@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 {70283, title = {Imp1 acts as a dosage- and stage-dependent temporal rheostat orchestrating radial glial fate transitions and cortical morphogenesis}, journal = {eLife}, year = {2026}, month = {2026 Feb 06}, abstract = {

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

}, doi = {10.7554/elife.109847.1}, url = {http://dx.doi.org/10.7554/eLife.109847.1}, author = {Azur, Romie Angelo G and Feliciano, Daniel and Espinosa-Medina, Isabel and Adhikari, Raghabendra and Lilao-Garz{\'o}n, Joaquin and Jansen, Ella and Yang, Ching-Po and Lee, Tzumin} } @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 {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 {70257, title = {Redefining colocalization analysis with a novel phasor mixing coefficient}, journal = {Journal of Cell Science}, volume = {139}, year = {2026}, month = {2026 Jan 19}, pages = {jcs264388}, abstract = {

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

}, issn = {0021-9533}, doi = {10.1242/jcs.264388}, url = {https://doi.org/10.1242/jcs.264388}, author = {Puls, Owen F. and Aaron, Jesse S. and Quarles, Ellen K. and Khuon, Satya and Eisenman, Leanna R. and Kamaid, Andres and Malacrida, Leonel and Chew, Teng-Leong} } @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 {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 {69796, title = {BPS2025 - Local cytoplasmic tradewinds direct soluble proteins to their targets}, journal = {Biophysical Journal}, volume = {124}, year = {2025}, month = {2025 Feb 13}, pages = {375a - 376a}, abstract = {

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

}, issn = {00063495}, doi = {10.1016/j.bpj.2024.11.2032}, url = {https://doi.org/10.1016/j.bpj.2024.11.2032}, author = {Galbraith, Catherine G. and English, Brian P. and Boehm, Ulrike and Galbraith, James} } @article {70035, title = {Cell type-specific contributions to a persistent aggressive internal state in female Drosophila}, journal = {Elife}, volume = {12}, year = {2025}, month = {2025 Jul 25}, abstract = {

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

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

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

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

}, doi = {10.7554/elife.104764.2}, url = {http://dx.doi.org/10.7554/eLife.104764.2}, author = {Wolff, Tanya and Eddison, Mark and Chen, Nan and Nern, Aljoscha and Sundaramurthi, Preeti and Sitaraman, Divya and Rubin, Gerald M} } @article {70026, title = {CHLOK: a chemigenetic multicolor labeling system to visualize neuronal birthdate and circuit integration}, journal = {Research Square}, year = {2025}, month = {2025 Jul 08}, abstract = {

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

}, doi = {10.21203/rs.3.rs-7039578/v1}, url = {https://doi.org/10.21203/rs.3.rs-7039578/v1}, author = {Faini, Giulia and Tuffery, Matthieu and Saleem, Amna and Zhang, Lixia and Du, Felix and Le Bourdelles, Guillaume and Duroure, Karine and Schreiter, Eric R and Tanese, Dimitrii and Emiliani, Valentina and Del Bene, Filippo and Koyama, Minoru} } @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 {69881, title = {Comparative connectomics of Drosophila descending and ascending neurons.}, journal = {Nature}, year = {2025}, month = {2025 Apr 30}, abstract = {

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

}, issn = {1476-4687}, doi = {10.1038/s41586-025-08925-z}, url = {https://doi.org/10.1038/s41586-025-08925-z}, author = {St{\"u}rner, Tomke and Brooks, Paul and Serratosa Capdevila, Laia and Morris, Billy J and Javier, Alexandre and Fang, Siqi and Gkantia, Marina and Cachero, Sebastian and Beckett, Isabella R and Marin, Elizabeth C and Schlegel, Philipp and Champion, Andrew S and Moitra, Ilina and Richards, Alana and Klemm, Finja and Kugel, Leonie and Namiki, Shigehiro and Cheong, Han S J and Kovalyak, Julie and Tenshaw, Emily and Parekh, Ruchi and Phelps, Jasper S and Mark, Brandon and Dorkenwald, Sven and Bates, Alexander S and Matsliah, Arie and Yu, Szi-Chieh and McKellar, Claire E and Sterling, Amy and Seung, H Sebastian and Murthy, Mala and Tuthill, John C and Lee, Wei-Chung Allen and Card, Gwyneth M and Costa, Marta and Jefferis, Gregory S X E and Eichler, Katharina} } @article {68955, title = {A competitive disinhibitory network for robust optic flow processing in Drosophila}, journal = {Nat Neurosci.}, year = {2025}, month = {2025 may 1}, abstract = {

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

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

}, doi = {10.1038/s41593-025-01948-9}, url = {https://doi.org/10.1038/s41593-025-01948-9}, author = {Mert Erginkaya and Tom{\'a}s Cruz and Margarida Brotas and Kathrin Steck and Aljoscha Nern and Filipa Torr{\~a}o and N{\'e}lia Varela and Davi Bock and Michael Reiser and M Eugenia Chiappe} } @article {69957, title = {Compressive streak microscopy for fast sampling of fluorescent reporters of neural activity.}, journal = {Neurophotonics}, volume = {12}, year = {2025}, month = {2025 Apr 12}, pages = {025013}, abstract = {

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

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

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

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

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

}, issn = {2329-423X}, doi = {10.1117/1.NPh.12.2.025013}, url = {https://doi.org/10.1117/1.nph.12.2.025013}, author = {Cai, Changjia and Traubert, Owen and Tormes-Vaquerano, Jovan and Eybposh, M Hossein and Turaga, Srinivas C and Rodriguez-Romaguera, Jose and Naumann, Eva A and P{\'e}gard, Nicolas C} } @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 {69718, title = {Design and Generation of TEMPO Reagents for Sequential Labeling and Manipulation of Vertebrate Cell Lineages.}, journal = {Methods Mol Biol}, volume = {2886}, year = {2025}, month = {01/2025}, pages = {327-353}, abstract = {

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

}, keywords = {Animals, Cell Lineage, CRISPR-Cas Systems, Luminescent Proteins, Mice, Staining and Labeling, Zebrafish}, issn = {1940-6029}, doi = {10.1007/978-1-0716-4310-5_17}, author = {Espinosa-Medina, Isabel} } @article {69772, title = {Discovering symbolic cognitive models from human and animal behavior.}, journal = {bioRxiv}, year = {2025}, month = {2025 Feb 13}, abstract = {

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

}, doi = {10.1101/2025.02.05.636732}, url = {https://doi.org/10.1101/2025.02.05.636732}, author = {Castro, P. S. and Tomasev, N. and Anand, A. and Sharma, N. and Mohanta, R. and Perlin, K. and Jain, S. and Levin, K. and {\'E}ltet{\H o}, N. and Dabney, W. and Novikov, A. and Eckstein, M. K. and Daw, N. D. and Miller, K. J. and Stachenfeld, K. L.} } @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 {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 {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 {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 {69825, title = {HortaCloud: An open and collaborative platform for whole brain neuronal reconstructions}, journal = {bioRxiv}, year = {2025}, month = {2025 Mar 13}, abstract = {

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

}, doi = {10.1101/2025.03.13.642887}, url = {https://www.biorxiv.org/content/early/2025/03/14/2025.03.13.642887}, author = {Rokicki, Konrad and Schauder, David and Olbris, Donald J. and Goina, Cristian and Clements, Jody and Edson, Patrick and Kawase, Takashi and Svirskas, Robert and Arshadi, Cameron and Feng, David and Chandrashekar, Jayaram and Ferreira, Tiago A. and MouseLight Project Team} } @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 {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 {70190, title = {Imp1 acts as a dosage- and stage-dependent temporal rheostat orchestrating radial glial fate transitions and cortical morphogenesis}, journal = {bioRxiv}, year = {2025}, month = {2025 Nov 18}, abstract = {

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

}, doi = {10.1101/2025.11.18.688993}, url = {https://www.biorxiv.org/content/early/2025/11/18/2025.11.18.688993}, author = {Azur, Romie Angelo G. and Feliciano, Daniel and Espinosa-Medina, Isabel and Adhikari, Raghabendra and Lilao-Garz{\'o}n, Joaquin and Jensen, Ella and Yang, Ching-Po and Lee, Tzumin} } @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 {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 {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 {70191, title = {Multimodal cell lineage reconstruction in the hindbrain reveals a link between progenitor origin and activity patterning}, journal = {bioRxiv}, year = {2025}, month = {2025 Nov 14}, abstract = {

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

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

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

}, doi = {10.1101/2025.09.29.679272}, url = {https://www.biorxiv.org/content/early/2025/10/01/2025.09.29.679272.1}, author = {Ludlow, B. Kemper and Dhawan, Serene and Whitehead, Samuel C and Teoh, Han Kheng and Ehrhardt, Erica and Cowan, Noah and Dickerson, Bradley H and Cohen, Itai} } @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 {70226, title = {Octopamine instructs head direction plasticity}, journal = {bioRxiv}, year = {2025}, month = {2025 Dec 15}, abstract = {

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

}, doi = {10.64898/2025.12.11.693783}, url = {https://www.biorxiv.org/content/early/2025/12/15/2025.12.11.693783}, author = {Plitt, Mark H. and Turner-Evans, Daniel B. and Co, Jessica C. and Layden, Aryanna and Eddison, Mark and Ray, Robert P. and Jayaraman, Vivek and Fisher, Yvette E.} } @article {70225, title = {Parallel neuronal ensembles control behavior across sensorimotor levels in Drosophila}, journal = {bioRxiv}, year = {2025}, month = {2025 Dec 16}, abstract = {

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

}, doi = {10.64898/2025.12.13.693955}, url = {https://www.biorxiv.org/content/early/2025/12/16/2025.12.13.693955}, author = {Liessem, Sander and Asinof, Samuel K. and Nern, Aljoscha and Sumathipala, Marissa and Rogers, Edward and Erginkaya, Mert and Dallmann, Chris J. and Card, Gwyneth M and Ache, Jan M.} } @article {70080, title = {RABGAP1 is a sensor that facilitates the sorting and processing of amyloid precursor protein}, journal = {The EMBO Journal}, year = {2025}, month = {2026 Aug 26}, pages = {1-20}, abstract = {

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

}, keywords = {Alzheimer{\textquoteright}s Disease, APP, RABGAP1, Trafficking}, doi = {10.1038/s44318-025-00530-0}, url = {https://www.embopress.org/doi/abs/10.1038/s44318-025-00530-0}, author = {Eden, Jessica and Kaufman, Jonathan G G and Pereira, Concei{\c c}{\~a}o and Fox, Eleanor and Cattin-Ortol{\'a}, Jerome and Benedetti, Lorena and Nieuwenhuis, Bart and Owen, David J and Lippincott-Schwartz, Jennifer and Munro, Sean and Gershlick, David C} } @article {70222, title = {Reconstructing a physiological state space via chronic jugular microdialysis in freely moving mice}, journal = {bioRxiv}, year = {2025}, month = {2025 Dec 11}, abstract = {

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

}, doi = {10.64898/2025.12.08.692974}, url = {https://www.biorxiv.org/content/early/2025/12/11/2025.12.08.692974}, author = {Nardin, Michele and Wang, Nan and Elziny, Soad and Boyer, Claire and Pjanovic, Vojko and Schuster, Luisa and Boklund, Peter and Lindo, Sarah and Morris, Kendra and Ilanges, Anoj and Voigts, Jakob and Dennis, Emily Jane} } @article {70198, title = {Redefining colocalization analysis with a novel Phasor Mixing Coefficient.}, journal = {J Cell Sci}, year = {2025}, month = {2025 Nov 24}, abstract = {

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

}, issn = {1477-9137}, doi = {10.1242/jcs.264388}, author = {Puls, Owen F and Aaron, Jesse S and Quarles, Ellen K and Khuon, Satya and Eisenman, Leanna R and Kamaid, Andres and Malacrida, Leonel and Chew, Teng-Leong} } @article {70203, title = {Redefining colocalization analysis with a novel Phasor Mixing Coefficient.}, journal = {J Cell Sci}, year = {2025}, month = {2025 Nov 24}, abstract = {

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

}, issn = {1477-9137}, doi = {10.1242/jcs.264388}, url = {https://doi.org/10.1242/jcs.264388}, author = {Puls, Owen F and Aaron, Jesse S and Quarles, Ellen K and Khuon, Satya and Eisenman, Leanna R and Kamaid, Andres and Malacrida, Leonel and Chew, Teng-Leong} } @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 {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 {68799, title = {Single-cell type analysis of wing premotor circuits in the ventral nerve cord of Drosophila melanogaster}, journal = {eLife}, year = {2025}, month = {2025 May 06}, abstract = {

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

}, doi = {10.7554/eLife.106548.1}, url = {https://doi.org/10.7554/eLife.106548.1}, author = {Erica Ehrhardt and Samuel C Whitehead and Shigehiro Namiki and Ryo Minegishi and Igor Siwanowicz and Kai Feng and Hideo Otsuna and FlyLight Project Team and Geoffrey W Meissner and David Stern and Jim Truman and David Shepherd and Michael H. Dickinson and Kei Ito and Barry J Dickson and Itai Cohen and Gwyneth M Card and Wyatt Korff} } @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 {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 {70091, title = {Synaptic targets of circadian clock neurons influence core clock parameters.}, journal = {Sci Adv}, volume = {11}, year = {2025}, month = {2025 Sep 05}, pages = {eadw4666}, abstract = {

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

}, keywords = {Animals, Circadian Clocks, Circadian Rhythm, Drosophila melanogaster, Drosophila Proteins, Neurons, Neuropeptides, Sleep, Synapses, Tetanus Toxin}, issn = {2375-2548}, doi = {10.1126/sciadv.adw4666}, url = {https://doi.org/10.1126/sciadv.adw4666}, author = {Scholz-Carlson, Eva and Iyer, Aishwarya R and Nern, Aljoscha and Ewer, John and Fernandez, Maria P} } @article {69764, title = {Targets of circadian clock neurons influence core clock parameters}, journal = {bioRxiv}, year = {2025}, month = {2025 Jan 31}, abstract = {

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

}, doi = {https://doi.org/10.1101/2025.01.30.635801v1}, author = {Scholz-Carson, E. and Iyer, A. R. and Ewer, J. and Fernandez, Maria P.} } @article {70030, title = {Transforming descending input into motor output: An analysis of the Drosophila Male Adult Nerve Cord connectome}, journal = {eLife}, year = {2025}, month = {2025 Jul 21}, abstract = {

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

}, doi = {10.7554/elife.96084.2}, url = {http://dx.doi.org/10.7554/eLife.96084.2}, author = {Cheong, Han Sj and Eichler, Katharina and St{\"u}rner, Tomke and Asinof, Samuel K and Champion, Andrew S and Marin, Elizabeth C and Oram, Tess B and Sumathipala, Marissa and Venkatasubramanian, Lalanti and Namiki, Shigehiro and Siwanowicz, Igor and Costa, Marta and Berg, Stuart and Jefferis, Gregory Sxe and Card, Gwyneth M} } @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 {69790, title = {An updated catalogue of split-GAL4 driver lines for descending neurons in Drosophila melanogaster}, journal = {bioRxiv}, year = {2025}, month = {2025 Feb 24}, abstract = {

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

}, doi = {10.1101/2025.02.22.639679}, url = {https://www.biorxiv.org/content/early/2025/02/24/2025.02.22.639679}, author = {Zung, Jessica L. and Namiki, Shigehiro and Meissner, Geoffrey W. and Costa, Marta and Eichler, Katharina and St{\"u}rner, Tomke and Jefferis, Gregory S.X.E. and Managan, Claire and FlyLight Project Team and Korff, Wyatt and Card, Gwyneth M.} } @article {70123, title = {An updated catalogue of split-GAL4 driver lines for descending neurons in Drosophila melanogaster}, journal = {eLife}, year = {2025}, month = {2025 Sept 19}, abstract = {

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

}, doi = {10.7554/elife.107450.1}, url = {http://dx.doi.org/10.7554/eLife.107450.1}, author = {Zung, Jessica L and Namiki, Shigehiro and Meissner, Geoffrey W and Cheong, Han Sj and Costa, Marta and Eichler, Katharina and St{\"u}rner, Tomke and Jefferis, Gregory Sxe and Managan, Claire and Korff, Wyatt and Card, Gwyneth M} } @article {69839, title = {Whole-brain, all-optical interrogation of neuronal dynamics underlying gut interoception in zebrafish}, journal = {bioRxiv}, year = {2025}, month = {2025 Mar 30}, abstract = {

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

}, doi = {10.1101/2025.03.26.645305}, url = {https://www.biorxiv.org/content/early/2025/03/30/2025.03.26.645305}, author = {Chen, Weiyu and James, Ben and Ruetten, Virginia M. S. and Banala, Sambashiva and Wei, Ziqiang and Fleishman, Greg and Rubinov, Mikail and Fishman, Mark C. and Engert, Florian and Lavis, Luke D. and Fitzgerald, James E. and Ahrens, Misha B.} } @article {69455, title = {Analysis of developmental gene expression using smFISH and in silico staging of C. elegans embryos}, journal = {bioRxiv}, year = {2024}, month = {2024 May 16}, abstract = {

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

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

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

}, doi = {10.1101/2024.05.15.594414}, url = {https://www.biorxiv.org/content/early/2024/05/16/2024.05.15.594414}, author = {Breimann, Laura and Bahry, Ella and Zouinkhi, Marwan and Kolyvanov, Klim and Street, Lena Annika and Preibisch, Stephan and Ercan, Sevin{\c c}} } @article {69654, title = {Back to the future - 20 years of progress and developments in photonic microscopy and biological imaging.}, journal = {J Cell Sci}, volume = {137}, year = {2024}, month = {2024 Oct 15}, abstract = {

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

}, keywords = {Animals, Humans, Microscopy, Photons}, issn = {1477-9137}, doi = {10.1242/jcs.262344}, url = {https://doi.org/10.1242/jcs.262344}, author = {Erard, Marie and Favard, Cyril and Lavis, Luke D and Recher, Ga{\"e}lle and Rigneault, Herv{\'e} and Sage, Daniel} } @article {69147, title = {Believing is seeing - the deceptive influence of bias in quantitative microscopy.}, journal = {Journal of Cell Science}, volume = {137}, year = {2024}, month = {2024 Jan 10}, abstract = {

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

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

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

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

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

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

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

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

}, doi = {10.1117/1.NPh.11.2.024207}, url = {https://doi.org/10.1117/1.NPh.11.2.024207}, author = {Abhi Aggarwal and Smrithi Sunil and Imane Bendifallah and Michael Moon and Mikhail Drobizhev and Landon Zarowny and Jihong Zheng and Sheng-Yi Wu and Alexander W. Lohman and Alison G. Tebo and Valentina Emiliani and Kaspar Podgorski and Yi Shen and Robert E. Campbell} } @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 {69650, title = {Cell type-specific driver lines targeting the Drosophila central complex and their use to investigate neuropeptide expression and sleep regulation}, journal = {bioRxiv}, year = {2024}, month = {2024 Oct 21}, abstract = {

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

}, doi = {10.1101/2024.10.21.619448}, url = {https://doi.org/10.1101/2024.10.21.619448}, author = {Wolff, Tanya and Eddison, Mark and Chen, Nan and Nern, Aljoscha and Sundaramurthi, Preeti and Sitaraman, Divya and Rubin, Gerald M.} } @article {69251, title = {The cell-type-specific spatial organization of the anterior thalamic nuclei of the mouse brain.}, journal = {Cell Reports}, volume = {43}, year = {2024}, month = {2024 Feb 29}, pages = {113842}, abstract = {

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

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2024.113842}, author = {Kapustina, Margarita and Zhang, Angela A and Tsai, Jennifer Y J and Bristow, Brianna N and Kraus, Larissa and Sullivan, Kaitlin E and Erwin, Sarah R and Wang, Lihua and Stach, Tara R and Clements, Jody and Lemire, Andrew L and Cembrowski, Mark S} } @article {69489, title = {Comparative connectomics of the descending and ascending neurons of the Drosophila nervous system: stereotypy and sexual dimorphism}, journal = {bioRxiv}, year = {2024}, month = {2024 Jun 06}, abstract = {

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

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

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

}, doi = {10.1101/2024.05.12.593794}, url = {https://www.biorxiv.org/content/early/2024/05/14/2024.05.12.593794}, author = {Galbraith, Catherine G and English, Brian P and Boehm, Ulrike and Galbraith, James A} } @article {69442, title = {Coumarin as a general switching auxiliary to prepare photochromic and spontaneously blinking fluorophores}, journal = {bioRxiv}, year = {2024}, month = {2024 May 12}, abstract = {

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

}, doi = {10.1101/2024.05.12.593749}, url = {https://www.biorxiv.org/content/early/2024/05/12/2024.05.12.593749}, author = {Jradi, Fadi M. and English, Brian P. and Brown, Timothy A. and Aaron, Jesse and Khuon, Satya and Galbraith, James A. and Galbraith, Catherine G. and Lavis, Luke D.} } @article {69328, title = {Cryo-electron tomographic investigation of native hippocampal glutamatergic synapses}, journal = {eLife}, year = {2024}, month = {2024 Nov 11}, abstract = {

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

}, doi = {10.7554/eLife.98458}, url = {https://doi.org/10.7554/eLife.98458}, author = {Aya Matsui and Catherine Spangler and Johannes Elferich and Momoko Shiozaki and Nikki Jean and Xiaowei Zhao and Maozhen Qin and Haining Zhong and Zhiheng Yu and Eric Gouaux} } @article {68794, title = {Direct measurement of dynamic attractant gradients reveals breakdown of the Patlak-Keller-Segel chemotaxis model}, journal = {Proceedings of the National Academy of Sciences}, year = {2024}, month = {2024 Jan 09}, abstract = {

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

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

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

}, doi = {10.1101/2024.12.30.630829}, url = {https://www.biorxiv.org/content/early/2024/12/31/2024.12.30.630829}, author = {The MouseLight Project Team and Ferreira, Tiago A. and Eddison, Mark and Copeland, Monique and Lay, Mary and Tenshaw, Emily and Weldon, Monet and Schauder, David and Olbris, Donald J. and Rokicki, Konrad and Spruston, Nelson and Tillberg, Paul W. and Korff, Wyatt and Dudman, Joshua T.} } @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 {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 {69576, title = {An Image Processing Tool for Automated Quantification of Bacterial Burdens in Zebrafish Larvae}, journal = {bioRxiv}, year = {2024}, month = {2024 Aug 19}, abstract = {

Zebrafish larvae are used to model the pathogenesis of multiple bacteria. This transparent model offers the unique advantage of allowing quantification of fluorescent bacterial burdens (fluorescent pixel counts: FPC) in vivo by facile microscopical methods, replacing enumeration of bacteria using time-intensive plating of lysates on bacteriological media. Accurate FPC measurements require laborious manual image processing to mark the outside borders of the animals so as to delineate the bacteria inside the animals from those in the culture medium that they are in. Here, we have developed an automated ImageJ/Fiji-based macro that accurately detect the outside borders of Mycobacterium marinum-infected larvae.

}, doi = {10.1101/2024.08.16.608298}, url = {hhtps://doi.org/10.1101/2024.08.16.608298}, author = {Yamaguchi, Naoya and Otsuna, Hideo and Eisenberg-Bord, Michal and Ramakrishnan, Lalita} } @article {69708, title = {An Image Processing Tool for Automated Quantification of Bacterial Burdens in Zebrafish Larvae.}, journal = {Zebrafish}, year = {2024}, month = {12/2024}, abstract = {

Zebrafish larvae are used to model the pathogenesis of multiple bacteria. This transparent model offers the unique advantage of allowing quantification of fluorescent bacterial burdens (fluorescent pixel counts [FPC]) by facile microscopical methods, replacing enumeration of bacteria using time-intensive plating of lysates on bacteriological media. Accurate FPC measurements require laborious manual image processing to mark the outside borders of the animals so as to delineate the bacteria inside the animals from those in the culture medium that they are in. Here, we have developed an automated ImageJ/Fiji-based macro that accurately detects the outside borders of -infected larvae.

}, issn = {1557-8542}, doi = {10.1089/zeb.2024.0170}, author = {Yamaguchi, Naoya and Otsuna, Hideo and Eisenberg-Bord, Michal and Ramakrishnan, Lalita} } @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 {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 {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 {68921, title = {Network statistics of the whole-brain connectome of Drosophila}, journal = {Nature}, volume = {634}, year = {2024}, month = {2024 Oct 02}, pages = {153{\textendash}165}, abstract = {

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

}, doi = {10.1038/s41586-024-07968-y}, url = {https://doi.org/10.1038/s41586-024-07968-y}, author = {Albert Lin and Runzhe Yang and Sven Dorkenwald and Arie Matsliah and Amy R. Sterling and Philipp Schlegel and Szi-chieh Yu and Claire E. McKellar and Marta Costa and Katharina Eichler and Alexander Shakeel Bates and Nils Eckstein and Jan Funke and Gregory S.X.E. Jefferis and Mala Murthy} } @article {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 {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 {69471, title = {Norepinephrine changes behavioral state via astroglial purinergic signaling}, journal = {Science}, year = {2024}, month = {2025 May 15}, abstract = {

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

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

}, doi = {10.1126/science.adq5233}, url = {https://www.science.org/stoken/author-tokens/ST-2654/full}, author = {Chen, Alex B. and Duque, Marc and Wang, Vickie M. and Dhanasekar, Mahalakshmi and Mi, Xuelong and Rymbek, Altyn and Tocquer, Loeva and Narayan, Sujatha and Prober, David and Yu, Guoqiang and Wyart, Claire and Engert, Florian and Ahrens, Misha B.} } @article {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 {69689, title = {Quantitative Attributions with Counterfactuals}, journal = {bioRxiv}, year = {2024}, month = {2024 Dec 02}, abstract = {

We address the problem of explaining the decision process of deep neural network classifiers on images, which is of particular importance in biomedical datasets where class-relevant differences are not always obvious to a human observer. Our proposed solution, termed quantitative attribution with counterfactuals (QuAC), generates visual explanations that highlight class-relevant differences by attributing the classifier decision to changes of visual features in small parts of an image. To that end, we train a separate network to generate counterfactual images (i.e., to translate images between different classes). We then find the most important differences using novel discriminative attribution methods. Crucially, QuAC allows scoring of the attribution and thus provides a measure to quantify and compare the fidelity of a visual explanation. We demonstrate the suitability and limitations of QuAC on two datasets: (1) a synthetic dataset with known class differences, representing different levels of protein aggregation in cells and (2) an electron microscopy dataset of D. melanogaster synapses with different neurotransmitters, where QuAC reveals so far unknown visual differences. We further discuss how QuAC can be used to interrogate mispredictions to shed light on unexpected inter-class similarities and intra-class differences.

}, doi = {10.1101/2024.11.26.625505}, url = {https://doi.org/10.1101/2024.11.26.625505}, author = {Adjavon, Diane-Yayra and Eckstein, Nils and Bates, Alexander S. and Jefferis, Gregory S.X.E. and Funke, Jan} } @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 {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 {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 {69612, title = {Synaptic Specializations at Dopamine Release Sites Orchestrate Efficient and Precise Neuromodulatory Signaling}, journal = {bioRxiv}, year = {2024}, month = {2024 Sep 16}, abstract = {

Dopamine is a key chemical neuromodulator that plays vital roles in various brain functions. Traditionally, neuromodulators like dopamine are believed to be released in a diffuse manner and are not commonly associated with synaptic structures where pre- and postsynaptic processes are closely aligned. Our findings challenge this conventional view. Using single-bouton optical measurements of dopamine release, we discovered that dopamine is predominantly released from varicosities that are juxtaposed against the processes of their target neurons. Dopamine axons specifically target neurons expressing dopamine receptors, forming synapses to release dopamine. Interestingly, varicosities that were not directly apposed to dopamine receptor-expressing processes or associated with neurons lacking dopamine receptors did not release dopamine, regardless of their vesicle content. The ultrastructure of dopamine release sites share common features of classical synapses. We further show that the dopamine released at these contact sites induces a precise, dopamine-gated biochemical response in the target processes. Our results indicate that dopamine release sites share key characteristics of conventional synapses that enable relatively precise and efficient neuromodulation of their targets.

}, doi = {10.1101/2024.09.16.613338}, url = {https://doi.org/10.1101/2024.09.16.613338}, author = {Bulumulla, Chandima and Walpita, Deepika and Iyer, Nirmala and Eddison, Mark and Patel, Ronak and Alcor, Damien and Ackerman, David and Beyene, Abraham G} } @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 {69674, title = {Tracking fructose 1,6-bisphosphate dynamics in liver cancer cells using a fluorescent biosensor}, journal = {iScience}, volume = {27}, year = {2024}, month = {2024 Nov 20}, pages = {111336}, abstract = {

Summary HYlight is a genetically encoded fluorescent biosensor that ratiometrically monitors fructose 1,6-bisphosphate (FBP), a key glycolytic metabolite. Given the role of glucose in liver cancer metabolism, we expressed HYlight in human liver cancer cells and primary mouse hepatocytes. Through in\ vitro, in silico, and in cellulo experiments, we showed HYlight{\textquoteright}s ability to monitor FBP changes linked to glycolysis, not gluconeogenesis. HYlight{\textquoteright}s affinity for FBP was \~{}1\ Î¼M and stable within physiological pH range. HYlight demonstrated weak binding to dihydroxyacetone phosphate, and its ratiometric response was influenced by both ionic strength and phosphate. Therefore, simulating cytosolic conditions in\ vitro was necessary to establish a reliable correlation between HYlight{\textquoteright}s cellular responses and FBP concentrations. FBP concentrations were found to be in the lower micromolar range, far lower than previous millimolar estimates. Altogether, this biosensor approach offers real-time monitoring of FBP concentrations at single-cell resolution, making it an invaluable tool for the understanding of cancer metabolism.

}, keywords = {biochemistry methods, cancer, metabolomics}, issn = {2589-0042}, doi = {https://doi.org/10.1016/j.isci.2024.111336}, url = {https://www.sciencedirect.com/science/article/pii/S2589004224025616}, author = {Israel P{\'e}rez-Ch{\'a}vez and John N. Koberstein and Julia Malo Pueyo and Eduardo H. Gilglioni and Didier Vertommen and Nicolas Baeyens and Daria Ezerina and Esteban N. Gurzov and Joris Messens} } @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 {69459, title = {Ultrastructural differences impact cilia shape and external exposure across cell classes in the visual cortex}, journal = {Curr Biol}, year = {2024}, month = {2024 May 13}, abstract = {

A primary cilium is a membrane-bound extension from the cell surface that contains receptors for perceiving and transmitting signals that modulate cell state and activity. Primary cilia in the brain are less accessible than cilia on cultured cells or epithelial tissues because in the brain they protrude into a deep, dense network of glial and neuronal processes. Here, we investigated cilia frequency, internal structure, shape, and position in large, high-resolution transmission electron microscopy volumes of mouse primary visual cortex. Cilia extended from the cell bodies of nearly all excitatory and inhibitory neurons, astrocytes, and oligodendrocyte precursor cells (OPCs) but were absent from oligodendrocytes and microglia. Ultrastructural comparisons revealed that the base of the cilium and the microtubule organization differed between neurons and glia. Investigating cilia-proximal features revealed that many cilia were directly adjacent to synapses, suggesting that cilia are poised to encounter locally released signaling molecules. Our analysis indicated that synapse proximity is likely due to random encounters in the neuropil, with no evidence that cilia modulate synapse activity as would be expected in tetrapartite synapses. The observed cell class differences in proximity to synapses were largely due to differences in external cilia length. Many key structural features that differed between neuronal and glial cilia influenced both cilium placement and shape and, thus, exposure to processes and synapses outside the cilium. Together, the ultrastructure both within and around neuronal and glial cilia suggest differences in cilia formation and function across cell types in the brain.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2024.04.043}, author = {Ott, Carolyn M and Torres, Russel and Kuan, Tung-Sheng and Kuan, Aaron and Buchanan, JoAnn and Elabbady, Leila and Seshamani, Sharmishtaa and Bodor, Agnes L and Collman, Forrest and Bock, Davi D and Lee, Wei Chung and da Costa, Nuno Ma{\c c}arico and Lippincott-Schwartz, Jennifer} } @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 {68808, title = {Cell type-specific contributions to a persistent aggressive internal state in female Drosophila}, journal = {bioRxiv}, year = {2023}, month = {2023 Jun 07}, abstract = {

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

}, doi = {10.1101/2023.06.07.543722}, url = {https://doi.org/10.1101/2023.06.07.543722}, author = {Hui Chiu and Alice A. Robie and Kristin M. Branson and Tanvi Vippa and Samantha Epstein and Gerald M. Rubin and David J. Anderson and Catherine E. Schretter} } @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 {68657, title = {Cristae formation is a mechanical buckling event controlled by the inner membrane lipidome}, journal = {bioRxiv}, year = {2023}, month = {2023 Mar 15}, abstract = {

The inner mitochondrial membrane (IMM) is the site of bulk ATP generation in cells and has a broadly conserved lipid composition enriched in unsaturated phospholipids and cardiolipin (CL). While proteins that shape the IMM and its characteristic cristae membranes (CM) have been defined, specific mechanisms by which mitochondrial lipids dictate its structure and function have yet to be elucidated. Here we combine experimental lipidome dissection with multi-scale modeling to investigate how lipid interactions shape CM morphology and ATP generation. When modulating fatty acid unsaturation in engineered yeast strains, we observed that loss of di-unsaturated phospholipids (PLs) led to a breakpoint in IMM topology and respiratory capacity. We found that PL unsaturation modulates the organization of ATP synthases that shape cristae ridges. Based on molecular modeling of mitochondrial-specific membrane adaptations, we hypothesized that conical lipids like CL buffer against the effects of saturation on the IMM. In cells, we discovered that loss of CL collapses the IMM at intermediate levels of PL saturation, an effect that is independent of ATP synthase oligomerization. To explain this interaction, we employed a continuum modeling approach, finding that lipid and protein-mediated curvatures are predicted to act in concert to form curved membranes in the IMM. The model highlighted a snapthrough instability in cristae tubule formation, which could drive IMM collapse upon small changes in composition. The interaction between CL and di-unsaturated PLs suggests that growth conditions that alter the fatty acid pool, such as oxygen availability, could define CL function. While loss of CL only has a minimal phenotype under standard laboratory conditions, we show that its synthesis is essential under microaerobic conditions that better mimic natural yeast fermentation. Lipid and protein-mediated mechanisms of curvature generation can thus act together to support mitochondrial architecture under changing environments.

}, doi = {10.1101/2023.03.13.532310}, url = {https://doi.org/10.1101/2023.03.13.532310}, author = {Kailash Venkatraman and Christopher T Lee and Guadalupe C. Garcia and Arijit Mahapatra and Guy Perkins and Keun-Young Kim and Hilda Amalia Pasolli and Sebastien Phan and Jennifer Lippincott-Schwartz and Mark Ellisman and Padmini Rangamani and Itay Budin} } @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 {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 {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 {69058, title = {Nanometer-scale views of visual cortex reveal anatomical features of primary cilia poised to detect synaptic spillover}, journal = {bioRxiv}, year = {2023}, month = {2023 Nov 01}, abstract = {

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

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

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

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

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

}, doi = {10.1101/2023.10.27.563951}, url = {https://doi.org/10.1101/2023.10.27.563951}, author = {Luis Wong-Dilworth and Gresy Bregu and Steffen Restel and Carmen Rodilla-Ramirez and Svenja Ebeling and Shelly Harel and Paula Leupold and Jonathan Grimm and Luke D. Lavis and Jessica Angulo-Capel and Felix Campelo and Francesca Bottanelli} } @article {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 {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 {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 {68838, title = {Small-field visual projection neurons detect translational optic flow and support walking control}, journal = {bioRxiv}, year = {2023}, month = {2023 Jun 22}, abstract = {

Animals rely on visual motion for navigating the world, and research in flies has clarified how neural circuits extract information from moving visual scenes. However, the major pathways connecting these patterns of optic flow to behavior remain poorly understood. Using a high-throughput quantitative assay of visually guided behaviors and genetic neuronal silencing, we discovered a region in\ Drosophila{\textquoteright}s protocerebrum critical for visual motion following. We used neuronal silencing, calcium imaging, and optogenetics to identify a single cell type, LPC1, that innervates this region, detects translational optic flow, and plays a key role in regulating forward walking. Moreover, the population of LPC1s can estimate the travelling direction, such as when gaze direction diverges from body heading. By linking specific cell types and their visual computations to specific behaviors, our findings establish a foundation for understanding how the nervous system uses vision to guide navigation.

}, doi = {10.1101/2023.06.21.546024}, url = {https://doi.org/10.1101/2023.06.21.546024}, author = {Mathew D. Isaacson and Jessica L. M. Eliason and Aljoscha Nern and Edward M. Rogers and Gus K. Lott and Tanya Tabachnik and William J. Rowell and Austin W. Edwards and Wyatt L. Korff and Gerald M. Rubin and Kristin Branson and Michael B. Reiser} } @article {68606, title = {TEMPO enables sequential genetic labeling and manipulation of vertebrate cell lineages.}, journal = {Neuron}, volume = {111}, year = {2023}, month = {2023 Feb 01}, pages = {345-361.e10}, abstract = {

During development, regulatory factors appear in a precise order to determine cell fates over time. Consequently, to investigate complex tissue development, it is necessary to visualize and manipulate cell lineages with temporal control. Current strategies for tracing vertebrate cell lineages lack genetic access to sequentially produced cells. Here, we present TEMPO (Temporal Encoding and Manipulation in a Predefined Order), an imaging-readable genetic tool allowing differential labeling and manipulation of consecutive cell generations in vertebrates. TEMPO is based on CRISPR and powered by a cascade of gRNAs that drive orderly activation and inactivation of reporters and/or effectors. Using TEMPO to visualize zebrafish and mouse neurogenesis, we recapitulated birth-order-dependent neuronal fates. Temporally manipulating cell-cycle regulators in mouse cortex progenitors altered the proportion and distribution of neurons and glia, revealing the effects of temporal gene perturbation on serial cell fates. Thus, TEMPO enables sequential manipulation of molecular factors, crucial to study cell-type specification.

}, keywords = {Animals, Cell Differentiation, Cell Lineage, Gene Expression Regulation, Developmental, Mice, Neurogenesis, Neuroglia, Neurons, Zebrafish}, issn = {1097-4199}, doi = {10.1016/j.neuron.2022.10.035}, author = {Espinosa-Medina, Isabel and Feliciano, Daniel and Belmonte-Mateos, Carla and Linda Miyares, Rosa and Garcia-Marques, Jorge and Foster, Benjamin and Lindo, Sarah and Pujades, Cristina and Koyama, Minoru and Lee, Tzumin} } @article {68884, title = {Ten-fold Robust Expansion Microscopy.}, journal = {Bio-Protocol}, volume = {13}, year = {2023}, month = {2023 Jun 20}, pages = {e4698}, abstract = {

Expansion microscopy (ExM) is a powerful technique to overcome the diffraction limit of light microscopy that can be applied in both tissues and cells. In ExM, samples are embedded in a swellable polymer gel to physically expand the sample and isotropically increase resolution in x, y, and z. By systematic exploration of the ExM recipe space, we developed a novel ExM method termed Ten-fold Robust Expansion Microscopy (TREx) that, as the original ExM method, requires no specialized equipment or procedures. TREx enables ten-fold expansion of both thick mouse brain tissue sections and cultured human cells, can be handled easily, and enables high-resolution subcellular imaging with a single expansion step. Furthermore, TREx can provide ultrastructural context to subcellular protein localization by combining antibody-stained samples with off-the-shelf small molecule stains for both total protein and membranes.

}, issn = {2331-8325}, doi = {10.21769/BioProtoc.4698}, author = {Damstra, Hugo G J and Mohar, Boaz and Eddison, Mark and Akhmanova, Anna and Kapitein, Lukas C and Tillberg, Paul W} } @article {68674, title = {Time-resolved correlation of distributed brain activity tracks E-I balance and accounts for diverse scale-free phenomena.}, journal = {Cell Reports}, volume = {42}, year = {2023}, month = {2023 Mar 24}, pages = {112254}, abstract = {

Much of systems neuroscience posits the functional importance of brain activity patterns that lack natural scales of sizes, durations, or frequencies. The field has developed prominent, and sometimes competing, explanations for the nature of this scale-free activity. Here, we reconcile these explanations across species and modalities. First, we link estimates of excitation-inhibition (E-I) balance with time-resolved correlation of distributed brain activity. Second, we develop an unbiased method for sampling time series constrained by this time-resolved correlation. Third, we use this method to show that estimates of E-I balance account for diverse scale-free phenomena without need to attribute additional function or importance to these phenomena. Collectively, our results simplify existing explanations of scale-free brain activity and provide stringent tests on future theories that seek to transcend these explanations.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2023.112254}, author = {Nanda, Aditya and Johnson, Graham W and Mu, Yu and Ahrens, Misha B and Chang, Catie and Englot, Dario J and Breakspear, Michael and Rubinov, Mikail} } @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 {68809, title = {Transforming descending input into behavior: The organization of premotor circuits in the Drosophila Male Adult Nerve Cord connectome}, journal = {bioRxiv}, year = {2023}, month = {2023 Jun 07}, abstract = {

In most animals, a relatively small number of descending neurons (DNs) connect higher brain centers in the animal{\textquoteright}s head to motor neurons (MNs) in the nerve cord of the animal{\textquoteright}s body that effect movement of the limbs. To understand how brain signals generate behavior, it is critical to understand how these descending pathways are organized onto the body MNs. In the fly, Drosophila melanogaster, MNs controlling muscles in the leg, wing, and other motor systems reside in a ventral nerve cord (VNC), analogous to the mammalian spinal cord. In companion papers, we introduced a densely-reconstructed connectome of the Drosophila Male Adult Nerve Cord (MANC,\ Takemura et al., 2023), including cell type and developmental lineage annotation (Marin et al., 2023), which provides complete VNC connectivity at synaptic resolution. Here, we present a first look at the organization of the VNC networks connecting DNs to MNs based on this new connectome information. We proofread and curated all DNs and MNs to ensure accuracy and reliability, then systematically matched DN axon terminals and MN dendrites with light microscopy data to link their VNC morphology with their brain inputs or muscle targets. We report both broad organizational patterns of the entire network and fine-scale analysis of selected circuits of interest. We discover that direct DN-MN connections are infrequent and identify communities of intrinsic neurons linked to control of different motor systems, including putative ventral circuits for walking, dorsal circuits for flight steering and power generation, and intermediate circuits in the lower tectulum for coordinated action of wings and legs. Our analysis generates hypotheses for future functional experiments and, together with the MANC connectome, empowers others to investigate these and other circuits of the Drosophila ventral nerve cord in richer mechanistic detail.

}, doi = {10.1101/2023.06.07.543976}, url = {https://doi.org/10.1101/2023.06.07.543976}, author = {H. S. J. Cheong and K. Eichler and T. Stuerner and S. K. Asinof and A. S. Champion and E. C. Marin and T. B. Oram and M. Sumathipala and L. Venkatasubramanian and S. Namiki and I. Siwanowicz and M. Costa and S. Berg and Janelia FlyEM Project Team and G. S. X. E. Jefferis and G. M. Card} } @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 {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 {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 {68462, title = {Cap-dependent translation initiation monitored in living cells.}, journal = {Nature Communications}, volume = {13}, year = {2022}, month = {2022 Nov 02}, pages = {6558}, abstract = {

mRNA translation is tightly regulated to preserve cellular homeostasis. Despite extensive biochemical, genetic, and structural studies, a detailed understanding of mRNA translation regulation is lacking. Imaging methodologies able to resolve the binding dynamics of translation factors at single-cell and single-mRNA resolution were necessary to fully elucidate regulation of this paramount process. Here live-cell spectroscopy and single-particle tracking were combined to interrogate the binding dynamics of endogenous initiation factors to the 5{\textquoteright}cap. The diffusion of initiation factors (IFs) changed markedly upon their association with mRNA. Quantifying their diffusion characteristics revealed the sequence of IFs assembly and disassembly in cell lines and the clustering of translation in neurons. This approach revealed translation regulation at high spatial and temporal resolution that can be applied to the formation of any endogenous complex that results in a measurable shift in diffusion.

