@article {69948, title = {Accelerating Neuron Reconstruction with PATHFINDER}, journal = {bioRxiv}, year = {2025}, month = {2025 May 21}, abstract = {

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

}, doi = {10.1101/2025.05.16.654254}, url = {https://www.biorxiv.org/content/early/2025/05/21/2025.05.16.654254}, author = {Januszewski, Micha{\l} and Templier, Thomas and Hayworth, Kenneth Jeffrey and Peale, David and Hess, Harald} } @article {69848, title = {A Bayesian Model to Count the Number of Two-State Emitters in a Diffraction Limited Spot.}, journal = {Nano Lett}, year = {2025}, month = {2025 Apr 04}, abstract = {

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

}, issn = {1530-6992}, doi = {10.1021/acs.nanolett.4c06304}, url = {https://doi.org/10.1021/acs.nanolett.4c06304}, author = {Hillsley, Alexander and Stein, Johannes and Tillberg, Paul W and Stern, David L and Funke, Jan} } @article {69987, title = {CalciumInsights: An Open-Source, Tissue-Agnostic Graphical Interface for High-Quality Analysis of Calcium Signals}, journal = {bioRxiv}, year = {2025}, month = {2025 Jun 04}, abstract = {

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

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

}, doi = {10.1101/2025.06.04.657923}, url = {https://www.biorxiv.org/content/early/2025/06/09/2025.06.04.657923}, author = {Suarez-Gomez, Deiver and Perez-Rosas, Norma C and Miranda-Contreras, Gabriel I and Colom-Bra{\~n}a, Santiago R and Zhang, Weiwei and Mim, Mayesha Sahir and Tan, Shelly and Gazzo, David and Tepole, Adrian Buganza and Deng, Qing and Reeves, Gregory T and Isaza-Brando, Clara E and Staiger, Christopher J. and Umulis, David and Zartman, Jeremiah and Cabrera-R{\'\i}os, Mauricio} } @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 {70130, title = {Combinatorial protein barcodes enable self-correcting neuron tracing with nanoscale molecular context}, journal = {bioRxiv}, year = {2025}, month = {2025 Sep 28}, abstract = {

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

}, doi = {10.1101/2025.09.26.678648}, url = {https://www.biorxiv.org/content/early/2025/09/28/2025.09.26.678648}, author = {Park, Sung Yun and Sheridan, Arlo and An, Bobae and Jarvis, Erin and Lyudchik, Julia and Patton, William and Axup, Jun Y. and Chan, Stephanie W. and Damstra, Hugo G.J. and Leible, Daniel and Leung, Kylie S. and Magno, Clarence A. and Meeran, Aashir and Michalska, Julia M. and Rieger, Franz and Wang, Claire and Wu, Michelle and Church, George M. and Funke, Jan and Huffman, Todd and Leeper, Kathleen G.C. and Truckenbrodt, Sven and Winnubst, Johan and Kornfeld, Joergen M.R. and Boyden, Edward S. and Rodriques, Samuel G. and Payne, Andrew C.} } @article {69854, title = {Combining spatial transcriptomics and ECM imaging in 3D for mapping cellular interactions in the tumor microenvironment.}, journal = {Cell Syst}, year = {2025}, month = {2025 Apr 09}, pages = {101261}, abstract = {

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

}, issn = {2405-4720}, doi = {10.1016/j.cels.2025.101261}, url = {https://doi.org10.1016/j.cels.2025.101261}, author = {Pentimalli, Tancredi Massimo and Schallenberg, Simon and Le{\'o}n-Peri{\~n}{\'a}n, Daniel and Legnini, Ivano and Theurillat, Ilan and Thomas, Gwendolin and Boltengagen, Anastasiya and Fritzsche, Sonja and Nimo, Jose and Ruff, Lukas and Dernbach, Gabriel and Jurmeister, Philipp and Murphy, Sarah and Gregory, Mark T and Liang, Yan and Cordenonsi, Michelangelo and Piccolo, Stefano and Coscia, Fabian and Woehler, Andrew and Karaiskos, Nikos and Klauschen, Frederick and Rajewsky, Nikolaus} } @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 {70138, title = {The Connectome Interpreter Toolkit}, journal = {bioRxiv}, year = {2025}, month = {2025 Sep 30}, abstract = {

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

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

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

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

}, doi = {10.1101/2025.06.10.658982}, url = {https://www.biorxiv.org/content/early/2025/06/15/2025.06.10.658982}, author = {Petkova, Mariela D. and Januszewski, Micha{\l} and Blakely, Tim and Herrera, Kristian J. and Schuhknecht, Gregor F.P. and Tiller, Robert and Choi, Jinhan and Schalek, Richard L. and Boulanger-Weill, Jonathan and Peleg, Adi and Wu, Yuelong and Wang, Shuohong and Troidl, Jakob and Kumar Vohra, Sumit and Wei, Donglai and Lin, Zudi and Bahl, Armin and Tapia, Juan Carlos and Iyer, Nirmala and Miller, Zachary T. and Hebert, Kathryn B. and Pavarino, Elisa C. and Taylor, Milo and Deng, Zixuan and Stingl, Moritz and Hockling, Dana and Hebling, Alina and Wang, Ruohong C. and Zhang, Lauren L. and Dvorak, Sam and Faik, Zainab and King, Kareem I. and Goel, Pallavi and Wagner-Carena, Julian and Aley, David and Chalyshkan, Selimzhan and Contreas, Dominick and Li, Xiong and Muthukumar, Akila V. and Vernaglia, Marina S. and Carrasco, Teodoro Tapia and Melnychuck, Sofia and Yan, TingTing and Dalal, Ananya and DiMartino, James M. and Brown, Sam and Safo-Mensa, Nana and Greenberg, Ethan and Cook, Michael and Finley-May, Samantha and Flynn, Miriam A. and Hopkins, Gary Patrick and Kovalyak, Julie and Leonard, Meghan and Lohff, Alanna and Ordish, Christopher and Scott, Ashley L. and Takemura, Satoko and Walsh, Claire and Walsh, John J. and Berger, Daniel R. and Pfister, Hanspeter and Berg, Stuart and Knecht, Christopher and Meissner, Geoffrey W. and Korff, Wyatt and Ahrens, Misha B. and Jain, Viren and Lichtman, Jeff W. and Engert, Florian} } @article {69457, title = {Deep-tissue transcriptomics and subcellular imaging at high spatial resolution}, journal = {Science}, year = {2025}, month = {2025 Feb 20}, abstract = {

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

bioRxiv preprint:\ 10.1101/2024.05.17.594641

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

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

}, issn = {1546-1726}, doi = {10.1038/s41593-025-01923-4}, url = {https://doi.org/10.1038/s41593-025-01923-4}, author = {Mohar, Boaz and Michel, Gabriela and Wang, Yi-Zhi and Hernandez, Veronica and Grimm, Jonathan B and Park, Jin-Yong and Patel, Ronak and Clarke, Morgan and Brown, Timothy A and Bergmann, Cornelius and Gebis, Kamil K and Wilen, Anika P and Liu, Bian and Johnson, Richard and Graves, Austin and Tchumatchenko, Tatjana and Savas, Jeffrey N and Fornasiero, Eugenio F and Huganir, Richard L and Tillberg, Paul W and Lavis, Luke D and Svoboda, Karel and Spruston, Nelson} } @article {70054, title = {Design of Orthogonal Far-Red, Orange and Green Fluorophore-binding Proteins for Multiplex Imaging}, journal = {bioRxiv}, year = {2025}, month = {2025 Aug 03}, abstract = {

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

}, doi = {10.1101/2025.08.03.668343}, url = {https://www.biorxiv.org/content/early/2025/08/03/2025.08.03.668343}, author = {Tran, Long and Sharma, Shajesh and Klein, Steffen and Jurgens, David and Decarreau, Justin and Liu, Bingxu and Wang, Yujia and Bera, Asim K. and Kang, Alex and Woods, Jon and Joyce, Emily and Vafeados, Dionne K and Roullier, Nicole and Chen, Wei and Lee, Gyu Rie and Mahamid, Julia and Lavis, Luke D. and An, Linna and Baker, David} } @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 {69840, title = {EPSILON: a method for pulse-chase labeling to probe synaptic AMPAR exocytosis during memory formation.}, journal = {Nat Neurosci}, year = {2025}, month = {2025 Mar 31}, abstract = {

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

}, issn = {1546-1726}, doi = {10.1038/s41593-025-01922-5}, url = {https://doi.org/10.1038/s41593-025-01922-5}, author = {Kim, Doyeon and Park, Pojeong and Li, Xiuyuan and Wong-Campos, J David and Tian, He and Moult, Eric M and Grimm, Jonathan B and Lavis, Luke D and Cohen, Adam E} } @article {68117, title = {An essential experimental control for functional connectivity mapping with optogenetics.}, journal = {Genetics}, volume = {231}, year = {2025}, month = {2025 Nov 12}, abstract = {

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

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

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

}, doi = {10.1101/2025.09.22.677893}, url = {https://www.biorxiv.org/content/early/2025/09/22/2025.09.22.677893}, author = {Yoo, Juyoun and Xie, Fangming and Butrus, Salwan and Xu, Runzhe and Tan, Zhiqun and Gorzek, Ryan and Mirshahidi, Parmis and Tring, Elaine and Suresh, Sanjana and Kim, Jinho and Fleishman, Greg and Tan, Liming and Ringach, Dario and Trachtenberg, Joshua and Xu, Xiangmin and Zipursky, S. Lawrence and Shekhar, Karthik and Jain, Saumya} } @article {69846, title = {Far-red fluorescent genetically encoded calcium ion indicators.}, journal = {Nat Commun}, volume = {16}, year = {2025}, month = {2025 Apr 07}, pages = {3318}, abstract = {

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

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

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

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

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

}, issn = {1097-4172}, doi = {10.1016/j.cell.2025.03.012}, url = {https://doi.org/10.1016/j.cell.2025.03.012}, author = {Mi, Xuelong and Chen, Alex Bo-Yuan and Duarte, Daniela and Carey, Erin and Taylor, Charlotte R and Braaker, Philipp N and Bright, Mark and Almeida, Rafael G and Lim, Jing-Xuan and Ruetten, Virginia M S and Wang, Yizhi and Wang, Mengfan and Zhang, Weizhan and Zheng, Wei and Reitman, Michael E and Huang, Yongkang and Wang, Xiaoyu and Li, Lei and Deng, Hanfei and Shi, Song-Hai and Poskanzer, Kira E and Lyons, David A and Nimmerjahn, Axel and Ahrens, Misha B and Yu, Guoqiang} } @article {70101, title = {Functional synapses between neurons and small cell lung cancer.}, journal = {Nature}, year = {2025}, month = {2025 Sep 10}, abstract = {

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

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

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

}, issn = {1754-8411}, doi = {10.1242/dmm.052329}, url = {https://doi.org/10.1242/dmm.052329}, author = {Banerjee, Animesh and Chatterjee, Moumita and Tan, Kah Junn and Tay, Shermaine and Duan, Kaibo and Andiappan, Anand Kumar and Howland, Shanshan Wu and Aso, Yoshinori and Aw, Sherry Shiying} } @article {69833, title = {Glutamate indicators with increased sensitivity and tailored deactivation rates}, journal = {bioRxiv}, year = {2025}, month = {2025 Mar 20}, abstract = {

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

}, doi = {10.1101/2025.03.20.643984}, url = {https://www.biorxiv.org/content/early/2025/03/24/2025.03.20.643984}, author = {Aggarwal, Abhi and Negrean, Adrian and Chen, Yang and Iyer, Rishyashring and Reep, Daniel and Liu, Anyi and Palutla, Anirudh and Xie, Michael E. and MacLennan, Bryan J. and Hagihara, Kenta M. and Kinsey, Lucas W. and Sun, Julianna L. and Yao, Pantong and Zheng, Jihong and Tsang, Arthur and Tsegaye, Getahun and Zhang, Yonghai and Patel, Ronak H. and Arthur, Benjamin J. and Hiblot, Julien and Leippe, Philipp and Tarnawski, Miroslaw and Marvin, Jonathan S. and Vevea, Jason D. and Turaga, Srinivas C. and Tebo, Alison G. and Carandini, Matteo and Rossi, L. F. and Kleinfeld, David and Konnerth, Arthur and Svoboda, Karel and Turner, Glenn C. and Hasseman, Jeremy and Podgorski, Kaspar} } @article {69856, title = {Glutamate indicators with increased sensitivity and tailored deactivation rates}, journal = {Research Square}, year = {2025}, month = {2025 Apr 8}, abstract = {

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

}, doi = {10.21203/rs.3.rs-6257403/v1}, url = {https://doi.org/10.21203/rs.3.rs-6257403/v1}, author = {Podgorski, Kaspar and Aggarwal, Abhi and Negrean, Adrian and Chen, Yang and Iyer, Rishyashring and Reep, Daniel and Liu, Anyi and Palutla, Anirudh and Xie, Michael and Maclennan, Bryan and Hagihara, Kenta and Kinsey, Lucas and Sun, Julianna and Yao, Pantong and Zheng, Jihong and Tsang, Arthur and Tsegaye, Getahun and Zhang, Yonghai and Patel, Ronak and Hasseman, Jeremy} } @article {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 {69831, title = {iGABASnFR2: Improved genetically encoded protein sensors of GABA}, journal = {bioRxiv}, year = {2025}, month = {2025 Mar 25}, abstract = {

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

}, doi = {10.1101/2025.03.25.644953}, url = {https://www.biorxiv.org/content/early/2025/03/26/2025.03.25.644953}, author = {Kolb, Ilya and Hasseman, Jeremy P. and Matsumoto, Akihiro and Arthur, Benjamin J. and Zhang, Yan and Tsang, Arthur and Reep, Daniel and Tsegaye, Getahun and Zheng, Jihong and Patel, Ronak and Looger, Loren L. and Marvin, Jonathan S. and Korff, Wyatt L. and Yonehara, Keisuke and Turner, Glenn C.} } @article {70093, title = {iGABASnFR2: Improved genetically encoded protein sensors of GABA}, journal = {eLife}, year = {2025}, month = {2025 Sept 03}, abstract = {

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

}, doi = {10.7554/elife.108319.1}, url = {http://dx.doi.org/10.7554/eLife.108319.1}, author = {Kolb, Ilya and Hasseman, Jeremy P and Matsumoto, Akihiro and Jensen, Thomas P and Kopach, Olga and Arthur, Benjamin J and Zhang, Yan and Tsang, Arthur and Reep, Daniel and Tsegaye, Getahun and Zheng, Jihong and Patel, Ronak H and Looger, Loren L and Marvin, Jonathan S and Korff, Wyatt L and Rusakov, Dmitri A and Yonehara, Keisuke and Turner, Glenn C} } @article {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 {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 {70006, title = {Large-scale high-density brain-wide neural recording in nonhuman primates.}, journal = {Nat Neurosci}, year = {2025}, month = {2025 Jun 23}, abstract = {

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

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

}, issn = {1546-1726}, doi = {10.1038/s41593-025-01976-5}, url = {https://doi.org/10.1038/s41593-025-01976-5}, author = {Trautmann, Eric M and Hesse, Janis K and Stine, Gabriel M and Xia, Ruobing and Zhu, Shude and O{\textquoteright}Shea, Daniel J and Karsh, Bill and Colonell, Jennifer and Lanfranchi, Frank F and Vyas, Saurabh and Zimnik, Andrew and Amematsro, Elom and Steinemann, Natalie A and Wagenaar, Daniel A and Pachitariu, Marius and Andrei, Alexandru and Lopez, Carolina Mora and O{\textquoteright}Callaghan, John and Putzeys, Jan and Raducanu, Bogdan C and Welkenhuysen, Marleen and Churchland, Mark and Moore, Tirin and Shadlen, Michael and Shenoy, Krishna and Tsao, Doris and Dutta, Barundeb and Harris, Timothy} } @article {69577, title = {Learning reshapes the hippocampal representation hierarchy}, journal = {Proc. Natl. Acad. Sci. U.S.A.}, year = {2025}, month = {2025 Mar 10}, abstract = {

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

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

}, doi = {10.1073/pnas.2417025122}, url = {https://doi.org/10.1073/pnas.2417025122}, author = {Chiossi, Heloisa S. C. and Nardin, Michele and Tka{\v c}ik, Ga{\v s}per and Csicsvari, Jozsef L.} } @article {69782, title = {Melanocortin 3 receptor regulates hepatic autophagy and systemic adiposity.}, journal = {Nat Commun}, volume = {16}, year = {2025}, month = {2025 Feb 16}, pages = {1690}, abstract = {

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

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

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

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

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

Preprint:\ 10.1101/2025.02.22.639343

}, keywords = {Animals, CRISPR-Cas Systems, Cryoelectron Microscopy, Endoplasmic Reticulum, HEK293 Cells, Hela Cells, Humans, Membrane Proteins, Mitochondria, Mitochondrial Membranes, Proteomics, Tacrolimus Binding Proteins}, issn = {2041-1723}, doi = {10.1038/s41467-025-58538-3}, url = {https://doi.org/10.1038/s41467-025-58538-3}, author = {Nakamura, Koki and Aoyama-Ishiwatari, Saeko and Nagao, Takahiro and Paaran, Mohammadreza and Obara, Christopher J and Sakurai-Saito, Yui and Johnston, Jake and Du, Yudan and Suga, Shogo and Tsuboi, Masafumi and Nakakido, Makoto and Tsumoto, Kouhei and Kishi, Yusuke and Gotoh, Yukiko and Kwak, Chulhwan and Rhee, Hyun-Woo and Seo, Jeong Kon and Kosako, Hidetaka and Potter, Clint and Carragher, Bridget and Lippincott-Schwartz, Jennifer and Polleux, Franck and Hirabayashi, Yusuke} } @article {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 {69960, title = {Myocardium and endocardium of the early mammalian heart tube arise from independent multipotent lineages specified at the primitive streak}, journal = {Dev Cell}, year = {2025}, month = {2025 May 20}, abstract = {

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

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

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

}, doi = {10.1101/2025.10.28.685015}, url = {https://www.biorxiv.org/content/early/2025/10/28/2025.10.28.685015}, author = {Denis, Silke and Van Deuren, Vincent and Frecot, Desiree I. and Rothbauer, Ulrich and Ismail, Shehab and Tebo, Alison G. and Dedecker, Peter} } @article {70162, title = {Networks of sexually dimorphic neurons that regulate social behaviors in Drosophila}, journal = {bioRxiv}, year = {2025}, month = {2025 Oct 21}, abstract = {

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

}, doi = {10.1101/2025.10.21.683766}, url = {https://www.biorxiv.org/content/early/2025/10/22/2025.10.21.683766}, author = {Rubin, Gerald M. and Managan, Claire and Dreher, Marisa and Kim, Elizabeth and Miller, Scott and Boone, Kaitlyn and Robie, Alice and Taylor, Adam L. and Branson, Kristin and Schretter, Catherine E. and Otopalik, Adriane G.} } @article {69996, title = {Neural substrates of cold nociception in Drosophila larva}, journal = {eLife}, volume = {12}, year = {2025}, month = {2025 Jun 13}, pages = {RP91582}, abstract = {

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

}, keywords = {cold nociception, somatosensory circuits, thermosensation, \textitDrosophila}, issn = {2050-084X}, doi = {10.7554/eLife.91582}, url = {https://doi.org/10.7554/eLife.91582}, author = {Patel, Atit A and Cardona, Albert and Cox, Daniel N}, editor = {Tuthill, John C and Sen, Sonia Q} } @article {69774, title = {Neuropixels Opto: Combining high-resolution electrophysiology and optogenetics}, journal = {bioRxiv}, year = {2025}, month = {2025 Feb 06}, abstract = {

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

}, doi = {10.1101/2025.02.04.636286}, url = {https://www.biorxiv.org/content/early/2025/02/06/2025.02.04.636286}, author = {Lakunina, Anna and Socha, Karolina Z and Ladd, Alexander and Bowen, Anna J and Chen, Susu and Colonell, Jennifer and Doshi, Anjal and Karsh, Bill and Krumin, Michael and Kulik, Pavel and Li, Anna and Neutens, Pieter and O{\textquoteright}Callaghan, John and Olsen, Meghan and Putzeys, Jan and Tilmans, Harrie AC and Ye, Zhiwen and Welkenhuysen, Marleen and H{\"a}usser, Michael and Koch, Christof and Ting, Jonathan T. and Neuropixels Opto Consortium and Dutta, Barun and Harris, Timothy D and Steinmetz, Nicholas A and Svoboda, Karel and Siegle, Joshua H and Carandini, Matteo} } @article {70169, title = {Optimizing multifunctional fluorescent ligands for intracellular labeling.}, journal = {Proc Natl Acad Sci U S A}, volume = {122}, year = {2025}, month = {2025 Nov 04}, pages = {e2510046122}, abstract = {

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

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

}, keywords = {Bromodomain Containing Proteins, Cell Cycle Proteins, Fluorescent Dyes, Humans, Ligands, Mitochondria, Nuclear Proteins, Rhodamines, Staining and Labeling, Transcription Factors}, issn = {1091-6490}, doi = {10.1073/pnas.2510046122}, url = {https://doi.org/10.1073/pnas.2510046122}, author = {Kumar, Pratik and Vevea, Jason D and Tkachuk, Ariana N and Campbell, Kirby R and Watson, Emma T and Ayala, Anthony X and Grimm, Jonathan B and Chapman, Edwin R and Solecki, David J and Lavis, Luke D} } @article {69949, title = {Proprioceptive limit detectors mediate sensorimotor control of the Drosophila leg}, journal = {bioRxiv}, year = {2025}, month = {2025 May 15}, abstract = {

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

}, doi = {10.1101/2025.05.15.654260}, url = {https://www.biorxiv.org/content/early/2025/05/19/2025.05.15.654260}, author = {Pratt, Brandon G. and Dallmann, Chris J. and Chou, Grant M. and Siwanowicz, Igor and Walling-Bell, Sarah and Cook, Andrew and Sustar, Anne and Azevedo, Anthony and Tuthill, John C.} } @article {69993, title = {RubyACRs Enable Red-Shifted Optogenetic Inhibition in Freely Behaving Drosophila}, journal = {eLife}, year = {2025}, month = {2025 Sep 05}, abstract = {

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

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

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

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

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

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

}, doi = {10.1101/2025.10.09.680999}, url = {https://www.biorxiv.org/content/early/2025/10/09/2025.10.09.680999}, author = {Berg, Stuart and Beckett, Isabella R and Costa, Marta and Schlegel, Philipp and Januszewski, Micha{\l} and Marin, Elizabeth C and Nern, Aljoscha and Preibisch, Stephan and Qiu, Wei and Takemura, Shin-ya and Fragniere, Alexandra MC and Champion, Andrew S and Adjavon, Diane-Yayra and Cook, Michael and Gkantia, Marina and Hayworth, Kenneth J and Huang, Gary B and Katz, William T and K{\"a}mpf, Florian and Lu, Zhiyuan and Ordish, Christopher and Paterson, Tyler and St{\"u}rner, Tomke and Trautman, Eric T and Whittle, Catherine R and Burnett, Laura E and Hoeller, Judith and Li, Feng and Loesche, Frank and Morris, Billy J and Pietzsch, Tobias and Pleijzier, Markus W and Silva, Valeria and Yin, Yijie and Ali, Iris and Badalamente, Griffin and Bates, Alexander Shakeel and Bogovic, John and Brooks, Paul and Cachero, Sebastian and Canino, Brandon S and Chaisrisawatsuk, Bhumpanya and Clements, Jody and Crowe, Arthur and de Haan Vicente, In{\^e}s and Dempsey, Georgia and Don{\`a}, Erika and dos Santos, M{\'a}rcia and Dreher, Marisa and Dunne, Christopher R and Eichler, Katharina and Finley-May, Samantha and Flynn, Miriam A and Hameed, Imran and Hopkins, Gary Patrick and Hubbard, Philip M and Kiassat, Ladann and Kovalyak, Julie and Lauchie, Shirley A and Leonard, Meghan and Lohff, Alanna and Longden, Kit D and Maldonado, Charli A and Mitletton, Myrto and Moitra, Ilina and Moon, Sung Soo and Mooney, Caroline and Munnelly, Eva J and Okeoma, Nneoma and Olbris, Donald J and Pai, Anika and Patel, Birava and Phillips, Emily M and Plaza, Stephen M and Richards, Alana and Rivas Salinas, Jennifer and Roberts, Ruair{\'\i} Jv and Rogers, Edward M and Scott, Ashley L and Scuderi, Louis A and Seenivasan, Pavithraa and Serratosa Capdevila, Laia and Smith, Claire and Svirskas, Rob and Takemura, Satoko and Tastekin, Ibrahim and Thomson, Alexander and Umayam, Lowell and Walsh, John J and Whittome, Holly and Xu, C Shan and Yakal, Emily A and Yang, Tansy and Zhao, Arthur and George, Reed and Jain, Viren and Jayaraman, Vivek and Korff, Wyatt and Meissner, Geoffrey W and Romani, Sandro and Funke, Jan and Knecht, Christopher and Saalfeld, Stephan and Scheffer, Louis K and Waddell, Scott and Card, Gwyneth M and Ribeiro, Carlos and Reiser, Michael B and Hess, Harald F and Rubin, Gerald M and Jefferis, Gregory Sxe} } @article {70136, title = {A single residue in the yellow fever virus envelope protein modulates virion architecture and antigenicity.}, journal = {Nat Commun}, volume = {16}, year = {2025}, month = {2025 Sep 26}, pages = {8449}, abstract = {

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

}, keywords = {Animals, Antibodies, Neutralizing, Antibodies, Viral, Antigens, Viral, Cross Reactions, Cryoelectron Microscopy, Epitopes, Humans, Viral Envelope Proteins, Virion, Yellow Fever, Yellow Fever Vaccine, Yellow fever virus}, issn = {2041-1723}, doi = {10.1038/s41467-025-63038-5}, url = {https://doi.org/10.1038/s41467-025-63038-5}, author = {Bibby, Summa and Jung, James and Low, Yu Shang and Amarilla, Alberto A and Newton, Natalee D and Scott, Connor A P and Balk, Jessica and Ting, Yi Tian and Freney, Morgan E and Liang, Benjamin and Grant, Timothy and Coulibaly, Fass{\'e}li and Young, Paul and Hall, Roy A and Hobson-Peters, Jody and Modhiran, Naphak and Watterson, Daniel} } @article {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 {69984, title = {Spatial reasoning via recurrent neural dynamics in mouse retrosplenial cortex}, journal = {Nat Neurosci}, volume = {28}, year = {2025}, month = {2025 Jun 06}, pages = {1293-1299}, abstract = {

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

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

}, keywords = {Animals, Cerebral Cortex, Gyrus Cinguli, Male, Mice, Mice, Inbred C57BL, Models, Neurological, Neural Networks, Computer, Neurons, Photic Stimulation, Space Perception}, issn = {1546-1726}, doi = {10.1038/s41593-025-01944-z}, url = {https://doi.org/10.1038/s41593-025-01944-z}, author = {Voigts, Jakob and Kanitscheider, Ingmar and Miller, Nicholas J and Toloza, Enrique H S and Newman, Jonathan P and Fiete, Ila R and Harnett, Mark T} } @article {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 {69702, title = {Structural dynamics and binding of Caenorhabditis elegans lifespan-extending lipid binding protein-3 to polyunsaturated fatty acids.}, journal = {Protein Sci}, volume = {34}, year = {2025}, month = {2025 Jan 01}, pages = {e5249}, abstract = {

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

}, keywords = {Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Crystallography, X-Ray, Fatty Acid-Binding Proteins, Fatty Acids, Unsaturated, Molecular Dynamics Simulation, Protein Binding}, issn = {1469-896X}, doi = {10.1002/pro.5249}, url = {https://doi.org/10.1002/pro.5249}, author = {Cuevas, Andr{\'e} R and Tillman, Matthew C and Wang, Meng C and Ortlund, Eric A} } @article {69803, title = {TEMI: Tissue Expansion Mass Spectrometry Imaging}, journal = {Nat Methods}, year = {2025}, month = {2025 Apr 22}, abstract = {

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

Preprint:\ 10.1101/2025.02.22.639343

}, doi = {10.1101/2025.02.22.639343}, url = {https://doi.org/ 10.1038/s41592-025-02664-9.}, author = {Zhang, Hua and Ding, Lang and Hu, Amy and Shi, Xudong and Huang, Penghsuan and Lu, Haiyan and Tillberg, Paul W. and Wang, Meng C. and Li, Lingjun} } @article {70085, title = {Time-deterministic cryo-optical microscopy.}, journal = {Light Sci Appl}, volume = {14}, year = {2025}, month = {2025 Aug 23}, pages = {275}, abstract = {

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

}, issn = {2047-7538}, doi = {10.1038/s41377-025-01941-8}, url = {https://doi.org/10.1038/s41377-025-01941-8}, author = {Tsuji, Kosuke and Yamanaka, Masahito and Kumamoto, Yasuaki and Tamura, Shoko and Miyamura, Wakana and Kubo, Toshiki and Mizushima, Kenta and Kono, Kakeru and Hirano, Hanae and Shiozaki, Momoko and Zhao, Xiaowei and Xi, Heqi and Sugiura, Kazunori and Fukushima, Shun-Ichi and Kunimoto, Takumi and Tanabe, Yoshino and Nishida, Kentaro and Mochizuki, Kentaro and Harada, Yoshinori and Smith, Nicholas I and Heintzmann, Rainer and Yu, Zhiheng and Wang, Meng C and Nagai, Takeharu and Tanaka, Hideo and Fujita, Katsumasa} } @article {70053, title = {Transgene-free generation of mouse post-gastrulation whole embryo models solely from naive ESCs and iPSCs.}, journal = {Cell Stem Cell}, year = {2025}, month = {2025 Aug 06}, abstract = {

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

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

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

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

}, doi = {10.1038/s41467-025-58017-9}, url = {https://doi.org/10.1038/s41467-025-58017-9}, author = {Lina El Hajji and Benjamin Bunel and Octave Joliot and Chenge Li and Alison G. Tebo and Christine Rampon and Michel Volovitch and Evelyne Fischer and Nicolas Pietrancosta and Franck Perez and Xavier Morin and Sophie Vriz and Arnaud Gautier} } @article {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 {69812, title = {Vimentin filament transport and organization revealed by single-particle tracking and 3D FIB-SEM}, journal = {Journal of Cell Biology}, volume = {224}, year = {2025}, month = {2025 Apr 03}, pages = {e202406054}, abstract = {

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

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

}, issn = {0021-9525}, doi = {10.1083/jcb.202406054}, url = {https://doi.org/10.1083/jcb.202406054}, author = {Renganathan, Bhuvanasundar and Moore, Andrew S. and Yeo, Wei-Hong and Petruncio, Alyson and Ackerman, David and Weigel, Aubrey V. and Team, The CellMap and Pasolli, H. Amalia and Xu, C. Shan and Shtengel, Gleb and Hess, Harald F. and Serpinskaya, Anna S. and Zhang, Hao F. and Lippincott-Schwartz, Jennifer and Gelfand, Vladimir I.} } @article {69290, title = {Whole-body simulation of realistic fruit fly locomotion with deep reinforcement learning}, journal = {Nature}, volume = {643}, year = {2025}, month = {2025 Jul}, abstract = {

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

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

}, doi = {10.1038/s41586-025-09029-4}, url = {https://doi.org/10.1038/s41586-025-09029-4}, author = {Roman Vaxenburg and Igor Siwanowicz and Josh Merel and Alice A Robie and Carmen Morrow and Guido Novati and Zinovia Stefanidi and Gwyneth M Card and Michael B Reiser and Matthew M Botvinick and Kristin M Branson and Yuval Tassa and Srinivas C Turaga} } @article {69601, title = {3D nanoscale architecture of the respiratory epithelium reveals motile cilia-rootlets-mitochondria axis of communication}, journal = {bioRxiv}, year = {2024}, month = {2024 Sep 08}, abstract = {

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

}, doi = {10.1101/2024.09.08.611854}, url = {https://www.doi.org/10.1101/2024.09.08.611854}, author = {Vijayakumaran, Aaran and Godbehere, Christopher and Abuammar, Analle and Breusegem, Sophia Y. and Hurst, Leah R. and Morone, Nobuhiro and Llodra, Jaime and Dalbay, Melis T. and Tanvir, Niaj M. and MacLellan-Gibson, K. and O{\textquoteright}Callaghan, Chris and Lorentzen, Esben and , and , and Murray, Andrew J. and Narayan, Kedar and Mennella, Vito} } @article {69641, title = {Assembloid model to study loop circuits of the human nervous system}, journal = {bioRxiv}, year = {2024}, month = {2024 Oct 14}, abstract = {

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

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

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

}, doi = {10.1101/2024.03.02.583085}, url = {https://www.biorxiv.org/content/early/2024/03/06/2024.03.02.583085}, author = {Advait Athreya and Liangqi Xie and Robert Tjian and Bin Zhang and Zhe J. Liu} } @article {69385, title = {A Bayesian Solution to Count the Number of Molecules within a Diffraction Limited Spot}, journal = {bioRxiv}, year = {2024}, month = {2024 Apr 22}, abstract = {

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

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

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

}, keywords = {Brain, Memory, Movement, Neurons, Thalamus}, issn = {1097-4172}, doi = {10.1016/j.cell.2023.12.035}, author = {Chen, Susu and Liu, Yi and Wang, Ziyue Aiden and Colonell, Jennifer and Liu, Liu D and Hou, Han and Tien, Nai-Wen and Wang, Tim and Harris, Timothy and Druckmann, Shaul and Li, Nuo and Svoboda, Karel} } @article {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 {68656, title = {Connectome-constrained networks predict neural activity across the fly visual system}, journal = {Nature}, year = {2024}, month = {2024 Sep 11}, abstract = {

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

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

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

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

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

}, doi = {10.1101/2024.04.21.590464}, url = {https://www.biorxiv.org/content/early/2024/04/25/2024.04.21.590464}, author = {Patricia K Rivlin and Michal Januszewski and Kit D Longden and Erika Neace and Louis K Scheffer and Christopher Ordish and Jody Clements and Elliott Phillips and Natalie Smith and Satoko Takemura and Lowell Umayam and Claire Walsh and Emily A Yakal and Stephen M Plaza and Stuart Berg} } @article {69286, title = {Coordinated head direction representations in mouse anterodorsal thalamic nucleus and retrosplenial cortex.}, journal = {Elife}, volume = {13}, year = {2024}, month = {2024 Mar 12}, abstract = {

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

}, keywords = {Animals, Anterior Thalamic Nuclei, Cerebral Cortex, Cues, Gyrus Cinguli, Mammals, Mice, Rotation}, issn = {2050-084X}, doi = {10.7554/eLife.82952}, author = {van der Goes, Marie-Sophie H and Voigts, Jakob and Newman, Jonathan P and Toloza, Enrique H S and Brown, Norma J and Murugan, Pranav and Harnett, Mark T} } @article {69568, title = {DaCapo: a modular deep learning framework for scalable 3D image segmentation}, journal = {arXiv}, year = {2024}, month = {2024 Aug 05}, abstract = {

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

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

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

}, doi = {10.1101/2024.09.05.611438}, url = {https://www.doi.org/10.1101/2024.09.05.611438}, author = {Ackerman, David and Avetissian, Emma and Bleck, Christopher K. E. and Bogovic, John A. and Innerberger, Michael and Korff, Wyatt and Li, Wei-Ping and Lu, Zhiyuan and Petruncio, Alyson and Preibisch, Stephan and Qiu, Wei and Jeff L Rhoades and Saalfeld, Stephan and Silva, Malan and Trautman, Eric T. and Vorimo, Rebecca and Weigel, Aubrey and Yu, Zhiheng and Zubov, Yurii and ,} } @article {69693, title = {Development of a novel methodology for ascertaining scientific opinion and extent of agreement.}, journal = {PLoS One}, volume = {19}, year = {2024}, month = {2024 Dec 06}, pages = {e0313541}, abstract = {

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

}, keywords = {COVID-19, Humans, Public Opinion, SARS-CoV-2, Science, Surveys and Questionnaires}, issn = {1932-6203}, doi = {10.1371/journal.pone.0313541}, author = {Vickers, Peter and Adamo, Ludovica and Alfano, Mark and Clark, Cory and Cresto, Eleonora and Cui, He and Dang, Haixin and Dells{\'e}n, Finnur and Dupin, Nathalie and Gradowski, Laura and Graf, Simon and Guevara, Aline and Hallap, Mark and Hamilton, Jesse and Hardey, Mariann and Helm, Paula and Landrum, Asheley and Levy, Neil and Machery, Edouard and Mills, Sarah and Muller, Se{\'a}n and Sheppard, Joanne and N K, Shinod and Slater, Matthew and Stegenga, Jacob and Strandin, Henning and Stuart, Michael T and Sweet, David and Tasdan, Ufuk and Taylor, Henry and Towler, Owen and Tulodziecki, Dana and Tworek, Heidi and Wallbank, Rebecca and Wiltsche, Harald and Mitchell Finnigan, Samantha} } @article {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 {69701, title = {Distinct roles of ascorbic acid in extracellular vesicles and free form: Implications for metabolism and oxidative stress in presymptomatic Huntington{\textquoteright}s disease.}, journal = {Free Radic Biol Med}, volume = {227}, year = {2024}, month = {2024 Dec 09}, pages = {521-535}, abstract = {

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

}, issn = {1873-4596}, doi = {10.1016/j.freeradbiomed.2024.12.001}, url = {https://doi.org/10.1016/j.freeradbiomed.2024.12.001}, author = {Beltr{\'a}n, Felipe A and Torres-D{\'\i}az L, Leandro and Troncoso-Escudero, Paulina and Villalobos-Gonz{\'a}lez, Juan and Mayorga-Weber, Gonzalo and Lara, Marcelo and Covarrubias-Pinto, Adriana and Valdivia, Sharin and Vicencio, Isidora and Papic, Eduardo and Paredes-Mart{\'\i}nez, Carolina and Silva-Janu{\`a}rio, Mara E and Rojas, Alejandro and daSilva, Luis L P and Court, Felipe and Rosas-Arellano, Abraham and B{\'a}tiz, Luis Federico and Rojas, Patricio and Rivera, Francisco J and Castro, Maite A} } @article {69692, title = {Elevated IL-22 as a result of stress-induced gut leakage suppresses septal neuron activation to ameliorate anxiety-like behavior.}, journal = {Immunity}, year = {2024}, month = {2024 Dec 04}, pages = {S1074-7613(24)00523-5}, abstract = {

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

}, issn = {1097-4180}, doi = {10.1016/j.immuni.2024.11.008}, author = {Xia, Mengyu and Lu, Junmei and Lan, Jiabin and Teng, Teng and Shiao, Rani and Sun, Hongbin and Jin, Zheyu and Liu, Xueer and Wang, Jie and Wu, Hongyan and Wang, Changchun and Yi, Han and Qi, Qingqing and Li, Jixi and Schneeberger, Marc and Shen, Wei and Lu, Boxun and Chen, Lei and Ilanges, Anoj and Zhou, Xinyu and Yu, Xiaofei} } @article {69145, title = {Epigenetic priming of embryonic lineages in the mammalian epiblast}, journal = {bioRxiv}, year = {2024}, month = {2024 Jan 11}, abstract = {

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

}, doi = {10.1101/2024.01.11.575188}, url = {https://doi.org/10.1101/2024.01.11.575188}, author = {Miquel Sendra and Katie McDole and Daniel Jimenez-Carretero and Juan de Dios Hourcade and Susana Temi{\~n}o and L{\'e}o Guignard and Philipp J Keller and F{\'a}tima S{\'a}nchez-Cabo and Jorge N. Dom{\'\i}nguez and Miguel Torres} } @article {69515, title = {Exploration and exploitation are flexibly balanced during local search in flies}, journal = {bioRxiv}, year = {2024}, month = {2024 Jun 28}, abstract = {

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

}, doi = {10.1101/2024.06.26.600764}, url = {https://www.biorxiv.org/content/early/2024/06/28/2024.06.26.600764}, author = {Goldschmidt, Dennis and Guo, Yipei and Chitnis, Shivam S and Christoforou, Christina and Turner-Evans, Dan and Ribeiro, Carlos and Hermundstad, Ann M and Jayaraman, Vivek and Haberkern, Hannah} } @article {69649, title = {FITM2 deficiency results in ER lipid accumulation, ER stress, and reduced apolipoprotein B lipidation and VLDL triglyceride secretion in vitro and in mouse liver.}, journal = {Mol Metab}, year = {2024}, month = {2024 Oct 18}, pages = {102048}, abstract = {

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

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

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

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

}, issn = {2212-8778}, doi = {10.1016/j.molmet.2024.102048}, url = {https://doi.org/10.1016/j.molmet.2024.102048}, author = {Wang, Haizhen and Nikain, Cyrus and Fortounas, Konstantinos I and Amengual, Jaime and Tufanli, Ozlem and La Forest, Maxwell and Yu, Yong and Wang, Meng C and Watts, Russell and Lehner, Richard and Qiu, Yunping and Cai, Min and Kurland, Irwin J and Goldberg, Ira J and Rajan, Sujith and Hussain, M Mahmood and Brodsky, Jeffrey L and Fisher, Edward A} } @article {69108, title = {A fluorogenic complementation tool kit for interrogating lipid droplet-organelle interaction}, journal = {J. Cell Biol.}, volume = {223}, year = {2024}, month = {2024 Jul 01}, pages = {e202311126}, abstract = {

Contact sites between lipid droplets and other organelles are essential for cellular lipid and energy homeostasis upon metabolic demands. Detection of these contact sites at the nanometer scale over time in living cells is challenging. We developed a tool kit for detecting contact sites based on fluorogen-activated bimolecular complementation at CONtact sites, FABCON, using a reversible, low-affinity split fluorescent protein, splitFAST. FABCON labels contact sites with minimal perturbation to organelle interaction. Via FABCON, we quantitatively demonstrated that endoplasmic reticulum (ER)- and mitochondria (mito)-lipid droplet contact sites are dynamic foci in distinct metabolic conditions, such as during lipid droplet biogenesis and consumption. An automated analysis pipeline further classified individual contact sites into distinct subgroups based on size, likely reflecting differential regulation and function. Moreover, FABCON is generalizable to visualize a repertoire of organelle contact sites including ER-mito. Altogether, FABCON reveals insights into the dynamic regulation of lipid droplet-organelle contact sites and generates new hypotheses for further mechanistical interrogation during metabolic regulation.

}, doi = {10.1083/jcb.202311126 }, url = {https://doi.org/10.1083/jcb.202311126 }, author = {Xiao Li and Rico Gamuyao and Ming-Lun Wu and Woo Jung Cho and Nathan B. Kurtz and Sharon V. King and R.A. Petersen and Daniel R. Stabley and Caleb Lindow and Leslie Climer and Abbas Shirinifard and Francesca Ferrara and Robert E. Throm and Camenzind G. Robinson and Alex Carisey and Alison G. Tebo and Chi-Lun Chang} } @article {69658, title = {The Fly Disco: Hardware and software for optogenetics and fine-grained fly behavior analysis}, journal = {bioRxiv}, year = {2024}, month = {2024 Nov 04}, abstract = {

In the fruit fly, Drosophila melanogaster, connectome data and genetic tools provide a unique opportunity to study complex behaviors including navigation, mating, aggression, and grooming in an organism with a tractable nervous system of 140,000 neurons. Here we present the Fly Disco, a flexible system for high quality video collection, optogenetic manipulation, and fine-grained behavioral analysis of freely walking and socializing fruit fly groups. The data collection hardware and software automates the collection of videos synced to programmable optogenetic stimuli. Key pipeline features include behavioral analysis based on trajectories of 21 keypoints and optogenetic-specific summary statistics and data visualization. We created the multifly dataset for pose estimation that includes 9701 examples enriched in complex behaviors. All hardware designs, software, and the multifly dataset are freely available.

}, doi = {10.1101/2024.11.04.621948}, url = {https://doi.org/10.1101/2024.11.04.621948}, author = {Robie, Alice A and Taylor, Adam L and Schretter, Catherine E and Kabra, Mayank and Branson, Kristin} } @article {69680, title = {Global Neuron Shape Reasoning with Point Affinity Transformers}, journal = {bioRxiv}, year = {2024}, month = {2024 Nov 24}, abstract = {

Connectomics is a subfield of neuroscience that aims to map the brain{\textquoteright}s intricate wiring diagram. Accurate neuron segmentation from microscopy volumes is essential for automating connectome reconstruction. However, current state-of-the-art algorithms use image-based convolutional neural networks that are limited to local neuron shape context. Thus, we introduce a new framework that reasons over global neuron shape with a novel point affinity transformer. Our framework embeds a (multi-)neuron point cloud into a fixed-length feature set from which we can decode any point pair affinities, enabling clustering neuron point clouds for automatic proofreading. We also show that the learned feature set can easily be mapped to a contrastive embedding space that enables neuron type classification using a simple KNN classifier. Our approach excels in two demanding connectomics tasks: proofreading segmentation errors and classifying neuron types. Evaluated on three benchmark datasets derived from state-of-the-art connectomes, our method outperforms point transformers, graph neural networks, and unsupervised clustering baselines.

}, doi = {10.1101/2024.11.24.625067}, url = {https://doi.org/10.1101/2024.11.24.625067}, author = {Troidl, Jakob and Knittel, Johannes and Li, Wanhua and Zhan, Fangneng and Pfister, Hanspeter and Turaga, Srinivas} } @article {69250, title = {High-Performance Genetically Encoded Green Fluorescent Biosensors for Intracellular l-Lactate.}, journal = {ACS Central Science}, volume = {10}, year = {2024}, month = {2024 Feb 28}, pages = {402-416}, abstract = {

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

}, issn = {2374-7943}, doi = {10.1021/acscentsci.3c01250}, author = {Hario, Saaya and Le, Giang N T and Sugimoto, Hikaru and Takahashi-Yamashiro, Kei and Nishinami, Suguru and Toda, Hirofumi and Li, Selene and Marvin, Jonathan S and Kuroda, Shinya and Drobizhev, Mikhail and Terai, Takuya and Nasu, Yusuke and Campbell, Robert E} } @article {68831, title = {Host ZCCHC3 blocks HIV-1 infection and production by a dual mechanism}, journal = {iScience}, year = {2024}, month = {05/2024}, abstract = {

Most mammalian cells prevent viral infection and proliferation by expressing various restriction factors and sensors that activate the immune system. While anti-human immunodeficiency virus type 1 (HIV-1) host restriction factors have been identified, most of them are antagonized by viral proteins. This has severely hindered their development in anti-HIV-1 therapy. Here, we describe CCHC-type zinc-finger-containing protein 3 (ZCCHC3) as a novel anti-HIV-1 factor that is not antagonized by viral proteins. ZCCHC3 suppresses production of HIV-1 and other retroviruses. We show that ZCCHC3 acts by binding to Gag nucleocapsid protein via zinc-finger motifs. This prevents interaction between the Gag nucleocapsid protein and viral genome and results in production of genome-deficient virions. ZCCHC3 also binds to the long terminal repeat on the viral genome via the middle-folded domain, sequestering the viral genome to P-bodies, which leads to decreased viral replication and production. Such a dual antiviral mechanism is distinct from that of any other known host restriction factors. Therefore, ZCCHC3 is a novel potential target in anti-HIV-1 therapy.

}, doi = {10.1101/2023.06.14.544911}, url = {https://doi.org/10.1101/2023.06.14.544911}, author = {Binbin Yi and Yuri L Tanaka and Hidetaka Kosako and Erika P Butlertanaka and Prabuddha Sengupta and Jennifer Lippincott-Schwartz and Akatsuki Saito and Shige H. Yoshimura} } @article {68969, title = {iATPSnFR2: a high dynamic range fluorescent sensor for monitoring intracellular ATP}, journal = {Proc Natl Acad Sci U S A}, year = {2024}, month = {2024 May 21}, abstract = {

We developed a significantly improved genetically encoded quantitative adenosine triphosphate (ATP) sensor to provide real-time dynamics of ATP levels in subcellular compartments. iATPSnFR2 is a variant of iATPSnFR1, a previously developed sensor that has circularly permuted super-folder GFP inserted between the ATP-binding helices of the\ ε-subunit of a bacterial F0-F1\ ATPase. Optimizing the linkers joining the two domains resulted in a \~{} 5-6 fold improvement in the dynamic range compared to the previous generation sensor, with excellent discrimination against other analytes and affinity variants varying from 4 μM to 500 μM. A chimeric version of this sensor fused to either the HaloTag protein or a suitably spectrally separated fluorescent protein, provides a ratiometric readout allowing comparisons of ATP across cellular regions. Subcellular targeting of the sensor to nerve terminals reveals previously uncharacterized single synapse metabolic signatures, while targeting to the mitochondrial matrix allowed direct quantitative probing of oxidative phosphorylation dynamics.

}, doi = {10.1073/pnas.2314604121 }, author = {Jonathan S. Marvin and Alexandros C. Kokotos and Mukesh Kumar and Camila Pulido and Ariana N. Tkachuk and Jocelyn Shuxin Yao and Timothy A. Brown and Timothy A. Ryan} } @article {69420, title = {An interphase actin wave promotes mitochondrial content mixing and organelle homeostasis.}, journal = {Nat Commun}, volume = {15}, year = {2024}, month = {2024 May 07}, pages = {3793}, abstract = {

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

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

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

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

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

}, doi = {10.1101/2024.05.28.595700}, url = {https://www.biorxiv.org/content/early/2024/06/01/2024.05.28.595700}, author = {Yang, Shang and Heckmann, Johanna and Taha, Abdulla and Gao, Shiqiang and Steinke, Stephan and Hust, Michael and Pr{\"u}{\ss}, Harald and Furukawa, Hiro and Geis, Christian and Heckmann, Manfred and Yu-Strzelczyk, Jing} } @article {69372, title = {Leptin Activated Hypothalamic BNC2 Neurons Acutely Suppress Food Intake}, journal = {bioRxiv}, year = {2024}, month = {12 Apr 2024}, abstract = {

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

}, doi = {10.1101/2024.01.25.577315}, url = {https://www.biorxiv.org/content/early/2024/04/12/2024.01.25.577315}, author = {Han L. Tan and Luping Yin and Yuqi Tan and Jessica Ivanov and Kaja Plucinska and Anoj Ilanges and Brian R. Herb and Putianqi Wang and Christin Kosse and Paul Cohen and Dayu Lin and Jeffrey M. Friedman} } @article {69226, title = {Live-cell imaging powered by computation.}, journal = {Nature Reviews Molecular Cell Biology}, year = {2024}, month = {2024 Feb 20}, abstract = {

The proliferation of microscopy methods for live-cell imaging offers many new possibilities for users but can also be challenging to navigate. The prevailing challenge in live-cell fluorescence microscopy is capturing intra-cellular dynamics while preserving cell viability. Computational methods can help to address this challenge and are now shifting the boundaries of what is possible to capture in living systems. In this Review, we discuss these computational methods focusing on artificial intelligence-based approaches that can be layered on top of commonly used existing microscopies as well as hybrid methods that integrate computation and microscope hardware. We specifically discuss how computational approaches can improve the signal-to-noise ratio, spatial resolution, temporal resolution and multi-colour capacity of live-cell imaging.

}, issn = {1471-0080}, doi = {10.1038/s41580-024-00702-6}, author = {Shroff, Hari and Testa, Ilaria and Jug, Florian and Manley, Suliana} } @article {68956, title = {Magnetic voluntary head-fixation in transgenic rats enables lifetime imaging of hippocampal neurons}, journal = {Nat. Commun.}, year = {2024}, month = {2024 May 16}, abstract = {

The precise neural mechanisms within the brain that contribute to the remarkable lifetime persistence of memory remain unknown. Existing techniques to record neurons in animals are either unsuitable for longitudinal recording from the same cells or make it difficult for animals to express their full naturalistic behavioral repertoire. We present a magnetic voluntary head-fixation system that provides stable optical access to the brain during complex behavior. Compared to previous systems that used mechanical restraint, there are no moving parts and animals can engage and disengage entirely at will. This system is failsafe, easy for animals to use and reliable enough to allow long-term experiments to be routinely performed. Together with a novel two-photon fluorescence collection scheme that increases two-photon signal and a transgenic rat line that stably expresses the calcium sensor GCaMP6f in dorsal CA1, we are able to track and record activity from the same hippocampal neurons, during behavior, over a large fraction of animals{\textquoteright} lives.

}, doi = {10.1038/s41467-024-48505-9}, author = {P. D. Rich and S. Y. Thiberge and B. B. Scott and C. Guo and D. G. Tervo and C. D. Brody and A. Y. Karpova and N. D. Daw and D. W. Tank} } @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 {69622, title = {A modular chemigenetic calcium indicator for multiplexed in vivo functional imaging.}, journal = {Nat Methods}, year = {2024}, month = {2024 Sep 20}, abstract = {

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

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

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

}, issn = {1097-4172}, doi = {10.1016/j.cell.2024.06.022}, author = {Xu, Chuanyun and Li, Zhuoran and Lyu, Cheng and Hu, Yixin and McLaughlin, Colleen N and Wong, Kenneth Kin Lam and Xie, Qijing and Luginbuhl, David J and Li, Hongjie and Udeshi, Namrata D and Svinkina, Tanya and Mani, D R and Han, Shuo and Li, Tongchao and Li, Yang and Guajardo, Ricardo and Ting, Alice Y and Carr, Steven A and Li, Jiefu and Luo, Liqun} } @article {69301, title = {Motor neurons generate pose-targeted movements via proprioceptive sculpting.}, journal = {Nature}, year = {2024}, month = {2024 Mar 20}, abstract = {

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

}, issn = {1476-4687}, doi = {10.1038/s41586-024-07222-5}, author = {Gorko, Benjamin and Siwanowicz, Igor and Close, Kari and Christoforou, Christina and Hibbard, Karen L and Kabra, Mayank and Lee, Allen and Park, Jin-Yong and Li, Si Ying and Chen, Alex B and Namiki, Shigehiro and Chen, Chenghao and Tuthill, John C and Bock, Davi D and Rouault, Herv{\'e} and Branson, Kristin and Ihrke, Gudrun and Huston, Stephen J} } @article {69542, title = {Neural circuit basis of placebo pain relief.}, journal = {Nature}, year = {2024}, month = {2024 Jul 24}, abstract = {

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

}, issn = {1476-4687}, doi = {10.1038/s41586-024-07816-z}, author = {Chen, Chong and Niehaus, Jesse K and Dinc, Fatih and Huang, Karen L and Barnette, Alexander L and Tassou, Adrien and Shuster, S Andrew and Wang, Lihua and Lemire, Andrew and Menon, Vilas and Ritola, Kimberly and Hantman, Adam and Zeng, Hongkui and Schnitzer, Mark J and Scherrer, Gr{\'e}gory} } @article {69045, title = {Neural-circuit basis of song preference learning in fruit flies}, journal = {iScience}, volume = {27}, year = {2024}, month = {2024 Jul 19}, abstract = {

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

}, doi = {10.1016/j.isci.2024.110266}, url = {https://doi.org/10.1016/j.isci.2024.110266}, author = {Keisuke Imoto and Yuki Ishikawa and Yoshinori Aso and Jan Funke and Ryoya Tanaka and Azusa Kamikouchi} } @article {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 {69010, title = {Olfactory sensory neuron population expansions influence projection neuron adaptation and enhance odour tracking}, journal = {Nat Commun}, volume = {15}, year = {2024}, month = {2024 Aug 15}, pages = {7041}, abstract = {

The evolutionary expansion of sensory neuron populations detecting important environmental cues is widespread, but functionally enigmatic. We investigated this phenomenon through comparison of homologous olfactory pathways of Drosophila melanogaster and its close relative Drosophila sechellia, an extreme specialist for Morinda citrifolia noni fruit. D. sechellia has evolved species-specific expansions in select, noni-detecting olfactory sensory neuron (OSN) populations, through multigenic changes. Activation and inhibition of defined proportions of neurons demonstrate that OSN number increases contribute to stronger, more persistent, noni-odour tracking behaviour. These expansions result in increased synaptic connections of sensory neurons with their projection neuron (PN) partners, which are conserved in number between species. Surprisingly, having more OSNs does not lead to greater odour-evoked PN sensitivity or reliability. Rather, pathways with increased sensory pooling exhibit reduced PN adaptation, likely through weakened lateral inhibition. Our work reveals an unexpected functional impact of sensory neuron population expansions to explain ecologically-relevant, species-specific behaviour.

}, doi = {10.1038/s41467-024-50808-w}, url = {https://doi.org/10.1038/s41467-024-50808-w}, author = {Suguru Takagi and Liliane Abuin and S. David Stupski and J. Roman Arguello and Lucia Prieto-Godino and David L. Stern and Steeve Cruchet and Raquel {\'A}lvarez-Oca{\~n}a and Carl F. R. Wienecke and Floris van Breugel and Thomas O. Auer and Richard Benton} } @article {69139, title = {Petascale pipeline for precise alignment of images from serial section electron microscopy.}, journal = {Nature Communications}, volume = {15}, year = {2024}, month = {2024 Jan 04}, pages = {289}, abstract = {

The reconstruction of neural circuits from serial section electron microscopy (ssEM) images is being accelerated by automatic image segmentation methods. Segmentation accuracy is often limited by the preceding step of aligning 2D section images to create a 3D image stack. Precise and robust alignment in the presence of image artifacts is challenging, especially as datasets are attaining the petascale. We present a computational pipeline for aligning ssEM images with several key elements. Self-supervised convolutional nets are trained via metric learning to encode and align image pairs, and they are used to initialize iterative fine-tuning of alignment. A procedure called vector voting increases robustness to image artifacts or missing image data. For speedup the series is divided into blocks that are distributed to computational workers for alignment. The blocks are aligned to each other by composing transformations with decay, which achieves a global alignment without resorting to a time-consuming global optimization. We apply our pipeline to a whole fly brain dataset, and show improved accuracy relative to prior state of the art. We also demonstrate that our pipeline scales to a cubic millimeter of mouse visual cortex. Our pipeline is publicly available through two open source Python packages.

}, keywords = {Animals, Brain, Image Processing, Computer-Assisted, Imaging, Three-Dimensional, Mice, Microscopy, Electron}, issn = {2041-1723}, doi = {10.1038/s41467-023-44354-0}, author = {Popovych, Sergiy and Macrina, Thomas and Kemnitz, Nico and Castro, Manuel and Nehoran, Barak and Jia, Zhen and Bae, J Alexander and Mitchell, Eric and Mu, Shang and Trautman, Eric T and Saalfeld, Stephan and Li, Kai and Seung, H Sebastian} } @article {69404, title = {Recognising the importance and impact of Imaging Scientists: Global guidelines for establishing career paths within core facilities}, journal = {J Microsc}, year = {2024}, month = {2024 May 01}, abstract = {

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

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

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

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

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

}, keywords = {Animals, Calcium, Cell Physiological Phenomena, Cells, Coloring Agents, Gene Expression Profiling, Protein Interaction Domains and Motifs, Staining and Labeling, Zebrafish}, issn = {1095-9203}, doi = {10.1126/science.adg0812}, author = {Huppertz, Magnus-Carsten and Wilhelm, Jonas and Grenier, Vincent and Schneider, Martin W and Falt, Tjalda and Porzberg, Nicola and Hausmann, David and Hoffmann, Dirk C and Hai, Ling and Tarnawski, Miroslaw and Pino, Gabriela and Slanchev, Krasimir and Kolb, Ilya and Acuna, Claudio and Fenk, Lisa M and Baier, Herwig and Hiblot, Julien and Johnsson, Kai} } @article {69253, title = {Sensory neuron population expansion enhances odor tracking without sensitizing projection neurons}, journal = {bioRxiv}, year = {2024}, month = {2024 Feb 28}, abstract = {

The evolutionary expansion of sensory neuron populations detecting important environmental cues is widespread, but functionally enigmatic. We investigated this phenomenon through comparison of homologous neural pathways of Drosophila melanogaster and its close relative Drosophila sechellia, an extreme specialist for Morinda citrifolia noni fruit. D. sechellia has evolved species-specific expansions in select, noni-detecting olfactory sensory neuron (OSN) populations, through multigenic changes. Activation and inhibition of defined proportions of neurons demonstrate that OSN population increases contribute to stronger, more persistent, noni-odor tracking behavior. These sensory neuron expansions result in increased synaptic connections with their projection neuron (PN) partners, which are conserved in number between species. Surprisingly, having more OSNs does not lead to greater odor-evoked PN sensitivity or reliability. Rather, pathways with increased sensory pooling exhibit reduced PN adaptation, likely through weakened lateral inhibition. Our work reveals an unexpected functional impact of sensory neuron expansions to explain ecologically-relevant, species-specific behavior.

}, doi = {10.1101/2023.09.15.556782}, url = {https://www.biorxiv.org/content/early/2024/02/28/2023.09.15.556782}, author = {Suguru Takagi and Gizem Sancer and Liliane Abuin and S. David Stupski and J. Roman Arguello and Lucia L. Prieto-Godino and David L. Stern and Steeve Cruchet and Raquel {\'A}lvarez-Oca{\~n}a and Carl F. R. Wienecke and Floris van Breugel and James M. Jeanne and Thomas O. Auer and Richard Benton} } @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 {68655, title = {Smart Lattice Light Sheet Microscopy for imaging rare and complex cellular events}, journal = {Nature Methods}, volume = {21}, year = {2024}, month = {2024 Feb 01}, pages = {301-310}, abstract = {

Light sheet microscopes enable rapid, high-resolution imaging of biological specimens; however, biological processes span a variety of spatiotemporal scales. Moreover, long-term phenotypes are often instigated by rare or fleeting biological events that are difficult to capture with a single imaging modality and constant imaging parameters. To overcome this limitation, we present smartLLSM, a microscope that incorporates AI-based instrument control to autonomously switch between epifluorescent inverted imaging and lattice light sheet microscopy. We apply this technology to two major scenarios. First, we demonstrate that the instrument provides population-level statistics of cell cycle states across thousands of cells on a coverslip. Second, we show that by using real-time image feedback to switch between imaging modes, the instrument autonomously captures multicolor 3D datasets or 4D time-lapse movies of dividing cells at rates that dramatically exceed human capabilities. Quantitative image analysis on high-content + high-throughput datasets reveal kinetochore and chromosome dynamics in dividing cells and determine the effects of drug perturbation on cells in specific mitotic stages. This new methodology enables efficient detection of rare events within a heterogeneous cell population and records these processes with high spatiotemporal 4D imaging over statistically significant replicates.

}, doi = {10.1038/s41592-023-02126-0}, url = {https://doi.org/10.1038/s41592-023-02126-0}, author = {Yu Shi and Jimmy S. Tabet and Daniel E. Milkie and Timothy A. Daugird and Chelsea Q. Yang and Andrea Giovannucci and Wesley R. Legant} } @article {69296, title = {Social state gates vision using three circuit mechanisms in Drosophila}, journal = {Nature}, year = {2024}, month = {2024 Nov 20}, abstract = {

Animals are often bombarded with visual information and must prioritize specific visual features based on their current needs. The neuronal circuits that detect and relay visual features have been well studied. Much less is known about how an animal adjusts its visual attention as its goals or environmental conditions change. During social behaviours, flies need to focus on nearby flies. Here we study how the flow of visual information is altered when female Drosophila enter an aggressive state. From the connectome, we identify three state-dependent circuit motifs poised to modify the response of an aggressive female to fly-sized visual objects: convergence of excitatory inputs from neurons conveying select visual features and internal state; dendritic disinhibition of select visual feature detectors; and a switch that toggles between two visual feature detectors. Using cell-type-specific genetic tools, together with behavioural and neurophysiological analyses, we show that each of these circuit motifs is used during female aggression. We reveal that features of this same switch operate in male Drosophila during courtship pursuit, suggesting that disparate social behaviours may share circuit mechanisms. Our study provides a compelling example of using the connectome to infer circuit mechanisms that underlie dynamic processing of sensory signals.

}, doi = {10.1038/s41586-024-08255-6}, url = {https://doi.org/10.1038/s41586-024-08255-6}, author = {Catherine E. Schretter and Tom Hindmarsh Sten and Nathan Klapoetke and Mei Shao and Aljoscha Nern and Marisa Dreher and Daniel Bushey and Alice A. Robie and Adam L. Taylor and Kristin M. Branson and Adriane Otopalik and Vanessa Ruta and Gerald M. Rubin} } @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 {69502, title = {Steering From the Rear: Coordination of Central Pattern Generators Underlying Navigation by Ascending Interneurons}, journal = {bioRxiv}, year = {2024}, month = {2024 Jun 17}, abstract = {

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

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

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

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

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

}, issn = {0028-0836}, doi = {10.1038/s41586-024-07937-5}, url = {https://www.nature.com/articles/s41586-024-07937-5https://www.nature.com/articles/s41586-024-07937-5.pdfhttps://www.nature.com/articles/s41586-024-07937-5.pdfhttps://www.nature.com/articles/s41586-024-07937-5}, author = {Hadas, Ron and Rubinstein, Hernan and Mittnenzweig, Markus and Mayshar, Yoav and Ben-Yair, Raz and Cheng, Saifeng and Aguilera-Castrejon, Alejandro and Reines, Netta and Orenbuch, Ayelet-Hashahar and Lifshitz, Aviezer and Chen, Dong-Yuan and Elowitz, Michael B. and Zernicka-Goetz, Magdalena and Hanna, Jacob H. and Tanay, Amos and Stelzer, Yonatan} } @article {69144, title = {Transforming chemigenetic bimolecular fluorescence complementation systems into chemical dimerizers using chemistry.}, journal = {bioRxiv}, year = {2024}, month = {2024 Jan 01}, abstract = {

Chemigenetic tags are versatile labels for fluorescence microscopy that combine some of the advantages of genetically encoded tags with small molecule fluorophores. The Fluorescence Activating and absorbance Shifting Tags (FASTs) bind a series of highly fluorogenic and cell-permeable chromophores. Furthermore, FASTs can be used in complementation-based systems for detecting or inducing protein-protein interactions, depending on the exact FAST protein variant chosen. In this study, we systematically explore substitution patterns on FAST fluorogens and generate a series of fluorogens that bind to FAST variants, thereby activating their fluorescence. This effort led to the discovery of a novel fluorogen with superior properties, as well as a fluorogen that transforms splitFAST systems into a fluorogenic dimerizer, eliminating the need for additional protein engineering.

}, doi = {10.1101/2023.12.30.573644}, url = {https://doi.org/10.1101/2023.12.30.573644}, author = {Pratik Kumar and Alina Gutu and Amelia Waring and Timothy A. Brown and Luke D. Lavis and Alison G. Tebo} } @article {69491, title = {Transport and Organization of Individual Vimentin Filaments Within Dense Networks Revealed by Single Particle Tracking and 3D FIB-SEM}, journal = {bioRxiv}, year = {2024}, month = {2024 Jun 10}, abstract = {

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

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

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

}, doi = {10.1101/2024.11.04.621531}, url = {https://doi.org/10.1101/2024.11.04.621531}, author = {Kivimaki, Sarah E. and Dempsey, Samantha and Tani, Julia M. and Camper, Colette and Hicklin, Ian K. and Blaby-Haas, Crysten E. and Brown, Anne M and Melville, Stephen} } @article {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 {69679, title = {Whole-body simulation of realistic fruit fly locomotion with deep reinforcement learning}, journal = {bioRxiv}, year = {2024}, month = {2024 Nov 22}, abstract = {

The body of an animal influences how the nervous system produces behavior. Therefore, detailed modeling of the neural control of sensorimotor behavior requires a detailed model of the body. Here we contribute an anatomically-detailed biomechanical whole-body model of the fruit fly Drosophila melanogaster in the MuJoCo physics engine. Our model is general-purpose, enabling the simulation of diverse fly behaviors, both on land and in the air. We demonstrate the generality of our model by simulating realistic locomotion, both flight and walking. To support these behaviors, we have extended MuJoCo with phenomenological models of fluid forces and adhesion forces. Through data-driven end-to-end reinforcement learning, we demonstrate that these advances enable the training of neural network controllers capable of realistic locomotion along complex trajectories based on high-level steering control signals. We demonstrate the use of visual sensors and the re-use of a pre-trained general-purpose flight controller by training the model to perform visually guided flight tasks. Our project is an open-source platform for modeling neural control of sensorimotor behavior in an embodied context.Competing Interest StatementThe authors have declared no competing interest.

}, doi = {10.1101/2024.03.11.584515}, url = {https://www.biorxiv.org/content/early/2024/11/22/2024.03.11.584515}, author = {Vaxenburg, Roman and Siwanowicz, Igor and Merel, Josh and Robie, Alice A. and Morrow, Carmen and Novati, Guido and Stefanidi, Zinovia and Both, Gert-Jan and Card, Gwyneth M. and Reiser, Michael B. and Botvinick, Matthew M. and Branson, Kristin M. and Tassa, Yuval and Turaga, Srinivas C.} } @article {68807, title = {Architecture and dynamics of a desmosome-endoplasmic reticulum complex.}, journal = {Nature Cell Biology}, volume = {25}, year = {2023}, month = {2023 Jun 16}, pages = {823-835}, abstract = {

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

}, keywords = {Cytoskeleton, Desmosomes, Endoplasmic Reticulum, Intermediate Filaments, Keratins}, issn = {1476-4679}, doi = {10.1038/s41556-023-01154-4}, author = {Bharathan, Navaneetha Krishnan and Giang, William and Hoffman, Coryn L and Aaron, Jesse S and Khuon, Satya and Chew, Teng-Leong and Preibisch, Stephan and Trautman, Eric T and Heinrich, Larissa and Bogovic, John and Bennett, Davis and Ackerman, David and Park, Woohyun and Petruncio, Alyson and Weigel, Aubrey V and Saalfeld, Stephan and Wayne Vogl, A and Stahley, Sara N and Kowalczyk, Andrew P} } @article {67907, title = {Ascending neurons convey behavioral state to integrative sensory and action selection centers in the brain}, journal = {Nature Neuroscience}, year = {2023}, month = {2023 Mar 31}, abstract = {

Knowledge of one{\textquoteright}s own behavioral state{\textemdash}whether one is walking, grooming, or resting{\textemdash}is critical for contextualizing sensory cues including interpreting visual motion and tracking odor sources. Additionally, awareness of one{\textquoteright}s own posture is important to avoid initiating destabilizing or physically impossible actions. Ascending neurons (ANs), interneurons in the vertebrate spinal cord or insect ventral nerve cord (VNC) that project to the brain, may provide such high-fidelity behavioral state signals. However, little is known about what ANs encode and where they convey signals in any brain. To address this gap, we performed a large-scale functional screen of AN movement encoding, brain targeting, and motor system patterning in the adult fly,\ Drosophila melanogaster. Using a new library of AN sparse driver lines, we measured the functional properties of 247 genetically-identifiable ANs by performing two-photon microscopy recordings of neural activity in tethered, behaving flies. Quantitative, deep network-based neural and behavioral analyses revealed that ANs nearly exclusively encode high-level behaviors{\textemdash}primarily walking as well as resting and grooming{\textemdash}rather than low-level joint or limb movements. ANs that convey self-motion{\textemdash}resting, walking, and responses to gust-like puff stimuli{\textemdash}project to the brain{\textquoteright}s anterior ventrolateral protocerebrum (AVLP), a multimodal, integrative sensory hub, while those that encode discrete actions{\textemdash}eye grooming, turning, and proboscis extension{\textemdash}project to the brain{\textquoteright}s gnathal ganglion (GNG), a locus for action selection. The structure and polarity of AN projections within the VNC are predictive of their functional encoding and imply that ANs participate in motor computations while also relaying state signals to the brain. Illustrative of this are ANs that temporally integrate proboscis extensions over tens-of-seconds, likely through recurrent interconnectivity. Thus, in line with long-held theoretical predictions, ascending populations convey high-level behavioral state signals almost exclusively to brain regions implicated in sensory feature contextualization and action selection.

}, doi = {10.1038/s41593-023-01281-z}, author = {Chin-Lin Chen and Florian Aymanns and Ryo Minegishi and Victor D. V. Matsuda and Nicolas Talabot and Semih G{\"u}nel and Barry J. Dickson and Pavan Ramdya} } @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 {68714, title = {The big warp: Registration of disparate retinal imaging modalities and an example overlay of ultrawide-field photos and en-face OCTA images.}, journal = {PLoS One}, volume = {18}, year = {2023}, month = {2023 Apr 25}, pages = {e0284905}, abstract = {

PURPOSE: To develop an algorithm and scripts to combine disparate multimodal imaging modalities and show its use by overlaying en-face optical coherence tomography angiography (OCTA) images and Optos ultra-widefield (UWF) retinal images using the Fiji (ImageJ) plugin BigWarp.

METHODS: Optos UWF images and Heidelberg en-face OCTA images were collected from various patients as part of their routine care. En-face OCTA images were generated and ten (10) images at varying retinal depths were exported. The Fiji plugin BigWarp was used to transform the Optos UWF image onto the en-face OCTA image using matching reference points in the retinal vasculature surrounding the macula. The images were then overlayed and stacked to create a series of ten combined Optos UWF and en-face OCTA images of increasing retinal depths. The first algorithm was modified to include two scripts that automatically aligned all the en-face OCTA images.

RESULTS: The Optos UWF image could easily be transformed to the en-face OCTA images using BigWarp with common vessel branch point landmarks in the vasculature. The resulting warped Optos image was then successfully superimposed onto the ten Optos UWF images. The scripts more easily allowed for automatic overlay of the images.

CONCLUSIONS: Optos UWF images can be successfully superimposed onto en-face OCTA images using freely available software that has been applied to ocular use. This synthesis of multimodal imaging may increase their potential diagnostic value. Script A is publicly available at https://doi.org/10.6084/m9.figshare.16879591.v1 and Script B is available at https://doi.org/10.6084/m9.figshare.17330048.

}, keywords = {Fluorescein Angiography, Fundus Oculi, Humans, Retina, Retinal Vessels, Tomography, Optical Coherence}, issn = {1932-6203}, doi = {10.1371/journal.pone.0284905}, author = {Thuma, Tobin B T and Bogovic, John A and Gunton, Kammi B and Jimenez, Hiram and Negreiros, Bernardo and Pulido, Jose S} } @article {68709, title = {BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets.}, journal = {Nature Methods}, volume = {20}, year = {2023}, month = {2023 Jun 01}, abstract = {

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

}, issn = {1548-7105}, doi = {10.1038/s41592-023-01848-5}, author = {Manubens-Gil, Linus and Zhou, Zhi and Chen, Hanbo and Ramanathan, Arvind and Liu, Xiaoxiao and Liu, Yufeng and Bria, Alessandro and Gillette, Todd and Ruan, Zongcai and Yang, Jian and Radojevi{\'c}, Miroslav and Zhao, Ting and Cheng, Li and Qu, Lei and Liu, Siqi and Bouchard, Kristofer E and Gu, Lin and Cai, Weidong and Ji, Shuiwang and Roysam, Badrinath and Wang, Ching-Wei and Yu, Hongchuan and Sironi, Amos and Iascone, Daniel Maxim and Zhou, Jie and Bas, Erhan and Conde-Sousa, Eduardo and Aguiar, Paulo and Li, Xiang and Li, Yujie and Nanda, Sumit and Wang, Yuan and Muresan, Leila and Fua, Pascal and Ye, Bing and He, Hai-Yan and Staiger, Jochen F and Peter, Manuel and Cox, Daniel N and Simonneau, Michel and Oberlaender, Marcel and Jefferis, Gregory and Ito, Kei and Gonzalez-Bellido, Paloma and Kim, Jinhyun and Rubel, Edwin and Cline, Hollis T and Zeng, Hongkui and Nern, Aljoscha and Chiang, Ann-Shyn and Yao, Jianhua and Roskams, Jane and Livesey, Rick and Stevens, Janine and Liu, Tianming and Dang, Chinh and Guo, Yike and Zhong, Ning and Tourassi, Georgia and Hill, Sean and Hawrylycz, Michael and Koch, Christof and Meijering, Erik and Ascoli, Giorgio A and Peng, Hanchuan} } @article {68933, title = {Biomechanical origins of proprioceptor feature selectivity and topographic maps in the Drosophila leg.}, journal = {Neuron}, year = {2023}, month = {2023 Aug 04}, abstract = {

Our ability to sense and move our bodies relies on proprioceptors, sensory neurons that detect mechanical forces within the body. Different subtypes of proprioceptors detect different kinematic features, such as joint position, movement, and vibration, but the mechanisms that underlie proprioceptor feature selectivity remain poorly understood. Using single-nucleus RNA sequencing (RNA-seq), we found that proprioceptor subtypes in the Drosophila leg lack differential expression of mechanosensitive ion channels. However, anatomical reconstruction of the proprioceptors and connected tendons revealed major biomechanical differences between subtypes. We built a model of the proprioceptors and tendons that identified a biomechanical mechanism for joint angle selectivity and predicted the existence of a topographic map of joint angle, which we confirmed using calcium imaging. Our findings suggest that biomechanical specialization is a key determinant of proprioceptor feature selectivity in Drosophila. More broadly, the discovery of proprioceptive maps reveals common organizational principles between proprioception and other topographically organized sensory systems.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2023.07.009}, author = {Mamiya, Akira and Sustar, Anne and Siwanowicz, Igor and Qi, Yanyan and Lu, Tzu-Chiao and Gurung, Pralaksha and Chen, Chenghao and Phelps, Jasper S and Kuan, Aaron T and Pacureanu, Alexandra and Lee, Wei-Chung Allen and Li, Hongjie and Mhatre, Natasha and Tuthill, John C} } @article {68647, title = {Brain-wide neural activity underlying memory-guided movement}, journal = {bioRxiv}, year = {2023}, month = {2023 Mar 02}, abstract = {

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

}, doi = {10.1101/2023.03.01.530520}, url = {https://doi.org/10.1101/2023.03.01.530520}, author = {Susu Chen and Yi Liu and Ziyue Wang and Jennifer Colonell and Liu D. Liu and Han Hou and Nai-Wen Tien and Tim Wang and Timothy Harris and Shaul Druckmann and Nuo Li and Karel Svoboda} } @article {69018, title = {Complete human day 14 post-implantation embryo models from na{\"\i}ve ES cells}, journal = {Nature}, year = {2023}, month = {09/2023}, abstract = {

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

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

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

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

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

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

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

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

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

}, keywords = {Astrocytes, Blood-Brain Barrier, Brain, Female, Humans, Male, Parkinson Disease, Substantia Nigra}, issn = {2041-1723}, doi = {10.1038/s41467-023-39038-8}, author = {de Rus Jacquet, A and Alpaugh, M and Denis, H L and Tancredi, J L and Boutin, M and Decaestecker, J and Beauparlant, C and Herrmann, L and Saint-Pierre, M and Parent, M and Droit, A and Breton, S and Cicchetti, F} } @article {69007, title = {Driver lines for studying associative learning in Drosophila}, journal = {bioRxiv}, year = {2023}, month = {2023 Sep 16}, abstract = {

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

}, doi = {https://doi.org/10.7554/elife.94168.4}, url = {https://doi.org/10.7554/elife.94168.4 }, author = {Yichun Shuai and Megan Sammons and Gabriella Sterne and Karen Hibbard and He Yang and Ching-Po Yang and Claire Managan and Igor Siwanowicz and Tzumin Lee and Gerald M. Rubin and Glenn Turner and Yoshinori Aso} } @article {69054, title = {Effects of stochastic coding on olfactory discrimination in flies and mice.}, journal = {PLoS Biology}, volume = {21}, year = {2023}, month = {2023 Oct 31}, pages = {e3002206}, abstract = {

Sparse coding can improve discrimination of sensory stimuli by reducing overlap between their representations. Two factors, however, can offset sparse coding{\textquoteright}s benefits: similar sensory stimuli have significant overlap and responses vary across trials. To elucidate the effects of these 2 factors, we analyzed odor responses in the fly and mouse olfactory regions implicated in learning and discrimination-the mushroom body (MB) and the piriform cortex (PCx). We found that neuronal responses fall along a continuum from extremely reliable across trials to extremely variable or stochastic. Computationally, we show that the observed variability arises from noise within central circuits rather than sensory noise. We propose this coding scheme to be advantageous for coarse- and fine-odor discrimination. More reliable cells enable quick discrimination between dissimilar odors. For similar odors, however, these cells overlap and do not provide distinguishing information. By contrast, more unreliable cells are decorrelated for similar odors, providing distinguishing information, though these benefits only accrue with extended training with more trials. Overall, we have uncovered a conserved, stochastic coding scheme in vertebrates and invertebrates, and we identify a candidate mechanism, based on variability in a winner-take-all (WTA) inhibitory circuit, that improves discrimination with training.

}, keywords = {Animals, Diptera, Learning, Mice, Odorants, Olfactory Pathways, Olfactory Perception, Smell}, issn = {1545-7885}, doi = {10.1371/journal.pbio.3002206}, author = {Srinivasan, Shyam and Daste, Simon and Modi, Mehrab N and Turner, Glenn C and Fleischmann, Alexander and Navlakha, Saket} } @article {68465, title = {Facemap: a framework for modeling neural activity based on orofacial tracking}, journal = {Nature Neuroscience}, year = {2023}, month = {2023 Nov 20}, abstract = {

Recent studies in mice have shown that orofacial behaviors drive a large fraction of neural activity across the brain. To understand the nature and function of these signals, we need better computational models to characterize the behaviors and relate them to neural activity. Here we developed Facemap, a framework consisting of a keypoint tracking algorithm and a deep neural network encoder for predicting neural activity. We used the Facemap keypoints as input for the deep neural network to predict the activity of \~{}50,000 simultaneously-recorded neurons and in visual cortex we doubled the amount of explained variance compared to previous methods. Our keypoint tracking algorithm was more accurate than existing pose estimation tools, while the inference speed was several times faster, making it a powerful tool for closed-loop behavioral experiments. The Facemap tracker was easy to adapt to data from new labs, requiring as few as 10 annotated frames for near-optimal performance. We used Facemap to find that the neuronal activity clusters which were highly driven by behaviors were more spatially spread-out across cortex. We also found that the deep keypoint features inferred by the model had time-asymmetrical state dynamics that were not apparent in the raw keypoint data. In summary, Facemap provides a stepping stone towards understanding the function of the brainwide neural signals and their relation to behavior.

}, doi = {10.1038/s41593-023-01490-6}, url = {https://doi.org/10.1038/s41593-023-01490-6}, author = {Atika Syeda and Lin Zhong and Renee Tung and Will Long and Marius Pachitariu and Carsen Stringer} } @article {68665, title = {Fast and sensitive GCaMP calcium indicators for imaging neural populations.}, journal = {Nature}, year = {2023}, month = {2023 Mar 15}, abstract = {

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

}, issn = {1476-4687}, doi = {10.1038/s41586-023-05828-9}, author = {Zhang, Yan and Rozsa, Marton and Liang, Yajie and Bushey, Daniel and Wei, Ziqiang and Zheng, Jihong and Reep, Daniel and Broussard, Gerard Joey and Tsang, Arthur and Tsegaye, Getahun and Narayan, Sujatha and Obara, Christopher J and Lim, Jing-Xuan and Patel, Ronak and Zhang, Rongwei and Ahrens, Misha B and Turner, Glenn C and Wang, Samuel S-H and Korff, Wyatt L and Schreiter, Eric R and Svoboda, Karel and Hasseman, Jeremy P and Kolb, Ilya and Looger, Loren L} } @article {68790, title = {Flexible specificity of memory in Drosophila depends on a comparison between choices}, journal = {eLife}, year = {2023}, month = {2023 Jun 15}, abstract = {

Memory guides behavior across widely varying environments and must therefore be both sufficiently specific and general. A memory too specific will be useless in even a slightly different environment, while an overly general memory may lead to suboptimal choices. Animals successfully learn to both distinguish between very similar stimuli and generalize across cues. Rather than forming memories that strike a balance between specificity and generality,\ Drosophila\ can flexibly categorize a given stimulus into different groups depending on the options available. We asked how this flexibility manifests itself in the well-characterized learning and memory pathways of the fruit fly. We show that flexible categorization in neuronal activity as well as behavior depends on the order and identity of the perceived stimuli. Our results identify the neural correlates of flexible stimulus-categorization in the fruit fly.

}, doi = {10.7554/eLife.80923}, url = {https://doi.org/10.7554/eLife.80923}, author = {Mehrab N Modi and Adithya Rajagopalan and Herv{\'e} Rouault and Yoshinori Aso and Glenn C Turner} } @article {68772, title = {Glutamate indicators with improved activation kinetics and localization for imaging synaptic transmission.}, journal = {Nature Methods}, volume = {20}, year = {2023}, month = {2023 Jun 01}, abstract = {

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

}, issn = {1548-7105}, doi = {10.1038/s41592-023-01863-6}, author = {Aggarwal, Abhi and Liu, Rui and Chen, Yang and Ralowicz, Amelia J and Bergerson, Samuel J and Tomaska, Filip and Mohar, Boaz and Hanson, Timothy L and Hasseman, Jeremy P and Reep, Daniel and Tsegaye, Getahun and Yao, Pantong and Ji, Xiang and Kloos, Marinus and Walpita, Deepika and Patel, Ronak and Mohr, Manuel A and Tillberg, Paul W and Looger, Loren L and Marvin, Jonathan S and Hoppa, Michael B and Konnerth, Arthur and Kleinfeld, David and Schreiter, Eric R and Podgorski, Kaspar} } @article {68595, title = {Hacking brain development to test models of sensory coding}, journal = {bioRxiv}, year = {2023}, month = {2023 Jan 26}, abstract = {

Animals can discriminate myriad sensory stimuli but can also generalize from learned experience. You can probably distinguish the favorite teas of your colleagues while still recognizing that all tea pales in comparison to coffee. Tradeoffs between detection, discrimination, and generalization are inherent at every layer of sensory processing. During development, specific quantitative parameters are wired into perceptual circuits and set the playing field on which plasticity mechanisms play out. A primary goal of systems neuroscience is to understand how material properties of a circuit define the logical operations{\textemdash} computations--that it makes, and what good these computations are for survival. A cardinal method in biology{\textemdash}and the mechanism of evolution--is to change a unit or variable within a system and ask how this affects organismal function. Here, we make use of our knowledge of developmental wiring mechanisms to modify hard-wired circuit parameters in the\ Drosophila melanogaster\ mushroom body and assess the functional and behavioral consequences. By altering the number of expansion layer neurons (Kenyon cells) and their dendritic complexity, we find that input number, but not cell number, tunes odor selectivity. Simple odor discrimination performance is maintained when Kenyon cell number is reduced and augmented by Kenyon cell expansion.

}, doi = {10.1101/2023.01.25.525425}, url = {https://doi.org/10.1101/2023.01.25.525425}, author = {Maria Ahmed and Adithya E. Rajagopalan and Yijie Pan and Ye Li and Donnell L. Williams and Erik A. Pedersen and Manav Thakral and Angelica Previero and Kari C. Close and Christina P. Christoforou and Dawen Cai and Glenn C. Turner and Josephine Clowney} } @article {68837, title = {Input density tunes Kenyon cell sensory responses in the Drosophila mushroom body.}, journal = {Current Biology}, year = {2023}, month = {2023 Jun 20}, abstract = {

The ability to discriminate sensory stimuli with overlapping features is thought to arise in brain structures called expansion layers, where neurons carrying information about sensory features make combinatorial connections onto a much larger set of cells. For 50 years, expansion coding has been a prime topic of theoretical neuroscience, which seeks to explain how quantitative parameters of the expansion circuit influence sensory sensitivity, discrimination, and generalization. Here, we investigate the developmental events that produce the quantitative parameters of the arthropod expansion layer, called the mushroom body. Using Drosophila melanogaster as a model, we employ genetic and chemical tools to engineer changes to circuit development. These allow us to produce living animals with hypothesis-driven variations on natural expansion layer wiring parameters. We then test the functional and behavioral consequences. By altering the number of expansion layer neurons (Kenyon cells) and their dendritic complexity, we find that input density, but not cell number, tunes neuronal odor selectivity. Simple odor discrimination behavior is maintained when the Kenyon cell number is reduced and augmented by Kenyon cell number expansion. Animals with increased input density to each Kenyon cell show increased overlap in Kenyon cell odor responses and become worse at odor discrimination tasks.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2023.05.064}, author = {Ahmed, Maria and Rajagopalan, Adithya E and Pan, Yijie and Li, Ye and Williams, Donnell L and Pedersen, Erik A and Thakral, Manav and Previero, Angelica and Close, Kari C and Christoforou, Christina P and Cai, Dawen and Turner, Glenn C and Clowney, E Josephine} } @article {68886, title = {Input density tunes Kenyon cell sensory responses in the Drosophila mushroom body.}, journal = {Current Biology}, volume = {33}, year = {2023}, month = {2023 Jul 10}, pages = {2742-2760.e12}, abstract = {

The ability to discriminate sensory stimuli with overlapping features is thought to arise in brain structures called expansion layers, where neurons carrying information about sensory features make combinatorial connections onto a much larger set of cells. For 50 years, expansion coding has been a prime topic of theoretical neuroscience, which seeks to explain how quantitative parameters of the expansion circuit influence sensory sensitivity, discrimination, and generalization. Here, we investigate the developmental events that produce the quantitative parameters of the arthropod expansion layer, called the mushroom body. Using Drosophila melanogaster as a model, we employ genetic and chemical tools to engineer changes to circuit development. These allow us to produce living animals with hypothesis-driven variations on natural expansion layer wiring parameters. We then test the functional and behavioral consequences. By altering the number of expansion layer neurons (Kenyon cells) and their dendritic complexity, we find that input density, but not cell number, tunes neuronal odor selectivity. Simple odor discrimination behavior is maintained when the Kenyon cell number is reduced and augmented by Kenyon cell number expansion. Animals with increased input density to each Kenyon cell show increased overlap in Kenyon cell odor responses and become worse at odor discrimination tasks.

}, keywords = {Animals, Drosophila, Drosophila melanogaster, Drosophila Proteins, Mushroom Bodies, Neurons, Odorants}, issn = {1879-0445}, doi = {10.1016/j.cub.2023.05.064}, author = {Ahmed, Maria and Rajagopalan, Adithya E and Pan, Yijie and Li, Ye and Williams, Donnell L and Pedersen, Erik A and Thakral, Manav and Previero, Angelica and Close, Kari C and Christoforou, Christina P and Cai, Dawen and Turner, Glenn C and Clowney, E Josephine} } @article {69053, title = {Lactate biosensors for spectrally and spatially multiplexed fluorescence imaging.}, journal = {Nature Communications}, volume = {14}, year = {2023}, month = {2023 Oct 27}, pages = {6598}, abstract = {

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

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

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

}, doi = {10.1101/2023.02.01.526664}, url = {https://doi.org/10.1101/2023.02.01.526664}, author = {Eric M. Trautmann and Janis K. Hesse and Gabriel M. Stine and Ruobing Xia and Shude Zhu and Daniel J. O{\textquoteright}Shea and Bill Karsh and Jennifer Colonell and Frank F. Lanfranchi and Saurabh Vyas and Andrew Zimnik and Natalie A. Steinmann and Daniel A. Wagenaar and Alexandru Andrei and Carolina Mora Lopez and John O{\textquoteright}Callaghan and Jan Putzeys and Bogdan C. Raducanu and Marleen Welkenhuysen and Mark Churchland and Tirin Moore and Michael Shadlen and Krishna Shenoy and Doris Tsao and Barundeb Dutta and Timothy Harris} } @article {68564, title = {Local shape descriptors for neuron segmentation.}, journal = {Nature Methods}, volume = {20}, year = {2023}, month = {2023 Feb 01}, pages = {295-303}, abstract = {

We present an auxiliary learning task for the problem of neuron segmentation in electron microscopy volumes. The auxiliary task consists of the prediction of local shape descriptors (LSDs), which we combine with conventional voxel-wise direct neighbor affinities for neuron boundary detection. The shape descriptors capture local statistics about the neuron to be segmented, such as diameter, elongation, and direction. On a study comparing several existing methods across various specimen, imaging techniques, and resolutions, auxiliary learning of LSDs consistently increases segmentation accuracy of affinity-based methods over a range of metrics. Furthermore, the addition of LSDs promotes affinity-based segmentation methods to be on par with the current state of the art for neuron segmentation (flood-filling networks), while being two orders of magnitudes more efficient-a critical requirement for the processing of future petabyte-sized datasets.

}, issn = {1548-7105}, doi = {10.1038/s41592-022-01711-z}, author = {Sheridan, Arlo and Nguyen, Tri M and Deb, Diptodip and Lee, Wei-Chung Allen and Saalfeld, Stephan and Turaga, Srinivas C and Manor, Uri and Funke, Jan} } @article {69009, title = {Low-latency extracellular spike assignment for high-density electrodes at single-neuron resolution}, journal = {bioRxiv}, year = {2023}, month = {2023 Sep 15}, abstract = {

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

}, doi = {10.1101/2023.09.14.557854}, url = {https://doi.org/10.1101/2023.09.14.557854}, author = {Chongxi Lai and Dohoung Kim and Brian Lustig and Shinsuke Tanaka and Brian Barbarits and Lakshmi Narayan and Jennifer Colonell and Ole Paulsen and Albert K. Lee and Timothy D. Harris} } @article {68791, title = {Mapping memories: pulse-chase labeling reveals AMPA receptor dynamics during memory formation.}, journal = {bioRxiv}, year = {2023}, month = {2023 May 29}, abstract = {

A tool to map changes in synaptic strength during a defined time window could provide powerful insights into the mechanisms governing learning and memory. We developed a technique, Extracellular Protein Surface Labeling in Neurons (EPSILON), to map α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) insertion\ in vivo\ by pulse-chase labeling of surface AMPARs with membrane-impermeable dyes. This approach allows for single-synapse resolution maps of plasticity in genetically targeted neurons during memory formation. We investigated the relationship between synapse-level and cell-level memory encodings by mapping synaptic plasticity and cFos expression in hippocampal CA1 pyramidal cells upon contextual fear conditioning (CFC). We observed a strong correlation between synaptic plasticity and cFos expression, suggesting a synaptic mechanism for the association of cFos expression with memory engrams. The EPSILON technique is a useful tool for mapping synaptic plasticity and may be extended to investigate trafficking of other transmembrane proteins.

}, doi = {10.1101/2023.05.26.541296}, url = {https://doi.org/10.1101/2023.05.26.541296}, author = {Doyeon Kim and Pojeong Park and Xiuyuan Li and J. David Wong Campos and He Tian and Eric M. Moult and Jonathan B. Grimm and Luke Lavis and Adam E. Cohen} } @article {68700, title = {Mental navigation and telekinesis with a hippocampal map-based brain-machine interface}, journal = {bioRxiv}, year = {2023}, month = {2023 Apr 10}, abstract = {

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

}, doi = {10.1101/2023.04.07.536077}, url = {https://doi.org/10.1101/2023.04.07.536077}, author = {Chongxi Lai and Shinsuke Tanaka and Timothy D. Harris and Albert K. Lee} } @article {68149, title = {Metamorphosis of memory circuits in Drosophila reveal a strategy for evolving a larval brain.}, journal = {eLife}, year = {2023}, month = {2023 Jan 25}, abstract = {

Insects like\ Drosophila\ produce a second brain adapted to the form and behavior of a larva. Neurons for both larval and adult brains are produced by the same stem cells (neuroblasts) but the larva possesses only the earliest born neurons produced from each. To understand how a functional larval brain is made from this reduced set of neurons, we examined the origins and metamorphic fates of the neurons of the larval and adult mushroom body circuits. The adult mushroom body core is built sequentially of γ Kenyon cells, that form a medial lobe, followed by α{\textquoteright}β{\textquoteright}, and αβ Kenyon cells that form additional medial lobes and two vertical lobes. Extrinsic input (MBINs) and output (MBONs) neurons divide this core into computational compartments. The larval mushroom body contains only γ neurons. Its medial lobe compartments are roughly homologous to those of the adult and same MBONs are used for both. The larval vertical lobe, however, is an analogous {\textquotedblleft}facsimile{\textquotedblright} that uses a larval-specific branch on the γ neurons to make up for the missing α{\textquoteright}β{\textquoteright}, and αβ neurons. The extrinsic cells for the facsimile are early-born neurons that trans-differentiate to serve a mushroom body function in the larva and then shift to other brain circuits in the adult. These findings are discussed in the context of the evolution of a larval brain in insects with complete metamorphosis.

