticity, Neurons, Pyramidal Cells, Rats, Spinal, Synapses, Synaptic Transmission, Wistar}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.6000-08.2009}, author = {Hardie, Jason and Spruston, Nelson} } @article {46620, title = {Too fat to fly? New brain circuits regulate obesity in Drosophila.}, journal = {Neuron}, volume = {63}, year = {2009}, month = {2009 Aug 13}, pages = {279-81}, abstract = {

In mammals, fat store levels are regulated by brain centers that control food intake and metabolism. A new study by Al-Anzi and colleagues in this issue of Neuron identifies neurons with similar functions in Drosophila, further establishing the fly as a legitimate model to study obesity.

}, keywords = {Animals, Brain, Disease Models, Animal, Drosophila, Drosophila Proteins, Nerve Net, Neurons, Obesity}, issn = {1097-4199}, doi = {10.1016/j.neuron.2009.07.023}, author = {Kaun, Karla R and Heberlein, Ulrike} } @article {2634, title = {Tweek, an evolutionarily conserved protein, is required for synaptic vesicle recycling.}, journal = {Neuron}, volume = {63}, year = {2009}, month = {2009 Jul 30}, pages = {203-15}, abstract = {

Synaptic vesicle endocytosis is critical for maintaining synaptic communication during intense stimulation. Here we describe Tweek, a conserved protein that is required for synaptic vesicle recycling. tweek mutants show reduced FM1-43 uptake, cannot maintain release during intense stimulation, and harbor larger than normal synaptic vesicles, implicating it in vesicle recycling at the synapse. Interestingly, the levels of a fluorescent PI(4,5)P(2) reporter are reduced at tweek mutant synapses, and the probe is aberrantly localized during stimulation. In addition, various endocytic adaptors known to bind PI(4,5)P(2) are mislocalized and the defects in FM1-43 dye uptake and adaptor localization are partially suppressed by removing one copy of the phosphoinositide phosphatase synaptojanin, suggesting a role for Tweek in maintaining proper phosphoinositide levels at synapses. Our data implicate Tweek in regulating synaptic vesicle recycling via an action mediated at least in part by the regulation of PI(4,5)P(2) levels or availability at the synapse.

}, keywords = {Animals, Blotting, Complementary, Diptera, DNA, Drosophila Proteins, Electron, Endocytosis, Eye Abnormalities, Immunohistochemistry, Microscopy, Molecular Sequence Data, Mutation, Nerve Tissue Proteins, Neurons, Phosphatidylinositol Phosphates, Pyridinium Compounds, Quaternary Ammonium Compounds, Reverse Transcriptase Polymerase Chain Reaction, Synapses, Synaptic Transmission, Synaptic Vesicles, Transmission, Western}, issn = {1097-4199}, doi = {10.1016/j.neuron.2009.06.017}, author = {Verstreken, Patrik and Ohyama, Tomoko and Haueter, Claire and Habets, Ron L P and Lin, Yong Q and Swan, Laura E and Ly, Cindy V and Venken, Koen J T and De Camilli, Pietro and Bellen, Hugo J} } @article {781, title = {Twin-spot MARCM to reveal the developmental origin and identity of neurons.}, journal = {Nature Neuroscience}, volume = {12}, year = {2009}, month = {2009 Jul}, pages = {947-53}, abstract = {

A comprehensive understanding of the brain requires the analysis of individual neurons. We used twin-spot mosaic analysis with repressible cell markers (twin-spot MARCM) to trace cell lineages at high resolution by independently labeling paired sister clones. We determined patterns of neurogenesis and the influences of lineage on neuron-type specification. Notably, neural progenitors were able to yield intermediate precursors that create one, two or more neurons. Furthermore, neurons acquired stereotyped projections according to their temporal position in various brain sublineages. Twin-spot MARCM also permitted birth dating of mutant clones, enabling us to detect a single temporal fate that required chinmo in a sublineage of six Drosophila central complex neurons. In sum, twin-spot MARCM can reveal the developmental origins of neurons and the mechanisms that underlie cell fate.

}, keywords = {Animals, Brain, Cell Lineage, Central Nervous System, Drosophila, Drosophila Proteins, Gene Knockout Techniques, Genetic Techniques, Genetically Modified, Mushroom Bodies, Nerve Tissue Proteins, Neurogenesis, Neurons, RNA Interference, Time Factors}, issn = {1546-1726}, doi = {10.1038/nn.2345}, author = {Yu, Hung-Hsiang and Chen, Chun-Hong and Shi, Lei and Huang, Yaling and Lee, Tzumin} } @article {48177, title = {Automatic Segmentation of the Pelvic Bones from CT Data Based on a Statistical Shape Model}, year = {2008}, abstract = {

We present an algorithm for automatic segmentation of the human pelvic bones from CT datasets that is based on the application of a statistical shape model. The proposed method is divided into three steps: 1) The averaged shape of the pelvis model is initially placed within the CT data using the Generalized Hough Transform, 2) the statistical shape model is then adapted to the image data by a transformation and variation of its shape modes, and 3) a final free-form deformation step based on optimal graph searching is applied to overcome the restrictive character of the statistical shape representation. We thoroughly evaluated the method on 50 manually segmented CT datasets by performing a leave-one-out study. The Generalized Hough Transform proved to be a reliable method for an automatic initial placement of the shape model within the CT data. Compared to the manual gold standard segmentations, our automatic segmentation approach produced an average surface distance of 1.2 {\textpm} 0.3mm after the adaptation of the statistical shape model, which could be reduced to 0.7{\textpm}0.3mm using a final free-form deformation step. Together with an average segmentation time of less than 5 minutes, the results of our study indicate that our method meets the requirements of clinical routine.

}, doi = {10.2312/VCBM/VCBM08/093-100}, author = {Kainmueller, Dagmar and Seim, Heiko and Heller, Markus and Lamecker, Hans and Zachow, Stefan and Hege, Hans-Christian} } @article {46037, title = {Behavioral and biological effects of chronic S18986, a positive AMPA receptor modulator, during aging.}, journal = {Exp Neurol}, volume = {210}, year = {2008}, month = {2008 Mar}, pages = {109-17}, abstract = {

AMPA receptors are a major subtype of ionotropic receptors that respond to glutamate. Positive allosteric modulators of AMPA receptors selectively enhance fast excitatory neurotransmission in the brain and increase overall neuronal excitability. In addition to enhancing cognitive performance, S18986 (Servier, France) and other AMPA receptor modulators have also been shown to be neuroprotective. A particularly relevant context for AMPAR modulator studies is during aging because of increased neuronal vulnerability. It is currently unknown if chronic AMPAR modulator treatment can alter the course of brain aging, a process characterized by impairment of cognitive function, reduced neuronal excitability, and increased inflammation in the brain. We examined the behavioral and some relevant CNS effects of chronic S18986 in rats from 14 to 18 months of age. Here we show that chronic, oral administration of S18986 increases locomotor activity and performance in a spatial memory task in aged rodents. In addition, chronic S18986 treatment retards the decline of forebrain cholinergic neurons by roughly 37\% and midbrain dopaminergic neurons by as much as 43\% during aging and attenuates the age-related increase in the expression of a microglial marker in the hippocampus. These results provide a framework for further studies of the potentially beneficial effects of AMPAR modulators on brain aging.

}, keywords = {Administration, Oral, Age Factors, Aging, Analysis of Variance, Animals, Antigens, CD11b, Behavior, Animal, Benzothiadiazines, Brain, Brain-Derived Neurotrophic Factor, Choline O-Acetyltransferase, Corticosterone, Dose-Response Relationship, Drug, Glial Fibrillary Acidic Protein, Male, Maze Learning, Motor Activity, Neurons, Radioimmunoassay, Rats, Rats, Sprague-Dawley, Tyrosine 3-Monooxygenase}, issn = {0014-4886}, doi = {10.1016/j.expneurol.2007.10.007}, author = {Bloss, Erik B and Hunter, Richard G and Waters, Elizabeth M and Munoz, Carmen and Bernard, Katie and McEwen, Bruce S} } @article {6349, title = {Calcium-sensing receptor activation depresses synaptic transmission.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {28}, year = {2008}, month = {2008 Nov 12}, pages = {12062-70}, abstract = {

At excitatory synapses, decreases in cleft [Ca] arising from activity-dependent transmembrane Ca flux reduce the probability of subsequent transmitter release. Intense neural activity, induced by physiological and pathological stimuli, disturb the external microenvironment reducing extracellular [Ca] ([Ca](o)) and thus may impair neurotransmission. Increases in [Ca](o) activate the extracellular calcium sensing receptor (CaSR) which in turn inhibits nonselective cation channels at the majority of cortical nerve terminals. This pathway may modulate synaptic transmission by attenuating the impact of decreases in [Ca](o) on synaptic transmission. Using patch-clamp recording from isolated cortical terminals, cortical neuronal pairs and isolated neuronal soma we examined the modulation of synaptic transmission by CaSR. EPSCs were increased on average by 88\% in reduced affinity CaSR-mutant (CaSR(-/-)) neurons compared with wild-type. Variance-mean analysis indicates that the enhanced synaptic transmission was due largely to an increase in average probability of release (0.27 vs 0.46 for wild-type vs CaSR(-/-) pairs) with little change in quantal size (23 +/- 4 pA vs 22 +/- 4 pA) or number of release sites (11 vs 13). In addition, the CaSR agonist spermidine reduced synaptic transmission and increased paired-pulse depression at physiological [Ca](o). Spermidine did not affect quantal size, consistent with a presynaptic mechanism of action, nor did it affect voltage-activated Ca channel currents. In summary, reduced CaSR function enhanced synaptic transmission and CaSR stimulation had the opposite effect. Thus CaSR provides a mechanism that may compensate for the fall in release probability that accompanies decreases in [Ca](o).

}, keywords = {Animals, Calcium, Calcium Signaling, Calcium-Sensing, Cells, Cerebral Cortex, Cultured, Down-Regulation, Excitatory Postsynaptic Potentials, Knockout, Mice, Neural Inhibition, Neuronal Plasticity, Neurons, Organ Culture Techniques, Patch-Clamp Techniques, Presynaptic Terminals, Receptors, Spermidine, Synaptic Transmission, Synaptic Vesicles, Synaptosomes}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4134-08.2008}, author = {Phillips, Cecilia G and Harnett, Mark T and Chen, Wenyan and Smith, Stephen M} } @article {46416, title = {Clathrin dependence of synaptic-vesicle formation at the Drosophila neuromuscular junction.}, journal = {Current Biology}, volume = {18}, year = {2008}, month = {2008 Mar 25}, pages = {401-9}, abstract = {

BACKGROUND: Among the most prominent molecular constituents of a recycling synaptic vesicle is the clathrin triskelion, composed of clathrin light chain (Clc) and clathrin heavy chain (Chc). Remarkably, it remains unknown whether clathrin is strictly necessary for the stimulus-dependent re-formation of a synaptic vesicle and, conversely, whether clathrin-independent vesicle endocytosis exists at the neuronal synapse.

RESULTS: We employ FlAsH-FALI-mediated protein photoinactivation to rapidly (3 min) and specifically disrupt Clc function at the Drosophila neuromuscular junction. We first demonstrate that Clc photoinactivation does not impair synaptic-vesicle fusion. We then provide electrophysiological and ultrastructural evidence that synaptic vesicles, once fused with the plasma membrane, cannot be re-formed after Clc photoinactivation. Finally, we demonstrate that stimulus-dependent membrane internalization occurs after Clc photoinactivation. However, newly internalized membrane fails to resolve into synaptic vesicles. Rather, newly internalized membrane forms large and extensive internal-membrane compartments that are never observed at a wild-type synapse.

CONCLUSIONS: We make three major conclusions. (1) FlAsH-FALI-mediated protein photoinactivation rapidly and specifically disrupts Clc function with no effect on synaptic-vesicle fusion. (2) Synaptic-vesicle re-formation does not occur after Clc photoinactivation. By extension, clathrin-independent "kiss-and-run" endocytosis does not sustain synaptic transmission during a stimulus train at this synapse. (3) Stimulus-dependent, clathrin-independent membrane internalization exists at this synapse, but it is unable to generate fusion-competent, small-diameter synaptic vesicles.

}, keywords = {Animals, Clathrin Light Chains, Drosophila, Electrophysiology, Endocytosis, Fluoresceins, Larva, Neuromuscular Junction, Organometallic Compounds, Synaptic Membranes, Synaptic Transmission, Synaptic Vesicles}, issn = {0960-9822}, doi = {10.1016/j.cub.2008.02.055}, author = {Heerssen, Heather and Fetter, Richard D and Davis, Graeme W} } @article {2392, title = {Codependent activators direct myoblast-specific MyoD transcription.}, journal = {Developmental Cell}, volume = {15}, year = {2008}, month = {2008 Oct}, pages = {534-46}, abstract = {

Although FoxO and Pax proteins represent two important families of transcription factors in determining cell fate, they had not been functionally or physically linked together in mediating regulation of a common target gene during normal cellular transcription programs. Here, we identify MyoD, a key regulator of myogenesis, as a direct target of FoxO3 and Pax3/7 in myoblasts. Our cell-based assays and in vitro studies reveal a tight codependent partnership between FoxO3 and Pax3/7 to coordinately recruit RNA polymerase II and form a preinitiation complex (PIC) to activate MyoD transcription in myoblasts. The role of FoxO3 in regulating muscle differentiation is confirmed in vivo by observed defects in muscle regeneration caused by MyoD downregulation in FoxO3 null mice. These data establish a mutual interdependence and functional link between two families of transcription activators serving as potential signaling sensors and regulators of cell fate commitment in directing tissue specific MyoD transcription.

}, keywords = {Animals, Cell Line, Forkhead Transcription Factors, Genetic, Immunohistochemistry, Knockout, Mice, Myoblasts, MyoD Protein, Paired Box Transcription Factors, RNA, RNA Interference, Small Interfering, Trans-Activators, Transcription, Transfection}, issn = {1878-1551}, doi = {10.1073/pnas.1100640108}, author = {Hu, Ping and Geles, Kenneth G and Paik, Ji-Hye and DePinho, Ronald A and Tjian, Robert} } @article {2291, title = {Coding and non-coding polymorphisms in alcohol dehydrogenase alters protein expression and alcohol-associated erythema.}, journal = {The Journal of Investigative Dermatology}, volume = {128}, year = {2008}, month = {2008 Mar}, pages = {616-27}, abstract = {

Ethanol (EtOH), isopropyl alcohol (IPA), and propylene glycol (PG) increase topical drug delivery, but are sometimes associated with erythema. A potential genetic basis for alcohol-associated erythema was investigated as the function of polymorphisms in coding and non-coding regions of class IB alcohol dehydrogenase (ADHIB) and evaluated for altered gene expression in vitro and metabolic activity in vivo via altered skin blood flow (Doppler velocimeter) and erythema (reflectance colorimeter a*) following topical challenge to 5 M EtOH, IPA, PG, and butanol (ButOH). Promoter polymorphisms G-887A and C-739T and exon G143A form eight ADHIB haplotypes with different frequencies in Caucasians vs Asians and exhibit variable gene expression and metabolic activity. Polymorphisms C-739T and G-887A independently alter gene expression, which is further increased by IPA and PG, but not EtOH or ButOH. EtOH and ButOH increase erythema as a function of skin blood flow. IPA increases skin blood flow without erythema and PG increased erythema with decreased skin blood flow, all as a function of ADHIB haplotype. PG-induced erythema was uniquely associated with tumor necrosis factor-alpha expression. Thus, erythema following alcohol exposure is alcohol type specific, has a pharmacogenetic basis related to ADHIB haplotype and can be functionally evaluated via Doppler velocimetry and reflectance colorimetry in vivo.

}, keywords = {Administration, Adolescent, Adult, Aged, Alcohol Dehydrogenase, Alcohols, Asian Continental Ancestry Group, Enzymologic, Erythema, European Continental Ancestry Group, Female, Gene Expression Regulation, Gene Frequency, Genetic, Haplotypes, Humans, Laser-Doppler Flowmetry, Male, Middle Aged, Patch Tests, Polymorphism, Promoter Regions, Single Nucleotide, Skin, Topical}, issn = {1523-1747}, doi = {10.1038/sj.jid.5701105}, author = {Pershing, Lynn K and Chen, Yuexian and Tkachuk, Ariana N and Rausch, Holly L and Petelenz-Rubin, Kasia and Corlett, Judy L and Hobbs, Maurine R} } @article {2802, title = {Design and characterization of a multisource hand-held tandem mass spectrometer.}, journal = {Analytical Chemistry}, volume = {80}, year = {2008}, month = {2008 Oct 1}, pages = {7198-205}, abstract = {

A wireless-controlled miniature rectilinear ion trap mass spectrometer system, total weight with batteries 5.0 kg, consuming less than 35 W of power, and having dimensions of 22 cm in length by 12 cm in width by 18 cm in height, is characterized. The design and construction of the mass spectrometer including mass analyzer, vacuum system, electronics system, and data acquisition and processing systems, is detailed. The mass spectrometer is compatible with various types of ionization sources including a glow discharge electron impact ionization source used in the internal ionization mode, and various atmospheric pressure ionization sources, including electrospray ionization, atmospheric pressure chemical ionization, and desorption electrospray ionization, which are employed for external, atmospheric pressure ionization. These external sources are coupled to the miniature mass spectrometer via a capillary interface that is operated in a discontinuous fashion (discontinuous atmospheric pressure interface) to maximize ion transport. The performance of the mass spectrometer for large and small molecules is characterized. Limits of detection in the parts-per-billion range were obtained for selected compounds examined using both the internal ionization and external ionization modes. Tandem mass spectrometry and fast in situ analysis capabilities are also demonstrated using a variety of compounds and ionization sources. Protein molecules are analyzed as the multiply protonated molecules with mass/charge ratios up to 1500 Da/charge.

}, keywords = {Miniaturization, Sensitivity and Specificity, Tandem Mass Spectrometry}, issn = {1520-6882}, doi = {10.1364/AO.50.001792}, author = {Gao, Liang and Sugiarto, Andy and Harper, Jason D and Cooks, R Graham and Ouyang, Zheng} } @article {5818, title = {Dynamics of zebrafish somitogenesis.}, journal = {Developmental Dynamics}, volume = {237}, year = {2008}, month = {2008 Mar}, pages = {545-53}, abstract = {

Vertebrate somitogenesis is a rhythmically repeated morphogenetic process. The dependence of somitogenesis dynamics on axial position and temperature has not been investigated systematically in any species. Here we use multiple embryo time-lapse imaging to precisely estimate somitogenesis period and somite length under various conditions in the zebrafish embryo. Somites form at a constant period along the trunk, but the period gradually increases in the tail. Somite length varies along the axis in a stereotypical manner, with tail somites decreasing in size. Therefore, our measurements prompt important modifications to the steady-state Clock and Wavefront model: somitogenesis period, somite length, and wavefront velocity all change with axial position. Finally, we show that somitogenesis period changes more than threefold across the standard developmental temperature range, whereas the axial somite length distribution is temperature invariant. This finding indicates that the temperature-induced change in somitogenesis period exactly compensates for altered axial growth.

}, keywords = {Animals, Body Patterning, Embryonic Development, Morphogenesis, Somites, Zebrafish}, issn = {1058-8388}, doi = {10.1002/dvdy.21458}, author = {Schr{\"o}ter, Christian and Herrgen, Leah and Cardona, Albert and Brouhard, Gary J and Feldman, Benjamin and Oates, Andrew C} } @article {2396, title = {ES cell pluripotency and germ-layer formation require the SWI/SNF chromatin remodeling component BAF250a.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, year = {2008}, month = {2008 May 6}, pages = {6656-61}, abstract = {

ATP-dependent chromatin remodeling complexes are a notable group of epigenetic modifiers that use the energy of ATP hydrolysis to change the structure of chromatin, thereby altering its accessibility to nuclear factors. BAF250a (ARID1a) is a unique and defining subunit of the BAF chromatin remodeling complex with the potential to facilitate chromosome alterations critical during development. Our studies show that ablation of BAF250a in early mouse embryos results in developmental arrest (about embryonic day 6.5) and absence of the mesodermal layer, indicating its critical role in early germ-layer formation. Moreover, BAF250a deficiency compromises ES cell pluripotency, severely inhibits self-renewal, and promotes differentiation into primitive endoderm-like cells under normal feeder-free culture conditions. Interestingly, this phenotype can be partially rescued by the presence of embryonic fibroblast cells. DNA microarray, immunostaining, and RNA analyses revealed that BAF250a-mediated chromatin remodeling contributes to the proper expression of numerous genes involved in ES cell self-renewal, including Sox2, Utf1, and Oct4. Furthermore, the pluripotency defects in BAF250a mutant ES cells appear to be cell lineage-specific. For example, embryoid body-based analyses demonstrated that BAF250a-ablated stem cells are defective in differentiating into fully functional mesoderm-derived cardiomyocytes and adipocytes but are capable of differentiating into ectoderm-derived neurons. Our results suggest that BAF250a is a key component of the gene regulatory machinery in ES cells controlling self-renewal, differentiation, and cell lineage decisions.

}, keywords = {Adipocytes, Animals, Cardiac, Cell Differentiation, Cell Line, Cell Lineage, Cell Proliferation, Chromatin Assembly and Disassembly, Chromosomal Proteins, Developmental, DNA-Binding Proteins, Embryo, Embryonic Development, Embryonic Stem Cells, Female, Genes, Germ Layers, Knockout, Male, Mammalian, Mice, Muscle, Myocytes, Non-Histone, Nuclear Proteins, Pluripotent Stem Cells, Skeletal, Transcription Factors}, issn = {1091-6490}, doi = {10.1073/pnas.1100640108}, author = {Gao, Xiaolin and Tate, Peri and Hu, Ping and Tjian, Robert and Skarnes, William C and Wang, Zhong} } @article {46624, title = {Ethanol sensitivity and tolerance in long-term memory mutants of Drosophila melanogaster.}, journal = {Alcoholism, Clinical and Experimental Research}, volume = {32}, year = {2008}, month = {2008 May}, pages = {895-908}, abstract = {

BACKGROUND: It has become increasingly clear that molecular and neural mechanisms underlying learning and memory and drug addiction are largely shared. To confirm and extend these findings, we analyzed ethanol-responsive behaviors of a collection of Drosophila long-term memory mutants.

METHODS: For each mutant, sensitivity to the acute uncoordinating effects of ethanol was quantified using the inebriometer. Additionally, 2 distinct forms of ethanol tolerance were measured: rapid tolerance, which develops in response to a single brief exposure to a high concentration of ethanol vapor; and chronic tolerance, which develops following a sustained low-level exposure.

RESULTS: Several mutants were identified with altered sensitivity, rapid or chronic tolerance, while a number of mutants exhibited multiple defects.

CONCLUSIONS: The corresponding genes in these mutants represent areas of potential overlap between learning and memory and behavioral responses to alcohol. These genes also define components shared between different ethanol behavioral responses.

}, keywords = {Animals, Behavior, Animal, Drosophila melanogaster, Drug Tolerance, Ethanol, Learning, Memory}, issn = {1530-0277}, doi = {10.1111/j.1530-0277.2008.00659.x}, author = {Berger, Karen H and Kong, Eric C and Dubnau, Josh and Tully, Tim and Moore, Monica S and Heberlein, Ulrike} } @article {5827, title = {Evaluating automated parameter constraining procedures of neuron models by experimental and surrogate data.}, journal = {Biological Cybernetics}, volume = {99}, year = {2008}, month = {2008 Nov}, pages = {371-9}, abstract = {

Neuron models, in particular conductance-based compartmental models, often have numerous parameters that cannot be directly determined experimentally and must be constrained by an optimization procedure. A common practice in evaluating the utility of such procedures is using a previously developed model to generate surrogate data (e.g., traces of spikes following step current pulses) and then challenging the algorithm to recover the original parameters (e.g., the value of maximal ion channel conductances) that were used to generate the data. In this fashion, the success or failure of the model fitting procedure to find the original parameters can be easily determined. Here we show that some model fitting procedures that provide an excellent fit in the case of such model-to-model comparisons provide ill-balanced results when applied to experimental data. The main reason is that surrogate and experimental data test different aspects of the algorithm{\textquoteright}s function. When considering model-generated surrogate data, the algorithm is required to locate a perfect solution that is known to exist. In contrast, when considering experimental target data, there is no guarantee that a perfect solution is part of the search space. In this case, the optimization procedure must rank all imperfect approximations and ultimately select the best approximation. This aspect is not tested at all when considering surrogate data since at least one perfect solution is known to exist (the original parameters) making all approximations unnecessary. Furthermore, we demonstrate that distance functions based on extracting a set of features from the target data (such as time-to-first-spike, spike width, spike frequency, etc.){\textendash}rather than using the original data (e.g., the whole spike trace) as the target for fitting-are capable of finding imperfect solutions that are good approximations of the experimental data.

}, keywords = {Algorithms, Animals, Models, Neocortex, Neurological, Neurons, Organ Culture Techniques, Patch-Clamp Techniques, Rats, Wistar}, issn = {1432-0770}, doi = {10.1007/s00422-008-0269-2}, author = {Druckmann, Shaul and Berger, Thomas K and Hill, Sean and Sch{\"u}rmann, Felix and Markram, Henry and Segev, Idan} } @article {46625, title = {Genetic dissociation of ethanol sensitivity and memory formation in Drosophila melanogaster.}, journal = {Genetics}, volume = {178}, year = {2008}, month = {2008 Apr}, pages = {1895-902}, abstract = {

The ad hoc genetic correlation between ethanol sensitivity and learning mechanisms in Drosophila could overemphasize a common process supporting both behaviors. To challenge directly the hypothesis that these mechanisms are singular, we examined the learning phenotypes of 10 new strains. Five of these have increased ethanol sensitivity, and the other 5 do not. We tested place and olfactory memory in each of these lines and found two new learning mutations. In one case, altering the tribbles gene, flies have a significantly reduced place memory, elevated olfactory memory, and normal ethanol response. In the second case, mutation of a gene we name ethanol sensitive with low memory (elm), place memory was not altered, olfactory memory was sharply reduced, and sensitivity to ethanol was increased. In sum, however, we found no overall correlation between ethanol sensitivity and place memory in the 10 lines tested. Furthermore, there was a weak but nonsignificant correlation between ethanol sensitivity and olfactory learning. Thus, mutations that alter learning and sensitivity to ethanol can occur independently of each other and this implies that the set of genes important for both ethanol sensitivity and learning is likely a subset of the genes important for either process.

}, keywords = {Animals, Behavior, Animal, Cell Cycle Proteins, DNA Transposable Elements, Drosophila melanogaster, Drosophila Proteins, Ethanol, Gene Expression Regulation, Head, Memory, Mutagenesis, Insertional, Phenotype, Protein-Serine-Threonine Kinases, RNA, Messenger}, issn = {0016-6731}, doi = {10.1534/genetics.107.084582}, author = {LaFerriere, Holly and Guarnieri, Douglas J and Sitaraman, Divya and Diegelmann, Soeren and Heberlein, Ulrike and Zars, Troy} } @article {4254, title = {A genetically encoded fluorescent sensor of ERK activity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, year = {2008}, month = {2008 Dec 9}, pages = {19264-9}, abstract = {

The activity of the ERK has complex spatial and temporal dynamics that are important for the specificity of downstream effects. However, current biochemical techniques do not allow for the measurement of ERK signaling with fine spatiotemporal resolution. We developed a genetically encoded, FRET-based sensor of ERK activity (the extracellular signal-regulated kinase activity reporter, EKAR), optimized for signal-to-noise ratio and fluorescence lifetime imaging. EKAR selectively and reversibly reported ERK activation in HEK293 cells after epidermal growth factor stimulation. EKAR signals were correlated with ERK phosphorylation, required ERK activity, and did not report the activities of JNK or p38. EKAR reported ERK activation in the dendrites and nucleus of hippocampal pyramidal neurons in brain slices after theta-burst stimuli or trains of back-propagating action potentials. EKAR therefore permits the measurement of spatiotemporal ERK signaling dynamics in living cells, including in neuronal compartments in intact tissues.

}, keywords = {Action Potentials, Animals, Artifacts, Bacterial Proteins, Cell Line, Dendrites, Endothelial Cells, Enzyme Activation, Extracellular Signal-Regulated MAP Kinases, Fluorescence Resonance Energy Transfer, Fluorescent Dyes, Genes, Green Fluorescent Proteins, Hippocampus, Humans, Kidney, Luminescent Proteins, MAP Kinase Signaling System, Organ Culture Techniques, Patch-Clamp Techniques, Pyramidal Cells, Rats, Reporter}, issn = {1091-6490}, doi = {10.1073/pnas.0804598105}, author = {Harvey, Christopher D and Ehrhardt, Anka G and Cellurale, Cristina and Zhong, Haining and Yasuda, Ryohei and Davis, Roger J and Svoboda, Karel} } @article {2679, title = {Genomic analysis of Drosophila neuronal remodeling: a role for the RNA-binding protein Boule as a negative regulator of axon pruning.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {28}, year = {2008}, month = {2008 Jun 11}, pages = {6092-103}, abstract = {

Drosophila mushroom body (MB) gamma neurons undergo axon pruning during metamorphosis through a process of localized degeneration of specific axon branches. Developmental axon degeneration is initiated by the steroid hormone ecdysone, acting through a nuclear receptor complex composed of USP (ultraspiracle) and EcRB1 (ecdysone receptor B1) to regulate gene expression in MB gamma neurons. To identify ecdysone-dependent gene expression changes in MB gamma neurons at the onset of axon pruning, we use laser capture microdissection to isolate wild-type and mutant MB neurons in which EcR (ecdysone receptor) activity is genetically blocked, and analyze expression changes by microarray. We identify several molecular pathways that are regulated in MB neurons by ecdysone. The most striking observation is the upregulation of genes involved in the UPS (ubiquitin-proteasome system), which is cell autonomously required for gamma neuron pruning. In addition, we characterize the function of Boule, an evolutionarily conserved RNA-binding protein previously implicated in spermatogenesis in flies and vertebrates. boule expression is downregulated by ecdysone in MB neurons at the onset of pruning, and forced expression of Boule in MB gamma neurons is sufficient to inhibit axon pruning. This activity is dependent on the RNA-binding domain of Boule and a conserved DAZ (deleted in azoospermia) domain implicated in interactions with other RNA-binding proteins. However, loss of Boule does not result in obvious defects in axon pruning or morphogenesis of MB neurons, suggesting that it acts redundantly with other ecdyonse-regulated genes. We propose a novel function for Boule in the CNS as a negative regulator of developmental axon pruning.

}, keywords = {Animals, Antigens, Axons, CD8, Developmental, Drosophila, Drosophila Proteins, Ecdysone, Gene Expression Regulation, Genetically Modified, Genomics, Green Fluorescent Proteins, Larva, Microarray Analysis, Mushroom Bodies, Mutation, Neurons, Receptors, RNA-Binding Proteins, Steroid}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0677-08.2008}, author = {Hoopfer, Eric D and Penton, Andrea and Watts, Ryan J and Luo, Liqun} } @article {2080, title = {High-density mapping of single-molecule trajectories with photoactivated localization microscopy. (With commentary)}, journal = {Nature Methods}, volume = {5}, year = {2008}, month = {2008 Feb}, pages = {155-7}, abstract = {

We combined photoactivated localization microscopy (PALM) with live-cell single-particle tracking to create a new method termed sptPALM. We created spatially resolved maps of single-molecule motions by imaging the membrane proteins Gag and VSVG, and obtained several orders of magnitude more trajectories per cell than traditional single-particle tracking enables. By probing distinct subsets of molecules, sptPALM can provide insight into the origins of spatial and temporal heterogeneities in membranes.

Commentary: As a stepping stone to true live cell PALM (see above), our collaborator Jennifer Lippincott-Schwartz suggested using the sparse photoactivation principle of PALM to track the nanoscale motion of thousands of individual molecules within a single living cell. Termed single particle tracking PALM (sptPALM), Jennifer{\textquoteright}s postdocs Suliana Manley and Jen Gillette used the method in our PALM rig to create spatially resolved maps of diffusion rates in the plasma membrane of live cells. sptPALM is a powerful tool to study the active cytoskeletal or passive diffusional transport of individual molecules with far more measurements per cell than is possible without sparse photoactivation.

}, keywords = {Animals, Cercopithecus aethiops, COS Cells, Fluorescence, Image Enhancement, Membrane Proteins, Microscopy}, issn = {1548-7105}, doi = {10.1038/nmeth.1176}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18193054}, author = {Manley, Suliana and Gillette, Jennifer M and Patterson, George H and Shroff, Hari and Hess, Harald F and Betzig, Eric and Lippincott-Schwartz, Jennifer} } @article {2347, title = {Induction of muscle thermogenesis by high-fat diet in mice: association with obesity-resistance.}, journal = {American Journal of Physiology. Endocrinology and Metabolism}, volume = {295}, year = {2008}, month = {2008 Aug}, pages = {E356-67}, abstract = {

The obesogenic effect of a high-fat (HF) diet is counterbalanced by stimulation of energy expenditure and lipid oxidation in response to a meal. The aim of this study was to reveal whether muscle nonshivering thermogenesis could be stimulated by a HF diet, especially in obesity-resistant A/J compared with obesity-prone C57BL/6J (B/6J) mice. Experiments were performed on male mice born and maintained at 30 degrees C. Four-week-old mice were randomly weaned onto a low-fat (LF) or HF diet for 2 wk. In the A/J LF mice, cold exposure (4 degrees C) resulted in hypothermia, whereas the A/J HF, B/6J LF, and B/6J HF mice were cold tolerant. Cold sensitivity of the A/J LF mice was associated with a relatively low whole body energy expenditure under resting conditions, which was normalized by the HF diet. In both strains, the HF diet induced uncoupling protein-1-mediated thermogenesis, with a stronger induction in A/J mice. Only in A/J mice: 1) the HF diet augmented activation of whole body lipid oxidation by cold; and 2) at 30 degrees C, oxygen consumption, total content, and phosphorylation of AMP-activated protein kinase (AMPK), and AICAR-stimulated palmitate oxidation in soleus muscle was increased by the HF diet in parallel with significantly increased leptinemia. Gene expression data in soleus muscle of the A/J HF mice indicated a shift from carbohydrate to fatty acid oxidation. Our results suggest a role for muscle nonshivering thermogenesis and lipid oxidation in the obesity-resistant phenotype of A/J mice and indicate that a HF diet could induce thermogenesis in oxidative muscle, possibly via the leptin-AMPK axis.

}, keywords = {Aminoimidazole Carboxamide, AMP-Activated Protein Kinases, Animals, Basal Metabolism, Body Temperature, Body Weight, Calorimetry, Dietary Fats, Fatty Acids, Inbred C57BL, Indirect, Male, Mice, Multienzyme Complexes, Muscle, Newborn, Nonesterified, Obesity, Oxygen Consumption, Protein-Serine-Threonine Kinases, Random Allocation, Ribonucleotides, Skeletal, Thermogenesis, Triglycerides}, issn = {0193-1849}, doi = {10.1523/JNEUROSCI.3773-10.2011}, author = {Kus, Vladimir and Prazak, Tomas and Brauner, Petr and Hensler, Michal and Kuda, Ondrej and Flachs, Pavel and Janovska, Petra and Medrikova, Dasa and Rossmeisl, Martin and Jilkova, Zuzana and Stefl, Bohumir and Pastalkova, Eva and Drahota, Zdenek and Houstek, Josef and Kopecky, Jan} } @article {45960, title = {Interactions of lipids with aquaporin-0 and other membrane proteins.}, journal = {Pfl{\"u}gers Archiv - European Journal of Physiology}, volume = {456}, year = {2008}, month = {2008 Jul}, pages = {651-61}, abstract = {

The structure of aquaporin-0 (AQP0) has recently been determined by electron crystallography of two-dimensional (2D) crystals and by X-ray crystallography of three-dimensional (3D) crystals. The electron crystallographic structure revealed nine lipids per AQP0 monomer, which form an almost complete bilayer. The lipids adopt a wide variety of conformations and tightly fill the space between adjacent AQP0 tetramers. The conformations of the lipid acyl chains appear to be determined not only by the protein surface but also by the acyl chains of adjacent lipid molecules. In the X-ray structure, the hydrophobic region of the protein is surrounded by a detergent micelle, with two ordered detergent molecules per AQP0 monomer. Despite the different environments, the electron crystallographic and X-ray structures of AQP0 are virtually identical, but they differ in the temperature factors of the atoms that either contact the lipids in the 2D crystals or are exposed to detergents in the 3D crystals. The temperature factors are higher in the X-ray structure, suggesting that the detergent-exposed AQP0 residues are less ordered than the corresponding ones contacting lipids in the 2D crystals. An examination of ordered detergent molecules in crystal structures of other aquaporins and of lipid molecules in 2D and 3D crystals of bacteriorhodopsin suggests that the increased conformational variability of detergent-exposed residues compared to lipid-contacting residues is a general feature.

}, keywords = {Animals, Aquaporins, Crystallization, Eye Proteins, Humans, Lipid Metabolism, Membrane Proteins, Models, Molecular, X-Ray Diffraction}, issn = {0031-6768}, doi = {10.1007/s00424-007-0353-9}, author = {Hite, Richard K and Gonen, Tamir and Harrison, Stephen C and Walz, Thomas} } @article {1248, title = {Local potential connectivity in cat primary visual cortex.}, journal = {Cerebral Cortex}, volume = {18}, year = {2008}, month = {2008 Jan}, pages = {13-28}, abstract = {

Time invariant description of synaptic connectivity in cortical circuits may be precluded by the ongoing growth and retraction of dendritic spines accompanied by the formation and elimination of synapses. On the other hand, the spatial arrangement of axonal and dendritic branches appears stable. This suggests that an invariant description of connectivity can be cast in terms of potential synapses, which are locations in the neuropil where an axon branch of one neuron is proximal to a dendritic branch of another neuron. In this paper, we attempt to reconstruct the potential connectivity in local cortical circuits of the cat primary visual cortex (V1). Based on multiple single-neuron reconstructions of axonal and dendritic arbors in 3 dimensions, we evaluate the expected number of potential synapses and the probability of potential connectivity among excitatory (pyramidal and spiny stellate) neurons and inhibitory basket cells. The results provide a quantitative description of structural organization of local cortical circuits. For excitatory neurons from different cortical layers, we compute local domains, which contain their potentially pre- and postsynaptic excitatory partners. These domains have columnar shapes with laminar specific radii and are roughly of the size of the ocular dominance column. Therefore, connections between most excitatory neurons in the ocular dominance column can be implemented by local synaptogenesis. Structural connectivity involving inhibitory basket cells is generally weaker than excitatory connectivity. Here, only nearby neurons are capable of establishing more than one potential synapse, implying that within the ocular dominance column these connections have more limited potential for circuit remodeling.

}, keywords = {Animals, Cats, Cells, Cultured, Nerve Net, Neural Pathways, Synapses, Visual Cortex}, issn = {1460-2199}, doi = {10.1093/cercor/bhm027}, author = {Stepanyants, Armen and Hirsch, Judith A and Martinez, Luis M and Kisv{\'a}rday, Zolt{\'a}n F and Ferecsk{\'o}, Alex S and Chklovskii, Dmitri B} } @article {46626, title = {Loss of RAB-3/A in Caenorhabditis elegans and the mouse affects behavioral response to ethanol.}, journal = {Genes, Brain, and Behavior}, volume = {7}, year = {2008}, month = {2008 Aug}, pages = {669-76}, abstract = {

The mechanisms by which ethanol induces changes in behavior are not well understood. Here, we show that Caenorhabditis elegans loss-of-function mutations in the synaptic vesicle-associated RAB-3 protein and its guanosine triphosphate exchange factor AEX-3 confer resistance to the acute locomotor effects of ethanol. Similarly, mice lacking one or both copies of Rab3A are resistant to the ataxic and sedative effects of ethanol, and Rab3A haploinsufficiency increases voluntary ethanol consumption. These data suggest a conserved role of RAB-3-/RAB3A-regulated neurotransmitter release in ethanol-related behaviors.

}, keywords = {Alcohol Drinking, Alcohol-Induced Disorders, Nervous System, Animals, Ataxia, Behavior, Animal, Brain, Brain Chemistry, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Central Nervous System Depressants, Consciousness Disorders, Drug Resistance, Ethanol, Haplotypes, Male, Mice, Mice, Inbred C57BL, Mice, Knockout, rab3 GTP-Binding Proteins, rab3A GTP-Binding Protein}, issn = {1601-183X}, doi = {10.1111/j.1601-183X.2008.00404.x}, author = {Kapfhamer, D and Bettinger, J C and Davies, A G and Eastman, C L and Smail, E A and Heberlein, U and McIntire, S L} } @article {1455, title = {Markov random field based automatic image alignment for electron tomography.}, journal = {Journal of Structural Biology}, volume = {161}, year = {2008}, month = {2008 Mar 28}, pages = {260-75}, abstract = {

We present a method for automatic full-precision alignment of the images in a tomographic tilt series. Full-precision automatic alignment of cryo electron microscopy images has remained a difficult challenge to date, due to the limited electron dose and low image contrast. These facts lead to poor signal to noise ratio (SNR) in the images, which causes automatic feature trackers to generate errors, even with high contrast gold particles as fiducial features. To enable fully automatic alignment for full-precision reconstructions, we frame the problem probabilistically as finding the most likely particle tracks given a set of noisy images, using contextual information to make the solution more robust to the noise in each image. To solve this maximum likelihood problem, we use Markov Random Fields (MRF) to establish the correspondence of features in alignment and robust optimization for projection model estimation. The resulting algorithm, called Robust Alignment and Projection Estimation for Tomographic Reconstruction, or RAPTOR, has not needed any manual intervention for the difficult datasets we have tried, and has provided sub-pixel alignment that is as good as the manual approach by an expert user. We are able to automatically map complete and partial marker trajectories and thus obtain highly accurate image alignment. Our method has been applied to challenging cryo electron tomographic datasets with low SNR from intact bacterial cells, as well as several plastic section and X-ray datasets.