}, keywords = {Peptide Chain Initiation, Translational, Peptide Initiation Factors, Protein Biosynthesis, RNA Caps, RNA, Messenger}, issn = {2041-1723}, doi = {10.1038/s41467-022-34052-8}, author = {Gandin, Valentina and English, Brian P and Freeman, Melanie and Leroux, Louis-Philippe and Preibisch, Stephan and Walpita, Deepika and Jaramillo, Maritza and Singer, Robert H} } @article {67857, title = {Characterization of ultrapotent chemogenetic ligands for research applications in non-human primates}, journal = {bioRxiv}, year = {2022}, month = {2022 Jan 07}, abstract = {

Chemogenetics is a technique for obtaining selective pharmacological control over a cell population by expressing an engineered receptor that is selectively activated by an exogenously administered ligand. A promising approach for neuronal modulation involves the use of {\textquotedblleft}Pharmacologically Selective Actuator Modules{\textquotedblright} (PSAMs); these chemogenetic receptors are selectively activated by ultrapotent {\textquotedblleft}Pharmacologically Selective Effector Molecules{\textquotedblright} (uPSEMs). To extend the use of PSAM/PSEMs to studies in nonhuman primates it is necessary to thoroughly characterize the efficacy and safety of these tools. We describe the time course and brain penetrance in rhesus monkeys of two compounds with promising binding specificity and efficacy profiles in\ in vitro\ studies, uPSEM792 and uPSEM817, after systemic administration. Rhesus macaques received subcutaneous (s.c.) or intravenous (i.v.) administration of uPSEM817(0.064 mg/kg) or uPSEM792 (0.87 mg/kg) and plasma and CSF samples were collected over the course of 48 hours. Both compounds exhibited good brain penetrance, relatively slow washout and negligible conversion to potential metabolites - varenicline or hydroxyvarenicline. In addition, we found that neither of these uPSEMs significantly altered heart rate or sleep. Our results indicate that both compounds are suitable candidates for neuroscience studies using PSAMs in nonhuman primates.

}, doi = {10.1101/2022.01.06.475241}, url = {https://doi.org/10.1101/2022.01.06.475241}, author = {Jessica Raper and Mark A. G. Eldridge and Scott. M. Sternson and Jalene Y. Shim and Grace P. Fomani and Barry J. Richmond and Thomas Wichmann and Adriana Galvan} } @article {68411, title = {Characterization of Ultrapotent Chemogenetic Ligands for Research Applications in Nonhuman Primates.}, journal = {ACS Chemical Neuroscience}, volume = {13}, year = {2022}, month = {2022 Nov 02}, pages = {3118-3125}, abstract = {

Chemogenetics is a technique for obtaining selective pharmacological control over a cell population by expressing an engineered receptor that is selectively activated by an exogenously administered ligand. A promising approach for neuronal modulation involves the use of "Pharmacologically Selective Actuator Modules" (PSAMs); these chemogenetic receptors are selectively activated by ultrapotent "Pharmacologically Selective Effector Molecules" (uPSEMs). To extend the use of PSAM/PSEMs to studies in nonhuman primates, it is necessary to thoroughly characterize the efficacy and safety of these tools. We describe the time course and brain penetrance in rhesus monkeys of two compounds with promising binding specificity and efficacy profiles in studies, uPSEM792 and uPSEM817, after systemic administration. Rhesus monkeys received subcutaneous (s.c.) or intravenous (i.v.) administration of uPSEM817 (0.064 mg/kg) or uPSEM792 (0.87 mg/kg), and plasma and cerebrospinal fluid samples were collected over 48 h. Both compounds exhibited good brain penetrance, relatively slow washout, and negligible conversion to potential metabolites-varenicline or hydroxyvarenicline. In addition, we found that neither of these uPSEMs significantly altered the heart rate or sleep. Our results indicate that both compounds are suitable candidates for neuroscience studies using PSAMs in nonhuman primates.

}, keywords = {Animals, Brain, Ligands, Macaca mulatta, Neurons, Varenicline}, issn = {1948-7193}, doi = {10.1021/acschemneuro.2c00525}, author = {Raper, Jessica and Eldridge, Mark A G and Sternson, Scott M and Shim, Jalene Y and Fomani, Grace P and Richmond, Barry J and Wichmann, Thomas and Galvan, Adriana} } @article {67990, title = {Cryo-EM structures of the human GATOR1-Rag-Ragulator complex reveal a spatial-constraint regulated GAP mechanism.}, journal = {Molecular Cell}, volume = {36}, year = {2022}, month = {2022 May 01}, abstract = {

mTORC1 controls cellular metabolic processes in response to nutrient availability. Amino acid signals are transmitted to mTORC1 through the Rag GTPases, which are localized on the lysosomal surface by the Ragulator complex. The Rag GTPases receive amino acid signals from multiple upstream regulators. One negative regulator, GATOR1, is a GTPase activating protein (GAP) for RagA. GATOR1 binds to the Rag GTPases via two modes: an inhibitory mode and a GAP mode. How these two binding interactions coordinate to process amino acid signals is unknown. Here, we resolved three cryo-EM structural models of the GATOR1-Rag-Ragulator complex, with the Rag-Ragulator subcomplex occupying the inhibitory site, the GAP site, and both binding sites simultaneously. When the Rag GTPases bind to GATOR1 at the GAP site, both Rag subunits contact GATOR1 to coordinate their nucleotide loading states. These results reveal a potential GAP mechanism of GATOR1 during the mTORC1 inactivation process.

}, issn = {1097-4164}, doi = {10.1016/j.molcel.2022.03.002}, author = {Egri, Shawn B and Ouch, Christna and Chou, Hui-Ting and Yu, Zhiheng and Song, Kangkang and Xu, Chen and Shen, Kuang} } @article {68147, title = {Drosophila gustatory projections are segregated by taste modality and connectivity.}, journal = {eLife}, volume = {11}, year = {2022}, month = {2022 May 25}, abstract = {

Gustatory sensory neurons detect caloric and harmful compounds in potential food and convey this information to the brain to inform feeding decisions. To examine the signals that gustatory neurons transmit and receive, we reconstructed gustatory axons and their synaptic sites in the adult brain, utilizing a whole-brain electron microscopy volume. We reconstructed 87 gustatory projections from the proboscis labellum in the right hemisphere and 57 from the left, representing the majority of labellar gustatory axons. Gustatory neurons contain a nearly equal number of interspersed pre- and postsynaptic sites, with extensive synaptic connectivity among gustatory axons. Morphology- and connectivity-based clustering revealed six distinct groups, likely representing neurons recognizing different taste modalities. The vast majority of synaptic connections are between neurons of the same group. This study resolves the anatomy of labellar gustatory projections, reveals that gustatory projections are segregated based on taste modality, and uncovers synaptic connections that may alter the transmission of gustatory signals.

}, keywords = {Animals, Drosophila, Drosophila melanogaster, Drosophila Proteins, Sensory Receptor Cells, Taste}, issn = {2050-084X}, doi = {10.7554/eLife.78110}, author = {Engert, Stefanie and Sterne, Gabriella R and Bock, Davi D and Scott, Kristin} } @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 {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 {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 {67858, title = {The importance of accounting for movement when relating neuronal activity to sensory and cognitive processes.}, journal = {Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {42}, year = {2022}, month = {2022 Feb 23}, pages = {1375-1382}, abstract = {

A surprising finding of recent studies in mouse is the dominance of widespread\ movement-related\ activity\ throughout the brain, including in early\ sensory\ areas. In awake subjects, failing to\ account\ for\ movement\ risks misattributing\ movement-related\ activity\ to other (e.g.,\ sensory\ or\ cognitive)\ processes. In this article, we 1) review task designs for separating task-related\ and\ movement-related\ activity, 2) review three {\textquoteright}case studies{\textquoteright} in which\ not\ considering\ movement\ would have resulted in critically different interpretations of\ neuronal\ function, and 3) discuss functional couplings that may prevent us from ever fully isolating\ sensory,\ motor, and\ cognitive-related\ activity. Our main thesis is that neural signals\ related\ to\ movement\ are ubiquitous, and therefore ought to be considered first and foremost when attempting to correlate\ neuronal\ activity\ with task-related\ processes.

}, doi = {10.1523/JNEUROSCI.1919-21.2021}, author = {Edward Zagha and Jeffrey C Erlich and Soohyun Lee and Gyorgy Lur and Daniel H O{\textquoteright}Connor and Nicholas A Steinmetz and Carsen Stringer and Hongdian Yang} } @article {68556, title = {Inhibition of coronavirus HCoV-OC43 by targeting the eIF4F complex.}, journal = {Frontiers in Pharmacology}, volume = {13}, year = {2022}, month = {2022 Dec 01}, pages = {1029093}, abstract = {

The translation initiation complex 4F (eIF4F) is a rate-limiting factor in protein synthesis. Alterations in eIF4F activity are linked to several diseases, including cancer and infectious diseases. To this end, coronaviruses require eIF4F complex activity to produce proteins essential for their life cycle. Efforts to target coronaviruses by abrogating translation have been largely limited to repurposing existing eIF4F complex inhibitors. Here, we report the results of a high throughput screen to identify small molecules that disrupt eIF4F complex formation and inhibit coronavirus RNA and protein levels. Of 338,000 small molecules screened for inhibition of the eIF4F-driven, CAP-dependent translation, we identified SBI-1232 and two structurally related analogs, SBI-5844 and SBI-0498, that inhibit human coronavirus OC43 (HCoV-OC43; OC43) with minimal cell toxicity. Notably, gene expression changes after OC43 infection of Vero E6 or A549 cells were effectively reverted upon treatment with SBI-5844 or SBI-0498. Moreover, SBI-5844 or SBI-0498 treatment effectively impeded the eIF4F complex assembly, with concomitant inhibition of newly synthesized OC43 nucleocapsid protein and OC43 RNA and protein levels. Overall, we identify SBI-5844 and SBI-0498 as small molecules targeting the eIF4F complex that may limit coronavirus transcripts and proteins, thereby representing a basis for developing novel therapeutic modalities against coronaviruses.

}, issn = {1663-9812}, doi = {10.3389/fphar.2022.1029093}, author = {Feng, Yongmei and Grotegut, Stefan and Jovanovic, Predrag and Gandin, Valentina and Olson, Steven H and Murad, Rabi and Beall, Anne and Colayco, Sharon and De-Jesus, Paul and Chanda, Sumit and English, Brian P and Singer, Robert H and Jackson, Michael and Topisirovic, Ivan and Ronai, Ze{\textquoteright}ev A} } @article {68273, title = {Neural network organization for courtship-song feature detection in Drosophila.}, journal = {Current Biology}, volume = {32}, year = {2022}, month = {2022 Aug 08}, pages = {3317-3333.e7}, abstract = {

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

}, keywords = {Animals, Auditory Perception, Courtship, Drosophila, Drosophila melanogaster, Neural Networks, Computer, Sexual Behavior, Animal, Vocalization, Animal}, issn = {1879-0445}, doi = {10.1016/j.cub.2022.06.019}, author = {Baker, Christa A and McKellar, Claire and Pang, Rich and Nern, Aljoscha and Dorkenwald, Sven and Pacheco, Diego A and Eckstein, Nils and Funke, Jan and Dickson, Barry J and Murthy, Mala} } @article {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 {67873, title = {Open-source, Python-based, hardware and software for controlling behavioural neuroscience experiments.}, journal = {eLife}, volume = {11}, year = {2022}, month = {2022 Jan 19}, abstract = {

Laboratory behavioural tasks are an essential research tool. As questions asked of behaviour and brain activity become more sophisticated, the ability to specify and run richly structured tasks becomes more important. An increasing focus on reproducibility also necessitates accurate communication of task logic to other researchers. To these ends, we developed pyControl, a system of open-source hardware and software for controlling behavioural experiments comprising a simple yet flexible Python-based syntax for specifying tasks as extended state machines, hardware modules for building behavioural setups, and a graphical user interface designed for efficiently running high-throughput experiments on many setups in parallel, all with extensive online documentation. These tools make it quicker, easier, and cheaper to implement rich behavioural tasks at scale. As important, pyControl facilitates communication and reproducibility of behavioural experiments through a highly readable task definition syntax and self-documenting features. Here, we outline the system{\textquoteright}s design and rationale, present validation experiments characterising system performance, and demonstrate example applications in freely moving and head-fixed mouse behaviour.

}, issn = {2050-084X}, doi = {10.7554/eLife.67846}, author = {Akam, Thomas and Lustig, Andy and Rowland, James M and Kapanaiah, Sampath Kt and Esteve-Agraz, Joan and Panniello, Mariangela and M{\'a}rquez, Cristina and Kohl, Michael M and K{\"a}tzel, Dennis and Costa, Rui M and Walton, Mark E} } @article {68370, title = {A proliferative to invasive switch is mediated by srGAP1 downregulation through the activation of TGF-β2 signaling.}, journal = {Cell Reports}, volume = {40}, year = {2022}, month = {2022 Sep 20}, pages = {111358}, abstract = {

Many breast cancer (BC) patients suffer from complications of metastatic disease. To form metastases, cancer cells must become migratory and coordinate both invasive and proliferative programs at distant organs. Here, we identify srGAP1 as a regulator of a proliferative-to-invasive switch in BC cells. High-resolution light-sheet microscopy demonstrates that BC cells can form actin-rich protrusions during extravasation. srGAP1 cells display a motile and invasive phenotype that facilitates their extravasation from blood vessels, as shown in zebrafish and mouse models, while attenuating tumor growth. Interestingly, a population of srGAP1 cells remain as solitary disseminated tumor cells in the lungs of mice bearing BC tumors. Overall, srGAP1 cells have increased Smad2 activation and TGF-β2 secretion, resulting in increased invasion and p27 levels to sustain quiescence. These findings identify srGAP1 as a mediator of a proliferative to invasive phenotypic switch in BC cells in\ vivo through a TGF-β2-mediated signaling axis.

}, keywords = {Actins, Animals, Cell Line, Tumor, Down-Regulation, Mice, Transforming Growth Factor beta2, Zebrafish}, issn = {2211-1247}, doi = {10.1016/j.celrep.2022.111358}, author = {Mondal, Chandrani and Gacha-Garay, Majo J and Larkin, Kathryn A and Adikes, Rebecca C and Di Martino, Julie S and Chien, Chen-Chi and Fraser, Madison and Eni-Aganga, Ireti and Agullo-Pascual, Esperanza and Cialowicz, Katarzyna and Ozbek, Umut and Naba, Alexandra and Gaitas, Angelo and Fu, Tian-Ming and Upadhyayula, Srigokul and Betzig, Eric and Matus, David Q and Martin, Benjamin L and Bravo-Cordero, Jose Javier} } @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 {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 {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 {67948, title = {Taste quality interactions and transformations in a sensorimotor circuit}, journal = {eLife}, year = {2022}, month = {2022 Jul 06}, abstract = {

Taste detection and hunger state dynamically regulate the decision to initiate feeding. To study how context-appropriate feeding decisions are generated, we combined synaptic resolution circuit reconstruction with targeted genetic access to specific neurons to elucidate a gustatory sensorimotor circuit for feeding initiation in\ Drosophila melanogaster. This circuit connects gustatory sensory neurons to proboscis motor neurons through three intermediate layers. Most of the neurons in this pathway are necessary and sufficient for proboscis extension, a feeding initiation behavior, and respond selectively to sugar taste detection. Hunger signals act at select second-order neurons to increase feeding initiation in food-deprived animals. In contrast, a bitter taste pathway inhibits premotor neurons, illuminating a central mechanism that weighs sugar and bitter tastes to promote or inhibit feeding. Together, these studies reveal the neural circuit basis for the integration of external taste detection and internal nutritive state to flexibly execute a critical feeding decision.

}, doi = {10.1101/2022.03.06.483180}, url = {https://doi.org/10.1101/2022.03.06.483180}, author = {Philip K. Shiu and Gabriella R. Sterne and Stefanie Engert and Barry J. Dickson and Kristin Scott} } @article {68518, title = {TEMPO enables sequential genetic labeling and manipulation of vertebrate cell lineages.}, journal = {Neuron}, year = {2022}, month = {2022 Nov 18}, abstract = {

During development, regulatory factors appear in a precise order to determine cell fates over time. Consequently, to investigate complex tissue development, it is necessary to visualize and manipulate cell lineages with temporal control. Current strategies for tracing vertebrate cell lineages lack genetic access to sequentially produced cells. Here, we present TEMPO (Temporal Encoding and Manipulation in a Predefined Order), an imaging-readable genetic tool allowing differential labeling and manipulation of consecutive cell generations in vertebrates. TEMPO is based on CRISPR and powered by a cascade of gRNAs that drive orderly activation and inactivation of reporters and/or effectors. Using TEMPO to visualize zebrafish and mouse neurogenesis, we recapitulated birth-order-dependent neuronal fates. Temporally manipulating cell-cycle regulators in mouse cortex progenitors altered the proportion and distribution of neurons and glia, revealing the effects of temporal gene perturbation on serial cell fates. Thus, TEMPO enables sequential manipulation of molecular factors, crucial to study cell-type specification.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2022.10.035}, author = {Espinosa-Medina, Isabel and Feliciano, Daniel and Belmonte-Mateos, Carla and Linda Miyares, Rosa and Garcia-Marques, Jorge and Foster, Benjamin and Lindo, Sarah and Pujades, Cristina and Koyama, Minoru and Lee, Tzumin} } @article {66029, title = {Visualizing cellular and tissue ultrastructure using Ten-fold Robust Expansion Microscopy (TREx)}, journal = {eLife}, year = {2022}, month = {2022 Feb 18}, abstract = {

Expansion microscopy (ExM) is a powerful technique to overcome the diffraction limit of light microscopy that can be applied in both tissues and cells. In ExM, samples are embedded in a swellable polymer gel to physically expand the sample and isotropically increase resolution in x, y and z. The maximum resolution increase is limited by the expansion factor of the polymer gel, which is four-fold for the original ExM protocol. Variations on the original ExM method have been reported that allow for greater expansion factors, for example using iterative expansion, but at the cost of ease of adoption or versatility. Here, we systematically explore the ExM recipe space and present a novel method termed Ten-fold Robust Expansion Microscopy (TREx) that, like the original ExM method, requires no specialized equipment or procedures to carry out. We demonstrate that TREx gels expand ten-fold, can be handled easily, and can be applied to both thick tissue sections and cells enabling high-resolution subcellular imaging in a single expansion step. We show that applying TREx on antibody-stained samples can be combined with off-the-shelf small molecule stains for both total protein and membranes to provide ultrastructural context to subcellular protein localization.

}, doi = {https://doi.org/10.1101/2021.02.03.428837}, author = {Hugo G.J. Damstra and Boaz Mohar and Mark Eddison and Anna Akhmanova and Lukas C. Kapitein and Paul W. Tillberg} } @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 {65319, title = {Accurate localization of linear probe electrodes across multiple brains.}, journal = {eNeuro}, volume = {8}, year = {2021}, month = {2021 Nov 12}, pages = {ENEURO.0241-21.2021}, author = {Liu, Liu D. and Chen, Susu and Economo, Michael N. and Li, Nuo and Svoboda, Karel} } @article {67299, title = {Algorithms underlying flexible phototaxis in larval zebrafish.}, journal = {Journal of Experimental Biology}, volume = {224}, year = {2021}, month = {2021 May 15}, abstract = {

To thrive, organisms must maintain physiological and environmental variables in suitable ranges. Given that these variables undergo constant fluctuations over varying time scales, how do biological control systems maintain control over these values? We explored this question in the context of phototactic behavior in larval zebrafish. We demonstrate that larval zebrafish use phototaxis to maintain environmental luminance at a set point, that the value of this set point fluctuates on a time scale of seconds when environmental luminance changes, and that it is determined by calculating the mean input across both sides of the visual field. These results expand on previous studies of flexible phototaxis in larval zebrafish; they suggest that larval zebrafish exert homeostatic control over the luminance of their surroundings, and that feedback from the surroundings drives allostatic changes to the luminance set point. As such, we describe a novel behavioral algorithm with which larval zebrafish exert control over a sensory variable.

}, issn = {1477-9145}, doi = {10.1242/jeb.238386}, author = {Chen, Alex B and Deb, Diptodip and Bahl, Armin and Engert, Florian} } @article {66903, title = {The art of lineage tracing: From worm to human.}, journal = {Progress in Neurobiology}, volume = {199}, year = {2021}, month = {2021 Apr}, pages = {101966}, abstract = {

Reconstructing the genealogy of every cell that makes up an organism remains a long-standing challenge in developmental biology. Besides its relevance for understanding the mechanisms underlying normal and pathological development, resolving the lineage origin of cell types will be crucial to create these types on-demand. Multiple strategies have been deployed towards the problem of lineage tracing, ranging from direct observation to sophisticated genetic approaches. Here we discuss the achievements and limitations of past and current technology. Finally, we speculate about the future of lineage tracing and how to reach the next milestones in the field.

}, issn = {1873-5118}, doi = {10.1016/j.pneurobio.2020.101966}, author = {Garcia-Marques, Jorge and Isabel Espinosa Medina and Lee, Tzumin} } @article {67231, title = {Attractor dynamics gate cortical information flow during decision-making.}, journal = {Nature Neuroscience}, volume = {24}, year = {2021}, month = {2021 Jun 1}, pages = {843-50}, abstract = {

Decisions are held in memory until enacted, which makes them potentially vulnerable to distracting sensory input. Gating of information flow from sensory to motor areas could protect memory from interference during decision-making, but the underlying network mechanisms are not understood. Here, we trained mice to detect optogenetic stimulation of the somatosensory cortex, with a delay separating sensation and action. During the delay, distracting stimuli lost influence on behavior over time, even though distractor-evoked neural activity percolated through the cortex without attenuation. Instead, choice-encoding activity in the motor cortex became progressively less sensitive to the impact of distractors. Reverse engineering of neural networks trained to reproduce motor cortex activity revealed that the reduction in sensitivity to distractors was caused by a growing separation in the neural activity space between attractors that encode alternative decisions. Our results show that communication between brain regions can be gated via attractor dynamics, which control the degree of commitment to an action.

}, issn = {1546-1726}, doi = {10.1038/s41593-021-00840-6}, author = {Finkelstein, Arseny and Fontolan, Lorenzo and Economo, Michael N and Li, Nuo and Romani, Sandro and Svoboda, Karel} } @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 {67793, title = {Circuits for integrating learned and innate valences in the insect brain.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Nov 10}, abstract = {

Animal behavior is shaped both by evolution and by individual experience. Parallel brain pathways encode innate and learned valences of cues, but the way in which they are integrated during action-selection is not well understood. We used electron microscopy to comprehensively map with synaptic resolution all neurons downstream of all Mushroom Body output neurons (encoding learned valences) and characterized their patterns of interaction with Lateral Horn neurons (encoding innate valences) in larva. The connectome revealed multiple types that receive convergent Mushroom Body and Lateral Horn inputs. A subset of these receives excitatory input from positive-valence MB and LH pathways and inhibitory input from negative-valence MB pathways. We confirmed functional connectivity from LH and MB pathways and behavioral roles of two of these neurons. These neurons encode integrated odor value and bidirectionally regulate turning. Based on this we speculate that learning could potentially skew the balance of excitation and inhibition onto these neurons and thereby modulate turning. Together, our study provides insights into the circuits that integrate learned and innate valences to modify behavior.

}, issn = {2050-084X}, doi = {10.7554/eLife.62567}, author = {Eschbach, Claire and Fushiki, Akira and Winding, Michael and Afonso, Bruno and Andrade, Ingrid V and Cocanougher, Benjamin T and Eichler, Katharina and Gepner, Ruben and Si, Guangwei and Valdes-Aleman, Javier and Fetter, Richard D and Gershow, Marc and Jefferis, Gregory Sxe and Samuel, Aravinthan Dt and Truman, James W and Cardona, Albert and Zlatic, Marta} } @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\ Î¼m) 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 {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 {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 {67712, title = {A genetic screen for Drosophila social isolation mutants and analysis of sex pistol.}, journal = {Scientific Reports}, volume = {11}, year = {2021}, month = {2021 Aug 30}, pages = {17395}, abstract = {

Prolonged periods of forced social isolation is detrimental to well-being, yet we know little about which genes regulate susceptibility to its effects. In the fruit fly, Drosophila melanogaster, social isolation induces stark changes in behavior including increased aggression, locomotor activity, and resistance to ethanol sedation. To identify genes regulating sensitivity to isolation, I screened a collection of sixteen hundred P-element insertion lines for mutants with abnormal levels of all three isolation-induced behaviors. The screen identified three mutants whose affected genes are likely central to regulating the effects of isolation in flies. One mutant, sex pistol (sxp), became extremely aggressive and resistant to ethanol sedation when socially isolated. sxp also had a high level of male-male courtship. The mutation in sxp reduced the expression of two minor isoforms of the actin regulator hts (adducin), as well as mildly reducing expression of CalpA, a calcium-dependent protease. As a consequence, sxp also had increased expression of the insulin-like peptide, dILP5. Analysis of the social behavior of sxp suggests that these minor hts isoforms function to limit isolation-induced aggression, while chronically high levels of dILP5 increase male-male courtship.

}, issn = {2045-2322}, doi = {10.1038/s41598-021-96871-x}, author = {Eddison, Mark} } @article {67263, title = {Hunger or thirst state uncertainty is resolved by outcome evaluation in medial prefrontal cortex to guide decision-making.}, journal = {Nature Neuroscience}, volume = {24}, year = {2021}, month = {2021 Jul 01}, pages = {907-912}, abstract = {

Physiological need states direct decision-making toward re-establishing homeostasis. Using a two-alternative forced choice task for mice that models elements of human decisions, we found that varying hunger and thirst states caused need-inappropriate choices, such as food seeking when thirsty. These results show limits on interoceptive knowledge of hunger and thirst states to guide decision-making. Instead, need states were identified after food and water consumption by outcome evaluation, which depended on the medial prefrontal cortex.

}, issn = {1546-1726}, doi = {10.1038/s41593-021-00850-4}, author = {Eiselt, Anne-Kathrin and Chen, Susu and Chen, Jim and Arnold, Jon and Kim, Tahnbee and Pachitariu, Marius and Sternson, Scott M} } @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 {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 {66900, title = {pyControl: Open source, Python based, hardware and software for controlling behavioural neuroscience experiments}, journal = {bioRxiv}, year = {2021}, month = {2021 Feb 23}, abstract = {

Laboratory behavioural tasks are an essential research tool. As questions asked of behaviour and brain activity become more sophisticated, the ability to specify and run richly structured tasks becomes more important. An increasing focus on reproducibility also necessitates accurate communication of task logic to other researchers. To these ends we developed pyControl, a system of open source hardware and software for controlling behavioural experiments comprising; a simple yet flexible Python-based syntax for specifying tasks as extended state machines, hardware modules for building behavioural setups, and a graphical user interface designed for efficiently running high throughput experiments on many setups in parallel, all with extensive online documentation. These tools make it quicker, easier and cheaper to implement rich behavioural tasks at scale. As important, pyControl facilitates communication and reproducibility of behavioural experiments through a highly readable task definition syntax and self-documenting features.

}, doi = {https://doi.org/10.1101/2021.02.22.432227}, author = {Thomas Akam and Andy Lustig and James Rowland and Sampath K.T. Kapanaiah and Joan Esteve-Agraz and Mariangela Panniello and Cristina Marquez and Michael Kohl and Dennis K{\"a}tzel and Rui M. Costa and Mark Walton} } @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 {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 {67673, title = {Spatially patterned excitatory neuron subtypes and projections of the claustrum.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Aug 16}, abstract = {

The claustrum is a functionally and structurally complex brain region, whose very spatial extent remains debated. Histochemical-based approaches typically treat the claustrum as a relatively narrow anatomical region that primarily projects to the neocortex, whereas circuit-based approaches can suggest a broader claustrum region containing projections to the neocortex and other regions. Here, in the mouse, we took a bottom-up and cell-type-specific approach to complement and possibly unite these seemingly disparate conclusions. Using single-cell RNA-sequencing, we found that the claustrum comprises two excitatory neuron subtypes that are differentiable from the surrounding cortex. Multicolor retrograde tracing in conjunction with 12-channel multiplexed in situ hybridization revealed a core-shell spatial arrangement of these subtypes, as well as differential downstream targets. Thus, the claustrum comprises excitatory neuron subtypes with distinct molecular and projection properties, whose spatial patterns reflect the narrower and broader claustral extents debated in previous research. This subtype-specific heterogeneity likely shapes the functional complexity of the claustrum.

}, issn = {2050-084X}, doi = {10.7554/eLife.68967}, author = {Erwin, Sarah R and Bristow, Brianna N and Sullivan, Kaitlin E and Kendrick, Rennie M and Marriott, Brian and Wang, Lihua and Clements, Jody and Lemire, Andrew L and Jackson, Jesse and Cembrowski, Mark S} } @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 {68342, title = {TEMPO: A system to sequentially label and genetically manipulate vertebrate cell lineages}, journal = {bioRxiv}, year = {2021}, month = {10/2021}, abstract = {

During development, regulatory factors appear in a precise order to determine cell fates over time. To investigate complex tissue development, one should not just label cell lineages but further visualize and manipulate cells with temporal control. Current strategies for tracing vertebrate cell lineages lack genetic access to sequentially produced cells. Here we present TEMPO (Temporal Encoding and Manipulation in a Predefined Order), an imaging-readable genetic tool allowing differential labelling and manipulation of consecutive cell generations in vertebrates. TEMPO is based on CRISPR and powered by a cascade of gRNAs that drive orderly activation/inactivation of reporters/effectors. Using TEMPO to visualize zebrafish and mouse neurogenesis, we recapitulated birth-order-dependent neuronal fates. Temporally manipulating cell-cycle regulators in mouse cortex progenitors altered the proportion and distribution of neurons and glia, revealing the effects of temporal gene perturbation on serial cell fates. Thus, TEMPO enables sequential manipulation of molecular factors, crucial to study cell-type specification.One-Sentence Summary Gaining sequential genetic access to vertebrate cell lineages.Competing Interest StatementThe authors have declared no competing interest.

}, doi = {10.1101/2021.10.27.466134}, url = {https://www.biorxiv.org/content/early/2021/10/28/2021.10.27.466134}, author = {Espinosa-Medina, Isabel and Feliciano, Daniel and Belmonte-Mateos, Carla and Garcia-Marques, Jorge and Foster, Benjamin and Miyares, Rosa Linda and Pujades, Cristina and Koyama, Minoru and Lee, Tzumin} } @article {67230, title = {VolPy: Automated and scalable analysis pipelines for voltage imaging datasets.}, journal = {PLoS Computational Biology}, volume = {17}, year = {2021}, month = {2021 Apr 14}, pages = {e1008806}, abstract = {

Voltage imaging enables monitoring neural activity at sub-millisecond and sub-cellular scale, unlocking the study of subthreshold activity, synchrony, and network dynamics with unprecedented spatio-temporal resolution. However, high data rates (\>800MB/s) and low signal-to-noise ratios create bottlenecks for analyzing such datasets. Here we present VolPy, an automated and scalable pipeline to pre-process voltage imaging datasets. VolPy features motion correction, memory mapping, automated segmentation, denoising and spike extraction, all built on a highly parallelizable, modular, and extensible framework optimized for memory and speed. To aid automated segmentation, we introduce a corpus of 24 manually annotated datasets from different preparations, brain areas and voltage indicators. We benchmark VolPy against ground truth segmentation, simulations and electrophysiology recordings, and we compare its performance with existing algorithms in detecting spikes. Our results indicate that VolPy{\textquoteright}s performance in spike extraction and scalability are state-of-the-art.

}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1008806}, author = {Cai, Changjia and Friedrich, Johannes and Singh, Amrita and Eybposh, M Hossein and Pnevmatikakis, Eftychios A and Podgorski, Kaspar and Giovannucci, Andrea} } @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 {67646, title = {YAP1 nuclear efflux and transcriptional reprograming follow membrane diminution upon VSV-G-induced cell fusion.}, journal = {Nature Communications}, volume = {12}, year = {2021}, month = {2021 Jul 23}, pages = {4502}, abstract = {

Cells in many tissues, such as bone, muscle, and placenta, fuse into syncytia to acquire new functions and transcriptional programs. While it is known that fused cells are specialized, it is unclear whether cell-fusion itself contributes to programmatic-changes that generate the new cellular state. Here, we address this by employing a fusogen-mediated, cell-fusion system to create syncytia from undifferentiated cells.\ RNA-Seq analysis reveals VSV-G-induced cell fusion precedes transcriptional changes. To gain mechanistic insights, we measure the plasma membrane surface area after cell-fusion and observe it diminishes through increases in endocytosis. Consequently, glucose transporters internalize, and cytoplasmic glucose and ATP transiently decrease. This reduced energetic state activates AMPK, which inhibits YAP1, causing transcriptional-reprogramming and cell-cycle arrest. Impairing either endocytosis or AMPK activity prevents YAP1 inhibition and cell-cycle arrest after fusion. Together, these data demonstrate plasma membrane diminishment upon cell-fusion causes transient nutrient stress that may promote transcriptional-reprogramming independent from extrinsic cues.

}, issn = {2041-1723}, doi = {10.1038/s41467-021-24708-2}, author = {Feliciano, Daniel and Ott, Carolyn M and Isabel Espinosa Medina and Weigel, Aubrey V and Benedetti, Lorena and Milano, Kristin M and Tang, Zhonghua and Lee, Tzumin and Kliman, Harvey J and Guller, Seth M and Lippincott-Schwartz, Jennifer} } @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 {65857, title = {The art of lineage tracing: from worm to human.}, journal = {Progress in Neurobiology}, year = {2020}, month = {2020 Nov 26}, pages = {101966}, abstract = {

Reconstructing the genealogy of every cell that makes up an organism remains a long-standing challenge in developmental biology. Besides its relevance for understanding the mechanisms underlying normal and pathological development, resolving the lineage origin of cell types will be crucial to create these types on-demand. Multiple strategies have been deployed towards the problem of lineage tracing, ranging from direct observation to sophisticated genetic approaches. Here we discuss the achievements and limitations of past and current technology. Finally, we speculate about the future of lineage tracing and how to reach the next milestones in the field.

}, issn = {1873-5118}, doi = {10.1016/j.pneurobio.2020.101966}, author = {Garcia-Marques, Jorge and Isabel Espinosa Medina and Lee, Tzumin} } @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 {65899, title = {The connectome of the adult mushroom body provides insights into function.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Dec 14}, abstract = {

Making inferences about the computations performed by neuronal circuits from synapse-level connectivity maps is an emerging opportunity in neuroscience. The mushroom body (MB) is well positioned for developing and testing such an approach due to its conserved neuronal architecture, recently completed dense connectome, and extensive prior experimental studies of its roles in learning, memory and activity regulation. Here we identify new components of the MB circuit in , including extensive visual input and MB output neurons (MBONs) with direct connections to descending neurons. We find unexpected structure in sensory inputs, in the transfer of information about different sensory modalities to MBONs, and in the modulation of that transfer by dopaminergic neurons (DANs). We provide insights into the circuitry used to integrate MB outputs, connectivity between the MB and the central complex and inputs to DANs, including feedback from MBONs. Our results provide a foundation for further theoretical and experimental work.

}, issn = {2050-084X}, doi = {10.7554/eLife.62576}, author = {Li, Feng and Lindsey, Jack W and Marin, Elizabeth C and Otto, Nils and Dreher, Marisa and Dempsey, Georgia and Stark, Ildiko and Bates, Alexander S and Pleijzier, Markus William and Schlegel, Philipp and Nern, Aljoscha and Takemura, Shin-ya and Eckstein, Nils and Yang, Tansy and Francis, Audrey and Braun, Amalia and Parekh, Ruchi and Costa, Marta and Scheffer, Louis K and Aso, Yoshi and Jefferis, Gregory Sxe and Abbott, Larry F and Litwin-Kumar, Ashok and Waddell, Scott and Rubin, Gerald M} } @article {68341, title = {Dense reconstruction of elongated cell lineages: overcoming suboptimum lineage encoding and sparse cell sampling}, journal = {bioRxiv}, year = {2020}, month = {07/2020}, abstract = {

Acquiring both lineage and cell-type information during brain development could elucidate transcriptional programs underling neuronal diversification. This is now feasible with single-cell RNA-seq combined with CRISPR-based lineage tracing, which generates genetic barcodes with cumulative CRISPR edits. This technique has not yet been optimized to deliver high-resolution lineage reconstruction of protracted lineages. Drosophila neuronal lineages are an ideal model to consider, as multiple lineages have been morphologically mapped at single-cell resolution. Here we find the parameter ranges required to encode a representative neuronal lineage emanating from 100 stem cell divisions. We derive the optimum editing rate to be inversely proportional to lineage depth, enabling encoding to persist across lineage progression. Further, we experimentally determine the editing rates of a Cas9-deaminase in cycling neural stem cells, finding near ideal rates to map elongated Drosophila neuronal lineages. Moreover, we propose and evaluate strategies to separate recurring cell-types for lineage reconstruction. Finally, we present a simple method to combine multiple experiments, which permits dense reconstruction of protracted cell lineages despite suboptimum lineage encoding and sparse cell sampling.Competing Interest StatementThe authors have declared no competing interest.

}, doi = {10.1101/2020.07.27.223321}, url = {https://www.biorxiv.org/content/early/2020/07/29/2020.07.27.223321}, author = {Sugino, Ken and Miyares, Rosa L. and Espinosa-Medina, Isabel and Chen, Hui-Min and Potter, Christopher J and Lee, Tzumin} } @article {65644, title = {Dielectric confinement and excitonic effects in two-dimensional nanoplatelets.}, journal = {ACS Nano}, year = {2020}, month = {2020 Jul 01}, abstract = {

Quasi-two-dimensional (2D) semiconductor nanoplatelets manifest strong quantum confinement with exceptional optical characteristics of narrow photoluminescence peaks with energies tunable by thickness with monolayer precision. We employed scanning tunneling spectroscopy (STS) in conjunction with optical measurements to probe the thickness-dependent band gap and density of excited states in a series of CdSe nanoplatelets. The tunneling spectra, measured in the double-barrier tunnel junction configuration, reveal the effect of quantum confinement on the band gap taking place mainly through a blue-shift of the conduction band edge, along with a signature of 2D electronic structure intermixed with finite lateral-size and/or defects effects. The STS fundamental band gaps are larger than the optical gaps as expected from the contributions of exciton binding in the absorption, as confirmed by theoretical calculations. The calculations also point to strong valence band mixing between the light- and split-off hole levels. Strikingly, the energy difference between the heavy-hole and light-hole levels in the tunneling spectra are significantly larger than the corresponding values extracted from the absorption spectra. Possible explanations for this, including an interplay of nanoplatelet charging, dielectric confinement, and difference in exciton binding energy for light and heavy holes, are analyzed and discussed.

}, issn = {1936-086X}, doi = {10.1021/acsnano.0c01950}, author = {Ji, Botao and Rabani, Eran and Efros, Alexander L and Vaxenburg, Roman and Ashkenazi, Or and Azulay, Doron and Banin, Uri and Millo, Oded} } @article {65295, title = {Estimating the power of sequence covariation for detecting conserved RNA structure.}, journal = {Bioinformatics}, volume = {36}, year = {2020}, month = {2020 May 01}, pages = {3072-76}, abstract = {

Pairwise sequence covariations are a signal of conserved RNA secondary structure. We describe a method for distinguishing when lack of covariation signal can be taken as evidence against a conserved RNA structure, as opposed to when a sequence alignment merely has insufficient variation to detect covariations. We find that alignments for several long noncoding RNAs previously shown to lack covariation support do have adequate covariation detection power, providing additional evidence against their proposed conserved structures.

}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btaa080}, url = {https://doi.org/10.1093/bioinformatics/btaa080}, author = {Rivas, Elena and Clements, Jody and Eddy, Sean R}, editor = {Ponty, Yann} } @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 {65377, title = {High-throughput cellular-resolution synaptic connectivity mapping in vivo with concurrent two-photon optogenetics and volumetric Ca2+ imaging}, journal = {bioRxiv}, year = {2020}, month = {2020 Feb 25}, abstract = {

The ability to measure synaptic connectivity and properties is essential for understanding neuronal circuits. However, existing methods that allow such measurements at cellular resolution are laborious and technically demanding. Here, we describe a system that allows such measurements in a high-throughput way by combining two-photon optogenetics and volumetric Ca2+\ imaging with whole-cell recording. We reveal a circuit motif for generating fast undulatory locomotion in zebrafish.

}, doi = {https://doi.org/10.1101/2020.02.21.959650}, author = {McRaven, Christopher and Tanese, Dimitrii and Zhang, Lixia and Yang, Chao-Tsung and Ahrens, Misha B and Emiliani, Valentina and Koyama, Minoru} } @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 {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 {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 {65366, title = {Layer 6b Is driven by intracortical long-range projection neurons.}, journal = {Cell Reports}, volume = {30}, year = {2020}, month = {2020 Mar 10}, pages = {3492 - 3505.e5}, abstract = {

Layer 6b (L6b), the deepest neocortical layer, projects to cortical targets and higher-order thalamus and is the only layer responsive to the wake-promoting neuropeptide orexin/hypocretin. These characteristics suggest that L6b can strongly modulate brain state, but projections to L6b and their influence remain unknown. Here, we examine the inputs to L6b\ ex\ vivo\ in the mouse primary somatosensory cortex with rabies-based retrograde tracing and channelrhodopsin-assisted circuit mapping in brain slices. We find that L6b receives its strongest excitatory input from intracortical long-range projection neurons, including those in the contralateral hemisphere. In contrast, local intracortical input and thalamocortical input were significantly weaker. Moreover, our data suggest that L6b receives far less thalamocortical input than other cortical layers. L6b was most strongly inhibited by PV and SST interneurons. This study shows that L6b integrates long-range intracortical information and is not part of the traditional thalamocortical loop.

}, issn = {22111247}, doi = {10.1016/j.celrep.2020.02.044}, url = {https://linkinghub.elsevier.com/retrieve/pii/S2211124720302059}, author = {Zolnik, Timothy A. and Ledderose, Julia and Toumazou, Maria and Trimbuch, Thorsten and Oram, Tess and Rosenmund, Christian and Eickholt, Britta J. and Sachdev, Robert N.S. and Larkum, Matthew E.} } @article {65581, title = {Live-cell single particle imaging reveals the role of RNA polymerase II in histone H2A.Z eviction.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Apr 27}, abstract = {

The H2A.Z histone variant, a genome-wide hallmark of permissive chromatin, is enriched near transcription start sites in all eukaryotes. H2A.Z is deposited by the SWR1 chromatin remodeler and evicted by unclear mechanisms. We tracked H2A.Z in living yeast at single-molecule resolution, and found that H2A.Z eviction is dependent on RNA Polymerase II (Pol II) and the Kin28/Cdk7 kinase, which phosphorylates Serine 5 of heptapeptide repeats on the carboxy-terminal domain of the largest Pol II subunit Rpb1. These findings link H2A.Z eviction to transcription initiation, promoter escape and early elongation activities of Pol II. Because passage of Pol II through +1 nucleosomes genome-wide would obligate H2A.Z turnover, we propose that global transcription at yeast promoters is responsible for eviction of H2A.Z. Such usage of yeast Pol II suggests a general mechanism coupling eukaryotic transcription to erasure of the H2A.Z epigenetic signal.