}, doi = {10.7554/eLife.80594}, url = {https://doi.org/110.7554/eLife.80594}, author = {James W. Truman and Jacquelyn Price and Rosa L. Miyares and Tzumin Lee} } @article {68836, title = {Method To Diversify Cyanine Chromophore Functionality Enables Improved Biomolecule Tracking and Intracellular Imaging.}, journal = {Journal of the American Chemical Society}, volume = {145}, year = {2023}, month = {2023 Jun 27}, pages = {14647{\textendash}14659}, abstract = {

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

}, issn = {1520-5126}, doi = {10.1021/jacs.3c01765}, author = {Usama, Syed Muhammad and Marker, Sierra C and Li, Dong-Hao and Caldwell, Donald R and Stroet, Marcus and Patel, Nimit L and Tebo, Alison G and Hernot, Sophie and Kalen, Joseph D and Schnermann, Martin} } @article {69127, title = {Model-Based Inference of Synaptic Plasticity Rules}, journal = {bioRxiv}, year = {2023}, month = {2023 Dec 12}, abstract = {

Understanding learning through synaptic plasticity rules in the brain is a grand challenge for neuroscience. Here we introduce a novel computational framework for inferring plasticity rules from experimental data on neural activity trajectories and behavioral learning dynamics. Our methodology parameterizes the plasticity function to provide theoretical interpretability and facilitate gradient-based optimization. For instance, we use Taylor series expansions or multilayer perceptrons to approximate plasticity rules, and we adjust their parameters via gradient descent over entire trajectories to closely match observed neural activity and behavioral data. Notably, our approach can learn intricate rules that induce long nonlinear time-dependencies, such as those incorporating postsynaptic activity and current synaptic weights. We validate our method through simulations, accurately recovering established rules, like Oja{\textquoteright}s, as well as more complex hypothetical rules incorporating reward-modulated terms. We assess the resilience of our technique to noise and, as a tangible application, apply it to behavioral data from\ Drosophila\ during a probabilistic reward-learning experiment. Remarkably, we identify an active forgetting component of reward learning in flies that enhances the predictive accuracy of previous models. Overall, our modeling framework provides an exciting new avenue to elucidate the computational principles governing synaptic plasticity and learning in the brain.

}, doi = {10.1101/2023.12.11.571103}, url = {https://doi.org/10.1101/2023.12.11.571103}, author = {Yash Mehta and Danil Tyulmankov and Adithya E. Rajagopalan and Glenn C. Turner and James E. Fitzgerald and Jan Funke} } @article {68783, title = {Modulation of calcium signaling {\textquotedblleft}on demand{\textquotedblright} to decipher the molecular mechanisms responsible for primary aldosteronism}, journal = {Archives of Cardiovascular Diseases Supplements}, volume = {15}, year = {2023}, month = {2023 May 01}, pages = {188}, abstract = {

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

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

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

}, doi = {10.7554/eLife.84262}, url = {https://doi.org/10.7554/eLife.84262}, author = {Yuhan Wang and Sabine Krabbe and Mark Eddison and Fredrick E. Henry and Greg Fleishman and Andrew L. Lemire and Lihua Wang and Wyatt Korff and Paul W. Tillberg and Andreas L{\"u}thi and Scott M. Sternson} } @article {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 {68635, title = {OME-Zarr: a cloud-optimized bioimaging file format with international community support.}, journal = {Histochemistry and Cell Biology}, volume = {160}, year = {2023}, month = {2023 Feb 25}, pages = {223-251}, abstract = {

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

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

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

}, issn = {0002-7863}, doi = {10.1021/jacs.3c0527310.1021/jacs.3c05273}, url = {https://pubs.acs.org/doi/10.1021/jacs.3c05273}, author = {Grimm, Jonathan B. and Tkachuk, Ariana N. and Patel, Ronak and Hennigan, S. Thomas and Gutu, Alina and Dong, Peng and Gandin, Valentina and Osowski, Anastasia M. and Holland, Katie L. and Liu, Zhe J. and Brown, Timothy A. and Lavis, Luke D.} } @article {68631, title = {Phase separation of Hippo signalling complexes.}, journal = {EMBO Journal}, volume = {42}, year = {2023}, month = {2023 Feb 20}, pages = {e112863}, abstract = {

The Hippo pathway was originally discovered to control tissue growth in Drosophila and includes the Hippo kinase (Hpo; MST1/2 in mammals), scaffold protein Salvador (Sav; SAV1 in mammals) and the Warts kinase (Wts; LATS1/2 in mammals). The Hpo kinase is activated by binding to Crumbs-Expanded (Crb-Ex) and/or Merlin-Kibra (Mer-Kib) proteins at the apical domain of epithelial cells. Here we show that activation of Hpo also involves the formation of supramolecular complexes with properties of a biomolecular condensate, including concentration dependence and\ sensitivity to starvation, macromolecular crowding, or 1,6-hexanediol treatment. Overexpressing Ex or Kib induces formation of micron-scale Hpo condensates in the cytoplasm, rather than at the apical membrane. Several Hippo pathway components contain unstructured low-complexity domains and purified Hpo-Sav complexes undergo phase separation in\ vitro. Formation of Hpo condensates is conserved in human cells. We propose that apical Hpo kinase activation occurs in phase separated "signalosomes" induced by clustering of upstream pathway components.

}, issn = {1460-2075}, doi = {10.15252/embj.2022112863}, author = {Bonello, Teresa T and Cai, Danfeng and Fletcher, Georgina C and Wiengartner, Kyler and Pengilly, Victoria and Lange, Kimberly S and Liu, Zhe and Lippincott-Schwartz, Jennifer and Kavran, Jennifer M and Thompson, Barry J} } @article {68770, title = {The power of peer networking for improving STEM faculty job applications: a successful pilot programme.}, journal = {Proceedings. Biological Sciences}, volume = {290}, year = {2023}, month = {2023 Apr 26}, pages = {20230124}, abstract = {

To attain a faculty position, postdoctoral fellows submit job applications that require considerable time and effort to produce. Although mentors and colleagues review these applications, postdocs rarely receive iterative feedback from reviewers with the breadth of expertise typically found on an academic search committee. To address this gap, we describe an international peer-reviewing programme for postdocs across disciplines to receive reciprocal, iterative feedback on faculty applications. A participant survey revealed that nearly all participants would recommend the programme to others. Furthermore, our programme was more likely to attract postdocs who struggled to find mentoring, possibly because of their identity as a woman or member of an underrepresented population in STEM or because they changed fields. Between 2018 and 2021, our programme provided nearly 150 early career academics with a diverse and supportive community of peer mentors during the difficult search for a faculty position and continues to do so today. As the transition from postdoc to faculty represents the largest {\textquoteright}leak{\textquoteright} in the academic pipeline, implementation of similar programmes by universities or professional societies would provide psycho-social support necessary to prevent attrition of individuals from underrepresented populations as well as increase the chances of success for early career academics in their search for independence.

}, keywords = {Faculty, Female, Humans, Mentoring, Mentors, Peer Group, Pilot Projects}, issn = {1471-2954}, doi = {10.1098/rspb.2023.0124}, author = {Guardia, Carlos M and Kane, Erin and Tebo, Alison G and Sanders, Anna A W M and Kaya, Devrim and Grogan, Kathleen E} } @article {68537, title = {Reward expectations direct learning and drive operant matching in Drosophila}, journal = {Proceedings of the National Academy of Sciences of the U.S.A.}, volume = {120}, year = {2023}, month = {2023 Sep 26}, pages = {e2221415120}, abstract = {

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

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

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

}, doi = {10.1101/2023.09.25.559373}, url = {https://doi.org/10.1101/2023.09.25.559373}, author = {Brad K Hulse and Angel Stanoev and Daniel B Turner-Evans and Johannes Seelig and Vivek Jayaraman} } @article {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 {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 {68666, title = {Social association predicts immunological similarity in rewilded mice}, journal = {bioRxiv}, year = {2023}, month = {2023 Mar 16}, abstract = {

Environmental influences on immune phenotypes are well-documented, but our understanding of which elements of the environment affect immune systems, and how, remains vague. Behaviors, including socializing with others, are central to an individual{\textquoteright}s interaction with its environment. We tracked behavior of rewilded laboratory mice of three inbred strains in outdoor enclosures and examined contributions of behavior, including social associations, to immune phenotypes. We found that the more associated two individuals were, the more similar their immune phenotypes were. Social association was particularly predictive of similar memory T and B cell profiles and was more influential than sibling relationships or worm infection status. These results highlight the importance of social networks for immune phenotype and reveal important immunological correlates of social life.

}, doi = {10.1101/2023.03.15.532825}, url = {https://doi.org/10.1101/2023.03.15.532825}, author = {A. E. Downie and O. Oyesola and R. S. Barre and Q. Caudron and Y.-H. Chen and E. J. Dennis and R. Garnier and K. Kiwanuka and A. Menezes and D. J. Navarrete and O. Mondrag{\'o}n-Palomino and J. B. Saunders and C. K. Tokita and K. Zaldana and K. Cadwell and P. Loke and A. L. Graham} } @article {69125, title = {Spatiotemporal-social association predicts immunological similarity in rewilded mice.}, journal = {Science Advances}, volume = {9}, year = {2023}, month = {2023 Dec 22}, pages = {eadh8310}, abstract = {

Environmental influences on immune phenotypes are well-documented, but our understanding of which elements of the environment affect immune systems, and how, remains vague. Behaviors, including socializing with others, are central to an individual{\textquoteright}s interaction with its environment. We therefore tracked behavior of rewilded laboratory mice of three inbred strains in outdoor enclosures and examined contributions of behavior, including associations measured from spatiotemporal co-occurrences, to immune phenotypes. We found extensive variation in individual and social behavior among and within mouse strains upon rewilding. In addition, we found that the more associated two individuals were, the more similar their immune phenotypes were. Spatiotemporal association was particularly predictive of similar memory T and B cell profiles and was more influential than sibling relationships or shared infection status. These results highlight the importance of shared spatiotemporal activity patterns and/or social networks for immune phenotype and suggest potential immunological correlates of social life.

}, keywords = {Animals, Immune System, Mice, Phenotype, Social Behavior}, issn = {2375-2548}, doi = {10.1126/sciadv.adh8310}, author = {Downie, Alexander E and Oyesola, Oyebola and Barre, Ramya S and Caudron, Quentin and Chen, Ying-Han and Dennis, Emily J and Garnier, Romain and Kiwanuka, Kasalina and Menezes, Arthur and Navarrete, Daniel J and Mondrag{\'o}n-Palomino, Octavio and Saunders, Jesse B and Tokita, Christopher K and Zaldana, Kimberly and Cadwell, Ken and Loke, P{\textquoteright}ng and Graham, Andrea L} } @article {68888, title = {Stochastic coding: a conserved feature of odor representations and its implications for odor discrimination}, journal = {bioRxiv}, year = {2023}, month = {2023 Jun 29}, abstract = {

Sparse coding is thought to improve discrimination of sensory stimuli by reducing overlap between their representations. Two factors, however, can offset sparse coding{\textquoteright}s advantages. Similar sensory stimuli have significant overlap, and responses vary across trials. To elucidate the effect of these two factors, we analyzed odor responses in the fly and mouse olfactory regions implicated in learning and discrimination --- the Mushroom Body (MB) and the Piriform Cortex (PCx). In both species, we show that neuronal responses fall along a continuum from extremely reliable across trials to extremely variable or stochastic. Computationally, we show that the range of observed variability arises from probabilistic synapses in inhibitory feedback connections within central circuits rather than sensory noise, as is traditionally assumed. We propose this coding scheme to be advantageous for coarse- and fine-odor discrimination. More reliable cells enable quick discrimination between dissimilar odors. For similar odors, however, these cells overlap, and do not provide distinguishing information. By contrast, more unreliable cells are decorrelated for similar odors, providing distinguishing information, though this requires extended training with more trials. Overall, we have uncovered a stochastic coding scheme that is conserved in vertebrates and invertebrates, and we identify a candidate mechanism, based on variability in a winner-take-all inhibitory circuit, that improves discrimination with training.

}, doi = {10.1101/2023.06.27.546757}, url = {https://doi.org/10.1101/2023.06.27.546757}, author = {Shyam Srinivasan and Simon Daste and Mehrab Modi and Glenn Turner and Alexander Fleischmann and Saket Navlakha} } @article {68517, title = {Structured cerebellar connectivity supports resilient pattern separation.}, journal = {Nature}, volume = {613}, year = {2023}, month = {2023 Jan 01}, pages = {543-549}, abstract = {

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

}, issn = {1476-4687}, doi = {10.1038/s41586-022-05471-w}, author = {Nguyen, Tri M and Thomas, Logan A and Jeff L Rhoades and Ricchi, Ilaria and Yuan, Xintong Cindy and Sheridan, Arlo and Hildebrand, David G C and Funke, Jan and Regehr, Wade G and Lee, Wei-Chung Allen} } @article {68566, title = {Synaptic gradients transform object location to action.}, journal = {Nature}, volume = {613}, year = {2023}, month = {2023 Jan 04}, pages = {534-42}, abstract = {

To survive, animals must convert sensory information into appropriate behaviours. Vision is a common sense for locating ethologically relevant stimuli and guiding motor responses. How circuitry converts object location in retinal coordinates to movement direction in body coordinates remains largely unknown. Here we show through behaviour, physiology, anatomy and connectomics in Drosophila that visuomotor transformation occurs by conversion of topographic maps formed by the dendrites of feature-detecting visual projection neurons (VPNs) into synaptic weight gradients of VPN outputs onto central brain neurons. We demonstrate how this gradient motif transforms the anteroposterior location of a visual looming stimulus into the fly{\textquoteright}s directional escape. Specifically, we discover that two neurons postsynaptic to a looming-responsive VPN type promote opposite takeoff directions. Opposite synaptic weight gradients onto these neurons from looming VPNs in different visual field regions convert localized looming threats into correctly oriented escapes. For a second looming-responsive VPN type, we demonstrate graded responses along the dorsoventral axis. We show that this synaptic gradient motif generalizes across all 20 primary VPN cell types and most often arises without VPN axon topography. Synaptic gradients may thus be a general mechanism for conveying spatial features of sensory information into directed motor outputs.

}, issn = {1476-4687}, doi = {10.1038/s41586-022-05562-8}, author = {Dombrovski, Mark and Peek, Martin Y and Park, Jin-Yong and Vaccari, Andrea and Sumathipala, Marissa and Morrow, Carmen and Breads, Patrick and Zhao, Arthur and Kurmangaliyev, Yerbol Z and Sanfilippo, Piero and Rehan, Aadil and Polsky, Jason and Alghailani, Shada and Tenshaw, Emily and Namiki, Shigehiro and Zipursky, S Lawrence and Card, Gwyneth M} } @article {68801, title = {Systematic annotation of a complete adult male Drosophila nerve cord connectome reveals principles of functional organisation}, journal = {bioRxiv}, year = {2023}, month = {2023 Jun 06}, abstract = {

Our companion paper (Takemura et al., 2023) introduces the first completely proofread connectome of the nerve cord of an animal that can walk or fly. The base connectome consists of neuronal morphologies and the connections between them. However, in order to efficiently navigate and understand this connectome, it is crucial to have a system of annotations that systematically categorises and names neurons, linking them to the existing literature. In this paper we describe the comprehensive annotation of the VNC connectome, first by a system of hierarchical coarse annotations, then by grouping left-right and serially homologous neurons and eventually by defining systematic cell types for the intrinsic interneurons and sensory neurons of the VNC; descending and motor neurons are typed in (Cheong et al., 2023). We assign a sensory modality to over 5000 sensory neurons, cluster them by connectivity, and identify serially homologous cell types and a layered organisation likely corresponding to peripheral topography. We identify the developmental neuroblast of origin of the large majority of VNC neurons and confirm that (in most cases) all secondary neurons of each hemilineage express a single neurotransmitter. Neuroblast hemilineages are serially repeated along the segments of the nerve cord and generally exhibit consistent hemilineage-to-hemilineage connectivity across neuromeres, supporting the idea that hemilineages are a major organisational feature of the VNC. We also find that more than a third of individual neurons belong to serially homologous cell types, which were crucial for identifying motor neurons and sensory neurons across leg neuropils. Categorising interneurons by their neuropil innervation patterns provides an additional organisation axis. Over half of the intrinsic neurons of the VNC appear dedicated to the legs, with the majority restricted to single leg neuropils; in contrast, inhibitory interneurons connecting different leg neuropils, especially those crossing the midline, appear rarer than anticipated by standard models of locomotor circuitry. Our annotations are being released as part of the neuprint.janelia.org web application and also serve as the basis of programmatic analysis of the connectome through dedicated tools that we describe in this paper.

}, doi = {10.1101/2023.06.05.543407}, url = {https://doi.org/10.1101/2023.06.05.543407}, author = {Elizabeth C Marin and Billy J Morris and Tomke Stuerner and Andrew S Champion and Dominik Krzeminski and Griffin Badalamente and Marina Gkantia and Imaan F M Tamimi and Siqi Fang and Sung Soo Moon and Han S J Cheong and Feng Li and Philipp Schlegel and Stuart Berg and FlyEM Project Team and Gwyneth M Card and Marta Costa and David Shepherd and Gregory S X E Jefferis} } @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 {68667, title = {Three-dimensional reconstructions of mechanosensory end organs suggest a unifying mechanism underlying dynamic, light touch}, journal = {Neuron}, year = {2023}, month = {2023 Oct 18}, abstract = {

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

}, doi = {10.1016/j.neuron.2023.08.023}, url = {https://doi.org/10.1016/j.neuron.2023.08.023}, author = {Annie Handler and Qiyu Zhang and Song Pang and Tri M. Nguyen and Michael Iskols and Michael Nolan-Tamariz and Stuart Cattel and Rebecca Plumb and Brianna Sanchez and Karyl Ashjian and Aria Shotland and Bartianna Brown and Madiha Kabeer and Josef Turecek and Genelle Rankin and Wangchu Xiang and Elisa C. Pavarino and Nusrat Africawala and Celine Santiago and Wei-Chung Allen Lee and C. Shan Xu and David D. Ginty} } @article {68561, title = {Time-tagged ticker tapes for intracellular recordings.}, journal = {Nature Biotechnology}, volume = {41}, year = {2023}, month = {2023 May 01}, pages = {631-9}, abstract = {

Recording transcriptional histories of a cell would enable deeper understanding of cellular developmental trajectories and responses to external perturbations. Here we describe an engineered protein fiber that incorporates diverse fluorescent marks during its growth to store a ticker tape-like history. An embedded HaloTag reporter incorporates user-supplied dyes, leading to colored stripes that map the growth of each individual fiber to wall clock time. A co-expressed eGFP tag driven by a promoter of interest records a history of transcriptional activation. High-resolution multi-spectral imaging on fixed samples reads the cellular histories, and interpolation of eGFP marks relative to HaloTag timestamps provides accurate absolute timing. We demonstrate recordings of doxycycline-induced transcription in HEK cells and cFos promoter activation in cultured neurons, with a single-cell absolute accuracy of 30-40 minutes over a 12-hour recording. The protein-based ticker tape design we present here could be generalized to achieve massively parallel single-cell recordings of diverse physiological modalities.

}, issn = {1546-1696}, doi = {10.1038/s41587-022-01524-7}, author = {Lin, Dingchang and Li, Xiuyuan and Moult, Eric and Park, Pojeong and Tang, Benjamin and Shen, Hao and Grimm, Jonathan B and Falco, Natalie and Jia, Bill Z and Baker, David and Lavis, Luke D and Cohen, Adam E} } @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 {69074, title = {Vagal sensory neurons mediate the Bezold-Jarisch reflex and induce syncope.}, journal = {Nature}, volume = {623}, year = {2023}, month = {2023 Nov 01}, pages = {387-396}, abstract = {

Visceral sensory pathways mediate homeostatic reflexes, the dysfunction of which leads to many neurological disorders. The Bezold-Jarisch reflex (BJR), first described in 1867, is a cardioinhibitory reflex that is speculated to be mediated by vagal sensory neurons (VSNs) that also triggers syncope. However, the molecular identity, anatomical organization, physiological characteristics and behavioural influence of cardiac VSNs remain mostly unknown. Here we leveraged single-cell RNA-sequencing data and HYBRiD tissue clearing to show that VSNs that express neuropeptide Y receptor Y2 (NPY2R) predominately connect the heart ventricular wall to the area postrema. Optogenetic activation of NPY2R VSNs elicits the classic triad of BJR responses-hypotension, bradycardia and suppressed respiration-and causes an animal to faint. Photostimulation during high-resolution echocardiography and laser Doppler flowmetry with behavioural observation revealed a range of phenotypes reflected in clinical syncope, including reduced cardiac output, cerebral hypoperfusion, pupil dilation and eye-roll. Large-scale Neuropixels brain recordings and machine-learning-based modelling showed that this manipulation causes the suppression of activity across a large distributed neuronal population that is not explained by changes in spontaneous behavioural movements. Additionally, bidirectional manipulation of the periventricular zone had a push-pull effect, with inhibition leading to longer syncope periods and activation inducing arousal. Finally, ablating NPY2R VSNs specifically abolished the BJR. Combined, these results demonstrate a genetically defined cardiac reflex that recapitulates characteristics of human syncope at physiological, behavioural and neural network levels.

}, keywords = {Area Postrema, Bradycardia, Cardiac Output, Low, Echocardiography, Heart, Heart Rate, Humans, Hypotension, Laser-Doppler Flowmetry, Nerve Net, Reflex, Sensory Receptor Cells, Single-Cell Gene Expression Analysis, Syncope, vagus nerve}, issn = {1476-4687}, doi = {10.1038/s41586-023-06680-7}, author = {Lovelace, Jonathan W and Ma, Jingrui and Yadav, Saurabh and Chhabria, Karishma and Shen, Hanbing and Pang, Zhengyuan and Qi, Tianbo and Sehgal, Ruchi and Zhang, Yunxiao and Bali, Tushar and Vaissiere, Thomas and Tan, Shawn and Liu, Yuejia and Rumbaugh, Gavin and Ye, Li and Kleinfeld, David and Stringer, Carsen and Augustine, Vineet} } @article {69073, title = {Volitional activation of remote place representations with a hippocampal brain-machine interface.}, journal = {Science}, volume = {382}, year = {2023}, month = {2023 Nov 03}, pages = {566-573}, abstract = {

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

}, keywords = {Animals, Brain-Computer Interfaces, Hippocampus, Humans, Imagination, Memory, Episodic, Mental Recall, Rats}, issn = {1095-9203}, doi = {10.1126/science.adh5206}, author = {Lai, Chongxi and Tanaka, Shinsuke and Harris, Timothy D and Lee, Albert K} } @article {68792, title = {Voltage dynamics of dendritic integration and back-propagation in vivo}, journal = {bioRxiv}, year = {2023}, month = {2023 May 26}, abstract = {

Neurons integrate synaptic inputs within their dendrites and produce spiking outputs, which then propagate down the axon and back into the dendrites where they contribute to plasticity. Mapping the voltage dynamics in dendritic arbors of live animals is crucial for understanding neuronal computation and plasticity rules. Here we combine patterned channelrhodopsin activation with dual-plane structured illumination voltage imaging, for simultaneous perturbation and monitoring of dendritic and somatic voltage in Layer 2/3 pyramidal neurons in anesthetized and awake mice. We examined the integration of synaptic inputs and compared the dynamics of optogenetically evoked, spontaneous, and sensory-evoked back-propagating action potentials (bAPs). Our measurements revealed a broadly shared membrane voltage throughout the dendritic arbor, and few signatures of electrical compartmentalization among synaptic inputs. However, we observed spike rate acceleration-dependent propagation of bAPs into distal dendrites. We propose that this dendritic filtering of bAPs may play a critical role in activity-dependent plasticity.

}, doi = {10.1101/2023.05.25.542363}, url = {https://doi.org/10.1101/2023.05.25.542363}, author = {J. David Wong-Campos and Pojeong Park and Hunter Davis and Yitong Qi and He Tian and Daniel G. Itkis and Doyeon Kim and Sarah E. Plutkis and Luke Lavis and Adam E. Cohen} } @article {67946, title = {2,7-Diaminobenzopyrylium Dyes Are Live-Cell Mitochondrial Stains2,7-Diaminobenzopyrylium Dyes Are Live-Cell Mitochondrial Stains}, journal = {ACS Bio \& Med Chem Au}, volume = {2}, year = {2022}, month = {2022 Jun 15}, pages = {307-12}, abstract = {

Small-molecule fluorescent stains enable the imaging of cellular structures without the need for genetic manipulation. Here, we introduce 2,7-diaminobenzopyrylium (DAB) dyes as live-cell mitochondrial stains excited with violet light. This amalgam of the coumarin and rhodamine fluorophore structures yields dyes with high photostability and tunable spectral properties.

}, issn = {2694-2437}, doi = {10.1021/acsbiomedchemau.1c00068}, url = {https://pubs.acs.org/doi/10.1021/acsbiomedchemau.1c00068}, author = {Banala, Sambashiva and Tkachuk, Ariana N. and Patel, Ronak and Kumar, Pratik and Brown, Timothy A. and Lavis, Luke D.} } @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 {68193, title = {Architecture and dynamics of a novel desmosome-endoplasmic reticulum organelle}, journal = {bioRxiv}, year = {2022}, month = {2022 Jul 08}, abstract = {

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

}, doi = {10.1101/2022.07.07.499185}, url = {https://doi.org/10.1101/2022.07.07.499185}, author = {Navaneetha Krishnan Bharathan and William Giang and Jesse S. Aaron and Satya Khuon and Teng-Leong Chew and Stephan Preibisch and Eric T. Trautman and Larissa Heinrich and John Bogovic and Davis Bennett and David Ackerman and Woohyun Park and Alyson Petruncio and Aubrey V. Weigel and Stephan Saalfeld and COSEM Project Team and A. Wayne Vogl and Sara N. Stahley and Andrew P. Kowalczyk} } @article {68165, title = {Binding partners regulate unfolding of myosin VI to activate the molecular motor.}, journal = {The Biochemical Journal}, volume = {479}, year = {2022}, month = {2022 Jul 15}, pages = {1409-1428}, abstract = {

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

}, issn = {1470-8728}, doi = {10.1042/BCJ20220025}, author = {Dos Santos, {\'A}lia and Fili, Natalia and Hari-Gupta, Yukti and Gough, Rosemarie E and Wang, Lin and Martin-Fernandez, Marisa and Arron, Jesse and Wait, Eric and Chew, Teng Leong and Toseland, Chris} } @article {68274, title = {Biomechanical origins of proprioceptive maps in the Drosophila leg}, journal = {bioRxiv}, year = {2022}, month = {2022 Aug 09}, abstract = {

Proprioception, the sense of body position and movement, is essential for effective motor control. Because proprioceptive sensory neurons are embedded in complex and dynamic tissues, it has been challenging to understand how they sense and encode mechanical stimuli. Here, we find that proprioceptor neurons in the\ Drosophila\ femur are organized into functional groups that are biomechanically specialized to detect features of tibia joint kinematics. The dendrites of position and vibration-tuned proprioceptors receive distinct mechanical signals via the\ arculum, an elegant mechanical structure that decomposes movement of the tibia joint into orthogonal components. The cell bodies of position-tuned proprioceptors form a\ goniotopic\ map of joint angle, whereas the dendrites of vibration-tuned proprioceptors form a\ tonotopic\ map of tibia vibration frequency. Our findings reveal biomechanical mechanisms that underlie proprioceptor feature selectivity and identify common organizational principles between proprioception and other topographically organized sensory systems.

}, doi = {10.1101/2022.08.08.503192}, url = {https://doi.org/10.1101/2022.08.08.503192}, author = {Akira Mamiya and Pralaksha Gurung and Igor Siwanowicz and Anne Sustar and Chenghao Chen and Jasper S. Phelps and Aaron T. Kuan and Alexandra Pacureanu and Wei-Chung Allen Lee and Natasha Mhatre and John C. Tuthill} } @article {68503, title = {Brain-wide measurement of protein turnover with high spatial and temporal resolution}, journal = {bioRxiv}, year = {2022}, month = {2022 Nov 13}, abstract = {

Cells regulate function by synthesizing and degrading proteins. This turnover ranges from minutes to weeks, as it varies across proteins, cellular compartments, cell types, and tissues. Current methods for tracking protein turnover lack the spatial and temporal resolution needed to investigate these processes, especially in the intact brain, which presents unique challenges. We describe a pulse-chase method (DELTA) for measuring protein turnover with high spatial and temporal resolution throughout the body, including the brain. DELTA relies on rapid covalent capture by HaloTag of fluorophores that were optimized for bioavailability\ in vivo. The nuclear protein MeCP2 showed brain region- and cell type-specific turnover. The synaptic protein PSD95 was destabilized in specific brain regions by behavioral enrichment. A novel variant of expansion microscopy further facilitated turnover measurements at individual synapses. DELTA enables studies of adaptive and maladaptive plasticity in brain-wide neural circuits.

}, doi = {10.1101/2022.11.12.516226}, url = {https://doi.org/10.1101/2022.11.12.516226}, author = {Boaz Mohar and Jonathan B. Grimm and Ronak Patel and Timothy A. Brown and Paul Tillberg and Luke D. Lavis and Nelson Spruston and Karel Svoboda} } @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} } @conference {67973, title = {Connectome-constrained Latent Variable Model of Whole-Brain Neural Activity}, booktitle = {International Conference on Learning Representations}, year = {2022}, month = {09/2021}, abstract = {

The availability of both anatomical connectivity and brain-wide neural activity measurements in C. elegans make the worm a promising system for learning detailed, mechanistic models of an entire nervous system in a data-driven way. However, one faces several challenges when constructing such a model. We often do not have direct experimental access to important modeling details such as single-neuron dynamics and the signs and strengths of the synaptic connectivity. Further, neural activity can only be measured in a subset of neurons, often indirectly via calcium imaging, and significant trial-to-trial variability has been observed. To address these challenges, we introduce a connectome-constrained latent variable model (CC-LVM) of the unobserved voltage dynamics of the entire C. elegans nervous system and the observed calcium signals. We used the framework of variational autoencoders to fit parameters of the mechanistic simulation constituting the generative model of the LVM to calcium imaging observations. A variational approximate posterior distribution over latent voltage traces for all neurons is efficiently inferred using an inference network, and constrained by a prior distribution given by the biophysical simulation of neural dynamics. We applied this model to an experimental whole-brain dataset, and found that connectomic constraints enable our LVM to predict the activity of neurons whose activity were withheld significantly better than models unconstrained by a connectome. We explored models with different degrees of biophysical detail, and found that models with realistic conductance-based synapses provide markedly better predictions than current-based synapses for this system.

}, url = {https://openreview.net/forum?id=CJzi3dRlJE-}, author = {Lu Mi and Richard Xu and Sridhama Prakhya and Albert Lin and Nir Shavit and Aravinthan Samuel and Srinivas C Turaga} } @article {67966, title = {The Consistency of Gastropod Identified Neurons Distinguishes Intra-Individual Plasticity From Inter-Individual Variability in Neural Circuits.}, journal = {Frontiers in Behavioral Neuroscience}, volume = {16}, year = {2022}, month = {2022 Mar 03}, pages = {855235}, abstract = {

Gastropod mollusks are known for their large, individually identifiable neurons, which are amenable to long-term intracellular recordings that can be repeated from animal to animal. The constancy of individual neurons can help distinguish state-dependent or temporal variation within an individual from actual variability between individual animals. Investigations into the circuitry underlying rhythmic swimming movements of the gastropod species, and have uncovered intra- and inter-individual variability in synaptic connectivity and serotonergic neuromodulation. has a reliably evoked escape swim behavior that is produced by a central pattern generator (CPG) composed of a small number of identifiable neurons. There is apparent individual variability in some of the connections between neurons that is inconsequential for the production of the swim behavior under normal conditions, but determines whether that individual can swim following a neural lesion. Serotonergic neuromodulation of synaptic strength intrinsic to the CPG creates neural circuit plasticity within an individual and contributes to reorganization of the network during recovery from injury and during learning. In , variability over time in the modulatory actions of serotonin and in expression of serotonin receptor genes in an identified neuron directly reflects variation in swimming behavior. Tracking behavior and electrophysiology over hours to days was necessary to identify the functional consequences of these intra-individual, time-dependent variations. This work demonstrates the importance of unambiguous neuron identification, properly assessing the animal and network states, and tracking behavior and physiology over time to distinguish plasticity within the same animal at different times from variability across individual animals.

}, issn = {1662-5153}, doi = {10.3389/fnbeh.2022.855235}, author = {Tamvacakis, Arianna N and Lillvis, Joshua L and Sakurai, Akira and Katz, Paul S} } @article {68984, title = {Embryo~model completes gastrulation to neurulation and organogenesis.}, journal = {Nature}, volume = {610}, year = {2022}, month = {10/2022}, pages = {143-153}, abstract = {

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

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

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

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

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

}, issn = {1546-1718}, doi = {10.1038/s41588-022-01177-x}, author = {Lange, Joshua T and Rose, John C and Chen, Celine Y and Pichugin, Yuriy and Xie, Liangqi and Tang, Jun and Hung, King L and Yost, Kathryn E and Shi, Quanming and Erb, Marcella L and Rajkumar, Utkrisht and Wu, Sihan and Taschner-Mandl, Sabine and Bernkopf, Marie and Swanton, Charles and Liu, Zhe and Huang, Weini and Chang, Howard Y and Bafna, Vineet and Henssen, Anton G and Werner, Benjamin and Mischel, Paul S} } @article {68570, title = {Eye structure shapes neuron function in Drosophila motion vision}, journal = {bioRxiv}, year = {2022}, month = {2022 Dec 15}, abstract = {

Many animals rely on vision to navigate through their environment. The pattern of changes in the visual scene induced by self-motion is the\ optic flow1, which is first estimated in local patches by directionally selective (DS) neurons2{\textendash}4. But how should the arrays of DS neurons, each responsive to motion in a preferred direction at a specific retinal position, be organized to support robust decoding of optic flow by downstream circuits? Understanding this global organization is challenging because it requires mapping fine, local features of neurons across the animal{\textquoteright}s field of view3. In\ Drosophila, the asymmetric dendrites of the T4 and T5 DS neurons establish their preferred direction, making it possible to predict DS responses from anatomy4,5. Here we report that the preferred directions of fly DS neurons vary at different retinal positions and show that this spatial variation is established by the anatomy of the compound eye. To estimate the preferred directions across the visual field, we reconstructed hundreds of T4 neurons in a full brain EM volume6\ and discovered unexpectedly stereotypical dendritic arborizations that are independent of location. We then used whole-head μCT scans to map the viewing directions of all compound eye facets and found a non-uniform sampling of visual space that explains the spatial variation in preferred directions. Our findings show that the organization of preferred directions in the fly is largely determined by the compound eye, exposing an intimate and unexpected connection between the peripheral structure of the eye, functional properties of neurons deep in the brain, and the control of body movements.

}, doi = {10.1101/2022.12.14.520178}, url = {https://doi.org/10.1101/2022.12.14.520178}, author = {Arthur Zhao and Eyal Gruntman and Aljoscha Nern and Nirmala A. Iyer and Edward M. Rogers and Sanna Koskela and Igor Siwanowicz and Marisa Dreher and Miriam A. Flynn and Connor W. Laughland and Henrique D.F. Ludwig and Alex G. Thomson and Cullen P. Moran and Bruck Gezahegn and Davi D. Bock and Michael B. Reiser} } @article {68558, title = {Fluorescence Screens for Identifying Central Nervous System-Acting Drug-Biosensor Pairs for Subcellular and Supracellular Pharmacokinetics.}, journal = {Bio-Protocol}, volume = {12}, year = {2022}, month = {2022 Nov 20}, abstract = {

Subcellular pharmacokinetic measurements have informed the study of central nervous system (CNS)-acting drug mechanisms. Recent investigations have been enhanced by the use of genetically encoded fluorescent biosensors for drugs of interest at the plasma membrane and in organelles. We describe screening and validation protocols for identifying hit pairs comprising a drug and biosensor, with each screen including 13-18 candidate biosensors and 44-84 candidate drugs. After a favorable hit pair is identified and validated via these protocols, the biosensor is then optimized, as described in other papers, for sensitivity and selectivity to the drug. We also show sample hit pair data that may lead to future intensity-based drug-sensing fluorescent reporters (iDrugSnFRs). These protocols will assist scientists to use fluorescence responses as criteria in identifying favorable fluorescent biosensor variants for CNS-acting drugs that presently have no corresponding biosensor partner. eLife (2022), DOI: 10.7554/eLife.74648 Graphical abstract.

}, issn = {2331-8325}, doi = {10.21769/BioProtoc.4551}, author = {Beatty, Zoe G and Muthusamy, Anand K and Unger, Elizabeth K and Dougherty, Dennis A and Tian, Lin and Looger, Loren L and Shivange, Amol V and Bera, Kallol and Lester, Henry A and Nichols, Aaron L} } @article {67863, title = {Fluorescent chemigenetic actuators and indicators for use in living animals.}, journal = {Current Opinion in Pharmacology}, volume = {62}, year = {2022}, month = {2022 Jan 15}, pages = {159-167}, abstract = {

Fluorescent indicators and actuators provide a means to optically observe and perturb dynamic events in living animals. Although chemistry and protein engineering have contributed many useful tools to observe and perturb cells, an emerging strategy is to use chemigenetics: systems in which a small molecule dye interacts with a genetically encoded protein domain. Here we review chemigenetic strategies that have been successfully employed in living animals as photosensitizers for photoablation experiments, fluorescent cell cycle indicators, and fluorescent indicators for studying dynamic biological signals. Although these strategies at times suffer from challenges, e.g. delivery of the small molecule and assembly of the chemigenetic unit in living animals, the advantages of using small molecules with high brightness, low photobleaching, no chromophore maturation time and expanded color palette, combined with the ability to genetically target them to specific cell types, make chemigenetic fluorescent actuators and indicators an attractive strategy for use in living animals.

}, issn = {1471-4973}, doi = {10.1016/j.coph.2021.12.007}, author = {Farrants, Helen and Tebo, Alison G} } @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} } @conference {68678, title = {FourierNets enable the design of highly non-local optical encoders for computational imaging}, booktitle = {Advances in Neural Information Processing Systems}, year = {2022}, month = {10/2022}, abstract = {

Differentiable simulations of optical systems can be combined with deep learning-based reconstruction networks to enable high performance computational imaging via end-to-end (E2E) optimization of both the optical encoder and the deep decoder. This has enabled imaging applications such as 3D localization microscopy, depth estimation, and lensless photography via the optimization of local optical encoders. More challenging computational imaging applications, such as 3D snapshot microscopy which compresses 3D volumes into single 2D images, require a highly non-local optical encoder. We show that existing deep network decoders have a locality bias which prevents the optimization of such highly non-local optical encoders. We address this with a decoder based on a shallow neural network architecture using global kernel Fourier convolutional neural networks (FourierNets). We show that FourierNets surpass existing deep network based decoders at reconstructing photographs captured by the highly non-local DiffuserCam optical encoder. Further, we show that FourierNets enable E2E optimization of highly non-local optical encoders for 3D snapshot microscopy. By combining FourierNets with a large-scale multi-GPU differentiable optical simulation, we are able to optimize non-local optical encoders 170{\texttimes}\ to 7372{\texttimes}\ larger than prior state of the art, and demonstrate the potential for ROI-type specific optical encoding with a programmable microscope.

}, keywords = {Computer Vision and Pattern Recognition (cs.CV), electronic engineering, FOS: Computer and information sciences, FOS: Electrical engineering, Image and Video Processing (eess.IV), information engineering, Machine Learning (cs.LG)}, doi = {https://doi.org/10.48550/arXiv.2104.10611}, url = {https://openreview.net/forum?id=Kx1VCs1treH}, author = {Diptodip Deb and Zhenfei Jiao and Ruth R Sims and Alex Bo-Yuan Chen and Michael Broxton and Misha Ahrens and Kaspar Podgorski and Srinivas C Turaga}, editor = {Alice H. Oh and Alekh Agarwal and Danielle Belgrave and Kyunghyun Cho} } @article {68985, title = {Human primed and na{\"\i}ve PSCs are both able to differentiate into trophoblast stem cells.}, journal = {Stem Cell Reports}, volume = {17}, year = {2022}, month = {11/2022}, pages = {2484-2500}, abstract = {

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

}, keywords = {Blastocyst, Cell Differentiation, Female, Humans, Placenta, Pluripotent Stem Cells, Pregnancy, Trophoblasts}, issn = {2213-6711}, doi = {10.1016/j.stemcr.2022.09.008}, author = {Viukov, Sergey and Shani, Tom and Bayerl, Jonathan and Aguilera-Castrejon, Alejandro and Oldak, Bernardo and Sheban, Daoud and Tarazi, Shadi and Stelzer, Yonatan and Hanna, Jacob H and Novershtern, Noa} } @article {67891, title = {Idiosyncratic learning performance in flies.}, journal = {Biology Letters}, volume = {18}, year = {2022}, month = {2022 Feb 01}, pages = {20210424}, abstract = {

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

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

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

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2022.09.025}, author = {Shuster, S Andrew and Li, Jiefu and Chon, URee and Sinantha-Hu, Miley C and Luginbuhl, David J and Udeshi, Namrata D and Carey, Dominique Kiki and Takeo, Yukari H and Xie, Qijing and Xu, Chuanyun and Mani, D R and Han, Shuo and Ting, Alice Y and Carr, Steven A and Luo, Liqun} } @article {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 {68226, title = {Kinetic principles underlying pioneer function of GAGA transcription factor in live cells.}, journal = {Nature Structural and Molecular Biology}, volume = {29}, year = {2022}, month = {2022 Jul 01}, pages = {665-676}, abstract = {

How pioneer factors interface with chromatin to promote accessibility for transcription control is poorly understood in vivo. Here, we directly visualize chromatin association by the prototypical GAGA pioneer factor (GAF) in live Drosophila hemocytes. Single-particle tracking reveals that most GAF is chromatin bound, with a stable-binding fraction showing nucleosome-like confinement residing on chromatin for more than 2 min, far longer than the dynamic range of most transcription factors. These kinetic properties require the full complement of GAF{\textquoteright}s DNA-binding, multimerization and intrinsically disordered domains, and are autonomous from recruited chromatin remodelers NURF and PBAP, whose activities primarily benefit GAF{\textquoteright}s neighbors such as Heat Shock Factor. Evaluation of GAF kinetics together with its endogenous abundance indicates that, despite on-off dynamics, GAF constitutively and fully occupies major chromatin targets, thereby providing a temporal mechanism that sustains open chromatin for transcriptional responses to homeostatic, environmental and developmental signals.

}, keywords = {Animals, Chromatin, DNA-Binding Proteins, Drosophila, Drosophila Proteins, Kinetics, Transcription Factors}, issn = {1545-9985}, doi = {10.1038/s41594-022-00800-z}, author = {Tang, Xiaona and Li, Taibo and Liu, Sheng and Wisniewski, Jan and Zheng, Qinsi and Rong, Yikang and Lavis, Luke D and Wu, Carl} } @article {67963, title = {Myosin VI regulates the spatial organisation of mammalian transcription initiation.}, journal = {Nature Communications}, volume = {13}, year = {2022}, month = {2022 Mar 15}, pages = {1346}, abstract = {

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

}, issn = {2041-1723}, doi = {10.1038/s41467-022-28962-w}, author = {Hari-Gupta, Yukti and Fili, Natalia and Dos Santos, {\'A}lia and Cook, Alexander W and Gough, Rosemarie E and Reed, Hannah C W and Wang, Lin and Aaron, Jesse and Venit, Tomas and Wait, Eric and Grosse-Berkenbusch, Andreas and Gebhardt, J Christof M and Percipalle, Piergiorgio and Chew, Teng-Leong and Martin-Fernandez, Marisa and Toseland, Christopher P} } @article {68379, title = {The Neurodata Without Borders ecosystem for neurophysiological data science.}, journal = {eLife}, volume = {11}, year = {2022}, month = {2022 Oct 04}, abstract = {

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

}, keywords = {Data Science, Ecosystem, Humans, Metadata, Neurophysiology, Software}, issn = {2050-084X}, doi = {10.7554/eLife.78362}, author = {Rubel, Oliver and Tritt, Andrew and Ly, Ryan and Dichter, Benjamin K and Ghosh, Satrajit and Niu, Lawrence and Baker, Pamela and Soltesz, Ivan and Ng, Lydia and Svoboda, Karel and Frank, Loren and Bouchard, Kristofer E} } @article {67801, title = {A neuropeptidergic circuit gates selective escape behavior of Drosophila larvae.}, journal = {Current Biology}, volume = {32}, year = {2022}, month = {2022 Jan 10}, pages = {149-63}, abstract = {

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

}, issn = {1879-0445}, doi = {10.1016/j.cub.2021.10.069}, author = {Imambocus, Bibi Nusreen and Zhou, Fangmin and Formozov, Andrey and Wittich, Annika and Tenedini, Federico M and Hu, Chun and Sauter, Kathrin and Macarenhas Varela, Ednilson and Her{\'e}dia, Fabiana and Casimiro, Andreia P and Macedo, Andr{\'e} and Schlegel, Philipp and Yang, Chung-Hui and Miguel-Aliaga, Irene and Wiegert, J Simon and Pankratz, Michael J and Gontijo, Alisson M and Cardona, Albert and Soba, Peter} } @article {68012, title = {Nuclear lamin isoforms differentially contribute to LINC complex-dependent nucleocytoskeletal coupling and whole-cell mechanics.}, journal = {Proceedings of the National Academy of Sciences of the U.S.A.}, volume = {119}, year = {2022}, month = {2022 Apr 19}, pages = {e2121816119}, abstract = {

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

}, keywords = {Animals, Cell Nucleus, Cytoskeleton, Fibroblasts, Lamin Type A, Lamin Type B, Mice, Nuclear Lamina, Nuclear Matrix, Protein Isoforms}, issn = {1091-6490}, doi = {10.1073/pnas.2121816119}, author = {Vahabikashi, Amir and Sivagurunathan, Suganya and Nicdao, Fiona Ann Sadsad and Han, Yu Long and Park, Chan Young and Kittisopikul, Mark and Wong, Xianrong and Tran, Joseph R and Gundersen, Gregg G and Reddy, Karen L and Luxton, G W Gant and Guo, Ming and Fredberg, Jeffrey J and Zheng, Yixian and Adam, Stephen A and Goldman, Robert D} } @article {68512, title = {Oligodendrocyte precursor cells ingest axons in the mouse neocortex.}, journal = {Proceedings of the National Academies of Science of the U.S.A.}, volume = {119}, year = {2022}, month = {2022 Nov 29}, pages = {e2202580119}, abstract = {

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

}, keywords = {Animals, Axons, Mice, Neocortex, Neurons, Oligodendrocyte Precursor Cells, Oligodendroglia}, issn = {1091-6490}, doi = {10.1073/pnas.2202580119}, author = {Buchanan, JoAnn and Elabbady, Leila and Collman, Forrest and Jorstad, Nikolas L and Bakken, Trygve E and Ott, Carolyn and Glatzer, Jenna and Bleckert, Adam A and Bodor, Agnes L and Brittain, Derrick and Bumbarger, Daniel J and Mahalingam, Gayathri and Seshamani, Sharmishtaa and Schneider-Mizell, Casey and Takeno, Marc M and Torres, Russel and Yin, Wenjing and Hodge, Rebecca D and Castro, Manuel and Dorkenwald, Sven and Ih, Dodam and Jordan, Chris S and Kemnitz, Nico and Lee, Kisuk and Lu, Ran and Macrina, Thomas and Mu, Shang and Popovych, Sergiy and Silversmith, William M and Tartavull, Ignacio and Turner, Nicholas L and Wilson, Alyssa M and Wong, William and Wu, Jingpeng and Zlateski, Aleksandar and Zung, Jonathan and Lippincott-Schwartz, Jennifer and Lein, Ed S and Seung, H Sebastian and Bergles, Dwight E and Reid, R Clay and da Costa, Nuno Ma{\c c}arico} } @article {68113, title = {One engram two readouts: stimulus dynamics switch a learned behavior in Drosophila}, journal = {bioRxiv}, year = {2022}, month = {2022 May 26}, abstract = {

Memory guides the choices an animal makes across widely varying conditions in dynamic environments. Consequently, the most adaptive choice depends on the options available. How can a single memory support optimal behavior across different sets of choice options? We address this using olfactory learning in Drosophila. Even when we restrict an odor-punishment association to a single set of synapses using optogenetics, we find that flies still show choice behavior that depends on the options it encounters. Here we show that how the odor choices are presented to the animal influences memory recall itself. Presenting two similar odors in sequence enabled flies to not only discriminate them behaviorally but also at the level of neural activity. However, when the same odors were encountered as solitary stimuli, no such differences were detectable. These results show that memory recall is not simply a comparison to a static learned template, but can be adaptively modulated by stimulus dynamics.

}, doi = {10.1101/2022.05.24.492551}, url = {https://doi.org/10.1101/2022.05.24.492551}, author = {Mehrab N Modi and Adithya Rajagopalan and Herv{\'e} Rouault and Yoshinori Aso and Glenn C Turner} } @article {67994, title = {Petascale pipeline for precise alignment of images from serial section electron microscopy.}, journal = {bioRxiv}, year = {2022}, month = {2022 Mar 27}, abstract = {

The reconstruction of neural circuits from serial section electron microscopy (ssEM) images is being accelerated by automatic image segmentation methods. Segmentation accuracy is often limited by the preceding step of aligning 2D section images to create a 3D image stack. Precise and robust alignment in the presence of image artifacts is challenging, especially as datasets are attaining the petascale. We present a computational pipeline for aligning ssEM images with several key elements. Self-supervised convolutional nets are trained via metric learning to encode and align image pairs, and they are used to initialize iterative fine-tuning of alignment. A procedure called vector voting increases robustness to image artifacts or missing image data. For speedup the series is divided into blocks that are distributed to computational workers for alignment. The blocks are aligned to each other by composing transformations with decay, which achieves a global alignment without resorting to a time-consuming global optimization. We apply our pipeline to a whole fly brain dataset, and show improved accuracy relative to prior state of the art. We also demonstrate that our pipeline scales to a cubic millimeter of mouse visual cortex. Our pipeline is publicly available through two open source Python packages.

}, doi = {10.1101/2022.03.25.485816}, url = {https://doi.org/10.1101/2022.03.25.485816}, author = {Sergiy Popovych and Thomas Macrina and Nico Kemnitz and Manuel Castro and Barak Nehoran and Zhen Jia and J. Alexander Bae and Eric Mitchell and Shang Mu and Eric T. Trautman and Stephan Saalfeld and Kai Li and Sebastian Seung} } @article {68983, title = {Post-gastrulation synthetic embryos generated ex utero from mouse naive ESCs}, journal = {Cell}, volume = {185}, year = {2022}, month = {09/2022}, pages = {3290-3306.e25}, abstract = {

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

}, keywords = {embryogenesis, embryoids, ESCs, ex utero, extra-embryonic Tissues, iPSCs, naive pluripotency, PGCs, synthetic embryos}, issn = {0092-8674}, doi = {https://doi.org/10.1016/j.cell.2022.07.028}, url = {https://www.sciencedirect.com/science/article/pii/S0092867422009813}, author = {Shadi Tarazi and Alejandro Aguilera-Castrejon and Carine Joubran and Nadir Ghanem and Shahd Ashouokhi and Francesco Roncato and Emilie Wildschutz and Montaser Haddad and Bernardo Oldak and Elidet Gomez-Cesar and Nir Livnat and Sergey Viukov and Dmitry Lokshtanov and Segev Naveh-Tassa and Max Rose and Suhair Hanna and Calanit Raanan and Ori Brenner and Merav Kedmi and Hadas Keren-Shaul and Tsvee Lapidot and Itay Maza and Noa Novershtern and Jacob H. Hanna} } @article {67849, title = {Rapid reconstruction of neural circuits using tissue expansion and lattice light sheet microscopy}, journal = {eLife}, year = {2022}, month = {2022 Oct 26}, abstract = {

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

}, doi = {10.7554/eLife.81248}, url = {https://doi.org/10.7554/eLife.81248}, author = {Joshua L. Lillvis and Hideo Otsuna and Xiaoyu Ding and Igor Pisarev and Takashi Kawase and Jennifer Colonell and Konrad Rokicki and Cristian Goina and Ruixuan Gao and Amy Hu and Kaiyu Wang and John Bogovic and Daniel E. Milkie and Edward S. Boyden and Stephan Saalfeld and Paul W. Tillberg and Barry J. Dickson} } @article {65821, title = {Robotic Multi-Probe-Single-Actuator Inchworm Neural Microdrive}, journal = {eLife}, year = {2022}, month = {2022 Nov 10}, abstract = {

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

}, doi = {10.7554/eLife.71876}, author = {Smith, R.D. and Kolb, Ilya and Tanaka, Shinsuke and Lee, A.K. and Harris, T.D. and Barbic, M.} } @article {68251, title = {A scalable and modular automated pipeline for stitching of large electron microscopy datasets.}, journal = {eLife}, volume = {11}, year = {2022}, month = {2022 Jul 26}, abstract = {

Serial-section electronmicroscopy (ssEM) is themethod of choice for studyingmacroscopic biological samples at extremely high resolution in three dimensions. In the nervous system, nanometer-scale images are necessary to reconstruct dense neural wiring diagrams in the brain, so called connectomes. In order to use this data, consisting of up to 10 individual EM images, it must be assembled into a volume, requiring seamless 2D stitching from each physical section followed by 3D alignment of the stitched sections. The high throughput of ssEM necessitates 2D stitching to be done at the pace of imaging, which currently produces tens of terabytes per day. To achieve this, we present a modular volume assembly software pipeline ASAP (Assembly Stitching and Alignment Pipeline) that is scalable to datasets containing petabytes of data and parallelized to work in a distributed computational environment. The pipeline is built on top of the Render (27) services used in the volume assembly of the brain of adult Drosophilamelanogaster (30). It achieves high throughput by operating on themeta-data and transformations of each image stored in a database, thus eliminating the need to render intermediate output. ASAP ismodular, allowing for easy incorporation of new algorithms without significant changes in the workflow. The entire software pipeline includes a complete set of tools for stitching, automated quality control, 3D section alignment, and final rendering of the assembled volume to disk. ASAP has been deployed for continuous stitching of several large-scale datasets of the mouse visual cortex and human brain samples including one cubic millimeter of mouse visual cortex (28; 8) at speeds that exceed imaging. The pipeline also has multi-channel processing capabilities and can be applied to fluorescence and multi-modal datasets like array tomography.

}, issn = {2050-084X}, doi = {10.7554/eLife.76534}, author = {Mahalingam, Gayathri and Torres, Russel and Kapner, Daniel and Trautman, Eric T and Fliss, Tim and Seshamani, Shamishtaa and Perlman, Eric and Young, Rob and Kinn, Samuel and Buchanan, JoAnn and Takeno, Marc M and Yin, Wenjing and Bumbarger, Daniel J and Gwinn, Ryder P and Nyhus, Julie and Lein, Ed and Smith, Steven J and Reid, R Clay and Khairy, Khaled A and Saalfeld, Stephan and Collman, Forrest and Macarico da Costa, Nuno} } @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 {68078, title = {Super-resolution microscopy reveals actomyosin dynamics in medioapical arrays.}, journal = {Molecular Biology of the Cell}, year = {2022}, month = {2022 May 11}, pages = {mbcE21110537}, abstract = {

Arrays of actin filaments (F-actin) near the apical surface of epithelial cells (medioapical arrays) contribute to apical constriction and morphogenesis throughout phylogeny. Here, super-resolution approaches (grazing incidence structured illumination, GI-SIM and lattice light sheet, LLSM) microscopy resolve individual, fluorescently labeled F-actin and bipolar myosin filaments that drive amnioserosa cell shape changes during dorsal closure in . In expanded cells, F-actin and myosin form loose, apically domed meshworks at the plasma membrane. The arrays condense as cells contract, drawing the domes into the plane of the junctional belts. As condensation continues, individual filaments are no longer uniformly apparent. As cells expand, arrays of actomyosin are again resolved - some F-actin turnover likely occurs, but a large fraction of existing filaments rearrange. In morphologically isotropic cells, actin filaments are randomly oriented and during contraction, are drawn together but remain essentially randomly oriented. In anisotropic cells, largely parallel actin filaments are drawn closer to one another. Our images offer unparalleled resolution of F-actin in embryonic tissue show that medioapical arrays are tightly apposed to the plasma membrane, are continuous with meshworks of lamellar F-actin and thereby constitute modified cell cortex. In concert with other tagged array components, super-resolution imaging of live specimens will offer new understanding of cortical architecture and function. [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text].

}, issn = {1939-4586}, doi = {10.1091/mbc.E21-11-0537}, author = {Moore, Regan P and Fogerson, Stephanie M and Tulu, U Serdar and Yu, Jason W and Cox, Amanda H and Sican, Melissa A and Li, Dong and Legant, Wesley R and Weigel, Aubrey V and Crawford, Janice M and Betzig, Eric and Kiehart, Daniel P} } @article {68328, title = {Superresolution microscopy reveals actomyosin dynamics in medioapical arrays.}, journal = {Molecular Biology of the Cell}, volume = {33}, year = {2022}, month = {2022 Sep 15}, pages = {ar94}, abstract = {

Arrays of actin filaments (F-actin) near the apical surface of epithelial cells (medioapical arrays) contribute to apical constriction and morphogenesis throughout phylogeny. Here, superresolution approaches (grazing incidence structured illumination, GI-SIM, and lattice light sheet, LLSM) microscopy resolve individual, fluorescently labeled F-actin and bipolar myosin filaments that drive amnioserosa cell shape changes during dorsal closure in . In expanded cells, F-actin and myosin form loose, apically domed meshworks at the plasma membrane. The arrays condense as cells contract, drawing the domes into the plane of the junctional belts. As condensation continues, individual filaments are no longer uniformly apparent. As cells expand, arrays of actomyosin are again resolved-some F-actin turnover likely occurs, but a large fraction of existing filaments rearrange. In morphologically isotropic cells, actin filaments are randomly oriented and during contraction are drawn together but remain essentially randomly oriented. In anisotropic cells, largely parallel actin filaments are drawn closer to one another. Our images offer unparalleled resolution of F-actin in embryonic tissue, show that medioapical arrays are tightly apposed to the plasma membrane and are continuous with meshworks of lamellar F-actin. Medioapical arrays thereby constitute modified cell cortex. In concert with other tagged array components, superresolution imaging of live specimens will offer new understanding of cortical architecture and function.

}, keywords = {Actin Cytoskeleton, Actins, Actomyosin, Animals, Drosophila, Microscopy, Myosins}, issn = {1939-4586}, doi = {10.1091/mbc.E21-11-0537}, author = {Moore, Regan P and Fogerson, Stephanie M and Tulu, U Serdar and Yu, Jason W and Cox, Amanda H and Sican, Melissa A and Li, Dong and Legant, Wesley R and Weigel, Aubrey V and Crawford, Janice M and Betzig, Eric and Kiehart, Daniel P} } @article {68145, title = {Targeting LIPA independent of its lipase activity is a therapeutic strategy in solid tumors via induction of endoplasmic reticulum stress.}, journal = {Nature Cancer}, volume = {3}, year = {2022}, month = {2022 Jun 02}, pages = {866-884}, abstract = {

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

}, issn = {2662-1347}, doi = {10.1038/s43018-022-00389-8}, author = {Liu, Xihui and Viswanadhapalli, Suryavathi and Kumar, Shourya and Lee, Tae-Kyung and Moore, Andrew and Ma, Shihong and Chen, Liping and Hsieh, Michael and Li, Mengxing and Sareddy, Gangadhara R and Parra, Karla and Blatt, Eliot B and Reese, Tanner C and Zhao, Yuting and Chang, Annabel and Yan, Hui and Xu, Zhenming and Pratap, Uday P and Liu, Zexuan and Roggero, Carlos M and Tan, Zhenqiu and Weintraub, Susan T and Peng, Yan and Tekmal, Rajeshwar R and Arteaga, Carlos L and Lippincott-Schwartz, Jennifer and Vadlamudi, Ratna K and Ahn, Jung-Mo and Raj, Ganesh V} } @article {68419, title = {Transcription factor Acj6 controls dendrite targeting via a combinatorial cell-surface code.}, journal = {Neuron}, volume = {110}, year = {2022}, month = {07/2022}, pages = {2299-2314.e8}, abstract = {

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

}, keywords = {Animals, Dendrites, Drosophila, Drosophila Proteins, Ion Channels, Membrane Proteins, Nerve Tissue Proteins, Olfactory Pathways, Olfactory Receptor Neurons, POU Domain Factors, Proteomics, Transcription Factors}, issn = {1097-4199}, doi = {10.1016/j.neuron.2022.04.026}, author = {Xie, Qijing and Li, Jiefu and Li, Hongjie and Udeshi, Namrata D and Svinkina, Tanya and Orlin, Daniel and Kohani, Sayeh and Guajardo, Ricardo and Mani, D R and Xu, Chuanyun and Li, Tongchao and Han, Shuo and Wei, Wei and Shuster, S Andrew and Luginbuhl, David J and Quake, Stephen R and Murthy, Swetha E and Ting, Alice Y and Carr, Steven A and Luo, Liqun} } @article {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 {68887, title = {Volume electron microscopy.}, journal = {Nature Reviews: Methods Primers}, volume = {2}, year = {2022}, month = {2022 Jul 07}, pages = {51}, abstract = {

Life exists in three dimensions, but until the turn of the century most electron microscopy methods provided only 2D image data. Recently, electron microscopy techniques capable of delving deep into the structure of cells and tissues have emerged, collectively called volume electron microscopy (vEM). Developments in vEM have been dubbed a quiet revolution as the field evolved from established transmission and scanning electron microscopy techniques, so early publications largely focused on the bioscience applications rather than the underlying technological breakthroughs. However, with an explosion in the uptake of vEM across the biosciences and fast-paced advances in volume, resolution, throughput and ease of use, it is timely to introduce the field to new audiences. In this Primer, we introduce the different vEM imaging modalities, the specialized sample processing and image analysis pipelines that accompany each modality and the types of information revealed in the data. We showcase key applications in the biosciences where vEM has helped make breakthrough discoveries and consider limitations and future directions. We aim to show new users how vEM can support discovery science in their own research fields and inspire broader uptake of the technology, finally allowing its full adoption into mainstream biological imaging.

}, issn = {2662-8449}, doi = {10.1038/s43586-022-00131-9}, author = {Peddie, Christopher J and Genoud, Christel and Kreshuk, Anna and Meechan, Kimberly and Micheva, Kristina D and Narayan, Kedar and Pape, Constantin and Parton, Robert G and Schieber, Nicole L and Schwab, Yannick and Titze, Benjamin and Verkade, Paul and Aubrey, Aubrey and Collinson, Lucy M} } @article {67177, title = {Actin cables and comet tails organize mitochondrial networks in mitosis.}, journal = {Nature}, volume = {591}, year = {2021}, month = {2021 Mar 03}, pages = {659-664}, abstract = {

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

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

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

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

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

}, issn = {2050-084X}, doi = {10.7554/eLife.61700}, author = {Koenecke, Allison and Powell, Michael and Xiong, Ruoxuan and Shen, Zhu and Fischer, Nicole and Huq, Sakibul and Khalafallah, Adham M and Trevisan, Marco and Sparen, P{\"a}r and Carrero, Juan J and Nishimura, Akihiko and Caffo, Brian and Stuart, Elizabeth A and Bai, Renyuan and Staedtke, Verena and Thomas, David L and Papadopoulos, Nickolas and Kinzler, Ken W and Vogelstein, Bert and Zhou, Shibin and Bettegowda, Chetan and Konig, Maximilian F and Mensh, Brett D and Vogelstein, Joshua T and Athey, Susan} } @article {67235, title = {The anterior cingulate cortex directs exploration of alternative strategies.}, journal = {Neuron}, volume = {109}, year = {2021}, month = {2021 Jun 2}, pages = {1876-87}, abstract = {

The ability to adjust one{\textquoteright}s behavioral strategy in complex environments is at the core of cognition. Doing so efficiently requires monitoring the reliability of the ongoing strategy and, when appropriate, switching away from it to evaluate alternatives. Studies in humans and non-human primates have uncovered signals in the anterior cingulate cortex (ACC) that reflect the pressure to switch away from the ongoing strategy, whereas other ACC signals relate to the pursuit of alternatives. However, whether these signals underlie computations that actually underpin strategy switching or merely reflect tracking of related variables remains unclear. Here we provide causal evidence that the rodent ACC actively arbitrates between persisting with the ongoing behavioral strategy and temporarily switching away to re-evaluate alternatives. Furthermore, by individually perturbing distinct output pathways, we establish that the two associated computations-determining whether to switch strategy and committing to the pursuit of a specific alternative-are segregated in the ACC microcircuitry.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2021.03.028}, author = {Tervo, D Gowanlock R and Kuleshova, Elena and Manakov, Maxim and Proskurin, Mikhail and Karlsson, Mattias and Lustig, Andy and Behnam, Reza and Karpova, Alla Y} } @article {65832, title = {Automatic Detection of Synaptic Partners in a Whole-Brain Drosophila EM Dataset}, journal = {Nature Methods}, volume = {18}, year = {2021}, month = {2021 Jul 1}, pages = {771-4}, abstract = {

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

}, doi = {10.1038/s41592-021-01183-7}, author = {Buhmann, Julia and Sheridan, Arlo and Gerhard, Stephan and Krause, Renate and Nguyen, Tri and Heinrich, Larissa and Schlegel, Philipp and Lee, Wei-Chung Allen and Wilson, Rachel and Saalfeld, Stephan and Jefferis, Gregory and Bock, Davi and Turaga, Srinivas and Cook, Matthew and Funke, Jan} } @article {65971, title = {Characterization of a common progenitor pool of the epicardium and myocardium.}, journal = {Science}, year = {2021}, month = {2021 Jan 07}, abstract = {

The mammalian heart is derived from multiple cell lineages; however, our understanding of when and how the diverse cardiac cell types arise is limited. We mapped the origin of the embryonic mouse heart at single-cell resolution using a combination of transcriptomic, imaging, and genetic lineage labeling approaches. This provided a transcriptional and anatomic definition of cardiac progenitor types. Furthermore, it revealed a cardiac progenitor pool that is anatomically and transcriptionally distinct from currently known cardiac progenitors. Besides contributing to cardiomyocytes, these cells also represent the earliest progenitor of the epicardium, a source of trophic factors and cells during cardiac development and injury. This study provides detailed insights into the formation of early cardiac cell types, with particular relevance to the development of cell-based cardiac regenerative therapies.

}, issn = {1095-9203}, doi = {10.1126/science.abb2986}, author = {Tyser, Richard C V and Ibarra-Soria, Ximena and McDole, Katie and A Jayaram, Satish and Godwin, Jonathan and van den Brand, Teun A H and Miranda, Antonio M A and Scialdone, Antonio and Keller, Philipp J and Marioni, John C and Srinivas, Shankar} } @article {67189, title = {Circuit reorganization in the Drosophila mushroom body calyx accompanies memory consolidation.}, journal = {Cell Reports}, volume = {34}, year = {2021}, month = {2021 Mar 16}, pages = {108871}, abstract = {

The formation and consolidation of memories are complex phenomena involving synaptic plasticity, microcircuit reorganization, and the formation of multiple representations within distinct circuits. To gain insight into the structural aspects of memory consolidation, we focus on the calyx of the Drosophila mushroom body. In this essential center, essential for olfactory learning, second- and third-order neurons connect through large synaptic microglomeruli, which we dissect at the electron microscopy level. Focusing on microglomeruli that respond to a specific odor, we reveal that appetitive long-term memory results in increased numbers of precisely those functional microglomeruli responding to the conditioned odor. Hindering memory consolidation by non-coincident presentation of odor and reward, by blocking protein synthesis, or by including memory mutants suppress these structural changes, revealing their tight correlation with the process of memory consolidation. Thus, olfactory long-term memory is associated with input-specific structural modifications in a high-order center of the fly brain.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2021.108871}, author = {Baltruschat, Lothar and Prisco, Luigi and Ranft, Philipp and Lauritzen, J Scott and Fiala, Andr{\'e} and Bock, Davi D and Tavosanis, Gaia} } @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 {67771, title = {A connectome of the central complex reveals network motifs suitable for flexible navigation and context-dependent action selection.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Oct 26}, abstract = {

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

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

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

}, issn = {1878-1551}, doi = {10.1016/j.devcel.2021.10.019}, author = {Willy, Nathan M and Ferguson, Joshua P and Akatay, Ata and Huber, Scott and Djakbarova, Umidahan and Silahli, Salih and Cakez, Cemal and Hasan, Farah and Chang, Henry C and Travesset, Alex and Li, Siyu and Zandi, Roya and Li, Dong and Betzig, Eric and Cocucci, Emanuele and Kural, Comert} } @article {67226, title = {Deep learning enables fast and dense single-molecule localization with high accuracy}, journal = {Nature Methods}, volume = {18}, year = {2021}, month = {2021 Sep 03}, abstract = {

Single-molecule localization microscopy (SMLM) has had remarkable success in imaging cellular structures with nanometer resolution, but the need for activating only single isolated emitters limits imaging speed and labeling density. Here, we overcome this major limitation using deep learning. We developed DECODE, a computational tool that can localize single emitters at high density in 3D with highest accuracy for a large range of imaging modalities and conditions. In a public software benchmark competition, it outperformed all other fitters on 12 out of 12 data-sets when comparing both detection accuracy and localization error, often by a substantial margin. DECODE allowed us to take live-cell SMLM data with reduced light exposure in just 3 seconds and to image microtubules at ultra-high labeling density. Packaged for simple installation and use, DECODE will enable many labs to reduce imaging times and increase localization density in SMLM.Competing Interest StatementThe authors have declared no competing interest.

}, doi = {10.1101/2020.10.26.355164}, url = {https://www.biorxiv.org/content/early/2020/10/26/2020.10.26.355164}, author = {Speiser, Artur and M{\"u}ller, Lucas-Raphael and Matti, Ulf and Obara, Christopher J. and Legant, Wesley R. and Kreshuk, Anna and Macke, Jakob H. and Ries, Jonas and Turaga, Srinivas C.} } @article {67262, title = {A developmental framework linking neurogenesis and circuit formation in the Drosophila CNS.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 May 11}, abstract = {

The mechanisms specifying neuronal diversity are well-characterized, yet it remains unclear how or if these mechanisms regulate neural circuit assembly. To address this, we mapped the developmental origin of 160 interneurons from seven bilateral neural progenitors (neuroblasts), and identify them in a synapse-scale TEM reconstruction of the larval CNS. We find that lineages concurrently build the sensory and motor neuropils by generating sensory and motor hemilineages in a Notch-dependent manner. Neurons in a hemilineage share common synaptic targeting within the neuropil, which is further refined based on neuronal temporal identity. Connectome analysis shows that hemilineage-temporal cohorts share common connectivity. Finally, we show that proximity alone cannot explain the observed connectivity structure, suggesting hemilineage/temporal identity confers an added layer of specificity. Thus, we demonstrate that the mechanisms specifying neuronal diversity also govern circuit formation and function, and that these principles are broadly applicable throughout the nervous system.

}, issn = {2050-084X}, doi = {10.7554/eLife.67510}, author = {Mark, Brandon and Lai, Sen-Lin and Zarin, Aref Arzan and Manning, Laurina and Pollington, Heather Q and Litwin-Kumar, Ashok and Cardona, Albert and Truman, James W and Doe, Chris Q} } @article {65970, title = {Direct detection of SARS-CoV-2 RNA using high-contrast pH-sensitive dyes.}, journal = {Journal of Biomolecular Techniques}, volume = {32}, year = {2021}, month = {2021 Sep 01}, pages = {121-133}, abstract = {

The worldwide COVID-19 pandemic has had devastating effects on health, healthcare infrastructure, social structure, and economics. One of the limiting factors in containing the spread of this virus has been the lack of widespread availability of fast, inexpensive, and reliable methods for testing of individuals. Frequent screening for infected and often asymptomatic people is a cornerstone of pandemic management plans. Here, we introduce two pH sensitive {\textquoteleft}LAMPshade{\textquoteright} dyes as novel readouts in an isothermal RT- LAMP amplification assay for SARS-CoV-2 RNA. The resulting JaneliaLAMP (jLAMP) assay is robust, simple, inexpensive, has low technical requirements and we describe its use and performance in direct testing of contrived and clinical samples without RNA extraction.

}, doi = {https://doi.org/10.1101/2020.12.26.20248878}, author = {Timothy A. Brown and Katherine S. Schaefer and Arthur Tsang and Hyun Ah Yi and Jonathan B. Grimm and Andrew L. Lemire and Fadi M. Jradi and Charles Kim and Kevin McGowan and Kimberly Ritola and Derek T. Armstrong and Heba H. Mostafa and Wyatt Korff and Ronald D. Vale and Luke D. Lavis} } @article {67815, title = {EASI-FISH for thick tissue defines lateral hypothalamus spatio-molecular organization.}, journal = {Cell}, volume = {184}, year = {2021}, month = {2021 Dec 01}, pages = {6361}, abstract = {

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

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

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

}, issn = {1476-4687}, doi = {10.1038/s41586-021-04116-8}, author = {Hung, King L and Yost, Kathryn E and Xie, Liangqi and Shi, Quanming and Helmsauer, Konstantin and Luebeck, Jens and Sch{\"o}pflin, Robert and Lange, Joshua T and Chamorro Gonz{\'a}lez, Roc{\'\i}o and Weiser, Natasha E and Chen, Celine and Valieva, Maria E and Wong, Ivy Tsz-Lo and Wu, Sihan and Dehkordi, Siavash R and Duffy, Connor V and Kraft, Katerina and Tang, Jun and Belk, Julia A and Rose, John C and Corces, M Ryan and Granja, Jeffrey M and Li, Rui and Rajkumar, Utkrisht and Friedlein, Jordan and Bagchi, Anindya and Satpathy, Ansuman T and Tjian, Robert and Mundlos, Stefan and Bafna, Vineet and Henssen, Anton G and Mischel, Paul S and Liu, Zhe and Chang, Howard Y} } @article {67633, title = {Enabling In Vivo Photocatalytic Activation of Rapid Bioorthogonal Chemistry by Repurposing Silicon-Rhodamine Fluorophores as Cytocompatible Far-Red Photocatalysts.}, journal = {Journal of the American Chemical Society}, volume = {143}, year = {2021}, month = {2021 Jul 21}, pages = {10793-10803}, abstract = {

Chromophores that absorb in the tissue-penetrant far-red/near-infrared window have long served as photocatalysts to generate singlet oxygen for photodynamic therapy. However, the cytotoxicity and side reactions associated with singlet oxygen sensitization have posed a problem for using long-wavelength photocatalysis to initiate other types of chemical reactions in biological environments. Herein, silicon-Rhodamine compounds (SiRs) are described as photocatalysts for inducing rapid bioorthogonal chemistry using 660 nm light through the oxidation of a dihydrotetrazine to a tetrazine in the presence of cyclooctene dienophiles. SiRs have been commonly used as fluorophores for bioimaging but have not been applied to catalyze chemical reactions. A series of SiR derivatives were evaluated, and the Janelia Fluor-SiR dyes were found to be especially effective in catalyzing photooxidation (typically 3\%). A dihydrotetrazine/tetrazine pair is described that displays high stability in both oxidation states. A protein that was site-selectively modified by cyclooctene was quantitatively conjugated upon exposure to 660 nm light and a dihydrotetrazine. By contrast, a previously described methylene blue catalyst was found to rapidly degrade the protein. SiR-red light photocatalysis was used to cross-link hyaluronic acid derivatives functionalized by dihydrotetrazine and cyclooctenes, enabling 3D culture of human prostate cancer cells. Photoinducible hydrogel formation could also be carried out in live mice through subcutaneous injection of a Cy7-labeled hydrogel precursor solution, followed by brief irradiation to produce a stable hydrogel. This cytocompatible method for using red light photocatalysis to activate bioorthogonal chemistry is anticipated to find broad applications where spatiotemporal control is needed in biological environments.

}, issn = {1520-5126}, doi = {10.1021/jacs.1c05547}, author = {Wang, Chuanqi and Zhang, He and Zhang, Tao and Zou, Xiaoyu and Wang, Hui and Rosenberger, Julia E and Vannam, Raghu and Trout, William S and Grimm, Jonathan B and Lavis, Luke D and Thorpe, Colin and Jia, Xinqiao and Li, Zibo and Fox, Joseph M} } @article {66006, title = {Endothelial junctional membrane protrusions serve as hotspots for neutrophil transmigration.}, journal = {bioRxiv}, year = {2021}, month = {2021 Jan 21}, abstract = {

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

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

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

}, issn = {2050-084X}, doi = {10.7554/eLife.66074}, author = {Arts, Janine Jg and Mahlandt, Eike K and Gr{\"o}nloh, Max and Schimmel, Lilian and Noordstra, Ivar and Gordon, Emma and van Steen, Abraham Ci and Tol, Simon and Walzog, Barbara and van Rijssel, Jos and Nolte, Martijn A and Postma, Marten and Khuon, Satya and Heddleston, John M and Wait, Eric and Chew, Teng Leong and Winter, Mark and Montanez, Eloi and Goedhart, Joachim and van Buul, Jaap D} } @article {67807, title = {Engineering of a fluorescent chemogenetic reporter with tunable color for advanced live-cell imaging.}, journal = {Nature Communications}, volume = {12}, year = {2021}, month = {2021 Nov 30}, pages = {6989}, abstract = {

Biocompatible fluorescent reporters with spectral properties spanning the entire visible spectrum are indispensable tools for imaging the biochemistry of living cells and organisms in real time. Here, we report the engineering of a fluorescent chemogenetic reporter with tunable optical and spectral properties. A collection of fluorogenic chromophores with various electronic properties enables to generate bimolecular fluorescent assemblies that cover the visible spectrum from blue to red using a single protein tag engineered and optimized by directed evolution and rational design. The ability to tune the fluorescence color and properties through simple molecular modulation provides a broad experimental versatility for imaging proteins in live cells, including neurons, and in multicellular organisms, and opens avenues for optimizing F{\"o}rster resonance energy transfer (FRET) biosensors in live cells. The ability to tune the spectral properties and fluorescence performance enables furthermore to match the specifications and requirements of advanced super-resolution imaging techniques.

}, issn = {2041-1723}, doi = {10.1038/s41467-021-27334-0}, author = {Benaissa, Hela and Ounoughi, Karim and Aujard, Isabelle and Fischer, Evelyne and Go{\"\i}ame, Rosette and Nguyen, Julie and Tebo, Alison G and Li, Chenge and Le Saux, Thomas and Bertolin, Giulia and Tramier, Marc and Danglot, Lydia and Pietrancosta, Nicolas and Morin, Xavier and Jullien, Ludovic and Gautier, Arnaud} } @article {67827, title = {Enhanced Photoinduced Electron Transfer Through a Tyrosine Relay in a De Novo Designed Protein Scaffold Bearing a Photoredox Unit and a Fe II S 4 Site}, journal = {ChemPhotoChem}, volume = {5}, year = {2021}, month = {03/2021}, pages = {665 - 668}, abstract = {

Electron transfer (ET) processes in biology over long distances often proceed via a series of hops, which reduces the distance dependence of the rate of ET. The protein matrix itself can be involved in mediating ET directly through the participation of redox-active amino acids. We have designed an electron transfer chain incorporated into a de novo protein scaffold, which is capable of photoinduced intramolecular electron transfer between a photoredox unit and a FeIIS4\ site through a tyrosine amino acid relay. The kinetics were characterized by nanosecond laser pulse photolysis and revealed that electron transfer from [RuIIIbpymal]3+\ proceeds most efficiently via a tyrosine located \~{}16 {\r A} from Rubpymal (bpymal=1-((1-([2,2'-bipyridin]-4-yl)-1H-1,2,3-triazol-4-yl)methyl)-1H-pyrrole-2,5-dione). Removal of the tyrosine as the electron relay station results in a 20-fold decrease in the apparent rate constant for the electron transfer.

}, issn = {2367-0932}, doi = {10.1002/cptc.v5.710.1002/cptc.202100014}, url = {https://onlinelibrary.wiley.com/toc/23670932/5/7}, author = {Tebo, Alison and Quaranta, Annamaria and Pecoraro, Vincent L. and Aukauloo, Ally} } @article {68989, title = {Ex utero mouse embryogenesis from pre-gastrulation to late organogenesis.}, journal = {Nature}, volume = {593}, year = {2021}, month = {05/2021}, pages = {119-124}, abstract = {

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

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

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

}, doi = {10.1101/2021.03.08.434304}, url = {https://doi.org/10.1101/2021.03.08.434304}, author = {Yuhan Wang and Mark Eddison and Greg Fleishman and Martin Weigert and Shengjin Xu and Frederick E. Henry and Tim Wang and Andrew L. Lemire and Uwe Schmidt and Hui Yang and Konrad Rokicki and Cristian Goina and Karel Svoboda and Eugene W. Myers and Stephan Saalfeld and Wyatt Korff and Scott M. Sternson and Paul W. Tillberg} } @article {67199, title = {Flexible scaling and persistence of social vocal communication.}, journal = {Nature}, volume = {593}, year = {2021}, month = {2021 May 01}, pages = {108-13}, abstract = {

Innate vocal sounds such as laughing, screaming or crying convey one{\textquoteright}s feelings to others. In many species, including humans, scaling the amplitude and duration of vocalizations is essential for effective social communication. In mice, female scent triggers male mice to emit innate courtship ultrasonic vocalizations (USVs). However, whether mice flexibly scale their vocalizations and how neural circuits are structured to generate flexibility remain largely unknown. Here we identify mouse neurons from the lateral preoptic area (LPOA) that express oestrogen receptor 1 (LPOA neurons) and, when activated, elicit the complete repertoire of USV syllables emitted during natural courtship. Neural anatomy and functional data reveal a two-step, di-synaptic circuit motif in which primary long-range inhibitory LPOA neurons relieve a clamp of local periaqueductal grey (PAG) inhibition, enabling excitatory PAG USV-gating neurons to trigger vocalizations. We find that social context shapes a wide range of USV amplitudes and bout durations. This variability is absent when PAG neurons are stimulated directly; PAG-evoked vocalizations are time-locked to neural activity and stereotypically loud. By contrast, increasing the activity of LPOA neurons scales the amplitude of vocalizations, and delaying the recovery of the inhibition clamp prolongs USV bouts. Thus, the LPOA disinhibition motif contributes to flexible loudness and the duration and persistence of bouts, which are key aspects of effective vocal social communication.

}, issn = {1476-4687}, doi = {10.1038/s41586-021-03403-8}, author = {Chen, Jingyi and Markowitz, Jeffrey E and Lilascharoen, Varoth and Taylor, Sandra and Sheurpukdi, Pete and Keller, Jason A and Jensen, Jennifer R and Lim, Byung Kook and Datta, Sandeep Robert and Stowers, Lisa} } @article {67751, title = {Functional architecture of neural circuits for leg proprioception in Drosophila.}, journal = {Current Biology}, volume = {31}, year = {2021}, month = {2021 Dec 06}, pages = {5163}, abstract = {

To effectively control their bodies, animals rely on feedback from proprioceptive mechanosensory neurons. In the Drosophila leg, different proprioceptor subtypes monitor joint position, movement direction, and vibration. Here, we investigate how these diverse sensory signals are integrated by central proprioceptive circuits. We find that signals for leg joint position and directional movement converge in second-order neurons, revealing pathways for local feedback control of leg posture. Distinct populations of second-order neurons integrate tibia vibration signals across pairs of legs, suggesting a role in detecting external substrate vibration. In each pathway, the flow of sensory information is dynamically gated and sculpted by inhibition. Overall, our results reveal parallel pathways for processing of internal and external mechanosensory signals, which we propose mediate feedback control of leg movement and vibration sensing, respectively. The existence of a functional connectivity map also provides a resource for interpreting connectomic reconstruction of neural circuits for leg proprioception.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2021.09.035}, author = {Chen, Chenghao and Agrawal, Sweta and Mark, Brandon and Mamiya, Akira and Sustar, Anne and Phelps, Jasper S and Lee, Wei-Chung Allen and Dickson, Barry J and Card, Gwyneth M and Tuthill, John C} } @article {67244, title = {A general method to improve fluorophores using deuterated auxochromes.}, journal = {JACS Au}, volume = {1}, year = {2021}, month = {2021 May 24}, pages = {690-6}, abstract = {

Fluorescence microscopy relies on dyes that absorb and then emit photons. In addition to fluorescence, fluorophores can undergo photochemical processes that decrease quantum yield or result in spectral shifts and irreversible photobleaching. Chemical strategies that suppress these undesirable pathways{\textemdash}thereby increasing the brightness and photostability of fluorophores{\textemdash}are crucial for advancing the frontier of bioimaging. Here, we describe a general method to improve small-molecule fluorophores by incorporating deuterium into the alkylamino auxochromes of rhodamines and other dyes. This strategy increases fluorescence quantum yield, inhibits photochemically induced spectral shifts, and slows irreparable photobleaching, yielding next-generation labels with improved performance in cellular imaging experiments.

}, issn = {2691-3704}, doi = {10.1021/jacsau.1c00006}, url = {https://doi.org/10.1021/jacsau.1c00006}, author = {Grimm, Jonathan B. and Xie, Liangqi and Casler, Jason C. and Patel, Ronak and Tkachuk, Ariana N. and Falco, Natalie and Choi, Heejun and Lippincott-Schwartz, Jennifer and Brown, Timothy A. and Glick, Benjamin S. and Liu, Zhe and Lavis, Luke D.} } @article {67234, title = {High-precision coding in visual cortex.}, journal = {Cell}, volume = {184}, year = {2021}, month = {2021 May 13}, pages = {2767-78}, abstract = {

Individual neurons in visual cortex provide the brain with unreliable estimates of visual features. It is not known whether the single-neuron variability is correlated across large neural populations, thus impairing the global encoding of stimuli. We recorded simultaneously from up to 50,000 neurons in mouse primary visual cortex (V1) and in higher order visual areas and measured stimulus discrimination thresholds of 0.35{\textdegree} and 0.37{\textdegree}, respectively, in an orientation decoding task. These neural thresholds were almost 100 times smaller than the behavioral discrimination thresholds reported in mice. This discrepancy could not be explained by stimulus properties or arousal states. Furthermore, behavioral variability during a sensory discrimination task could not be explained by neural variability in V1. Instead, behavior-related neural activity arose dynamically across a network of non-sensory brain areas. These results imply that perceptual discrimination in mice is limited by downstream decoders, not by neural noise in sensory representations.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2021.03.042}, author = {Stringer, Carsen and Michaelos, Michalis and Tsyboulski, Dmitri and Lindo, Sarah E and Pachitariu, Marius} } @article {66020, title = {Idiosyncratic learning performance in flies generalizes across modalities.}, journal = {bioRxiv}, year = {2021}, month = {2021 Jan 25}, abstract = {

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

}, author = {Matthew Smith and Kyle S. Honegger and Glenn Turner and Benjamin de Bivort} } @article {67303, title = {Information flow, cell types and stereotypy in a full olfactory connectome.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 May 25}, abstract = {

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

}, issn = {2050-084X}, doi = {10.7554/eLife.66018}, author = {Schlegel, Philipp and Bates, Alexander Shakeel and St{\"u}rner, Tomke and Jagannathan, Sridhar R and Drummond, Nikolas and Hsu, Joseph and Serratosa Capdevila, Laia and Javier, Alexandre and Marin, Elizabeth C and Barth-Maron, Asa and Tamimi, Imaan Fm and Li, Feng and Rubin, Gerald M and Plaza, Stephen M and Costa, Marta and Jefferis, Gregory Sxe} } @article {67210, title = {Intracellular mRNA transport and localized translation.}, journal = {Nature Reviews Molecular Cell Biology}, volume = {22}, year = {2021}, month = {2021 Jul 1}, pages = {483-504}, abstract = {

Fine-tuning cellular physiology in response to intracellular and environmental cues requires precise temporal and spatial control of gene expression. High-resolution imaging technologies to detect mRNAs and their translation state have revealed that all living organisms localize mRNAs in subcellular compartments and create translation hotspots, enabling cells to tune gene expression locally. Therefore, mRNA localization is a conserved and integral part of gene expression regulation from prokaryotic to eukaryotic cells. In this Review, we discuss the mechanisms of mRNA transport and local mRNA translation across the kingdoms of life and at organellar, subcellular and multicellular resolution. We also discuss the properties of messenger ribonucleoprotein and higher order RNA granules and how they may influence mRNA transport and local protein synthesis. Finally, we summarize the technological developments that allow us to study mRNA localization and local translation through the simultaneous detection of mRNAs and proteins in single cells, mRNA and nascent protein single-molecule imaging, and bulk RNA and protein detection methods.

}, issn = {1471-0080}, doi = {10.1038/s41580-021-00356-8}, author = {Das, Sulagna and Vera, Maria and Gandin, Valentina and Singer, Robert H and Tutucci, Evelina} } @article {67228, title = {Local Shape Descriptors for Neuron Segmentation}, journal = {bioRxiv}, year = {2021}, month = {2021/01}, abstract = {

We present a simple, yet effective, auxiliary learning task for the problem of neuron segmentation in electron microscopy volumes. The auxiliary task consists of the prediction of Local Shape Descriptors (LSDs), which we combine with conventional voxel-wise direct neighbor affinities for neuron boundary detection. The shape descriptors are designed to capture local statistics about the neuron to be segmented, such as diameter, elongation, and direction. On a large study comparing several existing methods across various specimen, imaging techniques, and resolutions, we find that auxiliary learning of LSDs consistently increases segmentation accuracy of affinity-based methods over a range of metrics. Furthermore, the addition of LSDs promotes affinitybased segmentation methods to be on par with the current state of the art for neuron segmentation (Flood-Filling Networks, FFN), while being two orders of magnitudes more efficient{\textemdash}a critical requirement for the processing of future petabyte-sized datasets. Implementations of the new auxiliary learning task, network architectures, training, prediction, and evaluation code, as well as the datasets used in this study are publicly available as a benchmark for future method contributions.Competing Interest StatementThe authors have declared no competing interest.

}, doi = {10.1101/2021.01.18.427039}, url = {https://www.biorxiv.org/content/early/2021/01/18/2021.01.18.427039}, author = {Sheridan, Arlo and Nguyen, Tri and Deb, Diptodip and Lee, Wei-Chung Allen and Saalfeld, Stephan and Turaga, Srini and Manor, Uri and Funke, Jan} } @article {67738, title = {The LRRK2 G2019S mutation alters astrocyte-to-neuron communication via extracellular vesicles and induces neuron atrophy in a human iPSC-derived model of Parkinson{\textquoteright}s disease}, journal = {eLife}, year = {2021}, month = {2021 Sep 30}, abstract = {

Astrocytes are essential cells of the central nervous system, characterized by dynamic relationships with neurons that range from functional metabolic interactions and regulation of neuronal firing activities, to the release of neurotrophic and neuroprotective factors. In Parkinson{\textquoteright}s disease (PD), dopaminergic neurons are progressively lost during the course of the disease, but the effects of PD on astrocytes and astrocyte-to-neuron communication remains largely unknown. This study focuses on the effects of the PD-related mutation LRRK2 G2019S in astrocytes generated from patient-derived induced pluripotent stem cells. We report the alteration of extracellular vesicle (EV) biogenesis in astrocytes, and we identify the abnormal accumulation of key PD-related proteins within multi vesicular bodies (MVBs). We found that dopaminergic neurons internalize astrocyte-secreted EVs and that LRRK2 G2019S EVs are abnormally enriched in neurites and fail to provide full neurotrophic support to dopaminergic neurons. Thus, dysfunctional astrocyte-to-neuron communication via altered EV biological properties may participate in the progression of PD.

}, doi = {https://doi.org/10.7554/eLife.73062}, author = {Aurelie de Rus Jacquet and Jenna L. Tancredi and Andrew L. Lemire and Michael C. DeSantis and Wei-Ping Li and Erin K. O{\textquoteright}Shea} } @article {67271, title = {Lupus susceptibility region containing CDKN1B rs34330 mechanistically influences expression and function of multiple target genes, also linked to proliferation and apoptosis.}, journal = {Arthritis Rheumatology}, volume = {73}, year = {2021}, month = {2021 Dec 01}, pages = {2303-13}, abstract = {

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

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

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

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

}, issn = {2326-5205}, doi = {10.1002/art.41799}, author = {Singh, Bhupinder and Maiti, Guru P and Zhou, Xujie and Fazel-Najafabadi, Mehdi and Bae, Sang-Cheol and Sun, Celi and Terao, Chikashi and Okada, Yukinori and Chua, Kek Heng and Kochi, Yuta and Guthridge, Joel M and Zhang, Hong and Weirauch, Matthew and James, Judith A and Harley, John B and Varshney, Gaurav K and Looger, Loren L and Nath, Swapan K} } @article {67826, title = {Nitrite reductase activity within an antiparallel de novo scaffold.}, journal = {JBIC Journal of Biological Inorganic Chemistry}, volume = {26}, year = {2021}, month = {09/2021}, pages = {855 - 862}, abstract = {

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

}, issn = {0949-8257}, doi = {10.1007/s00775-021-01889-1}, url = {https://link.springer.com/10.1007/s00775-021-01889-1}, author = {Koebke, Karl J. and Tebo, Alison G. and Manickas, Elizabeth C. and Deb, Aniruddha and Penner-Hahn, James E. and Pecoraro, Vincent L.} } @article {67753, title = {An open-access volume electron microscopy atlas of whole cells and tissues.}, journal = {Nature}, volume = {599}, year = {2021}, month = {2021 Nov 1}, pages = {147-51}, abstract = {

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

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

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

}, issn = {2045-2322}, doi = {10.1038/s41598-021-89676-5}, author = {Fuqua, Timothy and Jordan, Jeff and Halavatyi, Aliaksandr and Tischer, Christian and Richter, Kerstin and Crocker, Justin} } @article {67825, title = {The power of peer networking for improving STEM faculty job applications: a successful pilot program}, journal = {bioRxiv}, year = {2021}, month = {10/2021}, abstract = {

In order to successfully obtain a faculty position, postdoctoral fellows or {\textquoteleft}postdocs{\textquoteright}, must submit an application which requires considerable time and effort to produce. These job applications are often reviewed by mentors and colleagues, but rarely are postdocs offered the opportunity to solicit feedback multiple times from reviewers with the same breadth of expertise often found on an academic search committee. To address this gap, this manuscript describes an international peer reviewing program for small groups of postdocs with a broad range of expertise to reciprocally and iteratively provide feedback to each other on their application materials. Over 145 postdocs have participated, often multiple times, over three years. A survey of participants in this program revealed that nearly all participants would recommend participation in such a program to other faculty applicants. Furthermore, this program was more likely to attract participants who struggled to find mentoring and support elsewhere, either because they changed fields or because of their identity as a woman or member of an underrepresented population in STEM. Participation in programs like this one could provide early career academics like postdocs with a diverse and supportive community of peer mentors during the difficult search for a faculty position. Such psychosocial support and encouragement has been shown to prevent attrition of individuals from these populations and programs like this one target the largest {\textquoteleft}leak{\textquoteright} in the pipeline, that of postdoc to faculty. Implementation of similar peer reviewing programs by universities or professional scientific societies could provide a valuable mechanism of support and increased chances of success for early-career academics in their search for independence.Competing Interest StatementThe authors have declared no competing interest.

}, doi = {10.1101/2021.10.16.464662}, url = {https://www.biorxiv.org/content/early/2021/10/18/2021.10.16.464662}, author = {Guardia, Carlos M. and Kane, Erin and Tebo, Alison G. and Sanders, Anna A.W.M. and Kaya, Devrim and Grogan, Kathleen E.} } @article {68990, title = {Principles of signaling pathway modulation for enhancing human naive pluripotency induction.}, journal = {Cell Stem Cell}, volume = {28}, year = {2021}, month = {09/2021}, pages = {1549-1565.e12}, abstract = {

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

}, keywords = {Animals, Cell Differentiation, Embryo, Mammalian, Humans, Mice, Pluripotent Stem Cells, Signal Transduction, Trophoblasts}, issn = {1875-9777}, doi = {10.1016/j.stem.2021.04.001}, author = {Bayerl, Jonathan and Ayyash, Muneef and Shani, Tom and Manor, Yair Shlomo and Gafni, Ohad and Massarwa, Rada and Kalma, Yael and Aguilera-Castrejon, Alejandro and Zerbib, Mirie and Amir, Hadar and Sheban, Daoud and Geula, Shay and Mor, Nofar and Weinberger, Leehee and Naveh Tassa, Segev and Krupalnik, Vladislav and Oldak, Bernardo and Livnat, Nir and Tarazi, Shadi and Tawil, Shadi and Wildschutz, Emilie and Ashouokhi, Shahd and Lasman, Lior and Rotter, Varda and Hanna, Suhair and Ben-Yosef, Dalit and Novershtern, Noa and Viukov, Sergey and Hanna, Jacob H} } @booklet {67972, title = {Programmable 3D snapshot microscopy with Fourier convolutional networks}, year = {2021}, abstract = {

3D snapshot microscopy enables fast volumetric imaging by capturing a 3D volume in a single 2D camera image and performing computational reconstruction. Fast volumetric imaging has a variety of biological applications such as whole brain imaging of rapid neural activity in larval zebrafish. The optimal microscope design for this optical 3D-to-2D encoding is both sample- and task-dependent, with no general solution known. Deep learning based decoders can be combined with a differentiable simulation of an optical encoder for end-to-end optimization of both the deep learning decoder and optical encoder. This technique has been used to engineer local optical encoders for other problems such as depth estimation, 3D particle localization, and lensless photography. However, 3D snapshot microscopy is known to require a highly non-local optical encoder which existing UNet-based decoders are not able to engineer. We show that a neural network architecture based on global kernel Fourier convolutional neural networks can efficiently decode information from multiple depths in a volume, globally encoded across a 3D snapshot image. We show in simulation that our proposed networks succeed in engineering and reconstructing optical encoders for 3D snapshot microscopy where the existing state-of-the-art UNet architecture fails. We also show that our networks outperform the state-of-the-art learned reconstruction algorithms for a computational photography dataset collected on a prototype lensless camera which also uses a highly non-local optical encoding.