}, keywords = {Algorithms, Computer-Assisted, Cryoelectron Microscopy, Image Processing, Markov Chains, Tomography}, issn = {1095-8657}, doi = {10.1016/j.jsb.2007.07.007}, author = {Amat, Fernando and Moussavi, Farshid and Comolli, Luis R and Elidan, Gal and Downing, Kenneth H and Horowitz, Mark} } @article {2806, title = {Monitoring of toxic compounds in air using a handheld rectilinear ion trap mass spectrometer.}, journal = {Analytical Chemistry}, volume = {80}, year = {2008}, month = {2008 Feb 1}, pages = {734-41}, abstract = {

A miniature, handheld mass spectrometer, based on the rectilinear ion trap mass analyzer, has been applied to air monitoring for traces of toxic compounds. The instrument is battery-operated, hand-portable, and rugged. We anticipate its use in public safety, industrial hygiene, and environmental monitoring. Gaseous samples of nine toxic industrial compounds, phosgene, ethylene oxide, sulfur dioxide, acrylonitrile, cyanogen chloride, hydrogen cyanide, acrolein, formaldehyde, and ethyl parathion, were tested. A sorption trap inlet was constructed to serve as the interface between atmosphere and the vacuum chamber of the mass spectrometer. After selective collection of analytes on the sorbent bed, the sorbent tube was evacuated and then heated to desorb analyte into the instrument. Sampling, detection, identification, and quantitation of all compounds were readily achieved in times of less than 2 min, with detection limits ranging from 800 parts per trillion to 3 parts per million depending on the analyte. For all but one analyte, detection limits were well below (3.5-130 times below) permissible exposure limits. A linear dynamic range of 1-2 orders of magnitude was obtained over the concentration ranges studied (sub-ppbv to ppmv) for all analytes.

}, issn = {0003-2700}, doi = {10.1364/AO.50.001792}, author = {Keil, Adam and Hernandez-Soto, Heriberto and Noll, Robert J and Fico, Miriam and Gao, Liang and Ouyang, Zheng and Cooks, R Graham} } @article {2393, title = {MyoD targets TAF3/TRF3 to activate myogenin transcription.}, journal = {Molecular Cell}, volume = {32}, year = {2008}, month = {2008 Oct 10}, pages = {96-105}, abstract = {

Skeletal muscle differentiation requires a cascade of transcriptional events to control the spatial and temporal expression of muscle-specific genes. Until recently, muscle-specific transcription was primarily attributed to prototypic enhancer-binding factors, while the role of core promoter recognition complexes in directing myogenesis remained unknown. Here, we report the development of a purified reconstituted system to analyze the properties of a TAF3/TRF3 complex in directing transcription initiation at the Myogenin promoter. Importantly, this new complex is required to replace the canonical TFIID to recapitulate MyoD-dependent activation of Myogenin. In vitro and cell-based assays identify a domain of TAF3 that mediates coactivator functions targeted by MyoD. Our findings also suggest changes to CRSP/Mediator in terminally differentiated myotubes. This switching of the core promoter recognition complex during myogenesis allows a more balanced division of labor between activators and TAF coactivators, thus providing another strategy to accommodate cell-specific regulation during metazoan development.

}, keywords = {Animals, Cell Line, Genetic, Homeodomain Proteins, Mice, Multiprotein Complexes, Muscle Fibers, MyoD Protein, Myogenin, Promoter Regions, Protein Structure, Protein Subunits, Recombinant Proteins, Skeletal, TATA Box Binding Protein-Like Proteins, Tertiary, Trans-Activators, Transcription Factor TFIID, Transcription Initiation Site, Transcriptional Activation}, issn = {1097-4164}, doi = {10.1073/pnas.1100640108}, author = {Deato, Maria Divina E and Marr, Michael T and Sottero, Theo and Inouye, Carla and Hu, Ping and Tjian, Robert} } @article {45849, title = {The Pfam protein families database.}, journal = {Nucleic Acids Research}, volume = {36}, year = {2008}, month = {2008 Jan}, pages = {D281-8}, abstract = {

Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models. The current release of Pfam (22.0) contains 9318 protein families. Pfam is now based not only on the UniProtKB sequence database, but also on NCBI GenPept and on sequences from selected metagenomics projects. Pfam is available on the web from the consortium members using a new, consistent and improved website design in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/), as well as from mirror sites in France (http://pfam.jouy.inra.fr/) and South Korea (http://pfam.ccbb.re.kr/).

}, keywords = {Animals, Databases, Protein, Genomics, Internet, Protein Structure, Tertiary, Proteins, Sequence Alignment, Sequence Analysis, Protein, User-Computer Interface}, issn = {1362-4962}, doi = {10.1093/nar/gkm960}, author = {Finn, Robert D and Tate, John and Mistry, Jaina and Coggill, Penny C and Sammut, Stephen John and Hotz, Hans-Rudolf and Ceric, Goran and Forslund, Kristoffer and Eddy, Sean R and Sonnhammer, Erik L L and Bateman, Alex} } @article {1115, title = {Phenylglycine and phenylalanine derivatives as potent and selective HDAC1 inhibitors (SHI-1).}, journal = {Bioorganic \& Medicinal Chemistry Letters}, volume = {18}, year = {2008}, month = {2008 Mar 15}, pages = {1859-63}, abstract = {

An HTS screening campaign identified a series of low molecular weight phenols that showed excellent selectivity (\>100-fold) for HDAC1/HDAC2 over other Class I and Class II HDACs. Evolution and optimization of this HTS hit series provided HDAC1-selective (SHI-1) compounds with excellent anti-proliferative activity and improved physical properties. Dose-dependent efficacy in a mouse HCT116 xenograft model was demonstrated with a phenylglycine SHI-1 analog.

}, keywords = {Acetylation, Amides, Animals, Cell Proliferation, Colonic Neoplasms, Cultured, Dogs, Enzyme Inhibitors, Ether-A-Go-Go Potassium Channels, Glycine, Histone Deacetylase 1, Histone Deacetylase Inhibitors, Humans, Macaca mulatta, Mice, Molecular Structure, Phenylalanine, Structure-Activity Relationship, Tumor Cells, Xenograft Model Antitumor Assays}, issn = {1464-3405}, doi = {10.1016/j.bmcl.2008.02.012}, author = {Wilson, Kevin J and Witter, David J and Grimm, Jonathan B and Siliphaivanh, Phieng and Otte, Karin M and Kral, Astrid M and Fleming, Judith C and Harsch, Andreas and Hamill, Julie E and Cruz, Jonathan C and Chenard, Melissa and Szewczak, Alexander A and Middleton, Richard E and Hughes, Bethany L and Dahlberg, William K and Secrist, J Paul and Miller, Thomas A} } @article {45962, title = {Polymorphic assemblies and crystalline arrays of lens tetraspanin MP20.}, journal = {Journal of Molecular Biology}, volume = {376}, year = {2008}, month = {2008 Feb 15}, pages = {380-92}, abstract = {

Members of the tetraspanin superfamily function as transmembrane scaffold proteins that mediate the assembly of membrane proteins into specific signaling complexes. Tetraspanins also interact with each other and concentrate membrane proteins into tetraspanin-enriched microdomains (TEMs). Here we report that lens-specific tetraspanin MP20 can form multiple types of higher-order assemblies and we present crystalline arrays of MP20. When isolated in the absence of divalent cations, MP20 is solubilized predominantly in tetrameric form, whereas the presence of divalent cations during solubilization promotes the association of MP20 tetramers into higher-order species. This effect only occurs when divalent cations are present during solubilization but not when divalent cations are added to solubilized tetrameric MP20, suggesting that other factors may also be involved. When purified MP20 tetramers are reconstituted with native lens lipids in the presence of magnesium, MP20 forms two-dimensional (2D) crystals. A projection map at 18 A resolution calculated from negatively stained 2D crystals showed that the building block of the crystal is an octamer consisting of two tetramers related to each other by 2-fold symmetry. In addition to 2D crystals, reconstitution of MP20 with native lipids also produced a variety of large protein-lipid complexes, and we present three-dimensional (3D) reconstructions of the four most abundant of these complexes in negative stain. The various complexes formed by MP20 most likely reflect the many ways in which tetraspanins can interact with each other to allow formation of TEMs.

}, keywords = {Animals, Buffers, Cations, Divalent, Cell Membrane, Chelating Agents, Crystallization, Detergents, Edetic Acid, Egtazic Acid, Eye Proteins, Hydrogen-Ion Concentration, Imaging, Three-Dimensional, Lens, Crystalline, Lipid Metabolism, Magnesium, Membrane Microdomains, Membrane Proteins, Protein Structure, Secondary, Protein Structure, Tertiary, Sheep, Silver Staining, Solubility, Tromethamine}, issn = {1089-8638}, doi = {10.1016/j.jmb.2007.09.001}, author = {Gonen, Tamir and Hite, Richard K and Cheng, Yifan and Petre, Benjamin M and Kistler, Joerg and Walz, Thomas} } @article {1770, title = {Preserving cell shape under environmental stress.}, journal = {Nature}, volume = {452}, year = {2008}, month = {2008 Mar 20}, pages = {361-4}, abstract = {

Maintaining cell shape and tone is crucial for the function and survival of cells and tissues. Mechanotransduction relies on the transformation of minuscule mechanical forces into high-fidelity electrical responses. When mechanoreceptors are stimulated, mechanically sensitive cation channels open and produce an inward transduction current that depolarizes the cell. For this process to operate effectively, the transduction machinery has to retain integrity and remain unfailingly independent of environmental changes. This is particularly challenging for poikilothermic organisms, where changes in temperature in the environment may impact the function of mechanoreceptor neurons. Thus, we wondered how insects whose habitat might quickly vary over several tens of degrees of temperature manage to maintain highly effective mechanical senses. We screened for Drosophila mutants with defective mechanical responses at elevated ambient temperatures, and identified a gene, spam, whose role is to protect the mechanosensory organ from massive cellular deformation caused by heat-induced osmotic imbalance. Here we show that Spam protein forms an extracellular shield that guards mechanosensory neurons from environmental insult. Remarkably, heterologously expressed Spam protein also endowed other cells with superb defence against physically and chemically induced deformation. We studied the mechanical impact of Spam coating and show that spam-coated cells are up to ten times stiffer than uncoated controls. Together, these results help explain how poikilothermic organisms preserve the architecture of critical cells during environmental stress, and illustrate an elegant and simple solution to such challenge.

}, keywords = {Animals, Biological, Cell Line, Cell Shape, Cellular, Chemical, Drosophila melanogaster, Drosophila Proteins, Electrophysiology, Environment, Eye Proteins, Hot Temperature, Humidity, Mechanical, Mechanoreceptors, Mechanotransduction, Models, Osmotic Pressure, Stimulation, Stress}, issn = {1476-4687}, doi = {10.1038/nature06603}, author = {Cook, Boaz and Hardy, Robert W and McConnaughey, William B and Zuker, Charles S} } @article {4367, title = {Reporting neural activity with genetically encoded calcium indicators.}, journal = {Brain Cell Biology}, volume = {36}, year = {2008}, month = {2008 Aug 6}, pages = {69-86}, abstract = {

Genetically encoded calcium indicators (GECIs), based on recombinant fluorescent proteins, have been engineered to observe calcium transients in living cells and organisms. Through observation of calcium, these indicators also report neural activity. We review progress in GECI construction and application, particularly toward in vivo monitoring of sparse action potentials (APs). We summarize the extrinsic and intrinsic factors that influence GECI performance. A simple model of GECI response to AP firing demonstrates the relative significance of these factors. We recommend a standardized protocol for evaluating GECIs in a physiologically relevant context. A potential method of simultaneous optical control and recording of neuronal circuits is presented.

}, keywords = {Action Potentials, Animals, Calcium Signaling, Confocal, Electrophysiology, Luminescent Proteins, Microscopy, Neurons, Signal Transduction}, issn = {1559-7113}, doi = {10.1007/s11068-008-9029-4}, author = {Hires, S Andrew and Tian, Lin and Looger, Loren L} } @article {2201, title = {Single-molecule DNA sequencing of a viral genome.}, journal = {Science}, volume = {320}, year = {2008}, month = {2008 Apr 4}, pages = {106-9}, abstract = {

The full promise of human genomics will be realized only when the genomes of thousands of individuals can be sequenced for comparative analysis. A reference sequence enables the use of short read length. We report an amplification-free method for determining the nucleotide sequence of more than 280,000 individual DNA molecules simultaneously. A DNA polymerase adds labeled nucleotides to surface-immobilized primer-template duplexes in stepwise fashion, and the asynchronous growth of individual DNA molecules was monitored by fluorescence imaging. Read lengths of \>25 bases and equivalent phred software program quality scores approaching 30 were achieved. We used this method to sequence the M13 virus to an average depth of \>150x and with 100\% coverage; thus, we resequenced the M13 genome with high-sensitivity mutation detection. This demonstrates a strategy for high-throughput low-cost resequencing.

}, keywords = {Algorithms, Bacteriophage M13, Computational Biology, DNA, DNA Primers, Genetic, Genome, Mutation, Sequence Alignment, Sequence Analysis, Software, Templates, Viral}, issn = {1095-9203}, doi = {10.1038/nbt0510-426}, author = {Harris, Timothy D and Buzby, Phillip R and Babcock, Hazen and Beer, Eric and Bowers, Jayson and Braslavsky, Ido and Causey, Marie and Colonell, Jennifer and Dimeo, James and Efcavitch, J William and Giladi, Eldar and Gill, Jaime and Healy, John and Jarosz, Mirna and Lapen, Dan and Moulton, Keith and Quake, Stephen R and Steinmann, Kathleen and Thayer, Edward and Tyurina, Anastasia and Ward, Rebecca and Weiss, Howard and Xie, Zheng} } @article {5215, title = {Sparse optical microstimulation in barrel cortex drives learned behaviour in freely moving mice.}, journal = {Nature}, volume = {451}, year = {2008}, month = {2008 Jan 3}, pages = {61-4}, abstract = {

Electrical microstimulation can establish causal links between the activity of groups of neurons and perceptual and cognitive functions. However, the number and identities of neurons microstimulated, as well as the number of action potentials evoked, are difficult to ascertain. To address these issues we introduced the light-gated algal channel channelrhodopsin-2 (ChR2) specifically into a small fraction of layer 2/3 neurons of the mouse primary somatosensory cortex. ChR2 photostimulation in vivo reliably generated stimulus-locked action potentials at frequencies up to 50 Hz. Here we show that naive mice readily learned to detect brief trains of action potentials (five light pulses, 1 ms, 20 Hz). After training, mice could detect a photostimulus firing a single action potential in approximately 300 neurons. Even fewer neurons (approximately 60) were required for longer stimuli (five action potentials, 250 ms). Our results show that perceptual decisions and learning can be driven by extremely brief epochs of cortical activity in a sparse subset of supragranular cortical pyramidal neurons.

}, keywords = {Action Potentials, Algal Proteins, Animal, Animals, Behavior, Cerebral Cortex, Electric Stimulation, Learning, Mice, Microbial, Movement, Optics and Photonics, Photic Stimulation, Pyramidal Cells, Rhodopsins}, issn = {1476-4687}, doi = {10.1038/nature06445}, author = {Huber, Daniel and Petreanu, Leopoldo and Ghitani, Nima and Ranade, Sachin and Hrom{\'a}dka, Tom{\'a}s and Mainen, Zach and Svoboda, Karel} } @article {5213, title = {The spread of Ras activity triggered by activation of a single dendritic spine.}, journal = {Science}, volume = {321}, year = {2008}, month = {2008 Jul 4}, pages = {136-40}, abstract = {

In neurons, individual dendritic spines isolate N-methyl-d-aspartate (NMDA) receptor-mediated calcium ion (Ca2+) accumulations from the dendrite and other spines. However, the extent to which spines compartmentalize signaling events downstream of Ca2+ influx is not known. We combined two-photon fluorescence lifetime imaging with two-photon glutamate uncaging to image the activity of the small guanosine triphosphatase Ras after NMDA receptor activation at individual spines. Induction of long-term potentiation (LTP) triggered robust Ca2+-dependent Ras activation in single spines that decayed in approximately 5 minutes. Ras activity spread over approximately 10 micrometers of dendrite and invaded neighboring spines by diffusion. The spread of Ras-dependent signaling was necessary for the local regulation of the threshold for LTP induction. Thus, Ca2+-dependent synaptic signals can spread to couple multiple synapses on short stretches of dendrite.

}, keywords = {Animals, Calcium, Cell Membrane, Dendritic Spines, Diffusion, Fluorescence Resonance Energy Transfer, Glutamic Acid, GTPase-Activating Proteins, Guanine Nucleotide Exchange Factors, Hippocampus, Long-Term Potentiation, N-Methyl-D-Aspartate, Pyramidal Cells, ras Proteins, Rats, Receptors, Recombinant Fusion Proteins, Signal Transduction, Synapses, Transfection}, issn = {1095-9203}, doi = {10.1126/science.1159675}, author = {Harvey, Christopher D and Yasuda, Ryohei and Zhong, Haining and Svoboda, Karel} } @article {4980, title = {Standardized atlas of the brain of the desert locust, Schistocerca gregaria.}, journal = {Cell and Tissue Research}, volume = {333}, year = {2008}, month = {2008 Jul 27}, pages = {125-45}, abstract = {

In order to understand the connectivity of neuronal networks, their constituent neurons should ideally be studied in a common framework. Since morphological data from physiologically characterized and stained neurons usually arise from different individual brains, this can only be performed in a virtual standardized brain that compensates for interindividual variability. The desert locust, Schistocerca gregaria, is an insect species used widely for the analysis of olfactory and visual signal processing, endocrine functions, and neural networks controlling motor output. To provide a common multi-user platform for neural circuit analysis in the brain of this species, we have generated a standardized three-dimensional brain of this locust. Serial confocal images from whole-mount locust brains were used to reconstruct 34 neuropil areas in ten brains. For standardization, we compared two different methods: an iterative shape-averaging (ISA) procedure by using affine transformations followed by iterative nonrigid registrations, and the Virtual Insect Brain (VIB) protocol by using global and local rigid transformations followed by local nonrigid transformations. Both methods generated a standard brain, but for different applications. Whereas the VIB technique was designed to visualize anatomical variability between the input brains, the purpose of the ISA method was the opposite, i.e., to remove this variability. A novel individually labeled neuron, connecting the lobula to the midbrain and deutocerebrum, has been registered into the ISA atlas and demonstrates its usefulness and accuracy for future analysis of neural networks. The locust standard brain is accessible at http://www.3d-insectbrain.com .

}, keywords = {Anatomic, Anatomy, Animals, Artistic, Atlases as Topic, Brain, Brain Mapping, Grasshoppers, Imaging, Models, Neuroanatomy, Neurological, Neurons, Three-Dimensional}, issn = {0302-766X}, doi = {10.1007/s00441-008-0620-x}, author = {Kurylas, Angela E and Rohlfing, Torsten and Krofczik, Sabine and Jenett, Arnim and Homberg, Uwe} } @article {2957, title = {Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy.}, journal = {Science}, volume = {320}, year = {2008}, month = {2008 Jun 6}, pages = {1332-6}, abstract = {

Fluorescence light microscopy allows multicolor visualization of cellular components with high specificity, but its utility has until recently been constrained by the intrinsic limit of spatial resolution. We applied three-dimensional structured illumination microscopy (3D-SIM) to circumvent this limit and to study the mammalian nucleus. By simultaneously imaging chromatin, nuclear lamina, and the nuclear pore complex (NPC), we observed several features that escape detection by conventional microscopy. We could resolve single NPCs that colocalized with channels in the lamin network and peripheral heterochromatin. We could differentially localize distinct NPC components and detect double-layered invaginations of the nuclear envelope in prophase as previously seen only by electron microscopy. Multicolor 3D-SIM opens new and facile possibilities to analyze subcellular structures beyond the diffraction limit of the emitted light.

}, keywords = {Animals, Cell Line, Cell Nucleus, Chromatin, Confocal, Fluorescence, Fluorescent Dyes, Heterochromatin, Imaging, Indoles, Interphase, Lamins, Mice, Microscopy, Myoblasts, Nuclear Envelope, Nuclear Lamina, Nuclear Pore, Optics and Photonics, Three-Dimensional}, issn = {1095-9203}, doi = {10.1126/science.1156947}, author = {Schermelleh, Lothar and Carlton, Peter M and Haase, Sebastian and Shao, Lin and Winoto, Lukman and Kner, Peter and Burke, Brian and Cardoso, M Cristina and Agard, David A and Gustafsson, Mats G L and Leonhardt, Heinrich and Sedat, John W} } @article {2395, title = {TBP, Mot1, and NC2 establish a regulatory circuit that controls DPE-dependent versus TATA-dependent transcription.}, journal = {Genes \& Development}, volume = {22}, year = {2008}, month = {2008 Sep 1}, pages = {2353-8}, abstract = {

The RNA polymerase II core promoter is a structurally and functionally diverse transcriptional module. RNAi depletion and overexpression experiments revealed a genetic circuit that controls the balance of transcription from two core promoter motifs, the TATA box and the downstream core promoter element (DPE). In this circuit, TBP activates TATA-dependent transcription and represses DPE-dependent transcription, whereas Mot1 and NC2 block TBP function and thus repress TATA-dependent transcription and activate DPE-dependent transcription. This regulatory circuit is likely to be one means by which biological networks can transmit transcriptional signals, such as those from DPE-specific and TATA-specific enhancers, via distinct pathways.

}, keywords = {Animals, Cells, Cultured, Drosophila, Drosophila Proteins, Enhancer Elements, Gene Expression Regulation, Genetic, Promoter Regions, RNA Polymerase II, TATA Box, TATA-Box Binding Protein, Transcription, Transcription Factors}, issn = {0890-9369}, doi = {10.1073/pnas.1100640108}, author = {Hsu, Jer-Yuan and Juven-Gershon, Tamar and Marr, Michael T and Wright, Kevin J and Tjian, Robert and Kadonaga, James T} } @article {2346, title = {Theta-mediated dynamics of spatial information in hippocampus.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {28}, year = {2008}, month = {2008 Jun 4}, pages = {5959-64}, abstract = {

In rodent hippocampus, neuronal activity is organized by a 6-10 Hz theta oscillation. The spike timing of hippocampal pyramidal cells with respect to the theta rhythm correlates with an animal{\textquoteright}s position in space. This correlation has been suggested to indicate an explicit temporal code for position. Alternatively, it may be interpreted as a byproduct of theta-dependent dynamics of spatial information flow in hippocampus. Here we show that place cell activity on different phases of theta reflects positions shifted into the future or past along the animal{\textquoteright}s trajectory in a two-dimensional environment. The phases encoding future and past positions are consistent across recorded CA1 place cells, indicating a coherent representation at the network level. Consistent theta-dependent time offsets are not simply a consequence of phase-position correlation (phase precession), because they are no longer seen after data randomization that preserves the phase-position relationship. The scale of these time offsets, 100-300 ms, is similar to the latencies of hippocampal activity after sensory input and before motor output, suggesting that offset activity may maintain coherent brain activity in the face of information processing delays.

}, keywords = {Action Potentials, Animals, Hippocampus, Long-Evans, Male, Rats, Spatial Behavior, Theta Rhythm}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3773-10.2011}, author = {Itskov, Vladimir and Pastalkova, Eva and Mizuseki, Kenji and Buzs{\'a}ki, Gy{\"o}rgy and Harris, Kenneth D} } @article {988, title = {Tools for neuroanatomy and neurogenetics in Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, year = {2008}, month = {2008 Jul 15}, pages = {9715-20}, abstract = {

We demonstrate the feasibility of generating thousands of transgenic Drosophila melanogaster lines in which the expression of an exogenous gene is reproducibly directed to distinct small subsets of cells in the adult brain. We expect the expression patterns produced by the collection of 5,000 lines that we are currently generating to encompass all neurons in the brain in a variety of intersecting patterns. Overlapping 3-kb DNA fragments from the flanking noncoding and intronic regions of genes thought to have patterned expression in the adult brain were inserted into a defined genomic location by site-specific recombination. These fragments were then assayed for their ability to function as transcriptional enhancers in conjunction with a synthetic core promoter designed to work with a wide variety of enhancer types. An analysis of 44 fragments from four genes found that \>80\% drive expression patterns in the brain; the observed patterns were, on average, comprised of \<100 cells. Our results suggest that the D. melanogaster genome contains \>50,000 enhancers and that multiple enhancers drive distinct subsets of expression of a gene in each tissue and developmental stage. We expect that these lines will be valuable tools for neuroanatomy as well as for the elucidation of neuronal circuits and information flow in the fly brain.

}, keywords = {Animals, Biomedical Research, Brain, Developmental, Drosophila melanogaster, Enhancer Elements, Gene Expression Regulation, Genes, Genetic, Genetically Modified, Insect, Neurons, Neurosciences, Recombination}, issn = {1091-6490}, doi = {https://doi.org/10.1073/pnas.0803697105}, author = {Pfeiffer, Barret D and Jenett, Arnim and Hammonds, Ann S and Ngo, Teri-T B and Misra, Sima and Murphy, Christine and Scully, Audra and Carlson, Joseph W and Wan, Kenneth H and Laverty, Todd R and Mungall, Chris and Svirskas, Rob and Kadonaga, James T and Doe, Chris Q and Eisen, Michael B and Celniker, Susan E and Rubin, Gerald M} } @conference {6532, title = {Unfolding warping for object recognition.}, booktitle = {19TH International Conference on Pattern Recognition}, year = {2008}, month = {2008 December 11}, publisher = {IEEE}, organization = {IEEE}, address = {Tampa, FL}, abstract = {

In practice, understanding the spatial relationships between the surfaces of an object, can significantly improve the performance of object recognition systems. In this paper we propose a novel framework to recognize objects in pictures taken from arbitrary viewpoints. The idea is to maintain the frontal views of the major faces of objects in a global flat map. Then an unfolding warping technique is used to change the pose of the query object in the test view so that all visible surfaces of the object can be observed from a frontal viewpoint, improving the handling of serious occlusions and large viewpoint changes. We demonstrate the effectiveness of our approach through analysis of recognition trials of complex objects with comparison to popular methods.

}, isbn = {978-1-4244-2174-9}, doi = {10.1109/ICPR.2008.4761188}, author = {Xie, Jun and Hu, Min and Shah, Mubarak} } @article {46303, title = {Universal memory mechanism for familiarity recognition and identification.}, journal = {The Journal of Neuroscience : The Official Journal of the Society for Neuroscience}, volume = {28}, year = {2008}, month = {2008 Jan 2}, pages = {239-48}, abstract = {

Macaque monkeys were tested on a delayed-match-to-multiple-sample task, with either a limited set of well trained images (in randomized sequence) or with never-before-seen images. They performed much better with novel images. False positives were mostly limited to catch-trial image repetitions from the preceding trial. This result implies extremely effective one-shot learning, resembling Standing{\textquoteright}s finding that people detect familiarity for 10,000 once-seen pictures (with 80\% accuracy) (Standing, 1973). Familiarity memory may differ essentially from identification, which embeds and generates contextual information. When encountering another person, we can say immediately whether his or her face is familiar. However, it may be difficult for us to identify the same person. To accompany the psychophysical findings, we present a generic neural network model reproducing these behaviors, based on the same conservative Hebbian synaptic plasticity that generates delay activity identification memory. Familiarity becomes the first step toward establishing identification. Adding an inter-trial reset mechanism limits false positives for previous-trial images. The model, unlike previous proposals, relates repetition-recognition with enhanced neural activity, as recently observed experimentally in 92\% of differential cells in prefrontal cortex, an area directly involved in familiarity recognition. There may be an essential functional difference between enhanced responses to novel versus to familiar images: The maximal signal from temporal cortex is for novel stimuli, facilitating additional sensory processing of newly acquired stimuli. The maximal signal for familiar stimuli arising in prefrontal cortex facilitates the formation of selective delay activity, as well as additional consolidation of the memory of the image in an upstream cortical module.

}, keywords = {Animals, Behavior, Animal, Computer Simulation, Discrimination (Psychology), Haplorhini, Identification (Psychology), Models, Neurological, Neural Networks (Computer), Photic Stimulation, Recognition (Psychology), ROC Curve, Task Performance and Analysis}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4799-07.2008}, author = {Yakovlev, Volodya and Amit, Daniel J and Romani, Sandro and Hochstein, Shaul} } @article {68826, title = {V2a and V2b neurons are generated by the final divisions of pair-producing progenitors in the zebrafish spinal cord}, journal = {Development}, volume = {135}, year = {2008}, month = {09/2008}, pages = {3001-3005}, abstract = {

The p2 progenitor domain in the ventral spinal cord gives rise to two interneuron subtypes: V2a and V2b. Delta-Notch-mediated cell-cell interactions between postmitotic immature neurons have been implicated in the segregation of neuron subtypes. However, lineage relationships between V2a and V2b neurons have not been reported. We address this issue using Tg[vsx1:GFP]zebrafish, a model system in which high GFP expression is initiated near the final stage of p2 progenitors. Cell fates were followed in progeny using time-lapse microscopy. Results indicate that the vast majority, if not all, of GFP-labeled p2 progenitors divide once to produce V2a/V2b neuron pairs,indicating that V2a and V2b neurons are generated by the asymmetric division of pair-producing progenitor cells. Together with evidence that Notch signaling is involved in the cell fate specification process, our results strongly suggest that Delta-Notch interactions between sister cells play a crucial role in the final outcome of these asymmetric divisions. This mechanism for determining cell fate is similar to asymmetric divisions that occur during Drosophila neurogenesis, where ganglion mother cells divide once to produce distinct neurons. However, unlike in Drosophila, the divisional axes of p2 progenitors in zebrafish were not fixed. We report that the terminal division of pair-producing progenitor cells in vertebrate neurogenesis can reproducibly produce two distinct neurons through a mechanism that may not depend on the orientation of the division axis.

}, issn = {0950-1991}, doi = {10.1242/dev.024802}, url = {https://doi.org/10.1242/dev.024802}, author = {Kimura, Yukiko and Satou, Chie and Higashijima, Shin-Ichi} } @article {4431, title = {Visuomotor transformation in the fly gaze stabilization system.}, journal = {PLoS Biology}, volume = {6}, year = {2008}, month = {2008 Jul 22}, pages = {e173}, abstract = {

For sensory signals to control an animal{\textquoteright}s behavior, they must first be transformed into a format appropriate for use by its motor systems. This fundamental problem is faced by all animals, including humans. Beyond simple reflexes, little is known about how such sensorimotor transformations take place. Here we describe how the outputs of a well-characterized population of fly visual interneurons, lobula plate tangential cells (LPTCs), are used by the animal{\textquoteright}s gaze-stabilizing neck motor system. The LPTCs respond to visual input arising from both self-rotations and translations of the fly. The neck motor system however is involved in gaze stabilization and thus mainly controls compensatory head rotations. We investigated how the neck motor system is able to selectively extract rotation information from the mixed responses of the LPTCs. We recorded extracellularly from fly neck motor neurons (NMNs) and mapped the directional preferences across their extended visual receptive fields. Our results suggest that-like the tangential cells-NMNs are tuned to panoramic retinal image shifts, or optic flow fields, which occur when the fly rotates about particular body axes. In many cases, tangential cells and motor neurons appear to be tuned to similar axes of rotation, resulting in a correlation between the coordinate systems the two neural populations employ. However, in contrast to the primarily monocular receptive fields of the tangential cells, most NMNs are sensitive to visual motion presented to either eye. This results in the NMNs being more selective for rotation than the LPTCs. Thus, the neck motor system increases its rotation selectivity by a comparatively simple mechanism: the integration of binocular visual motion information.

}, keywords = {Animals, Diptera, Fixation, Motion Perception, Motor Neurons, Neck, Neurons, Ocular, Photic Stimulation, Visual Fields, Visual Pathways}, issn = {1545-7885}, doi = {10.1371/journal.pbio.0060173}, author = {Huston, Stephen J and Krapp, Holger G} } @article {4225, title = {Channelrhodopsin-2-assisted circuit mapping of long-range callosal projections.}, journal = {Nature Neuroscience}, volume = {10}, year = {2007}, month = {2007 May}, pages = {663-8}, abstract = {

The functions of cortical areas depend on their inputs and outputs, but the detailed circuits made by long-range projections are unknown. We show that the light-gated channel channelrhodopsin-2 (ChR2) is delivered to axons in pyramidal neurons in vivo. In brain slices from ChR2-expressing mice, photostimulation of ChR2-positive axons can be transduced reliably into single action potentials. Combining photostimulation with whole-cell recordings of synaptic currents makes it possible to map circuits between presynaptic neurons, defined by ChR2 expression, and postsynaptic neurons, defined by targeted patching. We applied this technique, ChR2-assisted circuit mapping (CRACM), to map long-range callosal projections from layer (L) 2/3 of the somatosensory cortex. L2/3 axons connect with neurons in L5, L2/3 and L6, but not L4, in both ipsilateral and contralateral cortex. In both hemispheres the L2/3-to-L5 projection is stronger than the L2/3-to-L2/3 projection. Our results suggest that laminar specificity may be identical for local and long-range cortical projections.

}, keywords = {Animals, Axons, Brain Mapping, Corpus Callosum, Embryo, Female, Functional Laterality, Inbred C57BL, Mammalian, Membrane Potentials, Mice, Nerve Net, Neural Pathways, Newborn, Patch-Clamp Techniques, Photic Stimulation, Pregnancy, Retinaldehyde, Rhodopsin, Somatosensory Cortex, Transgenic}, issn = {1097-6256}, doi = {10.1038/nn1891}, author = {Petreanu, Leopoldo and Huber, Daniel and Sobczyk, Aleksander and Svoboda, Karel} } @article {45889, title = {Coincidence detection of place and temporal context in a network model of spiking hippocampal neurons.}, journal = {PLoS Computational Biology}, volume = {3}, year = {2007}, month = {2007 Dec}, pages = {e234}, abstract = {

Recent advances in single-neuron biophysics have enhanced our understanding of information processing on the cellular level, but how the detailed properties of individual neurons give rise to large-scale behavior remains unclear. Here, we present a model of the hippocampal network based on observed biophysical properties of hippocampal and entorhinal cortical neurons. We assembled our model to simulate spatial alternation, a task that requires memory of the previous path through the environment for correct selection of the current path to a reward site. The convergence of inputs from entorhinal cortex and hippocampal region CA3 onto CA1 pyramidal cells make them potentially important for integrating information about place and temporal context on the network level. Our model shows how place and temporal context information might be combined in CA1 pyramidal neurons to give rise to splitter cells, which fire selectively based on a combination of place and temporal context. The model leads to a number of experimentally testable predictions that may lead to a better understanding of the biophysical basis of information processing in the hippocampus.

}, keywords = {Action Potentials, Algorithms, Animals, Computer Simulation, Hippocampus, Models, Neurological, Nerve Net, Neurons, Rats, Synaptic Transmission}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.0030234}, author = {Katz, Yael and Kath, William L and Spruston, Nelson and Hasselmo, Michael E} } @proceedings {3303, title = {Comparative analysis of spatial patterns of gene expression in Drosophila Melanogaster imaginal discs.}, year = {2007}, month = {2007 Apr 21}, abstract = {

Determining the precise spatial extent of expression of genes across different tissues, along with knowledge of the biochemical function of the genes is critical for understanding the roles of various genes in the development of metazoan organisms. To address this problem, we have developed high-throughput methods for generating images of gene expression in Drosophila melanogaster imaginal discs and for the automated analysis of these images. Our method automatically learns tissue shapes from a small number of manually segmented training examples and automatically aligns, extracts and scores new images, which are analyzed to generate gene expression maps for each gene. We have developed a reverse lookup procedure that enables us to identify genes that have spatial expression patterns most similar to a given gene of interest. Our methods enable us to cluster both the genes and the pixels that of the maps, thereby identifying sets of genes that have similar patterns, and regions of the tissues of interest that have similar gene expression profiles across a large number of genes.

}, author = {Harmon, C and Ahammad, Parvez and Hammonds, Ann S and Weiszmann, Richard and Celniker, Susan E and Sastry, S and Rubin, Gerald M} } @article {2506, title = {The coordination of the sequential appearance of MHR4 and dopa decarboxylase during the decline of the ecdysteroid titer at the end of the molt.}, journal = {Molecular and Cellular Endocrinology}, volume = {276}, year = {2007}, month = {2007 Sep 30}, pages = {71-9}, abstract = {

During the last larval molt in Manduca sexta, in response to an increasing, then decreasing ecdysteroid titer, a number of transcription factors such as E75B, MHR3, MHR4, and betaFTZ-F1 appear and disappear in the abdominal epidermis leading to dopa decarboxylase (DDC) expression. Messenger RNAs for both the 20E-induced transcription factors, MHR3 and E75B, are maximal near the peak of the ecdysteroid titer with MHR4 mRNA appearing as the titer declines followed by betaFTZ-F1 and DDC mRNAs. E75B and MHR4 mRNA were not expressed in Manduca GV1 cells, either during exposure to 20E or after its removal. When either MHR3 dsRNA was transfected or E75B was constitutively expressed in these cells, MHR4 mRNA appeared in response to 20E by 6h. E75B was found to form a heterodimer with MHR3 using the BacterioMatch II two-hybrid assay. We conclude that MHR3 apparently suppresses MHR4 expression in the presence of 20E; the appearance of E75B then removes MHR3 by dimerization, allowing MHR4 to be expressed. Because of significant basal activity of the ddc promoter in the GV1 cells, we could perform rescue experiments by adding various factors. Constitutive expression of either E75B or MHR4 in the cells suppressed the significant basal activity of the 3.2kb ddc promoter in the GV1 cells, but 20E had no effect on this activity. Thus, E75B and MHR4 are 20E-induced inhibitory factors that suppress ddc expression and therefore act as ecdysteroid-regulated timers to coordinate the onset of ddc expression at the end of the molt.

}, keywords = {Animals, Biological, Cell Line, Cytoplasmic and Nuclear, Developmental, Dopa Decarboxylase, Ecdysteroids, Gene Expression Regulation, Genetic, Insect Proteins, Manduca, Models, Molting, Promoter Regions, Protein Binding, Receptors}, issn = {0303-7207}, doi = {10.1016/j.mce.2007.07.002}, author = {Hiruma, Kiyoshi and Riddiford, Lynn M} } @proceedings {65004, title = {Developing photo activated localization microscopy}, year = {2007}, month = {2007 Apr 15}, abstract = {

In conventional biological imaging, diffraction places a limit on the minimal xy distance at which two marked objects can be discerned. Consequently, resolution of target molecules within cells is typically coarser by two orders of magnitude than the molecular scale at which the proteins are spatially distributed. Photoactivated localization microscopy (PALM) optically resolves selected subsets of protect fluorescent probes within cells at mean separations of \<25 nanometers. It involves serial photoactivation and subsequent photobleaching of numerous sparse subsets of photoactivated fluorescent protein molecules. Individual molecules are localized at near molecular resolution by determining their centers of fluorescent emission via a statistical fit of their point-spread-function. The position information from all subsets is then assembled into a super-resolution image, in which individual fluorescent molecules are isolated at high molecular densities. In this paper, some of the limitations for PALM imaging under current experimental conditions are discussed.

}, doi = {10.1109/isbi.2007.357008}, author = {George H. Patterson and Eric Betzig and Jennifer Lippincott-Schwartz and Harald F. Hess} } @article {6351, title = {Differential regulation of action potential- and metabotropic glutamate receptor-induced Ca2+ signals by inositol 1,4,5-trisphosphate in dopaminergic neurons.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {27}, year = {2007}, month = {2007 Apr 25}, pages = {4776-85}, abstract = {

Ca2+ signals associated with action potentials (APs) and metabotropic glutamate receptor (mGluR) activation exert distinct influences on neuronal activity and synaptic plasticity. However, it is not clear how these two types of Ca2+ signals are differentially regulated by neurotransmitter inputs in a single neuron. We investigated this issue in dopaminergic neurons of the ventral midbrain using brain slices. Intracellular Ca2+ was assessed by measuring Ca2+-sensitive K+ currents or imaging the fluorescence of Ca2+ indicator dyes. Tonic activation of metabotropic neurotransmitter receptors (mGluRs, alpha1 adrenergic receptors, and muscarinic acetylcholine receptors), attained by superfusion of agonists or weak, sustained (approximately 1 s) synaptic stimulation, augmented AP-induced Ca2+ transients. In contrast, Ca2+ signals elicited by strong, transient (50-200 ms) activation of mGluRs with aspartate iontophoresis were suppressed by superfusion of agonists. These opposing effects on Ca2+ signals were both mediated by an increase in intracellular inositol 1,4,5-trisphosphate (IP3) levels, because they were blocked by heparin, an IP3 receptor antagonist, and reproduced by photolytic application of IP3. Evoking APs repetitively at low frequency (2 Hz) caused inactivation of IP3 receptors and abolished IP3 facilitation of single AP-induced Ca2+ signals, whereas facilitation of Ca2+ signals triggered by bursts of APs (five at 20 Hz) was attenuated by less than half. We further obtained evidence suggesting that the psychostimulant amphetamine may augment burst-induced Ca2+ signals via both depression of basal firing and production of IP3. We propose that intracellular IP3 tone provides a mechanism to selectively amplify burst-induced Ca2+ signals in dopaminergic neurons.

}, keywords = {4, 5-Trisphosphate, 5-Trisphosphate Receptors, Action Potentials, Amphetamine, Animals, Aspartic Acid, Calcium Signaling, Central Nervous System Stimulants, Dopamine, Inositol 1, Mesencephalon, Metabotropic Glutamate, Neurons, Organ Culture Techniques, Patch-Clamp Techniques, Rats, Receptors, Ryanodine Receptor Calcium Release Channel, Sprague-Dawley}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0139-07.2007}, author = {Cui, Guohong and Bernier, Brian E and Harnett, Mark T and Morikawa, Hitoshi} } @article {46627, title = {Downregulation of mu opioid receptor by RNA interference in the ventral tegmental area reduces ethanol consumption in mice.}, journal = {Genes, Brain, and Behavior}, volume = {6}, year = {2007}, month = {2007 Nov}, pages = {728-35}, abstract = {

Pharmacological and genetic studies have implicated the mu opioid receptor (MOR) in the regulation of ethanol intake in animal models and humans. Non-specific antagonists of opioid receptors have been shown to affect ethanol consumption when infused directly into the ventral tegmental area (VTA) of rats. However, administration of MOR-selective antagonists into the VTA has yielded mixed results. We used RNA interference (RNAi) to specifically decrease levels of MOR messenger RNA in the VTA of mice and examined the effect on ethanol consumption in a two-bottle choice paradigm. Mice were injected in the VTA with lentivirus expressing either a small hairpin RNA (shRNA) targeting MOR or a control shRNA. One week after virus injection, mice were examined for ethanol consumption in a two-bottle choice experiment with increasing concentrations of ethanol over the course of 1 month. Expression of an shRNA targeting MOR in the VTA led to a significant reduction in ethanol consumption. These results strengthen the hypothesis that MOR in the VTA is one of the key brain substrates mediating alcohol consumption. The RNAi combined with lentiviral delivery can be used successfully in brain to effect a sustained reduction in expression of specific genes for behavioral analysis.