}, issn = {2050-084X}, doi = {10.7554/eLife.55667}, author = {Ranjan, Anand and Nguyen, Vu Q and Liu, Sheng and Wisniewski, Jan and Kim, Jee Min and Tang, Xiaona and Mizuguchi, Gaku and Elalaoui, Ejlal and Nickels, Timothy J and Jou, Vivian and English, Brian P and Zheng, Qinsi and Luk, Ed and Lavis, Luke D and Lionnet, Timoth{\'e}e and Wu, Carl} } @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} } @conference {65837, title = {Microtubule Tracking in Electron Microscopy Volumes}, booktitle = {International Conference on Medical Image Computing and Computer-Assisted Intervention}, year = {2020}, month = {2020 Sep 17}, abstract = {

We present a method for microtubule tracking in electron microscopy volumes. Our method first identifies a sparse set of voxels that likely belong to microtubules. Similar to prior work, we then enumerate potential edges between these voxels, which we represent in a candidate graph. Tracks of microtubules are found by selecting nodes and edges in the candidate graph by solving a constrained optimization problem incorporating biological priors on microtubule structure. For this, we present a novel integer linear programming formulation, which results in speed-ups of three orders of magnitude and an increase of 53\% in accuracy compared to prior art (evaluated on three 1 . 2 {\texttimes} 4 {\texttimes} 4{\textmu}m volumes of Drosophila neural tissue). We also propose a scheme to solve the optimization problem in a block-wise fashion, which allows distributed tracking and is necessary to process very large electron microscopy volumes. Finally, we release a benchmark dataset for microtubule tracking, here used for training, testing and validation, consisting of eight 30 x 1000 x 1000 voxel blocks (1 . 2 {\texttimes} 4 {\texttimes} 4{\textmu}m) of densely annotated microtubules in the CREMI data set (https://github.com/nilsec/micron).

}, author = {Nils Eckstein and Julia Buhmann and Matthew Cook and Jan Funke} } @article {65613, title = {mRNA stem-loops can pause the ribosome by hindering A-site tRNA binding.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 May 19}, abstract = {

Although the elongating ribosome is an efficient helicase, certain mRNA stem-loop structures are known to impede ribosome movement along mRNA and stimulate programmed ribosome frameshifting via mechanisms that are not well understood. Using biochemical and single-molecule F{\"o}rster resonance energy transfer (smFRET) experiments, we studied how frameshift-inducing stem-loops from mRNA and the transcript of Human Immunodeficiency Virus (HIV) perturb translation elongation. We find that upon encountering the ribosome, the stem-loops strongly inhibit A-site tRNA binding and ribosome intersubunit rotation that accompanies translation elongation. Electron cryo-microscopy (cryo-EM) reveals that the HIV stem-loop docks into the A site of the ribosome. Our results suggest that mRNA stem-loops can transiently escape the ribosome helicase by binding to the A site. Thus, the stem-loops can modulate gene expression by sterically hindering tRNA binding and inhibiting translation elongation.

}, issn = {2050-084X}, doi = {10.7554/eLife.55799}, author = {Bao, Chen and Loerch, Sarah and Ling, Clarence and Korostelev, Andrei A and Grigorieff, Nikolaus and Ermolenko, Dmitri N} } @article {65791, title = {The mTORC1/S6K/PDCD4/eIF4A axis determines outcome of mitotic arrest.}, journal = {Cell Reports}, volume = {33}, year = {2020}, month = {2020 Oct 06}, pages = {108230}, abstract = {

mTOR is a serine/threonine kinase and a master regulator of cell growth and proliferation. Raptor, a scaffolding protein that recruits substrates to mTOR complex 1 (mTORC1), is known to be phosphorylated during mitosis, but the significance of this phosphorylation remains largely unknown. Here we show that raptor expression and mTORC1 activity are dramatically reduced in cells arrested in mitosis. Expression of a non-phosphorylatable raptor mutant reactivates mTORC1 and significantly reduces cytotoxicity of the mitotic poison Taxol. This effect is mediated via degradation of PDCD4, a tumor suppressor protein that inhibits eIF4A activity and is negatively regulated by the mTORC1/S6K pathway. Moreover, pharmacological inhibition of eIF4A is able to enhance the effects of Taxol and restore sensitivity in Taxol-resistant cancer cells. These findings indicate that the mTORC1/S6K/PDCD4/eIF4A axis has a pivotal role in the death versus slippage decision during mitotic arrest and may be exploited clinically to treat tumors resistant to anti-mitotic agents.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2020.108230}, author = {Moustafa-Kamal, Mohamed and Kucharski, Thomas J and El-Assaad, Wissal and Abbas, Yazan M and Gandin, Valentina and Nagar, Bhushan and Pelletier, Jerry and Topisirovic, Ivan and Teodoro, Jose G} } @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 {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 {65669, title = {A programmable sequence of reporters for lineage analysis.}, journal = {Nature Neuroscience}, volume = {23}, year = {2020}, month = {2020 Dec 01}, pages = {1618-28}, abstract = {

We present CLADES (cell lineage access driven by an edition sequence), a technology for cell lineage studies based on CRISPR-Cas9 techniques. CLADES relies on a system of genetic switches to activate and inactivate reporter genes in a predetermined order. Targeting CLADES to progenitor cells allows the progeny to inherit a sequential cascade of reporters, thereby coupling birth order to reporter expression. This system, which can also be temporally induced by heat shock, enables the temporal resolution of lineage development and can therefore be used to deconstruct an extended cell lineage by tracking the reporters expressed in the progeny. When targeted to the germ line, the same cascade progresses across animal generations, predominantly marking each generation with the corresponding combination of reporters. CLADES therefore offers an innovative strategy for making programmable cascades of genes that can be used for genetic manipulation or to record serial biological events.

}, issn = {1546-1726}, doi = {10.1038/s41593-020-0676-9}, author = {Garcia-Marques, Jorge and Isabel Espinosa Medina and Ku, Kai-Yuan and Yang, Ching-Po and Koyama, Minoru and Yu, Hung-Hsiang and Lee, Tzumin} } @article {65668, title = {Rational design of bioavailable photosensitizers for manipulation and imaging of biological systems.}, journal = {Cell Chemical Biology}, volume = {27}, year = {2020}, month = {2020 Aug 20}, pages = {1063-72}, abstract = {

Light-mediated chemical reactions are powerful methods for manipulating and interrogating biological systems. Photosensitizers, compounds that generate reactive oxygen species upon excitation with light, can be utilized for numerous biological experiments, but the repertoire of bioavailable photosensitizers is limited. Here, we describe the synthesis, characterization, and utility of two photosensitizers based upon the widely used rhodamine scaffold and demonstrate their efficacy for chromophore-assisted light inactivation, cell ablation in culture and in\ vivo, and photopolymerization of diaminobenzidine for electron microscopy. These chemical tools will facilitate a broad range of applications spanning from targeted destruction of proteins to high-resolution imaging.

}, issn = {2451-9448}, doi = {10.1016/j.chembiol.2020.07.001}, author = {Binns, Thomas C and Ayala, Anthony X and Grimm, Jonathan B and Tkachuk, Ariana N and Castillon, Guillaume A and Phan, Sebastien and Zhang, Lixia and Brown, Timothy A and Liu, Zhe and Adams, Stephen R and Ellisman, Mark H and Koyama, Minoru and Lavis, Luke D} } @article {65373, title = {Recurrent architecture for adaptive regulation of learning in the insect brain.}, journal = {Nature Neuroscience}, volume = {23}, year = {2020}, month = {2020 Mar 23}, pages = {544-55}, abstract = {

Dopaminergic neurons (DANs) drive learning across the animal kingdom, but the upstream circuits that regulate their activity and thereby learning remain poorly understood. We provide a synaptic-resolution connectome of the circuitry upstream of all DANs in a learning center, the mushroom body of Drosophila larva. We discover afferent sensory pathways and a large population of neurons that provide feedback from mushroom body output neurons and link distinct memory systems (aversive and appetitive). We combine this with functional studies of DANs and their presynaptic partners and with comprehensive circuit modeling. We find that DANs compare convergent feedback from aversive and appetitive systems, which enables the computation of integrated predictions that may improve future learning. Computational modeling reveals that the discovered feedback motifs increase model flexibility and performance on learning tasks. Our study provides the most detailed view to date of biological circuit motifs that support associative learning.

}, issn = {1546-1726}, doi = {10.1038/s41593-020-0607-9}, author = {Eschbach, Claire and Fushiki, Akira and Winding, Michael and Schneider-Mizell, Casey M and Shao, Mei and Arruda, Rebecca and Eichler, Katharina and Valdes-Aleman, Javier and Ohyama, Tomoko and Thum, Andreas S and Gerber, Bertram and Fetter, Richard D and Truman, James W and Litwin-Kumar, Ashok and Cardona, Albert and Zlatic, Marta and Cardona, Albert and Zlatic, Marta} } @article {65584, title = {A Sparse, Spatially Biased Subtype of Mature Granule Cell Dominates Recruitment in Hippocampal-Associated Behaviors.}, journal = {Cell Reports}, volume = {31}, year = {2020}, month = {2020 Apr 28}, pages = {107551}, abstract = {

Animals can store information about experiences by activating specific neuronal populations, and subsequent reactivation of these neural ensembles can lead to recall of salient experiences. In the hippocampus, granule cells of the dentate gyrus participate in such memory engrams; however, whether there is an underlying logic to granule cell participation has not been examined. Here, we find that a range of novel experiences preferentially activates granule cells of the suprapyramidal blade relative to the infrapyramidal blade. Motivated by this, we identify a suprapyramidal-blade-enriched population of granule cells with distinct spatial, morphological, physiological, and developmental properties. Via transcriptomics, we map these traits onto a sparse and discrete granule cell subtype that is recruited at a 10-fold greater frequency than expected by subtype prevalence, constituting the majority of all recruited granule cells. Thus, in behaviors known to involve hippocampal-dependent memory formation, a rare and spatially localized subtype dominates overall granule cell recruitment.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2020.107551}, author = {Erwin, Sarah R and Sun, Weinan and Copeland, Monique and Lindo, Sarah and Spruston, Nelson and Cembrowski, Mark S} } @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 {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 {65253, title = {Tissue clearing and its applications in neuroscience}, journal = {Nature Reviews Neuroscience}, year = {2020}, month = {2020 Feb 1}, abstract = {

State-of-the-art tissue-clearing methods provide subcellular-level optical access to intact tissues from individual organs and even to some entire mammals. When combined with light-sheet microscopy and automated approaches to image analysis, existing tissue-clearing methods can speed up and may reduce the cost of conventional histology by several orders of magnitude. In addition, tissue-clearing chemistry allows whole-organ antibody labelling, which can be applied even to thick human tissues. By combining the most powerful labelling, clearing, imaging and data-analysis tools, scientists are extracting structural and functional cellular and subcellular information on complex mammalian bodies and large human specimens at an accelerated pace. The rapid generation of terabyte-scale imaging data furthermore creates a high demand for efficient computational approaches that tackle challenges in large-scale data analysis and management. In this Review, we discuss how tissue-clearing methods could provide an unbiased, system-level view of mammalian bodies and human specimens and discuss future opportunities for the use of these methods in human neuroscience.

}, issn = {1471-003X}, doi = {10.1038/s41583-019-0250-1}, url = {http://www.nature.com/articles/s41583-019-0250-1}, author = {Ueda, Hiroki R. and Ert{\"u}rk, Ali and Chung, Kwanghun and Gradinaru, Viviana and Ch{\'e}dotal, Alain and Tomancak, Pavel and Keller, Philipp J.} } @article {65264, title = {Tissue clearing and its applications in~neuroscience.}, journal = {Nature Reviews Neuroscience}, volume = {21}, year = {2020}, month = {2020 Jan 02}, pages = {61-79}, abstract = {

State-of-the-art tissue-clearing methods provide subcellular-level optical access to intact tissues from individual organs and even to some entire mammals. When combined with light-sheet microscopy and automated approaches to image analysis, existing tissue-clearing methods can speed up and may reduce the cost of conventional histology by several orders of magnitude. In addition, tissue-clearing chemistry allows whole-organ antibody labelling, which can be applied even to thick human tissues. By combining the most powerful labelling, clearing, imaging and data-analysis tools, scientists are extracting structural and functional cellular and subcellular information on complex mammalian bodies and large human specimens at an accelerated pace. The rapid generation of terabyte-scale imaging data furthermore creates a high demand for efficient computational approaches that tackle challenges in large-scale data analysis and management. In this Review, we discuss how tissue-clearing methods could provide an unbiased, system-level view of mammalian bodies and human specimens and discuss future opportunities for the use of these methods in human neuroscience.

}, issn = {1471-0048}, doi = {10.1038/s41583-019-0250-1}, author = {Ueda, Hiroki R and Ert{\"u}rk, Ali and Chung, Kwanghun and Gradinaru, Viviana and Ch{\'e}dotal, Alain and Tomancak, Pavel and Keller, Philipp J} } @article {65599, title = {Whole-brain profiling of cells and circuits in mammals by tissue clearing and light-sheet microscopy.}, journal = {Neuron}, volume = {106}, year = {2020}, month = {2020 May 06}, pages = {369-387}, abstract = {

Tissue clearing and light-sheet microscopy have a 100-year-plus history, yet these fields have been combined only recently to facilitate novel experiments and measurements in neuroscience. Since tissue-clearing methods were first combined with modernized light-sheet microscopy a decade ago, the performance of both technologies has rapidly improved, broadening their applications. Here, we review the state of the art of tissue-clearing methods and light-sheet microscopy and discuss applications of these techniques in profiling cells and circuits in mice. We examine outstanding challenges and future opportunities for expanding these techniques to achieve brain-wide profiling of cells and circuits in primates and humans. Such integration will help provide a systems-level understanding of the physiology and pathology of our central nervous system.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2020.03.004}, author = {Ueda, Hiroki R and Dodt, Hans-Ulrich and Osten, Pavel and Economo, Michael N and Chandrashekar, Jayaram and Keller, Philipp J} } @article {65633, title = {Whole-brain profiling of cells and circuits in mammals by tissue clearing and light-sheet microscopy.}, journal = {Neuron}, volume = {106}, year = {2020}, month = {2020 May 06}, pages = {369-387}, abstract = {

Tissue clearing and light-sheet microscopy have a 100-year-plus history, yet these fields have been combined only recently to facilitate novel experiments and measurements in neuroscience. Since tissue-clearing methods were first combined with modernized light-sheet microscopy a decade ago, the performance of both technologies has rapidly improved, broadening their applications. Here, we review the state of the art of tissue-clearing methods and light-sheet microscopy and discuss applications of these techniques in profiling cells and circuits in mice. We examine outstanding challenges and future opportunities for expanding these techniques to achieve brain-wide profiling of cells and circuits in primates and humans. Such integration will help provide a systems-level understanding of the physiology and pathology of our central nervous system.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2020.03.004}, author = {Ueda, Hiroki R and Dodt, Hans-Ulrich and Osten, Pavel and Economo, Michael N and Chandrashekar, Jayaram and Keller, Philipp J} } @article {65198, title = {A bidirectional network for appetite control in larval zebrafish.}, journal = {Elife}, volume = {8}, year = {2019}, month = {2019 Oct 18}, abstract = {

Medial and lateral hypothalamic loci are known to suppress and enhance appetite, respectively, but the dynamics and functional significance of their interaction have yet to be explored. Here we report that, in larval zebrafish, primarily serotonergic neurons of the ventromedial caudal hypothalamus (cH) become increasingly active during food deprivation, whereas activity in the lateral hypothalamus (LH) is reduced. Exposure to food sensory and consummatory cues reverses the activity patterns of these two nuclei, consistent with their representation of opposing internal hunger states. Baseline activity is restored as food-deprived animals return to satiety via voracious feeding. The antagonistic relationship and functional importance of cH and LH activity patterns were confirmed by targeted stimulation and ablation of cH neurons. Collectively, the data allow us to propose a model in which these hypothalamic nuclei regulate different phases of hunger and satiety and coordinate energy balance via antagonistic control of distinct behavioral outputs.

}, issn = {2050-084X}, doi = {10.7554/eLife.43775}, author = {Wee, Caroline Lei and Song, Erin Yue and Johnson, Robert Evan and Ailani, Deepak and Randlett, Owen and Kim, Ji-Yoon and Nikitchenko, Maxim and Bahl, Armin and Yang, Chao-Tsung and Ahrens, Misha B and Kawakami, Koichi and Engert, Florian and Kunes, Sam} } @article {65379, title = {CLADES: a programmable sequence of reporters for lineage analysis}, journal = {bioRxiv}, year = {2019}, month = {2019 May 30}, abstract = {

We present CLADES (Cell Lineage Access Driven by an Edition Sequence), a technology for cell lineage studies based on CRISPR/Cas9. CLADES relies on a system of genetic switches to activate and inactivate reporter genes in a pre-determined order. Targeting CLADES to progenitor cells allows the progeny to inherit a sequential cascade of reporters, coupling birth order with reporter expression. This gives us temporal resolution of lineage development that can be used to deconstruct an extended cell lineage by tracking the reporters expressed in the progeny. When targeted to the germ line, the same cascade progresses across animal generations, marking each generation with the corresponding combination of reporters. CLADES thus offers an innovative strategy for making programmable cascades of genes that can be used for genetic manipulation or to record serial biological events.

}, doi = {https://doi.org/10.1101/655308}, author = {Garcia-Marques, Jorge and Yang, Ching-Po and Isabel Espinosa Medina and Koyama, Minoru and Lee, Tzumin} } @article {64831, title = {Cytoskeletal actin patterns shape mast cell activation.}, journal = {Communications Biology}, volume = {2}, year = {2019}, month = {2019}, pages = {93}, abstract = {

Activation of immune cells relies on a dynamic actin cytoskeleton. Despite detailed knowledge of molecular actin assembly, the exact processes governing actin organization during activation remain elusive. Using advanced microscopy, we here show that Rat Basophilic Leukemia (RBL) cells, a model mast cell line, employ an orchestrated series of reorganization events within the cortical actin network during activation. In response to IgE antigen-stimulation of FCε receptors (FCεR) at the RBL cell surface, we observed symmetry breaking of the F-actin network and subsequent rapid disassembly of the actin cortex. This was followed by a reassembly process that may be driven by the coordinated transformation of distinct nanoscale F-actin architectures, reminiscent of self-organizing actin patterns. Actin patterns co-localized with zones of Arp2/3 nucleation, while network reassembly was accompanied by myosin-II activity. Strikingly, cortical actin disassembly coincided with zones of granule secretion, suggesting that cytoskeletal actin patterns contribute to orchestrate RBL cell activation.

}, issn = {2399-3642}, doi = {10.1038/s42003-019-0322-9}, author = {Colin-York, Huw and Li, Dong and Korobchevskaya, Kseniya and Chang, Veronica T and Betzig, Eric and Eggeling, Christian and Fritzsche, Marco} } @article {64852, title = {Cytoskeletal control of antigen-dependent T cell activation.}, journal = {Cell Reports}, volume = {26}, year = {2019}, month = {2019 Mar 19}, pages = {3369-3379.e5}, abstract = {

Cytoskeletal actin dynamics is essential for T\ cell activation. Here, we show evidence that the binding kinetics of the antigen engaging the T\ cell receptor influences the nanoscale actin organization and mechanics of the immune synapse. Using an engineered T\ cell system expressing a specific T\ cell receptor and stimulated by a range of antigens, we found that the peak force experienced by the T\ cell receptor during activation was independent of the unbinding kinetics of the stimulating antigen. Conversely, quantification of the actin retrograde flow velocity at the synapse revealed a striking dependence on the antigen unbinding kinetics. These findings suggest that the dynamics of the actin cytoskeleton actively adjusted to normalize the force experienced by the T\ cell receptor in an antigen-specific manner. Consequently, tuning actin dynamics in response to antigen kinetics may thus\ be a mechanism that allows T\ cells to adjust the lengthscale and timescale of T\ cell receptor signaling.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2019.02.074}, author = {Colin-York, Huw and Javanmardi, Yousef and Skamrahl, Mark and Kumari, Sudha and Chang, Veronica T and Khuon, Satya and Taylor, Aaron and Chew, Teng-Leong and Betzig, Eric and Moeendarbary, Emad and Cerundolo, Vincenzo and Eggeling, Christian and Fritzsche, Marco} } @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 {65244, title = {High-throughput dense reconstruction of cell lineages.}, journal = {Open Biology}, volume = {9}, year = {2019}, month = {2019 Dec 01}, pages = {190229}, abstract = {

The first meeting exclusively dedicated to the {\textquoteright}High-throughput dense reconstruction of cell lineages{\textquoteright} took place at Janelia Research Campus (Howard Hughes Medical Institute) from 14 to 18 April 2019. Organized by Tzumin Lee, Connie Cepko, Jorge Garcia-Marques and Isabel Espinosa-Medina, this meeting echoed the recent eruption of new tools that allow the reconstruction of lineages based on the phylogenetic analysis of DNA mutations induced during development. Combined with single-cell RNA sequencing, these tools promise to solve the lineage of complex model organisms at single-cell resolution. Here, we compile the conference consensus on the technological and computational challenges emerging from the use of the new strategies, as well as potential solutions.

}, issn = {2046-2441}, doi = {10.1098/rsob.190229}, author = {Isabel Espinosa Medina and Garcia-Marques, Jorge and Cepko, Connie and Lee, Tzumin} } @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 {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 {65141, title = {A neural circuit arbitrates between persistence and withdrawal in hungry drosophila.}, journal = {Neuron}, volume = {104}, year = {2019}, month = {2019 Nov 6}, pages = {544-58}, abstract = {

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

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

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

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2019.07.028}, author = {Sayin, Sercan and De Backer, Jean-Francois and Siju, K P and Wosniack, Marina E and Lewis, Laurence P and Frisch, Lisa-Marie and Gansen, Benedikt and Schlegel, Philipp and Edmondson-Stait, Amelia and Sharifi, Nadiya and Fisher, Corey B and Calle-Schuler, Steven A and Lauritzen, J Scott and Bock, Davi D and Costa, Marta and Jefferis, Gregory S X E and Gjorgjieva, Julijana and Grunwald Kadow, Ilona C} } @article {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 {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 {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 {65080, title = {Response to "Fallacies of mice experiments".}, journal = {Neuroinformatics}, year = {2019}, month = {2019 Aug 03}, abstract = {

In a recent Editorial, De Schutter commented on our recent study on the roles of a cortico-cerebellar loop in motor planning in mice (De Schutter 2019, Neuroinformatics, 17, 181-183, Gao et al. 2018, Nature, 563, 113-116). Two issues were raised. First, De Schutter questions the involvement of the fastigial nucleus in motor planning, rather than the dentate nucleus, given previous anatomical studies in non-human primates. Second, De Schutter suggests that our study design did not delineate different components of the behavior and the fastigial nucleus might play roles in sensory discrimination rather than motor planning. These comments are based on anatomical studies in other species and homology-based arguments and ignore key anatomical data and neurophysiological experiments from our study. Here we outline our interpretation of existing data and point out gaps in knowledge where future studies are needed.

}, issn = {1559-0089}, doi = {10.1007/s12021-019-09433-y}, author = {Gao, Zhenyu and Thomas, Alyse M and Economo, Michael N and Abrego, Amada M and Svoboda, Karel and De Zeeuw, Chris I and Li, Nuo} } @article {64830, title = {Single-neuron axonal reconstruction: The search for a wiring diagram of the brain.}, journal = {The Journal of Comparative Neurology}, year = {2019}, month = {2019 Mar 12}, abstract = {

Reconstruction of the axonal projection patterns of single neurons has been an important tool for understanding both the diversity of cell types in the brain and the logic of information flow between brain regions. Innovative approaches now enable the complete reconstruction of axonal projection patterns of individual neurons with vastly increased throughput. Here we review how advances in genetic, imaging, and computational techniques have been exploited for axonal reconstruction. We also discuss how new innovations could enable the integration of genetic and physiological information with axonal morphology for producing a census of cell types in the mammalian brain at scale. This article is protected by copyright. All rights reserved.

}, issn = {1096-9861}, doi = {10.1002/cne.24674}, author = {Economo, Michael N and Winnubst, Johan and Bas, Erhan and Ferreira, Tiago A and Chandrashekar, Jayaram} } @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 {67281, title = {Specialized coding of sensory, motor and cognitive variables in VTA dopamine neurons}, journal = {Nature}, volume = {570}, year = {2019}, month = {05/2019}, pages = {509 - 513}, abstract = {

There is increased appreciation that dopamine neurons in the midbrain respond not only to reward1\ and reward-predicting cues1,2, but also to other variables such as the distance to reward3, movements4,5,6,7,8,9\ and behavioural choices10,11. An important question is how the responses to these diverse variables are organized across the population of dopamine neurons. Whether individual dopamine neurons multiplex several variables, or whether there are subsets of neurons that are specialized in encoding specific behavioural variables remains unclear. This fundamental question has been difficult to resolve because recordings from large populations of individual dopamine neurons have not been performed in a behavioural task with sufficient complexity to examine these diverse variables simultaneously. Here, to address this gap, we used two-photon calcium imaging through an implanted lens to record the activity of more than 300 dopamine neurons from the ventral tegmental area of the mouse midbrain during a complex decision-making task. As mice navigated in a virtual-reality environment, dopamine neurons encoded an array of sensory, motor and cognitive variables. These responses were functionally clustered, such that subpopulations of neurons transmitted information about a subset of behavioural variables, in addition to encoding reward. These functional clusters were spatially organized, with neighbouring neurons more likely to be part of the same cluster. Together with the topography between dopamine neurons and their projections, this specialization and anatomical organization may aid downstream circuits in correctly interpreting the wide range of signals transmitted by dopamine neurons.

}, issn = {0028-0836}, doi = {10.1038/s41586-019-1261-9}, url = {http://www.nature.com/articles/s41586-019-1261-9}, author = {Engelhard, Ben and Finkelstein, Joel and Cox, Julia and Fleming, Weston and Jang, Hee Jae and Ornelas, Sharon and Koay, Sue Ann and Thiberge, Stephan Y. and Daw, Nathaniel D. and Tank, David W. and Witten, Ilana B.} } @article {68340, title = {Theoretical modeling on CRISPR-coded cell lineages: efficient encoding and optimal reconstruction}, journal = {bioRxiv}, year = {2019}, month = {04/2019}, abstract = {

Delineating cell lineages is a prerequisite for interrogating the genesis of cell types. CRISPR/Cas9 can edit genomic sequence during development which enables to trace cell lineages. Recent studies have demonstrated the feasibility of this idea. However, the optimality of the encoding or reconstruction processes has not been adequately addressed. Here, we surveyed a multitude of reconstruction algorithms and found hierarchical clustering, with a metric based on the number of shared Cas9 edits, delivers the best reconstruction. However, the trackable depth is ultimately limited by the number of available coding units that typically decrease exponentially across cell generations. To overcome this limit, we established two strategies that better sustain the coding capacity. One involves controlling target availability via use of parallel gRNA cascades, whereas the other strategy exploits adjustable Cas9/gRNA editing rates. In summary, we provide a theoretical basis in understanding, designing, and analyzing robust CRISPR barcodes for dense reconstruction of protracted cell lineages.

}, doi = {10.1101/538488}, url = {https://www.biorxiv.org/content/early/2019/04/14/538488}, author = {Sugino, Ken and Garcia-Marques, Jorge and Espinosa-Medina, Isabel and Lee, Tzumin} } @article {65078, title = {Unlimited genetic switches for cell-type-specific manipulation.}, journal = {Neuron}, volume = {104}, year = {2019}, month = {2019 Oct 23}, pages = {227-38}, abstract = {

Gaining independent genetic access to discrete cell types is critical to interrogate their biological functions as well as to deliver precise gene therapy. Transcriptomics has allowed us to profile cell populations with extraordinary precision, revealing that cell types are typically defined by a unique combination of genetic markers. Given the lack of adequate tools to target cell types based on multiple markers, most cell types remain inaccessible to genetic manipulation. Here we present CaSSA, a platform to create unlimited genetic switches based on CRISPR/Cas9 (Ca) and the DNA repair mechanism known as single-strand annealing (SSA). CaSSA allows engineering of independent genetic switches, each responding to a specific gRNA. Expressing multiple gRNAs in specific patterns enables multiplex cell-type-specific manipulations and combinatorial genetic targeting. CaSSA is a new genetic tool that conceptually works as an unlimited number of recombinases and will facilitate genetic access to cell types in diverse organisms.

}, doi = {https://doi.org/10.1016/j.neuron.2019.07.005}, author = {Garcia-Marques, Jorge and Yang, Ching-Po and Isabel Espinosa Medina and Mok, Kent and Koyama, Minoru and Lee, Tzumin} } @article {67283, title = {An Accumulation-of-Evidence Task Using Visual Pulses for Mice Navigating in Virtual Reality}, journal = {Frontiers in Behavioral Neuroscience}, volume = {12}, year = {2018}, month = {Jun-03-2018}, abstract = {

The gradual accumulation of sensory evidence is a crucial component of perceptual decision making, but its neural mechanisms are still poorly understood. Given the wide availability of genetic and optical tools for mice, they can be useful model organisms for the study of these phenomena; however, behavioral tools are largely lacking. Here, we describe a new evidence-accumulation task for head-fixed mice navigating in a virtual reality (VR) environment. As they navigate down the stem of a virtual T-maze, they see brief pulses of visual evidence on either side, and retrieve a reward on the arm with the highest number of pulses. The pulses occur randomly with Poisson statistics, yielding a diverse yet well-controlled stimulus set, making the data conducive to a variety of computational approaches. A large number of mice of different genotypes were able to learn and consistently perform the task, at levels similar to rats in analogous tasks. They are sensitive to side differences of a single pulse, and their memory of the cues is stable over time. Moreover, using non-parametric as well as modeling approaches, we show that the mice indeed accumulate evidence: they use multiple pulses of evidence from throughout the cue region of the maze to make their decision, albeit with a small overweighting of earlier cues, and their performance is affected by the magnitude but not the duration of evidence. Additionally, analysis of the mice{\textquoteright}s running patterns revealed that trajectories are fairly stereotyped yet modulated by the amount of sensory evidence, suggesting that the navigational component of this task may provide a continuous readout correlated to the underlying cognitive variables. Our task, which can be readily integrated with state-of-the-art techniques, is thus a valuable tool to study the circuit mechanisms and dynamics underlying perceptual decision making, particularly under more complex behavioral contexts.

}, doi = {10.3389/fnbeh.2018.00036}, url = {http://journal.frontiersin.org/article/10.3389/fnbeh.2018.00036/full}, author = {Pinto, Lucas and Koay, Sue A. and Engelhard, Ben and Yoon, Alice M. and Deverett, Ben and Thiberge, Stephan Y. and Witten, Ilana B. and Tank, David W. and Brody, Carlos D.} } @article {49223, title = {Atomic resolution cryo-EM structure of β-galactosidase.}, journal = {Structure (London, England : 1993)}, volume = {26}, year = {2018}, month = {2018 Apr 30}, pages = {848}, abstract = {

The advent of direct electron detectors has enabled the routine use of single-particle cryo-electron microscopy (EM) approaches to determine structures of a variety of protein complexes at near-atomic resolution. Here, we report the development of methods to account for local variations in defocus and beam-induced drift, and the implementation of a data-driven dose compensation scheme that significantly improves the extraction of high-resolution information recorded during exposure of the specimen to the electron beam. These advances enable determination of a cryo-EM density map for β-galactosidase bound to the inhibitor phenylethyl β-D-thiogalactopyranoside where the ordered regions are resolved at a level of detail seen in X-ray maps at \~{} 1.5\ {\r A} resolution. Using this density map in conjunction with constrained molecular dynamics simulations provides a measure of the local flexibility of the non-covalently bound inhibitor and offers further opportunities for structure-guided inhibitor design.

}, issn = {1878-4186}, doi = {10.1016/j.str.2018.04.004}, author = {Bartesaghi, Alberto and Aguerrebere, Cecilia and Falconieri, Veronica and Banerjee, Soojay and Earl, Lesley A and Zhu, Xing and Grigorieff, Nikolaus and Milne, Jacqueline L S and Sapiro, Guillermo and Wu, Xiongwu and Subramaniam, Sriram} } @article {49117, title = {Atomic-level evidence for packing and positional amyloid polymorphism by segment from TDP-43 RRM2.}, journal = {Nature Structural \& Molecular Biology}, year = {2018}, month = {2018 Mar 12}, abstract = {

Proteins in the fibrous amyloid state are a major hallmark of neurodegenerative disease. Understanding the multiple conformations, or polymorphs, of amyloid proteins at the molecular level is a challenge of amyloid research. Here, we detail the wide range of polymorphs formed by a segment of human TAR DNA-binding protein 43 (TDP-43) as a model for the polymorphic capabilities of pathological amyloid aggregation. Using X-ray diffraction, microelectron diffraction (MicroED) and single-particle cryo-EM, we show that theDLIIKGISVHIsegment from the second RNA-recognition motif (RRM2) forms an array of amyloid polymorphs. These associations include seven distinct interfaces displaying five different symmetry classes of steric zippers. Additionally, we find that this segment can adopt three different backbone conformations that contribute to its polymorphic capabilities. The polymorphic nature of this segment illustrates at the molecular level how amyloid proteins can form diverse fibril structures.

}, issn = {1545-9985}, doi = {10.1038/s41594-018-0045-5}, author = {Guenther, Elizabeth L and Ge, Peng and Trinh, Hamilton and Sawaya, Michael R and Cascio, Duilio and Boyer, David R and Gonen, Tamir and Zhou, Z Hong and Eisenberg, David S} } @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 {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 {49476, title = {A cortico-cerebellar loop for motor planning.}, journal = {Nature}, volume = {563}, year = {2018}, month = {2018 Oct 17}, pages = {113-6}, abstract = {

Persistent and ramping neural activity in the frontal cortex anticipates specific movements. Preparatory activity is distributed across several brain regions, but it is unclear which brain areas are involved and how this activity is mediated by multi-regional interactions. The cerebellum is thought to be primarily involved in the short-timescale control of movement; however, roles for this structure in cognitive processes have also been proposed. In humans, cerebellar damage can cause defects in planning and working memory. Here we show that persistent representation of information in the frontal cortex during motor planning is dependent on the cerebellum. Mice performed a sensory discrimination task in which they used short-term memory to plan a future directional movement. A transient perturbation in the medial deep cerebellar nucleus (fastigial nucleus) disrupted subsequent correct responses without hampering movement execution. Preparatory activity was observed in both the frontal cortex and the cerebellar nuclei, seconds before the onset of movement. The silencing of frontal cortex activity abolished preparatory activity in the cerebellar nuclei, and fastigial activity was necessary to maintain cortical preparatory activity. Fastigial output selectively targeted the behaviourally relevant part of the frontal cortex through the thalamus, thus closing a cortico-cerebellar loop. Our results support the view that persistent neural dynamics during motor planning is maintained by neural circuits that span multiple brain regions, and that cerebellar computations extend beyond online motor control.

}, issn = {1476-4687}, doi = {10.1038/s41586-018-0633-x}, author = {Gao, Zhenyu and Davis, Courtney and Thomas, Alyse M and Economo, Michael N and Abrego, Amada M and Svoboda, Karel and De Zeeuw, Chris I and Li, Nuo} } @article {49496, title = {Distinct descending motor cortex pathways and their roles in movement.}, journal = {Nature}, volume = {563}, year = {2018}, month = {2018 Nov}, pages = {79-84}, abstract = {

Activity in the motor cortex predicts movements, seconds before they are initiated. This preparatory activity has been observed across cortical layers, including in descending pyramidal tract neurons in layer 5. A key question is how preparatory activity is maintained without causing movement, and is ultimately converted to a motor command to trigger appropriate movements. Here, using single-cell transcriptional profiling and axonal reconstructions, we identify two types of pyramidal tract neuron. Both types project to several targets in the basal ganglia and brainstem. One type projects to thalamic regions that connect back to motor cortex; populations of these neurons produced early preparatory activity that persisted until the movement was initiated. The second type projects to motor centres in the medulla and mainly\ produced late preparatory activity and motor commands. These results indicate that two types of motor cortex output neurons have specialized roles in motor control.

}, issn = {1476-4687}, doi = {10.1038/s41586-018-0642-9}, author = {Economo, Michael N and Viswanathan, Sarada and Tasic, Bosiljka and Bas, Erhan and Winnubst, Johan and Menon, Vilas and Graybuck, Lucas T and Nguyen, Thuc Nghi and Smith, Kimberly A and Yao, Zizhen and Wang, Lihua and Gerfen, Charles R and Chandrashekar, Jayaram and Zeng, Hongkui and Looger, Loren L and Svoboda, Karel} } @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 {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 {49093, title = {Functional architecture of reward learning in mushroom body extrinsic neurons of larval Drosophila.}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {2018 Mar 16}, pages = {1104}, abstract = {

The brain adaptively integrates present sensory input, past experience, and options for future action. The insect mushroom body exemplifies how a central brain structure brings about such integration. Here we use a combination of systematic single-cell labeling, connectomics, transgenic silencing, and activation experiments to study the mushroom body at single-cell resolution, focusing on the behavioral architecture of its input and output neurons (MBINs and MBONs), and of the mushroom body intrinsic APL neuron. Our results reveal the identity and morphology of almost all of these 44 neurons in stage 3 Drosophila larvae. Upon an initial screen, functional analyses focusing on the mushroom body medial lobe uncover sparse and specific functions of its dopaminergic MBINs, its MBONs, and of the GABAergic APL neuron across three behavioral tasks, namely odor preference, taste preference, and associative learning between odor and taste. Our results thus provide a cellular-resolution study case of how brains organize behavior.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-03130-1}, author = {Saumweber, Timo and Rohwedder, Astrid and Schleyer, Michael and Eichler, Katharina and Chen, Yi-chun and Aso, Yoshinori and Cardona, Albert and Eschbach, Claire and Kobler, Oliver and Voigt, Anne and Durairaja, Archana and Mancini, Nino and Zlatic, Marta and Truman, James W and Thum, Andreas S and Gerber, Bertram} } @article {49509, title = {A GAL80 collection to inhibit GAL4 transgenes in olfactory sensory neurons.}, journal = {G3 (Bethesda, Md.)}, volume = {8}, year = {2018}, month = {2018 Nov 06}, pages = {3661-3668}, abstract = {

Fruit flies recognize hundreds of ecologically relevant odors and respond appropriately to them. The complexity, redundancy and interconnectedness of the olfactory machinery complicate efforts to pinpoint the functional contributions of any component neuron or receptor to behavior. Some contributions can only be elucidated in flies that carry multiple mutations and transgenes, but the production of such flies is currently labor-intensive and time-consuming. Here, we describe a set of transgenic flies that express the GAL80 in specific olfactory sensory neurons (). The GAL80s effectively and specifically subtract the activities of GAL4-driven transgenes that impart anatomical and physiological phenotypes. can allow researchers to efficiently activate only one or a few types of functional neurons in an otherwise nonfunctional olfactory background. Such experiments will improve our understanding of the mechanistic connections between odorant inputs and behavioral outputs at the resolution of only a few functional neurons.

}, issn = {2160-1836}, doi = {10.1534/g3.118.200569}, author = {Eliason, Jessica and Afify, Ali and Potter, Christopher and Matsumura, Lchiro} } @article {51794, title = {High-resolution transcriptional dissection of in vivo Atoh1-mediated hair cell conversion in mature cochleae identifies Isl1 as a co-reprogramming factor.}, journal = {PLoS Genetics}, volume = {14}, year = {2018}, month = {2018 07}, pages = {e1007552}, abstract = {

In vivo direct conversion of differentiated cells holds promise for regenerative medicine; however, improving the conversion efficiency and producing functional target cells remain challenging. Ectopic Atoh1 expression in non-sensory supporting cells (SCs) in mouse cochleae induces their partial conversion to hair cells (HCs) at low efficiency. Here, we performed single-cell RNA sequencing of whole mouse sensory epithelia harvested at multiple time points after conditional overexpression of Atoh1. Pseudotemporal ordering revealed that converted HCs (cHCs) are present along a conversion continuum that correlates with both endogenous and exogenous Atoh1 expression. Bulk sequencing of isolated cell populations and single-cell qPCR confirmed 51 transcription factors, including Isl1, are differentially expressed among cHCs, SCs and HCs. In transgenic mice, co-overexpression of Atoh1 and Isl1 enhanced the HC conversion efficiency. Together, our study shows how high-resolution transcriptional profiling of direct cell conversion can identify co-reprogramming factors required for efficient conversion.

}, keywords = {Animals, Animals, Newborn, Basic Helix-Loop-Helix Transcription Factors, Cellular Reprogramming, Gene Expression Profiling, Hair Cells, Auditory, LIM-Homeodomain Proteins, Mice, Mice, Inbred C57BL, Mice, Transgenic, Regeneration, Sequence Analysis, RNA, Single-Cell Analysis, Transcription Factors}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1007552}, author = {Yamashita, Tetsuji and Zheng, Fei and Finkelstein, David and Kellard, Zoe and Carter, Robert and Rosencrance, Celeste D and Sugino, Ken and Easton, John and Gawad, Charles and Zuo, Jian} } @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 {49435, title = {Integration of parallel opposing memories underlies memory extinction.}, journal = {Cell}, volume = {175}, year = {2018}, month = {2018 Sep 06}, pages = {709-22}, abstract = {

Accurately predicting an outcome requires that animals learn supporting and conflicting evidence from sequential experience. In mammals and invertebrates, learned fear responses can be suppressed by experiencing predictive cues without punishment,\ a process called memory extinction. Here, we show that extinction of aversive memories in Drosophila requires specific dopaminergic neurons, which indicate that omission of punishment is remembered as a positive experience. Functional imaging revealed co-existence of intracellular calcium traces in different places in the mushroom body output neuron network for both the original aversive memory and a new appetitive extinction memory. Light and ultrastructural anatomy are consistent with parallel competing memories being combined within mushroom body output neurons that direct avoidance. Indeed, extinction-evoked plasticity in a pair of these neurons neutralizes the potentiated odor response imposed in the network by aversive learning. Therefore, flies track the accuracy of learned expectations by accumulating and integrating memories of conflicting events.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2018.08.021}, author = {Felsenberg, Johannes and Jacob, Pedro F and Walker, Thomas and Barnstedt, Oliver and Edmondson-Stait, Amelia J and Pleijzier, Markus W and Otto, Nils and Schlegel, Philipp and Sharifi, Nadiya and Perisse, Emmanuel and Smith, Carlas S and Lauritzen, J Scott and Costa, Marta and Jefferis, Gregory S X E and Bock, Davi D and Waddell, Scott} } @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 {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 {65768, title = {Macroscale fluorescence imaging against autofluorescence under ambient light}, journal = {Light: Science \& Applications}, year = {2018}, month = {11/2018}, pages = {1 {\textendash} 12}, abstract = {

Macroscale fluorescence imaging is increasingly used to observe biological samples. However, it may suffer from spectral interferences that originate from ambient light or autofluorescence of the sample or its support. In this manuscript, we built a simple and inexpensive fluorescence macroscope, which has been used to evaluate the performance of Speed OPIOM (Out of Phase Imaging after Optical Modulation), which is a reference-free dynamic contrast protocol, to selectively image reversibly photoswitchable fluorophores as labels against detrimental autofluorescence and ambient light. By tuning the intensity and radial frequency of the modulated illumination to the Speed OPIOM resonance and adopting a phase-sensitive detection scheme that ensures noise rejection, we enhanced the sensitivity and the signal-to-noise ratio for fluorescence detection in blot assays by factors of 50 and 10, respectively, over direct fluorescence observation under constant illumination. Then, we overcame the strong autofluorescence of growth media that are currently used in microbiology and realized multiplexed fluorescence observation of colonies of spectrally similar fluorescent bacteria with a unique configuration of excitation and emission wavelengths. Finally, we easily discriminated fluorescent labels from the autofluorescent and reflective background in labeled leaves, even under the interference of incident light at intensities that are comparable to sunlight. The proposed approach is expected to find multiple applications, from biological assays to outdoor observations, in fluorescence macroimaging.