}, keywords = {Computer Vision and Pattern Recognition (cs.CV), electronic engineering, FOS: Computer and information sciences, FOS: Electrical engineering, Image and Video Processing (eess.IV), information engineering, Machine Learning (cs.LG)}, doi = {10.48550/ARXIV.2104.10611}, url = {https://arxiv.org/abs/2104.10611}, author = {Deb, Diptodip and Jiao, Zhenfei and Chen, Alex B. and Broxton, Michael and Ahrens, Misha B. and Podgorski, Kaspar and Turaga, Srinivas C.} } @article {67300, title = {Protein-Retention Expansion Microscopy (ExM): Scalable and Convenient Super-Resolution Microscopy.}, journal = {Methods in Molecular Biology}, volume = {2304}, year = {2021}, month = {2021 May 28}, pages = {147-156}, abstract = {

Expansion microscopy (ExM) is a method to expand biological specimens ~fourfold in each dimension by embedding in a hyper-swellable gel material. The expansion is uniform across observable length scales, enabling imaging of structures previously too small to resolve. ExM is compatible with any microscope and does not require expensive materials or specialized software, offering effectively sub-diffraction-limited imaging capabilities to labs that are not equipped to use traditional super-resolution imaging methods. Expanded specimens are ~99\% water, resulting in strongly reduced optical scattering and enabling imaging of sub-diffraction-limited structures throughout specimens up to several hundred microns in (pre-expansion) thickness.

}, issn = {1940-6029}, doi = {10.1007/978-1-0716-1402-0_7}, author = {Tillberg, Paul} } @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 {65833, title = {Reconstruction of motor control circuits in adult Drosophila using automated transmission electron microscopy}, journal = {Cell}, volume = {184}, year = {2021}, month = {2021 Feb 04}, abstract = {

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

}, doi = {10.1101/2020.01.10.902478}, author = {Maniates-Selvin, Jasper T. and Hildebrand, David Grant Colburn and Graham, Brett J. and Kuan, Aaron T. and Thomas, Logan A. and Nguyen, Tri and Buhmann, Julia and Azevedo, Anthony W. and Shanny, Brendan L. and Funke, Jan and Tuthill, John C. and Lee, Wei-Chung Allen} } @article {67647, title = {Single-molecule imaging of chromatin remodelers reveals role of ATPase in promoting fast kinetics of target search and dissociation from chromatin.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Jul 27}, abstract = {

Conserved ATP-dependent chromatin remodelers establish and maintain genome-wide chromatin architectures of regulatory DNA during cellular lifespan, but the temporal interactions between remodelers and chromatin targets have been obscure. We performed live-cell single-molecule tracking for RSC, SWI/SNF, CHD1, ISW1, ISW2, and INO80 remodeling complexes in budding yeast and detected hyperkinetic behaviors for chromatin-bound molecules that frequently transition to the free state for all complexes. Chromatin-bound remodelers display notably higher diffusion than nucleosomal histones, and strikingly fast dissociation kinetics with 4-7 s mean residence times. These enhanced dynamics require ATP binding or hydrolysis by the catalytic ATPase, uncovering an additional function to its established role in nucleosome remodeling. Kinetic simulations show that multiple remodelers can repeatedly occupy the same promoter region on a timescale of minutes, implicating an unending {\textquoteright}tug-of-war{\textquoteright} that controls a temporally shifting window of accessibility for the transcription initiation machinery.

}, issn = {2050-084X}, doi = {10.7554/eLife.69387}, author = {Kim, Jee Min and Visanpattanasin, Pat and Jou, Vivian and Liu, Sheng and Tang, Xiaona and Zheng, Qinsi and Li, Kai Yu and Snedeker, Jonathan and Lavis, Luke D and Lionnet, Timoth{\'e}e and Wu, Carl} } @article {67229, title = {SongExplorer: A deep learning workflow for discovery and segmentation of animal acoustic communication signals}, journal = {bioRxiv}, year = {2021}, month = {03/2021}, abstract = {

Many animals produce distinct sounds or substrate-borne vibrations, but these signals have proved challenging to segment with automated algorithms. We have developed SongExplorer, a web-browser based interface wrapped around a deep-learning algorithm that supports an interactive workflow for (1) discovery of animal sounds, (2) manual annotation, (3) supervised training of a deep convolutional neural network, and (4) automated segmentation of recordings. Raw data can be explored by simultaneously examining song events, both individually and in the context of the entire recording, watching synced video, and listening to song. We provide a simple way to visualize many song events from large datasets within an interactive low-dimensional visualization, which facilitates detection and correction of incorrectly labelled song events. The machine learning model we implemented displays higher accuracy than existing heuristic algorithms and similar accuracy as two expert human annotators. We show that SongExplorer allows rapid detection of all song types from new species and of novel song types in previously well-studied species.Competing Interest StatementThe authors have declared no competing interest.

}, doi = {10.1101/2021.03.26.437280}, url = {https://www.biorxiv.org/content/early/2021/03/26/2021.03.26.437280}, author = {Arthur, Benjamin J. and Ding, Yun and Sosale, Medhini and Khalif, Faduma and Kim, Elizabeth and Waddell, Peter and Turaga, Srinivas C. and Stern, David L.} } @article {67671, title = {Spatiotemporal coordination of transcription preinitiation complex assembly in live cells.}, journal = {Molecular Cell}, volume = {81}, year = {2021}, month = {2021 Sep 02}, pages = {3560-3575}, abstract = {

Transcription initiation by RNA polymerase II (RNA Pol II) requires preinitiation complex (PIC) assembly at gene promoters. In the dynamic nucleus, where thousands of promoters are broadly distributed in chromatin, it is unclear how multiple individual components converge on any target to establish the PIC. Here we use live-cell, single-molecule tracking in S.\ cerevisiae to visualize constrained exploration of the nucleoplasm by PIC components and Mediator{\textquoteright}s key role in guiding this process. On chromatin, TFIID/TATA-binding protein (TBP), Mediator, and RNA Pol II instruct assembly of a short-lived PIC, which occurs infrequently but efficiently within a few seconds on average. Moreover, PIC exclusion by nucleosome encroachment underscores regulated promoter accessibility by chromatin remodeling. Thus, coordinated nuclear exploration and recruitment to accessible targets underlies dynamic PIC establishment in yeast. Our study provides a global spatiotemporal model for transcription initiation in live cells.

}, issn = {1097-4164}, doi = {10.1016/j.molcel.2021.07.022}, author = {Nguyen, Vu Q and Ranjan, Anand and Liu, Sheng and Tang, Xiaona and Ling, Yick Hin and Wisniewski, Jan and Mizuguchi, Gaku and Li, Kai Yu and Jou, Vivian and Zheng, Qinsi and Lavis, Luke D and Lionnet, Timoth{\'e}e and Wu, Carl} } @article {67820, title = {Structure and RNA template requirements of RNA-DEPENDENT RNA POLYMERASE 2.}, journal = {Proceedings of the National Academy of Sciences of the U.S.A.}, volume = {118}, year = {2021}, month = {2021 Dec 21}, abstract = {

RNA-dependent RNA polymerases play essential roles in RNA-mediated gene silencing in eukaryotes. In , RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) physically interacts with DNA-dependent NUCLEAR RNA POLYMERASE IV (Pol IV) and their activities are tightly coupled, with Pol IV transcriptional arrest, induced by the nontemplate DNA strand, somehow enabling RDR2 to engage Pol IV transcripts and generate double-stranded RNAs. The double-stranded RNAs are then released from the Pol IV-RDR2 complex and diced into short-interfering RNAs that guide RNA-directed DNA methylation and silencing. Here we report the structure of full-length RDR2, at an overall resolution of 3.1 {\r A}, determined by cryoelectron microscopy. The N-terminal region contains an RNA-recognition motif adjacent to a positively charged channel that leads to a catalytic center with striking structural homology to the catalytic centers of multisubunit DNA-dependent RNA polymerases. We show that RDR2 initiates 1 to 2 nt internal to the 3{\textquoteright} ends of its templates and can transcribe the RNA of an RNA/DNA hybrid, provided that 9 or more nucleotides are unpaired at the RNA{\textquoteright}s 3{\textquoteright} end. Using a nucleic acid configuration that mimics the arrangement of RNA and DNA strands upon Pol IV transcriptional arrest, we show that displacement of the RNA 3{\textquoteright} end occurs as the DNA template and nontemplate strands reanneal, enabling RDR2 transcription. These results suggest a model in which Pol IV arrest and backtracking displaces the RNA 3{\textquoteright} end as the DNA strands reanneal, allowing RDR2 to engage the RNA and synthesize the complementary strand.

}, issn = {1091-6490}, doi = {10.1073/pnas.2115899118}, author = {Fukudome, Akihito and Singh, Jasleen and Mishra, Vibhor and Reddem, Eswar and Martinez-Marquez, Francisco and Wenzel, Sabine and Yan, Rui and Shiozaki, Momoko and Yu, Zhiheng and Wang, Joseph Che-Yen and Takagi, Yuichiro and Pikaard, Craig S} } @article {66028, title = {Structure-Function Dataset Reveals Environment Effects within a Fluorescent Protein Model System.}, journal = {Angew Chemie (International Edition English)}, year = {2021}, month = {2021 Feb 04}, abstract = {

Anisotropic environments can drastically alter the spectroscopy and photochemistry of molecules, leading to complex structure-function relationships. We examined this using fluorescent proteins as easy-to-modify model systems. Starting from a single scaffold, we have developed a range of 27 photochromic fluorescent proteins that cover a broad range of spectroscopic properties, including the determination of 43 crystal structures. Correlation and principal component analysis confirmed the complex relationship between structure and spectroscopy, but also allowed us to identify consistent trends and to relate these to the spatial organization. We find that changes in spectroscopic properties can come about through multiple underlying mechanisms, of which polarity, hydrogen bonding and presence of water molecules are key modulators. We anticipate that our findings and rich structure/spectroscopy dataset can open opportunities for the development and evaluation of new and existing protein engineering methods.

}, issn = {1521-3773}, doi = {10.1002/anie.202015201}, author = {De Zitter, Elke and Hugelier, Siewert and Duw{\'e}, Sam and Vandenberg, Wim and Tebo, Alison G and Van Meervelt, Luc and Dedecker, Peter} } @article {66008, title = {Survey of spiking in the mouse visual system reveals functional hierarchy.}, journal = {Nature}, volume = {592(7852):86-92}, year = {2021}, month = {2021 Jan 20}, pages = {86-92}, abstract = {

The anatomy of the mammalian visual system, from the retina to the neocortex, is organized hierarchically. However, direct observation of cellular-level functional interactions across this hierarchy is lacking due to the challenge of simultaneously recording activity across numerous regions. Here we describe a large, open dataset-part of the Allen Brain Observatory-that surveys spiking from tens of thousands of units in six cortical and two thalamic regions in the brains of mice responding to a battery of visual stimuli. Using cross-correlation analysis, we reveal that the organization of inter-area functional connectivity during visual stimulation mirrors the anatomical hierarchy from the Allen Mouse Brain Connectivity Atlas. We find that four classical hierarchical measures-response latency, receptive-field size, phase-locking to drifting gratings and response decay timescale-are all correlated with the hierarchy. Moreover, recordings obtained during a visual task reveal that the correlation between neural activity and behavioural choice also increases along the hierarchy. Our study provides a foundation for understanding coding and signal propagation across hierarchically organized cortical and thalamic visual areas.

}, issn = {1476-4687}, doi = {10.1038/s41586-020-03171-x}, author = {Siegle, Joshua H and Jia, Xiaoxuan and Durand, Severine and Gale, Sam and Bennett, Corbett and Graddis, Nile and Heller, Greggory and Ramirez, Tamina K and Choi, Hannah and Luviano, Jennifer A and Groblewski, Peter A and Ahmed, Ruweida and Arkhipov, Anton and Bernard, Amy and Billeh, Yazan N and Brown, Dillan and Buice, Michael A and Cain, Nicolas and Caldejon, Shiella and Casal, Linzy and Cho, Andrew and Chvilicek, Maggie and Cox, Timothy C and Dai, Kael and Denman, Daniel J and de Vries, Saskia E J and Dietzman, Roald and Esposito, Luke and Farrell, Colin and Feng, David and Galbraith, John and Garrett, Marina and Gelfand, Emily C and Hancock, Nicole and Harris, Julie A and Howard, Robert and Hu, Brian and Hytnen, Ross and Iyer, Ramakrishnan and Jessett, Erika and Johnson, Katelyn and Kato, India and Kiggins, Justin and Lambert, Sophie and Lecoq, Jerome and Ledochowitsch, Peter and Lee, Jung Hoon and Leon, Arielle and Li, Yang and Liang, Elizabeth and Long, Fuhui and Mace, Kyla and Melchior, Jose and Millman, Daniel and Mollenkopf, Tyler and Nayan, Chelsea and Ng, Lydia and Ngo, Kiet and Nguyen, Thuyahn and Nicovich, Philip R and North, Kat and Ocker, Gabriel Koch and Ollerenshaw, Doug and Oliver, Michael and Pachitariu, Marius and Perkins, Jed and Reding, Melissa and Reid, David and Robertson, Miranda and Ronellenfitch, Kara and Seid, Sam and Slaughterbeck, Cliff and Stoecklin, Michelle and Sullivan, David and Sutton, Ben and Swapp, Jackie and Thompson, Carol and Turner, Kristen and Wakeman, Wayne and Whitesell, Jennifer D and Williams, Derric and Williford, Ali and Young, Rob and Zeng, Hongkui and Naylor, Sarah and Phillips, John W and Reid, R Clay and Mihalas, Stefan and Olsen, Shawn R and Koch, Christof} } @article {67843, title = {Synaptic targets of photoreceptors specialized to detect color and skylight polarization in .}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Dec 16}, abstract = {

Color and polarization provide complementary information about the world and are detected by specialized photoreceptors. However, the downstream neural circuits that process these distinct modalities are incompletely understood in any animal. Using electron microscopy, we have systematically reconstructed the synaptic targets of the photoreceptors specialized to detect color and skylight polarization in Drosophila, and we have used light microscopy to confirm many of our findings. We identified known and novel downstream targets that are selective for different wavelengths or polarized light, and followed their projections to other areas in the optic lobes and the central brain. Our results revealed many synapses along the photoreceptor axons between brain regions, new pathways in the optic lobes, and spatially segregated projections to central brain regions. Strikingly, photoreceptors in the polarization-sensitive dorsal rim area target fewer cell types, and lack strong connections to the lobula, a neuropil involved in color processing. Our reconstruction identifies shared wiring and modality-specific specializations for color and polarization vision, and provides a comprehensive view of the first steps of the pathways processing color and polarized light inputs.

}, issn = {2050-084X}, doi = {10.7554/eLife.71858}, author = {Kind, Emil and Longden, Kit D and Nern, Aljoscha and Zhao, Arthur and Sancer, Gizem and Flynn, Miriam A and Laughland, Connor W and Gezahegn, Bruck and Ludwig, Henrique Df and Thomson, Alex G and Obrusnik, Tessa and Alarc{\'o}n, Paula G and Dionne, Heather and Bock, Davi D and Rubin, Gerald M and Reiser, Michael B and Wernet, Mathias F} } @article {67713, title = {Synchronous and opponent thermosensors use flexible cross-inhibition to orchestrate thermal homeostasis.}, journal = {Science Advances}, volume = {7}, year = {2021}, month = {2021 Aug 27}, abstract = {

Body temperature homeostasis is essential and reliant upon the integration of outputs from multiple classes of cooling- and warming-responsive cells. The computations that integrate these outputs are not understood. Here, we discover a set of warming cells (WCs) and show that the outputs of these WCs combine with previously described cooling cells (CCs) in a cross-inhibition computation to drive thermal homeostasis in larval WCs and CCs detect temperature changes using overlapping combinations of ionotropic receptors: Ir68a, Ir93a, and Ir25a for WCs and Ir21a, Ir93a, and Ir25a for CCs. WCs mediate avoidance to warming while cross-inhibiting avoidance to cooling, and CCs mediate avoidance to cooling while cross-inhibiting avoidance to warming. Ambient temperature-dependent regulation of the strength of WC- and CC-mediated cross-inhibition keeps larvae near their homeostatic set point. Using neurophysiology, quantitative behavioral analysis, and connectomics, we demonstrate how flexible integration between warming and cooling pathways can orchestrate homeostatic thermoregulation.

}, issn = {2375-2548}, doi = {10.1126/sciadv.abg6707}, author = {Hernandez-Nunez, Luis and Chen, Alicia and Budelli, Gonzalo and Berck, Matthew E and Richter, Vincent and Rist, Anna and Thum, Andreas S and Cardona, Albert and Klein, Mason and Garrity, Paul and Samuel, Aravinthan D T} } @article {66001, title = {Systems Neuroscience of Natural Behaviors in Rodents.}, journal = {Journal of Neuroscience}, volume = {41}, year = {2021}, month = {2021 Feb 03}, pages = {911-1}, abstract = {

Animals evolved in complex environments, producing a wide range of behaviors, including navigation, foraging, prey capture, and conspecific interactions, which vary over timescales ranging from milliseconds to days. Historically, these behaviors have been the focus of study for ecology and ethology, while systems neuroscience has largely focused on short timescale behaviors that can be repeated thousands of times and occur in highly artificial environments. Thanks to recent advances in machine learning, miniaturization, and computation, it is newly possible to study freely moving animals in more natural conditions while applying systems techniques: performing temporally specific perturbations, modeling behavioral strategies, and recording from large numbers of neurons while animals are freely moving. The authors of this review are a group of scientists with deep appreciation for the common aims of systems neuroscience, ecology, and ethology. We believe it is an extremely exciting time to be a neuroscientist, as we have an opportunity to grow as a field, to embrace interdisciplinary, open, collaborative research to provide new insights and allow researchers to link knowledge across disciplines, species, and scales. Here we discuss the origins of ethology, ecology, and systems neuroscience in the context of our own work and highlight how combining approaches across these fields has provided fresh insights into our research. We hope this review facilitates some of these interactions and alliances and helps us all do even better science, together.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.1877-20.2020}, author = {Dennis, Emily Jane and El Hady, Ahmed and Michaiel, Angie and Clemens, Ann and Gowan Tervo, Dougal R and Voigts, Jakob and Datta, Sandeep Robert} } @article {67853, title = {Systems Neuroscience of Natural Behaviors in Rodents}, journal = {Journal of Neuroscience}, volume = {41}, year = {2021}, month = {02/2021}, pages = {911{\textendash}919}, abstract = {

Animals evolved in complex environments, producing a wide range of behaviors, including navigation, foraging, prey capture, and conspecific interactions, which vary over timescales ranging from milliseconds to days. Historically, these behaviors have been the focus of study for ecology and ethology, while systems neuroscience has largely focused on short timescale behaviors that can be repeated thousands of times and occur in highly artificial environments. Thanks to recent advances in machine learning, miniaturization, and computation, it is newly possible to study freely moving animals in more natural conditions while applying systems techniques: performing temporally specific perturbations, modeling behavioral strategies, and recording from large numbers of neurons while animals are freely moving. The authors of this review are a group of scientists with deep appreciation for the common aims of systems neuroscience, ecology, and ethology. We believe it is an extremely exciting time to be a neuroscientist, as we have an opportunity to grow as a field, to embrace interdisciplinary, open, collaborative research to provide new insights and allow researchers to link knowledge across disciplines, species, and scales. Here we discuss the origins of ethology, ecology, and systems neuroscience in the context of our own work and highlight how combining approaches across these fields has provided fresh insights into our research. We hope this review facilitates some of these interactions and alliances and helps us all do even better science, together.

}, issn = {0270-6474}, doi = {10.1523/JNEUROSCI.1877-20.2020}, url = {https://www.jneurosci.org/content/41/5/911}, author = {Dennis, Emily Jane and El Hady, Ahmed and Michaiel, Angie and Clemens, Ann and Tervo, Dougal R. Gowan and Voigts, Jakob and Datta, Sandeep Robert} } @article {67310, title = {Unveiling the sensory and interneuronal pathways of the neuroendocrine connectome in Drosophila.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Jun 04}, abstract = {

Neuroendocrine systems in animals maintain organismal homeostasis and regulate stress response. Although a great deal of work has been done on the neuropeptides and hormones that are released and act on target organs in the periphery, the synaptic inputs onto these neuroendocrine outputs in the brain are less well understood. Here, we use the transmission electron microscopy reconstruction of a whole central nervous system in the larva to elucidate the sensory pathways and the interneurons that provide synaptic input to the neurosecretory cells projecting to the endocrine organs. Predicted by network modeling, we also identify a new carbon dioxide-responsive network that acts on a specific set of neurosecretory cells and that includes those expressing corazonin (Crz) and diuretic hormone 44 (Dh44) neuropeptides. Our analysis reveals a neuronal network architecture for combinatorial action based on sensory and interneuronal pathways that converge onto distinct combinations of neuroendocrine outputs.

}, issn = {2050-084X}, doi = {10.7554/eLife.65745}, author = {H{\"u}ckesfeld, Sebastian and Schlegel, Philipp and Miroschnikow, Anton and Schoofs, Andreas and Zinke, Ingo and Haubrich, Andr{\'e} N and Schneider-Mizell, Casey M and Truman, James W and Fetter, Richard D and Cardona, Albert and Pankratz, Michael J} } @article {67833, title = {Versatile On-Demand Fluorescent Labeling of Fusion Proteins Using Fluorescence-Activating and Absorption-Shifting Tag (FAST).}, journal = {Methods Mol Biol}, volume = {2350}, year = {2021}, month = {2021}, pages = {253-265}, abstract = {

Observing the localization, the concentration, and the distribution of proteins in cells or organisms is essential to understand theirs functions. General and versatile methods allowing multiplexed imaging of proteins under a large variety of experimental conditions are thus essential for deciphering the inner workings of cells and organisms. Here, we present a general method based on the non-covalent labeling of a small protein tag, named FAST (fluorescence-activating and absorption-shifting tag), with various fluorogenic ligands that light up upon labeling, which makes the simple, robust, and versatile on-demand labeling of fusion proteins in a wide range of experimental systems possible.

}, keywords = {Animals, Cell Line, Flow Cytometry, Fluorescent Dyes, Humans, Microscopy, Fluorescence, Molecular Structure, Recombinant Fusion Proteins, Staining and Labeling, Zebrafish}, issn = {1940-6029}, doi = {10.1007/978-1-0716-1593-5_16}, author = {Gautier, Arnaud and Jullien, Ludovic and Li, Chenge and Plamont, Marie-Aude and Tebo, Alison G and Thauvin, Marion and Volovitch, Michel and Vriz, Sophie} } @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 {65276, title = {Accurate measurement of fast endocytic recycling kinetics in real time.}, journal = {Journal of Cell Science}, volume = {133}, year = {2020}, month = {2020 Jan 22}, abstract = {

The fast turnover of membrane components through endocytosis and recycling allows precise control of the composition of the plasma membrane. Endocytic recycling can be rapid with some molecules returning to the plasma membrane with a \<5 minutes. Existing methods to study these trafficking pathways utilize chemical, radioactive, or fluorescent labeling of cell surface receptors in pulse-chase experiments, which require tedious washing steps and manual collection of samples. Here, we introduce a live-cell endocytic recycling assay, based on a newly designed cell-impermeable, fluorogenic ligand for HaloTag: {\textquoteright}Janelia Fluor 635i{\textquoteright} (JFi; i=impermeant) which allows real-time detection of membrane receptor recycling at steady state. We used this method to study the effect of iron depletion on transferrin receptor (TfR) recycling using the chelator desferrioxamine. We found this perturbation significantly increases the TfR recycling rate. The high temporal resolution and simplicity of this assay provides a clear advantage over extant methods and makes it ideal for large scale cellular imaging studies. This assay can be adapted to examine other cellular kinetic parameters such as protein turnover and biosynthetic trafficking.

}, issn = {1477-9137}, doi = {10.1242/jcs.231225}, author = {Jonker, Caspar T H and Deo, Claire and Zager, Patrick J and Tkachuk, Ariana N and Weinstein, Alan M and Rodriguez-Boulan, Enrique and Lavis, Luke D and Schreiner, Ryan} } @article {65240, title = {Aurora B functions at the apical surface after specialized cytokinesis during morphogenesis in C. elegans.}, journal = {Development}, volume = {147}, year = {2020}, month = {2020 Jan}, pages = {1-16}, abstract = {

While cytokinesis has been intensely studied, the way it is executed during development is not well understood, despite a long-standing appreciation that various aspects of cytokinesis vary across cell and tissue types. To address this, we investigated cytokinesis during the invariant embryonic divisions and found several reproducibly altered parameters at different stages. During early divisions, furrow ingression asymmetry and midbody inheritance is consistent, suggesting specific regulation of these events. During morphogenesis, we found several unexpected alterations to cytokinesis including apical midbody migration in polarizing epithelial cells of the gut, pharynx and sensory neurons. Aurora B kinase, which is essential for several aspects of cytokinesis, remains apically localized in each of these tissues after internalization of midbody ring components. Aurora B inactivation disrupts cytokinesis and causes defects in apical structures, even if inactivated post-mitotically. Therefore, cytokinesis is implemented in a specialized way during epithelial polarization and Aurora B has a new role in the formation of the apical surface.

}, issn = {1477-9129}, doi = {10.1242/dev.181099}, author = {Bai, Xiaofei and Melesse, Michael and Sorensen Turpin, Christopher G and Sloan, Dillon and Chen, Chin-Yi and Wang, Wen-Cheng and Lee, Po-Yi and Simmons, James R and Nebenfuehr, Benjamin and Mitchell, Diana and Klebanow, Lindsey R and Mattson, Nicholas and Betzig, Eric and Chen, Bi-Chang and Cheerambathur, Dhanya and Bembenek, Joshua N} } @article {65798, title = {Behavioral state coding by molecularly defined paraventricular hypothalamic cell type ensembles.}, journal = {Science}, volume = {370}, year = {2020}, month = {2020 Oct 16}, abstract = {

Brains encode behaviors using neurons amenable to systematic classification by gene expression. The contribution of molecular identity to neural coding is not understood because of the challenges involved with measuring neural dynamics and molecular information from the same cells. We developed CaRMA (calcium and RNA multiplexed activity) imaging based on recording in vivo single-neuron calcium dynamics followed by gene expression analysis. We simultaneously monitored activity in hundreds of neurons in mouse paraventricular hypothalamus (PVH). Combinations of cell-type marker genes had predictive power for neuronal responses across 11 behavioral states. The PVH uses combinatorial assemblies of molecularly defined neuron populations for grouped-ensemble coding of survival behaviors. The neuropeptide receptor neuropeptide Y receptor type 1 (Npy1r) amalgamated multiple cell types with similar responses. Our results show that molecularly defined neurons are important processing units for brain function.

}, issn = {1095-9203}, doi = {10.1126/science.abb2494}, author = {Xu, Shengjin and Yang, Hui and Menon, Vilas and Lemire, Andrew L and Wang, Lihua and Henry, Fredrick E and Turaga, Srinivas C and Sternson, Scott M} } @article {65659, title = {Cell types promoting goosebumps form a niche to regulate hair follicle stem cells.}, journal = {Cell}, volume = {182}, year = {2020}, month = {2020 Aug 6}, pages = {578}, abstract = {

Piloerection (goosebumps) requires concerted actions of the hair follicle, the arrector pili muscle (APM), and the sympathetic nerve, providing a model to study interactions across epithelium, mesenchyme, and nerves. Here, we show that APMs and sympathetic nerves form a dual-component niche to modulate hair follicle stem cell (HFSC) activity. Sympathetic nerves form synapse-like structures with HFSCs and regulate HFSCs through norepinephrine, whereas APMs maintain sympathetic innervation to HFSCs. Without norepinephrine signaling, HFSCs enter deep quiescence by down-regulating the cell cycle and metabolism while up-regulating quiescence regulators Foxp1 and Fgf18. During development, HFSC progeny secretes Sonic Hedgehog (SHH) to direct the formation of this APM-sympathetic nerve niche, which in turn controls hair follicle regeneration in adults. Our results reveal a reciprocal interdependence between a regenerative tissue and its niche at different stages and demonstrate sympathetic nerves can modulate stem cells through synapse-like connections and neurotransmitters to couple tissue production with demands.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2020.06.031}, author = {Shwartz, Yulia and Gonzalez-Celeiro, Meryem and Chen, Chih-Lung and Pasolli, H Amalia and Sheu, Shu-Hsien and Fan, Sabrina Mai-Yi and Shamsi, Farnaz and Assaad, Steven and Lin, Edrick Tai-Yu and Zhang, Bing and Tsai, Pai-Chi and He, Megan and Tseng, Yu-Hua and Lin, Sung-Jan and Hsu, Ya-Chieh} } @article {68429, title = {Cell-Surface Proteomic Profiling in the Fly Brain Uncovers Wiring Regulators.}, journal = {Cell}, volume = {180}, year = {2020}, month = {01/2020}, pages = {373-386.e15}, abstract = {

Molecular interactions at the cellular interface mediate organized assembly of single cells into tissues and, thus, govern the development and physiology of multicellular organisms. Here, we developed a cell-type-specific, spatiotemporally resolved approach to profile cell-surface proteomes in intact tissues. Quantitative profiling of cell-surface proteomes of Drosophila olfactory projection neurons (PNs) in pupae and adults revealed global downregulation of wiring molecules and upregulation of synaptic molecules in the transition from developing to mature PNs. A proteome-instructed in\ vivo screen identified 20 cell-surface molecules regulating neural circuit assembly, many of which belong to evolutionarily conserved protein families not previously linked to neural development. Genetic analysis further revealed that the lipoprotein receptor LRP1 cell-autonomously controls PN dendrite targeting, contributing to the formation of a precise olfactory map. These findings highlight the power of temporally resolved in situ cell-surface proteomic profiling in discovering regulators of brain wiring.

}, keywords = {Animals, Axons, Brain, Dendrites, Drosophila melanogaster, Drosophila Proteins, Gene Expression Profiling, Gene Expression Regulation, Developmental, Membrane Proteins, Neurogenesis, Olfactory Nerve, Olfactory Pathways, Olfactory Receptor Neurons, Proteomics, Receptors, Lipoprotein, Smell}, issn = {1097-4172}, doi = {10.1016/j.cell.2019.12.029}, author = {Li, Jiefu and Han, Shuo and Li, Hongjie and Udeshi, Namrata D and Svinkina, Tanya and Mani, D R and Xu, Chuanyun and Guajardo, Ricardo and Xie, Qijing and Li, Tongchao and Luginbuhl, David J and Wu, Bing and McLaughlin, Colleen N and Xie, Anthony and Kaewsapsak, Pornchai and Quake, Stephen R and Carr, Steven A and Ting, Alice Y and Luo, Liqun} } @article {65361, title = {Cell-type specific outcome representation in primary motor cortex.}, journal = {Neuron}, volume = {107}, year = {2020}, month = {2020 Sep 9}, pages = {954-71}, abstract = {

Adaptive movements are critical to animal survival. To guide future actions, the brain monitors different outcomes, including achievement of movement and appetitive goals. The nature of outcome signals and their neuronal and network realization in motor cortex (M1), which commands the performance of skilled movements, is largely unknown. Using a dexterity task, calcium imaging, optogenetic perturbations, and behavioral manipulations, we studied outcome signals in murine M1. We find two populations of layer 2-3 neurons, {\textquotedblleft}success{\textquotedblright}- and {\textquotedblleft}failure{\textquotedblright} related neurons that develop with training and report end-result of trials. In these neurons, prolonged responses were recorded after success or failure trials, independent of reward and kinematics. In contrast, the initial state of layer-5 pyramidal tract neurons contains a memory trace of the previous trial{\textquoteright}s outcome. Inter-trial cortical activity was needed to learn new task requirements. These M1 reflective layer-specific performance outcome signals, can support reinforcement motor learning of skilled behavior.

}, doi = {10.1016/j.neuron.2020.06.006}, author = {Lavzin, Maria and Levy, Shahar and Benisty, Hadas and Dubin, Uri and Brosh, Zohar and Aeed, Fadi and Mensh, Brett D. and Schiller, Yitzhak and Meir, Ron and Barak, Omri and Talmon, Ronen and Hantman, Adam W. and Schiller, Jackie} } @article {65860, title = {Central processing of leg proprioception in Drosophila.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Dec 02}, abstract = {

Proprioception, the sense of self-movement and position, is mediated by mechanosensory neurons that detect diverse features of body kinematics. Although proprioceptive feedback is crucial for accurate motor control, little is known about how downstream circuits transform limb sensory information to guide motor output. Here, we investigate neural circuits in that process proprioceptive information from the fly leg. We identify three cell-types from distinct developmental lineages that are positioned to receive input from proprioceptor subtypes encoding tibia position, movement, and vibration. 13Bα neurons encode femur-tibia joint angle and mediate postural changes in tibia position. 9Aα neurons also drive changes in leg posture, but encode a combination of directional movement, high frequency vibration, and joint angle. Activating 10Bα neurons, which encode tibia vibration at specific joint angles, elicits pausing in walking flies. Altogether, our results reveal that central circuits integrate information across proprioceptor subtypes to construct complex sensorimotor representations that mediate diverse behaviors, including reflexive control of limb posture and detection of leg vibration.

}, issn = {2050-084X}, doi = {10.7554/eLife.60299}, author = {Agrawal, Sweta and Dickinson, Evyn S and Sustar, Anne and Gurung, Pralaksha and Shepherd, David and Truman, James W and Tuthill, John C} } @article {65614, title = {Chloroplast Sec14-like 1 (CPSFL1) is essential for normal chloroplast development and affects carotenoid accumulation in Chlamydomonas.}, journal = {Proceedings of the National Academy of Sciences of the U S A}, volume = {117}, year = {2020}, month = {2020 Jun 2}, pages = {1-12}, abstract = {

Plastid isoprenoid-derived carotenoids serve essential roles in chloroplast development and photosynthesis. Although nearly all enzymes that participate in the biosynthesis of carotenoids in plants have been identified, the complement of auxiliary proteins that regulate synthesis, transport, sequestration, and degradation of these molecules and their isoprenoid precursors have not been fully described. To identify such proteins that are necessary for the optimal functioning of oxygenic photosynthesis, we screened a large collection of nonphotosynthetic (acetate-requiring) DNA insertional mutants of and isolated The mutant is extremely light-sensitive and susceptible to photoinhibition and photobleaching. The gene encodes a CRAL-TRIO hydrophobic ligand-binding (Sec14) domain protein. Proteins containing this domain are limited to eukaryotes, but some may have been retargeted to function in organelles of endosymbiotic origin. The mutant showed decreased accumulation of plastidial isoprenoid-derived pigments, especially carotenoids, and whole-cell focused ion-beam scanning-electron microscopy revealed a deficiency of carotenoid-rich chloroplast structures (e.g., eyespot and plastoglobules). The low carotenoid content resulted from impaired biosynthesis at a step prior to phytoene, the committed precursor to carotenoids. The CPSFL1 protein bound phytoene and β-carotene when expressed in and phosphatidic acid in vitro. We suggest that CPSFL1 is involved in the regulation of phytoene synthesis and carotenoid transport and thereby modulates carotenoid accumulation in the chloroplast.

}, issn = {1091-6490}, doi = {10.1073/pnas.1916948117}, author = {Garc{\'\i}a-Cerd{\'a}n, Jos{\'e} G and Schmid, Eva M and Takeuchi, Tomomi and McRae, Ian and McDonald, Kent L and Yordduangjun, Nichakarn and Hassan, Ahmed M and Grob, Patricia and Xu, C Shan and Hess, Harald F and Fletcher, Daniel A and Nogales, Eva and Niyogi, Krishna K} } @article {67225, title = {Comparative single-cell transcriptomics of complete insect nervous systems}, journal = {bioRxiv}, year = {2020}, month = {01/2020}, abstract = {

Molecular profiles of neurons influence information processing, but bridging the gap between genes, circuits, and behavior has been very difficult. Furthermore, the behavioral state of an animal continuously changes across development and as a result of sensory experience. How behavioral state influences molecular cell state is poorly understood. Here we present a complete atlas of the Drosophila larval central nervous system composed of over 200,000 single cells across four developmental stages. We develop polyseq, a python package, to perform cell-type analyses. We use single-molecule RNA-FISH to validate our scRNAseq findings. To investigate how internal state affects cell state, we optogentically altered internal state with high-throughput behavior protocols designed to mimic wasp sting and over activation of the memory system. We found nervous system-wide and neuron-specific gene expression changes. This resource is valuable for developmental biology and neuroscience, and it advances our understanding of how genes, neurons, and circuits generate behavior.

}, doi = {10.1101/785931}, url = {https://www.biorxiv.org/content/early/2020/01/16/785931}, author = {Cocanougher, Benjamin T. and Wittenbach, Jason D. and Long, Xi Salina and Kohn, Andrea B. and Norekian, Tigran P. and Yan, Jinyao and Colonell, Jennifer and Masson, Jean-Baptiste and Truman, James W. and Cardona, Albert and Turaga, Srinivas C. and Singer, Robert H. and Moroz, Leonid L. and Zlatic, Marta} } @article {65645, title = {Complete connectomic reconstruction of olfactory projection neurons in the fly brain.}, journal = {Current Biology}, volume = {30}, year = {2020}, month = {2020 Aug 17}, pages = {3183-99}, abstract = {

Nervous systems contain sensory neurons, local neurons, projection neurons, and motor neurons. To understand how these building blocks form whole circuits, we must distil these broad classes into neuronal cell types and describe their network connectivity. Using an electron micrograph dataset for an entire Drosophila melanogaster brain, we reconstruct the first complete inventory of olfactory projections connecting the antennal lobe, the insect analog of the mammalian olfactory bulb, to higher-order brain regions in an adult animal brain. We then connect this inventory to extant data in the literature, providing synaptic-resolution "holotypes" both for heavily investigated and previously unknown cell types. Projection neurons are approximately twice as numerous as reported by light level studies; cell types are stereotyped, but not identical, in cell and synapse numbers between brain hemispheres. The lateral horn, the insect analog of the mammalian cortical amygdala, is the main target for this olfactory information and has been shown to guide innate behavior. Here, we find new connectivity motifs, including axo-axonic connectivity between projection neurons, feedback, and lateral inhibition of these axons by a large population of neurons, and the convergence of different inputs, including non-olfactory inputs and memory-related feedback onto third-order olfactory neurons. These features are less prominent in the mushroom body calyx, the insect analog of the mammalian piriform cortex and a center for associative memory. Our work provides a complete neuroanatomical platform for future studies of the adult Drosophila olfactory system.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2020.06.042}, author = {Bates, Alexander S and Schlegel, Philipp and Roberts, Ruair{\'\i} J V and Drummond, Nikolas and Tamimi, Imaan F M and Turnbull, Robert and Zhao, Xincheng and Marin, Elizabeth C and Popovici, Patricia D and Dhawan, Serene and Jamasb, Arian and Javier, Alexandre and Serratosa Capdevila, Laia and Li, Feng and Rubin, Gerald M and Waddell, Scott and Bock, Davi D and Costa, Marta and Jefferis, Gregory S X E} } @article {65646, title = {Comprehensive imaging of sensory-evoked activity of entire neurons within the awake developing brain using ultrafast AOD-based random-access two-photon microscopy.}, journal = {Frontiers in Neural Circuits}, volume = {14}, year = {2020}, month = {2020 Jun 16}, pages = {33}, abstract = {

Determining how neurons transform synaptic input and encode information in action potential (AP) firing output is required for understanding dendritic integration, neural transforms and encoding. Limitations in the speed of imaging 3D volumes of brain encompassing complex dendritic arbors using conventional galvanometer mirror-based laser-scanning microscopy has hampered fully capturing fluorescent sensors of activity throughout an individual neuron{\textquoteright}s entire complement of synaptic inputs and somatic APs. To address this problem, we have developed a two-photon microscope that achieves high-speed scanning by employing inertia-free acousto-optic deflectors (AODs) for laser beam positioning, enabling random-access sampling of hundreds to thousands of points-of-interest restricted to a predetermined neuronal structure, avoiding wasted scanning of surrounding extracellular tissue. This system is capable of comprehensive imaging of the activity of single neurons within the intact and awake vertebrate brain. Here, we demonstrate imaging of tectal neurons within the brains of albino tadpoles labeled using single-cell electroporation for expression of a red space-filling fluorophore to determine dendritic arbor morphology, and either the calcium sensor jGCaMP7s or the glutamate sensor iGluSnFR as indicators of neural activity. Using discrete, point-of-interest scanning we achieve sampling rates of 3 Hz for saturation sampling of entire arbors at 2 μm resolution, 6 Hz for sequentially sampling 3 volumes encompassing the dendritic arbor and soma, and 200-250 Hz for scanning individual planes through the dendritic arbor. This system allows investigations of sensory-evoked information input-output relationships of neurons within the intact and awake brain.

}, issn = {1662-5110}, doi = {10.3389/fncir.2020.00033}, author = {Sakaki, Kelly D R and Podgorski, Kaspar and Dellazizzo Toth, Tristan A and Coleman, Patrick and Haas, Kurt} } @article {68507, title = {A connectome and analysis of the adult Drosophila central brain.}, journal = {Elife}, volume = {9}, year = {2020}, month = {2020 Sep 07}, abstract = {

The neural circuits responsible for animal behavior remain largely unknown. We summarize new methods and present the circuitry of a large fraction of the brain of the fruit fly . Improved methods include new procedures to prepare, image, align, segment, find synapses in, and proofread such large data sets. We define cell types, refine computational compartments, and provide an exhaustive atlas of cell examples and types, many of them novel. We provide detailed circuits consisting of neurons and their chemical synapses for most of the central brain. We make the data public and simplify access, reducing the effort needed to answer circuit questions, and provide procedures linking the neurons defined by our analysis with genetic reagents. Biologically, we examine distributions of connection strengths, neural motifs on different scales, electrical consequences of compartmentalization, and evidence that maximizing packing density is an important criterion in the evolution of the fly{\textquoteright}s brain.

}, keywords = {Animals, Brain, Connectome, Drosophila melanogaster, Female, Male, Neurons, Synapses}, issn = {2050-084X}, doi = {10.7554/eLife.57443}, author = {Scheffer, Louis K and Xu, C Shan and Januszewski, Michal and Lu, Zhiyuan and Takemura, Shin-ya and Hayworth, Kenneth J and Huang, Gary B and Shinomiya, Kazunori and Maitlin-Shepard, Jeremy and Berg, Stuart and Clements, Jody and Hubbard, Philip M and Katz, William T and Umayam, Lowell and Zhao, Ting and Ackerman, David and Blakely, Tim and Bogovic, John and Dolafi, Tom and Kainmueller, Dagmar and Kawase, Takashi and Khairy, Khaled A and Leavitt, Laramie and Li, Peter H and Lindsey, Larry and Neubarth, Nicole and Olbris, Donald J and Otsuna, Hideo and Trautman, Eric T and Ito, Masayoshi and Bates, Alexander S and Goldammer, Jens and Wolff, Tanya and Svirskas, Robert and Schlegel, Philipp and Neace, Erika and Knecht, Christopher J and Alvarado, Chelsea X and Bailey, Dennis A and Ballinger, Samantha and Borycz, Jolanta A and Canino, Brandon S and Cheatham, Natasha and Cook, Michael and Dreher, Marisa and Duclos, Octave and Eubanks, Bryon and Fairbanks, Kelli and Finley, Samantha and Forknall, Nora and Francis, Audrey and Hopkins, Gary Patrick and Joyce, Emily M and Kim, SungJin and Kirk, Nicole A and Kovalyak, Julie and Lauchie, Shirley A and Lohff, Alanna and Maldonado, Charli and Manley, Emily A and McLin, Sari and Mooney, Caroline and Ndama, Miatta and Ogundeyi, Omotara and Okeoma, Nneoma and Ordish, Christopher and Padilla, Nicholas and Patrick, Christopher M and Paterson, Tyler and Phillips, Elliott E and Phillips, Emily M and Rampally, Neha and Ribeiro, Caitlin and Robertson, Madelaine K and Rymer, Jon Thomson and Ryan, Sean M and Sammons, Megan and Scott, Anne K and Scott, Ashley L and Shinomiya, Aya and Smith, Claire and Smith, Kelsey and Smith, Natalie L and Sobeski, Margaret A and Suleiman, Alia and Swift, Jackie and Takemura, Satoko and Talebi, Iris and Tarnogorska, Dorota and Tenshaw, Emily and Tokhi, Temour and Walsh, John J and Yang, Tansy and Horne, Jane Anne and Li, Feng and Parekh, Ruchi and Rivlin, Patricia K and Jayaraman, Vivek and Costa, Marta and Jefferis, Gregory Sxe and Ito, Kei and Saalfeld, Stephan and George, Reed and Meinertzhagen, Ian A and Rubin, Gerald M and Hess, Harald F and Jain, Viren and Plaza, Stephen M} } @article {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 {65643, title = {Connectomics analysis reveals first-, second-, and third-order thermosensory and hygrosensory neurons in the adult Drosophila brain.}, journal = {Current Biology}, volume = {30}, year = {2020}, month = {2020 Aug 17}, pages = {3167-82}, abstract = {

Animals exhibit innate and learned preferences for temperature and humidity-conditions critical for their survival and reproduction. Leveraging a whole-brain electron microscopy volume, we studied the adult Drosophila melanogaster circuitry associated with antennal thermo- and hygrosensory neurons. We have identified two new target glomeruli in the antennal lobe, in addition to the five known ones, and the ventroposterior projection neurons (VP PNs) that relay thermo- and hygrosensory information to higher brain centers, including the mushroom body and lateral horn, seats of learned and innate behavior. We present the first connectome of a thermo- and hygrosensory neuropil, the lateral accessory calyx (lACA), by reconstructing neurons downstream of heating- and cooling-responsive VP PNs. A few mushroom body-intrinsic neurons solely receive thermosensory input from the lACA, while most receive additional olfactory and thermo- and/or hygrosensory PN inputs. Furthermore, several classes of lACA-associated neurons form a local network with outputs to other brain neuropils, suggesting that the lACA serves as a hub for thermo- and hygrosensory circuitry. For example, DN1a neurons link thermosensory PNs in the lACA to the circadian clock via the accessory medulla. Finally, we survey strongly connected downstream partners of VP PNs across the protocerebrum; these include a descending neuron targeted by dry-responsive VP PNs, meaning that just two synapses might separate hygrosensory inputs from motor circuits. These data provide a comprehensive first- and second-order layer analysis of Drosophila thermo- and hygrosensory systems and an initial survey of third-order neurons that could directly modulate behavior.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2020.06.028}, author = {Marin, Elizabeth C and B{\"u}ld, Laurin and Theiss, Maria and Sarkissian, Tatevik and Roberts, Ruair{\'\i} J V and Turnbull, Robert and Tamimi, Imaan F M and Pleijzier, Markus W and Laursen, Willem J and Drummond, Nik and Schlegel, Philipp and Bates, Alexander S and Li, Feng and Landgraf, Matthias and Costa, Marta and Bock, Davi D and Garrity, Paul A and Jefferis, Gregory S X E} } @article {68991, title = {Context-dependent functional compensation between Ythdf mA reader proteins.}, journal = {Genes Dev}, volume = {34}, year = {2020}, month = {10/2020}, pages = {1373-1391}, abstract = {

The N6-methyladenosine (mA) modification is the most prevalent post-transcriptional mRNA modification, regulating mRNA decay and splicing. It plays a major role during normal development, differentiation, and disease progression. The modification is regulated by a set of writer, eraser, and reader proteins. The YTH domain family of proteins consists of three homologous mA-binding proteins, Ythdf1, Ythdf2, and Ythdf3, which were suggested to have different cellular functions. However, their sequence similarity and their tendency to bind the same targets suggest that they may have overlapping roles. We systematically knocked out (KO) the Mettl3 writer, each of the Ythdf readers, and the three readers together (triple-KO). We then estimated the effect in vivo in mouse gametogenesis, postnatal viability, and in vitro in mouse embryonic stem cells (mESCs). In gametogenesis, severity is increased as the deletion occurs earlier in the process, and Ythdf2 has a dominant role that cannot be compensated by Ythdf1 or Ythdf3, due to differences in readers{\textquoteright} expression pattern across different cell types, both in quantity and in spatial location. Knocking out the three readers together and systematically testing viable offspring genotypes revealed a redundancy in the readers{\textquoteright} role during early development that is gene dosage-dependent. Finally, in mESCs there is compensation between the three Ythdf reader proteins, since the resistance to differentiate and the significant effect on mRNA decay occur only in the triple-KO cells and not in the single KOs. Thus, we suggest a new model for the Ythdf readers function, in which there is profound dosage-dependent redundancy when all three readers are equivalently coexpressed in the same cell types.

}, keywords = {Animals, Cell Line, Dosage Compensation, Genetic, Embryonic Stem Cells, Fertility, Gametogenesis, Gene Deletion, Gene Expression Profiling, Gene Expression Regulation, Developmental, Methyltransferases, Mice, Mice, Knockout, RNA-Binding Proteins}, issn = {1549-5477}, doi = {10.1101/gad.340695.120}, author = {Lasman, Lior and Krupalnik, Vladislav and Viukov, Sergey and Mor, Nofar and Aguilera-Castrejon, Alejandro and Schneir, Dan and Bayerl, Jonathan and Mizrahi, Orel and Peles, Shani and Tawil, Shadi and Sathe, Shashank and Nachshon, Aharon and Shani, Tom and Zerbib, Mirie and Kilimnik, Itay and Aigner, Stefan and Shankar, Archana and Mueller, Jasmine R and Schwartz, Schraga and Stern-Ginossar, Noam and Yeo, Gene W and Geula, Shay and Novershtern, Noa and Hanna, Jacob H} } @article {65600, title = {The corazonin-PTTH neuronal axis controls systemic body growth by regulating basal ecdysteroid biosynthesis in Drosophila melanogaster.}, journal = {Current Biology}, volume = {30}, year = {2020}, month = {2020 Jun 8}, pages = {2156-65}, abstract = {

Steroid hormones play key roles in development, growth, and reproduction in various animal phyla [1]. The insect steroid hormone, ecdysteroid, coordinates growth and maturation, represented by molting and metamorphosis [2]. In Drosophila melanogaster, the prothoracicotropic hormone (PTTH)-producing neurons stimulate peak levels of ecdysteroid biosynthesis for maturation [3]. Additionally, recent studies on PTTH signaling indicated that basal levels of ecdysteroid negatively affect systemic growth prior to maturation [4-8]. However, it remains unclear how PTTH signaling is regulated for basal ecdysteroid biosynthesis. Here, we report that Corazonin (Crz)-producing neurons regulate basal ecdysteroid biosynthesis by affecting PTTH neurons. Crz belongs to gonadotropin-releasing hormone (GnRH) superfamily, implying an analogous role in growth and maturation [9]. Inhibition of Crz neuronal activity increased pupal size, whereas it hardly affected pupariation timing. This phenotype resulted from enhanced growth rate and a delay in ecdysteroid elevation during the mid-third instar larval (L3) stage. Interestingly, Crz receptor (CrzR) expression in PTTH neurons was higher during the mid- than the late-L3 stage. Silencing of CrzR in PTTH neurons increased pupal size, phenocopying the inhibition of Crz neuronal activity. When Crz neurons were optogenetically activated, a strong calcium response was observed in PTTH neurons during the mid-L3, but not the late-L3, stage. Furthermore, we found that octopamine neurons contact Crz neurons in the subesophageal zone (SEZ), transmitting signals for systemic growth. Together, our results suggest that the Crz-PTTH neuronal axis modulates ecdysteroid biosynthesis in response to octopamine, uncovering a regulatory neuroendocrine system in the developmental transition from growth to maturation.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2020.03.050}, author = {Imura, Eisuke and Shimada-Niwa, Yuko and Nishimura, Takashi and H{\"u}ckesfeld, Sebastian and Schlegel, Philipp and Ohhara, Yuya and Kondo, Shu and Tanimoto, Hiromu and Cardona, Albert and Pankratz, Michael J and Niwa, Ryusuke} } @article {65697, title = {Cortical RORβ is required for layer 4 transcriptional identity and barrel integrity.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Aug 27}, abstract = {

Retinoic Acid-Related Orphan Receptor Beta (RORβ) is a transcription factor (TF) and marker of layer 4 (L4) neurons, which are distinctive both in transcriptional identity and the ability to form aggregates such as barrels in rodent somatosensory cortex. However, the relationship between transcriptional identity and L4 cytoarchitecture is largely unknown. We find RORβ is required in the cortex for L4 aggregation into barrels and thalamocortical afferent (TCA) segregation. Interestingly, barrel organization also degrades with age in wildtype mice. Loss of RORβ delays excitatory input and disrupts gene expression and chromatin accessibility, with down-regulation of L4 and up-regulation of L5 genes, suggesting a disruption in cellular specification. Expression and binding site accessibility change for many other TFs, including closure of neurodevelopmental TF binding sites and increased expression and binding capacity of activity-regulated TFs. Lastly, a putative target of RORβ, , is down-regulated without RORβ, and knock-out alone disrupts TCA organization in adult barrels.

}, issn = {2050-084X}, doi = {10.7554/eLife.52370}, author = {Clark, Erin A and Rutlin, Michael and Capano, Lucia and Aviles, Samuel and Saadon, Jordan R and Taneja, Praveen and Zhang, Qiyu and Bullis, James B and Lauer, Timothy and Myers, Emma and Schulmann, Anton and Forrest, Douglas and Nelson, Sacha B} } @article {65869, title = {Cryo-EM structure of the inhibited (10S) form of myosin II.}, journal = {Nature}, volume = {588}, year = {2020}, month = {2020 Dec 02}, pages = {521-25}, abstract = {

Myosin II is the motor protein that enables muscle cells to contract and nonmuscle cells to move and change shape. The molecule has two identical heads attached to an elongated tail, and can exist in two conformations: 10S and 6S, named for their sedimentation coefficients. The 6S conformation has an extended tail and assembles into polymeric filaments, which pull on actin filaments to generate force and motion. In 10S myosin, the tail is folded into three segments and the heads bend back and interact with each other and the tail, creating a compact conformation in which ATPase activity, actin activation and filament assembly are all highly inhibited. This switched-off structure appears to function as a key energy-conserving storage molecule in muscle and nonmuscle cells, which can be activated to form functional filaments as needed-but the mechanism of its inhibition is not understood. Here we have solved the structure of smooth muscle 10S myosin by cryo-electron microscopy with sufficient resolution to enable improved understanding of the function of the head and tail regions of the molecule and of the key intramolecular contacts that cause inhibition. Our results suggest an atomic model for\ the off state of myosin II, for its activation and unfolding by phosphorylation, and for understanding the clustering of disease-causing mutations near sites of intramolecular interaction.

}, issn = {1476-4687}, doi = {10.1038/s41586-020-3007-0}, author = {Yang, Shixin and Tiwari, Prince and Lee, Kyoung Hwan and Sato, Osamu and Ikebe, Mitsuo and Padr{\'o}n, Ra{\'u}l and Craig, Roger} } @article {65799, title = {Dense and pleiotropic regulatory information in a developmental enhancer.}, journal = {Nature}, volume = {587}, year = {2020}, month = {2020 Nov 01}, pages = {235-39}, abstract = {

Changes in gene regulation underlie much of phenotypic evolution. However, our understanding of the potential for regulatory evolution is biased, because most evidence comes from either natural variation or limited experimental perturbations. Using an automated robotics pipeline, we surveyed an unbiased mutation library for a developmental enhancer in Drosophila melanogaster. We found that almost all mutations altered gene expression and that parameters of gene expression-levels, location, and state-were convolved. The widespread pleiotropic effects of most mutations may constrain the evolvability of developmental enhancers. Consistent with these observations, comparisons of diverse Drosophila larvae revealed apparent biases in the phenotypes influenced by the enhancer. Developmental enhancers may encode a higher density of regulatory information than has been appreciated previously, imposing constraints on regulatory evolution.

}, issn = {1476-4687}, doi = {10.1038/s41586-020-2816-5}, author = {Fuqua, Timothy and Jordan, Jeff and van Breugel, Maria Elize and Halavatyi, Aliaksandr and Tischer, Christian and Polidoro, Peter and Abe, Namiko and Tsai, Albert and Mann, Richard S and Stern, David L and Crocker, Justin} } @article {65725, title = {Dense neuronal reconstruction through X-ray holographic nano-tomography.}, journal = {Nature Neuroscience}, volume = {23}, year = {2020}, month = {2020 Dec -1}, pages = {1637-43}, abstract = {

Imaging neuronal networks provides a foundation for understanding the nervous system, but resolving dense nanometer-scale structures over large volumes remains challenging for light microscopy (LM) and electron microscopy (EM). Here we show that X-ray holographic nano-tomography (XNH) can image millimeter-scale volumes with sub-100-nm resolution, enabling reconstruction of dense wiring in Drosophila melanogaster and mouse nervous tissue. We performed correlative XNH and EM to reconstruct hundreds of cortical pyramidal cells and show that more superficial cells receive stronger synaptic inhibition on their apical dendrites. By combining multiple XNH scans, we imaged an adult Drosophila leg with sufficient resolution to comprehensively catalog mechanosensory neurons and trace individual motor axons from muscles to the central nervous system. To accelerate neuronal reconstructions, we trained a convolutional neural network to automatically segment neurons from XNH volumes. Thus, XNH bridges a key gap between LM and EM, providing a new avenue for neural circuit discovery.

}, issn = {1546-1726}, doi = {10.1038/s41593-020-0704-9}, author = {Kuan, Aaron T and Phelps, Jasper S and Thomas, Logan A and Nguyen, Tri M and Han, Julie and Chen, Chiao-Lin and Azevedo, Anthony W and Tuthill, John C and Funke, Jan and Cloetens, Peter and Pacureanu, Alexandra and Lee, Wei-Chung Allen} } @article {65902, title = {Directed Evolution of a Selective and Sensitive Serotonin Sensor via Machine Learning.}, journal = {Cell}, volume = {183}, year = {2020}, month = {2020 Dec 23}, pages = {1986-2002.e26}, abstract = {

Serotonin plays a central role in cognition and is the target of most pharmaceuticals for psychiatric disorders. Existing drugs have limited efficacy; creation of improved versions will require better understanding of serotonergic circuitry, which has been hampered by our inability to monitor serotonin release and transport with high spatial and temporal resolution. We developed and applied a binding-pocket redesign strategy, guided by machine learning, to create a high-performance, soluble, fluorescent serotonin sensor (iSeroSnFR), enabling optical detection of millisecond-scale serotonin transients. We demonstrate that iSeroSnFR can be used to detect serotonin release in freely behaving mice during fear conditioning, social interaction, and sleep/wake transitions. We also developed a robust assay of serotonin transporter function and modulation by drugs. We expect that both machine-learning-guided binding-pocket redesign and iSeroSnFR will have broad utility for the development of other sensors and in\ vitro and in\ vivo serotonin detection, respectively.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2020.11.040}, author = {Unger, Elizabeth K and Keller, Jacob P and Altermatt, Michael and Liang, Ruqiang and Matsui, Aya and Dong, Chunyang and Hon, Olivia J and Yao, Zi and Sun, Junqing and Banala, Samba and Flanigan, Meghan E and Jaffe, David A and Hartanto, Samantha and Carlen, Jane and Mizuno, Grace O and Borden, Phillip M and Shivange, Amol V and Cameron, Lindsay P and Sinning, Steffen and Underhill, Suzanne M and Olson, David E and Amara, Susan G and Temple Lang, Duncan and Rudnick, Gary and Marvin, Jonathan S and Lavis, Luke D and Lester, Henry A and Alvarez, Veronica A and Fisher, Andrew J and Prescher, Jennifer A and Kash, Thomas L and Yarov-Yarovoy, Vladimir and Gradinaru, Viviana and Looger, Loren L and Tian, Lin} } @article {65904, title = {DNA damage alters nuclear mechanics through chromatin reorganization.}, journal = {Nucleic Acids Research}, year = {2020}, month = {2020 Dec 16}, abstract = {

DNA double-strand breaks drive genomic instability. However, it remains unknown how these processes may affect the biomechanical properties of the nucleus and what role nuclear mechanics play in DNA damage and repair efficiency. Here, we have used Atomic Force Microscopy to investigate nuclear mechanical changes, arising from externally induced DNA damage. We found that nuclear stiffness is significantly reduced after cisplatin treatment, as a consequence of DNA damage signalling. This softening was linked to global chromatin decondensation, which improves molecular diffusion within the organelle. We propose that this can increase recruitment for repair factors. Interestingly, we also found that reduction of nuclear tension, through cytoskeletal relaxation, has a protective role to the cell and reduces accumulation of DNA damage. Overall, these changes protect against further genomic instability and promote DNA repair. We propose that these processes may underpin the development of drug resistance.

}, issn = {1362-4962}, doi = {10.1093/nar/gkaa1202}, author = {Dos Santos, {\'A}lia and Cook, Alexander W and Gough, Rosemarie E and Schilling, Martin and Olszok, Nora A and Brown, Ian and Wang, Lin and Aaron, Jesse and Martin-Fernandez, Marisa L and Rehfeldt, Florian and Toseland, Christopher P} } @article {65655, title = {The Drosophila mushroom body: From architecture to algorithm in a learning circuit.}, journal = {Annual Review of Neuroscience}, volume = {43}, year = {2020}, month = {2020 Jul 08}, pages = {465-484}, abstract = {

The brain contains a relatively simple circuit for forming Pavlovian associations, yet it achieves many operations common across memory systems. Recent advances have established a clear framework for learning and revealed the following key operations: ) pattern separation, whereby dense combinatorial representations of odors are preprocessed to generate highly specific, nonoverlapping odor patterns used for learning; ) convergence, in which sensory information is funneled to a small set of output neurons that guide behavioral actions; ) plasticity, where changing the mapping of sensory input to behavioral output requires a strong reinforcement signal, which is also modulated by internal state and environmental context; and ) modularization, in which a memory consists of multiple parallel traces, which are distinct in stability and flexibility and exist in anatomically well-defined modules within the network. Cross-module interactions allow for higher-order effects where past experience influences future learning. Many of these operations have parallels with processes of memory formation and action selection in more complex brains.

}, issn = {1545-4126}, doi = {10.1146/annurev-neuro-080317-0621333}, author = {Modi, Mehrab N and Shuai, Yichun and Turner, Glenn C} } @article {68477, title = {Eco-evolutionary significance of "loners".}, journal = {PLoS Biol}, volume = {18}, year = {2020}, month = {03/2020}, pages = {e3000642}, abstract = {

Loners-individuals out of sync with a coordinated majority-occur frequently in nature. Are loners incidental byproducts of large-scale coordination attempts, or are they part of a mosaic of life-history strategies? Here, we provide empirical evidence of naturally occurring heritable variation in loner behavior in the model social amoeba Dictyostelium discoideum. We propose that Dictyostelium loners-cells that do not join the multicellular life stage-arise from a dynamic population-partitioning process, the result of each cell making a stochastic, signal-based decision. We find evidence that this imperfectly synchronized multicellular development is affected by both abiotic (environmental porosity) and biotic (signaling) factors. Finally, we predict theoretically that when a pair of strains differing in their partitioning behavior coaggregate, cross-signaling impacts slime-mold diversity across spatiotemporal scales. Our findings suggest that loners could be critical to understanding collective and social behaviors, multicellular development, and ecological dynamics in D. discoideum. More broadly, across taxa, imperfect coordination of collective behaviors might be adaptive by enabling diversification of life-history strategies.

}, keywords = {Biological Evolution, Dictyostelium, Models, Biological, Quorum Sensing, Spatio-Temporal Analysis, Stochastic Processes}, issn = {1545-7885}, doi = {10.1371/journal.pbio.3000642}, author = {Rossine, Fernando W and Martinez-Garcia, Ricardo and Sgro, Allyson E and Gregor, Thomas and Tarnita, Corina E} } @article {65675, title = {Efficient coding of natural scene statistics predicts discrimination thresholds for grayscale textures.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Aug 3}, abstract = {

Previously, in (Hermundstad et al., 2014), we showed that when sampling is limiting, the efficient coding principle leads to a {\textquoteright}variance is salience{\textquoteright} hypothesis, and that this hypothesis accounts for visual sensitivity to binary image statistics. Here, using extensive new psychophysical data and image analysis, we show that this hypothesis accounts for visual sensitivity to a large set of grayscale image statistics at a striking level of detail, and also identify the limits of the prediction. We define a 66-dimensional space of local grayscale light-intensity correlations, and measure the relevance of each direction to natural scenes. The {\textquoteright}variance is salience{\textquoteright} hypothesis predicts that two-point correlations are most salient, and predicts their relative salience. We tested these predictions in a texture-segregation task using un-natural, synthetic textures. As predicted, correlations beyond second order are not salient, and predicted thresholds for over 300 second-order correlations match psychophysical thresholds closely (median fractional error \< 0:13).

}, doi = {10.7554/eLife.54347}, url = {https://elifesciences.org/articles/54347}, author = {Tesileanu, Tiberiu and Conte, Mary M and Briguglio, John J and Hermundstad, Ann M and Victor, Jonathan D and Balasubramanian, Vijay} } @article {65763, title = {A far-red fluorescent chemogenetic reporter for in vivo molecular imaging}, journal = {Angewandte Chemie International Edition}, year = {2020}, month = {06/2020}, abstract = {

Far-red emitting fluorescent labels are highly desirable for spectral multiplexing and deep tissue imaging. Here, we describe the generation of frFAST (far-red Fluorescence Activating and absorption Shifting Tag), a 14-kDa monomeric protein that forms a bright far-red fluorescent assembly with (4-hydroxy-3-methoxy-phenyl)allylidene rhodanine (HPAR-3OM). As HPAR-3OM is essentially non- fluorescent in solution and in cells, frFAST can be imaged with high contrast in presence of free HPAR-3OM, which allowed the rapid and efficient imaging of frFAST fusions in live cells, zebrafish embryo/larvae and chicken embryo. Beyond enabling genetic encoding of far-red fluorescence, frFAST allowed the design of a far- red chemogenetic reporter of protein-protein interactions, demonstrating its great potential for the design of innovative far-red emitting biosensors.

}, issn = {1433-7851}, doi = {10.1002/anie.202006576}, author = {Li, Chenge and Tebo, Alison G and Thauvin, Marion and Plamont, Marie-Aude and Volovitch, Michel and Morin, Xavier and Vriz, Sophie and Gautier, Arnaud} } @article {65300, title = {A fast genetically encoded fluorescent sensor for faithful in vivo acetylcholine detection in mice, fish, worms and flies.}, journal = {bioRxiv}, year = {2020}, month = {2020 Feb 8}, abstract = {

Here we design and optimize a genetically encoded fluorescent indicator, iAChSnFR, for the ubiquitous neurotransmitter acetylcholine, based on a bacterial periplasmic binding protein. iAChSnFR shows large fluorescence changes, rapid rise and decay kinetics, and insensitivity to most cholinergic drugs. iAChSnFR revealed large transients in a variety of slice and\ in vivo\ preparations in mouse, fish, fly and worm. iAChSnFR will be useful for the study of acetylcholine in all animals.

}, doi = {https://doi.org/10.1101/2020.02.07.939504}, author = {Borden, Philip and Zhang, Peng and Shivange, Amol V and Marvin, Jonathan S and Cichon, Joseph and Dan, Chuntao and Podgorski, Kaspar and Figueiredo, Antonio and Novak, Ondrej and Tanimoto, Masashi and Shigetomi, Eiji and Lobas, Mark A and Kim, Hyuntae and Zhu, Paula and Zhang, Yajun and Zheng, W. Sharon and Fan, ChengCheng and Wang, Guangfu and Xiang, Bowen and Gan, Li and Zhang, Guang-Xian and Guo, Kaiming and Lin, Li and Cai, Yuan and Yee, Andrew G. and Aggarwal, Aman and Ford, Christopher P. and Rees, Douglas C. and Dietrich, Dirk and Khakh, Baljit S. and Dittman, Jeremy S. and Gan, Wen-Biao and Koyama, Minoru and Jayaraman, Vivek and Cheer, Joseph F. and Lester, Henry A. and Zhu, J. Julius and Looger, Loren L.} } @article {65283, title = {Fundamental law of memory recall.}, journal = {Physical Review Letters}, volume = {124}, year = {2020}, month = {2020 Jan 10}, pages = {018101}, abstract = {

Human memory appears to be fragile and unpredictable. Free recall of random lists of words is a standard paradigm used to probe episodic memory. We proposed an associative search process that can be reduced to a deterministic walk on random graphs defined by the structure of memory representations. The corresponding graph model can be solved analytically, resulting in a novel parameter-free prediction for the average number of memory items recalled (R) out of M items in memory: R=sqrt[3πM/2]. This prediction was verified with a specially designed experimental protocol combining large-scale crowd-sourced free recall and recognition experiments with randomly assembled lists of words or common facts. Our results show that human memory can be described by universal laws derived from first principles.

}, issn = {1079-7114}, doi = {10.1103/PhysRevLett.124.018101}, author = {Naim, Michelangelo and Katkov, Mikhail and Romani, Sandro and Tsodyks, Misha} } @article {65667, title = {A general method to optimize and functionalize red-shifted rhodamine dyes.}, journal = {Nature Methods}, year = {2020}, month = {2020 Jul 27}, abstract = {

Expanding the palette of fluorescent dyes is vital to push the frontier of biological imaging. Although rhodamine dyes remain the premier type of small-molecule fluorophore owing to their bioavailability and brightness, variants excited with far-red or near-infrared light suffer from poor performance due to their propensity to adopt a lipophilic, nonfluorescent form. We report a framework for rationalizing rhodamine behavior in biological environments and a general chemical modification for rhodamines that optimizes long-wavelength variants and enables facile functionalization with different chemical groups. This strategy yields red-shifted {\textquoteright}Janelia Fluor{\textquoteright} (JF) dyes useful for biological imaging experiments in cells and in vivo.

}, issn = {1548-7105}, doi = {10.1038/s41592-020-0909-6}, author = {Grimm, Jonathan B and Tkachuk, Ariana N and Xie, Liangqi and Choi, Heejun and Mohar, Boaz and Falco, Natalie and Schaefer, Kathy and Patel, Ronak and Zheng, Qinsi and Liu, Zhe and Lippincott-Schwartz, Jennifer and Brown, Timothy A and Lavis, Luke D} } @article {65739, title = {A genetically defined compartmentalized striatal direct pathway for negative reinforcement.}, journal = {Cell}, volume = {181}, year = {2020}, month = {2020 Oct 1}, pages = {211}, abstract = {

The striosome compartment within the dorsal striatum has been implicated in reinforcement learning and regulation of motivation, but how striosomal neurons contribute to these functions remains elusive. Here, we show that a genetically identified striosomal population, which expresses the Teashirt family zinc finger 1 (Tshz1) and belongs to the direct pathway, drives negative reinforcement and is essential for aversive learning in mice. Contrasting a "conventional" striosomal direct pathway, the Tshz1 neurons cause aversion, movement suppression, and negative reinforcement once activated, and they receive a distinct set of synaptic inputs. These neurons are predominantly excited by punishment rather than reward and represent the anticipation of punishment or the motivation for avoidance. Furthermore, inhibiting these neurons impairs punishment-based learning without affecting reward learning or movement. These results establish a major role of striosomal neurons in behaviors reinforced by punishment and moreover uncover functions of the direct pathway unaccounted for in classic models.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2020.08.032}, author = {Xiao, Xiong and Deng, Hanfei and Furlan, Alessandro and Yang, Tao and Zhang, Xian and Hwang, Ga-Ram and Tucciarone, Jason and Wu, Priscilla and He, Miao and Palaniswamy, Ramesh and Ramakrishnan, Charu and Ritola, Kimberly and Hantman, Adam and Deisseroth, Karl and Osten, Pavel and Huang, Z Josh and Li, Bo} } @article {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 {65130, title = {Idiosyncratic neural coding and neuromodulation of olfactory individuality in Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, year = {2020}, month = {2020 Sep 22}, pages = {23292-23297}, abstract = {

Innate behavioral biases and preferences can vary significantly among individuals of the same genotype. Though individuality is a fundamental property of behavior, it is not currently understood how individual differences in brain structure and physiology produce idiosyncratic behaviors. Here we present evidence for idiosyncrasy in olfactory behavior and neural responses in We show that individual female from a highly inbred laboratory strain exhibit idiosyncratic odor preferences that persist for days. We used in vivo calcium imaging of neural responses to compare projection neuron (second-order neurons that convey odor information from the sensory periphery to the central brain) responses to the same odors across animals. We found that, while odor responses appear grossly stereotyped, upon closer inspection, many individual differences are apparent across antennal lobe (AL) glomeruli (compact microcircuits corresponding to different odor channels). Moreover, we show that neuromodulation, environmental stress in the form of altered nutrition, and activity of certain AL local interneurons affect the magnitude of interfly behavioral variability. Taken together, this work demonstrates that individual exhibit idiosyncratic olfactory preferences and idiosyncratic neural responses to odors, and that behavioral idiosyncrasies are subject to neuromodulation and regulation by neurons in the AL.

}, issn = {1091-6490}, doi = {10.1073/pnas.1901623116}, author = {Honegger, Kyle S and Smith, Matthew A-Y and Churgin, Matthew A and Turner, Glenn C and de Bivort, Benjamin L} } @inbook {65285, title = {Imaging Cellular Proteins and Structures}, booktitle = {The Liver : Biology and Pathobiology}, year = {2020}, pages = {965 - 978}, publisher = {Wiley}, organization = {Wiley}, edition = {1}, abstract = {

This chapter describes many of the technologies, which have the potential to provide new insights into fundamental aspects of liver biology. Imaging live liver tissue in an animal with multiphoton microscopy coupled with photoactivatable fluorescent proteins and/or additional fluorescent proteins could be used to follow the lineage and fates of individual transplanted stem cells or developing transgenic cells in liver. Proteins or other molecules are labeled with a dye that can be excited with light source. Cells and proteins are generally too small to detect with the naked eye, relatively transparent when imaged by light microscopy, and are highly dynamic. With the increased signal to noise, isotropic and volumetric imaging and high speeds lattice light sheet allows for 3D super-resolution microscopy, as well. Photomultiplier tubes, while capable of detecting and counting single photons, are less useful for high-speed imaging because they normally only detect a single pixel at a time.

}, isbn = {9781119436829}, doi = {10.1002/978111943681210.1002/9781119436812.ch72}, url = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/9781119436812.ch72}, author = {Weigel, Aubrey V. and Snapp, Erik Lee}, editor = {Arias, Irwin M. and Alter, Harvey J. and Boyer, James L. and Cohen, David E. and Shafritz, David A. and Thorgeirsson, Snorri S. and Wolkoff, Allan W.} } @article {65275, title = {Improved HaloTag Ligand Enables BRET Imaging With NanoLuc}, journal = {Frontiers in Chemistry}, volume = {7}, year = {2020}, month = {2020 Jan 14}, doi = {10.3389/fchem.2019.0093810.3389/fchem.2019.00938.s001}, url = {https://www.frontiersin.org/article/10.3389/fchem.2019.00938/fullhttps://www.frontiersin.org/article/10.3389/fchem.2019.00938/fullhttps://www.frontiersin.org/articles/10.3389/fchem.2019.00938/supplementary-material/10.3389/fchem.2019.00938.s001}, author = {Thirukkumaran, Ovia Margaret and Wang, Congrong and Asouzu, Nnamdi Joseph and Fron, Eduard and Rocha, Susana and Hofkens, Johan and Lavis, Luke D. and Mizuno, Hideaki} } @article {65762, title = {Integrated structure-function dataset reveals key mechanisms underlying photochromic fluorescent proteins}, journal = {bioRxiv}, year = {2020}, month = {09/2020}, pages = {2020.09.25.313528}, abstract = {

Photochromic fluorescent proteins have become versatile tools in the life sciences, though our understanding of their structure-function relation is limited. Starting from a single scaffold, we have developed a range of 27 photochromic fluorescent proteins that cover a broad range of spectroscopic properties, yet differ only in one or two mutations. We also determined 43 different crystal structures of these mutants. Correlation and principal component analysis of the spectroscopic and structural properties confirmed the complex relationship between structure and spectroscopy, suggesting that the observed variability does not arise from a limited number of mechanisms, but also allowed us to identify consistent trends and to relate these to the spatial organization around the chromophore. We find that particular changes in spectroscopic properties can come about through multiple different underlying mechanisms, of which the polarity of the chromophore environment and hydrogen bonding of the chromophore are key modulators. Furthermore, some spectroscopic parameters, such as the photochromism, appear to be largely determined by a single or a few structural properties, while other parameters, such as the absorption maximum, do not allow a clear identification of a single cause. We also highlight the role of water molecules close to the chromophore in influencing photochromism. We anticipate that our dataset can open opportunities for the development and evaluation of new and existing protein engineering methods.

}, doi = {10.1101/2020.09.25.313528}, author = {Zitter, Elke De and Hugelier, Siewert and Duw{\'e}, Sam and Vandenberg, Wim and Tebo, Alison G. and Meervelt, Luc Van and Dedecker, Peter} } @article {65618, title = {jYCaMP: an optimized calcium indicator for two-photon imaging at fiber laser wavelengths.}, journal = {Nature Methods}, volume = {17}, year = {2020}, month = {2020 May 25}, pages = {694-97}, abstract = {

Femtosecond lasers at fixed wavelengths above 1,000 nm are powerful, stable and inexpensive, making them promising sources for two-photon microscopy. Biosensors optimized for these wavelengths are needed for both next-generation microscopes and affordable turn-key systems. Here we report jYCaMP1, a yellow variant of the calcium indicator jGCaMP7 that outperforms its parent in mice and flies at excitation wavelengths above 1,000 nm and enables improved two-color calcium imaging with red fluorescent protein-based indicators.

}, issn = {1548-7105}, doi = {10.1038/s41592-020-0835-7}, author = {Mohr, Manuel Alexander and Bushey, Daniel and Abhi Aggarwal and Marvin, Jonathan S and Kim, Jeong Jun and Marquez, Emiliano Jimenez and Liang, Yajie and Patel, Ronak and Macklin, John J and Lee, Chi-Yu and Tsang, Arthur and Tsegaye, Getahun and Ahrens, Allison M and Chen, Jerry L and Kim, Douglas S and Wong, Allan M and Looger, Loren L and Schreiter, Eric R and Podgorski, Kaspar} } @article {65322, title = {Kilohertz two-photon fluorescence microscopy imaging of neural activity in vivo.}, journal = {Nature Methods}, volume = {17}, year = {2020}, month = {2020 Mar 02}, pages = {287-290}, abstract = {

Understanding information processing in the brain requires monitoring neuronal activity at high spatiotemporal resolution. Using an ultrafast two-photon fluorescence microscope empowered by all-optical laser scanning, we imaged neuronal activity in vivo at up to 3,000 frames per second and submicrometer spatial resolution. This imaging method enabled monitoring of both supra- and subthreshold electrical activity down to 345 μm below the brain surface in head-fixed awake mice.

}, issn = {1548-7105}, doi = {10.1038/s41592-020-0762-7}, author = {Wu, Jianglai and Liang, Yajie and Chen, Shuo and Hsu, Ching-Lung and Chavarha, Mariya and Evans, Stephen W and Shi, Dongqing and Lin, Michael Z and Tsia, Kevin K and Ji, Na} } @article {68842, title = {Latent Feature Representation via Unsupervised Learning for Pattern Discovery in Massive Electron Microscopy Image Volumes}, journal = {arXiv}, year = {2020}, month = {2020 Dec 22}, abstract = {

We propose a method to facilitate exploration and analysis of new large data sets. In particular, we give an unsupervised deep learning approach to learning a latent representation that captures semantic similarity in the data set. The core idea is to use data augmentations that preserve semantic meaning to generate synthetic examples of elements whose feature representations should be close to one another.
We demonstrate the utility of our method applied to nano-scale electron microscopy data, where even relatively small portions of animal brains can require terabytes of image data. Although supervised methods can be used to predict and identify known patterns of interest, the scale of the data makes it difficult to mine and analyze patterns that are not known a priori. We show the ability of our learned representation to enable query by example, so that if a scientist notices an interesting pattern in the data, they can be presented with other locations with matching patterns. We also demonstrate that clustering of data in the learned space correlates with biologically-meaningful distinctions. Finally, we introduce a visualization tool and software ecosystem to facilitate user-friendly interactive analysis and uncover interesting biological patterns. In short, our work opens possible new avenues in understanding of and discovery in large data sets, arising in domains such as EM analysis.

}, doi = {10.48550/arXiv.2012.12175}, url = {http://doi.org/10.48550/arXiv.2012.12175}, author = {Gary B Huang and Huei-Fang Yang and Shin-ya Takemura and Pat Rivlin and Stephen M Plaza} } @article {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.} } @conference {67227, title = {Learning Guided Electron Microscopy with Active Acquisition}, booktitle = {Medical Image Computing and Computer Assisted Intervention {\textendash} MICCAI 2020}, year = {2020}, month = {10/2020}, publisher = {Springer International Publishing}, organization = {Springer International Publishing}, address = {Cham}, abstract = {

Single-beam scanning electron microscopes (SEM) are widely used to acquire massive datasets for biomedical study, material analysis, and fabrication inspection. Datasets are typically acquired with uniform acquisition: applying the electron beam with the same power and duration to all image pixels, even if there is great variety in the pixels{\textquoteright} importance for eventual use. Many SEMs are now able to move the beam to any pixel in the field of view without delay, enabling them, in principle, to invest their time budget more effectively with non-uniform imaging.

}, isbn = {978-3-030-59722-1}, url = {https://link.springer.com/chapter/10.1007/978-3-030-59722-1_8}, author = {Mi, Lu and Wang, Hao and Meirovitch, Yaron and Schalek, Richard and Turaga, Srinivas C. and Lichtman, Jeff W. and Samuel, Aravinthan D. T. and Shavit, Nir}, editor = {Martel, Anne L. and Abolmaesumi, Purang and Stoyanov, Danail and Mateus, Diana and Zuluaga, Maria A. and Zhou, S. Kevin and Racoceanu, Daniel and Joskowicz, Leo} } @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 {65738, title = {The mind of a mouse.}, journal = {Cell}, volume = {182}, year = {2020}, month = {2020 Sep 17}, pages = {1372-1376}, abstract = {

Large scientific projects in genomics and astronomy are influential not because they answer any single question but because they enable investigation of continuously arising new questions from the same data-rich sources. Advances in automated mapping of the brain{\textquoteright}s synaptic connections (connectomics) suggest that the complicated circuits underlying brain function are ripe for analysis. We discuss benefits of mapping a mouse brain at the level of synapses.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2020.08.010}, author = {Abbott, Larry F and Bock, Davi D and Callaway, Edward M and Denk, Winfried and Dulac, Catherine and Fairhall, Adrienne L and Fiete, Ila and Harris, Kristen M and Helmstaedter, Moritz and Jain, Viren and Kasthuri, Narayanan and LeCun, Yann and Lichtman, Jeff W and Littlewood, Peter B and Luo, Liqun and Maunsell, John H R and Reid, R Clay and Rosen, Bruce R and Rubin, Gerald M and Sejnowski, Terrence J and Seung, H Sebastian and Svoboda, Karel and Tank, David W and Tsao, Doris and Van Essen, David C} } @article {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} } @conference {65385, title = {Multiplexed 3-photon microscopy for functional connectomics of mammalian brains.}, booktitle = {Multiphoton Microscopy in the Biomedical Sciences XXMultiphoton Microscopy in the Biomedical Sciences XX}, year = {2020}, month = {2020 Feb 14}, publisher = {SPIE}, organization = {SPIE}, address = {San Francisco, United States}, abstract = {

3-photon excitation enables in vivo fluorescence microscopy deep in densely labeled and highly scattering samples, while maintaining high resolution and contrast. We designed and characterized a dual-plane 3-photon microscope with temporal multiplexing and remote focusing, and performed simultaneous in vivo calcium imaging of two planes deep in the cortex of a transgenic mouse expressing GCaMP6s in nearly all excitatory neurons.

}, doi = {10.1117/12.2543232 }, url = {https://www.spiedigitallibrary.org/conference-proceedings-of-spie/11244/2543232/Multiplexed-3-photon-microscopy-for-functional-connectomics-of-mammalian-brains/10.1117/12.2543232.full}, author = {Takasaki, Kevin and Tsyboulski, Dmitri A. and Waters, Jack} } @article {65386, title = {The Mushroom Body: From Architecture to Algorithm in a Learning Circuit.}, journal = {Annual Review of Neuroscience}, year = {2020}, month = {2020 Apr 13}, abstract = {

The brain contains a relatively simple circuit for forming Pavlovian associations, yet it achieves many operations common across memory systems. Recent advances have established a clear framework for learning and revealed the following key operations: ) pattern separation, whereby dense combinatorial representations of odors are preprocessed to generate highly specific, nonoverlapping odor patterns used for learning; ) convergence, in which sensory information is funneled to a small set of output neurons that guide behavioral actions; ) plasticity, where changing the mapping of sensory input to behavioral output requires a strong reinforcement signal, which is also modulated by internal state and environmental context; and ) modularization, in which a memory consists of multiple parallel traces, which are distinct in stability and flexibility and exist in anatomically well-defined modules within the network. Cross-module interactions allow for higher-order effects where past experience influences future learning. Many of these operations have parallels with processes of memory formation and action selection in more complex brains. Expected final online publication date for the , Volume 43 is July 8, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

}, issn = {1545-4126}, doi = {10.1146/annurev-neuro-080317-0621333}, author = {Modi, Mehrab N and Shuai, Yichun and Turner, Glenn C} } @article {65722, title = {The neuroanatomical ultrastructure and function of a biological ring attractor.}, journal = {Neuron}, volume = {108}, year = {2020}, month = {2020 Oct 14}, pages = {145-63}, abstract = {

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

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2020.08.006}, author = {Turner-Evans, Daniel B and Jensen, Kristopher T and Ali, Saba and Paterson, Tyler and Sheridan, Arlo and Ray, Robert P and Wolff, Tanya and Lauritzen, J Scott and Rubin, Gerald M and Bock, Davi D and Jayaraman, Vivek} } @article {65761, title = {Orthogonal fluorescent chemogenetic reporters for multicolor imaging}, journal = {Nature Chemical Biology}, year = {2020}, month = {04/2020}, pages = {1{\textendash}9}, abstract = {

Spectrally separated fluorophores allow the observation of multiple targets simultaneously inside living cells, leading to a deeper understanding of the molecular interplay that regulates cell function and fate. Chemogenetic systems combining a tag and a synthetic fluorophore provide certain advantages over fluorescent proteins since there is no requirement for chromophore maturation. Here, we present the engineering of a set of spectrally orthogonal fluorogen-activating tags based on the fluorescence-activating and absorption shifting tag (FAST) that are compatible with two-color, live-cell imaging. The resulting tags, greenFAST and redFAST, demonstrate orthogonality not only in their fluorogen recognition capabilities, but also in their one- and two-photon absorption profiles. This pair of orthogonal tags allowed the creation of a two-color cell cycle sensor capable of detecting very short, early cell cycles in zebrafish development and the development of split complementation systems capable of detecting multiple protein{\textendash}protein interactions by live-cell fluorescence microscopy. The fluorescent chemogenetic reporters greenFAST and redFAST were engineered by protein engineering. They display orthogonal fluorogen recognition and spectral properties allowing efficient multicolor imaging of proteins in live cells and organisms.

}, issn = {1552-4450}, doi = {10.1038/s41589-020-0611-0}, author = {Tebo, Alison G. and Moeyaert, Benjamien and Thauvin, Marion and Carlon-Andres, Irene and B{\"o}ken, Dorothea and Volovitch, Michel and Padilla-Parra, Sergi and Dedecker, Peter and Vriz, Sophie and Gautier, Arnaud} } @article {65694, title = {A post-invasion role for type III effector TarP in modulating the dynamics and organization of host cell focal adhesions.}, journal = {Journal of Biological Chemistry}, volume = {295}, year = {2020}, month = {2020 Oct 23}, pages = {14763-14779}, abstract = {

The human pathogen targets epithelial cells lining the genital mucosa. We observed that infection of various cell types, including fibroblasts and epithelial cells resulted in the formation of unusually stable and mature focal adhesions that resisted disassembly induced by the myosin II inhibitor, blebbistatin. Super-resolution microscopy revealed in infected cells the vertical displacement of paxillin and FAK from the signaling layer of focal adhesions; while vinculin remained in its normal position within the force transduction layer. The candidate type III effector TarP which localized to focal adhesions during infection and when expressed ectopically, was sufficient to mimic both the reorganization and blebbistatin-resistant phenotypes. These effects of TarP, including its localization to focal adhesions, required a post-invasion interaction with the host protein vinculin through a specific domain at the C-terminus of TarP. This interaction is repurposed from an actin-recruiting and -remodeling complex to one that mediates nano-architectural and dynamic changes of focal adhesions. The consequence of -stabilized focal adhesions was restricted cell motility and enhanced attachment to the extracellular matrix. Thus, via a novel mechanism, inserts TarP within focal adhesions to alter their organization and stability.

}, issn = {1083-351X}, doi = {10.1074/jbc.RA120.015219}, author = {Pedrosa, Antonio T and Murphy, Korinn N and Nogueira, Ana T and Brinkworth, Amanda J and Thwaites, Tristan R and Aaron, Jesse and Chew, Teng-Leong and Carabeo, Rey A} } @article {65634, title = {Precision Calcium Imaging of Dense Neural Populations via a Cell-Body-Targeted Calcium Indicator.}, journal = {Neuron}, volume = {107}, year = {2020}, month = {2020 Aug 01}, pages = {470}, abstract = {

Methods for one-photon fluorescent imaging of calcium dynamics can capture the activity of hundreds of neurons across large fields of view at a low equipment complexity and cost. In contrast to two-photon methods, however, one-photon methods suffer from higher levels of crosstalk from neuropil, resulting in a decreased signal-to-noise ratio and artifactual correlations of neural activity. We address this problem by engineering cell-body-targeted variants of the fluorescent calcium indicators GCaMP6f and GCaMP7f. We screened fusions of GCaMP to natural, as well as artificial, peptides and identified fusions that localized GCaMP to within 50\ μm of the cell body of neurons in mice and larval zebrafish. One-photon imaging of soma-targeted GCaMP in dense neural circuits reported fewer artifactual spikes from neuropil, an increased signal-to-noise ratio, and decreased artifactual correlation across neurons. Thus, soma-targeting of fluorescent calcium indicators facilitates usage of simple, powerful, one-photon methods for imaging neural calcium dynamics.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2020.05.029}, author = {Shemesh, Or A and Linghu, Changyang and Piatkevich, Kiryl D and Goodwin, Daniel and Celiker, Orhan Tunc and Gritton, Howard J and Romano, Michael F and Gao, Ruixuan and Yu, Chih-Chieh Jay and Tseng, Hua-An and Bensussen, Seth and Narayan, Sujatha and Yang, Chao-Tsung and Freifeld, Limor and Siciliano, Cody A and Gupta, Ishan and Wang, Joyce and Pak, Nikita and Yoon, Young-Gyu and Ullmann, Jeremy F P and Guner-Ataman, Burcu and Noamany, Habiba and Sheinkopf, Zoe R and Park, Won Min and Asano, Shoh and Keating, Amy E and Trimmer, James S and Reimer, Jacob and Tolias, Andreas S and Bear, Mark F and Tye, Kay M and Han, Xue and Ahrens, Misha B and Boyden, Edward S} } @article {65721, title = {Preventing cytokine storm syndrome in COVID-19 using α-1 adrenergic receptor antagonists.}, journal = {The Journal of Clinical Investigatio}, volume = {130}, year = {2020}, month = {2020 Jul 01}, pages = {3345-47}, keywords = {Adrenergic alpha-1 Receptor Antagonists, Clinical Trials as Topic, Coronavirus Infections, Cytokine Release Syndrome, Humans, Pandemics, Pneumonia, Viral}, issn = {1558-8238}, doi = {10.1172/JCI139642}, author = {Konig, Maximilian F and Powell, Mike and Staedtke, Verena and Bai, Ren-Yuan and Thomas, David L and Fischer, Nicole and Huq, Sakibul and Khalafallah, Adham M and Koenecke, Allison and Xiong, Ruoxuan and Mensh, Brett and Papadopoulos, Nickolas and Kinzler, Kenneth W and Vogelstein, Bert and Vogelstein, Joshua T and Athey, Susan and Zhou, Shibin and Bettegowda, Chetan} } @article {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 {65760, title = {Sensing cellular biochemistry with fluorescent chemical{\textendash}genetic hybrids}, journal = {Current Opinion in Chemical Biology}, volume = {57}, year = {2020}, month = {08/2020}, pages = {58{\textendash}64}, abstract = {

Fluorescent biosensors are powerful tools\ for the detection of biochemical events inside cells with high spatiotemporal resolution. Biosensors based on fluorescent proteins often suffer from issues with photostability and brightness. On the other hand, hybrid, chemical{\textendash}genetic systems present unique opportunities to combine the strengths of synthetic, organic chemistry with biological macromolecules to generate exquisitely tailored semisynthetic sensors.

}, issn = {1367-5931}, doi = {10.1016/j.cbpa.2020.04.005}, author = {Gautier, Arnaud and Tebo, Alison G.} } @article {65286, title = {Structure and assembly of calcium homeostasis modulator proteins.}, journal = {Nature Structural and Molecular Biology}, volume = {27}, year = {2020}, month = {2020 Jan 27}, pages = {150-9}, abstract = {

The biological membranes of many cell types contain large-pore channels through which a wide variety of ions and metabolites permeate. Examples include connexin, innexin and pannexin, which form gap junctions and/or bona fide cell surface channels. The most recently identified large-pore channels are the calcium homeostasis modulators (CALHMs), through which ions and ATP permeate in a voltage-dependent manner to control neuronal excitability, taste signaling and pathologies of depression and Alzheimer{\textquoteright}s disease. Despite such critical biological roles, the structures and patterns of their oligomeric assembly remain unclear. Here, we reveal the structures of two CALHMs, chicken CALHM1 and human CALHM2, by single-particle cryo-electron microscopy (cryo-EM), which show novel assembly of the four transmembrane helices into channels of octamers and undecamers, respectively. Furthermore, molecular dynamics simulations suggest that lipids can favorably assemble into a bilayer within the larger CALHM2 pore, but not within CALHM1, demonstrating the potential correlation between pore size, lipid accommodation and channel activity.

}, issn = {1545-9985}, doi = {10.1038/s41594-019-0369-9}, author = {Syrjanen, Johanna L and Michalski, Kevin and Chou, Tsung-Han and Grant, Timothy and Rao, Shanlin and Simorowski, Noriko and Tucker, Stephen J and Grigorieff, Nikolaus and Furukawa, Hiro} } @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 {65723, title = {A systematic nomenclature for the Drosophila ventral nerve cord.}, journal = {Neuron}, volume = {107}, year = {2020}, month = {2020 Sep 14}, pages = {1071-79}, abstract = {

Drosophila melanogaster is an established model for neuroscience research with relevance in biology and medicine. Until recently, research on the Drosophila brain was hindered by the lack of a complete and uniform nomenclature. Recognizing this, Ito et\ al. (2014) produced an authoritative nomenclature for the adult insect brain, using Drosophila as the reference. Here, we extend this nomenclature to the adult thoracic and abdominal neuromeres, the ventral nerve cord (VNC), to provide an anatomical description of this major component of the Drosophila nervous system. The VNC is the locus for the reception and integration of sensory information and involved in generating most of the locomotor actions that underlie fly behaviors. The aim is to create a nomenclature, definitions, and spatial boundaries for the Drosophila VNC that are consistent with other insects. The work establishes an anatomical framework that provides a powerful tool for analyzing the functional organization of the VNC.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2020.08.005}, author = {Court, Robert and Namiki, Shigehiro and Armstrong, J Douglas and Borner, Jana and Card, Gwyneth and Costa, Marta and Dickinson, Michael and Duch, Carsten and Korff, Wyatt and Mann, Richard and Merritt, David and Murphey, Rod K and Seeds, Andrew M and Shirangi, Troy and Simpson, Julie H and Truman, James W and Tuthill, John C and Williams, Darren W and Shepherd, David} } @booklet {67224, title = {Teaching deep neural networks to localize single molecules for super-resolution microscopy}, year = {2020}, abstract = {

Single-molecule localization fluorescence microscopy constructs super-resolution images by sequential imaging and computational localization of sparsely activated fluorophores. Accurate and efficient fluorophore localization algorithms are key to the success of this computational microscopy method. We present a novel localization algorithm based on deep learning which significantly improves upon the state of the art. Our contributions are a novel network architecture for simultaneous detection and localization, and new loss function which phrases detection and localization as a Bayesian inference problem, and thus allows the network to provide uncertainty-estimates. In contrast to standard methods which independently process imaging frames, our network architecture uses temporal context from multiple sequentially imaged frames to detect and localize molecules. We demonstrate the power of our method across a variety of datasets, imaging modalities, signal to noise ratios, and fluorophore densities. While existing localization algorithms can achieve optimal localization accuracy at low fluorophore densities, they are confounded by high densities. Our method is the first deep-learning based approach which achieves state-of-the-art on the SMLM2016 challenge. It achieves the best scores on 12 out of 12 data-sets when comparing both detection accuracy and precision, and excels at high densities. Finally, we investigate how unsupervised learning can be used to make the network robust against mismatch between simulated and real data. The lessons learned here are more generally relevant for the training of deep networks to solve challenging Bayesian inverse problems on spatially extended domains in biology and physics.