}, keywords = {Administration, Oral, Alcohol Drinking, Animals, Choice Behavior, Dose-Response Relationship, Drug, Down-Regulation, Ethanol, Female, Gene Transfer Techniques, Lentivirus, Mice, Mice, Inbred C57BL, Receptors, Opioid, mu, RNA Interference, RNA, Messenger, RNA, Small Interfering, Ventral Tegmental Area}, issn = {1601-1848}, doi = {10.1111/j.1601-183X.2007.00303.x}, author = {Lasek, A W and Janak, P H and He, L and Whistler, J L and Heberlein, U} } @article {6494, title = {Evolution of genes and genomes on the Drosophila phylogeny.}, journal = {Nature}, volume = {450}, year = {2007}, month = {2007 Nov 8}, pages = {203-18}, abstract = {

Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

}, keywords = {Animals, Codon, DNA, DNA Transposable Elements, Drosophila, Drosophila Proteins, Evolution, Gene Order, Genes, Genome, Genomics, Immunity, Insect, Mitochondrial, Molecular, Multigene Family, Phylogeny, Reproduction, RNA, Sequence Alignment, Sequence Analysis, Synteny, Untranslated}, issn = {1476-4687}, doi = {10.1038/nature06341}, author = {Clark, Andrew G and Eisen, Michael B and Smith, Douglas R and Bergman, Casey M and Oliver, Brian and Markow, Therese A and Kaufman, Thomas C and Kellis, Manolis and Gelbart, William and Iyer, Venky N and Pollard, Daniel A and Sackton, Timothy B and Larracuente, Amanda M and Singh, Nadia D and Abad, Jose P and Abt, Dawn N and Adryan, Boris and Aguade, Montserrat and Akashi, Hiroshi and Anderson, Wyatt W and Aquadro, Charles F and Ardell, David H and Arguello, Roman and Artieri, Carlo G and Barbash, Daniel A and Barker, Daniel and Barsanti, Paolo and Batterham, Phil and Batzoglou, Serafim and Begun, Dave and Bhutkar, Arjun and Blanco, Enrico and Bosak, Stephanie A and Bradley, Robert K and Brand, Adrianne D and Brent, Michael R and Brooks, Angela N and Brown, Randall H and Butlin, Roger K and Caggese, Corrado and Calvi, Brian R and Bernardo de Carvalho, A and Caspi, Anat and Castrezana, Sergio and Celniker, Susan E and Chang, Jean L and Chapple, Charles and Chatterji, Sourav and Chinwalla, Asif and Civetta, Alberto and Clifton, Sandra W and Comeron, Josep M and Costello, James C and Coyne, Jerry A and Daub, Jennifer and David, Robert G and Delcher, Arthur L and Delehaunty, Kim and Do, Chuong B and Ebling, Heather and Edwards, Kevin and Eickbush, Thomas and Evans, Jay D and Filipski, Alan and Findeiss, Sven and Freyhult, Eva and Fulton, Lucinda and Fulton, Robert and Garcia, Ana C L and Gardiner, Anastasia and Garfield, David A and Garvin, Barry E and Gibson, Greg and Gilbert, Don and Gnerre, Sante and Godfrey, Jennifer and Good, Robert and Gotea, Valer and Gravely, Brenton and Greenberg, Anthony J and Griffiths-Jones, Sam and Gross, Samuel and Guigo, Roderic and Gustafson, Erik A and Haerty, Wilfried and Hahn, Matthew W and Halligan, Daniel L and Halpern, Aaron L and Halter, Gillian M and Han, Mira V and Heger, Andreas and Hillier, LaDeana and Hinrichs, Angie S and Holmes, Ian and Hoskins, Roger A and Hubisz, Melissa J and Hultmark, Dan and Huntley, Melanie A and Jaffe, David B and Jagadeeshan, Santosh and Jeck, William R and Johnson, Justin and Jones, Corbin D and Jordan, William C and Karpen, Gary H and Kataoka, Eiko and Keightley, Peter D and Kheradpour, Pouya and Kirkness, Ewen F and Koerich, Leonardo B and Kristiansen, Karsten and Kudrna, Dave and Kulathinal, Rob J and Kumar, Sudhir and Kwok, Roberta and Lander, Eric and Langley, Charles H and Lapoint, Richard and Lazzaro, Brian P and Lee, So-Jeong and Levesque, Lisa and Li, Ruiqiang and Lin, Chiao-Feng and Lin, Michael F and Lindblad-Toh, Kerstin and Llopart, Ana and Long, Manyuan and Low, Lloyd and Lozovsky, Elena and Lu, Jian and Luo, Meizhong and Machado, Carlos A and Makalowski, Wojciech and Marzo, Mar and Matsuda, Muneo and Matzkin, Luciano and McAllister, Bryant and McBride, Carolyn S and McKernan, Brendan and McKernan, Kevin and Mendez-Lago, Maria and Minx, Patrick and Mollenhauer, Michael U and Montooth, Kristi and Mount, Stephen M and Mu, Xu and Myers, Eugene and Negre, Barbara and Newfeld, Stuart and Nielsen, Rasmus and Noor, Mohamed A F and O{\textquoteright}Grady, Patrick and Pachter, Lior and Papaceit, Montserrat and Parisi, Matthew J and Parisi, Michael and Parts, Leopold and Pedersen, Jakob S and Pesole, Graziano and Phillippy, Adam M and Ponting, Chris P and Pop, Mihai and Porcelli, Damiano and Powell, Jeffrey R and Prohaska, Sonja and Pruitt, Kim and Puig, Marta and Quesneville, Hadi and Ram, Kristipati Ravi and Rand, David and Rasmussen, Matthew D and Reed, Laura K and Reenan, Robert and Reily, Amy and Remington, Karin A and Rieger, Tania T and Ritchie, Michael G and Robin, Charles and Rogers, Yu-Hui and Rohde, Claudia and Rozas, Julio and Rubenfield, Marc J and Ruiz, Alfredo and Russo, Susan and Salzberg, Steven L and Sanchez-Gracia, Alejandro and Saranga, David J and Sato, Hajime and Schaeffer, Stephen W and Schatz, Michael C and Schlenke, Todd and Schwartz, Russell and Segarra, Carmen and Singh, Rama S and Sirot, Laura and Sirota, Marina and Sisneros, Nicholas B and Smith, Chris D and Smith, Temple F and Spieth, John and Stage, Deborah E and Stark, Alexander and Stephan, Wolfgang and Strausberg, Robert L and Strempel, Sebastian and Sturgill, David and Sutton, Granger and Sutton, Granger G and Tao, Wei and Teichmann, Sarah and Tobari, Yoshiko N and Tomimura, Yoshihiko and Tsolas, Jason M and Valente, Vera L S and Venter, Eli and Venter, J Craig and Vicario, Saverio and Vieira, Filipe G and Vilella, Albert J and Villasante, Alfredo and Walenz, Brian and Wang, Jun and Wasserman, Marvin and Watts, Thomas and Wilson, Derek and Wilson, Richard K and Wing, Rod A and Wolfner, Mariana F and Wong, Alex and Wong, Gane Ka-Shu and Wu, Chung-I and Wu, Gabriel and Yamamoto, Daisuke and Yang, Hsiao-Pei and Yang, Shiaw-Pyng and Yorke, James A and Yoshida, Kiyohito and Zdobnov, Evgeny and Zhang, Peili and Zhang, Yu and Zimin, Aleksey V and Baldwin, Jennifer and Abdouelleil, Amr and Abdulkadir, Jamal and Abebe, Adal and Abera, Brikti and Abreu, Justin and Acer, St Christophe and Aftuck, Lynne and Alexander, Allen and An, Peter and Anderson, Erica and Anderson, Scott and Arachi, Harindra and Azer, Marc and Bachantsang, Pasang and Barry, Andrew and Bayul, Tashi and Berlin, Aaron and Bessette, Daniel and Bloom, Toby and Blye, Jason and Boguslavskiy, Leonid and Bonnet, Claude and Boukhgalter, Boris and Bourzgui, Imane and Brown, Adam and Cahill, Patrick and Channer, Sheridon and Cheshatsang, Yama and Chuda, Lisa and Citroen, Mieke and Collymore, Alville and Cooke, Patrick and Costello, Maura and D{\textquoteright}Aco, Katie and Daza, Riza and De Haan, Georgius and DeGray, Stuart and DeMaso, Christina and Dhargay, Norbu and Dooley, Kimberly and Dooley, Erin and Doricent, Missole and Dorje, Passang and Dorjee, Kunsang and Dupes, Alan and Elong, Richard and Falk, Jill and Farina, Abderrahim and Faro, Susan and Ferguson, Diallo and Fisher, Sheila and Foley, Chelsea D and Franke, Alicia and Friedrich, Dennis and Gadbois, Loryn and Gearin, Gary and Gearin, Christina R and Giannoukos, Georgia and Goode, Tina and Graham, Joseph and Grandbois, Edward and Grewal, Sharleen and Gyaltsen, Kunsang and Hafez, Nabil and Hagos, Birhane and Hall, Jennifer and Henson, Charlotte and Hollinger, Andrew and Honan, Tracey and Huard, Monika D and Hughes, Leanne and Hurhula, Brian and Husby, M Erii and Kamat, Asha and Kanga, Ben and Kashin, Seva and Khazanovich, Dmitry and Kisner, Peter and Lance, Krista and Lara, Marcia and Lee, William and Lennon, Niall and Letendre, Frances and LeVine, Rosie and Lipovsky, Alex and Liu, Xiaohong and Liu, Jinlei and Liu, Shangtao and Lokyitsang, Tashi and Lokyitsang, Yeshi and Lubonja, Rakela and Lui, Annie and MacDonald, Pen and Magnisalis, Vasilia and Maru, Kebede and Matthews, Charles and McCusker, William and McDonough, Susan and Mehta, Teena and Meldrim, James and Meneus, Louis and Mihai, Oana and Mihalev, Atanas and Mihova, Tanya and Mittelman, Rachel and Mlenga, Valentine and Montmayeur, Anna and Mulrain, Leonidas and Navidi, Adam and Naylor, Jerome and Negash, Tamrat and Nguyen, Thu and Nguyen, Nga and Nicol, Robert and Norbu, Choe and Norbu, Nyima and Novod, Nathaniel and O{\textquoteright}Neill, Barry and Osman, Sahal and Markiewicz, Eva and Oyono, Otero L and Patti, Christopher and Phunkhang, Pema and Pierre, Fritz and Priest, Margaret and Raghuraman, Sujaa and Rege, Filip and Reyes, Rebecca and Rise, Cecil and Rogov, Peter and Ross, Keenan and Ryan, Elizabeth and Settipalli, Sampath and Shea, Terry and Sherpa, Ngawang and Shi, Lu and Shih, Diana and Sparrow, Todd and Spaulding, Jessica and Stalker, John and Stange-Thomann, Nicole and Stavropoulos, Sharon and Stone, Catherine and Strader, Christopher and Tesfaye, Senait and Thomson, Talene and Thoulutsang, Yama and Thoulutsang, Dawa and Topham, Kerri and Topping, Ira and Tsamla, Tsamla and Vassiliev, Helen and Vo, Andy and Wangchuk, Tsering and Wangdi, Tsering and Weiand, Michael and Wilkinson, Jane and Wilson, Adam and Yadav, Shailendra and Young, Geneva and Yu, Qing and Zembek, Lisa and Zhong, Danni and Zimmer, Andrew and Zwirko, Zac and Jaffe, David B and Alvarez, Pablo and Brockman, Will and Butler, Jonathan and Chin, CheeWhye and Gnerre, Sante and Grabherr, Manfred and Kleber, Michael and Mauceli, Evan and MacCallum, Iain} } @article {955, title = {Global analysis of patterns of gene expression during Drosophila embryogenesis.}, journal = {Genome Biology}, volume = {8}, year = {2007}, month = {2007 July 23}, pages = {R145}, abstract = {

Cell and tissue specific gene expression is a defining feature of embryonic development in multi-cellular organisms. However, the range of gene expression patterns, the extent of the correlation of expression with function, and the classes of genes whose spatial expression are tightly regulated have been unclear due to the lack of an unbiased, genome-wide survey of gene expression patterns.

}, keywords = {Animals, Drosophila melanogaster, Embryonic Development, Gene Expression Profiling}, issn = {1465-6914}, doi = {10.1186/gb-2007-8-7-r145}, author = {Tomancak, Pavel and Berman, Benjamin P and Beaton, Amy and Weiszmann, Richard and Kwan, Elaine and Hartenstein, Volker and Celniker, Susan E and Rubin, Gerald M} } @article {46628, title = {GSK-3/Shaggy regulates olfactory habituation in Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, year = {2007}, month = {2007 Mar 13}, pages = {4653-7}, abstract = {

Habituation is a universal form of nonassociative learning that results in the devaluation of sensory inputs that have little information content. Although habituation is found throughout nature and has been studied in many organisms, the underlying molecular mechanisms remain poorly understood. We performed a forward genetic screen in Drosophila to search for mutations that modified habituation of an olfactory-mediated locomotor startle response, and we isolated a mutation in the glycogen synthase kinase-3 (GSK-3) homolog Shaggy. Decreases in Shaggy levels blunted habituation, whereas increases promoted habituation. Additionally, habituation acutely regulated Shaggy by an inhibitory phosphorylation mechanism, suggesting that a signal transduction pathway that regulates Shaggy is engaged during habituation. Although shaggy mutations also affected circadian rhythm period, this requirement was genetically separable from its role in habituation. Thus, shaggy functions in different neuronal circuits to regulate behavioral plasticity to an olfactory startle and circadian rhythmicity.

}, keywords = {Alleles, Animals, Behavior, Animal, Circadian Rhythm, Drosophila, Drosophila Proteins, Female, Glycogen Synthase Kinase 3, Habituation, Psychophysiologic, Male, Models, Genetic, Mutation, Phosphorylation, Signal Transduction, Smell}, issn = {0027-8424}, doi = {10.1073/pnas.0700493104}, author = {Wolf, Fred W and Eddison, Mark and Lee, Seonok and Cho, William and Heberlein, Ulrike} } @article {46630, title = {Guidelines on nicotine dose selection for in vivo research.}, journal = {Psychopharmacology (Berl)}, volume = {190}, year = {2007}, month = {2007 Feb}, pages = {269-319}, abstract = {

RATIONALE: This review provides insight for the judicious selection of nicotine dose ranges and routes of administration for in vivo studies. The literature is replete with reports in which a dosaging regimen chosen for a specific nicotine-mediated response was suboptimal for the species used. In many cases, such discrepancies could be attributed to the complex variables comprising species-specific in vivo responses to acute or chronic nicotine exposure.

OBJECTIVES: This review capitalizes on the authors{\textquoteright} collective decades of in vivo nicotine experimentation to clarify the issues and to identify the variables to be considered in choosing a dosaging regimen. Nicotine dose ranges tolerated by humans and their animal models provide guidelines for experiments intended to extrapolate to human tobacco exposure through cigarette smoking or nicotine replacement therapies. Just as important are the nicotine dosaging regimens used to provide a mechanistic framework for acquisition of drug-taking behavior, dependence, tolerance, or withdrawal in animal models.

RESULTS: Seven species are addressed: humans, nonhuman primates, rats, mice, Drosophila, Caenorhabditis elegans, and zebrafish. After an overview on nicotine metabolism, each section focuses on an individual species, addressing issues related to genetic background, age, acute vs chronic exposure, route of administration, and behavioral responses.

CONCLUSIONS: The selected examples of successful dosaging ranges are provided, while emphasizing the necessity of empirically determined dose-response relationships based on the precise parameters and conditions inherent to a specific hypothesis. This review provides a new, experimentally based compilation of species-specific dose selection for studies on the in vivo effects of nicotine.

}, keywords = {Animals, Behavioral Research, Dose-Response Relationship, Drug, Ganglionic Stimulants, Guidelines as Topic, Humans, Models, Biological, Nicotine, Species Specificity}, issn = {0033-3158}, doi = {10.1007/s00213-006-0441-0}, author = {Matta, Shannon G and Balfour, David J and Benowitz, Neal L and Boyd, R Thomas and Buccafusco, Jerry J and Caggiula, Anthony R and Craig, Caroline R and Collins, Allan C and Damaj, M Imad and Donny, Eric C and Gardiner, Phillip S and Grady, Sharon R and Heberlein, Ulrike and Leonard, Sherry S and Levin, Edward D and Lukas, Ronald J and Markou, Athina and Marks, Michael J and McCallum, Sarah E and Parameswaran, Neeraja and Perkins, Kenneth A and Picciotto, Marina R and Quik, Maryka and Rose, Jed E and Rothenfluh, Adrian and Schafer, William R and Stolerman, Ian P and Tyndale, Rachel F and Wehner, Jeanne M and Zirger, Jeffrey M} } @article {2670, title = {Huntingtin-interacting protein 14, a palmitoyl transferase required for exocytosis and targeting of CSP to synaptic vesicles.}, journal = {The Journal of Cell Biology}, volume = {179}, year = {2007}, month = {2007 Dec 31}, pages = {1481-96}, abstract = {

Posttranslational modification through palmitoylation regulates protein localization and function. In this study, we identify a role for the Drosophila melanogaster palmitoyl transferase Huntingtin-interacting protein 14 (HIP14) in neurotransmitter release. hip14 mutants show exocytic defects at low frequency stimulation and a nearly complete loss of synaptic transmission at higher temperature. Interestingly, two exocytic components known to be palmitoylated, cysteine string protein (CSP) and SNAP25, are severely mislocalized at hip14 mutant synapses. Complementary DNA rescue and localization experiments indicate that HIP14 is required solely in the nervous system and is essential for presynaptic function. Biochemical studies indicate that HIP14 palmitoylates CSP and that CSP is not palmitoylated in hip14 mutants. Furthermore, the hip14 exocytic defects can be suppressed by targeting CSP to synaptic vesicles using a chimeric protein approach. Our data indicate that HIP14 controls neurotransmitter release by regulating the trafficking of CSP to synapses.

}, keywords = {Acyltransferases, Adaptor Proteins, Animals, Drosophila melanogaster, Drosophila Proteins, Exocytosis, Ganglia, Invertebrate, Nerve Tissue Proteins, Nervous System, Neuromuscular Junction, Neurotransmitter Agents, Post-Translational, Protein Processing, Protein Transport, Signal Transducing, Synaptic Transmission, Synaptic Vesicles}, issn = {1540-8140}, doi = {10.1083/jcb.200710061}, author = {Ohyama, Tomoko and Verstreken, Patrik and Ly, Cindy V and Rosenmund, Tanja and Rajan, Akhila and Tien, An-Chi and Haueter, Claire and Schulze, Karen L and Bellen, Hugo J} } @article {46405, title = {IL-33 and ST2 comprise a critical biomechanically induced and cardioprotective signaling system.}, journal = {The Journal of Clinical Investigation}, volume = {117}, year = {2007}, month = {2007 Jun}, pages = {1538-49}, abstract = {

ST2 is an IL-1 receptor family member with transmembrane (ST2L) and soluble (sST2) isoforms. sST2 is a mechanically induced cardiomyocyte protein, and serum sST2 levels predict outcome in patients with acute myocardial infarction or chronic heart failure. Recently, IL-33 was identified as a functional ligand of ST2L, allowing exploration of the role of ST2 in myocardium. We found that IL-33 was a biomechanically induced protein predominantly synthesized by cardiac fibroblasts. IL-33 markedly antagonized angiotensin II- and phenylephrine-induced cardiomyocyte hypertrophy. Although IL-33 activated NF-kappaB, it inhibited angiotensin II- and phenylephrine-induced phosphorylation of inhibitor of NF-kappa B alpha (I kappa B alpha) and NF-kappaB nuclear binding activity. sST2 blocked antihypertrophic effects of IL-33, indicating that sST2 functions in myocardium as a soluble decoy receptor. Following pressure overload by transverse aortic constriction (TAC), ST2(-/-) mice had more left ventricular hypertrophy, more chamber dilation, reduced fractional shortening, more fibrosis, and impaired survival compared with WT littermates. Furthermore, recombinant IL-33 treatment reduced hypertrophy and fibrosis and improved survival after TAC in WT mice, but not in ST2(-/-) littermates. Thus, IL-33/ST2 signaling is a mechanically activated, cardioprotective fibroblast-cardiomyocyte paracrine system, which we believe to be novel. IL-33 may have therapeutic potential for beneficially regulating the myocardial response to overload.

}, keywords = {Animals, Biomechanical Phenomena, Cardiotonic Agents, Cells, Cultured, Fibroblasts, Humans, Interleukins, Membrane Proteins, Mice, Mice, Inbred C57BL, Mice, Knockout, Myocytes, Cardiac, NF-kappa B, Rats, Receptors, Cell Surface, Receptors, Interleukin, Recombinant Proteins, Signal Transduction}, issn = {0021-9738}, doi = {10.1172/JCI30634}, author = {Sanada, Shoji and Hakuno, Daihiko and Higgins, Luke J and Schreiter, Eric R and McKenzie, Andrew N J and Lee, Richard T} } @article {4222, title = {Locally dynamic synaptic learning rules in pyramidal neuron dendrites.}, journal = {Nature}, volume = {450}, year = {2007}, month = {2007 Dec 20}, pages = {1195-200}, abstract = {

Long-term potentiation (LTP) of synaptic transmission underlies aspects of learning and memory. LTP is input-specific at the level of individual synapses, but neural network models predict interactions between plasticity at nearby synapses. Here we show in mouse hippocampal pyramidal cells that LTP at individual synapses reduces the threshold for potentiation at neighbouring synapses. After input-specific LTP induction by two-photon glutamate uncaging or by synaptic stimulation, subthreshold stimuli, which by themselves were too weak to trigger LTP, caused robust LTP and spine enlargement at neighbouring spines. Furthermore, LTP induction broadened the presynaptic-postsynaptic spike interval for spike-timing-dependent LTP within a dendritic neighbourhood. The reduction in the threshold for LTP induction lasted approximately 10 min and spread over approximately 10 microm of dendrite. These local interactions between neighbouring synapses support clustered plasticity models of memory storage and could allow for the binding of behaviourally linked information on the same dendritic branch.

}, keywords = {Animals, Dendrites, Excitatory Postsynaptic Potentials, Glutamic Acid, Learning, Long-Term Potentiation, Mice, Models, Neurological, Pyramidal Cells, Synapses}, issn = {1476-4687}, doi = {10.1038/nature06416}, author = {Harvey, Christopher D and Svoboda, Karel} } @article {6350, title = {Modulation of neuronal voltage-activated calcium and sodium channels by polyamines and pH.}, journal = {Channels }, volume = {1}, year = {2007}, month = {2007 Jul-Aug}, pages = {281-90}, abstract = {

The endogenous polyamines spermine, spermidine and putrescine are present at high concentrations inside neurons and can be released into the extracellular space where they have been shown to modulate ion channels. Here, we have examined polyamine modulation of voltage-activated Ca(2+) channels (VACCs) and voltage-activated Na(+) channels (VANCs) in rat superior cervical ganglion neurons using whole-cell voltage-clamp at physiological divalent concentrations. Polyamines inhibited VACCs in a concentration-dependent manner with IC(50)s for spermine, spermidine, and putrescine of 4.7 +/- 0.7, 11.2 +/- 1.4 and 90 +/- 36 mM, respectively. Polyamines caused inhibition by shifting the VACC half-activation voltage (V(0.5)) to depolarized potentials and by reducing total VACC permeability. The shift was described by Gouy-Chapman-Stern theory with a surface charge density of 0.120 +/- 0.005 e(-) nm(-2) and a surface potential of -19 mV. Attenuation of spermidine and spermine inhibition of VACC at decreased pH was explained by H(+) titration of surface charge. Polyamine-mediated effects also decreased at elevated pH due to the inhibitors having lower valence and being less effective at screening surface charge. Polyamines affected VANC currents indirectly by reducing TTX inhibition of VANCs at high pH. This may reflect surface charge induced decreases in the local TTX concentration or polyamine-TTX interactions. In conclusion, polyamines inhibit neuronal VACCs via complex interactions with extracellular H(+) and Ca. Many of the observed effects can be explained by a model incorporating polyamine binding, H(+) binding and surface charge screening.

}, keywords = {Animals, Calcium, Calcium Channels, Cell Membrane Permeability, Cells, Cultured, Hydrogen-Ion Concentration, Membrane Potentials, Models, Neurological, Neurons, Patch-Clamp Techniques, Polyamines, Putrescine, Rats, Sodium, Sodium Channel Blockers, Sodium Channels, Spermidine, Spermine, Superior Cervical Ganglion, Tetrodotoxin, Time Factors}, issn = {1933-6969}, author = {Chen, Wenyan and Harnett, Mark T and Smith, Stephen M} } @article {4979, title = {Multiple memory traces for olfactory reward learning in Drosophila.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {27}, year = {2007}, month = {2007 Oct 10}, pages = {11132-8}, abstract = {

Physical traces underlying simple memories can be confined to a single group of cells in the brain. In the fly Drosophila melanogaster, the Kenyon cells of the mushroom bodies house traces for both appetitive and aversive odor memories. The adenylate cyclase protein, Rutabaga, has been shown to mediate both traces. Here, we show that, for appetitive learning, another group of cells can additionally accommodate a Rutabaga-dependent memory trace. Localized expression of rutabaga in either projection neurons, the first-order olfactory interneurons, or in Kenyon cells, the second-order interneurons, is sufficient for rescuing the mutant defect in appetitive short-term memory. Thus, appetitive learning may induce multiple memory traces in the first- and second-order olfactory interneurons using the same plasticity mechanism. In contrast, aversive odor memory of rutabaga is rescued selectively in the Kenyon cells, but not in the projection neurons. This difference in the organization of memory traces is consistent with the internal representation of reward and punishment.

}, keywords = {Animals, Drosophila melanogaster, Female, Learning, Male, Nerve Net, Olfactory Pathways, Reward, Smell}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.2712-07.2007}, author = {Thum, Andreas S and Jenett, Arnim and Ito, Kei and Heisenberg, Martin and Tanimoto, Hiromu} } @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 {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 {67285, title = {Observability of Higgs produced with top quarks and decaying to bottom quarks}, journal = {Journal of Physics G: Nuclear and Particle Physics}, volume = {34}, year = {2007}, month = {04/20027}, pages = {N221 - N250}, abstract = {

The decay,\ , is dominant for a Standard Model Higgs boson in the mass range just above the exclusion limit of 114.4 GeV/c2\ reported by the LEP experiments. Unfortunately, an overwhelming abundance of\ \ events arising from more mundane sources, together with the lack of precision inherent in the reconstruction of the Higgs mass, renders this decay mode\ a priori\ undetectable in the case of direct Higgs production at the LHC. It is therefore of no small interest to investigate whether\ \ can be observed in those cases where the Higgs is produced in association with other massive particles. In this note, the results of a study of Higgs bosons produced in association with top quarks and decaying via\ \ are presented. The study was performed as realistically as possible by employing a full and detailed Monte Carlo simulation of the CMS detector followed by the application of trigger and reconstruction algorithms that were developed for use with real data. Important systematic effects resulting from such sources as the uncertainties in the jet energy scale and the estimated rates for correctly tagging b jets or mistagging non-b jets have been taken into account. The impact of large theoretical uncertainties in the cross sections for\ \ plus\ N\ jets processes due to an absence of next-to-leading order calculations is also considered.

}, issn = {0954-3899}, doi = {10.1088/0954-3899/34/5/N03}, url = {https://iopscience.iop.org/article/10.1088/0954-3899/34/5/N03}, author = {Benedetti, D and Cucciarelli, S and Hill, C and Incandela, J and Koay, S A and Riccardi, C and Santocchia, A and Schmidt, A and Torre, P and Weiser, C} } @article {2807, title = {[Role of Bid protein in the mitochondria and endoplasmic reticulum associated apoptotic pathway].}, journal = {Zhonghua Xue Ye Xue Za Zhi = Zhonghua Xueyexue Zazhi}, volume = {28}, year = {2007}, month = {2007 Jul}, pages = {466-9}, abstract = {

To explore the role of Bid protein in the mitochondria and endoplasmic reticulum (ER) associated apoptotic pathway.

}, keywords = {Apoptosis, BH3 Interacting Domain Death Agonist Protein, Calcium, Caspase 3, Caspases, Cell Line, DNA-Binding Proteins, Endoplasmic Reticulum, Harringtonines, Humans, Initiator, Mitochondria, Transcription Factors}, issn = {0253-2727}, doi = {10.1364/AO.50.001792}, author = {Hu, Jie and He, Dong-Hua and Gao, Liang and Yang, Chun-Hu and Cai, Zhen} } @proceedings {4528, title = {Supervised learning of image restoration with convolutional networks.}, volume = {2}, year = {2007}, month = {2007 Oct 14}, pages = {1-8}, publisher = {IEEE}, edition = {ICCV}, author = {Jain, Viren and Murray, Joseph F and Roth, Fabian and Turaga, Srinivas and Zhigulin, Valentin and Briggman, Kevin L and Helmstaedter, Moritz N. and Denk, Winfried and Seung, H Sebastian} } @conference {46328, title = {Supervised Learning of Image Restoration with Convolutional Networks}, booktitle = {IEEE 11th International Conference on Computer Vision, 2007. ICCV 2007}, year = {2007}, month = {2007-10}, publisher = {IEEE}, organization = {IEEE}, address = {Rio de Janeiro}, abstract = {

Convolutional networks have achieved a great deal of success in high-level vision problems such as object recognition. Here we show that they can also be used as a general method for low-level image processing. As an example of our approach, convolutional networks are trained using gradient learning to solve the problem of restoring noisy or degraded images. For our training data, we have used electron microscopic images of neural circuitry with ground truth restorations provided by human experts. On this dataset, Markov random field (MRF), conditional random field (CRF), and anisotropic diffusion algorithms perform about the same as simple thresholding, but superior performance is obtained with a convolutional network containing over 34,000 adjustable parameters. When restored by this convolutional network, the images are clean enough to be used for segmentation, whereas the other approaches fail in this respect. We do not believe that convolutional networks are fundamentally superior to MRFs as a representation for image processing algorithms. On the contrary, the two approaches are closely related. But in practice, it is possible to train complex convolutional networks, while even simple MRF models are hindered by problems with Bayesian learning and inference procedures. Our results suggest that high model complexity is the single most important factor for good performance, and this is possible with convolutional networks.

}, isbn = {978-1-4244-1630-1}, doi = {10.1109/ICCV.2007.4408909}, author = {Jain, V. and Murray, J.F. and Roth, F. and Turaga, S. and Zhigulin, V. and Briggman, K.L. and Helmstaedter, M.N. and Denk, W. and Seung, H.S.} } @article {4005, title = {Tracking silence: adjusting vocal production to avoid acoustic interference.}, journal = {Journal of Comparative Physiology. A, Neuroethology, Sensory, Neural, and Behavioral Physiology}, volume = {193}, year = {2007}, month = {2007 Apr}, pages = {477-83}, abstract = {

Organisms that use vocal signals to communicate often modulate their vocalizations to avoid being masked by other sounds in the environment. Although some environmental noise is continuous, both biotic and abiotic noise can be intermittent, or even periodic. Interference from intermittent noise can be avoided if calls are timed to coincide with periods of silence, a capacity that is unambiguously present in insects, amphibians, birds, and humans. Surprisingly, we know virtually nothing about this fundamental capacity in nonhuman primates. Here we show that a New World monkey, the cotton-top tamarin (Saguinus oedipus), can restrict calls to periodic silent intervals in loud white noise. In addition, calls produced during these silent intervals were significantly louder than calls recorded in silent baseline sessions. Finally, average call duration dropped across sessions, indicating that experience with temporally patterned noise caused tamarins to compress their calls. Taken together, these results show that in the presence of a predictable, intermittent environmental noise, cotton-top tamarins are able to modify the duration, timing, and amplitude of their calls to avoid acoustic interference.

}, keywords = {Adaptation, Animal, Animals, Auditory Perception, Auditory Threshold, Behavior, Environment, Feedback, Female, Male, Noise, Physiological, Saguinus, Vocalization}, issn = {0340-7594}, doi = {10.1007/s00359-006-0205-7}, author = {Egnor, S E Roian and Wickelgren, Jeanette Graham and Hauser, Marc D} } @article {2400, title = {Transcription of histone gene cluster by differential core-promoter factors.}, journal = {Genes \& Development}, volume = {21}, year = {2007}, month = {2007 Nov 15}, pages = {2936-49}, abstract = {

The 100 copies of tandemly arrayed Drosophila linker (H1) and core (H2A/B and H3/H4) histone gene cluster are coordinately regulated during the cell cycle. However, the molecular mechanisms that must allow differential transcription of linker versus core histones prevalent during development remain elusive. Here, we used fluorescence imaging, biochemistry, and genetics to show that TBP (TATA-box-binding protein)-related factor 2 (TRF2) selectively regulates the TATA-less Histone H1 gene promoter, while TBP/TFIID targets core histone transcription. Importantly, TRF2-depleted polytene chromosomes display severe chromosomal structural defects. This selective usage of TRF2 and TBP provides a novel mechanism to differentially direct transcription within the histone cluster. Moreover, genome-wide chromatin immunoprecipitation (ChIP)-on-chip analyses coupled with RNA interference (RNAi)-mediated functional studies revealed that TRF2 targets several classes of TATA-less promoters of \>1000 genes including those driving transcription of essential chromatin organization and protein synthesis genes. Our studies establish that TRF2 promoter recognition complexes play a significantly more central role in governing metazoan transcription than previously appreciated.

}, keywords = {Animals, Base Sequence, Biological, Cells, Chromatin Immunoprecipitation, Chromosomes, Cluster Analysis, Cultured, Drosophila, Firefly, Fluorescence, Genes, Genetic, Histones, Immunohistochemistry, In Situ Hybridization, Insect, Luciferases, Models, Molecular Sequence Data, Multigene Family, Nucleic Acid, Promoter Regions, Reporter, RNA Interference, Sequence Homology, TATA Box Binding Protein-Like Proteins, TATA-Box Binding Protein, Transcription}, issn = {0890-9369}, doi = {10.1073/pnas.1100640108}, author = {Isogai, Yoh and Keles, S{\"u}nd{\"u}z and Prestel, Matthias and Hochheimer, Andreas and Tjian, Robert} } @article {2407, title = {An ARC/Mediator subunit required for SREBP control of cholesterol and lipid homeostasis.}, journal = {Nature}, volume = {442}, year = {2006}, month = {2006 Aug 10}, pages = {700-4}, abstract = {

The sterol regulatory element binding protein (SREBP) family of transcription activators are critical regulators of cholesterol and fatty acid homeostasis. We previously demonstrated that human SREBPs bind the CREB-binding protein (CBP)/p300 acetyltransferase KIX domain and recruit activator-recruited co-factor (ARC)/Mediator co-activator complexes through unknown mechanisms. Here we show that SREBPs use the evolutionarily conserved ARC105 (also called MED15) subunit to activate target genes. Structural analysis of the SREBP-binding domain in ARC105 by NMR revealed a three-helix bundle with marked similarity to the CBP/p300 KIX domain. In contrast to SREBPs, the CREB and c-Myb activators do not bind the ARC105 KIX domain, although they interact with the CBP KIX domain, revealing a surprising specificity among structurally related activator-binding domains. The Caenorhabditis elegans SREBP homologue SBP-1 promotes fatty acid homeostasis by regulating the expression of lipogenic enzymes. We found that, like SBP-1, the C. elegans ARC105 homologue MDT-15 is required for fatty acid homeostasis, and show that both SBP-1 and MDT-15 control transcription of genes governing desaturation of stearic acid to oleic acid. Notably, dietary addition of oleic acid significantly rescued various defects of nematodes targeted with RNA interference against sbp-1 and mdt-15, including impaired intestinal fat storage, infertility, decreased size and slow locomotion, suggesting that regulation of oleic acid levels represents a physiologically critical function of SBP-1 and MDT-15. Taken together, our findings demonstrate that ARC105 is a key effector of SREBP-dependent gene regulation and control of lipid homeostasis in metazoans.

}, keywords = {Amino Acid Sequence, Animals, Biomolecular, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Cholesterol, Homeostasis, Humans, Lipid Metabolism, Mediator Complex, Mice, Models, Molecular, Molecular Sequence Data, Nuclear Magnetic Resonance, Protein Binding, Protein Structure, Sterol Regulatory Element Binding Proteins, Tertiary, Transcription Factors, Transcriptional Activation}, issn = {1476-4687}, doi = {10.1073/pnas.1100640108}, author = {Yang, Fajun and Vought, Bryan W and Satterlee, John S and Walker, Amy K and Jim Sun, Z-Y and Watts, Jennifer L and DeBeaumont, Rosalie and Saito, R Mako and Hyberts, Sven G and Yang, Shaosong and Macol, Christine and Iyer, Lakshmanan and Tjian, Robert and van den Heuvel, Sander and Hart, Anne C and Wagner, Gerhard and N{\"a}{\"a}r, Anders M} } @article {1734, title = {Atomic and molecular parity nonconservation and sum frequency generation solutions to the ozma problem.}, journal = {The Journal of Physical Chemistry}, volume = {110}, year = {2006}, month = {2006 Sep 28}, pages = {18744-7}, abstract = {

Two Ozma problems are defined. Parity nonconservation is necessary for their solutions. Both problems may be solved by beta decay or atomic optical activity. Atomic and molecular sum frequency generation is chosen, as it supplies rich methods of effecting "gedanken" solutions to the Ozma problems. A new method of measuring a parameter manifesting molecular parity violations is advanced.

}, issn = {1520-6106}, doi = {10.1021/jp055038i}, author = {Ji, Na and Harris, Robert A} } @article {1490, title = {Boundary enhancement and speckle reduction for ultrasound images via salient structure extraction.}, journal = {IEEE Transactions on Bio-Medical Engineering}, volume = {53}, year = {2006}, month = {2006 Nov}, pages = {2300-9}, abstract = {

In this paper, we present an approach for medical ultrasound (US) image enhancement. It is based on a novel perceptual saliency measure which favors smooth, long curves with constant curvature. The perceptual salient boundaries of tissues in US images are enhanced by computing the saliency of directional vectors in the image space, via a local searching algorithm. Our measure is generally determined by curvature changes, intensity gradient and the interaction of neighboring vectors. To restrain speckle noise during the enhancement process, an adaptive speckle suspension term is also combined into the proposed saliency measure. The results obtained on both simulated images and medical US data reveal superior performance of the novel approach over a number of commonly used speckle filters. Applications of US image segmentation show that although the proposed algorithm cannot remove the speckle noise completely and may discard weak anatomical structures in some case, it still provides a considerable gain to US image processing for computer-aided diagnosis.

}, keywords = {Algorithms, Automated, Computer-Assisted, Humans, Image Enhancement, Image Interpretation, Pattern Recognition, Reproducibility of Results, Sensitivity and Specificity, Ultrasonography}, issn = {0018-9294}, doi = {10.1109/TBME.2006.878088}, author = {Xie, Jun and Jiang, Yifeng and Tsui, Hung-Tat and Heng, Pheng-Ann} } @article {1773, title = {The cells and logic for mammalian sour taste detection.}, journal = {Nature}, volume = {442}, year = {2006}, month = {2006 Aug 24}, pages = {934-8}, abstract = {

Mammals taste many compounds yet use a sensory palette consisting of only five basic taste modalities: sweet, bitter, sour, salty and umami (the taste of monosodium glutamate). Although this repertoire may seem modest, it provides animals with critical information about the nature and quality of food. Sour taste detection functions as an important sensory input to warn against the ingestion of acidic (for example, spoiled or unripe) food sources. We have used a combination of bioinformatics, genetic and functional studies to identify PKD2L1, a polycystic-kidney-disease-like ion channel, as a candidate mammalian sour taste sensor. In the tongue, PKD2L1 is expressed in a subset of taste receptor cells distinct from those responsible for sweet, bitter and umami taste. To examine the role of PKD2L1-expressing taste cells in vivo, we engineered mice with targeted genetic ablations of selected populations of taste receptor cells. Animals lacking PKD2L1-expressing cells are completely devoid of taste responses to sour stimuli. Notably, responses to all other tastants remained unaffected, proving that the segregation of taste qualities even extends to ionic stimuli. Our results now establish independent cellular substrates for four of the five basic taste modalities, and support a comprehensive labelled-line mode of taste coding at the periphery. Notably, PKD2L1 is also expressed in specific neurons surrounding the central canal of the spinal cord. Here we demonstrate that these PKD2L1-expressing neurons send projections to the central canal, and selectively trigger action potentials in response to decreases in extracellular pH. We propose that these cells correspond to the long-sought components of the cerebrospinal fluid chemosensory system. Taken together, our results suggest a common basis for acid sensing in disparate physiological settings.