}, doi = {10.1038/s41377-018-0098-6}, author = {Zhang, Ruikang and Chouket, Raja and Plamont, Marie-Aude and Kelemen, Zsolt and Espagne, Agathe and Tebo, Alison G and Gautier, Arnaud and Gissot, Lionel and Faure, Jean-Denis and Jullien, Ludovic and Croquette, Vincent and Saux, Thomas Le} } @article {65030, title = {Membrane bending moduli of coexisting liquid phases containing transmembrane peptide.}, journal = {Biophys J}, volume = {114}, year = {2018}, month = {2018 May 08}, pages = {2152-2164}, abstract = {

A number of highly curved membranes in\ vivo, such as epithelial cell microvilli, have the relatively high sphingolipid content associated with "raft-like" composition. Given the much lower bending energy measured for bilayers with "nonraft" low sphingomyelin and low cholesterol content, observing high curvature for presumably more rigid compositions seems counterintuitive. To understand this behavior, we measured membrane rigidity by fluctuation analysis of giant unilamellar vesicles. We found that including a transmembrane helical GWALP peptide increases the membrane bending modulus of the liquid-disordered (Ld) phase. We observed this increase at both low-cholesterol fraction and higher, more physiological cholesterol fraction. We find that simplified, commonly used Ld and liquid-ordered (Lo) phases are not representative of those that coexist. When Ld and Lo phases coexist, GWALP peptide favors the Ld phase with a partition coefficient of 3-10 depending on mixture composition. In model membranes at high cholesterol fractions, Ld phases with GWALP have greater bending moduli than the Lo phase that would coexist.

}, keywords = {Amino Acid Sequence, Biomechanical Phenomena, Cell Membrane, Cholesterol, Mechanical Phenomena, Models, Molecular, Oligopeptides, Protein Conformation, alpha-Helical}, issn = {1542-0086}, doi = {10.1016/j.bpj.2018.03.026}, author = {Usery, Rebecca D and Enoki, Thais A and Wickramasinghe, Sanjula P and Nguyen, Vanessa P and Ackerman, David G and Greathouse, Denise V and Koeppe, Roger E and Barrera, Francisco N and Feigenson, Gerald W} } @article {49370, title = {mTOR-dependent phosphorylation controls TFEB nuclear export.}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {2018 Aug 17}, pages = {3312}, abstract = {

During starvation the transcriptional activation of catabolic processes is induced by the nuclear translocation and consequent activation of transcription factor EB (TFEB), a master modulator of autophagy and lysosomal biogenesis. However, how TFEB is inactivated upon nutrient refeeding is currently unknown. Here we show that TFEB subcellular localization is dynamically controlled by its continuous shuttling between the cytosol and the nucleus, with the nuclear export representing a limiting step. TFEB nuclear export is mediated by CRM1 and is modulated by nutrient availability via mTOR-dependent hierarchical multisite phosphorylation of serines S142 and S138, which are localized in proximity of a nuclear export signal (NES). Our data on TFEB nucleo-cytoplasmic shuttling suggest an unpredicted role of mTOR in nuclear export.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-05862-6}, author = {Napolitano, Gennaro and Esposito, Alessandra and Choi, Heejun and Matarese, Maria and Benedetti, Valerio and Di Malta, Chiara and Monfregola, Jlenia and Medina, Diego Luis and Lippincott-Schwartz, Jennifer and Ballabio, Andrea} } @conference {49417, title = {Multiple animals tracking in video using part affinity fields}, booktitle = {Visual observation and analysis of Vertebrate And Insect Behavior 2018}, year = {2018}, month = {2018 Aug 20}, abstract = {

In this work, we address the problem of pose detection and tracking of multiple individuals for the study of behaviour in insects and animals. Using a Deep Neural Network architecture, precise detection and association of the body parts can be performed. The models are learned based on user-annotated training videos, which gives flexibility to the approach. This is illustrated on two different animals: honeybees and mice, where very good performance in part recognition and association are observed despite the presence of multiple interacting individuals.

}, url = {http://homepages.inf.ed.ac.uk/rbf/VAIB18PAPERS/vaib18rodriguez.pdf}, author = {Rodriguez, Ivan F and Megret, Remi and Egnor, Roian and Branson, Kristin and Agosto, Jose L and Giray, Tugrul and Acuna, Edgar} } @article {49095, title = {NeuroStorm: accelerating brain science discovery in the cloud.}, journal = {arXiv}, year = {2018}, month = {2018 Mar 09}, abstract = {

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

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

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

}, keywords = {Animals, Cells, Cultured, DNA Helicases, DNA-Binding Proteins, Female, GATA Transcription Factors, Induced Pluripotent Stem Cells, Male, Mi-2 Nucleosome Remodeling and Deacetylase Complex, Mice, Mice, Inbred C57BL, Mice, Inbred CBA, Mice, Knockout, Mice, Transgenic, Transcription Factors}, issn = {1875-9777}, doi = {10.1016/j.stem.2018.07.004}, author = {Mor, Nofar and Rais, Yoach and Sheban, Daoud and Peles, Shani and Aguilera-Castrejon, Alejandro and Zviran, Asaf and Elinger, Dalia and Viukov, Sergey and Geula, Shay and Krupalnik, Vladislav and Zerbib, Mirie and Chomsky, Elad and Lasman, Lior and Shani, Tom and Bayerl, Jonathan and Gafni, Ohad and Hanna, Suhair and Buenrostro, Jason D and Hagai, Tzachi and Masika, Hagit and Vainorius, Gintautas and Bergman, Yehudit and Greenleaf, William J and Esteban, Miguel A and Elling, Ulrich and Levin, Yishai and Massarwa, Rada and Merbl, Yifat and Novershtern, Noa and Hanna, Jacob H} } @conference {65885, title = {Point process latent variable models of larval zebrafish behavior}, booktitle = {NeurIPS}, year = {2018}, month = {12/2018}, abstract = {

A fundamental goal of systems neuroscience is to understand how neural activity gives rise to natural behavior. In order to achieve this goal, we must first build comprehensive models that offer quantitative descriptions of behavior. We develop a new class of probabilistic models to tackle this challenge in the study of larval zebrafish, an important model organism for neuroscience. Larval zebrafish locomote via sequences of punctate swim bouts--brief flicks of the tail--which are naturally modeled as a marked point process. However, these sequences of swim bouts belie a set of discrete and continuous internal states, latent variables that are not captured by standard point process models. We incorporate these variables as latent marks of a point process and explore various models for their dynamics. To infer the latent variables and fit the parameters of this model, we develop an amortized variational inference algorithm that targets the collapsed posterior distribution, analytically marginalizing out the discrete latent variables. With a dataset of over 120,000 swim bouts, we show that our models reveal interpretable discrete classes of swim bouts and continuous internal states like hunger that modulate their dynamics. These models are a major step toward understanding the natural behavioral program of the larval zebrafish and, ultimately, its neural underpinnings.

}, url = {http://papers.nips.cc/paper/8289-point-process-latent-variable-models-of-larval-zebrafish-behavior}, author = {Anuj Sharma and Robert Johnson and Florian Engert and Scott W. Linderman} } @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 {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 {68339, title = {The "sacral parasympathetic": ontogeny and anatomy of a myth.}, journal = {Clin Auton Res}, volume = {28}, year = {2018}, month = {2018 02}, pages = {13-21}, abstract = {

We recently defined genetic traits that distinguish sympathetic from parasympathetic neurons, both preganglionic and ganglionic (Espinosa-Medina et al., Science 354:893-897, 2016). By this set of criteria, we found that the sacral autonomic outflow is sympathetic, not parasympathetic as has been thought for more than a century. Proposing such a belated shift in perspective begs the question why the new criterion (cell types defined by their genetic make-up and dependencies) should be favored over the anatomical, physiological and pharmacological considerations of long ago that inspired the "parasympathetic" classification. After a brief reminder of the former, we expound the weaknesses of the latter and argue that the novel genetic definition helps integrating neglected anatomical and physiological observations and clearing the path for future research.

}, keywords = {Ganglia, Parasympathetic, Ganglia, Sympathetic, Humans, Sacrococcygeal Region, Spinal Cord}, issn = {1619-1560}, doi = {10.1007/s10286-017-0478-7}, author = {Espinosa-Medina, Isabel and Saha, Orthis and Boismoreau, Franck and Brunet, Jean-Fran{\c c}ois} } @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 {67288, title = {Specialized and spatially organized coding of sensory, motor, and cognitive variables in midbrain dopamine neurons}, journal = {bioRxiv}, year = {2018}, month = {10/2018}, abstract = {

There is increased appreciation that dopamine (DA) neurons in the midbrain respond not only to reward 1,2 and reward-predicting cues 1,3,4, but also to other variables such as distance to reward 5, movements 6{\textendash}11 and behavioral choices 12{\textendash}15. Based on these findings, a major open question is how the responses to these diverse variables are organized across the population of DA neurons. In other words, do individual DA neurons multiplex multiple variables, or are subsets of neurons specialized in encoding specific behavioral variables? The reason that this fundamental question has been difficult to resolve is that recordings from large populations of individual DA neurons have not been performed in a behavioral task with sufficient complexity to examine these diverse variables simultaneously. To address this gap, we used 2-photon calcium imaging through an implanted lens to record activity of \>300 midbrain DA neurons in the VTA during a complex decision-making task. As mice navigated in a virtual reality (VR) environment, DA neurons encoded an array of sensory, motor, and cognitive variables. These responses were functionally clustered, such that subpopulations of neurons transmitted information about a subset of behavioral variables, in addition to encoding reward. These functional clusters were spatially organized, such that neighboring neurons were more likely to be part of the same cluster. Taken together with the topography between DA neurons and their projections, this specialization and anatomical organization may aid downstream circuits in correctly interpreting the wide range of signals transmitted by DA neurons.

}, doi = {10.1101/456194}, url = {https://www.biorxiv.org/content/early/2018/10/29/456194}, author = {Engelhard, Ben and Finkelstein, Joel and Cox, Julia and Fleming, Weston and Jang, Hee Jae and Ornelas, Sharon and Koay, Sue Ann and Thiberge, Stephan and Daw, Nathaniel and Tank, David W. and Witten, Ilana B.} } @article {49014, title = {Structure-based inhibitors of tau aggregation.}, journal = {Nature Chemistry}, volume = {10}, year = {2018}, month = {2018 Feb}, pages = {170-176}, abstract = {

Aggregated tau protein is associated with over 20 neurological disorders, which include Alzheimer{\textquoteright}s disease. Previous work has shown that tau{\textquoteright}s sequence segments VQIINK and VQIVYK drive its aggregation, but inhibitors based on the structure of the VQIVYK segment only partially inhibit full-length tau aggregation and are ineffective at inhibiting seeding by full-length fibrils. Here we show that the VQIINK segment is the more powerful driver of tau aggregation. Two structures of this segment determined by the cryo-electron microscopy method micro-electron diffraction explain its dominant influence on tau aggregation. Of practical significance, the structures lead to the design of inhibitors that not only inhibit tau aggregation but also inhibit the ability of exogenous full-length tau fibrils to seed intracellular tau in HEK293 biosensor cells into amyloid. We also raise the possibility that the two VQIINK structures represent amyloid polymorphs of tau that may account for a subset of prion-like strains of tau.

}, issn = {1755-4349}, doi = {10.1038/nchem.2889}, author = {Seidler, P M and Boyer, D R and Rodriguez, J A and Sawaya, M R and Cascio, D and Murray, K and Gonen, T and Eisenberg, D S} } @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 {49292, title = {Synaptic partner prediction from point annotations in insect brains.}, journal = {MICCAI 2018: Medical Image Computing and Computer Assisted Intervention}, year = {2018}, month = {2018 Sep 26}, abstract = {

High-throughput electron microscopy allows recording of lar- ge stacks of neural tissue with sufficient resolution to extract the wiring diagram of the underlying neural network. Current efforts to automate this process focus mainly on the segmentation of neurons. However, in order to recover a wiring diagram, synaptic partners need to be identi- fied as well. This is especially challenging in insect brains like Drosophila melanogaster, where one presynaptic site is associated with multiple post- synaptic elements. Here we propose a 3D U-Net architecture to directly identify pairs of voxels that are pre- and postsynaptic to each other. To that end, we formulate the problem of synaptic partner identification as a classification problem on long-range edges between voxels to encode both the presence of a synaptic pair and its direction. This formulation allows us to directly learn from synaptic point annotations instead of more ex- pensive voxel-based synaptic cleft or vesicle annotations. We evaluate our method on the MICCAI 2016 CREMI challenge and improve over the current state of the art, producing 3\% fewer errors than the next best method.

}, doi = {10.1007/978-3-030-00934-2_35}, author = {Buhmann, Julia and Krause, Renate and Lentini, Rodrigo Ceballos and Eckstein, Nils and Cook, Matthew and Turaga, Srinivas C and Funke, Jan} } @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 {49058, title = {VPS4 is a dynamic component of the centrosome that regulates centrosome localization of γ-tubulin, centriolar satellite stability and ciliogenesis.}, journal = {Scientific Reports}, volume = {8}, year = {2018}, month = {2018 Feb 20}, pages = {3353}, abstract = {

The hexameric AAA ATPase VPS4 facilitates ESCRT III filament disassembly on diverse intracellular membranes. ESCRT III components and VPS4 have been localized to the ciliary transition zone and spindle poles and reported to affect centrosome duplication and spindle pole stability. How the canonical ESCRT pathway could mediate these events is unclear. We studied the association of VPS4 with centrosomes and found that GFP-VPS4 was a dynamic component of both mother and daughter centrioles. A mutant, VPS4, which can{\textquoteright}t hydrolyze ATP, was less dynamic and accumulated at centrosomes. Centrosome localization of the VPS4mutant, caused reduced γ-tubulin levels at centrosomes and consequently decreased microtubule growth and altered centrosome positioning. In addition, preventing VPS4 ATP hydrolysis nearly eliminated centriolar satellites and paused ciliogensis after formation of the ciliary vesicle. Zebrafish embryos injected with GFP-VPS4mRNA were less viable, exhibited developmental defects and had fewer cilia in Kupffer{\textquoteright}s vesicle. Surprisingly, ESCRT III proteins seldom localized to centrosomes and their depletion did not lead to these phenotypes. Our data support an ESCRT III-independent function for VPS4 at the centrosome and reveal that this evolutionary conserved AAA ATPase influences diverse centrosome functions and, as a result, global cellular architecture and development.

}, issn = {2045-2322}, doi = {10.1038/s41598-018-21491-x}, author = {Ott, Carolyn and Nachmias, Dikla and Adar, Shai and Jarnik, Michal and Sherman, Shachar and Birnbaum, Ramon Y and Lippincott-Schwartz, Jennifer and Elia, Natalie} } @article {48449, title = {An Amidase_3 domain-containing N-acetylmuramyl-L-alanine amidase is required for mycobacterial cell division.}, journal = {Scientific Reports}, volume = {7}, year = {2017}, month = {2017 Apr 25}, pages = {1140}, abstract = {

Mycobacteria possess a multi-layered cell wall that requires extensive remodelling during cell division. We investigated the role of an amidase_3 domain-containing N-acetylmuramyl-L-alanine amidase, a peptidoglycan remodelling enzyme implicated in cell division. We demonstrated that deletion of MSMEG_6281 (Ami1) in Mycobacterium smegmatis resulted in the formation of cellular chains, illustrative of cells that were unable to complete division. Suprisingly, viability in the Δami1 mutant was maintained through atypical lateral branching, the products of which proceeded to form viable daughter cells. We showed that these lateral buds resulted from mislocalization of DivIVA, a major determinant in facilitating polar elongation in mycobacterial cells. Failure of Δami1 mutant cells to separate also led to dysregulation of FtsZ ring bundling. Loss of Ami1 resulted in defects in septal peptidoglycan turnover with release of excess cell wall material from the septum or newly born cell poles. We noted signficant accumulation of 3-3 crosslinked muropeptides in the Δami1 mutant. We further demonstrated that deletion of ami1 leads to increased cell wall permeability and enhanced susceptiblity to cell wall targeting antibiotics. Collectively, these data provide novel insight on cell division in actinobacteria and highlights a new class of potential drug targets for mycobacterial diseases.

}, issn = {2045-2322}, doi = {10.1038/s41598-017-01184-7}, author = {Senzani, Sibusiso and Li, Dong and Bhaskar, Ashima and Ealand, Christopher and Chang, James and Rimal, Binayak and Liu, Chengyin and Joon Kim, Sung and Dhar, Neeraj and Kana, Bavesh} } @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 {48982, title = {Behavioral state modulates the ON visual motion pathway of Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, year = {2017}, month = {2017 Dec 18}, pages = {E102-11}, abstract = {

The behavioral state of an animal can dynamically modulate visual processing. In flies, the behavioral state is known to alter the temporal tuning of neurons that carry visual motion information into the central brain. However, where this modulation occurs and how it tunes the properties of this neural circuit are not well understood. Here, we show that the behavioral state alters the baseline activity levels and the temporal tuning of the first directionally selective neuron in the ON motion pathway (T4) as well as its primary input neurons (Mi1, Tm3, Mi4, Mi9). These effects are especially prominent in the inhibitory neuron Mi4, and we show that central octopaminergic neurons provide input to Mi4 and increase its excitability. We further show that octopamine neurons are required for sustained behavioral responses to fast-moving, but not slow-moving, visual stimuli in walking flies. These results indicate that behavioral-state modulation acts directly on the inputs to the directionally selective neurons and supports efficient neural coding of motion stimuli.

}, issn = {1091-6490}, doi = {10.1073/pnas.1703090115}, author = {Strother, James A and Wu, Shiuan-Tze and Rogers, Edward M and Eliason, Jessica L M and Wong, Allan M and Nern, Aljoscha and Reiser, Michael B} } @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 {48960, title = {Cell dynamics underlying oriented growth of the Drosophila wing imaginal disc.}, journal = {Development (Cambridge, England)}, volume = {144}, year = {2017}, month = {2017 Dec 01}, pages = {4406-4421}, abstract = {

Quantitative analysis of the dynamic cellular mechanisms shaping the Drosophila wing during its larval growth phase has been limited, impeding our ability to understand how morphogen patterns regulate tissue shape. Such analysis requires explants to be imaged under conditions that maintain both growth and patterning, as well as methods to quantify how much cellular behaviors change tissue shape. Here, we demonstrate a key requirement for the steroid hormone 20-hydroxyecdysone (20E) in the maintenance of numerous patterning systems in vivo and in explant culture. We find that low concentrations of 20E support prolonged proliferation in explanted wing discs in the absence of insulin, incidentally providing novel insight into the hormonal regulation of imaginal growth. We use 20E-containing media to observe growth directly and to apply recently developed methods for quantitatively decomposing tissue shape changes into cellular contributions. We discover that whereas cell divisions drive tissue expansion along one axis, their contribution to expansion along the orthogonal axis is cancelled by cell rearrangements and cell shape changes. This finding raises the possibility that anisotropic mechanical constraints contribute to growth orientation in the wing disc.

}, keywords = {Animals, Animals, Genetically Modified, Body Patterning, Cell Proliferation, Drosophila melanogaster, Ecdysterone, Gene Expression Profiling, Gene Expression Regulation, Developmental, Genes, Insect, Imaginal Discs, Insulin, Morphogenesis, Signal Transduction, Transcription, Genetic, Wings, Animal}, issn = {1477-9129}, doi = {10.1242/dev.155069}, author = {Dye, Natalie A and Popovi{\'c}, Marko and Spannl, Stephanie and Etournay, Rapha{\"e}l and Kainm{\"u}ller, Dagmar and Ghosh, Suhrid and Myers, Eugene W and J{\"u}licher, Frank and Eaton, Suzanne} } @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 {48991, title = {Common fibrillar spines of amyloid-β and human Islet Amyloid Polypeptide revealed by Micro Electron Diffraction and inhibitors developed using structure-based design.}, journal = {The Journal of Biological Chemistry}, volume = {293}, year = {2017}, month = {2017 Dec 27}, pages = {2888-902}, abstract = {

Amyloid-β (Aβ) and human islet amyloid polypeptide (hIAPP) aggregate to form amyloid fibrils that deposit in tissues, and are associated with Alzheimer{\textquoteright}s disease (AD) and Type-II Diabetes (T2D), respectively. Individuals with T2D have an increased risk of developing AD, and conversely, AD patients have an increased risk of developing T2D. Evidence suggests that this link between AD and T2D might originate from a structural similarity between aggregates of Aβ and hIAPP. Using the cryoEM method Micro-Electron Diffraction (MicroED) we determined the atomic structures of 11-residue segments from both Aβ and hIAPP, termed Aβ 24-34 WT and hIAPP 19-29 S20G, with 64\% sequence similarity. We observe a high degree of structural similarity between their backbone atoms (0.96 {\r A} RMSD). Moreover, fibrils of these segments induce amyloid formation through self- and cross-seeding. Furthermore, inhibitors designed for one segment show cross-efficacy for full-length Aβ and hIAPP and reduce cytotoxicity of both proteins, though by apparently blocking different cytotoxic mechanisms. The similarity of the atomic structures of Aβ 24-34 WT and hIAPP 19-29 S20G offers a molecular model for cross-seeding between Aβ and hIAPP.

}, issn = {1083-351X}, doi = {10.1074/jbc.M117.806109}, author = {Krotee, Pascal and Griner, Sarah L and Sawaya, Michael R and Cascio, Duilio and Rodriguez, Jose A and Shi, Dan and Philipp, Stephan and Murray, Kevin and Saelices, Lorena and Lee, Ji and Seidler, Paul and Glabe, Charles G and Jiang, Lin and Gonen, Tamir and Eisenberg, David S} } @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 {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 {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 {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 {68338, title = {Dual origin of enteric neurons in vagal Schwann cell precursors and the sympathetic neural crest}, journal = {Proceedings of the National Academy of Sciences}, volume = {114}, year = {2017}, month = {10/2017}, pages = {11980-11985}, abstract = {

Most of the enteric nervous system derives from the {\textquotedblleft}vagal{\textquotedblright} neural crest, lying at the level of somites 1{\textendash}7, which invades the digestive tract rostro-caudally from the foregut to the hindgut. Little is known about the initial phase of this colonization, which brings enteric precursors into the foregut. Here we show that the {\textquotedblleft}vagal crest{\textquotedblright} subsumes two populations of enteric precursors with contrasted origins, initial modes of migration, and destinations. Crest cells adjacent to somites 1 and 2 produce Schwann cell precursors that colonize the vagus nerve, which in turn guides them into the esophagus and stomach. Crest cells adjacent to somites 3{\textendash}7 belong to the crest streams contributing to sympathetic chains: they migrate ventrally, seed the sympathetic chains, and colonize the entire digestive tract thence. Accordingly, enteric ganglia, like sympathetic ones, are atrophic when deprived of signaling through the tyrosine kinase receptor ErbB3, while half of the esophageal ganglia require, like parasympathetic ones, the nerve-associated form of the ErbB3 ligand, Neuregulin-1. These dependencies might bear relevance to Hirschsprung disease, with which alleles of Neuregulin-1 are associated.

}, doi = {10.1073/pnas.1710308114}, url = {https://www.pnas.org/doi/abs/10.1073/pnas.1710308114}, author = {Isabel Espinosa-Medina and Ben Jevans and Franck Boismoreau and Zoubida Chettouh and Hideki Enomoto and Thomas M{\"u}ller and Carmen Birchmeier and Alan J. Burns and Jean-Fran{\c c}ois Brunet} } @article {48478, title = {Genetic tools to study juvenile hormone action in Drosophila.}, journal = {Scientific Reports}, volume = {7}, year = {2017}, month = {2017 May 18}, pages = {2132}, abstract = {

The insect juvenile hormone receptor is a basic helix-loop-helix (bHLH), Per-Arnt-Sim (PAS) domain protein, a novel type of hormone receptor. In higher flies like\ Drosophila, the ancestral receptor\ germ cell-expressed\ (gce) gene has duplicated to yield the paralog\ Methoprene-tolerant\ (Met). These paralogous receptors share redundant function during development but play unique roles in adults. Some aspects of JH function apparently require one receptor or the other. To provide a foundation for studying JH receptor function, we have recapitulated endogenous JH receptor expression with single cell resolution. Using Bacteria Artificial Chromosome (BAC) recombineering and a transgenic knock-in, we have generated a spatiotemporal expressional atlas of\ Metand\ gce\ throughout development. We demonstrate JH receptor expression in known JH target tissues, in which temporal expression corresponds with periods of hormone sensitivity. Larval expression largely supports the notion of functional redundancy. Furthermore, we provide the neuroanatomical distribution of JH receptors in both the larval and adult central nervous system, which will serve as a platform for future studies regarding JH action on insect behavior.

}, doi = {10.1038/s41598-017-02264-4}, author = {Baumann, Aaron A and Texada, Michael J and Chen, Hui-Min and Etheredge, Jack N and Miller, D L and Picard, Serge and Warner, Raechel D and Truman, James W and Riddiford, Lynn M} } @article {48318, title = {Imaging mRNA and protein interactions within neurons.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, year = {2017}, month = {2017 Mar 07}, pages = {E1875-E1884}, abstract = {

RNA-protein interactions are essential for proper gene expression regulation, particularly in neurons with unique spatial constraints. Currently, these interactions are defined biochemically, but a method is needed to evaluate them quantitatively within morphological context. Colocalization of two-color labels using wide-field microscopy is a method to infer these interactions. However, because of chromatic aberrations in the objective lens, this approach lacks the resolution to determine whether two molecules are physically in contact or simply nearby by chance. Here, we developed a robust super registration methodology that corrected the chromatic aberration across the entire image field to within 10 nm, which is capable of determining whether two molecules are physically interacting or simply in proximity by random chance. We applied this approach to image single-molecule FISH in combination with immunofluorescence (smFISH-IF) and determined whether the association between an mRNA and binding protein(s) within a neuron was significant or accidental. We evaluated several mRNA-binding proteins identified from RNA pulldown assays to determine which of these exhibit bona fide interactions. Surprisingly, many known mRNA-binding proteins did not bind the mRNA in situ, indicating that adventitious interactions are significant using existing technology. This method provides an ability to evaluate two-color registration compatible with the scale of molecular interactions.

}, issn = {1091-6490}, doi = {10.1073/pnas.1621440114}, author = {Eliscovich, Carolina and Shenoy, Shailesh M and Singer, Robert H} } @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 {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,\ Î±-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 {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 {48160, title = {Machine vision methods for analyzing social interactions.}, journal = {The Journal of Experimental Biology}, volume = {220}, year = {2017}, month = {2017 Jan 01}, pages = {25-34}, abstract = {

Recent developments in machine vision methods for automatic, quantitative analysis of social behavior have immensely improved both the scale and level of resolution with which we can dissect interactions between members of the same species. In this paper, we review these methods, with a particular focus on how biologists can apply them to their own work. We discuss several components of machine vision-based analyses: methods to record high-quality video for automated analyses, video-based tracking algorithms for estimating the positions of interacting animals, and machine learning methods for recognizing patterns of interactions. These methods are extremely general in their applicability, and we review a subset of successful applications of them to biological questions in several model systems with very different types of social behaviors.

}, issn = {1477-9145}, doi = {10.1242/jeb.142281}, author = {Robie, Alice A and Seagraves, Kelly M and Egnor, S E Roian and Branson, Kristin} } @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 {48906, title = {Membrane dynamics and organelle biogenesis-lipid pipelines and vesicular carriers.}, journal = {BMC Biology}, volume = {15}, year = {2017}, month = {2017 Oct 31}, pages = {102}, abstract = {

Discoveries spanning several decades have pointed to vital membrane lipid trafficking pathways involving both vesicular and non-vesicular carriers. But the relative contributions for distinct membrane delivery pathways in cell growth and organelle biogenesis continue to be a puzzle. This is because lipids flow from many sources and across many paths via transport vesicles, non-vesicular transfer proteins, and dynamic interactions between organelles at membrane contact sites. This forum presents our latest understanding, appreciation, and queries regarding the lipid transport mechanisms necessary to drive membrane expansion during organelle biogenesis and cell growth.

}, issn = {1741-7007}, doi = {10.1186/s12915-017-0432-0}, author = {Stefan, Christopher J and Trimble, William S and Grinstein, Sergio and Drin, Guillaume and Reinisch, Karin and De Camilli, Pietro and Cohen, Sarah and Valm, Alex M and Lippincott-Schwartz, Jennifer and Levine, Tim P and Iaea, David B and Maxfield, Frederick R and Futter, Clare E and Eden, Emily R and Judith, Delphine and van Vliet, Alexander R and Agostinis, Patrizia and Tooze, Sharon A and Sugiura, Ayumu and McBride, Heidi M} } @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 {48433, title = {Pavlovian conditioning of larval Drosophila: an illustrated, multilingual, hands-on manual for odor-taste associative learning in maggots.}, journal = {Frontiers in Behavioral Neuroscience}, volume = {11}, year = {2017}, month = {2017 Apr 19}, pages = {45}, abstract = {

Larval Drosophila offer a study case for behavioral neurogenetics that is simple enough to be experimentally tractable, yet complex enough to be worth the effort. We provide a detailed, hands-on manual for Pavlovian odor-reward learning in these animals. Given the versatility of Drosophila for genetic analyses, combined with the evolutionarily shared genetic heritage with humans, the paradigm has utility not only in behavioral neurogenetics and experimental psychology, but for translational biomedicine as well. Together with the upcoming total synaptic connectome of the Drosophila nervous system and the possibilities of single-cell-specific transgene expression, it offers enticing opportunities for research. Indeed, the paradigm has already been adopted by a number of labs and is robust enough to be used for teaching in classroom settings. This has given rise to a demand for a detailed, hands-on manual directed at newcomers and/or at laboratory novices, and this is what we here provide. The paradigm and the present manual have a unique set of features: {\textbullet} The paradigm is cheap, easy, and robust; {\textbullet} The manual is detailed enough for newcomers or laboratory novices; {\textbullet} It briefly covers the essential scientific context; {\textbullet} It includes sheets for scoring, data analysis, and display; {\textbullet} It is multilingual: in addition to an English version we provide German, French, Japanese, Spanish and Italian language versions as well. The present manual can thus foster science education at an earlier age and enable research by a broader community than has been the case to date.

}, doi = {10.3389/fnbeh.2017.00045}, author = {Michels, Birgit and Saumweber, Timo and Biernacki, Roland and Thur, Jeanette and Glasgow, Rupert DV and Schleyer, Michael and Chen, Yi-chun and Eschbach, Claire and Stocker, Reinhard F and Toshima, Naoko and Tanimura, Teiichi and Louis, Matthieu and Arias-Gil, Gonzalo and Marescotti, Manuela and Benfenati, Fabio and Gerber, Bertram} } @article {48418, title = {PreMosa: Extracting 2D surfaces from 3D microscopy mosaics.}, journal = {Bioinformatics (Oxford, England)}, volume = {33}, year = {2017}, month = {2017 Apr 05}, pages = {2563-9}, abstract = {

Motivation: A significant focus of biological research is to understand the development, organization and function of tissues. A particularly productive area of study is on single layer epithelial tissues in which the adherence junctions of cells form a 2D manifold that is fluorescently labeled. Given the size of the tissue, a microscope must collect a mosaic of overlapping 3D stacks encompassing the stained surface. Downstream interpretation is greatly simplified by preprocessing such a dataset as follows: (a) extracting and mapping the stained manifold in each stack into a single 2D projection plane, (b) correcting uneven illumination artifacts, (c) stitching the mosaic planes into a single, large 2D image, and (d) adjusting the contrast.

Results: We have developed PreMosa, an efficient, fully automatic pipeline to perform the four preprocessing tasks above resulting in a single 2D image of the stained manifold across which contrast is optimized and illumination is even. Notable features are as follows. First, the 2D projection step employs a specially developed algorithm that actually finds the manifold in the stack based on maximizing contrast, intensity and smoothness. Second, the projection step comes first, implying all subsequent tasks are more rapidly solved in 2D. And last, the mosaic melding employs an algorithm that globally adjusts contrasts amongst the 2D tiles so as to produce a seamless, high-contrast image. We conclude with an evaluation using ground-truth datasets and present results on datasets from Drosophila melanogaster wings and Schmidtae mediterranea ciliary components.

Availability: PreMosa is available under https://cblasse.github.io/premosa.

Contact: blasse@mpi-cbg.de, myers@mpi-cbg.de.

}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btx195}, author = {Blasse, Corinna and Saalfeld, Stephan and Etournay, Rapha{\"e}l and Sagner, Andreas and Eaton, Suzanne and Myers, Eugene W} } @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 {48303, title = {RNP transport in cell biology: the long and winding road.}, journal = {Current Opinion in Cell Biology}, volume = {45}, year = {2017}, month = {2017 Feb 28}, pages = {38-46}, abstract = {

Regulation of gene expression is key determinant to cell structure and function. RNA localization, where specific mRNAs are transported to subcellular regions and then translated, is highly conserved in eukaryotes ranging from yeast to extremely specialized and polarized cells such as neurons. Messenger RNA and associated proteins (mRNP) move from the site of transcription in the nucleus to their final destination in the cytoplasm both passively through diffusion and actively via directed transport. Dysfunction of RNA localization, transport and translation machinery can lead to pathology. Single-molecule live-cell imaging techniques have revealed unique features of this journey with unprecedented resolution. In this review, we highlight key recent findings that have been made using these approaches and possible implications for spatial control of gene function.

}, issn = {1879-0410}, doi = {10.1016/j.ceb.2017.02.008}, author = {Eliscovich, Carolina and Singer, Robert H} } @article {48269, title = {Self-organizing actin patterns shape membrane architecture but not cell mechanics.}, journal = {Nature Communications}, volume = {8}, year = {2017}, month = {2017 Feb 13}, pages = {14347}, abstract = {

Cell-free studies have demonstrated how collective action of actin-associated proteins can organize actin filaments into dynamic patterns, such as vortices, asters and stars. Using complementary microscopic techniques, we here show evidence of such self-organization of the actin cortex in living HeLa cells. During cell adhesion, an active multistage process naturally leads to pattern transitions from actin vortices over stars into asters. This process is primarily driven by Arp2/3 complex nucleation, but not by myosin motors, which is in contrast to what has been theoretically predicted and observed in vitro. Concomitant measurements of mechanics and plasma membrane fluidity demonstrate that changes in actin patterning alter membrane architecture but occur functionally independent of macroscopic cortex elasticity. Consequently, tuning the activity of the Arp2/3 complex to alter filament assembly may thus be a mechanism allowing cells to adjust their membrane architecture without affecting their macroscopic mechanical properties.

}, issn = {2041-1723}, doi = {10.1038/ncomms14347}, author = {Fritzsche, M and Li, D and Colin-York, H and Chang, V T and Moeendarbary, E and Felce, J H and Sezgin, E and Charras, G and Betzig, E and Eggeling, C} } @article {48495, title = {Semiparametric spectral modeling of the Drosophila connectome.}, journal = {arXiv}, year = {2017}, month = {2017 May 9}, pages = {1705.03297}, abstract = {

We present semiparametric spectral modeling of the complete larval Drosophila mushroom body connectome. Motivated by a thorough exploratory data analysis of the network via Gaussian mixture modeling (GMM) in the adjacency spectral embedding (ASE) representation space, we introduce the latent structure model (LSM) for network modeling and inference. LSM is a generalization of the stochastic block model (SBM) and a special case of the random dot product graph (RDPG) latent position model, and is amenable to semiparametric GMM in the ASE representation space. The resulting connectome code derived via semiparametric GMM composed with ASE captures latent connectome structure and elucidates biologically relevant neuronal properties.

}, url = {https://arxiv.org/abs/1705.03297}, author = {Priebe, Carey E. and Park, Youngser and Tang, Minh and Athreya, Avanti and Lyzinski, Vince and Vogelstein, Joshua T and Qin, Yichen and Cocanougher, Benjamin and Eichler, Katharina and Zlatic, Marta and Cardona, Albert} } @article {48509, title = {Spatial Memory: Mice Quickly Learn a Safe Haven.}, journal = {Current Biology : CB}, volume = {27}, year = {2017}, month = {2017 May 22}, pages = {R388-R390}, abstract = {

New work on innate escape behavior shows that mice spontaneously form a spatially precise memory of the location of shelter, which is laid down quickly and updated continuously.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2017.04.007}, author = {Egnor, S E Roian} } @article {48009, title = {A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs.}, journal = {Nature Methods}, volume = {14}, year = {2017}, month = {2017 Jan 31}, pages = {45-8}, abstract = {

Many functional RNAs have an evolutionarily conserved secondary structure. Conservation of RNA base pairing induces pairwise covariations in sequence alignments. We developed a computational method, R-scape (RNA Structural Covariation Above Phylogenetic Expectation), that quantitatively tests whether covariation analysis supports the presence of a conserved RNA secondary structure. R-scape analysis finds no statistically significant support for proposed secondary structures of the long noncoding RNAs HOTAIR, SRA, and Xist.

}, author = {Rivas, Elena and Clements, Jody and Eddy, Sean R.} } @article {48958, title = {Structure-based inhibitors of tau aggregation.}, journal = {Nature Chemistry}, year = {2017}, month = {2017 Nov 20}, abstract = {

Aggregated tau protein is associated with over 20 neurological disorders, which include Alzheimer{\textquoteright}s disease. Previous work has shown that tau{\textquoteright}s sequence segments VQIINK and VQIVYK drive its aggregation, but inhibitors based on the structure of the VQIVYK segment only partially inhibit full-length tau aggregation and are ineffective at inhibiting seeding by full-length fibrils. Here we show that the VQIINK segment is the more powerful driver of tau aggregation. Two structures of this segment determined by the cryo-electron microscopy method micro-electron diffraction explain its dominant influence on tau aggregation. Of practical significance, the structures lead to the design of inhibitors that not only inhibit tau aggregation but also inhibit the ability of exogenous full-length tau fibrils to seed intracellular tau in HEK293 biosensor cells into amyloid. We also raise the possibility that the two VQIINK structures represent amyloid polymorphs of tau that may account for a subset of prion-like strains of tau.

}, doi = {10.1038/nchem.2889}, author = {Seidler, P M and Boyer, D R and Rodriguez, J A and Sawaya, Michael R and Cascio, Duilio and Murray, K and Gonen, Tamir and Eisenberg, David S} } @article {48804, title = {Synthesis of Janelia Fluor HaloTag and SNAP-Tag Ligands and Their Use in Cellular Imaging Experiments.}, journal = {Methods in Molecular Biology (Clifton, N.J.)}, volume = {1663}, year = {2017}, month = {2017}, pages = {179-188}, abstract = {

The development of genetically encoded self-labeling protein tags such as the HaloTag and SNAP-tag has expanded the utility of chemical dyes in microscopy. Intracellular labeling using these systems requires small, cell-permeable dyes with high brightness and photostability. We recently discovered a general method to improve the properties of classic fluorophores by replacing N,N-dimethylamino groups with four-membered azetidine rings to create the "Janelia Fluor" dyes. Here, we describe the synthesis of the HaloTag and SNAP-tag ligands of Janelia Fluor 549 and Janelia Fluor 646 as well as standard labeling protocols for use in ensemble and single-molecule cellular imaging.

}, issn = {1940-6029}, doi = {10.1007/978-1-4939-7265-4_15}, author = {Grimm, Jonathan B and Brown, Timothy A and English, Brian P and Lionnet, Timoth{\'e}e and Lavis, Luke D} } @article {48623, title = {Taking the measure of MicroED.}, journal = {Current Opinion in Structural Biology}, volume = {46}, year = {2017}, month = {2017 Jun 22}, pages = {79-86}, abstract = {

It is now possible to routinely determine atomic resolution structures by electron cryo-microscopy (cryoEM), facilitated in part by the method known as micro electron-diffraction (MicroED). Since its initial demonstration in 2013, MicroED has helped determine a variety of protein structures ranging in molecular weight from a few hundred Daltons to several hundred thousand Daltons. Some of these structures were novel while others were previously known. The resolutions of structures obtained thus far by MicroED range from 3.2{\r A} to 1.0{\r A}, with most better than 2.5{\r A}. Crystals of various sizes and shapes, with different space group symmetries, and with a range of solvent content have all been studied by MicroED. The wide range of crystals explored to date presents the community with a landscape of opportunity for structure determination from nano crystals. Here we summarize the lessons we have learned during the first few years of MicroED, and from our attempts at the first ab initio structure determined by the method. We re-evaluate theoretical considerations in choosing the appropriate crystals for MicroED and for extracting the most meaning out of measured data. With more laboratories worldwide adopting the technique, we speculate what the first decade might hold for MicroED.

}, issn = {1879-033X}, doi = {10.1016/j.sbi.2017.06.004}, author = {Rodriguez, Jose A and Eisenberg, David S and Gonen, Tamir} } @article {48367, title = {Trainable Weka Segmentation: a machine learning tool for microscopy pixel classification.}, journal = {Bioinformatics (Oxford, England)}, volume = {33}, year = {2017}, month = {2017 Mar 29}, pages = {2424-6}, abstract = {

Summary: State-of-the-art light and electron microscopes are capable of acquiring large image datasets, but quantitatively evaluating the data often involves manually annotating structures of interest. This processis time-consuming and often a major bottleneck in the evaluation pipeline. To overcome this problem, we have introduced the Trainable Weka Segmentation (TWS), a machine learning tool that leveragesa limited number of manual annotations in order to train a classifier and segment the remaining dataautomatically. In addition, TWS can provide unsupervised segmentation learning schemes (clustering) and can be customized to employ user-designed image features or classifiers.

Availability and Implementation: TWS is distributed as open-source software as part of the Fiji image processing distribution of ImageJ at http://imagej.net/Trainable_Weka_Segmentation.

Contact: ignacio.arganda@ehu.eus.

Supplementary information: Supplementary data are available at Bioinformatics online.

}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btx180}, author = {Arganda-Carreras, Ignacio and Kaynig, Verena and Rueden, Curtis and Eliceiri, Kevin W and Schindelin, Johannes and Cardona, Albert and Seung, H Sebastian} } @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 {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 {47711, title = {Accurate design of megadalton-scale two-component icosahedral protein complexes.}, journal = {Science (New York, N.Y.)}, volume = {353}, year = {2016}, month = {2016 Jul 22}, pages = {389-94}, abstract = {

Nature provides many examples of self- and co-assembling protein-based molecular machines, including icosahedral protein cages that serve as scaffolds, enzymes, and compartments for essential biochemical reactions and icosahedral virus capsids, which encapsidate and protect viral genomes and mediate entry into host cells. Inspired by these natural materials, we report the computational design and experimental characterization of co-assembling, two-component, 120-subunit icosahedral protein nanostructures with molecular weights (1.8 to 2.8 megadaltons) and dimensions (24 to 40 nanometers in diameter) comparable to those of small viral capsids. Electron microscopy, small-angle x-ray scattering, and x-ray crystallography show that 10 designs spanning three distinct icosahedral architectures form materials closely matching the design models. In vitro assembly of icosahedral complexes from independently purified components occurs rapidly, at rates comparable to those of viral capsids, and enables controlled packaging of molecular cargo through charge complementarity. The ability to design megadalton-scale materials with atomic-level accuracy and controllable assembly opens the door to a new generation of genetically programmable protein-based molecular machines.