}, url = {https://arxiv.org/abs/1907.00770}, author = {Artur Speiser and Lucas-Raphael M{\"u}ller and Ulf Matti and Christopher J. Obara and Wesley R. Legant and Jonas Ries and Jakob H. Macke and Srinivas C. Turaga} } @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 {65256, title = {Trans-endocytosis of intact IL-15Rα-IL-15 complex from presenting cells into NK cells favors signaling for proliferation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, year = {2020}, month = {2020 Jan 07}, pages = {522-531}, abstract = {

Interleukin 15 (IL-15) is an essential cytokine for the survival and proliferation of natural killer (NK) cells. IL-15 activates signaling by the β and common γ (γ) chain heterodimer of the IL-2 receptor through -presentation by cells expressing IL-15 bound to the α chain of the IL-15 receptor (IL-15Rα). We show here that membrane-associated IL-15Rα-IL-15 complexes are transferred from presenting cells to NK cells through -endocytosis and contribute to the phosphorylation of ribosomal protein S6 and NK cell proliferation. NK cell interaction with soluble or surface-bound IL-15Rα-IL-15 complex resulted in Stat5 phosphorylation and NK cell survival at a concentration or density of the complex much lower than required to stimulate S6 phosphorylation. Despite this efficient response, Stat5 phosphorylation was reduced after inhibition of metalloprotease-induced IL-15Rα-IL-15 shedding from -presenting cells, whereas S6 phosphorylation was unaffected. Conversely, inhibition of -endocytosis by silencing of the small GTPase TC21 or expression of a dominant-negative TC21 reduced S6 phosphorylation but not Stat5 phosphorylation. Thus, -endocytosis of membrane-associated IL-15Rα-IL-15 provides a mode of regulating NK cells that is not afforded to IL-2 and is distinct from activation by soluble IL-15. These results may explain the strict IL-15 dependence of NK cells and illustrate how the cellular compartment in which receptor-ligand interaction occurs can influence functional outcome.

}, issn = {1091-6490}, doi = {10.1073/pnas.1911678117}, author = {Anton, Olga M and Peterson, Mary E and Hollander, Michael J and Dorward, David W and Arora, Gunjan and Traba, Javier and Rajagopalan, Sumati and Snapp, Erik L and Garcia, K Christopher and Waldmann, Thomas A and Long, Eric O} } @article {65603, title = {Ultrastructural visualization of 3D chromatin folding using volume electron microscopy and DNA in situ hybridization.}, journal = {Nature Communications}, volume = {11}, year = {2020}, month = {2020 May 01}, pages = {2120}, abstract = {

The human genome is extensively folded into 3-dimensional organization. However, the detailed 3D chromatin folding structures have not been fully visualized due to the lack of robust and ultra-resolution imaging capability. Here, we report the development of an electron microscopy method that combines serial block-face scanning electron microscopy with in situ hybridization (3D-EMISH) to visualize 3D chromatin folding at targeted genomic regions with ultra-resolution (5 {\texttimes} 5 {\texttimes} 30 nm in xyz dimensions) that is superior to the current super-resolution by fluorescence light microscopy. We apply 3D-EMISH to human lymphoblastoid cells at a 1.7 Mb segment of the genome and visualize a large number of distinctive 3D chromatin folding structures in ultra-resolution. We further quantitatively characterize the reconstituted chromatin folding structures by identifying sub-domains, and uncover a high level heterogeneity of chromatin folding ultrastructures in individual nuclei, suggestive of extensive dynamic fluidity in 3D chromatin states.

}, issn = {2041-1723}, doi = {10.1038/s41467-020-15987-2}, author = {Trzaskoma, Pawe{\l} and Ruszczycki, B{\l}a{\.z}ej and Lee, Byoungkoo and Pels, Katarzyna K and Krawczyk, Katarzyna and Bokota, Grzegorz and Szczepankiewicz, Andrzej A and Aaron, Jesse and Walczak, Agnieszka and {\'S}liwi{\'n}ska, Ma{\l}gorzata A and Magalska, Adriana and Kadlof, Michal and Wolny, Artur and Parteka, Zofia and Arabasz, Sebastian and Kiss-Arabasz, Magdalena and Plewczy{\'n}ski, Dariusz and Ruan, Yijun and Wilczy{\'n}ski, Grzegorz M} } @article {65375, title = {Unc-4 acts to promote neuronal identity and development of the take-off circuit in the Drosophila CNS.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Mar 27}, doi = {10.7554/eLife.55007}, url = {https://elifesciences.org/articles/55007}, author = {Lacin, Haluk and Williamson, W Ryan and Card, Gwyneth M and Skeath, James B and Truman, James W} } @article {64890, title = {Amino acid signatures of HLA Class-I and II molecules are strongly associated with SLE susceptibility and autoantibody production in Eastern Asians.}, journal = {PLoS Genetics}, volume = {15}, year = {2019}, month = {2019 Apr 25}, pages = {e1008092}, abstract = {

Human leukocyte antigen (HLA) is a key genetic factor conferring risk of systemic lupus erythematosus (SLE), but precise independent localization of HLA effects is extremely challenging. As a result, the contribution of specific HLA alleles and amino-acid residues to the overall risk of SLE and to risk of specific autoantibodies are far from completely understood. Here, we dissected (a) overall SLE association signals across HLA, (b) HLA-peptide interaction, and (c) residue-autoantibody association. Classical alleles, SNPs, and amino-acid residues of eight HLA genes were imputed across 4,915 SLE cases and 13,513 controls from Eastern Asia. We performed association followed by conditional analysis across HLA, assessing both overall SLE risk and risk of autoantibody production. DR15 alleles HLA-DRB1*15:01 (P = 1.4x10-27, odds ratio (OR) = 1.57) and HLA-DQB1*06:02 (P = 7.4x10-23, OR = 1.55) formed the most significant haplotype (OR = 2.33). Conditioned protein-residue signals were stronger than allele signals and mapped predominantly to HLA-DRB1 residue 13 (P = 2.2x10-75) and its proxy position 11 (P = 1.1x10-67), followed by HLA-DRB1-37 (P = 4.5x10-24). After conditioning on HLA-DRB1, novel associations at HLA-A-70 (P = 1.4x10-8), HLA-DPB1-35 (P = 9.0x10-16), HLA-DQB1-37 (P = 2.7x10-14), and HLA-B-9 (P = 6.5x10-15) emerged. Together, these seven residues increased the proportion of explained heritability due to HLA to 2.6\%. Risk residues for both overall disease and hallmark autoantibodies (i.e., nRNP: DRB1-11, P = 2.0x10-14; DRB1-13, P = 2.9x10-13; DRB1-30, P = 3.9x10-14) localized to the peptide-binding groove of HLA-DRB1. Enrichment for specific amino-acid characteristics in the peptide-binding groove correlated with overall SLE risk and with autoantibody presence. Risk residues were in primarily negatively charged side-chains, in contrast with rheumatoid arthritis. We identified novel SLE signals in HLA Class I loci (HLA-A, HLA-B), and localized primary Class II signals to five residues in HLA-DRB1, HLA-DPB1, and HLA-DQB1. These findings provide insights about the mechanisms by which the risk residues interact with each other to produce autoantibodies and are involved in SLE pathophysiology.

}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1008092}, author = {Molineros, Julio E and Looger, Loren L and Kim, Kwangwoo and Okada, Yukinori and Terao, Chikashi and Sun, Celi and Zhou, Xu-Jie and Raj, Prithvi and Kochi, Yuta and Suzuki, Akari and Akizuki, Shuji and Nakabo, Shuichiro and Bang, So-Young and Lee, Hye-Soon and Kang, Young Mo and Suh, Chang-Hee and Chung, Won Tae and Park, Yong-Beom and Choe, Jung-Yoon and Shim, Seung-Cheol and Lee, Shin-Seok and Zuo, Xiaoxia and Yamamoto, Kazuhiko and Li, Quan-Zhen and Shen, Nan and Porter, Lauren L and Harley, John B and Chua, Kek Heng and Zhang, Hong and Wakeland, Edward K and Tsao, Betty P and Bae, Sang-Cheol and Nath, Swapan K} } @article {64847, title = {Attachment of the blastoderm to the vitelline envelope affects gastrulation of insects.}, journal = {Nature}, year = {2019}, month = {2019 Mar 27}, abstract = {

During gastrulation, physical forces reshape the simple embryonic tissue to form the complex body plans of multicellular organisms. These forces often cause large-scale asymmetric movements of the embryonic tissue. In many embryos, the gastrulating tissue is surrounded by a rigid protective shell. Although it is well-recognized that gastrulation movements depend on forces that are generated by tissue-intrinsic contractility,\ it is not known whether interactions between the tissue and the protective shell provide additional forces that affect gastrulation. Here we show that a particular part of the blastoderm tissue of the red flour beetle (Tribolium castaneum) tightly adheres in a temporally coordinated manner to the vitelline envelope that surrounds the embryo. This attachment generates an additional force that counteracts tissue-intrinsic contractile forces to create asymmetric tissue movements. This localized attachment depends on an αPS2 integrin (inflated), and the knockdown of this integrin leads to a gastrulation phenotype that is consistent with complete loss of attachment. Furthermore, analysis of another integrin (the αPS3 integrin, scab) in the fruit fly (Drosophila melanogaster) suggests that gastrulation in this organism also relies on adhesion between the blastoderm and the vitelline envelope. Our findings reveal a conserved mechanism through which the spatiotemporal pattern of tissue adhesion to the vitelline envelope provides controllable, counteracting forces that shape gastrulation movements in insects.

}, doi = {10.1038/s41586-019-1044-3}, author = {Muenster, Stefan and Jain, Akanksha and Mietke, Alexander and Pavlopoulos, Anastasios and Grill, Stephan W and Tomancak, Pavel} } @article {65001, title = {Automated reconstruction of a serial-section EM drosophila brain with flood-filling networks and local realignment.}, journal = {bioRxiv}, year = {2019}, month = {2019 Apr 11}, abstract = {

Reconstruction of neural circuitry at single-synapse resolution is an attractive target for improving understanding of the nervous system in health and disease. Serial section transmission electron microscopy (ssTEM) is among the most prolific imaging methods employed in pursuit of such reconstructions. We demonstrate how Flood-Filling Networks (FFNs) can be used to computationally segment a forty-teravoxel whole-brain\ Drosophila\ ssTEM volume. To compensate for data irregularities and imperfect global alignment, FFNs were combined with procedures that locally re-align serial sections and dynamically adjust image content. The proposed approach produced a largely merger-free segmentation of the entire ssTEM\ Drosophila\ brain, which we make freely available. As compared to manual tracing using an efficient skeletonization strategy, the segmentation enabled circuit reconstruction and analysis workflows that were an order of magnitude faster.

}, doi = {10.1101/605634}, author = {Peter H. Li and Larry F. Lindsey and Micha{\l} Januszewski and Zhihao Zheng and Alexander Shakeel Bates and Istv{\'a}n Taisz and Mike Tyka and Matthew Nichols and Feng Li and Eric Perlman and Jeremy Maitin-Shepard and Tim Blakely and Laramie Leavitt and Gregory S.X.E. Jefferis and Davi Bock and Viren Jain} } @article {65079, title = {BigStitcher: reconstructing high-resolution image datasets of cleared and expanded samples.}, journal = {Nature Methods}, volume = {16}, year = {2019}, month = {2019 Sep}, pages = {870-74}, abstract = {

Light-sheet imaging of cleared and expanded samples creates terabyte-sized datasets that consist of many unaligned three-dimensional image tiles, which must be reconstructed before analysis. We developed the BigStitcher software to address this challenge. BigStitcher enables interactive visualization, fast and precise alignment, spatially resolved quality estimation, real-time fusion and deconvolution of dual-illumination, multitile, multiview datasets. The software also compensates for optical effects, thereby improving accuracy and enabling subsequent biological analysis.

}, issn = {1548-7091}, doi = {10.1038/s41592-019-0501-0}, url = {http://www.nature.com/articles/s41592-019-0501-0http://www.nature.com/articles/s41592-019-0501-0.pdfhttp://www.nature.com/articles/s41592-019-0501-0.pdfhttp://www.nature.com/articles/s41592-019-0501-0}, author = {H{\"o}rl, David and Rojas Rusak, Fabio and Preusser, Friedrich and Tillberg, Paul and Randel, Nadine and Chhetri, Raghav K. and Cardona, Albert and Keller, Philipp J. and Harz, Hartmann and Leonhardt, Heinrich and Treier, Mathias and Preibisch, Stephan} } @article {65242, title = {Biosensors show the pharmacokinetics of S-Ketamine in the endoplasmic reticulum.}, journal = {Frontiers in Cellular Neuroscience}, volume = {13}, year = {2019}, month = {2019 Nov 12}, pages = {499}, abstract = {

The target for the "rapid" (\<24 h) antidepressant effects of S-ketamine is unknown, vitiating programs to rationally develop more effective rapid antidepressants. To describe a drug{\textquoteright}s target, one must first understand the compartments entered by the drug, at all levels-the organ, the cell, and the organelle. We have, therefore, developed molecular tools to measure the subcellular, organellar pharmacokinetics of S-ketamine. The tools are genetically encoded intensity-based S-ketamine-sensing fluorescent reporters, iSKetSnFR1 and iSKetSnFR2. In solution, these biosensors respond to S-ketamine with a sensitivity, S-slope = delta(F/F)/(delta[S-ketamine]) of 0.23 and 1.9/μM, respectively. The iSKetSnFR2 construct allows measurements at \<0.3 μM S-ketamine. The iSKetSnFR1 and iSKetSnFR2 biosensors display \>100-fold selectivity over other ligands tested, including R-ketamine. We targeted each of the sensors to either the plasma membrane (PM) or the endoplasmic reticulum (ER). Measurements on these biosensors expressed in Neuro2a cells and in human dopaminergic neurons differentiated from induced pluripotent stem cells (iPSCs) show that S-ketamine enters the ER within a few seconds after appearing in the external solution near the PM, then leaves as rapidly after S-ketamine is removed from the extracellular solution. In cells, S-slopes for the ER and PM-targeted sensors differ by \<2-fold, indicating that the ER [S-ketamine] is less than 2-fold different from the extracellular [S-ketamine]. Organelles represent potential compartments for the engagement of S-ketamine with its antidepressant target, and potential S-ketamine targets include organellar ion channels, receptors, and transporters.

}, issn = {1662-5102}, doi = {10.3389/fncel.2019.00499}, author = {Bera, Kallol and Kamajaya, Aron and Shivange, Amol V and Muthusamy, Anand K and Nichols, Aaron L and Borden, Philip M and Grant, Stephen and Jeon, Janice and Lin, Elaine and Bishara, Ishak and Chin, Theodore M and Cohen, Bruce N and Kim, Charlene H and Unger, Elizabeth K and Tian, Lin and Marvin, Jonathan S and Looger, Loren L and Lester, Henry A} } @article {65081, title = {Bright and photostable chemigenetic indicators for extended in vivo voltage imaging.}, journal = {Science}, volume = {365}, year = {2019}, month = {2019 Aug 13}, pages = {699-704}, abstract = {

Imaging changes in membrane potential using genetically encoded fluorescent voltage indicators (GEVIs) has great potential for monitoring neuronal activity with high spatial and temporal resolution. Brightness and photostability of fluorescent proteins and rhodopsins have limited the utility of existing GEVIs. We engineered a novel GEVI, "Voltron", that utilizes bright and photostable synthetic dyes instead of protein-based fluorophores, extending the combined duration of imaging and number of neurons imaged simultaneously by more than tenfold relative to existing GEVIs. We used Voltron for in vivo voltage imaging in mice, zebrafish, and fruit flies. In mouse cortex, Voltron allowed single-trial recording of spikes and subthreshold voltage signals from dozens of neurons simultaneously, over 15 min of continuous imaging. In larval zebrafish, Voltron enabled the precise correlation of spike timing with behavior.

}, issn = {1095-9203}, doi = {10.1126/science.aav6416}, author = {Abdelfattah, Ahmed S and Kawashima, Takashi and Singh, Amrita and Novak, Ondrej and Liu, Hui and Shuai, Yichun and Huang, Yi-Chieh and Campagnola, Luke and Seeman, Stephanie C and Yu, Jianing and Zheng, Jihong and Grimm, Jonathan B and Patel, Ronak and Friedrich, Johannes and Mensh, Brett D and Paninski, Liam and Macklin, John J and Murphy, Gabe J and Podgorski, Kaspar and Lin, Bei-Jung and Chen, Tsai-Wen and Turner, Glenn C and Liu, Zhe and Koyama, Minoru and Svoboda, Karel and Ahrens, Misha B and Lavis, Luke D and Schreiter, Eric R} } @article {67280, title = {CaImAn an open source tool for scalable calcium imaging data analysis}, journal = {eLife}, volume = {8}, year = {2019}, month = {01/2019}, abstract = {

Advances in fluorescence microscopy enable monitoring larger brain areas in-vivo with finer time resolution. The resulting data rates require reproducible analysis pipelines that are reliable, fully automated, and scalable to datasets generated over the course of months. We present CaImAn, an open-source library for calcium imaging data analysis. CaImAn\ provides automatic and scalable methods to address problems common to pre-processing, including motion correction, neural activity identification, and registration across different sessions of data collection. It does this while requiring minimal user intervention, with good scalability on computers ranging from laptops to high-performance computing clusters. CaImAn\ is suitable for two-photon and one-photon imaging, and also enables real-time analysis on streaming data. To benchmark the performance of CaImAn\ we collected and combined a corpus of manual annotations from multiple labelers on nine mouse two-photon datasets. We demonstrate that CaImAn\ achieves near-human performance in detecting locations of active neurons

}, doi = {10.7554/eLife.38173}, url = {https://elifesciences.org/articles/38173}, author = {Giovannucci, Andrea and Friedrich, Johannes and Gunn, Pat and Kalfon, J{\'e}r{\'e}mie and Brown, Brandon L and Koay, Sue Ann and Taxidis, Jiannis and Najafi, Farzaneh and Gauthier, Jeffrey L and Zhou, Pengcheng and Khakh, Baljit S and Tank, David W and Chklovskii, Dmitri B and Pnevmatikakis, Eftychios A} } @article {64850, title = {Cellular localization of tolyporphins, unusual tetrapyrroles, in a microbial photosynthetic community determined using hyperspectral confocal fluorescence microscopy.}, journal = {Photosynthesis Research}, volume = {141}, year = {2019}, month = {2019 Sep 1}, pages = {259-71}, abstract = {

The cyanobacterial culture HT-58-2, composed of a filamentous cyanobacterium and accompanying community bacteria, produces chlorophyll a as well as the tetrapyrrole macrocycles known as tolyporphins. Almost all known tolyporphins (A-M except K) contain a dioxobacteriochlorin chromophore and exhibit an absorption spectrum somewhat similar to that of chlorophyll a. Here, hyperspectral confocal fluorescence microscopy was employed to noninvasively probe the locale of tolyporphins within live cells under various growth conditions (media, illumination, culture age). Cultures grown in nitrate-depleted media (BG-11 vs. nitrate-rich, BG-11) are known to increase the production of tolyporphins by orders of magnitude (rivaling that of chlorophyll a) over a period of 30-45 days. Multivariate curve resolution (MCR) was applied to an image set containing images from each condition to obtain pure component spectra of the endogenous pigments. The relative abundances of these components were then calculated for individual pixels in each image in the entire set, and 3D-volume renderings were obtained. At 30 days in media with or without nitrate, the chlorophyll a and phycobilisomes (combined phycocyanin and phycobilin components) co-localize in the filament outer cytoplasmic region. Tolyporphins localize in a distinct peripheral pattern in cells grown in BG-11 versus a diffuse pattern (mimicking the chlorophyll a localization) upon growth in BG-11. In BG-11, distinct puncta of tolyporphins were commonly found at the septa between cells and at the end of filaments. This work quantifies the relative abundance and envelope localization of tolyporphins in single cells, and illustrates the ability to identify novel tetrapyrroles in the presence of chlorophyll a in a photosynthetic microorganism within a non-axenic culture.

}, issn = {1573-5079}, doi = {10.1007/s11120-019-00625-w}, author = {Barnhart-Dailey, Meghan and Zhang, Yunlong and Zhang, Ran and Anthony, Stephen M and Aaron, Jesse S and Miller, Eric S and Lindsey, Jonathan S and Timlin, Jerilyn A} } @article {49582, title = {Characterization of neurite dystrophy after trauma by high speed structured illumination microscopy and lattice light sheet microscopy.}, journal = {Journal of Neuroscience Methods}, volume = {312}, year = {2019}, month = {2019 Jan 15}, pages = {154-61}, abstract = {

BACKGROUND: Unbiased screening studies have repeatedly identified actin-related proteins as one of the families of proteins most influenced by neurotrauma. Nevertheless, the status quo model of cytoskeletal reorganization after neurotrauma excludes actin and incorporates only changes in microtubules and intermediate filaments. Actin is excluded in part because it is difficult to image with conventional techniques. However, recent innovations in fluorescent microscopy provide an opportunity to image the actin cytoskeleton at super-resolution resolution in living cells. This study applied these innovations to an in vitro model of neurotrauma.

NEW METHOD: New methods are introduced for traumatizing neurons before imaging them with high speed structured illumination microscopy or lattice light sheet microscopy. Also, methods for analyzing structured illumination microscopy images to quantify post-traumatic neurite dystrophy are presented.

RESULTS: Human induced pluripotent stem cell-derived neurons exhibited actin organization typical of immature neurons. Neurite dystrophy increased after trauma but was not influenced by jasplakinolide treatment. The F-actin content of dystrophies varied greatly from one dystrophy to another.

COMPARISON WITH EXISTING METHODS: In contrast to fixation dependent methods, these methods capture the evolution of the actin cytoskeleton over time in a living cell. In contrast to prior methods based on counting dystrophies, this quantification scheme parameterizes the severity of a given dystrophy as it evolves from a local swelling to an almost-perfect spheroid that threatens to transect the neurite.

CONCLUSIONS: These methods can be used to investigate genetic factors and therapeutic interventions that modulate the course of neurite dystrophy after trauma.

}, issn = {1872-678X}, doi = {10.1016/j.jneumeth.2018.12.005}, author = {Phillips, Jack K and Sherman, Sydney A and Cotton, Kristen Y and Heddleston, John M and Taylor, Aaron B and Finan, John D} } @article {51252, title = {Comparisons between the ON- and OFF-edge motion pathways in the brain.}, journal = {eLife}, volume = {8}, year = {2019}, month = {2019 Jan 09}, abstract = {

Understanding the circuit mechanisms behind motion detection is a long-standing question in visual neuroscience. In , recent synapse-level connectomes in the optic lobe, particularly in ON-pathway (T4) receptive-field circuits, in concert with physiological studies, suggest an increasingly intricate motion model compared with the ubiquitous Hassenstein-Reichardt model, while our knowledge of OFF-pathway (T5) has been incomplete. Here we present a conclusive and comprehensive connectome that for the first time integrates detailed connectivity information for inputs to both T4 and T5 pathways in a single EM dataset covering the entire optic lobe. With novel reconstruction methods using automated synapse prediction suited to such a large connectome, we successfully corroborate previous findings in the T4 pathway and comprehensively identify inputs and receptive fields for T5. While the two pathways are likely evolutionarily linked and indeed exhibit many similarities, we uncover interesting differences and interactions that may underlie their distinct functional properties.

}, issn = {2050-084X}, doi = {10.7554/eLife.40025}, author = {Shinomiya, Kazunori and Huang, Gary and Lu, Zhiyuan and Parag, Toufiq and Xu, C Shan and Aniceto, Roxanne and Ansari, Namra and Cheatham, Natasha and Lauchie, Shirley and Neace, Erika and Ogundeyi, Omotara and Ordish, Christopher and Peel, David and Shinomiya, Aya and Smith, Claire and Takemura, Satoko and Talebi, Iris and Rivlin, Patricia K and Nern, Aljoscha and Scheffer, Louis K and Plaza, Stephen M and Meinertzhagen, Ian A} } @article {65128, title = {Constraining computational models using electron microscopy wiring diagrams.}, journal = {Current Opinion in Neurobiology}, volume = {58}, year = {2019}, month = {2019 Aug 27}, pages = {94-100}, abstract = {

Numerous efforts to generate "connectomes," or synaptic wiring diagrams, of large neural circuits or entire nervous systems are currently underway. These efforts promise an abundance of data to guide theoretical models of neural computation and test their predictions. However, there is not yet a standard set of tools for incorporating the connectivity constraints that these datasets provide into the models typically studied in theoretical neuroscience. This article surveys recent approaches to building models with constrained wiring diagrams and the insights they have provided. It also describes challenges and the need for new techniques to scale these approaches to ever more complex datasets.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2019.07.007}, author = {Litwin-Kumar, Ashok and Turaga, Srinivas C} } @article {51795, title = {Cortical column and whole-brain imaging with molecular contrast and nanoscale resolution.}, journal = {Science (New York, N.Y.)}, volume = {363}, year = {2019}, month = {2019 Jan 18}, pages = {eaau8302}, abstract = {

Optical and electron microscopy have made tremendous inroads toward understanding the complexity of the brain. However, optical microscopy offers insufficient resolution to reveal subcellular details, and electron microscopy lacks the throughput and molecular contrast to visualize specific molecular constituents over millimeter-scale or larger dimensions. We combined expansion microscopy and lattice light-sheet microscopy to image the nanoscale spatial relationships between proteins across the thickness of the mouse cortex or the entire\ Drosophila\ brain. These included synaptic proteins at dendritic spines, myelination along axons, and presynaptic densities at dopaminergic neurons in every fly brain region. The technology should enable statistically rich, large-scale studies of neural development, sexual dimorphism, degree of stereotypy, and structural correlations to behavior or neural activity, all with molecular contrast.

}, doi = {10.1126/science.aau8302}, author = {Gao, Ruixuan and Asano, Shoh M and Upadhyayula, Srigokul and Pisarev, Igor and Milkie, Daniel E and Liu, Tsung-Li and Singh, Ved and Graves, Austin R and Huynh, Grace H and Zhao, Yongxin and Bogovic, John A and Colonell, Jennifer and Ott, Carolyn M and Zugates, Christopher T and Tappan, Susan and Rodriguez, Alfredo and Mosaliganti, Kishore R and Sheu, Shu-Hsien and Pasolli, H Amalia and et al} } @article {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 {68993, title = {Deterministic Somatic Cell Reprogramming Involves Continuous Transcriptional Changes Governed by Myc and Epigenetic-Driven Modules.}, journal = {Cell Stem Cell}, volume = {24}, year = {2019}, month = {02/2019}, pages = {328-341.e9}, abstract = {

The epigenetic dynamics of induced pluripotent stem cell (iPSC) reprogramming in correctly reprogrammed cells at high resolution and throughout the entire process remain largely undefined. Here, we characterize conversion of mouse fibroblasts into iPSCs using Gatad2a-Mbd3/NuRD-depleted and highly efficient reprogramming systems. Unbiased high-resolution profiling of dynamic changes in levels of gene expression, chromatin engagement, DNA accessibility, and DNA methylation were obtained. We identified two distinct and synergistic transcriptional modules that dominate successful reprogramming, which are associated with cell identity and biosynthetic genes. The pluripotency module is governed by dynamic alterations in epigenetic modifications to promoters and binding by Oct4, Sox2, and Klf4, but not Myc. Early DNA demethylation at certain enhancers prospectively marks cells fated to reprogram. Myc activity drives expression of the essential biosynthetic module and is associated with optimized changes in tRNA codon usage. Our functional validations highlight interweaved epigenetic- and Myc-governed essential reconfigurations that rapidly commission and propel deterministic reprogramming toward naive pluripotency.

}, keywords = {Animals, Cell Lineage, Cellular Reprogramming, Chromatin, Demethylation, Epigenesis, Genetic, Humans, Induced Pluripotent Stem Cells, Kruppel-Like Factor 4, Mice, Protein Binding, Proto-Oncogene Proteins c-myc, RNA, Transfer, Transcription Factors, Transcription, Genetic}, issn = {1875-9777}, doi = {10.1016/j.stem.2018.11.014}, author = {Zviran, Asaf and Mor, Nofar and Rais, Yoach and Gingold, Hila and Peles, Shani and Chomsky, Elad and Viukov, Sergey and Buenrostro, Jason D and Scognamiglio, Roberta and Weinberger, Leehee and Manor, Yair S and Krupalnik, Vladislav and Zerbib, Mirie and Hezroni, Hadas and Jaitin, Diego Adhemar and Larastiaso, David and Gilad, Shlomit and Benjamin, Sima and Gafni, Ohad and Mousa, Awni and Ayyash, Muneef and Sheban, Daoud and Bayerl, Jonathan and Aguilera-Castrejon, Alejandro and Massarwa, Rada and Maza, Itay and Hanna, Suhair and Stelzer, Yonatan and Ulitsky, Igor and Greenleaf, William J and Tanay, Amos and Trumpp, Andreas and Amit, Ido and Pilpel, Yitzhak and Novershtern, Noa and Hanna, Jacob H} } @article {65168, title = {Developmental organization of central neurons in the adult Drosophila ventral nervous system.}, journal = {Journal of Comparative Neurology}, volume = {527}, year = {2019}, month = {2019 Oct 15}, pages = {2573-2598}, abstract = {

We have used MARCM to reveal the adult morphology of the post embryonically produced neurons in the thoracic neuromeres of the Drosophila VNS. The work builds on previous studies of the origins of the adult VNS neurons to describe the clonal organization of the adult VNS. We present data for 58 of 66 postembryonic thoracic lineages, excluding the motor neuron producing lineages (15 and 24) which have been described elsewhere. MARCM labels entire lineages but where both A and B hemilineages survive (e.g., lineages 19, 12, 13, 6, 1, 3, 8, and 11), the two hemilineages can be discriminated and we have described each hemilineage separately. Hemilineage morphology is described in relation to the known functional domains of the VNS neuropil and based on the anatomy we are able to assign broad functional roles for each hemilineage. The data show that in a thoracic hemineuromere, 16 hemilineages are primarily involved in controlling leg movements and walking, 9 are involved in the control of wing movements, and 10 interface between both leg and wing control. The data provide a baseline of understanding of the functional organization of the adult Drosophila VNS. By understanding the morphological organization of these neurons, we can begin to define and test the rules by which neuronal circuits are assembled during development and understand the functional logic and evolution of neuronal networks.

}, issn = {1096-9861}, doi = {10.1002/cne.24690}, author = {Shepherd, David and Sahota, Virender and Court, Robert and Williams, Darren W and Truman, James W} } @article {65241, title = {Dual-plane 3-photon microscopy with remote focusing.}, journal = {Biomedical Optics Express}, volume = {10}, year = {2019}, month = {2019 Nov 1}, pages = {5585-5599}, abstract = {

3-photon excitation enables fluorescence microscopy deep in densely labeled and highly scattering samples. To date, 3-photon excitation has been restricted to scanning a single focus, limiting the speed of volume acquisition. Here, for the first time to our knowledge, we implemented and characterized dual-plane 3-photon microscopy with temporal multiplexing and remote focusing, and performed simultaneous calcium imaging of two planes beyond 600 {\textmu}m deep in the cortex of a pan-excitatory GCaMP6s transgenic mouse with a per-plane framerate of 7 Hz and an effective 2 MHz laser repetition rate. This method is a straightforward and generalizable modification to single-focus 3PE systems, doubling the rate of volume (column) imaging with off-the-shelf components and minimal technical constraints.

}, issn = {2156-7085}, doi = {10.1364/BOE.10.005585}, author = {Takasaki, Kevin T and Tsyboulski, Dmitri and Waters, Jack} } @article {64889, title = {Dynamic super-resolution structured illumination imaging in the living brain.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, year = {2019}, month = {2019 Apr 26}, pages = {9586-91}, abstract = {

Cells in the brain act as components of extended networks. Therefore, to understand neurobiological processes in a physiological context, it is essential to study them in vivo. Super-resolution microscopy has spatial resolution beyond the diffraction limit, thus promising to provide structural and functional insights that are not accessible with conventional microscopy. However, to apply it to in vivo brain imaging, we must address the challenges of 3D imaging in an optically heterogeneous tissue that is constantly in motion. We optimized image acquisition and reconstruction to combat sample motion and applied adaptive optics to correcting sample-induced optical aberrations in super-resolution structured illumination microscopy (SIM) in vivo. We imaged the brains of live zebrafish larvae and mice and observed the dynamics of dendrites and dendritic spines at nanoscale resolution.

}, issn = {1091-6490}, doi = {10.1073/pnas.1819965116}, author = {Turcotte, Raphael and Liang, Yajie and Tanimoto, Masashi and Zhang, Qinrong and Li, Ziwei and Koyama, Minoru and Betzig, Eric and Ji, Na} } @article {64797, title = {Dystroglycan is a scaffold for extracellular axon guidance decisions.}, journal = {eLife}, volume = {8}, year = {2019}, month = {2019 Feb 13}, abstract = {

Axon guidance requires interactions between extracellular signaling molecules and transmembrane receptors, but how appropriate context-dependent decisions are coordinated outside the cell remains unclear. Here we show that the transmembrane glycoprotein Dystroglycan interacts with a changing set of environmental cues that regulate the trajectories of extending axons throughout the mammalian brain and spinal cord. Dystroglycan operates primarily as an extracellular scaffold during axon guidance, as it functions non-cell autonomously and does not require signaling through its intracellular domain. We identify the transmembrane receptor Celsr3/Adgrc3 as a binding partner for Dystroglycan, and show that this interaction is critical for specific axon guidance events . These findings establish Dystroglycan as a multifunctional scaffold that coordinates extracellular matrix proteins, secreted cues, and transmembrane receptors to regulate axon guidance.

}, issn = {2050-084X}, doi = {10.7554/eLife.42143}, author = {Lindenmaier, L Bailey and Parmentier, Nicolas and Guo, Caiying and Tissir, Fadel and Wright, Kevin M} } @article {64958, title = {Evolution of Mechanisms that Control Mating in Drosophila Males.}, journal = {Cell Reports}, volume = {27}, year = {2019}, month = {2019 May 28}, pages = {2527-2536.e4}, abstract = {

Genetically wired neural mechanisms inhibit mating between species because even naive animals rarely mate with other species. These mechanisms can evolve through changes in expression or function of key genes in sensory pathways or central circuits. Gr32a is a gustatory chemoreceptor that, in D.\ melanogaster, is essential to inhibit interspecies courtship and sense quinine. Similar to D.\ melanogaster, we find that D.\ simulans Gr32a is expressed in foreleg tarsi, sensorimotor appendages that inhibit interspecies courtship, and it is required to sense quinine. Nevertheless, Gr32a is not required to inhibit interspecies mating by D.\ simulans males. However, and similar to its function in D.\ melanogaster, Ppk25, a member of the Pickpocket family, promotes conspecific courtship in D.\ simulans. Together, we have identified distinct evolutionary mechanisms underlying chemosensory control of taste and courtship in closely related Drosophila species.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2019.04.104}, author = {Ahmed, Osama M and Avila-Herrera, Aram and Tun, Khin May and Serpa, Paula H and Peng, Justin and Parthasarathy, Srinivas and Knapp, Jon-Michael and Stern, David L and Davis, Graeme W and Pollard, Katherine S and Shah, Nirao M} } @article {65110, title = {Expansion microscopy: scalable and convenient super-resolution microscopy.}, journal = {Annual Review of Cell and Developmental Biology}, volume = {35}, year = {2019}, month = {2019 Oct 6}, pages = {683-701}, abstract = {

Expansion microscopy (ExM) is a physical form of magnification that increases the effective resolving power of any microscope. Here, we describe the fundamental principles of ExM, as well as how recently developed ExM variants build upon and apply those principles. We examine applications of ExM in cell and developmental biology for the study of nanoscale structures as well as ExM{\textquoteright}s potential for scalable mapping of nanoscale structures across large sample volumes. Finally, we explore how the unique anchoring and hydrogel embedding properties enable postexpansion molecular interrogation in a purified chemical environment. ExM promises to play an important role complementary to emerging live-cell imaging techniques, because of its relative ease of adoption and modification and its compatibility with tissue specimens up to at least 200 μm thick. Expected final online publication date for the , Volume 35 is October 7, 2019. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

}, issn = {1530-8995}, doi = {10.1146/annurev-cellbio-100818-125320}, author = {Tillberg, Paul W and Chen, Fei} } @article {64934, title = {Functional and anatomical specificity in a higher olfactory centre.}, journal = {Elife}, volume = {8}, year = {2019}, month = {2019 May 21}, abstract = {

Most sensory systems are organized into parallel neuronal pathways that process distinct aspects of incoming stimuli. In the insect olfactory system, second order projection neurons target both the mushroom body, required for learning, and the lateral horn (LH), proposed to mediate innate olfactory behavior. Mushroom body neurons form a sparse olfactory population code, which is not stereotyped across animals. In contrast, odor coding in the LH remains poorly understood. We combine genetic driver lines, anatomical and functional criteria to show that the LH has ~1400 neurons and \>165 cell types. Genetically labeled LHNs have stereotyped odor responses across animals and on average respond to three times more odors than single projection neurons. LHNs are better odor categorizers than projection neurons, likely due to stereotyped pooling of related inputs. Our results reveal some of the principles by which a higher processing area can extract innate behavioral significance from sensory stimuli.

}, issn = {2050-084X}, doi = {10.7554/eLife.44590}, author = {Frechter, Shahar and Bates, Alexander Shakeel and Tootoonian, Sina and Dolan, Michael-John and Manton, James D and Jamasb, Arian Rokkum and Kohl, Johannes and Bock, Davi and Jefferis, Gregory Sxe} } @article {64796, title = {A genetically encoded single-wavelength sensor for imaging cytosolic and cell surface ATP.}, journal = {Nature Communications}, volume = {10}, year = {2019}, month = {2019 Feb 12}, pages = {711}, abstract = {

Adenosine 5{\textquoteright} triphosphate (ATP) is a universal intracellular energy source and an evolutionarily ancient, ubiquitous extracellular signal in diverse species. Here, we report the generation and characterization of single-wavelength genetically encoded fluorescent sensors (iATPSnFRs) for imaging extracellular and cytosolic ATP from insertion of circularly permuted superfolder GFP into the epsilon subunit of FF-ATPase from Bacillus PS3. On the cell surface and within the cytosol, iATPSnFR responds to relevant ATP concentrations (30 μM to 3 mM) with fast increases in fluorescence. iATPSnFRs can be genetically targeted to specific cell types and sub-cellular compartments, imaged with standard light microscopes, do not respond to other nucleotides and nucleosides, and when fused with a red fluorescent protein function as ratiometric indicators. After careful consideration of their modest pH sensitivity, iATPSnFRs represent promising reagents for imaging ATP in the extracellular space and within cells during a variety of settings, and for further application-specific refinements.

}, issn = {2041-1723}, doi = {10.1038/s41467-019-08441-5}, author = {Lobas, Mark A and Tao, Rongkun and Nagai, Jun and Kronschl{\"a}ger, Mira T and Borden, Philip M and Marvin, Jonathan S and Looger, Loren L and Khakh, Baljit S} } @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 {65023, title = {Glia accumulate evidence that actions are futile and suppress unsuccessful behavior.}, journal = {Cell}, volume = {178}, year = {2019}, month = {2019 Jun 27}, pages = {27-43}, abstract = {

When a behavior repeatedly fails to achieve its goal, animals often give up and become passive, which can be strategic for preserving energy or regrouping between attempts. It is unknown how the brain identifies behavioral failures and mediates this behavioral-state switch. In larval zebrafish swimming in virtual reality, visual feedback can be withheld so that swim attempts fail to trigger expected visual flow. After tens of seconds of such motor futility, animals became passive for similar durations. Whole-brain calcium imaging revealed noradrenergic neurons that responded specifically to failed swim attempts and radial astrocytes whose calcium levels accumulated with increasing numbers of failed attempts. Using cell ablation and optogenetic or chemogenetic activation, we found that noradrenergic neurons progressively activated brainstem radial astrocytes, which then suppressed swimming. Thus, radial astrocytes perform a computation critical for behavior: they accumulate evidence that current actions are ineffective and consequently drive changes in behavioral states.

}, doi = {10.1016/j.cell.2019.05.050}, author = {Mu, Yu and Bennett, Davis V and Rubinov, Mikail and Narayan, Sujatha and Yang, Chao-Tsung and Tanimoto, Masashi and Mensh, Brett D and Looger, Loren L and Ahrens, Misha B} } @article {64986, title = {High-performance calcium sensors for imaging activity in neuronal populations and microcompartments.}, journal = {Nature Methods}, volume = {16}, year = {2019}, month = {2019 Jun 17}, pages = {649-57}, abstract = {

Calcium imaging with genetically encoded calcium indicators (GECIs) is routinely used to measure neural activity in intact nervous systems. GECIs are frequently used in one of two different modes: to track activity in large populations of neuronal cell bodies, or to follow dynamics in subcellular compartments such as axons, dendrites and individual synaptic compartments. Despite major advances, calcium imaging is still limited by the biophysical properties of existing GECIs, including affinity, signal-to-noise ratio, rise and decay kinetics and dynamic range. Using structure-guided mutagenesis and neuron-based screening, we optimized the green fluorescent protein-based GECI GCaMP6 for different modes of in vivo imaging. The resulting jGCaMP7 sensors provide improved detection of individual spikes (jGCaMP7s,f), imaging in neurites and neuropil (jGCaMP7b), and may allow tracking larger populations of neurons using two-photon (jGCaMP7s,f) or wide-field (jGCaMP7c) imaging.

}, issn = {1548-7105}, doi = {10.1038/s41592-019-0435-6}, author = {Dana, Hod and Sun, Yi and Mohar, Boaz and Hulse, Brad K and Kerlin, Aaron M and Hasseman, Jeremy P and Tsegaye, Getahun and Tsang, Arthur and Wong, Allan and Patel, Ronak and Macklin, John J and Chen, Yang and Konnerth, Arthur and Jayaraman, Vivek and Looger, Loren L and Schreiter, Eric R and Svoboda, Karel and Kim, Douglas S} } @article {64971, title = {High-resolution cryo-EM structures of outbreak strain human norovirus shells reveal size variations.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, year = {2019}, month = {2019 Jun 25}, pages = {12828-32}, abstract = {

Noroviruses are a leading cause of foodborne illnesses worldwide. Although GII.4 strains have been responsible for most norovirus outbreaks, the assembled virus shell structures have been available in detail for only a single strain (GI.1). We present high-resolution (2.6- to 4.1-{\r A}) cryoelectron microscopy (cryo-EM) structures of GII.4, GII.2, GI.7, and GI.1 human norovirus outbreak strain virus-like particles (VLPs). Although norovirus VLPs have been thought to exist in a single-sized assembly, our structures reveal polymorphism between and within genogroups, with small, medium, and large particle sizes observed. Using asymmetric reconstruction, we were able to resolve a Zn2+\ metal ion adjacent to the coreceptor binding site, which affected the structural stability of the shell. Our structures serve as valuable templates for facilitating vaccine formulations.

}, doi = {10.1073/pnas.1903562116}, author = {Jung, James and Grant, Timothy and Thomas, Dennis R. and Diehnelt, Chris W. and Grigorieff, Nikolaus and Leemor, Joshua-Tor} } @article {65092, title = {Imaging striatal dopamine release using a nongenetically encoded near infrared fluorescent catecholamine nanosensor.}, journal = {Science Advances}, volume = {5}, year = {2019}, month = {2019 Jul 10}, pages = {eaaw3108}, abstract = {

Neuromodulation plays a critical role in brain function in both health and disease, and new tools that capture neuromodulation with high spatial and temporal resolution are needed. Here, we introduce a synthetic catecholamine nanosensor with fluorescent emission in the near infrared range (1000{\textendash}1300 nm), near infrared catecholamine nanosensor (nIRCat). We demonstrate that nIRCats can be used to measure electrically and optogenetically evoked dopamine release in brain tissue, revealing hotspots with a median size of 2 {\textmu}m. We also demonstrated that nIRCats are compatible with dopamine pharmacology and show D2 autoreceptor modulation of evoked dopamine release, which varied as a function of initial release magnitude at different hotspots. Together, our data demonstrate that nIRCats and other nanosensors of this class can serve as versatile synthetic optical tools to monitor neuromodulatory neurotransmitter release with high spatial resolution.

}, doi = {10.1126/sciadv.aaw3108}, url = {http://advances.sciencemag.org/lookup/doi/10.1126/sciadv.aaw3108https://syndication.highwire.org/content/doi/10.1126/sciadv.aaw3108}, author = {Beyene, Abraham G. and Delevich, Kristen and Del Bonis-O{\textquoteright}Donnell, Jackson Travis and Piekarski, David J. and Lin, Wan Chen and Thomas, A. Wren and Yang, Sarah J. and Kosillo, Polina and Yang, Darwin and Prounis, George S. and Wilbrecht, Linda and Landry, Markita P.} } @article {67223, title = {Importance Weighted Adversarial Variational Autoencoders for Spike Inference from Calcium Imaging Data}, journal = {CoRR}, volume = {abs/1906.03214}, year = {2019}, month = {10/2019}, abstract = {

The Importance Weighted Auto Encoder (IWAE) objective has been shown to improve the training of generative models over the standard Variational Auto Encoder (VAE) objective. Here, we derive importance weighted extensions to Adversarial Variational Bayes (AVB) and Adversarial Autoencoder (AAE). These latent variable models use implicitly defined inference networks whose approximate posterior density qφ(z|x) cannot be directly evaluated, an essential ingredient for importance weighting. We show improved training and inference in latent variable models with our adversarially trained importance weighting method, and derive new theoretical connections between adversarial generative model training criteria and marginal likelihood based methods. We apply these methods to the important problem of inferring spiking neural activity from calcium imaging data, a challenging posterior inference problem in neuroscience, and show that posterior samples from the adversarial methods outperform factorized posteriors used in VAEs.

}, url = {http://arxiv.org/abs/1906.03214}, author = {Daniel Jiwoong Im and Sridhama Prakhya and Jinyao Yan and Srinivas C. Turaga and Kristin Branson} } @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 {65212, title = {Interactions between Dpr11 and DIP-γ control selection of amacrine neurons in color vision circuits.}, journal = {eLife}, volume = {8}, year = {2019}, month = {2019 Nov 06}, abstract = {

R7 UV photoreceptors (PRs) are divided into yellow (y) and pale (p) subtypes. yR7 PRs express the Dpr11 cell surface protein and are presynaptic to Dm8 amacrine neurons (yDm8) that express Dpr11{\textquoteright}s binding partner DIP-g, while pR7 PRs synapse onto DIP-g-negative pDm8. Dpr11 and DIP-g expression patterns define {\textquoteright}yellow{\textquoteright} and {\textquoteright}pale{\textquoteright} color vision circuits. We examined Dm8 neurons in these circuits by electron microscopic reconstruction and expansion microscopy. and mutations affect the morphologies of yDm8 distal ({\textquoteright}home column{\textquoteright}) dendrites. yDm8 neurons are generated in excess during development and compete for presynaptic yR7 PRs, and interactions between Dpr11 and DIP-g are required for yDm8 survival. These interactions also allow yDm8 neurons to select yR7 PRs as their appropriate home column partners. yDm8 and pDm8 neurons do not normally compete for survival signals or R7 partners, but can be forced to do so by manipulation of R7 subtype fate.

}, issn = {2050-084X}, doi = {10.7554/eLife.48935}, author = {Menon, Kaushiki P and Kulkarni, Vivek and Takemura, Shin-ya and Anaya, Michael and Zinn, Kai} } @article {64851, title = {Interfacial actin protrusions mechanically enhance killing by cytotoxic T cells.}, journal = {Science Immunology}, volume = {4}, year = {2019}, month = {2019 Mar 22}, abstract = {

Cytotoxic T lymphocytes (CTLs) kill by forming immunological synapses with target cells and secreting toxic proteases and the pore-forming protein perforin into the intercellular space. Immunological synapses are highly dynamic structures that boost perforin activity by applying mechanical force against the target cell. Here, we used high-resolution imaging and microfabrication to investigate how CTLs exert synaptic forces and coordinate their mechanical output with perforin secretion. Using micropatterned stimulatory substrates that enable synapse growth in three dimensions, we found that perforin release occurs at the base of actin-rich protrusions that extend from central and intermediate locations within the synapse. These protrusions, which depended on the cytoskeletal regulator WASP and the Arp2/3 actin nucleation complex, were required for synaptic force exertion and efficient killing. They also mediated physical deformation of the target cell surface during CTL-target cell interactions. Our results reveal the mechanical basis of cellular cytotoxicity and highlight the functional importance of dynamic, three-dimensional architecture in immune cell-cell interfaces.

}, issn = {2470-9468}, doi = {10.1126/sciimmunol.aav5445}, author = {Tamzalit, Fella and Wang, Mitchell S and Jin, Weiyang and Tello-Lafoz, Maria and Boyko, Vitaly and Heddleston, John M and Black, Charles T and Kam, Lance C and Huse, Morgan} } @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 {48806, title = {Large scale image segmentation with structured loss based deep learning for connectome reconstruction.}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, volume = {41}, year = {2019}, month = {2019 Jul 1}, pages = {1669-80}, abstract = {

We present a method combining affinity prediction with region agglomeration, which improves significantly upon the state of the art of neuron segmentation from electron microscopy (EM) in accuracy and scalability. Our method consists of a 3D U-net, trained to predict affinities between voxels, followed by iterative region agglomeration. We train using a structured loss based on MALIS, encouraging topologically correct segmentations obtained from affinity thresholding. Our extension consists of two parts: First, we present a quasi-linear method to compute the loss gradient, improving over the original quadratic algorithm. Second, we compute the gradient in two separate passes to avoid spurious gradient contributions in early training stages. Our predictions are accurate enough that simple learning-free percentile-based agglomeration outperforms more involved methods used earlier on inferior predictions. We present results on three diverse EM datasets, achieving relative improvements over previous results of 27\%, 15\%, and 250\%. Our findings suggest that a single method can be applied to both nearly isotropic block-face EM data and anisotropic serial sectioned EM data. The runtime of our method scales linearly with the size of the volume and achieves a throughput of ~2.6 seconds per megavoxel, qualifying our method for the processing of very large datasets.

}, doi = {10.1109/TPAMI.2018.2835450}, author = {Funke, Jan and Tschopp, Fabian D and Grisaitis, William and Sheridan, Arlo and Singh, Chandan and Saalfeld, Stephan and Turaga, Srinivas C} } @article {64874, title = {Mapping the transcriptional diversity of genetically and anatomically defined cell populations in the mouse brain.}, journal = {Elife}, volume = {8}, year = {2019}, month = {2019 Apr 12}, abstract = {

Understanding the principles governing neuronal diversity is a fundamental goal for neuroscience. Here we provide an anatomical and transcriptomic database of nearly 200 genetically identified cell populations. By separately analyzing the robustness and pattern of expression differences across these cell populations, we identify two gene classes contributing distinctly to neuronal diversity. Short homeobox transcription factors distinguish neuronal populations combinatorially, and exhibit extremely low transcriptional noise, enabling highly robust expression differences. Long neuronal effector genes, such as channels and cell adhesion molecules, contribute disproportionately to neuronal diversity, based on their patterns rather than robustness of expression differences. By linking transcriptional identity to genetic strains and anatomical atlases we provide an extensive resource for further investigation of mouse neuronal cell types.

}, issn = {2050-084X}, doi = {10.7554/eLife.38619}, author = {Sugino, Ken and Clark, Erin and Schulmann, Anton and Shima, Yasuyuki and Wang, Lihua and Hunt, David L and Hooks, Bryan M and Traenkner, Dimitri and Chandrashekar, Jayaram and Picard, Serge and Lemire, Andrew L and Spruston, Nelson and Hantman, Adam W and Nelson, Sacha B} } @article {64973, title = {Mechanistic characterization of RASGRP1 variants identifies an hnRNP K-regulated transcriptional enhancer contributing to SLE susceptibility.}, journal = {Frontiers in Immunology}, year = {2019}, month = {2019 May 20}, abstract = {

Systemic lupus erythematosus (SLE) is an autoimmune disease with a strong genetic component. We recently identified a novel SLE susceptibility locus near\ RASGRP1, which governs the ERK/MAPK kinase cascade and B-/T-cell differentiation and development. However, precise causal\ RASGRP1functional variant(s) and their mechanisms of action in SLE pathogenesis remain undefined. Our goal was to fine-map this locus, prioritize genetic variants likely to be functional, experimentally validate their biochemical mechanisms, and determine the contribution of these SNPs to SLE risk. We performed a meta-analysis across six Asian and European cohorts (9,529 cases; 22,462 controls), followed by\ in silico\ bioinformatic and epigenetic analyses to prioritize potentially functional SNPs. We experimentally validated the functional significance and mechanism of action of three SNPs in cultured T-cells. Meta-analysis identified 18 genome-wide significant (p\ \< 5 {\texttimes} 10-8) SNPs, mostly concentrated in two haplotype blocks, one intronic and the other intergenic. Epigenetic fine-mapping, allelic, eQTL, and imbalance analyses predicted three transcriptional regulatory regions with four SNPs (rs7170151, rs11631591-rs7173565, and rs9920715) prioritized for functional validation. Luciferase reporter assays indicated significant allele-specific enhancer activity for intronic rs7170151 and rs11631591-rs7173565 in T-lymphoid (Jurkat) cells, but not in HEK293 cells. Following up with EMSA, mass spectrometry, and ChIP-qPCR, we detected allele-dependent interactions between heterogeneous nuclear ribonucleoprotein K (hnRNP-K) and rs11631591. Furthermore, inhibition of hnRNP-K in Jurkat and primary T-cells downregulated\ RASGRP1\ and ERK/MAPK signaling. Comprehensive association, bioinformatics, and epigenetic analyses yielded putative functional variants of\ RASGRP1, which were experimentally validated. Notably, intronic variant (rs11631591) is located in a cell type-specific enhancer sequence, where its risk allele binds to the hnRNP-K protein and modulates\ RASGRP1\ expression in Jurkat and primary T-cells. As risk allele dosage of rs11631591 correlates with increased\ RASGRP1\ expression and ERK activity, we suggest that this SNP may underlie SLE risk at this locus.

}, doi = {10.3389/fimmu.2019.01066}, author = {Molineros, Julio E. and Singh, Bhupinder and Terao, Chikashi and Okada, Yukinori and Kaplan, Jakub and McDaniel, Barbara and Akizuki, Shuji and Sun, Celi and Webb, Carol F. and Looger, Loren L and Nath, Swapan K.} } @article {65257, title = {MeCP2 nuclear dynamics in live neurons results from low and high affinity chromatin interactions.}, journal = {eLife}, volume = {8}, year = {2019}, month = {2019 Dec 23}, abstract = {

Methyl-CpG-binding-Protein 2 (MeCP2) is an abundant nuclear protein highly enriched in neurons. Here we report live-cell single-molecule imaging studies of the kinetic features of mouse MeCP2 at high spatial-temporal resolution. MeCP2 displays dynamic features that are distinct from both highly mobile transcription factors and immobile histones. Stable binding of MeCP2 in living neurons requires its methyl-binding domain and is sensitive to DNA modification levels. Diffusion of unbound MeCP2 is strongly constrained by weak, transient interactions mediated primarily by its AT-hook domains, and varies with the level of chromatin compaction and cell type. These findings extend previous studies of the role of the MeCP2 MBD in high affinity DNA binding to living neurons, and identify a new role for its AT-hooks domains as critical determinants of its kinetic behavior. They suggest that limited nuclear diffusion of MeCP2 in live neurons contributes to its local impact on chromatin structure and gene expression.

}, issn = {2050-084X}, doi = {10.7554/eLife.51449}, author = {Piccolo, Francesco M and Liu, Zhe and Dong, Peng and Hsu, Ching-Lung and Stoyanova, Elitsa I and Rao, Anjana and Tjian, Robert and Heintz, Nathaniel} } @article {64972, title = {Multi-color single molecule imaging uncovers extensive heterogeneity in mRNA decoding.}, journal = {Cell}, volume = {178}, year = {2019}, month = {2019 Jul 11}, pages = {458-72}, abstract = {

mRNA translation is a key step in decoding genetic information. Genetic decoding is surprisingly heterogeneous, as multiple distinct polypeptides can be synthesized from a single mRNA sequence. To study translational heterogeneity, we developed the MoonTag, a new fluorescence labeling system to visualize translation of single mRNAs. When combined with the orthogonal SunTag system, the MoonTag enables dual readouts of translation, greatly expanding the possibilities to interrogate complex translational heterogeneity. By placing MoonTag and SunTag sequences in different translation reading frames, each driven by distinct translation start sites, start site selection of individual ribosomes can be visualized in real-time. We find that start site selection is largely stochastic, but that the probability of using a particular start site differs among mRNA molecules, and can be dynamically regulated over time. Together, this study provides key insights into translation start site selection heterogeneity, and provides a powerful toolbox to visualize complex translation dynamics.

}, doi = {10.1016/j.cell.2019.05.001}, author = {Boersma, Sanne and Khuperkar, Deepak and Verhagen, Bram M.P. and Sonneveld, Stijn and Grimm, Jonathan B. and Lavis, Luke D. and Tanenbaum, Marvin E.} } @conference {67294, title = {Neural Correlates of Cognition in Primary Visual versus Downstream Posterior Cortices During Evidence Accumulation}, booktitle = {APS March Meeting Abstracts}, year = {2019}, month = {01/2019}, abstract = {

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

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

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

}, doi = {10.1101/568766}, url = {https://www.biorxiv.org/content/early/2019/03/06/568766}, author = {Koay, Sue Ann and Thiberge, Stephan Y. and Brody, Carlos D. and Tank, David W.} } @article {64785, title = {Neural substrates of Drosophila larval anemotaxis.}, journal = {Current Biology : CB}, volume = {29}, year = {2019}, month = {2019 Jan 29}, pages = {554-66}, abstract = {

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

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

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

}, issn = {2050-084X}, doi = {10.7554/eLife.43079}, author = {Dolan, Michael-John and Frechter, Shahar and Bates, Alexander Shakeel and Dan, Chuntao and Huoviala, Paavo and Roberts, Ruair{\'\i} Jv and Schlegel, Philipp and Dhawan, Serene and Tabano, Remy and Dionne, Heather and Christoforou, Christina and Close, Kari and Sutcliffe, Ben and Giuliani, Bianca and Li, Feng and Costa, Marta and Ihrke, Gudrun and Meissner, Geoffrey Wilson and Bock, Davi D and Aso, Yoshinori and Rubin, Gerald M and Jefferis, Gregory Sxe} } @conference {65315, title = {The Neuropixels probe: A CMOS based integrated microsystems platform for neuroscience and brain-computer interfaces.}, booktitle = {2019 IEEE International Electron Devices Meeting (IEDM)}, year = {2019}, month = {2020 Feb 13}, publisher = {IEEE}, organization = {IEEE}, address = {San Francisco, CA, USA}, abstract = {

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

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

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

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

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

}, issn = {2050-084X}, doi = {10.7554/eLife.49257}, author = {Aso, Yoshinori and Ray, Robert P and Long, Xi and Bushey, Daniel and Cichewicz, Karol and Ngo, Teri-Tb and Sharp, Brandi and Christoforou, Christina and Hu, Amy and Lemire, Andrew L and Tillberg, Paul and Hirsh, Jay and Litwin-Kumar, Ashok and Rubin, Gerald M} } @article {59912, title = {NWB:N 2.0: An accessible data standard for neurophysiology.}, journal = {bioRxiv}, year = {2019}, month = {2019 Jan 17}, abstract = {

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

}, doi = {10.1101/523035}, author = {Rubel, Oliver and Tritt, Andrew and Dichter, Benjamin and Braun, Thomas and Cain, Nicholas and Clack, Nathan G and Davidson, Thomas J and Dougherty, Max and Fillion-Rubin, Jean-Christophe and Graddis, Nile and Grauer, Michael and Kiggins, Justin T and Niu, Lawrence and Ozturk, Doruk and Schroeder, William and Soltesz, Ivan and Sommer, Friedrich T and Svoboda, Karel and Ng, Lydia and et al} } @article {51254, title = {The Pearson{\textquoteright}s correlation coefficient is not a universally superior colocalization metric. Response to {\textquoteright}Quantifying colocalization: the MOC is a hybrid coefficient - an uninformative mix of co-occurrence and correlation{\textquoteright}.}, journal = {Journal of Cell Science}, volume = {132}, year = {2019}, month = {2019 Jan 09}, issn = {1477-9137}, doi = {10.1242/jcs.227074}, author = {Aaron, Jesse S and Taylor, Aaron B and Chew, Teng-Leong} } @article {64944, title = {Pleiotropic effects of ebony and tan on pigmentation and cuticular hydrocarbon composition in Drosophila melanogaster.}, journal = {Frontiers in Physiology}, volume = {10}, year = {2019}, month = {05/2019}, pages = {518}, abstract = {

Pleiotropic genes are genes that affect more than one trait. For example, many genes required for pigmentation in the fruit fly also affect traits such as circadian rhythms, vision, and mating behavior. Here, we present evidence that two pigmentation genes, and , which encode enzymes catalyzing reciprocal reactions in the melanin biosynthesis pathway, also affect cuticular hydrocarbon (CHC) composition in females. More specifically, we report that loss-of-function mutants have a CHC profile that is biased toward long (\>25C) chain CHCs, whereas loss-of-function mutants have a CHC profile that is biased toward short (\<25C) chain CHCs. Moreover, pharmacological inhibition of dopamine synthesis, a key step in the melanin synthesis pathway, reversed the changes in CHC composition seen in mutants, making the CHC profiles similar to those seen in mutants. These observations suggest that genetic variation affecting and/or activity might cause correlated changes in pigmentation and CHC composition in natural populations. We tested this possibility using the Genetic Reference Panel (DGRP) and found that CHC composition covaried with pigmentation as well as levels of and expression in newly eclosed adults in a manner consistent with the and mutant phenotypes. These data suggest that the pleiotropic effects of and might contribute to covariation of pigmentation and CHC profiles in .

}, issn = {1664-042X}, doi = {10.3389/fphys.2019.00518}, author = {Massey, Jonathan H and Akiyama, Noriyoshi and Bien, Tanja and Dreisewerd, Klaus and Wittkopp, Patricia J and Yew, Joanne Y and Takahashi, Aya} } @article {65176, title = {Rational design of fluorogenic and spontaneously blinking labels for super-resolution imaging.}, journal = {ACS Central Science}, volume = {5}, year = {2019}, month = {2019 Sep 25}, pages = {1602-1613}, abstract = {

Rhodamine dyes exist in equilibrium between a fluorescent zwitterion and a nonfluorescent lactone. Tuning this equilibrium toward the nonfluorescent lactone form can improve cell-permeability and allow creation of "fluorogenic" compounds-ligands that shift to the fluorescent zwitterion upon binding a biomolecular target. An archetype fluorogenic dye is the far-red tetramethyl-Si-rhodamine (SiR), which has been used to create exceptionally useful labels for advanced microscopy. Here, we develop a quantitative framework for the development of new fluorogenic dyes, determining that the lactone-zwitterion equilibrium constant () is sufficient to predict fluorogenicity. This rubric emerged from our analysis of known fluorophores and yielded new fluorescent and fluorogenic labels with improved performance in cellular imaging experiments. We then designed a novel fluorophore-Janelia Fluor 526 (JF)-with SiR-like properties but shorter fluorescence excitation and emission wavelengths. JF is a versatile scaffold for fluorogenic probes including ligands for self-labeling tags, stains for endogenous structures, and spontaneously blinking labels for super-resolution immunofluorescence. JF constitutes a new label for advanced microscopy experiments, and our quantitative framework will enable the rational design of other fluorogenic probes for bioimaging.

}, issn = {2374-7943}, doi = {10.1021/acscentsci.9b00676}, author = {Zheng, Qinsi and Ayala, Anthony X and Chung, Inhee and Weigel, Aubrey V and Ranjan, Anand and Falco, Natalie and Grimm, Jonathan B and Tkachuk, Ariana N and Wu, Carl and Lippincott-Schwartz, Jennifer and Singer, Robert H and Lavis, Luke D} } @article {65111, title = {Regionalized tissue fluidization by an actomyosin cable is required for epithelial gap closure during insect gastrulation.}, journal = {Nature Communications}, volume = {11}, year = {2019}, month = {2020 Aug 22}, pages = {5604}, abstract = {

Many animal embryos face early on in development the problem of having to pull and close an epithelial sheet around the spherical yolk-sac. During this gastrulation process, known as epiboly, the spherical geometry of the egg dictates that the epithelial sheet first expands and subsequently compacts to close around the sphere. While it is well recognized that contractile actomyosin cables can drive epiboly movements, it is unclear how pulling on the leading edge can lead to simultaneous tissue expansion and compaction. Moreover, the epithelial sheet spreading over the sphere is mechanically stressed and this stress needs to be dissipated for seamless closure. While oriented cell division is known to dissipate tissue stresses during epiboly, it is unclear how this can be achieved without cell division. Here we show that during extraembryonic tissue (serosa) epiboly in the red flour beetle Tribolium castaneum, the non-proliferative serosa becomes regionalized into two distinct territories: a dorsal region under higher tension away from the leading edge with larger, isodiametric and non-rearranging cells, and a more fluid ventral region under lower tension surrounding the leading edge with smaller, anisotropic cells undergoing cell intercalation. Our results suggest that fluidization of the leading edge is effected by a heterogeneous actomyosin cable that drives sequential eviction and intercalation of individual cells away from the serosa margin. Since this developmental solution utilized during epiboly resembles the mechanism of wound healing in other systems, we propose actomyosin cable-driven local tissue fluidization as a conserved morphogenetic module for closure of epithelial gaps.

}, doi = {https://doi.org/10.1101/744193}, author = {Jain, Akanksha and Ulman, Vladimir and Mukherjee, Argo and Prakash, Mangal and Pimpale, Lokesh and Munster, Stefan and Panfilio, Kristen A. and Jug, Florian and Grill, Stephan WA. and Tomancak, Pavel and Pavlopoulos, Anastasios} } @article {64988, title = {Regulation of forward and backward locomotion through intersegmental feedback circuits in Drosophila larvae.}, journal = {Nature Communications}, volume = {10}, year = {2019}, month = {2019 Jun 14}, pages = {2654}, abstract = {

Animal locomotion requires spatiotemporally coordinated contraction of muscles throughout the body. Here, we investigate how contractions of antagonistic groups of muscles are intersegmentally coordinated during bidirectional crawling of Drosophila larvae. We identify two pairs of higher-order premotor excitatory interneurons present in each abdominal neuromere that intersegmentally provide feedback to the adjacent neuromere during motor propagation. The two feedback neuron pairs are differentially active during either forward or backward locomotion but commonly target a group of premotor interneurons that together provide excitatory inputs to transverse muscles and inhibitory inputs to the antagonistic longitudinal muscles. Inhibition of either feedback neuron pair compromises contraction of transverse muscles in a direction-specific manner. Our results suggest that the intersegmental feedback neurons coordinate contraction of synergistic muscles by acting as delay circuits representing the phase lag between segments. The identified circuit architecture also shows how bidirectional motor networks could be economically embedded in the nervous system.

}, issn = {2041-1723}, doi = {10.1038/s41467-019-10695-y}, author = {Kohsaka, Hiroshi and Zwart, Maarten F and Fushiki, Akira and Fetter, Richard D and Truman, James W and Cardona, Albert and Nose, Akinao} } @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 {67290, title = {Sequential and efficient neural-population coding of complex task information}, journal = {bioRxiv}, year = {2019}, month = {10/2019}, abstract = {

Recent work has highlighted that many types of variables are represented in each neocortical area. How can these many neural representations be organized together without interference, and coherently maintained/updated through time? We recorded from large neural populations in posterior cortices as mice performed a complex, dynamic task involving multiple interrelated variables. The neural encoding implied that correlated task variables were represented by uncorrelated modes in an information-coding subspace. We show via theory that this can enable optimal decoding directions to be insensitive to neural noise levels. Across posterior cortex, principles of efficient coding thus applied to task-specific information, with neural-population modes as the encoding unit. Remarkably, this encoding function was multiplexed with rapidly changing, sequential neural dynamics, yet reliably followed slow changes in task-variable correlations through time. We can explain this as due to a mathematical property of high-dimensional spaces that the brain might exploit as a temporal scaffold.

}, doi = {10.1101/801654}, url = {https://www.biorxiv.org/content/early/2019/10/13/801654}, author = {Koay, Sue Ann and Thiberge, Stephan Y. and Brody, Carlos D. and Tank, David W.} } @article {65225, title = {ShuTu: Open-source software for efficient and accurate reconstruction of dendritic morphology.}, journal = {Frontiers in Neuroinformatics}, volume = {13}, year = {2019}, month = {2019 Oct 31}, pages = {68}, abstract = {

Neurons perform computations by integrating inputs from thousands of synapses-mostly in the dendritic tree-to drive action potential firing in the axon. One fruitful approach to studying this process is to record from neurons using patch-clamp electrodes, fill the recorded neurons with a substance that allows subsequent staining, reconstruct the three-dimensional architectures of the dendrites, and use the resulting functional and structural data to develop computer models of dendritic integration. Accurately producing quantitative reconstructions of dendrites is typically a tedious process taking many hours of manual inspection and measurement. Here we present ShuTu, a new software package that facilitates accurate and efficient reconstruction of dendrites imaged using bright-field microscopy. The program operates in two steps: (1) automated identification of dendritic processes, and (2) manual correction of errors in the automated reconstruction. This approach allows neurons with complex dendritic morphologies to be reconstructed rapidly and efficiently, thus facilitating the use of computer models to study dendritic structure-function relationships and the computations performed by single neurons.

}, issn = {1662-5196}, doi = {10.3389/fninf.2019.00068}, author = {Jin, Dezhe Z and Zhao, Ting and Hunt, David L and Tillage, Rachel P and Hsu, Ching-Lung and Spruston, Nelson} } @article {65764, title = {Simple imaging protocol for autofluorescence elimination and optical sectioning in fluorescence endomicroscopy}, journal = {Optica}, volume = {6}, year = {2019}, month = {07/2019}, pages = {972}, abstract = {

Fiber-optic epifluorescence imaging with one-photon excitation benefits from its ease of use, cheap light sources, and full-frame acquisition, which enables it for favorable temporal resolution of image acquisition. However, it suffers from a lack of robustness against autofluorescence and light scattering. Moreover, it cannot easily eliminate the out-of-focus background, which generally results in low-contrast images. In order to overcome these limitations, we have implemented fast out-of-phase imaging after optical modulation (Speed OPIOM) for dynamic contrast in fluorescence endomicroscopy. Using a simple and cheap optical-fiber bundle-based endomicroscope integrating modulatable light sources, we first showed that Speed OPIOM provides intrinsic optical sectioning, which restricts the observation of fluorescent labels at targeted positions within a sample. We also demonstrated that this imaging protocol efficiently eliminates the interference of autofluorescence arising from both the fiber bundle and the specimen in several biological samples. Finally, we could perform multiplexed observations of two spectrally similar fluorophores differing by their photoswitching dynamics. Such attractive features of Speed OPIOM in fluorescence endomicroscopy should find applications in bioprocessing, clinical diagnostics, plant observation, and surface imaging.

}, doi = {10.1364/optica.6.000972}, author = {Zhang, Ruikang and Chouket, Raja and Tebo, Alison G and Plamont, Marie-Aude and Kelemen, Zsolt and Gissot, Lionel and Faure, Jean-Denis and Gautier, Arnaud and Croquette, Vincent and Jullien, Ludovic and Saux, Thomas Le} } @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 {65765, title = {A split fluorescent reporter with rapid and reversible complementation.}, journal = {Nature communications}, volume = {10}, year = {2019}, month = {06/2019}, pages = {2822}, abstract = {

Interactions between proteins play an essential role in metabolic and signaling pathways, cellular processes and organismal systems. We report the development of splitFAST, a fluorescence complementation system for the visualization of transient protein-protein interactions in living cells. Engineered from the fluorogenic reporter FAST (Fluorescence-Activating and absorption-Shifting Tag), which specifically and reversibly binds fluorogenic hydroxybenzylidene rhodanine (HBR) analogs, splitFAST displays rapid and reversible complementation, allowing the real-time visualization of both the formation and the dissociation of a protein assembly.

}, doi = {10.1038/s41467-019-10855-0}, author = {Tebo, Alison G and Gautier, Arnaud} } @article {65260, title = {Structure of an endosomal signaling GPCR-G protein-β-arrestin megacomplex.}, journal = {Nature Structural and Molecular Biology}, volume = {26}, year = {2019}, month = {2019 Dec 26}, pages = {1123-1131}, abstract = {

Classically, G-protein-coupled receptors (GPCRs) are thought to activate G protein from the plasma membrane and are subsequently desensitized by β-arrestin (β-arr). However, some GPCRs continue to signal through G protein from internalized compartments, mediated by a GPCR-G protein-β-arr {\textquoteright}megaplex{\textquoteright}. Nevertheless, the molecular architecture of the megaplex remains unknown. Here, we present its cryo-electron microscopy structure, which shows simultaneous engagement of human G protein and bovine β-arr to the core and phosphorylated tail, respectively, of a single active human chimeric β-adrenergic receptor with the C-terminal tail of the arginine vasopressin type 2 receptor (βVR). All three components adopt their canonical active conformations, suggesting that a single megaplex GPCR is capable of simultaneously activating G protein and β-arr. Our findings provide a structural basis for GPCR-mediated sustained internalized G protein signaling.

}, issn = {1545-9985}, doi = {10.1038/s41594-019-0330-y}, author = {Nguyen, Anthony H and Thomsen, Alex R B and Cahill, Thomas J and Huang, Rick and Huang, Li-Yin and Marcink, Tara and Clarke, Oliver B and Heissel, S{\o}ren and Masoudi, Ali and Ben-Hail, Danya and Samaan, Fadi and Dandey, Venkata P and Tan, Yong Zi and Hong, Chuan and Mahoney, Jacob P and Triest, Sarah and Little, John and Chen, Xin and Sunahara, Roger and Steyaert, Jan and Molina, Henrik and Yu, Zhiheng and des Georges, Amedee and Lefkowitz, Robert J} } @article {67222, title = {Teaching deep neural networks to localize single molecules for super-resolution microscopy}, journal = {arXiv e-prints}, year = {2019}, month = {06/2019}, pages = {arXiv:1907.00770}, abstract = {

Single-molecule localization fluorescence microscopy constructs super-resolution images by sequential imaging and computational localization of sparsely activated fluorophores. Accurate and efficient fluorophore localization algorithms are key to the success of this computational microscopy method. We present a novel localization algorithm based on deep learning which significantly improves upon the state of the art. Our contributions are a novel network architecture for simultaneous detection and localization, and new loss function which phrases detection and localization as a Bayesian inference problem, and thus allows the network to provide uncertainty-estimates. In contrast to standard methods which independently process imaging frames, our network architecture uses temporal context from multiple sequentially imaged frames to detect and localize molecules. We demonstrate the power of our method across a variety of datasets, imaging modalities, signal to noise ratios, and fluorophore densities. While existing localization algorithms can achieve optimal localization accuracy at low fluorophore densities, they are confounded by high densities. Our method is the first deep-learning based approach which achieves state-of-the-art on the SMLM2016 challenge. It achieves the best scores on 12 out of 12 data-sets when comparing both detection accuracy and precision, and excels at high densities. Finally, we investigate how unsupervised learning can be used to make the network robust against mismatch between simulated and real data. The lessons learned here are more generally relevant for the training of deep networks to solve challenging Bayesian inverse problems on spatially extended domains in biology and physics.

}, keywords = {Computer Science - Machine Learning, Electrical Engineering and Systems Science - Image and Video Processing, Statistics - Machine Learning}, url = {https://arxiv.org/abs/1907.00770}, author = {Speiser, Artur and M{\"u}ller, Lucas-Raphael and Matti, Ulf and Obara, Christopher J. and Legant, Wesley R. and Ries, Jonas and Macke, Jakob H. and Turaga, Srinivas C.} } @article {64871, title = {Thirst regulates motivated behavior through modulation of brainwide neural population dynamics.}, journal = {Science}, volume = {364}, year = {2019}, month = {2019 Apr 04}, pages = {253}, abstract = {

Physiological needs produce motivational drives, such as thirst and hunger, that regulate behaviors essential to survival. Hypothalamic neurons sense these needs and must coordinate relevant brainwide neuronal activity to produce the appropriate behavior. We studied dynamics from ~24,000 neurons in 34 brain regions during thirst-motivated choice behavior, as mice consumed water and became sated. Water-predicting sensory cues elicited activity that rapidly spread throughout the brain of thirsty animals. These dynamics were gated by a brainwide mode of population activity that encoded motivational state. Focal optogenetic activation of hypothalamic thirst-sensing neurons, after satiation, returned global activity to the pre-satiation state. Thus, motivational states specify initial conditions determining how a brainwide dynamical system transforms sensory input into behavioral output.

}, issn = {1095-9203}, doi = {10.1126/science.aav3932}, author = {Allen, William E and Chen, Michael Z and Pichamoorthy, Nandini and Tien, Rebecca H and Pachitariu, Marius and Luo, Liqun and Deisseroth, Karl} } @article {65254, title = {Two-photon imaging with silicon photomultipliers.}, journal = {Optics Express}, volume = {27}, year = {2019}, month = {2019 Nov 25}, pages = {35830-35841}, abstract = {

We compared performance of recently developed silicon photomultipliers (SiPMs) to GaAsP photomultiplier tubes (PMTs) for two-photon imaging of neural activity. Despite higher dark counts, SiPMs match or exceed the signal-to-noise ratio of PMTs at photon rates encountered in typical calcium imaging experiments due to their low pulse height variability. At higher photon rates encountered during high-speed voltage imaging, SiPMs substantially outperform PMTs.

}, issn = {1094-4087}, doi = {10.1364/OE.27.035830}, author = {Modi, Mehrab N and Daie, Kayvon and Turner, Glenn C and Podgorski, Kaspar} } @article {49151, title = {50 Hz volumetric functional imaging with continuously adjustable depth of focus.}, journal = {Biomedical Optics Express}, volume = {9}, year = {2018}, month = {2018 Apr}, pages = {1964-76}, abstract = {

Understanding how neural circuits control behavior requires monitoring a large population of neurons with high spatial resolution and volume rate. Here we report an axicon-based Bessel beam module with continuously adjustable depth of focus (CADoF), that turns frame rate into volume rate by extending the excitation focus in the axial direction while maintaining high lateral resolutions. Cost-effective and compact, this CADoF Bessel module can be easily integrated into existing two-photon fluorescence microscopes. Simply translating one of the relay lenses along its optical axis enabled continuous adjustment of the axial length of the Bessel focus. We used this module to simultaneously monitor activity of spinal projection neurons extending over 60 {\textmu}m depth in larval zebrafish at 50 Hz volume rate with adjustable axial extent of the imaged volume.

}, doi = {10.1364/BOE.9.001964}, author = {Lu, Rongwen and Tanimoto, Masashi and Koyama, Minoru and Na, Ji} } @article {49023, title = {Aberrant calcium signaling in astrocytes inhibits neuronal excitability in a human Down syndrome stem cell model.}, journal = {Cell Reports}, volume = {24}, year = {2018}, month = {2018 Jul 10}, pages = {355-65}, abstract = {

Down syndrome (DS) is a genetic disorder that causes cognitive impairment. The staggering effects associated with an extra copy of human chromosome 21 (HSA21) complicates mechanistic understanding of DS pathophysiology. We examined the neuron-astrocyte interplay in a fully recapitulated HSA21 trisomy cellular model differentiated from DS-patient-derived induced pluripotent stem cells (iPSCs). By combining calcium imaging with genetic approaches, we discovered the functional defects of DS astroglia and their effects on neuronal excitability. Compared with control isogenic astroglia, DS astroglia exhibited more-frequent spontaneous calcium fluctuations, which reduced the excitability of co-cultured neurons. Furthermore, suppressed neuronal activity could be rescued by abolishing astrocytic spontaneous calcium activity either chemically by blocking adenosine-mediated signaling or genetically by knockdown of inositol triphosphate (IP3) receptors or S100B, a calcium binding protein coded on HSA21. Our results suggest a mechanism by which DS alters the function of astrocytes, which subsequently disturbs neuronal excitability.

}, doi = {10.1101/247585}, author = {Tian, Lin and Or, Grace and Wang, Yinxue and Shi, Guilai and Wang, Yizhi and Sun, Junqing and Papadopoulos, Stelios and Broussard, Gerard and Unger, Elizabeth and Deng, Wenbin and Weick, Jason and Bhattacharyya, Anita and Chen, Chao-Yin and Yu, Guoqiang and Looger, Loren L} } @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 {49341, title = {The actin cytoskeletal architecture of estrogen receptor positive breast cancer cells suppresses invasion.}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {2018 Jul 30}, pages = {2980}, abstract = {

Estrogen promotes growth of estrogen receptor-positive (ER+) breast tumors. However, epidemiological studies examining the prognostic characteristics of breast cancer in postmenopausal women receiving hormone replacement therapy reveal a significant decrease in tumor dissemination, suggesting that estrogen has potential protective effects against cancer cell invasion. Here, we show that estrogen suppresses invasion of ER+ breast cancer cells by increasing transcription of the Ena/VASP protein, EVL, which promotes the generation of suppressive cortical actin bundles that inhibit motility dynamics, and is crucial for the ER-mediated suppression of invasion in vitro and in vivo. Interestingly, despite its benefits in suppressing tumor growth, anti-estrogenic endocrine therapy decreases EVL expression and increases local invasion in patients. Our results highlight the dichotomous effects of estrogen on tumor progression and suggest that, in contrast to its established role in promoting growth of ER+ tumors, estrogen has a significant role in suppressing invasion through actin cytoskeletal remodeling.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-05367-2}, author = {Padilla-Rodriguez, Marco and Parker, Sara S and Adams, Deanna G and Westerling, Thomas and Puleo, Julieann I and Watson, Adam W and Hill, Samantha M and Noon, Muhammad and Gaudin, Rapha{\"e}l and Aaron, Jesse and Tong, Daoqin and Roe, Denise J and Knudsen, Beatrice and Mouneimne, Ghassan} } @article {49316, title = {Apical and basal matrix remodeling control epithelial morphogenesis.}, journal = {Developmental Cell}, volume = {46}, year = {2018}, month = {2018 Jul 02}, pages = {23-39.e5}, abstract = {

Epithelial tissues can elongate in two dimensions by polarized cell intercalation, oriented cell division, or cell shape change, owing to local or global actomyosin contractile forces acting in the plane of the tissue. In addition, epithelia can undergo morphogenetic change in three dimensions. We show that elongation of the wings and legs of Drosophila involves a columnar-to-cuboidal cell shape change that reduces cell height and expands cell width. Remodeling of the apical extracellular matrix by the Stubble protease and basal matrix by MMP1/2 proteases induces wing and leg elongation. Matrix remodeling does not occur in the haltere, a limb that fails to elongate. Limb elongation is made anisotropic by planar polarized Myosin-II, which drives convergent extension along the proximal-distal axis. Subsequently, Myosin-II relocalizes to lateral membranes to accelerate columnar-to-cuboidal transition and isotropic tissue expansion. Thus, matrix remodeling induces dynamic changes in actomyosin contractility\ to drive epithelial morphogenesis in three dimensions.

}, issn = {1878-1551}, doi = {10.1016/j.devcel.2018.06.006}, author = {Diaz-de-la-Loza, Maria-Del-Carmen and Ray, Robert P and Ganguly, Poulami S and Alt, Silvanus and Davis, John R and Hoppe, Andreas and Tapon, Nic and Salbreux, Guillaume and Thompson, Barry J} } @article {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 {49535, title = {Brain-wide circuit interrogation at the cellular level guided by online analysis of neuronal function.}, journal = {Nature Methods}, volume = {15}, year = {2018}, month = {2018 Nov 30}, pages = {1117-1125}, abstract = {

Whole-brain imaging allows for comprehensive functional mapping of distributed neural pathways, but neuronal perturbation experiments are usually limited to targeting predefined regions or genetically identifiable cell types. To complement whole-brain measures of activity with brain-wide manipulations for testing causal interactions, we introduce a system that uses measuredactivity patterns to guide optical perturbations of any subset of neurons in the same fictively behaving larval zebrafish. First, a light-sheet microscope collects whole-brain data that are rapidly analyzed by a distributed computing system to generate functional brain maps. On the basis of these maps, the experimenter can then optically ablate neurons and image activity changes across the brain. We applied this method to characterize contributions of behaviorally tuned populations to the optomotor response. We extended the system to optogenetically stimulate arbitrary subsets of neurons during whole-brain imaging. These open-source methods enable delineating the contributions of neurons to brain-wide circuit dynamics and behavior in individual animals.

}, doi = {10.1038/s41592-018-0221-x}, author = {Vladimirov, Nikita and Wang, Chen and H{\"o}ckendorf, Burkhard and Pujala, Avinash and Tanimoto, Masashi and Mu, Yu and Yang, Chao-Tsung and Wittenbach, Jason and Freeman, Jeremy and Preibisch, Stephan and Koyama, Minoru and Keller, Philipp J and Ahrens, Misha B} } @article {67289, title = {CalmAn: An open source tool for scalable Calcium Imaging data Analysis}, journal = {bioRxiv}, year = {2018}, month = {06/2018}, abstract = {

Advances in fluorescence microscopy enable monitoring larger brain areas in-vivo with finer time resolution. The resulting data rates require reproducible analysis pipelines that are reliable, fully automated, and scalable to datasets generated over the course of months. Here we present CaImAn, an open-source library for calcium imaging data analysis. CaImAn provides automatic and scalable methods to address problems common to pre-processing, including motion correction, neural activity identification, and registration across different sessions of data collection. It does this while requiring minimal user intervention, with good performance on computers ranging from laptops to high-performance computing clusters. CaImAn is suitable for two-photon and one-photon imaging, and also enables real-time analysis on streaming data. To benchmark the performance of CaImAn we collected a corpus of ground truth annotations from multiple labelers on nine mouse two-photon datasets. We demonstrate that CaImAn achieves near-human performance in detecting locations of active neurons.

}, doi = {10.1101/339564}, url = {https://www.biorxiv.org/content/early/2018/06/05/339564}, author = {Giovannucci, Andrea and Friedrich, Johannes and Gunn, Pat and Kalfon, J{\'e}r{\'e}mie and Koay, Sue Ann and Taxidis, Jiannis and Najafi, Farzaneh and Gauthier, Jeffrey L. and Zhou, Pengcheng and Tank, David W. and Chklovskii, Dmitri and Pnevmatikakis, Eftychios A.} } @article {49406, title = {Cell-specific chemical delivery using a selective Nitroreductase-Nitroaryl pair.}, journal = {ACS Chemical Biology}, volume = {13}, year = {2018}, month = {2018 Aug 29}, pages = {1888-96}, abstract = {

The utility of small molecules to probe or perturb biological systems is limited by the lack of cell-specificity. "Masking" the activity of small molecules using a general chemical modification and "unmasking" it only within target cells overcomes this limitation. To this end, we have developed a selective enzyme-substrate pair consisting of engineered variants of E. coli nitroreductase (NTR) and a 2-nitro- N-methylimidazolyl (NM) masking group. To discover and optimize this NTR-NM system, we synthesized a series of fluorogenic substrates containing different nitroaromatic masking groups, confirmed their stability in cells, and identified the best substrate for NTR. We then engineered the enzyme for improved activity in mammalian cells, ultimately yielding an enzyme variant (enhanced NTR, or eNTR) that possesses up to 100-fold increased activity over wild-type NTR. These improved NTR enzymes combined with the optimal NM masking group enable rapid, selective unmasking of dyes, indicators, and drugs to genetically defined populations of cells.

}, issn = {1554-8937}, doi = {10.1021/acschembio.8b00524}, author = {Gruber, Todd D and Krishnamurthy, Chithra and Grimm, Jonathan B and Tadross, Michael R and Wysocki, Laura M and Gartner, Zev J and Lavis, Luke D} } @article {49021, title = {The Chlamydia type III effector TarP alters the dynamics and organization of host focal adhesions.}, journal = {bioRxiv}, year = {2018}, month = {2018 Jan 23}, abstract = {

Bacterial infection of mucosal epithelial cells triggers cell exfoliation to limit the dissemination of infection within the tissue. Therefore, mucosal pathogens must possess strategies to counteract cell extrusion in response to infection. Chlamydia trachomatis spends most of its intracellular development in the non-infectious form. Thus, premature host cell extrusion is detrimental to the pathogen. We demonstrate that C. trachomatis alters the dynamics of focal adhesions. Live-cell microscopy showed that focal adhesions in C. trachomatis-infected cells displayed increased stability. In contrast, focal adhesions in mock-infected cells readily disassembled upon inhibition of myosin II by blebbisttin. Super-resolution microscopy revealed a reorganization of paxillin and FAK in infected cells. Ectopically expressed type III effector TarP localized to focal adhesions, leading to their stabilization and reorganization in a vinculin-dependent manner. Overall, the results indicate that C. trachomatis possesses a dedicated mechanism to regulate host cell focal adhesion dynamics.

}, doi = {10.1101/250563}, author = {Pedrosa, Antonio T and Nogueira, Ana T and Thwaites, Tristan R and Aaron, Jesse and Chew, Teng-Leong and Carabeo, Rey A} } @article {65772, title = {Circularly Permuted Fluorogenic Proteins for the Design of Modular Biosensors.}, journal = {ACS Chemical Biology}, volume = {13}, year = {2018}, month = {09/2018}, pages = {2392 {\textendash} 2397}, abstract = {

Fluorescent reporters are essential components for the design of optical biosensors that are able to image intracellular analytes in living cells. Herein, we describe the development of circularly permuted variants of Fluorescence-Activating and absorption-Shifting Tag (FAST) and demonstrate their potential as reporting module in biosensors. Circularly permutated FAST (cpFAST) variants allow one to condition the binding and activation of a fluorogenic ligand (and thus fluorescence) to analyte recognition by coupling them with analyte-binding domains. We demonstrated their use for biosensor design by generating multicolor plug-and-play fluorogenic biosensors for imaging the intracellular levels of Ca2+ in living mammalian cells in real time.

}, doi = {10.1021/acschembio.8b00417}, author = {Tebo, Alison G and Pimenta, Frederico M and Zoumpoulaki, Martha and Kikuti, Carlos and Sirkia, Helena and Plamont, Marie-Aude and Houdusse, Anne and Gautier, Arnaud} } @article {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 {49149, title = {A community-developed Open-Source computational ecosystem for big neuro data.}, journal = {Nature Methods}, volume = {15}, year = {2018}, month = {2018 Nov}, pages = {846-7}, abstract = {

Big imaging data is becoming more prominent in brain sciences across spatiotemporal scales and phylogenies. We have developed a computational ecosystem that enables storage, visualization, and analysis of these data in the cloud, thusfar spanning 20+ publications and 100+ terabytes including nanoscale ultrastructure, microscale synaptogenetic diversity, and mesoscale whole brain connectivity, making NeuroData the largest and most diverse open repository of brain data.

}, doi = {10.1038/s41592-018-0181-1}, author = {Vogelstein, Joshua T and Perlman, Eric and Falk, Benjamin and Baden, Alex and Roncal, William Gray and Chandrashekhar, Vikram and Collman, Forrest and Seshamani, Sharmishtaa and Patsolic, Jesse and Lillaney, Kunal and Kazhdan, Michael and Hider Jr., Robert and Pryor, Derek and Matelsky, Jordan and Gion, Timothy and Manavalan, Priya and Wester, Brock and Chevillet, Mark and Trautman, Eric T and Khairy, Khaled} } @article {48620, title = {A complete electron microscopy volume of the brain of adult Drosophila melanogaster.}, journal = {Cell}, volume = {174}, year = {2018}, month = {2018 Jul 12}, pages = {730-43}, abstract = {

Drosophila melanogaster has a rich repertoire of innate and learned behaviors. Its 100,000-neuron brain is a large but tractable target for comprehensive neural circuit mapping. Only electron microscopy (EM) enables complete, unbiased mapping of synaptic connectivity; however, the fly brain is too large for conventional EM. We developed a custom high-throughput EM platform and imaged the entire brain of an adult female fly at synaptic resolution. To validate the dataset, we traced brain-spanning circuitry involving the mushroom body (MB), which has been extensively studied for its role in learning. All inputs to Kenyon cells (KCs), the intrinsic neurons of the MB, were mapped, revealing a previously unknown cell type, postsynaptic partners of KC dendrites, and unexpected clustering of olfactory projection neurons. These reconstructions show that this freely available EM volume supports mapping of brain-spanning circuits, which will significantly accelerate Drosophila neuroscience..

}, doi = {10.1016/j.cell.2018.06.019}, author = {Zheng, Zhihao and Lauritzen, J Scott and Perlman, Eric and Robinson, Camenzind G and Nichols, Matthew and Milkie, Daniel E and Torrens, Omar and Price, John and Fisher, Corey B and Sharifi, Nadiya and Calle-Schuler, Steven A and Kmecova, Lucia and Ali, Iqbal J and Karsh, Bill and Trautman, Eric T and Bogovic, John A and Hanslovsky, Philipp and Jefferis, Gregory S X E and Kazhdan, Michael and Khairy, Khaled} } @article {49290, title = {A connectome based hexagonal lattice convolutional network model of the Drosophila visual system.}, journal = {arXiv}, year = {2018}, month = {2018 Jun 12}, pages = {1806.04793 }, abstract = {

What can we learn from a connectome? We constructed a simplified model of the first two stages of the fly visual system, the lamina and medulla. The resulting hexagonal lattice convolutional network was trained using backpropagation through time to perform object tracking in natural scene videos. Networks initialized with weights from connectome reconstructions automatically discovered well-known orientation and direction selectivity properties in T4 neurons and their inputs, while networks initialized at random did not. Our work is the first demonstration, that knowledge of the connectome can enable in silico predictions of the functional properties of individual neurons in a circuit, leading to an understanding of circuit function from structure alone.

}, url = {https://arxiv.org/abs/1806.04793}, author = {Tschopp, Fabian D and Reiser, Michael B and Turaga, Srinivas C} } @article {49583, title = {Convergence of monosynaptic and polysynaptic sensory paths onto common motor outputs in a feeding connectome.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Dec 11}, abstract = {

We reconstructed, from a whole CNS EM volume, the synaptic map of input and output neurons that underlie food intake behavior of larvae. Input neurons originate from enteric, pharyngeal and external sensory organs and converge onto seven distinct sensory synaptic compartments within the CNS. Output neurons consist of feeding motor, serotonergic modulatory and neuroendocrine neurons. Monosynaptic connections from a set of sensory synaptic compartments cover the motor, modulatory and neuroendocrine targets in overlapping domains. Polysynaptic routes are superimposed on top of monosynaptic connections, resulting in divergent sensory paths that converge on common outputs. A completely different set of sensory compartments is connected to the mushroom body calyx. The mushroom body output neurons are connected to interneurons that directly target the feeding output neurons. Our results illustrate a circuit architecture in which monosynaptic and multisynaptic connections from sensory inputs traverse onto output neurons via a series of converging paths.

}, issn = {2050-084X}, doi = {10.7554/eLife.40247}, author = {Miroschnikow, Anton and Schlegel, Philipp and Schoofs, Andreas and Hueckesfeld, Sebastian and Li, Feng and Schneider-Mizell, Casey M and Fetter, Richard D and Truman, James W and Cardona, Albert and Pankratz, Michael J} } @article {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 {49315, title = {Cryo-EM structure of an essential Plasmodium vivax invasion complex.}, journal = {Nature}, volume = {559}, year = {2018}, month = {2018 Jul}, pages = {135-139}, abstract = {

Plasmodium vivax is the most widely distributed malaria parasite that infects humans. P. vivax invades reticulocytes exclusively, and successful entry depends on specific interactions between the P. vivax reticulocyte-binding protein 2b (PvRBP2b) and transferrin receptor 1 (TfR1). TfR1-deficient erythroid cells are refractory to invasion by P. vivax, and anti-PvRBP2b monoclonal antibodies inhibit reticulocyte binding and block P. vivax invasion in field isolates. Here we report a high-resolution cryo-electron microscopy structure of a ternary complex of PvRBP2b bound to human TfR1 and transferrin, at 3.7 {\r A} resolution. Mutational analyses show that PvRBP2b residues involved in complex formation are conserved; this suggests that antigens could be designed that act across P. vivax strains. Functional analyses of TfR1 highlight how P. vivax hijacks TfR1, an essential housekeeping protein, by binding to sites that govern host specificity, without affecting its cellular function of transporting iron. Crystal and solution structures of PvRBP2b in complex with antibody fragments characterize the inhibitory epitopes. Our results establish a structural framework for understanding how P. vivax reticulocyte-binding protein engages its receptor and the molecular mechanism of inhibitory monoclonal antibodies, providing important information for the design of novel vaccine candidates.