}, keywords = {Action Potentials, Animals, Calcium Channels, Cell Surface, Computational Biology, Gene Expression Profiling, Hydrogen-Ion Concentration, Membrane Glycoproteins, Mice, Neurons, Phosphoproteins, Receptors, Spinal Cord, Taste, Tongue, Transgenic}, issn = {1476-4687}, doi = {10.1038/nature05084}, author = {Huang, Angela L and Chen, Xiaoke and Hoon, Mark A and Chandrashekar, Jayaram and Guo, Wei and Tr{\"a}nkner, Dimitri and Ryba, Nicholas J P and Zuker, Charles S} } @article {1410, title = {Cre recombinase-mediated restoration of nigrostriatal dopamine in dopamine-deficient mice reverses hypophagia and bradykinesia.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, year = {2006}, month = {2006 Jun 6}, pages = {8858-63}, abstract = {

A line of dopamine-deficient (DD) mice was generated to allow selective restoration of normal dopamine signaling to specific brain regions. These DD floxed stop (DDfs) mice have a nonfunctional Tyrosine hydroxylase (Th) gene because of insertion of a NeoR gene flanked by lox P sites targeted to the first intron of the Th gene. DDfs mice have trace brain dopamine content, severe hypoactivity, and aphagia, and they die without intervention. However, they can be maintained by daily treatment with l-3,4-dihydroxyphenylalanine (L-dopa). Injection of a canine adenovirus (CAV-2) engineered to express Cre recombinase into the central caudate putamen restores normal Th gene expression to the midbrain dopamine neurons that project there because CAV-2 efficiently transduces axon terminals and is retrogradely transported to neuronal cell bodies. Bilateral injection of Cre recombinase into the central caudate putamen restores feeding and normalizes locomotion in DDfs mice. Analysis of feeding behavior by using lickometer cages revealed that virally rescued DDfs mice are hyperphagic and have modified meal structures compared with control mice. The virally rescued DDfs mice are also hyperactive at night, have reduced motor coordination, and are thigmotactic compared with controls. These results highlight the critical role for dopamine signaling in the dorsal striatum for most dopamine-dependent behaviors but suggest that dopamine signaling in other brain regions is important to fine-tune these behaviors. This approach offers numerous advantages compared with previous models aimed at examining dopamine signaling in discrete dopaminergic circuits.

}, keywords = {Adenoviridae, Animals, Brain, Dogs, Dopamine, Eating Disorders, Feeding Behavior, Gene Therapy, Hypokinesia, Inbred C57BL, Integrases, Mice, Motor Activity, Tyrosine 3-Monooxygenase, Viral Proteins}, issn = {0027-8424}, doi = {10.1073/pnas.0603081103}, author = {Hnasko, Thomas S and Perez, Francisco A and Scouras, Alex D and Stoll, Elizabeth A and Gale, Samuel D and Luquet, Serge and Phillips, Paul E M and Kremer, Eric J and Palmiter, Richard D} } @article {45891, title = {Dendritic patch-clamp recording.}, journal = {Nature Protocols}, volume = {1}, year = {2006}, month = {2006}, pages = {1235-47}, abstract = {

The patch-clamp technique allows investigation of the electrical excitability of neurons and the functional properties and densities of ion channels. Most patch-clamp recordings from neurons have been made from the soma, the largest structure of individual neurons, while their dendrites, which form the majority of the surface area and receive most of the synaptic input, have been relatively neglected. This protocol describes techniques for recording from the dendrites of neurons in brain slices under direct visual control. Although the basic technique is similar to that used for somatic patching, we describe refinements and optimizations of slice quality, microscope optics, setup stability and electrode approach that are required for maximizing the success rate for dendritic recordings. Using this approach, all configurations of the patch-clamp technique (cell-attached, inside-out, whole-cell, outside-out and perforated patch) can be achieved, even for relatively distal dendrites, and simultaneous multiple-electrode dendritic recordings are also possible. The protocol--from the beginning of slice preparation to the end of the first successful recording--can be completed in 3 h.

}, keywords = {Dendrites, Patch-Clamp Techniques}, issn = {1750-2799}, doi = {10.1038/nprot.2006.164}, author = {Davie, Jenny T and Kole, Maarten H P and Letzkus, Johannes J and Rancz, Ede A and Spruston, Nelson and Stuart, Greg J and H{\"a}usser, Michael} } @article {5487, title = {Distinct behavioral responses to ethanol are regulated by alternate RhoGAP18B isoforms.}, journal = {Cell}, volume = {127}, year = {2006}, month = {2006 Oct 6}, pages = {199-211}, abstract = {

In most organisms, low ethanol doses induce increased activity, while high doses are sedating. To investigate the underlying mechanisms, we isolated Drosophila mutants with altered ethanol responsiveness. Mutations in white rabbit (whir), disrupting RhoGAP18B, are strongly resistant to the sedating effects of ethanol. This resistance can be suppressed by reducing the levels of Rho1 or Rac, implicating these GTPases in the behavioral response to ethanol. Indeed, expression of constitutively active forms of Rho1 or Rac1 in adult flies results in ethanol resistance similar to that observed in whir mutants. The whir locus produces several transcripts, RA-RD, which are predicted to encode three distinct RhoGAPs that share only the GAP domain. The RC transcript mediates the sedating effects of ethanol, while the RA transcript regulates its stimulant effects. Thus, distinct RhoGAPs, encoded by the same gene, regulate different manifestations of acute ethanol intoxication.

}, keywords = {Animal, Animals, Behavior, Brain, Central Nervous System Depressants, Drosophila melanogaster, Drosophila Proteins, Enzyme Activation, Ethanol, Female, GTPase-Activating Proteins, Humans, Molecular Sequence Data, Motor Activity, Mutation, Protein Isoforms, Rabbits, rho GTP-Binding Proteins, Transgenes}, issn = {0092-8674}, doi = {10.1016/j.cell.2006.09.010}, author = {Rothenfluh, Adrian and Threlkeld, Robert J and Bainton, Roland J and Tsai, Linus T-Y and Lasek, Amy W and Heberlein, Ulrike} } @article {45750, title = {A dual-genome microarray for the pea aphid, Acyrthosiphon pisum, and its obligate bacterial symbiont, Buchnera aphidicola.}, journal = {BMC Genomics}, volume = {7}, year = {2006}, month = {Mar 2006}, pages = {50}, abstract = {

BACKGROUND: The best studied insect-symbiont system is that of aphids and their primary bacterial endosymbiont Buchnera aphidicola. Buchnera inhabits specialized host cells called bacteriocytes, provides nutrients to the aphid and has co-speciated with its aphid hosts for the past 150 million years. We have used a single microarray to examine gene expression in the pea aphid, Acyrthosiphon pisum, and its resident Buchnera. Very little is known of gene expression in aphids, few studies have examined gene expression in Buchnera, and no study has examined simultaneously the expression profiles of a host and its symbiont. Expression profiling of aphids, in studies such as this, will be critical for assigning newly discovered A. pisum genes to functional roles. In particular, because aphids possess many genes that are absent from Drosophila and other holometabolous insect taxa, aphid genome annotation efforts cannot rely entirely on homology to the best-studied insect systems. Development of this dual-genome array represents a first attempt to characterize gene expression in this emerging model system.

RESULTS: We chose to examine heat shock response because it has been well characterized both in Buchnera and in other insect species. Our results from the Buchnera of A. pisum show responses for the same gene set as an earlier study of heat shock response in Buchnera for the host aphid Schizaphis graminum. Additionally, analyses of aphid transcripts showed the expected response for homologs of known heat shock genes as well as responses for several genes with unknown functional roles.

CONCLUSION: We examined gene expression under heat shock of an insect and its bacterial symbiont in a single assay using a dual-genome microarray. Further, our results indicate that microarrays are a useful tool for inferring functional roles of genes in A. pisum and other insects and suggest that the pea aphid genome may contain many gene paralogs that are differentially regulated.

}, keywords = {Animals, Aphids, Buchnera, Expressed Sequence Tags, Gene Expression Profiling, Gene Expression Regulation, Genome, Insect, Genomics, Heat-Shock Response, Oligonucleotide Array Sequence Analysis, Symbiosis}, issn = {1471-2164}, doi = {10.1186/1471-2164-7-50}, author = {Wilson, Alex C C and Dunbar, Helen E and Davis, Gregory K and Hunter, Wayne B and Stern, David L and Moran, Nancy A} } @article {5820, title = {Early embryogenesis of planaria: a cryptic larva feeding on maternal resources.}, journal = {Development Genes \& Evolution}, volume = {216}, year = {2006}, month = {2006 Nov}, pages = {667-81}, abstract = {

The early planarian embryo presents a complete ciliated epidermis and a pharynx and feeds on maternal yolk cells. In this paper, we report on all the elements involved in the formation of such an autonomous embryo, which we name cryptic larva. First, we provide a description of the spherical and fusiform yolk cells and their relationship with the blastomeres, from the laying of the egg capsule up to their final fate in mid embryonic stages. Then, we describe the early cleavage and the subsequent development of the tissues of the cryptic larva, namely, the primary epidermis, the embryonic pharynx, and a new cell type, the star cells. Finally, we discuss the possibility that the cryptic larva either constitutes a vestigial larva or, more likely, is the evolutionary result of the competition between multiple embryos for the limited and shared maternal resources in the egg capsule.

}, keywords = {Animals, Electron, Feeding Behavior, In Situ Hybridization, Larva, Microscopy, Planarians}, issn = {0949-944X}, doi = {10.1007/s00427-006-0094-3}, author = {Cardona, Albert and Hartenstein, Volker and Romero, Rafael} } @article {5530, title = {Efficient estimation of detailed single-neuron models.}, journal = {Journal of Neurophysiology}, volume = {96}, year = {2006}, month = {2006 Aug}, pages = {872-90}, abstract = {

Biophysically accurate multicompartmental models of individual neurons have significantly advanced our understanding of the input-output function of single cells. These models depend on a large number of parameters that are difficult to estimate. In practice, they are often hand-tuned to match measured physiological behaviors, thus raising questions of identifiability and interpretability. We propose a statistical approach to the automatic estimation of various biologically relevant parameters, including 1) the distribution of channel densities, 2) the spatiotemporal pattern of synaptic input, and 3) axial resistances across extended dendrites. Recent experimental advances, notably in voltage-sensitive imaging, motivate us to assume access to: i) the spatiotemporal voltage signal in the dendrite and ii) an approximate description of the channel kinetics of interest. We show here that, given i and ii, parameters 1-3 can be inferred simultaneously by nonnegative linear regression; that this optimization problem possesses a unique solution and is guaranteed to converge despite the large number of parameters and their complex nonlinear interaction; and that standard optimization algorithms efficiently reach this optimum with modest computational and data requirements. We demonstrate that the method leads to accurate estimations on a wide variety of challenging model data sets that include up to about 10(4) parameters (roughly two orders of magnitude more than previously feasible) and describe how the method gives insights into the functional interaction of groups of channels.

}, keywords = {Algorithms, Biophysical Phenomena, Biophysics, Cell Membrane, Data Interpretation, Dendrites, Electrophysiology, Ion Channel Gating, Ion Channels, Kinetics, Ligands, Likelihood Functions, Models, Monte Carlo Method, N-Methyl-D-Aspartate, Neurological, Neurons, Patch-Clamp Techniques, Receptors, Statistical, Synapses}, issn = {0022-3077}, author = {Huys, Quentin J M and Ahrens, Misha B and Paninski, Liam} } @article {1587, title = {Evidence supporting a cis-enediol-based mechanism for Pyrococcus furiosus phosphoglucose isomerase.}, journal = {Journal of Molecular Biology}, volume = {358}, year = {2006}, month = {2006 May 19}, pages = {1353-66}, abstract = {

The enzymatic aldose ketose isomerisation of glucose and fructose sugars involves the transfer of a hydrogen between their C1 and C2 carbon atoms and, in principle, can proceed through either a direct hydride shift or via a cis-enediol intermediate. Pyrococcus furiosus phosphoglucose isomerase (PfPGI), an archaeal metalloenzyme, which catalyses the interconversion of glucose 6-phosphate and fructose 6-phosphate, has been suggested to operate via a hydride shift mechanism. In contrast, the structurally distinct PGIs of eukaryotic or bacterial origin are thought to catalyse isomerisation via a cis-enediol intermediate. We have shown by NMR that hydrogen exchange between substrate and solvent occurs during the reaction catalysed by PfPGI eliminating the possibility of a hydride-shift-based mechanism. In addition, kinetic measurements on this enzyme have shown that 5-phospho-d-arabinonohydroxamate, a stable analogue of the putative cis-enediol intermediate, is the most potent inhibitor of the enzyme yet discovered. Furthermore, determination and analysis of crystal structures of PfPGI with bound zinc and the substrate F6P, and with a number of competitive inhibitors, and EPR analysis of the coordination of the metal ion within PfPGI, have suggested that a cis-enediol intermediate-based mechanism is used by PfPGI with Glu97 acting as the catalytic base responsible for isomerisation.

}, keywords = {Biomolecular, Catalytic Domain, Chemical, Crystallography, Electron Spin Resonance Spectroscopy, Enzyme Inhibitors, Glucose-6-Phosphate Isomerase, Hydrogen, Hydroxamic Acids, Isomerism, Kinetics, Macromolecular Substances, Metals, Models, Molecular, Nuclear Magnetic Resonance, Pyrococcus furiosus, Stereoisomerism, Substrate Specificity, Sugar Phosphates, X-Ray}, issn = {0022-2836}, doi = {10.1016/j.jmb.2006.03.015}, author = {Berrisford, John M and Hounslow, Andrea M and Akerboom, Jasper and Hagen, Wilfred R and Brouns, Stan J J and van der Oost, John and Murray, Iain A and Michael Blackburn, G and Waltho, Jonathan P and Rice, David W and Baker, Patrick J} } @article {4142, title = {Functional dissection of a neuronal network required for cuticle tanning and wing expansion in Drosophila.}, journal = {The Journal of Neuroscience The Official Journal of the Society for Neuroscience}, volume = {26}, year = {2006}, month = {2006 Jan 11}, pages = {573-84}, abstract = {

A subset of Drosophila neurons that expresses crustacean cardioactive peptide (CCAP) has been shown previously to make the hormone bursicon, which is required for cuticle tanning and wing expansion after eclosion. Here we present evidence that CCAP-expressing neurons (NCCAP) consist of two functionally distinct groups, one of which releases bursicon into the hemolymph and the other of which regulates its release. The first group, which we call NCCAP-c929, includes 14 bursicon-expressing neurons of the abdominal ganglion that lie within the expression pattern of the enhancer-trap line c929-Gal4. We show that suppression of activity within this group blocks bursicon release into the hemolymph together with tanning and wing expansion. The second group, which we call NCCAP-R, consists of NCCAP neurons outside the c929-Gal4 pattern. Because suppression of synaptic transmission and protein kinase A (PKA) activity throughout NCCAP, but not in NCCAP-c929, also blocks tanning and wing expansion, we conclude that neurotransmission and PKA are required in NCCAP-R to regulate bursicon secretion from NCCAP-c929. Enhancement of electrical activity in NCCAP-R by expression of the bacterial sodium channel NaChBac also blocks tanning and wing expansion and leads to depletion of bursicon from central processes. NaChBac expression in NCCAP-c929 is without effect, suggesting that the abdominal bursicon-secreting neurons are likely to be silent until stimulated to release the hormone. Our results suggest that NCCAP form an interacting neuronal network responsible for the regulation and release of bursicon and suggest a model in which PKA-mediated stimulation of inputs to normally quiescent bursicon-expressing neurons activates release of the hormone.

}, keywords = {Animals, Bacterial Proteins, Cyclic AMP-Dependent Protein Kinases, Drosophila melanogaster, Drosophila Proteins, Electroretinography, Ganglia, Gene Targeting, Genetically Modified, Invertebrate, Invertebrate Hormones, Nerve Net, Neurons, Neuropeptides, Phenotype, Pigmentation, Recombinant Fusion Proteins, Shaker Superfamily of Potassium Channels, Sodium Channels, Synaptic Transmission, Wing}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3916-05.2006}, author = {Luan, Haojiang and Lemon, William C and Peabody, Nathan C and Pohl, Jascha B and Zelensky, Paul K and Wang, Ding and Nitabach, Michael N and Holmes, Todd C and White, Benjamin H} } @article {48655, title = {High-speed pollen release in the white mulberry tree, Morus alba L.}, journal = {Sexual Plant Reproduction}, volume = {19}, year = {2006}, month = {2006 Mar}, pages = {19-24}, abstract = {

Anemophilous plants described as catapulting pollen explosively into the air have rarely attracted detailed examination. We investigated floral anthesis in a male mulberry tree with high-speed video and a force probe. The stamen was inflexed within the floral bud. Exposure to dry air initially resulted in a gradual movement of the stamen. This caused fine threads to tear at the stomium, ensuring dehiscence of the anther, and subsequently enabled the anther to slip off a restraining pistillode. The sudden release of stored elastic energy in the spring-like filament drove the stamen to straighten in less than 25\ μs, and reflex the petals to velocities in excess of half the speed of sound. This is the fastest motion yet observed in biology, and approaches the theoretical physical limits for movements in plants.

}, doi = {10.1007/s00497-005-0018-9}, author = {Taylor, Philip E and Card, Gwyneth M and House, James and Dickinson, Michael H and Flagan, Richard C} } @article {6353, title = {Hyperpolarization-activated cation current (Ih) is an ethanol target in midbrain dopamine neurons of mice.}, journal = {Journal of Neurophysiology}, volume = {95}, year = {2006}, month = {2006 Feb}, pages = {619-26}, abstract = {

Ethanol stimulates the firing activity of midbrain dopamine (DA) neurons, leading to enhanced dopaminergic transmission in the mesolimbic system. This effect is thought to underlie the behavioral reinforcement of alcohol intake. Ethanol has been shown to directly enhance the intrinsic pacemaker activity of DA neurons, yet the cellular mechanism mediating this excitation remains poorly understood. The hyperpolarization-activated cation current, Ih, is known to contribute to the pacemaker firing of DA neurons. To determine the role of Ih in ethanol excitation of DA neurons, we performed patch-clamp recordings in acutely prepared mouse midbrain slices. Superfusion of ethanol increased the spontaneous firing frequency of DA neurons in a reversible fashion. Treatment with ZD7288, a blocker of Ih, irreversibly depressed basal firing frequency and significantly attenuated the stimulatory effect of ethanol on firing. Furthermore, ethanol reversibly augmented Ih amplitude and accelerated its activation kinetics. This effect of ethanol was accompanied by a shift in the voltage dependence of Ih activation to more depolarized potentials and an increase in the maximum Ih conductance. Cyclic AMP mediated the depolarizing shift in Ih activation but not the increase in the maximum conductance. Finally, repeated ethanol treatment in vivo induced downregulation of Ih density in DA neurons and an accompanying reduction in the magnitude of ethanol stimulation of firing. These results suggest an important role of Ih in the reinforcing actions of ethanol and in the neuroadaptations underlying escalation of alcohol consumption associated with alcoholism.

}, keywords = {Action Potentials, Animals, Antiporters, Biological Clocks, Dopamine, Ethanol, Inbred C57BL, Ion Channel Gating, Membrane Potentials, Mesencephalon, Mice, Neurons}, issn = {0022-3077}, doi = {10.1152/jn.00682.2005}, author = {Okamoto, Takashi and Harnett, Mark T and Morikawa, Hitoshi} } @article {1489, title = {Image diffusion using saliency bilateral filter.}, journal = {Medical Image Computing and Computer-Assisted Intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention}, volume = {9}, year = {2006}, month = {2006}, pages = {67-75}, abstract = {

Image diffusion can smooth away noise and small-scale structures while retaining important features, thereby enhancing the performances of many image processing algorithms such as image compression, segmentation and recognition. In this paper, we present a novel diffusion algorithm for which the filtering kernels vary according to the perceptual saliency of boundaries in the input images. The boundary saliency is estimated through a saliency measure which is generally determined by curvature changes, intensity gradient and the interaction of neighboring vectors. The connection between filtering kernels and perceptual saliency makes it possible to remove small-scale structures and preserves significant boundaries adaptively. The effectiveness of the proposed approach is validated by experiments on various medical images including the color Chinese Visible Human data set and gray MRI brain images.

}, keywords = {Algorithms, Artificial Intelligence, Automated, Brain, Cluster Analysis, Computer-Assisted, Diffusion Magnetic Resonance Imaging, Humans, Image Enhancement, Image Interpretation, Magnetic Resonance Imaging, Pattern Recognition, Reproducibility of Results, Sensitivity and Specificity}, author = {Xie, Jun and Heng, Pheng-Ann and Ho, Simon S M and Shah, Mubarak} } @article {2083, title = {Imaging intracellular fluorescent proteins at nanometer resolution. (With commentary)}, journal = {Science}, volume = {313}, year = {2006}, month = {2006 Sep 15}, pages = {1642-5}, abstract = {

We introduce a method for optically imaging intracellular proteins at nanometer spatial resolution. Numerous sparse subsets of photoactivatable fluorescent protein molecules were activated, localized (to approximately 2 to 25 nanometers), and then bleached. The aggregate position information from all subsets was then assembled into a superresolution image. We used this method{\textendash}termed photoactivated localization microscopy{\textendash}to image specific target proteins in thin sections of lysosomes and mitochondria; in fixed whole cells, we imaged vinculin at focal adhesions, actin within a lamellipodium, and the distribution of the retroviral protein Gag at the plasma membrane.

Commentary: The original PALM paper by myself and my friend and co-inventor Harald Hess, spanning the before- and after-HHMI eras. Submitted and publicly presented months before other publications in the same year, the lessons of the paper remain widely misunderstood: 1) localization precision is not resolution; 2) the ability to resolve a few molecules by the Rayleigh criterion in a diffraction limited region (DLR) does not imply the ability to resolve structures of arbitrary complexity at the same scale; 3) true resolution well beyond the Abbe limit requires the ability to isolate and localize hundreds or thousands of molecules in one DLR; and 4) certain photoactivatable fluorescent proteins (PA-FPs) and caged dyes can be isolated and precisely localized at such densities; yielding true resolution down to \ 20 nm. The molecular densities we demonstrate (105 molecules/m2) are more than two orders of magnitude greater than in later papers that year (implying ten-fold better true resolution) {\textendash} indeed, these papers demonstrate densities only comparable to earlier spectral or photobleaching based isolation methods. We validate our claims by correlative electron microscopy, and demonstrate the outstanding advantages of PA-FPs for superresolution microscopy: minimally perturbative sample preparation; high labeling densities; close binding to molecular targets; and zero non-specific background.

}, keywords = {Actins, Algorithms, Animals, Cell Line, Cell Membrane, Cercopithecus aethiops, COS Cells, Fluorescence, Focal Adhesions, gag, Gene Products, HIV-1, Light, Luminescent Proteins, Lysosomes, Microscopy, Mitochondria, Nanotechnology, Organelles, Photobleaching, Proteins, Pseudopodia, Recombinant Fusion Proteins, Vinculin}, issn = {1095-9203}, doi = {10.1126/science.1127344}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16902090}, author = {Betzig, Eric and Patterson, George H and Sougrat, Rachid and Lindwasser, O Wolf and Olenych, Scott and Bonifacino, Juan S and Davidson, Michael W and Lippincott-Schwartz, Jennifer and Hess, Harald F} } @article {46629, title = {Increased ethanol resistance and consumption in Eps8 knockout mice correlates with altered actin dynamics.}, journal = {Cell}, volume = {127}, year = {2006}, month = {2006 Oct 6}, pages = {213-26}, abstract = {

Dynamic modulation of the actin cytoskeleton is critical for synaptic plasticity, abnormalities of which are thought to contribute to mental illness and addiction. Here we report that mice lacking Eps8, a regulator of actin dynamics, are resistant to some acute intoxicating effects of ethanol and show increased ethanol consumption. In the brain, the N-methyl-D-aspartate (NMDA) receptor is a major target of ethanol. We show that Eps8 is localized to postsynaptic structures and is part of the NMDA receptor complex. Moreover, in Eps8 null mice, NMDA receptor currents and their sensitivity to inhibition by ethanol are abnormal. In addition, Eps8 null neurons are resistant to the actin-remodeling activities of NMDA and ethanol. We propose that proper regulation of the actin cytoskeleton is a key determinant of cellular and behavioral responses to ethanol.

}, keywords = {Actins, Adaptor Proteins, Signal Transducing, Alcohol Drinking, Animals, Behavior, Animal, Cells, Cultured, Central Nervous System Depressants, Cerebellum, Cytoskeletal Proteins, Cytoskeleton, Ethanol, Female, Humans, Male, Mice, Mice, Knockout, Neurons, Receptors, N-Methyl-D-Aspartate, Recombinant Proteins, Signal Transduction}, issn = {0092-8674}, doi = {10.1016/j.cell.2006.09.011}, author = {Offenh{\"a}user, Nina and Castelletti, Daniela and Mapelli, Lisa and Soppo, Blanche Ekalle and Regondi, Maria Cristina and Rossi, Paola and D{\textquoteright}Angelo, Egidio and Frassoni, Carolina and Amadeo, Alida and Tocchetti, Arianna and Pozzi, Benedetta and Disanza, Andrea and Guarnieri, Douglas and Betsholtz, Christer and Scita, Giorgio and Heberlein, Ulrike and Di Fiore, Pier Paolo} } @article {2508, title = {Juvenile hormone is required to couple imaginal disc formation with nutrition in insects.}, journal = {Science }, volume = {312}, year = {2006}, month = {2006 Jun 2}, pages = {1385-8}, abstract = {

In starved larvae of the tobacco hornworm moth Manduca sexta, larval and imaginal tissues stop growing, the former because they lack nutrient-dependent signals but the latter because of suppression by juvenile hormone. Without juvenile hormone, imaginal discs form and grow despite severe starvation. This hormone inhibits the intrinsic signaling needed for disc morphogenesis and does so independently of ecdysteroid action. Starvation and juvenile hormone treatments allowed the separation of intrinsic and nutrient-dependent aspects of disc growth and showed that both aspects must occur during the early phases of disc morphogenesis to ensure normal growth leading to typical-sized adults.

}, keywords = {Animal Nutritional Physiological Phenomena, Animals, Ecdysteroids, Juvenile Hormones, Larva, Manduca, Morphogenesis, Pyridines}, issn = {1095-9203}, doi = {10.1126/science.1123652}, author = {Truman, J W and Hiruma, K and Allee, J P and Macwhinnie, S G B and Champlin, D T and Riddiford, L M} } @proceedings {5679, title = {Large-scale biophysical parameter estimation in single neurons via constrained linear regression.}, volume = {18}, year = {2006}, month = {2006}, publisher = {MIT press}, abstract = {

Our understanding of the input-output function of single cells has been substantially advanced by biophysically accurate multi-compartmental models. The large number of parameters needing hand tuning in these models has, however, somewhat hampered their applicability and interpretability. Here we propose a simple and well-founded method for automatic estimation of many of these key parameters: 1) the spatial distribution of channel densities on the cell{\textquoteright}s membrane; 2) the spatiotemporal pattern of synaptic input; 3) the channels{\textquoteright} reversal potentials; 4) the intercompartmental conductances; and 5) the noise level in each compartment. We assume experimental access to: a) the spatiotemporal voltage signal in the dendrite (or some contiguous subpart thereof, e.g. via voltage sensitive imaging techniques), b) an approximate kinetic description of the channels and synapses present in each compartment, and c) the morphology of the part of the neuron under investigation. The key observation is that, given data a)-c), all of the parameters 1)-4) may be simultaneously inferred by a version of constrained linear regression; this regression, in turn, is efficiently solved using standard algorithms, without any {\textquotedblleft}local minima{\textquotedblright} problems despite the large number of parameters and complex dynamics. The noise level 5) may also be estimated by standard techniques. We demonstrate the method{\textquoteright}s accuracy on several model datasets, and describe techniques for quantifying the uncertainty in our estimates.

}, author = {Ahrens, MB and Huys, QJM and Paninski, L} } @article {45751, title = {Large-scale gene discovery in the pea aphid Acyrthosiphon pisum (Hemiptera).}, journal = {Genome Biol}, volume = {7}, year = {2006}, month = {2006}, pages = {R21}, abstract = {

Aphids are the leading pests in agricultural crops. A large-scale sequencing of 40,904 ESTs from the pea aphid Acyrthosiphon pisum was carried out to define a catalog of 12,082 unique transcripts. A strong AT bias was found, indicating a compositional shift between Drosophila melanogaster and A. pisum. An in silico profiling analysis characterized 135 transcripts specific to pea-aphid tissues (relating to bacteriocytes and parthenogenetic embryos). This project is the first to address the genetics of the Hemiptera and of a hemimetabolous insect.

}, keywords = {Animals, Aphids, Base Composition, Base Sequence, DNA, DNA, Complementary, Expressed Sequence Tags, Gene Library, Microsatellite Repeats, Peas, Phylogeny, Plant Diseases, Population Density, Transcription, Genetic}, issn = {1465-6914}, doi = {10.1186/gb-2006-7-3-r21}, author = {Sabater-Mu{\~n}oz, Beatriz and Legeai, Fabrice and Rispe, Claude and Bonhomme, Jo{\"e}l and Dearden, Peter and Dossat, Carole and Duclert, Aymeric and Gauthier, Jean-Pierre and Ducray, Dani{\`e}le Giblot and Hunter, Wayne and Dang, Phat and Kambhampati, Srini and Martinez-Torres, David and Cortes, Teresa and Moya, Andr{\`e}s and Nakabachi, Atsushi and Philippe, Cathy and Prunier-Leterme, Nathalie and Rahb{\'e}, Yvan and Simon, Jean-Christophe and Stern, David L and Wincker, Patrick and Tagu, Denis} } @article {2444, title = {Local caspase activity directs engulfment of dendrites during pruning.}, journal = {Nature Neuroscience}, volume = {9}, year = {2006}, month = {2006 Oct}, pages = {1234-6}, abstract = {

Pruning is important for sculpting neural circuits, as it removes excessive or inaccurate projections. Here we show that the removal of sensory neuron dendrites during pruning in Drosophila melanogaster is directed by local caspase activity. Suppressing caspase activity prevented dendrite removal, whereas a global activation of caspases within a neuron caused cell death. A new genetically encoded caspase probe revealed that caspase activity is confined to the degenerating dendrites of pruning neurons.

}, keywords = {Afferent, Analysis of Variance, Animals, Apoptosis, Caspases, Dendrites, Drosophila melanogaster, Drosophila Proteins, Enzyme Activation, Enzyme Inhibitors, Fluorescent Antibody Technique, Ganglia, Genetically Modified, Neurons, Spinal, Time Factors}, issn = {1097-6256}, doi = {10.1038/nn1774}, author = {Williams, Darren W and Kondo, Shu and Krzyzanowska, Agnieszka and Hiromi, Yasushi and Truman, James W} } @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 {4007, title = {Perturbation of auditory feedback causes systematic perturbation in vocal structure in adult cotton-top tamarins.}, journal = {The Journal of Experimental Biology}, volume = {209}, year = {2006}, month = {2006 Sep}, pages = {3652-63}, abstract = {

Auditory feedback is critical for the development and maintenance of speech in humans. In contrast, studies of nonhuman primate vocal production generally report that subjects show little reliance on auditory input. We examined the extent to which cotton-top tamarin (Saguinus oedipus) vocal production is sensitive to perturbation of auditory feedback by manipulating the predictability of presentation of a 1 s burst of white noise during the production of the species-specific contact call, the combination long call (CLC). We used three experimental conditions: the Begin condition, in which white noise was presented only during the first half of a recording session, the End condition, in which white noise was presented only in the last half, and the Random condition, in which each call had a 50\% probability of receiving white noise playback throughout the recording session, making the auditory feedback unpredictable. In addition we recorded calls before and after the experimental series (Baseline condition) to determine whether any changes induced by modification of auditory feedback persisted. Results showed that playback of white noise during the production of the CLC produced changes in the temporal structure of the CLC: calls were shorter and had fewer pulses, indicating that modification of auditory feedback can interrupt vocal production. In addition, calls that received modified feedback were louder and had longer inter-pulse intervals than those that did not, consistent with an adaptive response to the masking effect of white noise playback. The magnitude of this compensatory effect and the interruption rate were both sensitive to whether the feedback modification occurred at the beginning or end of the experimental session: early feedback produced less interruption and more compensation. Finally, when auditory feedback modification was unpredictable, adaptive changes were observed in both calls that received modified feedback and those that received normal feedback, suggesting that tamarins can generate an expectation of noise playback and increase vocal amplitude in anticipation of masking.

}, keywords = {Acoustic Stimulation, Adaptation, Animal, Animals, Female, Male, Perceptual Masking, Psychological, Saguinus, Vocalization}, issn = {0022-0949}, doi = {10.1242/jeb.02420}, author = {Egnor, S E Roian and Iguina, Carmen G and Hauser, Marc D} } @article {5414, title = {Purification, characterization, and crystallization of human pyrroline-5-carboxylate reductase.}, journal = {Protein Expression and Purification}, volume = {49}, year = {2006}, month = {2006 Sep}, pages = {83-7}, abstract = {

Pyrroline-5-carboxylate reductase (P5CR) catalyzes the reduction of Delta1-pyrroline-5-carboxylate (P5C) to proline with concomitant oxidation of NAD(P)H to NAD(P)(+). The enzymatic cycle between P5C and proline is very important in many physiological and pathological processes. Human P5CR was over-expressed in Escherichia coli and purified to homogeneity by chromatography. Enzymatic assays of the wild-type protein were carried out using 3,4-dehydro-L-proline as substrate and NAD(+) as cofactor. The homopolymer was characterized by cross-linking and size exclusion gel filtration chromatography. Human P5CR was crystallized by the hanging-drop vapor-diffusion method at 37 degrees C. Diffraction data were obtained to a resolution of 2.8A and were suitable for high resolution X-ray structure determination.

}, keywords = {Crystallization, Crystallography, Gene Expression, Humans, Polymers, Proline, Pyrroline Carboxylate Reductases, Solubility, Water, X-Ray}, issn = {1046-5928}, doi = {10.1016/j.pep.2006.02.019}, author = {Meng, Zhaohui and Lou, Zhiyong and Liu, Zhe and Hui, Dong and Bartlam, Mark and Rao, Zihe} } @article {1771, title = {The receptors and cells for mammalian taste.}, journal = {Nature}, volume = {444}, year = {2006}, month = {2006 Nov 16}, pages = {288-94}, abstract = {

The emerging picture of taste coding at the periphery is one of elegant simplicity. Contrary to what was generally believed, it is now clear that distinct cell types expressing unique receptors are tuned to detect each of the five basic tastes: sweet, sour, bitter, salty and umami. Importantly, receptor cells for each taste quality function as dedicated sensors wired to elicit stereotypic responses.

}, keywords = {Animals, G-Protein-Coupled, Humans, Receptors, Signal Transduction, Taste, Taste Buds}, issn = {1476-4687}, doi = {10.1038/nature05401}, author = {Chandrashekar, Jayaram and Hoon, Mark A and Ryba, Nicholas J P and Zuker, Charles S} } @article {2130, title = {Sleep deprivation-induced alterations in excitatory synaptic transmission in the CA1 region of the rat hippocampus.}, journal = {The Journal of Physiology}, volume = {570}, year = {2006}, month = {2006 Feb 1}, pages = {553-65}, abstract = {

Although the function of sleep remains elusive, there is compelling evidence to suggest that sleep plays an important role in learning and memory. A number of studies have now shown that sleep deprivation (SD) results in significant impairment of long-term potentiation (LTP) in the hippocampus. In this study, we have attempted to determine the mechanisms responsible for this impairment. After 72 h SD using the multiple-platform technique, we observed a reduction in the whole-cell recorded NMDA/AMPA ratio of CA1 pyramidal cells in response to Schaffer collateral stimulation. This impairment was specific to sleep deprivation as rats placed over a single large platform, which allowed sleep, had a normal NMDA/AMPA ratio. mEPSCs evoked by local application of a high osmolarity solution revealed no differences in the AMPA receptor function. NMDA currents recorded from outside-out patches excised from the distal dendrites of CA1 cells displayed a reduction in amplitude after SD. While there were no alterations in the glutamate sensitivity, channel open probability or the single channel conductance of the receptor, a crosslinking assay demonstrated that the NR1 and NR2A subunits of NMDA receptors were preferentially retained in the cytoplasm after SD, indicating that SD alters NMDAR surface expression. In summary, we have identified a potential mechanism underlying SD-induced LTP impairment. This synaptic alteration may underlie the cognitive deficits seen following sleep deprivation and could represent a target for future intervention studies.

}, keywords = {AMPA, Animals, Electric Stimulation, Excitatory Postsynaptic Potentials, Glutamic Acid, Glycine, Hippocampus, Ion Channel Gating, Kinetics, Long-Term Potentiation, Male, N-Methyl-D-Aspartate, Patch-Clamp Techniques, Rats, Receptors, Sleep Deprivation, Sprague-Dawley, Synaptic Transmission}, issn = {0022-3751}, doi = {10.1002/cbic.201000254}, author = {McDermott, Carmel M and Hardy, Mattie N and Bazan, Nicolas G and Magee, Jeffrey C} } @article {6352, title = {Transcriptional signatures of cellular plasticity in mice lacking the alpha1 subunit of GABAA receptors.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {26}, year = {2006}, month = {2006 May 24}, pages = {5673-83}, abstract = {

GABAA receptors mediate the majority of inhibitory neurotransmission in the CNS. Genetic deletion of the alpha1 subunit of GABAA receptors results in a loss of alpha1-mediated fast inhibitory currents and a marked reduction in density of GABAA receptors. A grossly normal phenotype of alpha1-deficient mice suggests the presence of neuronal adaptation to these drastic changes at the GABA synapse. We used cDNA microarrays to identify transcriptional fingerprints of cellular plasticity in response to altered GABAergic inhibition in the cerebral cortex and cerebellum of alpha1 mutants. In silico analysis of 982 mutation-regulated transcripts highlighted genes and functional groups involved in regulation of neuronal excitability and synaptic transmission, suggesting an adaptive response of the brain to an altered inhibitory tone. Public gene expression databases permitted identification of subsets of transcripts enriched in excitatory and inhibitory neurons as well as some glial cells, providing evidence for cellular plasticity in individual cell types. Additional analysis linked some transcriptional changes to cellular phenotypes observed in the knock-out mice and suggested several genes, such as the early growth response 1 (Egr1), small GTP binding protein Rac1 (Rac1), neurogranin (Nrgn), sodium channel beta4 subunit (Scn4b), and potassium voltage-gated Kv4.2 channel (Kcnd2) as cell type-specific markers of neuronal plasticity. Furthermore, transcriptional activation of genes enriched in Bergman glia suggests an active role of these astrocytes in synaptic plasticity. Overall, our results suggest that the loss of alpha1-mediated fast inhibition produces diverse transcriptional responses that act to regulate neuronal excitability of individual neurons and stabilize neuronal networks, which may account for the lack of severe abnormalities in alpha1 null mutants.

}, keywords = {Animals, GABA-A, Gene Expression Profiling, Knockout, Male, Mice, Neural Inhibition, Neuroglia, Neuronal Plasticity, Neurons, Receptors, Synaptic Transmission, Transcription Factors}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0860-06.2006}, author = {Ponomarev, Igor and Maiya, Rajani and Harnett, Mark T and Schafer, Gwen L and Ryabinin, Andrey E and Blednov, Yuri A and Morikawa, Hitoshi and Boehm, Stephen L and Homanics, Gregg E and Berman, Ari E and Berman, Ari and Lodowski, Kerrie H and Bergeson, Susan E and Harris, R Adron} } @article {1772, title = {Transforming the architecture of compound eyes.}, journal = {Nature}, volume = {443}, year = {2006}, month = {2006 Oct 12}, pages = {696-9}, abstract = {

Eyes differ markedly in the animal kingdom, and are an extreme example of the evolution of multiple anatomical solutions to light detection and image formation. A salient feature of all photoreceptor cells is the presence of a specialized compartment (disc outer segments in vertebrates, and microvillar rhabdomeres in insects), whose primary role is to accommodate the millions of light receptor molecules required for efficient photon collection. In insects, compound eyes can have very different inner architectures. Fruitflies and houseflies have an open rhabdom system, in which the seven rhabdomeres of each ommatidium are separated from each other and function as independent light guides. In contrast, bees and various mosquitoes and beetle species have a closed system, in which rhabdomeres within each ommatidium are fused to each other, thus sharing the same visual axis. To understand the transition between open and closed rhabdom systems, we isolated and characterized the role of Drosophila genes involved in rhabdomere assembly. Here we show that Spacemaker, a secreted protein expressed only in the eyes of insects with open rhabdom systems, acts together with Prominin and the cell adhesion molecule Chaoptin to choreograph the partitioning of rhabdomeres into an open system. Furthermore, the complete loss of spacemaker (spam) converts an open rhabdom system to a closed one, whereas its targeted expression to photoreceptors of a closed system markedly reorganizes the architecture of the compound eyes to resemble an open system. Our results provide a molecular atlas for the construction of microvillar assemblies and illustrate the critical effect of differences in a single structural protein in morphogenesis.

}, keywords = {Adhesiveness, Animals, Bees, Drosophila melanogaster, Drosophila Proteins, Eye, Eye Proteins, Membrane Glycoproteins, Molecular Sequence Data, Morphogenesis, Mutation}, issn = {1476-4687}, doi = {10.1038/nature05128}, author = {Zelhof, Andrew C and Hardy, Robert W and Becker, Ann and Zuker, Charles S} } @article {2152, title = {Transitive closure and metric inequality of weighted graphs: detecting protein interaction modules using cliques.}, journal = {International Journal of Data Mining and Bioinformatics}, volume = {1}, year = {2006}, month = {2006 Jun 2}, pages = {162-77}, abstract = {

We study transitivity properties of edge weights in complex networks. We show that enforcing transitivity leads to a transitivity inequality which is equivalent to ultra-metric inequality. This can be used to define transitive closure on weighted undirected graphs, which can be computed using a modified Floyd-Warshall algorithm. These new concepts are extended to dissimilarity graphs and triangle inequalities. From this, we extend the clique concept from unweighted graph to weighted graph. We outline several applications and present results of detecting protein functional modules in a protein interaction network.

}, keywords = {Algorithms, Computational Biology, Fungal Proteins, Models, Protein Binding, Protein Interaction Mapping, Systems Biology, Theoretical}, issn = {1748-5673}, doi = {10.1007/s12021-010-9090-x}, author = {Ding, Chris and He, Xiaofeng and Xiong, Hui and Peng, Hanchuan and Holbrook, Stephen R} } @article {4981, title = {The virtual insect brain protocol: creating and comparing standardized neuroanatomy.}, journal = {BMC Bioinformatics}, volume = {7}, year = {2006}, month = {2006 Dec 29}, pages = {544}, abstract = {

In the fly Drosophila melanogaster, new genetic, physiological, molecular and behavioral techniques for the functional analysis of the brain are rapidly accumulating. These diverse investigations on the function of the insect brain use gene expression patterns that can be visualized and provide the means for manipulating groups of neurons as a common ground. To take advantage of these patterns one needs to know their typical anatomy.