}, issn = {1095-9203}, doi = {10.1126/science.aaf8818}, author = {Bale, Jacob B and Gonen, Shane and Liu, Yuxi and Sheffler, William and Ellis, Daniel and Thomas, Chantz and Cascio, Duilio and Yeates, Todd O and Gonen, Tamir and King, Neil P and Baker, David} } @article {47380, title = {Brain-wide mapping of neural activity controlling zebrafish exploratory locomotion.}, journal = {eLife}, year = {2016}, month = {2016 Mar 22}, abstract = {

In the absence of salient sensory cues to guide behavior, animals must still execute sequences of motor actions in order to forage and explore. How such successive motor actions are coordinated to form global locomotion trajectories is unknown. We mapped the structure of larval zebrafish swim trajectories in homogeneous environments and found that trajectories were characterized by alternating sequences of repeated turns to the left and to the right. Using whole-brain light-sheet imaging, we identified activity relating to the behavior in specific neural populations that we termed the anterior rhombencephalic turning region (ARTR). ARTR perturbations biased swim direction and reduced the dependence of turn direction on turn history, indicating that the ARTR is part of a network generating the temporal correlations in turn direction. We also find suggestive evidence for ARTR mutual inhibition and ARTR projections to premotor neurons. Finally, simulations suggest the observed turn sequences may underlie efficient exploration of local environments.

}, doi = {10.7554/eLife.12741}, url = {http://dx.doi.org/10.7554/eLife.12741}, author = {Dunn, Timothy W. and Mu, Yu and Narayan, Sujatha and Randlett, Owen and Naumann, Eva A. and Yang, Chao-Tsung and Schier, Alexander F. and Freeman, Jeremy and Engert, Florian and Ahrens, Misha B.} } @article {47729, title = {Bright photoactivatable fluorophores for single-molecule imaging.}, journal = {Nature Methods}, volume = {13}, year = {2016}, month = {2016 Oct 24}, pages = {985-8}, abstract = {

Small molecule fluorophores are important tools for advanced imaging experiments. The development of self-labeling protein tags such as the HaloTag and SNAP-tag has expanded the utility of chemical dyes in live-cell microscopy. We recently described a general method for improving the brightness and photostability of small, cell-permeable fluorophores, resulting in the novel azetidine-containing "Janelia Fluor" (JF) dyes. Here, we refine and extend the utility of the JF dyes by synthesizing photoactivatable derivatives that are compatible with live cell labeling strategies. These compounds retain the superior brightness of the JF dyes once activated, but their facile photoactivation also enables improved single-particle tracking and localization microscopy experiments.

}, doi = {10.1038/nmeth.4034}, author = {Lavis, Luke D and Grimm, Jonathan B and English, Brian P and Choi, Heejin and Muthusamy, Anand K and Mehl, Brian P and Dong, Peng and Brown, Timothy A and Lippincott-Schwartz, Jennifer and Liu, Zhe and Lionnet, Timoth{\'e}e} } @article {47433, title = {Computational Analysis of Behavior.}, journal = {Annual Review of Neuroscience}, volume = {39}, year = {2016}, month = {2016 Apr 18}, pages = {217-36}, abstract = {

In this review, we discuss the emerging field of computational behavioral analysis-the use of modern methods from computer science and engineering to quantitatively measure animal behavior. We discuss aspects of experiment design important to both obtaining biologically relevant behavioral data and enabling the use of machine vision and learning techniques for automation. These two goals are often in conflict. Restraining or restricting the environment of the animal can simplify automatic behavior quantification, but it can also degrade the quality or alter important aspects of behavior. To enable biologists to design experiments to obtain better behavioral measurements, and computer scientists to pinpoint fruitful directions for algorithm improvement, we review known effects of artificial manipulation of the animal on behavior. We also review machine vision and learning techniques for tracking, feature extraction, automated behavior classification, and automated behavior discovery, the assumptions they make, and the types of data they work best with. Expected final online publication date for the Annual Review of Neuroscience Volume 39 is July 08, 2016. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates.

}, issn = {1545-4126}, doi = {10.1146/annurev-neuro-070815-013845}, author = {Egnor, S E Roian and Branson, Kristin} } @article {47259, title = {The contribution of ultrasonic vocalizations to mouse courtship.}, journal = {Current Opinion in Neurobiology}, volume = {38}, year = {2016}, month = {2016 Jan 11}, pages = {1-5}, abstract = {

Vocalizations transmit information to social partners, and mice use these signals to exchange information during courtship. Ultrasonic vocalizations from adult males are tightly associated with their interactions with females, and vary as a function of male quality. Work in the last decade has established that the spectrotemporal features of male vocalizations are not learned, but that female attention toward specific vocal features is modified by social experience. Additionally, progress has been made on elucidating how mouse vocalizations are encoded in the auditory system, and on the olfactory circuits that trigger their production. Together these findings provide us with important insights into how vocal communication can contribute to social interactions.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2015.12.009}, author = {Egnor, Se Roian and Seagraves, Kelly M} } @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 {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 {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 {47510, title = {Evidence for an audience effect in mice: male social partners alter the male vocal response to female cues.}, journal = {The Journal of Experimental Biology}, volume = {219}, year = {2016}, month = {2016 May 15}, pages = {1437-48}, abstract = {

Mice (Mus musculus) form large and dynamic social groups and emit ultrasonic vocalizations in a variety of social contexts. Surprisingly, these vocalizations have been studied almost exclusively in the context of cues from only one social partner, despite the observation that in many social species the presence of additional listeners changes the structure of communication signals. Here, we show that male vocal behavior elicited by female odor is affected by the presence of a male audience - with changes in vocalization count, acoustic structure and syllable complexity. We further show that single sensory cues are not sufficient to elicit this audience effect, indicating that multiple cues may be necessary for an audience to be apparent. Together, these experiments reveal that some features of mouse vocal behavior are only expressed in more complex social situations, and introduce a powerful new assay for measuring detection of the presence of social partners in mice.

}, issn = {1477-9145}, doi = {10.1242/jeb.129361}, author = {Seagraves, Kelly M and Arthur, Ben J and Egnor, S E Roian} } @article {48386, title = {From Whole-Brain Data to Functional Circuit Models: The Zebrafish Optomotor Response.}, journal = {Cell}, volume = {167}, year = {2016}, month = {2016 11 03}, pages = {947-960.e20}, abstract = {

Detailed descriptions of brain-scale sensorimotor circuits underlying vertebrate behavior remain elusive. Recent advances in zebrafish neuroscience offer new opportunities to dissect such circuits via whole-brain imaging, behavioral analysis, functional perturbations, and network modeling. Here, we harness these tools to generate a brain-scale circuit\ model of the optomotor response, an orienting behavior evoked by visual motion. We show that such motion is processed by diverse neural response types distributed across multiple brain regions. To transform sensory input into action, these regions sequentially integrate eye- and direction-specific sensory streams, refine representations via interhemispheric inhibition, and demix locomotor instructions to independently drive turning and forward swimming. While experiments revealed many neural response types throughout the brain, modeling identified the dimensions of functional connectivity most critical for the behavior. We thus reveal how distributed neurons collaborate to generate behavior and illustrate a paradigm for distilling functional circuit models from whole-brain data.

}, keywords = {Animals, Brain, Feedback, Sensory, Neural Pathways, Neuroimaging, Neurons, Swimming, Visual Perception, Zebrafish}, issn = {1097-4172}, doi = {10.1016/j.cell.2016.10.019}, author = {Naumann, Eva A and Fitzgerald, James E and Dunn, Timothy W and Rihel, Jason and Sompolinsky, Haim and Engert, Florian} } @article {47726, title = {The genome of the crustacean Parhyale hawaiensis: a model for animal development, regeneration, immunity and lignocellulose digestion.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Nov 16}, pages = {e20062}, abstract = {

Parhyale hawaiensis is a blossoming model system for studies of developmental mechanisms and more recently adult regeneration. We have sequenced the genome allowing annotation of all key signaling pathways, small non-coding RNAs and transcription factors that will enhance ongoing functional studies. Parhayle is a member of the Malacostraca, which includes crustacean food crop species. We analysed the immunity related genes of Parhyale as an important comparative system for these species, where immunity related aquaculture problems have increased as farming has intensified. We also find that Parhyale and other species within Multicrustacea contain the enzyme sets necessary to perform lignocellulose digestion (wood eating), suggesting this ability may predate the diversification of this lineage. Our data provide an essential resource for further development of the Parhyale model. The first Malacostracan genome sequence will underpin ongoing comparative work in important food crop species and research investigating lignocellulose as energy source.

Publication first appeared in BioRxiv on August 2, 2016.\ http://dx.doi.org/10.1101/065789

}, doi = {10.7554/eLife.20062}, author = {Kao, Damian and Lai, Alvina G and Stamataki, Evangelia and Rosic, Silvana and Konstantinides, Nikolaos and Jarvis, Erin and Di Donfrancesco, Alessia and Pouchkina-Stantcheva, Natalia and Semon, Marie and Grillo, Marco and Bruce, Heather and Kumar, Suyash and Siwanowicz, Igor and Le, Andy and Lemire, Andrew and Extavour, Cassandra and Browne, William and Wolff, Carsten and Averof, Michalis and et al} } @article {47967, title = {Glutamate-induced RNA localization and translation in neurons.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, year = {2016}, month = {2016 Sep 13}, abstract = {

Localization of mRNA is required for protein synthesis to occur within discrete intracellular compartments. Neurons represent an ideal system for studying the precision of mRNA trafficking because of their polarized structure and the need for synapse-specific targeting. To investigate this targeting, we derived a quantitative and analytical approach. Dendritic spines were stimulated by glutamate uncaging at a diffraction-limited spot, and the localization of single β-actin mRNAs was measured in space and time. Localization required NMDA receptor activity, a dynamic actin cytoskeleton, and the transacting RNA-binding protein, Zipcode-binding protein 1 (ZBP1). The ability of the mRNA to direct newly synthesized proteins to the site of localization was evaluated using a Halo-actin reporter so that RNA and protein were detected simultaneously. Newly synthesized Halo-actin was enriched at the site of stimulation, required NMDA receptor activity, and localized preferentially at the periphery of spines. This work demonstrates that synaptic activity can induce mRNA localization and local translation of β-actin where the new actin participates in stabilizing the expanding synapse in dendritic spines.

}, doi = {10.1073/pnas.1614267113}, author = {Yoon, Young J and Wu, Bin and Buxbaum, Adina R and Das, Sulagna and Tsai, Albert and English, Brian P and Grimm, Jonathan B and Lavis, Luke D and Singer, Robert H} } @article {48005, title = {Learning recurrent representations for hierarchical behavior modeling.}, journal = {arXiv}, volume = {arXiv:1611.00094}, year = {2016}, month = {2016 Nov 1}, abstract = {

We propose a framework for detecting action patterns from motion sequences and modeling the sensory-motor relationship of animals, using a generative recurrent neural network. The network has a discriminative part (classifying actions) and a generative part (predicting motion), whose recurrent cells are laterally connected, allowing higher levels of the network to represent high level phenomena. We test our framework on two types of data, fruit fly behavior and online handwriting. Our results show that 1) taking advantage of unlabeled sequences, by predicting future motion, significantly improves action detection performance when training labels are scarce, 2) the network learns to represent high level phenomena such as writer identity and fly gender, without supervision, and 3) simulated motion trajectories, generated by treating motion prediction as input to the network, look realistic and may be used to qualitatively evaluate whether the model has learnt generative control rules.

}, author = {Eyjolfsdottir, Eyrun and Branson, Kristin and Yue, Yisong and Perona, Pietro} } @article {48044, title = {Long distance projections of cortical pyramidal neurons.}, journal = {Journal of Neuroscience Research}, year = {2016}, month = {2016 Nov 12}, abstract = {

The neuronal circuits defined by the axonal projections of pyramidal neurons in the cerebral cortex are responsible for processing sensory and other information to plan and execute behavior. Subtypes of cortical pyramidal neurons are organized across layers, with those in different layers distinguished by their patterns of axonal projections and connectivity. For example, those in layers 2 and 3 project between cortical areas to integrate sensory and other information with motor areas; while those in layers 5 and 6 also integrate information between cortical areas, but also project to subcortical structures involved in the generation of behavior. Recent advances in neuroanatomical techniques allow one to target specific subtypes of cortical pyramidal neurons and label both their inputs and projections. Combining these methods with neurophysiological recording techniques and newly introduced atlases of the mouse brain provide the opportunity to achieve a detailed view of the organization of cerebral cortical circuits.

}, doi = {10.1002/jnr.23978}, author = {Gerfen, Charles R and Economo, Michael N and Chandrashekar, Jayaram} } @article {47398, title = {Mapping translation {\textquoteright}hot-spots{\textquoteright} in live cells by tracking single molecules of mRNA and ribosomes.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016}, abstract = {

Messenger RNA localization is important for cell motility by local protein translation. However, while single mRNAs can be imaged and their movements tracked in single cells, it has not yet been possible to determine whether these mRNAs are actively translating. Therefore, we imaged single β-actin mRNAs tagged with MS2 stem loops colocalizing with labeled ribosomes to determine when polysomes formed. A dataset of tracking information consisting of thousands of trajectories per cell demonstrated that mRNAs co-moving with ribosomes have significantly different diffusion properties from non-translating mRNAs that were exposed to translation inhibitors. These data indicate that ribosome load changes mRNA movement and therefore highly translating mRNAs move slower. Importantly, β-actin mRNA near focal adhesions exhibited sub-diffusive corralled movement characteristic of increased translation. This method can identify where ribosomes become engaged for local protein production and how spatial regulation of mRNA-protein interactions mediates cell directionality.

}, issn = {2050-084X}, doi = {10.7554/eLife.10415}, author = {Katz, Zachary B and English, Brian P and Lionnet, Timoth{\'e}e and Yoon, Young J and Monnier, Nilah and Ovryn, Ben and Bathe, Mark and Singer, Robert H} } @article {47283, title = {Neural circuits underlying visually evoked escapes in larval zebrafish.}, journal = {Neuron}, volume = {89}, year = {2016}, month = {2016 Feb 3}, pages = {613-628}, abstract = {

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

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.12.021}, author = {Dunn, Timothy W and Gebhardt, Christoph and Naumann, Eva A and Riegler, Clemens and Ahrens, Misha B and Engert, Florian and Del Bene, Filippo} } @article {47274, title = {A platform for brain-wide imaging and reconstruction of individual neurons.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Jan 20}, abstract = {

The structure of axonal arbors controls how signals from individual neurons are routed within the mammalian brain. However, the arbors of very few long-range projection neurons have been reconstructed in their entirety, as axons with diameters as small as 100 nm arborize in target regions dispersed over many millimeters of tissue. We introduce a platform for high-resolution, three-dimensional fluorescence imaging of complete tissue volumes that enables the visualization and reconstruction of long-range axonal arbors. This platform relies on a high-speed two-photon microscope integrated with a tissue vibratome and a suite of computational tools for large-scale image data. We demonstrate the power of this approach by reconstructing the axonal arbors of multiple neurons in the motor cortex across a single mouse brain.

}, issn = {2050-084X}, doi = {10.7554/eLife.10566}, author = {Economo, Michael N and Clack, Nathan G and Lavis, Luke D and Gerfen, Charles R and Svoboda, Karel and Myers, Eugene W and Chandrashekar, Jayaram} } @article {47602, title = {Protein-retention expansion microscopy of cells and tissues labeled using standard fluorescent proteins and antibodies.}, journal = {Nature Biotechnology}, volume = {34}, year = {2016}, month = {2016 Jul 4}, pages = {987-92}, abstract = {

Expansion microscopy (ExM) enables imaging of preserved specimens with nanoscale precision on diffraction-limited instead of specialized super-resolution microscopes. ExM works by physically separating fluorescent probes after anchoring them to a swellable gel. The first ExM method did not result in the retention of native proteins in the gel and relied on custom-made reagents that are not widely available. Here we describe protein retention ExM (proExM), a variant of ExM in which proteins are anchored to the swellable gel, allowing the use of conventional fluorescently labeled antibodies and streptavidin, and fluorescent proteins. We validated and demonstrated the utility of proExM for multicolor super-resolution (\~{}70 nm) imaging of cells and mammalian tissues on conventional microscopes.

}, issn = {1546-1696}, doi = {10.1038/nbt.3625}, author = {Tillberg, Paul and Chen, Fei and Piatkevich, Kiryl D and Zhao, Yongxin and Yu, Chih-Chieh Jay and English, Brian P and Gao, Linyi and Martorell, Anthony and Suk, Ho-Jun and Yoshida, Fumiaki and DeGennaro, Ellen M and Roossien, Douglas H and Gong, Guanyu and Seneviratne, Uthpala and Tannenbaum, Steven R and Desimone, Robert and Cai, Dawen and Boyden, Edward S} } @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 {47512, title = {Real-time quantification of single RNA translation dynamics in living cells.}, journal = {Science}, volume = {352}, year = {2016}, month = {2016 May 05}, pages = {1425-9}, abstract = {

Although mRNA translation is a fundamental biological process, it has never been imaged in real-time with single molecule precision in vivo. To achieve this, we developed Nascent Chain Tracking (NCT), a technique that uses multi-epitope tags and antibody-based fluorescent probes to quantify single mRNA protein synthesis dynamics. NCT reveals an elongation rate of ~10 amino acids per second, with initiation occurring stochastically every ~30 s. Polysomes contain ~1 ribosome every 200-900 nucleotides and are globular rather than elongated in shape. By developing multi-color probes, we show most polysomes act independently; however, a small fraction (~5\%) form complexes in which two distinct mRNAs can be translated simultaneously. The sensitivity and versatility of NCT make it a powerful new tool for quantifying mRNA translation kinetics.

}, doi = {10.1126/science.aaf0899}, author = {Morisaki, Tatsuya and Lyon, Kenneth and DeLuca, Keith F and DeLuca, Jennifer G and English, Brian P and Zhang, Zhengjian and Lavis, Luke D and Grimm, Jonathan B and Viswanathan, Sarada and Looger, Loren L} } @article {47753, title = {RNA Polymerase II cluster dynamics predict mRNA output in living cells.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 May 03}, abstract = {

Protein clustering is a hallmark of genome regulation in mammalian cells. However, the dynamic molecular processes involved make it difficult to correlate clustering with functional consequences in vivo. We developed a live-cell super-resolution approach to uncover the correlation between mRNA synthesis and the dynamics of RNA Polymerase II (Pol II) clusters at a gene locus. For endogenous β-actin genes in mouse embryonic fibroblasts, we observe that short-lived (~8 s) Pol II clusters correlate with basal mRNA output. During serum stimulation, a stereotyped increase in Pol II cluster lifetime correlates with a proportionate increase in the number of mRNAs synthesized. Our findings suggest that transient clustering of Pol II may constitute a pre-transcriptional regulatory event that predictably modulates nascent mRNA output.

}, issn = {2050-084X}, doi = {10.7554/eLife.13617}, author = {Cho, Won-Ki and Jayanth, Namrata and English, Brian P and Inoue, Takuma and Andrews, J Owen and Conway, William and Grimm, Jonathan B and Spille, Jan-Hendrik and Lavis, Luke D and Lionnet, Timoth{\'e}e and Cisse, Ibrahim I} } @article {68337, title = {The sacral autonomic outflow is sympathetic}, journal = {Science}, volume = {354}, year = {2016}, month = {11/2016}, pages = {893-897}, abstract = {

The autonomic nervous system regulates the function of internal organs such as the gut. The parasympathetic and sympathetic arms of this system tend to operate antagonistically. Espinosa-Medina et al. used anatomical and molecular analyses to reevaluate the assignment of neurons in the sacral autonomic nervous system (see the Perspective by Adameyko). Previously categorized as parasympathetic, these neurons are now identified as sympathetic. The results resolve a persistent confusion about how the two systems developed and open the avenue to more predictable outcomes in developing treatments targeted to the pelvic autonomic nervous system. Science, this issue p. 893; see also p. 833 Contrary to a century-old dogma, the pelvic nerves and ganglia do not belong to the parasympathetic nervous system but to the sympathetic one. A kinship between cranial and pelvic visceral nerves of vertebrates has been accepted for a century. Accordingly, sacral preganglionic neurons are considered parasympathetic, as are their targets in the pelvic ganglia that prominently control rectal, bladder, and genital functions. Here, we uncover 15 phenotypic and ontogenetic features that distinguish pre- and postganglionic neurons of the cranial parasympathetic outflow from those of the thoracolumbar sympathetic outflow in mice. By every single one, the sacral outflow is indistinguishable from the thoracolumbar outflow. Thus, the parasympathetic nervous system receives input from cranial nerves exclusively and the sympathetic nervous system from spinal nerves, thoracic to sacral inclusively. This simplified, bipartite architecture offers a new framework to understand pelvic neurophysiology as well as development and evolution of the autonomic nervous system.

}, doi = {10.1126/science.aah5454}, url = {https://www.science.org/doi/abs/10.1126/science.aah5454}, author = {I. Espinosa-Medina and O. Saha and F. Boismoreau and Z. Chettouh and F. Rossi and W. D. Richardson and J.-F. Brunet} } @article {47487, title = {Shared and distinct retinal input to the mouse superior colliculus and dorsal lateral geniculate nucleus.}, journal = {Journal of Neurophysiology}, volume = {116}, year = {2016}, month = {2016 May 11}, pages = {602-10}, abstract = {

The mammalian retina conveys the vast majority of information about visual stimuli to two brain regions: the dorsal lateral geniculate nucleus (dLGN) and the superior colliculus (SC). The degree to which retinal ganglion cells (RGCs) send similar or distinct information to the two areas remains unclear despite the important constraints that different patterns of RGC input place on downstream visual processing. To resolve this ambiguity we injected a glycoprotein-deficient rabies virus coding for the expression of a fluorescent protein into the dLGN or SC; rabies virus labeled a smaller fraction of RGCs than lipophilic dyes like DiI but, crucially, did not label RGC axons of passage. ~80\% of the RGCs infected by rabies virus injected into the dLGN were co-labeled with DiI injected into the SC, suggesting that many dLGN-projecting RGCs also project to the SC. However, functional characterization of RGCs revealed that the SC receives input from several classes of RGCs that largely avoid the dLGN - in particular, RGCs in which (1) sustained changes in light intensity elicit transient changes in firing rate and/or (2) a small range of stimulus sizes or temporal fluctuations in light intensity elicit robust activity. Taken together, our results illustrate several unexpected asymmetries in the information that the mouse retina conveys to two major downstream targets and suggest that differences in the output of dLGN and SC neurons reflect, at least in part, differences in the functional properties of RGCs that innervate the SC but not the dLGN.

}, issn = {1522-1598}, doi = {10.1152/jn.00227.2016}, author = {Ellis, Erika M and Gauvain, Gregory and Sivyer, Benjamin and Murphy, Gabe J} } @article {47990, title = {Single-cell coding of sensory, spatial and numerical magnitudes in primate prefrontal, premotor and cingulate motor cortices.}, journal = {Experimental Brain Research}, volume = {234}, year = {2016}, month = {2016 Jan}, pages = {241-54}, abstract = {

The representation of magnitude information enables humans and animal species alike to successfully interact with the external environment. However, how various types of magnitudes are processed by single neurons to guide goal-directed behavior remains elusive. Here, we recorded single-cell activity from the dorsolateral prefrontal (PFC), dorsal premotor (PMd) and cingulate motor (CMA) cortices in monkeys discriminating discrete numerical (numerosity), continuous spatial (line length) and basic sensory (spatial frequency) stimuli. We found that almost exclusively PFC neurons represented the different magnitude types during sample presentation and working memory periods. The frequency of magnitude-selective cells in PMd and CMA did not exceed chance level. The proportion of PFC neurons selectively tuned to each of the three magnitude types were comparable. Magnitude coding was mainly dissociated at the single-neuron level, with individual neurons representing only one of the three tested magnitude types. Neuronal magnitude discriminability, coding strength and temporal evolution were comparable between magnitude types encoded by PFC neuron populations. Our data highlight the importance of PFC neurons in representing various magnitude categories. Such magnitude representations are based on largely distributed coding by single neurons that are anatomically intermingled within the same cortical area.

}, keywords = {Animals, Gyrus Cinguli, Judgment, Macaca mulatta, Male, Mathematical Concepts, Motor Cortex, Neurons, Patch-Clamp Techniques, Pattern Recognition, Visual, Prefrontal Cortex, Space Perception}, issn = {1432-1106}, doi = {10.1007/s00221-015-4449-8}, author = {Eiselt, Anne-Kathrin and Nieder, Andreas} } @article {48106, title = {Three pillars for the neural control of appetite.}, journal = {Annual Review of Physiology}, volume = {79}, year = {2016}, month = {2016 Nov 28}, pages = {401-23}, abstract = {

The neural control of appetite is important for understanding motivated behavior along with the present rising prevalence of obesity. Over the past several years, new tools for cell type-specific neuron activity monitoring and perturbation have enabled increasingly detailed analyses of the mechanisms underlying appetite-control systems. Three major neural circuits strongly and acutely influence appetite but with notably different characteristics. Although these circuits interact, they have distinct properties and thus appear to contribute to separate but interlinked processes influencing appetite, thereby forming three pillars of appetite control. Here, we summarize some of the key characteristics of appetite circuits that are emerging from recent work and synthesize the findings into a provisional framework that can guide future studies. Expected final online publication date for the Annual Review of Physiology Volume 79 is February 10, 2017. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

}, issn = {1545-1585}, doi = {10.1146/annurev-physiol-021115-104948}, author = {Sternson, Scott M and Eiselt, Anne-Kathrin} } @article {47521, title = {Translation dynamics of single mRNAs in live cells and neurons.}, journal = {Science (New York, N.Y.)}, volume = {352}, year = {2016}, month = {2016 May 05}, pages = {1430-5}, abstract = {

Translation is the fundamental biological process converting mRNA information into proteins. Single molecule imaging in live cells has illuminated the dynamics of RNA transcription; however, it is not yet applicable to translation. Here we report Single molecule Imaging of NAscent PeptideS (SINAPS) to assess translation in live cells. The approach provides direct readout of initiation, elongation, and location of translation. We show that mRNAs coding for endoplasmic reticulum (ER) proteins are translated when they encounter the ER membrane. Single molecule fluorescence recovery after photobleaching provides direct measurement of elongation speed (5 AA/s). In primary neurons mRNAs are translated in proximal dendrites but repressed in distal dendrites and display {\textquotedblleft}bursting{\textquotedblright} translation. This technology provides a tool to address the spatiotemporal translation mechanism of single mRNAs in living cells.

}, doi = {10.1126/science.aaf1084}, author = {Wu, Bin and Eliscovich, Carolina and Yoon, Young J and Singer, Robert H} } @article {68445, title = {Transmembrane channel-like (tmc) gene regulates Drosophila larval locomotion.}, journal = {Proc Natl Acad Sci U S A}, volume = {113}, year = {2016}, month = {06/2016}, pages = {7243-8}, abstract = {

Drosophila larval locomotion, which entails rhythmic body contractions, is controlled by sensory feedback from proprioceptors. The molecular mechanisms mediating this feedback are little understood. By using genetic knock-in and immunostaining, we found that the Drosophila melanogaster transmembrane channel-like (tmc) gene is expressed in the larval class I and class II dendritic arborization (da) neurons and bipolar dendrite (bd) neurons, both of which are known to provide sensory feedback for larval locomotion. Larvae with knockdown or loss of tmc function displayed reduced crawling speeds, increased head cast frequencies, and enhanced backward locomotion. Expressing Drosophila TMC or mammalian TMC1 and/or TMC2 in the tmc-positive neurons rescued these mutant phenotypes. Bending of the larval body activated the tmc-positive neurons, and in tmc mutants this bending response was impaired. This implicates TMC{\textquoteright}s roles in Drosophila proprioception and the sensory control of larval locomotion. It also provides evidence for a functional conservation between Drosophila and mammalian TMCs.

}, keywords = {Animals, Animals, Genetically Modified, Cell Line, Drosophila melanogaster, Drosophila Proteins, Larva, Locomotion, Membrane Proteins, Mutation, Neurons}, issn = {1091-6490}, doi = {10.1073/pnas.1606537113}, author = {Guo, Yanmeng and Wang, Yuping and Zhang, Wei and Meltzer, Shan and Zanini, Damiano and Yu, Yue and Li, Jiefu and Cheng, Tong and Guo, Zhenhao and Wang, Qingxiu and Jacobs, Julie S and Sharma, Yashoda and Eberl, Daniel F and G{\"o}pfert, Martin C and Jan, Lily Yeh and Jan, Yuh Nung and Wang, Zuoren} } @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 {47035, title = {Combinatorial DNA rearrangement facilitates the origin of new genes in ciliates.}, journal = {Genome Biology and Evolution}, volume = {7}, year = {2015}, month = {2015 Sep 2}, pages = {2859-70}, abstract = {

Programmed genome rearrangements in the unicellular eukaryote Oxytricha trifallax produce a transcriptionally active somatic nucleus from a copy of its germline nucleus during development. This process eliminates noncoding sequences that interrupt coding regions in the germline genome, and joins over 225,000 remaining DNA segments, some of which require inversion or complex permutation to build functional genes. This dynamic genomic organization permits some single DNA segments in the germline to contribute to multiple, distinct somatic genes via alternative processing. Like alternative mRNA splicing, the combinatorial assembly of DNA segments contributes to genetic variation and facilitates the evolution of new genes. In this study, we use comparative genomic analysis to demonstrate that the emergence of alternative DNA splicing is associated with the origin of new genes. Short duplications give rise to alternative gene segments that are spliced to the shared gene segments. Alternative gene segments evolve faster than shared, constitutive segments. Genes with shared segments frequently have different expression profiles, permitting functional divergence. This study reports alternative DNA splicing as a mechanism of new gene origination, illustrating how the process of programmed genome rearrangement gives rise to evolutionary innovation.

}, issn = {1759-6653}, doi = {10.1093/gbe/evv172}, author = {Chen, Xiao and Jung, Seolkyoung and Beh, Leslie Y and Eddy, Sean R and Landweber, Laura F} } @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 {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 {46818, title = {Female mice ultrasonically interact with males during courtship displays.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 May 28}, pages = {e06203}, abstract = {

During courtship males attract females with elaborate behaviors. In mice, these displays include ultrasonic vocalizations. Ultrasonic courtship vocalizations were previously attributed to the courting male, despite evidence that both sexes produce virtually indistinguishable vocalizations. Because of this similarity, and the difficulty of assigning vocalizations to individuals, the vocal contribution of each individual during courtship is unknown. To address this question, we developed a microphone array system to localize vocalizations from socially interacting, individual adult mice. With this system, we show that female mice vocally interact with males during courtship. Males and females jointly increased their vocalization rates during chases. Furthermore, a female{\textquoteright}s participation in these vocal interactions may function as a signal that indicates a state of increased receptivity. Our results reveal a novel form of vocal communication during mouse courtship, and lay the groundwork for a mechanistic dissection of communication during social behavior.

}, issn = {2050-084X}, doi = {10.7554/eLife.06203}, author = {Neunuebel, Joshua P and Taylor, Adam L and Arthur, Ben J and Egnor, Se Roian} } @article {47179, title = {Free RNA polymerase in Escherichia coli.}, journal = {Biochimie}, volume = {119}, year = {2015}, month = {2015 Oct 19}, pages = {80-91}, abstract = {

The frequencies of transcription initiation of regulated and constitutive genes depend on the concentration of free RNA polymerase holoenzyme [Rf] near their promoters. Although RNA polymerase is largely confined to the nucleoid, it is difficult to determine absolute concentrations of [Rf] at particular locations within the nucleoid structure. However, relative concentrations of free RNA polymerase at different growth rates, [Rf]rel, can be estimated from the activities of constitutive promoters. Previous studies indicated that the rrnB P2 promoter is constitutive and that [Rf]rel in the vicinity of rrnB P2 increases with increasing growth rate. Recently it has become possible to directly visualize Rf in growing Escherichia coli cells. Here we examine some of the important issues relating to gene expression based on these new observations. We conclude that: (i) At a growth rate of 2 doublings/h, there are about 1000 free and 2350 non-specifically DNA-bound RNA polymerase molecules per average cell (12 and 28\%, respectively, of 8400 total) which are in rapid equilibrium. (ii) The reversibility of the non-specific binding generates more than 1000 free RNA polymerase molecules every second in the immediate vicinity of the DNA. Of these, most rebind non-specifically to the DNA within a few ms; the frequency of non-specific binding is at least two orders of magnitude greater than specific binding and transcript initiation. (iii) At a given amount of RNA polymerase per cell, [Rf] and the density of non-specifically DNA-bound RNA polymerase molecules along the DNA both vary reciprocally with the amount of DNA in the cell. (iv) At 2 doublings/h an E.\ coli cell contains, on the average, about 1 non-specifically bound RNA polymerase per 9\ kbp of DNA and 1 free RNA polymerase per 20\ kbp of DNA. However some DNA regions (i.e. near active rRNA operons) may have significantly higher than average [Rf].

}, issn = {1638-6183}, doi = {10.1016/j.biochi.2015.10.015}, author = {Patrick, Michael and Dennis, Patrick P and Ehrenberg, Mans and Bremer, Hans} } @article {46267, title = {A general method to improve fluorophores for live-cell and single-molecule microscopy.}, journal = {Nature Methods}, volume = {12}, year = {2015}, month = {2015 Jan 19}, pages = {244-50}, abstract = {

Specific labeling of biomolecules with bright fluorophores is the keystone of fluorescence microscopy. Genetically encoded self-labeling tag proteins can be coupled to synthetic dyes inside living cells, resulting in brighter reporters than fluorescent proteins. Intracellular labeling using these techniques requires cell-permeable fluorescent ligands, however, limiting utility to a small number of classic fluorophores. Here we describe a simple structural modification that improves the brightness and photostability of dyes while preserving spectral properties and cell permeability. Inspired by molecular modeling, we replaced the N,N-dimethylamino substituents in tetramethylrhodamine with four-membered azetidine rings. This addition of two carbon atoms doubles the quantum efficiency and improves the photon yield of the dye in applications ranging from in vitro single-molecule measurements to super-resolution imaging. The novel substitution is generalizable, yielding a palette of chemical dyes with improved quantum efficiencies that spans the UV and visible range.

}, issn = {1548-7105}, doi = {10.1038/nmeth.3256}, author = {Grimm, Jonathan B and English, Brian P and Chen, Jiji and Slaughter, Joel P and Zhang, Zhengjian and Revyakin, Andrey and Patel, Ronak and Macklin, John J and Normanno, Davide and Singer, Robert H and Lionnet, Timoth{\'e}e and Lavis, Luke D} } @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 {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 {46742, title = {HMMER web server: 2015 update.}, journal = {Nucleic Acids Research}, year = {2015}, month = {2015 May 5}, abstract = {

The HMMER website, available at http://www.ebi.ac.uk/Tools/hmmer/, provides access to the protein homology search algorithms found in the HMMER software suite. Since the first release of the website in 2011, the search repertoire has been expanded to include the iterative search algorithm, jackhmmer. The continued growth of the target sequence databases means that traditional tabular representations of significant sequence hits can be overwhelming to the user. Consequently, additional ways of presenting homology search results have been developed, allowing them to be summarised according to taxonomic distribution or domain architecture. The taxonomy and domain architecture representations can be used in combination to filter the results according to the needs of a user. Searches can also be restricted prior to submission using a new taxonomic filter, which not only ensures that the results are specific to the requested taxonomic group, but also improves search performance. The repertoire of profile hidden Markov model libraries, which are used for annotation of query sequences with protein families and domains, has been expanded to include the libraries from CATH-Gene3D, PIRSF, Superfamily and TIGRFAMs. Finally, we discuss the relocation of the HMMER webserver to the European Bioinformatics Institute and the potential impact that this will have.

}, issn = {1362-4962}, doi = {10.1093/nar/gkv397}, author = {Finn, Robert D and Clements, Jody and Arndt, William and Miller, Benjamin L and Wheeler, Travis J and Schreiber, Fabian and Bateman, Alex and Eddy, Sean R} } @article {46480, title = {Homology searches for structural RNAs: from proof of principle to practical use.}, journal = {RNA}, volume = {21}, year = {2015}, month = {2015 Apr}, pages = {605-7}, issn = {1469-9001}, doi = {10.1261/rna.050484.115}, author = {Eddy, Sean R} } @article {46929, title = {Inferring transient particle transport dynamics in live cells.}, journal = {Nature Methods}, volume = {12}, year = {2015}, month = {2015 Jul 20}, pages = {838-40}, abstract = {

Live-cell imaging and particle tracking provide rich information on mechanisms of intracellular transport. However, trajectory analysis procedures to infer complex transport dynamics involving stochastic switching between active transport and diffusive motion are lacking. We applied Bayesian model selection to hidden Markov modeling to infer transient transport states from trajectories of mRNA-protein complexes in live mouse hippocampal neurons and metaphase kinetochores in dividing human cells. The software is available at http://hmm-bayes.org/.

}, issn = {1548-7105}, doi = {10.1038/nmeth.3483}, author = {Monnier, Nilah and Barry, Zachary and Park, Hye Yoon and Su, Kuan-Chung and Katz, Zachary and English, Brian P and Dey, Arkajit and Pan, Keyao and Cheeseman, Iain M and Singer, Robert H and Bathe, Mark} } @article {46532, title = {Large-scale imaging in small brains.}, journal = {Current Opinion in Neurobiology}, volume = {32C}, year = {2015}, month = {2015 Jun 1}, pages = {78-86}, abstract = {

The dense connectivity in the brain means that one neuron{\textquoteright}s activity can influence many others. To observe this interconnected system comprehensively, an aspiration within neuroscience is to record from as many neurons as possible at the same time. There are two useful routes toward this goal: one is to expand the spatial extent of functional imaging techniques, and the second is to use animals with small brains. Here we review recent progress toward imaging many neurons and complete populations of identified neurons in small vertebrates and invertebrates.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2015.01.007}, author = {Ahrens, Misha B and Engert, Florian} } @article {46506, title = {Numb is not a critical regulator of Notch-mediated cell fate decisions in the developing chick inner ear.}, journal = {Frontiers in Cellular Neuroscience}, volume = {9}, year = {2015}, month = {2015}, pages = {74}, abstract = {

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

}, issn = {1662-5102}, doi = {10.3389/fncel.2015.00074}, author = {Eddison, Mark and Weber, Sara J and Ariza-McNaughton, Linda and Lewis, Julian and Daudet, Nicolas} } @article {46185, title = {Rfam 12.0: updates to the RNA families database.}, journal = {Nucleic Acids Research}, volume = {43}, year = {2015}, month = {2015 Jan 28}, pages = {D130-7}, abstract = {

The Rfam database (available at http://rfam.xfam.org) is a collection of non-coding RNA families represented by manually curated sequence alignments, consensus secondary structures and annotation gathered from corresponding Wikipedia, taxonomy and ontology resources. In this article, we detail updates and improvements to the Rfam data and website for the Rfam 12.0 release. We describe the upgrade of our search pipeline to use Infernal 1.1 and demonstrate its improved homology detection ability by comparison with the previous version. The new pipeline is easier for users to apply to their own data sets, and we illustrate its ability to annotate RNAs in genomic and metagenomic data sets of various sizes. Rfam has been expanded to include 260 new families, including the well-studied large subunit ribosomal RNA family, and for the first time includes information on short sequence- and structure-based RNA motifs present within families.

}, issn = {1362-4962}, doi = {10.1093/nar/gku1063}, author = {Nawrocki, Eric P and Burge, Sarah W and Bateman, Alex and Daub, Jennifer and Eberhardt, Ruth Y and Eddy, Sean R and Floden, Evan W and Gardner, Paul P and Jones, Thomas A and Tate, John and Finn, Robert D} } @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 {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 {47266, title = {A three-camera imaging microscope for high-speed single-molecule tracking and super-resolution imaging in living cells.}, journal = {Proceedings of SPIE}, volume = {9550}, year = {2015}, month = {2015 Aug 21}, pages = {955008 }, abstract = {

Our aim is to develop quantitative single-molecule assays to study when and where molecules are interacting inside living cells and where enzymes are active. To this end we present a three-camera imaging microscope for fast tracking of multiple interacting molecules simultaneously, with high spatiotemporal resolution. The system was designed around an ASI RAMM frame using three separate tube lenses and custom multi-band dichroics to allow for enhanced detection efficiency. The frame times of the three Andor iXon Ultra EMCCD cameras are hardware synchronized to the laser excitation pulses of the three excitation lasers, such that the fluorophores are effectively immobilized during frame acquisitions and do not yield detections that are motion-blurred. Stroboscopic illumination allows robust detection from even rapidly moving molecules while minimizing bleaching, and since snapshots can be spaced out with varying time intervals, stroboscopic illumination enables a direct comparison to be made between fast and slow molecules under identical light dosage. We have developed algorithms that accurately track and co-localize multiple interacting biomolecules. The three-color microscope combined with our co-movement algorithms have made it possible for instance to simultaneously image and track how the chromosome environment affects diffusion kinetics or determine how mRNAs diffuse during translation. Such multiplexed single-molecule measurements at a high spatiotemporal resolution inside living cells will provide a major tool for testing models relating molecular architecture and biological dynamics.

}, doi = {10.1117/12.2190246}, author = {English, Brian P and Singer, Robert H} } @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 {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 {48388, title = {Whole-brain activity mapping onto a zebrafish brain atlas.}, journal = {Nature methods}, volume = {12}, year = {2015}, month = {2015 Nov}, pages = {1039-46}, abstract = {

In order to localize the neural circuits involved in generating behaviors, it is necessary to assign activity onto anatomical maps of the nervous system. Using brain registration across hundreds of larval zebrafish, we have built an expandable open-source atlas containing molecular labels and definitions of anatomical regions, the Z-Brain. Using this platform and immunohistochemical detection of phosphorylated extracellular signal{\textendash}regulated kinase (ERK) as a readout of neural activity, we have developed a system to create and contextualize whole-brain maps of stimulus- and behavior-dependent neural activity. This mitogen-activated protein kinase (MAP)-mapping assay is technically simple, and data analysis is completely automated. Because MAP-mapping is performed on freely swimming fish, it is applicable to studies of nearly any stimulus or behavior. Here we demonstrate our high-throughput approach using pharmacological, visual and noxious stimuli, as well as hunting and feeding. The resultant maps outline hundreds of areas associated with behaviors.

}, keywords = {Algorithms, Animals, Automation, Behavior, Animal, Brain, Brain Mapping, Calcium, Extracellular Signal-Regulated MAP Kinases, Image Processing, Computer-Assisted, Immunohistochemistry, Microscopy, Confocal, Neurites, Neurons, Phosphorylation, Principal Component Analysis, Reproducibility of Results, Software, Swimming, Zebrafish}, issn = {1548-7105}, doi = {10.1038/nmeth.3581}, author = {Randlett, Owen and Wee, Caroline L and Naumann, Eva A and Nnaemeka, Onyeka and Schoppik, David and Fitzgerald, James E and Portugues, Ruben and Lacoste, Alix M B and Riegler, Clemens and Engert, Florian and Schier, Alexander F} } @article {45856, title = {Computational analysis of conserved RNA secondary structure in transcriptomes and genomes.}, journal = {Annual Review of Biophysics and Biomolecular Structure}, volume = {43}, year = {2014}, month = {2014}, pages = {433-56}, abstract = {

Transcriptomics experiments and computational predictions both enable systematic discovery of new functional RNAs. However, many putative noncoding transcripts arise instead from artifacts and biological noise, and current computational prediction methods have high false positive rates. I discuss prospects for improving computational methods for analyzing and identifying functional RNAs, with a focus on detecting signatures of conserved RNA secondary structure. An interesting new front is the application of chemical and enzymatic experiments that probe RNA structure on a transcriptome-wide scale. I review several proposed approaches for incorporating structure probing data into the computational prediction of RNA secondary structure. Using probabilistic inference formalisms, I show how all these approaches can be unified in a well-principled framework, which in turn allows RNA probing data to be easily integrated into a wide range of analyses that depend on RNA secondary structure inference. Such analyses include homology search and genome-wide detection of new structural RNAs.