}, issn = {1476-4687}, doi = {10.1038/s41586-018-0249-1}, author = {Gruszczyk, Jakub and Huang, Rick K and Chan, Li-Jin and Menant, S{\'e}bastien and Hong, Chuan and Murphy, James M and Mok, Yee-Foong and Griffin, Michael D W and Pearson, Richard D and Wong, Wilson and Cowman, Alan F and Yu, Zhiheng and Tham, Wai-Hong} } @article {65000, title = {Cryo-EM structure of the receptor-activated TRPC5 ion channel at 2.9 angstrom resolution.}, year = {2018}, month = {2018 Nov 11}, abstract = {

The transient receptor potential canonical subfamily member 5 (TRPC5) is a non-selective calcium-permeant cation channel. As a depolarizing channel, its function is studied in the central nervous system and kidney. TRPC5 forms heteromultimers with TRPC1, but also forms homomultimers. It can be activated by reducing agents through reduction of the extracellular disulfide bond. Here we present the 2.9 {\r A} resolution electron cryo-microscopy (cryo-EM) structure of TRPC5. The structure of TRPC5 in its apo state is partially open, which may be related to the weak activation of TRPC5 in response to extracellular pH. We also report the conserved negatively charged residues of the cation binding site located in the hydrophilic pocket between S2 and S3. Comparison of the TRPC5 structure to previously determined structures of other TRPC and TRP channels reveals differences in the extracellular pore domain and in the length of the S3 helix. Together, these results shed light on the structural features that contribute to the specific activation mechanism of the receptor-activated TRPC5.

}, doi = {10.1101/467969}, author = {Jingjing Duan and Jian Li and Gui-Lan Chen and Bo Zeng and Kechen Xie and Xiaogang Peng and Wei Zhou and Jianing Zhong and Yixing Zhang and Jie Xu and Changhu Xue and Lan Zhu and Wei Liu and Xiao-Li Tian and Jianbin Wang and David E. Clapham and Zongli Li and Jin Zhang} } @article {49125, title = {Dedicated photoreceptor pathways in Drosophila larvae mediate navigation by processing either spatial or temporal cues.}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {2018 Mar 28}, pages = {1260}, abstract = {

To integrate changing environmental cues with high spatial and temporal resolution is critical for animals to orient themselves. Drosophila larvae show an effective motor program to navigate away from light sources. How the larval visual circuit processes light stimuli to control navigational decision remains unknown. The larval visual system is composed of two sensory input channels, Rhodopsin5 (Rh5) and Rhodopsin6 (Rh6) expressing photoreceptors (PRs). We here characterize how spatial and temporal information are used to control navigation. Rh6-PRs are required to perceive temporal changes of light intensity during head casts, while Rh5-PRs are required to control behaviors that allow navigation in response to spatial cues. We characterize how distinct behaviors are modulated and identify parallel acting and converging features of the visual circuit. Functional features of the larval visual circuit highlight the principle of how early in a sensory circuit distinct behaviors may be computed by partly overlapping sensory pathways.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-03520-5}, author = {Humberg, Tim-Henning and Bruegger, Pascal and Afonso, Bruno and Zlatic, Marta and Truman, James W and Gershow, Marc and Samuel, Aravinthan and Sprecher, Simon G} } @article {49415, title = {Defective cortex glia plasma membrane structure underlies light-induced epilepsy in mutants.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, year = {2018}, month = {2018 Sep 05}, pages = {E8919-28}, abstract = {

Seizures induced by visual stimulation (photosensitive epilepsy; PSE) represent a common type of epilepsy in humans, but the molecular mechanisms and genetic drivers underlying PSE remain unknown, and no good genetic animal models have been identified as yet. Here, we show an animal model of PSE, in , owing to defective cortex glia. The cortex glial membranes are severely compromised in ceramide phosphoethanolamine synthase ()-null mutants and fail to encapsulate the neuronal cell bodies in the neuronal cortex. Expression of human sphingomyelin synthase 1, which synthesizes the closely related ceramide phosphocholine (sphingomyelin), rescues the cortex glial abnormalities and PSE, underscoring the evolutionarily conserved role of these lipids in glial membranes. Further, we show the compromise in plasma membrane structure that underlies the glial cell membrane collapse in mutants and leads to the PSE phenotype.

}, issn = {1091-6490}, doi = {10.1073/pnas.1808463115}, author = {Kunduri, Govind and Turner-Evans, Daniel and Konya, Yutaka and Izumi, Yoshihiro and Nagashima, Kunio and Lockett, Stephen and Holthuis, Joost and Bamba, Takeshi and Acharya, Usha and Acharya, Jairaj K} } @article {67291, title = {Detecting and Correcting False Transients in Calcium Imaging}, journal = {bioRxiv}, year = {2018}, month = {11/2018}, abstract = {

Population recordings of calcium activity are a major source of insight into neural function. Large dataset sizes often require automated methods, but automation can introduce errors that are difficult to detect. Here we show that automatic time course estimation can sometimes lead to significant misattribution errors, in which fluorescence is ascribed to the wrong cell. Misattribution arises when the shapes of overlapping cells are imperfectly defined, or when entire cells or processes are not identified, and misattribution can even be produced by methods specifically designed to handle overlap. To diagnose this problem, we develop a transient-by-transient metric and a visualization tool that allow users to quickly assess the degree of misattribution in large populations. To filter out misattribution, we also design a robust estimator that explicitly accounts for contaminating signals in a generative model. Our methods can be combined with essentially any cell finding technique, empowering users to diagnose and correct at large scale a problem that has the potential to significantly alter scientific conclusions.

}, doi = {10.1101/473470}, url = {https://www.biorxiv.org/content/early/2018/11/19/473470}, author = {Gauthier, Jeff L. and Koay, Sue Ann and Nieh, Edward H. and Tank, David W. and Pillow, Jonathan W. and Charles, Adam S.} } @article {65771, title = {Development of a Rubredoxin-Type Center Embedded in a de Dovo-Designed Three-Helix Bundle}, journal = {Biochemistry}, volume = {57}, year = {2018}, month = {03/2018}, pages = {2308 {\textendash} 2316}, abstract = {

Protein design is a powerful tool for interrogating the basic requirements for the function of a metal site in a way that allows for the selective incorporation of elements that are important for function. Rubredoxins are small electron transfer proteins with a reduction potential centered near 0 mV (vs normal hydrogen electrode). All previous attempts to design a rubredoxin site have focused on incorporating the canonical CXXC motifs in addition to reproducing the peptide fold or using flexible loop regions to define the morphology of the site. We have produced a rubredoxin site in an utterly different fold, a three-helix bundle. The spectra of this construct mimic the ultraviolet{\textendash}visible, M{\"o}ssbauer, electron paramagnetic resonance, and magnetic circular dichroism spectra of native rubredoxin. Furthermore, the measured reduction potential suggests that this rubredoxin analogue could function similarly. Thus, we have shown that an α-helical scaffold sustains a rubredoxin site that can cycle with the desired potential between the Fe(II) and Fe(III) states and reproduces the spectroscopic characteristics of this electron transport protein without requiring the classic rubredoxin protein fold.

}, doi = {10.1021/acs.biochem.8b00091}, url = {https://pubs-acs-org.accesdistant.sorbonne-universite.fr/doi/pdf/10.1021/acs.biochem.8b00091}, author = {Tebo, Alison G and Pinter, Tyler B J and Garc{\'\i}a-Serres, Ricardo and Speelman, Amy L and Tard, C{\'e}dric and S{\'e}n{\`e}que, Olivier and Blondin, Genevi{\`e}ve and Latour, Jean-Marc and Penner-Hahn, James and Lehnert, Nicolai and Pecoraro, Vincent L} } @article {49255, title = {Discrete flow posteriors for variational inference in discrete dynamical systems.}, journal = {arXiv}, year = {2018}, month = {2018 May 28}, pages = {1805.10958}, abstract = {

Each training step for a variational autoencoder (VAE) requires us to sample from the approximate posterior, so we usually choose simple (e.g. factorised) approximate posteriors in which sampling is an efficient computation that fully exploits GPU parallelism. However, such simple approximate posteriors are often insufficient, as they eliminate statistical dependencies in the posterior. While it is possible to use normalizing flow approximate posteriors for continuous latents, some problems have discrete latents and strong statistical dependencies. The most natural approach to model these dependencies is an autoregressive distribution, but sampling from such distributions is inherently sequential and thus slow. We develop a fast, parallel sampling procedure for autoregressive distributions based on fixed-point iterations which enables efficient and accurate variational inference in discrete state-space latent variable dynamical systems. To optimize the variational bound, we considered two ways to evaluate probabilities: inserting the relaxed samples directly into the pmf for the discrete distribution, or converting to continuous logistic latent variables and interpreting the K-step fixed-point iterations as a normalizing flow. We found that converting to continuous latent variables gave considerable additional scope for mismatch between the true and approximate posteriors, which resulted in biased inferences, we thus used the former approach. Using our fast sampling procedure, we were able to realize the benefits of correlated posteriors, including accurate uncertainty estimates for one cell, and accurate connectivity estimates for multiple cells, in an order of magnitude less time.

}, url = {https://arxiv.org/abs/1805.10958}, author = {Aitchison, Laurence and Adam, Vincent and Turaga, Srinivas C} } @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 {49195, title = {Ejaculation induced by the activation of Crz neurons is rewarding to Drosophila males.}, journal = {Current Biology : CB}, volume = {28}, year = {2018}, month = {2018 May 07}, pages = {1445-1452.e3}, abstract = {

The reward system is a collection of circuits that reinforce behaviors necessary for survival [1, 2]. Given the importance of reproduction for survival, actions that promote successful mating induce pleasurable feeling and are positively reinforced [3, 4]. This principle is conserved in Drosophila, where successful copulation is naturally rewarding to male flies, induces long-term appetitive memories [5], increases brain levels of neuropeptide F (NPF, the fly homolog of neuropeptide Y), and prevents ethanol, known otherwise as rewarding to flies [6, 7], from being rewarding [5]. It is not clear which of the multiple sensory and motor responses performed during mating induces perception of reward. Sexual interactions with female flies that do not reach copulation are not sufficient to reduce ethanol consumption [5], suggesting that only successful mating encounters are rewarding. Here, we uncoupled the initial steps of mating from its final steps and tested the ability of ejaculation to mimic the rewarding value of full copulation. We induced ejaculation by activating neurons that express the neuropeptide corazonin (CRZ) [8] and subsequently measured different aspects of reward. We show that activating Crz-expressing neurons is rewarding to male flies, as they choose to reside in a zone that triggers optogenetic stimulation of Crz neurons and display conditioned preference for an odor paired with the activation. Reminiscent of successful mating, repeated activation of Crz neurons increases npf levels and reduces ethanol consumption. Our results demonstrate that ejaculation stimulated by Crz/Crz-receptor signaling serves as an essential part of the mating reward mechanism in Drosophila. VIDEO ABSTRACT.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2018.03.039}, author = {Zer-Krispil, Shir and Zak, Hila and Shao, Lisha and Ben-Shaanan, Shir and Tordjman, Lea and Bentzur, Assa and Shmueli, Anat and Shohat-Ophir, Galit} } @article {49474, title = {Expanding the optogenetics toolkit by topological inversion of rhodopsins.}, journal = {Cell}, volume = {175}, year = {2018}, month = {2018 Oct 16}, pages = {1131-40}, abstract = {

Targeted manipulation of activity in specific populations of neurons is important for investigating the neural circuit basis of behavior. Optogenetic approaches using light-sensitive microbial rhodopsins have permitted manipulations to reach a level of temporal precision that is enabling functional circuit dissection. As demand for more precise perturbations to serve specific experimental goals increases, a palette of opsins with diverse selectivity, kinetics, and spectral properties will be needed. Here, we introduce a novel approach of "topological engineering"-inversion of opsins in the plasma membrane-and demonstrate that it can produce variants with unique functional properties of interest for circuit neuroscience. In one striking example, inversion of a Channelrhodopsin variant converted it from a potent activator into a fast-acting inhibitor that operates as a cation pump. Our findings argue that membrane topology provides a useful orthogonal dimension of protein engineering that immediately permits as much as a doubling of the available toolkit.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2018.09.026}, author = {Brown, Jennifer and Behnam, Reza and Coddington, Luke and Tervo, D G R and Martin, Kathleen and Proskurin, Mikhail and Kuleshova, Elena and Park, Junchol and Phillips, James and Bergs, Amelie C F and Gottschalk, Alexander and Dudman, Joshua T and Karpova, Alla Y} } @article {49346, title = {Expansion microscopy: protocols for imaging proteins and RNA in cells and tissues.}, journal = {Current Protocols in Cell Biology}, volume = {80}, year = {2018}, month = {2018 Aug 02}, pages = {e56}, abstract = {

Expansion microscopy (ExM) is a recently developed technique that enables nanoscale-resolution imaging of preserved cells and tissues on conventional diffraction-limited microscopes via isotropic physical expansion of the specimens before imaging. In ExM, biomolecules and/or fluorescent labels in the specimen are linked to a dense, expandable polymer matrix synthesized evenly throughout the specimen, which undergoes 3-dimensional expansion by \~{}4.5 fold linearly when immersed in water. Since our first report, versions of ExM optimized for visualization of proteins, RNA, and other biomolecules have emerged. Here we describe best-practice, step-by-step ExM protocols for performing analysis of proteins (protein retention ExM, or proExM) as well as RNAs (expansion fluorescence in situ hybridization, or ExFISH), using chemicals and hardware found in a typical biology lab. Furthermore, a detailed protocol for handling and mounting expanded samples and for imaging them with confocal and light-sheet microscopes is provided. {\textcopyright} 2018 by John Wiley \& Sons, Inc.

}, issn = {1934-2616}, doi = {10.1002/cpcb.56}, author = {Asano, Shoh M and Gao, Ruixuan and Wassie, Asmamaw T and Tillberg, Paul W and Chen, Fei and Boyden, Edward S} } @article {65770, title = {Fluorogenic Protein-Based Strategies for Detection, Actuation, and Sensing}, journal = {BioEssays}, volume = {40}, year = {2018}, month = {08/2018}, pages = {1800118}, abstract = {

Fluorescence imaging has become an indispensable tool in cell and molecular biology. GFP-like fluorescent proteins have revolutionized fluorescence microscopy, giving experimenters exquisite control over the localization and specificity of tagged constructs. However, these systems present certain drawbacks and as such, alternative systems based on a fluorogenic interaction between a chromophore and a protein have been developed. While these systems are initially designed as fluorescent labels, they also present new opportunities for the development of novel labeling and detection strategies. This review focuses on new labeling protocols, actuation methods, and biosensors based on fluorogenic protein systems. This review presents recently developed fluorogenic protein-based systems made of a protein tag incorporating an external chromophore. Beyond addressing some limitations of classical fluorescent proteins, these unique systems present characteristics than can be used to creatively push the limits of biological imaging, in particular for the development of new labeling protocols, actuation methods and biosensors.

}, issn = {0265-9247}, doi = {10.1002/bies.201800118}, url = {https://onlinelibrary-wiley-com.accesdistant.sorbonne-universite.fr/doi/pdf/10.1002/bies.201800118}, author = {Gautier, Arnaud and Tebo, Alison G.} } @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 {49813, title = {High-performance GFP-based calcium indicators for imaging activity in neuronal populations and microcompartments.}, journal = {bioRxiv}, year = {2018}, month = {2018 Oct 3}, abstract = {

Calcium imaging with genetically encoded calcium indicators (GECIs) is routinely used to measure neural activity in intact nervous systems. GECIs are frequently used in one of two different modes: to track activity in large populations of neuronal cell bodies, or to follow dynamics in subcellular compartments such as axons, dendrites and individual synaptic compartments. Despite major advances, calcium imaging is still limited by the biophysical properties of existing GECIs, including affinity, signal-to-noise ratio, rise and decay kinetics, and dynamic range. Using structure-guided mutagenesis and neuron-based screening, we optimized the green fluorescent protein-based GECI GCaMP6 for different modes of in vivo imaging. The jGCaMP7 sensors provide improved detection of individual spikes (jGCaMP7s,f), imaging in neurites and neuropil (jGCaMP7b), and tracking large populations of neurons using 2-photon (jGCaMP7s,f) or wide-field (jGCaMP7c) imaging.

}, doi = {10.1101/434589}, author = {Dana, Hod and Sun, Yi and Mohar, Boaz and Hulse, Brad and Hasseman, Jeremy P and Tsegaye, Getahun and Tsang, Arthur and Wong, Allan and Patel, Ronak and Macklin, John J and Chen, Yang and Konnerth, Arthur and Jayaraman, Vivek and Looger, Loren L and Schreiter, Eric R and Svoboda, Karel and Kim, Douglas S} } @article {49043, title = {Image co-localization - co-occurrence versus correlation.}, journal = {Journal of Cell Science}, volume = {131}, year = {2018}, month = {2018 Feb 08}, abstract = {

Fluorescence image co-localization analysis is widely utilized to suggest biomolecular interaction. However, there exists some confusion as to its correct implementation and interpretation. In reality, co-localization analysis consists of at least two distinct sets of methods, termed co-occurrence and correlation. Each approach has inherent and often contrasting strengths and weaknesses. Yet, neither one can be considered to always be preferable for any given application. Rather, each method is most appropriate for answering different types of biological question. This Review discusses the main factors affecting multicolor image co-occurrence and correlation analysis, while giving insight into the types of biological behavior that are better suited to one approach or the other. Further, the limits of pixel-based co-localization analysis are discussed in the context of increasingly popular super-resolution imaging techniques.

}, issn = {1477-9137}, doi = {10.1242/jcs.211847}, author = {Aaron, Jesse S and Taylor, Aaron B and Chew, Teng-Leong} } @article {49545, title = {Imaging cortical dynamics in GCaMP transgenic rats with a head-mounted widefield macroscope.}, journal = {Neuron}, year = {2018}, month = {2018 Oct 22}, abstract = {

Widefield imaging of calcium dynamics is an emerging method for mapping regional neural activity but is currently limited to restrained animals. Here we describe cScope, a head-mounted widefield macroscope\ developed to image large-scale cortical dynamics in rats during natural behavior. cScope provides a 7.8\ {\texttimes} 4\ mm field of view and dual illumination paths for both fluorescence and hemodynamic correction and can be fabricated at low cost using readily attainable components. We also report the development of Thy-1 transgenic rat strains with widespread neuronal expression of the calcium indicator GCaMP6f. We combined these two technologies to image large-scale calcium dynamics in the dorsal neocortex during a visual evidence accumulation\ task. Quantitative analysis of task-related dynamics revealed multiple regions having neural signals that encode behavioral choice and sensory evidence. Our results provide a new transgenic resource for calcium imaging in rats and extend the domain of head-mounted microscopes to larger-scale cortical dynamics.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2018.09.050}, author = {Scott, Benjamin B and Thiberge, Stephan Y and Guo, Caiying and Tervo, D Gowanlock R and Brody, Carlos D and Karpova, Alla Y and Tank, David W} } @article {49293, title = {Imaging dynamic and selective low-complexity domain interactions that control gene transcription.}, journal = {Science (New York, N.Y.)}, volume = {361}, year = {2018}, month = {2018 Jun 21}, pages = {eaar2555}, abstract = {

Many eukaryotic transcription factors (TFs) contain intrinsically disordered low-complexity domains (LCDs), but how they drive transactivation remains unclear. Here, live-cell single-molecule imaging reveals that TF-LCDs form local high-concentration interaction hubs at synthetic and endogenous genomic loci. TF-LCD hubs stabilize DNA binding, recruit RNA polymerase II (Pol II), and activate transcription. LCD-LCD interactions within hubs are highly dynamic, display selectivity with binding partners, and are differentially sensitive to disruption by hexanediols. Under physiological conditions, rapid and reversible LCD-LCD interactions occur between TFs and the Pol II machinery without detectable phase separation. Our findings reveal fundamental mechanisms underpinning transcriptional control and suggest a framework for developing single-molecule imaging screens for novel drugs targeting gene regulatory interactions implicated in disease.

}, issn = {1095-9203}, doi = {10.1126/science.aar2555}, author = {Chong, Shasha and Dugast-Darzacq, Claire and Liu, Zhe and Dong, Peng and Dailey, Gina M and Cattoglio, Claudia and Heckert, Alec and Banala, Sambashiva and Lavis, Luke and Darzacq, Xavier and Tjian, Robert} } @article {49245, title = {Imaging mRNA in vivo, from birth to death.}, journal = {Annual Review of Biophysics}, volume = {47}, year = {2018}, month = {2018 May 20}, pages = {85-106}, abstract = {

RNA is the fundamental information transfer system in the cell. The ability to follow single messenger RNAs (mRNAs) from transcription to degradation with fluorescent probes gives quantitative information about how the information is transferred from DNA to proteins. This review focuses on the latest technological developments in the field of single-mRNA detection and their usage to study gene expression in both fixed and live cells. By describing the application of these imaging tools, we follow the journey of mRNA from transcription to decay in single cells, with single-molecule resolution. We review current theoretical models for describing transcription and translation that were generated by single-molecule and single-cell studies. These methods provide a basis to study how single-molecule interactions generate phenotypes, fundamentally changing our understating of gene expression regulation.

}, issn = {1936-1238}, doi = {10.1146/annurev-biophys-070317-033037}, author = {Tutucci, Evelina and Livingston, Nathan M and Singer, Robert H and Wu, Bin} } @article {65769, title = {Improved Chemical-Genetic Fluorescent Markers for Live Cell Microscopy}, journal = {Biochemistry}, volume = {57}, year = {2018}, month = {11/2018}, pages = {5648 {\textendash} 5653}, abstract = {

Inducible chemical-genetic fluorescent markers are promising tools for live cell imaging requiring high spatiotemporal resolution and low background fluorescence. The fluorescence-activating and absorption shifting tag (FAST) was recently developed to form fluorescent molecular complexes with a family of small, synthetic fluorogenic chromophores (so-called fluorogens). Here, we use rational design to modify the binding pocket of the protein and screen for improved fluorescence performances with four different fluorogens. The introduction of a single mutation results in improvements in both quantum yield and dissociation constant with nearly all fluorogens tested. Our improved FAST (iFAST) allowed the generation of a tandem iFAST (td-iFAST) that forms green and red fluorescent reporters 1.6-fold and 2-fold brighter than EGFP and mCherry, respectively, while having a comparable size.

}, doi = {10.1021/acs.biochem.8b00649}, url = {https://pubs-acs-org.accesdistant.sorbonne-universite.fr/doi/pdf/10.1021/acs.biochem.8b00649}, author = {Tebo, Alison G and Pimenta, Frederico M and Zhang, Yu and Gautier, Arnaud} } @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 {49466, title = {In toto imaging and reconstruction of post-implantation mouse development at the single-cell level.}, journal = {Cell}, volume = {175}, year = {2018}, month = {2018 Oct 10}, pages = {859-876}, abstract = {

The mouse embryo has long been central to the study of mammalian development; however, elucidating the cell behaviors governing gastrulation and the formation of tissues and organs remains a fundamental challenge. A major obstacle is the lack of live imaging and image analysis technologies capable of systematically following cellular dynamics across the developing embryo. We developed a light-sheet microscope that adapts itself to the dramatic changes in size, shape, and optical properties of the post-implantation\ mouse embryo and captures its development from gastrulation to early organogenesis at\ the cellular level. We furthermore developed a computational framework for reconstructing long-term cell tracks, cell divisions, dynamic fate maps, and maps of tissue morphogenesis across the entire embryo. By jointly analyzing cellular dynamics in multiple embryos registered in space and time, we built a dynamic atlas of post-implantation mouse development that, together with our microscopy and computational methods, is provided as a resource.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2018.09.031}, author = {McDole, Katie and Guignard, Leo and Amat, Fernando and Berger, Andrew and Malandain, Gr{\'e}goire and Royer, Lo{\"\i}c A and Turaga, Srinivas C and Branson, Kristin and Keller, Philipp J} } @article {49367, title = {In vivo measurement of afferent activity with axon-specific calcium imaging.}, journal = {Nature Neuroscience}, year = {2018}, month = {2018 Aug 20}, abstract = {

In vivo calcium imaging from axons provides direct interrogation of afferent neural activity, informing the neural representations that a local circuit receives. Unlike in somata and dendrites, axonal recording of neural activity-both electrically and optically-has been difficult to achieve, thus preventing comprehensive understanding of neuronal circuit function. Here we developed an active transportation strategy to enrich GCaMP6, a genetically encoded calcium indicator, uniformly in axons with sufficient brightness, signal-to-noise ratio, and photostability to allow robust, structure-specific imaging of presynaptic activity in awake mice. Axon-targeted GCaMP6 enables frame-to-frame correlation for motion correction in axons and permits subcellular-resolution recording of axonal activity in previously inaccessible deep-brain areas. We used axon-targeted GCaMP6 to record layer-specific local afferents without contamination from somata or from intermingled dendrites in the cortex. We expect that axon-targeted GCaMP6 will facilitate new applications in investigating afferent signals relayed by genetically defined neuronal populations within and across specific brain regions.

}, issn = {1546-1726}, doi = {10.1038/s41593-018-0211-4}, author = {Broussard, Gerard Joey and Liang, Yajie and Fridman, Marina and Unger, Elizabeth K and Meng, Guanghan and Xiao, Xian and Ji, Na and Petreanu, Leopoldo and Tian, Lin} } @article {49451, title = {Integrin-mediated attachment of the blastoderm to the vitelline envelope impacts gastrulation of insects.}, journal = {bioRxiv}, year = {2018}, month = {2018 Oct 2}, abstract = {

During gastrulation, physical forces reshape the simple embryonic tissue to form a complex body plan of multicellular organisms. These forces often cause large-scale asymmetric movements of the embryonic tissue. In many embryos, the tissue undergoing gastrulation movements is surrounded by a rigid protective shell. While it is well recognized that gastrulation movements depend on forces generated by tissue-intrinsic contractility, it is not known if interactions between the tissue and the protective shell provide additional forces that impact gastrulation. Here we show that a particular part of the blastoderm tissue of the red flour beetle Tribolium castaneum tightly adheres in a temporally coordinated manner to the vitelline envelope surrounding the embryo. This attachment generates an additional force that counteracts the tissue-intrinsic contractile forces to create asymmetric tissue movements. Furthermore, this localized attachment is mediated by a specific integrin, and its knock-down leads to a gastrulation phenotype consistent with complete loss of attachment. Moreover, analysis of another integrin in the fruit fly Drosophila melanogaster suggests that gastrulation in this organism also relies on adhesion between the blastoderm and the vitelline. Together, our findings reveal a conserved mechanism whereby the spatiotemporal pattern of tissue adhesion to the vitelline envelope provides controllable counter-forces that shape gastrulation movements in insects.

}, doi = {10.1101/421701}, author = {Muenster, Stefan and Jain, Akanksha and Mietke, Alexander and Pavlopoulos, Anastasios and Grill, Stephan W and Tomancak, Pavel} } @article {49143, title = {Juvenile hormone reveals mosaic developmental programs in the metamorphosing optic lobe of Drosophila melanogaster.}, journal = {Biology Open}, year = {2018}, month = {2018 Apr 04}, abstract = {

The development of the adult optic lobe (OL) of is directed by a wave of ingrowth of the photoreceptors over a two day period at the outset of metamorphosis which is accompanied by the appearance of the pupal-specific transcription factor Broad-Z3 (Br-Z3) and expression of early drivers in OL neurons. During this time, there are pulses of ecdysteroids that time the metamorphic events. At the outset, the transient appearance of juvenile hormone (JH) prevents precocious development of the OL caused by the ecdysteroid peak that initiates pupariation, but the artificial maintenance of JH after this time misdirects subsequent development. Axon ingrowth, Br-Z3 appearance and the expression of early drivers were unaffected, but aspects of later development such as the dendritic expansion of the lamina monopolar neurons and the expression of late drivers were suppressed. This effect of the exogenous JH mimic (JHM) pyriproxifen is lost by 24 hr after pupariation. Part of this effect of JHM is due to its suppression of the appearance of ecdysone receptor EcR-B1 that occurs after pupation and during early adult development.

}, issn = {2046-6390}, doi = {10.1242/bio.034025}, author = {Riddiford, Lynn M and Truman, James W and Nern, Aljoscha} } @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 {48937, title = {larvalign: Aligning gene expression patterns from the larval brain of Drosophila melanogaster.}, journal = {Neuroinformatics}, volume = {16}, year = {2018}, month = {2018 Jan 1}, pages = {65-80}, abstract = {

The larval brain of the fruit fly Drosophila melanogaster is a small, tractable model system for neuroscience. Genes for fluorescent marker proteins can be expressed in defined, spatially restricted neuron populations. Here, we introduce the methods for 1) generating a standard template of the larval central nervous system (CNS), 2) spatial mapping of expression patterns from different larvae into a reference space defined by the standard template. We provide a manually annotated gold standard that serves for evaluation of the registration framework involved in template generation and mapping. A method for registration quality assessment enables the automatic detection of registration errors, and a semi-automatic registration method allows one to correct registrations, which is a prerequisite for a high-quality, curated database of expression patterns. All computational methods are available within the larvalign software package: https://github.com/larvalign/larvalign/releases/tag/v1.0.

}, issn = {1559-0089}, doi = {10.1007/s12021-017-9349-6}, author = {Muenzing, Sascha E A and Strauch, Martin and Truman, James W and B{\"u}hler, Katja and Thum, Andreas S and Merhof, Dorit} } @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 {49085, title = {Model-free quantification and visualization of colocalization in fluorescence images.}, journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology}, year = {2018}, month = {2018 Mar 13}, abstract = {

The spatial association between fluorescently tagged biomolecules in situ provides valuable insight into their biological relationship. Within the limits of diffraction, such association can be measured using either Pearson{\textquoteright}s Correlation Coefficient (PCC) or Spearman{\textquoteright}s Rank Coefficient (SRC), which are designed to measure linear and monotonic correlations, respectively. However, the relationship between real biological signals is often more complex than these measures assume, rendering their results difficult to interpret. Here, we have adapted methods from the field of information theory to measure the association between two probes{\textquoteright} concentrations based on their statistical dependence. Our approach is mathematically more general than PCC or SRC, making no assumptions about the type of relationship between the probes. We show that when applied to biological images, our measures provide more intuitive results that are also more robust to outliers and the presence of multiple relationships than PCC or SRC. We also devise a display technique to highlight regions in the input images where the probes{\textquoteright} association is higher versus lower. We expect that our methods will allow biologists to more accurately and robustly quantify and visualize the association between two probes in a pair of fluorescence images. {\textcopyright} 2018 International Society for Advancement of Cytometry.

}, issn = {1552-4930}, doi = {10.1002/cyto.a.23356}, author = {Taylor, Aaron B and Ioannou, Maria S and Aaron, Jesse and Chew, Teng-Leong} } @article {65766, title = {Modifying the Steric Properties in the Second Coordination Sphere of Designed Peptides Leads to Enhancement of Nitrite Reductase Activity}, journal = {Angewandte Chemie International Edition}, volume = {57}, year = {2018}, month = {01/2018}, pages = {3954 {\textendash} 3957}, abstract = {

Protein design is a useful strategy to interrogate the protein structure-function relationship. We demonstrate using a highly modular 3-stranded coiled coil (TRI-peptide system) that a functional type 2 copper center exhibiting copper nitrite reductase (NiR) activity exhibits the highest homogeneous catalytic efficiency under aqueous conditions for the reduction of nitrite to NO and H2O. Modification of the amino acids in the second coordination sphere of the copper center increases the nitrite reductase activity up to 75-fold compared to previously reported systems. We find also that steric bulk can be used to enforce a three-coordinate CuI in a site, which tends toward two-coordination with decreased steric bulk. This study demonstrates the importance of the second coordination sphere environment both for controlling metal-center ligation and enhancing the catalytic efficiency of metalloenzymes and their analogues.

}, doi = {10.1002/anie.201712757}, url = {https://onlinelibrary.wiley.com/doi/full/10.1002/anie.201712757}, author = {Koebke, Karl J and Yu, Fangting and Salerno, Elvin and Stappen, Casey Van and Tebo, Alison G and Penner-Hahn, James E and Pecoraro, Vincent L} } @article {49527, title = {MYC induces a hybrid energetics program early in cell reprogramming.}, journal = {Stem Cell Reports}, volume = {11}, year = {2018}, month = {2018 Dec 11}, pages = {1479-92}, abstract = {

Cell reprogramming is thought to be associated with a full metabolic switch from an oxidative- to a glycolytic-based metabolism. However, neither the dynamics nor the factors controlling this metabolic switch are fully understood. By using cellular, biochemical, protein array, metabolomic, and respirometry analyses, we found that c-MYC establishes a robust bivalent energetics program early in cell reprogramming. Cells prone to undergo reprogramming exhibit high mitochondrial membrane potential and display a hybrid metabolism. We conclude that MYC proteins orchestrate a rewiring of somatic cell metabolism early in cell reprogramming, whereby somatic cells acquire the phenotypic plasticity necessary for their transition to pluripotency in response to either intrinsic or external cues.

}, issn = {2213-6711}, doi = {10.1016/j.stemcr.2018.10.018}, author = {Prieto, Javier and Seo, Arnold Y and Le{\'o}n, Marian and Santacatterina, Fulvio and Torresano, Laura and Palomino-Sch{\"a}tzlein, Martina and Gim{\'e}nez, Karen and Vallet-S{\'a}nchez, Azahara and Ponsoda, Xavier and Pineda-Lucena, Antonio and Cuezva, Jos{\'e} M and Lippincott-Schwartz, Jennifer and Torres, Josema} } @article {49001, title = {Neural substrates of navigational decision-making in Drosophila larva anemotaxis.}, journal = {bioRxiv}, year = {2018}, month = {2018 Jan 08}, pages = {244608}, abstract = {

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

}, doi = {10.1101/244608}, author = {Jovanic, Tihana and Truman, James W and Gershow, Marc and Zlatic, Marta} } @article {49529, title = {Neuron-subtype-specific expression, interaction affinities, and specificity determinants of DIP/Dpr cell recognition proteins.}, journal = {Neuron}, volume = {100}, year = {2018}, month = {2018 Nov 12}, pages = {1385-1400}, abstract = {

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

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2018.10.046}, author = {Cosmanescu, Filip and Katsamba, Phinikoula S and Sergeeva, Alina P and Ahlsen, Goran and Patel, Saurabh D and Brewer, Joshua J and Tan, Liming and Xu, Shuwa and Xiao, Qi and Nagarkar-Jaiswal, Sonal and Nern, Aljoscha and Bellen, Hugo J and Zipursky, S Lawrence and Honig, Barry and Shapiro, Lawrence} } @article {49086, title = {Nociceptive interneurons control modular motor pathways to promote escape behavior in Drosophila.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Mar 12}, abstract = {

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

}, issn = {2050-084X}, doi = {10.7554/eLife.26016}, author = {Burgos, Anita and Honjo, Ken and Ohyama, Tomoko and Qian, Cheng Sam and Shin, Grace Ji-Eun and Gohl, Daryl M and Silies, Marion and Tracey, W Daniel and Zlatic, Marta and Cardona, Albert and Grueber, Wesley B} } @article {49381, title = {Optical alignment device for two-photon microscopy.}, journal = {Biomedical Optics Express}, volume = {9}, year = {2018}, month = {2018 Aug 1}, pages = {3624-9}, abstract = {

Two-photon excitation fluorescence microscopy has revolutionized our understanding of brain structure and function through the high resolution and large penetration depth it offers. Investigating neural structures\ in vivo\ requires gaining optical access to the brain, which is typically achieved by replacing a part of the skull with one or several layers of cover glass windows. To compensate for the spherical aberrations caused by the presence of these layers of glass, collar-correction objectives are typically used. However, the efficiency of this correction has been shown to depend significantly on the tilt angle between the glass window surface and the optical axis of the imaging system. Here, we first expand these observations and characterize the effect of the tilt angle on the collected fluorescence signal with thicker windows (double cover slide) and compare these results with an objective devoid of collar-correction. Second, we present a simple optical alignment device designed to rapidly minimize the tilt angle\ in vivo\ and align the optical axis of the microscope perpendicularly to the glass window to an angle below 0.25{\textdegree}, thereby significantly improving the imaging quality. Finally, we describe a tilt-correction procedure for users in an\ in vivo\ setting, enabling the accurate alignment with a resolution of \<0.2{\textdegree} in only few iterations.

}, doi = {10.1364/BOE.9.003624}, author = {Gali{\~n}anes, Gregorio L and Marchand, Paul J and Turcotte, Raphael and Pellat, Sebastien and Ji, Na and Huber, Daniel} } @article {68434, title = {Proximity labeling: spatially resolved proteomic mapping for neurobiology.}, journal = {Curr Opin Neurobiol}, volume = {50}, year = {2018}, month = {06/2018}, pages = {17-23}, abstract = {

Understanding signaling pathways in neuroscience requires high-resolution maps of the underlying protein networks. Proximity-dependent biotinylation with engineered enzymes, in combination with mass spectrometry-based quantitative proteomics, has emerged as a powerful method to dissect molecular interactions and the localizations of endogenous proteins. Recent applications to neuroscience have provided insights into the composition of sub-synaptic structures, including the synaptic cleft and inhibitory post-synaptic density. Here we compare the different enzymes and small-molecule probes for proximity labeling in the context of cultured neurons and tissue, review existing studies, and provide technical suggestions for the in vivo application of proximity labeling.

}, keywords = {Animals, Biotinylation, Humans, Neurobiology, Neuroimaging, Proteome, Proteomics}, issn = {1873-6882}, doi = {10.1016/j.conb.2017.10.015}, author = {Han, Shuo and Li, Jiefu and Ting, Alice Y} } @article {49013, title = {Repetitive aggressive encounters generate a long-lasting internal state in Drosophila melanogaster males.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, year = {2018}, month = {2018 Jan 16}, pages = {1099-104}, abstract = {

Multiple studies have investigated the mechanisms of aggressive behavior in Drosophila; however, little is known about the effects of chronic fighting experience. Here, we investigated if repeated fighting encounters would induce an internal state that could affect the expression of subsequent behavior. We trained wild-type males to become winners or losers by repeatedly pairing them with hypoaggressive or hyperaggressive opponents, respectively. As described previously, we observed that chronic losers tend to lose subsequent fights, while chronic winners tend to win them. Olfactory conditioning experiments showed that winning is perceived as rewarding, while losing is perceived as aversive. Moreover, the effect of chronic fighting experience generalized to other behaviors, such as gap-crossing and courtship. We propose that in response to repeatedly winning or losing aggressive encounters, male flies form an internal state that displays persistence and generalization; fight outcomes can also have positive or negative valence. Furthermore, we show that the activities of the PPL1-γ1pedc dopaminergic neuron and the MBON-γ1pedc\>α/β mushroom body output neuron are required for aversion to an olfactory cue associated with losing fights.

}, issn = {1091-6490}, doi = {10.1073/pnas.1716612115}, author = {Kim, Yong-Kyu and Saver, Mathias and Simon, Jasper and Kent, Clement F and Shao, Lisha and Eddison, Mark and Agrawal, Pavan and Texada, Michael and Truman, James W and Heberlein, Ulrike} } @article {48997, title = {Robust model-based analysis of single-particle tracking experiments with Spot-On.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Jan 04}, abstract = {

Single-particle tracking (SPT) has become an important method to bridge biochemistry and cell biology since it allows direct observation of protein binding and diffusion dynamics in live cells. However, accurately inferring information from SPT studies is challenging due to biases in both data analysis and experimental design. To address analysis bias, we introduce {\textquoteright}Spot-On{\textquoteright}, an intuitive web-interface. Spot-On implements a kinetic modeling framework that accounts for known biases, including molecules moving out-of-focus, and robustly infers diffusion constants and subpopulations from pooled single-molecule trajectories. To minimize inherent experimental biases, we implement and validate stroboscopic photo-activation SPT (spaSPT), which minimizes motion-blur bias and tracking errors. We validate Spot-On using experimentally realistic simulations and show that Spot-On outperforms other methods. We then apply Spot-On to spaSPT data from live mammalian cells spanning a wide range of nuclear dynamics and demonstrate that Spot-On consistently and robustly infers subpopulation fractions and diffusion constants.

}, issn = {2050-084X}, doi = {10.7554/eLife.33125}, author = {Hansen, Anders S and Woringer, Maxime and Grimm, Jonathan B and Lavis, Luke D and Tjian, Robert and Darzacq, Xavier} } @article {49523, title = {Sensorimotor pathway controlling stopping behavior during chemotaxis in the larva.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Nov 22}, abstract = {

Sensory navigation results from coordinated transitions between distinct behavioral programs. During chemotaxis in the larva, the detection of positive odor gradients extends runs while negative gradients promote stops and turns. This algorithm represents a foundation for the control of sensory navigation across phyla. In the present work, we identified an olfactory descending neuron, PDM-DN, which plays a pivotal role in the organization of stops and turns in response to the detection of graded changes in odor concentrations. Artificial activation of this descending neuron induces deterministic stops followed by the initiation of turning maneuvers through head casts. Using electron microscopy, we reconstructed the main pathway that connects the PDM-DN neuron to the peripheral olfactory system and to the pre-motor circuit responsible for the actuation of forward peristalsis. Our results set the stage for a detailed mechanistic analysis of the sensorimotor conversion of graded olfactory inputs into action selection to perform goal-oriented navigation.

}, issn = {2050-084X}, doi = {10.7554/eLife.38740}, author = {Tastekin, Ibrahim and Khandelwal, Avinash and Tadres, David and Fessner, Nico D and Truman, James W and Zlatic, Marta and Cardona, Albert and Louis, Matthieu} } @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 {48984, title = {Stability, affinity and chromatic variants of the glutamate sensor iGluSnFR.}, journal = {Nature Methods}, volume = {15}, year = {2018}, month = {2018 Nov}, pages = {9386-9}, abstract = {

Single-wavelength fluorescent reporters allow visualization of specific neurotransmitters with high spatial and temporal resolution. We report variants of intensity-based glutamate-sensing fluorescent reporter (iGluSnFR) that are functionally brighter; detect submicromolar to millimolar amounts of glutamate; and have blue, cyan, green, or yellow emission profiles. These variants could be imaged in vivo in cases where original iGluSnFR was too dim, resolved glutamate transients in dendritic spines and axonal boutons, and allowed imaging at kilohertz rates.

}, doi = {10.1038/s41592-018-0171-3}, author = {Marvin, Jonathan S and Scholl, Benjamin and Wilson, Daniel E and Podgorski, Kaspar and Kazemipour, Abbas and Mueller, Johannes Alexander and Schoch-McGovern, Susanne and Wang, Samuel S-H and Quiroz, Francisco Jose Urra and Rebola, Nelson and Bao, Huan and Little, Justin P and Tkachuk, Ariana N and Hantman, Adam W and Chapman, Edwin R and Dietrich, Dirk and DiGregorio, David A and Fitzpatrick, David and Looger, Loren L} } @article {49152, title = {Structural mechanism of functional modulation by gene splicing in NMDA receptors.}, journal = {Neuron}, volume = {98}, year = {2018}, month = {2018 Apr 10}, pages = {521-9}, abstract = {

Alternative gene splicing gives rise to N-methyl-D-aspartate (NMDA) receptor ion channels with defined functional properties and unique contributions to calcium signaling in a given chemical environment in the mammalian brain. Splice variants possessing the exon-5-encoded motif at the amino-terminal domain (ATD) of the GluN1 subunit are known to display robustly altered deactivation rates and pH sensitivity, but the underlying mechanism for this functional modification is largely unknown. Here, we show through cryoelectron microscopy (cryo-EM) that the presence of the exon 5 motif in GluN1 alters the local architecture of heterotetrameric GluN1-GluN2 NMDA receptors and creates contacts with the ligand-binding domains (LBDs) of the GluN1 and GluN2 subunits, which are absent in NMDA receptors lacking the exon 5 motif. The unique interactions established by the exon 5 motif are essential to the stability of the ATD/LBD and LBD/LBD interfaces that are critically involved in controlling proton sensitivity and deactivation.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2018.03.034}, author = {Regan, Michael C and Grant, Timothy and McDaniel, Miranda J and Karakas, Erkan and Zhang, Jing and Traynelis, Stephen F and Grigorieff, Nikolaus and Furukawa, Hiro} } @article {49574, title = {Structure of Plasmodium falciparum Rh5-CyRPA-Ripr invasion complex.}, journal = {Nature}, volume = {565}, year = {2018}, month = {2018 Dec 12}, pages = {118-21}, abstract = {

Plasmodium falciparum causes the severe form of malaria that has high levels of mortality in humans. Blood-stage merozoites of P. falciparum invade erythrocytes, and this requires interactions between multiple ligands from the parasite and receptors in hosts. These interactions include the binding of the Rh5-CyRPA-Ripr complex with the erythrocyte receptor basigin, which is an essential step for entry into human erythrocytes. Here we show that the Rh5-CyRPA-Ripr complex binds the erythrocyte cell line JK-1 significantly better than does Rh5 alone, and that this binding occurs through the insertion of Rh5 and Ripr into host membranes as a complex with high molecular weight. We report a cryo-electron microscopy structure of the Rh5-CyRPA-Ripr complex at subnanometre resolution, which reveals the organization of this essential invasion complex and the mode of interactions between members of the complex, and shows that CyRPA is a critical mediator of complex assembly. Our structure identifies blades 4-6 of the β-propeller of CyRPA as contact sites for Rh5 and Ripr. The limited contacts between Rh5-CyRPA and CyRPA-Ripr are consistent with the dissociation of Rh5 and Ripr from CyRPA for membrane insertion. A comparision of the crystal structure of Rh5-basigin with the cryo-electron microscopy structure of Rh5-CyRPA-Ripr suggests that Rh5 and Ripr are positioned parallel to the erythrocyte membrane before membrane insertion. This provides information on the function of this complex, and thereby provides insights into invasion by P. falciparum.

}, issn = {1476-4687}, doi = {10.1038/s41586-018-0779-6}, author = {Wong, Wilson and Huang, Rick and Menant, S{\'e}bastien and Hong, Chuan and Sandow, Jarrod J and Birkinshaw, Richard W and Healer, Julie and Hodder, Anthony N and Kanjee, Usheer and Tonkin, Christopher J and Heckmann, Denise and Soroka, Vladislav and S{\o}gaard, Teit Max Moscote and J{\o}rgensen, Thomas and Duraisingh, Manoj T and Czabotar, Peter E and de Jongh, Willem A and Tham, Wai-Hong and Webb, Andrew I and Yu, Zhiheng and Cowman, Alan F} } @article {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 {49182, title = {Transvection Goes Live-Visualizing Enhancer-Promoter Communication between Chromosomes.}, journal = {Molecular Cell}, volume = {70}, year = {2018}, month = {2018 Apr 19}, pages = {195-196}, abstract = {

Lim et\ al. (2018) use live imaging in Drosophila embryos to show that enhancers can drive transcription from promoters on another chromosome when they are in close proximity. In addition, they show that multiple promoters can access the same enhancer without competition, potentially sharing a pool of factors in a transcriptional "hub."

}, issn = {1097-4164}, doi = {10.1016/j.molcel.2018.04.004}, author = {Tsai, Albert and Singer, Robert H and Crocker, Justin} } @article {49512, title = {Visualizing intracellular organelle and cytoskeletal interactions at nanoscale resolution on millisecond timescales. }, journal = {Cell}, volume = {175}, year = {2018}, month = {2018 Nov 15}, pages = {1430-42}, abstract = {In eukaryotic cells, organelles and the cytoskeleton undergo highly dynamic yet organized interactions capable of orchestrating complex cellular functions. Visualizing these interactions requires noninvasive, long-duration imaging of the intracellular environment at high spatiotemporal resolution and low background. To achieve these normally opposing goals, we developed grazing incidence structured illumination microscopy (GI-SIM) that is capable of imaging dynamic events near the basal cell cortex at 97-nm resolution and 266 frames/s over thousands of time points. We employed multi-color GI-SIM to characterize the fast dynamic interactions of diverse organelles and the cytoskeleton, shedding new light on the complex behaviors of these structures. Precise measurements of microtubule growth or shrinkage events helped distinguish among models of microtubule dynamic instability. Analysis of endoplasmic reticulum (ER) interactions with other organelles or microtubules uncovered new ER remodeling mechanisms, such as hitchhiking of the ER on motile organelles. Finally, ER-mitochondria contact sites were found to promote both mitochondrial fission and fusion.}, doi = {10.1016/j.cell.2018.09.057}, author = {Guo, Yuting and Li, Di and Zhang, Siwei and Yang, Yanrui and Liu, Jia-Jia and Wang, Xinyu and Liu, Chong and Milkie, Daniel E and Moore, Regan P and Tulu, U Serdar and Kiehart, Daniel P and Hu, Junjie and Lippincott-Schwartz, Jennifer and Betzig, Eric and Li, Dong} } @article {49022, title = {Visualizing transcription factor dynamics in living cells.}, journal = {The Journal of Cell Biology}, volume = {217}, year = {2018}, month = {2018 Jan 29}, pages = {1181-91}, abstract = {

The assembly of sequence-specific enhancer-binding transcription factors (TFs) at cis-regulatory elements in the genome has long been regarded as the fundamental mechanism driving cell type-specific gene expression. However, despite extensive biochemical, genetic, and genomic studies in the past three decades, our understanding of molecular mechanisms underlying enhancer-mediated gene regulation remains incomplete. Recent advances in imaging technologies now enable direct visualization of TF-driven regulatory events and transcriptional activities at the single-cell, single-molecule level. The ability to observe the remarkably dynamic behavior of individual TFs in live cells at high spatiotemporal resolution has begun to provide novel mechanistic insights and promises new advances in deciphering causal-functional relationships of TF targeting, genome organization, and gene activation. In this review, we review current transcription imaging techniques and summarize converging results from various lines of research that may instigate a revision of models to describe key features of eukaryotic gene regulation.

}, issn = {1540-8140}, doi = {10.1083/jcb.201710038}, author = {Liu, Zhe and Tjian, Robert} } @article {48507, title = {Angular velocity integration in a fly heading circuit.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 May 22}, abstract = {

Many animals maintain an internal representation of their heading as they move through their surroundings. Such a compass representation was recently discovered in a neural population in the Drosophila melanogaster central complex, a brain region implicated in spatial navigation. Here, we use two-photon calcium imaging and electrophysiology in head-fixed walking flies to identify a different neural population that conjunctively encodes heading and angular velocity, and is excited selectively by turns in either the clockwise or counterclockwise direction. We show how these mirror-symmetric turn responses combine with the neurons{\textquoteright} connectivity to the compass neurons to create an elegant mechanism for updating the fly{\textquoteright}s heading representation when the animal turns in darkness. This mechanism, which employs recurrent loops with an angular shift, bears a resemblance to those proposed in theoretical models for rodent head direction cells. Our results provide a striking example of structure matching function for a broadly relevant computation.

}, issn = {2050-084X}, doi = {10.7554/eLife.23496}, author = {Turner-Evans, Daniel and Wegener, Stephanie and Rouault, Herv{\'e} and Franconville, Romain and Wolff, Tanya and Seelig, Johannes D and Druckmann, Shaul and Jayaraman, Vivek} } @article {67220, title = {Anisotropic EM Segmentation by 3D Affinity Learning and Agglomeration}, journal = {CoRR}, volume = {abs/1707.08935}, year = {2017}, abstract = {

The field of connectomics has recently produced neuron wiring diagrams from relatively large brain regions from multiple animals. Most of these neural reconstructions were computed from isotropic (e.g., FIBSEM) or near isotropic (e.g., SBEM) data. In spite of the remarkable progress on algorithms in recent years, automatic dense reconstruction from anisotropic data remains a challenge for the connectomics community. One significant hurdle in the segmentation of anisotropic data is the difficulty in generating a suitable initial over-segmentation. In this study, we present a segmentation method for anisotropic EM data that agglomerates a 3D over-segmentation computed from the 3D affinity prediction. A 3D U-net is trained to predict 3D affinities by the MALIS approach. Experiments on multiple datasets demonstrates the strength and robustness of the proposed method for anisotropic EM segmentation.

}, url = {https://arxiv.org/abs/1707.08935v2}, author = {Toufiq Parag and Fabian Tschopp and William Grisaitis and Srinivas C. Turaga and Xuewen Zhang and Brian Matejek and Lee Kamentsky and Jeff W. Lichtman and Hanspeter Pfister} } @article {65893, title = {Antibodies to biotin enable large-scale detection of biotinylation sites on proteins}, journal = {Nature Methods}, volume = {14}, year = {2017}, month = {Jan-12-2017}, pages = {1167 - 1170}, abstract = {

Although purification of biotinylated molecules is highly efficient, identifying specific sites of biotinylation remains challenging. We show that anti-biotin antibodies enable unprecedented enrichment of biotinylated peptides from complex peptide mixtures. Live-cell proximity labeling using APEX peroxidase followed by anti-biotin enrichment and mass spectrometry yielded over 1,600 biotinylation sites on hundreds of proteins, an increase of more than 30-fold in the number of biotinylation sites identified compared to streptavidin-based enrichment of proteins.

}, issn = {1548-7091}, doi = {10.1038/nmeth.4465}, url = {http://www.nature.com/articles/nmeth.4465http://www.nature.com/doifinder/10.1038/nmeth.4465http://www.nature.com/articles/nmeth.4465.pdfhttp://www.nature.com/articles/nmeth.4465.pdfhttp://www.nature.com/articles/nmeth.4465}, author = {Udeshi, Namrata D and Pedram, Kayvon and Svinkina, Tanya and Fereshetian, Shaunt and Myers, Samuel A and Aygun, Ozan and Krug, Karsten and Clauser, Karl and Ryan, Dominic and Ast, Tslil and Mootha, Vamsi K and Ting, Alice Y and Carr, Steven A} } @article {48645, title = {Building bridges between cellular and molecular structural biology.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Jul 06}, abstract = {

The integration of cellular and molecular structural data is key to understanding the function of macromolecular assemblies and complexes in their in vivo context. Here we report on the outcomes of a workshop that discussed how to integrate structural data from a range of public archives. The workshop identified two main priorities: the development of tools and file formats to support segmentation (that is, the decomposition of a three-dimensional volume into regions that can be associated with defined objects), and the development of tools to support the annotation of biological structures.

}, issn = {2050-084X}, doi = {10.7554/eLife.25835}, author = {Patwardhan, Ardan and Brandt, Robert and Butcher, Sarah J and Collinson, Lucy and Gault, David and Gr{\"u}newald, Kay and Hecksel, Corey and Huiskonen, Juha T and Iudin, Andrii and Jones, Martin L and Korir, Paul K and Koster, Abraham J and Lagerstedt, Ingvar and Lawson, Catherine L and Mastronarde, David and McCormick, Matthew and Parkinson, Helen and Rosenthal, Peter B and Saalfeld, Stephan and Saibil, Helen R and Sarntivijai, Sirarat and Solanes Valero, Irene and Subramaniam, Sriram and Swedlow, Jason R and Tudose, Ilinca and Winn, Martyn and Kleywegt, Gerard J} } @article {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 {48836, title = {Community-based benchmarking improves spike inference from two-photon calcium imaging data.}, journal = {PLoS Computational Biology}, volume = {14}, year = {2017}, month = {2018 May 21}, pages = {e1006157}, abstract = {

In recent years, two-photon calcium imaging has become a standard tool to probe the function of neural circuits and to study computations in neuronal populations. However, the acquired signal is only an indirect measurement of neural activity due to the comparatively slow dynamics of fluorescent calcium indicators. Different algorithms for estimating spike rates from noisy calcium measurements have been proposed in the past, but it is an open question how far performance can be improved. Here, we report the results of the spikefinder challenge, launched to catalyze the development of new spike rate inference algorithms through crowd-sourcing. We present ten of the submitted algorithms which show improved performance compared to previously evaluated methods. Interestingly, the top-performing algorithms are based on a wide range of principles from deep neural networks to generative models, yet provide highly correlated estimates of the neural activity. The competition shows that benchmark challenges can drive algorithmic developments in neuroscience.

}, doi = {10.1371/journal.pcbi.1006157}, author = {Berens, Philipp and Freeman, Jeremy and Deneux, Thomas and Chenkov, Nicolay and McColgan, Thomas and Speiser, Artur and Macke, Jakob H and Turaga, Srinivas C and Mineault, Patrick and Rupprecht, Peter and Gerhard, Stephan and Friedrich, Rainer W and Friedrich, Johannes and Paninski, Liam and Pachitariu, Marius and Harris, Kenneth D and Bolte, Ben and Machado, Timothy A and Ringach, Dario and etal} } @article {48720, title = {The complete connectome of a learning and memory centre in an insect brain.}, journal = {Nature}, volume = {548}, year = {2017}, month = {2017 Aug 09}, pages = {175-182}, abstract = {

Associating stimuli with positive or negative reinforcement is essential for survival, but a complete wiring diagram of a higher-order circuit supporting associative memory has not been previously available. Here we reconstruct one such circuit at synaptic resolution, the Drosophila larval mushroom body. We find that most Kenyon cells integrate random combinations of inputs but that a subset receives stereotyped inputs from single projection neurons. This organization maximizes performance of a model output neuron on a stimulus discrimination task. We also report a novel canonical circuit in each mushroom body compartment with previously unidentified connections: reciprocal Kenyon cell to modulatory neuron connections, modulatory neuron to output neuron connections, and a surprisingly high number of recurrent connections between Kenyon cells. Stereotyped connections found between output neurons could enhance the selection of learned behaviours. The complete circuit map of the mushroom body should guide future functional studies of this learning and memory centre.

}, issn = {1476-4687}, doi = {10.1038/nature23455}, author = {Eichler, Katharina and Li, Feng and Litwin-Kumar, Ashok and Park, Youngser and Andrade, Ingrid and Schneider-Mizell, Casey M and Saumweber, Timo and Huser, Annina and Eschbach, Claire and Gerber, Bertram and Fetter, Richard D and Truman, James W and Priebe, Carey E and Abbott, L F and Thum, Andreas S and Zlatic, Marta and Cardona, Albert} } @article {48436, title = {The comprehensive connectome of a neural substrate for {\textquoteright}ON{\textquoteright} motion detection in Drosophila.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Apr 22}, abstract = {

Analysing computations in neural circuits often uses simplified models because the actual neuronal implementation is not known. For example, a problem in vision, how the eye detects image motion, has long been analysed using Hassenstein-Reichardt (HR) detector or Barlow-Levick (BL) models. These both simulate motion detection well, but the exact neuronal circuits undertaking these tasks remain elusive. We reconstructed a comprehensive connectome of the circuits of Drosophila{\textquoteright}s motion-sensing T4 cells using a novel EM technique. We uncover complex T4 inputs and reveal that putative excitatory inputs cluster at T4{\textquoteright}s dendrite shafts, while inhibitory inputs localize to the bases. Consistent with our previous study, we reveal that Mi1 and Tm3 cells provide most synaptic contacts onto T4. We are, however, unable to reproduce the spatial offset between these cells reported previously. Our comprehensive connectome reveals complex circuits that include candidate anatomical substrates for both HR and BL types of motion detectors.

}, issn = {2050-084X}, doi = {10.7554/eLife.24394}, author = {Takemura, Shin-ya and Nern, Aljoscha and Chklovskii, Dmitri B and Scheffer, Louis K and Rubin, Gerald M and Meinertzhagen, Ian A} } @article {48658, title = {A connectome of a learning and memory center in the adult Drosophila brain.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Jul 18}, pages = {e26975}, abstract = {

Understanding memory formation, storage and retrieval requires knowledge of the underlying neuronal circuits. In\ Drosophila, the mushroom body (MB) is the major site of associative learning. We reconstructed the morphologies and synaptic connections of all 983 neurons within the three functional units, or compartments, that compose the adult MB{\textquoteright}s α lobe, using a dataset of isotropic 8-nm voxels collected by focused ion-beam milling scanning electron microscopy. We found that Kenyon cells (KCs), whose sparse activity encodes sensory information, each make multiple\ en passant\ synapses to MB output neurons (MBONs) in each compartment. Some MBONs have inputs from all KCs, while others differentially sample sensory modalities. Only six percent of KC\>MBON synapses receive a direct synapse from a dopaminergic neuron (DAN). We identified two unanticipated classes of synapses, KC\>DAN and DAN\>MBON. DAN activation produces a slow depolarization of the MBON in these DAN\>MBON synapses and can weaken memory recall.

}, doi = {10.7554/eLife.26975}, author = {Takemura, Shin-ya and Aso, Yoshinori and Hige, Toshihide and Wong, Allan M and Lu, Zhiyuan and Xu, C Shan and Rivlin, Patricia K and Hess, Harald F and Zhao, Ting and Parag, Toufiq and Berg, Stuart and Huang, Gary and Katz, William T and Olbris, Donald J and Plaza, Stephen M and Umayam, Lowell A and Aniceto, Roxanne and Chang, Lei-Ann and Lauchie, Shirley and et al} } @article {48413, title = {Deconstructing behavioral neuropharmacology with cellular specificity.}, journal = {Science (New York, N.Y.)}, volume = {356}, year = {2017}, month = {2017 Apr 07}, abstract = {

Behavior has molecular, cellular, and circuit determinants. However, because many proteins are broadly expressed, their acute manipulation within defined cells has been difficult. Here, we combined the speed and molecular specificity of pharmacology with the cell type specificity of genetic tools. DART (drugs acutely restricted by tethering) is a technique that rapidly localizes drugs to the surface of defined cells, without prior modification of the native target. We first developed an AMPAR antagonist DART, with validation in cultured neuronal assays, in slices of mouse dorsal striatum, and in behaving mice. In parkinsonian animals, motor deficits were causally attributed to AMPARs in indirect spiny projection neurons (iSPNs) and to excess phasic firing of tonically active interneurons (TANs). Together, iSPNs and TANs (i.e., D2 cells) drove akinesia, whereas movement execution deficits reflected the ratio of AMPARs in D2 versus D1 cells. Finally, we designed a muscarinic antagonist DART in one iteration, demonstrating applicability of the method to diverse targets.

}, issn = {1095-9203}, doi = {10.1126/science.aaj2161}, author = {Shields, Brenda C and Kahuno, Elizabeth and Kim, Charles and Apostolides, Pierre F and Brown, Jennifer and Lindo, Sarah and Mensh, Brett D and Dudman, Joshua T and Lavis, Luke D and Tadross, Michael R} } @article {65780, title = {Discovery of chemoautotrophic symbiosis in the giant shipworm Kuphus polythalamia (Bivalvia: Teredinidae) extends wooden-steps theory}, journal = {Proceedings of the National Academy of Sciences}, volume = {114}, year = {2017}, month = {05/2017}, pages = {E3652{\textendash}E3658}, abstract = {

Certain marine invertebrates harbor chemosynthetic bacterial symbionts, giving them the remarkable ability to consume inorganic chemicals such as hydrogen sulfide (H2S) rather than organic matter as food. These chemosynthetic animals are found near geochemical (e.g., hydrothermal vents) or biological (e.g., decaying wood or large animal carcasses) sources of H2S on the seafloor. Although many such symbioses have been discovered, little is known about how or where they originated. Here, we demonstrate a new chemosynthetic symbiosis in the giant teredinid bivalve (shipworm) Kuphus polythalamia and show that this symbiosis arose in a wood-eating ancestor via the displacement of ancestral cellulolytic symbionts by sulfur-oxidizing invaders. Here, wood served as an evolutionary stepping stone for a dramatic transition from heterotrophy to chemoautotrophy.The {\textquotedblleft}wooden-steps{\textquotedblright} hypothesis [Distel DL, et al. (2000) Nature 403:725{\textendash}726] proposed that large chemosynthetic mussels found at deep-sea hydrothermal vents descend from much smaller species associated with sunken wood and other organic deposits, and that the endosymbionts of these progenitors made use of hydrogen sulfide from biogenic sources (e.g., decaying wood) rather than from vent fluids. Here, we show that wood has served not only as a stepping stone between habitats but also as a bridge between heterotrophic and chemoautotrophic symbiosis for the giant mud-boring bivalve Kuphus polythalamia. This rare and enigmatic species, which achieves the greatest length of any extant bivalve, is the only described member of the wood-boring bivalve family Teredinidae (shipworms) that burrows in marine sediments rather than wood. We show that K. polythalamia harbors sulfur-oxidizing chemoautotrophic (thioautotrophic) bacteria instead of the cellulolytic symbionts that allow other shipworm species to consume wood as food. The characteristics of its symbionts, its phylogenetic position within Teredinidae, the reduction of its digestive system by comparison with other family members, and the loss of morphological features associated with wood digestion indicate that K. polythalamia is a chemoautotrophic bivalve descended from wood-feeding (xylotrophic) ancestors. This is an example in which a chemoautotrophic endosymbiosis arose by displacement of an ancestral heterotrophic symbiosis and a report of pure culture of a thioautotrophic endosymbiont.

}, issn = {0027-8424}, doi = {10.1073/pnas.1620470114}, url = {https://www.pnas.org/content/114/18/E3652}, author = {Distel, Daniel L. and Altamia, Marvin A. and Lin, Zhenjian and Shipway, J. Reuben and Han, Andrew and Forteza, Imelda and Antemano, Rowena and Limbaco, Ma. Gwen J. Pe{\~n}aflor and Tebo, Alison G. and Dechavez, Rande and Albano, Julie and Rosenberg, Gary and Concepcion, Gisela P. and Schmidt, Eric W. and Haygood, Margo G.} } @article {48983, title = {Divergent connectivity of homologous command-like neurons mediates segment-specific touch responses in Drosophila.}, journal = {Neuron}, volume = {96}, year = {2017}, month = {2017 Dec 20}, pages = {1373-87}, abstract = {

Animals adaptively respond to a tactile stimulus by choosing an ethologically relevant behavior depending on the location of the stimuli. Here, we investigate how somatosensory inputs on different body segments are linked to distinct motor outputs in Drosophila larvae. Larvae escape by backward locomotion when touched on the head, while they crawl forward when touched on the tail. We identify a class of segmentally repeated second-order somatosensory interneurons, that we named Wave, whose activation in anterior and posterior segments elicit backward and forward locomotion, respectively. Anterior and posterior Wave neurons extend their dendrites in opposite directions to receive somatosensory inputs from the head and tail, respectively. Downstream of anterior Wave neurons, we identify premotor circuits including the neuron A03a5, which together with Wave, is necessary for the backward locomotion touch response. Thus, Wave neurons match their receptive field to appropriate motor programs by participating in different circuits in different segments.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2017.10.030}, author = {Takagi, Suguru and Cocanougher, Benjamin Thomas and Niki, Sawako and Miyamoto, Dohjin and Kohsaka, Hiroshi and Kazama, Hokto and Fetter, Richard Doty and Truman, James William and Zlatic, Marta and Cardona, Albert and Nose, Akinao} } @article {48416, title = {Diverse protocols for correlative super-resolution fluorescence imaging and electron microscopy of chemically fixed samples.}, journal = {Nature Protocols}, volume = {12}, year = {2017}, month = {2017 May}, pages = {916-946}, abstract = {

Our groups have recently developed related approaches for sample preparation for super-resolution imaging within endogenous cellular environments using correlative light and electron microscopy (CLEM). Four distinct techniques for preparing and acquiring super-resolution CLEM data sets for aldehyde-fixed specimens are provided, including Tokuyasu cryosectioning, whole-cell mount, cell unroofing and platinum replication, and resin embedding and sectioning. The choice of the best protocol for a given application depends on a number of criteria that are discussed in detail. Tokuyasu cryosectioning is relatively rapid but is limited to small, delicate specimens. Whole-cell mount has the simplest sample preparation but is restricted to surface structures. Cell unroofing and platinum replication creates high-contrast, 3D images of the cytoplasmic surface of the plasma membrane but is more challenging than whole-cell mount. Resin embedding permits serial sectioning of large samples but is limited to osmium-resistant probes, and is technically difficult. Expected results from these protocols include super-resolution localization (\~{}10-50 nm) of fluorescent targets within the context of electron microscopy ultrastructure, which can help address cell biological questions. These protocols can be completed in 2-7 d, are compatible with a number of super-resolution imaging protocols, and are broadly applicable across biology.

}, issn = {1750-2799}, doi = {10.1038/nprot.2017.017}, author = {Kopek, Benjamin G and Paez-Segala, Maria G and Shtengel, Gleb and Sochacki, Kem A and Sun, Mei G and Wang, Yalin and Xu, C Shan and Van Engelenburg, Schuyler B and Taraska, Justin W and Looger, Loren L and Hess, Harald F} } @article {65095, title = {Dual near-Infrared two-photon microscopy for deep-tissue dopamine nanosensor imaging.}, journal = {Advanced Functional Materials}, volume = {27}, year = {2017}, month = {2017 August 15}, pages = {1702112}, abstract = {

A key limitation for achieving deep imaging in biological structures lies in photon absorption and scattering leading to attenuation of fluorescence. In particular, neurotransmitter imaging is challenging in the biologically relevant context of the intact brain for which photons must traverse the cranium, skin, and bone. Thus, fluorescence imaging is limited to the surface cortical layers of the brain, only achievable with craniotomy. Herein, this study describes optimal excitation and emission wavelengths for through-cranium imaging, and demonstrates that near-infrared emissive nanosensors can be photoexcited using a two-photon 1560 nm excitation source. Dopamine-sensitive nanosensors can undergo two-photon excitation, and provide chirality-dependent responses selective for dopamine with fluorescent turn-on responses varying between 20\% and 350\%. The two-photon absorption cross-section and quantum yield of dopamine nanosensors are further calculated, and a two-photon power law relationship for the nanosensor excitation process is confirmed. Finally, the improved image quality of the nanosensors embedded 2-mm-deep into a brain-mimetic tissue phantom is shown, whereby one-photon excitation yields 42\% scattering, in contrast to 4\% scattering when the same object is imaged under two-photon excitation. The approach overcomes traditional limitations in deep-tissue fluorescence microscopy, and can enable neurotransmitter imaging in the biologically relevant milieu of the intact and living brain.

}, doi = {10.1002/adfm.v27.3910.1002/adfm.201702112}, url = {http://doi.wiley.com/10.1002/adfm.v27.39http://doi.wiley.com/10.1002/adfm.201702112https://onlinelibrary.wiley.com/doi/full/10.1002/adfm.201702112https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002\%2Fadfm.201702112}, author = {Bonis-O{\textquoteright}Donnell, Jackson T. Del and Page, Ralph H. and Beyene, Abraham G. and Tindall, Eric G. and McFarlane, Ian R. and Landry, Markita P.} } @article {48859, title = {A dynamic interplay of enhancer elements regulates Klf4 expression in na{\"\i}ve pluripotency.}, journal = {Genes \& Development}, volume = {31}, year = {2017}, month = {2017 Sep 01}, pages = {1795-1808}, abstract = {

Transcription factor (TF)-directed enhanceosome assembly constitutes a fundamental regulatory mechanism driving spatiotemporal gene expression programs during animal development. Despite decades of study, we know little about the dynamics or order of events animating TF assembly at cis-regulatory elements in living cells and the long-range molecular "dialog" between enhancers and promoters. Here, combining genetic, genomic, and imaging approaches, we characterize a complex long-range enhancer cluster governing Kr{\"u}ppel-like factor 4 (Klf4) expression in na{\"\i}ve pluripotency. Genome editing by CRISPR/Cas9 revealed that OCT4 and SOX2 safeguard an accessible chromatin neighborhood to assist the binding of other TFs/cofactors to the enhancer. Single-molecule live-cell imaging uncovered that two na{\"\i}ve pluripotency TFs, STAT3 and ESRRB, interrogate chromatin in a highly dynamic manner, in which SOX2 promotes ESRRB target search and chromatin-binding dynamics through a direct protein-tethering mechanism. Together, our results support a highly dynamic yet intrinsically ordered enhanceosome assembly to maintain the finely balanced transcription program underlying na{\"\i}ve pluripotency.

}, issn = {1549-5477}, doi = {10.1101/gad.303321.117}, author = {Xie, Liangqi and Torigoe, Sharon E and Xiao, Jifang and Mai, Daniel H and Li, Li and Davis, Fred P and Dong, Peng and Marie-Nelly, Herve and Grimm, Jonathan and Lavis, Luke and Darzacq, Xavier and Cattoglio, Claudia and Liu, Zhe and Tjian, Robert} } @proceedings {48802, title = {Extracting low-dimensional dynamics from multiple large-scale neural population recordings by learning to predict correlations.}, year = {2017}, month = {2017 Dec 04}, abstract = {

A powerful approach for understanding neural population dynamics is to extract low-dimensional trajectories from population recordings using dimensionality reduction methods. Current approaches for dimensionality reduction on neural data are limited to single population recordings, and can not identify dynamics embedded across multiple measurements. We propose an approach for extracting low-dimensional dynamics from multiple, sequential recordings. Our algorithm scales to data comprising millions of observed dimensions, making it possible to access dynamics distributed across large populations or multiple brain areas. Building on subspace-identification approaches for dynamical systems, we perform parameter estimation by minimizing a moment-matching objective using a scalable stochastic gradient descent algorithm: The model is optimized to predict temporal covariations across neurons and across time. We show how this approach naturally handles missing data and multiple partial recordings, and can identify dynamics and predict correlations even in the presence of severe subsampling and small overlap between recordings. We demonstrate the effectiveness of the approach both on simulated data and a whole-brain larval zebrafish imaging dataset.\ 

}, url = {http://www.mackelab.org/pubs/Nonnenmacher_Turaga_NIPS_2017.pdf}, author = {Nonnenmacher, Marcel and Turaga, Srinivas C and Macke, Jakob H} } @proceedings {48805, title = {Fast amortized inference of neural activity from calcium imaging data with variational autoencoders.}, year = {2017}, month = {2017 Dec 04}, abstract = {

Calcium imaging permits optical measurement of neural activity. Since intracellular calcium concentration is an indirect measurement of neural activity, computational tools are necessary to infer the true underlying spiking activity from fluorescence measurements. Bayesian model inversion can be used to solve this problem, but typically requires either computationally expensive MCMC sampling, or faster but approximate maximum-a-posteriori optimization. Here, we introduce a flexible algorithmic framework for fast, efficient and accurate extraction of neural spikes from imaging data. Using the framework of variational autoencoders, we propose to amortize inference by training a deep neural network to perform model inversion efficiently. The recognition network is trained to produce samples from the posterior distribution over spike trains. Once trained, performing inference amounts to a fast single forward pass through the network, without the need for iterative optimization or sampling. We show that amortization can be applied flexibly to a wide range of nonlinear generative models and significantly improves upon the state of the art in computation time, while achieving competitive accuracy. Our framework is also able to represent posterior distributions over spike-trains. We demonstrate the generality of our method by proposing the first probabilistic approach for separating backpropagating action potentials from putative synaptic inputs in calcium imaging of dendritic spines.\ 

}, url = {http://www.mackelab.org/pubs/Speiser_NIPS_2017.pdf}, author = {Speiser, Artur and Yan, Jinyao and Archer, Evan and Buesing, Lars and Turaga, Srinivas C and Macke, Jakob H} } @article {48204, title = {A fluorescent Hsp90 probe demonstrates the unique association between extracellular Hsp90 and malignancy in vivo.}, journal = {ACS chemical biology}, year = {2017}, month = {2017 Jan 19}, abstract = {

Extracellular expression of heat shock protein 90 (eHsp90) by tumor cells is correlated with malignancy. Development of small molecule probes that can detect eHsp90 in vivo may therefore have utility in the early detection of malignancy. We synthesized a cell impermeable far-red fluorophore-tagged Hsp90 inhibitor to target eHsp90 in vivo. High resolution confocal and lattice light sheet microscopy show that probe-bound eHsp90 accumulates in punctate structures on the plasma membrane of breast tumor cells and is actively internalized. The extent of internalization correlates with tumor cell aggressiveness, and this process can be induced in benign cells by over-expressing p110HER2. Whole body cryoslicing, imaging and histology of flank and spontaneous tumor-bearing mice strongly suggests that eHsp90 expression and internalization is a phenomenon unique to tumor cells in vivo and may provide an {\textquoteright}Achilles heel{\textquoteright} for the early diagnosis of metastatic disease and targeted drug delivery.

}, issn = {1554-8937}, doi = {10.1021/acschembio.7b00006}, author = {Crowe, Lauren B and Hughes, Philip F and Alcorta, David A and Osada, Takuya and Smith, Aaron P and Totzke, Juliane and Loiselle, David R and Lutz, Isaac D and Gargesha, Madhusudhana and Roy, Debasish and Roques, Jose and Darr, David and Lyerly, H Kim and Spector, Neil L and Haystead, Timothy Aj} } @article {65777, title = {Fluorogenic Labeling Strategies for Biological Imaging}, journal = {International Journal of Molecular Sciences}, volume = {18}, year = {2017}, month = {07/2017}, pages = {1473 {\textendash} 11}, abstract = {

The spatiotemporal fluorescence imaging of biological processes requires effective tools to label intracellular biomolecules in living systems. This review presents a brief overview of recent labeling strategies that permits one to make protein and RNA strongly fluorescent using synthetic fluorogenic probes. Genetically encoded tags selectively binding the exogenously applied molecules ensure high labeling selectivity, while high imaging contrast is achieved using fluorogenic chromophores that are fluorescent only when bound to their cognate tag, and are otherwise dark. Beyond avoiding the need for removal of unbound synthetic dyes, these approaches allow the development of sophisticated imaging assays, and open exciting prospects for advanced imaging, particularly for multiplexed imaging and super-resolution microscopy.

}, doi = {10.3390/ijms18071473}, url = {http://www.mdpi.com/1422-0067/18/7/1473}, author = {Li, Chenge and Tebo, Alison G. and Gautier, Arnaud} } @article {48157, title = {A fully synthetic transcriptional platform for a multicellular eukaryote.}, journal = {Cell Reports}, volume = {18}, year = {2017}, month = {2017 Jan 03}, pages = {287-296}, abstract = {

Regions of genomic DNA called enhancers encode binding sites for transcription factor proteins. Binding of activators and repressors increase and reduce transcription, respectively, but it is not understood how combinations of activators and repressors generate precise patterns of transcription during development. Here, we explore this problem using\ a fully synthetic transcriptional platform in Drosophila consisting of engineered transcription factor gradients and artificial enhancers. We found that binding sites for a transcription factor that makes DNA accessible are required together with binding sites for transcriptional activators to produce a functional enhancer. Only in this context can changes in the number of activator binding sites mediate quantitative control of transcription. Using an engineered transcriptional repressor gradient, we demonstrate that overlapping repressor and activator binding sites provide more robust repression and sharper expression boundaries than non-overlapping sites. This may explain why this common motif is observed in many developmental enhancers.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2016.12.025}, author = {Crocker, Justin and Tsai, Albert and Stern, David L} } @article {48733, title = {General synthetic method for Si-Fluoresceins and Si-Rhodamines.}, journal = {ACS Central Science}, volume = {3}, year = {2017}, month = {2017 Aug 09}, pages = {975-85}, abstract = {

The century-old fluoresceins and rhodamines persist as flexible scaffolds for fluorescent and fluorogenic compounds. Extensive exploration of these xanthene dyes has yielded general structure{\textendash}activity relationships where the development of new probes is limited only by imagination and organic chemistry. In particular, replacement of the xanthene oxygen with silicon has resulted in new red-shifted Si-fluoresceins and Si-rhodamines, whose high brightness and photostability enable advanced imaging experiments. Nevertheless, efforts to tune the chemical and spectral properties of these dyes have been hindered by difficult synthetic routes. Here, we report a general strategy for the efficient preparation of Si-fluoresceins and Si-rhodamines from readily synthesized bis(2-bromophenyl)silane intermediates. These dibromides undergo metal/bromide exchange to give bis-aryllithium or bis(aryl Grignard) intermediates, which can then add to anhydride or ester electrophiles to afford a variety of Si-xanthenes. This strategy enabled efficient (3{\textendash}5 step) syntheses of known and novel Si-fluoresceins, Si-rhodamines, and related dye structures. In particular, we discovered that previously inaccessible tetrafluorination of the bottom aryl ring of the Si-rhodamines resulted in dyes with improved visible absorbance in solution, and a convenient derivatization through fluoride-thiol substitution. This modular, divergent synthetic method will expand the palette of accessible xanthenoid dyes across the visible spectrum, thereby pushing further the frontiers of biological imaging.

}, doi = {10.1021/acscentsci.7b00247}, author = {Grimm, Jonathan B and Brown, Timothy A and Tkachuk, Ariana N and Lavis, Luke D} } @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 {65886, title = {Homeostatic plasticity shapes the visual system{\textquoteright}s first synapse}, journal = {Nature Communications}, volume = {8}, year = {2017}, month = {10/2017}, abstract = {

Vision in dim light depends on synapses between rods and rod bipolar cells (RBCs). Here, we find that these synapses exist in multiple configurations, in which single release sites of rods are apposed by one to three postsynaptic densities (PSDs). Single RBCs often form multiple PSDs with one rod; and neighboring RBCs share ~13\% of their inputs. Rod-RBC synapses develop while ~7\% of RBCs undergo programmed cell death (PCD). Although PCD is common throughout the nervous system, its influences on circuit development and function are not well understood. We generate mice in which ~53 and ~93\% of RBCs, respectively, are removed during development. In these mice, dendrites of the remaining RBCs expand in graded fashion independent of light-evoked input. As RBC dendrites expand, they form fewer multi-PSD contacts with rods. Electrophysiological recordings indicate that this homeostatic co-regulation of neurite and synapse development preserves retinal function in dim light.

}, doi = {10.1038/s41467-017-01332-7}, url = {http://www.nature.com/articles/s41467-017-01332-7http://www.nature.com/articles/s41467-017-01332-7.pdfhttp://www.nature.com/articles/s41467-017-01332-7.pdfhttp://www.nature.com/articles/s41467-017-01332-7}, author = {Johnson, Robert E. and Tien, Nai-Wen and Shen, Ning and Pearson, James T. and Soto, Florentina and Kerschensteiner, Daniel} } @article {65773, title = {Intramolecular Photogeneration of a Tyrosine Radical in a Designed Protein}, journal = {ChemPhotoChem}, volume = {1}, year = {2017}, month = {02/2017}, pages = {89 {\textendash} 92}, abstract = {

Long-distance biological electron transfer occurs through a hopping mechanism and often involves tyrosine as a high potential intermediate, for example in the early charge separation steps during photosynthesis. Protein design allows for the development of minimal systems to study the underlying principles of complex systems. Herein, we report the development of the first ruthenium-linked designed protein for the photogeneration of a tyrosine radical by intramolecular electron transfer.

}, doi = {10.1002/cptc.201600044}, url = {https://chemistry-europe.onlinelibrary.wiley.com/doi/abs/10.1002/cptc.201600044}, author = {Tebo, Alison G and Quaranta, Annamaria and Herrero, Christian and Pecoraro, Vincent L and Aukauloo, Ally} } @article {48219, title = {Long-range self-organization of cytoskeletal myosin II filament stacks.}, journal = {Nature Cell Biology}, volume = {19}, year = {2017}, month = {2017 Jan 23}, pages = {133-41}, abstract = {

Although myosin II filaments are known to exist in non-muscle cells, their dynamics and organization are incompletely understood. Here, we combined structured illumination microscopy with pharmacological and genetic perturbations, to study the process of actomyosin cytoskeleton self-organization into arcs and stress fibres. A striking feature of the myosin II filament organization was their {\textquoteright}registered{\textquoteright} alignment into stacks, spanning up to several micrometres in the direction orthogonal to the parallel actin bundles. While turnover of individual myosin II filaments was fast (characteristic half-life time 60 s) and independent of actin filament turnover, the process of stack formation lasted a longer time (in the range of several minutes) and required myosin II contractility, as well as actin filament assembly/disassembly and crosslinking (dependent on formin Fmnl3, cofilin1 and α-actinin-4). Furthermore, myosin filament stack formation involved long-range movements of individual myosin filaments towards each other suggesting the existence of attractive forces between myosin II filaments. These forces, possibly transmitted via mechanical deformations of the intervening actin filament network, may in turn remodel the actomyosin cytoskeleton and drive its self-organization.

}, issn = {1476-4679}, doi = {10.1038/ncb3466}, author = {Hu, Shiqiong and Dasbiswas, Kinjal and Guo, Zhenhuan and Tee, Yee-Han and Thiagarajan, Visalatchi and Hersen, Pascal and Chew, Teng-Leong and Safran, Samuel A and Zaidel-Bar, Ronen and Bershadsky, Alexander D} } @article {48560, title = {Mechanisms underlying a thalamocortical transformation during active tactile sensation.}, journal = {PLoS Computational Biology}, volume = {13}, year = {2017}, month = {2017 Jun 07}, pages = {e1005576}, abstract = {

During active somatosensation, neural signals expected from movement of the sensors are suppressed in the cortex, whereas information related to touch is enhanced. This tactile suppression underlies low-noise encoding of relevant tactile features and the brain{\textquoteright}s ability to make fine tactile discriminations. Layer (L) 4 excitatory neurons in the barrel cortex, the major target of the somatosensory thalamus (VPM), respond to touch, but have low spike rates and low sensitivity to the movement of whiskers. Most neurons in VPM respond to touch and also show an increase in spike rate with whisker movement. Therefore, signals related to self-movement are suppressed in L4. Fast-spiking (FS) interneurons in L4 show similar dynamics to VPM neurons. Stimulation of halorhodopsin in FS interneurons causes a reduction in FS neuron activity and an increase in L4 excitatory neuron activity. This decrease of activity of L4 FS neurons contradicts the "paradoxical effect" predicted in networks stabilized by inhibition and in strongly-coupled networks. To explain these observations, we constructed a model of the L4 circuit, with connectivity constrained by in vitro measurements. The model explores the various synaptic conductance strengths for which L4 FS neurons actively suppress baseline and movement-related activity in layer 4 excitatory neurons. Feedforward inhibition, in concert with recurrent intracortical circuitry, produces tactile suppression. Synaptic delays in feedforward inhibition allow transmission of temporally brief volleys of activity associated with touch. Our model provides a mechanistic explanation of a behavior-related computation implemented by the thalamocortical circuit.

}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1005576}, author = {Gutnisky, Diego Adrian and Yu, Jianing and Hires, Samuel Andrew and To, Minh-Son and Bale, Michael and Svoboda, Karel and Golomb, David} } @article {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 {48557, title = {Memory retrieval from first principles.}, journal = {Neuron}, volume = {94}, year = {2017}, month = {2017 Jun 07}, pages = {1027-1032}, abstract = {

The dilemma that neurotheorists face is that (1) detailed biophysical models that can be constrained by direct measurements, while being of great importance, offer no immediate insights into cognitive processes in the brain, and (2) high-level abstract cognitive models, on the other hand, while relevant for understanding behavior, are largely detached from neuronal processes and typically have many free, experimentally unconstrained parameters that have to be tuned to a particular data set and, hence, cannot be readily generalized to other experimental paradigms. In this contribution, we propose a set of "first principles" for neurally inspired cognitive modeling of memory retrieval that has no biologically unconstrained parameters and can be analyzed mathematically both at neuronal and cognitive levels. We apply this framework to the classical cognitive paradigm of free recall. We show that the resulting model accounts well for puzzling behavioral data on human participants and makes predictions that could potentially be tested with neurophysiological recording techniques.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2017.03.048}, author = {Katkov, M and Romani, S and Tsodyks, M} } @proceedings {48942, title = {Model-based Bayesian inference of neural activity and connectivity from all-optical interrogation of a neural circuit.}, year = {2017}, month = {2017 Dec 04}, abstract = {

Population activity measurement by calcium imaging can be combined with cellular resolution optogenetic activity perturbations to enable the mapping of neural connectivity in vivo. This requires accurate inference of perturbed and unperturbed neural activity from calcium imaging measurements, which are noisy and indirect, and can also be contaminated by photostimulation artifacts. We have developed a new fully Bayesian approach to jointly inferring spiking activity and neural connectivity from in vivo all-optical perturbation experiments. In contrast to standard approaches that perform spike inference and analysis in two separate maximum-likelihood phases, our joint model is able to propagate uncertainty in spike inference to the inference of connectivity and vice versa. We use the framework of variational autoencoders to model spiking activity using discrete latent variables, low-dimensional latent common input, and sparse spike-and-slab generalized linear coupling between neurons. Additionally, we model two properties of the optogenetic perturbation: off-target photostimulation and photostimulation transients. Our joint model includes at least two sets of discrete random variables; to avoid the dramatic slowdown typically caused by being unable to differentiate such variables, we introduce two strategies that have not, to our knowledge, been used with variational autoencoders. Using this model, we were able to fit models on 30 minutes of data in just 10 minutes. We performed an all-optical circuit mapping experiment in primary visual cortex of the awake mouse, and use our approach to predict neural connectivity between excitatory neurons in layer 2/3. Predicted connectivity is sparse and consistent with known correlations with stimulus tuning, spontaneous correlation and distance.

}, url = {https://papers.nips.cc/paper/6940-model-based-bayesian-inference-of-neural-activity-and-connectivity-from-all-optical-interrogation-of-a-neural-circuit}, author = {Aitchison, Laurence and Russell, Lloyd and Packer, Adam M and Yan, Jinyao and Castonguaye, Philippe and H{\"a}usser, Michael and Turaga, Srinivas C} } @conference {67221, title = {Model-based Bayesian inference of neural activity and connectivity from all-optical interrogation of a neural circuit}, booktitle = {Advances in Neural Information Processing Systems}, year = {2017}, publisher = {Curran Associates, Inc.}, organization = {Curran Associates, Inc.}, abstract = {

Population activity measurement by calcium imaging can be combined with cellular resolution optogenetic activity perturbations to enable the mapping of neural connectivity in vivo. This requires accurate inference of perturbed and unperturbed neural activity from calcium imaging measurements, which are noisy and indirect, and can also be contaminated by photostimulation artifacts. We have developed a new fully Bayesian approach to jointly inferring spiking activity and neural connectivity from in vivo all-optical perturbation experiments. In contrast to standard approaches that perform spike inference and analysis in two separate maximum-likelihood phases, our joint model is able to propagate uncertainty in spike inference to the inference of connectivity and vice versa. We use the framework of variational autoencoders to model spiking activity using discrete latent variables, low-dimensional latent common input, and sparse spike-and-slab generalized linear coupling between neurons. Additionally, we model two properties of the optogenetic perturbation: off-target photostimulation and photostimulation transients. Using this model, we were able to fit models on 30 minutes of data in just 10 minutes. We performed an all-optical circuit mapping experiment in primary visual cortex of the awake mouse, and use our approach to predict neural connectivity between excitatory neurons in layer 2/3. Predicted connectivity is sparse and consistent with known correlations with stimulus tuning, spontaneous correlation and distance.

}, url = {https://discovery.ucl.ac.uk/id/eprint/10072143/}, author = {Aitchison, Laurence and Russell, Lloyd and Packer, Adam M and Yan, Jinyao and Castonguay, Philippe and H{\"a}usser, Michael and Turaga, Srinivas C}, editor = {I. Guyon and U. V. Luxburg and S. Bengio and H. Wallach and R. Fergus and S. Vishwanathan and R. Garnett} } @article {48595, title = {mRNA quantification using single-molecule FISH in Drosophila embryos.}, journal = {Nature Protocols}, volume = {12}, year = {2017}, month = {2017 Jul}, pages = {1326-1348}, abstract = {

Spatial information is critical to the interrogation of developmental and tissue-level regulation of gene expression. However, this information is usually lost when global mRNA levels from tissues are measured using reverse transcriptase PCR, microarray analysis or high-throughput sequencing. By contrast, single-molecule fluorescence in situ hybridization (smFISH) preserves the spatial information of the cellular mRNA content with subcellular resolution within tissues. Here we describe an smFISH protocol that allows for the quantification of single mRNAs in Drosophila embryos, using commercially available smFISH probes (e.g., short fluorescently labeled DNA oligonucleotides) in combination with wide-field epifluorescence, confocal or instant structured illumination microscopy (iSIM, a super-resolution imaging approach) and a spot-detection algorithm. Fixed Drosophila embryos are hybridized in solution with a mixture of smFISH probes, mounted onto coverslips and imaged in 3D. Individual fluorescently labeled mRNAs are then localized within tissues and counted using spot-detection software to generate quantitative, spatially resolved gene expression data sets. With minimum guidance, a graduate student can successfully implement this protocol. The smFISH procedure described here can be completed in 4-5 d.

}, issn = {1750-2799}, doi = {10.1038/nprot.2017.030}, author = {Trcek, Tatjana and Lionnet, Timoth{\'e}e and Shroff, Hari and Lehmann, Ruth} } @article {48278, title = {Multi-view light-sheet imaging and tracking with the MaMuT software reveals the cell lineage of a direct developing arthropod limb.}, journal = {eLife}, volume = {7}, year = {2017}, month = {2018 Mar 29}, pages = {e34410}, abstract = {

During development, coordinated cell behaviors orchestrate tissue and organ morphogenesis. Detailed descriptions of cell lineages and behaviors provide a powerful framework to elucidate the mechanisms of morphogenesis. To study the cellular basis of limb development, we imaged transgenic fluorescently-labeled embryos from the crustacean Parhyale hawaiensis with multi-view light-sheet microscopy at high spatiotemporal resolution over several days of embryogenesis. The cell lineage of outgrowing thoracic limbs was reconstructed at single-cell resolution with new software called Massive Multi-view Tracker (MaMuT). In silico clonal analyses suggested that the early limb primordium becomes subdivided into anterior-posterior and dorsal-ventral compartments whose boundaries intersect at the distal tip of the growing limb. Limb-bud formation is associated with spatial modulation of cell proliferation, while limb elongation is also driven by preferential orientation of cell divisions along the proximal-distal growth axis. Cellular reconstructions were predictive of the expression patterns of limb development genes including the BMP morphogen Decapentaplegic.

}, doi = {10.7554/eLife.34410}, author = {Wolff, Carsten and Tinevez, Jean-Yves and Pietzsch, Tobias and Stamataki, Evangelia and Harich, Benjamin and Guignard, Leo and Preibisch, Stephan and Shorte, Spencer and Keller, Philipp J and Tomancak, Pavel and Pavlopoulos, Anastasios} } @article {48731, title = {Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation.}, journal = {Molecular Cell}, volume = {67}, year = {2017}, month = {2017 Jul 28}, pages = {566-78}, abstract = {

50 years ago, Vincent Allfrey and colleagues discovered that lymphocyte activation triggers massive acetylation of chromatin. However, the molecular mechanisms driving epigenetic accessibility are still unknown. We here show that stimulated lymphocytes decondense chromatin by three differentially regulated steps. First, chromatin is repositioned away from the nuclear periphery in response to global acetylation. Second, histone nanodomain clusters decompact into mononucleosome fibers through a mechanism that requires Myc and continual energy input. Single-molecule imaging shows that this step lowers transcription factor residence time and non-specific collisions during sampling for DNA targets. Third, chromatin interactions shift from long range to predominantly short range, and CTCF-mediated loops and contact domains double in numbers. This architectural change facilitates cognate promoter-enhancer contacts and also requires Myc and continual ATP production. Our results thus define the nature and transcriptional impact of chromatin decondensation and reveal an unexpected role for Myc in the establishment of nuclear topology in mammalian cells.

}, issn = {1097-4164}, doi = {10.1016/j.molcel.2017.07.013}, author = {Kieffer-Kwon, Kyong-Rim and Nimura, Keisuke and Rao, Suhas S P and Xu, Jianliang and Jung, Seolkyoung and Pekowska, Aleksandra and Dose, Marei and Stevens, Evan and Mathe, Ewy and Dong, Peng and Huang, Su-Chen and Ricci, Maria Aurelia and Baranello, Laura and Zheng, Ying and Ardori, Francesco Tomassoni and Resch, Wolfgang and Stavreva, Diana and Nelson, Steevenson and McAndrew, Michael and Casellas, Adriel and Finn, Elizabeth and Gregory, Charles and St Hilaire, Brian Glenn and Johnson, Steven M and Dubois, Wendy and Cosma, Maria Pia and Batchelor, Eric and Levens, David and Phair, Robert D and Misteli, Tom and Tessarollo, Lino and Hager, Gordon and Lakadamyali, Melike and Liu, Zhe and Floer, Monique and Shroff, Hari and Aiden, Erez Lieberman and Casellas, Rafael} } @article {48713, title = {Near-atomic resolution cryoelectron microscopy structure of the 30-fold homooligomeric SpoIIIAG channel essential to spore formation in Bacillus subtilis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, year = {2017}, month = {2017 Aug 07}, abstract = {

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

}, issn = {1091-6490}, doi = {10.1073/pnas.1704310114}, author = {Zeytuni, Natalie and Hong, Chuan and Flanagan, Kelly A and Worrall, Liam J and Theiltges, Kate A and Vuckovic, Marija and Huang, Rick K and Massoni, Shawn C and Camp, Amy H and Yu, Zhiheng and Strynadka, Natalie C} } @article {48920, title = {Nuclear microenvironments modulate transcription from low-affinity enhancers.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Nov 02}, abstract = {

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

}, issn = {2050-084X}, doi = {10.7554/eLife.28975}, author = {Tsai, Albert and Muthusamy, Anand K and Alves, Mariana Rp and Lavis, Luke D and Singer, Robert H and Stern, David L and Crocker, Justin} } @article {48642, title = {The Ol1mpiad: concordance of behavioural faculties of stage 1 and stage 3 Drosophila larvae.}, journal = {The Journal of Experimental Biology}, volume = {220}, year = {2017}, month = {2017 Jul 01}, pages = {2452-2475}, abstract = {

Mapping brain function to brain structure is a fundamental task for neuroscience. For such an endeavour, the Drosophila larva is simple enough to be tractable, yet complex enough to be interesting. It features about 10,000 neurons and is capable of various taxes, kineses and Pavlovian conditioning. All its neurons are currently being mapped into a light-microscopical atlas, and Gal4 strains are being generated to experimentally access neurons one at a time. In addition, an electron microscopic reconstruction of its nervous system seems within reach. Notably, this electron microscope-based connectome is being drafted for a stage 1 larva - because stage 1 larvae are much smaller than stage 3 larvae. However, most behaviour analyses have been performed for stage 3 larvae because their larger size makes them easier to handle and observe. It is therefore warranted to either redo the electron microscopic reconstruction for a stage 3 larva or to survey the behavioural faculties of stage 1 larvae. We provide the latter. In a community-based approach we called the Ol1mpiad, we probed stage 1 Drosophila larvae for free locomotion, feeding, responsiveness to substrate vibration, gentle and nociceptive touch, burrowing, olfactory preference and thermotaxis, light avoidance, gustatory choice of various tastants plus odour-taste associative learning, as well as light/dark-electric shock associative learning. Quantitatively, stage 1 larvae show lower scores in most tasks, arguably because of their smaller size and lower speed. Qualitatively, however, stage 1 larvae perform strikingly similar to stage 3 larvae in almost all cases. These results bolster confidence in mapping brain structure and behaviour across developmental stages.