}, keywords = {Anatomic, Animals, Brain, Computer Graphics, Computer Simulation, Drosophila melanogaster, Imaging, Models, Neuroanatomy, Neurological, Software, Subtraction Technique, Three-Dimensional, User-Computer Interface}, issn = {1471-2105}, doi = {10.1186/1471-2105-7-544}, author = {Jenett, Arnim and Schindelin, Johannes E and Heisenberg, Martin} } @article {1239, title = {Wiring optimization can relate neuronal structure and function.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, year = {2006}, month = {2006 Mar 21}, pages = {4723-8}, abstract = {

We pursue the hypothesis that neuronal placement in animals minimizes wiring costs for given functional constraints, as specified by synaptic connectivity. Using a newly compiled version of the Caenorhabditis elegans wiring diagram, we solve for the optimal layout of 279 nonpharyngeal neurons. In the optimal layout, most neurons are located close to their actual positions, suggesting that wiring minimization is an important factor. Yet some neurons exhibit strong deviations from "optimal" position. We propose that biological factors relating to axonal guidance and command neuron functions contribute to these deviations. We capture these factors by proposing a modified wiring cost function.

}, keywords = {Animals, Caenorhabditis elegans, Models, Neurological, Neurons, Synapses}, issn = {0027-8424}, doi = {10.1371/journal.pcbi.1001066}, author = {Chen, Beth L and Hall, David H and Chklovskii, Dmitri B} } @article {2680, title = {Wlds protection distinguishes axon degeneration following injury from naturally occurring developmental pruning.}, journal = {Neuron}, volume = {50}, year = {2006}, month = {2006 Jun 15}, pages = {883-95}, abstract = {

Axon pruning by degeneration remodels exuberant axonal connections and is widely required for the development of proper circuitry in the nervous system from insects to mammals. Developmental axon degeneration morphologically resembles injury-induced Wallerian degeneration, suggesting similar underlying mechanisms. As previously reported for mice, we show that Wlds protein substantially delays Wallerian degeneration in flies. Surprisingly, Wlds has no effect on naturally occurring developmental axon degeneration in flies or mice, although it protects against injury-induced degeneration of the same axons at the same developmental age. By contrast, the ubiquitin-proteasome system is intrinsically required for both developmental and injury-induced axon degeneration. We also show that the glial cell surface receptor Draper is required for efficient clearance of axon fragments during developmental axon degeneration, similar to its function in injury-induced degeneration. Thus, mechanistically, naturally occurring developmental axon pruning by degeneration and injury-induced axon degeneration differ significantly in early steps, but may converge onto a common execution pathway.

}, keywords = {Animals, Axons, Developmental, Drosophila, Drosophila Proteins, Gene Expression Regulation, Genetically Modified, Inbred C57BL, Mice, Nerve Tissue Proteins, Wallerian Degeneration}, issn = {0896-6273}, doi = {10.1016/j.neuron.2006.05.013}, author = {Hoopfer, Eric D and McLaughlin, Todd and Watts, Ryan J and Schuldiner, Oren and O{\textquoteright}Leary, Dennis D M and Luo, Liqun} } @article {3937, title = {A conserved processing mechanism regulates the activity of transcription factors Cubitus interruptus and NF-kappaB.}, journal = {Nature Structural \& Molecular Biology}, volume = {12}, year = {2005}, month = {2005 Dec}, pages = {1045-53}, abstract = {

The proteasome degrades some proteins, such as transcription factors Cubitus interruptus (Ci) and NF-kappaB, to generate biologically active protein fragments. Here we have identified and characterized the signals in the substrate proteins that cause this processing. The minimum signal consists of a simple sequence preceding a tightly folded domain in the direction of proteasome movement. The strength of the processing signal depends primarily on the complexity of the simple sequence rather than on amino acid identity, the resistance of the folded domain to unraveling by the proteasome and the spacing between the simple sequence and folded domain. We show that two unrelated transcription factors, Ci and NF-kappaB, use this mechanism to undergo partial degradation by the proteasome in vivo. These findings suggest that the mechanism is conserved evolutionarily and that processing signals may be widespread in regulatory proteins.

}, keywords = {Amino Acid Sequence, Animals, Cells, Cultured, DNA-Binding Proteins, Drosophila Proteins, Humans, NF-kappa B p50 Subunit, Proteasome Endopeptidase Complex, Protein Folding, Transcription Factors}, issn = {1545-9993}, doi = {10.1038/nsmb1018}, author = {Tian, Lin and Holmgren, Robert A and Matouschek, Andreas} } @article {5822, title = {The embryonic development of the triclad Schmidtea polychroa.}, journal = {Development Genes \& Evolution}, volume = {215}, year = {2005}, month = {2005 Mar}, pages = {109-31}, abstract = {

Triclad flatworms are well studied for their regenerative properties, yet little is known about their embryonic development. We here describe the embryonic development of the triclaty 120d Schmidtea polychroa, using histological and immunocytochemical analysis of whole-mount preparations and sections. During early cleavage (stage 1), yolk cells fuse and enclose the zygote into a syncytium. The zygote divides into blastomeres that dissociate and migrate into the syncytium. During stage 2, a subset of blastomeres differentiate into a transient embryonic epidermis that surrounds the yolk syncytium, and an embryonic pharynx. Other blastomeres divide as a scattered population of cells in the syncytium. During stage 3, the embryonic pharynx imbibes external yolk cells and a gastric cavity is formed in the center of the syncytium. The syncytial yolk and the blastomeres contained within it are compressed into a thin peripheral rind. From a location close to the embryonic pharynx, which defines the posterior pole, bilaterally symmetric ventral nerve cord pioneers extend forward. Stage 4 is characterized by massive proliferation of embryonic cells. Large yolk-filled cells lining the syncytium form the gastrodermis. During stage 5 the external syncytial yolk mantle is resorbed and the embryonic cells contained within differentiate into an irregular scaffold of muscle and nerve cells. Epidermal cells differentiate and replace the transient embryonic epidermis. Through stages 6-8, the embryo adopts its worm-like shape, and loosely scattered populations of differentiating cells consolidate into structurally defined organs. Our analysis reveals a picture of S. polychroa embryogenesis that resembles the morphogenetic events underlying regeneration.

}, keywords = {Animals, Blastomeres, Embryo, Epidermis, Female, Morphogenesis, Nonmammalian, Ovum, Turbellaria}, issn = {0949-944X}, doi = {10.1007/s00427-004-0455-8}, author = {Cardona, Albert and Hartenstein, Volker and Romero, Rafael} } @article {46631, title = {GPCR signaling is required for blood-brain barrier formation in drosophila.}, journal = {Cell}, volume = {123}, year = {2005}, month = {2005 Oct 7}, pages = {133-44}, abstract = {

The blood-brain barrier of Drosophila is established by surface glia, which ensheath the nerve cord and insulate it against the potassium-rich hemolymph by forming intercellular septate junctions. The mechanisms underlying the formation of this barrier remain obscure. Here, we show that the G protein-coupled receptor (GPCR) Moody, the G protein subunits G alpha i and G alpha o, and the regulator of G protein signaling Loco are required in the surface glia to achieve effective insulation. Our data suggest that the four proteins act in a complex common pathway. At the cellular level, the components function by regulating the cortical actin and thereby stabilizing the extended morphology of the surface glia, which in turn is necessary for the formation of septate junctions of sufficient length to achieve proper sealing of the nerve cord. Our study demonstrates the importance of morphogenetic regulation in blood-brain barrier development and places GPCR signaling at its core.

}, keywords = {Actins, Alternative Splicing, Animals, Blood-Brain Barrier, Brain, Drosophila melanogaster, Drosophila Proteins, Endothelium, Vascular, GTP-Binding Protein alpha Subunits, Gi-Go, Microscopy, Electron, Transmission, Nerve Tissue Proteins, Neuroglia, Receptors, G-Protein-Coupled, Signal Transduction, Tight Junctions}, issn = {0092-8674}, doi = {10.1016/j.cell.2005.08.037}, author = {Schwabe, Tina and Bainton, Roland J and Fetter, Richard D and Heberlein, Ulrike and Gaul, Ulrike} } @article {5489, title = {The hangover gene defines a stress pathway required for ethanol tolerance development.}, journal = {Nature}, volume = {436}, year = {2005}, month = {2005 Aug 11}, pages = {845-7}, abstract = {

Repeated alcohol consumption leads to the development of tolerance, simply defined as an acquired resistance to the physiological and behavioural effects of the drug. This tolerance allows increased alcohol consumption, which over time leads to physical dependence and possibly addiction. Previous studies have shown that Drosophila develop ethanol tolerance, with kinetics of acquisition and dissipation that mimic those seen in mammals. This tolerance requires the catecholamine octopamine, the functional analogue of mammalian noradrenaline. Here we describe a new gene, hangover, which is required for normal development of ethanol tolerance. hangover flies are also defective in responses to environmental stressors, such as heat and the free-radical-generating agent paraquat. Using genetic epistasis tests, we show that ethanol tolerance in Drosophila relies on two distinct molecular pathways: a cellular stress pathway defined by hangover, and a parallel pathway requiring octopamine. hangover encodes a large nuclear zinc-finger protein, suggesting a role in nucleic acid binding. There is growing recognition that stress, at both the cellular and systemic levels, contributes to drug- and addiction-related behaviours in mammals. Our studies suggest that this role may be conserved across evolution.

}, keywords = {Alcoholism, Animals, Drosophila melanogaster, Drosophila Proteins, Drug Tolerance, Ethanol, Heat-Shock Response, Mutation, Physiological, Stress, Zinc Fingers}, issn = {1476-4687}, doi = {10.1038/nature03864}, author = {Scholz, Henrike and Franz, Mirjam and Heberlein, Ulrike} } @article {5490, title = {Insulin signaling in the nervous system regulates ethanol intoxication in Drosophila melanogaster.}, journal = {Nature Neuroscience}, volume = {8}, year = {2005}, month = {2005 Jan}, pages = {18-9}, abstract = {

The insulin signaling pathway regulates multiple physiological processes, including energy metabolism, organismal growth, aging and reproduction. Here we show that genetic manipulations in Drosophila melanogaster that impair the function of insulin-producing cells or of the insulin-receptor signaling pathway in the nervous system lead to increased sensitivity to the intoxicating effects of ethanol. These findings suggest a previously unknown role for this highly conserved pathway in regulating the behavioral responses to an addictive drug.

}, keywords = {Alcoholic Intoxication, Animals, Brain, Drosophila melanogaster, Ethanol, Insulin, Neurons, Receptor, Signal Transduction}, issn = {1097-6256}, doi = {10.1038/nn1363}, author = {Corl, Ammon B and Rodan, Aylin R and Heberlein, Ulrike} } @proceedings {3305, title = {Joint nonparametric alignment for analyzing spatial gene expression patterns of Drosophila imaginal discs.}, volume = {2}, year = {2005}, month = {2005 Jun 20}, pages = {755-60}, abstract = {

To compare spatial patterns of gene expression, one must analyze a large number of images as current methods are only able to measure a small number of genes at a time. Bringing images of corresponding tissues into alignment is a critical first step in making a meaningful comparative analysis of these spatial patterns. Significant image noise and variability in the shapes make it hard to pick a canonical shape model. In this paper, we address these problems by combining segmentation and unsupervised shape learning algorithms. We first segment images to acquire structures of interest, then jointly align the shapes of these acquired structures using an unsupervised nonparametric maximum likelihood algorithm along the lines of congealing, while simultaneously learning the underlying shape model and associated transformations. The learned transformations are applied to corresponding images to bring them into alignment in one step. We demonstrate the results for images of various classes of Drosophila imaginal discs and discuss the methodology used for a quantitative analysis of spatial gene expression patterns.

}, author = {Ahammad, Parvez and Harmon, C and Hammonds, Ann S and Sastry, S and Rubin, Gerald M} } @article {45957, title = {Lipid-protein interactions in double-layered two-dimensional AQP0 crystals.}, journal = {Nature}, volume = {438}, year = {2005}, month = {2005 Dec 1}, pages = {633-8}, abstract = {

Lens-specific aquaporin-0 (AQP0) functions as a specific water pore and forms the thin junctions between fibre cells. Here we describe a 1.9 A resolution structure of junctional AQP0, determined by electron crystallography of double-layered two-dimensional crystals. Comparison of junctional and non-junctional AQP0 structures shows that junction formation depends on a conformational switch in an extracellular loop, which may result from cleavage of the cytoplasmic amino and carboxy termini. In the centre of the water pathway, the closed pore in junctional AQP0 retains only three water molecules, which are too widely spaced to form hydrogen bonds with each other. Packing interactions between AQP0 tetramers in the crystalline array are mediated by lipid molecules, which assume preferred conformations. We were therefore able to build an atomic model for the lipid bilayer surrounding the AQP0 tetramers, and we describe lipid-protein interactions.

}, keywords = {Animals, Aquaporins, Crystallization, Crystallography, Hydrogen Bonding, Lens, Crystalline, Lipid Bilayers, Membrane Lipids, Models, Molecular, Protein Binding, Protein Structure, Quaternary, Sheep, Water}, issn = {1476-4687}, doi = {10.1038/nature04321}, author = {Gonen, Tamir and Cheng, Yifan and Sliz, Piotr and Hiroaki, Yoko and Fujiyoshi, Yoshinori and Harrison, Stephen C and Walz, Thomas} } @article {2414, title = {Maintenance of spermatogenesis requires TAF4b, a gonad-specific subunit of TFIID.}, journal = {Genes \& Development}, volume = {19}, year = {2005}, month = {2005 Apr 1}, pages = {794-803}, abstract = {

The establishment and maintenance of spermatogenesis in mammals requires specialized networks of gene expression programs in the testis. The gonad-specific TAF4b component of TFIID (formerly TAF(II)105) is a transcriptional regulator enriched in the mouse testis. Herein we show that TAF4b is required for maintenance of spermatogenesis in the mouse. While young Taf4b-null males are initially fertile, Taf4b-null males become infertile by 3 mo of age and eventually exhibit seminiferous tubules devoid of germ cells. At birth, testes of Taf4b-null males appear histologically normal; however, at post-natal day 3 gonocyte proliferation is impaired and expression of spermatogonial stem cell markers c-Ret, Plzf, and Stra8 is reduced. Together, these data indicate that TAF4b is required for the precise expression of gene products essential for germ cell proliferation and suggest that TAF4b may be required for the regulation of spermatogonial stem cell specification and proliferation that is obligatory for normal spermatogenic maintenance in the adult.

}, keywords = {Aging, Animals, Cell Division, Infertility, Male, Mice, Spermatids, Spermatogenesis, Spermatogonia, TATA-Binding Protein Associated Factors, Testis, Transcription Factor TFIID}, issn = {0890-9369}, doi = {10.1073/pnas.1100640108}, author = {Falender, Allison E and Freiman, Richard N and Geles, Kenneth G and Lo, Kirk C and Hwang, KeumSil and Lamb, Dolores J and Morris, Patricia L and Tjian, Robert and Richards, JoAnne S} } @article {1409, title = {A major role for zygotic hunchback in patterning the Nasonia embryo.}, journal = {Development }, volume = {132}, year = {2005}, month = {2005 Aug}, pages = {3705-15}, abstract = {

Developmental genetic analysis has shown that embryos of the parasitoid wasp Nasonia vitripennis depend more on zygotic gene products to direct axial patterning than do Drosophila embryos. In Drosophila, anterior axial patterning is largely established by bicoid, a rapidly evolving maternal-effect gene, working with hunchback, which is expressed both maternally and zygotically. Here, we focus on a comparative analysis of Nasonia hunchback function and expression. We find that a lesion in Nasonia hunchback is responsible for the severe zygotic headless mutant phenotype, in which most head structures and the thorax are deleted, as are the three most posterior abdominal segments. This defines a major role for zygotic Nasonia hunchback in anterior patterning, more extensive than the functions described for hunchback in Drosophila or Tribolium. Despite the major zygotic role of Nasonia hunchback, we find that it is strongly expressed maternally, as well as zygotically. Nasonia Hunchback embryonic expression appears to be generally conserved; however, the mRNA expression differs from that of Drosophila hunchback in the early blastoderm. We also find that the maternal hunchback message decays at an earlier developmental stage in Nasonia than in Drosophila, which could reduce the relative influence of maternal products in Nasonia embryos. Finally, we extend the comparisons of Nasonia and Drosophila hunchback mutant phenotypes, and propose that the more severe Nasonia hunchback mutant phenotype may be a consequence of differences in functionally overlapping regulatory circuitry.

}, keywords = {Animals, Base Sequence, Body Patterning, Developmental, DNA-Binding Proteins, Drosophila Proteins, Gene Expression Regulation, Genetic Linkage, HMGB Proteins, In Situ Hybridization, Insect Proteins, Messenger, Molecular Sequence Data, RNA, Sequence Alignment, Stored, TCF Transcription Factors, Transcription Factor 7-Like 1 Protein, Transcription Factors, Wasps}, issn = {0950-1991}, doi = {10.1242/dev.01939}, author = {Pultz, Mary Anne and Westendorf, Lori and Gale, Samuel D and Hawkins, Kyle and Lynch, Jeremy and Pitt, Jason N and Reeves, Nick L and Yao, Jennifer C Y and Small, Stephen and Desplan, Claude and Leaf, David S} } @article {1138, title = {Male-specific fruitless specifies the neural substrates of Drosophila courtship behaviour.}, journal = {Nature}, volume = {436}, year = {2005}, month = {2005 Jul 21}, pages = {395-400}, abstract = {

Robust innate behaviours are attractive systems for genetically dissecting how environmental cues are perceived and integrated to generate complex behaviours. During courtship, Drosophila males engage in a series of innate, stereotyped behaviours that are coordinated by specific sensory cues. However, little is known about the specific neural substrates mediating this complex behavioural programme. Genetic, developmental and behavioural studies have shown that the fruitless (fru) gene encodes a set of male-specific transcription factors (FruM) that act to establish the potential for courtship in Drosophila. FruM proteins are expressed in approximately 2\% of central nervous system neurons, at least one subset of which coordinates the component behaviours of courtship. Here we have inserted the yeast GAL4 gene into the fru locus by homologous recombination and show that (1) FruM is expressed in subsets of all peripheral sensory systems previously implicated in courtship, (2) inhibition of FruM function in olfactory system components reduces olfactory-dependent changes in courtship behaviour, (3) transient inactivation of all FruM-expressing neurons abolishes courtship behaviour, with no other gross changes in general behaviour, and (4) {\textquoteright}masculinization{\textquoteright} of FruM-expressing neurons in females is largely sufficient to confer male courtship behaviour. Together, these data demonstrate that FruM proteins specify the neural substrates of male courtship.

}, keywords = {Animal, Animals, Central Nervous System, Courtship, Developmental, Drosophila melanogaster, Drosophila Proteins, Female, Gene Expression Regulation, Male, Nerve Tissue Proteins, Neurons, Sex Characteristics, Sexual Behavior, Transcription Factors}, issn = {1476-4687}, doi = {10.1038/nature03859}, author = {Manoli, Devanand S and Foss, Margit and Villella, Adriana and Taylor, Barbara J and Hall, Jeffrey C and Baker, Bruce S} } @article {5898, title = {Molecular and genetic features of a labeled class of spinal substantia gelatinosa neurons in a transgenic mouse.}, journal = {Journal of Computational Neuroscience}, volume = {492}, year = {2005}, month = {2005 Nov 7}, pages = {90-100}, abstract = {

Genetic incorporation in a mouse of a transgene containing the prion promoter and the green fluorescent protein (GFP) coding sequence labels a set of substantia gelatinosa (SG) neurons (SG-GFP) homogenous in morphology, electrophysiology, and γ-amino-butyric acid expression. In the present analysis the SG-GFP neurons are established to have protein kinase C-βII immunoreactivity and to lack evidence for the presence of calbindin D-28k, parvalbumin, and protein kinase C-γ. These neurons were hyperpolarized by mediators of descending control, norepinephrine and serotonin. Sequential polymerase chain reactions established the insertion of the transgene to be in the receptor protein tyrosine phosphatase kappa (RPTP-κ) and the laminin receptor 1 (ribosomal protein SA) pseudogene 1 locus. RPTP-κ expression in both GFP-labeled dorsal root ganglia and SG neurons raises the possibility that homophilic interactions of RPTP-κ contribute to establishment of connections between specific classes of primary afferent and SG neurons.

}, issn = {0021-9967}, doi = {doi: 10.1002/cne.20709}, author = {Hantman, Adam W. and Perl, Edward R} } @article {5488, title = {Moody encodes two GPCRs that regulate cocaine behaviors and blood-brain barrier permeability in Drosophila.}, journal = {Cell}, volume = {123}, year = {2005}, month = {2005 Oct 7}, pages = {145-56}, abstract = {

We identified moody in a genetic screen for Drosophila mutants with altered cocaine sensitivity. Hypomorphic mutations in moody cause an increased sensitivity to cocaine and nicotine exposure. In contrast, sensitivity to the acute intoxicating effects of ethanol is reduced. The moody locus encodes two novel GPCRs, Moody-alpha and Moody-beta. While identical in their membrane-spanning domains, the two Moody proteins differ in their long carboxy-terminal domains, which are generated by use of alternative reading frames. Both Moody forms are required for normal cocaine sensitivity, suggesting that they carry out distinct but complementary functions. Moody-alpha and Moody-beta are coexpressed in surface glia that surround the nervous system, where they are actively required to maintain the integrity of the blood-brain barrier in the adult fly. We propose that a Moody-mediated signaling pathway functions in glia to regulate nervous system insulation and drug-related behaviors.

}, keywords = {Alternative Splicing, Animal, Animals, Behavior, Blood-Brain Barrier, Brain, Cocaine, Cocaine-Related Disorders, Disease Models, Dopamine Uptake Inhibitors, Drosophila melanogaster, Drosophila Proteins, Drug Tolerance, G-Protein-Coupled, Male, Motor Activity, Neuroglia, Nicotine, Protein Structure, Receptors, Substance-Related Disorders, Tertiary}, issn = {0092-8674}, doi = {10.1016/j.cell.2005.07.029}, author = {Bainton, Roland J and Tsai, Linus T-Y and Schwabe, Tina and DeSalvo, Michael and Gaul, Ulrike and Heberlein, Ulrike} } @article {45753, title = {Pleiotropic functions of a conserved insect-specific Hox peptide motif.}, journal = {Development}, volume = {132}, year = {2005}, month = {2005 Dec}, pages = {5261-70}, abstract = {

The proteins that regulate developmental processes in animals have generally been well conserved during evolution. A few cases are known where protein activities have functionally evolved. These rare examples raise the issue of how highly conserved regulatory proteins with many roles evolve new functions while maintaining old functions. We have investigated this by analyzing the function of the ;QA{\textquoteright} peptide motif of the Hox protein Ultrabithorax (Ubx), a motif that has been conserved throughout insect evolution since its establishment early in the lineage. We precisely deleted the QA motif at the endogenous locus via allelic replacement in Drosophila melanogaster. Although the QA motif was originally characterized as involved in the repression of limb formation, we have found that it is highly pleiotropic. Curiously, deleting the QA motif had strong effects in some tissues while barely affecting others, suggesting that QA function is preferentially required for a subset of Ubx target genes. QA deletion homozygotes had a normal complement of limbs, but, at reduced doses of Ubx and the abdominal-A (abd-A) Hox gene, ectopic limb primordia and adult abdominal limbs formed when the QA motif was absent. These results show that redundancy and the additive contributions of activity-regulating peptide motifs play important roles in moderating the phenotypic consequences of Hox protein evolution, and that pleiotropic peptide motifs that contribute quantitatively to several functions are subject to intense purifying selection.

}, keywords = {Amino Acid Motifs, Animals, Conserved Sequence, Drosophila melanogaster, Drosophila Proteins, Extremities, Genes, Homeobox, Homeodomain Proteins, Phenotype, Sequence Deletion, Transcription Factors}, issn = {0950-1991}, doi = {10.1242/dev.02146}, author = {Hittinger, Chris Todd and Stern, David L and Carroll, Sean B} } @article {1774, title = {The receptors and coding logic for bitter taste.}, journal = {Nature}, volume = {434}, year = {2005}, month = {2005 Mar 10}, pages = {225-9}, abstract = {

The sense of taste provides animals with valuable information about the nature and quality of food. Bitter taste detection functions as an important sensory input to warn against the ingestion of toxic and noxious substances. T2Rs are a family of approximately 30 highly divergent G-protein-coupled receptors (GPCRs) that are selectively expressed in the tongue and palate epithelium and are implicated in bitter taste sensing. Here we demonstrate, using a combination of genetic, behavioural and physiological studies, that T2R receptors are necessary and sufficient for the detection and perception of bitter compounds, and show that differences in T2Rs between species (human and mouse) can determine the selectivity of bitter taste responses. In addition, we show that mice engineered to express a bitter taste receptor in {\textquoteright}sweet cells{\textquoteright} become strongly attracted to its cognate bitter tastants, whereas expression of the same receptor (or even a novel GPCR) in T2R-expressing cells resulted in mice that are averse to the respective compounds. Together these results illustrate the fundamental principle of bitter taste coding at the periphery: dedicated cells act as broadly tuned bitter sensors that are wired to mediate behavioural aversion.

}, keywords = {Animals, Food Preferences, G-Protein-Coupled, Humans, Inbred BALB C, Inbred C57BL, Knockout, Mice, Palate, Physical Stimulation, Receptors, Species Specificity, Substrate Specificity, Taste, Tongue}, issn = {1476-4687}, doi = {10.1038/nature03352}, author = {Mueller, Ken L and Hoon, Mark A and Erlenbach, Isolde and Chandrashekar, Jayaram and Zuker, Charles S and Ryba, Nicholas J P} } @article {1108, title = {Template-dependent morphogenesis of oriented calcite crystals in the presence of magnesium ions.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {44}, year = {2005}, month = {2005 Apr 15}, pages = {2386-90}, issn = {1433-7851}, doi = {10.1002/anie.200462296}, author = {Han, Yong-Jin and Wysocki, Laura M and Thanawala, Monica S and Siegrist, Theo and Aizenberg, Joanna} } @article {2160, title = {A Bayesian morphometry algorithm.}, journal = {IEEE Transactions on Medical Imaging}, volume = {23}, year = {2004}, month = {2004 Jun}, pages = {723-37}, abstract = {

Most methods for structure-function analysis of the brain in medical images are usually based on voxel-wise statistical tests performed on registered magnetic resonance (MR) images across subjects. A major drawback of such methods is the inability to accurately locate regions that manifest nonlinear associations with clinical variables. In this paper, we propose Bayesian morphological analysis methods, based on a Bayesian-network representation, for the analysis of MR brain images. First, we describe how Bayesian networks (BNs) can represent probabilistic associations among voxels and clinical (function) variables. Second, we present a model-selection framework, which generates a BN that captures structure-function relationships from MR brain images and function variables. We demonstrate our methods in the context of determining associations between regional brain atrophy (as demonstrated on MR images of the brain), and functional deficits. We employ two data sets for this evaluation: the first contains MR images of 11 subjects, where associations between regional atrophy and a functional deficit are almost linear; the second data set contains MR images of the ventricles of 84 subjects, where the structure-function association is nonlinear. Our methods successfully identify voxel-wise morphological changes that are associated with functional deficits in both data sets, whereas standard statistical analysis (i.e., t-test and paired t-test) fails in the nonlinear-association case.

}, keywords = {Aged, Algorithms, Atrophy, Automated, Bayes Theorem, Brain, Brain Diseases, Cluster Analysis, Computer-Assisted, Humans, Image Interpretation, Magnetic Resonance Imaging, Pattern Recognition, Reproducibility of Results, Sensitivity and Specificity, Signal Processing, Subtraction Technique}, issn = {0278-0062}, doi = {10.1007/s12021-010-9090-x}, author = {Herskovits, Edward H and Peng, Hanchuan and Davatzikos, Christos} } @article {1262, title = {Biophysical constraints on neuronal branching.}, journal = {Neurocomputing}, volume = {58-60}, year = {2004}, month = {2004 Jun}, pages = {487-95}, abstract = {

We investigate rules that govern neuronal arborization, speci\%cally the local geometry of the

bifurcation of a neurite into its sub-branches. In the present study we set out to determine

the relationship between branch diameter and angle. Existing theories are based on minimizing a

neuronal volume cost function, or, alternatively, on the equilibrium of mechanical tension forces,

whichdepend on branchdiameters. Our experimental results utilizing two-dimensional cultured

neural networks partly corroborate both the volume optimization principles and the tension theory.

Deviation from pure tension forces equilibrium is explained by an additional force exerted by

the anchoring of the junction to the substrate.

}, author = {Shefi, Orit and Harel, Amir and Chklovskii, Dmitri B and Ben-Jacob, Eshel and Ayali, Amir} } @article {2512, title = {Differential control of MHR3 promoter activity by isoforms of the ecdysone receptor and inhibitory effects of E75A and MHR3.}, journal = {Developmental Biology}, volume = {272}, year = {2004}, month = {2004 Aug 15}, pages = {510-21}, abstract = {

MHR3 is an ecdysone-inducible transcription factor whose expression in both Manduca sexta epidermis and the Manduca GV1 cell line is induced by 20-hydroxyecdysone (20E) in vitro. There are four putative ecdysone response elements (EcRE) in the 2.6-kb flanking region of the MHR3 promoter. The most proximal, EcRE1, is necessary for activation of the promoter by 20E in the GV1 cells because the mutation of EcRE1 caused the loss of responsiveness to 20E. Previous studies showed that EcR-B1/USP-1 bound only to EcRE1 and high levels of this complex increased the 20E-induced activation, whereas the presence of high USP-2 prevented this increased activation. When we expressed EcR-A alone or in combination with USP-1 under the control of Autographa californica baculovirus promoter (pIE1hr), the activation of the 2.6-kb promoter by 20E was reduced by about 50\%. Moreover, when EcR-A was expressed together with both EcR-B1 and USP-1, it reduced the normal activation caused by EcR-B1 and USP-1 by 50\%. Gel mobility shift assays showed no binding of EcR-A/USP-1 to EcRE1. The presence of EcR-A, however, reduced the binding of EcR-B1/USP-1 by about 50\%. These findings suggest that EcR-A competes with EcR-B1 for binding of USP-1, leading to a decline in activity of the promoter. In addition, E75A, another ecdysone-induced transcription factor, and MHR3 itself suppressed MHR3 promoter activity by binding to the monomeric response element (MRE2). Therefore, MHR3 can be down-regulated both by itself and by E75A.

}, keywords = {Animals, Base Sequence, Binding Sites, Cell Line, DNA-Binding Proteins, Ecdysterone, Epidermis, Gene Expression Regulation, Genetic, Glycoproteins, Insect Proteins, Manduca, Molecular Sequence Data, Mutation, Promoter Regions, Protein Isoforms, Receptors, Response Elements, Serpins, Steroid, Transcription Factors}, issn = {0012-1606}, doi = {10.1016/j.ydbio.2004.04.028}, author = {Hiruma, Kiyoshi and Riddiford, Lynn M} } @article {6442, title = {Functional magnetic resonance imaging of macaque monkeys performing visually guided saccade tasks: comparison of cortical eye fields with humans.}, journal = {Neuron}, volume = {41}, year = {2004}, month = {2004 Mar 4}, pages = {795-807}, abstract = {

The frontal and parietal eye fields serve as functional landmarks of the primate brain, although their correspondences between humans and macaque monkeys remain unclear. We conducted fMRI at 4.7 T in monkeys performing visually-guided saccade tasks and compared brain activations with those in humans using identical paradigms. Among multiple parietal activations, the dorsal lateral intraparietal area in monkeys and an area in the posterior superior parietal lobule in humans exhibited the highest selectivity to saccade directions. In the frontal cortex, the selectivity was highest at the junction of the precentral and superior frontal sulci in humans and in the frontal eye field (FEF) in monkeys. BOLD activation peaks were also found in premotor areas (BA6) in monkeys, which suggests that the apparent discrepancy in location between putative human FEF (BA6, suggested by imaging studies) and monkey FEF (BA8, identified by microstimulation studies) partly arose from methodological differences.

}, keywords = {Analysis of Variance, Animals, Cerebral Cortex, Female, Humans, Macaca, Magnetic Resonance Imaging, Male, Photic Stimulation, Psychomotor Performance, Rats, Saccades, Species Specificity, Visual Fields}, issn = {0896-6273}, author = {Koyama, Minoru and Hasegawa, Isao and Osada, Takahiro and Adachi, Yusuke and Nakahara, Kiyoshi and Miyashita, Yasushi} } @article {45801, title = {Gene Expression in Acyrthosiphon Pisum (Hemiptera: Aphididae)}, journal = {National Center for Biotechnology Information (NCBI)}, year = {2004}, month = {03/2004}, abstract = {

Examination of the genetic differences between aphids that can transmit citrus tristeza virus, CTV, and those which cannot, may lead to a greater understanding of the virus-aphid interactions necessitating virus acquisition and transmission. Since a cDNA library had been completed the previous year for the brown citrus aphid, a vector of CTV, a second aphid cDNA library was made to a non-CTV aphid vector, the pea aphid, Acyrthosiphon pisum. Comparisons between these two genetic datasets will provide a better understanding of the dynamics of aphid feeding, digestion, development, and may elucidate elements related to virus interactions that were previously unknown. Identification of the numerous proteins actively involved in feeding and digestion from aphids will provide specific targets for the development of new methods of control aimed at disrupting aphid feeding and ultimately reducing the acquisition and transmission of plant viruses which cause disease.

}, url = {http://www.ars.usda.gov/research/publications/publications.htm?SEQ_NO_115=168710}, author = {WB Hunter and PM Dang and D Stern} } @article {46634, title = {Habituation of an odorant-induced startle response in Drosophila.}, journal = {Genes, Brain, and Behavior}, volume = {3}, year = {2004}, month = {2004 Jun}, pages = {127-37}, abstract = {

Habituation is a fundamental form of behavioral plasticity that permits organisms to ignore inconsequential stimuli. Here we describe the habituation of a locomotor response to ethanol and other odorants in Drosophila, measured by an automated high-throughput locomotor tracking system. Flies exhibit an immediate and transient startle response upon exposure to a novel odor. Surgical removal of the antennae, the fly{\textquoteright}s major olfactory organs, abolishes this startle response. With repeated discrete exposures to ethanol vapor, the startle response habituates. Habituation is reversible by a mechanical stimulus and is not due to the accumulation of ethanol in the organism, nor to non-specific mechanisms. Ablation or inactivation of the mushroom bodies, central brain structures involved in olfactory and courtship conditioning, results in decreased olfactory habituation. In addition, olfactory habituation to ethanol generalizes to odorants that activate separate olfactory receptors. Finally, habituation is impaired in rutabaga, an adenylyl cyclase mutant isolated based on a defect in olfactory associative learning. These data demonstrate that olfactory habituation operates, at least in part, through central mechanisms. This novel model of olfactory habituation in freely moving Drosophila provides a scalable method for studying the molecular and neural bases of this simple and ubiquitous form of learning.

}, keywords = {Adenylate Cyclase, Animals, Chemoreceptor Cells, Denervation, Drosophila melanogaster, Ethanol, Female, Habituation, Psychophysiologic, Learning, Male, Models, Animal, Motor Activity, Mushroom Bodies, Mutation, Odors, Physical Stimulation, Reflex, Startle, Smell}, issn = {1601-1848}, doi = {10.1111/j.1601-183x.2004.00061.x}, author = {Cho, W and Heberlein, U and Wolf, F W} } @article {2319, title = {Individual differences in trait anxiety predict the response of the basolateral amygdala to unconsciously processed fearful faces.}, journal = {Neuron}, volume = {44}, year = {2004}, month = {2004 Dec 16}, pages = {1043-55}, abstract = {

Responses to threat-related stimuli are influenced by conscious and unconscious processes, but the neural systems underlying these processes and their relationship to anxiety have not been clearly delineated. Using fMRI, we investigated the neural responses associated with the conscious and unconscious (backwardly masked) perception of fearful faces in healthy volunteers who varied in threat sensitivity (Spielberger trait anxiety scale). Unconscious processing modulated activity only in the basolateral subregion of the amygdala, while conscious processing modulated activity only in the dorsal amygdala (containing the central nucleus). Whereas activation of the dorsal amygdala by conscious stimuli was consistent across subjects and independent of trait anxiety, activity in the basolateral amygdala to unconscious stimuli, and subjects{\textquoteright} reaction times, were predicted by individual differences in trait anxiety. These findings provide a biological basis for the unconscious emotional vigilance characteristic of anxiety and a means for investigating the mechanisms and efficacy of treatments for anxiety.

}, keywords = {Adult, Amygdala, Anxiety, Brain Mapping, Emotions, Facial Expression, Fear, Female, Humans, Individuality, Male, Photic Stimulation, Predictive Value of Tests, Reaction Time, Unconscious (Psychology)}, issn = {0896-6273}, doi = {10.3389/fnana.2010.00147}, author = {Etkin, Amit and Klemenhagen, Kristen C and Dudman, Joshua T and Rogan, Michael T and Hen, Ren{\'e} and Kandel, Eric R and Hirsch, Joy} } @article {5491, title = {Lmo mutants reveal a novel role for circadian pacemaker neurons in cocaine-induced behaviors.}, journal = {PLoS Biology}, volume = {2}, year = {2004}, month = {2004 Dec}, pages = {e408}, abstract = {

Drosophila has been developed recently as a model system to investigate the molecular and neural mechanisms underlying responses to drugs of abuse. Genetic screens for mutants with altered drug-induced behaviors thus provide an unbiased approach to define novel molecules involved in the process. We identified mutations in the Drosophila LIM-only (LMO) gene, encoding a regulator of LIM-homeodomain proteins, in a genetic screen for mutants with altered cocaine sensitivity. Reduced Lmo function increases behavioral responses to cocaine, while Lmo overexpression causes the opposite effect, reduced cocaine responsiveness. Expression of Lmo in the principal Drosophila circadian pacemaker cells, the PDF-expressing ventral lateral neurons (LN(v)s), is sufficient to confer normal cocaine sensitivity. Consistent with a role for Lmo in LN(v)function,Lmomutants also show defects in circadian rhythms of behavior. However, the role for LN(v)s in modulating cocaine responses is separable from their role as pacemaker neurons: ablation or functional silencing of the LN(v)s reduces cocaine sensitivity, while loss of the principal circadian neurotransmitter PDF has no effect. Together, these results reveal a novel role for Lmo in modulating acute cocaine sensitivity and circadian locomotor rhythmicity, and add to growing evidence that these behaviors are regulated by shared molecular mechanisms. The finding that the degree of cocaine responsiveness is controlled by the Drosophila pacemaker neurons provides a neuroanatomical basis for this overlap. We propose that Lmo controls the responsiveness of LN(v)s to cocaine, which in turn regulate the flies{\textquoteright} behavioral sensitivity to the drug.

}, keywords = {Alleles, Animal, Animals, Behavior, Biological, Biological Clocks, Circadian Rhythm, Cocaine, Drosophila melanogaster, Drosophila Proteins, Gene Expression Regulation, Gene Silencing, Genetic, Homeodomain Proteins, Models, Mutation, Neurons, Neuropeptides, Neurotransmitter Agents, Protein Structure, Reverse Transcriptase Polymerase Chain Reaction, Tertiary}, issn = {1545-7885}, doi = {10.1371/journal.pbio.0020408}, author = {Tsai, Linus T-Y and Bainton, Roland J and Blau, Justin and Heberlein, Ulrike} } @article {2188, title = {Modular synthesis and preliminary biological evaluation of stereochemically diverse 1,3-dioxanes.}, journal = {Chemistry \& Biology}, volume = {11}, year = {2004}, month = {2004 Sep}, pages = {1279-91}, abstract = {

Modular synthesis and substrate stereocontrol were combined to furnish 18,000 diverse 1,3-dioxanes whose distribution in chemical space rivals that of a reference set of over 2,000 bioactive small molecules. Library quality was assessed at key synthetic stages, culminating in a detailed postsynthesis analysis of purity, yield, and structural characterizability, and the resynthesis of library subsets that did not meet quality standards. The importance of this analysis-resynthesis process is highlighted by the discovery of new biological probes through organismal and protein binding assays, and by determination of the building block and stereochemical basis for their bioactivity. This evaluation of a portion of the 1,3-dioxane library suggests that many additional probes for chemical genetics will be identified as the entire library becomes biologically annotated.

}, keywords = {Amines, Animals, Calmodulin, Combinatorial Chemistry Techniques, Dioxanes, Molecular Structure, Stereoisomerism, Surface Plasmon Resonance, Zebrafish}, issn = {1074-5521}, doi = {10.1016/j.chembiol.2004.07.012}, author = {Wong, Jason C and Sternson, Scott M and Louca, Joseph B and Hong, Roger and Schreiber, Stuart L} } @article {46633, title = {Molecular Genetic Analysis of Ethanol Intoxication in Drosophila melanogaster.}, journal = {Integrative and Comparative Biology}, volume = {44}, year = {2004}, month = {2004 Aug}, pages = {269-74}, abstract = {

Recently, the fruit fly Drosophila melanogaster has been introduced as a model system to study the molecular bases of a variety of ethanol-induced behaviors. It became immediately apparent that the behavioral changes elicited by acute ethanol exposure are remarkably similar in flies and mammals. Flies show signs of acute intoxication, which range from locomotor stimulation at low doses to complete sedation at higher doses and they develop tolerance upon intermittent ethanol exposure. Genetic screens for mutants with altered responsiveness to ethanol have been carried out and a few of the disrupted genes have been identified. This analysis, while still in its early stages, has already revealed some surprising molecular parallels with mammals. The availability of powerful tools for genetic manipulation in Drosophila, together with the high degree of conservation at the genomic level, make Drosophila a promising model organism to study the mechanism by which ethanol regulates behavior and the mechanisms underlying the organism{\textquoteright}s adaptation to long-term ethanol exposure.

}, issn = {1540-7063}, doi = {10.1093/icb/44.4.269}, author = {Heberlein, Ulrike and Wolf, Fred W and Rothenfluh, Adrian and Guarnieri, Douglas J} } @article {5904, title = {Morphological and physiological features of a set of spinal substantia gelatinosa neurons defined by green fluorescent protein expression.}, journal = {The Journal of Neuroscience}, volume = {24}, year = {2004}, month = {2004 Jan 28}, pages = {836-42}, abstract = {

The spinal substantia gelatinosa (SG) is known to be involved in the manipulation of nociceptive and thermal primary afferent input; however, the interrelationships of its neuronal components are poorly understood. As a step toward expanding understanding, we took a relatively unique approach by concentrating on a set of SG neurons selectively labeled by green fluorescent protein (GFP) in a transgenic mouse. These GFP-expressing SG neurons prove to have homogenous morphological and electrophysiological properties, are systematically spaced in the SG, contain GABA, receive C-fiber primary afferent input, and upregulate c-Fos protein in response to noxious stimuli. Together, the properties established for these GFP-labeled neurons are consistent with a modular SG organization in which afferent activity related to nociception or other C-fiber signaling are subject to integration/modulation by repeating, similar circuits of neurons.