}, keywords = {Algorithms, Animals, Bacteria, Computational Biology, Humans, Nucleic Acid Conformation, RNA}, issn = {1936-1238}, doi = {10.1146/annurev-biophys-051013-022950}, author = {Eddy, Sean R} } @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 {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 {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 {47218, title = {OpenStage: a low-cost motorized microscope stage with sub-micron positioning accuracy.}, journal = {PloS One}, volume = {9}, year = {2014}, month = {2014 Feb 26}, pages = {e88977}, abstract = {

Recent progress in intracellular calcium sensors and other fluorophores has promoted the widespread adoption of functional optical imaging in the life sciences. Home-built multiphoton microscopes are easy to build, highly customizable, and cost effective. For many imaging applications a 3-axis motorized stage is critical, but commercially available motorization hardware (motorized translators, controller boxes, etc) are often very expensive. Furthermore, the firmware on commercial motor controllers cannot easily be altered and is not usually designed with a microscope stage in mind. Here we describe an open-source motorization solution that is simple to construct, yet far cheaper and more customizable than commercial offerings. The cost of the controller and motorization hardware are under $1000. Hardware costs are kept low by replacing linear actuators with high quality stepper motors. Electronics are assembled from commonly available hobby components, which are easy to work with. Here we describe assembly of the system and quantify the positioning accuracy of all three axes. We obtain positioning repeatability of the order of 1 μm in X/Y and 0.1 μm in Z. A hand-held control-pad allows the user to direct stage motion precisely over a wide range of speeds (10(-1) to 10(2) μm{\textperiodcentered}s(-1)), rapidly store and return to different locations, and execute "jumps" of a fixed size. In addition, the system can be controlled from a PC serial port. Our "OpenStage" controller is sufficiently flexible that it could be used to drive other devices, such as micro-manipulators, with minimal modifications.

}, keywords = {Costs and Cost Analysis, Equipment Design, Microscopy, Reproducibility of Results}, issn = {1932-6203}, doi = {10.1371/journal.pone.0088977}, author = {Campbell, Robert A A and Eifert, Robert W and Turner, Glenn C} } @article {68336, title = {Parasympathetic ganglia derive from Schwann cell precursors}, journal = {Science}, volume = {345}, year = {2014}, month = {06/2014}, pages = {87-90}, abstract = {

The parasympathetic nervous system helps regulate the functions of many tissues and organs, including the salivary glands and the esophagus. To do so, it needs to reach throughout the body, connecting central systems to peripheral ones. Dyachuk et al. and Espinosa-Medina et al. explored how these connections are established in mice (see the Perspective by Kalcheim and Rohrer). Progenitor cells that travel along with the developing nerves can give rise to both myelinforming Schwann cells and to parasympathetic neurons. That means the interacting nerves do not have to find each other. Instead, the beginnings of the connections are laid down as the nervous system develops. Science, this issue p. 82, p. 87; see also p. 32 Parasympathetic neurons are born from Schwann cell precursors located in the nerves that carry preganglionic fibers. [Also see Perspective by Kalcheim and Rohrer] Neural crest cells migrate extensively and give rise to most of the peripheral nervous system, including sympathetic, parasympathetic, enteric, and dorsal root ganglia. We studied how parasympathetic ganglia form close to visceral organs and what their precursors are. We find that many cranial nerve-associated crest cells coexpress the pan-autonomic determinant Paired-like homeodomain 2b (Phox2b) together with markers of Schwann cell precursors. Some give rise to Schwann cells after down-regulation of PHOX2b. Others form parasympathetic ganglia after being guided to the site of ganglion formation by the nerves that carry preganglionic fibers, a parsimonious way of wiring the pathway. Thus, cranial Schwann cell precursors are the source of parasympathetic neurons during normal development.

}, doi = {10.1126/science.1253286}, url = {https://www.science.org/doi/abs/10.1126/science.1253286}, author = {I. Espinosa-Medina and E. Outin and C. A. Picard and Z. Chettouh and S. Dymecki and G. G. Consalez and E. Coppola and J.-F. Brunet} } @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 {45699, title = {Photoswitchable red fluorescent protein with a large stokes shift.}, journal = {Chemistry \& Biology}, volume = {21}, year = {2014}, month = {2014 Oct 23}, pages = {1402-14}, abstract = {

A subclass of fluorescent proteins (FPs), large Stokes shift (LSS) FP, are characterized by increased spread between excitation and emission maxima. We report a photoswitchable variant of a red FP with an LSS, PSLSSmKate, which initially exhibits excitation and emission at 445 and 622\ nm, but violet irradiation photoswitches PSLSSmKate into a common red form with excitation and emission at 573 and 621\ nm. We characterize spectral, photophysical, and biochemical properties of PSLSSmKate in\ vitro and in mammalian cells and determine its crystal structure in the LSS form. Mass spectrometry, mutagenesis, and spectroscopy of PSLSSmKate allow us\ to propose molecular mechanisms for the LSS, pH dependence, and light-induced chromophore transformation. We demonstrate the applicability of PSLSSmKate to superresolution photoactivated localization microscopy and protein dynamics in live cells. Given its promising properties, we expect that PSLSSmKate-like phenotype will be further used for photoactivatable imaging and tracking multiple populations of intracellular objects.

}, issn = {1879-1301}, doi = {10.1016/j.chembiol.2014.08.010}, author = {Piatkevich, Kiryl D and English, Brian P and Malashkevich, Vladimir N and Xiao, Hui and Almo, Steven C and Singer, Robert H and Verkhusha, Vladislav V} } @article {47625, title = {Probing the stochastic, motor-driven properties of the cytoplasm using force spectrum microscopy.}, journal = {Cell}, volume = {158}, year = {2014}, month = {2014 Aug 14}, pages = {822-32}, abstract = {

Molecular motors in cells typically produce highly directed motion; however, the aggregate, incoherent effect of all active processes also creates randomly fluctuating forces, which drive diffusive-like, nonthermal motion. Here, we introduce force-spectrum-microscopy (FSM) to directly quantify random forces within the cytoplasm of cells and thereby probe stochastic motor activity. This technique combines measurements of the random motion of probe particles with independent micromechanical measurements of the cytoplasm to quantify the spectrum of force fluctuations. Using FSM, we show that force\ fluctuations substantially enhance intracellular movement of small and large components. The fluctuations are three times larger in malignant cells than in their benign counterparts. We further demonstrate that vimentin acts globally to anchor organelles against randomly fluctuating forces in the cytoplasm, with no effect on their magnitude. Thus, FSM has broad applications for understanding the cytoplasm and its intracellular processes in relation to cell physiology in healthy and diseased states.

}, keywords = {Animals, Biomechanical Phenomena, Cytoplasm, Embryo, Mammalian, Fibroblasts, Mice, Microscopy, Atomic Force, Proteins, Vimentin}, issn = {1097-4172}, doi = {10.1016/j.cell.2014.06.051}, author = {Guo, Ming and Ehrlicher, Allen J and Jensen, Mikkel H and Renz, Malte and Moore, Jeffrey R and Goldman, Robert D and Lippincott-Schwartz, Jennifer and Mackintosh, Frederick C and Weitz, David A} } @article {6938, title = {Rapid adaptive optical recovery of optimal resolution over large volumes.}, journal = {Nature Methods}, volume = {11}, year = {2014}, month = {2014 Apr}, pages = {625-8}, abstract = {

Using a descanned, laser-induced guide star and direct wavefront sensing, we demonstrate adaptive correction of complex optical aberrations at high numerical aperture (NA) and a 14-ms update rate. This correction permits us to compensate for the rapid spatial variation in aberration often encountered in biological specimens and to recover diffraction-limited imaging over large volumes (\>240 mm per side). We applied this to image fine neuronal processes and subcellular dynamics within the zebrafish brain.

}, doi = {10.1038/nmeth.2925}, author = {Wang, Kai and Milkie, Daniel E and Saxena, Ankur and Engerer, Peter and Misgeld, Thomas and Bronner, Marianne E. and Mumm, Jeff and Betzig, Eric} } @article {46327, title = {Space-time wiring specificity supports direction selectivity in the retina.}, journal = {Nature}, volume = {509}, year = {2014}, month = {2014 May 15}, pages = {331-6}, abstract = {

How does the mammalian retina detect motion? This classic problem in visual neuroscience has remained unsolved for 50 years. In search of clues, here we reconstruct Off-type starburst amacrine cells (SACs) and bipolar cells (BCs) in serial electron microscopic images with help from EyeWire, an online community of {\textquoteright}citizen neuroscientists{\textquoteright}. On the basis of quantitative analyses of contact area and branch depth in the retina, we find evidence that one BC type prefers to wire with a SAC dendrite near the SAC soma, whereas another BC type prefers to wire far from the soma. The near type is known to lag the far type in time of visual response. A mathematical model shows how such {\textquoteright}space-time wiring specificity{\textquoteright} could endow SAC dendrites with receptive fields that are oriented in space-time and therefore respond selectively to stimuli that move in the outward direction from the soma.

}, keywords = {Amacrine Cells, Animals, Artificial Intelligence, Brain Mapping, Crowdsourcing, Dendrites, Mice, Models, Neurological, Motion, Neural Pathways, Presynaptic Terminals, Retina, Retinal Bipolar Cells, Spatio-Temporal Analysis}, issn = {1476-4687}, doi = {10.1038/nature13240}, author = {Kim, Jinseop S and Greene, Matthew J and Zlateski, Aleksandar and Lee, Kisuk and Richardson, Mark and Turaga, Srinivas C and Purcaro, Michael and Balkam, Matthew and Robinson, Amy and Behabadi, Bardia F and Campos, Michael and Denk, Winfried and Seung, H Sebastian} } @article {48277, title = {Unilateral whisker trimming in newborn rats alters neuronal coincident discharge among mature barrel cortex neurons.}, journal = {Journal of neurophysiology}, volume = {112}, year = {2014}, month = {2014 Oct 15}, pages = {1925-35}, abstract = {

It is known that sensory deprivation, including postnatal whisker trimming, can lead to severe deficits in the firing rate properties of cortical neurons. Recent results indicate that development of synchronous discharge among cortical neurons is also activity influenced, and that correlated discharge is significantly impaired following loss of bilateral sensory input in rats. Here we investigate whether unilateral whisker trimming (unilateral deprivation or UD) after birth interferes in the same way with the development of synchronous discharge in cortex. We measured the coincidence of spikes among pairs of neurons recorded under urethane anesthesia in one whisker barrel field deprived by trimming all contralateral whiskers for 60 days after birth (UD), and in untrimmed controls (CON). In the septal columns around barrels, UD significantly increased the coincident discharge among cortical neurons compared with CON, most notably in layers II/III. In contrast, synchronous discharge was normal between layer IV UD barrel neurons: i.e., not different from CON. Thus, while bilateral whisker deprivation (BD) produced a global deficit in the development of synchrony in layer IV, UD did not block the development of synchrony between neurons in layer IV barrels and increased synchrony within septal circuits. We conclude that changes in synchronous discharge after UD are unexpectedly different from those recorded after BD, and we speculate that this effect may be due to the driven activity from active commissural inputs arising from the contralateral hemisphere that received normal activity levels during postnatal development.

}, keywords = {Animals, Animals, Newborn, Female, Male, Neurons, Physical Stimulation, Rats, Rats, Long-Evans, Sensory Deprivation, Somatosensory Cortex, Touch, Touch Perception, Vibrissae}, issn = {1522-1598}, doi = {10.1152/jn.00562.2013}, author = {Ghoshal, Ayan and Lustig, Brian and Popescu, Maria and Ebner, Ford and Pouget, Pierre} } @article {45041, title = {Whole-cell patch-clamp recordings in freely moving animals.}, journal = {Methods in Molecular Biology}, volume = {1183}, year = {2014}, month = {2014 Jun 20}, pages = {263-76}, abstract = {

The patch-clamp technique and the whole-cell measurements derived from it have greatly advanced our understanding of the coding properties of individual neurons by allowing for a detailed analysis of their excitatory/inhibitory synaptic inputs, intrinsic electrical properties, and morphology. Because such measurements require a high level of mechanical stability they have for a long time been limited to in vitro and anesthetized preparations. Recently, however, a considerable amount of effort has been devoted to extending these techniques to awake restrained/head-fixed preparations allowing for the study of the input-output functions of neurons during behavior. In this chapter we describe a technique extending patch-clamp recordings to awake animals free to explore their environments.

}, issn = {1940-6029}, doi = {10.1007/978-1-4939-1096-0_17}, author = {Lee, Albert K and Epsztein, J{\'e}r{\^o}me and Brecht, Michael} } @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 {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 {6148, title = {Automated multi-day tracking of marked mice for the analysis of social behaviour.}, journal = {Journal of Neuroscience Methods}, volume = {219}, year = {2013}, month = {2013 Sep 30}, pages = {10-19}, abstract = {

A quantitative description of animal social behaviour is informative for behavioural biologists and clinicians developing drugs to treat social disorders. Social interaction in a group of animals has been difficult to measure because behaviour develops over long periods of time and requires tedious manual scoring, which is subjective and often non-reproducible. Computer-vision systems with the ability to measure complex social behaviour automatically would have a transformative impact on biology. Here, we present a method for tracking group-housed mice individually as they freely interact over multiple days. Each mouse is bleach-marked with a unique fur pattern. The patterns are automatically learned by the tracking software and used to infer identities. Trajectories are analysed to measure behaviour as it develops over days, beyond the range of acute experiments. We demonstrate how our system may be used to study the development of place preferences, associations and social relationships by tracking four mice continuously for five days. Our system enables accurate and reproducible characterisation of wild-type mouse social behaviour and paves the way for high-throughput long-term observation of the effects of genetic, pharmacological and environmental manipulations.

}, issn = {1872-678X}, doi = {10.1016/j.jneumeth.2013.05.013}, author = {Ohayon, Shay and Avni, Ofer and Taylor, Adam L and Perona, Pietro and Roian Egnor, S E} } @article {6282, title = {Cbl-associated protein regulates assembly and function of two tension-sensing structures in Drosophila.}, journal = {Development}, volume = {140}, year = {2013}, month = {2013 Feb 1}, pages = {627-38}, abstract = {

Cbl-associated protein (CAP) localizes to focal adhesions and associates with numerous cytoskeletal proteins; however, its physiological roles remain unknown. Here, we demonstrate that Drosophila CAP regulates the organization of two actin-rich structures in Drosophila: muscle attachment sites (MASs), which connect somatic muscles to the body wall; and scolopale cells, which form an integral component of the fly chordotonal organs and mediate mechanosensation. Drosophila CAP mutants exhibit aberrant junctional invaginations and perturbation of the cytoskeletal organization at the MAS. CAP depletion also results in collapse of scolopale cells within chordotonal organs, leading to deficits in larval vibration sensation and adult hearing. We investigate the roles of different CAP protein domains in its recruitment to, and function at, various muscle subcellular compartments. Depletion of the CAP-interacting protein Vinculin results in a marked reduction in CAP levels at MASs, and vinculin mutants partially phenocopy Drosophila CAP mutants. These results show that CAP regulates junctional membrane and cytoskeletal organization at the membrane-cytoskeletal interface of stretch-sensitive structures, and they implicate integrin signaling through a CAP/Vinculin protein complex in stretch-sensitive organ assembly and function.

}, keywords = {Actin Cytoskeleton, Amino Acid, Amino Acid Sequence, Animal Structures, Animals, Binding Sites, Cell Membrane, Cell-Matrix Junctions, Cellular, Cytoskeletal Proteins, Developmental, Drosophila, Electron, Electrophysiological Phenomena, Gene Expression Regulation, Genome, Hearing Disorders, Insect, Integrins, Larva, Mechanotransduction, Microscopy, Multiprotein Complexes, Muscles, Protein Interaction Mapping, Sequence Homology, Signal Transduction, src Homology Domains, Talin, Transmission, Vibration, Vinculin}, issn = {1477-9129}, doi = {10.1242/dev.085100}, author = {Bharadwaj, Rajnish and Roy, Madhuparna and Ohyama, Tomoko and Sivan-Loukianova, Elena and Delannoy, Michael and Lloyd, Thomas E and Zlatic, Marta and Eberl, Daniel F and Kolodkin, Alex L} } @article {6272, title = {Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions.}, journal = {Nucleic Acids Research}, volume = {41}, year = {2013}, month = {2013 Jul}, pages = {e121}, abstract = {

Detection of protein homology via sequence similarity has important applications in biology, from protein structure and function prediction to reconstruction of phylogenies. Although current methods for aligning protein sequences are powerful, challenges remain, including problems with homologous overextension of alignments and with regions under convergent evolution. Here, we test the ability of the profile hidden Markov model method HMMER3 to correctly assign homologous sequences to \>13,000 manually curated families from the Pfam database. We identify problem families using protein regions that match two or more Pfam families not currently annotated as related in Pfam. We find that HMMER3 E-value estimates seem to be less accurate for families that feature periodic patterns of compositional bias, such as the ones typically observed in coiled-coils. These results support the continued use of manually curated inclusion thresholds in the Pfam database, especially on the subset of families that have been identified as problematic in experiments such as these. They also highlight the need for developing new methods that can correct for this particular type of compositional bias.

}, issn = {1362-4962}, doi = {10.1093/nar/gkt263}, author = {Mistry, Jaina and Finn, Robert D and Eddy, Sean R. and Bateman, Alex and Punta, Marco} } @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 {6266, title = {Computational identification of functional RNA homologs in metagenomic data.}, journal = {RNA Biology}, volume = {10}, year = {2013}, month = {2013 Jul 1}, pages = {1170-9}, abstract = {

A key step toward understanding a metagenomics data set is the identification of functional sequence elements within it, such as protein coding genes and structural RNAs. Relative to protein coding genes, structural RNAs are more difficult to identify because of their reduced alphabet size, lack of open reading frames, and short length. Infernal is a software package that implements "covariance models" (CMs) for RNA homology search, which harness both sequence and structural conservation when searching for RNA homologs. Thanks to the added statistical signal inherent in the secondary structure conservation of many RNA families, Infernal is more powerful than sequence-only based methods such as BLAST and profile HMMs. Together with the Rfam database of CMs, Infernal is a useful tool for identifying RNAs in metagenomics data sets.

}, issn = {1555-8584}, doi = {10.4161/rna.25038}, author = {Nawrocki, Eric P and Eddy, Sean R.} } @article {6586, title = {Decoupled roles for the atypical, bifurcated binding pocket of the ybfF hydrolase.}, journal = {Chembiochem : A European Journal of Chemical Biology}, volume = {14}, year = {2013}, month = {2013 Jun 17}, pages = {1134-44}, abstract = {

Serine hydrolases have diverse intracellular substrates, biological functions, and structural plasticity, and are thus important for biocatalyst design. Amongst serine hydrolases, the recently described ybfF enzyme family are promising novel biocatalysts with an unusual bifurcated substrate-binding cleft and the ability to recognize commercially relevant substrates. We characterized in detail the substrate selectivity of a novel ybfF enzyme from Vibrio cholerae (Vc-ybfF) by using a 21-member library of fluorogenic ester substrates. We assigned the roles of the two substrate-binding clefts in controlling the substrate selectivity and folded stability of Vc-ybfF by comprehensive substitution analysis. The overall substrate preference of Vc-ybfF was for short polar chains, but it retained significant activity with a range of cyclic and extended esters. This broad substrate specificity combined with the substitutional analysis demonstrates that the larger binding cleft controls the substrate specificity of Vc-ybfF. Key selectivity residues (Tyr116, Arg120, Tyr209) are also located at the larger binding pocket and control the substrate specificity profile. In the structure of ybfF the narrower binding cleft contains water molecules prepositioned for hydrolysis, but based on substitution this cleft showed only minimal contribution to catalysis. Instead, the residues surrounding the narrow binding cleft and at the entrance to the binding pocket contributed significantly to the folded stability of Vc-ybfF. The relative contributions of each cleft of the binding pocket to the catalytic activity and folded stability of Vc-ybfF provide a valuable map for designing future biocatalysts based on the ybfF scaffold.

}, issn = {1439-7633}, doi = {10.1002/cbic.201300085}, author = {Ellis, Elizabeth E and Adkins, Chinessa T and Galovska, Natalie M and Lavis, Luke D and Johnson, R Jeremy} } @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 {6846, title = {Dual functions of TAF7L in adipocyte differentiation.}, journal = {eLife}, volume = {2}, year = {2013}, month = {2013 Jan 8}, pages = {e00170}, abstract = {

The diverse transcriptional mechanisms governing cellular differentiation and development of mammalian tissue remains poorly understood. Here we report that TAF7L, a paralogue of TFIID subunit TAF7, is enriched in adipocytes and white fat tissue (WAT) in mouse. Depletion of TAF7L reduced adipocyte-specific gene expression, compromised adipocyte differentiation, and WAT development as well. Ectopic expression of TAF7L in myoblasts reprograms these muscle precursors into adipocytes upon induction. Genome-wide mRNA-seq expression profiling and ChIP-seq binding studies confirmed that TAF7L is required for activating adipocyte-specific genes via a dual mechanism wherein it interacts with PPARγ at enhancers and TBP/Pol II at core promoters. In vitro binding studies confirmed that TAF7L forms complexes with both TBP and PPARγ. These findings suggest that TAF7L plays an integral role in adipocyte gene expression by targeting enhancers as a cofactor for PPARγ and promoters as a component of the core transcriptional machinery.DOI:http://dx.doi.org/10.7554/eLife.00170.001.

}, issn = {2050-084X}, doi = {10.7554/eLife.00170}, author = {Zhou, Haiying and Kaplan, Tommy and Li, Yan and Grubisic, Ivan and Zhang, Zhengjian and Wang, P Jeremy and Eisen, Michael B and Tjian, Robert} } @article {6287, title = {The ENCODE project: missteps overshadowing a success.}, journal = {Current Biology}, volume = {23}, year = {2013}, month = {2013 Apr 8}, pages = {R259-61}, abstract = {

Two clich{\'e}s of science journalism have now played out around the ENCODE project. ENCODE{\textquoteright}s publicity first presented a misleading "all the textbooks are wrong" narrative about noncoding human DNA. Now several critiques of ENCODE{\textquoteright}s narrative have been published, and one was so vitriolic that it fueled "undignified academic squabble" stories that focused on tone more than substance. Neither story line does justice to our actual understanding of genomes, to ENCODE{\textquoteright}s results, or to the role of big science in biology.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2013.03.023}, author = {Eddy, Sean R.} } @article {4056, title = {High throughput methods for electron crystallography.}, journal = {Methods in Molecular Biology}, volume = {955}, year = {2013}, month = {2013}, pages = {273-96}, abstract = {

Membrane proteins play a tremendously important role in cell physiology and serve as a target for an increasing number of drugs. Structural information is key to understanding their function and for developing new strategies for combating disease. However, the complex physical chemistry associated with membrane proteins has made them more difficult to study than their soluble cousins. Electron crystallography has historically been a successful method for solving membrane protein structures and has the advantage of providing a native lipid environment for these proteins. Specifically, when membrane proteins form two-dimensional arrays within a lipid bilayer, electron microscopy can be used to collect images and diffraction and the corresponding data can be combined to produce a three-dimensional reconstruction, which under favorable conditions can extend to atomic resolution. Like X-ray crystallography, the quality of the structures are very much dependent on the order and size of the crystals. However, unlike X-ray crystallography, high-throughput methods for screening crystallization trials for electron crystallography are not in general use. In this chapter, we describe two alternative methods for high-throughput screening of membrane protein crystallization within the lipid bilayer. The first method relies on the conventional use of dialysis for removing detergent and thus reconstituting the bilayer; an array of dialysis wells in the standard 96-well format allows the use of a liquid-handling robot and greatly increases throughput. The second method relies on titration of cyclodextrin as a chelating agent for detergent; a specialized pipetting robot has been designed not only to add cyclodextrin in a systematic way, but to use light scattering to monitor the reconstitution process. In addition, the use of liquid-handling robots for making negatively stained grids and methods for automatically imaging samples in the electron microscope are described.

}, doi = {10.1007/978-1-62703-176-9_15}, author = {Stoke, DL and Ubarretxena-Belandia, I and Gonen, T and Engel, A} } @article {5840, title = {Identification of nonvisual photomotor response cells in the vertebrate hindbrain.}, journal = {The Journal of Neuroscience}, volume = {33}, year = {2013}, month = {2013 Feb 27}, pages = {3834-43}, abstract = {

Nonvisual photosensation enables animals to sense light without sight. However, the cellular and molecular mechanisms of nonvisual photobehaviors are poorly understood, especially in vertebrate animals. Here, we describe the photomotor response (PMR), a robust and reproducible series of motor behaviors in zebrafish that is elicited by visual wavelengths of light but does not require the eyes, pineal gland, or other canonical deep-brain photoreceptive organs. Unlike the relatively slow effects of canonical nonvisual pathways, motor circuits are strongly and quickly (seconds) recruited during the PMR behavior. We find that the hindbrain is both necessary and sufficient to drive these behaviors. Using in vivo calcium imaging, we identify a discrete set of neurons within the hindbrain whose responses to light mirror the PMR behavior. Pharmacological inhibition of the visual cycle blocks PMR behaviors, suggesting that opsin-based photoreceptors control this behavior. These data represent the first known light-sensing circuit in the vertebrate hindbrain.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3689-12.2013}, author = {Kokel, David and Dunn, Timothy W. and Ahrens, Misha B and Alshut, R{\"u}diger and Cheung, Chung Yan J. and Saint-Amant, Louis and Bruni, Giancarlo and Mateus, Rita and van Ham, Tjakko J. and Shiraki, Tomoya and Fukada, Yoshitaka and Kojima, Daisuke and Yeh, Jing-Ruey J. and Mikut, Ralf and von Lintig, Johannes and Engert, Florian and Peters, Randall T.} } @article {47634, title = {Incisive imaging and computation for cellular mysteries: lessons from abscission.}, journal = {Cell}, volume = {155}, year = {2013}, month = {2013 Dec 5}, pages = {1220-31}, abstract = {

The final cleavage event that terminates cell division, abscission of the small, dense intercellular bridge, has been particularly challenging to resolve. Here, we describe imaging innovations that helped answer long-standing questions about the mechanism of abscission. We further explain how computational modeling of high-resolution data was employed to test hypotheses and generate additional insights. We present the model that emerges from application of these complimentary approaches. Similar experimental strategies will undoubtedly reveal exciting details about other underresolved cellular structures.

}, keywords = {Animals, Cell Physiological Processes, Cytokinesis, Humans, Models, Biological, Plant Cells}, issn = {1097-4172}, doi = {10.1016/j.cell.2013.11.011}, author = {Elia, Natalie and Ott, Carolyn and Lippincott-Schwartz, Jennifer} } @article {6453, title = {Infernal 1.1: 100-fold faster RNA homology searches.}, journal = {Bioinformatics}, volume = {29}, year = {2013}, month = {2013 Sep 19}, pages = {2933-5}, abstract = {

SUMMARY: Infernal builds probabilistic profiles of the sequence and secondary structure of an RNA family called covariance models (CMs) from structurally annotated multiple sequence alignments given as input. Infernal uses CMs to search for new family members in sequence databases and to create potentially large multiple sequence alignments. Version 1.1 of Infernal introduces a new filter pipeline for RNA homology search based on accelerated profile hidden Markov model (HMM) methods and HMM-banded CM alignment methods. This enables \~{}100-fold acceleration over the previous version and \~{}10 000-fold acceleration over exhaustive non-filtered CM searches. AVAILABILITY: Source code, documentation and the benchmark are downloadable from http://infernal.janelia.org. Infernal is freely licensed under the GNU GPLv3 and should be portable to any POSIX-compliant operating system, including Linux and Mac OS/X. Documentation includes a user{\textquoteright}s guide with a tutorial, a discussion of file formats and user options and additional details on methods implemented in the software. CONTACT: nawrockie@janelia.hhmi.org.

}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btt509}, author = {Nawrocki, Eric P and Eddy, Sean R.} } @article {6578, title = {Intrinsic disorder within an AKAP-protein kinase A complex guides local substrate phosphorylation.}, journal = {eLife}, volume = {2}, year = {2013}, month = {2013 Nov 5}, pages = {e01319}, abstract = {

Anchoring proteins sequester kinases with their substrates to locally disseminate intracellular signals and avert indiscriminate transmission of these responses throughout the cell. Mechanistic understanding of this process is hampered by limited structural information on these macromolecular complexes. A-kinase anchoring proteins (AKAPs) spatially constrain phosphorylation by cAMP-dependent protein kinases (PKA). Electron microscopy and three-dimensional reconstructions of type-II PKA-AKAP18γ complexes reveal hetero-pentameric assemblies that adopt a range of flexible tripartite configurations. Intrinsically disordered regions within each PKA regulatory subunit impart the molecular plasticity that affords an \~{}16 nanometer radius of motion to the associated catalytic subunits. Manipulating flexibility within the PKA holoenzyme augmented basal and cAMP responsive phosphorylation of AKAP-associated substrates. Cell-based analyses suggest that the catalytic subunit remains within type-II PKA-AKAP18γ complexes upon cAMP elevation. We propose that the dynamic movement of kinase sub-structures, in concert with the static AKAP-regulatory subunit interface, generates a solid-state signaling microenvironment for substrate phosphorylation. DOI: http://dx.doi.org/10.7554/eLife.01319.001.

}, issn = {2050-084X}, doi = {10.7554/eLife.01319}, author = {Smith, F Donelson and Reichow, Steve L and Esseltine, Jessica L and Shi, Dan and Langeberg, Lorene K and Scott, John D and Gonen, Tamir} } @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 {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 {46710, title = {mRNA on the move: the road to its biological destiny.}, journal = {The Journal of Biological Chemistry}, volume = {288}, year = {2013}, month = {2013 Jul 12}, pages = {20361-8}, abstract = {

Cells have evolved to regulate the asymmetric distribution of specific mRNA targets to institute spatial and temporal control over gene expression. Over the last few decades, evidence has mounted as to the importance of localization elements in the mRNA sequence and their respective RNA-binding proteins. Live imaging methodologies have shown mechanistic details of this phenomenon. In this minireview, we focus on the advanced biochemical and cell imaging techniques used to tweeze out the finer aspects of mechanisms of mRNA movement.

}, keywords = {Animals, Cytoplasm, Humans, In Situ Hybridization, Microscopy, Fluorescence, Models, Genetic, RNA Precursors, RNA Transport, RNA, Messenger, RNA-Binding Proteins}, issn = {1083-351X}, doi = {10.1074/jbc.R113.452094}, author = {Eliscovich, Carolina and Buxbaum, Adina R and Katz, Zachary B and Singer, Robert H} } @article {6435, title = {nhmmer: DNA homology search with profile HMMs.}, journal = {Bioinformatics}, volume = {29}, year = {2013}, month = {2013 Oct 1}, pages = {2487-9}, abstract = {

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

}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btt403}, author = {Wheeler, Travis J and Eddy, Sean R.} } @article {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 {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 {45716, title = {Pupariation site preference within and between Drosophila sibling species.}, journal = {Evolution}, volume = {67}, year = {2013}, month = {2013 Sep}, pages = {2714-27}, abstract = {

Holometabolous insects pass through a sedentary pupal stage and often choose a location for pupation that is different from the site of larval feeding. We have characterized a difference in pupariation site choice within and between sibling species of Drosophila. We found that, in nature, Drosophila sechellia pupariate within their host fruit, Morinda citrifolia, and that they perform this behavior in laboratory assays. In contrast, in the laboratory, geographically diverse strains of Drosophila simulans vary in their pupariation site preference; D. simulans lines from the ancestral range in southeast Africa pupariate on fruit, or a fruit substitute, whereas populations from Europe or the New World select sites off of fruit. We explored the genetic basis for the evolved preference in puariation site preference by performing quantitative trait locus mapping within and between species. We found that the interspecific difference is controlled largely by loci on chromosomes X and II. In contrast, variation between two strains of D. simulans appears to be highly polygenic, with the majority of phenotypic effects due to loci on chromosome III. These data address the genetic basis of how new traits arise as species diverge and populations disperse.

}, keywords = {Africa, Animal Distribution, Animals, Chromosomes, Insect, Drosophila, Europe, Evolution, Molecular, Genetic Speciation, Genetic Variation, Morinda, Phylogeography, Pupa, Quantitative Trait Loci, X Chromosome}, issn = {1558-5646}, doi = {10.1111/evo.12146}, author = {Erezyilmaz, Deniz F and Stern, David L} } @article {6298, title = {Rfam 11.0: 10 years of RNA families.}, journal = {Nucleic Acids Research}, volume = {41}, year = {2013}, month = {2013 Jan}, pages = {D226-32}, abstract = {

The Rfam database (available via the website at http://rfam.sanger.ac.uk and through our mirror at http://rfam.janelia.org) is a collection of non-coding RNA families, primarily RNAs with a conserved RNA secondary structure, including both RNA genes and mRNA cis-regulatory elements. Each family is represented by a multiple sequence alignment, predicted secondary structure and covariance model. Here we discuss updates to the database in the latest release, Rfam 11.0, including the introduction of genome-based alignments for large families, the introduction of the Rfam Biomart as well as other user interface improvements. Rfam is available under the Creative Commons Zero license.

}, keywords = {Base Sequence, Databases, Genomics, Internet, Molecular Sequence Annotation, Nucleic Acid, Nucleic Acid Conformation, RNA, Sequence Alignment, Untranslated, User-Computer Interface}, issn = {1362-4962}, doi = {10.1093/nar/gks1005}, author = {Burge, Sarah W and Daub, Jennifer and Eberhardt, Ruth and Tate, John and Barquist, Lars and Nawrocki, Eric P and Eddy, Sean R. and Gardner, Paul P and Bateman, Alex} } @article {65031, title = {A Schnurri/Mad/Medea complex attenuates the dorsal-twist gradient readout at vnd.}, journal = {Dev Biol}, volume = {378}, year = {2013}, month = {2013 Jun 01}, pages = {64-72}, abstract = {

Morphogen gradients are used in developing embryos, where they subdivide a field of cells into territories characterized by distinct cell fate potentials. Such systems require both a spatially-graded distribution of the morphogen, and an ability to encode different responses at different target genes. However, the potential for different temporal responses is also present because morphogen gradients typically provide temporal cues, which may be a potential source of conflict. Thus, a low threshold response adapted for an early temporal onset may be inappropriate when the desired spatial response is a spatially-limited, high-threshold expression pattern. Here, we identify such a case with the Drosophila vnd locus, which is a target of the dorsal (dl) nuclear concentration gradient that patterns the dorsal/ventral (D/V) axis of the embryo. The vnd gene plays a critical role in the "ventral dominance" hierarchy of vnd, ind, and msh, which individually specify distinct D/V neural columnar fates in increasingly dorsal ectodermal compartments. The role of vnd in this regulatory hierarchy requires early temporal expression, which is characteristic of low-threshold responses, but its specification of ventral neurogenic ectoderm demands a relatively high-threshold response to dl. We show that the Neurogenic Ectoderm Enhancer (NEE) at vnd takes additional input from the complementary Dpp gradient via a conserved Schnurri/Mad/Medea silencer element (SSE) unlike NEEs at brk, sog, rho, and vn. These results show how requirements for conflicting temporal and spatial responses to the same gradient can be solved by additional inputs from complementary gradients.

}, keywords = {Animals, Base Sequence, Computational Biology, DNA-Binding Proteins, Drosophila melanogaster, Drosophila Proteins, Ectoderm, Enhancer Elements, Genetic, Gene Expression Profiling, Gene Expression Regulation, Developmental, Gene Silencing, Homeodomain Proteins, Molecular Sequence Data, Smad4 Protein, Time Factors, Tissue Distribution, Transcription Factors}, issn = {1095-564X}, doi = {10.1016/j.ydbio.2013.03.002}, author = {Crocker, Justin and Erives, Albert} } @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 {6265, title = {Transcription factors that convert adult cell identity are differentially polycomb repressed.}, journal = {PLoS One}, volume = {8}, year = {2013}, month = {2013 May}, pages = {e63407}, abstract = {

Transcription factors that can convert adult cells of one type to another are usually discovered empirically by testing factors with a known developmental role in the target cell. Here we show that standard genomic methods (RNA-seq and ChIP-seq) can help identify these factors, as most are more strongly Polycomb repressed in the source cell and more highly expressed in the target cell. This criterion is an effective genome-wide screen that significantly enriches for factors that can transdifferentiate several mammalian cell types including neural stem cells, neurons, pancreatic islets, and hepatocytes. These results suggest that barriers between adult cell types, as depicted in Waddington{\textquoteright}s "epigenetic landscape", consist in part of differentially Polycomb-repressed transcription factors. This genomic model of cell identity helps rationalize a growing number of transdifferentiation protocols and may help facilitate the engineering of cell identity for regenerative medicine.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0063407}, author = {Davis, Fred P and Eddy, Sean R.} } @article {6537, title = {Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila.}, journal = {BMC Bioinformatics}, volume = {14}, year = {2013}, month = {2013 Sep 3}, pages = {265}, abstract = {

BACKGROUND: Every genome contains a large number of uncharacterized proteins that may encode entirely novel biological systems. Many of these uncharacterized proteins fall into related sequence families. By applying sequence and structural analysis we hope to provide insight into novel biology. RESULTS: We analyze a previously uncharacterized Pfam protein family called DUF4424 [Pfam:PF14415]. The recently solved three-dimensional structure of the protein lpg2210 from Legionella pneumophila provides the first structural information pertaining to this family. This protein additionally includes the first representative structure of another Pfam family called the YARHG domain [Pfam:PF13308]. The Pfam family DUF4424 adopts a 19-stranded beta-sandwich fold that shows similarity to the N-terminal domain of leukotriene A-4 hydrolase. The YARHG domain forms an all-helical domain at the C-terminus. Structure analysis allows us to recognize distant similarities between the DUF4424 domain and individual domains of M1 aminopeptidases and tricorn proteases, which form massive proteasome-like capsids in both archaea and bacteria. CONCLUSIONS: Based on our analyses we hypothesize that the DUF4424 domain may have a role in forming large, multi-component enzyme complexes. We suggest that the YARGH domain may play a role in binding a moiety in proximity with peptidoglycan, such as a hydrophobic outer membrane lipid or lipopolysaccharide.

}, issn = {1471-2105}, doi = {10.1186/1471-2105-14-265}, author = {Coggill, Penelope and Eberhardt, Ruth Y and Finn, Robert D and Chang, Yuanyuan and Jaroszewski, Lukasz and Godzik, Adam and Das, Debanu and Xu, Qingping and Axelrod, Herbert L and Aravind, L and Murzin, Alexey G and Bateman, Alex} } @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 {48276, title = {Voltage-sensitive dye imaging reveals shifting spatiotemporal spread of whisker-induced activity in rat barrel cortex.}, journal = {Journal of neurophysiology}, volume = {109}, year = {2013}, month = {2013 May}, pages = {2382-92}, abstract = {

In rats, navigating through an environment requires continuous information about objects near the head. Sensory information such as object location and surface texture are encoded by spike firing patterns of single neurons within rat barrel cortex. Although there are many studies using single-unit electrophysiology, much less is known regarding the spatiotemporal pattern of activity of populations of neurons in barrel cortex in response to whisker stimulation. To examine cortical response at the population level, we used voltage-sensitive dye (VSD) imaging to examine ensemble spatiotemporal dynamics of barrel cortex in response to stimulation of single or two adjacent whiskers in urethane-anesthetized rats. Single whisker stimulation produced a poststimulus fluorescence response peak within 12-16 ms in the barrel corresponding to the stimulated whisker (principal whisker). This fluorescence subsequently propagated throughout the barrel field, spreading anisotropically preferentially along a barrel row. After paired whisker stimulation, the VSD signal showed sublinear summation (less than the sum of 2 single whisker stimulations), consistent with previous electrophysiological and imaging studies. Surprisingly, we observed a spatial shift in the center of activation occurring over a 10- to 20-ms period with shift magnitudes of 1-2 barrels. This shift occurred predominantly in the posteromedial direction within the barrel field. Our data thus reveal previously unreported spatiotemporal patterns of barrel cortex activation. We suggest that this nontopographical shift is consistent with known functional and anatomic asymmetries in barrel cortex and that it may provide an important insight for understanding barrel field activation during whisking behavior.

}, keywords = {Action Potentials, Animals, Rats, Rats, Long-Evans, Sensory Receptor Cells, Somatosensory Cortex, Time Factors, Vibrissae, Voltage-Sensitive Dye Imaging}, issn = {1522-1598}, doi = {10.1152/jn.00430.2012}, author = {Lustig, Brian R and Friedman, Robert M and Winberry, Jeremy E and Ebner, Ford F and Roe, Anna W} } @article {4984, title = {Biological imaging software tools.}, journal = {Nature Methods}, volume = {9}, year = {2012}, month = {2012 Jun 28}, pages = {697-710}, abstract = {

Few technologies are more widespread in modern biological laboratories than imaging. Recent advances in optical technologies and instrumentation are providing hitherto unimagined capabilities. Almost all these advances have required the development of software to enable the acquisition, management, analysis and visualization of the imaging data. We review each computational step that biologists encounter when dealing with digital images, the inherent challenges and the overall status of available software for bioimage informatics, focusing on open-source options.

}, issn = {1548-7105}, doi = {10.1038/nmeth.2084}, author = {Eliceiri, Kevin W and Berthold, Michael R and Goldberg, Ilya G and Ib{\'a}{\~n}ez, Luis and Manjunath, B S and Martone, Maryann E and Murphy, Robert F and Peng, Hanchuan and Plant, Anne L and Roysam, Badrinath and Stuurmann, Nico and Swedlow, Jason R and Tomancak, Pavel and Carpenter, Anne E.} } @article {5671, title = {Brain-wide neuronal dynamics during motor adaptation in zebrafish.}, journal = {Nature}, volume = {485}, year = {2012}, month = {2012 May 24}, pages = {471-7}, abstract = {

A fundamental question in neuroscience is how entire neural circuits generate behaviour and adapt it to changes in sensory feedback. Here we use two-photon calcium imaging to record the activity of large populations of neurons at the cellular level, throughout the brain of larval zebrafish expressing a genetically encoded calcium sensor, while the paralysed animals interact fictively with a virtual environment and rapidly adapt their motor output to changes in visual feedback. We decompose the network dynamics involved in adaptive locomotion into four types of neuronal response properties, and provide anatomical maps of the corresponding sites. A subset of these signals occurred during behavioural adjustments and are candidates for the functional elements that drive motor learning. Lesions to the inferior olive indicate a specific functional role for olivocerebellar circuitry in adaptive locomotion. This study enables the analysis of brain-wide dynamics at single-cell resolution during behaviour.

}, keywords = {Adaptation, Animals, Brain, Genetically Modified, Larva, Learning, Locomotion, Models, Nerve Net, Neurological, Neurons, Neuropil, Photic Stimulation, Physiological, Psychomotor Performance, Single-Cell Analysis, Zebrafish}, issn = {1476-4687}, doi = {10.1038/nature11057}, author = {Ahrens, Misha B and Li, Jennifer M and Orger, Michael B. and Robson, Drew N and Schier, Alexander F and Engert, Florian and Portugues, Ruben} } @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 {47649, title = {Computational model of cytokinetic abscission driven by ESCRT-III polymerization and remodeling.}, journal = {Biophysical journal}, volume = {102}, year = {2012}, month = {2012 May 16}, pages = {2309-20}, abstract = {

The endosomal sorting complex required for transport (ESCRT)-III complex, capable of polymerization and remodeling, participates in abscission of the intercellular membrane bridge connecting two daughter cells at the end of cytokinesis. Here, we integrate quantitative imaging of ESCRT-III during cytokinetic abscission with biophysical properties of ESCRT-III complexes to formulate and test a computational model for ESCRT-mediated cytokinetic abscission. We propose that cytokinetic abscission is driven by an ESCRT-III fission complex, which arises from ESCRT-III polymerization at the edge of the cytokinetic midbody structure, located at the center of the intercellular bridge. Formation of the fission complex is completed by remodeling and breakage of the ESCRT-III polymer assisted by VPS4. Subsequent spontaneous constriction of the fission complex generates bending deformation of the intercellular bridge membrane. The related membrane elastic force propels\ the fission complex along the intercellular bridge away from the midbody until it reaches an equilibrium position, determining the scission site. Membrane attachment to the dome-like end-cap of the fission complex drives membrane fission, completing the abscission process. We substantiate the model by theoretical analysis of the membrane elastic energy and by experimental verification of the major model assumptions.