}, issn = {1477-9145}, doi = {10.1242/jeb.156646}, author = {Almeida-Carvalho, Maria J and Berh, Dimitri and Braun, Andreas and Chen, Yi-chun and Eichler, Katharina and Eschbach, Claire and Fritsch, Pauline M J and Gerber, Bertram and Hoyer, Nina and Jiang, Xiaoyi and Kleber, J{\"o}rg and Kl{\"a}mbt, Christian and K{\"o}nig, Christian and Louis, Matthieu and Michels, Birgit and Miroschnikow, Anton and Mirth, Christen and Miura, Daisuke and Niewalda, Thomas and Otto, Nils and Paisios, Emmanouil and Pankratz, Michael J and Petersen, Meike and Ramsperger, Noel and Randel, Nadine and Risse, Benjamin and Saumweber, Timo and Schlegel, Philipp and Schleyer, Michael and Soba, Peter and Sprecher, Simon G and Tanimura, Teiichi and Thum, Andreas S and Toshima, Naoko and Truman, Jim W and Yarali, Ayse and Zlatic, Marta} } @article {48799, title = {Optogenetic control with a photocleavable protein, PhoCl.}, journal = {Nature Methods}, volume = {14}, year = {2017}, month = {2017 Apr}, pages = {391-394}, abstract = {

To expand the range of experiments that are accessible with optogenetics, we developed a photocleavable protein (PhoCl) that spontaneously dissociates into two fragments after violet-light-induced cleavage of a specific bond in the protein backbone. We demonstrated that PhoCl can be used to engineer light-activatable Cre recombinase, Gal4 transcription factor, and a viral protease that in turn was used to activate opening of the large-pore ion channel Pannexin-1.

}, keywords = {Connexins, Directed Molecular Evolution, Green Fluorescent Proteins, HEK293 Cells, HSP90 Heat-Shock Proteins, Humans, Luminescent Proteins, Nerve Tissue Proteins, Nuclear Localization Signals, Optogenetics, Patch-Clamp Techniques, Photochemistry, Protein Engineering, Recombinant Proteins, Viral Nonstructural Proteins}, issn = {1548-7105}, doi = {10.1038/nmeth.4222}, author = {Zhang, Wei and Lohman, Alexander W and Zhuravlova, Yevgeniya and Lu, Xiaocen and Wiens, Matthew D and Hoi, Hiofan and Yaganoglu, Sine and Mohr, Manuel A and Kitova, Elena N and Klassen, John S and Pantazis, Periklis and Thompson, Roger J and Campbell, Robert E} } @article {48847, title = {Organization of the drosophila larval visual circuit.}, journal = {eLife}, year = {2017}, month = {2017 Aug 8}, pages = {e28387}, abstract = {

Visual systems transduce, process and transmit light-dependent environmental cues. Computation of visual features depends on photoreceptor neuron types (PR) present, organization of the eye and wiring of the underlying neural circuit. Here, we describe the circuit architecture of the visual system of\ Drosophila\ larvae by mapping the synaptic wiring diagram and neurotransmitters. By contacting different targets, the two larval PR-subtypes create two converging pathways potentially underlying the computation of ambient light intensity and temporal light changes already within this first visual processing center. Locally processed visual information then signals via dedicated projection interneurons to higher brain areas including the lateral horn and mushroom body. The stratified structure of the larval optic neuropil (LON) suggests common organizational principles with the adult fly and vertebrate visual systems. The complete synaptic wiring diagram of the LON paves the way to understanding how circuits with reduced numerical complexity control wide ranges of behaviors.

}, doi = {10.7554/eLife.28387}, author = {Larderet, Ivan and Fritsch, Pauline M J and Gendre, Nanae and Neagu-Maier, G Larisa and Fetter, Richard D and Schneider-Mizell, Casey M and Truman, James W and Zlatic, Marta and Cardona, Albert and Sprecher, Simon G} } @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 {48535, title = {Perceptually accurate display of two greyscale images as a single colour image.}, journal = {Journal of Microscopy}, year = {2017}, month = {2017 May 30}, abstract = {

Life scientists often desire to display the signal from two different molecular probes as a single colour image, so as to convey information about the probes{\textquoteright} relative concentrations as well as their spatial corelationship. Traditionally, such colour images are created through a merge display, where each greyscale signal is assigned to different channels of an RGB colour image. However, human perception of colour and greyscale intensity is not equivalent. Thus, a merged image display conveys to the typical viewer only a subset of the absolute and relative intensity information present in and between two greyscale images. The Commission Internationale de l{\textquoteright}Eclairage L*a*b* colour space (CIELAB) has been designed to specify colours according to the perceptually defined quantities of hue (perceived colour) and luminosity (perceived brightness). Here, we use the CIELAB colour space to encode two dimensions of information about two greyscale images within these two perceptual dimensions of a single colour image. We term our method a Perceptually Uniform Projection display and show using biological image examples how these displays convey more information about two greyscale signals than comparable RGB colour space-based techniques.

}, issn = {1365-2818}, doi = {10.1111/jmi.12588}, author = {Taylor, A B and Ioannou, M S and Watanabe, T and Hahn, K and Chew, T-L} } @article {67286, title = {Predictive Coding of Novel versus Familiar Stimuli in the Primary Visual Cortex}, journal = {bioRxiv}, year = {2017}, month = {10/2017}, abstract = {

To explore theories of predictive coding, we presented mice with repeated sequences of images with novel images sparsely substituted. Under these conditions, mice could be rapidly trained to lick in response to a novel image, demonstrating a high level of performance on the first day of testing. Using 2-photon calcium imaging to record from layer 2/3 neurons in the primary visual cortex, we found that novel images evoked excess activity in the majority of neurons. When a new stimulus sequence was repeatedly presented, a majority of neurons had similarly elevated activity for the first few presentations, which then decayed to almost zero activity. The decay time of these transient responses was not fixed, but instead scaled with the length of the stimulus sequence. However, at the same time, we also found a small fraction of the neurons within the population (\~2\%) that continued to respond strongly and periodically to the repeated stimulus. Decoding analysis demonstrated that both the transient and sustained responses encoded information about stimulus identity. We conclude that the layer 2/3 population uses a two-channel predictive code: a dense transient code for novel stimuli and a sparse sustained code for familiar stimuli. These results extend and unify existing theories about the nature of predictive neural codes.

}, doi = {10.1101/197608}, url = {https://www.biorxiv.org/content/early/2017/10/03/197608}, author = {Homann, Jan and Koay, Sue Ann and Glidden, Alistair M. and Tank, David W. and Berry, Michael J.} } @article {48787, title = {The role of disulfide bond replacements in analogues of the tarantula toxin ProTx-II and their effects on inhibition of the voltage-gated sodium ion channel Nav1.7.}, journal = {Journal of the American Chemical Society}, volume = {139}, year = {2017}, month = {2017 Sep 07}, pages = {13063-75}, abstract = {

Spider venom toxins, such as Protoxin-II (ProTx-II), have recently received much attention as selective Nav1.7 channel blockers, with potential to be developed as leads for the treatment of chronic nocioceptive pain. ProTx-II is a 30-amino acid peptide with three disulfide bonds that has been reported to adopt a well-defined inhibitory cystine knot (ICK) scaffold structure. Potential drawbacks with such peptides include poor pharmacodynamics and potential scrambling of the disulfide bonds in vivo. In order to address these issues, in the present study we report the solid-phase synthesis of lanthionine-bridged analogues of ProTx-II, in which one of the three disulfide bridges is replaced with a thioether linkage, and evaluate the biological properties of these analogues. We have also investigated the folding and disulfide bridging patterns arising from different methods of oxidation of the linear peptide precursor. Finally, we report the X-ray crystal structure of ProTx-II to atomic resolution; to our knowledge this is the first crystal structure of an ICK spider venom peptide not bound to a substrate.

}, issn = {1520-5126}, doi = {10.1021/jacs.7b06506}, author = {Wright, Zo{\"e} V F and McCarthy, Stephen and Dickman, Rachael and Reyes, Francis E and Sanchez-Martinez, Silvia and Cryar, Adam and Kilford, Ian and Hall, Adrian and Takle, Andrew K and Topf, Maya and Gonen, Tamir and Thalassinos, Konstantinos and Tabor, Alethea B} } @article {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 {48938, title = {Semisynthetic fluorescent pH sensors for imaging exocytosis and endocytosis.}, journal = {Nature Communications}, volume = {8}, year = {2017}, month = {2017 Nov 10}, pages = {1412}, abstract = {

The GFP-based superecliptic pHluorin (SEP) enables detection of exocytosis and endocytosis, but its performance has not been duplicated in red fluorescent protein scaffolds. Here we describe "semisynthetic" pH-sensitive protein conjugates with organic fluorophores, carbofluorescein, and Virginia Orange that match the properties of SEP. Conjugation to genetically encoded self-labeling tags or antibodies allows visualization of both exocytosis and endocytosis, constituting new bright sensors for these key steps of synaptic transmission.

}, issn = {2041-1723}, doi = {10.1038/s41467-017-01752-5}, author = {Martineau, Magalie and Somasundaram, Agila and Grimm, Jonathan B and Gruber, Todd D and Choquet, Daniel and Taraska, Justin W and Lavis, Luke D and Perrais, David} } @conference {67293, title = {Stochastic filtering of two-photon imaging using reweighted l1}, booktitle = {2017 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)}, year = {2017}, month = {03/2017}, publisher = {IEEE}, organization = {IEEE}, address = {New Orleans, LA}, abstract = {
Two-photon (TP) calcium imaging is an important imaging modality in neuroscience, allowing for large-scale recording of neural activity in awake, behaving animals at behavior-relevant timescales. Interpretation of TP data requires the accurate extraction of temporal neural activity traces, which can be accomplished via manual or automated methods. In this work we seek to improve the accuracy of both manual and automated TP microscopy demixing methods by introducing a denoising algorithm based on a statistical model of TP data which includes spatial contiguity, sparse activity and Poisson observations. Our method leverages recent developments in stochastic filtering of structured signals based on Laplacian-scale mixture models (LSMs) to model the neural activity in TP data as a set of spatially correlated sparse variables. We apply our method on TP images taken from the visual cortex of an awake, behaving mouse, and demonstrate improved neural activity demixing over current pre-processing techniques.
}, doi = {10.1109/ICASSP.2017.7952314}, url = {https://ieeexplore.ieee.org/abstract/document/7952314}, author = {Charles, Adam S. and Song, Alexander and Koay, Sue Ann and Tank, David W. and Pillow, Jonathan W.} } @article {48657, title = {A systematic nomenclature for the Drosophila ventral nervous system.}, journal = {bioRxiv}, year = {2017}, month = {2017 Apr 26}, abstract = {

Insect nervous systems are proven and powerful model systems for neuroscience research with wide relevance in biology and medicine. However, descriptions of insect brains have suffered from a lack of a complete and uniform nomenclature. Recognising this problem the Insect Brain Name Working Group produced the first agreed hierarchical nomenclature system for the adult insect brain, using Drosophila melanogaster as the reference framework, with other insect taxa considered to ensure greater consistency and expandability (Ito et al., 2014). Ito et al. (2014) purposely focused on the gnathal regions that account for approximately 50\% of the adult CNS. We extend this nomenclature system to the sub-gnathal regions of the adult Drosophila nervous system to provide a nomenclature of the so-called ventral nervous system (VNS), which includes the thoracic and abdominal neuromeres that was not included in the original work and contains the neurons that play critical roles underpinning most fly behaviours.

}, doi = {10.1101/122952}, author = {Court, Robert Christopher and Armstrong, James Douglas and Borner, Jana and Card, Gwyneth M and Costa, Marta and Dickinson, Michael H and Duch, Carsten and Korff, Wyatt and Mann, Richard S and Merritt, David and Murphey, Rodney K and Namiki, Shigehiro and Seeds, Andrew M and Shepherd, David and Shirangi, Troy R and Simpson, Julie H and Truman, James W and Tuthill, John C and Williams, Darren W} } @article {48533, title = {Theta-paced flickering between place-cell maps in the hippocampus: A model based on short-term synaptic plasticity.}, journal = {Hippocampus}, volume = {27}, year = {2017}, month = {2017 May 30}, pages = {959-70}, abstract = {

Hippocampal place cells represent different environments with distinct neural activity patterns. Following an abrupt switch between two familiar configurations of visual cues defining two environments, the hippocampal neural activity pattern switches almost immediately to the corresponding representation. Surprisingly, during a transient period following the switch to the new environment, occasional fast transitions of activity patterns between the representations (flickering) were observed (Jezek et al. 2011). Here we show that an attractor neural network model of place cells with connections endowed with short-term synaptic plasticity can account for this phenomenon. A memory trace of the recent history of network activity is maintained in the state of the synapses, allowing the network to temporarily reactivate the representation of the previous environment in the absence of the corresponding sensory cues. The model predicts that the number of flickering events depends on the amplitude of the ongoing theta rhythm and the distance between the current position of the animal and its position at the time of cue switching. We test these predictions with new analysis of experimental data. These results suggest a potential role of short-term synaptic plasticity in recruiting the activity of different cell assemblies and in shaping hippocampal activity of behaving animals. This article is protected by copyright. All rights reserved.

}, issn = {1098-1063}, doi = {10.1002/hipo.22743}, author = {Mark, Shirley and Romani, Sandro and Jezek, Karel and Tsodyks, Misha} } @article {68761, title = {A toolkit for GFP-mediated tissue-specific protein degradation in C. elegans}, journal = {Development}, volume = {144}, year = {2017}, month = {07/2017}, pages = {2694-2701}, abstract = {

Proteins that are essential for embryo production, cell division and early embryonic events are frequently reused later in embryogenesis, during organismal development or in the adult. Examining protein function across these different biological contexts requires tissue-specific perturbation. Here, we describe a method that uses expression of a fusion between a GFP-targeting nanobody and a SOCS-box containing ubiquitin ligase adaptor to target GFP-tagged proteins for degradation. When combined with endogenous locus GFP tagging by CRISPR-Cas9 or with rescue of a null mutant with a GFP fusion, this approach enables routine and efficient tissue-specific protein ablation. We show that this approach works in multiple tissues {\textendash} the epidermis, intestine, body wall muscle, ciliated sensory neurons and touch receptor neurons {\textendash} where it recapitulates expected loss-of-function mutant phenotypes. The transgene toolkit and the strain set described here will complement existing approaches to enable routine analysis of the tissue-specific roles of C. elegans proteins.

}, issn = {0950-1991}, doi = {10.1242/dev.150094}, url = {https://doi.org/10.1242/dev.150094}, author = {Wang, Shaohe and Tang, Ngang Heok and Lara-Gonzalez, Pablo and Zhao, Zhiling and Cheerambathur, Dhanya K. and Prevo, Bram and Chisholm, Andrew D. and Desai, Arshad and Oegema, Karen} } @article {48921, title = {Topological and modality-specific representation of somatosensory information in the fly brain.}, journal = {Science (New York, N.Y.)}, volume = {358}, year = {2017}, month = {2017 11 03}, pages = {615-623}, abstract = {

Insects and mammals share similarities of neural organization underlying the perception of odors, taste, vision, sound, and gravity. We observed that insect somatosensation also corresponds to that of mammals. In Drosophila, the projections of all the somatosensory neuron types to the insect{\textquoteright}s equivalent of the spinal cord segregated into modality-specific layers comparable to those in mammals. Some sensory neurons innervate the ventral brain directly to form modality-specific and topological somatosensory maps. Ascending interneurons with dendrites in matching layers of the nerve cord send axons that converge to respective brain regions. Pathways arising from leg somatosensory neurons encode distinct qualities of leg movement information and play different roles in ground detection. Establishment of the ground pattern and genetic tools for neuronal manipulation should provide the basis for elucidating the mechanisms underlying somatosensation.

}, issn = {1095-9203}, doi = {10.1126/science.aan4428}, author = {Tsubouchi, Asako and Yano, Tomoko and Yokoyama, Takeshi K and Murtin, Chlo{\'e} and Otsuna, Hideo and Ito, Kei} } @article {48304, title = {Video-rate volumetric functional imaging of the brain at synaptic resolution.}, journal = {Nature Neuroscience}, volume = {20}, year = {2017}, month = {2017 Feb 27}, pages = {620-8}, abstract = {

Neurons and neural networks often extend hundreds of micrometers in three dimensions. Capturing the calcium transients associated with their activity requires volume imaging methods with subsecond temporal resolution. Such speed is a challenge for conventional two-photon laser-scanning microscopy, because it depends on serial focal scanning in 3D and indicators with limited brightness. Here we present an optical module that is easily integrated into standard two-photon laser-scanning microscopes to generate an axially elongated Bessel focus, which when scanned in 2D turns frame rate into volume rate. We demonstrated the power of this approach in enabling discoveries for neurobiology by imaging the calcium dynamics of volumes of neurons and synapses in fruit flies, zebrafish larvae, mice and ferrets in vivo. Calcium signals in objects as small as dendritic spines could be resolved at video rates, provided that the samples were sparsely labeled to limit overlap in their axially projected images.

}, issn = {1546-1726}, doi = {10.1038/nn.4516}, author = {Lu, Rongwen and Sun, Wenzhi and Liang, Yajie and Kerlin, Aaron and Bierfeld, Jens and Seelig, Johannes D and Wilson, Daniel E and Scholl, Benjamin and Mohar, Boaz and Tanimoto, Masashi and Koyama, Minoru and Fitzpatrick, David and Orger, Michael B and Ji, Na} } @article {67282, title = {Volumetric two-photon imaging of neurons using stereoscopy (vTwINS)}, journal = {Nature Methods}, volume = {14}, year = {2017}, month = {03/2017}, pages = {420 - 426}, abstract = {

Two-photon laser scanning microscopy of calcium dynamics using fluorescent indicators is a widely used imaging method for large-scale recording of neural activity\ in vivo. Here, we introduce volumetric two-photon imaging of neurons using stereoscopy (vTwINS), a volumetric calcium imaging method that uses an elongated, V-shaped point spread function to image a 3D brain volume. Single neurons project to spatially displaced {\textquoteright}image pairs{\textquoteright} in the resulting 2D image, and the separation distance between projections is proportional to depth in the volume. To demix the fluorescence time series of individual neurons, we introduce a modified orthogonal matching pursuit algorithm that also infers source locations within the 3D volume. We illustrated vTwINS by imaging neural population activity in the mouse primary visual cortex and hippocampus. Our results demonstrated that vTwINS provides an effective method for volumetric two-photon calcium imaging that increases the number of neurons recorded while maintaining a high frame rate.

}, issn = {1548-7091}, doi = {10.1038/nmeth.4226}, url = {http://www.nature.com/articles/nmeth.4226http://www.nature.com/articles/nmeth.4226.pdfhttp://www.nature.com/articles/nmeth.4226.pdfhttp://www.nature.com/articles/nmeth.4226}, author = {Song, Alexander and Charles, Adam S and Koay, Sue Ann and Gauthier, Jeff L and Thiberge, Stephan Y and Pillow, Jonathan W and Tank, David W} } @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 {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 {47509, title = {Activation of NMDA receptors and the mechanism of inhibition by ifenprodil.}, journal = {Nature}, volume = {534}, year = {2016}, month = {2016 Jun 2}, pages = {63-8}, abstract = {

The physiology of N-methyl-d-aspartate (NMDA) receptors is fundamental to brain development and function. NMDA receptors are ionotropic glutamate receptors that function as heterotetramers composed mainly of GluN1 and GluN2 subunits. Activation of NMDA receptors requires binding of neurotransmitter agonists to a ligand-binding domain (LBD) and structural rearrangement of an amino-terminal domain (ATD). Recent crystal structures of GluN1-GluN2B NMDA receptors bound to agonists and an allosteric inhibitor, ifenprodil, represent the allosterically inhibited state. However, how the ATD and LBD move to activate the NMDA receptor ion channel remains unclear. Here we applied X-ray crystallography, single-particle electron cryomicroscopy and electrophysiology to rat NMDA receptors to show that, in the absence of ifenprodil, the bi-lobed structure of GluN2 ATD adopts an open conformation accompanied by rearrangement of the GluN1-GluN2 ATD heterodimeric interface, altering subunit orientation in the ATD and LBD and forming an active receptor conformation that gates the ion channel.

}, issn = {1476-4687}, doi = {10.1038/nature17679}, author = {Tajima, Nami and Karakas, Erkan and Grant, Timothy and Simorowski, Noriko and Diaz-Avalos, Ruben and Grigorieff, Nikolaus and Furukawa, Hiro} } @article {47260, title = {Adaptive and background-aware GAL4 expression enhancement of co-registered confocal microscopy images.}, journal = {Neuroinformatics}, volume = {14}, year = {2016}, month = {2016 Jan 7}, pages = {221-33}, abstract = {

GAL4 gene expression imaging using confocal microscopy is a common and powerful technique used to study the nervous system of a model organism such as Drosophila melanogaster. Recent research projects focused on high throughput screenings of thousands of different driver lines, resulting in large image databases. The amount of data generated makes manual assessment tedious or even impossible. The first and most important step in any automatic image processing and data extraction pipeline is to enhance areas with relevant signal. However, data acquired via high throughput imaging tends to be less then ideal for this task, often showing high amounts of background signal. Furthermore, neuronal structures and in particular thin and elongated projections with a weak staining signal are easily lost. In this paper we present a method for enhancing the relevant signal by utilizing a Hessian-based filter to augment thin and weak tube-like structures in the image. To get optimal results, we present a novel adaptive background-aware enhancement filter parametrized with the local background intensity, which is estimated based on a common background model. We also integrate recent research on adaptive image enhancement into our approach, allowing us to propose an effective solution for known problems present in confocal microscopy images. We provide an evaluation based on annotated image data and compare our results against current state-of-the-art algorithms. The results show that our algorithm clearly outperforms the existing solutions.

}, issn = {1559-0089}, doi = {10.1007/s12021-015-9289-y}, author = {Trapp, Martin and Schulze, Florian and Novikov, Alexey A and Tirian, Laszlo and J Dickson, Barry and B{\"u}hler, Katja} } @article {47894, title = {Adult mouse cortical cell taxonomy revealed by single cell transcriptomics.}, journal = {Nature neuroscience}, volume = {19}, year = {2016}, month = {2016 Feb}, pages = {335-46}, abstract = {

Nervous systems are composed of various cell types, but the extent of cell type diversity is poorly understood. We constructed a cellular taxonomy of one cortical region, primary visual cortex, in adult mice on the basis of single-cell RNA sequencing. We identified 49 transcriptomic cell types, including 23 GABAergic, 19 glutamatergic and 7 non-neuronal types. We also analyzed cell type-specific mRNA processing and characterized genetic access to these transcriptomic types by many transgenic Cre lines. Finally, we found that some of our transcriptomic cell types displayed specific and differential electrophysiological and axon projection properties, thereby confirming that the single-cell transcriptomic signatures can be associated with specific cellular properties.

}, keywords = {Animals, Cell Line, Cerebral Cortex, Classification, gamma-Aminobutyric Acid, Gene Library, Genetic Markers, Glutamic Acid, Interneurons, Male, Mice, Mice, Inbred C57BL, Mice, Transgenic, Neurons, RNA, Sequence Analysis, RNA, Transcriptome, Visual Cortex}, issn = {1546-1726}, doi = {10.1038/nn.4216}, author = {Tasic, Bosiljka and Menon, Vilas and Nguyen, Thuc Nghi and Kim, Tae Kyung and Jarsky, Tim and Yao, Zizhen and Levi, Boaz and Gray, Lucas T and Sorensen, Staci A and Dolbeare, Tim and Bertagnolli, Darren and Goldy, Jeff and Shapovalova, Nadiya and Parry, Sheana and Lee, Changkyu and Smith, Kimberly and Bernard, Amy and Madisen, Linda and Sunkin, Susan M and Hawrylycz, Michael and Koch, Christof and Zeng, Hongkui} } @article {47994, title = {AMPK activation prevents and reverses drug-induced mitochondrial and hepatocyte injury by promoting mitochondrial fusion and function.}, journal = {PLoS One}, volume = {11}, year = {2016}, month = {2016 Oct 31}, pages = {e0165638}, abstract = {

Mitochondrial damage is the major factor underlying drug-induced liver disease but whether conditions that thwart mitochondrial injury can prevent or reverse drug-induced liver damage is unclear. A key molecule regulating mitochondria quality control is AMP activated kinase (AMPK). When activated, AMPK causes mitochondria to elongate/fuse and proliferate, with mitochondria now producing more ATP and less reactive oxygen species. Autophagy is also triggered, a process capable of removing damaged/defective mitochondria. To explore whether AMPK activation could potentially prevent or reverse the effects of drug-induced mitochondrial and hepatocellular damage, we added an AMPK activator to collagen sandwich cultures of rat and human hepatocytes exposed to the hepatotoxic drugs, acetaminophen or diclofenac. In the absence of AMPK activation, the drugs caused hepatocytes to lose polarized morphology and have significantly decreased ATP levels and viability. At the subcellular level, mitochondria underwent fragmentation and had decreased membrane potential due to decreased expression of the mitochondrial fusion proteins Mfn1, 2 and/or Opa1. Adding AICAR, a specific AMPK activator, at the time of drug exposure prevented and reversed these effects. The mitochondria became highly fused and ATP production increased, and hepatocytes maintained polarized morphology. In exploring the mechanism responsible for this preventive and reversal effect, we found that AMPK activation prevented drug-mediated decreases in Mfn1, 2 and Opa1. AMPK activation also stimulated autophagy/mitophagy, most significantly in acetaminophen-treated cells. These results suggest that activation of AMPK prevents/reverses drug-induced mitochondrial and hepatocellular damage through regulation of mitochondrial fusion and autophagy, making it a potentially valuable approach for treatment of drug-induced liver injury.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0165638}, author = {Kang, Sun Woo Sophie and Haydar, Ghada and Taniane, Caitlin and Farrell, Geoffrey and Arias, Irwin M and Lippincott-Schwartz, Jennifer and Fu, Dong} } @article {47421, title = {Astrocytic glutamate transport regulates a Drosophila CNS synapse that lacks astrocyte ensheathment.}, journal = {The Journal of Comparative Neurology}, volume = {524}, year = {2016}, month = {2016 Apr 12}, pages = {1979-98}, abstract = {

Anatomical, molecular, and physiological interactions between astrocytes and neuronal synapses regulate information processing in the brain. The fruit fly Drosophila melanogaster has become a valuable experimental system for genetic manipulation of the nervous system and has enormous potential for elucidating mechanisms that mediate neuron-glia interactions. Here, we show the first electrophysiological recordings from Drosophila astrocytes and characterize their spatial and physiological relationship with particular synapses. Astrocyte intrinsic properties were found to be strongly analogous to those of vertebrate astrocytes, including a passive current-voltage relationship, low membrane resistance, high capacitance, and dye-coupling to local astrocytes. Responses to optogenetic stimulation of glutamatergic pre-motor neurons were correlated directly with anatomy using serial electron microscopy reconstructions of homologous identified neurons and surrounding astrocytic processes. Robust bidirectional communication was present: neuronal activation triggered astrocytic glutamate transport via Eaat1, and blocking Eaat1 extended glutamatergic interneuron-evoked inhibitory post-synaptic currents in motor neurons. The neuronal synapses were always located within a micron of an astrocytic process, but none were ensheathed by those processes. Thus, fly astrocytes can modulate fast synaptic transmission via neurotransmitter transport within these anatomical parameters. This article is protected by copyright. All rights reserved.

}, issn = {1096-9861}, doi = {10.1002/cne.24016}, author = {MacNamee, Sarah E and Liu, Kendra E and Gerhard, Stephan and Tran, Cathy T and Fetter, Richard D and Cardona, Albert and Tolbert, Leslie P and Oland, Lynne A} } @article {47463, title = {Brain derived neurotrophic factor differentially modulates excitability of two classes of hippocampal output neurons.}, journal = {Journal of Neurophysiology}, volume = {116}, year = {2016}, month = {2016 May 4}, pages = {466-71}, abstract = {

Brain-derived neurotrophic factor (BDNF) plays an important role in hippocampus-dependent learning and memory. Canonically, this has been ascribed to an enhancing effect on neuronal excitability and synaptic plasticity in the CA1 region. However, it is the pyramidal neurons in the subiculum that form the primary efferent pathways conveying hippocampal information to other areas of the brain, and yet the effect of BDNF on these neurons has remained unexplored. We present new data that BDNF regulates neuronal excitability and cellular plasticity in a much more complex manner than previously suggested. Subicular pyramidal neurons can be divided into two major classes, which have different electrophysiological and morphological properties, different requirements for the induction of plasticity and different extra-hippocampal projections. We found that BDNF increases excitability in one class of subicular pyramidal neurons, yet decreases excitability of the other class. Further, while endogenous BDNF was necessary for the induction of synaptic plasticity in both cell types, BDNF enhanced intrinsic plasticity in one class of pyramidal neurons, yet suppressed intrinsic plasticity in the other. Taken together, these data suggest a novel role for BDNF signaling, as it appears to dynamically and bidirectionally regulate the output of hippocampal information to different regions of the brain.

}, issn = {1522-1598}, doi = {10.1152/jn.00186.2016}, author = {Graves, Austin R and Moore, Shannon J and Spruston, Nelson and Tryba, Andrew Kieran and Kaczorowski, Catherine C} } @article {47527, title = {A bright cyan-excitable orange fluorescent protein facilitates dual-emission microscopy and enhances bioluminescence imaging in vivo.}, journal = {Nature Biotechnology}, volume = {34}, year = {2016}, month = {2016 May 30}, pages = {760-7}, abstract = {

Orange-red fluorescent proteins (FPs) are widely used in biomedical research for multiplexed epifluorescence microscopy with GFP-based probes, but their different excitation requirements make multiplexing with new advanced microscopy methods difficult. Separately, orange-red FPs are useful for deep-tissue imaging in mammals owing to the relative tissue transmissibility of orange-red light, but their dependence on illumination limits their sensitivity as reporters in deep tissues. Here we describe CyOFP1, a bright, engineered, orange-red FP that is excitable by cyan light. We show that CyOFP1 enables single-excitation multiplexed imaging with GFP-based probes in single-photon and two-photon microscopy, including time-lapse imaging in light-sheet systems. CyOFP1 also serves as an efficient acceptor for resonance energy transfer from the highly catalytic blue-emitting luciferase NanoLuc. An optimized fusion of CyOFP1 and NanoLuc, called Antares, functions as a highly sensitive bioluminescent reporter in vivo, producing substantially brighter signals from deep tissues than firefly luciferase and other bioluminescent proteins.

}, issn = {1546-1696}, doi = {10.1038/nbt.3550}, author = {Chu, Jun and Oh, Younghee and Sens, Alex and Ataie, Niloufar and Dana, Hod and Macklin, John J and Laviv, Tal and Welf, Erik S and Dean, Kevin M and Zhang, Feijie and Kim, Benjamin B and Tang, Clement Tran and Hu, Michelle and Baird, Michelle A and Davidson, Michael W and Kay, Mark A and Fiolka, Reto and Yasuda, Ryohei and Kim, Douglas S and Ng, Ho-Leung and Lin, Michael Z} } @article {47935, title = {Competitive disinhibition mediates behavioral choice and sequences in Drosophila.}, journal = {Cell}, volume = {167}, year = {2016}, month = {2016 Oct 5}, pages = {858-70}, abstract = {

Even a simple sensory stimulus can elicit distinct innate behaviors and sequences. During sensorimotor decisions, competitive interactions among neurons that promote distinct behaviors must ensure the selection and maintenance of one behavior, while suppressing others. The circuit implementation of these competitive interactions is still an open question. By combining comprehensive electron microscopy reconstruction of inhibitory interneuron networks, modeling, electrophysiology, and behavioral studies, we determined the circuit mechanisms that\ contribute to the Drosophila larval sensorimotor decision to startle, explore, or perform a sequence of the two in response to a mechanosensory stimulus. Together, these studies reveal that, early in sensory processing, (1) reciprocally connected feedforward inhibitory interneurons implement behavioral choice, (2) local feedback disinhibition provides positive feedback that consolidates and maintains the chosen behavior, and (3) lateral disinhibition promotes sequence transitions. The combination of these interconnected circuit motifs can implement both behavior selection and the serial organization of behaviors into a sequence.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2016.09.009}, author = {Jovanic, Tihana and Schneider-Mizell, Casey M and Shao, Mei and Masson, Jean-Baptiste and Denisov, Gennady and Fetter, Richard D and Mensh, Brett D and Truman, James W and Cardona, Albert and Zlatic, Marta} } @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 {47934, title = {A designer AAV variant permits efficient retrograde access to projection neurons.}, journal = {Neuron}, volume = {92}, year = {2016}, month = {2016 Oct 19}, pages = {372-82}, abstract = {

Efficient retrograde access to projection neurons for the delivery of sensors and effectors constitutes an important and enabling capability for neural circuit dissection. Such an approach would also be useful for gene therapy, including the treatment of neurodegenerative disorders characterized by pathological spread through functionally connected and highly distributed networks. Viral vectors, in particular, are powerful gene delivery vehicles for the nervous system, but all available tools suffer from inefficient retrograde transport or limited clinical potential. To address this need, we applied in\ vivo directed evolution to engineer potent retrograde functionality into the capsid of adeno-associated virus (AAV), a vector that has shown promise in neuroscience research and the clinic. A newly evolved variant, rAAV2-retro, permits robust retrograde access to projection neurons with efficiency comparable to classical synthetic retrograde tracers and enables sufficient sensor/effector expression for functional circuit interrogation and in\ vivo genome editing in targeted neuronal populations. VIDEO ABSTRACT.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2016.09.021}, author = {Tervo, D Gowanlock R and Hwang, Bum-Yeol and Viswanathan, Sarada and Gaj, Thomas and Lavzin, Maria and Ritola, Kimberly D and Lindo, Sarah and Michael, Susan and Kuleshova, Elena and Ojala, David and Huang, Cheng-Chiu and Gerfen, Charles R and Schiller, Jackie and Dudman, Joshua T and Hantman, Adam W and Looger, Loren L and Schaffer, David V and Karpova, Alla Y} } @article {47434, title = {Direct neural pathways convey distinct visual information to Drosophila mushroom bodies.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Apr 15}, pages = {e14009}, abstract = {

Previously, we identified that visual and olfactory associative memories of Drosophila share the mushroom body (MB) circuits (Vogt et al. 2014). Despite well-characterized odor representations in the Drosophila MB, the MB circuit for visual information is totally unknown. Here we show that a small subset of MB Kenyon cells (KCs) selectively responds to visual but not olfactory stimulation. The dendrites of these atypical KCs form a ventral accessory calyx (vAC), distinct from the main calyx that receives olfactory input. We identified two types of visual projection neurons (VPNs) directly connecting the optic lobes and the vAC. Strikingly, these VPNs are differentially required for visual memories of color and brightness. The segregation of visual and olfactory domains in the MB allows independent processing of distinct sensory memories and may be a conserved form of sensory representations among insects.

}, issn = {2050-084X}, doi = {10.7554/eLife.14009}, author = {Vogt, Katrin and Aso, Yoshinori and Hige, Toshihide and Knapek, Stephan and Ichinose, Toshiharu and Friedrich, Anja B and Turner, Glenn C and Rubin, Gerald M and Tanimoto, Hiromu} } @booklet {67218, title = {Discovering Neuronal Cell Types and Their Gene Expression Profiles Using a Spatial Point Process Mixture Model}, year = {2016}, abstract = {

Cataloging the neuronal cell types that comprise circuitry of individual brain regions is a major goal of modern neuroscience and the BRAIN initiative. Single-cell RNA sequencing can now be used to measure the gene expression profiles of individual neurons and to categorize neurons based on their gene expression profiles. While the single-cell techniques are extremely powerful and hold great promise, they are currently still labor intensive, have a high cost per cell, and, most importantly, do not provide information on spatial distribution of cell types in specific regions of the brain. We propose a complementary approach that uses computational methods to infer the cell types and their gene expression profiles through analysis of brain-wide single-cell resolution in situ hybridization (ISH) imagery contained in the Allen Brain Atlas (ABA). We measure the spatial distribution of neurons labeled in the ISH image for each gene and model it as a spatial point process mixture, whose mixture weights are given by the cell types which express that gene. By fitting a point process mixture model jointly to the ISH images, we infer both the spatial point process distribution for each cell type and their gene expression profile. We validate our predictions of cell type-specific gene expression profiles using single cell RNA sequencing data, recently published for the mouse somatosensory cortex. Jointly with the gene expression profiles, cell features such as cell size, orientation, intensity and local density level are inferred per cell type.

}, author = {Furong Huang and Animashree Anandkumar and Christian Borgs and Jennifer Chayes and Ernest Fraenkel and Michael Hawrylycz and Ed Lein and Alessandro Ingrosso and Srinivas Turaga} } @article {47553, title = {Doublesex regulates the connectivity of a neural circuit controlling Drosophila male courtship song.}, journal = {Developmental Cell}, volume = {37}, year = {2016}, month = {2016 Jun 20}, pages = {533-44}, abstract = {

It is unclear how regulatory genes establish neural circuits that compose sex-specific behaviors. The\ Drosophila melanogaster\ male courtship song provides a powerful model to study this problem. Courting males vibrate a wing to sing bouts of pulses and hums, called pulse and sine song, respectively. We report the discovery of male-specific thoracic interneurons{\textemdash}the TN1A neurons{\textemdash}that are required specifically for sine song. The TN1A neurons can drive the activity of a sex-non-specific wing motoneuron,\ hg1, which is also required for sine song. The male-specific connection between the TN1A neurons and the\ hg1\ motoneuron is regulated by the sexual differentiation gene\ doublesex. We find that\ doublesex\ is required in the TN1A neurons during development to increase the density of the TN1A arbors that interact with dendrites of the\ hg1motoneuron. Our findings demonstrate how a sexual differentiation gene can build a sex-specific circuit motif by modulating neuronal arborization.

{\textbullet}Doublesex-expressing TN1 neurons are necessary and sufficient for the male sine song{\textbullet}A subclass of TN1 neurons, TN1A, contributes to the sine song{\textbullet}TN1A neurons are functionally coupled to a sine song motoneuron,\ hg1{\textbullet}Doublesex\ regulates the connectivity between the TN1A and\ hg1\ neurons

It is unclear how developmental regulatory genes specify sex-specific behaviors. Shirangi et\ al. demonstrate that the\ Drosophila\ sexual differentiation gene\ doublesex\ encodes a sex-specific behavior{\textemdash}male song{\textemdash}by promoting the connectivity between the male-specific TN1A neurons and the sex-non-specific\ hg1\ neurons, which are required for production of the song.

}, doi = {10.1016/j.devcel.2016.05.012}, author = {Shirangi, Troy R and Wong, Allen M and Truman, James W and Stern, David L} } @article {47749, title = {Drosophila larval to pupal switch under nutrient stress requires IP3R/Ca(2+) signalling in glutamatergic interneurons.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Aug 5}, abstract = {

Neuronal circuits are known to integrate nutritional information, but the identity of the circuit components is not completely understood. Amino acids are a class of nutrients that are vital for the growth and function of an organism. Here, we report a neuronal circuit that allows Drosophila larvae to overcome amino acid deprivation and pupariate. We find that nutrient stress is sensed by the class IV multidendritic cholinergic neurons. Through live calcium imaging experiments, we show that these cholinergic stimuli are conveyed to glutamatergic neurons in the ventral ganglion through mAChR. We further show that IP3R-dependent calcium transients in the glutamatergic neurons convey this signal to downstream medial neurosecretory cells (mNSCs). The circuit ultimately converges at the ring gland and regulates expression of ecdysteroid biosynthetic genes. Activity in this circuit is thus likely to be an adaptation that provides a layer of regulation to help surpass nutritional stress during development.

}, issn = {2050-084X}, doi = {10.7554/eLife.17495}, author = {Jayakumar, Siddharth and Richhariya, Shlesha and Reddy, O Venkateswara and Texada, Michael J and Hasan, Gaiti} } @conference {47736, title = {Efficient convolutional neural networks for pixelwise classification on heterogeneous hardware systems.}, booktitle = { IEEE 13th International Symposium on Biomedical Imaging: From Nano to Macro}, year = {2016}, month = {2016 Jun 15}, address = {Clarion Congress Hotel in Prague Prague; Czech Republic}, abstract = {

With recent advances in high-throughput Electron Microscopy (EM) imaging it is now possible to image an entire nervous system of organisms like Drosophila melanogaster. One of the bottlenecks to reconstruct a connectome from these large volumes ({\oe} 100 TiB) is the pixel-wise prediction of membranes. The time it would typically take to process such a volume using a convolutional neural network (CNN) with a sliding window approach is in the order of years on a current GPU. With sliding windows, however, a lot of redundant computations are carried out. In this paper, we present an extension to the Caffe library to increase throughput by predicting many pixels at once. On a sliding window network successfully used for membrane classification, we show that our method achieves a speedup of up to 57{\texttimes}, maintaining identical prediction results.

}, isbn = {978-147992350-2}, doi = {10.1109/ISBI.2016.7493487}, author = {Tschopp, F and Martel, J N P and Turaga, Srinivas C and Cook, M and Funke, Jan} } @article {48132, title = {An empirical analysis of deep network loss surfaces.}, journal = {arXiv}, year = {2016}, month = {2016 Dec 13}, pages = {arXiv:1612.04010}, abstract = {

The training of deep neural networks is a high-dimension optimization problem with respect to the loss function of a model. Unfortunately, these functions are of high dimension and non-convex and hence difficult to characterize. In this paper, we empirically investigate the geometry of the loss functions for state-of-the-art networks with multiple stochastic optimization methods. We do this through several experiments that are visualized on polygons to understand how and when these stochastic optimization methods find minima.

}, url = {https://arxiv.org/pdf/1612.04010.pdf}, author = {Im, Daniel Jiwoong and Tao, Michael and Branson, Kristin} } @article {48042, title = {Engulfed cadherin fingers are polarized junctional structures between collectively migrating endothelial~cells.}, journal = {Nature Cell Biology}, volume = {18}, year = {2016}, month = {2016 Nov 14}, pages = {1311-23}, abstract = {

The development and maintenance of tissues requires collective cell movement, during which neighbouring cells coordinate the polarity of their migration machineries. Here, we ask how polarity signals are transmitted from one cell to another across symmetrical cadherin junctions, during collective migration. We demonstrate that collectively migrating endothelial cells have polarized VE-cadherin-rich membrane protrusions, {\textquoteleft}cadherin fingers{\textquoteright}, which leading cells extend from their rear and follower cells engulf at their front, thereby generating opposite membrane curvatures and asymmetric recruitment of curvature-sensing proteins. In follower cells, engulfment of cadherin fingers occurs along with the formation of a lamellipodia-like zone with low actomyosin contractility, and requires VE-cadherin/catenin complexes and Arp2/3-driven actin polymerization. Lateral accumulation of cadherin fingers in follower cells precedes turning, and increased actomyosin contractility can initiate cadherin finger extension as well as engulfment by a neighbouring cell, to promote follower behaviour. We propose that cadherin fingers serve as guidance cues that direct collective cell migration.

}, doi = {10.1038/ncb3438}, author = {Hayer, Arnold and Shao, Lin and Chung, Mingyu and Joubert, Lydia-Marie and Yang, Hee Won and Tsai, Feng-Chiao and Bisaria, Anjali and Betzig, Eric and Meyer, Tobias} } @article {47303, title = {Four individually identified paired dopamine neurons signal reward in larval Drosophila.}, journal = {Current Biology : CB}, year = {2016}, month = {2016 Feb 10}, abstract = {

Dopaminergic neurons serve multiple functions, including reinforcement processing during associative learning [1-12]. It is thus warranted to understand which dopaminergic neurons mediate which function. We study larval Drosophila, in which only approximately 120 of a total of 10,000 neurons are dopaminergic, as judged by the expression of tyrosine hydroxylase (TH), the rate-limiting enzyme of dopamine biosynthesis [5, 13]. Dopaminergic neurons mediating reinforcement in insect olfactory learning target the mushroom bodies, a higher-order "cortical" brain region [1-5, 11, 12, 14, 15]. We discover four previously undescribed paired neurons, the primary protocerebral anterior medial (pPAM) neurons. These neurons are TH positive and subdivide the medial lobe of the mushroom body into four distinct subunits. These pPAM neurons are acutely necessary for odor-sugar reward learning and require intact TH function in this process. However, they are dispensable for aversive learning and innate behavior toward the odors and sugars employed. Optogenetical activation of pPAM neurons is sufficient as a reward. Thus, the pPAM neurons convey a likely dopaminergic reward signal. In contrast, DL1 cluster neurons convey a corresponding punishment signal [5], suggesting a cellular division of labor to convey dopaminergic reward and punishment signals. On the level of individually identified neurons, this uncovers an organizational principle shared with adult Drosophila and mammals [1-4, 7, 9, 10] (but see [6]). The numerical simplicity and connectomic tractability of the larval nervous system [16-19] now offers a prospect for studying circuit principles of dopamine function at unprecedented resolution.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2016.01.012}, author = {Rohwedder, Astrid and Wenz, Nana L and Stehle, Bernhard and Huser, Annina and Yamagata, Nobuhiro and Zlatic, Marta and Truman, James W and Tanimoto, Hiromu and Saumweber, Timo and Gerber, Bertram and Thum, Andreas S} } @article {47524, title = {Genetic and environmental control of neurodevelopmental robustness in Drosophila.}, journal = {PLoS One}, volume = {11}, year = {2016}, month = {2016 May 25}, pages = {e0155957}, abstract = {

Interindividual differences in neuronal wiring may contribute to behavioral individuality and affect susceptibility to neurological disorders. To investigate the causes and potential consequences of wiring variation in Drosophila melanogaster, we focused on a hemilineage of ventral nerve cord interneurons that exhibits morphological variability. We find that late-born subclasses of the 12A hemilineage are highly sensitive to genetic and environmental variation. Neurons in the second thoracic segment are particularly variable with regard to two developmental decisions, whereas its segmental homologs are more robust. This variability "hotspot" depends on Ultrabithorax expression in the 12A neurons, indicating variability is cell-intrinsic and under genetic control. 12A development is more variable and sensitive to temperature in long-established laboratory strains than in strains recently derived from the wild. Strains with a high frequency of one of the 12A variants also showed a high frequency of animals with delayed spontaneous flight initiation, whereas other wing-related behaviors did not show such a correlation and were thus not overtly affected by 12A variation. These results show that neurodevelopmental robustness is variable and under genetic control in Drosophila and suggest that the fly may serve as a model for identifying conserved gene pathways that stabilize wiring in stressful developmental environments. Moreover, some neuronal lineages are variation hotspots and thus may be more amenable to evolutionary change.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0155957}, author = {Mellert, David J and Williamson, W Ryan and Shirangi, Troy R and Card, Gwyneth M and Truman, James W} } @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 {47728, title = {Identification of excitatory premotor interneurons which regulate local muscle contraction during Drosophila larval locomotion.}, journal = {Scientific Reports}, volume = {6}, year = {2016}, month = {2016}, pages = {30806}, abstract = {

We use Drosophila larval locomotion as a model to elucidate the working principles of motor circuits. Larval locomotion is generated by rhythmic and sequential contractions of body-wall muscles from the posterior to anterior segments, which in turn are regulated by motor neurons present in the corresponding neuromeres. Motor neurons are known to receive both excitatory and inhibitory inputs, combined action of which likely regulates patterned motor activity during locomotion. Although recent studies identified candidate inhibitory premotor interneurons, the identity of premotor interneurons that provide excitatory drive to motor neurons during locomotion remains unknown. In this study, we searched for and identified two putative excitatory premotor interneurons in this system, termed CLI1 and CLI2 (cholinergic lateral interneuron 1 and 2). These neurons were segmentally arrayed and activated sequentially from the posterior to anterior segments during peristalsis. Consistent with their being excitatory premotor interneurons, the CLIs formed GRASP- and ChAT-positive putative synapses with motoneurons and were active just prior to motoneuronal firing in each segment. Moreover, local activation of CLI1s induced contraction of muscles in the corresponding body segments. Taken together, our results suggest that the CLIs directly activate motoneurons sequentially along the segments during larval locomotion.

}, issn = {2045-2322}, doi = {10.1038/srep30806}, author = {Hasegawa, Eri and Truman, James W and Nose, Akinao} } @article {48990, title = {The insect central complex.}, journal = {Current Biology : CB}, volume = {26}, year = {2016}, month = {2016 Jun 06}, pages = {R453-7}, abstract = {

Hordes of tourists flock to Washington, D.C. every spring to see the cherry trees blossom. Once in the city, they must find their way to the Tidal Basin where the Japanese trees grow. Fortunately, a number of visual landmarks can help them to navigate. In 1910, the United States Congress passed The Height of Buildings Act, limiting the elevation of commercial and residential structures in D.C. to 130 feet. Thus, the 555-foot-tall Washington Monument often looms large against the horizon, serving as an anchor point to help set the tourists{\textquoteright} sense of direction. Once their heading is set, they can lose sight of the monument behind buildings or groups of tall Scandinavian visitors and still use their internal compass to navigate to the Basin. This compass keeps track of their paces and turns and updates their sense of where they are and where they need to go. Yet while their heading informs their actions, it does not dictate them. Tourists who have been to D.C. in the past can, for example, use remembered views to alter their routes to avoid crowds. On an even finer scale, their leg movements also depend on their current state - they might increase the frequency and length of their strides if hunger pangs compete with their desire to see cherry blossoms, for example. The way in which these disparate cues and motivations influence exploration is a neuroscience mystery across creatures large and small.

}, keywords = {Animals, Brain, Cues, Insecta, Spatial Navigation, Vision, Ocular}, issn = {1879-0445}, doi = {10.1016/j.cub.2016.04.006}, author = {Turner-Evans, Daniel B and Jayaraman, Vivek} } @conference {48194, title = {Learning a metric for class-conditional KNN.}, booktitle = {International Joint Conference on Neural Networks, IJCNN 2016}, year = {2016}, month = {2016 Oct 31}, address = {Vancouver, British Columbia, Canada}, abstract = {

Na{\"\i}ve Bayes Nearest Neighbour (NBNN) is a simple and effective framework which addresses many of the pitfalls of K-Nearest Neighbour (KNN) classification. It has yielded competitive results on several computer vision benchmarks. Its central tenet is that during NN search, a query is not compared to every example in a database, ignoring class information. Instead, NN searches are performed within each class, generating a score per class. A key problem with NN techniques, including NBNN, is that they fail when the data representation does not capture perceptual (e.g. class-based) similarity. NBNN circumvents this by using independent engineered descriptors (e.g. SIFT). To extend its applicability outside of image-based domains, we propose to learn a metric which captures perceptual similarity. Similar to how Neighbourhood Components Analysis optimizes a differentiable form of KNN classification, we propose {\textquoteright}Class Conditional{\textquoteright} metric learning (CCML), which optimizes a soft form of the NBNN selection rule. Typical metric learning algorithms learn either a global or local metric. However, our proposed method can be adjusted to a particular level of locality by tuning a single parameter. An empirical evaluation on classification and retrieval tasks demonstrates that our proposed method clearly outperforms existing learned distance metrics across a variety of image and non-image datasets.

}, doi = {10.1109/IJCNN.2016.7727436}, author = {Im, Daniel Jiwoong and Taylor, Graham W} } @article {47399, title = {Lineage mapping identifies molecular and architectural similarities between the larval and adult Drosophila central nervous system.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016}, abstract = {

Neurogenesis in Drosophila occurs in two phases, embryonic and post-embryonic, in which the same set of neuroblasts give rise to the distinct larval and adult nervous systems, respectively. Here, we identified the embryonic neuroblast origin of the adult neuronal lineages in the ventral nervous system via lineage-specific GAL4 lines and molecular markers. Our lineage mapping revealed that neurons born late in the embryonic phase show axonal morphology and transcription factor profiles that are similar to the neurons born post-embryonically from the same neuroblast. Moreover, we identified three thorax-specific neuroblasts not previously characterized and show that HOX genes confine them to the thoracic segments. Two of these, NB2-3 and NB3-4, generate leg motor neurons. The other neuroblast is novel and appears to have arisen recently during insect evolution. Our findings provide a comprehensive view of neurogenesis and show how proliferation of individual neuroblasts is dictated by temporal and spatial cues.

}, issn = {2050-084X}, doi = {10.7554/eLife.13399}, author = {Lacin, Haluk and Truman, James W} } @article {47933, title = {Live-cell single-molecule tracking reveals co-recognition of H3K27me3 and DNA targets polycomb Cbx7-PRC1 to chromatin.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Oct 10}, abstract = {

The Polycomb PRC1 plays essential roles in development and disease pathogenesis. Targeting of PRC1 to chromatin is thought to be mediated by the Cbx family proteins (Cbx2/4/6/7/8) binding to histone H3 with a K27me3 modification (H3K27me3). Despite this prevailing view, the molecular mechanisms of targeting remain poorly understood. Here, by combining live-cell single-molecule tracking (SMT) and genetic engineering, we reveal that H3K27me3 contributes significantly to the targeting of Cbx7 and Cbx8 to chromatin, but less to Cbx2, Cbx4, and Cbx6. Genetic disruption of the complex formation of PRC1 facilitates the targeting of Cbx7 to chromatin. Biochemical analyses uncover that the CD and AT-hook-like (ATL) motif of Cbx7 constitute a functional DNA-binding unit. Live-cell SMT of Cbx7 mutants demonstrates that Cbx7 is targeted to chromatin by co-recognizing of H3K27me3 and DNA. Our data suggest a novel hierarchical cooperation mechanism by which histone modifications and DNA coordinate to target chromatin regulatory complexes.

}, issn = {2050-084X}, doi = {10.7554/eLife.17667}, author = {Zhen, Chao Yu and Tatavosian, Roubina and Huynh, Thao Ngoc and Duc, Huy Nguyen and Das, Raibatak and Kokotovic, Marko and Grimm, Jonathan B and Lavis, Luke D and Lee, Jun and Mejia, Frances J and Li, Yang and Yao, Tingting and Ren, Xiaojun} } @article {47383, title = {A mammalian enhancer trap resource for discovering and manipulating neuronal cell types.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Mar 21}, abstract = {

There is a continuing need for driver strains to enable cell type-specific manipulation in the nervous system. Each cell type expresses a unique set of genes, and recapitulating expression of marker genes by BAC transgenesis or knock-in has generated useful transgenic mouse lines. However since genes are often expressed in many cell types, many of these lines have relatively broad expression patterns. We report an alternative transgenic approach capturing distal enhancers for more focused expression. We identified an enhancer trap probe often producing restricted reporter expression and developed efficient enhancer trap screening with the PiggyBac transposon. We established more than 200 lines and found many lines that label small subsets of neurons in brain substructures, including known and novel cell types. Images and other information about each line are available online (enhancertrap.bio.brandeis.edu).

}, issn = {2050-084X}, doi = {10.7554/eLife.13503}, author = {Shima, Yasuyuki and Sugino, Ken and Hempel, Chris and Shima, Masami and Taneja, Praveen and Bullis, James B and Mehta, Sonam and Lois, Carlos and Nelson, Sacha B} } @article {47752, title = {MLlib: Machine learning in Apache Spark.}, journal = {Journal of Machine Learning Research}, volume = {17}, year = {2016}, month = {2016 Apr 01}, pages = {1-7}, abstract = {

Apache Spark is a popular open-source platform for large-scale data processing that is well-suited for iterative machine learning tasks. In this paper we present MLlib, Spark{\textquoteright}s open-source distributed machine learning library. MLlib provides efficient functionality for a wide range of learning settings and includes several underlying statistical, optimization, and linear algebra primitives. Shipped with Spark, MLlib supports several languages and provides a high-level API that leverages Spark{\textquoteright}s rich ecosystem to simplify the development of end-to-end machine learning pipelines. MLlib has experienced a rapid growth due to its vibrant open-source community of over 140 contributors, and includes extensive documentation to support further growth and to let users quickly get up to speed.\ 

}, url = {http://www.jmlr.org/papers/volume17/15-237/15-237.pdf}, author = {Meng, Xiangrui and Bradley, Joseph and Yavus, Burak and Sparks, Evan and Venkataraman, Shivaram and Liu, Davies and Freeman, Jeremy and Tsai, D B and Amde, Manish and Owen, Sean and Xin, Doris and Franklin, Michael J and Zadeh, Reza and Zaharia, Matei and Talwalkar, Ameet} } @article {47424, title = {Movement and structure of mitochondria in oligodendrocytes and their myelin sheaths.}, journal = {Glia}, volume = {64}, year = {2016}, month = {2016 May}, pages = {810-25}, abstract = {

Mitochondria play several crucial roles in the life of oligodendrocytes. During development of the myelin sheath they are essential providers of carbon skeletons and energy for lipid synthesis. During normal brain function their consumption of pyruvate will be a key determinant of how much lactate is available for oligodendrocytes to export to power axonal function. Finally, during calcium-overload induced pathology, as occurs in ischemia, mitochondria may buffer calcium or induce apoptosis. Despite their important functions, very little is known of the properties of oligodendrocyte mitochondria, and mitochondria have never been observed in the myelin sheaths. We have now used targeted expression of fluorescent mitochondrial markers to characterize the location and movement of mitochondria within oligodendrocytes. We show for the first time that mitochondria are able to enter and move within the myelin sheath. Within the myelin sheath the highest number of mitochondria was in the cytoplasmic ridges along the sheath. Mitochondria moved more slowly than in neurons and, in contrast to their behavior in neurons and astrocytes, their movement was increased rather than inhibited by glutamate activating NMDA receptors. By electron microscopy we show that myelin sheath mitochondria have a low surface area of cristae, which suggests a low ATP production. These data specify fundamental properties of the oxidative phosphorylation system in oligodendrocytes, the glial cells that enhance cognition by speeding action potential propagation and provide metabolic support to axons. GLIA 2016;64:810-825.

}, issn = {1098-1136}, doi = {10.1002/glia.22965}, author = {Rinholm, Johanne E and Vervaeke, Koen and Tadross, Michael R and Tkachuk, Ariana N and Kopek, Benjamin G and Brown, Timothy A and Bergersen, Linda H and Clayton, David A} } @article {47552, title = {Near-perfect synaptic integration by Nav1.7 in hypothalamic neurons regulates body weight.}, journal = {Cell}, volume = {165}, year = {2016}, month = {2016 Jun 16}, pages = {1749-61}, abstract = {

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

}, doi = {10.1016/j.cell.2016.05.019}, author = {Branco, Tiago and Tozer, Adam and Magnus, Christopher J and Sugino, Ken and Tanaka, Shinsuke and Lee, Albert K and Wood, John N and Sternson, Scott M} } @article {47305, title = {Postembryonic lineages of the Drosophila ventral nervous system: Neuroglian expression reveals the adult hemilineage associated fiber tracts in the adult thoracic neuromeres.}, journal = {The Journal of Comparative Neurology}, volume = {524}, year = {2016}, month = {2016 Feb 15}, pages = {2677-95}, abstract = {

During larval life most of the thoracic neuroblasts (NBs) in Drosophila undergo a second phase of neurogenesis to generate adult-specific neurons that remain in an immature, developmentally stalled state until pupation. Using a combination of MARCM and immunostaining with a neurotactin antibody Truman et al. (2004) identified 24 adult specific NB lineages within each thoracic hemineuromere of the larval ventral nervous system (VNS) but because the neurotactin labeling of lineage tracts disappearing early in metamorphosis they were unable extend the identification of the these lineages into the adult. Here we show that immunostaining with an antibody against the cell adhesion molecule Neuroglian reveals the same larval secondary lineage projections through metamorphosis and by identifying each neuroglian positive tract at selected stages we have traced the larval hemilineage tracts for all three thoracic neuromeres through metamorphosis into the adult. To validate tract identifications we used the genetic toolkit developed by Harris et al. (2015) to preserve hemilineage specific GAL4 expression patterns from larval into the adult stage. The immortalized expression proved a powerful confirmation of the analysis of the neuroglian scaffold. This work has enabled us to directly link the secondary, larval NB lineages to their adult counterparts. The data provide an anatomical framework that 1) makes it possible to assign most neurons to their parent lineage and 2) allows more precise definitions of the neuronal organization of the adult VNS based in developmental units/rules. This article is protected by copyright. All rights reserved.

}, issn = {1096-9861}, doi = {10.1002/cne.23988}, author = {Shepherd, David and Harris, Robin and Williams, Darren and Truman, James W} } @article {47382, title = {Practice makes perfect in memory recall.}, journal = {Learning \& Memory (Cold Spring Harbor, N.Y.)}, volume = {23}, year = {2016}, month = {2016 Apr}, pages = {169-73}, abstract = {

A large variability in performance is observed when participants recall briefly presented lists of words. The sources of such variability are not known. Our analysis of a large data set of free recall revealed a small fraction of participants that reached an extremely high performance, including many trials with the recall of complete lists. Moreover, some of them developed a number of consistent input-position-dependent recall strategies, in particular recalling words consecutively ("chaining") or in groups of consecutively presented words ("chunking"). The time course of acquisition and particular choice of positional grouping were variable among participants. Our results show that acquiring positional strategies plays a crucial role in improvement of recall performance.

}, issn = {1549-5485}, doi = {10.1101/lm.041178.115}, author = {Romani, Sandro and Katkov, Mikhail and Tsodyks, Misha} } @article {47410, title = {A primer on the Bayesian approach to high-density single-molecule trajectories analysis.}, journal = {Biophysical Journal}, volume = {110}, year = {2016}, month = {2016 Mar 29}, pages = {1209-15}, abstract = {

Tracking single molecules in living cells provides invaluable information on their environment and on the interactions that underlie their motion. New experimental techniques now permit the recording of large amounts of individual trajectories, enabling the implementation of advanced statistical tools for data analysis. In this primer, we present a Bayesian approach toward treating these data, and we discuss how it can be fruitfully employed to infer physical and biochemical parameters from single-molecule trajectories.

}, issn = {1542-0086}, doi = {10.1016/j.bpj.2016.01.018}, author = {El Beheiry, Mohamed and T{\"u}rkcan, Silvan and Richly, Maximilian U and Triller, Antoine and Alexandrou, Antigone and Dahan, Maxime and Masson, Jean-Baptiste} } @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 {47741, title = {Real-time imaging of Huntingtin aggregates diverting target search and gene transcription.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Aug 03}, abstract = {

The presumptive altered dynamics of transient molecular interactions in vivo contributing to neurodegenerative diseases have remained elusive. Here, using single-molecule localization microscopy, we show that disease-inducing Huntingtin (mHtt) protein fragments display three distinct dynamic states in living cells - 1) fast diffusion, 2) dynamic clustering and 3) stable aggregation. Large, stable aggregates of mHtt exclude chromatin and form {\textquoteright}sticky{\textquoteright} decoy traps that impede target search processes of key regulators involved in neurological disorders. Functional domain mapping based on super-resolution imaging reveals an unexpected role of aromatic amino acids in promoting protein-mHtt aggregate interactions. Genome-wide expression analysis and numerical simulation experiments suggest mHtt aggregates reduce transcription factor target site sampling frequency and impair critical gene expression programs in striatal neurons. Together, our results provide insights into how mHtt dynamically forms aggregates and disrupts the finely-balanced gene control mechanisms in neuronal cells.

}, issn = {2050-084X}, doi = {10.7554/eLife.17056}, author = {Li, Li and Liu, Hui and Dong, Peng and Li, Dong and Legant, Wesley R and Grimm, Jonathan B and Lavis, Luke D and Betzig, Eric and Tjian, Robert and Liu, Zhe} } @article {47267, title = {Real-time three-dimensional cell segmentation in large-scale microscopy data of developing embryos.}, journal = {Developmental Cell}, volume = {36}, year = {2016}, month = {2016 Jan 25}, pages = {225-40}, abstract = {

We present the Real-time Accurate Cell-shape Extractor (RACE), a high-throughput image analysis framework for automated three-dimensional cell segmentation in large-scale images. RACE is 55{\textendash}330 times faster and 2{\textendash}5 times more accurate than state-of-the-art methods. We demonstrate the generality of RACE by extracting cell-shape information from entire Drosophila, zebrafish, and mouse embryos imaged with confocal and light-sheet microscopes. Using RACE, we automatically reconstructed cellular-resolution tissue anisotropy maps across developing Drosophila embryos and quantified differences in cell-shape dynamics in wild-type and mutant embryos. We furthermore integrated RACE with our framework for automated cell lineaging and performed joint segmentation and cell tracking in entire Drosophila embryos. RACE processed these terabyte-sized datasets on a single computer within 1.4\ days. RACE is easy to use, as it requires adjustment of only three parameters, takes full advantage of state-of-the-art multi-core processors and graphics cards, and is available as open-source software for Windows, Linux, and Mac\ OS.

}, doi = {10.1016/j.devcel.2015.12.028}, author = {Stegmaier, Johannes and Amat, Fernando and Lemon, William C and McDole, Katie and Wan, Yinan and Teodoro, George and Mikut, Ralf and Keller, Philipp J} } @article {47440, title = {Repulsive cues combined with physical barriers and cell{\textendash}cell adhesion determine progenitor cell positioning during organogenesis}, journal = {Nature Communications}, volume = {7}, year = {2016}, month = {2016 Apr 18}, pages = {11288}, abstract = {

The precise positioning of organ progenitor cells constitutes an essential, yet poorly understood step during organogenesis. Using primordial germ cells that participate in gonad formation, we present the developmental mechanisms maintaining a motile progenitor cell population at the site where the organ develops. Employing high-resolution live-cell microscopy, we find that repulsive cues coupled with physical barriers confine the cells to the correct bilateral positions. This analysis revealed that cell polarity changes on interaction with the physical barrier and that the establishment of compact clusters involves increased cell-cell interaction time. Using particle-based simulations, we demonstrate the role of reflecting barriers, from which cells turn away on contact, and the importance of proper cell-cell adhesion level for maintaining the tight cell clusters and their correct positioning at the target region. The combination of these developmental and cellular mechanisms prevents organ fusion, controls organ positioning and is thus critical for its proper function.

}, doi = {10.1038/ncomms11288}, author = {Paksa, Azadeh and Bandemer, Jan and H{\"o}ckendorf, Burkhard and Razin, Nitzan and Tarbashevich, Katsiaryna and Minina, Sofia and Meyen, Dana and Gov, Nir S and Keller, Philipp J and Raz, Erez} } @article {47538, title = {A screen for constituents of motor control and decision making in Drosophila reveals visual distance-estimation neurons.}, journal = {Scientific Reports}, volume = {6}, year = {2016}, month = {2016}, pages = {27000}, abstract = {

Climbing over chasms larger than step size is vital to fruit flies, since foraging and mating are achieved while walking. Flies avoid futile climbing attempts by processing parallax-motion vision to estimate gap width. To identify neuronal substrates of climbing control, we screened a large collection of fly lines with temporarily inactivated neuronal populations in a novel high-throughput assay described here. The observed climbing phenotypes were classified; lines in each group are reported. Selected lines were further analysed by high-resolution video cinematography. One striking class of flies attempts to climb chasms of unsurmountable width; expression analysis guided us to C2 optic-lobe interneurons. Inactivation of C2 or the closely related C3 neurons with highly specific intersectional driver lines consistently reproduced hyperactive climbing whereas strong or weak artificial depolarization of C2/C3 neurons strongly or mildly decreased climbing frequency. Contrast-manipulation experiments support our conclusion that C2/C3 neurons are part of the distance-evaluation system.

}, issn = {2045-2322}, doi = {10.1038/srep27000}, author = {Triphan, Tilman and Nern, Aljoscha and Roberts, Sonia F and Korff, Wyatt and Naiman, Daniel Q and Strauss, Roland} } @article {47698, title = {Selective inhibition mediates the sequential recruitment of motor pools.}, journal = {Neuron}, volume = {91}, year = {2016}, month = {2016 Jul 12}, pages = {615-28}, abstract = {

Locomotor systems generate diverse motor patterns to produce the movements underlying behavior, requiring that motor neurons be recruited at various phases of the locomotor cycle. Reciprocal inhibition produces alternating motor patterns; however, the mechanisms that generate other phasic relationships between intrasegmental motor pools are unknown. Here, we investigate one such motor pattern in the Drosophila larva, using a multidisciplinary approach including electrophysiology and ssTEM-based circuit reconstruction. We find that two motor pools that are sequentially recruited during locomotion have identical excitable properties. In contrast, they receive input from divergent premotor circuits. We find that this motor pattern is not orchestrated by differential excitatory input but by a GABAergic interneuron acting as a delay line to the later-recruited motor pool. Our findings show how a motor pattern is generated as a function of the modular organization of locomotor networks through segregation of\ inhibition, a potentially general mechanism for sequential motor patterns.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2016.06.031}, author = {Zwart, Maarten F and Pulver, Stefan R and Truman, James W and Fushiki, Akira and Cardona, Albert and Landgraf, Matthias} } @article {47396, title = {Sensitive red protein calcium indicators for imaging neural activity.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Mar 24}, abstract = {

Genetically encoded calcium indicators (GECIs) allow measurement of activity in large populations of neurons and in small neuronal compartments, over times of milliseconds to months. Although GFP-based GECIs are widely used for in vivo neurophysiology, GECIs with red-shifted excitation and emission spectra have advantages for in vivo imaging because of reduced scattering and absorption in tissue, and a consequent reduction in phototoxicity. However, current red GECIs are inferior to the state-of-the-art GFP-based GCaMP6 indicators for detecting and quantifying neural activity. Here we present improved red GECIs based on mRuby (jRCaMP1a, b) and mApple (jRGECO1a), with sensitivity comparable to GCaMP6. We characterized the performance of the new red GECIs in cultured neurons and in mouse, Drosophila, zebrafish and C. elegans in vivo. Red GECIs facilitate deep-tissue imaging, dual-color imaging together with GFP-based reporters, and the use of optogenetics in combination with calcium imaging.

}, issn = {2050-084X}, doi = {10.7554/eLife.12727}, author = {Dana, Hod and Mohar, Boaz and Sun, Yi and Narayan, Sujatha and Gordus, Andrew and Hasseman, Jeremy P and Tsegaye, Getahun and Holt, Graham T and Hu, Amy and Walpita, Deepika and Patel, Ronak and Macklin, John J and Bargmann, Cornelia I and Ahrens, Misha B and Schreiter, Eric R and Jayaraman, Vivek and Looger, Loren L and Svoboda, Karel and Kim, Douglas S} } @article {47315, title = {Sequential ionic and conformational signaling by calcium channels drives neuronal gene expression.}, journal = {Science (New York, N.Y.)}, volume = {351}, year = {2016}, month = {2016 Feb 19}, pages = {863-7}, abstract = {

Voltage-gated CaV1.2 channels (L-type calcium channel α1C subunits) are critical mediators of transcription-dependent neural plasticity. Whether these channels signal via the influx of calcium ion (Ca2+), voltage-dependent conformational change (VΔC), or a combination of the two has thus far been equivocal. We fused CaV1.2 to a ligand-gated Ca2+-permeable channel, enabling independent control of localized Ca2+\ and VΔC signals. This revealed an unexpected dual requirement: Ca2+\ must first mobilize actin-bound Ca2+/calmodulin-dependent protein kinase II, freeing it for subsequent VΔC-mediated accumulation. Neither signal alone sufficed to activate transcription. Signal order was crucial: Efficiency peaked when Ca2+\ preceded VΔC by 10 to 20 seconds. CaV1.2 VΔC synergistically augmented signaling by\ N-methyl-D-aspartate receptors. Furthermore, VΔC mistuning correlated with autistic symptoms in Timothy syndrome. Thus, nonionic VΔC signaling is vital to the function of CaV1.2 in synaptic and neuropsychiatric processes.

}, doi = {10.1126/science.aad3647}, author = {Li, Boxing and Tadross, Michael R and Tsien, Richard W} } @article {47323, title = {Sex-specific regulation of Lgr3 in Drosophila neurons.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, year = {2016}, month = {2016 Feb 18}, abstract = {

The development of sexually dimorphic morphology and the potential for sexually dimorphic behavior in Drosophila are regulated by the Fruitless (Fru) and Doublesex (Dsx) transcription factors. Several direct targets of Dsx have been identified, but direct Fru targets have not been definitively identified. We show that Drosophila leucine-rich repeat G protein-coupled receptor 3 (Lgr3) is regulated by Fru and Dsx in separate populations of neurons. Lgr3 is a member of the relaxin-receptor family and a receptor for Dilp8, necessary for control of organ growth. Lgr3 expression in the anterior central brain of males is inhibited by the B isoform of Fru, whose DNA binding domain interacts with a short region of an Lgr3 intron. Fru A and C isoform mutants had no observed effect on Lgr3 expression. The female form of Dsx (Dsx(F)) separately up- and down-regulates Lgr3 expression in distinct neurons in the abdominal ganglion through female- and male-specific Lgr3 enhancers. Excitation of neural activity in the Dsx(F)-up-regulated abdominal ganglion neurons inhibits female receptivity, indicating the importance of these neurons for sexual behavior. Coordinated regulation of Lgr3 by Fru and Dsx marks a point of convergence of the two branches of the sex-determination hierarchy.

}, issn = {1091-6490}, doi = {10.1073/pnas.1600241113}, author = {Meissner, Geoffrey W and Luo, Shengzhan D and Dias, Brian G and Texada, Michael J and Baker, Bruce S} } @article {48116, title = {Sonic Hedgehog Pathway activation increases mitochondrial abundance and activity in hippocampal neurons.}, journal = {Molecular Biology of the Cell}, year = {2016}, month = {2016 Dec 08}, abstract = {

Mitochondria are essential organelles whose biogenesis, structure, and function are regulated by many signaling pathways. In this study we present evidence that, in hippocampal neurons, activation of the Sonic hedgehog (Shh) signaling pathway impacts multiple aspects of mitochondria. Mitochondrial mass was increased significantly in neurons treated with Shh. Using biochemical and fluorescence imaging analyses, we show that Shh signaling activity reduces mitochondrial fission and promotes mitochondrial elongation, at least in part, via suppression of the mitochondrial fission protein dynamin-like GTPase Drp1. Mitochondria from Shh-treated neurons were more electron-dense as revealed by electron microscopy, and had higher membrane potential and respiratory activity. We further show that Shh protects neurons against a variety of stresses, including the mitochondrial poison rotenone, amyloid β-peptide, hydrogen peroxide, and high levels of glutamate. Collectively, our data suggest a link between Shh pathway activity and the physiological properties of mitochondria in hippocampal neurons.

}, issn = {1939-4586}, doi = {10.1091/mbc.E16-07-0553}, author = {Yao, Pamela J and Manor, Uri and Petralia, Ronald S and Brose, Rebecca D and Wu, Ryan T Y and Ott, Carolyn and Wang, Ya-Xian and Charnoff, Ari and Lippincott-Schwartz, Jennifer and Mattson, Mark P} } @article {65891, title = {Spatially resolved proteomic mapping in living cells with the engineered peroxidase APEX2}, journal = {Nature Protocols}, volume = {11}, year = {2016}, month = {Jan-03-2016}, pages = {456 - 475}, abstract = {

This protocol describes a method to obtain spatially resolved proteomic maps of specific compartments within living mammalian cells. An engineered peroxidase, APEX2, is genetically targeted to a cellular region of interest. Upon the addition of hydrogen peroxide for 1 min to cells preloaded with a biotin-phenol substrate, APEX2 generates biotin-phenoxyl radicals that covalently tag proximal endogenous proteins. Cells are then lysed, and biotinylated proteins are enriched with streptavidin beads and identified by mass spectrometry. We describe the generation of an appropriate APEX2 fusion construct, proteomic sample preparation, and mass spectrometric data acquisition and analysis. A two-state stable isotope labeling by amino acids in cell culture (SILAC) protocol is used for proteomic mapping of membrane-enclosed cellular compartments from which APEX2-generated biotin-phenoxyl radicals cannot escape. For mapping of open cellular regions, we instead use a {\textquoteright}ratiometric{\textquoteright} three-state SILAC protocol for high spatial specificity. Isotopic labeling of proteins takes 5{\textendash}7 cell doublings. Generation of the biotinylated proteomic sample takes 1 d, acquiring the mass spectrometric data takes 2{\textendash}5 d and analysis of the data to obtain the final proteomic list takes 1 week.

}, issn = {1754-2189}, doi = {10.1038/nprot.2016.018}, url = {http://www.nature.com/articles/nprot.2016.018http://www.nature.com/articles/nprot.2016.018.pdfhttp://www.nature.com/articles/nprot.2016.018.pdfhttp://www.nature.com/articles/nprot.2016.018}, author = {Hung, Victoria and Udeshi, Namrata D and Lam, Stephanie S and Loh, Ken H and Cox, Kurt J and Pedram, Kayvon and Carr, Steven A and Ting, Alice Y} } @article {48093, title = {Structure of a Holliday junction complex reveals mechanisms governing a highly regulated DNA transaction.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 May 25}, abstract = {

The molecular machinery responsible for DNA expression, recombination, and compaction has been difficult to visualize as functionally complete entities due to their combinatorial and structural complexity. We report here the structure of the intact functional assembly responsible for regulating and executing a site-specific DNA recombination reaction. The assembly is a 240-bp Holliday junction (HJ) bound specifically by 11 protein subunits. This higher-order complex is a key intermediate in the tightly regulated pathway for the excision of bacteriophage λ viral DNA out of the E. coli host chromosome, an extensively studied paradigmatic model system for the regulated rearrangement of DNA. Our results provide a structural basis for pre-existing data describing the excisive and integrative recombination pathways, and they help explain their regulation.

}, issn = {2050-084X}, doi = {10.7554/eLife.14313}, author = {Laxmikanthan, Gurunathan and Xu, Chen and Brilot, Axel F and Warren, David and Steele, Lindsay and Seah, Nicole and Tong, Wenjun and Grigorieff, Nikolaus and Landy, Arthur and Van Duyne, Gregory D} } @article {48045, title = {Synaptic transmission parallels neuromodulation in a central food-intake circuit.}, journal = {eLife}, year = {2016}, month = {2016 Nov 15}, abstract = {

NeuromedinU is a potent regulator of food intake and activity in mammals. In\ Drosophila, neurons producing the homologous neuropeptide hugin regulate feeding and locomotion in a similar manner. Here, we use EM-based reconstruction to generate the entire connectome of hugin-producing neurons in the\ Drosophila\ larval CNS. We demonstrate that hugin neurons use synaptic transmission in addition to peptidergic neuromodulation and identify acetylcholine as a key transmitter. Hugin neuropeptide and acetylcholine are both necessary for the regulatory effect on feeding. We further show that subtypes of hugin neurons connect chemosensory to endocrine system by combinations of synaptic and peptide-receptor connections. Targets include endocrine neurons producing DH44, a CRH-like peptide, and insulin-like peptides. Homologs of these peptides are likewise downstream of neuromedinU, revealing striking parallels in flies and mammals. We propose that hugin neurons are part of an ancient physiological control system that has been conserved at functional and molecular level.

}, doi = {10.7554/eLife.16799}, author = {Schlegel, Philipp and Texada, Michael J and Miroschnikow, Anton and Schoofs, Andreas and H{\"u}ckesfeld, Sebastian and Peters, Marc and Schneider-Mizell, Casey M and Lacin, Haluk and Li, Feng and Fetter, Richard D and Truman, James W and Cardona, Albert and Pankratz, Michael J} } @article {47265, title = {Thalamus provides layer 4 of primary visual cortex with orientation- and direction-tuned inputs.}, journal = {Nature Neuroscience}, volume = {19}, year = {2016}, month = {2016 Feb}, pages = {308-15}, abstract = {

Understanding the functions of a brain region requires knowing the neural representations of its myriad inputs, local neurons and outputs. Primary visual cortex (V1) has long been thought to compute visual orientation from untuned thalamic inputs, but very few thalamic inputs have been measured in any mammal. We determined the response properties of ~28,000 thalamic boutons and ~4,000 cortical neurons in layers 1{\textendash}5 of awake mouse V1. Using adaptive optics that allows accurate measurement of bouton activity deep in cortex, we found that around half of the boutons in the main thalamorecipient L4 carried orientation-tuned information and that their orientation and direction biases were also dominant in the L4 neuron population, suggesting that these neurons may inherit their selectivity from tuned thalamic inputs. Cortical neurons in all layers exhibited sharper tuning than thalamic boutons and a greater diversity of preferred orientations. Our results provide data-rich constraints for refining mechanistic models of cortical computation.

}, doi = {10.1038/nn.4196}, author = {Sun, Wenzhi and Tan, Zhongchao and Mensh, Brett D and Ji, Na} } @article {47306, title = {Toward the neural implementation of structure learning.}, journal = {Current Opinion in Neurobiology}, volume = {37}, year = {2016}, month = {2016 Feb 11}, pages = {99-105}, abstract = {

Despite significant advances in neuroscience, the neural bases of intelligence remain poorly understood. Arguably the most elusive aspect of intelligence is the ability to make robust inferences that go far beyond one{\textquoteright}s experience. Animals categorize objects, learn to vocalize and may even estimate causal relationships - all in the face of data that is often ambiguous and sparse. Such inductive leaps are thought to result from the brain{\textquoteright}s ability to infer latent structure that governs the environment. However, we know little about the neural computations that underlie this ability. Recent advances in developing computational frameworks that can support efficient structure learning and inductive inference may provide insight into the underlying component processes and help pave the path for uncovering their neural implementation.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2016.01.014}, author = {Tervo, D Gowan and Tenenbaum, Joshua B and Gershman, Samuel J} } @article {47486, title = {The wiring diagram of a glomerular olfactory system.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 May 13}, abstract = {

The sense of smell enables animals to react to long-distance cues according to learned and innate valences. Here, we have mapped with electron microscopy the complete wiring diagram of the Drosophila larval antennal lobe, an olfactory neuropil similar to the vertebrate olfactory bulb. We found a canonical circuit with uniglomerular projection neurons (uPNs) relaying gain-controlled ORN activity to the mushroom body and the lateral horn. A second, parallel circuit with multiglomerular projection neurons (mPNs) and hierarchically connected local neurons (LNs) selectively integrates multiple ORN signals already at the first synapse. LN-LN synaptic connections putatively implement a bistable gain control mechanism that either computes odor saliency through panglomerular inhibition, or allows some glomeruli to respond to faint aversive odors in the presence of strong appetitive odors. This complete wiring diagram will support experimental and theoretical studies towards bridging the gap between circuits and behavior.

}, issn = {2050-084X}, doi = {10.7554/eLife.14859}, author = {Berck, Matthew E and Khandelwal, Avinash and Claus, Lindsey and Hernandez-Nunez, Luis and Si, Guangwei and Tabone, Christopher J and Li, Feng and Truman, James W and Fetter, Richard D and Louis, Matthieu and Samuel, Aravinthan Dt and Cardona, Albert} } @article {47162, title = {The 2015 super-resolution microscopy roadmap.}, journal = {Journal of Physics D: Applied Physics}, volume = {48}, year = {2015}, month = {2015 Oct 14}, pages = {443001}, abstract = {

Far-field optical microscopy using focused light is an important tool in a number of scientific disciplines including chemical, (bio)physical and biomedical research, particularly with respect to the study of living cells and organisms. Unfortunately, the applicability of the optical microscope is limited, since the diffraction of light imposes limitations on the spatial resolution of the image. Consequently the details of, for example, cellular protein distributions, can be visualized only to a certain extent. Fortunately, recent years have witnessed the development of {\textquoteright}super-resolution{\textquoteright} far-field optical microscopy (nanoscopy) techniques such as stimulated emission depletion (STED), ground state depletion (GSD), reversible saturated optical (fluorescence) transitions (RESOLFT), photoactivation localization microscopy (PALM), stochastic optical reconstruction microscopy (STORM), structured illumination microscopy (SIM) or saturated structured illumination microscopy (SSIM), all in one way or another addressing the problem of the limited spatial resolution of far-field optical microscopy. While SIM achieves a two-fold improvement in spatial resolution compared to conventional optical microscopy, STED, RESOLFT, PALM/STORM, or SSIM have all gone beyond, pushing the limits of optical image resolution to the nanometer scale. Consequently, all super-resolution techniques open new avenues of biomedical research. Because the field is so young, the potential capabilities of different super-resolution microscopy approaches have yet to be fully explored, and uncertainties remain when considering the best choice of methodology. Thus, even for experts, the road to the future is sometimes shrouded in mist. The super-resolution optical microscopy roadmap of\ Journal of Physics D: Applied Physicsaddresses this need for clarity. It provides guidance to the outstanding questions through a collection of short review articles from experts in the field, giving a thorough discussion on the concepts underlying super-resolution optical microscopy, the potential of different approaches, the importance of label optimization (such as reversible photoswitchable proteins) and applications in which these methods will have a significant impact.

}, doi = {10.1088/0022-3727/48/44/443001}, author = {Hell, Stefan W and Sahl, Steffen J and Bates, Mark and Zhuang, Xiaowei and Heintzmann, Rainer and Booth, Martin J and Bewersdorf, Joerg and Shtengel, Gleb and Hess, Harald F and Tinnefeld, Philip} } @article {65782, title = {Artificial metalloenzymes derived from three-helix bundles.}, journal = {Current Opinion in Chemical Biology}, volume = {25C}, year = {2015}, month = {01/2015}, pages = {65 {\textendash} 70}, abstract = {

Three-helix bundles and coiled-coil motifs are well-established de novo designed scaffolds that have been investigated for their metal-binding and catalytic properties. Satisfaction of the primary coordination sphere for a given metal is sufficient to introduce catalytic activity and a given structure may catalyze different reactions dependent on the identity of the incorporated metal. Here we describe recent contributions in the de novo design of metalloenzymes based on three-helix bundles and coiled-coil motifs, focusing on non-heme systems for hydrolytic and redox chemistry.

}, doi = {10.1016/j.cbpa.2014.12.034}, author = {Tebo, Alison G and Pecoraro, Vincent L} } @article {46753, title = {Behavioral responses to a repetitive visual threat stimulus express a persistent state of defensive arousal in Drosophila}, journal = {Current Biology}, volume = {25}, year = {2015}, month = {2015 May 14}, pages = {1401-15}, abstract = {

The neural circuit mechanisms underlying emotion states remain poorly understood. Drosophila offers powerful genetic approaches for dissecting neural circuit function, but whether flies exhibit emotion-like behaviors has not been clear. We recently proposed that model organisms may express internal states displaying {\textquotedblleft}emotion primitives,{\textquotedblright} which are general characteristics common to different emotions, rather than specific anthropomorphic emotions such as {\textquotedblleft}fear{\textquotedblright} or {\textquotedblleft}anxiety.{\textquotedblright} These emotion primitives include scalability, persistence, valence, and generalization to multiple contexts. Here, we have applied this approach to determine whether flies{\textquoteright} defensive responses to moving overhead translational stimuli ({\textquotedblleft}shadows{\textquotedblright}) are purely reflexive or may express underlying emotion states. We describe a new behavioral assay in which flies confined in an enclosed arena are repeatedly exposed to an overhead translational stimulus. Repetitive stimuli promoted graded (scalable) and persistent increases in locomotor velocity and hopping, and occasional freezing. The stimulus also dispersed feeding flies from a food resource, suggesting both negative valence and context generalization. Strikingly, there was a significant delay before the flies returned to the food following stimulus-induced dispersal, suggestive of a slowly decaying internal defensive state. The length of this delay was increased when more stimuli were delivered for initial dispersal. These responses can be mathematically modeled by assuming an internal state that behaves as a leaky integrator of stimulus exposure. Our results suggest that flies{\textquoteright} responses to repetitive visual threat stimuli express an internal state exhibiting canonical emotion primitives, possibly analogous to fear in mammals. The mechanistic basis of this state can now be investigated in a genetically tractable insect species.

}, doi = {10.1016/j.cub.2015.03.058}, author = {Gibson, William T. and Gonzalez, Carlos R. and Fernandez, Conchi and Ramasamy, Lakshminarayanan and Tabachnik, Tanya and Du, Rebecca R. and Felsen, Panna D. and Maire, Michael M. and Perona, Pietro and Anderson, David J.} } @article {46817, title = {BigDataViewer: visualization and processing for large image data sets.}, journal = {Nature Methods}, volume = {12}, year = {2015}, month = {2015 May 28}, pages = {481-3}, issn = {1548-7105}, doi = {10.1038/nmeth.3392}, author = {Pietzsch, Tobias and Saalfeld, Stephan and Preibisch, Stephan and Tomancak, Pavel} } @article {47032, title = {CASFISH: CRISPR/Cas9-mediated in situ labeling of genomic loci in fixed cells.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, year = {2015}, month = {2015 Aug 31}, pages = {11870-5}, abstract = {

Direct visualization of genomic loci in the 3D nucleus is important for understanding the spatial organization of the genome and its association with gene expression. Various DNA FISH methods have been developed in the past decades, all involving denaturing dsDNA and hybridizing fluorescent nucleic acid probes. Here we report a novel approach that uses in vitro constituted nuclease-deficient clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated caspase 9 (Cas9) complexes as probes to label sequence-specific genomic loci fluorescently without global DNA denaturation (Cas9-mediated fluorescence in situ hybridization, CASFISH). Using fluorescently labeled nuclease-deficient Cas9 (dCas9) protein assembled with various single-guide RNA (sgRNA), we demonstrated rapid and robust labeling of repetitive DNA elements in pericentromere, centromere, G-rich telomere, and coding gene loci. Assembling dCas9 with an array of sgRNAs tiling arbitrary target loci, we were able to visualize nonrepetitive genomic sequences. The dCas9/sgRNA binary complex is stable and binds its target DNA with high affinity, allowing sequential or simultaneous probing of multiple targets. CASFISH assays using differently colored dCas9/sgRNA complexes allow multicolor labeling of target loci in cells. In addition, the CASFISH assay is remarkably rapid under optimal conditions and is applicable for detection in primary tissue sections. This rapid, robust, less disruptive, and cost-effective technology adds a valuable tool for basic research and genetic diagnosis.

}, issn = {1091-6490}, doi = {10.1073/pnas.1515692112}, author = {Deng, Wulan and Shi, Xinghua and Tjian, Robert and Lionnet, Timoth{\'e}e and Singer, Robert H} } @article {47015, title = {C/D box sRNA-guided 2{\textquoteright}-O-methylation patterns of archaeal rRNA molecules.}, journal = {BMC Genomics}, volume = {16}, year = {2015}, month = {2015 Aug 22}, pages = {632}, abstract = {

BACKGROUND: In archaea and eukaryotes, ribonucleoprotein complexes containing small C/D box s(no)RNAs use base pair complementarity to target specific sites within ribosomal RNA for 2{\textquoteright}-O-ribose methylation. These modifications aid in the folding and stabilization of nascent rRNA molecules and their assembly into ribosomal particles. The genomes of hyperthermophilic archaea encode large numbers of C/D box sRNA genes, suggesting an increased necessity for rRNA stabilization at extreme growth temperatures.

RESULTS: We have identified the complete sets of C/D box sRNAs from seven archaea using RNA-Seq methodology. In total, 489 C/D box sRNAs were identified, each containing two guide regions. A combination of computational and manual analyses predicts 719 guide interactions with 16S and 23S rRNA molecules. This first pan-archaeal description of guide sequences identifies (i) modified rRNA nucleotides that are frequently conserved between species and (ii) regions within rRNA that are hotspots for 2{\textquoteright}-O-methylation. Gene duplication, rearrangement, mutational drift and convergent evolution of sRNA genes and guide sequences were observed. In addition, several C/D box sRNAs were identified that use their two guides to target locations distant in the rRNA sequence but close in the secondary and tertiary structure. We propose that they act as RNA chaperones and facilitate complex folding events between distant sequences.

CONCLUSIONS: This pan-archaeal analysis of C/D box sRNA guide regions identified conserved patterns of rRNA 2{\textquoteright}-O-methylation in archaea. The interaction between the sRNP complexes and the nascent rRNA facilitates proper folding and the methyl modifications stabilize higher order rRNA structure within the assembled ribosome.

}, issn = {1471-2164}, doi = {10.1186/s12864-015-1839-z}, author = {Dennis, Patrick P and Tripp, Vanessa and Lui, Lauren and Lowe, Todd and Randau, Lennart} } @article {47033, title = {Cell type-specific transcriptomics of hypothalamic energy-sensing neuron responses to weight-loss.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Sep 2}, abstract = {

Molecular and cellular processes in neurons are critical for sensing and responding to energy deficit states, such as during weight-loss. AGRP neurons are a key hypothalamic population that is activated during energy deficit and increases appetite and weight-gain. Cell type-specific transcriptomics can be used to identify pathways that counteract weight-loss, and here we report high-quality gene expression profiles of AGRP neurons from well-fed and food-deprived young adult mice. For comparison, we also analyzed POMC neurons, an intermingled population that suppresses appetite and body weight. We find that AGRP neurons are considerably more sensitive to energy deficit than POMC neurons. Furthermore, we identify cell type-specific pathways involving endoplasmic reticulum-stress, circadian signaling, ion channels, neuropeptides, and receptors. Combined with methods to validate and manipulate these pathways, this resource greatly expands molecular insight into neuronal regulation of body weight, and may be useful for devising therapeutic strategies for obesity and eating disorders.

}, issn = {2050-084X}, doi = {10.7554/eLife.09800}, author = {Henry, Fredrick E and Sugino, Ken and Tozer, Adam and Branco, Tiago and Sternson, Scott M} } @article {46546, title = {Cellular levels of signaling factors are sensed by β-actin alleles to modulate transcriptional pulse intensity.}, journal = {Cell Reports}, volume = {11}, year = {2015}, month = {2015 Apr 7}, pages = {419-32}, abstract = {

The transcriptional response of β-actin to extra-cellular stimuli is a paradigm for transcription factor complex assembly and regulation. Serum induction leads to a precisely timed pulse of β-actin transcription in the cell population. Actin protein is proposed to be involved in this response, but it is not known whether cellular actin levels affect nuclear β-actin transcription. We perturbed the levels of key signaling factors and examined the effect on the induced transcriptional pulse by following endogenous β-actin alleles in single living cells. Lowering serum response factor (SRF) protein levels leads to loss of pulse integrity, whereas reducing actin protein levels reveals positive feedback regulation, resulting in elevated gene activation and a prolonged transcriptional response. Thus, transcriptional pulse fidelity requires regulated amounts of signaling proteins, and perturbations in factor levels eliminate the physiological response, resulting in either tuning down or exaggeration of the transcriptional pulse.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2015.03.039}, author = {Kalo, Alon and Kanter, Itamar and Shraga, Amit and Sheinberger, Jonathan and Tzemach, Hadar and Kinor, Noa and Singer, Robert H and Lionnet, Timoth{\'e}e and Shav-Tal, Yaron} } @article {47034, title = {Chemical perturbation of an intrinsically disordered region of TFIID distinguishes two modes of transcription initiation.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Aug 28}, abstract = {

Intrinsically disordered protein regions (IDRs) are peptide segments that fail to form stable 3-dimensional structures in the absence of partner proteins. They are abundant in eukaryotic proteomes and are often associated with human diseases, but their biological functions have been elusive to study. Here we report the identification of a tin(IV) oxochloride-derived cluster that binds an evolutionarily conserved IDR within the metazoan TFIID transcription complex. Binding arrests an isomerization of promoter-bound TFIID that is required for the engagement of Pol II during the first (de novo) round of transcription initiation. However, the specific chemical probe does not affect reinitiation, which requires the re-entry of Pol II, thus, mechanistically distinguishing these two modes of transcription initiation. This work also suggests a new avenue for targeting the elusive IDRs by harnessing certain features of metal-based complexes for mechanistic studies, and for the development of novel pharmaceutical interventions.