}, keywords = {Animals, Biological Markers, Electrophysiology, gamma-Aminobutyric Acid, Ganglia, Green Fluorescent Proteins, Luminescent Proteins, Lysine, Mice, Nerve Fibers, Neurons, Pain Measurement, Patch-Clamp Techniques, Proto-Oncogene Proteins c-fos, Spinal, Substantia Gelatinosa, Transgenic, Unmyelinated}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4221-03.2004}, author = {Hantman, Adam W and van den Pol, Anthony N and Perl, Edward R} } @article {4008, title = {A paradox in the evolution of primate vocal learning.}, journal = {Trends in Neurosciences}, volume = {27}, year = {2004}, month = {2004 Nov}, pages = {649-54}, abstract = {

The importance of auditory feedback in the development of spoken language in humans is striking. Paradoxically, although auditory-feedback-dependent vocal plasticity has been shown in a variety of taxonomic groups, there is little evidence that our nearest relatives{\textendash}non-human primates{\textendash}require auditory feedback for the development of species-typical vocal signals. Because of the apparent lack of developmental plasticity in the vocal production system, neuroscientists have largely ignored the neural mechanisms of non-human primate vocal production and perception. Recently, the absence of evidence for vocal plasticity from developmental studies has been contrasted with evidence for vocal plasticity in adults. We argue that this new evidence makes non-human primate vocal behavior an attractive model system for neurobiological analysis.

}, keywords = {Acoustic Stimulation, Animal, Animals, Biological Evolution, Humans, Learning, Vocalization}, issn = {0166-2236}, doi = {10.1016/j.tins.2004.08.009}, author = {Egnor, S E Roian and Hauser, Marc D} } @conference {45802, title = {Prospects in aphid genetics}, booktitle = {Aphids in a new millennium. Proceedings of the Sixth International Symposium on Aphids}, year = {2004}, month = {09/2004}, publisher = {Institut National de la Recherche Agronomique}, organization = {Institut National de la Recherche Agronomique}, address = {Rennes, France}, abstract = {

This paper identifies the prospects of using aphid species as ideal genetic model systems for the study of evolutionary developmental biology and genetic control of polyphenisms. The advantages and disadvantages of using aphids as genetic model organisms are discussed.

}, isbn = {2-7380-1113-6}, url = {http://www.cabdirect.org/abstracts/20043046841.html;jsessionid=4C6865DD4D971042FEB329F0DD6166E5}, author = {DL Stern and JC Simon and CA Dedryver and C Rispe and M Hull{\'e}} } @article {46632, title = {Rapid and chronic: two distinct forms of ethanol tolerance in Drosophila.}, journal = {Alcoholism, Clinical and Experimental Research}, volume = {28}, year = {2004}, month = {2004 Oct}, pages = {1469-80}, abstract = {

BACKGROUND: Ethanol tolerance, defined as a reduction in the intensity of the effects of ethanol upon continuous or repeated exposure, is a hallmark of alcoholism. Tolerance may develop at the cellular or neural systems levels. The molecular changes underlying ethanol tolerance are not well understood. We therefore explored the utility of Drosophila, with its accessibility to genetic, molecular, and behavioral analyses, as a model organism to study tolerance development in response to different ethanol-exposure regimens.

METHODS: We describe a new assay that quantifies recovery from ethanol intoxication in Drosophila. Using this recovery assay, we define ethanol pre-exposure paradigms that lead to the development of tolerance. We also use the inebriometer, an assay that measures the onset of intoxication, to study the effects of pharmacological and genetic manipulations on tolerance development.

RESULTS: We show that flies develop different forms of ethanol tolerance: rapid tolerance, induced by a single short exposure to a high concentration of ethanol, and chronic tolerance, elicited by prolonged exposure to a low concentration of the drug. Neither rapid nor chronic tolerance involves changes in ethanol pharmacokinetics, implying that they represent functional rather than dispositional tolerance. Chronic and rapid tolerance can be distinguished mechanistically: chronic tolerance is disrupted by treatment with the protein synthesis inhibitor cycloheximide, whereas rapid tolerance is resistant to this treatment. Furthermore, rapid and chronic tolerance rely on distinct genetic pathways: a mutant defective for octopamine biosynthesis shows reduced rapid tolerance but normal chronic tolerance.

CONCLUSIONS: Flies, like mammals, develop tolerance in response to different ethanol-exposure regimens, and this tolerance affects both the onset of and the recovery from acute intoxication. Two forms of tolerance, rapid and chronic, are mechanistically distinct, because they can be dissociated genetically and pharmacologically.

}, keywords = {Animals, Drosophila, Drug Tolerance, Ethanol, Male, Models, Animal, Time Factors}, issn = {0145-6008}, author = {Berger, Karen H and Heberlein, Ulrike and Moore, Monica S} } @article {1590, title = {The structures of inhibitor complexes of Pyrococcus furiosus phosphoglucose isomerase provide insights into substrate binding and catalysis.}, journal = {Journal of Molecular Biology}, volume = {343}, year = {2004}, month = {2004 Oct 22}, pages = {649-57}, abstract = {

Pyrococcus furiosus phosphoglucose isomerase (PfPGI) is a metal-containing enzyme that catalyses the interconversion of glucose 6-phosphate (G6P) and fructose 6-phosphate (F6P). The recent structure of PfPGI has confirmed the hypothesis that the enzyme belongs to the cupin superfamily and identified the position of the active site. This fold is distinct from the alphabetaalpha sandwich fold commonly seen in phosphoglucose isomerases (PGIs) that are found in bacteria, eukaryotes and some archaea. Whilst the mechanism of the latter family is thought to proceed through a cis-enediol intermediate, analysis of the structure of PfPGI in the presence of inhibitors has led to the suggestion that the mechanism of this enzyme involves the metal-dependent direct transfer of a hydride between C1 and C2 atoms of the substrate. To gain further insight in the reaction mechanism of PfPGI, the structures of the free enzyme and the complexes with the inhibitor, 5-phospho-d-arabinonate (5PAA) in the presence and absence of metal have been determined. Comparison of these structures with those of equivalent complexes of the eukaryotic PGIs reveals similarities at the active site in the disposition of possible catalytic residues. These include the presence of a glutamic acid residue, Glu97 in PfPGI, which occupies the same position relative to the inhibitor as that of the glutamate that is thought to function as the catalytic base in the eukaryal-type PGIs. These similarities suggest that aspects of the catalytic mechanisms of these two structurally unrelated PGIs may be similar and based on an enediol intermediate.

}, keywords = {Archaeal Proteins, Binding Sites, Catalysis, Crystallography, Dimerization, Fructosephosphates, Glucose-6-Phosphate, Glucose-6-Phosphate Isomerase, Manganese, Models, Molecular, Molecular Structure, Pentosephosphates, Protein Binding, Protein Conformation, Pyrococcus furiosus, X-Ray}, issn = {0022-2836}, doi = {10.1016/j.jmb.2004.08.061}, author = {Berrisford, John M and Akerboom, Jasper and Brouns, Stan and Sedelnikova, Svetlana E and Turnbull, Andrew P and van der Oost, John and Salmon, Laurent and Hardr{\'e}, Renaud and Murray, Iain A and Blackburn, G Michael and Rice, David W and Baker, Patrick J} } @article {2682, title = {Axon pruning during Drosophila metamorphosis: evidence for local degeneration and requirement of the ubiquitin-proteasome system.}, journal = {Neuron}, volume = {38}, year = {2003}, month = {2003 Jun 19}, pages = {871-85}, abstract = {

Axon pruning is widely used for the refinement of neural circuits in both vertebrates and invertebrates, and may also contribute to the pathogenesis of neurodegenerative diseases. However, little is known about the cellular and molecular mechanisms of axon pruning. We use the stereotyped pruning of gamma neurons of the Drosophila mushroom bodies (MB) during metamorphosis to investigate these mechanisms. Detailed time course analyses indicate that MB axon pruning is mediated by local degeneration rather than retraction and that the disruption of the microtubule cytoskeleton precedes axon pruning. In addition, multiple lines of genetic evidence demonstrate an intrinsic role of the ubiquitin-proteasome system in axon pruning; for example, loss-of-function mutations of the ubiquitin activating enzyme (E1) or proteasome subunits in MB neurons block axon pruning. Our findings suggest that some forms of axon pruning during development may share similarities with degeneration of axons in response to injury.

}, keywords = {Animals, Axons, Biological, Cell Adhesion Molecules, Cysteine Endopeptidases, Cytoskeletal Proteins, Cytoskeleton, Cytosol, Drosophila, Endocytosis, Endopeptidases, Gene Expression, Ligases, Metamorphosis, Microtubules, Multienzyme Complexes, Mutation, Nerve Degeneration, Neurons, Proteasome Endopeptidase Complex, Saccharomyces cerevisiae, Synapses, Transfection, Ubiquitin, Ubiquitin-Activating Enzymes, Ubiquitin-Protein Ligases}, issn = {0896-6273}, author = {Watts, Ryan J and Hoopfer, Eric D and Luo, Liqun} } @article {1777, title = {Coding of sweet, bitter, and umami tastes: different receptor cells sharing similar signaling pathways.}, journal = {Cell}, volume = {112}, year = {2003}, month = {2003 Feb 7}, pages = {293-301}, abstract = {

Mammals can taste a wide repertoire of chemosensory stimuli. Two unrelated families of receptors (T1Rs and T2Rs) mediate responses to sweet, amino acids, and bitter compounds. Here, we demonstrate that knockouts of TRPM5, a taste TRP ion channel, or PLCbeta2, a phospholipase C selectively expressed in taste tissue, abolish sweet, amino acid, and bitter taste reception, but do not impact sour or salty tastes. Therefore, despite relying on different receptors, sweet, amino acid, and bitter transduction converge on common signaling molecules. Using PLCbeta2 taste-blind animals, we then examined a fundamental question in taste perception: how taste modalities are encoded at the cellular level. Mice engineered to rescue PLCbeta2 function exclusively in bitter-receptor expressing cells respond normally to bitter tastants but do not taste sweet or amino acid stimuli. Thus, bitter is encoded independently of sweet and amino acids, and taste receptor cells are not broadly tuned across these modalities.

}, keywords = {Action Potentials, Afferent, Animals, Cell Membrane, Cell Surface, Cells, Citric Acid, Cultured, Female, Glutamic Acid, GTP-Binding Proteins, Isoenzymes, Knockout, Male, Membrane Proteins, Mice, Neurons, Phospholipase C beta, Quinine, Receptors, Sensory Receptor Cells, Signal Transduction, Sucrose, Taste, Taste Buds, TRPM Cation Channels, Type C Phospholipases}, issn = {0092-8674}, author = {Zhang, Yifeng and Hoon, Mark A and Chandrashekar, Jayaram and Mueller, Ken L and Cook, Boaz and Wu, Dianqing and Zuker, Charles S and Ryba, Nicholas J P} } @article {2424, title = {Diversified transcription initiation complexes expand promoter selectivity and tissue-specific gene expression.}, journal = {Genes \& Development}, volume = {17}, year = {2003}, month = {2003 Jun 1}, pages = {1309-20}, keywords = {Animals, Developmental, Drosophila, Drosophila Proteins, Gene Expression Regulation, Genetic, Male, Messenger, Organ Specificity, Promoter Regions, RNA, RNA Polymerase III, Spermatogenesis, TATA Box Binding Protein-Like Proteins, Telomeric Repeat Binding Protein 2, Transcription}, issn = {0890-9369}, doi = {10.1073/pnas.1100640108}, author = {Hochheimer, Andreas and Tjian, Robert} } @article {2322, title = {Dopamine D1 receptors mediate CREB phosphorylation via phosphorylation of the NMDA receptor at Ser897-NR1.}, journal = {Journal of Neurochemistry}, volume = {87}, year = {2003}, month = {2003 Nov}, pages = {922-34}, abstract = {

Addictive drugs such as amphetamine and cocaine stimulate the dopaminergic system, activate dopamine receptors and induce gene expression throughout the striatum. The signal transduction pathway leading from dopamine receptor stimulation at the synapse to gene expression in the nucleus has not been fully elucidated. Here, we present evidence that D1 receptor stimulation leads to phosphorylation of the transcription factor Ca2+ and cyclic AMP response element binding protein (CREB) in the nucleus by means of NMDA receptor-mediated Ca2+ signaling. Stimulation of D1 receptors induces the phosphorylation of Ser897 on the NR1 subunit by protein kinase A (PKA). This phosphorylation event is crucial for D1 receptor-mediated CREB phosphorylation. Dopamine cannot induce CRE-mediated gene expression in neurons transfected with a phosphorylation-deficient NR1 construct. Moreover, stimulation of D1 receptors or increase in cyclic AMP levels leads to an increase in cytosolic Ca2+ in the presence of glutamate, but not in the absence of glutamate, indicating the ability of dopamine and cyclic AMP to facilitate NMDA channel activity. The recruitment of the NMDA receptor signal transduction pathway by D1 receptors may provide a general mechanism for gene regulation that is fundamental for mechanisms of drug addiction and long-term memory.

}, keywords = {Animals, Calcium, Calcium-Calmodulin-Dependent Protein Kinases, Cells, Corpus Striatum, Cultured, Cyclic AMP Response Element-Binding Protein, Cyclic AMP-Dependent Protein Kinases, Dopamine D1, Glutamic Acid, Mutagenesis, N-Methyl-D-Aspartate, Neurons, Phosphorylation, Rats, Receptors, Signal Transduction, Site-Directed, Sprague-Dawley}, issn = {0022-3042}, doi = {10.3389/fnana.2010.00147}, author = {Dudman, Joshua T and Eaton, Molly E and Rajadhyaksha, Anjali and Mac{\'\i}as, Wendy and Taher, Muffadal and Barczak, Amy and Kameyama, Kimihiko and Huganir, Richard and Konradi, Christine} } @article {46636, title = {Drosophila melanogaster, a genetic model system for alcohol research.}, journal = {International Review of Neurobiology}, volume = {54}, year = {2003}, month = {2003}, pages = {199-228}, abstract = {

In its natural environment, which consists of fermenting plant materials, the fruit fly Drosophila melanogaster encounters high levels of ethanol. Flies are well equipped to deal with the toxic effects of ethanol; they use it as an energy source and for lipid biosynthesis. The primary ethanol-metabolizing pathway in flies involves the enzymes alcohol dehydrogenase (ADH) and acetaldehyde dehydrogenase (ALDH); their role in adaptation to ethanol-rich environments has been studied extensively. The similarity between Drosophila and mammals is not restricted to the manner in which they metabolize ethanol; behaviors elicited by ethanol exposure are also remarkably similar in these organisms. Flies show signs of acute intoxication, which range from locomotor stimulation at low doses to complete sedation at higher doses, they develop tolerance upon intermittent ethanol exposure, and they appear to like ethanol, showing preference for ethanol-containing media. Molecular genetic analysis of ethanol-induced behaviors in Drosophila, while still in its early stages, has already revealed some surprising parallels with mammals. The availability of powerful tools for genetic manipulation in Drosophila, together with the high degree of conservation at the genomic level, make Drosophila a promising model organism to study the mechanism by which ethanol regulates behavior and the mechanisms underlying the organism{\textquoteright}s adaptation to long-term ethanol exposure.

}, keywords = {Alcohol Dehydrogenase, Alcoholism, Aldehyde Oxidoreductases, Animals, Behavior, Animal, Cell Membrane, Conditioning (Psychology), Drosophila melanogaster, Drug Tolerance, Ethanol, Humans, Models, Animal, Mutation}, issn = {0074-7742}, author = {Guarnieri, Douglas J and Heberlein, Ulrike} } @article {2514, title = {E74 exhibits stage-specific hormonal regulation in the epidermis of the tobacco hornworm, manduca sexta.}, journal = {Developmental Biology}, volume = {258}, year = {2003}, month = {2003 Jun 1}, pages = {76-90}, abstract = {

The transcription factor E74 is one of the early genes induced by ecdysteroids during metamorphosis of Drosophila melanogaster. Here, we report the cloning and hormonal regulation of E74 from the tobacco hornworm, Manduca sexta (MsE74). MsE74 is 98\% identical to that of D. melanogaster within the DNA-binding ETS domain of the protein. The 5{\textquoteright}-isoform-specific regions of MsE74A and MsE74B share significantly lower sequence similarity (30-40\%). Developmental expression by Northern blot analysis reveals that, during the 5th larval instar, MsE74B expression correlates with pupal commitment on day 3 and is induced to maximal levels within 12h by low levels of 20-hydroxyecdysone (20E) and repressed by physiologically relevant levels of juvenile hormone I (JH I). Immunocytochemical analysis shows that MsE74B appears in the epidermis before the 20E-induced Broad transcription factor that is correlated with pupal commitment (Zhou and Riddiford, 2001). In contrast, MsE74A is expressed late in the larval and the pupal molts when the ecdysteroid titer has declined to low levels and in the adult molt just as the ecdysteroid titer begins to decline. This change in timing during the adult molt appears not to be due to the absence of JH as there was no change during the pupal molt of allatectomized animals. When either 4th or 5th instar larval epidermis was explanted and subjected to hormonal manipulations, MsE74A induction occurred only after exposure to 20E followed by its removal. Thus, MsE74B appears to have a similar role at the onset of metamorphosis in Manduca as it does in Drosophila, whereas MsE74A is regulated differently at pupation in Manduca than at pupariation in Drosophila.

}, keywords = {Amino Acid, Amino Acid Sequence, Animals, Base Sequence, Biological, Cells, Cultured, Developmental, Drosophila, Ecdysterone, Epidermis, Gene Expression Regulation, Genes, Insect, Insect Proteins, Juvenile Hormones, Larva, Manduca, Messenger, Metamorphosis, Molecular Sequence Data, Open Reading Frames, Protein Isoforms, Protein Structure, Pupa, RNA, Sequence Homology, Tertiary, Transcription Factors}, issn = {0012-1606}, author = {Stilwell, Geoffrey E and Nelson, Charles A and Weller, John and Cui, Haiyang and Hiruma, Kiyoshi and Truman, James W and Riddiford, Lynn M} } @article {6354, title = {Functional properties of a brain-specific NH2-terminally spliced modulator of Kv4 channels.}, journal = {American Journal of Physiology. Cell Physiology}, volume = {285}, year = {2003}, month = {2003 Jul}, pages = {C161-70}, abstract = {

Kv4/K channel-interacting protein (KChIP) potassium channels are a major class of rapidly inactivating K channels in brain and heart. Considering the importance of alternative splicing to the quantitative features of KChIP gating modulation, a previously uncharacterized splice form of KChIP1 was functionally characterized. The KChIP1b splice variant differs from the previously characterized KChIP1a splice form by the inclusion of a novel amino-terminal region that is encoded by an alternative exon that is conserved in mouse, rat, and human genes. The expression of KChIP1b mRNA was high in brain but undetectable in heart or liver by RT-PCR. In cerebellar tissue, KChIP1b and KChIP1a transcripts were expressed at nearly equal levels. Coexpression of KChIP1b or KChIP1a with Kv4.2 channels in oocytes slowed K current decay and destabilized open-inactivated channel gating. Like other KChIP subunits, KChIP1b increased Kv4.2 current amplitude and KChIP1b also shifted Kv4.2 conductance-voltage curves by -10 mV. The development of Kv4.2 channel inactivation accessed from closed gating states was faster with KChIP1b coexpression. Deletion of the novel amino-terminal region in KChIP1b selectively altered the subunit{\textquoteright}s modulation of Kv4.2 closed inactivation gating. The role of the KChIP1b NH2-terminal region was further confirmed by direct comparison of the properties of the NH2-terminal deletion mutant and the KChIP1a subunit, which is encoded by a transcript that lacks the novel exon. The features of KChIP1b modulation of Kv4 channels are likely to be conserved in mammals and demonstrate a role for the KChIP1 NH2-terminal region in the regulation of closed inactivation gating.

}, keywords = {Alternative Splicing, Amino Acid Sequence, Animals, Brain, Calcium-Binding Proteins, Exons, Ion Channel Gating, Kv Channel-Interacting Proteins, Mammals, Molecular Sequence Data, Mutagenesis, Oocytes, Potassium Channels, Protein Structure, Rats, Shal Potassium Channels, Tertiary, Voltage-Gated, Xenopus}, issn = {0363-6143}, doi = {10.1152/ajpcell.00416.2002}, author = {Boland, Linda M and Jiang, Min and Lee, So Yeong and Fahrenkrug, Scott C and Harnett, Mark T and O{\textquoteright}Grady, Scott M} } @article {2292, title = {Inducible nitric oxide synthase (NOS2) promoter CCTTT repeat polymorphism: relationship to in vivo nitric oxide production/NOS activity in an asymptomatic malaria-endemic population.}, journal = {The American Journal of Tropical Medicine and Hygiene}, volume = {69}, year = {2003}, month = {2003 Dec}, pages = {569-73}, abstract = {

Polymorphisms in the inducible nitric oxide synthase gene (NOS2) promoter have been associated with clinical outcome from malaria. These include a CCTTT repeat (CCTTTn) 2.5 kilobases upstream from the NOS2 transcription start site, and two single nucleotide substitutions: G{\textendash}\>C at position -954 (G-954C), and C{\textendash}\>T at position -1173 (C-1173T). Although hypothesized to influence NO production in vivo, the functional relevance of (CCTTT)n and G-954C is uncertain because disease association studies have yielded inconsistent results. This study found no association between CCTTT repeat number and levels of plasma NO metabolites or peripheral blood mononuclear cell NOS activity in a cohort of asymptomatic malaria-exposed coastal Papua New Guineans 1-60 years old. This suggests that (CCTTT)n does not independently influence NOS2 transcription in vivo. Neither the G-954C nor the C-1173T polymorphisms were identified in this population, indicating the variability and complexity of selection for NOS2 promoter polymorphisms in different malaria-endemic populations.

}, keywords = {Endemic Diseases, Female, Genetic, Genetic Predisposition to Disease, Humans, Malaria, Male, Nitric Oxide, Nitric Oxide Synthase, Nitric Oxide Synthase Type II, Nucleic Acid, Oceanic Ancestry Group, Papua New Guinea, Polymorphism, Promoter Regions, Repetitive Sequences}, issn = {0002-9637}, author = {Boutlis, Craig S and Hobbs, Maurine R and Marsh, Robyn L and Misukonis, Mary A and Tkachuk, Ariana N and Lagog, Moses and Booth, Jennifer and Granger, Donald L and Bockarie, Moses J and Mgone, Charles S and Levesque, Marc C and Weinberg, J Brice and Anstey, Nicholas M} } @article {46639, title = {Invertebrate models of drug abuse.}, journal = {Journal of Neurobiology}, volume = {54}, year = {2003}, month = {2003 Jan}, pages = {161-78}, abstract = {

Susceptibility to drug addiction depends on genetic and environmental factors and their complex interactions. Studies with mammalian models have identified molecular targets, neurochemical systems, and brain regions that mediate some of the addictive properties of abused drugs. Yet, our understanding of how the primary effects of drugs lead to addiction remains incomplete. Recently, researchers have turned to the invertebrate model systems Drosophila melanogaster and Caenorhabditis elegans to dissect the mechanisms by which abused drugs modulate behavior. Due to their sophisticated genetics, relatively simple anatomy, and their remarkable molecular similarity to mammals, these invertebrate models should provide useful insights into the mechanisms of drug action. Here we review recent behavioral and genetic studies in flies and worms on the effects of ethanol, cocaine, and nicotine, three of the most widely abused drugs in the world.

}, keywords = {Alcoholic Intoxication, Animals, Behavior, Animal, Caenorhabditis elegans, Cocaine, Disease Models, Animal, Dopamine, Drosophila melanogaster, Drug Tolerance, Ethanol, Learning, Memory, Nicotine, Substance-Related Disorders}, issn = {0022-3034}, doi = {10.1002/neu.10166}, author = {Wolf, Fred W and Heberlein, Ulrike} } @article {2681, title = {Involvement of the ubiquitin-proteasome system in the early stages of wallerian degeneration.}, journal = {Neuron}, volume = {39}, year = {2003}, month = {2003 Jul 17}, pages = {217-25}, abstract = {

Local axon degeneration is a common pathological feature of many neurodegenerative diseases and peripheral neuropathies. While it is believed to operate with an apoptosis-independent molecular program, the underlying molecular mechanisms are largely unknown. In this study, we used the degeneration of transected axons, termed "Wallerian degeneration," as a model to examine the possible involvement of the ubiquitin proteasome system (UPS). Inhibiting UPS activity by both pharmacological and genetic means profoundly delays axon degeneration both in vitro and in vivo. In addition, we found that the fragmentation of microtubules is the earliest detectable change in axons undergoing Wallerian degeneration, which among other degenerative events, can be delayed by proteasome inhibitors. Interestingly, similar to transected axons, degeneration of axons from nerve growth factor (NGF)-deprived sympathetic neurons could also be suppressed by proteasome inhibitors. Our findings suggest a possibility that inhibiting UPS activity may serve to retard axon degeneration in pathological conditions.

}, keywords = {Amino Acids, Animal, Animals, Axons, Benzimidazoles, Blotting, Calpain, Cells, Chelating Agents, Cultured, Cysteine Endopeptidases, Cysteine Proteinase Inhibitors, Cytoskeleton, Disease Models, Drug Interactions, Egtazic Acid, Endopeptidases, Ganglia, Immunohistochemistry, Leupeptins, Microtubules, Multienzyme Complexes, Nerve Growth Factor, Newborn, Optic Nerve, Optic Nerve Injuries, Peptide Fragments, Proteasome Endopeptidase Complex, Rats, Sympathetic, Time Factors, Tubulin, Ubiquitin, Wallerian Degeneration, Western}, issn = {0896-6273}, author = {Zhai, Qiwei and Wang, Jing and Kim, Anna and Liu, Qing and Watts, Ryan and Hoopfer, Eric and Mitchison, Timothy and Luo, Liqun and He, Zhigang} } @article {46637, title = {Mechanism of hedgehog signaling during Drosophila eye development.}, journal = {Development}, volume = {130}, year = {2003}, month = {2003 Jul}, pages = {3053-62}, abstract = {

Although Hedgehog (Hh) signaling is essential for morphogenesis of the Drosophila eye, its exact link to the network of tissue-specific genes that regulate retinal determination has remained elusive. In this report, we demonstrate that the retinal determination gene eyes absent (eya) is the crucial link between the Hedgehog signaling pathway and photoreceptor differentiation. Specifically, we show that the mechanism by which Hh signaling controls initiation of photoreceptor differentiation is to alleviate repression of eya and decapentaplegic (dpp) expression by the zinc-finger transcription factor Cubitus interruptus (Ci(rep)). Furthermore, our results suggest that stabilized, full length Ci (Ci(act)) plays little or no role in Drosophila eye development. Moreover, while the effects of Hh are primarily concentration dependent in other tissues, hh signaling in the eye acts as a binary switch to initiate retinal morphogenesis by inducing expression of the tissue-specific factor Eya.

}, keywords = {Animals, Cell Differentiation, DNA-Binding Proteins, Drosophila melanogaster, Drosophila Proteins, Eye Proteins, Hedgehog Proteins, Models, Biological, Morphogenesis, Organisms, Genetically Modified, Photoreceptor Cells, Invertebrate, Signal Transduction, Transcription Factors, Wing}, issn = {0950-1991}, author = {Pappu, Kartik S and Chen, Rui and Middlebrooks, Brooke W and Woo, Catherine and Heberlein, Ulrike and Mardon, Graeme} } @article {4481, title = {Microwave oven synthesis of esters promoted by imidazole.}, journal = {Tetrahedron Letters}, volume = {44}, year = {2003}, month = {2003 Feb 24}, pages = {1831-3}, abstract = {

Using imidazole as promotion agent, primary, secondary and phenolic alcohol compounds were esterified with aliphatic and aromatic carboxylic acid anhydrides. Heating a ternary mixture of alcohol, anhydride and imidazole in an unmodified microwave oven produced esters in low to high yields, depending on the steric bulk of the alcohol.

}, url = {http://www.sciencedirect.com/science/article/pii/S0040403903001047}, author = {Hirose, Takuji and Kopek, Benjamin G and Wang, Zhao-Hui and Yusa, Ritsuko and Baldwin, Bruce W.} } @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 {1591, title = {Purification, crystallization and preliminary crystallographic analysis of phosphoglucose isomerase from the hyperthermophilic archaeon Pyrococcus furiosus.}, journal = {Acta Crystallographica. Section D, Biological Crystallography}, volume = {59}, year = {2003}, month = {2003 Oct 19}, pages = {1822-3}, abstract = {

The glycolytic enzyme phosphoglucose isomerase catalyses the reversible isomerization of glucose 6-phosphate to fructose 6-phosphate. The phosphoglucose isomerase from the hyperthermophilic archaeon Pyrococcus furiosus, which shows no sequence similarity to any known bacterial or eukaryotic phosphoglucose isomerase, has been cloned and overexpressed in Escherichia coli, purified and subsequently crystallized by the hanging-drop method of vapour diffusion using 1.6 M sodium citrate as the precipitant at pH 6.5. Multiple-wavelength anomalous dispersive X-ray data have been collected to a maximum resolution of 1.92 A on a single selenomethionine-incorporated crystal. This crystal belongs to space group C2, with approximate unit-cell parameters a = 84.7

}, keywords = {Crystallization, Crystallography, Escherichia coli, Glucose-6-Phosphate Isomerase, Protein Conformation, Pyrococcus furiosus, Recombinant Proteins, Selenomethionine, X-Ray}, issn = {0907-4449}, author = {Akerboom, Jasper and Turnbull, Andrew P and Hargreaves, David and Fisher, Martin and de Geus, Daniel and Sedelnikova, Svetlana E and Berrisford, John M and Baker, Patrick J and Verhees, Corn{\'e} H and van der Oost, John and Rice, David W} } @article {1776, title = {The receptors for mammalian sweet and umami taste.}, journal = {Cell}, volume = {115}, year = {2003}, month = {2003 Oct 31}, pages = {255-66}, abstract = {

Sweet and umami (the taste of monosodium glutamate) are the main attractive taste modalities in humans. T1Rs are candidate mammalian taste receptors that combine to assemble two heteromeric G-protein-coupled receptor complexes: T1R1+3, an umami sensor, and T1R2+3, a sweet receptor. We now report the behavioral and physiological characterization of T1R1, T1R2, and T1R3 knockout mice. We demonstrate that sweet and umami taste are strictly dependent on T1R-receptors, and show that selective elimination of T1R-subunits differentially abolishes detection and perception of these two taste modalities. To examine the basis of sweet tastant recognition and coding, we engineered animals expressing either the human T1R2-receptor (hT1R2), or a modified opioid-receptor (RASSL) in sweet cells. Expression of hT1R2 in mice generates animals with humanized sweet taste preferences, while expression of RASSL drives strong attraction to a synthetic opiate, demonstrating that sweet cells trigger dedicated behavioral outputs, but their tastant selectivity is determined by the nature of the receptors.

}, keywords = {Animals, Flavoring Agents, G-Protein-Coupled, Gene Deletion, Humans, In Situ Hybridization, kappa, Knockout, Mice, Opioid, Protein Isoforms, Protein Subunits, Receptors, Sodium Glutamate, Sucrose, Taste, Taste Buds}, issn = {0092-8674}, author = {Zhao, Grace Q and Zhang, Yifeng and Hoon, Mark A and Chandrashekar, Jayaram and Erlenbach, Isolde and Ryba, Nicholas J P and Zuker, Charles S} } @article {788, title = {TGF-beta signaling activates steroid hormone receptor expression during neuronal remodeling in the Drosophila brain.}, journal = {Cell}, volume = {112}, year = {2003}, month = {2003 Feb 7}, pages = {303-15}, abstract = {

Metamorphosis of the Drosophila brain involves pruning of many larval-specific dendrites and axons followed by outgrowth of adult-specific processes. From a genetic mosaic screen, we recovered two independent mutations that block neuronal remodeling in the mushroom bodies (MBs). These phenotypically indistinguishable mutations affect Baboon function, a Drosophila TGF-beta/activin type I receptor, and dSmad2, its downstream transcriptional effector. We also show that Punt and Wit, two type II receptors, act redundantly in this process. In addition, knocking out dActivin around the mid-third instar stage interferes with remodeling. Binding of the insect steroid hormone ecdysone to distinct ecdysone receptor isoforms induces different metamorphic responses in various larval tissues. Interestingly, expression of the ecdysone receptor B1 isoform (EcR-B1) is reduced in activin pathway mutants, and restoring EcR-B1 expression significantly rescues remodeling defects. We conclude that the Drosophila Activin signaling pathway mediates neuronal remodeling in part by regulating EcR-B1 expression.

}, keywords = {Activin Receptors, Animals, Brain, Cell Differentiation, Cell Surface, DNA-Binding Proteins, Drosophila, Drosophila Proteins, Female, Genes, Larva, Lethal, Male, Missense, Mushroom Bodies, Mutation, Neural Pathways, Neuronal Plasticity, Neurons, Protein Isoforms, Proteins, Receptors, Signal Transduction, Smad2 Protein, Steroid, Trans-Activators, Transforming Growth Factor beta, Type I, Type II}, issn = {0092-8674}, author = {Zheng, Xiaoyan and Wang, Jian and Haerry, Theodor E and Wu, Ann Y-H and Martin, Josephine and O{\textquoteright}Connor, Michael B and Lee, Ching-Hsien J and Lee, Tzumin} } @article {46635, title = {Tre1, a G protein-coupled receptor, directs transepithelial migration of Drosophila germ cells.}, journal = {PLoS Biology}, volume = {1}, year = {2003}, month = {2003 Dec}, pages = {E80}, abstract = {

In most organisms, germ cells are formed distant from the somatic part of the gonad and thus have to migrate along and through a variety of tissues to reach the gonad. Transepithelial migration through the posterior midgut (PMG) is the first active step during Drosophila germ cell migration. Here we report the identification of a novel G protein-coupled receptor (GPCR), Tre1, that is essential for this migration step. Maternal tre1 RNA is localized to germ cells, and tre1 is required cell autonomously in germ cells. In tre1 mutant embryos, most germ cells do not exit the PMG. The few germ cells that do leave the midgut early migrate normally to the gonad, suggesting that this gene is specifically required for transepithelial migration and that mutant germ cells are still able to recognize other guidance cues. Additionally, inhibiting small Rho GTPases in germ cells affects transepithelial migration, suggesting that Tre1 signals through Rho1. We propose that Tre1 acts in a manner similar to chemokine receptors required during transepithelial migration of leukocytes, implying an evolutionarily conserved mechanism of transepithelial migration. Recently, the chemokine receptor CXCR4 was shown to direct migration in vertebrate germ cells. Thus, germ cells may more generally use GPCR signaling to navigate the embryo toward their target.

}, keywords = {Animals, Cell Movement, Cell Transplantation, Cloning, Molecular, Crosses, Genetic, Drosophila melanogaster, Drosophila Proteins, Embryo, Nonmammalian, Epithelium, Evolution, Molecular, Female, Gene Expression Regulation, Germ Cells, Humans, Immunohistochemistry, In Situ Hybridization, Inflammation, Leukocytes, Male, Models, Biological, Molecular Sequence Data, Mutation, Phenotype, Phylogeny, Receptors, Chemokine, Receptors, G-Protein-Coupled, rho GTP-Binding Proteins, RNA, Signal Transduction}, issn = {1545-7885}, doi = {10.1371/journal.pbio.0000080}, author = {Kunwar, Prabhat S and Starz-Gaiano, Michelle and Bainton, Roland J and Heberlein, Ulrike and Lehmann, Ruth} } @article {1778, title = {An amino-acid taste receptor.}, journal = {Nature}, volume = {416}, year = {2002}, month = {2002 Mar 14}, pages = {199-202}, abstract = {

The sense of taste provides animals with valuable information about the nature and quality of food. Mammals can recognize and respond to a diverse repertoire of chemical entities, including sugars, salts, acids and a wide range of toxic substances. Several amino acids taste sweet or delicious (umami) to humans, and are attractive to rodents and other animals. This is noteworthy because L-amino acids function as the building blocks of proteins, as biosynthetic precursors of many biologically relevant small molecules, and as metabolic fuel. Thus, having a taste pathway dedicated to their detection probably had significant evolutionary implications. Here we identify and characterize a mammalian amino-acid taste receptor. This receptor, T1R1+3, is a heteromer of the taste-specific T1R1 and T1R3 G-protein-coupled receptors. We demonstrate that T1R1 and T1R3 combine to function as a broadly tuned L-amino-acid sensor responding to most of the 20 standard amino acids, but not to their D-enantiomers or other compounds. We also show that sequence differences in T1R receptors within and between species (human and mouse) can significantly influence the selectivity and specificity of taste responses.

}, keywords = {Alleles, Amino Acids, Animals, Calcium Signaling, Cell Line, Cell Surface, Chorda Tympani Nerve, Dose-Response Relationship, Drug, G-Protein-Coupled, Genetic, Heterotrimeric GTP-Binding Proteins, Humans, Inosine Monophosphate, Mice, Mutation, Polymorphism, Protein Subunits, Receptors, Stereoisomerism, Structure-Activity Relationship, Substrate Specificity, Taste, Taste Buds, Transfection}, issn = {0028-0836}, doi = {10.1038/nature726}, author = {Nelson, Greg and Chandrashekar, Jayaram and Hoon, Mark A and Feng, Luxin and Zhao, Grace and Ryba, Nicholas J P and Zuker, Charles S} } @article {2683, title = {Basic transcription element binding protein is a thyroid hormone-regulated transcription factor expressed during metamorphosis in Xenopus laevis.}, journal = {Development, Growth \& Differentiation}, volume = {44}, year = {2002}, month = {2002 Oct}, pages = {365-81}, abstract = {

Basic transcription element binding protein (BTEB) is a member of the Kr{\"u}ppel family of zinc finger transcription factors. It has been shown that BTEB plays a role in promoting neuronal process formation during postembryonic development. In the present study, the biochemical properties, transactivation function, and the developmental and hormone-regulated expression of BTEB in Xenopus laevis (xBTEB) are described. xBTEB binds the GC-rich basic transcription element (BTE) with high affinity and functions as a transcriptional activator on promoters containing multiple or single GC boxes. xBTEB mRNA levels increase in the tadpole brain, intestine and tail during metamorphosis, and are correlated with tissue-specific morphological and biochemical transformations. xBTEB mRNA expression can be induced precociously in premetamorphic tadpole tissues by treatment with thyroid hormone. In situ hybridization histochemistry showed that thyroid hormone upregulates xBTEB mRNA throughout the brain of premetamorphic tadpoles, with the highest expression found in the subventricular zones of the telencephalon, diencephalon, optic tectum, cerebellum and spinal cord. xBTEB protein parallels changes in its mRNA, and it was found that xBTEB is not expressed in mitotic cells in the developing brain, but is expressed just distal to the proliferative zone, supporting the hypothesis that this protein plays a role in neural cell differentiation.

}, keywords = {Animals, Biological, Blotting, Brain, Cell Division, DNA-Binding Proteins, Genetic, Kruppel-Like Transcription Factors, Metamorphosis, Northern, Promoter Regions, Rats, Receptors, Thyroid Hormone, Transcription Factors, Triiodothyronine, Up-Regulation, Xenopus laevis, Xenopus Proteins}, issn = {0012-1592}, author = {Hoopfer, Eric D and Huang, Liyue and Denver, Robert J} } @article {2143, title = {Conditional loss of Nkx3.1 in adult mice induces prostatic intraepithelial neoplasia.}, journal = {Molecular and Cellular Biology}, volume = {22}, year = {2002}, month = {2002 Mar}, pages = {1495-503}, abstract = {

The homeodomain-containing transcription factor NKX3.1 is a putative prostate tumor suppressor that is expressed in a largely prostate-specific and androgen-regulated manner. Loss of NKX3.1 protein expression is common in human prostate carcinomas and prostatic intraepithelial neoplasia (PIN) lesions and correlates with tumor progression. Disruption of the murine Nkx3.1 gene results in defects in prostate branching morphogenesis, secretions, and growth. To more closely mimic the pattern of NKX3.1 loss that occurs in human prostate tumors, we have used Cre- and loxP-mediated recombination to delete the Nkx3.1 gene in the prostates of adult transgenic mice. Conditional deletion of one or both alleles of Nkx3.1 leads to the development of preinvasive lesions that resemble PIN. The pattern of expression of several biomarkers (Ki-67, E-cadherin, and high-molecular-weight cytokeratins) in these PIN lesions resembled that observed in human cases of PIN. Furthermore, PIN foci in mice with conditional deletion of a single Nkx3.1 allele lose expression of the wild-type allele. Our results support the role of NKX3.1 as a prostate tumor suppressor and indicate a role for this gene in tumor initiation.

}, keywords = {Animals, Gene Deletion, Genes, Genetic Predisposition to Disease, Homeodomain Proteins, Homozygote, Hyperplasia, Integrases, Male, Mice, Prostate, Prostatic Intraepithelial Neoplasia, Prostatic Neoplasms, Transcription Factors, Transgenic, Tumor Suppressor, Viral Proteins}, issn = {0270-7306}, doi = {10.1002/cbic.201000254}, author = {Abdulkadir, Sarki A and Magee, Jeffrey A and Peters, Thomas J and Kaleem, Zahid and Naughton, Cathy K and Humphrey, Peter A and Milbrandt, Jeffrey} } @article {2189, title = {Dissecting glucose signalling with diversity-oriented synthesis and small-molecule microarrays.}, journal = {Nature}, volume = {416}, year = {2002}, month = {2002 Apr 11}, pages = {653-7}, abstract = {

Small molecules that alter protein function provide a means to modulate biological networks with temporal resolution. Here we demonstrate a potentially general and scalable method of identifying such molecules by application to a particular protein, Ure2p, which represses the transcription factors Gln3p and Nil1p. By probing a high-density microarray of small molecules generated by diversity-oriented synthesis with fluorescently labelled Ure2p, we performed 3,780 protein-binding assays in parallel and identified several compounds that bind Ure2p. One compound, which we call uretupamine, specifically activates a glucose-sensitive transcriptional pathway downstream of Ure2p. Whole-genome transcription profiling and chemical epistasis demonstrate the remarkable Ure2p specificity of uretupamine and its ability to modulate the glucose-sensitive subset of genes downstream of Ure2p. These results demonstrate that diversity-oriented synthesis and small-molecule microarrays can be used to identify small molecules that bind to a protein of interest, and that these small molecules can regulate specific functions of the protein.