}, keywords = {Adenosine Triphosphate, Animals, Cell Line, Cell Membrane, Computer Simulation, Cytokinesis, Dogs, Endosomal Sorting Complexes Required for Transport, Extracellular Space, Humans, Models, Biological, Polymerization, Reproducibility of Results, Vacuolar Proton-Translocating ATPases}, issn = {1542-0086}, doi = {10.1016/j.bpj.2012.04.007}, author = {Elia, Natalie and Fabrikant, Gur and Kozlov, Michael M and Lippincott-Schwartz, Jennifer} } @article {6280, title = {The C-value paradox, junk DNA and ENCODE.}, journal = {Current Biology}, volume = {22}, year = {2012}, month = {2012 Nov 6}, pages = {R898-9}, abstract = {

paradox? You might expect more complex organisms to have progressively larger genomes, but eukaryotic genome size fails to correlate well with apparent complexity, and instead varies wildly over more than a 100,000-fold range. Single-celled amoebae have some of the largest genomes, up to 100-fold larger than the human genome. This variation suggested that genomes can contain a substantial fraction of DNA other than for genes and their regulatory sequences. C.A. Thomas Jr dubbed it the {\textquoteleft}C-value paradox{\textquoteright} in 1971.

}, keywords = {Animals, DNA, DNA Transposable Elements, Genetic, Genome, Genome Size, Human, Humans, Intergenic, Models}, issn = {1879-0445}, doi = {10.1016/j.cub.2012.10.002}, author = {Eddy, Sean R.} } @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 {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} } @proceedings {5767, title = {Learning animal social behavior from trajectory features.}, year = {2012}, month = {2012 Nov}, address = {Tsukuba, Japan}, author = {Eyjolfsdottir, Eyrun and Burgos-Artizzu, Xavier P. and Branson, Steven and Branson, Kristin and Anderson, David and Perona, Pietro} } @article {5164, title = {Optimization of a GCaMP calcium indicator for neural activity imaging.}, journal = {The Journal of Neuroscience}, volume = {32}, year = {2012}, month = {2012 Oct 3}, pages = {13819-40}, chapter = {13819}, abstract = {

Genetically encoded calcium indicators (GECIs) are powerful tools for systems neuroscience. Recent efforts in protein engineering have significantly increased the performance of GECIs. The state-of-the art single-wavelength GECI, GCaMP3, has been deployed in a number of model organisms and can reliably detect three or more action potentials in short bursts in several systems in vivo . Through protein structure determination, targeted mutagenesis, high-throughput screening, and a battery of in vitro assays, we have increased the dynamic range of GCaMP3 by severalfold, creating a family of {\textquotedblleft}GCaMP5{\textquotedblright} sensors. We tested GCaMP5s in several systems: cultured neurons and astrocytes, mouse retina, and in vivo in Caenorhabditis chemosensory neurons, Drosophila larval neuromuscular junction and adult antennal lobe, zebrafish retina and tectum, and mouse visual cortex. Signal-to-noise ratio was improved by at least 2- to 3-fold. In the visual cortex, two GCaMP5 variants detected twice as many visual stimulus-responsive cells as GCaMP3. By combining in vivo imaging with electrophysiology we show that GCaMP5 fluorescence provides a more reliable measure of neuronal activity than its predecessor GCaMP3.GCaMP5allows more sensitive detection of neural activity in vivo andmayfind widespread applications for cellular imaging in general.

}, doi = {10.1523/​JNEUROSCI.2601-12.2012}, author = {Akerboom, Jasper and Chen, Tsai-Wen and Wardill, Trevor J. and Marvin, Jonathan S and Mutlu, Sevinc and Carreras Caldero, Nicole and Esposti, Federico and Borghuis, Bart G and Sun, Xiaonan Richard and Gordus, Andrew and Orger, Michael B. and Portugues, Ruben and Engert, Florian and Macklin, John J and Filosa, Alessandro and Aggarwal, Aman and Kerr, Rex and Takagi, Ryousuke and Kracun, Sebastian and Shigetomi, Eiji and Khakh, Baljit S. and Baier, Herwig and Lagnado, Leon and Wang, Samuel S-H and Bargmann, Cornelia and Kimmel, Bruce and Jayaraman, Vivek and Svoboda, Karel and Kim, Douglas S. and Schreiter, Eric R and Looger, Loren L} } @article {6501, title = {Organization and metamorphosis of glia in the Drosophila visual system.}, journal = {The Journal of Comparative Neurology}, volume = {520}, year = {2012}, month = {2012 Jul 1}, pages = {2067-85}, abstract = {

The visual system of Drosophila is an excellent model for determining the interactions that direct the differentiation of the nervous system{\textquoteright}s many unique cell types. Glia are essential not only in the development of the nervous system, but also in the function of those neurons with which they become associated in the adult. Given their role in visual system development and adult function we need to both accurately and reliably identify the different subtypes of glia, and to relate the glial subtypes in the larval brain to those previously described for the adult. We viewed driver expression in subsets of larval eye disc glia through the earliest stages of pupal development to reveal the counterparts of these cells in the adult. Two populations of glia exist in the lamina, the first neuropil of the adult optic lobe: those that arise from precursors in the eye-disc/optic stalk and those that arise from precursors in the brain. In both cases, a single larval source gives rise to at least three different types of adult glia. Furthermore, analysis of glial cell types in the second neuropil, the medulla, has identified at least four types of astrocyte-like (reticular) glia. Our clarification of the lamina{\textquoteright}s adult glia and identification of their larval origins, particularly the respective eye disc and larval brain contributions, begin to define developmental interactions which establish the different subtypes of glia.

}, keywords = {Animals, Biological, Drosophila, Drosophila Proteins, Electron, Eye, Genetically Modified, Green Fluorescent Proteins, Horseradish Peroxidase, Metamorphosis, Microscopy, Neuroglia, Neuropil, Nonmammalian, Optic Chiasm, Optic Lobe, Transmission, Visual Pathways}, issn = {1096-9861}, doi = {10.1002/cne.23071}, author = {Edwards, Tara N and Nuschke, Andrea C and Nern, Aljoscha and Meinertzhagen, Ian A.} } @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 {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 {4597, title = {A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more.}, journal = {RNA}, volume = {18}, year = {2012}, month = {2012 Feb}, pages = {193-212}, abstract = {

The standard approach for single-sequence RNA secondary structure prediction uses a nearest-neighbor thermodynamic model with several thousand experimentally determined energy parameters. An attractive alternative is to use statistical approaches with parameters estimated from growing databases of structural RNAs. Good results have been reported for discriminative statistical methods using complex nearest-neighbor models, including CONTRAfold, Simfold, and ContextFold. Little work has been reported on generative probabilistic models (stochastic context-free grammars [SCFGs]) of comparable complexity, although probabilistic models are generally easier to train and to use. To explore a range of probabilistic models of increasing complexity, and to directly compare probabilistic, thermodynamic, and discriminative approaches, we created TORNADO, a computational tool that can parse a wide spectrum of RNA grammar architectures (including the standard nearest-neighbor model and more) using a generalized super-grammar that can be parameterized with probabilities, energies, or arbitrary scores. By using TORNADO, we find that probabilistic nearest-neighbor models perform comparably to (but not significantly better than) discriminative methods. We find that complex statistical models are prone to overfitting RNA structure and that evaluations should use structurally nonhomologous training and test data sets. Overfitting has affected at least one published method (ContextFold). The most important barrier to improving statistical approaches for RNA secondary structure prediction is the lack of diversity of well-curated single-sequence RNA secondary structures in current RNA databases.

}, issn = {1469-9001}, doi = {10.1261/rna.030049.111}, author = {Rivas, Elena and Lang, Raymond and Eddy, Sean R.} } @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 {6506, title = {A survey of 6,300 genomic fragments for cis-regulatory activity in the imaginal discs of Drosophila melanogaster.}, journal = {Cell Reports}, volume = {2}, year = {2012}, month = {2012 Oct 25}, pages = {1014-24}, abstract = {

Over 6,000 fragments from the genome of Drosophila melanogaster were analyzed for their ability to drive expression of GAL4 reporter genes in the third-instar larval imaginal discs. About 1,200 reporter genes drove expression in the eye, antenna, leg, wing, haltere, or genital imaginal discs. The patterns ranged from large regions to individual cells. About 75\% of the active fragments drove expression in multiple discs; 20\% were expressed in ventral, but not dorsal, discs (legs, genital, and antenna), whereas \~{}23\% were expressed in dorsal but not ventral discs (wing, haltere, and eye). Several patterns, for example, within the leg chordotonal organ, appeared a surprisingly large\ number of times. Unbiased searches for DNA sequence motifs suggest candidate transcription factors that may regulate enhancers with shared activities. Together, these expression patterns provide a valuable resource to the community and offer a broad overview of how transcriptional regulatory information is distributed in the Drosophila genome.

}, keywords = {Animals, Arthropod Antennae, Blastodisc, Databases, Drosophila melanogaster, Drosophila Proteins, Eye, Factual, Genes, Genetically Modified, Genome, Imaginal Discs, Regulatory Elements, Reporter, Transcription Factors, Transcriptional, Wing}, issn = {2211-1247}, doi = {10.1016/j.celrep.2012.09.010}, author = {Jory, Aur{\'e}lie and Estella, Carlos and Giorgianni, Matt W and Slattery, Matthew and Laverty, Todd R and Rubin, Gerald M and Mann, Richard S} } @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 {5271, title = {Accelerated profile HMM searches.}, journal = {PLoS Computational Biology}, volume = {7}, year = {2011}, month = {2011 Oct}, pages = {e1002195}, abstract = {

Profile hidden Markov models (profile HMMs) and probabilistic inference methods have made important contributions to the theory of sequence database homology search. However, practical use of profile HMM methods has been hindered by the computational expense of existing software implementations. Here I describe an acceleration heuristic for profile HMMs, the "multiple segment Viterbi" (MSV) algorithm. The MSV algorithm computes an optimal sum of multiple ungapped local alignment segments using a striped vector-parallel approach previously described for fast Smith/Waterman alignment. MSV scores follow the same statistical distribution as gapped optimal local alignment scores, allowing rapid evaluation of significance of an MSV score and thus facilitating its use as a heuristic filter. I also describe a 20-fold acceleration of the standard profile HMM Forward/Backward algorithms using a method I call "sparse rescaling". These methods are assembled in a pipeline in which high-scoring MSV hits are passed on for reanalysis with the full HMM Forward/Backward algorithm. This accelerated pipeline is implemented in the freely available HMMER3 software package. Performance benchmarks show that the use of the heuristic MSV filter sacrifices negligible sensitivity compared to unaccelerated profile HMM searches. HMMER3 is substantially more sensitive and 100- to 1000-fold faster than HMMER2. HMMER3 is now about as fast as BLAST for protein searches.

}, keywords = {Algorithms, Computational Biology, Databases, Information Storage and Retrieval, Markov Chains, Protein, Sequence Alignment, Software}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1002195}, author = {Eddy, Sean R.} } @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 {5411, title = {Control of embryonic stem cell lineage commitment by core promoter factor, TAF3.}, journal = {Cell}, volume = {146}, year = {2011}, month = {2011 Sep 2}, pages = {720-31}, abstract = {

Deciphering the molecular basis of pluripotency is fundamental to our understanding of development and embryonic stem cell function. Here, we report that TAF3, a TBP-associated core promoter factor, is highly enriched in ES cells. In this context, TAF3 is required for endoderm lineage differentiation and prevents premature specification of neuroectoderm and mesoderm. In addition to its role in the core promoter recognition complex TFIID, genome-wide binding studies reveal that TAF3 localizes to a subset of chromosomal regions bound by CTCF/cohesin that are selectively associated with genes upregulated by TAF3. Notably, CTCF directly recruits TAF3 to promoter distal sites and TAF3-dependent DNA looping is observed between the promoter distal sites and core promoters occupied by TAF3/CTCF/cohesin. Together, our findings support a new role of TAF3 in mediating long-range chromatin regulatory interactions that safeguard the finely-balanced transcriptional programs underlying pluripotency.

}, keywords = {Animals, Cell Cycle Proteins, Cell Proliferation, Chromosomal Proteins, Developmental, Embryonic Stem Cells, Endoderm, Gene Expression Regulation, Genetic, Homeodomain Proteins, Humans, Mice, Non-Histone, Promoter Regions, Repressor Proteins, Teratoma, Transcription, Transcription Factor TFIID}, issn = {1097-4172}, doi = {10.1016/j.cell.2011.08.005}, author = {Liu, Zhe and Scannell, Devin R and Eisen, Michael B and Tjian, Robert} } @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 {6507, title = {Exploiting Oxytricha trifallax nanochromosomes to screen for non-coding RNA genes.}, journal = {Nucleic Acids Research}, volume = {39}, year = {2011}, month = {2011 Sep 1}, pages = {7529-47}, abstract = {

We took advantage of the unusual genomic organization of the ciliate Oxytricha trifallax to screen for eukaryotic non-coding RNA (ncRNA) genes. Ciliates have two types of nuclei: a germ line micronucleus that is usually transcriptionally inactive, and a somatic macronucleus that contains a reduced, fragmented and rearranged genome that expresses all genes required for growth and asexual reproduction. In some ciliates including Oxytricha, the macronuclear genome is particularly extreme, consisting of thousands of tiny {\textquoteright}nanochromosomes{\textquoteright}, each of which usually contains only a single gene. Because the organism itself identifies and isolates most of its genes on single-gene nanochromosomes, nanochromosome structure could facilitate the discovery of unusual genes or gene classes, such as ncRNA genes. Using a draft Oxytricha genome assembly and a custom-written protein-coding genefinding program, we identified a subset of nanochromosomes that lack any detectable protein-coding gene, thereby strongly enriching for nanochromosomes that carry ncRNA genes. We found only a small proportion of non-coding nanochromosomes, suggesting that Oxytricha has few independent ncRNA genes besides homologs of already known RNAs. Other than new members of known ncRNA classes including C/D and H/ACA snoRNAs, our screen identified one new family of small RNA genes, named the Arisong RNAs, which share some of the features of small nuclear RNAs.

}, keywords = {Base Sequence, Chromosomes, Conserved Sequence, Genes, Genome, Genomics, Introns, Oxytricha, Protozoan, RNA, Small Nuclear, Small Nucleolar, Untranslated}, issn = {1362-4962}, doi = {10.1093/nar/gkr501}, author = {Jung, Seolkyoung and Swart, Estienne C and Minx, Patrick J and Magrini, Vincent and Mardis, Elaine R and Landweber, Laura F and Eddy, Sean R.} } @article {5280, title = {Fast filtering for RNA homology search.}, journal = {Bioinformatics}, volume = {27}, year = {2011}, month = {2011 Nov 15}, pages = {3102-9}, abstract = {

MOTIVATION: Homology search for RNAs can use secondary structure information to increase power by modeling base pairs, as in covariance models, but the resulting computational costs are high. Typical acceleration strategies rely on at least one filtering stage using sequence-only search. RESULTS: Here we present the multi-segment CYK (MSCYK) filter, which implements a heuristic of ungapped structural alignment for RNA homology search. Compared to gapped alignment, this approximation has lower computation time requirements (O(N$^{4}$) reduced to O(N{\textthreesuperior}), and space requirements (O(N{\textthreesuperior}) reduced to O(N{\texttwosuperior}). A vector-parallel implementation of this method gives up to 100-fold speed-up; vector-parallel implementations of standard gapped alignment at two levels of precision give 3- and 6-fold speed-ups. These approaches are combined to create a filtering pipeline that scores RNA secondary structure at all stages, with results that are synergistic with existing methods.

}, keywords = {Algorithms, Base Sequence, Consensus Sequence, Humans, Nucleic Acid, Nucleic Acid Conformation, RNA, Sequence Alignment, Sequence Analysis, Sequence Homology, Software}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btr545}, author = {Kolbe, Diana L and Eddy, Sean R.} } @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 {4371, title = {A genetically encoded, high-signal-to-noise maltose sensor.}, journal = {Proteins}, volume = {79}, year = {2011}, month = {2011 Nov}, pages = {3025-36}, abstract = {

We describe the generation of a family of high-signal-to-noise single-wavelength genetically encoded indicators for maltose. This was achieved by insertion of circularly permuted fluorescent proteins into a bacterial periplasmic binding protein (PBP), Escherichia coli maltodextrin-binding protein, resulting in a four-color family of maltose indicators. The sensors were iteratively optimized to have sufficient brightness and maltose-dependent fluorescence increases for imaging, under both one- and two-photon illumination. We demonstrate that maltose affinity of the sensors can be tuned in a fashion largely independent of the fluorescent readout mechanism. Using literature mutations, the binding specificity could be altered to moderate sucrose preference, but with a significant loss of affinity. We use the soluble sensors in individual E. coli bacteria to observe rapid maltose transport across the plasma membrane, and membrane fusion versions of the sensors on mammalian cells to visualize the addition of maltose to extracellular media. The PBP superfamily includes scaffolds specific for a number of analytes whose visualization would be critical to the reverse engineering of complex systems such as neural networks, biosynthetic pathways, and signal transduction cascades. We expect the methodology outlined here to be useful in the development of indicators for many such analytes.

}, issn = {1097-0134}, doi = {10.1002/prot.23118}, author = {Marvin, Jonathan S and Schreiter, Eric R and Echevarr{\'\i}a, Ileabett M and Looger, Loren L} } @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 {4302, title = {HMMER web server: interactive sequence similarity searching.}, journal = {Nucleic Acids Research}, volume = {39}, year = {2011}, month = {2011 Jul}, pages = {W29-37}, abstract = {

HMMER is a software suite for protein sequence similarity searches using probabilistic methods. Previously, HMMER has mainly been available only as a computationally intensive UNIX command-line tool, restricting its use. Recent advances in the software, HMMER3, have resulted in a 100-fold speed gain relative to previous versions. It is now feasible to make efficient profile hidden Markov model (profile HMM) searches via the web. A HMMER web server (http://hmmer.janelia.org) has been designed and implemented such that most protein database searches return within a few seconds. Methods are available for searching either a single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence database, and for searching a protein sequence against Pfam. The web server is designed to cater to a range of different user expertise and accepts batch uploading of multiple queries at once. All search methods are also available as RESTful web services, thereby allowing them to be readily integrated as remotely executed tasks in locally scripted workflows. We have focused on minimizing search times and the ability to rapidly display tabular results, regardless of the number of matches found, developing graphical summaries of the search results to provide quick, intuitive appraisement of them.

}, keywords = {Internet, Protein, Sequence Alignment, Sequence Analysis, Software}, issn = {1362-4962}, doi = {10.1093/nar/gkr367}, author = {Finn, Robert D and Clements, Jody and Eddy, Sean R.} } @article {3522, title = {In search of the structure of human olfactory space.}, journal = {Frontiers in Systems Neuroscience}, volume = {5}, year = {2011}, month = {2011 Jun 2}, pages = {65}, abstract = {

We analyze the responses of human observers to an ensemble of monomolecular odorants. Each odorant is characterized by a set of 146 perceptual descriptors obtained from a database of odor character profiles. Each odorant is therefore represented by a point in a highly multidimensional sensory space. In this work we study the arrangement of odorants in this perceptual space. We argue that odorants densely sample a two-dimensional curved surface embedded in the multidimensional sensory space. This surface can account for more than half of the variance of the perceptual data. We also show that only 12\% of experimental variance cannot be explained by curved surfaces of substantially small dimensionality (\<10). We suggest that these curved manifolds represent the relevant spaces sampled by the human olfactory system, thereby providing surrogates for olfactory sensory space. For the case of 2D approximation, we relate the two parameters on the curved surface to the physico-chemical parameters of odorant molecules. We show that one of the dimensions is related to eigenvalues of molecules{\textquoteright} connectivity matrix, while the other is correlated with measures of molecules{\textquoteright} polarity. We discuss the behavioral significance of these findings.

}, author = {Koulakov, Alexei and Kolterman, Brian E. and Enikolopov, Armen and Rinberg, Dmitry} } @article {2694, title = {Intracellular determinants of hippocampal CA1 place and silent cell activity in a novel environment.}, journal = {Neuron}, volume = {70}, year = {2011}, month = {2011 Apr 14}, pages = {109-20}, abstract = {

For each environment a rodent has explored, its hippocampus contains a map consisting of a unique subset of neurons, called place cells, that have spatially tuned spiking there, with the remaining neurons being essentially silent. Using whole-cell recording in freely moving rats exploring a novel maze, we observed differences in intrinsic cellular properties and input-based subthreshold membrane potential levels underlying this division into place and silent cells. Compared to silent cells, place cells had lower spike thresholds and peaked versus flat subthreshold membrane potentials as a function of animal location. Both differences were evident from the beginning of exploration. Additionally, future place cells exhibited higher burst propensity before exploration. Thus, internal settings appear to predetermine which cells will represent the next novel environment encountered. Furthermore, place cells fired spatially tuned bursts with large, putatively calcium-mediated depolarizations that could trigger plasticity and stabilize the new map for long-term storage. Our results provide new insight into hippocampal memory formation.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2011.03.006}, author = {Epsztein, J{\'e}r{\^o}me and Brecht, Michael and Lee, Albert K} } @article {4650, title = {Morphological evolution caused by many subtle-effect substitutions in regulatory DNA.}, journal = {Nature}, volume = {474}, year = {2011}, month = {2011 Jun 30}, pages = {598-603}, abstract = {

Morphology evolves often through changes in developmental genes, but the causal mutations, and their effects, remain largely unknown. The evolution of naked cuticle on larvae of Drosophila sechellia resulted from changes in five transcriptional enhancers of shavenbaby (svb), a transcript of the ovo locus that encodes a transcription factor that governs morphogenesis of microtrichiae, hereafter called {\textquoteright}trichomes{\textquoteright}. Here we show that the function of one of these enhancers evolved through multiple single-nucleotide substitutions that altered both the timing and level of svb expression. The consequences of these nucleotide substitutions on larval morphology were quantified with a novel functional assay. We found that each substitution had a relatively small phenotypic effect, and that many nucleotide changes account for this large morphological difference. In addition, we observed that the substitutions had non-additive effects. These data provide unprecedented resolution of the phenotypic effects of substitutions and show how individual nucleotide changes in a transcriptional enhancer have caused morphological evolution.

}, keywords = {Animals, Base Sequence, Biological Evolution, Developmental, DNA-Binding Proteins, Drosophila, Drosophila melanogaster, Drosophila Proteins, Embryo, Enhancer Elements, Female, Gene Expression Regulation, Genetic, Larva, Male, Nonmammalian, Nucleic Acid, Phenotype, Sequence Alignment, Sequence Homology, Transcription Factors}, issn = {1476-4687}, doi = {10.1038/nature10200}, author = {Frankel, Nicol{\'a}s and Erezyilmaz, Deniz F and McGregor, Alistair P and Wang, Shu and Payre, Fran\c cois and Stern, David L} } @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 {2908, title = {N-WASp is required for Schwann cell cytoskeletal dynamics, normal myelin gene expression and peripheral nerve myelination.}, journal = {Development}, volume = {138}, year = {2011}, month = {2011 Apr}, pages = {1329-37}, abstract = {

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

}, keywords = {Animals, Axons, Blotting, Cells, Cultured, Cytoskeleton, Fluorescent Antibody Technique, Gait, Gene Expression, Knockout, Mice, Myelin Sheath, Neuronal, Peripheral Nerves, Reverse Transcriptase Polymerase Chain Reaction, Schwann Cells, Western, Wiskott-Aldrich Syndrome Protein}, issn = {1477-9129}, doi = {10.1242/dev.058677}, author = {Jin, Fuzi and Dong, Baoxia and Georgiou, John and Jiang, Qiuhong and Zhang, Jinyi and Bharioke, Arjun and Qiu, Frank and Lommel, Silvia and Feltri, M Laura and Wrabetz, Lawrence and Roder, John C and Eyer, Joel and Chen, Xiequn and Peterson, Alan C and Siminovitch, Katherine A} } @article {1927, title = {Rfam: Wikipedia, clans and the "decimal" release.}, journal = {Nucleic Acids Research}, volume = {39}, year = {2011}, month = {2011 Jan}, pages = {D141-5}, abstract = {

The Rfam database aims to catalogue non-coding RNAs through the use of sequence alignments and statistical profile models known as covariance models. In this contribution, we discuss the pros and cons of using the online encyclopedia, Wikipedia, as a source of community-derived annotation. We discuss the addition of groupings of related RNA families into clans and new developments to the website. Rfam is available on the Web at http://rfam.sanger.ac.uk.

}, issn = {1362-4962}, doi = {10.1093/nar/gkq1129}, author = {Gardner, Paul P and Daub, Jennifer and Tate, John and Moore, Benjamin L and Osuch, Isabelle H and Griffiths-Jones, Sam and Finn, Robert D and Nawrocki, Eric P and Kolbe, Diana L and Eddy, Sean R. and Bateman, Alex} } @article {4373, title = {Structure of the escherichia coli phosphonate binding protein PhnD and rationally optimized phosphonate biosensors.}, journal = {Journal of Molecular Biology}, volume = {414}, year = {2011}, month = {2011 Dec 2}, pages = {356-69}, abstract = {

The phnD gene of Escherichia coli encodes the periplasmic binding protein of the phosphonate (Pn) uptake and utilization pathway. We have crystallized and determined structures of E. coli PhnD (EcPhnD) in the absence of ligand and in complex with the environmentally abundant 2-aminoethylphosphonate (2AEP). Similar to other bacterial periplasmic binding proteins, 2AEP binds near the center of mass of EcPhnD in a cleft formed between two lobes. Comparison of the open, unliganded structure with the closed 2AEP-bound structure shows that the two lobes pivot around a hinge by \~{}70{\textdegree} between the two states. Extensive hydrogen bonding and electrostatic interactions stabilize 2AEP, which binds to EcPhnD with low nanomolar affinity. These structures provide insight into Pn uptake by bacteria and facilitated the rational design of high signal-to-noise Pn biosensors based on both coupled small-molecule dyes and autocatalytic fluorescent proteins.

}, issn = {1089-8638}, doi = {10.1016/j.jmb.2011.09.047}, author = {Alicea, Ismael and Marvin, Jonathan S and Miklos, Aleksandr E and Ellington, Andrew D and Looger, Loren L and Schreiter, Eric R} } @conference {2844, title = {Supervised hypergraph labeling.}, booktitle = {IEEE Conference on Computer Vision Pattern Recognition}, year = {2011}, month = {2011}, abstract = {

We address the problem of labeling individual datapoints given some knowledge about (small) subsets or groups of them. The knowledge we have for a group is the likelihood value for each group member to satisfy a certain model. This problem is equivalent to hypergraph labeling problem where each datapoint corresponds to a node and the each subset correspond to a hyperedge with likelihood value as its weight. We propose a novel method to model the label dependence using an Undirected Graphical Model and reduce the problem of hypergraph labeling into an inference problem. This paper describes the structure and necessary components of such model and proposes useful cost functions. We discuss the behavior of proposed algorithm with different forms of the cost functions, identify suitable algorithms for inference and analyze required properties when it is theoretically guaranteed to have exact solution. Examples of several real world problems are shown as applications of the proposed method.

}, author = {Parag, Toufiq and Elgammal, Ahmed} } @article {47669, title = {Tubular network formation protects mitochondria from autophagosomal degradation during nutrient starvation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, year = {2011}, month = {2011 Jun 21}, pages = {10190-5}, abstract = {

Mitochondria are highly dynamic organelles that mediate essential cell functions such as apoptosis and cell-cycle control in addition to their role as efficient ATP generators. Mitochondrial morphology changes are tightly regulated, and their shape can shift between small, fragmented units and larger networks of elongated mitochondria. We demonstrate that mitochondrial elements become significantly elongated and interconnected shortly after nutrient depletion. This mitochondrial morphological shift depends on the type of starvation, with an additive effect observed when multiple nutrients are depleted simultaneously. We further show that starvation-induced mitochondrial elongation is mediated by down-regulation of dynamin-related protein 1 (Drp1) through modulation of two Drp1 phosphorylation sites, leading to unopposed mitochondrial fusion. Finally, we establish that mitochondrial tubulation upon nutrient deprivation protects mitochondria from autophagosomal degradation, which could permit mitochondria to maximize energy production and supply autophagosomal membranes during starvation.

}, keywords = {Animals, Autophagy, Cells, Cultured, Dynamins, Fibroblasts, GTP Phosphohydrolases, Mice, Microtubule-Associated Proteins, Mitochondria, Mitochondrial Proteins, Phagosomes, Protein Processing, Post-Translational, Starvation}, issn = {1091-6490}, doi = {10.1073/pnas.1107402108}, author = {Rambold, Angelika S and Kostelecky, Brenda and Elia, Natalie and Lippincott-Schwartz, Jennifer} } @article {46737, title = {Variegated gene expression caused by cell-specific long-range DNA interactions.}, journal = {Nature Cell Biology}, volume = {13}, year = {2011}, month = {2011 Aug}, pages = {944-51}, abstract = {

Mammalian genomes contain numerous regulatory DNA sites with unknown target genes. We used mice with an extra β-globin locus control region (LCR) to investigate how a regulator searches the genome for target genes. We find that the LCR samples a restricted nuclear subvolume, wherein it preferentially contacts genes controlled by shared transcription factors. No contacted gene is detectably upregulated except for endogenous β-globin genes located on another chromosome. This demonstrates genetically that mammalian trans activation is possible, but suggests that it will be rare. Trans activation occurs not pan-cellularly, but in {\textquoteright}jackpot{\textquoteright} cells enriched for the interchromosomal interaction. Therefore, cell-specific long-range DNA contacts can cause variegated expression.

}, keywords = {Animals, beta-Globins, DNA, GATA1 Transcription Factor, Gene Expression, In Situ Hybridization, Fluorescence, Kruppel-Like Transcription Factors, Locus Control Region, Mice, Mice, Transgenic, RNA, Messenger, Transcriptional Activation}, issn = {1476-4679}, doi = {10.1038/ncb2278}, author = {Noordermeer, Daan and de Wit, Elzo and Klous, Petra and van de Werken, Harmen and Simonis, Marieke and Lopez-Jones, Melissa and Eussen, Bert and de Klein, Annelies and Singer, Robert H and de Laat, Wouter} } @article {4286, title = {Hidden Markov model speed heuristic and iterative HMM search procedure.}, journal = {BMC Bioinformatics}, volume = {11}, year = {2010}, month = {2010}, pages = {431}, abstract = {

Profile hidden Markov models (profile-HMMs) are sensitive tools for remote protein homology detection, but the main scoring algorithms, Viterbi or Forward, require considerable time to search large sequence databases.

}, keywords = {Algorithms, Artificial Intelligence, Base Sequence, Databases, Markov Chains, Protein, Proteins, Sequence Alignment, Software}, issn = {1471-2105}, doi = {10.1186/1471-2105-11-431}, author = {Johnson, L Steven and Eddy, Sean R. and Portugaly, Elon} } @article {1344, title = {Impact of spikelets on hippocampal CA1 pyramidal cell activity during spatial exploration.}, journal = {Science}, volume = {327}, year = {2010}, month = {2010 Jan 22}, pages = {474-7}, abstract = {

In vivo intracellular recordings of hippocampal neurons reveal the occurrence of fast events of small amplitude called spikelets or fast prepotentials. Because intracellular recordings have been restricted to anesthetized or head-fixed animals, it is not known how spikelet activity contributes to hippocampal spatial representations. We addressed this question in CA1 pyramidal cells by using in vivo whole-cell recording in freely moving rats. We observed a high incidence of spikelets that occurred either in isolation or in bursts and could drive spiking as fast prepotentials of action potentials. Spikelets strongly contributed to spiking activity, driving approximately 30\% of all action potentials. CA1 pyramidal cell firing and spikelet activity were comodulated as a function of the animal{\textquoteright}s location in the environment. We conclude that spikelets have a major impact on hippocampal activity during spatial exploration.

}, keywords = {Action Potentials, Animals, CA1 Region, Exploratory Behavior, Hippocampal, Male, Maze Learning, Patch-Clamp Techniques, Pyramidal Cells, Rats, Space Perception, Wistar}, issn = {1095-9203}, doi = {10.1126/science.1182773}, author = {Epsztein, J{\'e}r{\^o}me and Lee, Albert K and Chorev, Edith and Brecht, Michael} } @article {5676, title = {Multilinear models of single cell responses in the medial nucleus of the trapezoid body.}, journal = {Network}, volume = {21}, year = {2010}, month = {2010}, pages = {91-124}, abstract = {

The representation of acoustic stimuli in the brainstem forms the basis for higher auditory processing. While some characteristics of this representation (e.g. tuning curve) are widely accepted, it remains a challenge to predict the firing rate at high temporal resolution in response to complex stimuli. In this study we explore models for in vivo, single cell responses in the medial nucleus of the trapezoid body (MNTB) under complex sound stimulation. We estimate a family of models, the multilinear models, encompassing the classical spectrotemporal receptive field and allowing arbitrary input-nonlinearities and certain multiplicative interactions between sound energy and its short-term auditory context. We compare these to models of more traditional type, and also evaluate their performance under various stimulus representations. Using the context model, 75\% of the explainable variance could be predicted based on a cochlear-like, gamma-tone stimulus representation. The presence of multiplicative contextual interactions strongly reduces certain inhibitory/suppressive regions of the linear kernels, suggesting an underlying nonlinear mechanism, e.g. cochlear or synaptic suppression, as the source of the suppression in MNTB neuronal responses. In conclusion, the context model provides a rich and still interpretable extension over many previous phenomenological models for modeling responses in the auditory brainstem at submillisecond resolution.

}, keywords = {Action Potentials, Animals, Auditory Pathways, Computer Simulation, Gerbillinae, Linear Models, Models, Neural Inhibition, Neurological, Neurons, Olivary Nucleus, Predictive Value of Tests, Sound Localization, Synaptic Transmission}, issn = {1361-6536}, doi = {10.3109/09548981003801996}, author = {Englitz, B and Ahrens, M and Tolnai, S and R{\"u}bsamen, R and Sahani, M and Jost, J} } @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 {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 {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 {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 {1343, title = {Head-anchored whole-cell recordings in freely moving rats.}, journal = {Nature Protocols}, volume = {4}, year = {2009}, month = {2009}, pages = {385-92}, abstract = {

Intracellular recordings are routinely used to study the synaptic and intrinsic properties of neurons in vitro. A key requirement for these recordings is a mechanically very stable preparation; thus their use in vivo had been limited previously to head-restrained animals. We have recently demonstrated that anchoring the electrode rigidly in place with respect to the skull provides sufficient stabilization for long-lasting, high-quality whole-cell recordings in awake, freely moving rats. This protocol describes our procedure in detail, adds specific instructions for targeting hippocampal CA1 pyramidal neurons and updates it with changes that facilitate patching and improve the success rate. The changes involve combining a standard, nonhead-mounted micromanipulator with a gripper to firmly hold the recording pipette during the anchoring process then gently release it afterwards. The procedure from the beginning of surgery to the end of a recording takes approximately 5 h. This technique allows new studies of the mechanisms underlying neuronal integration and cellular/synaptic plasticity in identified cells during natural behaviors.

}, keywords = {Animals, Brain, Electrodes, Implanted, Neurology, Neurons, Patch-Clamp Techniques, Rats, Wakefulness}, issn = {1750-2799}, doi = {10.1038/nprot.2009.5}, author = {Lee, Albert K and Epsztein, J{\'e}r{\^o}me and Brecht, Michael} } @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 {4277, title = {Infernal 1.0: inference of RNA alignments.}, journal = {Bioinformatics}, volume = {25}, year = {2009}, month = {2009 May 15}, pages = {1335-7}, abstract = {

SUMMARY: INFERNAL builds consensus RNA secondary structure profiles called covariance models (CMs), and uses them to search nucleic acid sequence databases for homologous RNAs, or to create new sequence- and structure-based multiple sequence alignments. AVAILABILITY: Source code, documentation and benchmark downloadable from http://infernal.janelia.org. INFERNAL is freely licensed under the GNU GPLv3 and should be portable to any POSIX-compliant operating system, including Linux and Mac OS/X.

}, keywords = {Databases, Nucleic Acid, Nucleic Acid Conformation, RNA, Sequence Alignment, Sequence Analysis, Software}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btp157}, author = {Nawrocki, Eric P and Kolbe, Diana L and Eddy, Sean R.} } @article {4605, title = {Leptin targets in the mouse brain.}, journal = {The Journal of Comparative Neurology}, volume = {514}, year = {2009}, month = {2009 Jun 10}, pages = {518-32}, abstract = {

The central actions of leptin are essential for homeostatic control of adipose tissue mass, glucose metabolism, and many autonomic and neuroendocrine systems. In the brain, leptin acts on numerous different cell types via the long-form leptin receptor (LepRb) to elicit its effects. The precise identification of leptin{\textquoteright}s cellular targets is fundamental to understanding the mechanism of its pleiotropic central actions. We have systematically characterized LepRb distribution in the mouse brain using in situ hybridization in wildtype mice as well as by EYFP immunoreactivity in a novel LepRb-IRES-Cre EYFP reporter mouse line showing high levels of LepRb mRNA/EYFP coexpression. We found substantial LepRb mRNA and EYFP expression in hypothalamic and extrahypothalamic sites described before, including the dorsomedial nucleus of the hypothalamus, ventral premammillary nucleus, ventral tegmental area, parabrachial nucleus, and the dorsal vagal complex. Expression in insular cortex, lateral septal nucleus, medial preoptic area, rostral linear nucleus, and in the Edinger-Westphal nucleus was also observed and had been previously unreported. The LepRb-IRES-Cre reporter line was used to chemically characterize a population of leptin receptor-expressing neurons in the midbrain. Tyrosine hydroxylase and Cre reporter were found to be coexpressed in the ventral tegmental area and in other midbrain dopaminergic neurons. Lastly, the LepRb-IRES-Cre reporter line was used to map the extent of peripheral leptin sensing by central nervous system (CNS) LepRb neurons. Thus, we provide data supporting the use of the LepRb-IRES-Cre line for the assessment of the anatomic and functional characteristics of neurons expressing leptin receptor.

}, keywords = {Animals, Brain, Cell Count, Gene Expression, Immunohistochemistry, In Situ Hybridization, Lac Operon, Leptin, Male, Messenger, Mice, Photomicrography, Receptors, RNA, STAT3 Transcription Factor, Transgenic, Tyrosine 3-Monooxygenase}, issn = {1096-9861}, doi = {10.1002/cne.22025}, author = {Scott, Michael M and Lachey, Jennifer L and Sternson, Scott M and Lee, Charlotte E and Elias, Carol F and Friedman, Jeffrey M and Elmquist, Joel K} } @article {5243, title = {Local RNA structure alignment with incomplete sequence.}, journal = {Bioinformatics}, volume = {25}, year = {2009}, month = {2009 May 15}, pages = {1236-43}, abstract = {

Accuracy of automated structural RNA alignment is improved by using models that consider not only primary sequence but also secondary structure information. However, current RNA structural alignment approaches tend to perform poorly on incomplete sequence fragments, such as single reads from metagenomic environmental surveys, because nucleotides that are expected to be base paired are missing.

}, keywords = {Algorithms, Databases, Genetic, Models, Molecular, Nucleic Acid Conformation, RNA, Sequence Alignment, Sequence Analysis}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btp154}, author = {Kolbe, Diana L and Eddy, Sean R.} } @article {1236, title = {Maximization of the connectivity repertoire as a statistical principle governing the shapes of dendritic arbors.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, year = {2009}, month = {2009 Jul 28}, pages = {12536-41}, abstract = {

The shapes of dendritic arbors are fascinating and important, yet the principles underlying these complex and diverse structures remain unclear. Here, we analyzed basal dendritic arbors of 2,171 pyramidal neurons sampled from mammalian brains and discovered 3 statistical properties: the dendritic arbor size scales with the total dendritic length, the spatial correlation of dendritic branches within an arbor has a universal functional form, and small parts of an arbor are self-similar. We proposed that these properties result from maximizing the repertoire of possible connectivity patterns between dendrites and surrounding axons while keeping the cost of dendrites low. We solved this optimization problem by drawing an analogy with maximization of the entropy for a given energy in statistical physics. The solution is consistent with the above observations and predicts scaling relations that can be tested experimentally. In addition, our theory explains why dendritic branches of pyramidal cells are distributed more sparsely than those of Purkinje cells. Our results represent a step toward a unifying view of the relationship between neuronal morphology and function.

}, keywords = {Action Potentials, Algorithms, Animals, Axons, Dendrites, Haplorhini, Models, Neural Pathways, Neurological, Purkinje Cells, Pyramidal Cells, Rats, Synapses}, issn = {1091-6490}, doi = {10.1371/journal.pcbi.1001066}, author = {Wen, Quan and Stepanyants, Armen and Elston, Guy N and Grosberg, Alexander Y and Chklovskii, Dmitri B} } @article {4265, title = {A new generation of homology search tools based on probabilistic inference.}, journal = {Genome Informatics. International Conference on Genome Informatics}, volume = {23}, year = {2009}, month = {2009 Oct}, pages = {205-11}, abstract = {

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

}, keywords = {Markov Chains, Probability, Sequence Alignment}, issn = {0919-9454}, author = {Eddy, Sean R.} } @article {2501, title = {The nuclear receptor E75A has a novel pair-rule-like function in patterning the milkweed bug, Oncopeltus fasciatus.}, journal = {Developmental Biology}, volume = {334}, year = {2009}, month = {2009 Oct 1}, pages = {300-10}, abstract = {

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

}, keywords = {Animals, Blastoderm, Body Patterning, Cytoplasmic and Nuclear, Embryo, Hemiptera, Insect Proteins, Nonmammalian, Receptors, RNA Interference}, issn = {1095-564X}, doi = {10.1016/j.ydbio.2009.06.038}, author = {Erezyilmaz, Deniz F and Kelstrup, Hans C and Riddiford, Lynn M} } @article {4266, title = {Rfam: updates to the RNA families database.}, journal = {Nucleic Acids Research}, volume = {37}, year = {2009}, month = {2009 Jan}, pages = {D136-40}, abstract = {

Rfam is a collection of RNA sequence families, represented by multiple sequence alignments and covariance models (CMs). The primary aim of Rfam is to annotate new members of known RNA families on nucleotide sequences, particularly complete genomes, using sensitive BLAST filters in combination with CMs. A minority of families with a very broad taxonomic range (e.g. tRNA and rRNA) provide the majority of the sequence annotations, whilst the majority of Rfam families (e.g. snoRNAs and miRNAs) have a limited taxonomic range and provide a limited number of annotations. Recent improvements to the website, methodologies and data used by Rfam are discussed. Rfam is freely available on the Web at http://rfam.sanger.ac.uk/and http://rfam.janelia.org/.