}, issn = {2050-084X}, doi = {10.7554/eLife.07777}, author = {Zhang, Zhengjian and Boskovic, Zarko and Hussain, Mahmud M and Hu, Wenxin and Inouye, Carla and Kim, Han-Je and Abole, A Katherine and Doud, Mary K and Lewis, Timothy A and Koehler, Angela N and Schreiber, Stuart L and Tjian, Robert} } @article {46940, title = {A common evolutionary origin for the ON- and OFF-edge motion detection pathways of the Drosophila visual system.}, journal = {Frontiers in Neural Circuits}, volume = {9}, year = {2015}, month = {2015}, pages = {33}, abstract = {

Synaptic circuits for identified behaviors in the Drosophila brain have typically been considered from either a developmental or functional perspective without reference to how the circuits might have been inherited from ancestral forms. For example, two candidate pathways for ON- and OFF-edge motion detection in the visual system act via circuits that use respectively either T4 or T5, two cell types of the fourth neuropil, or lobula plate (LOP), that exhibit narrow-field direction-selective responses and provide input to wide-field tangential neurons. T4 or T5 both have four subtypes that terminate one each in the four strata of the LOP. Representatives are reported in a wide range of Diptera, and both cell types exhibit various similarities in: (1) the morphology of their dendritic arbors; (2) their four morphological and functional subtypes; (3) their cholinergic profile in Drosophila; (4) their input from the pathways of L3 cells in the first neuropil, or lamina (LA), and by one of a pair of LA cells, L1 (to the T4 pathway) and L2 (to the T5 pathway); and (5) their innervation by a single, wide-field contralateral tangential neuron from the central brain. Progenitors of both also express the gene atonal early in their proliferation from the inner anlage of the developing optic lobe, being alone among many other cell type progeny to do so. Yet T4 receives input in the second neuropil, or medulla (ME), and T5 in the third neuropil or lobula (LO). Here we suggest that these two cell types were originally one, that their ancestral cell population duplicated and split to innervate separate ME and LO neuropils, and that a fiber crossing-the internal chiasma-arose between the two neuropils. The split most plausibly occurred, we suggest, with the formation of the LO as a new neuropil that formed when it separated from its ancestral neuropil to leave the ME, suggesting additionally that ME input neurons to T4 and T5 may also have had a common origin.

}, issn = {1662-5110}, doi = {10.3389/fncir.2015.00033}, author = {Shinomiya, Kazunori and Takemura, Shin-ya and Rivlin, Patricia K and Plaza, Stephen M and Scheffer, Louis K and Meinertzhagen, Ian A} } @article {46918, title = {Conjunctive input processing drives feature selectivity in hippocampal CA1 neurons.}, journal = {Nature Neuroscience}, year = {2015}, month = {2015 Jul 13}, abstract = {

Feature-selective firing allows networks to produce representations of the external and internal environments. Despite its importance, the mechanisms generating neuronal feature selectivity are incompletely understood. In many cortical microcircuits the integration of two functionally distinct inputs occurs nonlinearly through generation of active dendritic signals that drive burst firing and robust plasticity. To examine the role of this processing in feature selectivity, we recorded CA1 pyramidal neuron membrane potential and local field potential in mice running on a linear treadmill. We found that dendritic plateau potentials were produced by an interaction between properly timed input from entorhinal cortex and hippocampal CA3. These conjunctive signals positively modulated the firing of previously established place fields and rapidly induced new place field formation to produce feature selectivity in CA1 that is a function of both entorhinal cortex and CA3 input. Such selectivity could allow mixed network level representations that support context-dependent spatial maps.

}, issn = {1546-1726}, doi = {10.1038/nn.4062}, author = {Bittner, Katie C and Grienberger, Christine and Vaidya, Sachin P and Milstein, Aaron D and Macklin, John J and Suh, Junghyup and Tonegawa, Susumu and Magee, Jeffrey C} } @article {46263, title = {Connectome of the fly visual circuitry.}, journal = {Microscopy}, volume = {64}, year = {2015}, month = {2015 Feb}, pages = {37-44}, abstract = {

Recent powerful tools for reconstructing connectomes using electron microscopy (EM) have made outstanding contributions to the field of neuroscience. As a prime example, the detection of visual motion is a classic problem of neural computation, yet our understanding of the exact mechanism has been frustrated by our incomplete knowledge of the relevant neurons and synapses. Recent connectomic studies have successfully identified the concrete neuronal circuit in the fly{\textquoteright}s visual system that computes the motion signals. This identification was greatly aided by the comprehensiveness of the EM reconstruction. Compared with light microscopy, which gives estimated connections from arbor overlap, EM gives unequivocal connections with precise synaptic counts. This paper reviews the recent study of connectomics in a brain of the fruit fly Drosophila and highlights how connectomes can provide a foundation for understanding the mechanism of neuronal functions by identifying the underlying neural circuits.

}, issn = {2050-5701}, doi = {10.1093/jmicro/dfu102}, author = {Takemura, Shin-ya} } @article {46890, title = {Continuous volumetric imaging via an optical phase-locked ultrasound lens.}, journal = {Nature Methods}, volume = {12}, year = {2015}, month = {2015-Jul 13}, pages = {759-62}, abstract = {

In vivo imaging at high spatiotemporal resolution is key to the understanding of complex biological systems. We integrated an optical phase-locked ultrasound lens into a two-photon fluorescence microscope and achieved microsecond-scale axial scanning, thus enabling volumetric imaging at tens of hertz. We applied this system to multicolor volumetric imaging of processes sensitive to motion artifacts, including calcium dynamics in behaving mouse brain and transient morphology changes and trafficking of immune cells.

}, doi = {10.1038/nmeth.3476}, author = {Kong, Lingjie and Tang, Jianyong and Little, Justin P and Yu, Yang and L{\"a}mmermann, Tim and Lin, Charles P and Germain, Ronald N and Cui, Meng} } @article {47159, title = {Crowdsourcing the creation of image segmentation algorithms for connectomics.}, journal = {Frontiers in Neuroanatomy}, volume = {9}, year = {2015}, month = {2015 Nov 05}, pages = {142}, abstract = {

To stimulate progress in automating the reconstruction of neural circuits, we organized the first international challenge on 2D segmentation of electron microscopic (EM) images of the brain. Participants submitted boundary maps predicted for a test set of images, and were scored based on their agreement with a consensus of human expert annotations. The winning team had no prior experience with EM images, and employed a convolutional network. This {\textquotedblleft}deep learning{\textquotedblright} approach has since become accepted as a standard for segmentation of EM images. The challenge has continued to accept submissions, and the best so far has resulted from cooperation between two teams. The challenge has probably saturated, as algorithms cannot progress beyond limits set by ambiguities inherent in 2D scoring and the size of the test dataset. Retrospective evaluation of the challenge scoring system reveals that it was not sufficiently robust to variations in the widths of neurite borders. We propose a solution to this problem, which should be useful for a future 3D segmentation challenge.

}, doi = {10.3389/fnana.2015.00142}, author = {Arganda-Carreras, Ignacio and Turaga, Srinivas C and Berger, Daniel R and Ciresan, Dan and Giusti, Alessandro and Gambardella, Luca M and Schmidhuber, Juergen and Laptev, Dmitry and Dwivedi, Sarvesh and Buhmann, Joachim M} } @article {47215, title = {Direct in~vivo manipulation and imaging of calcium transients in neutrophils identify a critical role for leading-edge calcium flux.}, journal = {Cell Reports}, volume = {13}, year = {2015}, month = {2015 Dec 15}, pages = {2107-17}, abstract = {

Calcium signaling has long been associated with key events of immunity, including chemotaxis, phagocytosis, and activation. However, imaging and manipulation of calcium flux in motile immune cells in live animals remain challenging. Using light-sheet microscopy for in\ vivo calcium imaging in zebrafish, we observe characteristic patterns of calcium flux triggered by distinct events, including phagocytosis of pathogenic bacteria and migration of neutrophils toward inflammatory stimuli. In contrast to findings from ex\ vivo studies, we observe enriched calcium influx at the leading edge of migrating neutrophils. To directly manipulate calcium dynamics in\ vivo, we have developed transgenic lines with cell-specific expression of the mammalian TRPV1 channel, enabling ligand-gated, reversible, and spatiotemporal control of calcium influx. We find that controlled calcium influx can function to help define the neutrophil{\textquoteright}s leading edge. Cell-specific TRPV1 expression may have broad utility for precise control of calcium dynamics in other immune cell types and organisms.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2015.11.010}, author = {Beerman, Rebecca W and Matty, Molly A and Au, Gina G and Looger, Loren L and Choudhury, Kingshuk Roy and Keller, Philipp J and Tobin, David M} } @article {45979, title = {Distinct dopamine neurons mediate reward signals for short- and long-term memories.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, year = {2015}, month = {2015 Jan 13}, pages = {578-83}, abstract = {

Drosophila melanogaster can acquire a stable appetitive olfactory memory when the presentation of a sugar reward and an odor are paired. However, the neuronal mechanisms by which a single training induces long-term memory are poorly understood. Here we show that two distinct subsets of dopamine neurons in the fly brain signal reward for short-term (STM) and long-term memories (LTM). One subset induces memory that decays within several hours, whereas the other induces memory that gradually develops after training. They convey reward signals to spatially segregated synaptic domains of the mushroom body (MB), a potential site for convergence. Furthermore, we identified a single type of dopamine neuron that conveys the reward signal to restricted subdomains of the mushroom body lobes and induces long-term memory. Constant appetitive memory retention after a single training session thus comprises two memory components triggered by distinct dopamine neurons.

}, issn = {1091-6490}, doi = {10.1073/pnas.1421930112}, author = {Yamagata, Nobuhiro and Ichinose, Toshiharu and Aso, Yoshinori and Placais, Pierre-Yves and Friedrich, Anja B and Sima, Richard J and Preat, Thomas and Rubin, Gerald M and Tanimoto, Hiromu} } @article {46975, title = {Drosophila germ granules are structured and contain homotypic mRNA clusters.}, journal = {Nature Communications}, volume = {6}, year = {2015}, month = {2015 Aug 5}, pages = {7962}, abstract = {

Germ granules, specialized ribonucleoprotein particles, are a hallmark of all germ cells. In Drosophila, an estimated 200 mRNAs are enriched in the germ plasm, and some of these have important, often conserved roles in germ cell formation, specification, survival and migration. How mRNAs are spatially distributed within a germ granule and whether their position defines functional properties is unclear. Here we show, using single-molecule FISH and structured illumination microscopy, a super-resolution approach, that mRNAs are spatially organized within the granule whereas core germ plasm proteins are distributed evenly throughout the granule. Multiple copies of single mRNAs organize into {\textquoteright}homotypic clusters{\textquoteright} that occupy defined positions within the center or periphery of the granule. This organization, which is maintained during embryogenesis and independent of the translational or degradation activity of mRNAs, reveals new regulatory mechanisms for germ plasm mRNAs that may be applicable to other mRNA granules.

}, issn = {2041-1723}, doi = {10.1038/ncomms8962}, author = {Trcek, Tatjana and Grosch, Markus and York, Andrew and Shroff, Hari and Lionnet, Timoth{\'e}e and Lehmann, Ruth} } @article {47146, title = {Drosophila Lgr3 couples organ growth with maturation and ensures developmental stability.}, journal = {Current biology : CB}, volume = {25}, year = {2015}, month = {2015 Oct 19}, pages = {2723-9}, abstract = {

Early transplantation and grafting experiments suggest that body organs follow autonomous growth programs [1-3], therefore pointing to a need for coordination mechanisms to produce fit\ individuals with proper proportions. We recently\ identified Drosophila insulin-like peptide 8 (Dilp8) as a relaxin and insulin-like molecule secreted from growing tissues that plays a central role in coordinating growth between organs and coupling organ growth with animal maturation [4, 5]. Deciphering the function of Dilp8 in growth coordination relies on the identification of the receptor and tissues relaying Dilp8 signaling. We show here that the orphan receptor leucine-rich repeat-containing G protein-coupled receptor 3 (Lgr3), a member of the highly conserved family of relaxin family peptide receptors (RXFPs), mediates the checkpoint function of Dilp8 for entry into maturation. We functionally identify two Lgr3-positive neurons in each brain lobe that are required to induce a developmental delay upon overexpression of Dilp8. These neurons are located in the pars intercerebralis, an important neuroendocrine area in the brain, and make physical contacts with the PTTH neurons that ultimately control the\ production and release of the molting steroid ecdysone. Reducing Lgr3 levels in these neurons\ results in adult flies exhibiting increased fluctuating bilateral asymmetry, therefore recapitulating the phenotype of dilp8 mutants. Our work reveals a novel Dilp8/Lgr3 neuronal circuitry involved in a feedback mechanism that ensures coordination between organ growth and developmental transitions and prevents developmental variability.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2015.09.020}, author = {Colombani, Julien and Andersen, Ditte S and Boulan, Laura and Boone, Emilie and Romero, Nuria and Virolle, Virginie and Texada, Michael and L{\'e}opold, Pierre} } @article {46835, title = {Dynamical feature extraction at the sensory periphery guides chemotaxis.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Jun 16}, abstract = {

Behavioral strategies employed for chemotaxis have been described across phyla, but the sensorimotor basis of this phenomenon has seldom been studied in naturalistic contexts. Here, we examine how signals experienced during free olfactory behaviors are processed by first-order olfactory sensory neurons (OSNs) of the Drosophila larva. We find that OSNs can act as differentiators that transiently normalize stimulus intensity-a property potentially derived from a combination of integral feedback and feed-forward regulation of olfactory transduction. In olfactory virtual reality experiments, we report that high activity levels of the OSN suppress turning, whereas low activity levels facilitate turning. Using a generalized linear model, we explain how peripheral encoding of olfactory stimuli modulates the probability of switching from a run to a turn. Our work clarifies the link between computations carried out at the sensory periphery and action selection underlying navigation in odor gradients.

}, issn = {2050-084X}, doi = {10.7554/eLife.06694}, author = {Schulze, Aljoscha and Gomez-Marin, Alex and Rajendran, Vani G and Lott, Gus and Musy, Marco and Ahammad, Parvez and Deogade, Ajinkya and Sharpe, James and Riedl, Julia and Jarriault, David and Trautman, Eric T and Werner, Christopher and Venkadesan, Madhusudhan and Druckmann, Shaul and Jayaraman, Vivek and Louis, Matthieu} } @article {47160, title = {Dynamics of CRISPR-Cas9 genome interrogation in living cells.}, journal = {Science (New York, N.Y.)}, volume = {350}, year = {2015}, month = {2015 Nov 13}, pages = {823-6}, abstract = {

The RNA-guided CRISPR-associated protein Cas9 is used for genome editing, transcriptional modulation, and live-cell imaging. Cas9-guide RNA complexes recognize and cleave double-stranded DNA sequences on the basis of 20-nucleotide RNA-DNA complementarity, but the mechanism of target searching in mammalian cells is unknown. Here, we use single-particle tracking to visualize diffusion and chromatin binding of Cas9 in living cells. We show that three-dimensional diffusion dominates Cas9 searching in vivo, and off-target binding events are, on average, short-lived (\<1 second). Searching is dependent on the local chromatin environment, with less sampling and slower movement within heterochromatin. These results reveal how the bacterial Cas9 protein interrogates mammalian genomes and navigates eukaryotic chromatin structure.

}, issn = {1095-9203}, doi = {10.1126/science.aac6572}, author = {Knight, Spencer C and Xie, Liangqi and Deng, Wulan and Guglielmi, Benjamin and Witkowsky, Lea B and Bosanac, Lana and Zhang, Elisa T and El Beheiry, Mohamed and Masson, Jean-Baptiste and Dahan, Maxime and Liu, Zhe and Doudna, Jennifer A and Tjian, Robert} } @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 {46283, title = {Effects of long-term representations on free recall of unrelated words.}, journal = {Learning \& Memory}, volume = {22}, year = {2015}, month = {2015 Jan 15}, pages = {101-8}, abstract = {

Human memory stores vast amounts of information. Yet recalling this information is often challenging when specific cues are lacking. Here we consider an associative model of retrieval where each recalled item triggers the recall of the next item based on the similarity between their long-term neuronal representations. The model predicts that different items stored in memory have different probability to be recalled depending on the size of their representation. Moreover, items with high recall probability tend to be recalled earlier and suppress other items. We performed an analysis of a large data set on free recall and found a highly specific pattern of statistical dependencies predicted by the model, in particular negative correlations between the number of words recalled and their average recall probability. Taken together, experimental and modeling results presented here reveal complex interactions between memory items during recall that severely constrain recall capacity.

}, issn = {1549-5485}, doi = {10.1101/lm.035238.114}, author = {Katkov, Mikhail and Romani, Sandro and Tsodyks, Misha} } @article {47135, title = {Even-Skipped(+) interneurons are core components of a sensorimotor circuit that maintains left-right symmetric muscle contraction amplitude.}, journal = {Neuron}, volume = {88}, year = {2015}, month = {2015 Oct 21}, pages = {314-29}, abstract = {

Bilaterally symmetric motor patterns-those in which left-right pairs of muscles contract synchronously and with equal amplitude (such as breathing, smiling,\ whisking, and locomotion)-are widespread throughout the animal kingdom. Yet, surprisingly little is known about the underlying neural circuits. We performed a thermogenetic screen to identify neurons required for bilaterally symmetric locomotion in Drosophila larvae and identified the evolutionarily conserved Even-skipped(+) interneurons (Eve/Evx). Activation or ablation of Eve(+) interneurons disrupted bilaterally symmetric muscle contraction amplitude, without affecting the timing of motor output. Eve(+) interneurons are not rhythmically active and thus function independently of the locomotor CPG. GCaMP6 calcium imaging of Eve(+) interneurons in freely moving larvae showed left-right asymmetric activation that correlated with larval behavior. TEM reconstruction of Eve(+) interneuron inputs and outputs showed that the Eve(+) interneurons are at the core of a sensorimotor circuit capable of detecting and modifying body wall muscle contraction.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.09.009}, author = {Heckscher, Ellie S and Zarin, Aref Arzan and Faumont, Serge and Clark, Matthew Q and Manning, Laurina and Fushiki, Akira and Schneider-Mizell, Casey M and Fetter, Richard D and Truman, James W and Zwart, Maarten F and Landgraf, Matthias and Cardona, Albert and Lockery, Shawn R and Doe, Chris Q} } @article {48036, title = {Expansion microscopy.}, year = {2015}, abstract = {

In optical microscopy, fine structural details are resolved by using refraction to magnify images of a specimen. We discovered that by synthesizing a swellable polymer network within a specimen, it can be physically expanded, resulting in physical magnification. By covalently anchoring specific labels located within the specimen directly to the polymer network, labels spaced closer than the optical diffraction limit can be isotropically separated and optically resolved, a process we call expansion microscopy (ExM). Thus, this process can be used to perform scalable superresolution microscopy with diffraction-limited microscopes. We demonstrate ExM with apparent ~70-nanometer lateral resolution in both cultured cells and brain tissue, performing three-color superresolution imaging of ~107 cubic micrometers of the mouse hippocampus with a conventional confocal microscope.

}, author = {Fei Chen and Paul Tillberg and Edward Boyden} } @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 {68482, title = {Fitness tradeoffs between spores and nonaggregating cells can explain the coexistence of diverse genotypes in cellular slime molds.}, journal = {Proc Natl Acad Sci U S A}, volume = {112}, year = {2015}, month = {03/2015}, pages = {2776-81}, abstract = {

Cellular slime molds, including the well-studied Dictyostelium discoideum, are amoebae whose life cycle includes both a single-cellular and a multicellular stage. To achieve the multicellular stage, individual amoebae aggregate upon starvation to form a fruiting body made of dead stalk cells and reproductive spores, a process that has been described in terms of cooperation and altruism. When amoebae aggregate they do not perfectly discriminate against nonkin, leading to chimeric fruiting bodies. Within chimeras, complex interactions among genotypes have been documented, which should theoretically reduce genetic diversity. This is however inconsistent with the great diversity of genotypes found in nature. Recent work has shown that a little-studied component of D. discoideum fitness--the loner cells that do not participate in the aggregation--can be selected for depending on environmental conditions and that, together with the spores, they could represent a bet-hedging strategy. We suggest that in all cellular slime molds the existence of loners could resolve the apparent diversity paradox in two ways. First, if loners are accounted for, then apparent genotypic skew in the spores of chimeras could simply be the result of different investments into spores versus loners. Second, in an ecosystem with multiple local environments differing in their food recovery characteristics and connected globally via weak-to-moderate dispersal, coexistence of multiple genotypes can occur. Finally, we argue that the loners make it impossible to define altruistic behavior, winners or losers, without a clear description of the ecology.

}, keywords = {Dictyostelium, Ecosystem, Life Cycle Stages, Spores, Protozoan}, issn = {1091-6490}, doi = {10.1073/pnas.1424242112}, author = {Tarnita, Corina E and Washburne, Alex and Martinez-Garcia, Ricardo and Sgro, Allyson E and Levin, Simon A} } @article {46535, title = {Genetic architecture and functional characterization of genes underlying the rapid diversification of male external genitalia between Drosophila simulans and Drosophila mauritiana.}, journal = {Genetics}, year = {2015}, month = {2015 Mar 16}, abstract = {

Male sexual characters are often among the first traits to diverge between closely related species and identifying the genetic basis of such changes can contribute to our understanding of their evolutionary history. However, little is known about the genetic architecture or the specific genes underlying the evolution of male genitalia. The morphology of the claspers, posterior lobes and anal plates exhibit striking differences between Drosophila mauritiana and Drosophila simulans. Using QTL and introgression-based high-resolution mapping, we identified several small regions on chromosome arms 3L and 3R that contribute to differences in these traits. However, we found that the loci underlying the evolution of clasper differences between these two species are independent from those that contribute to posterior lobe and anal plate divergence. Furthermore, while most of the loci affect each trait in the same direction and act additively, we also found evidence for epistasis between loci for clasper bristle number. In addition, we conducted an RNAi screen in D. melanogaster to investigate if positional and expression candidate genes located on chromosome 3L, are also involved in genital development. We found that six of these genes, including components of Wnt signaling and male-specific lethal 3 (msl3), regulate the development of genital traits consistent with the effects of the introgressed regions where they are located and that thus represent promising candidate genes for the evolution these traits.

}, issn = {1943-2631}, doi = {10.1534/genetics.114.174045}, author = {Tanaka, Kentaro M and Hopfen, Corinna and Herbert, Matthew R and Schl{\"o}tterer, Christian and Stern, David L and Masly, John P and McGregor, Alistair P and Nunes, Maria D S} } @article {46756, title = {Genomic signatures of evolutionary transitions from solitary to group living.}, journal = {Science}, year = {2015}, month = {2015 May 14}, abstract = {

The evolution of eusociality is one of the major transitions in evolution, but the underlying genomic changes are unknown. We compared the genomes of ten bee species that vary in social complexity, representing multiple independent transitions in social evolution, and report three major findings. First, many important genes show evidence of neutral evolution as a consequence of relaxed selection with increasing social complexity. Second, there is no single road map to eusociality; independent evolutionary transitions in sociality have independent genetic underpinnings. Third, though clearly independent in detail, these transitions do have similar general features, including an increase in constrained protein evolution accompanied by increases in the potential for gene regulation and decreases in diversity and abundance of transposable elements. Eusociality may arise through different mechanisms each time, but would likely always involve an increase in the complexity of gene networks.

}, issn = {1095-9203}, doi = {10.1126/science.aaa4788}, author = {Kapheim, Karen M and Pan, Hailin and Li, Cai and Salzberg, Steven L and Puiu, Daniela and Magoc, Tanja and Robertson, Hugh M and Hudson, Matthew E and Venkat, Aarti and Fischman, Brielle J and Hernandez, Alvaro and Yandell, Mark and Ence, Daniel and Holt, Carson and Yocum, George D and Kemp, William P and Bosch, Jordi and Waterhouse, Robert M and Zdobnov, Evgeny M and Stolle, Eckart and Kraus, F Bernhard and Helbing, Sophie and Moritz, Robin F A and Glastad, Karl M and Hunt, Brendan G and Goodisman, Michael A D and Hauser, Frank and Grimmelikhuijzen, Cornelis J P and Pinheiro, Daniel Guariz and Nunes, Francis Morais Franco and Soares, Michelle Prioli Miranda and Tanaka, {\'E}rica Donato and Sim{\~o}es, Zil{\'a} Luz Paulino and Hartfelder, Klaus and Evans, Jay D and Barribeau, Seth M and Johnson, Reed M and Massey, Jonathan H and Southey, Bruce R and Hasselmann, Martin and Hamacher, Daniel and Biewer, Matthias and Kent, Clement F and Zayed, Amro and Blatti, Charles and Sinha, Saurabh and Johnston, J Spencer and Hanrahan, Shawn J and Kocher, Sarah D and Wang, Jun and Robinson, Gene E and Zhang, Guojie} } @article {47180, title = {Heterosynaptic plasticity underlies aversive olfactory learning in Drosophila}, journal = {Neuron}, volume = {88}, year = {2015}, month = {2015 Dec 2}, pages = {985-98}, abstract = {

Although associative learning has been localized to specific brain areas in many animals, identifying the underlying synaptic processes in vivo has been difficult. Here, we provide the first demonstration of long-term synaptic plasticity at the output site of the Drosophila mushroom body. Pairing an odor with activation of specific dopamine neurons induces both learning and odor-specific synaptic depression. The plasticity induction strictly depends on the temporal order of the two stimuli, replicating the logical requirement for associative learning. Furthermore, we reveal that dopamine action is confined to and distinct across different anatomical compartments of the mushroom body lobes. Finally, we find that overlap between sparse representations of different odors defines both stimulus specificity of the plasticity and generalizability of associative memories across odors. Thus, the plasticity we find here not only manifests important features of associative learning but also provides general insights into how a sparse sensory code is read out.

}, doi = {10.1016/j.neuron.2015.11.003}, author = {Hige, Toshihide and Aso, Yoshinori and Modi, Mehrab and Rubin, Gerald M and Turner, Glenn C} } @article {46576, title = {High-performance probes for light and electron microscopy.}, journal = {Nature Methods}, volume = {12}, year = {2015}, month = {2015 Apr 27}, pages = {568-76}, abstract = {

We describe an engineered family of highly antigenic molecules based on GFP-like fluorescent proteins. These molecules contain numerous copies of peptide epitopes and simultaneously bind IgG antibodies at each location. These {\textquoteright}spaghetti monster{\textquoteright} fluorescent proteins (smFPs) distributed well in neurons, notably into small dendrites, spines and axons. smFP immunolabeling localized weakly expressed proteins not well resolved with traditional epitope tags. By varying epitope and scaffold, we generated a diverse family of mutually orthogonal antigens. In cultured neurons and mouse and fly brains, smFP probes allowed robust, orthogonal multicolor visualization of proteins, cell populations and neuropil. smFP variants complement existing tracers and greatly increase the number of simultaneous imaging channels, and they performed well in advanced preparations such as array tomography, super-resolution fluorescence imaging and electron microscopy. In living cells, the probes improved single-molecule image tracking and increased yield for RNA-seq. These probes facilitate new experiments in connectomics, transcriptomics and protein localization.

}, issn = {1548-7105}, doi = {10.1038/nmeth.3365}, author = {Viswanathan, Sarada and Williams, Megan E. and Bloss, Erik B. and Stasevich, Timothy J. and Speer, Colenso M. and Nern, Aljoscha and Pfeiffer, Barret D. and Hooks, Bryan M. and Li, Wei-Ping and English, Brian P. and Tian, Teresa and Henry, Gilbert L. and Macklin, John J. and Patel, Ronak and Gerfen, Charles R and Zhuang, Xiaowei and Wang, Yalin and Rubin, Gerald M and Looger, Loren L} } @article {47145, title = {Histone H3 threonine phosphorylation regulates asymmetric histone inheritance in the Drosophila male germline.}, journal = {Cell}, volume = {163}, year = {2015}, month = {2015 Nov 5}, pages = {920-33}, abstract = {

A long-standing question concerns how stem cells maintain their identity through multiple divisions. Previously, we reported that pre-existing and newly synthesized histone H3 are asymmetrically distributed during Drosophila male germline stem cell (GSC) asymmetric division. Here, we show that phosphorylation at threonine 3 of H3 (H3T3P) distinguishes pre-existing versus newly synthesized H3. Converting T3 to the unphosphorylatable residue alanine (H3T3A) or to the phosphomimetic aspartate (H3T3D) disrupts asymmetric H3 inheritance. Expression of H3T3A or H3T3D specifically in early-stage germline also leads to cellular defects, including GSC loss and germline tumors. Finally, compromising the activity of the H3T3 kinase Haspin enhances the H3T3A but suppresses the H3T3D phenotypes. These studies demonstrate that H3T3P distinguishes sister chromatids enriched with distinct pools of H3 in order to coordinate asymmetric segregation of "old" H3 into GSCs and that tight regulation of H3T3 phosphorylation is required for male germline activity.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2015.10.002}, author = {Xie, Jing and Wooten, Matthew and Tran, Vuong and Chen, Bi-Chang and Pozmanter, Caitlin and Simbolon, Christine and Betzig, Eric and Chen, Xin} } @article {47237, title = {Ig superfamily ligand and receptor pairs expressed in synaptic partners in Drosophila.}, journal = {Cell}, volume = {163}, year = {2015}, month = {2015 Dec 17}, pages = {1756-69}, abstract = {

Information processing relies on precise patterns of synapses between neurons. The cellular recognition mechanisms regulating this specificity are poorly understood. In the medulla of the Drosophila visual system, different neurons form synaptic connections in different layers. Here, we sought to identify candidate cell recognition molecules underlying this specificity. Using RNA sequencing (RNA-seq), we show that neurons with different synaptic specificities express unique combinations of mRNAs encoding hundreds of cell surface and secreted proteins. Using RNA-seq and protein tagging, we demonstrate that 21 paralogs of the Dpr family, a subclass of immunoglobulin (Ig)-domain containing proteins, are expressed in unique combinations in homologous neurons with different layer-specific synaptic connections. Dpr interacting proteins (DIPs), comprising nine paralogs of another subclass of Ig-containing proteins, are expressed in a complementary layer-specific fashion in a subset of synaptic partners. We propose that pairs of Dpr/DIP paralogs contribute to layer-specific patterns of synaptic connectivity.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2015.11.021}, author = {Tan, Liming and Zhang, Kelvin Xi and Pecot, Matthew Y and Nagarkar-Jaiswal, Sonal and Lee, Pei-Tseng and Takemura, Shin-ya and McEwen, Jason M and Nern, Aljoscha and Xu, Shuwa and Tadros, Wael and Chen, Zhenqing and Zinn, Kai and Bellen, Hugo J and Morey, Marta and Zipursky, S Lawrence} } @article {47161, title = {Imaging fictive locomotor patterns in larval Drosophila.}, journal = {Journal of Neurophysiology}, volume = {114}, year = {2015}, month = {2015 Nov 06}, pages = {2564-77}, abstract = {

We have established a preparation in larval Drosophila to monitor fictive locomotion simultaneously across abdominal and thoracic segments of the isolated CNS with genetically encoded Ca(2+) indicators. The Ca(2+) signals closely followed spiking activity measured electrophysiologically in nerve roots. Three motor patterns are analyzed. Two comprise waves of Ca(2+) signals that progress along the longitudinal body axis in a posterior-to-anterior or anterior-to-posterior direction. These waves had statistically indistinguishable intersegmental phase delays compared with segmental contractions during forward and backward crawling behavior, despite being \~{}10 times slower. During these waves, motor neurons of the dorsal longitudinal and transverse muscles were active in the same order as the muscle groups are recruited during crawling behavior. A third fictive motor pattern exhibits a left-right asymmetry across segments and bears similarities with turning behavior in intact larvae, occurring equally frequently and involving asymmetry in the same segments. Ablation of the segments in which forward and backward waves of Ca(2+) signals were normally initiated did not eliminate production of Ca(2+) waves. When the brain and subesophageal ganglion (SOG) were removed, the remaining ganglia retained the ability to produce both forward and backward waves of motor activity, although the speed and frequency of waves changed. Bilateral asymmetry of activity was reduced when the brain was removed and abolished when the SOG was removed. This work paves the way to studying the neural and genetic underpinnings of segmentally coordinated motor pattern generation in Drosophila with imaging techniques.

}, issn = {1522-1598}, doi = {10.1152/jn.00731.2015}, author = {Pulver, Stefan R and Bayley, Timothy G and Taylor, Adam L and Berni, Jimena and Bate, Michael and Hedwig, Berthold} } @article {47734, title = {Imaging transcription: past, present, and future.}, journal = {Cold Spring Harbor Symposia on Quantitative Biology}, volume = {80}, year = {2015}, month = {2015}, pages = {1-8}, abstract = {

Transcription, the first step of gene expression, is exquisitely regulated in higher eukaryotes to ensure correct development and homeostasis. Traditional biochemical, genetic, and genomic approaches have proved successful at identifying factors, regulatory sequences, and potential pathways that modulate transcription. However, they typically only provide snapshots or population averages of the highly dynamic, stochastic biochemical processes involved in transcriptional regulation. Single-molecule live-cell imaging has, therefore, emerged as a complementary approach capable of circumventing these limitations. By observing sequences of molecular events in real time as they occur in their native context, imaging has the power to derive cause-and-effect relationships and quantitative kinetics to build predictive models of transcription. Ongoing progress in fluorescence imaging technology has brought new microscopes and labeling technologies that now make it possible to visualize and quantify the transcription process with single-molecule resolution in living cells and animals. Here we provide an overview of the evolution and current state of transcription imaging technologies. We discuss some of the important concepts they uncovered and present possible future developments that might solve long-standing questions in transcriptional regulation.

}, issn = {1943-4456}, doi = {10.1101/sqb.2015.80.027201}, author = {Coleman, Robert A and Liu, Zhe and Darzacq, Xavier and Tjian, Robert and Singer, Robert H and Lionnet, Timoth{\'e}e} } @article {47284, title = {The innate immune receptor PGRP-LC controls presynaptic homeostatic plasticity.}, journal = {Neuron}, volume = {88}, year = {2015}, month = {2015 Dec 16}, pages = {1157-64}, abstract = {

It is now appreciated that the brain is immunologically active. Highly conserved innate immune signaling responds to pathogen invasion and injury and promotes structural refinement of neural circuitry. However, it remains generally unknown whether innate immune signaling has a function during the day-to-day regulation of neural function in the absence of pathogens and irrespective of cellular damage or developmental change. Here we show that an innate immune receptor, a member of the peptidoglycan pattern recognition receptor family (PGRP-LC), is required for the induction and sustained expression of homeostatic synaptic plasticity. This receptor functions presynaptically, controlling the homeostatic modulation of the readily releasable pool of synaptic vesicles following inhibition of postsynaptic glutamate receptor function. Thus, PGRP-LC is a candidate receptor for retrograde, trans-synaptic signaling, a novel activity for innate immune signaling and the first known function of a PGRP-type receptor in the nervous system of any organism.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.10.049}, author = {Harris, Nathan and Braiser, Daniel J and Dickman, Dion K and Fetter, Richard D and Tong, Amy and Davis, Graeme W} } @article {46368, title = {Labeling of active neural circuits in vivo with designed calcium integrators.}, journal = {Science}, volume = {347}, year = {2015}, month = {2015 Feb 13}, pages = {755-60}, abstract = {

The identification of active neurons and circuits in vivo is a fundamental challenge in understanding the neural basis of behavior. Genetically encoded calcium (Ca(2+)) indicators (GECIs) enable quantitative monitoring of cellular-resolution activity during behavior. However, such indicators require online monitoring within a limited field of view. Alternatively, post hoc staining of immediate early genes (IEGs) indicates highly active cells within the entire brain, albeit with poor temporal resolution. We designed a fluorescent sensor, CaMPARI, that combines the genetic targetability and quantitative link to neural activity of GECIs with the permanent, large-scale labeling of IEGs, allowing a temporally precise "activity snapshot" of a large tissue volume. CaMPARI undergoes efficient and irreversible green-to-red conversion only when elevated intracellular Ca(2+) and experimenter-controlled illumination coincide. We demonstrate the utility of CaMPARI in freely moving larvae of zebrafish and flies, and in head-fixed mice and adult flies.

}, issn = {1095-9203}, doi = {10.1126/science.1260922}, author = {Fosque, Benjamin F and Sun, Yi and Dana, Hod and Yang, Chao-Tsung and Ohyama, Tomoko and Tadross, Michael R and Patel, Ronak and Zlatic, Marta and Kim, Douglas S and Ahrens, Misha B and Jayaraman, Vivek and Looger, Loren L and Schreiter, Eric R} } @article {47744, title = {Learning: the good, the bad, and the fly.}, journal = {Neuron}, volume = {86}, year = {2015}, month = {2015 Apr 22}, pages = {343-5}, abstract = {

Olfactory memories can be very good-your mother{\textquoteright}s baking-or very bad-your father{\textquoteright}s cooking. We go through life forming these different associations with the smells we encounter. But what makes one association pleasant and another repulsive? Work in deep areas of the Drosophila brain has revealed the beginnings of an answer, as reported in this issue of Neuron by Owald et al. (2015).

}, keywords = {Animals, Appetitive Behavior, Dopaminergic Neurons, Drosophila, Mushroom Bodies, Smell}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.04.012}, author = {Hige, Toshihide and Turner, Glenn} } @article {46326, title = {Mapping social behavior-induced brain activation at cellular resolution in the mouse.}, journal = {Cell Reports}, volume = {10}, year = {2015}, month = {2015 Jan 13}, pages = {292-305}, abstract = {

Understanding how brain activation mediates behaviors is a central goal of systems neuroscience. Here, we apply an automated method for mapping brain activation in the mouse in order to probe how sex-specific social behaviors are represented in the male brain. Our method uses the immediate-early-gene c-fos, a marker of neuronal activation, visualized by serial two-photon tomography: the c-fos-GFP+ neurons are computationally detected, their distribution is registered to a reference brain and a brain atlas, and their numbers are analyzed by statistical tests. Our results reveal distinct and shared female and male interaction-evoked patterns of male brain activation representing sex discrimination and social recognition. We also identify brain regions whose degree of activity correlates to specific features of social behaviors and estimate the total numbers and the densities of activated neurons per brain areas. Our study opens the door to automated screening of behavior-evoked brain activation in the mouse.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2014.12.014}, author = {Kim, Yongsoo and Venkataraju, Kannan Umadevi and Pradhan, Kith and Mende, Carolin and Taranda, Julian and Turaga, Srinivas C and Arganda-Carreras, Ignacio and Ng, Lydia and Hawrylycz, Michael J and Rockland, Kathleen S and Seung, H Sebastian and Osten, Pavel} } @article {48311, title = {Mitochondrial transcription factor A (TFAM) binds to RNA containing 4-way junctions and mitochondrial tRNA.}, journal = {PloS one}, volume = {10}, year = {2015}, month = {2015 nov 6}, pages = {e0142436}, abstract = {

Mitochondrial DNA (mtDNA) is maintained within nucleoprotein complexes known as nucleoids. These structures are highly condensed by the DNA packaging protein, mitochondrial Transcription Factor A (TFAM). Nucleoids also include RNA, RNA:DNA hybrids, and are associated with proteins involved with RNA processing and mitochondrial ribosome biogenesis. Here we characterize the ability of TFAM to bind various RNA containing substrates in order to determine their role in TFAM distribution and function within the nucleoid. We find that TFAM binds to RNA-containing 4-way junctions but does not bind appreciably to RNA hairpins, internal loops, or linear RNA:DNA hybrids. Therefore the RNA within nucleoids largely excludes TFAM, and its distribution is not grossly altered with removal of RNA. Within the cell, TFAM binds to mitochondrial tRNAs, consistent with our RNA 4-way junction data. Kinetic binding assays and RNase-insensitive TFAM distribution indicate that DNA remains the preferred substrate within the nucleoid. However, TFAM binds to tRNA with nanomolar affinity and these complexes are not rare. TFAM-immunoprecipitated tRNAs have processed ends, suggesting that binding is not specific to RNA precursors. The amount of each immunoprecipitated tRNA is not well correlated with tRNA celluar abundance, indicating unequal TFAM binding preferences. TFAM-mt-tRNA interaction suggests potentially new functions for this protein.

}, keywords = {Animals, DNA-Binding Proteins, High Mobility Group Proteins, Kinetics, Mice, Nucleic Acid Conformation, Protein Binding, RNA, RNA, Transfer, Surface Plasmon Resonance, Swiss 3T3 Cells}, issn = {1932-6203}, doi = {10.1371/journal.pone.0142436}, author = {Brown, Timothy A and Tkachuk, Ariana N and Clayton, David A} } @article {46557, title = {A multilevel multimodal circuit enhances action selection in Drosophila.}, journal = {Nature}, volume = {520}, year = {2015}, month = {2015 Apr 20}, pages = {633-9}, abstract = {

Natural events present multiple types of sensory cues, each detected by a specialized sensory modality. Combining information from several modalities is essential for the selection of appropriate actions. Key to understanding multimodal computations is determining the structural patterns of multimodal convergence and how these patterns contribute to behaviour. Modalities could converge early, late or at multiple levels in the sensory processing hierarchy. Here we show that combining mechanosensory and nociceptive cues synergistically enhances the selection of the fastest mode of escape locomotion in Drosophila larvae. In an electron microscopy volume that spans the entire insect nervous system, we reconstructed the multisensory circuit supporting the synergy, spanning multiple levels of the sensory processing hierarchy. The wiring diagram revealed a complex multilevel multimodal convergence architecture. Using behavioural and physiological studies, we identified functionally connected circuit nodes that trigger the fastest locomotor mode, and others that facilitate it, and we provide evidence that multiple levels of multimodal integration contribute to escape mode selection. We propose that the multilevel multimodal convergence architecture may be a general feature of multisensory circuits enabling complex input{\textendash}output functions and selective tuning to ecologically relevant combinations of cues.

}, doi = {10.1038/nature14297}, author = {Ohyama, Tomoko and Schneider-Mizell, Casey M. and Fetter, Richard D. and Aleman, Javier Valdes and Franconville, Romain and Rivera-Alba, Marta and Mensh, Brett D. and Branson, Kristin M. and Simpson, Julie H. and Truman, James W. and Cardona, Albert and Zlatic, Marta} } @article {46527, title = {Myosin 18A coassembles with nonmuscle myosin 2 to form mixed bipolar filaments.}, journal = {Current Biology}, volume = {25}, year = {2015}, month = {2015 Mar 30}, pages = {942-8}, abstract = {

Class-18 myosins are most closely related to conventional class-2 nonmuscle myosins (NM2). Surprisingly, the purified head domains of Drosophila, mouse, and human myosin 18A (M18A) lack actin-activated ATPase activity and the ability to translocate actin filaments, suggesting that the functions of M18A in\ vivo do not depend on intrinsic motor activity. M18A has the longest coiled coil of any myosin outside of the class-2 myosins, suggesting that it might form bipolar filaments similar to conventional myosins. To address this possibility, we expressed and purified full-length mouse M18A using the baculovirus/Sf9 system. M18A did not form large bipolar filaments under any of the conditions tested. Instead, M18A formed an \~{}65-nm-long bipolar structure with two heads at each end. Importantly, when NM2 was polymerized in the presence of M18A, the two myosins formed mixed bipolar filaments, as evidenced by cosedimentation, electron microscopy, and single-molecule imaging. Moreover, super-resolution imaging of NM2 and M18A using fluorescently tagged proteins and immunostaining of endogenous proteins showed that NM2 and M18A are present together within individual filaments inside living cells. Together, our in\ vitro and live-cell imaging data argue strongly that M18A coassembles with NM2 into mixed bipolar filaments. M18A could regulate the biophysical properties of these filaments and, by virtue of its extra N- and C-terminal domains, determine the localization and/or molecular interactions of the filaments. Given the numerous, fundamental cellular and developmental roles attributed to NM2, our results have far-reaching biological implications.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2015.02.012}, author = {Billington, Neil and Beach, Jordan R and Heissler, Sarah M and Remmert, Kirsten and Guzik-Lendrum, Stephanie and Nagy, Attila and Takagi, Yasuharu and Shao, Lin and Li, Dong and Yang, Yi and Zhang, Yingfan and Barzik, Melanie and Betzig, Eric and Hammer, John A and Sellers, James R} } @article {47240, title = {Neural Network Model of Memory Retrieval.}, journal = {Frontiers in Computational Neuroscience}, volume = {9}, year = {2015}, month = {2015 Dec 17}, pages = {149}, abstract = {

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

}, issn = {1662-5188}, doi = {10.3389/fncom.2015.00149}, author = {Recanatesi, Stefano and Katkov, Mikhail and Romani, Sandro and Tsodyks, Misha} } @article {47158, title = {Neurodata without borders: creating a common data format for neurophysiology}, journal = {Neuron}, volume = {88}, year = {2015}, month = {2015 Nov 18}, pages = {629-34}, abstract = {

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

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

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

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

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

}, issn = {2045-2322}, doi = {10.1038/srep12597}, author = {Tan, Zhongchao and Sun, Wenzhi and Chen, Tsai-Wen and Kim, Douglas and Ji, Na} } @article {46816, title = {The nutrient-responsive hormone CCHamide-2 controls growth by regulating insulin-like peptides in the brain of Drosophila melanogaster.}, journal = {PLoS Genetics}, volume = {11}, year = {2015}, month = {2015 May}, pages = {e1005209}, abstract = {

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

}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1005209}, author = {Sano, Hiroko and Nakamura, Akira and Texada, Michael J and Truman, James W and Ishimoto, Hiroshi and Kamikouchi, Azusa and Nibu, Yutaka and Kume, Kazuhiko and Ida, Takanori and Kojima, Masayasu} } @article {47017, title = {Optogenetics: 10 years after ChR2 in neurons-views from the community.}, journal = {Nature Neuroscience}, volume = {18}, year = {2015}, month = {2015 Aug 26}, pages = {1202-12}, issn = {1546-1726}, doi = {10.1038/nn.4106}, author = {Adamantidis, Antoine and Arber, Silvia and Bains, Jaideep S and Bamberg, Ernst and Bonci, Antonello and Buzs{\'a}ki, Gy{\"o}rgy and Cardin, Jessica A and Costa, Rui M and Dan, Yang and Goda, Yukiko and Graybiel, Ann M and H{\"a}usser, Michael and Hegemann, Peter and Huguenard, John R and Insel, Thomas R and Janak, Patricia H and Johnston, Daniel and Josselyn, Sheena A and Koch, Christof and Kreitzer, Anatol C and L{\"u}scher, Christian and Malenka, Robert C and Miesenb{\"o}ck, Gero and Nagel, Georg and Roska, Botond and Schnitzer, Mark J and Shenoy, Krishna V and Soltesz, Ivan and Sternson, Scott M and Tsien, Richard W and Tsien, Roger Y and Turrigiano, Gina G and Tye, Kay M and Wilson, Rachel I} } @article {47409, title = {Plasticity-driven individualization of olfactory coding in mushroom body output neurons.}, journal = {Nature}, volume = {526}, year = {2015}, month = {2015 Oct 8}, pages = {258-62}, abstract = {

Although all sensory circuits ascend to higher brain areas where stimuli are represented in sparse, stimulus-specific activity patterns, relatively little is known about sensory coding on the descending side of neural circuits, as a network converges. In insects, mushroom bodies have been an important model system for studying sparse coding in the olfactory system, where this format is important for accurate memory formation. In Drosophila, it has recently been shown that the 2,000 Kenyon cells of the mushroom body converge onto a population of only 34 mushroom body output neurons (MBONs), which fall into 21 anatomically distinct cell types. Here we provide the first, to our knowledge, comprehensive view of olfactory representations at the fourth layer of the circuit, where we find a clear transition in the principles of sensory coding. We show that MBON tuning curves are highly correlated with one another. This is in sharp contrast to the process of progressive decorrelation of tuning in the earlier layers of the circuit. Instead, at the population level, odour representations are reformatted so that positive and negative correlations arise between representations of different odours. At the single-cell level, we show that uniquely identifiable MBONs display profoundly different tuning across different animals, but that tuning of the same neuron across the two hemispheres of an individual fly was nearly identical. Thus, individualized coordination of tuning arises at this level of the olfactory circuit. Furthermore, we find that this individualization is an active process that requires a learning-related gene, rutabaga. Ultimately, neural circuits have to flexibly map highly stimulus-specific information in sparse layers onto a limited number of different motor outputs. The reformatting of sensory representations we observe here may mark the beginning of this sensory-motor transition in the olfactory system.

}, keywords = {Adenylyl Cyclases, Animals, Drosophila melanogaster, Drosophila Proteins, Female, Learning, Male, Mushroom Bodies, Mutation, Neuronal Plasticity, Neurons, Olfactory Pathways, Olfactory Perception, Psychomotor Performance}, issn = {1476-4687}, doi = {10.1038/nature15396}, author = {Hige, Toshihide and Aso, Yoshinori and Rubin, Gerald M and Turner, Glenn C} } @article {47182, title = {Reward signal in a recurrent circuit drives appetitive long-term memory formation.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Nov 18}, abstract = {

Dopamine signals reward in animal brains. A single presentation of a sugar reward to Drosophila activates distinct subsets of dopamine neurons that independently induce short- and long-term olfactory memories (STM and LTM, respectively). In this study, we show that a recurrent reward circuit underlies the formation and consolidation of LTM. This feedback circuit is composed of a single class of reward-signaling dopamine neurons (PAM-α1) projecting to a restricted region of the mushroom body (MB), and a specific MB output cell type, MBON-α1, whose dendrites arborize that same MB compartment. Both MBON-α1 and PAM-α1 neurons are required during the acquisition and consolidation of appetitive LTM. MBON-α1 additionally mediates the retrieval of LTM, which is dependent on the dopamine receptor signaling in the MB α/β neurons. Our results suggest that a reward signal transforms a nascent memory trace into a stable LTM using a feedback circuit at the cost of memory specificity.

}, issn = {2050-084X}, doi = {10.7554/eLife.10719}, author = {Ichinose, Toshiharu and Aso, Yoshinori and Yamagata, Nobuhiro and Abe, Ayako and Rubin, Gerald M and Tanimoto, Hiromu} } @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 {46743, title = {Role of the subesophageal zone in sensorimotor control of orientation in Drosophila larva.}, journal = {Current Biology}, volume = {25}, year = {2015}, month = {2015 May 6}, pages = {1448-60}, abstract = {

Chemotaxis is a powerful paradigm to investigate how nervous systems represent and integrate changes in sensory signals to direct navigational decisions. In the Drosophila melanogaster larva, chemotaxis mainly consists of an alternation of distinct behavioral modes: runs and directed turns. During locomotion, turns are triggered by the integration of temporal changes in the intensity of the stimulus. Upon completion of a turning maneuver, the direction of motion is typically realigned toward the odor gradient. While the anatomy of the peripheral olfactory circuits and the locomotor system of the larva are reasonably well documented, the neural circuits connecting the sensory neurons to the motor neurons remain unknown. We combined a loss-of-function behavioral screen with optogenetics-based clonal gain-of-function manipulations to identify neurons that are necessary and sufficient for the initiation of reorientation maneuvers in odor gradients. Our results indicate that a small subset of neurons residing in the subesophageal zone controls the rate of transition from runs to turns-a premotor function compatible with previous observations made in other invertebrates. After having shown that this function pertains to the processing of inputs from different sensory modalities (olfaction, vision, thermosensation), we conclude that the subesophageal zone operates as a general premotor center that regulates the selection of different behavioral programs based on the integration of sensory stimuli. The present analysis paves the way for a systematic investigation of the neural computations underlying action selection in a miniature brain amenable to genetic manipulations.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2015.04.016}, author = {Tastekin, Ibrahim and Riedl, Julia and Schilling-Kurz, Verena and Gomez-Marin, Alex and Truman, James W and Louis, Matthieu} } @article {46187, title = {Sensory determinants of behavioral dynamics in Drosophila thermotaxis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, year = {2015}, month = {2015 Jan 13}, pages = {E220-9}, abstract = {

Complex animal behaviors are built from dynamical relationships between sensory inputs, neuronal activity, and motor outputs in patterns with strategic value. Connecting these patterns illuminates how nervous systems compute behavior. Here, we study Drosophila larva navigation up temperature gradients toward preferred temperatures (positive thermotaxis). By tracking the movements of animals responding to fixed spatial temperature gradients or random temperature fluctuations, we calculate the sensitivity and dynamics of the conversion of thermosensory inputs into motor responses. We discover three thermosensory neurons in each dorsal organ ganglion (DOG) that are required for positive thermotaxis. Random optogenetic stimulation of the DOG thermosensory neurons evokes behavioral patterns that mimic the response to temperature variations. In vivo calcium and voltage imaging reveals that the DOG thermosensory neurons exhibit activity patterns with sensitivity and dynamics matched to the behavioral response. Temporal processing of temperature variations carried out by the DOG thermosensory neurons emerges in distinct motor responses during thermotaxis.

}, issn = {1091-6490}, doi = {10.1073/pnas.1416212112}, author = {Klein, Mason and Afonso, Bruno and Vonner, Ashley J and Hernandez-Nunez, Luis and Berck, Matthew and Tabone, Christopher J and Kane, Elizabeth A and Pieribone, Vincent A and Nitabach, Michael N and Cardona, Albert and Zlatic, Marta and Sprecher, Simon G and Gershow, Marc and Garrity, Paul A and Samuel, Aravinthan D T} } @article {46285, title = {Short-term plasticity based network model of place cells dynamics.}, journal = {Hippocampus}, volume = {25}, year = {2015}, month = {2015 Jan}, pages = {94-105}, abstract = {

Rodent hippocampus exhibits strikingly different regimes of population activity in different behavioral states. During locomotion, hippocampal activity oscillates at theta frequency (5-12 Hz) and cells fire at specific locations in the environment, the place fields. As the animal runs through a place field, spikes are emitted at progressively earlier phases of the theta cycles. During immobility, hippocampus exhibits sharp irregular bursts of activity, with occasional rapid orderly activation of place cells expressing a possible trajectory of the animal. The mechanisms underlying this rich repertoire of dynamics are still unclear. We developed a novel recurrent network model that accounts for the observed phenomena. We assume that the network stores a map of the environment in its recurrent connections, which are endowed with short-term synaptic depression. We show that the network dynamics exhibits two different regimes that are similar to the experimentally observed population activity states in the hippocampus. The operating regime can be solely controlled by external inputs. Our results suggest that short-term synaptic plasticity is a potential mechanism contributing to shape the population activity in hippocampus.

}, issn = {1098-1063}, doi = {10.1002/hipo.22355}, author = {Romani, Sandro and Tsodyks, Misha} } @article {47085, title = {A specific E3 ligase/deubiquitinase pair modulates TBP protein levels during muscle differentiation.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015}, abstract = {

TFIID-a complex of TATA-binding protein (TBP) and TBP-associated factors (TAFs)-is a central component of the Pol II promoter recognition apparatus. Recent studies have revealed significant downregulation of TFIID subunits in terminally differentiated myocytes, hepatocytes and adipocytes. Here, we report that TBP protein levels are tightly regulated by the ubiquitin-proteasome system. Using an in vitro ubiquitination assay coupled with biochemical fractionation, we identified Huwe1 as an E3 ligase targeting TBP for K48-linked ubiquitination and proteasome-mediated degradation. Upregulation of Huwe1 expression during myogenesis induces TBP degradation and myotube differentiation. We found that Huwe1 activity on TBP is antagonized by the deubiquitinase USP10, which protects TBP from degradation. Thus, modulating the levels of both Huwe1 and USP10 appears to fine-tune the requisite degradation of TBP during myogenesis. Together, our study unmasks a previously unknown interplay between an E3 ligase and a deubiquitinating enzyme regulating TBP levels during cellular differentiation.

}, issn = {2050-084X}, doi = {10.7554/eLife.08536}, author = {Li, Li and Martinez, Silvia Sanchez and Hu, Wenxin and Liu, Zhe and Tjian, Robert} } @article {46379, title = {Stimulation-evoked Ca2+ signals in astrocytic processes at hippocampal CA3-CA1 synapses of adult mice are modulated by glutamate and ATP.}, journal = {The Journal of Neuroscience}, volume = {35}, year = {2015}, month = {2015 Feb 18}, pages = {3016-21}, abstract = {

To date, it has been difficult to reveal physiological Ca(2+) events occurring within the fine astrocytic processes of mature animals. The objective of the study was to explore whether neuronal activity evokes astrocytic Ca(2+) signals at glutamatergic synapses of adult mice. We stimulated the Schaffer collateral/commissural fibers in acute hippocampal slices from adult mice transduced with the genetically encoded Ca(2+) indicator GCaMP5E driven by the glial fibrillary acidic protein promoter. Two-photon imaging revealed global stimulation-evoked astrocytic Ca(2+) signals with distinct latencies, rise rates, and amplitudes in fine processes and somata. Specifically, the Ca(2+) signals in the processes were faster and of higher amplitude than those in the somata. A combination of P2 purinergic and group I/II metabotropic glutamate receptor (mGluR) antagonists reduced the amplitude of the Ca(2+) transients by 30-40\% in both astrocytic compartments. Blockage of the mGluRs alone only modestly reduced the magnitude of the stimulation-evoked Ca(2+) signals in processes and failed to affect the somatic Ca(2+) response. Local application of group I or I/II mGluR agonists or adenosine triphosphate (ATP) elicited global astrocytic Ca(2+) signals that mimicked the stimulation-evoked astrocytic Ca(2+) responses. We conclude that stimulation-evoked Ca(2+) signals in astrocytic processes at CA3-CA1 synapses of adult mice (1) differ from those in astrocytic somata and (2) are modulated by glutamate and ATP.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3319-14.2015}, author = {Tang, Wannan and Szokol, Karolina and Jensen, Vidar and Enger, Rune and Trivedi, Chintan A and Hvalby, {\O}ivind and Helm, P Johannes and Looger, Loren L and Sprengel, Rolf and Nagelhus, Erlend A} } @article {47204, title = {Sweet and bitter taste in the brain of awake behaving animals.}, journal = {Nature}, volume = {527}, year = {2015}, month = {2015 Nov 26}, pages = {512-5}, abstract = {

Taste is responsible for evaluating the nutritious content of food, guiding essential appetitive behaviours, preventing the ingestion of toxic substances, and helping to ensure the maintenance of a healthy diet. Sweet and bitter are two of the most salient sensory percepts for humans and other animals; sweet taste allows the identification of energy-rich nutrients whereas bitter warns against the intake of potentially noxious chemicals. In mammals, information from taste receptor cells in the tongue is transmitted through multiple neural stations to the primary gustatory cortex in the brain. Recent imaging studies have shown that sweet and bitter are represented in the primary gustatory cortex by neurons organized in a spatial map, with each taste quality encoded by distinct cortical fields. Here we demonstrate that by manipulating the brain fields representing sweet and bitter taste we directly control an animal{\textquoteright}s internal representation, sensory perception, and behavioural actions. These results substantiate the segregation of taste qualities in the cortex, expose the innate nature of appetitive and aversive taste responses, and illustrate the ability of gustatory cortex to recapitulate complex behaviours in the absence of sensory input.

}, keywords = {Animals, Appetitive Behavior, Avoidance Learning, Brain Mapping, Cerebral Cortex, Discrimination (Psychology), Male, Mice, Mice, Inbred C57BL, Optogenetics, Stereotaxic Techniques, Taste, Taste Perception, Wakefulness}, issn = {1476-4687}, doi = {10.1038/nature15763}, author = {Peng, Yueqing and Gillis-Smith, Sarah and Jin, Hao and Tr{\"a}nkner, Dimitri and Ryba, Nicholas J P and Zuker, Charles S} } @article {47152, title = {Synaptic circuits and their variations within different columns in the visual system of Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, year = {2015}, month = {2015 Nov 3}, pages = {13711-6}, abstract = {

We reconstructed the synaptic circuits of seven columns in the second neuropil or medulla behind the fly{\textquoteright}s compound eye. These neurons embody some of the most stereotyped circuits in one of the most miniaturized of animal brains. The reconstructions allow us, for the first time to our knowledge, to study variations between circuits in the medulla{\textquoteright}s neighboring columns. This variation in the number of synapses and the types of their synaptic partners has previously been little addressed because methods that visualize multiple circuits have not resolved detailed connections, and existing connectomic studies, which can see such connections, have not so far examined multiple reconstructions of the same circuit. Here, we address the omission by comparing the circuits common to all seven columns to assess variation in their connection strengths and the resultant rates of several different and distinct types of connection error. Error rates reveal that, overall, \<1\% of contacts are not part of a consensus circuit, and we classify those contacts that supplement (E+) or are missing from it (E-). Autapses, in which the same cell is both presynaptic and postsynaptic at the same synapse, are occasionally seen; two cells in particular, Dm9 and Mi1, form >=20-fold more autapses than do other neurons. These results delimit the accuracy of developmental events that establish and normally maintain synaptic circuits with such precision, and thereby address the operation of such circuits. They also establish a precedent for error rates that will be required in the new science of connectomics.

}, issn = {1091-6490}, doi = {10.1073/pnas.1509820112}, author = {Takemura, Shin-ya and Xu, C Shan and Lu, Zhiyuan and Rivlin, Patricia K and Parag, Toufiq and Olbris, Donald J and Plaza, Stephen and Zhao, Ting and Katz, William T and Umayam, Lowell and Weaver, Charlotte and Hess, Harald F and Horne, Jane Anne and Nunez-Iglesias, Juan and Aniceto, Roxanne and Chang, Lei-Ann and Lauchie, Shirley and Nasca, Ashley and Ogundeyi, Omotara and Sigmund, Christopher and Takemura, Satoko and Tran, Julie and Langille, Carlie and Le Lacheur, Kelsey and McLin, Sari and Shinomiya, Aya and Chklovskii, Dmitri B and Meinertzhagen, Ian A and Scheffer, Louis K} } @article {46887, title = {Synaptic Orb2A bridges memory acquisition and late memory consolidation in Drosophila.}, journal = {Cell Reports}, volume = {11}, year = {2015}, month = {2015 Jun 30}, pages = {1953-65}, abstract = {

To adapt to an ever-changing environment, animals consolidate some, but not all, learning experiences to long-term memory. In mammals, long-term memory consolidation often involves neural pathway reactivation hours after memory acquisition. It is not known whether this delayed-reactivation schema is\ common across the animal kingdom or how information is stored during the delay period. Here, we show\ that, during courtship suppression learning, Drosophila exhibits delayed long-term memory consolidation. We also show that the same class of dopaminergic neurons engaged earlier in memory acquisition is also both necessary and sufficient for delayed long-term memory consolidation. Furthermore, we present evidence that, during learning, the translational regulator Orb2A tags specific synapses of mushroom body neurons for later consolidation. Consolidation involves the subsequent recruitment of Orb2B and the activity-dependent synthesis of CaMKII. Thus, our results provide evidence for the role of a neuromodulated, synapse-restricted molecule bridging memory acquisition and long-term memory consolidation in a learning animal.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2015.05.037}, author = {Kr{\"u}ttner, Sebastian and Traunm{\"u}ller, Lisa and Dag, Ugur and Jandrasits, Katharina and Stepien, Barbara and Iyer, Nirmala and Fradkin, Lee G and Noordermeer, Jasprina N and Mensh, Brett D and Keleman, Krystyna} } @article {46697, title = {Synonymous modification results in high-fidelity gene expression of repetitive protein and nucleotide sequences.}, journal = {Genes \& Development}, volume = {29}, year = {2015}, month = {2015 Apr 15}, pages = {876-86}, abstract = {

Repetitive nucleotide or amino acid sequences are often engineered into probes and biosensors to achieve functional readouts and robust signal amplification. However, these repeated sequences are notoriously prone to aberrant deletion and degradation, impacting the ability to correctly detect and interpret biological functions. Here, we introduce a facile and generalizable approach to solve this often unappreciated problem by modifying the nucleotide sequences of the target mRNA to make them nonrepetitive but still functional ("synonymous"). We first demonstrated the procedure by designing a cassette of synonymous MS2 RNA motifs and tandem coat proteins for RNA imaging and showed a dramatic improvement in signal and reproducibility in single-RNA detection in live cells. The same approach was extended to enhancing the stability of engineered fluorescent biosensors containing a fluorescent resonance energy transfer (FRET) pair of fluorescent proteins on which a great majority of systems thus far in the field are based. Using the synonymous modification to FRET biosensors, we achieved correct expression of full-length sensors, eliminating the aberrant truncation products that often were assumed to be due to nonspecific proteolytic cleavages. Importantly, the biological interpretations of the sensor are significantly different when a correct, full-length biosensor is expressed. Thus, we show here a useful and generally applicable method to maintain the integrity of expressed genes, critical for the correct interpretation of probe readouts.

}, issn = {1549-5477}, doi = {10.1101/gad.259358.115}, author = {Wu, Bin and Miskolci, Veronika and Sato, Hanae and Tutucci, Evelina and Kenworthy, Charles A and Donnelly, Sara K and Yoon, Young J and Cox, Dianne and Singer, Robert H and Hodgson, Louis} } @article {46787, title = {Systematic imaging reveals features and changing localization of mRNAs in Drosophila development.}, journal = {Elife}, volume = {4}, year = {2015}, month = {2015}, abstract = {

mRNA localization is critical for eukaryotic cells and affects numerous transcripts, yet how cells regulate distribution of many mRNAs to their subcellular destinations is still unknown. We combined transcriptomics and systematic imaging to determine the tissue-specific expression and subcellular distribution of 5862 mRNAs during Drosophila oogenesis. mRNA localization is widespread in the ovary and detectable in all of its cell types-the somatic epithelial, the nurse cells, and the oocyte. Genes defined by a common RNA localization share distinct gene features and differ in expression level, 3{\textquoteright}UTR length and sequence conservation from unlocalized mRNAs. Comparison of mRNA localizations in different contexts revealed that localization of individual mRNAs changes over time in the oocyte and between ovarian and embryonic cell types. This genome scale image-based resource (Dresden Ovary Table, DOT, http://tomancak-srv1.mpi-cbg.de/DOT/main.html) enables the transition from mechanistic dissection of singular mRNA localization events towards global understanding of how mRNAs transcribed in the nucleus distribute in cells.

}, issn = {2050-084X}, doi = {10.7554/eLife.05003}, author = {Jambor, Helena and Surendranath, Vineeth and Kalinka, Alex T and Mejstrik, Pavel and Saalfeld, Stephan and Tomancak, Pavel} } @article {47025, title = {The transgenic RNAi project at Harvard Medical School: resources and validation.}, journal = {Genetics}, volume = {201}, year = {2015}, month = {2015 Aug 28}, pages = {843-52}, abstract = {

To facilitate large scale functional studies in Drosophila, the Drosophila Transgenic RNAi Project (TRiP) at Harvard Medical School (HMS) was established along with several goals: developing efficient vectors for RNAi that work in all tissues, generating a genome scale collection of RNAi stocks with input from the community, distributing the lines as they are generated through existing stock centers, validating as many lines as possible using RT-qPCR and phenotypic analyses, and developing tools and web resources for identifying RNAi lines and retrieving existing information on their quality. With these goals in mind, here we describe in detail the various tools we developed and the status of the collection, which is currently comprised of 11,491 lines and covering 71\% of Drosophila genes. Data on the characterization of the lines either by RT-qPCR or phenotype is available on a dedicated web site, the RNAi Stock Validation and Phenotypes Project (RSVP; www.flyrnai.org/RSVP.html), and stocks are available from three stock centers, the Bloomington Drosophila Stock Center (USA), National Institute of Genetics (Japan), and TsingHua Fly Center (China).

}, issn = {1943-2631}, doi = {10.1534/genetics.115.180208}, author = {Perkins, L A and Holderbaum, L and Tao, R and Hu, Y and Sopko, R and McCall, K and Yang-Zhou, D and Flockhart, I and Binari, R and Shim, H-S and Miller, A and Housden, A and Foos, M and Randkelv, S and Kelley, C and Namgyal, P and Villalta, C and Liu, L-P and Jiang, X and Huan-Huan, Q and Xia, W and Fujiyama, A and Toyoda, A and Ayers, K and Blum, A and Czech, B and Neumuller, R and Yan, D and Cavallaro, A and Hibbard, K and Hall, D and Cooley, L and Hannon, G J and Lehmann, R and Parks, A and Mohr, S E and Ueda, R and Kondo, S and Ni, J-Q and Perrimon, Norbert} } @article {46325, title = {Ultrastructurally smooth thick partitioning and volume stitching for large-scale connectomics.}, journal = {Nature Methods}, volume = {12}, year = {2015}, month = {2015 Feb 16}, pages = {319-22}, abstract = {

Focused-ion-beam scanning electron microscopy (FIB-SEM) has become an essential tool for studying neural tissue at resolutions below 10 nm {\texttimes} 10 nm {\texttimes} 10 nm, producing data sets optimized for automatic connectome tracing. We present a technical advance, ultrathick sectioning, which reliably subdivides embedded tissue samples into chunks (20 μm thick) optimally sized and mounted for efficient, parallel FIB-SEM imaging. These chunks are imaged separately and then {\textquoteright}volume stitched{\textquoteright} back together, producing a final three-dimensional data set suitable for connectome tracing.

}, issn = {1548-7105}, doi = {10.1038/nmeth.3292}, author = {Hayworth, Kenneth J and Xu, C Shan and Lu, Zhiyuan and Knott, Graham W and Fetter, Richard D and Tapia, Juan Carlos and Lichtman, Jeff W and Hess, Harald F} } @article {65781, title = {Variable primary coordination environments of Cd(II) binding to three helix bundles provide a pathway for rapid metal exchange.}, journal = {Metallomics}, volume = {7}, year = {2015}, month = {10/2015}, pages = {1555 {\textendash} 1561}, abstract = {

Members of the ArsR/SmtB family of transcriptional repressors, such as CadC, regulate the intracellular levels of heavy metals like Cd(II), Hg(II), and Pb(II). These metal sensing proteins bind their target metals with high specificity and affinity, however, a lack of structural information about these proteins makes defining the coordination sphere of the target metal difficult. Lingering questions as to the identity of Cd(II) coordination in CadC are addressed via protein design techniques. Two designed peptides with tetrathiolate metal binding sites were prepared and characterized, revealing fast exchange between CdS3O and CdS4 coordination spheres. Correlation of (111m)Cd PAC spectroscopy and (113)Cd NMR spectroscopy suggests that Cd(II) coordinated to CadC is in fast exchange between CdS3O and CdS4 forms, which may provide a mechanism for rapid sensing of heavy metal contaminants by this regulatory protein.

}, doi = {10.1039/c5mt00228a}, author = {Tebo, Alison G and Hemmingsen, Lars and Pecoraro, Vincent L} } @article {46922, title = {Vinculin is required for cell polarization, migration, and extracellular matrix remodeling in 3D collagen.}, journal = {FASEB Journal}, volume = {29}, year = {2015}, month = {2015 Nov}, pages = {4555-67}, abstract = {

Vinculin is filamentous (F)-actin-binding protein enriched in integrin-based adhesions to the extracellular matrix (ECM). Whereas studies in 2-dimensional (2D) tissue culture models have suggested that vinculin negatively regulates cell migration by promoting cytoskeleton-ECM coupling to strengthen and stabilize adhesions, its role in regulating cell migration in more physiologic, 3-dimensional (3D) environments is unclear. To address the role of vinculin in 3D cell migration, we analyzed the morphodynamics, migration, and ECM remodeling of primary murine embryonic fibroblasts (MEFs) with cre/loxP-mediated vinculin gene disruption in 3D collagen I cultures. We found that vinculin promoted 3D cell migration by increasing directional persistence. Vinculin was necessary for persistent cell protrusion, cell elongation, and stable cell orientation in 3D collagen, but was dispensable for lamellipodia formation, suggesting that vinculin-mediated cell adhesion to the ECM is needed to convert actin-based cell protrusion into persistent cell shape change and migration. Consistent with this finding, vinculin was necessary for efficient traction force generation in 3D collagen without affecting myosin II activity and promoted 3D collagen fiber alignment and macroscopical gel contraction. Our results suggest that vinculin promotes directionally persistent cell migration and tension-dependent ECM remodeling in complex 3D environments by increasing cell-ECM adhesion and traction force generation.-Thievessen, I., Fakhri, N., Steinwachs, J., Kraus, V., McIsaac, R. S., Gao, L., Chen, B.-C., Baird, M. A., Davidson, M. W., Betzig, E., Oldenbourg, R., Waterman, C., M., Fabry, B. Vinculin is required for cell polarization, migration, and extracellular matrix remodeling in 3D collagen.

}, issn = {1530-6860}, doi = {10.1096/fj.14-268235}, author = {Thievessen, Ingo and Fakhri, Nikta and Steinwachs, Julian and Kraus, Viola and McIsaac, R Scott and Gao, Liang and Chen, Bi-Chang and Baird, Michelle A and Davidson, Michael W and Betzig, Eric and Oldenbourg, Rudolf and Waterman, Clare M and Fabry, Ben} } @article {45886, title = {3D imaging of Sox2 enhancer clusters in embryonic stem cells.}, journal = {eLife}, volume = {3}, year = {2014}, month = {2014 Dec 24}, abstract = {

Combinatorial cis-regulatory networks encoded in animal genomes represent the foundational gene expression mechanism for directing cell-fate commitment and maintenance of cell identity by transcription factors (TFs). However, the 3D spatial organization of cis-elements and how such sub-nuclear structures influence TF activity remain poorly understood. Here, we combine lattice light-sheet imaging, single-molecule tracking, numerical simulations, and ChIP-exo mapping to localize and functionally probe Sox2 enhancer-organization in living embryonic stem cells. Sox2 enhancers form 3D-clusters that are segregated from heterochromatin but overlap with a subset of Pol II enriched regions. Sox2 searches for specific binding targets via a 3D-diffusion dominant mode when shuttling long-distances between clusters while chromatin-bound states predominate within individual clusters. Thus, enhancer clustering may reduce global search efficiency but enables rapid local fine-tuning of TF search parameters. Our results suggest an integrated model linking cis-element 3D spatial distribution to local-versus-global target search modalities essential for regulating eukaryotic gene transcription.

}, issn = {2050-084X}, doi = {10.7554/eLife.04236}, author = {Liu, Zhe and Legant, Wesley R and Chen, Bi-Chang and Li, Li and Grimm, Jonathan B and Lavis, Luke D and Betzig, Eric and Tjian, Robert} } @article {6932, title = {Amphotericin forms an extramembranous and fungicidal sterol sponge.}, journal = {Nature Chemical Biology}, volume = {10}, year = {2014}, month = {2014 Mar 30}, pages = {400-6}, abstract = {

For over 50 years, amphotericin has remained the powerful but highly toxic last line of defense in treating life-threatening fungal infections in humans with minimal development of microbial resistance. Understanding how this small molecule kills yeast is thus critical for guiding development of derivatives with an improved therapeutic index and other resistance-refractory antimicrobial agents. In the widely accepted ion channel model for its mechanism of cytocidal action, amphotericin forms aggregates inside lipid bilayers that permeabilize and kill cells. In contrast, we report that amphotericin exists primarily in the form of large, extramembranous aggregates that kill yeast by extracting ergosterol from lipid bilayers. These findings reveal that extraction of a polyfunctional lipid underlies the resistance-refractory antimicrobial action of amphotericin and suggests a roadmap for separating its cytocidal and membrane-permeabilizing activities. This new mechanistic understanding is also guiding development of what are to our knowledge the first derivatives of amphotericin that kill yeast but not human cells.

}, issn = {1552-4469}, doi = {10.1038/nchembio.1496}, author = {Anderson, Thomas M and Clay, Mary C and Cioffi, Alexander G and Diaz, Katrina A and Hisao, Grant S and Tuttle, Marcus D and Nieuwkoop, Andrew J and Comellas, Gemma and Maryum, Nashrah and Wang, Shu and Uno, Brice E and Wildeman, Erin L and Gonen, Tamir and Rienstra, Chad M and Burke, Martin D} } @article {45048, title = {Ascending SAG neurons control sexual receptivity of Drosophila females.}, journal = {Neuron}, volume = {83}, year = {2014}, month = {2014 Jul 2}, pages = {135-48}, abstract = {

Mating induces pronounced changes in female reproductive behavior, typically including a dramatic reduction in sexual receptivity. In Drosophila, postmating behavioral changes are triggered by sex peptide (SP), a male seminal fluid peptide that acts via a\ receptor (SPR) expressed in sensory neurons (SPSNs) of the female reproductive tract. Here, we identify second-order neurons that mediate the behavioral changes induced by SP. These SAG neurons receive synaptic input from SPSNs in the abdominal ganglion and project to the dorsal protocerebrum. Silencing SAG neurons renders virgin females unreceptive, whereas activating them increases the receptivity of females that have already mated. Physiological experiments demonstrate that SP downregulates the excitability of the SPSNs, and hence their input onto SAG neurons. These data thus provide a physiological correlate of mating status in the female central nervous system and a key entry point into the brain circuits that control sexual receptivity.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2014.05.017}, author = {Feng, Kai and Palfreyman, Mark T and H{\"a}semeyer, Martin and Talsma, Aaron and Dickson, Barry J} } @article {45458, title = {Behavioral variability through stochastic choice and its gating by anterior cingulate cortex.}, journal = {Cell}, volume = {159}, year = {2014}, month = {2014 Sep 25}, pages = {21-32}, abstract = {

Behavioral choices that ignore prior experience promote exploration and unpredictability but are seemingly at odds with the brain{\textquoteright}s tendency to use experience to optimize behavioral choice. Indeed, when faced with virtual competitors, primates resort to strategic counterprediction rather than to stochastic choice. Here, we show that rats also use history- and model-based strategies when faced with similar competitors but can switch to a "stochastic" mode when challenged with a competitor that they cannot defeat by counterprediction. In this mode, outcomes associated with an animal{\textquoteright}s actions are ignored, and normal engagement of anterior cingulate cortex (ACC) is suppressed. Using circuit perturbations in\ transgenic rats, we demonstrate that switching between strategic and stochastic behavioral modes is controlled by locus coeruleus input into ACC. Our\ findings suggest that, under conditions of uncertainty about environmental rules, changes in noradrenergic input alter ACC output and prevent erroneous beliefs from guiding decisions, thus enabling behavioral variation.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2014.08.037}, author = {Tervo, Dougal G R and Proskurin, Mikhail and Manakov, Maxim and Kabra, Mayank and Vollmer, Alison and Branson, Kristin and Karpova, Alla Y} } @article {45049, title = {Bioimage informatics in the context of Drosophila research.}, journal = {Methods}, volume = {68}, year = {2014}, month = {2014 Jun 15}, pages = {60-73}, abstract = {

Modern biological research relies heavily on microscopic imaging. The advanced genetic toolkit of Drosophila makes it possible to label molecular and cellular components with unprecedented level of specificity necessitating the application of the most sophisticated imaging technologies. Imaging in Drosophila spans all scales from single molecules to the entire populations of adult organisms, from electron microscopy to live imaging of developmental processes. As the imaging approaches become more complex and ambitious, there is an increasing need for quantitative, computer-mediated image processing and analysis to make sense of the imagery. Bioimage Informatics is an emerging research field that covers all aspects of biological image analysis from data handling, through processing, to quantitative measurements, analysis and data presentation. Some of the most advanced, large scale projects, combining cutting edge imaging with complex bioimage informatics pipelines, are realized in the Drosophila research community. In this review, we discuss the current research in biological image analysis specifically relevant to the type of systems level image datasets that are uniquely available for the Drosophila model system. We focus on how state-of-the-art computer vision algorithms are impacting the ability of Drosophila researchers to analyze biological systems in space and time. We pay particular attention to how these algorithmic advances from computer science are made usable to practicing biologists through open source platforms and how biologists can themselves participate in their further development.

}, issn = {1095-9130}, doi = {10.1016/j.ymeth.2014.04.004}, author = {Jug, Florian and Pietzsch, Tobias and Preibisch, Stephan and Tomancak, Pavel} } @article {45700, title = {Bone-free: soft mechanics for adaptive locomotion.}, journal = {Integrative and Comparative Biology}, volume = {54}, year = {2014}, month = {2014 Dec}, pages = {1122-35}, abstract = {

Muscular hydrostats (such as mollusks), and fluid-filled animals (such as annelids), can exploit their constant-volume tissues to transfer forces and displacements in predictable ways, much as articulated animals use hinges and levers. Although larval insects contain pressurized fluids, they also have internal air tubes that are compressible and, as a result, they have more uncontrolled degrees of freedom. Therefore, the mechanisms by which larval insects control their movements are expected to reveal useful strategies for designing soft biomimetic robots. Using caterpillars as a tractable model system, it is now possible to identify the biomechanical and neural strategies for controlling movements in such highly deformable animals. For example, the tobacco hornworm, Manduca sexta, can stiffen its body by increasing muscular tension (and therefore body pressure) but the internal cavity (hemocoel) is not iso-barometric, nor is pressure used to directly control the movements of its limbs. Instead, fluid and tissues flow within the hemocoel and the body is soft and flexible to conform to the substrate. Even the gut contributes to the biomechanics of locomotion; it is decoupled from the movements of the body wall and slides forward within the body cavity at the start of each step. During crawling the body is kept in tension for part of the stride and compressive forces are exerted on the substrate along the axis of the caterpillar, thereby using the environment as a skeleton. The timing of muscular activity suggests that crawling is coordinated by proleg-retractor motoneurons and that the large segmental muscles produce anterograde waves of lifting that do not require precise timing. This strategy produces a robust form of locomotion in which the kinematics changes little with orientation. In different species of caterpillar, the presence of prolegs on particular body segments is related to alternative kinematics such as "inching." This suggests a mechanism for the evolution of different gaits through changes in the usage of prolegs, rather than, through extensive alterations in the motor program controlling the body wall. Some of these findings are being used to design and test novel control-strategies for highly deformable robots. These "softworm" devices are providing new insights into the challenges faced by any soft animal navigating in a terrestrial environment.

}, issn = {1557-7023}, doi = {10.1093/icb/icu076}, author = {Trimmer, B A and Lin, Huai-Ti} } @article {46347, title = {Cell types and coincident synapses in the ellipsoid body of Drosophila.}, journal = {The European Journal of Neuroscience}, volume = {39}, year = {2014}, month = {2014 May}, pages = {1586-601}, abstract = {

Cellular ultrastructures for signal integration are unknown in any nervous system. The ellipsoid body (EB) of the Drosophila brain is thought to control locomotion upon integration of various modalities of sensory signals with the animal internal status. However, the expected excitatory and inhibitory input convergence that virtually all brain centres exhibit is not yet described in the EB. Based on the EB expression domains of genetic constructs from the choline acetyl transferase (Cha), glutamic acid decarboxylase (GAD) and tyrosine hydroxylase (TH) genes, we identified a new set of neurons with the characteristic ring-shaped morphology (R\ neurons) which are presumably cholinergic, in addition to the existing GABA-expressing neurons. The R1 morphological subtype is represented in the Cha- and TH-expressing classes. In addition, using transmission electron microscopy, we identified a novel type of synapse in the EB, which exhibits the precise array of two independent active zones over the same postsynaptic dendritic domain, that we named {\textquoteright}agora{\textquoteright}. This array is compatible with a coincidence detector role, and represents ~8\% of all EB synapses in Drosophila. Presumably excitatory R\ neurons contribute to coincident synapses. Functional silencing of EB neurons by driving genetically tetanus toxin expression either reduces walking speed or alters movement orientation depending on the targeted R\ neuron subset, thus revealing functional specialisations in the EB for locomotion control.

}, keywords = {Animals, Animals, Genetically Modified, Bees, Brain, Choline O-Acetyltransferase, Drosophila, Drosophila Proteins, Female, gamma-Aminobutyric Acid, Green Fluorescent Proteins, Male, Microscopy, Electron, Transmission, Nerve Tissue Proteins, Neurons, Orientation, Paired Box Transcription Factors, Synapses, Tetanus Toxin, Transcription Factors, Visual Perception, Walking}, issn = {1460-9568}, doi = {10.1111/ejn.12537}, author = {Mart{\'\i}n-Pe{\~n}a, Alfonso and Acebes, Angel and Rodr{\'\i}guez, Jos{\'e}-Rodrigo and Chevalier, Valerie and Casas-Tinto, Sergio and Triphan, Tilman and Strauss, Roland and Ferr{\'u}s, Alberto} } @article {6890, title = {Cell-type-specific labeling of synapses in vivo through synaptic tagging with recombination.}, journal = {Neuron}, volume = {81}, year = {2014}, month = {2014 Jan 22}, pages = {280-93}, abstract = {

The study of synaptic specificity and plasticity in the CNS is limited by the inability to efficiently visualize synapses in identified neurons using light microscopy. Here, we describe synaptic tagging with recombination (STaR), a method for labeling endogenous presynaptic and postsynaptic proteins in a cell-type-specific fashion. We modified genomic loci encoding synaptic proteins within bacterial artificial chromosomes such that these proteins, expressed at endogenous levels and with normal spatiotemporal patterns, were labeled in an inducible fashion in specific neurons through targeted expression of site-specific recombinases. Within the Drosophila visual system, the number and distribution of synapses correlate with electron microscopy studies. Using two different recombination systems, presynaptic and postsynaptic specializations of synaptic pairs can be colabeled. STaR also allows synapses within the CNS to be studied in live animals noninvasively. In principle, STaR can be adapted to the mammalian nervous system.

}, keywords = {Animals, Drosophila, Drosophila Proteins, Electron, Genetic, Genetically Modified, Luminescent Proteins, Medulla Oblongata, Microscopy, Nerve Tissue Proteins, Neurons, Neurotransmitter, Presynaptic Terminals, Receptors, Recombinases, Recombination, Synapses, Transcription Factors, Transmission, Visual Pathways}, issn = {1097-4199}, doi = {10.1016/j.neuron.2013.12.021}, author = {Chen, Yi and Akin, Orkun and Nern, Aljoscha and Tsui, C Y Kimberly and Pecot, Matthew Y and Zipursky, S Lawrence} } @article {6826, title = {Cellular and behavioral functions of fruitless isoforms in Drosophila courtship.}, journal = {Current Biology }, volume = {24}, year = {2014}, month = {2014 Feb 3}, pages = {242-51}, abstract = {

BACKGROUND: Male-specific products of the fruitless (fru) gene control the development and function of neuronal circuits that underlie male-specific behaviors in Drosophila, including courtship. Alternative splicing generates at least three distinct Fru isoforms, each containing a different zinc-finger domain. Here, we examine the expression and function of each of these isoforms. RESULTS: We show that most fru(+) cells express all three isoforms, yet each isoform has a distinct function in the elaboration of sexually dimorphic circuitry and behavior. The strongest impairment in courtship behavior is observed in fru(C) mutants, which fail to copulate, lack sine song, and do not generate courtship song in the absence of visual stimuli. Cellular dimorphisms in the fru circuit are dependent on Fru(C) rather than other single Fru isoforms. Removal of Fru(C) from the neuronal classes vAB3 or aSP4 leads to cell-autonomous feminization of arborizations and loss of courtship in the dark. CONCLUSIONS: These data map specific aspects of courtship behavior to the level of single fru isoforms and fru(+) cell types-an important step toward elucidating the chain of causality from gene to circuit to behavior.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2013.12.015}, author = {von Philipsborn, Anne C and J{\"o}rchel, Sabrina and Tirian, Laszlo and Demir, Ebru and Morita, Tomoko and Stern, David L and Dickson, Barry J} } @article {6894, title = {Charting Brachyury-mediated developmental pathways during early mouse embryogenesis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, year = {2014}, month = {2014 Mar 10}, pages = {4478-83}, abstract = {

To gain insights into coordinated lineage-specification and morphogenetic processes during early embryogenesis, here we report a systematic identification of transcriptional programs mediated by a key developmental regulator-Brachyury. High-resolution chromosomal localization mapping of Brachyury by ChIP sequencing and ChIP-exonuclease revealed distinct sequence signatures enriched in Brachyury-bound enhancers. A combination of genome-wide in vitro and in vivo perturbation analysis and cross-species evolutionary comparison unveiled a detailed Brachyury-dependent gene-regulatory network that directly links the function of Brachyury to diverse developmental pathways and cellular housekeeping programs. We also show that Brachyury functions primarily as a transcriptional activator genome-wide and that an unexpected gene-regulatory feedback loop consisting of Brachyury, Foxa2, and Sox17 directs proper stem-cell lineage commitment during streak formation. Target gene and mRNA-sequencing correlation analysis of the T(c) mouse model supports a crucial role of Brachyury in up-regulating multiple key hematopoietic and muscle-fate regulators. Our results thus chart a comprehensive map of the Brachyury-mediated gene-regulatory network and how it influences in vivo developmental homeostasis and coordination.

}, issn = {1091-6490}, doi = {10.1073/pnas.1402612111}, author = {Lolas, Macarena and Valenzuela, Pablo D T and Tjian, Robert and Liu, Zhe} } @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 {46286, title = {Continuous attractor network model for conjunctive position-by-velocity tuning of grid cells.}, journal = {PLoS Computational Biology}, volume = {10}, year = {2014}, month = {2014 Apr 17}, pages = {e1003558}, abstract = {

The spatial responses of many of the cells recorded in layer II of rodent medial entorhinal cortex (MEC) show a triangular grid pattern, which appears to provide an accurate population code for animal spatial position. In layer III, V and VI of the rat MEC, grid cells are also selective to head-direction and are modulated by the speed of the animal. Several putative mechanisms of grid-like maps were proposed, including attractor network dynamics, interactions with theta oscillations or single-unit mechanisms such as firing rate adaptation. In this paper, we present a new attractor network model that accounts for the conjunctive position-by-velocity selectivity of grid cells. Our network model is able to perform robust path integration even when the recurrent connections are subject to random perturbations.

}, keywords = {Animals, Models, Theoretical, Movement, Rodentia}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1003558}, author = {Si, Bailu and Romani, Sandro and Tsodyks, Misha} } @article {6711, title = {Correlative super-resolution fluorescence and metal-replica transmission electron microscopy.}, journal = {Nature Methods}, volume = {11}, year = {2014}, month = {2014 Jan 26}, pages = {305-8}, abstract = {

We combine super-resolution localization fluorescence microscopy with transmission electron microscopy of metal replicas to locate proteins on the landscape of the cellular plasma membrane at the nanoscale. We validate robust correlation on the scale of 20 nm by imaging endogenous clathrin (in two and three dimensions) and apply the method to find the previously unknown three-dimensional position of the endocytic protein epsin on clathrin-coated structures at the plasma membrane.

}, issn = {1548-7105}, doi = {10.1038/nmeth.2816}, author = {Sochacki, Kem A and Shtengel, Gleb and Van Engelenburg, Schuyler B and Hess, Harald F and Taraska, Justin W} } @article {45419, title = {Development of the annelid axochord: insights into notochord evolution.}, journal = {Science}, volume = {345}, year = {2014}, month = {2014 Sep 12}, pages = {1365-8}, abstract = {

The origin of chordates has been debated for more than a century, with one key issue being the emergence of the notochord. In vertebrates, the notochord develops by convergence and extension of the chordamesoderm, a population of midline cells of unique molecular identity. We identify a population of mesodermal cells in a developing invertebrate, the marine annelid Platynereis dumerilii, that converges and extends toward the midline and expresses a notochord-specific combination of genes. These cells differentiate into a longitudinal muscle, the axochord, that is positioned between central nervous system and axial blood vessel and secretes a strong collagenous extracellular matrix. Ancestral state reconstruction suggests that contractile mesodermal midline cells existed in bilaterian ancestors. We propose that these cells, via vacuolization and stiffening, gave rise to the chordate notochord.

}, issn = {1095-9203}, doi = {10.1126/science.1253396}, author = {Lauri, Antonella and Brunet, Thibaut and Handberg-Thorsager, Mette and Fischer, Antje H L and Simakov, Oleg and Steinmetz, Patrick R H and Tomer, Raju and Keller, Philipp J and Arendt, Detlev} } @article {6911, title = {Discovery of brainwide neural-behavioral maps via multiscale unsupervised structure learning}, journal = {Science}, volume = {344}, year = {2014}, month = {2014 Mar 27}, pages = {386-92}, chapter = {386}, abstract = {

A single nervous system can generate many distinct motor patterns. Identifying which neurons and circuits control which behaviors has been a laborious piecemeal process, usually for one observer-defined behavior at a time. We present a fundamentally different approach to neuron-behavior mapping. We optogenetically activated 1,054 identified neuron lines in Drosophila larva and tracked the behavioral responses from 37,780 animals. Applying multiscale unsupervised structure learning methods to the behavioral data identified 29 discrete statistically distinguishable and observer-unbiased behavioral phenotypes. Mapping the neural lines to the behavior(s) they evoke provides a behavioral reference atlas for neuron subsets covering a large fraction of larval neurons. This atlas is a starting point for connectivity- and activity-mapping studies to further investigate the mechanisms by which neurons mediate diverse behaviors.

}, issn = {1095-9203}, doi = {10.1126/science.1250298}, author = {Vogelstein, Joshua T and Park, Youngser and Ohyama, Tomoko and Kerr, Rex and Truman, James W and Priebe, Carey E. and Zlatic, Marta} } @article {6962, title = {Efficient Bayesian-based multiview deconvolution.}, journal = {Nature Methods}, volume = {11}, year = {2014}, month = {2014 Apr 20}, pages = {645-8}, abstract = {

Light-sheet fluorescence microscopy is able to image large specimens with high resolution by capturing the samples from multiple angles. Multiview deconvolution can substantially improve the resolution and contrast of the images, but its application has been limited owing to the large size of the data sets. Here we present a Bayesian-based derivation of multiview deconvolution that drastically improves the convergence time, and we provide a fast implementation using graphics hardware.

}, issn = {1548-7105}, doi = {10.1038/nmeth.2929}, author = {Preibisch, Stephan and Amat, Fernando and Stamataki, Evangelia and Sarov, Mihail and Singer, Robert H and Myers, Eugene and Tomancak, Pavel} } @article {6879, title = {Flow of cortical activity underlying a tactile decision in mice.}, journal = {Neuron}, volume = {81}, year = {2014}, month = {2014 Jan 8}, pages = {179-94}, abstract = {

Perceptual decisions involve distributed cortical activity. Does information flow sequentially from one cortical area to another, or do networks of interconnected areas contribute at the same time? Here we delineate when and how activity in specific areas drives a whisker-based decision in mice. A short-term memory component temporally separated tactile "sensation" and "action" (licking). Using optogenetic inhibition (spatial resolution, 2 mm; temporal resolution, 100 ms), we surveyed the neocortex for regions driving behavior during specific behavioral epochs. Barrel cortex was critical for sensation. During the short-term memory, unilateral inhibition of anterior lateral motor cortex biased responses to the ipsilateral side. Consistently, barrel cortex showed stimulus-specific activity during sensation, whereas motor cortex showed choice-specific preparatory activity and movement-related activity, consistent with roles in motor planning and movement. These results suggest serial information flow from sensory to motor areas during perceptual decision making.

}, keywords = {Action Potentials, Afferent Pathways, Animals, Cerebral Cortex, Conditioning, Decision Making, Discrimination (Psychology), Female, Green Fluorescent Proteins, Male, Mice, Motion Perception, Nerve Net, Neurons, Operant, Photic Stimulation, Rhodopsin, Touch, Transgenic, Vesicular Inhibitory Amino Acid Transport Proteins, Vibrissae}, issn = {1097-4199}, doi = {10.1016/j.neuron.2013.10.020}, author = {Guo, Zengcai V and Li, Nuo and Huber, Daniel and Ophir, Eran and Gutnisky, Diego and Ting, Jonathan T and Feng, Guoping and Svoboda, Karel} } @article {48037, title = {A fully genetically encoded protein architecture for optical control of peptide ligand concentration.}, year = {2014}, abstract = {

Ion channels are among the most important proteins in biology, regulating the activity of excitable cells and changing in diseases. Ideally it would be possible to actuate endogenous ion channels, in a temporally precise and reversible manner, and without requiring chemical cofactors. Here we present a modular protein architecture for fully genetically encoded, light-modulated control of ligands that modulate ion channels of a targeted cell. Our reagent, which we call a lumitoxin, combines a photoswitch and an ion channel-blocking peptide toxin. Illumination causes the photoswitch to unfold, lowering the toxin{\textquoteright}s local concentration near the cell surface, and enabling the ion channel to function. We explore lumitoxin modularity by showing operation with peptide toxins that target different voltage-dependent K+\ channels. The lumitoxin architecture may represent a new kind of modular protein-engineering strategy for designing light-activated proteins, and thus may enable development of novel tools for modulating cellular physiology.

}, author = {Daniel Schmidt and Paul Tillberg and Fei Chen and Edward Boyden} } @article {45334, title = {A GAL4 driver resource for developmental and behavioral studies on the larval CNS of Drosophila.}, journal = {Cell Reports}, volume = {8}, year = {2014}, month = {2014 Aug 7}, pages = {897-908}, abstract = {

We report the larval CNS expression patterns for 6,650 GAL4 lines based on cis-regulatory regions (CRMs) from the Drosophila genome. Adult CNS expression patterns were previously reported for this collection, thereby providing a unique resource for determining the origins of adult cells. An illustrative example reveals the origin of the astrocyte-like glia of the ventral\ CNS. Besides larval neurons and glia, the larval CNS\ contains scattered lineages of immature, adult-specific\ neurons. Comparison of lineage expression within this large collection of CRMs provides insight into the codes used for designating neuronal types. The CRMs encode both dense and sparse patterns of lineage expression. There is little correlation between brain and thoracic lineages in patterns of sparse expression, but expression in the two regions is highly correlated in the dense mode. The optic lobes, by comparison, appear to use a different set of genetic instructions in their development.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2014.06.065}, author = {Li, Hsing-Hsi and Kroll, Jason R and Lennox, Sara M and Ogundeyi, Omotara and Jeter, Jennifer and Depasquale, Gina and Truman, James W} } @article {47897, title = {A high-resolution spatiotemporal atlas of gene expression of the developing mouse brain.}, journal = {Neuron}, volume = {83}, year = {2014}, month = {2014 Jul 16}, pages = {309-23}, abstract = {

To provide a temporal framework for the genoarchitecture of brain development, we generated in situ hybridization data for embryonic and postnatal mouse brain at seven developmental stages for \~{}2,100 genes, which were processed with an automated informatics pipeline and manually annotated. This resource comprises 434,946 images, seven reference atlases, an ontogenetic ontology, and tools to explore coexpression of genes across neurodevelopment. Gene sets coinciding with developmental phenomena were identified. A temporal shift in the principles governing the molecular organization of the brain was detected, with transient neuromeric, plate-based organization of the brain present at E11.5 and E13.5. Finally, these data provided a transcription factor code that discriminates brain structures and identifies the developmental age of a tissue, providing a foundation for eventual genetic manipulation or tracking of specific brain structures over development. The resource is available as the Allen Developing Mouse Brain Atlas (http://developingmouse.brain-map.org).