}, keywords = {Biological, Dioxanes, Dose-Response Relationship, Drug, Fungal, Gene Expression Profiling, Gene Expression Regulation, Genetic, Glucose, Glutathione Peroxidase, Ligands, Messenger, Models, Oligonucleotide Array Sequence Analysis, Oxazoles, Prions, Protein Binding, Repressor Proteins, RNA, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Signal Transduction, Structure-Activity Relationship, Substrate Specificity, Transcription}, issn = {0028-0836}, doi = {10.1038/416653a}, author = {Kuruvilla, Finny G and Shamji, Alykhan F and Sternson, Scott M and Hergenrother, Paul J and Schreiber, Stuart L} } @article {46638, title = {Drugs, flies, and videotape: the effects of ethanol and cocaine on Drosophila locomotion.}, journal = {Current Opinion in Neurobiology}, volume = {12}, year = {2002}, month = {2002 Dec}, pages = {639-45}, abstract = {

Drosophila melanogaster has been introduced recently as a model organism in which to study the mechanisms by which drugs of abuse change behavior and by which the nervous system changes upon repeated drug exposure. Surprising similarities between flies and mammals have begun to emerge at the behavioral, neurochemical and molecular levels.

}, keywords = {Animals, Behavior, Animal, Circadian Rhythm, Cocaine, Cyclic AMP, Dopamine, Drosophila melanogaster, Drug Tolerance, Ethanol, Locomotion}, issn = {0959-4388}, author = {Rothenfluh, Adrian and Heberlein, Ulrike} } @article {5493, title = {Functional dissection of neuroanatomical loci regulating ethanol sensitivity in Drosophila.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {22}, year = {2002}, month = {2002 Nov 1}, pages = {9490-501}, abstract = {

Ethanol has complex but similar effects on behavior in mammals and the fruit fly Drosophila melanogaster. In addition, genetic and pharmacological approaches have implicated the cAMP pathway in the regulation of ethanol-induced behaviors in both flies and rodents. Here we examine the neuroanatomical loci that modulate ethanol sensitivity in Drosophila by targeting the expression of an inhibitor of cAMP-dependent protein kinase (PKA) to specific regions in the fly{\textquoteright}s brain. Expression of the inhibitor in most brain regions or in muscle has no effect on behavior. In contrast, inhibition of PKA in a relatively small number of cells, possibly neurosecretory cells, in the fly{\textquoteright}s brain is sufficient to decrease sensitivity to the incoordinating effects of ethanol. Additional brain areas are, however, also involved. The mushroom bodies, brain structures where cAMP signaling is required for olfactory classical conditioning, are dispensable for the regulation of ethanol sensitivity. Finally, different behavioral effects of ethanol, motor incoordination and sedation, appear to be regulated by PKA function in distinct brain regions. We conclude that the regulation of ethanol-induced behaviors by PKA involves complex interactions among groups of cells that mediate either increased or reduced sensitivity to the acute intoxicating effects of ethanol.

}, keywords = {Administration, Animal, Animals, Behavior, Catalytic Domain, Cyclic AMP-Dependent Protein Kinases, DNA-Binding Proteins, Drosophila melanogaster, Drug Resistance, Ethanol, Gene Expression, Genes, Genetically Modified, Hydroxyurea, Inhalation, Larva, Locomotion, Male, Motor Activity, Mushroom Bodies, Nervous System, Organ Specificity, Protein Subunits, Reporter, Saccharomyces cerevisiae Proteins, Transcription Factors, Transgenes}, issn = {1529-2401}, author = {Rodan, Aylin R and Kiger, John A and Heberlein, Ulrike} } @article {1259, title = {Geometry and structural plasticity of synaptic connectivity.}, journal = {Neuron}, volume = {34}, year = {2002}, month = {2002 Apr 11}, pages = {275-88}, abstract = {

Changes in synaptic connectivity patterns through the formation and elimination of dendritic spines may contribute to structural plasticity in the brain. We characterize this contribution quantitatively by estimating the number of different synaptic connectivity patterns attainable without major arbor remodeling. This number depends on the ratio of the synapses on a dendrite to the axons that pass within a spine length of that dendrite. We call this ratio the filling fraction and calculate it from geometrical analysis and anatomical data. The filling fraction is 0.26 in mouse neocortex, 0.22-0.34 in rat hippocampus. In the macaque visual cortex, the filling fraction increases by a factor of 1.6-1.8 from area V1 to areas V2, V4, and 7a. Since the filling fraction is much smaller than 1, spine remodeling can make a large contribution to structural plasticity.

}, keywords = {Animals, Macaca fascicularis, Male, Models, Neural Pathways, Neurological, Neuronal Plasticity, Synapses}, issn = {0896-6273}, doi = {10.1016/j.tins.2005.05.006}, author = {Stepanyants, Armen and Hof, Patrick R and Chklovskii, Dmitri B} } @article {5492, title = {High-resolution analysis of ethanol-induced locomotor stimulation in Drosophila.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {22}, year = {2002}, month = {2002 Dec 15}, pages = {11035-44}, abstract = {

Understanding how ethanol influences behavior is key to deciphering the mechanisms of ethanol action and alcoholism. In mammals, low doses of ethanol stimulate locomotion, whereas high doses depress it. The acute stimulant effect of ethanol has been proposed to be a manifestation of its rewarding effects. In Drosophila, ethanol exposure transiently potentiates locomotor activity in a biphasic dose- and time-dependent manner. An initial short-lived peak of activity corresponds to an olfactory response to ethanol. A second, longer-lasting period of increased activity coincides with rising internal ethanol concentrations; these closely parallel concentrations that stimulate locomotion in mammals. High-resolution analysis of the walking pattern of individual flies revealed that locomotion consists of bouts of activity; bout structure can be quantified by bout frequency, bout length, and the time spent walking at high speeds. Ethanol exposure induces both dramatic and dynamic changes in bout structure. Mutants with increased ethanol sensitivity show distinct changes in ethanol-induced locomotor behavior, as well as genotype-specific changes in activity bout structure. Thus, the overall effect of ethanol on locomotor behavior in Drosophila is caused by changes in discrete quantifiable parameters of walking pattern. The effects of ethanol on locomotion are comparable in flies and mammals, suggesting that Drosophila is a suitable model system to study the underlying mechanisms.

}, keywords = {Afferent Pathways, Animal, Animals, Automation, Behavior, Cyclic AMP, Dose-Response Relationship, Drosophila, Drug, Ethanol, Kinetics, Locomotion, Male, Mutation, Sensitivity and Specificity}, issn = {1529-2401}, author = {Wolf, Fred W and Rodan, Aylin R and Tsai, Linus T-Y and Heberlein, Ulrike} } @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 {46640, title = {Rough eye is a gain-of-function allele of amos that disrupts regulation of the proneural gene atonal during Drosophila retinal differentiation.}, journal = {Genetics}, volume = {160}, year = {2002}, month = {2002 Feb}, pages = {623-35}, abstract = {

The regular organization of the ommatidial lattice in the Drosophila eye originates in the precise regulation of the proneural gene atonal (ato), which is responsible for the specification of the ommatidial founder cells R8. Here we show that Rough eye (Roi), a dominant mutation manifested by severe roughening of the adult eye surface, causes defects in ommatidial assembly and ommatidial spacing. The ommatidial spacing defect can be ascribed to the irregular distribution of R8 cells caused by a disruption of the patterning of ato expression. Disruptions in the recruitment of other photoreceptors and excess Hedgehog production in differentiating cells may further contribute to the defects in ommatidial assembly. Our molecular characterization of the Roi locus demonstrates that it is a gain-of-function mutation of the bHLH gene amos that results from a chromosomal inversion. We show that Roi can rescue the retinal developmental defect of ato1 mutants and speculate that amos substitutes for some of ato{\textquoteright}s function in the eye or activates a residual function of the ato1 allele.

}, keywords = {Alleles, Animals, Basic Helix-Loop-Helix Transcription Factors, DNA-Binding Proteins, Drosophila melanogaster, Drosophila Proteins, Epistasis, Genetic, Gene Expression Regulation, Developmental, Nerve Growth Factors, Nerve Tissue Proteins, Retina, Signal Transduction, Transgenes}, issn = {0016-6731}, author = {Chanut, Fran{\c c}oise and Woo, Katherine and Pereira, Shalini and Donohoe, Terrence J and Chang, Shang-Yu and Laverty, Todd R and Jarman, Andrew P and Heberlein, Ulrike} } @article {2427, title = {TRF2 associates with DREF and directs promoter-selective gene expression in Drosophila.}, journal = {Nature}, volume = {420}, year = {2002}, month = {2002 Nov 28}, pages = {439-45}, abstract = {

Drosophila TATA-box-binding protein (TBP)-related factor 2 (TRF2) is a member of a family of TBP-related factors present in metazoan organisms. Recent evidence suggests that TRF2s are required for proper embryonic development and differentiation. However, true target promoters and the mechanisms by which TRF2 operates to control transcription remain elusive. Here we report the antibody affinity purification of a Drosophila TRF2-containing complex that contains components of the nucleosome remodelling factor (NURF) chromatin remodelling complex as well as the DNA replication-related element (DRE)-binding factor DREF. This latter finding led us to potential target genes containing TRF2-responsive promoters. We have used a combination of in vitro and in vivo assays to show that the DREF-containing TRF2 complex directs core promoter recognition of the proliferating cell nuclear antigen (PCNA) gene. We also identified additional TRF2-responsive target genes involved in DNA replication and cell proliferation. These data suggest that TRF2 functions as a core promoter-selectivity factor responsible for coordinating transcription of a subset of genes in Drosophila.

}, keywords = {Animals, Cell Line, Chromatin, Drosophila, Drosophila Proteins, Gene Expression Regulation, Genes, Genetic, Insect, Macromolecular Substances, Nuclease Protection Assays, Oligonucleotide Array Sequence Analysis, Precipitin Tests, Proliferating Cell Nuclear Antigen, Promoter Regions, Protein Binding, RNA Interference, Substrate Specificity, Telomeric Repeat Binding Protein 2, Transcription Factors, Transcription Initiation Site}, issn = {0028-0836}, doi = {10.1073/pnas.1100640108}, author = {Hochheimer, Andreas and Zhou, Sharleen and Zheng, Shuang and Holmes, Michael C and Tjian, Robert} } @article {1142, title = {Are complex behaviors specified by dedicated regularoty genes? Reasoning from Drosophila.}, journal = {Cell}, volume = {105}, year = {2001}, month = {2001 Apr 6}, pages = {13-24}, issn = {0092-8674}, author = {Baker, B.S. and Taylor, B.T. and Hall, Jeffrey C} } @article {1561, title = {Conversion of a maltose receptor into a zinc biosensor by computational design.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {98}, year = {2001}, month = {2001 Apr 24}, pages = {4955-60}, abstract = {

We have demonstrated that it is possible to radically change the specificity of maltose binding protein by converting it into a zinc sensor using a rational design approach. In this new molecular sensor, zinc binding is transduced into a readily detected fluorescence signal by use of an engineered conformational coupling mechanism linking ligand binding to reporter group response. An iterative progressive design strategy led to the construction of variants with increased zinc affinity by combining binding sites, optimizing the primary coordination sphere, and exploiting conformational equilibria. Intermediates in the design series show that the adaptive process involves both introduction and optimization of new functions and removal of adverse vestigial interactions. The latter demonstrates the importance of the rational design approach in uncovering cryptic phenomena in protein function, which cannot be revealed by the study of naturally evolved systems.

}, keywords = {Alanine, Allosteric Regulation, Bacterial Proteins, Binding Sites, Biosensing Techniques, Calorimetry, Carrier Proteins, Computer Simulation, Fluorescence, Kinetics, Ligands, Maltose, Maltose-Binding Proteins, Models, Molecular, Mutation, Protein Conformation, Protein Engineering, Signal Transduction, Software, Substrate Specificity, Temperature, Thermodynamics, Zinc}, issn = {0027-8424}, doi = {10.1073/pnas.091083898}, author = {Marvin, J S and Hellinga, H W} } @article {46641, title = {Drosophila fasciclinII is required for the formation of odor memories and for normal sensitivity to alcohol.}, journal = {Cell}, volume = {105}, year = {2001}, month = {2001 Jun 15}, pages = {757-68}, abstract = {

Drosophila fasciclinII (fasII) mutants perform poorly after olfactory conditioning due to a defect in encoding, stabilizing, or retrieving short-term memories. Performance was rescued by inducing the expression of a normal transgene just before training and immediate testing. Induction after training but before testing failed to rescue performance, showing that Fas II does not have an exclusive role in memory retrieval processes. The stability of odor memories in fasII mutants are indistinguishable from control animals when initial performance is normalized. Like several other mutants deficient in odor learning, fasII mutants exhibit a heightened sensitivity to ethanol vapors. A combination of behavioral and genetic strategies have therefore revealed a role for Fas II in the molecular operations of encoding short-term odor memories and conferring alcohol sensitivity. The preferential expression of Fas II in the axons of mushroom body neurons furthermore suggests that short-term odor memories are formed in these neurites.

}, keywords = {Animals, Animals, Genetically Modified, Axons, Brain Chemistry, Cell Adhesion Molecules, Neuronal, Conditioning, Classical, Drosophila melanogaster, Electroshock, Ethanol, Gene Expression Regulation, Male, Memory, Short-Term, Mutation, Neurons, Odors, Smell}, issn = {0092-8674}, author = {Cheng, Y and Endo, K and Wu, K and Rodan, A R and Heberlein, U and Davis, R L} } @article {46417, title = {Life on carbon monoxide: X-ray structure of Rhodospirillum rubrum Ni-Fe-S carbon monoxide dehydrogenase. }, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {98}, year = {2001}, month = {2001-10-09}, pages = {11973-8}, abstract = {

A crystal structure of the anaerobic Ni-Fe-S carbon monoxide dehydrogenase (CODH) from Rhodospirillum rubrum has been determined to 2.8-{\r A} resolution. The CODH family, for which the R. rubrum enzyme is the prototype, catalyzes the biological oxidation of CO at an unusual Ni-Fe-S cluster called the C-cluster. The Ni-Fe-S C-cluster contains a mononuclear site and a four-metal cubane. Surprisingly, anomalous dispersion data suggest that the mononuclear site contains Fe and not Ni, and the four-metal cubane has the form [NiFe3S4] and not [Fe4S4]. The mononuclear site and the four-metal cluster are bridged by means of Cys531 and one of the sulfides of the cube. CODH is organized as a dimer with a previously unidentified [Fe4S4] cluster bridging the two subunits. Each monomer is comprised of three domains: a helical domain at the N terminus, an α/β (Rossmann-like) domain in the middle, and an α/β (Rossmann-like) domain at the C terminus. The helical domain contributes ligands to the bridging [Fe4S4] cluster and another [Fe4S4] cluster, the B-cluster, which is involved in electron transfer. The two Rossmann domains contribute ligands to the active site C-cluster. This x-ray structure provides insight into the mechanism of biological CO oxidation and has broader significance for the roles of Ni and Fe in biological systems.

}, issn = {1091-6490}, doi = {10.1073/pnas.211429998}, author = {Drennan, Catherine L and Heo, Jongyun and Sintchak, Michael D and Schreiter, Eric R and Ludden, Paul W.} } @article {1780, title = {Mammalian sweet taste receptors.}, journal = {Cell}, volume = {106}, year = {2001}, month = {2001 Aug 10}, pages = {381-90}, abstract = {

The sense of taste provides animals with valuable information about the quality and nutritional value of food. Previously, we identified a large family of mammalian taste receptors involved in bitter taste perception (the T2Rs). We now report the characterization of mammalian sweet taste receptors. First, transgenic rescue experiments prove that the Sac locus encodes T1R3, a member of the T1R family of candidate taste receptors. Second, using a heterologous expression system, we demonstrate that T1R2 and T1R3 combine to function as a sweet receptor, recognizing sweet-tasting molecules as diverse as sucrose, saccharin, dulcin, and acesulfame-K. Finally, we present a detailed analysis of the patterns of expression of T1Rs and T2Rs, thus providing a view of the representation of sweet and bitter taste at the periphery.

}, keywords = {Animals, Calcium Signaling, Cell Line, Cell Surface, Chromosomes, Cricetinae, Evolution, G-Protein-Coupled, Gene Expression Profiling, Genetic Complementation Test, Heterotrimeric GTP-Binding Proteins, Human, Humans, Messenger, Mice, Molecular, Molecular Sequence Data, Multigene Family, Pair 4, Phenylurea Compounds, Physical Chromosome Mapping, Receptors, RNA, Saccharin, Substrate Specificity, Sucrose, Sweetening Agents, Taste, Taste Buds, Thiazines, Transgenic}, issn = {0092-8674}, author = {Nelson, G and Hoon, M A and Chandrashekar, J and Zhang, Y and Ryba, N J and Zuker, C S} } @article {1560, title = {Manipulation of ligand binding affinity by exploitation of conformational coupling.}, journal = {Nature Structural Biology}, volume = {8}, year = {2001}, month = {2001 Sep 27}, pages = {795-8}, abstract = {

Traditional approaches for increasing the affinity of a protein for its ligand focus on constructing improved surface complementarity in the complex by altering the protein binding site to better fit the ligand. Here we present a novel strategy that leaves the binding site intact, while residues that allosterically affect binding are mutated. This method takes advantage of conformationally distinct states, each with different ligand-binding affinities, and manipulates the equilibria between these conformations. We demonstrate this approach in the Escherichia coli maltose binding protein by introducing mutations, located at some distance from the ligand binding pocket, that sterically affect the equilibrium between an open, apo-state and a closed, ligand-bound state. A family of 20 variants was generated with affinities ranging from an approximately 100-fold improvement (7.4 nM) to an approximately two-fold weakening (1.8 mM) relative to the wild type protein (800 nM).

}, keywords = {Allosteric Regulation, Allosteric Site, Apoproteins, ATP-Binding Cassette Transporters, Calorimetry, Carrier Proteins, Escherichia coli, Escherichia coli Proteins, Kinetics, Ligands, Maltose, Maltose-Binding Proteins, Models, Molecular, Monosaccharide Transport Proteins, Mutation, Protein Binding, Protein Conformation, Protein Engineering, Temperature, Thermodynamics}, issn = {1072-8368}, doi = {10.1038/nsb0901-795}, author = {Marvin, J S and Hellinga, H W} } @article {2707, title = {The sequence of the human genome.}, journal = {Science}, volume = {291}, year = {2001}, month = {2001 Feb 16}, pages = {1304-51}, abstract = {

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90\% of the genome is in scaffold assemblies of 100,000 bp or more, and 25\% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1\% of the genome is spanned by exons, whereas 24\% is in introns, with 75\% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1\% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

}, keywords = {Algorithms, Animals, Artificial, Bacterial, Chromosome Banding, Chromosome Mapping, Chromosomes, Computational Biology, Consensus Sequence, CpG Islands, Databases, DNA, Evolution, Exons, Factual, Female, Gene Duplication, Genes, Genetic Variation, Genome, Human, Human Genome Project, Humans, Intergenic, Introns, Male, Molecular, Nucleic Acid, Phenotype, Physical Chromosome Mapping, Polymorphism, Proteins, Pseudogenes, Repetitive Sequences, Retroelements, Sequence Analysis, Single Nucleotide, Species Specificity}, issn = {0036-8075}, doi = {10.1126/science.1058040}, author = {Venter, J C and Adams, M D and Myers, E W and Li, P W and Mural, R J and Sutton, G G and Smith, H O and Yandell, M and Evans, C A and Holt, R A and Gocayne, J D and Amanatides, P and Ballew, R M and Huson, D H and Wortman, J R and Zhang, Q and Kodira, C D and Zheng, X H and Chen, L and Skupski, M and Subramanian, G and Thomas, P D and Zhang, J and Gabor Miklos, G L and Nelson, C and Broder, S and Clark, A G and Nadeau, J and McKusick, V A and Zinder, N and Levine, A J and Roberts, R J and Simon, M and Slayman, C and Hunkapiller, M and Bolanos, R and Delcher, A and Dew, I and Fasulo, D and Flanigan, M and Florea, L and Halpern, A and Hannenhalli, S and Kravitz, S and Levy, S and Mobarry, C and Reinert, K and Remington, K and Abu-Threideh, J and Beasley, E and Biddick, K and Bonazzi, V and Brandon, R and Cargill, M and Chandramouliswaran, I and Charlab, R and Chaturvedi, K and Deng, Z and Di Francesco, V and Dunn, P and Eilbeck, K and Evangelista, C and Gabrielian, A E and Gan, W and Ge, W and Gong, F and Gu, Z and Guan, P and Heiman, T J and Higgins, M E and Ji, R R and Ke, Z and Ketchum, K A and Lai, Z and Lei, Y and Li, Z and Li, J and Liang, Y and Lin, X and Lu, F and Merkulov, G V and Milshina, N and Moore, H M and Naik, A K and Narayan, V A and Neelam, B and Nusskern, D and Rusch, D B and Salzberg, S and Shao, W and Shue, B and Sun, J and Wang, Z and Wang, A and Wang, X and Wang, J and Wei, M and Wides, R and Xiao, C and Yan, C and Yao, A and Ye, J and Zhan, M and Zhang, W and Zhang, H and Zhao, Q and Zheng, L and Zhong, F and Zhong, W and Zhu, S and Zhao, S and Gilbert, D and Baumhueter, S and Spier, G and Carter, C and Cravchik, A and Woodage, T and Ali, F and An, H and Awe, A and Baldwin, D and Baden, H and Barnstead, M and Barrow, I and Beeson, K and Busam, D and Carver, A and Center, A and Cheng, M L and Curry, L and Danaher, S and Davenport, L and Desilets, R and Dietz, S and Dodson, K and Doup, L and Ferriera, S and Garg, N and Gluecksmann, A and Hart, B and Haynes, J and Haynes, C and Heiner, C and Hladun, S and Hostin, D and Houck, J and Howland, T and Ibegwam, C and Johnson, J and Kalush, F and Kline, L and Koduru, S and Love, A and Mann, F and May, D and McCawley, S and McIntosh, T and McMullen, I and Moy, M and Moy, L and Murphy, B and Nelson, K and Pfannkoch, C and Pratts, E and Puri, V and Qureshi, H and Reardon, M and Rodriguez, R and Rogers, Y H and Romblad, D and Ruhfel, B and Scott, R and Sitter, C and Smallwood, M and Stewart, E and Strong, R and Suh, E and Thomas, R and Tint, N N and Tse, S and Vech, C and Wang, G and Wetter, J and Williams, S and Williams, M and Windsor, S and Winn-Deen, E and Wolfe, K and Zaveri, J and Zaveri, K and Abril, J F and Guig{\'o}, R and Campbell, M J and Sjolander, K V and Karlak, B and Kejariwal, A and Mi, H and Lazareva, B and Hatton, T and Narechania, A and Diemer, K and Muruganujan, A and Guo, N and Sato, S and Bafna, V and Istrail, S and Lippert, R and Schwartz, R and Walenz, B and Yooseph, S and Allen, D and Basu, A and Baxendale, J and Blick, L and Caminha, M and Carnes-Stine, J and Caulk, P and Chiang, Y H and Coyne, M and Dahlke, C and Mays, A and Dombroski, M and Donnelly, M and Ely, D and Esparham, S and Fosler, C and Gire, H and Glanowski, S and Glasser, K and Glodek, A and Gorokhov, M and Graham, K and Gropman, B and Harris, M and Heil, J and Henderson, S and Hoover, J and Jennings, D and Jordan, C and Jordan, J and Kasha, J and Kagan, L and Kraft, C and Levitsky, A and Lewis, M and Liu, X and Lopez, J and Ma, D and Majoros, W and McDaniel, J and Murphy, S and Newman, M and Nguyen, T and Nguyen, N and Nodell, M and Pan, S and Peck, J and Peterson, M and Rowe, W and Sanders, R and Scott, J and Simpson, M and Smith, T and Sprague, A and Stockwell, T and Turner, R and Venter, E and Wang, M and Wen, M and Wu, D and Wu, M and Xia, A and Zandieh, A and Zhu, X} } @article {958, title = {Comparative genomics of the eukaryotes.}, journal = {Science}, volume = {287}, year = {2000}, month = {2000 Mar 24}, pages = {2204-15}, abstract = {

A comparative analysis of the genomes of Drosophila melanogaster, Caenorhabditis elegans, and Saccharomyces cerevisiae-and the proteins they are predicted to encode-was undertaken in the context of cellular, developmental, and evolutionary processes. The nonredundant protein sets of flies and worms are similar in size and are only twice that of yeast, but different gene families are expanded in each genome, and the multidomain proteins and signaling pathways of the fly and worm are far more complex than those of yeast. The fly has orthologs to 177 of the 289 human disease genes examined and provides the foundation for rapid analysis of some of the basic processes involved in human disease.

}, keywords = {Animals, Apoptosis, Biological Evolution, Caenorhabditis elegans, Cell Adhesion, Cell Cycle, Drosophila melanogaster, Duplicate, Fungal Proteins, Genes, Genetic Diseases, Genetics, Genome, Helminth Proteins, Humans, Immunity, Inborn, Insect Proteins, Medical, Multigene Family, Neoplasms, Protein Structure, Proteome, Saccharomyces cerevisiae, Signal Transduction, Tertiary}, issn = {0036-8075}, doi = {10.1186/gb-2007-8-7-r145}, author = {Rubin, G M and Yandell, M D and Wortman, J R and Gabor Miklos, G L and Nelson, C R and Hariharan, I K and Fortini, M E and Li, P W and Apweiler, R and Fleischmann, W and Cherry, J M and Henikoff, S and Skupski, M P and Misra, S and Ashburner, M and Birney, E and Boguski, M S and Brody, T and Brokstein, P and Celniker, S E and Chervitz, S A and Coates, D and Cravchik, A and Gabrielian, A and Galle, R F and Gelbart, W M and George, R A and Goldstein, L S and Gong, F and Guan, P and Harris, N L and Hay, B A and Hoskins, R A and Li, J and Li, Z and Hynes, R O and Jones, S J and Kuehl, P M and Lemaitre, B and Littleton, J T and Morrison, D K and Mungall, C and O{\textquoteright}Farrell, P H and Pickeral, O K and Shue, C and Vosshall, L B and Zhang, J and Zhao, Q and Zheng, X H and Lewis, S} } @article {45914, title = {Diversity and dynamics of dendritic signaling.}, journal = {Science}, volume = {290}, year = {2000}, month = {2000 Oct 27}, pages = {739-44}, abstract = {

Communication between neurons in the brain occurs primarily through synapses made onto elaborate treelike structures called dendrites. New electrical and optical recording techniques have led to tremendous advances in our understanding of how dendrites contribute to neuronal computation in the mammalian brain. The varied morphology and electrical and chemical properties of dendrites enable a spectrum of local and long-range signaling, defining the input-output relationship of neurons and the rules for induction of synaptic plasticity. In this way, diversity in dendritic signaling allows individual neurons to carry out specialized functions within their respective networks.

}, keywords = {Action Potentials, Animals, Brain, Calcium Signaling, Dendrites, Electrophysiology, Humans, Ion Channel Gating, Ion Channels, Neuronal Plasticity, Neurons, Neurotransmitter Agents, Protein Biosynthesis, Signal Transduction, Synapses, Synaptic Transmission}, issn = {0036-8075}, author = {H{\"a}usser, M and Spruston, N and Stuart, G J} } @article {5495, title = {Dopamine modulates acute responses to cocaine, nicotine and ethanol in Drosophila.}, journal = {Current Biology}, volume = {10}, year = {2000}, month = {2000 Feb 24}, pages = {187-94}, abstract = {

Drugs of abuse have a common property in mammals, which is their ability to facilitate the release of the neurotransmitter and neuromodulator dopamine in specific brain regions involved in reward and motivation. This increase in synaptic dopamine levels is believed to act as a positive reinforcer and to mediate some of the acute responses to drugs. The mechanisms by which dopamine regulates acute drug responses and addiction remain unknown.

}, keywords = {Animal, Animals, Behavior, Cocaine, Dopamine, Drosophila, Ethanol, Male, Nicotine}, issn = {0960-9822}, author = {Bainton, R J and Tsai, L T and Singh, C M and Moore, M S and Neckameyer, W S and Heberlein, U} } @article {46644, title = {Early retinal development in Drosophila.}, journal = {Results and Problems in Cell Differentiation}, volume = {31}, year = {2000}, month = {2000}, pages = {37-50}, keywords = {Animals, Cell Differentiation, Drosophila melanogaster, Retina}, issn = {0080-1844}, author = {Heberlein, U and Treisman, J E} } @article {5494, title = {Functional ethanol tolerance in Drosophila.}, journal = {Neuron}, volume = {28}, year = {2000}, month = {2000 Oct}, pages = {261-71}, abstract = {

In humans, repeated alcohol consumption leads to the development of tolerance, manifested as a reduced physiological and behavioral response to a particular dose of alcohol. Here we show that adult Drosophila develop tolerance to the sedating and motor-impairing effects of ethanol with kinetics of acquisition and dissipation that mimic those seen in mammals. Importantly, this tolerance is not caused by changes in ethanol absorption or metabolism. Rather, the development of tolerance requires the functional and structural integrity of specific central brain regions. Mutants unable to synthesize the catecholamine octopamine are also impaired in their ability to develop tolerance. Taken together, these data show that Drosophila is a suitable model system in which to study the molecular and neuroanatomical bases of ethanol tolerance.

}, keywords = {Animal, Animals, Behavior, Biological, Central Nervous System, Dose-Response Relationship, Drosophila, Drug, Drug Tolerance, Ethanol, Inhalation Exposure, Male, Models, Motor Activity, Mutation, Octopamine}, issn = {0896-6273}, author = {Scholz, H and Ramond, J and Singh, C M and Heberlein, U} } @article {46643, title = {Genetic control of acute ethanol-induced behaviors in Drosophila.}, journal = {Alcoholism, Clinical and Experimental Research}, volume = {24}, year = {2000}, month = {2000 Aug}, pages = {1127-36}, abstract = {

BACKGROUND: In most organisms in which acute ethanol exposure has been studied, it leads to similar changes in behavior. Generally, low ethanol doses activate the central nervous system, whereas high doses are sedative. Sensitivity to the acute intoxicating effects of ethanol is in part under genetic control in rodents and humans, and reduced sensitivity in humans predicts the development of alcoholism (Crabbe et al., 1994; Schuckit, 1994). We have established Drosophila melanogaster as a model organism to study the mechanisms that regulate acute sensitivity to ethanol.

METHODS: We measured the effects of ethanol vapor on Drosophila locomotor behaviors by using three different assays. Horizontal locomotion was quantified in a locomotor chamber, turning behavior was assayed in narrow tubes, and ethanol-induced loss of postural control was measured in an inebriometer. Mutants with altered sensitivity to the acute effects of ethanol were generated by treatment with ethyl methane sulfonate and isolated by selection in the inebriometer. We ascertained the effects of these mutations on ethanol pharmacokinetics by measuring ethanol levels in extracts of flies at various times during and after ethanol exposure.

RESULTS: Among nearly 30,000 potentially mutant flies tested, we isolated 19 mutant strains with reduced and 4 strains with increased sensitivity to the acute effects of ethanol as measured in the inebriometer. Of these mutants, four showed changes in ethanol absorption. Two mutants, named barfly and tipsy to reflect their reduced and increased ethanol sensitivity in the inebriometer, respectively, were analyzed for locomotor behaviors. Both mutants exhibited ethanol-induced hyperactivity that was indistinguishable from wild type. However, barfly and tipsy displayed reduced and increased sensitivity to the sedative effects of ethanol, respectively. Finally, both mutants showed an increased rate of ethanol-induced turning behavior.

CONCLUSIONS: The effects of acute ethanol exposure on Drosophila locomotor behaviors are remarkably similar to those described for mammals. The analysis of mutants with altered sensitivity to ethanol revealed that the genetic pathways which regulate these responses are complex and that single genes can affect hyperactivity, turning, and sedation independently.

}, keywords = {Absorption, Animals, Behavior, Animal, Drosophila melanogaster, Drug Resistance, Ethanol, Kinetics, Motor Activity, Mutation}, issn = {0145-6008}, author = {Singh, C M and Heberlein, U} } @article {957, title = {The genome sequence of Drosophila melanogaster.}, journal = {Science}, volume = {287}, year = {2000}, month = {2000 Mar 24}, pages = {2185-95}, abstract = {

The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes approximately 13,600 genes, somewhat fewer than the smaller Caenorhabditis elegans genome, but with comparable functional diversity.

}, keywords = {Animals, Biological Transport, Chromatin, Cloning, Computational Biology, Contig Mapping, Cytochrome P-450 Enzyme System, DNA, DNA Repair, DNA Replication, Drosophila melanogaster, Euchromatin, Gene Library, Genes, Genetic, Genome, Heterochromatin, Insect, Insect Proteins, Molecular, Nuclear Proteins, Protein Biosynthesis, Sequence Analysis, Transcription}, issn = {0036-8075}, doi = {10.1186/gb-2007-8-7-r145}, author = {Adams, M D and Celniker, S E and Holt, R A and Evans, C A and Gocayne, J D and Amanatides, P G and Scherer, S E and Li, P W and Hoskins, R A and Galle, R F and George, R A and Lewis, S E and Richards, S and Ashburner, M and Henderson, S N and Sutton, G G and Wortman, J R and Yandell, M D and Zhang, Q and Chen, L X and Brandon, R C and Rogers, Y H and Blazej, R G and Champe, M and Pfeiffer, B D and Wan, K H and Doyle, C and Baxter, E G and Helt, G and Nelson, C R and Gabor, G L and Abril, J F and Agbayani, A and An, H J and Andrews-Pfannkoch, C and Baldwin, D and Ballew, R M and Basu, A and Baxendale, J and Bayraktaroglu, L and Beasley, E M and Beeson, K Y and Benos, P V and Berman, B P and Bhandari, D and Bolshakov, S and Borkova, D and Botchan, M R and Bouck, J and Brokstein, P and Brottier, P and Burtis, K C and Busam, D A and Butler, H and Cadieu, E and Center, A and Chandra, I and Cherry, J M and Cawley, S and Dahlke, C and Davenport, L B and Davies, P and de Pablos, B and Delcher, A and Deng, Z and Mays, A D and Dew, I and Dietz, S M and Dodson, K and Doup, L E and Downes, M and Dugan-Rocha, S and Dunkov, B C and Dunn, P and Durbin, K J and Evangelista, C C and Ferraz, C and Ferriera, S and Fleischmann, W and Fosler, C and Gabrielian, A E and Garg, N S and Gelbart, W M and Glasser, K and Glodek, A and Gong, F and Gorrell, J H and Gu, Z and Guan, P and Harris, M and Harris, N L and Harvey, D and Heiman, T J and Hernandez, J R and Houck, J and Hostin, D and Houston, K A and Howland, T J and Wei, M H and Ibegwam, C and Jalali, M and Kalush, F and Karpen, G H and Ke, Z and Kennison, J A and Ketchum, K A and Kimmel, B E and Kodira, C D and Kraft, C and Kravitz, S and Kulp, D and Lai, Z and Lasko, P and Lei, Y and Levitsky, A A and Li, J and Li, Z and Liang, Y and Lin, X and Liu, X and Mattei, B and McIntosh, T C and McLeod, M P and McPherson, D and Merkulov, G and Milshina, N V and Mobarry, C and Morris, J and Moshrefi, A and Mount, S M and Moy, M and Murphy, B and Murphy, L and Muzny, D M and Nelson, D L and Nelson, D R and Nelson, K A and Nixon, K and Nusskern, D R and Pacleb, J M and Palazzolo, M and Pittman, G S and Pan, S and Pollard, J and Puri, V and Reese, M G and Reinert, K and Remington, K and Saunders, R D and Scheeler, F and Shen, H and Shue, B C and Sid{\'e}n-Kiamos, I and Simpson, M and Skupski, M P and Smith, T and Spier, E and Spradling, A C and Stapleton, M and Strong, R and Sun, E and Svirskas, R and Tector, C and Turner, R and Venter, E and Wang, A H and Wang, X and Wang, Z Y and Wassarman, D A and Weinstock, G M and Weissenbach, J and Williams, S M and Williams, S M and Worley, K C and Wu, D and Yang, S and Yao, Q A and Ye, J and Yeh, R F and Zaveri, J S and Zhan, M and Zhang, G and Zhao, Q and Zheng, L and Zheng, X H and Zhong, F N and Zhong, W and Zhou, X and Zhu, S and Zhu, X and Smith, H O and Gibbs, R A and Myers, E W and Rubin, G M and Venter, J C} } @article {1783, title = {A molecular pathway for light-dependent photoreceptor apoptosis in Drosophila.}, journal = {Neuron}, volume = {28}, year = {2000}, month = {2000 Oct 5}, pages = {139-52}, abstract = {

Light-induced photoreceptor apoptosis occurs in many forms of inherited retinal degeneration resulting in blindness in both vertebrates and invertebrates. Though mutations in several photoreceptor signaling proteins have been implicated in triggering this process, the molecular events relating light activation of rhodopsin to photoreceptor death are yet unclear. Here, we uncover a pathway by which activation of rhodopsin in Drosophila mediates apoptosis through a G protein-independent mechanism. This process involves the formation of membrane complexes of phosphorylated, activated rhodopsin and its inhibitory protein arrestin, and subsequent clathrin-dependent endocytosis of these complexes into a cytoplasmic compartment. Together, these data define the proapoptotic molecules in Drosophila photoreceptors and indicate a novel signaling pathway for light-activated rhodopsin molecules in control of photoreceptor viability.

}, keywords = {Animals, Apoptosis, Arrestins, Binding, Calcium-Binding Proteins, Clathrin, Competitive, Drosophila, Drosophila Proteins, Endocytosis, Gene Expression Regulation, Invertebrate, Light, Mutation, Phosphoprotein Phosphatases, Phosphoproteins, Phosphorylation, Photoreceptor Cells, Retinal Degeneration, Rhodopsin}, issn = {0896-6273}, author = {Kiselev, A and Socolich, M and Vin{\'o}s, J and Hardy, R W and Zuker, C S and Ranganathan, R} } @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 {46642, title = {A screen for dominant modifiers of ro(Dom), a mutation that disrupts morphogenetic furrow progression in Drosophila, identifies groucho and hairless as regulators of atonal expression.}, journal = {Genetics}, volume = {156}, year = {2000}, month = {2000 Nov}, pages = {1203-17}, abstract = {

ro(Dom) is a dominant allele of rough (ro) that results in reduced eye size due to premature arrest in morphogenetic furrow (MF) progression. We found that the ro(Dom) stop-furrow phenotype was sensitive to the dosage of genes known to affect retinal differentiation, in particular members of the hedgehog (hh) signaling cascade. We demonstrate that ro(Dom) interferes with Hh{\textquoteright}s ability to induce the retina-specific proneural gene atonal (ato) in the MF and that normal eye size can be restored by providing excess Ato protein. We used ro(Dom) as a sensitive genetic background in which to identify mutations that affect hh signal transduction or regulation of ato expression. In addition to mutations in several unknown loci, we recovered multiple alleles of groucho (gro) and Hairless (H). Analysis of their phenotypes in somatic clones suggests that both normally act to restrict neuronal cell fate in the retina, although they control different aspects of ato{\textquoteright}s complex expression pattern.

}, keywords = {Animals, Basic Helix-Loop-Helix Transcription Factors, Crosses, Genetic, DNA-Binding Proteins, Drosophila melanogaster, Embryo, Nonmammalian, Ethyl Methanesulfonate, Female, Genes, Dominant, Genes, Insect, Helix-Loop-Helix Motifs, Male, Morphogenesis, Mutagenesis, Nerve Tissue Proteins, Phenotype, Signal Transduction}, issn = {0016-6731}, author = {Chanut, F and Luk, A and Heberlein, U} } @article {1784, title = {T2Rs function as bitter taste receptors.}, journal = {Cell}, volume = {100}, year = {2000}, month = {2000 Mar 17}, pages = {703-11}, abstract = {

Bitter taste perception provides animals with critical protection against ingestion of poisonous compounds. In the accompanying paper, we report the characterization of a large family of putative mammalian taste receptors (T2Rs). Here we use a heterologous expression system to show that specific T2Rs function as bitter taste receptors. A mouse T2R (mT2R-5) responds to the bitter tastant cycloheximide, and a human and a mouse receptor (hT2R-4 and mT2R-8) responded to denatonium and 6-n-propyl-2-thiouracil. Mice strains deficient in their ability to detect cycloheximide have amino acid substitutions in the mT2R-5 gene; these changes render the receptor significantly less responsive to cycloheximide. We also expressed mT2R-5 in insect cells and demonstrate specific tastant-dependent activation of gustducin, a G protein implicated in bitter signaling. Since a single taste receptor cell expresses a large repertoire of T2Rs, these findings provide a plausible explanation for the uniform bitter taste that is evoked by many structurally unrelated toxic compounds.

}, keywords = {Afferent Pathways, Amino Acid Sequence, Animals, Calcium, Cell Line, Cell Surface, Chemoreceptor Cells, Cycloheximide, G-Protein-Coupled, Gene Expression, Humans, Inbred C57BL, Inbred DBA, Kidney, Mice, Molecular Sequence Data, Protein Synthesis Inhibitors, Quaternary Ammonium Compounds, Receptors, Recombinant Fusion Proteins, Signal Transduction, Taste, Taste Buds, Transducin, Transfection}, issn = {0092-8674}, author = {Chandrashekar, J and Mueller, K L and Hoon, M A and Adler, E and Feng, L and Guo, W and Zuker, C S and Ryba, N J} } @article {2705, title = {A whole-genome assembly of Drosophila.}, journal = {Science}, volume = {287}, year = {2000}, month = {2000 Mar 24}, pages = {2196-204}, abstract = {

We report on the quality of a whole-genome assembly of Drosophila melanogaster and the nature of the computer algorithms that accomplished it. Three independent external data sources essentially agree with and support the assembly{\textquoteright}s sequence and ordering of contigs across the euchromatic portion of the genome. In addition, there are isolated contigs that we believe represent nonrepetitive pockets within the heterochromatin of the centromeres. Comparison with a previously sequenced 2.9- megabase region indicates that sequencing accuracy within nonrepetitive segments is greater than 99. 99\% without manual curation. As such, this initial reconstruction of the Drosophila sequence should be of substantial value to the scientific community.