}, keywords = {Computer Graphics, Databases, Internet, Nucleic Acid, RNA, Sequence Alignment, Sequence Analysis}, issn = {1362-4962}, doi = {10.1093/nar/gkn766}, author = {Gardner, Paul P and Daub, Jennifer and Tate, John G and Nawrocki, Eric P and Kolbe, Diana L and Lindgreen, Stinus and Wilkinson, Adam C and Finn, Robert D and Griffiths-Jones, Sam and Eddy, Sean R. and Bateman, Alex} } @article {2500, title = {The role of the pupal determinant broad during embryonic development of a direct-developing insect.}, journal = {Development Genes \& Evolution}, volume = {219}, year = {2009}, month = {2009 Dec 30}, pages = {535-44}, abstract = {

Metamorphosis is one of the most common, yet dramatic of life history strategies. In insects, complete metamorphosis with morphologically distinct larval stages arose from hemimetabolous ancestors that were more direct developing. Over the past century, several ideas have emerged that suggest the holometabolous pupa is developmentally homologous to the embryonic stages of the hemimetabolous ancestor. Other theories consider the pupal stage to be a modification of a hemimetabolous nymph. To address this question, we have isolated an ortholog of the pupal determinant, broad (br), from the hemimetabolous milkweed bug and examined its role during embryonic development. We show that Oncopeltus fasciatus br (Of{\textquoteright}br) is expressed in two phases. The first occurs during germ band invagination and segmentation when Of{\textquoteright}br is expressed ubiquitously in the embryonic tissues. The second phase of Of{\textquoteright}br expression appears during the pronymphal phase of embryogenesis and persists through nymphal differentiation to decline just before hatching. Knock-down of Of{\textquoteright}br transcripts results in defects that range from posterior truncations in the least-affected phenotypes to completely fragmented embryonic tissues in the most severe cases. Analysis of the patterning genes engrailed and hunchback reveal loss of segments and a failure in neural differentiation after Of{\textquoteright}br depletion. Finally, we show that br is constitutively expressed during embyrogenesis of the ametabolous firebrat, Thermobia domestica. This suggests that br expression is prominent during embryonic development of ametabolous and hemimetabolous insects but was lost with the emergence of the completely metamorphosing insects.

}, keywords = {Animals, Biological, Biological Evolution, Body Patterning, Cloning, Developmental, DNA Primers, Drosophila Proteins, Gene Expression Regulation, Heteroptera, In Situ Hybridization, Insect Proteins, Metamorphosis, Molecular, Reverse Transcriptase Polymerase Chain Reaction, Transcription Factors}, issn = {1432-041X}, doi = {10.1007/s00427-009-0315-7}, author = {Erezyilmaz, Deniz F and Rynerson, Melody R and Truman, James W and Riddiford, Lynn M} } @article {4268, title = {A survey of nematode SmY RNAs.}, journal = {RNA Biology}, volume = {6}, year = {2009}, month = {2009 Jan-Mar}, pages = {5-8}, abstract = {

SmY RNAs are a family of approximately 70-90 nt small nuclear RNAs found in nematodes. In C. elegans, SmY RNAs copurify in a small ribonucleoprotein (snRNP) complex related to the SL1 and SL2 snRNPs that are involved in nematode mRNA trans-splicing. Here we describe a comprehensive computational analysis of SmY RNA homologs found in the currently available genome sequences. We identify homologs in all sequenced nematode genomes in class Chromadorea. We are unable to identify homologs in a more distantly related nematode species, Trichinella spiralis (class: Dorylaimia), and in representatives of non-nematode phyla that use trans-splicing. Using comparative RNA sequence analysis, we infer a conserved consensus SmY RNA secondary structure consisting of two stems flanking a consensus Sm protein binding site. A representative seed alignment of the SmY RNA family, annotated with the inferred consensus secondary structure, has been deposited with the Rfam RNA families database.

}, keywords = {Animals, Base Sequence, Binding Sites, Caenorhabditis elegans, Genome, Molecular Sequence Data, Nematoda, Nucleic Acid Conformation, Phylogeny, RNA, Small Nuclear, snRNP Core Proteins, Trichinella spiralis}, issn = {1555-8584}, author = {Jones, Thomas A and Otto, Wolfgang and Marz, Manja and Eddy, Sean R. and Stadler, Peter F} } @article {65012, title = {T cells require Foxo1 to populate the peripheral lymphoid organs.}, journal = {Eur J Immunol}, volume = {39}, year = {2009}, month = {2009 Oct 30}, pages = {2991-9}, abstract = {

Forkhead transcription factors play critical roles in leukocyte homeostasis. To study further the immunological functions of Foxo1, we generated mice that selectively lack Foxo1 in T cells (Foxo1(flox/flox) Lck.cre(+)conditional knockout mice (cKO)). Although thymocyte development appeared relatively normal, Foxo1 cKO mice harbored significantly increased percentages of mature single positive T cells in the thymus as compared with WT mice, yet possessed smaller lymph nodes and spleens that contained fewer T cells. Foxo1 cKO T cells were not more prone to apoptosis, but instead were characterized by a CD62L(lo) CCR7(lo) CD44(hi) surface phenotype, a poorly populated lymphoid compartment in the periphery, and were relatively refractory to TCR stimulation, all of which were associated with reduced expression of Sell, Klf2, Ccr7, and S1pr1. Thus, Foxo1 is critical for na{\"\i}ve T cells to populate the peripheral lymphoid organs by coordinating a molecular program that maintains homeostasis and regulates trafficking.

}, keywords = {Animals, Apoptosis, Cell Proliferation, Chemotaxis, Leukocyte, Flow Cytometry, Forkhead Box Protein O1, Forkhead Transcription Factors, Lymphoid Tissue, Mice, Mice, Knockout, Phenotype, Reverse Transcriptase Polymerase Chain Reaction, T-Lymphocyte Subsets, T-Lymphocytes}, issn = {1521-4141}, doi = {10.1002/eji.200939427}, author = {Gubbels Bupp, Melanie R and Edwards, Bonnie and Guo, Caiying and Wei, Datsen and Chen, Gang and Wong, Brian and Masteller, Emma and Peng, Stanford L} } @article {4264, title = {A tool for identification of genes expressed in patterns of interest using the Allen Brain Atlas.}, journal = {Bioinformatics}, volume = {25}, year = {2009}, month = {2009 Jul 1}, pages = {1647-54}, abstract = {

Gene expression patterns can be useful in understanding the structural organization of the brain and the regulatory logic that governs its myriad cell types. A particularly rich source of spatial expression data is the Allen Brain Atlas (ABA), a comprehensive genome-wide in situ hybridization study of the adult mouse brain. Here, we present an open-source program, ALLENMINER, that searches the ABA for genes that are expressed, enriched, patterned or graded in a user-specified region of interest.

}, keywords = {Animals, Brain, Computer Graphics, Gene Expression, Gene Expression Profiling, Genome, Mice, Oligonucleotide Array Sequence Analysis}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btp288}, author = {Davis, Fred P and Eddy, Sean R.} } @conference {2845, title = {Boosting adaptive linear weak classifiers for online learning and tracking.}, booktitle = {IEEE Conference on Computer Vision and Pattern Recognition}, year = {2008}, month = {2008 Jun 28}, author = {Parag, Toufiq and Porikli, Fatih and Elgammal, Ahmed} } @article {4638, title = {Even illumination in total internal reflection fluorescence microscopy using laser light.}, journal = {Microscopy Research and Technique}, volume = {71}, year = {2008}, month = {2008 Jan}, pages = {45-50}, abstract = {

In modern fluorescence microscopy, lasers are a widely used source of light, both for imaging in total internal reflection and epi-illumination modes. In wide-field imaging, scattering of highly coherent laser light due to imperfections in the light path typically leads to nonuniform illumination of the specimen, compromising image analysis. We report the design and construction of an objective-launch total internal reflection fluorescence microscopy system with excellent evenness of specimen illumination achieved by azimuthal rotation of the incoming illuminating laser beam. The system allows quick and precise changes of the incidence angle of the laser beam and thus can also be used in an epifluorescence mode.

}, keywords = {Fluorescence, Lasers, Microscopy, Reproducibility of Results}, issn = {1059-910X}, doi = {10.1002/jemt.20527}, author = {Fiolka, R and Belyaev, Y and Ewers, H and Stemmer, A} } @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 {45964, title = {Junction-forming aquaporins.}, journal = {Current Opinion in Structural Biology}, volume = {18}, year = {2008}, month = {2008 Apr}, pages = {229-35}, abstract = {

Aquaporins (AQPs) are a family of ubiquitous membrane channels that conduct water and solutes across membranes. This review focuses on AQP0 and AQP4, which in addition to forming water channels also appear to play a role in cell adhesion. We discuss the recently determined structures of the membrane junctions mediated by these two AQPs, the mechanisms that regulate junction formation, and evidence that supports a role for AQP0 and AQP4 in cell adhesion.

}, keywords = {Animals, Aquaporin 4, Aquaporins, Eye Proteins, Humans, Intercellular Junctions, Models, Molecular, Protein Structure, Quaternary}, issn = {0959-440X}, doi = {10.1016/j.sbi.2007.11.003}, author = {Engel, Andreas and Fujiyoshi, Yoshinori and Gonen, Tamir and Walz, Thomas} } @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 {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 {4252, title = {A probabilistic model of local sequence alignment that simplifies statistical significance estimation.}, journal = {PLoS Computational Biology}, volume = {4}, year = {2008}, month = {2008 May 30}, pages = {e1000069}, abstract = {

Sequence database searches require accurate estimation of the statistical significance of scores. Optimal local sequence alignment scores follow Gumbel distributions, but determining an important parameter of the distribution (lambda) requires time-consuming computational simulation. Moreover, optimal alignment scores are less powerful than probabilistic scores that integrate over alignment uncertainty ("Forward" scores), but the expected distribution of Forward scores remains unknown. Here, I conjecture that both expected score distributions have simple, predictable forms when full probabilistic modeling methods are used. For a probabilistic model of local sequence alignment, optimal alignment bit scores ("Viterbi" scores) are Gumbel-distributed with constant lambda = log 2, and the high scoring tail of Forward scores is exponential with the same constant lambda. Simulation studies support these conjectures over a wide range of profile/sequence comparisons, using 9,318 profile-hidden Markov models from the Pfam database. This enables efficient and accurate determination of expectation values (E-values) for both Viterbi and Forward scores for probabilistic local alignments.

}, keywords = {Algorithms, Base Sequence, Chromosome Mapping, Computer Simulation, Data Interpretation, DNA, Genetic, Models, Molecular Sequence Data, Sequence Alignment, Sequence Analysis, Statistical}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1000069}, author = {Sean R. Eddy} } @article {4259, title = {Probabilistic phylogenetic inference with insertions and deletions.}, journal = {PLoS Computational Biology}, volume = {4}, year = {2008}, month = {2008 Sep 19}, pages = {e1000172}, abstract = {

A fundamental task in sequence analysis is to calculate the probability of a multiple alignment given a phylogenetic tree relating the sequences and an evolutionary model describing how sequences change over time. However, the most widely used phylogenetic models only account for residue substitution events. We describe a probabilistic model of a multiple sequence alignment that accounts for insertion and deletion events in addition to substitutions, given a phylogenetic tree, using a rate matrix augmented by the gap character. Starting from a continuous Markov process, we construct a non-reversible generative (birth-death) evolutionary model for insertions and deletions. The model assumes that insertion and deletion events occur one residue at a time. We apply this model to phylogenetic tree inference by extending the program dnaml in phylip. Using standard benchmarking methods on simulated data and a new "concordance test" benchmark on real ribosomal RNA alignments, we show that the extended program dnamlepsilon improves accuracy relative to the usual approach of ignoring gaps, while retaining the computational efficiency of the Felsenstein peeling algorithm.

}, keywords = {Algorithms, Computational Biology, Computer Simulation, DNA, Evolution, Genetic, Insertional, Markov Chains, Models, Molecular, Mutagenesis, Phylogeny, Poisson Distribution, Ribosomal, RNA, Sequence Alignment, Sequence Deletion, Software, Statistical}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1000172}, author = {Rivas, Elena and Sean R. Eddy} } @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 {68488, title = {Single-synapse ablation and long-term imaging in live C. elegans.}, journal = {J Neurosci Methods}, volume = {173}, year = {2008}, month = {09/2008}, pages = {20-6}, abstract = {

Synapses are individually operated, computational units for neural communication. To manipulate physically individual synapses in a living organism, we have developed a laser ablation technique for removing single synapses in live neurons in C. elegans that operates without apparent damage to the axon. As a complementary technique, we applied microfluidic immobilization of C. elegans to facilitate long-term fluorescence imaging and observation of neuronal development. With this technique, we directly demonstrated the existence of competition between developing synapses in the HSNL motor neuron.

}, keywords = {Animals, Axons, Behavior, Animal, Caenorhabditis elegans, Diagnostic Imaging, Laser Therapy, Microfluidic Analytical Techniques, Movement, Neurons, Synapses, Time Factors}, issn = {0165-0270}, doi = {10.1016/j.jneumeth.2008.05.007}, author = {Allen, Peter B and Sgro, Allyson E and Chao, Daniel L and Doepker, Byron E and Scott Edgar, J and Shen, Kang and Chiu, Daniel T} } @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} } @article {2154, title = {Automatic image analysis for gene expression patterns of fly embryos.}, journal = {BMC Cell Biology}, volume = {8}, year = {2007}, month = {2007 Jul 10}, pages = {S7}, abstract = {

Staining the mRNA of a gene via in situ hybridization (ISH) during the development of a D. melanogaster embryo delivers the detailed spatio-temporal pattern of expression of the gene. Many biological problems such as the detection of co-expressed genes, co-regulated genes, and transcription factor binding motifs rely heavily on the analyses of these image patterns. The increasing availability of ISH image data motivates the development of automated computational approaches to the analysis of gene expression patterns.

}, keywords = {Algorithms, Animals, Computational Biology, Computer-Assisted, Drosophila, Embryo, Gene Expression Profiling, Genes, Image Processing, In Situ Hybridization, Insect, Nonmammalian, Reproducibility of Results, Software Design}, issn = {1471-2121}, doi = {10.1007/s12021-010-9090-x}, author = {Peng, Hanchuan and Long, Fuhui and Zhou, Jie and Leung, Garmay and Eisen, Michael B and Myers, Eugene W} } @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 {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 {4224, title = {Query-dependent banding (QDB) for faster RNA similarity searches.}, journal = {PLoS Computational Biology}, volume = {3}, year = {2007}, month = {2007 Mar 30}, pages = {e56}, abstract = {

When searching sequence databases for RNAs, it is desirable to score both primary sequence and RNA secondary structure similarity. Covariance models (CMs) are probabilistic models well-suited for RNA similarity search applications. However, the computational complexity of CM dynamic programming alignment algorithms has limited their practical application. Here we describe an acceleration method called query-dependent banding (QDB), which uses the probabilistic query CM to precalculate regions of the dynamic programming lattice that have negligible probability, independently of the target database. We have implemented QDB in the freely available Infernal software package. QDB reduces the average case time complexity of CM alignment from LN(2.4) to LN(1.3) for a query RNA of N residues and a target database of L residues, resulting in a 4-fold speedup for typical RNA queries. Combined with other improvements to Infernal, including informative mixture Dirichlet priors on model parameters, benchmarks also show increased sensitivity and specificity resulting from improved parameterization.

}, keywords = {Base Sequence, Database Management Systems, Databases, Genetic, Information Storage and Retrieval, Molecular Sequence Data, Nucleic Acid, RNA, Sequence Alignment, Sequence Analysis, Sequence Homology}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.0030056}, author = {Nawrocki, Eric P and Eddy, Sean R.} } @article {1542, title = {Three-dimensional analysis of a viral RNA replication complex reveals a virus-induced mini-organelle.}, journal = {PLoS Biology}, volume = {5}, year = {2007}, month = {2007 Sep}, pages = {e220}, abstract = {

Positive-strand RNA viruses are the largest genetic class of viruses and include many serious human pathogens. All positive-strand RNA viruses replicate their genomes in association with intracellular membrane rearrangements such as single- or double-membrane vesicles. However, the exact sites of RNA synthesis and crucial topological relationships between relevant membranes, vesicle interiors, surrounding lumens, and cytoplasm generally are poorly defined. We applied electron microscope tomography and complementary approaches to flock house virus (FHV)-infected Drosophila cells to provide the first 3-D analysis of such replication complexes. The sole FHV RNA replication factor, protein A, and FHV-specific 5-bromouridine 5{\textquoteright}-triphosphate incorporation localized between inner and outer mitochondrial membranes inside approximately 50-nm vesicles (spherules), which thus are FHV-induced compartments for viral RNA synthesis. All such FHV spherules were outer mitochondrial membrane invaginations with interiors connected to the cytoplasm by a necked channel of approximately 10-nm diameter, which is sufficient for ribonucleotide import and product RNA export. Tomographic, biochemical, and other results imply that FHV spherules contain, on average, three RNA replication intermediates and an interior shell of approximately 100 membrane-spanning, self-interacting protein As. The results identify spherules as the site of protein A and nascent RNA accumulation and define spherule topology, dimensions, and stoichiometry to reveal the nature and many details of the organization and function of the FHV RNA replication complex. The resulting insights appear relevant to many other positive-strand RNA viruses and support recently proposed structural and likely evolutionary parallels with retrovirus and double-stranded RNA virus virions.

}, keywords = {Animals, Drosophila, Electron, Imaging, Microscopy, Mitochondrial Membranes, Nodaviridae, Organelles, RNA, Three-Dimensional, Viral, Virus Replication}, issn = {1545-7885}, doi = {10.1371/journal.pbio.0050220}, author = {Kopek, Benjamin G and Perkins, Guy and Miller, David J and Ellisman, Mark H and Ahlquist, Paul} } @article {4479, title = {Three-dimensional analysis of a viral RNA replication complex reveals a virus-induced mini-organelle.}, journal = {PLoS biology}, volume = {5}, year = {2007}, month = {2007 Sep}, pages = {e220}, abstract = {

Positive-strand RNA viruses are the largest genetic class of viruses and include many serious human pathogens. All positive-strand RNA viruses replicate their genomes in association with intracellular membrane rearrangements such as single- or double-membrane vesicles. However, the exact sites of RNA synthesis and crucial topological relationships between relevant membranes, vesicle interiors, surrounding lumens, and cytoplasm generally are poorly defined. We applied electron microscope tomography and complementary approaches to flock house virus (FHV)-infected Drosophila cells to provide the first 3-D analysis of such replication complexes. The sole FHV RNA replication factor, protein A, and FHV-specific 5-bromouridine 5{\textquoteright}-triphosphate incorporation localized between inner and outer mitochondrial membranes inside approximately 50-nm vesicles (spherules), which thus are FHV-induced compartments for viral RNA synthesis. All such FHV spherules were outer mitochondrial membrane invaginations with interiors connected to the cytoplasm by a necked channel of approximately 10-nm diameter, which is sufficient for ribonucleotide import and product RNA export. Tomographic, biochemical, and other results imply that FHV spherules contain, on average, three RNA replication intermediates and an interior shell of approximately 100 membrane-spanning, self-interacting protein As. The results identify spherules as the site of protein A and nascent RNA accumulation and define spherule topology, dimensions, and stoichiometry to reveal the nature and many details of the organization and function of the FHV RNA replication complex. The resulting insights appear relevant to many other positive-strand RNA viruses and support recently proposed structural and likely evolutionary parallels with retrovirus and double-stranded RNA virus virions.

}, keywords = {Animals, Drosophila, Electron, Imaging, Microscopy, Mitochondrial Membranes, Nodaviridae, Organelles, RNA, Three-Dimensional, Viral, Virus Replication}, issn = {1545-7885}, doi = {10.1371/journal.pbio.0050220}, url = {http://www.plosbiology.org/article/info\%3Adoi\%2F10.1371\%2Fjournal.pbio.0050220}, author = {Kopek, Benjamin G and Perkins, Guy and Miller, David J and Ellisman, Mark H and Ahlquist, Paul} } @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} } @conference {2846, title = {A framework for feature selection for background subtraction.}, booktitle = {IEEE Conference on Computer Vision and Pattern Recognition}, year = {2006}, month = {2006}, author = {Parag, Toufiq and Elgammal, Ahmed and Mittal, Anurag} } @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 {2446, title = {The pupal specifier broad directs progressive morphogenesis in a direct-developing insect.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, year = {2006}, month = {2006 May 2}, pages = {6925-30}, abstract = {

A key regulatory gene in metamorphosing (holometabolous) insect life histories is the transcription factor broad (br), which specifies pupal development. To determine the role of br in a direct-developing (hemimetabolous) insect that lacks a pupal stage, we cloned br from the milkweed bug, Oncopeltus fasciatus (Of{\textquoteright}br). We find that, unlike metamorphosing insects, in which br expression is restricted to the larval-pupal transition, Of{\textquoteright}br mRNA is expressed during embryonic development and is maintained at each nymphal molt but then disappears at the molt to the adult. Induction of a supernumerary nymphal stage with a juvenile hormone (JH) mimic prevented the disappearance of br mRNA. In contrast, induction of a precocious adult molt by application of precocene II to third-stage nymphs caused a loss of br mRNA at the precocious adult molt. Thus, JH is necessary to maintain br expression during the nymphal stages. Injection of Of{\textquoteright}br dsRNA into either early third- or fourth-stage nymphs caused a repetition of stage-specific pigmentation patterns and prevented the normal anisometric growth of the wing pads without affecting isometric growth or molting. Therefore, br is necessary for the mutable (heteromorphic) changes that occur during hemimetabolous development. Our results suggest that metamorphosis in insects arose as expression of br, which conveys competence for change, became restricted to one postembryonic instar. After this shift in br expression, the progressive changes that occur within the nymphal series in basal insects became compressed to the one short period of morphogenesis seen in the larva-to-pupa transition of holometabolous insects.

}, keywords = {Animals, Biological, Drosophila Proteins, Heteroptera, Insect Proteins, Juvenile Hormones, Metamorphosis, Molecular Sequence Data, Morphogenesis, Nymph, Pigmentation, RNA, Transcription Factors, Wing}, issn = {0027-8424}, doi = {10.1073/pnas.0509983103}, author = {Erezyilmaz, Deniz F and Riddiford, Lynn M and Truman, James W} } @conference {2847, title = {Unsupervised learning of boosted tree classifier using graph cuts for hand pose recognition.}, booktitle = {British Machine Vision Conference}, year = {2006}, month = {2006 Sep 4}, author = {Parag, Toufiq and Elgammal, Ahmed} } @article {2318, title = {Antipsychotic drugs elevate mRNA levels of presynaptic proteins in the frontal cortex of the rat.}, journal = {Biological Psychiatry}, volume = {57}, year = {2005}, month = {2005 May 1}, pages = {1041-51}, abstract = {

Molecular adaptations are believed to contribute to the mechanism of action of antipsychotic drugs (APDs). We attempted to establish common gene regulation patterns induced by chronic treatment with APDs.

}, keywords = {Animals, Antipsychotic Agents, Cluster Analysis, Corpus Striatum, Frontal Lobe, Gene Expression, Male, Messenger, Microtubules, Oligonucleotide Array Sequence Analysis, Presynaptic Terminals, Rats, Reverse Transcriptase Polymerase Chain Reaction, RNA, Sprague-Dawley, Synaptic Vesicles}, issn = {0006-3223}, doi = {10.3389/fnana.2010.00147}, author = {MacDonald, Matthew L and Eaton, Molly E and Dudman, Joshua T and Konradi, Christine} } @article {2471, title = {Drosophila retained/dead ringer is necessary for neuronal pathfinding, female receptivity and repression of fruitless independent male courtship behaviors.}, journal = {Development}, volume = {132}, year = {2005}, month = {2005 Jan}, pages = {155-64}, abstract = {

Mutations in the Drosophila retained/dead ringer (retn) gene lead to female behavioral defects and alter a limited set of neurons in the CNS. retn is implicated as a major repressor of male courtship behavior in the absence of the fruitless (fru) male protein. retn females show fru-independent male-like courtship of males and females, and are highly resistant to courtship by males. Males mutant for retn court with normal parameters, although feminization of retn cells in males induces bisexuality. Alternatively spliced RNAs appear in the larval and pupal CNS, but none shows sex specificity. Post-embryonically, retn RNAs are expressed in a limited set of neurons in the CNS and eyes. Neural defects of retn mutant cells include mushroom body beta-lobe fusion and pathfinding errors by photoreceptor and subesophageal neurons. We posit that some of these retn-expressing cells function to repress a male behavioral pathway activated by fruM.

}, keywords = {Alternative Splicing, Animal, Animals, Behavior, Central Nervous System, Complementary, Crosses, DNA, Drosophila melanogaster, Drosophila Proteins, Female, Genetic, Homeodomain Proteins, Male, Mice, Models, Mutation, Nerve Tissue Proteins, Neurons, Nuclear Proteins, Point Mutation, Reverse Transcriptase Polymerase Chain Reaction, RNA, Sequence Analysis, Sex Factors, Sexual Behavior, Transcription Factors}, issn = {0950-1991}, doi = {10.1242/dev.01568}, author = {Ditch, Lynn M and Shirangi, Troy and Pitman, Jeffrey L and Latham, Kristin L and Finley, Kim D and Edeen, Philip T and Taylor, Barbara J and McKeown, Michael} } @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 {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 {2320, title = {L-type Ca2+ channel blockers promote Ca2+ accumulation when dopamine receptors are activated in striatal neurons.}, journal = {Brain Research. Molecular Brain Research}, volume = {131}, year = {2004}, month = {2004 Nov 24}, pages = {65-72}, abstract = {

Dopamine (DA) receptor-mediated signal transduction and gene expression play a central role in many brain disorders from schizophrenia to Parkinson{\textquoteright}s disease to addiction. While trying to evaluate the role of L-type Ca2+ channels in dopamine D1 receptor-mediated phosphorylation of the transcription factor cyclic AMP response element-binding protein (CREB), we found that activation of dopamine D1 receptors alters the properties of L-type Ca2+ channel inhibitors and turns them into facilitators of Ca2+ influx. In D1 receptor-stimulated neurons, L-type Ca2+ channel blockers promote cytosolic Ca2+ accumulation. This leads to the activation of a molecular signal transduction pathway and CREB phosphorylation. In the absence of dopamine receptor stimulation, L-type Ca2+ channel blockers inhibit CREB phosphorylation. The effect of dopamine on L-type Ca2+ channel blockers is dependent on protein kinase A (PKA), suggesting that protein phosphorylation plays a role in this phenomenon. Because of the adverse effect of activated dopamine receptors on L-type Ca2+ channel blocker action, the role of L-type Ca2+ channels in the dopamine D1 receptor signal transduction pathway cannot be assessed with pharmacological tools. However, with antisense technology, we demonstrate that L-type Ca2+ channels contribute to D1 receptor-mediated CREB phosphorylation. We conclude that the D1 receptor signal transduction pathway depends on L-type Ca2+ channels to mediate CREB phosphorylation.

}, keywords = {2, 3, 4, 5-Tetrahydro-7, 8-dihydroxy-1-phenyl-1H-3-benzazepine, Animals, Antisense, Calcium, Calcium Channel Blockers, Calcium Channels, Cells, Corpus Striatum, Cultured, Cyclic AMP Response Element-Binding Protein, Dizocilpine Maleate, Dopamine Antagonists, Dopamine D1, Drug Interactions, Excitatory Amino Acid Antagonists, Female, L-Type, N-Methyl-D-Aspartate, Neurons, Nifedipine, Oligonucleotides, Phosphorylation, Pregnancy, Rats, Receptors, Sprague-Dawley}, issn = {0169-328X}, doi = {10.3389/fnana.2010.00147}, author = {Eaton, Molly E and Mac{\'\i}as, Wendy and Youngs, Rachael M and Rajadhyaksha, Anjali and Dudman, Joshua T and Konradi, Christine} } @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} } @article {1189, title = {Recombination of human mitochondrial DNA.}, journal = {Science}, volume = {304}, year = {2004}, month = {2004 May 14}, pages = {981}, keywords = {DNA, DNA Replication, Fathers, Female, Genetic, Humans, Male, Mitochondria, Mitochondrial, Mothers, Muscle, Polymerase Chain Reaction, Recombination}, issn = {1095-9203}, doi = {10.1126/science.1096342}, author = {Kraytsberg, Yevgenya and Schwartz, Marianne and Brown, Timothy A and Ebralidse, Konstantin and Kunz, Wolfram S and Clayton, David A and Vissing, John and Khrapko, Konstantin} } @proceedings {4534, title = {A smorgasbord of features for statistical machine translation.}, year = {2004}, month = {2004 May}, abstract = {

We describe a methodology for rapid experimentation in statistical machine translation which we use to add a large number of features to a baseline system exploiting features from a wide range of levels of syntactic representation. Feature values were combined in a log-linear model to select the highest scoring candidate translation from an n-best list. Feature weights were optimized directly against the BLEU evaluation metric on held-out data. We present results for a small selection of features at each level of syntactic representation.

}, author = {Och, Franz J. and Gildea, Daniel and Khudanpur, Sanjeev and Sarkar, Anoop and Yamada, Kenji and Fraser, Alex and Kumar, Shankar and Shen, Libin and Smith, David and Eng, Katherine and Jain, Viren and Jin, Zhen and Radev, Dragomir} } @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 {2140, title = {Mechanism of the distance-dependent scaling of Schaffer collateral synapses in rat CA1 pyramidal neurons.}, journal = {The Journal of Physiology}, volume = {548}, year = {2003}, month = {2003 Apr 1}, pages = {245-58}, abstract = {

Schaffer collateral axons form excitatory synapses that are distributed across much of the dendritic arborization of hippocampal CA1 pyramidal neurons. Remarkably, AMPA-receptor-mediated miniature EPSP amplitudes at the soma are relatively independent of synapse location, despite widely different degrees of dendritic filtering. A progressive increase with distance in synaptic conductance is thought to produce this amplitude normalization. In this study we examined the mechanism(s) responsible for spatial scaling by making whole-cell recordings from the apical dendrites of CA1 pyramidal neurons. We found no evidence to suggest that there is any location dependence to the range of cleft glutamate concentrations found at Schaffer collateral synapses. Furthermore, we observed that release probability (Pr), paired-pulse facilitation and the size of the readily releasable vesicular pool are not dependent on synapse location. Thus, there do not appear to be any changes in the fundamental presynaptic properties of Schaffer collateral synapses that could account for distance-dependent scaling. On the other hand, two-photon uncaging of 4-methoxy-7-nitroindolinyl-caged L-glutamate onto isolated dendritic spines shows that the number of postsynaptic AMPA receptors per spine increases with distance from the soma. We conclude, therefore, that the main synaptic mechanism involved in the production of distance-dependent scaling of Schaffer collateral synapses is an elevated postsynaptic AMPA receptor density.

}, keywords = {Algorithms, alpha-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid, AMPA, Animals, Computer Simulation, Dendrites, Electrophysiology, Excitatory Amino Acid Antagonists, Excitatory Postsynaptic Potentials, Glutamates, Glutamic Acid, Hippocampus, Indoles, Kinetics, Kynurenic Acid, N-Methyl-D-Aspartate, Neurotransmitter Agents, Patch-Clamp Techniques, Pyramidal Cells, Rats, Receptors, Sprague-Dawley, Synapses, Tetrodotoxin}, issn = {0022-3751}, doi = {10.1002/cbic.201000254}, author = {Smith, Mark A and Ellis-Davies, Graham C R and Magee, Jeffrey C} } @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 {48325, title = {Visualization of the domain structure of an L-type Ca2+ channel using electron cryo-microscopy.}, journal = {Journal of Molecular Biology}, volume = {332}, year = {2003}, month = {2003 Sep 05}, pages = {171-82}, abstract = {

The three-dimensional structure of the skeletal muscle voltage-gated L-type calcium channel (Ca(v)1.1; dihydropyridine receptor, DHPR) was determined using electron cryo-microscopy and single-particle averaging. The structure shows a single channel complex with an approximate total molecular mass of 550 kDa, corresponding to the five known subunits of the DHPR, and bound detergent and lipid. Features visible in our structure together with antibody labeling of the beta and alpha(2) subunits allowed us to assign locations for four of the five subunits within the structure. The most striking feature of the structure is the extra-cellular alpha(2) subunit that protrudes from the membrane domain in close proximity to the alpha(1) subunit. The cytosolic beta subunit is located close to the membrane and adjacent to subunits alpha(1), gamma and delta. Our structure correlates well with the functional and biochemical data available for this channel and suggests a three-dimensional model for the excitation-contraction coupling complex consisting of DHPR tetrads and the calcium release channel.

}, keywords = {Animals, Calcium Channels, L-Type, Cryoelectron Microscopy, Models, Molecular, Molecular Weight, Protein Structure, Quaternary, Protein Subunits, Rabbits, Ryanodine Receptor Calcium Release Channel}, issn = {0022-2836}, author = {Wolf, M and Eberhart, A and Glossmann, H and Striessnig, J and Grigorieff, N} } @article {2178, title = {Detection of large interaural delays and its implication for models of binaural interaction.}, journal = {Journal of the Association for Research in Otolaryngology: JARO}, volume = {3}, year = {2002}, month = {2002 Mar}, pages = {80-8}, abstract = {

The interaural time difference (ITD) is a major cue to sound localization along the horizontal plane. The maximum natural ITD occurs when a sound source is positioned opposite to one ear. We examined the ability of owls and humans to detect large ITDs in sounds presented through headphones. Stimuli consisted of either broad or narrow bands of Gaussian noise, 100 ms in duration. Using headphones allowed presentation of ITDs that are greater than the maximum natural ITD. Owls were able to discriminate a sound leading to the left ear from one leading to the right ear, for ITDs that are 5 times the maximum natural delay. Neural recordings from optic-tectum neurons, however, show that best ITDs are usually well within the natural range and are never as large as ITDs that are behaviorally discriminable. A model of binaural crosscorrelation with short delay lines is shown to explain behavioral detection of large ITDs. The model uses curved trajectories of a cross-correlation pattern as the basis for detection. These trajectories represent side peaks of neural ITD-tuning curves and successfully predict localization reversals by both owls and human subjects.

}, keywords = {Animals, Biological, Ear, Hearing, Humans, Models, Neurons, Noise, Strigiformes, Superior Colliculi, Time Factors}, issn = {1525-3961}, author = {Saberi, Kourosh and Takahashi, Yoshifumi and Egnor, Roian and Farahbod, Haleh and Mazer, James and Konishi, Masakazu} } @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 {4009, title = {Effects of binaural decorrelation on neural and behavioral processing of interaural level differences in the barn owl (Tyto alba).}, journal = {Journal of Comparative Physiology. A, Neuroethology, Sensory, Neural, and Behavioral Physiology}, volume = {187}, year = {2001}, month = {2001 Oct}, pages = {589-95}, abstract = {

The effect of binaural decorrelation on the processing of interaural level difference cues in the barn owl (Tyto alba) was examined behaviorally and electrophysiologically. The electrophysiology experiment measured the effect of variations in binaural correlation on the first stage of interaural level difference encoding in the central nervous system. The responses of single neurons in the posterior part of the ventral nucleus of the lateral lemniscus were recorded to stimulation with binaurally correlated and binaurally uncorrelated noise. No significant differences in interaural level difference sensitivity were found between conditions. Neurons in the posterior part of the ventral nucleus of the lateral lemniscus encode the interaural level difference of binaurally correlated and binaurally uncorrelated noise with equal accuracy and precision. This nucleus therefore supplies higher auditory centers with an undegraded interaural level difference signal for sound stimuli that lack a coherent interaural time difference. The behavioral experiment measured auditory saccades in response to interaural level differences presented in binaurally correlated and binaurally uncorrelated noise. The precision and accuracy of sound localization based on interaural level difference was reduced but not eliminated for binaurally uncorrelated signals. The observation that barn owls continue to vary auditory saccades with the interaural level difference of binaurally uncorrelated stimuli suggests that neurons that drive head saccades can be activated by incomplete auditory spatial information.

}, keywords = {Animal, Animals, Auditory Pathways, Behavior, Brain Stem, Electrophysiology, Inferior Colliculi, Sound Localization, Strigiformes}, issn = {0340-7594}, author = {Egnor, S E} } @article {2015, title = {Rapid atomic density methods for molecular shape characterization.}, journal = {Journal of Molecular Graphics \& Modelling}, volume = {19}, year = {2001}, month = {2001 Jun}, pages = {325-30, 388-90}, abstract = {

Two methods for rapid characterization of molecular shape are presented. Both techniques are based on the density of atoms near the molecular surface. The Fast Atomic Density Evaluation (FADE) algorithm uses fast Fourier transforms to quickly estimate densities. The Pairwise Atomic Density Reverse Engineering (PADRE) method derives modified density measures from the relationship between atomic density and total potentials. While many shape-characterization techniques define shape relative to a surface, the descriptors returned by FADE and PADRE can measure local geometry from points within the three-dimensional space surrounding a molecule. The methods can be used to find crevices and protrusions near the surface of a molecule and to test shape complementarity at the interface between docking molecules.

}, keywords = {Algorithms, Binding Sites, Computer Simulation, Fourier Analysis, Models, Molecular, Protein Binding, Protein Conformation, Proteins}, issn = {1093-3263}, author = {Mitchell, J C and Kerr, R and Ten Eyck, L F} } @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 {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 {45772, title = {The developmental basis for allometry in insects.}, journal = {Development}, volume = {126}, year = {1999}, month = {1999 Mar}, pages = {1091-101}, abstract = {

Within all species of animals, the size of each organ bears a specific relationship to overall body size. These patterns of organ size relative to total body size are called static allometry and have enchanted biologists for centuries, yet the mechanisms generating these patterns have attracted little experimental study. We review recent and older work on holometabolous insect development that sheds light on these mechanisms. In insects, static allometry can be divided into at least two processes: (1) the autonomous specification of organ identity, perhaps including the approximate size of the organ, and (2) the determination of the final size of organs based on total body size. We present three models to explain the second process: (1) all organs autonomously absorb nutrients and grow at organ-specific rates, (2) a centralized system measures a close correlate of total body size and distributes this information to all organs, and (3) autonomous organ growth is combined with feedback between growing organs to modulate final sizes. We provide evidence supporting models 2 and 3 and also suggest that hormones are the messengers of size information. Advances in our understanding of the mechanisms of allometry will come through the integrated study of whole tissues using techniques from development, genetics, endocrinology and population biology.

}, keywords = {Animals, Biological Evolution, Body Constitution, Insect Hormones, Insects, Metamorphosis, Biological, Organ Size, Vertebrates}, issn = {0950-1991}, author = {Stern, D L and Emlen, D J} } @article {1192, title = {Regulation of nuclear genes encoding mitochondrial proteins in Saccharomyces cerevisiae.}, journal = {Journal of Bacteriology}, volume = {177}, year = {1995}, month = {1995 Dec}, pages = {6836-43}, abstract = {

Selection for mutants which release glucose repression of the CYB2 gene was used to identify genes which regulate repression of mitochondrial biogenesis. We have identified two of these as the previously described GRR1/CAT80 and ROX3 genes. Mutations in these genes not only release glucose repression of CYB2 but also generally release respiration of the mutants from glucose repression. In addition, both mutants are partially defective in CYB2 expression when grown on nonfermentable carbon sources, indicating a positive regulatory role as well. ROX3 was cloned by complementation of a glucose-inducible flocculating phenotype of an amber mutant and has been mapped as a new leftmost marker on chromosome 2. The ROX3 mutant has only a modest defect in glucose repression of GAL1 but is substantially compromised in galactose induction of GAL1 expression. This mutant also has increased SUC2 expression on nonrepressing carbon sources. We have also characterized the regulation of CYB2 in strains carrying null mutation in two other glucose repression genes, HXK2 and SSN6, and show that HXK2 is a negative regulator of CYB2, whereas SSN6 appears to be a positive effector of CYB2 expression.

}, keywords = {Base Sequence, Cell Compartmentation, Cell Nucleus, Chromosome Mapping, Chromosomes, Fermentation, Fungal, Fungal Proteins, Gene Expression Regulation, Genes, Genetic, Glucose, Mitochondria, Molecular Sequence Data, Mutagenesis, Oxygen Consumption, Saccharomyces cerevisiae, Selection, Telomere}, issn = {0021-9193}, author = {Brown, T A and Evangelista, C and Trumpower, B L} } @article {4010, title = {The uncertain response in the bottlenosed dolphin (Tursiops truncatus).}, journal = {Journal of Experimental Psychology}, volume = {124}, year = {1995}, month = {1995 Dec}, pages = {391-408}, abstract = {

Humans respond adaptively to uncertainty by escaping or seeking additional information. To foster a comparative study of uncertainty processes, we asked whether humans and a bottlenosed dolphin (Tursiops truncatus) would use similarly a psychophysical uncertain response. Human observers and the dolphin were given 2 primary discrimination responses and a way to escape chosen trials into easier ones. Humans escaped sparingly from the most difficult trials near threshold that left them demonstrably uncertain of the stimulus. The dolphin performed nearly identically. The behavior of both species is considered from the perspectives of signal detection theory and optimality theory, and its appropriate interpretation is discussed. Human and dolphin uncertain responses seem to be interesting cognitive analogs and may depend on cognitive or controlled decisional mechanisms. The capacity to monitor ongoing cognition, and use uncertainty appropriately, would be a valuable adaptation for animal minds. This recommends uncertainty processes as an important but neglected area for future comparative research.

}, keywords = {Animal, Animals, Auditory Threshold, Behavior, Biological, Cognition, Discrimination (Psychology), Humans, Kinetics, Models, Probability, Psychiatric Status Rating Scales, Reinforcement (Psychology), Task Performance and Analysis}, issn = {0096-3445}, author = {Smith, J D and Schull, J and Strote, J and McGee, K and Egnor, R and Erb, L} } @article {2461, title = {Neuropeptide induction of cyclic GMP increases in the insect CNS: resolution at the level of single identifiable neurons.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {14}, year = {1994}, month = {1994 Dec}, pages = {7704-12}, abstract = {

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

}, keywords = {Animals, Central Nervous System, Cyclic GMP, Enzyme Activation, Guanylate Cyclase, Immunohistochemistry, Insect Hormones, Manduca, Neurons, Synapses, Time Factors}, issn = {0270-6474}, author = {Ewer, J and de Vente, J and Truman, J W} } @article {972, title = {The glass gene encodes a zinc-finger protein required by Drosophila photoreceptor cells.}, journal = {Nature}, volume = {340}, year = {1989}, month = {1989 Aug 17}, pages = {531-6}, abstract = {

Null mutations of glass specifically remove photoreceptor cells, leaving other cell types intact. We have isolated the glass gene and have shown that its transcript encodes a putative protein of 604 amino acids with five zinc-fingers. The glass product may be a transcription factor required for the development of a single neuronal cell type.

}, keywords = {Animals, Base Sequence, DNA, Drosophila, Gene Expression Regulation, Molecular Sequence Data, Mutation, Photoreceptor Cells}, issn = {0028-0836}, doi = {10.1186/gb-2007-8-7-r145}, author = {Moses, K and Ellis, M C and Rubin, G M} } @article {1149, title = {The sex determination locus transformer-2 of Drosophila encodes a polypeptide with similarity to RNA binding proteins.}, journal = {Cell}, volume = {56}, year = {1989}, month = {1989 Mar 24}, pages = {1011-18}, abstract = {

The D. melanogaster transformer-2 (tra-2) gene regulates somatic sexual differentiation in females and is necessary for spermatogenesis in males. Wild-type tra-2 function is required for the female-specific splicing of the pre-mRNA of the next known gene (doublesex) downstream of tra-2 in the sex determination regulatory hierarchy. The tra-2 gene was cloned, and P element-mediated transformation was used to demonstrate that a 3.9 kb genomic fragment contains all sequences necessary for tra-2 function. A 1.7 kb transcript was shown to be the product of the tra-2 locus based on its reduced level in flies containing a tra-2 mutant allele. The sequence of a cDNA corresponding to this transcript indicates that it encodes a polypeptide with strong similarity to a family of RNA binding proteins that includes proteins found associated with hnRNPs and snRNPs, suggesting that the tra-2 product may directly regulate the processing of the double-sex pre-mRNA in females.

}, issn = {0092-8674}, author = {Baker, B.S. and Goralski, T.J. and Edstrom, J.E.} } @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} }