}, keywords = {Algorithms, Animals, Chromatin, Computational Biology, Contig Mapping, DNA, Drosophila melanogaster, Euchromatin, Genes, Genome, Heterochromatin, Insect, Molecular Sequence Data, Nucleic Acid, Physical Chromosome Mapping, Repetitive Sequences, Sequence Analysis, Sequence Tagged Sites}, issn = {0036-8075}, author = {Myers, E W and Sutton, G G and Delcher, A L and Dew, I M and Fasulo, D P and Flanigan, M J and Kravitz, S A and Mobarry, C M and Reinert, K H and Remington, K A and Anson, E L and Bolanos, R A and Chou, H H and Jordan, C M and Halpern, A L and Lonardi, S and Beasley, E M and Brandon, R C and Chen, L and Dunn, P J and Lai, Z and Liang, Y and Nusskern, D R and Zhan, M and Zhang, Q and Zheng, X and Rubin, G M and Adams, M D and Venter, J C} } @article {46647, title = {Dorsoventral patterning in the Drosophila retina by wingless.}, journal = {Development}, volume = {125}, year = {1998}, month = {1998 Feb}, pages = {567-77}, abstract = {

The eye imaginal disc displays dorsal-ventral (D-V) and anterior-posterior polarity prior to the onset of differentiation, which initiates at the intersection of the D-V midline with the posterior margin. As the wave of differentiation progresses anteriorly, additional asymmetry develops as ommatidial clusters rotate coordinately in opposite directions in the dorsal and ventral halves of the disc; this forms a line of mirror-image symmetry, the equator, which coincides with the D-V midline of the disc. How D-V pattern is established and how it relates to ommatidial rotation are unknown. Here we address this question by assaying the expression of various asymmetric markers under conditions that lead to ectopic differentiation, such as removal of patched or wingless function. We find that D-V patterning develops gradually and that wingless plays an important role in setting up this pattern. We show that wingless is necessary and sufficient to induce dorsal expression of the gene mirror prior to the start of differentiation and also to restrict the expression of the WR122 marker to differentiating photoreceptors near the equator. In addition, we find that manipulations in wingless expression shift the D-V axis of the disc as evidenced by changes in the expression domains of asymmetric markers, the position of the site of initiation and the equator, and the pattern of epithelial growth. Thus, Wg appears to coordinately regulate multiple events related to D-V patterning in the developing retina.

}, keywords = {Animals, Animals, Genetically Modified, Crosses, Genetic, Drosophila, Drosophila Proteins, Eye Proteins, Female, Gene Expression Regulation, Developmental, Genes, Insect, Genetic Markers, Homeodomain Proteins, Lac Operon, Larva, Male, Proto-Oncogene Proteins, Retina, Transcription Factors, Wnt1 Protein}, issn = {0950-1991}, author = {Heberlein, U and Borod, E R and Chanut, F A} } @inbook {2557, title = {The effect of cross-linking on thermal inactivation of cellulases. In stability of stabilization of biocatalyst.}, booktitle = {Progress in Biotechnology}, year = {1998}, author = {Bilen, Julide and Bakir, U}, editor = {Ballesteros, A and Plou, FJ and Iborra, JL and Hallings, PJ} } @article {5496, title = {Ethanol intoxication in Drosophila: genetic and pharmacological evidence for regulation by the cAMP signaling pathway.}, journal = {Cell}, volume = {93}, year = {1998}, month = {1998 Jun 12}, pages = {997-1007}, abstract = {

Upon exposure to ethanol, Drosophila display behaviors that are similar to ethanol intoxication in rodents and humans. Using an inebriometer to measure ethanol-induced loss of postural control, we identified cheapdate, a mutant with enhanced sensitivity to ethanol. Genetic and molecular analyses revealed that cheapdate is an allele of the memory mutant amnesiac. amnesiac has been postulated to encode a neuropeptide that activates the cAMP pathway. Consistent with this, we find that enhanced ethanol sensitivity of cheapdate can be reversed by treatment with agents that increase cAMP levels or PKA activity. Conversely, genetic or pharmacological reduction in PKA activity results in increased sensitivity to ethanol. Taken together, our results provide functional evidence for the involvement of the cAMP signal transduction pathway in the behavioral response to intoxicating levels of ethanol.

}, keywords = {Adenylate Cyclase, Alleles, Amino Acid Sequence, Animal, Animals, Base Sequence, Behavior, Cloning, Cyclic AMP, Cyclic AMP-Dependent Protein Kinases, Drosophila melanogaster, Drosophila Proteins, Enzyme Activation, Enzyme Inhibitors, Ethanol, Forskolin, Genes, Genetic Complementation Test, Genetically Modified, Insect, Male, Messenger, Molecular, Molecular Sequence Data, Mutation, Neuropeptides, RNA, Signal Transduction}, issn = {0092-8674}, author = {Moore, M S and DeZazzo, J and Luk, A Y and Tully, T and Singh, C M and Heberlein, U} } @article {46648, title = {Eye development in Drosophila: formation of the eye field and control of differentiation.}, journal = {Current Topics in Developmental Biology}, volume = {39}, year = {1998}, month = {1998}, pages = {119-58}, keywords = {Animals, Cell Differentiation, Drosophila, Eye, Gene Expression Regulation, Developmental, Larva, Morphogenesis, Mutation, Visual Fields}, issn = {0070-2153}, author = {Treisman, J E and Heberlein, U} } @article {1567, title = {Introduction of fluorescent allosteric signal transduction elements into glucose-binding protein: construction of a novel glucose sensor.}, journal = {Journal of the American Chemical Society}, year = {1998}, month = {1998}, pages = {7-11}, author = {Marvin, Jonathan S and Hellinga, H W} } @article {46646, title = {Mutual regulation of decapentaplegic and hedgehog during the initiation of differentiation in the Drosophila retina.}, journal = {Devopemental Biology}, volume = {197}, year = {1998}, month = {1998 May 15}, pages = {187-97}, abstract = {

Neuronal differentiation in the Drosophila retinal primordium, the eye imaginal disc, begins at the posterior tip of the disc and progresses anteriorly as a wave. The morphogenetic furrow (MF) marks the boundary between undifferentiated anterior cells and differentiating posterior cells. Anterior progression of differentiation is driven by Hedgehog, synthesized by cells located posterior to the MF. We report here that hedgehog (hh), which is expressed prior to the start of differentiation along the disc{\textquoteright}s posterior margin, also plays a crucial role in the initiation of differentiation. Using a temperature-sensitive allele we show that hh is normally required at the posterior margin to maintain the expression of decapentaplegic (dpp) and of the proneural gene atonal. In addition, we find that ectopic differentiation driven by ectopic dpp expression or loss of wingless function requires hh. Consistent with this is our observation that ectopic dpp induces the expression of hh along the anterior margin even in the absence of differentiation. Taken together, these data reveal a novel positive regulatory loop between dpp and hh that is essential for the initiation of differentiation in the eye disc.

}, keywords = {Animals, Animals, Genetically Modified, Basic Helix-Loop-Helix Transcription Factors, Cell Differentiation, DNA-Binding Proteins, Drosophila, Drosophila Proteins, Female, Gene Expression Regulation, Developmental, Genes, Insect, Hedgehog Proteins, Immunohistochemistry, Insect Proteins, Larva, Male, Nerve Tissue Proteins, Neurons, Retina}, issn = {0012-1606}, doi = {10.1006/dbio.1998.8888}, author = {Borod, E R and Heberlein, U} } @article {1562, title = {Protein engineering and the development of generic biosensors.}, journal = {Trends in Biotechnology}, volume = {16}, year = {1998}, month = {1998 Apr}, pages = {183-9}, abstract = {

Biosensors exploit the remarkable specificity of biomolecular recognition to provide analytical tools that can measure the presence of a single molecular species in a complex mixture. A new strategy is emerging in the development of biosensor technologies: molecular-engineering techniques are being used to adapt the properties of proteins to simple, generic detector instrumentation, rather than adapting instruments to the unique requirements of a natural molecule.

}, keywords = {Binding Sites, Biosensing Techniques, Protein Binding, Protein Engineering, Proteins, Signal Transduction}, issn = {0167-7799}, author = {Hellinga, H W and Marvin, J S} } @article {46645, title = {Y do we drink?}, journal = {Cell}, volume = {95}, year = {1998}, month = {1998 Dec 11}, pages = {733-5}, keywords = {Alcohol Drinking, Alcoholic Intoxication, Animals, Ethanol, Feeding Behavior, Humans, Mice, Mice, Mutant Strains, Neuropeptide Y, Rats}, issn = {0092-8674}, author = {Tecott, L H and Heberlein, U} } @article {45923, title = {Action potential initiation and backpropagation in neurons of the mammalian CNS.}, journal = {Trends Neurosci}, volume = {20}, year = {1997}, month = {1997 Mar}, pages = {125-31}, abstract = {

Most neurons in the mammalian CNS encode and transmit information via action potentials. Knowledge of where these electrical events are initiated and how they propagate within neurons is therefore fundamental to an understanding of neuronal function. While work from the 1950s suggested that action potentials are initiated in the axon, many subsequent investigations have suggested that action potentials can also be initiated in the dendrites. Recently, experiments using simultaneous patch-pipette recordings from different locations on the same neuron have been used to address this issue directly. These studies show that the site of action potential initiation is in the axon, even when synaptic activation is powerful enough to elicit dendritic electrogenesis. Furthermore, these and other studies also show that following initiation, action potentials actively backpropagate into the dendrites of many neuronal types, providing a retrograde signal of neuronal output to the dendritic tree.

}, keywords = {Action Potentials, Animals, Central Nervous System, Neurons}, issn = {0166-2236}, author = {Stuart, G and Spruston, N and Sakmann, B and H{\"a}usser, M} } @article {46649, title = {eyelid antagonizes wingless signaling during Drosophila development and has homology to the Bright family of DNA-binding proteins.}, journal = {Genes \& Development}, volume = {11}, year = {1997}, month = {1997 Aug 1}, pages = {1949-62}, abstract = {

In Drosophila, pattern formation at multiple stages of embryonic and imaginal development depends on the same intercellular signaling pathways. We have identified a novel gene, eyelid (eld), which is required for embryonic segmentation, development of the notum and wing margin, and photoreceptor differentiation. In these tissues, eld mutations have effects opposite to those caused by wingless (wg) mutations. eld encodes a widely expressed nuclear protein with a region homologous to a novel family of DNA-binding domains. Based on this homology and on the phenotypic analysis, we suggest that Eld could act as a transcription factor antagonistic to the Wg pathway.

}, keywords = {Amino Acid Sequence, Animals, Body Patterning, Cell Differentiation, Cloning, Molecular, DNA-Binding Proteins, Drosophila, Drosophila Proteins, Gene Expression Regulation, Developmental, Genes, Insect, Molecular Sequence Data, Mutation, Phenotype, Photoreceptor Cells, Invertebrate, Proto-Oncogene Proteins, Recombinant Fusion Proteins, Restriction Mapping, Sequence Homology, Amino Acid, Signal Transduction, Trans-Activators, Transcription Factors, Wing, Wnt1 Protein}, issn = {0890-9369}, author = {Treisman, J E and Luk, A and Rubin, G M and Heberlein, U} } @article {1563, title = {The rational design of allosteric interactions in a monomeric protein and its applications to the construction of biosensors.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {94}, year = {1997}, month = {1997 Apr 29}, pages = {4366-71}, abstract = {

Rational protein design is an emerging approach for testing general theories of structure and function. The ability to manipulate function rationally also offers the possibility of creating new proteins of biotechnological value. Here we use the design approach to test the current understanding of the structural principles of allosteric interactions in proteins and demonstrate how a simple allosteric system can form the basis for the construction of a generic biosensor molecular engineering system. We have identified regions in Escherichia coli maltose-binding protein that are predicted to be allosterically linked to its maltose-binding site. Environmentally sensitive fluorophores were covalently attached to unique thiols introduced by cysteine mutations at specific sites within these regions. The fluorescence of such conjugates changes cooperatively with respect to maltose binding, as predicted. Spatial separation of the binding site and reporter groups allows the intrinsic properties of each to be manipulated independently. Provided allosteric linkage is maintained, ligand binding can therefore be altered without affecting transduction of the binding event by fluorescence. To demonstrate applicability to biosensor technology, we have introduced a series of point mutations in the maltose-binding site that lower the affinity of the protein for its ligand. These mutant proteins have been combined in a composite biosensor capable of measuring substrate concentration within 5\% accuracy over a concentration range spanning five orders of magnitude.

}, keywords = {Allosteric Regulation, ATP-Binding Cassette Transporters, Binding Sites, Biosensing Techniques, Biotechnology, Carrier Proteins, Computer Simulation, Escherichia coli Proteins, Fluorescent Dyes, Maltose, Maltose-Binding Proteins, Models, Molecular, Monosaccharide Transport Proteins, Mutation, Protein Conformation}, issn = {0027-8424}, author = {Marvin, J S and Corcoran, E E and Hattangadi, N A and Zhang, J V and Gere, S A and Hellinga, H W} } @article {46650, title = {Retinal morphogenesis in Drosophila: hints from an eye-specific decapentaplegic allele.}, journal = {Developmental Genetics}, volume = {20}, year = {1997}, month = {1997}, pages = {197-207}, abstract = {

Decapentaplegic (dpp) regulates many aspects of imaginal disc growth and patterning in Drosophila. We have analyzed the phenotype of an eye-specific dpp allele, dppblk, which causes a reduction in the size of the retina due to a loss of ventral ommatidia. Prior to the onset of differentiation, dppblk eye discs are normal regarding size, shape, and ability to express dorsal and ventral markers. However, expression of a dpp-lacZ reporter is reduced at the ventral margin. Additional dorsoventral asymmetry appears during retinal differentiation: the morphogenetic furrow (MF) initiates normally at the posterior tip of the disc, but fails to propagate into the ventral epithelium. This defect can be rescued by increasing dpp expression along the ventral margin by local removal of patched function. We propose that the primary defect in dppblk is an inability to activate dpp expression properly at the ventral margin. This has two consequences: it prevents initiation from the ventral margin, and it renders the ventral epithelium unresponsive to differentiation signals emanating from the MF.

}, keywords = {Animals, Drosophila, Drosophila Proteins, Insect Proteins, Morphogenesis, Mutation, Phenotype, Photoreceptor Cells, Invertebrate, Retina}, issn = {0192-253X}, doi = {10.1002/(SICI)1520-6408(1997)20:3<197::AID-DVG3>3.0.CO;2-2}, author = {Chanut, F and Heberlein, U} } @article {46651, title = {Role of decapentaplegic in initiation and progression of the morphogenetic furrow in the developing Drosophila retina.}, journal = {Development}, volume = {124}, year = {1997}, month = {1997 Jan}, pages = {559-67}, abstract = {

Morphogenesis in the Drosophila retina initiates at the posterior margin of the eye imaginal disc by an unknown mechanism. Upon initiation, a wave of differentiation, its forward edge marked by the morphogenetic furrow (MF), proceeds anteriorly across the disc. Progression of the MF is driven by hedgehog (hh), expressed by differentiating photoreceptor cells. The TGF-beta homolog encoded by decapentaplegic (dpp) is expressed at the disc{\textquoteright}s posterior margin prior to initiation and in the furrow, under the control of hh, during MF progression. While dpp has been implicated in eye disc growth and morphogenesis, its precise role in retinal differentiation has not been determined. To address the role of dpp in initiation and progression of retinal differentiation we analyzed the consequences of reduced and increased dpp function during eye development. We find that dpp is not only required for normal MF initiation, but is sufficient to induce ectopic initiation of differentiation. Inappropriate initiation is normally inhibited by wingless (wg). Loss of dpp function is accompanied by expansion of wg expression, while increased dpp function leads to loss of wg transcription. In addition, dpp is required to maintain, and sufficient to induce, its own expression along the disc{\textquoteright}s margins. We postulate that dpp autoregulation and dpp-mediated inhibition of wg expression are required for the coordinated regulation of furrow initiation and progression. Finally, we show that in the later stages of retinal differentiation, reduction of dpp function leads to an arrest in MF progression.

}, keywords = {Animals, Cell Differentiation, Chromosome Mapping, Drosophila, Drosophila Proteins, Embryo, Nonmammalian, Embryonic Induction, Gene Expression Regulation, Developmental, Genes, Insect, Hedgehog Proteins, Insect Proteins, Morphogenesis, Proto-Oncogene Proteins, Retina, Transcription, Genetic, Wnt1 Protein}, issn = {0950-1991}, author = {Chanut, F and Heberlein, U} } @article {1163, title = {Control of male sexual behavior and sexual orientation in Drosophila by the fruitless gene.}, journal = {Cell}, volume = {87}, year = {1996}, month = {1996 Dec 13}, pages = {1079-89}, abstract = {

Sexual orientation and courtship behavior in Drosophila are regulated by fruitless (fru), the first gene in a branch of the sex-determination hierarchy functioning specifically in the central nervous system (CNS). The phenotypes of new fru mutants encompass nearly all aspects of male sexual behavior. Alternative splicing of fru transcripts produces sex-specific proteins belonging to the BTB-ZF family of transcriptional regulators. The sex-specific fru products are produced in only about 500 of the 10(5) neurons that comprise the CNS. The properties of neurons expressing these fru products suggest that fru specifies the fates or activities of neurons that carry out higher order control functions to elicit and coordinate the activities comprising male courtship behavior.

}, issn = {0092-8674}, author = {Baker, B.S. and Ryner, L.C. and Goodwin, S.F. and Castrillon, D.H. and Anand, A and Villella, A and Hall, J.C. and Taylor, B.J. and Wasserman, S.A.} } @article {2559, title = {Modal aproximation for the electromagnetic field of a near-field optical probe.}, journal = {Applied Optics}, volume = {35}, year = {1996}, month = {1996 Jul 1}, pages = {3488-95}, abstract = {

A formalism is given in which the optical field generated by a near-field optical aperture is described as an analytic expansion over a complete set of optical modes. This vectoral solution preserves the divergent behavior of the near field and the dipolar nature of the far field. Numerical calculation of the fields requires only evaluation of a well behaved, one-dimensional integral. The formalism is directly applicable to experiments in near-field scanning optical microscopy when relatively flat samples are evaluated.

}, issn = {0003-6935}, doi = {10.1364/AO.35.003488}, author = {Grober, R D and Rutherford, T and Harris, T D} } @article {961, title = {Drosophila homologs of baculovirus inhibitor of apoptosis proteins function to block cell death.}, journal = {Cell}, volume = {83}, year = {1995}, month = {1995 Dec 29}, pages = {1253-62}, abstract = {

Apoptotic cell death is a mechanism by which organisms eliminate superfluous or harmful cells. Expression of the cell death regulatory protein REAPER (RPR) in the developing Drosophila eye results in a small eye owing to excess cell death. We show that mutations in thread (th) are dominant enhancers of RPR-induced cell death and that th encodes a protein homologous to baculovirus inhibitors of apoptosis (IAPs), which we call Drosophila IAP1 (DIAP1). Overexpression of DIAP1 or a related protein, DIAP2, in the eye suppresses normally occurring cell death as well as death due to overexpression of rpr or head involution defective. IAP death-preventing activity localizes to the N-terminal baculovirus IAP repeats, a motif found in both viral and cellular proteins associated with death prevention.

}, keywords = {Amino Acid, Amino Acid Sequence, Animals, Apoptosis, Biological Evolution, Chromosome Deletion, Drosophila, Drosophila Proteins, Electron, Enhancer Elements, Eye, Genes, Genetic, Genetic Testing, Humans, Inhibitor of Apoptosis Proteins, Insect, Insect Proteins, Mammals, Microscopy, Molecular Sequence Data, Mutation, Neurons, Nucleic Acid, Peptides, Repetitive Sequences, Scanning, Sequence Homology, Viral Proteins}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Hay, B A and Wassarman, D A and Rubin, G M} } @article {46654, title = {Growth and differentiation in the Drosophila eye coordinated by hedgehog.}, journal = {Nature}, volume = {373}, year = {1995}, month = {1995 Feb 23}, pages = {709-11}, abstract = {

Differentiation of the Drosophila retina is asynchronous: it starts at the posterior margin of the eye imaginal disc and progresses anteriorly over two days. During this time the disc continues to grow, increasing in size by approximately eightfold. An indentation in the epithelium, the morphogenetic furrow, marks the front edge of the differentiation wave. Anterior progression of the furrow is thought to be driven by signals emanating from differentiating photoreceptor cells in the posterior eye disc. A good candidate for such a signal is the product of the hedgehog (hh) gene; it is expressed, and presumably secreted, by differentiating photoreceptors and its function is required for continued furrow movement. Here we show that ectopic expression of hedgehog sets in motion ectopic furrows in the anterior eye disc. In addition to changes in cell shape, these ectopic furrows are associated with a tightly orchestrated series of events, including proliferation, cell cycle synchronization and pattern formation, that parallel normal furrow progression. We propose that the morphogenetic furrow coincides with a transient boundary that coordinates growth and differentiation of the eye disc, and that hedgehog is necessary and sufficient to propagate this boundary across the epithelium.

}, keywords = {Animals, Basic Helix-Loop-Helix Transcription Factors, Cell Cycle, Cell Cycle Proteins, DNA-Binding Proteins, Drosophila, Drosophila Proteins, Embryonic Induction, Eye, Hedgehog Proteins, Helix-Loop-Helix Motifs, Insect Hormones, Insect Proteins, Nerve Tissue Proteins, Phosphoprotein Phosphatases, Protein Tyrosine Phosphatases, Proteins, Repressor Proteins, Signal Transduction, Transcription Factors}, issn = {0028-0836}, doi = {10.1038/373709a0}, author = {Heberlein, U and Singh, C M and Luk, A Y and Donohoe, T J} } @article {46653, title = {Mechanisms of Drosophila retinal morphogenesis: the virtues of being progressive.}, journal = {Cell}, volume = {81}, year = {1995}, month = {1995 Jun 30}, pages = {987-90}, keywords = {Animals, Cell Differentiation, Drosophila, Morphogenesis, Retina, Signal Transduction}, issn = {0092-8674}, author = {Heberlein, U and Moses, K} } @article {46652, title = {Role of the morphogenetic furrow in establishing polarity in the Drosophila eye.}, journal = {Development}, volume = {121}, year = {1995}, month = {1995 Dec}, pages = {4085-94}, abstract = {

The Drosophila retina is a crystalline array of 800 ommatidia whose organization and assembly suggest polarization of the retinal epithelium along anteroposterior and dorsoventral axes. The retina develops by a stepwise process following the posterior-to-anterior progression of the morphogenetic furrow across the eye disc. Ectopic expression of hedgehog or local removal of patched function generates ectopic furrows that can progress in any direction across the disc leaving in their wake differentiating fields of ectopic ommatidia. We have studied the effect of these ectopic furrows on the polarity of ommatidial assembly and rotation. We find that the anteroposterior asymmetry of ommatidial assembly parallels the progression of ectopic furrows, regardless of their direction. In addition, ommatidia developing behind ectopic furrows rotate coordinately, forming equators in various regions of the disc. Interestingly, the expression of a marker normally restricted to the equator is induced in ectopic ommatidial fields. Ectopic equators are stable as they persist to adulthood, where they can coexist with the normal equator. Our results suggest that ectopic furrows can impart polarity to the disc epithelium, regarding the direction of both assembly and rotation of ommatidia. We propose that these processes are polarized as a consequence of furrow propagation, while more global determinants of dorsoventral and anteroposterior polarity may act less directly by determining the site of furrow initiation.

}, keywords = {Animals, Drosophila, Drosophila Proteins, Eye, Gene Expression, Genes, Insect, Hedgehog Proteins, Immunohistochemistry, Insect Hormones, Membrane Proteins, Models, Biological, Morphogenesis, Proteins, Receptors, Cell Surface, Retina}, issn = {0950-1991}, author = {Chanut, F and Heberlein, U} } @article {1158, title = {Behavioral and neurobiological implications of sex-determining factors in Drosophila.}, journal = {Developmental. Genetics}, volume = {15}, year = {1994}, month = {1994}, pages = {275-96}, abstract = {

The function of the central nervous system as it controls sex-specific behaviors in Drosophila has been studied with renewed intensity, in the context of genetic factors that influence the development of sexually differentiated aspects of this insect. Three categories of genetic variations that cause anomalies in courtship and mating behaviors are discussed: (1) mutants isolated with regard to courtship defects, of which putatively courtship-specific variants such as the fruitless mutant are a subset; (2) general behavioral and neurological variants (including sensory and learning mutants), whose defects include subnormal reproductive performance; and (3) mutations of genes within the sex-determination regulatory hierarchy of Drosophila, the analysis of which has included studies of reproductive behavior. Recent studies of mutations in two of these categories have provided new insights into the control of neuronally based aspects of sex-specific behavior. The doublesex gene, the final factor acting in the sex-determination hierarchy, had been previously thought to regulate all aspects of sexual differentiation. Yet, it has been recently shown that doublesex does not control at least one neuronally-determined feature of sex-specific anatomy--a muscle in the male{\textquoteright}s abdomen, whose normal development is, however, dependent on the action of fruitless. These considerations prompted us to examine further (and in some cases re-examine) the influences exerted by sex-determination hierarchy genes on behavior. Our results--notably those obtained from assessments of doublesex mutations{\textquoteright} effects on general reproductive actions and on a particular component of the courtship sequence (male "singing" behavior)--lead to the suggestion that there is a previously unrecognized branch within the sex-determination hierarchy, which controls the differentiation of the male- and female- specific phenotypes of Drosophila. This new branch separates from the doublesex-related one immediately before the action of that gene (just after transformer and transformer-2) and appears to control as least some aspects of neuronally determined sexual differentiation of males.

}, issn = {0192-253X}, author = {Baker, B.S. and Taylor, B.J. and Villella. A. and Ryner, L.C. and Hall, J.C.} } @article {2561, title = {Dimensions of luminescent oxidized and porous silicon structures.}, journal = {Physical Review Letters}, volume = {72}, year = {1994}, month = {1994 Apr 18}, pages = {2648-51}, abstract = {

X-ray absorption measurements from H-passivated porous Si and from oxidized Si nanocrystals, combined with electron microscopy, ir absorption, α recoil, and luminescence emission data, provide a consistent structural picture of the species responsible for the visible luminescence observed in these samples. The mass-weighted average structures in por-Si are particles, not wires, with dimensions significantly smaller than previously reported or proposed.

}, issn = {1079-7114}, author = {Schuppler, S and Friedman, SL and Marcus, MA and Adler, DL and Xie, Y and Ross, FM and Harris, T D and Brown, WL and Chabal, YJ and Brus, LE and Citrin, PH} } @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 {2562, title = {Raman studies of steric hindrance and surface relaxation of stepped H-terminated silicon surfaces.}, journal = {Physical Review Letters}, volume = {71}, year = {1993}, month = {1993 Oct 4}, pages = {2280-83}, abstract = {

Polarized angle-resolved Raman spectra of the Si-H stretching vibrations on stepped H-terminated Si(111) surfaces confirm the constrained orientation of the step dihydride derived from ab initio cluster calculations. They further show that the step normal modes involve little concerted motion of the step atoms, indicating that step relaxation reduces the steric interaction much further than predicted.

}, issn = {1079-7114}, author = {Hines, MA and Chabal, YJ and Harris, T D and Harris, AL} } @article {964, title = {The TGF beta homolog dpp and the segment polarity gene hedgehog are required for propagation of a morphogenetic wave in the Drosophila retina.}, journal = {Cell}, volume = {75}, year = {1993}, month = {1993 Dec 3}, pages = {913-26}, abstract = {

Development of the Drosophila retina occurs asynchronously; differentiation, its front marked by the morphogenetic furrow, progresses across the eye disc epithelium over a 2 day period. We have investigated the mechanism by which this front advances, and our results suggest that developing retinal cells drive the progression of morphogenesis utilizing the products of the hedgehog (hh) and decapentaplegic (dpp) genes. Analysis of hh and dpp genetic mosaics indicates that the products of these genes act as diffusible signals in this process. Expression of dpp in the morphogenetic furrow is closely correlated with the progression of the furrow under a variety of conditions. We show that hh, synthesized by differentiating cells, induces the expression of dpp, which appears to be a primary mediator of furrow movement.

}, keywords = {Animals, Cell Differentiation, Drosophila melanogaster, Drosophila Proteins, Eye, Gene Expression, Genes, Hedgehog Proteins, Insect, Insect Hormones, Invertebrate, Messenger, Morphogenesis, Mosaicism, Photoreceptor Cells, Proteins, Retina, RNA, Transforming Growth Factor beta}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Heberlein, U and Wolff, T and Rubin, G M} } @article {2563, title = {Polarization contrast in near-field scanning optical microscopy.}, journal = {Applied Optics}, volume = {31}, year = {1992}, month = {1992 Aug 1}, pages = {4563-8}, abstract = {

Recent advances in probe design have led to enhanced resolution (currently as significant as \  12 nm) in optical microscopes based on near-field imaging. We demonstrate that the polarization of emitted and detected light in such microscopes can be manipulated sensitively to generate contrast. We show that the contrast on certain patterns is consistent with a simple interpretation of the requisite boundary conditions, whereas in other cases a more complicated interaction between the probe and the sample is involved. Finally application of the technique to near-filed magneto-optic imaging is demonstrated.

}, issn = {0003-6935}, doi = {10.1364/AO.31.004563}, author = {Betzig, E and Trautman, J K and Weiner, J S and Harris, T D and Wolfe, R} } @article {2564, title = {Breaking the diffraction barrier: optical microscopy on a nanometric scale.}, journal = {Science}, volume = {251}, year = {1991}, month = {1991 Mar 22}, pages = {1468-70}, abstract = {

In near-field scanning optical microscopy, a light source or detector with dimensions less than the wavelength (lambda) is placed in close proximity (lambda/50) to a sample to generate images with resolution better than the diffraction limit. A near-field probe has been developed that yields a resolution of approximately 12 nm ( approximately lambda/43) and signals approximately 10(4)- to 10(6)-fold larger than those reported previously. In addition, image contrast is demonstrated to be highly polarization dependent. With these probes, near-field microscopy appears poised to fulfill its promise by combining the power of optical characterization methods with nanometric spatial resolution.

}, issn = {0036-8075}, doi = {10.1126/science.251.5000.1468}, author = {Betzig, E and Trautman, J K and Harris, T D and Weiner, J S and Kostelak, R L} } @article {2095, title = {Breaking the diffraction barrier: optical microscopy on a nanometric scale. (With commentary)}, journal = {Science}, volume = {251}, year = {1991}, month = {1991 Mar 22}, pages = {1468-70}, abstract = {

In near-field scanning optical microscopy, a light source or detector with dimensions less than the wavelength (lambda) is placed in close proximity (lambda/50) to a sample to generate images with resolution better than the diffraction limit. A near-field probe has been developed that yields a resolution of approximately 12 nm ( approximately lambda/43) and signals approximately 10(4)- to 10(6)-fold larger than those reported previously. In addition, image contrast is demonstrated to be highly polarization dependent. With these probes, near-field microscopy appears poised to fulfill its promise by combining the power of optical characterization methods with nanometric spatial resolution.

Commentary: Introduced the adiabatically tapered single mode fiber probe to near-field scanning optical microscopy which, together with shear force feedback, made the technique a practical reality. Although earlier claims of superresolution via near-field microscopy existed for nearly a decade, this paper was the first to convincingly break Abbe{\textquoteright}s limit with visible light, as demonstrated by reproducibly resolving known, complex nanoscale patterns having features separated by much less than the wavelength. Whereas our fiber probe and shear force technologies were soon widely adopted and key to many novel applications (see above), the earlier methods proved to be technological dead ends, never achieving the results of their original claims. This experience taught me the most valuable lesson of my career: while it{\textquoteright}s bad to bullshit others, it{\textquoteright}s even worse to bullshit yourself. It{\textquoteright}s a lesson sadly unheeded by many current practitioners of superresolution microscopy.

}, issn = {0036-8075}, doi = {10.1126/science.251.5000.1468}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17779440}, author = {Betzig, E and Trautman, J K and Harris, T D and Weiner, J S and Kostelak, R L} } @article {1173, title = {Impairment of mitochondrial transcription termination by a point mutation associated with the MELAS subgroup of mitochondrial encephalomyopathies.}, journal = {Nature}, volume = {351}, year = {1991}, month = {1991 May 16}, pages = {236-9}, abstract = {

Defects in mitochondrial DNA (mtDNA) are associated with several different human diseases, including the mitochondrial encephalomyopathies. The mutations include deletions but also duplications and point mutations. Individuals with MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes) carry a common A-to-G substitution in a highly conserved portion of the gene for transfer RNA(Leu(UUR)). Although the MELAS mutation may be comparable to the defect in the tRNA(Lys) gene associated with MERRF (myoclonus epilepsy associated with ragged-red fibres), it is also embedded in the middle of a tridecamer sequence necessary for the formation of the 3{\textquoteright} ends of 16S ribosomal RNA in vitro. We found that the MELAS mutation results in severe impairment of 16S rRNA transcription termination, which correlates with a reduced affinity of the partially purified termination protein for the MELAS template. This suggests that the molecular defect in MELAS is the inability to produce the correct type and quantity of rRNA relative to other mitochondrial gene products.

}, keywords = {Base Sequence, Blotting, Brain Diseases, Chromosome Mapping, DNA, DNA Mutational Analysis, Genetic, Humans, Mitochondria, Mitochondrial, Molecular Sequence Data, Muscle, Mutation, Peptide Termination Factors, Ribosomal, RNA, Transcription, Transfer, Western}, issn = {0028-0836}, doi = {10.1101/gad.1352105}, author = {Hess, J F and Parisi, M A and Bennett, J L and Clayton, D A} } @article {969, title = {The homeo domain protein rough is expressed in a subset of cells in the developing Drosophila eye where it can specify photoreceptor cell subtype.}, journal = {Genes \& Development}, volume = {4}, year = {1990}, month = {1990 May}, pages = {712-27}, abstract = {

The Drosophila homeo box gene rough is required in photoreceptor cells R2 and R5 for normal eye development. We show here that rough protein expression is limited to a subset of cells in the developing retina where it is transiently expressed for 30-60 hr. The rough protein is first expressed broadly in the morphogenetic furrow but is rapidly restricted to the R2, R3, R4, and R5 precursor cells. Ubiquitous expression of rough under the control of the hsp70 promoter in third-instar larvae suppresses the initial steps of ommatidial assembly. Structures derived from other imaginal discs are not affected. Ectopic expression of rough in the R7 precursor, through the use of the sevenless promoter, causes this cell to develop into an R1-6 photoreceptor subtype; however, this cell still requires sevenless function for its neural differentiation. Taken together with previous analyses of the rough mutant phenotype, these results suggest that the normal role of rough is to establish the unique cell identity of photoreceptors R2 and R5.

}, keywords = {Animals, Base Sequence, Cell Cycle Proteins, DNA-Binding Proteins, Drosophila melanogaster, Drosophila Proteins, Eye, Gene Expression, Genes, Genetic, Heat-Shock Proteins, Homeobox, Hot Temperature, Microtubule-Associated Proteins, Molecular Sequence Data, Morphogenesis, Phenotype, Photoreceptor Cells, Promoter Regions, Transcription Factors}, issn = {0890-9369}, doi = {10.1186/gb-2007-8-7-r145}, author = {Kimmel, B E and Heberlein, U and Rubin, G M} } @article {924, title = {Evaporative cooling of spin-polarized atomic hydrogen.}, journal = {Physical Review Letters}, volume = {61}, year = {1988}, month = {1988 Aug 22}, pages = {935-8}, abstract = {

A gas of hydrogen atoms, confined in a static magnetic trap, has been evaporatively cooled to temperatures of a few millikelvin. The initial trap configuration held the gas at 38 mK for as long as 5 h. Evaporative cooling reduced the temperature to 3.0 mK while maintaining the central density at 7.6{\texttimes}10\ 12\ \  cm\ -3\ \  . These values were determined by measurement of the rate of electronic spin relaxation and are in agreement with model calculations. Further cooling to 1 mK (inferred from the model) has been achieved. Measurements were made of the efficiency of the evaporative cooling process.

}, issn = {1079-7114}, author = {Masuhara, N and Doyle, JM and Sandberg, JC and Kleppner, D and Greytak, TJ and Hess, H F and Kochanski, GP} } @article {974, title = {Localization of the sevenless protein, a putative receptor for positional information, in the eye imaginal disc of Drosophila.}, journal = {Cell}, volume = {51}, year = {1987}, month = {1987 Oct 9}, pages = {143-50}, abstract = {

The Drosophila gene sevenless encodes a putative trans-membrane receptor required for the formation of one particular cell, the R7 photoreceptor, in each ommatidium of the compound eye. Mutations in this gene result in the cell normally destined to form the R7 cell forming a non-neuronal cell type instead. These observations have led to the proposal that the sevenless protein receives at least part of the positional information required for the R7 developmental pathway. We have generated antibodies specific for sevenless and have examined expression of the protein by light and electron microscopy. sevenless protein is present transiently at high levels in at least 9 cells in each developing ommatidium and is detectable several hours before any overt differentiation of R7. The protein is mostly localized at the apices of the cells, in microvilli, but is also found deeper in the tissue where certain cells contact the R8 cell. This finding suggests that R8 expresses a ligand for the sevenless protein.

}, keywords = {Animals, Drosophila melanogaster, Electron, Epithelium, Eye, Eye Proteins, Histocytochemistry, Immunologic Techniques, Insect Hormones, Microscopy, Microvilli, Peptide Fragments, Photoreceptor Cells}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Tomlinson, A and Bowtell, D D and Hafen, E and Rubin, G M} } @article {975, title = {Sevenless, a cell-specific homeotic gene of Drosophila, encodes a putative transmembrane receptor with a tyrosine kinase domain.}, journal = {Science}, volume = {236}, year = {1987}, month = {1987 Apr 3}, pages = {55-63}, abstract = {

The determination of cell fates during the assembly of the ommatidia in the compound eye of Drosophila appears to be controlled by cell-cell interactions. In this process, the sevenless gene is essential for the development of a single type of photoreceptor cell. In the absence of proper sevenless function the cells that would normally become the R7 photoreceptors instead become nonneuronal cells. Previous morphological and genetic analysis has indicated that the product of the sevenless gene is involved in reading or interpreting the positional information that specifies this particular developmental pathway. The sevenless gene has now been isolated and characterized. The data indicate that sevenless encodes a transmembrane protein with a tyrosine kinase domain. This structural similarity between sevenless and certain hormone receptors suggests that similar mechanisms are involved in developmental decisions based on cell-cell interaction and physiological or developmental changes induced by diffusible factors.

}, keywords = {Amino Acid Sequence, Animals, Base Sequence, Cell Surface, Chromosome Mapping, Cloning, DNA Restriction Enzymes, Drosophila melanogaster, Eye, Gene Expression Regulation, Genes, Genetic, Growth Substances, Homeobox, Membrane Proteins, Molecular, Phenotype, Protein-Tyrosine Kinases, Receptors, Transcription}, issn = {0036-8075}, doi = {10.1186/gb-2007-8-7-r145}, author = {Hafen, E and Basler, K and Edstroem, J E and Rubin, G M} } @article {1182, title = {Replication priming and transcription initiate from precisely the same site in mouse mitochondrial DNA.}, journal = {The EMBO Journal}, volume = {4}, year = {1985}, month = {1985 Jun}, pages = {1559-67}, abstract = {

Mammalian mitochondrial DNA maintains a novel displacement-loop region containing the major sites of transcriptional initiation and the origin of heavy strand DNA replication. Because the exact map positions of the 5{\textquoteright} termini of nascent mouse displacement-loop strands are known, it is possible to examine directly a potential relationship between replication priming and transcription. Analyses of in vivo nucleic acids complementary to the displacement-loop region reveal two species with identical 5{\textquoteright} ends at map position 16 183. One is entirely RNA and the other is RNA covalently linked to DNA. In the latter the transition from RNA to DNA is sharp, occurring near or within a series of previously identified conserved sequences 74-163 nucleotides downstream from the transcriptional initiation site. These data suggest that the initial events in replication priming and transcription are the same and that the decision to synthesize DNA or RNA is a downstream event under the control of short, conserved displacement-loop template sequences.

}, keywords = {Animals, Base Sequence, Chromosome Mapping, DNA, DNA Replication, Genetic, Mice, Mitochondrial, Operon, Ribonucleases, RNA, Transcription}, issn = {0261-4189}, doi = {10.1101/gad.1352105}, author = {Chang, D D and Hauswirth, W W and Clayton, D A} } @article {1147, title = {Sex-specific regulation of yolk protein gene expression in Drosophila.}, journal = {Cell}, volume = {40}, year = {1985}, month = {1985 Feb}, pages = {339-48}, abstract = {

Many of the genes in the regulatory hierarchy controlling sex determination in Drosophila melanogaster are known. Here we examine how this regulatory hierarchy controls the expression of the structural genes encoding the female-specific yolk polypeptides. Temperature shift experiments with a temperature-sensitive allele of the sex determination regulatory gene transformer-2 (tra-2) showed that tra-2+ function is required in the adult for both the sex-specific initiation and maintenance of YP synthesis. Control of the YP genes by this regulatory hierarchy is at the level of transcription, or transcript stability. The results of temperature shift experiments with abdomens isolated from tra-2ts homozygotes support the notion that the tra-2+ function acts in a cell-autonomous manner to control YP synthesis. These results provide a paradigm for the way this regulatory hierarchy controls the terminal differentiation functions for sexually dimorphic development.

}, issn = {0092-8674}, author = {Baker, B.S. and Belote, J.M. and Handler, A.M. and Wolfner, M.F. and Livak, K.J.} }