}, keywords = {Animals, Brain, Brain Mapping, Gene Expression, Gene Expression Profiling, Gene Expression Regulation, Developmental, Mice}, issn = {1097-4199}, doi = {10.1016/j.neuron.2014.05.033}, author = {Thompson, Carol L and Ng, Lydia and Menon, Vilas and Martinez, Salvador and Lee, Chang-Kyu and Glattfelder, Katie and Sunkin, Susan M and Henry, Alex and Lau, Christopher and Dang, Chinh and Garcia-Lopez, Raquel and Martinez-Ferre, Almudena and Pombero, Ana and Rubenstein, John L R and Wakeman, Wayne B and Hohmann, John and Dee, Nick and Sodt, Andrew J and Young, Rob and Smith, Kimberly and Nguyen, Thuc-Nghi and Kidney, Jolene and Kuan, Leonard and Jeromin, Andreas and Kaykas, Ajamete and Miller, Jeremy and Page, Damon and Orta, Geri and Bernard, Amy and Riley, Zackery and Smith, Simon and Wohnoutka, Paul and Hawrylycz, Michael J and Puelles, Luis and Jones, Allan R} } @article {6719, title = {Independent optical excitation of distinct neural populations.}, journal = {Nature Methods}, volume = {11}, year = {2014}, month = {2014 Feb 9}, pages = {338-46}, abstract = {

Optogenetic tools enable examination of how specific cell types contribute to brain circuit functions. A long-standing question is whether it is possible to independently activate two distinct neural populations in mammalian brain tissue. Such a capability would enable the study of how different synapses or pathways interact to encode information in the brain. Here we describe two channelrhodopsins, Chronos and Chrimson, discovered through sequencing and physiological characterization of opsins from over 100 species of alga. Chrimson{\textquoteright}s excitation spectrum is red shifted by 45 nm relative to previous channelrhodopsins and can enable experiments in which red light is preferred. We show minimal visual system-mediated behavioral interference when using Chrimson in neurobehavioral studies in Drosophila melanogaster. Chronos has faster kinetics than previous channelrhodopsins yet is effectively more light sensitive. Together these two reagents enable two-color activation of neural spiking and downstream synaptic transmission in independent neural populations without detectable cross-talk in mouse brain slice.

}, issn = {1548-7105}, doi = {10.1038/nmeth.2836}, author = {Klapoetke, Nathan C and Murata, Yasunobu and Kim, Sung Soo and Pulver, Stefan R and Birdsey-Benson, Amanda and Cho, Yong Ku and Morimoto, Tania K and Chuong, Amy S and Carpenter, Eric J and Tian, Zhijian and Wang, Jun and Xie, Yinlong and Yan, Zhixiang and Zhang, Yong and Chow, Brian Y and Surek, Barbara and Melkonian, Michael and Jayaraman, Vivek and Constantine-Paton, Martha and Wong, Gane Ka-Shu and Boyden, Edward S} } @article {45190, title = {Juvenile hormone regulates body size and perturbs insulin signaling in Drosophila.}, journal = {Proceedings of the National Academy of Science of the United States of America}, volume = {111}, year = {2014}, month = {2014 May 13}, pages = {7018-23}, abstract = {

The role of juvenile hormone (JH) in regulating the timing and nature of insect molts is well-established. Increasing evidence suggests that JH is also involved in regulating final insect size. Here we elucidate the developmental mechanism through which JH regulates body size in developing Drosophila larvae by genetically ablating the JH-producing organ, the corpora allata (CA). We found that larvae that lack CA pupariated at smaller sizes than control larvae due to a reduced larval growth rate. Neither the timing of the metamorphic molt nor the duration of larval growth was affected by the loss of JH. Further, we show that the effects of JH on growth rate are dependent on the forkhead box O transcription factor (FOXO), which is negatively regulated by the insulin-signaling pathway. Larvae that lacked the CA had elevated levels of FOXO activity, whereas a loss-of-function mutation of FOXO rescued the effects of CA ablation on final body size. Finally, the effect of JH on growth appears to be mediated, at least in part, via ecdysone synthesis in the prothoracic gland. These results indicate a role of JH in regulating growth rate via the ecdysone- and insulin-signaling pathways.

}, keywords = {Animals, Basic Helix-Loop-Helix Transcription Factors, Body Size, Corpora Allata, Denervation, Drosophila melanogaster, Drosophila Proteins, Ecdysone, Forkhead Transcription Factors, Insulin, Juvenile Hormones, Larva, Signal Transduction}, issn = {1091-6490}, doi = {10.1073/pnas.1313058111}, author = {Mirth, C K and Tang, H Y and Makohon-Moore, S C and Salhadar, S and Gokhale, R H and Warner, R D and Koyama, T and Riddiford, L M and Shingleton, A W} } @article {45182, title = {Kainate receptors mediate signaling in both transient and sustained OFF bipolar cell pathways in mouse retina.}, journal = {Journal of Neuroscience}, volume = {34}, year = {2014}, month = {2014 Apr 30}, pages = {6128-39}, abstract = {

A fundamental question in sensory neuroscience is how parallel processing is implemented at the level of molecular and circuit mechanisms. In the retina, it has been proposed that distinct OFF cone bipolar cell types generate fast/transient and slow/sustained pathways by the differential expression of AMPA- and kainate-type glutamate receptors, respectively. However, the functional significance of these receptors in the intact circuit during light stimulation remains unclear. Here, we measured glutamate release from mouse bipolar cells by two-photon imaging of a glutamate sensor (iGluSnFR) expressed on postsynaptic amacrine and ganglion cell dendrites. In both transient and sustained OFF layers, cone-driven glutamate release from bipolar cells was blocked by antagonists to kainate receptors but not AMPA receptors. Electrophysiological recordings from bipolar and ganglion cells confirmed the essential role of kainate receptors for signaling in both transient and sustained OFF pathways. Kainate receptors mediated responses to contrast modulation up to 20 Hz. Light-evoked responses in all mouse OFF bipolar pathways depend on kainate, not AMPA, receptors.

}, keywords = {Action Potentials, Animals, Drug Interactions, Excitatory Amino Acid Antagonists, Female, Glutamic Acid, Hexamethonium, Light, Male, Mice, Mice, Inbred C57BL, Nicotinic Antagonists, Patch-Clamp Techniques, Photic Stimulation, Propionates, Receptors, Kainic Acid, Retina, Retinal Bipolar Cells, Signal Transduction, Visual Pathways}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4941-13.2014}, author = {Borghuis, Bart G and Looger, Loren L and Tomita, Susumu and Demb, Jonathan B} } @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 {45852, title = {Live imaging of endogenous PSD-95 using ENABLED: a conditional strategy to fluorescently label endogenous proteins.}, journal = {Journal of Neuroscience}, volume = {34}, year = {2014}, month = {2014 Dec 10}, pages = {16698-712}, abstract = {

Stoichiometric labeling of endogenous synaptic proteins for high-contrast live-cell imaging in brain tissue remains challenging. Here, we describe a conditional mouse genetic strategy termed endogenous labeling via exon duplication (ENABLED), which can be used to fluorescently label endogenous proteins with near ideal properties in all neurons, a sparse subset of neurons, or specific neuronal subtypes. We used this method to label the postsynaptic density protein PSD-95 with mVenus without overexpression side effects. We demonstrated that mVenus-tagged PSD-95 is functionally equivalent to wild-type PSD-95 and that PSD-95 is present in nearly all dendritic spines in CA1 neurons. Within spines, while PSD-95 exhibited low mobility under basal conditions, its levels could be regulated by chronic changes in neuronal activity. Notably, labeled PSD-95 also allowed us to visualize and unambiguously examine otherwise-unidentifiable excitatory shaft synapses in aspiny neurons, such as parvalbumin-positive interneurons and dopaminergic neurons. Our results demonstrate that the ENABLED strategy provides a valuable new approach to study the dynamics of endogenous synaptic proteins in vivo.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3888-14.2014}, author = {Fortin, Dale A and Tillo, Shane E and Yang, Guang and Rah, Jong-Cheol and Melander, Joshua B and Bai, Suxia and Soler-Cede{\~n}o, Omar and Qin, Maozhen and Zemelman, Boris V and Guo, Caiying and Mao, Tianyi and Zhong, Haining} } @article {45373, title = {Multiplexed aberration measurement for deep tissue imaging in vivo.}, journal = {Nature Methods}, year = {2014}, month = {2014 Aug 17}, abstract = {

We describe an adaptive optics method that modulates the intensity or phase of light rays at multiple pupil segments in parallel to determine the sample-induced aberration. Applicable to fluorescent protein-labeled structures of arbitrary complexity, it allowed us to obtain diffraction-limited resolution in various samples in vivo. For the strongly scattering mouse brain, a single aberration correction improved structural and functional imaging of fine neuronal processes over a large imaging volume.

}, issn = {1548-7105}, doi = {10.1038/nmeth.3068}, author = {Wang, Chen and Liu, Rui and Milkie, Daniel E and Sun, Wenzhi and Tan, Zhongchao and Kerlin, Aaron and Chen, Tsai-Wen and Kim, Douglas S and Ji, Na} } @article {45811, title = {Mushroom body output neurons encode valence and guide memory-based action selection in Drosophila.}, journal = {eLife}, volume = {4}, year = {2014}, month = {12/2014}, abstract = {

Animals discriminate stimuli, learn their predictive value and use this knowledge to modify their behavior. In Drosophila, the mushroom body (MB) plays a key role in these processes. Sensory stimuli are sparsely represented by \~{}2000 Kenyon cells, which converge onto 34 output neurons (MBONs) of 21 types. We studied the role of MBONs in several associative learning tasks and in sleep regulation, revealing the extent to which information flow is segregated into distinct channels and suggesting possible roles for the multi-layered MBON network. We also show that optogenetic activation of MBONs can, depending on cell type, induce repulsion or attraction in flies. The behavioral effects of MBON perturbation are combinatorial, suggesting that the MBON ensemble collectively represents valence. We propose that local, stimulus-specific dopaminergic modulation selectively alters the balance within the MBON network for those stimuli. Our results suggest that valence encoded by the MBON ensemble biases memory-based action selection.

}, issn = {2050-084X}, doi = {10.7554/eLife.04580}, author = {Aso, Yoshinori and Sitaraman, Divya and Ichinose, Toshiharu and Kaun, Karla R and Vogt, Katrin and Belliart-Gu{\'e}rin, Ghislain and Placais, Pierre-Yves and Robie, Alice A and Yamagata, Nobuhiro and Schnaitmann, Christopher and Rowell, William J and Johnston, Rebecca M and Ngo, Teri-T B and Chen, Nan and Korff, Wyatt and Nitabach, Michael N and Heberlein, Ulrike and Preat, Thomas and Branson, Kristin M and Tanimoto, Hiromu and Rubin, Gerald M} } @article {45810, title = {The neuronal architecture of the mushroom body provides a logic for associative learning.}, journal = {eLife}, volume = {3}, year = {2014}, month = {2014 Dec 23}, abstract = {

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

}, issn = {2050-084X}, doi = {10.7554/eLife.04577}, author = {Aso, Yoshinori and Hattori, Daisuke and Yu, Yang and Johnston, Rebecca M and Iyer, Nirmala A and Ngo, Teri-Tb and Dionne, Heather and Abbott, Lf and Axel, Richard and Tanimoto, Hiromu and Rubin, Gerald M} } @article {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 {6892, title = {Optimized ratiometric calcium sensors for functional in vivo imaging of neurons and T lymphocytes.}, journal = {Nature Methods}, volume = {11}, year = {2014}, month = {2014 Feb}, pages = {175-82}, abstract = {

The quality of genetically encoded calcium indicators (GECIs) has improved dramatically in recent years, but high-performing ratiometric indicators are still rare. Here we describe a series of fluorescence resonance energy transfer (FRET)-based calcium biosensors with a reduced number of calcium binding sites per sensor. These {\textquoteright}Twitch{\textquoteright} sensors are based on the C-terminal domain of Opsanus troponin C. Their FRET responses were optimized by a large-scale functional screen in bacterial colonies, refined by a secondary screen in rat hippocampal neuron cultures. We tested the in vivo performance of the most sensitive variants in the brain and lymph nodes of mice. The sensitivity of the Twitch sensors matched that of synthetic calcium dyes and allowed visualization of tonic action potential firing in neurons and high resolution functional tracking of T lymphocytes. Given their ratiometric readout, their brightness, large dynamic range and linear response properties, Twitch sensors represent versatile tools for neuroscience and immunology.

}, issn = {1548-7105}, doi = {10.1038/nmeth.2773}, author = {Thestrup, Thomas and Litzlbauer, Julia and Bartholom{\"a}us, Ingo and Mues, Marsilius and Russo, Luigi and Dana, Hod and Kovalchuk, Yuri and Liang, Yajie and Kalamakis, Georgios and Laukat, Yvonne and Becker, Stefan and Witte, Gregor and Geiger, Anselm and Allen, Taylor and Rome, Lawrence C and Chen, Tsai-Wen and Kim, Douglas S. and Garaschuk, Olga and Griesinger, Christian and Griesbeck, Oliver} } @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 {45336, title = {Population of sensory neurons essential for asthmatic hyperreactivity of inflamed airways.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, year = {2014}, month = {2014 Aug 5}, pages = {11515-20}, abstract = {

Asthma is a common debilitating inflammatory lung disease affecting over 200 million people worldwide. Here, we investigated neurogenic components involved in asthmatic-like attacks using the ovalbumin-sensitized murine model of the disease, and identified a specific population of neurons that are required for airway hyperreactivity. We show that ablating or genetically silencing these neurons abolished the hyperreactive broncho-constrictions, even in the presence of a fully developed lung inflammatory immune response. These neurons are found in the vagal ganglia and are characterized by the expression of the transient receptor potential vanilloid 1 (TRPV1) ion channel. However, the TRPV1 channel itself is not required for the asthmatic-like hyperreactive airway response. We also demonstrate that optogenetic stimulation of this population of TRP-expressing cells with channelrhodopsin dramatically exacerbates airway hyperreactivity of inflamed airways. Notably, these cells express the sphingosine-1-phosphate receptor 3 (S1PR3), and stimulation with a S1PR3 agonist efficiently induced broncho-constrictions, even in the absence of ovalbumin sensitization and inflammation. Our results show that the airway hyperreactivity phenotype can be physiologically dissociated from the immune component, and provide a platform for devising therapeutic approaches to asthma that target these pathways separately.

}, issn = {1091-6490}, doi = {10.1073/pnas.1411032111}, author = {Tr{\"a}nkner, Dimitri and Hahne, Nadeau and Sugino, Ken and Hoon, Mark A and Zuker, Charles} } @inbook {65784, title = {Porphyrins and Metalloporphyrins at Components in Artificial Photosynthesis Research}, booktitle = {Handbook of Porphyrin Science}, volume = {34}, year = {2014}, pages = {196 {\textendash} 233}, publisher = {World Scientific Pulishing}, organization = {World Scientific Pulishing}, isbn = {978-981-4425-10-0}, doi = {10.1142/9789814417297_0016}, author = {Tebo, Alison G. and Herrero, C and Aukauloo, A}, editor = {Kadish, Karl M and Smith, Kevin M and undefined, and Guilard, Roger} } @article {65783, title = {Protein design: toward functional metalloenzymes.}, journal = {Chemical reviews}, volume = {114}, year = {2014}, month = {03/2014}, pages = {3495 {\textendash} 3578}, doi = {10.1021/cr400458x}, author = {Yu, Fangting and Cangelosi, Virginia M and Zastrow, Melissa L and Tegoni, Matteo and Plegaria, Jefferson S and Tebo, Alison G and Mocny, Catherine S and Ruckthong, Leela and Qayyum, Hira and Pecoraro, Vincent L} } @article {45843, title = {Regulation of RNA polymerase II activation by histone acetylation in single living cells.}, journal = {Nature}, volume = {516}, year = {2014}, month = {2014 Dec 11}, pages = {272-5}, abstract = {

In eukaryotic cells, post-translational histone modifications have an important role in gene regulation. Starting with early work on histone acetylation, a variety of residue-specific modifications have now been linked to RNA polymerase II (RNAP2) activity, but it remains unclear if these markers are active regulators of transcription or just passive byproducts. This is because studies have traditionally relied on fixed cell populations, meaning temporal resolution is limited to minutes at best, and correlated factors may not actually be present in the same cell at the same time. Complementary approaches are therefore needed to probe the dynamic interplay of histone modifications and RNAP2 with higher temporal resolution in single living cells. Here we address this problem by developing a system to track residue-specific histone modifications and RNAP2 phosphorylation in living cells by fluorescence microscopy. This increases temporal resolution to the tens-of-seconds range. Our single-cell analysis reveals histone H3 lysine-27 acetylation at a gene locus can alter downstream transcription kinetics by as much as 50\%, affecting two temporally separate events. First acetylation enhances the search kinetics of transcriptional activators, and later the acetylation accelerates the transition of RNAP2 from initiation to elongation. Signatures of the latter can be found genome-wide using chromatin immunoprecipitation followed by sequencing. We argue that this regulation leads to a robust and potentially tunable transcriptional response.

}, issn = {1476-4687}, doi = {10.1038/nature13714}, author = {Stasevich, Timothy J and Hayashi-Takanaka, Yoko and Sato, Yuko and Maehara, Kazumitsu and Ohkawa, Yasuyuki and Sakata-Sogawa, Kumiko and Tokunaga, Makio and Nagase, Takahiro and Nozaki, Naohito and McNally, James G and Kimura, Hiroshi} } @article {45416, title = {Shared mushroom body circuits underlie visual and olfactory memories in Drosophila.}, journal = {eLife}, volume = {3}, year = {2014}, month = {2014}, pages = {e02395}, abstract = {

In nature, animals form memories associating reward or punishment with stimuli from different sensory modalities, such as smells and colors. It is unclear, however, how distinct sensory memories are processed in the brain. We established appetitive and aversive visual learning assays for Drosophila that are comparable to the widely used olfactory learning assays. These assays share critical features, such as reinforcing stimuli (sugar reward and electric shock punishment), and allow direct comparison of the cellular requirements for visual and olfactory memories. We found that the same subsets of dopamine neurons drive formation of both sensory memories. Furthermore, distinct yet partially overlapping subsets of mushroom body intrinsic neurons are required for visual and olfactory memories. Thus, our results suggest that distinct sensory memories are processed in a common brain center. Such centralization of related brain functions is an economical design that avoids the repetition of similar circuit motifs.

}, issn = {2050-084X}, doi = {10.7554/eLife.02395}, author = {Vogt, Katrin and Schnaitmann, Christopher and Dylla, Kristina V and Knapek, Stephan and Aso, Yoshinori and Rubin, Gerald M and Tanimoto, Hiromu} } @article {6919, title = {Single-molecule dynamics of enhanceosome assembly in embryonic stem cells.}, journal = {Cell}, volume = {156}, year = {2014}, month = {2014 Mar 13}, pages = {1274-85}, abstract = {

Enhancer-binding pluripotency regulators (Sox2 and Oct4) play a seminal role in embryonic stem (ES) cell-specific gene regulation. Here, we combine in\ vivo and in\ vitro single-molecule imaging, transcription factor (TF) mutagenesis, and ChIP-exo mapping to\ determine how TFs dynamically search for and assemble on their cognate DNA target sites. We find that enhanceosome assembly is hierarchically ordered with kinetically favored Sox2 engaging the target DNA first, followed by assisted binding of Oct4. Sox2/Oct4 follow a trial-and-error sampling mechanism involving 84-97 events of 3D diffusion (3.3-3.7 s) interspersed with brief nonspecific collisions (0.75-0.9 s) before acquiring and dwelling at specific target DNA (12.0-14.6 s). Sox2 employs a 3D diffusion-dominated search mode facilitated by 1D sliding along open DNA to efficiently locate targets. Our findings also reveal fundamental aspects of gene and developmental regulation by fine-tuning TF dynamics and influence of the epigenome on target search parameters.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2014.01.062}, author = {Chen, Jiji and Zhang, Zhengjian and Li Li and Chen, Bi-Chang and Revyakin, Andrey and Hajj, Bassam and Legant, Wesley and Dahan, Maxime and Lionnet, Timoth{\'e}e and Betzig, Eric and Tjian, Robert and Liu, Zhe} } @article {6845, title = {Single-molecule tracking of the transcription cycle by sub-second RNA detection.}, journal = {eLife}, volume = {3}, year = {2014}, month = {2014 Jan 28}, pages = {e01775}, abstract = {

Transcription is an inherently stochastic, noisy, and multi-step process, in which fluctuations at every step can cause variations in RNA synthesis, and affect physiology and differentiation decisions in otherwise identical cells. However, it has been an experimental challenge to directly link the stochastic events at the promoter to transcript production. Here we established a fast fluorescence in situ hybridization (fastFISH) method that takes advantage of intrinsically unstructured nucleic acid sequences to achieve exceptionally fast rates of specific hybridization (\~{}10e7 M(-1)s(-1)), and allows deterministic detection of single nascent transcripts. Using a prototypical RNA polymerase, we demonstrated the use of fastFISH to measure the kinetic rates of promoter escape, elongation, and termination in one assay at the single-molecule level, at sub-second temporal resolution. The principles of fastFISH design can be used to study stochasticity in gene regulation, to select targets for gene silencing, and to design nucleic acid nanostructures. DOI: http://dx.doi.org/10.7554/eLife.01775.001.

}, issn = {2050-084X}, doi = {10.7554/eLife.01775}, author = {Zhang, Zhengjian and Revyakin, Andrey and Grimm, Jonathan B and Lavis, Luke D and Tjian, Robert} } @article {6957, title = {A small subset of fruitless subesophageal neurons modulate early courtship in Drosophila.}, journal = {PLoS One}, volume = {9}, year = {2014}, month = {2014 Apr 16}, pages = {e95472}, abstract = {

We show that a small subset of two to six subesophageal neurons, expressing the male products of the male courtship master regulator gene products fruitlessMale (fruM), are required in the early stages of the Drosophila melanogaster male courtship behavioral program. Loss of fruM expression or inhibition of synaptic transmission in these fruM(+) neurons results in delayed courtship initiation and a failure to progress to copulation primarily under visually-deficient conditions. We identify a fruM-dependent sexually dimorphic arborization in the tritocerebrum made by two of these neurons. Furthermore, these SOG neurons extend descending projections to the thorax and abdominal ganglia. These anatomical and functional characteristics place these neurons in the position to integrate gustatory and higher-order signals in order to properly initiate and progress through early courtship.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0095472}, author = {Tran, David H and Meissner, Geoffrey W and French, Rachael L and Baker, Bruce S} } @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 {47704, title = {Structurally-constrained relationships between cognitive states in the human brain.}, journal = {PLoS computational biology}, volume = {10}, year = {2014}, month = {2014 May}, pages = {e1003591}, abstract = {

The anatomical connectivity of the human brain supports diverse patterns of correlated neural activity that are thought to underlie cognitive function. In a manner sensitive to underlying structural brain architecture, we examine the extent to which such patterns of correlated activity systematically vary across cognitive states. Anatomical white matter connectivity is compared with functional correlations in neural activity measured via blood oxygen level dependent (BOLD) signals. Functional connectivity is separately measured at rest, during an attention task, and during a memory task. We assess these structural and functional measures within previously-identified resting-state functional networks, denoted task-positive and task-negative networks, that have been independently shown to be strongly anticorrelated at rest but also involve regions of the brain that routinely increase and decrease in activity during task-driven processes. We find that the density of anatomical connections within and between task-positive and task-negative networks is differentially related to strong, task-dependent correlations in neural activity. The space mapped out by the observed structure-function relationships is used to define a quantitative measure of separation between resting, attention, and memory states. We find that the degree of separation between states is related to both general measures of behavioral performance and relative differences in task-specific measures of attention versus memory performance. These findings suggest that the observed separation between cognitive states reflects underlying organizational principles of human brain structure and function.

}, keywords = {Attention, Brain, Cognition, Computer Simulation, Connectome, Humans, Memory, Models, Anatomic, Models, Neurological, Nerve Net, White Matter}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1003591}, author = {Hermundstad, Ann M and Brown, Kevin S and Bassett, Danielle S and Aminoff, Elissa M and Frithsen, Amy and Johnson, Arianne and Tipper, Christine M and Miller, Michael B and Grafton, Scott T and Carlson, Jean M} } @article {6825, title = {Structure-based neuron retrieval across Drosophila brains.}, journal = {Neuroinformatics}, volume = {12}, year = {2014}, month = {2014 Jan 21}, pages = {423-34}, abstract = {

Comparing local neural structures across large sets of examples is crucial when studying gene functions, and their effect in the Drosophila brain. The current practice of aligning brain volume data to a joint reference frame is based on the neuropil. However, even after alignment neurons exhibit residual location and shape variability that, together with image noise, hamper direct quantitative comparison and retrieval of similar structures on an intensity basis. In this paper, we propose and evaluate an image-based retrieval method for neurons, relying on local appearance, which can cope with spatial variability across the population. For an object of interest marked in a query case, the method ranks cases drawn from a large data set based on local neuron appearance in confocal microscopy data. The approach is based on capturing the orientation of neurons based on structure tensors and expanding this field via Gradient Vector Flow. During retrieval, the algorithm compares fields across cases, and calculates a corresponding ranking of most similar cases with regard to the local structure of interest. Experimental results demonstrate that the similarity measure and ranking mechanisms yield high precision and recall in realistic search scenarios.

}, issn = {1559-0089}, doi = {10.1007/s12021-014-9219-4}, author = {Ganglberger, Florian and Schulze, Florian and Tirian, Laszlo and Novikov, Alexey and Dickson, Barry and B{\"u}hler, Katja and Langs, Georg} } @article {45372, title = {A type VI secretion-related pathway in bacteroidetes mediates interbacterial antagonism.}, journal = {Cell Host Microbe}, volume = {16}, year = {2014}, month = {2014 Aug 13}, pages = {227-36}, abstract = {

Bacteroidetes are a phylum of Gram-negative bacteria abundant in mammalian-associated polymicrobial communities, where they impact digestion, immunity, and resistance to infection. Despite the extensive competition at high cell density that occurs in these settings, cell contact-dependent mechanisms of interbacterial antagonism, such as the type VI secretion system (T6SS), have not been defined in this group of organisms. Herein we report the bioinformatic and functional characterization of a T6SS-like pathway in diverse Bacteroidetes. Using prominent human gut commensal and soil-associated species, we demonstrate that these systems localize dynamically within the cell, export antibacterial proteins, and target competitor bacteria. The Bacteroidetes system is a distinct pathway with marked differences in gene content and high evolutionary divergence from the canonical T6S pathway. Our findings offer a potential molecular explanation for the abundance of Bacteroidetes in polymicrobial environments, the observed stability of Bacteroidetes in healthy humans, and the barrier presented by the microbiota against pathogens.

}, issn = {1934-6069}, doi = {10.1016/j.chom.2014.07.007}, author = {Russell, Alistair B and Wexler, Aaron G and Harding, Brittany N and Whitney, John C and Bohn, Alan J and Goo, Young Ah and Tran, Bao Q and Barry, Natasha A and Zheng, Hongjin and Peterson, S Brook and Chou, Seemay and Gonen, Tamir and Goodlett, David R and Goodman, Andrew L and Mougous, Joseph D} } @article {47703, title = {Variance predicts salience in central sensory processing.}, journal = {eLife}, volume = {3}, year = {2014}, month = {2014}, abstract = {

Information processing in the sensory periphery is shaped by natural stimulus statistics. In the periphery, a transmission bottleneck constrains performance; thus efficient coding implies that natural signal components with a predictably wider range should be compressed. In a different regime--when sampling limitations constrain performance--efficient coding implies that more resources should be allocated to informative features that are more variable. We propose that this regime is relevant for sensory cortex when it extracts complex features from limited numbers of sensory samples. To test this prediction, we use central visual processing as a model: we show that visual sensitivity for local multi-point spatial correlations, described by dozens of independently-measured parameters, can be quantitatively predicted from the structure of natural images. This suggests that efficient coding applies centrally, where it extends to higher-order sensory features and operates in a regime in which sensitivity increases with feature variability.

}, keywords = {Humans, Sensory Receptor Cells, Visual Cortex, Visual Perception}, issn = {2050-084X}, doi = {10.7554/eLife.03722}, author = {Hermundstad, Ann M and Briguglio, John J and Conte, Mary M and Victor, Jonathan D and Balasubramanian, Vijay and Tka{\v c}ik, Ga{\v s}per} } @article {45064, title = {Virtual finger boosts three-dimensional imaging and microsurgery as well as terabyte volume image visualization and analysis.}, journal = {Nature Communications}, volume = {5}, year = {2014}, month = {2014 Jul 11}, pages = {4342}, abstract = {

Three-dimensional (3D) bioimaging, visualization and data analysis are in strong need of powerful 3D exploration techniques. We develop virtual finger (VF) to generate 3D curves, points and regions-of-interest in the 3D space of a volumetric image with a single finger operation, such as a computer mouse stroke, or click or zoom from the 2D-projection plane of an image as visualized with a computer. VF provides efficient methods for acquisition, visualization and analysis of 3D images for roundworm, fruitfly, dragonfly, mouse, rat and human. Specifically, VF enables instant 3D optical zoom-in imaging, 3D free-form optical microsurgery, and 3D visualization and annotation of terabytes of whole-brain image volumes. VF also leads to orders of magnitude better efficiency of automated 3D reconstruction of neurons and similar biostructures over our previous systems. We use VF to generate from images of 1,107 Drosophila GAL4 lines a projectome of a Drosophila brain.

}, issn = {2041-1723}, doi = {10.1038/ncomms5342}, author = {Peng, Hanchuan and Tang, Jianyong and Xiao, Hang and Bria, Alessandro and Zhou, Jianlong and Butler, Victoria and Zhou, Zhi and Gonzalez-Bellido, Paloma T and Oh, Seung W and Chen, Jichao and Mitra, Ananya and Tsien, Richard W and Zeng, Hongkui and Ascoli, Giorgio A and Iannello, Giulio and Hawrylycz, Michael and Myers, Eugene and Long, Fuhui} } @article {45176, title = {Wide-field feedback neurons dynamically tune early visual processing.}, journal = {Neuron}, volume = {82}, year = {2014}, month = {2014 May 21}, pages = {887-95}, abstract = {

An important strategy for efficient neural coding is to match the range of cellular responses to the distribution of relevant input signals. However, the structure and relevance of sensory signals depend on behavioral state. Here, we show that behavior modifies neural activity at the earliest stages of fly vision. We describe a class of wide-field neurons that provide feedback to the most peripheral layer of the Drosophila visual system, the lamina. Using in vivo patch-clamp electrophysiology, we found that lamina wide-field neurons respond to low-frequency luminance fluctuations. Recordings in flying flies revealed that the gain and frequency tuning of wide-field neurons change during flight, and that these effects are mimicked by the neuromodulator octopamine. Genetically silencing wide-field neurons increased behavioral responses to slow-motion stimuli. Together, these findings identify a cell type that is gated by behavior to enhance neural coding by subtracting low-frequency signals from the inputs to motion detection circuits.

}, keywords = {Adrenergic alpha-Agonists, Anesthetics, Local, Animals, Animals, Genetically Modified, Brain, Choline O-Acetyltransferase, Drosophila, Drosophila Proteins, Feedback, Sensory, Flight, Animal, Green Fluorescent Proteins, Membrane Potentials, Motion Perception, Neurons, Octopamine, Photic Stimulation, Tetrodotoxin, Transcription Factors, Visual Pathways}, issn = {1097-4199}, doi = {10.1016/j.neuron.2014.04.023}, author = {Tuthill, John C and Nern, Aljoscha and Rubin, Gerald M and Reiser, Michael B} } @article {46284, title = {Word length effect in free recall of randomly assembled word lists.}, journal = {Frontiers in Computational Neuroscience}, volume = {8}, year = {2014}, month = {2014 Oct 14}, pages = {129}, abstract = {

In serial recall experiments, human subjects are requested to retrieve a list of words in the same order as they were presented. In a classical study, participants were reported to recall more words from study lists composed of short words compared to lists of long words, the word length effect. The world length effect was also observed in free recall experiments, where subjects can retrieve the words in any order. Here we analyzed a large dataset from free recall experiments of unrelated words, where short and long words were randomly mixed, and found a seemingly opposite effect: long words are recalled better than the short ones. We show that our recently proposed mechanism of associative retrieval can explain both these observations. Moreover, the direction of the effect depends solely on the way study lists are composed.

}, issn = {1662-5188}, doi = {10.3389/fncom.2014.00129}, author = {Katkov, Mikhail and Romani, Sandro and Tsodyks, Misha} } @article {6127, title = {Admixture mapping in lupus identifies multiple functional variants within IFIH1 associated with apoptosis, inflammation, and autoantibody production.}, journal = {PLoS Genetics}, volume = {9}, year = {2013}, month = {2013 Feb 18}, pages = {e1003222}, abstract = {

Systemic lupus erythematosus (SLE) is an inflammatory autoimmune disease with a strong genetic component. African-Americans (AA) are at increased risk of SLE, but the genetic basis of this risk is largely unknown. To identify causal variants in SLE loci in AA, we performed admixture mapping followed by fine mapping in AA and European-Americans (EA). Through genome-wide admixture mapping in AA, we identified a strong SLE susceptibility locus at 2q22-24 (LOD=6.28), and the admixture signal is associated with the European ancestry (ancestry risk ratio \ 1.5). Large-scale genotypic analysis on 19,726 individuals of African and European ancestry revealed three independently associated variants in the IFIH1 gene: an intronic variant, rs13023380 [P(meta) = 5.20{\texttimes}10(-14); odds ratio, 95\% confidence interval = 0.82 (0.78-0.87)], and two missense variants, rs1990760 (Ala946Thr) [P(meta) = 3.08{\texttimes}10(-7); 0.88 (0.84-0.93)] and rs10930046 (Arg460His) [P(dom) = 1.16{\texttimes}10(-8); 0.70 (0.62-0.79)]. Both missense variants produced dramatic phenotypic changes in apoptosis and inflammation-related gene expression. We experimentally validated function of the intronic SNP by DNA electrophoresis, protein identification, and in vitro protein binding assays. DNA carrying the intronic risk allele rs13023380 showed reduced binding efficiency to a cellular protein complex including nucleolin and lupus autoantigen Ku70/80, and showed reduced transcriptional activity in vivo. Thus, in SLE patients, genetic susceptibility could create a biochemical imbalance that dysregulates nucleolin, Ku70/80, or other nucleic acid regulatory proteins. This could promote antibody hypermutation and auto-antibody generation, further destabilizing the cellular network. Together with molecular modeling, our results establish a distinct role for IFIH1 in apoptosis, inflammation, and autoantibody production, and explain the molecular basis of these three risk alleles for SLE pathogenesis.

}, keywords = {African Americans, Alleles, Antigens, Apoptosis, Autoantibodies, Chromosome Mapping, DEAD-box RNA Helicases, DNA-Binding Proteins, European Continental Ancestry Group, Genetic Predisposition to Disease, Genome, Haplotypes, Human, Humans, Inflammation, Lupus Erythematosus, Nuclear, Polymorphism, Protein Binding, Single Nucleotide, Systemic}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1003222}, author = {Molineros, Julio E and Maiti, Amit K and Sun, Celi and Looger, Loren L and Han, Shizhong and Kim-Howard, Xana and Glenn, Stuart and Adler, Adam and Kelly, Jennifer A and Niewold, Timothy B and Gilkeson, Gary S and Brown, Elizabeth E and Alarc{\'o}n, Graciela S and Edberg, Jeffrey C and Petri, Michelle and Ramsey-Goldman, Rosalind and Reveille, John D and Vil{\'a}, Luis M and Freedman, Barry I and Tsao, Betty P and Criswell, Lindsey A and Jacob, Chaim O and Moore, Jason H and Vyse, Timothy J and Langefeld, Carl L and Guthridge, Joel M and Gaffney, Patrick M and Moser, Kathy L and Scofield, R Hal and Alarc{\'o}n-Riquelme, Marta E and Williams, Scott M and Merrill, Joan T and James, Judith A and Kaufman, Kenneth M and Kimberly, Robert P and Harley, John B and Nath, Swapan K} } @article {6252, title = {Allosteric mechanism of water-channel gating by Ca(2+)-calmodulin.}, journal = {Nature Structural \& Molecular Biology}, volume = {20}, year = {2013}, month = {2013 Jul 28}, pages = {1085-92}, abstract = {

Calmodulin (CaM) is a universal regulatory protein that communicates the presence of calcium to its molecular targets and correspondingly modulates their function. This key signaling protein is important for controlling the activity of hundreds of membrane channels and transporters. However, understanding of the structural mechanisms driving CaM regulation of full-length membrane proteins has remained elusive. In this study, we determined the pseudoatomic structure of full-length mammalian aquaporin-0 (AQP0, Bos taurus) in complex with CaM, using EM to elucidate how this signaling protein modulates water-channel function. Molecular dynamics and functional mutation studies reveal how CaM binding inhibits AQP0 water permeability by allosterically closing the cytoplasmic gate of AQP0. Our mechanistic model provides new insight, only possible in the context of the fully assembled channel, into how CaM regulates multimeric channels by facilitating cooperativity between adjacent subunits.

}, issn = {1545-9985}, doi = {10.1038/nsmb.2630}, author = {Reichow, Steve L and Clemens, Daniel M and Freites, J Alfredo and N{\'e}meth-Cahalan, Karin L and Heyden, Matthias and Tobias, Douglas J and Hall, James E and Gonen, Tamir} } @article {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 {6268, title = {Aβ induces astrocytic glutamate release, extrasynaptic NMDA receptor activation, and synaptic loss.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, year = {2013}, month = {2013 Jul 2}, pages = {E2518-27}, abstract = {

Synaptic loss is the cardinal feature linking neuropathology to cognitive decline in Alzheimer{\textquoteright}s disease (AD). However, the mechanism of synaptic damage remains incompletely understood. Here, using FRET-based glutamate sensor imaging, we show that amyloid-β peptide (Aβ) engages α7 nicotinic acetylcholine receptors to induce release of astrocytic glutamate, which in turn activates extrasynaptic NMDA receptors (eNMDARs) on neurons. In hippocampal autapses, this eNMDAR activity is followed by reduction in evoked and miniature excitatory postsynaptic currents (mEPSCs). Decreased mEPSC frequency may reflect early synaptic injury because of concurrent eNMDAR-mediated NO production, tau phosphorylation, and caspase-3 activation, each of which is implicated in spine loss. In hippocampal slices, oligomeric Aβ induces eNMDAR-mediated synaptic depression. In AD-transgenic mice compared with wild type, whole-cell recordings revealed excessive tonic eNMDAR activity accompanied by eNMDAR-sensitive loss of mEPSCs. Importantly, the improved NMDAR antagonist NitroMemantine, which selectively inhibits extrasynaptic over physiological synaptic NMDAR activity, protects synapses from Aβ-induced damage both in vitro and in vivo.

}, issn = {1091-6490}, doi = {10.1073/pnas.1306832110}, author = {Talantova, Maria and Sanz-Blasco, Sara and Zhang, Xiaofei and Xia, Peng and Akhtar, Mohd Waseem and Okamoto, Shu-ichi and Dziewczapolski, Gustavo and Nakamura, Tomohiro and Cao, Gang and Pratt, Alexander E and Kang, Yeon-Joo and Tu, Shichun and Molokanova, Elena and McKercher, Scott R and Hires, Samuel Andrew and Sason, Hagit and Stouffer, David G and Buczynski, Matthew W and Solomon, James P and Michael, Sarah and Powers, Evan T and Kelly, Jeffery W and Roberts, Amanda and Tong, Gary and Fang-Newmeyer, Traci and Parker, James and Holland, Emily A and Zhang, Dongxian and Nakanishi, Nobuki and Chen, H-S Vincent and Wolosker, Herman and Wang, Yuqiang and Parsons, Loren H and Ambasudhan, Rajesh and Masliah, Eliezer and Heinemann, Stephen F and Pi{\~n}a-Crespo, Juan C and Lipton, Stuart A} } @article {6261, title = {Connectomic reconstruction of the inner plexiform layer in the mouse retina.}, journal = {Nature}, volume = {500}, year = {2013}, month = {2013 Aug 8}, pages = {168-74}, abstract = {

Comprehensive high-resolution structural maps are central to functional exploration and understanding in biology. For the nervous system, in which high resolution and large spatial extent are both needed, such maps are scarce as they challenge data acquisition and analysis capabilities. Here we present for the mouse inner plexiform layer{\textendash}the main computational neuropil region in the mammalian retina{\textendash}the dense reconstruction of 950 neurons and their mutual contacts. This was achieved by applying a combination of crowd-sourced manual annotation and machine-learning-based volume segmentation to serial block-face electron microscopy data. We characterize a new type of retinal bipolar interneuron and show that we can subdivide a known type based on connectivity. Circuit motifs that emerge from our data indicate a functional mechanism for a known cellular response in a ganglion cell that detects localized motion, and predict that another ganglion cell is motion sensitive.

}, keywords = {Amacrine Cells, Animals, Biological, Cell Communication, Computer-Assisted, Connectome, Electron, Image Processing, Inbred C57BL, Mice, Microscopy, Models, Neuropil, Retina, Retinal Ganglion Cells}, issn = {1476-4687}, doi = {10.1038/nature12346}, author = {Helmstaedter, Moritz and Briggman, Kevin L and Turaga, Srinivas C and Jain, Viren and Seung, H Sebastian and Denk, Winfried} } @article {6091, title = {Contributions of the 12 neuron classes in the fly lamina to motion vision.}, journal = {Neuron}, volume = {79}, year = {2013}, month = {07/2013}, pages = {128-140}, abstract = {

Motion detection is a fundamental neural computation performed by many sensory systems. In the fly, local motion computation is thought to occur within the first two layers of the visual system, the lamina and medulla. We constructed specific genetic driver lines for each of the 12 neuron classes in the lamina. We then depolarized and hyperpolarized each neuron type and quantified fly behavioral responses to a diverse set of motion stimuli. We found that only a small number of lamina output neurons are essential for motion detection, while most neurons serve to sculpt and enhance these feedforward pathways. Two classes of feedback neurons (C2 and C3), and lamina output neurons (L2 and L4), are required for normal detection of directional motion stimuli. Our results reveal a prominent role for feedback and lateral interactions in motion processing and demonstrate that motion-dependent behaviors rely on contributions from nearly all lamina neuron classes.

}, doi = {http://dx.doi.org/10.1016/j.neuron.2013.05.024}, author = {Tuthill, John C and Nern, Aljoscha and Stephen L. Holtz and Rubin, Gerald M and Reiser, Michael B} } @article {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 {6454, title = {Extremes of lineage plasticity in the Drosophila brain.}, journal = {Current Biology}, volume = {23}, year = {2013}, month = {2013 Sep 19}, pages = {1908-13}, abstract = {

An often-overlooked aspect of neural plasticity is the plasticity of neuronal composition, in which the numbers of neurons of particular classes are altered in response to environment and experience. The Drosophila brain features several well-characterized lineages in which a single neuroblast gives rise to multiple neuronal classes in a stereotyped sequence during development [1]. We find that in the\ intrinsic mushroom body neuron lineage, the numbers for each class are highly plastic, depending on the timing of temporal fate transitions and the rate of neuroblast proliferation. For example, mushroom body neuroblast cycling can continue under starvation conditions, uncoupled from\ temporal fate transitions that depend on extrinsic cues reflecting organismal growth and development. In contrast, the proliferation rates of antennal lobe lineages are closely associated with organismal development, and\ their temporal fate changes appear to be cell cycle-dependent, such that the same numbers and types of uniglomerular projection neurons innervate the antennal lobe following various perturbations. We propose that this surprising difference in plasticity for these brain lineages is adaptive, given their respective roles as parallel\ processors versus discrete carriers of olfactory information.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2013.07.074}, author = {Lin, Suewei and Marin, Elizabeth C and Yang, Ching-Po and Kao, Chih-Fei and Apenteng, Bettye A and Huang, Yaling and O{\textquoteright}Connor, Michael B and Truman, James W and Lee, Tzumin} } @article {46714, title = {The fate of the messenger is pre-determined: a new model for regulation of gene expression.}, journal = {Biochimica et Biophysica Acta (BBA)}, volume = {1829}, year = {2013}, month = {2013 Jun-Jul}, pages = {643-53}, abstract = {

Recent years have seen a rise in publications demonstrating coupling between transcription and mRNA decay. This coupling most often accompanies cellular processes that involve transitions in gene expression patterns, for example during mitotic division and cellular differentiation and in response to cellular stress. Transcription can affect the mRNA fate by multiple mechanisms. The most novel finding is the process of co-transcriptional imprinting of mRNAs with proteins, which in turn regulate cytoplasmic mRNA stability. Transcription therefore is not only a catalyst of mRNA synthesis but also provides a platform that enables imprinting, which coordinates between transcription and mRNA decay. Here we present an overview of the literature, which provides the evidence of coupling between transcription and decay, review the mechanisms and regulators by which the two processes are coupled, discuss why such coupling is beneficial and present a new model for regulation of gene expression. This article is part of a Special Issue entitled: RNA Decay mechanisms.

}, keywords = {Cytoplasm, Gene Expression Regulation, Fungal, Genomic Imprinting, Humans, Poly(A)-Binding Proteins, Ribonucleases, RNA Polymerase II, RNA Stability, RNA, Messenger, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Transcription, Genetic}, issn = {0006-3002}, doi = {10.1016/j.bbagrm.2013.01.004}, author = {Haimovich, Gal and Choder, Mordechai and Singer, Robert H and Trcek, Tatjana} } @article {6133, title = {Functional labeling of neurons and their projections using the synthetic activity-dependent promoter E-SARE.}, journal = {Nature Methods}, volume = {10}, year = {2013}, month = {2013 Jul 14}, pages = {889-95}, abstract = {

Identifying the neuronal ensembles that respond to specific stimuli and mapping their projection patterns in living animals are fundamental challenges in neuroscience. To this end, we engineered a synthetic promoter, the enhanced synaptic activity-responsive element (E-SARE), that drives neuronal activity-dependent gene expression more potently than other existing immediate-early gene promoters. Expression of a drug-inducible Cre recombinase downstream of E-SARE enabled imaging of neuronal populations that respond to monocular visual stimulation and tracking of their long-distance thalamocortical projections in living mice. Targeted cell-attached recordings and calcium imaging of neurons in sensory cortices revealed that E-SARE reporter expression correlates with sensory-evoked neuronal activity at the single-cell level and is highly specific to the type of stimuli presented to the animals. This activity-dependent promoter can expand the repertoire of genetic approaches for high-resolution anatomical and functional analysis of neural circuits.

}, issn = {1548-7105}, doi = {10.1038/nmeth.2559}, author = {Kawashima, Takashi and Kitamura, Kazuo and Suzuki, Kanzo and Nonaka, Mio and Kamijo, Satoshi and Takemoto-Kimura, Sayaka and Kano, Masanobu and Okuno, Hiroyuki and Ohki, Kenichi and Bito, Haruhiko} } @article {6126, title = {Genetically encoded calcium indicators and astrocyte calcium microdomains.}, journal = {The Neuroscientist : A Review Journal Bringing Neurobiology, Neurology and Psychiatry}, volume = {19}, year = {2013}, month = {2013 Jun}, pages = {274-91}, abstract = {

The discovery of intracellular Ca(2+) signals within astrocytes has changed our view of how these ubiquitous cells contribute to brain function. Classically thought merely to serve supportive functions, astrocytes are increasingly thought to respond to, and regulate, neurons. The use of organic Ca(2+) indicator dyes such as Fluo-4 and Fura-2 has proved instrumental in the study of astrocyte physiology. However, progress has recently been accelerated by the use of cytosolic and membrane targeted genetically encoded calcium indicators (GECIs). Herein, we review these recent findings, discuss why studying astrocyte Ca(2+) signals is important to understand brain function, and summarize work that led to the discovery of TRPA1 channel-mediated near-membrane Ca(2+) signals in astrocytes and their indirect neuromodulatory roles at inhibitory synapses in the CA1 stratum radiatum region of the hippocampus. We suggest that the use of membrane-targeted and cytosolic GECIs holds great promise to explore the diversity of Ca(2+) signals within single astrocytes and also to study diversity of function for astrocytes in different parts of the brain.

}, issn = {1089-4098}, doi = {10.1177/1073858412468794}, author = {Tong, Xiaoping and Shigetomi, Eiji and Looger, Loren L and Khakh, Baljit S.} } @article {6541, title = {Genetically encoded calcium indicators for multi-color neural activity imaging and combination with optogenetics.}, journal = {Frontiers in Molecular Neuroscience}, volume = {6}, year = {2013}, month = {2013 Mar 4}, pages = {2}, abstract = {

Genetically encoded calcium indicators (GECIs) are powerful tools for systems neuroscience. Here we describe red, single-wavelength GECIs, "RCaMPs," engineered from circular permutation of the thermostable red fluorescent protein mRuby. High-resolution crystal structures of mRuby, the red sensor RCaMP, and the recently published red GECI R-GECO1 give insight into the chromophore environments of the Ca(2+)-bound state of the sensors and the engineered protein domain interfaces of the different indicators. We characterized the biophysical properties and performance of RCaMP sensors in vitro and in vivo in Caenorhabditis elegans, Drosophila larvae, and larval zebrafish. Further, we demonstrate 2-color calcium imaging both within the same cell (registering mitochondrial and somatic [Ca(2+)]) and between two populations of cells: neurons and astrocytes. Finally, we perform integrated optogenetics experiments, wherein neural activation via channelrhodopsin-2 (ChR2) or a red-shifted variant, and activity imaging via RCaMP or GCaMP, are conducted simultaneously, with the ChR2/RCaMP pair providing independently addressable spectral channels. Using this paradigm, we measure calcium responses of naturalistic and ChR2-evoked muscle contractions in vivo in crawling C. elegans. We systematically compare the RCaMP sensors to R-GECO1, in terms of action potential-evoked fluorescence increases in neurons, photobleaching, and photoswitching. R-GECO1 displays higher Ca(2+) affinity and larger dynamic range than RCaMP, but exhibits significant photoactivation with blue and green light, suggesting that integrated channelrhodopsin-based optogenetics using R-GECO1 may be subject to artifact. Finally, we create and test blue, cyan, and yellow variants engineered from GCaMP by rational design. This engineered set of chromatic variants facilitates new experiments in functional imaging and optogenetics.

}, issn = {1662-5099}, doi = {10.3389/fnmol.2013.00002}, author = {Akerboom, Jasper and Carreras Calder{\'o}n, Nicole and Tian, Lin and Wabnig, Sebastian and Prigge, Matthias and Tol{\"o}, Johan and Gordus, Andrew and Orger, Michael B. and Severi, Kristen E and Macklin, John J and Patel, Ronak and Pulver, Stefan R and Wardill, Trevor J. and Fischer, Elisabeth and Sch{\"u}ler, Christina and Chen, Tsai-Wen and Sarkisyan, Karen S and Marvin, Jonathan S and Bargmann, Cornelia I and Kim, Douglas S. and K{\"u}gler, Sebastian and Lagnado, Leon and Hegemann, Peter and Gottschalk, Alexander and Schreiter, Eric R and Looger, Loren L} } @article {47220, title = {Imaging a population code for odor identity in the Drosophila mushroom body.}, journal = {The Journal of Neuroscience : the official journal of the Society for Neuroscience}, volume = {33}, year = {2013}, month = {2013 Jun 19}, pages = {10568-81}, abstract = {

The brain represents sensory information in the coordinated activity of neuronal ensembles. Although the microcircuits underlying olfactory processing are well characterized in Drosophila, no studies to date have examined the encoding of odor identity by populations of neurons and related it to the odor specificity of olfactory behavior. Here we used two-photon Ca(2+) imaging to record odor-evoked responses from \>100 neurons simultaneously in the Drosophila mushroom body (MB). For the first time, we demonstrate quantitatively that MB population responses contain substantial information on odor identity. Using a series of increasingly similar odor blends, we identified conditions in which odor discrimination is difficult behaviorally. We found that MB ensemble responses accounted well for olfactory acuity in this task. Kenyon cell ensembles with as few as 25 cells were sufficient to match behavioral discrimination accuracy. Using a generalization task, we demonstrated that the MB population code could predict the flies{\textquoteright} responses to novel odors. The degree to which flies generalized a learned aversive association to unfamiliar test odors depended upon the relative similarity between the odors{\textquoteright} evoked MB activity patterns. Discrimination and generalization place different demands on the animal, yet the flies{\textquoteright} choices in these tasks were reliably predicted based on the amount of overlap between MB activity patterns. Therefore, these different behaviors can be understood in the context of a single physiological framework.

}, keywords = {Animals, Calcium, Discrimination (Psychology), Drosophila, Generalization (Psychology), Image Processing, Computer-Assisted, Learning, Linear Models, Mushroom Bodies, Neuroimaging, Odors, Olfactory Pathways, Olfactory Perception, Psychomotor Performance, Synaptic Transmission}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0682-12.2013}, author = {Campbell, Robert A A and Honegger, Kyle S and Qin, Hongtao and Li, Wanhe and Demir, Ebru and Turner, Glenn C} } @article {46575, title = {Inferring neural population dynamics from multiple partial recordings of the same neural circuit.}, journal = {Advances in Neural Information Processing Systems (NIPS) }, volume = {26}, year = {2013}, month = {2013}, abstract = {

Simultaneous recordings of the activity of large neural populations are extremely valuable as they can be used to infer the dynamics and interactions of neurons in a local circuit, shedding light on the computations performed. It is now possible to measure the activity of hundreds of neurons using 2-photon calcium imaging. However, many computations are thought to involve circuits consisting of thousands of neurons, such as cortical barrels in rodent somatosensory cortex. Here we contribute a statistical method for stitching" together sequentially imaged sets of neurons into one model by phrasing the problem as fitting a latent dynamical system with missing observations. This method allows us to substantially expand the population-sizes for which population dynamics can be characterized---beyond the number of simultaneously imaged neurons. In particular, we demonstrate using recordings in mouse somatosensory cortex that this method makes it possible to predict noise correlations between non-simultaneously recorded neuron pairs.

}, url = {http://papers.nips.cc/paper/4874-inferring-neural-population-dynamics-from-multiple-partial-recordings-of-the-same-neural-circuit}, author = {Turaga, Srinivas C and Buesing, Lars and Packer, Adam M. and Dalgleish, Henry and Pettit, Noah and H{\"a}usser, Michael and Macke, Jakob H.} } @article {47746, title = {Integration of the olfactory code across dendritic claws of single mushroom body neurons.}, journal = {Nature Neuroscience}, volume = {16}, year = {2013}, month = {2013 Oct 20}, pages = {1821-9}, abstract = {

In the olfactory system, sensory inputs are arranged in different glomerular channels, which respond in combinatorial ensembles to the various chemical features of an odor. Here we investigate where and how this combinatorial code is read out deeper in the brain. We exploit the unique morphology of neurons in the mushroom body (MB), which receive input on large dendritic claws. Imaging odor responses of these dendritic claws shows that input channels with distinct odor tuning converge on individual MB neurons. We determined how these inputs interact to drive the cell to spike threshold using intracellular recordings to examine MB responses to optogenetically controlled input. Our results provide an elegant explanation for the characteristic selectivity of MB neurons: these cells receive different types of input, and require those inputs to be coactive in order to spike. These results establish the MB as an important site of integration in the fly olfactory system.

}, doi = {10.1038/nn.3547}, author = {Gruntman, Eyal and Turner, Glenn C} } @article {47219, title = {Integration of the olfactory code across dendritic claws of single mushroom body neurons.}, journal = {Nature Neuroscience}, volume = {16}, year = {2013}, month = {2013 Dec}, pages = {1821-9}, abstract = {

In the olfactory system, sensory inputs are arranged in different glomerular channels, which respond in combinatorial ensembles to the various chemical features of an odor. We investigated where and how this combinatorial code is read out deeper in the brain. We exploited the unique morphology of neurons in the Drosophila mushroom body, which receive input on large dendritic claws. Imaging odor responses of these dendritic claws revealed that input channels with distinct odor tuning converge on individual mushroom body neurons. We determined how these inputs interact to drive the cell to spike threshold using intracellular recordings to examine mushroom body responses to optogenetically controlled input. Our results provide an elegant explanation for the characteristic selectivity of mushroom body neurons: these cells receive different types of input and require those inputs to be coactive to spike. These results establish the mushroom body as an important site of integration in the fly olfactory system.

}, keywords = {Animals, Animals, Genetically Modified, Calcium, Dendrites, Drosophila, Drosophila Proteins, Electric Stimulation, Female, Luminescent Proteins, Membrane Potentials, Models, Neurological, Mushroom Bodies, Neurons, Odors, Olfactory Pathways, Patch-Clamp Techniques, Photic Stimulation, Rhodopsin, Synapses}, issn = {1546-1726}, doi = {10.1038/nn.3547}, author = {Gruntman, Eyal and Turner, Glenn C} } @article {6528, title = {Intensity discrimination deficits cause habituation changes in middle-aged Caenorhabditis elegans.}, journal = {Neurobiology of Aging}, volume = {34}, year = {2013}, month = {2013 Feb}, pages = {621-31}, abstract = {

The ability to learn and remember is critical for all animals to survive in the ever-changing environment. As we age, many of our biological faculties decay and of these, decline in learning and memory can be the most distressing. To carefully define age-dependent changes in learning during reproductive age in the nematode Caenorhabditis elegans, we performed a parametric behavioral study of habituation to nonlocalized mechanical stimuli (petri plate taps) over a range of intensities in middle-aged worms. We found that as worms age (from the onset of reproduction to the end of egg laying), response probability habituation increases (at both 10- and 60-second interstimulus intervals) and that these age-related changes were associated with a decrease in the discrimination between stimuli of different intensities. We also used optogenetics to investigate where these age-dependent changes occur. Our data suggest that the changes occur upstream of mechanosensory neuron depolarization. These data support the idea that declines in stimulus intensity discrimination abilities during aging may be one variable underlying age-related cognitive deficits.

}, keywords = {Age Factors, Aging, Animal, Animals, Behavior, Caenorhabditis elegans, Discrimination (Psychology), Habituation, Memory, Physical Stimulation, Psychophysiologic, Short-Term}, issn = {1558-1497}, doi = {10.1016/j.neurobiolaging.2012.03.016}, author = {Timbers, Tiffany A and Giles, Andrew C and Ardiel, Evan L and Kerr, Rex A and Rankin, Catharine H} } @article {5346, title = {Light sheet microscopy in cell biology.}, journal = {Methods in Molecular Biology}, volume = {931}, year = {2013}, month = {2013}, pages = {123-37}, abstract = {

Light sheet-based fluorescence microscopy (LSFM) is emerging as a powerful imaging technique for the life sciences. LSFM provides an exceptionally high imaging speed, high signal-to-noise ratio, low level of photo-bleaching, and good optical penetration depth. This unique combination of capabilities makes light sheet-based microscopes highly suitable for live imaging applications. Here, we provide an overview of light sheet-based microscopy assays for in vitro and in vivo imaging of biological samples, including cell extracts, soft gels, and large multicellular organisms. We furthermore describe computational tools for basic image processing and data inspection.

}, issn = {1940-6029}, doi = {10.1007/978-1-62703-056-4_7}, author = {Tomer, Raju and Khairy, Khaled and Keller, Philipp J} } @article {6318, title = {Likelihood-based classification of cryo-EM images using FREALIGN.}, journal = {Journal of Structural Biology}, volume = {183}, year = {2013}, month = {2013 Sep}, pages = {377-88}, abstract = {

We describe an implementation of maximum likelihood classification for single particle electron cryo-microscopy that is based on the FREALIGN software. Particle alignment parameters are determined by maximizing a joint likelihood that can include hierarchical priors, while classification is performed by expectation maximization of a marginal likelihood. We test the FREALIGN implementation using a simulated dataset containing computer-generated projection images of three different 70S ribosome structures, as well as a publicly available dataset of 70S ribosomes. The results show that the mixed strategy of the new FREALIGN algorithm yields performance on par with other maximum likelihood implementations, while remaining computationally efficient.

}, issn = {1095-8657}, doi = {10.1016/j.jsb.2013.07.005}, author = {Lyumkis, Dmitry and Brilot, Axel F and Theobald, Douglas L and Grigorieff, Nikolaus} } @article {6291, title = {A localized Wnt signal orients asymmetric stem cell division in vitro.}, journal = {Science}, volume = {339}, year = {2013}, month = {2013 Mar 22}, pages = {1445-8}, abstract = {

Developmental signals such as Wnts are often presented to cells in an oriented manner. To examine the consequences of local Wnt signaling, we immobilized Wnt proteins on beads and introduced them to embryonic stem cells in culture. At the single-cell level, the Wnt-bead induced asymmetric distribution of Wnt-β-catenin signaling components, oriented the plane of mitotic division, and directed asymmetric inheritance of centrosomes. Before cytokinesis was completed, the Wnt-proximal daughter cell expressed high levels of nuclear β-catenin and pluripotency genes, whereas the distal daughter cell acquired hallmarks of differentiation. We suggest that a spatially restricted Wnt signal induces an oriented cell division that generates distinct cell fates at predictable positions relative to the Wnt source.

}, keywords = {Animals, Asymmetric Cell Division, beta Catenin, Cell Differentiation, Cells, Centrosome, Cultured, Cytokinesis, Embryonic Stem Cells, Gene Expression, Homeodomain Proteins, Mice, Mitosis, Octamer Transcription Factor-3, Pluripotent Stem Cells, Recombinant Proteins, Single-Cell Analysis, Transcription Factors, Wnt Proteins, Wnt Signaling Pathway, Wnt3A Protein}, issn = {1095-9203}, doi = {10.1126/science.1231077}, author = {Habib, Shukry J and Chen, Bi-Chang and Tsai, Feng-Chiao and Anastassiadis, Konstantinos and Meyer, Tobias and Betzig, Eric and Nusse, Roel} } @article {6144, title = {A low-bandwidth camera sensor platform with applications in smart camera networks.}, journal = {ACM Transactions on Sensor Networks}, volume = {9}, year = {2013}, month = {2013 Mar}, abstract = {

Smart camera networks have recently emerged as a new class of sensor network infrastructure that is capable of supporting high-power in-network signal processing and enabling a wide range of applications. In this article, we provide an exposition of our efforts to build a low-bandwidth wireless camera network platform, called CITRIC, and its applications in smart camera networks. The platform integrates a camera, a microphone, a frequency-scalable (up to 624 MHz) CPU, 16 MB FLASH, and 64 MB RAM onto a single device. The device then connects with a standard sensor network mote to form a wireless camera mote. With reasonably low power consumption and extensive algorithmic libraries running on a decent operating system that is easy to program, CITRIC is ideal for research and applications in distributed image and video processing. Its capabilities of in-network image processing also reduce communication requirements, which has been high in other existing camera networks with centralized processing. Furthermore, the mote easily integrates with other low-bandwidth sensor networks via the IEEE 802.15.4 protocol. To justify the utility of CITRIC, we present several representative applications. In particular, concrete research results will be demonstrated in two areas, namely, distributed coverage hole identification and distributed object recognition.

}, issn = {1550-4859}, url = {http://dl.acm.org/citation.cfm?doid=2422966.2422978}, author = {Phoebus Chen and Kirak Hong and Nikhil Naikal and S. Shankar Sastry and Doug Tygar and Yan, Posu and Yang, Allen and Chang, Lung-Chung and Lin, Leon and Wang, Simon and Lobaton, Edgar and Oh, Songhwai and Ahammad, Parvez} } @article {6383, title = {A molt timer is involved in the metamorphic molt in Manduca sexta larvae.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, year = {2013}, month = {2013 Jul 30}, pages = {12518-25}, abstract = {

Manduca sexta larvae are a model for growth control in insects, particularly for the demonstration of critical weight, a threshold weight that the larva must surpass before it can enter metamorphosis on a normal schedule, and the inhibitory action of juvenile hormone on this checkpoint. We examined the effects of nutrition on allatectomized (CAX) larvae that lack juvenile hormone to impose the critical weight checkpoint. Normal larvae respond to prolonged starvation at the start of the last larval stage, by extending their subsequent feeding period to ensure that they begin metamorphosis above critical weight. CAX larvae, by contrast, show no homeostatic adjustment to starvation but start metamorphosis 4 d after feeding onset, regardless of larval size or the state of development of their imaginal discs. By feeding starved CAX larvae for various durations, we found that feeding for only 12-24 h was sufficient to result in metamorphosis on day 4, regardless of further feeding or body size. Manipulation of diet composition showed that protein was the critical macronutrient to initiate this timing. This constant period between the start of feeding and the onset of metamorphosis suggests that larvae possess a molt timer that establishes a minimal time to metamorphosis. Ligation experiments indicate that a portion of the timing may occur in the prothoracic glands. This positive system that promotes molting and the negative control via the critical weight checkpoint provide antagonistic pathways that evolution can modify to adapt growth to the ecological needs of different insects.

}, issn = {1091-6490}, doi = {10.1073/pnas.1311405110}, author = {Suzuki, Yuichiro and Koyama, Takashi and Hiruma, Kiyoshi and Riddiford, Lynn M and Truman, James W} } @article {6671, title = {Motor control of Drosophila courtship song.}, journal = {Cell Reports}, volume = {5}, year = {2013}, month = {2013 Nov 14}, pages = {678-86}, abstract = {

Many animals utilize acoustic signals-or songs-to attract mates. During courtship, Drosophila melanogaster males vibrate a wing to produce trains of pulses and extended tone, called pulse and sine song, respectively. Courtship songs in the genus Drosophila are exceedingly diverse, and different song features appear to have evolved independently of each other. How the nervous system allows such diversity to evolve is not understood. Here, we identify a wing muscle in D.\ melanogaster (hg1) that is uniquely male-enlarged. The hg1 motoneuron and the sexually dimorphic development of the hg1 muscle are required specifically for the sine component of the male song. In contrast, the motoneuron innervating a sexually monomorphic wing muscle, ps1, is required specifically for a feature of pulse song. Thus, individual wing motor pathways can control separate aspects of courtship song and may provide a "modular" anatomical substrate for the evolution of diverse songs.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2013.09.039}, author = {Shirangi, Troy R and Stern, David L and Truman, James W} } @article {6926, title = {Multiple interactions control synaptic layer specificity in the Drosophila visual system.}, journal = {Neuron}, volume = {77}, year = {2013}, month = {2013 Jan 23}, pages = {299-310}, abstract = {

How neurons form synapses within specific layers remains poorly understood. In the Drosophila medulla, neurons target to discrete layers in a precise fashion. Here we demonstrate that the targeting of L3 neurons to a specific layer occurs in two steps. Initially, L3 growth cones project to a common domain in the outer medulla, overlapping with the growth cones of other neurons destined for a different layer through the redundant functions of N-Cadherin (CadN) and Semaphorin-1a (Sema-1a). CadN mediates adhesion within the domain and Sema-1a mediates repulsion through Plexin A (PlexA) expressed in an adjacent region. Subsequently, L3 growth cones segregate from the domain into their target layer in part through Sema-1a/PlexA-dependent remodeling. Together, our results and recent studies argue that the early medulla is organized into common domains, comprising processes bound for different layers, and that discrete layers later emerge through successive interactions between processes within domains and developing layers.

}, keywords = {Animals, Cell Communication, Drosophila, Drosophila Proteins, Genetically Modified, Growth Cones, Medulla Oblongata, Protein Interaction Mapping, Synapses, Visual Pathways}, issn = {1097-4199}, doi = {10.1016/j.neuron.2012.11.007}, author = {Pecot, Matthew Y and Tadros, Wael and Nern, Aljoscha and Bader, Maya and Chen, Yi and Zipursky, S Lawrence} } @article {6130, title = {Nanotools for neuroscience and brain activity mapping.}, journal = {ACS Nano}, volume = {7}, year = {2013}, month = {2013 Mar 26}, pages = {1850-66}, abstract = {

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

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

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

}, keywords = {Animals, Brain Mapping, Humans, Models, Neurological, Nanomedicine, Nanoparticles, Nanotechnology, Nervous System Physiological Phenomena}, issn = {1936-086X}, doi = {10.1021/nn4012847}, author = {Alivisatos, A Paul and Andrews, Anne M and Boyden, Edward S and Chun, Miyoung and Church, George M and Deisseroth, Karl and Donoghue, John P and Fraser, Scott E and Lippincott-Schwartz, Jennifer and Looger, Loren L and Masmanidis, Sotiris and McEuen, Paul L and Nurmikko, Arto V and Park, Hongkun and Peterka, Darcy S and Reid, Clay and Roukes, Michael L and Scherer, Axel and Schnitzer, Mark and Sejnowski, Terrence J and Shepard, Kenneth L and Tsao, Doris and Turrigiano, Gina and Weiss, Paul S and Xu, Chris and Yuste, Rafael and Zhuang, Xiaowei} } @conference {45640, title = {A neuron as a signal processing device}, booktitle = {2013 Asilomar Conference on Signals, Systems and Computers}, year = {2013}, month = {05/2014}, publisher = {IEEE}, organization = {IEEE}, address = {Pacific Grove, CA}, abstract = {

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

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

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

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0077728}, author = {Wardill, Trevor J. and Chen, Tsai-Wen and Schreiter, Eric R and Hasseman, Jeremy P and Tsegaye, Getahun and Fosque, Benjamin F and Behnam, Reza and Shields, Brenda C and Ramirez, Melissa and Kimmel, Bruce E and Kerr, Rex A and Jayaraman, Vivek and Looger, Loren L and Svoboda, Karel and Kim, Douglas S.} } @article {6128, title = {An optimized fluorescent probe for visualizing glutamate neurotransmission.}, journal = {Nature Methods}, volume = {10}, year = {2013}, month = {2013 Feb}, pages = {162-70}, abstract = {

We describe an intensity-based glutamate-sensing fluorescent reporter (iGluSnFR) with signal-to-noise ratio and kinetics appropriate for in vivo imaging. We engineered iGluSnFR in vitro to maximize its fluorescence change, and we validated its utility for visualizing glutamate release by neurons and astrocytes in increasingly intact neurological systems. In hippocampal culture, iGluSnFR detected single field stimulus-evoked glutamate release events. In pyramidal neurons in acute brain slices, glutamate uncaging at single spines showed that iGluSnFR responds robustly and specifically to glutamate in situ, and responses correlate with voltage changes. In mouse retina, iGluSnFR-expressing neurons showed intact light-evoked excitatory currents, and the sensor revealed tonic glutamate signaling in response to light stimuli. In worms, glutamate signals preceded and predicted postsynaptic calcium transients. In zebrafish, iGluSnFR revealed spatial organization of direction-selective synaptic activity in the optic tectum. Finally, in mouse forelimb motor cortex, iGluSnFR expression in layer V pyramidal neurons revealed task-dependent single-spine activity during running.

}, keywords = {Animals, Astrocytes, Biosensing Techniques, Caenorhabditis elegans, Calcium Signaling, Escherichia coli Proteins, Excitatory Postsynaptic Potentials, Fluorescent Dyes, Glutamic Acid, Green Fluorescent Proteins, Hippocampus, Mice, Motor Cortex, Neurons, Photic Stimulation, Pyramidal Cells, Recombinant Fusion Proteins, Retina, Signal-To-Noise Ratio, Synaptic Transmission, Zebrafish}, issn = {1548-7105}, doi = {10.1038/nmeth.2333}, author = {Marvin, Jonathan S and Borghuis, Bart G and Tian, Lin and Cichon, Joseph and Harnett, Mark T and Akerboom, Jasper and Gordus, Andrew and Renninger, Sabine L. and Chen, Tsai-Wen and Bargmann, Cornelia I and Orger, Michael B. and Schreiter, Eric R and Demb, Jonathan B and Gan, Wen-Biao and Hires, S Andrew and Looger, Loren L} } @article {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 {46299, title = {Scaling laws of associative memory retrieval.}, journal = {Neural Computation}, volume = {25}, year = {2013}, month = {2013 Oct}, pages = {2523-44}, abstract = {

Most people have great difficulty in recalling unrelated items. For example, in free recall experiments, lists of more than a few randomly selected words cannot be accurately repeated. Here we introduce a phenomenological model of memory retrieval inspired by theories of neuronal population coding of information. The model predicts nontrivial scaling behaviors for the mean and standard deviation of the number of recalled words for lists of increasing length. Our results suggest that associative information retrieval is a dominating factor that limits the number of recalled items.

}, keywords = {Algorithms, Association Learning, Computer Simulation, Humans, Memory, Mental Recall, Models, Neurological, Neural Networks (Computer)}, issn = {1530-888X}, doi = {10.1162/NECO_a_00499}, author = {Romani, Sandro and Pinkoviezky, Itai and Rubin, Alon and Tsodyks, Misha} } @article {6125, title = {{\ss}-synuclein aggregates and induces neurodegeneration in dopaminergic neurons.}, journal = {Annals of Neurology}, volume = {74}, year = {2013}, month = {2013 Mar 28}, pages = {109-18}, abstract = {

Objective: While the contribution of α-Synuclein to neurodegeneration in Parkinson{\textquoteright}s disease is well accepted, the putative impact of its close homologue, β-Synuclein, is enigmatic. β-Synuclein is widely expressed throughout the central nervous system as is α-Synuclein, but the physiological functions of both proteins remain unknown. Recent findings supported the view that β-Synuclein can act as an ameliorating regulator of α-Synuclein-induced neurotoxicity, having neuroprotective rather than neurodegenerative capabilities, and being non-aggregating due to absence of most part of the aggregation-promoting NAC domain. However, a mutation of β-Synuclein linked to dementia with Lewy bodies rendered the protein neurotoxic in transgenic mice and fibrillation of β-Synuclein has been demonstrated in vitro. Methods / Results: Supporting the hypothesis that β-Synuclein can act as a neurodegeneration-inducing factor we now demonstrate that wild-type β-Synuclein is neurotoxic for cultured primary neurons. Furthermore, β-Synuclein formed proteinase K resistant aggregates in dopaminergic neurons in vivo, leading to pronounced and progressive neurodegeneration in rats. Expression of β-Synuclein caused mitochondrial fragmentation, but this fragmentation did not render mitochondria non-functional in terms of ion handling and respiration even in late stages of neurodegeneration. A comparison of the neurodegenerative effects induced by α-, β-, and γ-Synuclein revealed that β-Synuclein was eventually as neurotoxic as α-Synuclein for nigral dopaminergic neurons, while γ-Synuclein proved to be non-toxic and had very low aggregation propensity. Interpretation: Our results suggest that the role of β-Synuclein as a putative modulator of neuropathology in aggregopathies like Parkinson{\textquoteright}s disease and dementia with Lewy bodies needs to be revisited. ANN NEUROL 2013. {\textcopyright} 2013 American Neurological Association.

}, issn = {1531-8249}, doi = {10.1002/ana.23905}, author = {Taschenberger, G and Toloe, J and Tereshchenko, J and Akerboom, J and Wales, P and Benz, R and Becker, S and Outeiro, Tf and Looger, L and B{\"a}hr, M and Zweckstetter, M and K{\"u}gler, S} } @article {47705, title = {Structural foundations of resting-state and task-based functional connectivity in the human brain.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, year = {2013}, month = {2013 Apr 9}, pages = {6169-74}, abstract = {

Magnetic resonance imaging enables the noninvasive mapping of both anatomical white matter connectivity and dynamic patterns of neural activity in the human brain. We examine the relationship between the structural properties of white matter streamlines (structural connectivity) and the functional properties of correlations in neural activity (functional connectivity) within 84 healthy human subjects both at rest and during the performance of attention- and memory-demanding tasks. We show that structural properties, including the length, number, and spatial location of white matter streamlines, are indicative of and can be inferred from the strength of resting-state and task-based functional correlations between brain regions. These results, which are both representative of the entire set of subjects and consistently observed within individual subjects, uncover robust links between structural and functional connectivity in the human brain.

}, keywords = {Aging, Attention, Brain, Brain Mapping, Cognition, Computational Biology, Diffusion Magnetic Resonance Imaging, Humans, Magnetic Resonance Imaging, Memory, Models, Statistical, Neural Pathways, Software}, issn = {1091-6490}, doi = {10.1073/pnas.1219562110}, author = {Hermundstad, Ann M and Bassett, Danielle S and Brown, Kevin S and Aminoff, Elissa M and Clewett, David and Freeman, Scott and Frithsen, Amy and Johnson, Arianne and Tipper, Christine M and Miller, Michael B and Grafton, Scott T and Carlson, Jean M} } @article {46606, title = {Taok2 controls behavioral response to ethanol in mice.}, journal = {Genes, Brain, and Behavior}, volume = {12}, year = {2013}, month = {2013 Feb}, pages = {87-97}, abstract = {

Despite recent advances in the understanding of ethanol{\textquoteright}s biological action, many of the molecular targets of ethanol and mechanisms behind ethanol{\textquoteright}s effect on behavior remain poorly understood. In an effort to identify novel genes, the products of which regulate behavioral responses to ethanol, we recently identified a mutation in the dtao gene that confers resistance to the locomotor stimulating effect of ethanol in Drosophila. dtao encodes a member of the Ste20 family of serine/threonine kinases implicated in MAP kinase signaling pathways. In this study, we report that conditional ablation of the mouse dtao homolog, Taok2, constitutively and specifically in the nervous system, results in strain-specific and overlapping alterations in ethanol-dependent behaviors. These data suggest a functional conservation of dtao and Taok2 in mediating ethanol{\textquoteright}s biological action and identify Taok2 as a putative candidate gene for ethanol use disorders in humans.

}, keywords = {Alcohol Drinking, Alcoholism, Animals, Behavior, Animal, Conditioning, Classical, Ethanol, Gait Ataxia, Locomotion, MAP Kinase Kinase Kinases, Mice, Mice, Inbred C57BL, Mice, Transgenic, Protein-Serine-Threonine Kinases}, issn = {1601-183X}, doi = {10.1111/j.1601-183X.2012.00834.x}, author = {Kapfhamer, D and Taylor, S and Zou, M E and Lim, J P and Kharazia, V and Heberlein, U} } @article {46713, title = {Temporal and spatial characterization of nonsense-mediated mRNA decay.}, journal = {Genes \& Development}, volume = {27}, year = {2013}, month = {2013 Mar 1}, pages = {541-51}, abstract = {

Nonsense-mediated mRNA decay (NMD) is a quality control mechanism responsible for "surveying" mRNAs during translation and degrading those that harbor a premature termination codon (PTC). Currently the intracellular spatial location of NMD and the kinetics of its decay step in mammalian cells are under debate. To address these issues, we used single-RNA fluorescent in situ hybridization (FISH) and measured the NMD of PTC-containing β-globin mRNA in intact single cells after the induction of β-globin gene transcription. This approach preserves temporal and spatial information of the NMD process, both of which would be lost in an ensemble study. We determined that decay of the majority of PTC-containing β-globin mRNA occurs soon after its export into the cytoplasm, with a half-life of \<1 min; the remainder is degraded with a half-life of \>12 h, similar to the half-life of normal PTC-free β-globin mRNA, indicating that it had evaded NMD. Importantly, NMD does not occur within the nucleoplasm, thus countering the long-debated idea of nuclear degradation of PTC-containing transcripts. We provide a spatial and temporal model for the biphasic decay of NMD targets.

}, keywords = {Animals, beta-Globins, Cell Line, Cell Nucleus, Cytoplasm, Humans, In Situ Hybridization, Fluorescence, Nonsense Mediated mRNA Decay, RNA, Messenger, Time Factors}, issn = {1549-5477}, doi = {10.1101/gad.209635.112}, author = {Trcek, Tatjana and Sato, Hanae and Singer, Robert H and Maquat, Lynne E} } @article {6178, title = {A visual motion detection circuit suggested by Drosophila connectomics.}, journal = {Nature}, volume = {500}, year = {2013}, month = {2013 Aug 7}, pages = {175{\textendash}81}, abstract = {

Animal behaviour arises from computations in neuronal circuits, but our understanding of these computations has been frustrated by the lack of detailed synaptic connection maps, or connectomes. For example, despite intensive investigations over half a century, the neuronal implementation of local motion detection in the insect visual system remains elusive. Here we develop a semi-automated pipeline using electron microscopy to reconstruct a connectome, containing 379 neurons and 8,637 chemical synaptic contacts, within the Drosophila optic medulla. By matching reconstructed neurons to examples from light microscopy, we assigned neurons to cell types and assembled a connectome of the repeating module of the medulla. Within this module, we identified cell types constituting a motion detection circuit, and showed that the connections onto individual motion-sensitive neurons in this circuit were consistent with their direction selectivity. Our results identify cellular targets for future functional investigations, and demonstrate that connectomes can provide key insights into neuronal computations.

}, issn = {1476-4687}, doi = {doi:10.1038/nature12450}, url = {http://www.nature.com/nature/journal/v500/n7461/full/nature12450.html}, author = {Takemura, Shin-ya and Bharioke, Arjun and Lu, Zhiyuan and Nern, Aljoscha and Vitaladevuni, Shiv and Rivlin, Patricia K. and Katz, William T. and Olbris, Donald J. and Plaza, Stephen M and Winston, Philip and Zhao, Ting and Horne, Jane Anne and Fetter, Richard D and Takemura, Satoko and Blazek, Katerina and Chang, Lei-Ann and Ogundeyi, Omotara and Saunders, Mathew A. and Shapiro, Victor and Sigmund, Christopher and Rubin, Gerald M and Scheffer, Louis K and Meinertzhagen, Ian A. and Chklovskii, Dmitri B} } @article {5162, title = {Activity in motor-sensory projections reveals distributed coding in somatosensation.}, journal = {Nature}, volume = {489}, year = {2012}, month = {2012 Sep 13}, pages = {299-303}, abstract = {

Cortical-feedback projections to primary sensory areas terminate most heavily in layer 1 (L1) of the neocortex, where they make synapses with tuft dendrites of pyramidal neurons. L1 input is thought to provide {\textquoteleft}contextual{\textquoteright} information, but the signals transmitted by L1 feedback remain uncharacterized. In the rodent somatosensory system, the spatially diffuse feedback projection from vibrissal motor cortex (vM1) to vibrissal somatosensory cortex (vS1, also known as the barrel cortex) may allow whisker touch to be interpreted in the context of whisker position to compute object location. When mice palpate objects with their whiskers to localize object features, whisker touch excites vS1 and later vM1 in a somatotopic manner. Here we use axonal calcium imaging to track activity in vM1{\textendash}\>vS1 afferents in L1 of the barrel cortex while mice performed whisker-dependent object localization. Spatially intermingled individual axons represent whisker movements, touch and other behavioural features. In a subpopulation of axons, activity depends on object location and persists for seconds after touch. Neurons in the barrel cortex thus have information to integrate movements and touches of multiple whiskers over time, key components of object identification and navigation by active touch.

}, issn = {1476-4687}, doi = {10.1038/nature11321}, author = {Petreanu, Leopoldo and Gutnisky, Diego A and Huber, Daniel and Xu, Ning-long and O{\textquoteright}Connor, Dan H and Tian, Lin and Looger, Loren and Svoboda, Karel} } @proceedings {46790, title = {Advanced Programming with ImgLib2}, year = {2012}, month = {2012 Oct 24}, address = {Mondorf-les-Bains, Luxembourg}, author = {Pietzsch, Tobias and Preibisch, Stephan and Tomancak, Pavel and Saalfeld, Stephan} } @article {6527, title = {A battery-free multichannel digital neural/EMG telemetry system for flying insects.}, journal = {IEEE Transactions on Biomedical Circuits and Systems}, volume = {6}, year = {2012}, month = {2012 Oct}, pages = {424-36}, abstract = {

This paper presents a digital neural/EMG telemetry system small enough and lightweight enough to permit recording from insects in flight. It has a measured flight package mass of only 38 mg. This system includes a single-chip telemetry integrated circuit (IC) employing RF power harvesting for battery-free operation, with communication via modulated backscatter in the UHF (902-928 MHz) band. An on-chip 11-bit ADC digitizes 10 neural channels with a sampling rate of 26.1 kSps and 4 EMG channels at 1.63 kSps, and telemeters this data wirelessly to a base station. The companion base station transceiver includes an RF transmitter of +36 dBm (4 W) output power to wirelessly power the telemetry IC, and a digital receiver with a sensitivity of -70 dBm for 10$^{-}$$^{5}$ BER at 5.0 Mbps to receive the data stream from the telemetry IC. The telemetry chip was fabricated in a commercial 0.35 μ m 4M1P (4 metal, 1 poly) CMOS process. The die measures 2.36 {\texttimes} 1.88 mm, is 250 μm thick, and is wire bonded into a flex circuit assembly measuring 4.6 {\texttimes} 6.8 mm.

}, issn = {1940-9990}, doi = {10.1109/TBCAS.2012.2222881}, author = {Thomas, Stewart J and Harrison, Reid R. and Leonardo, Anthony and Reynolds, Matthew S} } @article {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 {4601, title = {A Cre-dependent GCaMP3 reporter mouse for neuronal imaging in vivo.}, journal = {The Journal of Neuroscience}, volume = {32}, year = {2012}, month = {2012 Feb 29}, pages = {3131-41}, abstract = {

Fluorescent calcium indicator proteins, such as GCaMP3, allow imaging of activity in genetically defined neuronal populations. GCaMP3 can be expressed using various gene delivery methods, such as viral infection or electroporation. However, these methods are invasive and provide inhomogeneous and nonstationary expression. Here, we developed a genetic reporter mouse, Ai38, which expresses GCaMP3 in a Cre-dependent manner from the ROSA26 locus, driven by a strong CAG promoter. Crossing Ai38 with appropriate Cre mice produced robust GCaMP3 expression in defined cell populations in the retina, cortex, and cerebellum. In the primary visual cortex, visually evoked GCaMP3 signals showed normal orientation and direction selectivity. GCaMP3 signals were rapid, compared with virally expressed GCaMP3 and synthetic calcium indicators. In the retina, Ai38 allowed imaging spontaneous calcium waves in starburst amacrine cells during development, and light-evoked responses in ganglion cells in adult tissue. Our results show that the Ai38 reporter mouse provides a flexible method for targeted expression of GCaMP3.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4469-11.2012}, author = {Zariwala, Hatim A and Borghuis, Bart G and Hoogland, Tycho M and Madisen, Linda and Tian, Lin and De Zeeuw, Chris I and Zeng, Hongkui and Looger, Loren L and Svoboda, Karel and Chen, Tsai-Wen} } @article {5653, title = {Current challenges in open-source bioimage informatics.}, journal = {Nature Methods}, volume = {9}, year = {2012}, month = {2012 Jul}, pages = {661-5}, abstract = {

We discuss the advantages and challenges of the open-source strategy in biological image analysis and argue that its full impact will not be realized without better support and recognition of software engineers{\textquoteright} contributions to the biological sciences and more support of this development model from funders and institutions.

}, keywords = {Algorithms, Computational Biology, Computer-Assisted, Image Processing, Information Dissemination, Internet, Software, Software Design}, issn = {1548-7105}, doi = {10.1038/nmeth.2082}, author = {Cardona, Albert and Tomancak, Pavel} } @article {46605, title = {DlgS97/SAP97, a neuronal isoform of discs large, regulates ethanol tolerance.}, journal = {PLoS One}, volume = {7}, year = {2012}, month = {2012 Nov 7}, pages = {e48967}, abstract = {

From a genetic screen for Drosophila melanogaster mutants with altered ethanol tolerance, we identified intolerant (intol), a novel allele of discs large 1 (dlg1). Dlg1 encodes Discs Large 1, a MAGUK (Membrane Associated Guanylate Kinase) family member that is the highly conserved homolog of mammalian PSD-95 and SAP97. The intol mutation disrupted specifically the expression of DlgS97, a SAP97 homolog, and one of two major protein isoforms encoded by dlg1 via alternative splicing. Expression of the major isoform, DlgA, a PSD-95 homolog, appeared unaffected. Ethanol tolerance in the intol mutant could be partially restored by transgenic expression of DlgS97, but not DlgA, in specific neurons of the fly{\textquoteright}s brain. Based on co-immunoprecipitation, DlgS97 forms a complex with N-methyl-D-aspartate (NMDA) receptors, a known target of ethanol. Consistent with these observations, flies expressing reduced levels of the essential NMDA receptor subunit dNR1 also showed reduced ethanol tolerance, as did mutants in the gene calcium/calmodulin-dependent protein kinase (caki), encoding the fly homolog of mammalian CASK, a known binding partner of DlgS97. Lastly, mice in which SAP97, the mammalian homolog of DlgS97, was conditionally deleted in adults failed to develop rapid tolerance to ethanol{\textquoteright}s sedative/hypnotic effects. We propose that DlgS97/SAP97 plays an important and conserved role in the development of tolerance to ethanol via NMDA receptor-mediated synaptic plasticity.

}, keywords = {Alleles, Alternative Splicing, Animals, Drosophila melanogaster, Drosophila Proteins, Ethanol, Female, Guanylate Kinase, Male, Membrane Proteins, Mice, Mice, Inbred C57BL, Mutation, Neurons, Protein Isoforms, Receptors, N-Methyl-D-Aspartate, Repressor Proteins, Tumor Suppressor Proteins}, issn = {1932-6203}, doi = {10.1371/journal.pone.0048967}, author = {Maiya, Rajani and Lee, Seonok and Berger, Karen H and Kong, Eric C and Slawson, Justin B and Griffith, Leslie C and Takamiya, Kogo and Huganir, Richard L and Margolis, Ben and Heberlein, Ulrike} } @article {6859, title = {The Drosophila female aphrodisiac pheromone activates ppk23(+) sensory neurons to elicit male courtship behavior.}, journal = {Cell Reports}, volume = {1}, year = {2012}, month = {2012 Jun 28}, pages = {599-607}, abstract = {

Females of many animal species emit chemical signals that attract and arouse males for mating. For example, the major aphrodisiac pheromone of Drosophila melanogaster females, 7,11-heptacosadiene (7,11-HD), is a potent inducer of male-specific courtship and copulatory behaviors. Here, we demonstrate that a set of gustatory sensory neurons on the male foreleg, defined by expression of the ppk23 marker, respond to 7,11-HD. Activity of these neurons is required for males to robustly court females or to court males perfumed with 7,11-HD. Artificial activation of these ppk23(+) neurons stimulates male-male courtship even without 7,11-HD perfuming. These data identify the ppk23(+) sensory neurons as the primary targets for female sex pheromones in Drosophila.

}, keywords = {Alkadienes, Animal, Animals, Aphrodisiacs, Courtship, Drosophila melanogaster, Drosophila Proteins, Female, Ion Channels, Male, Pheromones, Sensilla, Sensory Receptor Cells, Sexual Behavior, Taste}, issn = {2211-1247}, doi = {10.1016/j.celrep.2012.05.007}, author = {Toda, Hirofumi and Zhao, Xiaoliang and Dickson, Barry J} } @article {5681, title = {Elastic volume reconstruction from series of ultra-thin microscopy sections.}, journal = {Nature Methods}, volume = {9}, year = {2012}, month = {2012 Jul}, pages = {717-20}, abstract = {

Anatomy of large biological specimens is often reconstructed from serially sectioned volumes imaged by high-resolution microscopy. We developed a method to reassemble a continuous volume from such large section series that explicitly minimizes artificial deformation by applying a global elastic constraint. We demonstrate our method on a series of transmission electron microscopy sections covering the entire 558-cell Caenorhabditis elegans embryo and a segment of the Drosophila melanogaster larval ventral nerve cord.

}, keywords = {Animals, Automated, Caenorhabditis elegans, Computer-Assisted, Drosophila melanogaster, Elasticity, Electron, Embryo, Image Processing, Larva, Microscopy, Microtomy, Nonmammalian, Pattern Recognition, Transmission}, issn = {1548-7105}, doi = {10.1038/nmeth.2072}, author = {Saalfeld, Stephan and Fetter, Richard D and Cardona, Albert and Tomancak, Pavel.} } @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 {3933, title = {Imaging neural activity with genetically encoded calcium indicator.}, journal = {Cold Spring Harbor Protocols}, volume = {2012}, year = {2012}, month = {2012 Jun 1}, pages = {647-56}, abstract = {

Genetically encoded calcium indicators (GECIs), which are based on chimeric fluorescent proteins, can be used to monitor calcium transients in living cells and organisms. Because they are encoded by DNA, GECIs can be delivered to the intact brain noninvasively and targeted to defined populations of neurons and specific subcellular compartments for long-term, repeated measurements in vivo. GECIs have improved iteratively and are becoming useful for imaging neural activity in vivo. Here we summarize extrinsic and intrinsic factors that influence a GECI{\textquoteright}s performance and provides guidelines for selecting the appropriate GECI for a given application. We also review recent progress in GECI design, optimization, and standardized testing protocols.

}, author = {Tian, Lin and Hires, A and Looger, Loren L} } @article {5851, title = {Imaging the post-fusion release and capture of a vesicle membrane protein.}, journal = {Nature Communications}, volume = {3}, year = {2012}, month = {2012}, pages = {1154}, abstract = {

The molecular mechanism responsible for capturing, sorting and retrieving vesicle membrane proteins following triggered exocytosis is not understood. Here we image the post-fusion release and then capture of a vesicle membrane protein, the vesicular acetylcholine transporter, from single vesicles in living neuroendocrine cells. We combine these measurements with super-resolution interferometric photo-activation localization microscopy and electron microscopy, and modelling to map the nanometer-scale topography and architecture of the structures responsible for the transporter{\textquoteright}s capture following exocytosis. We show that after exocytosis, the transporter rapidly diffuses into the plasma membrane, but most travels only a short distance before it is locally captured over a dense network of membrane-resident clathrin-coated structures. We propose that the extreme density of these structures acts as a short-range diffusion trap. They quickly sequester diffusing vesicle material and limit its spread across the membrane. This system could provide a means for clathrin-mediated endocytosis to quickly recycle vesicle proteins in highly excitable cells.

}, issn = {2041-1723}, doi = {10.1038/ncomms2158}, author = {Sochacki, Kem A and Larson, Ben T and Sengupta, Deepali C and Daniels, Mathew P and Shtengel, Gleb and Hess, Harald F and Taraska, Justin W} } @article {46160, title = {ImgLib2--generic image processing in Java.}, journal = {Bioinformatics}, volume = {28}, year = {2012}, month = {2012 Nov 15}, pages = {3009-11}, abstract = {

SUMMARY: ImgLib2 is an open-source Java library for n-dimensional data representation and manipulation with focus on image processing. It aims at minimizing code duplication by cleanly separating pixel-algebra, data access and data representation in memory. Algorithms can be implemented for classes of pixel types and generic access patterns by which they become independent of the specific dimensionality, pixel type and data representation. ImgLib2 illustrates that an elegant high-level programming interface can be achieved without sacrificing performance. It provides efficient implementations of common data types, storage layouts and algorithms. It is the data model underlying ImageJ2, the KNIME Image Processing toolbox and an increasing number of Fiji-Plugins.

AVAILABILITY: ImgLib2 is licensed under BSD. Documentation and source code are available at http://imglib2.net and in a public repository at https://github.com/imagej/imglib.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Online.

CONTACT: saalfeld@mpi-cbg.de

}, keywords = {Algorithms, Image Processing, Computer-Assisted, Programming Languages, Software}, issn = {1367-4811}, doi = {10.1093/bioinformatics/bts543}, author = {Pietzsch, Tobias and Preibisch, Stephan and Tomancak, Pavel and Saalfeld, Stephan} } @proceedings {46789, title = {ImgLib2{\textemdash}Generic Image Processing in Java}, year = {2012}, month = {2012 Oct 24}, address = {Mondorf-les-Bains, Luxembourg}, author = {Saalfeld, Stephan and Pietzsch, Tobias and Tomancak, Pavel and Preibisch, Stephan} } @article {65029, title = {An intra-cerebral drug delivery system for freely moving animals.}, journal = {Biomed Microdevices}, volume = {14}, year = {2012}, month = {2012 Oct 01}, pages = {799-809}, abstract = {

Microinfusions of drugs directly into the central nervous system of awake animals represent a widely used means of unravelling brain functions related to behaviour. However, current approaches generally use tethered liquid infusion systems and a syringe pump to deliver drugs into the brain, which often interfere with behaviour. We address this shortfall with a miniaturised electronically-controlled drug delivery system (20 {\texttimes} 17.5 {\texttimes} 5 mm{\textthreesuperior}) designed to be skull-mounted in rats. The device features a micropump connected to two 8-mm-long silicon microprobes with a cross section of 250 {\texttimes} 250 μm{\texttwosuperior} and integrated fluid microchannels. Using an external electronic control unit, the device allows infusion of 16 metered doses (0.25 μL each, 8 per silicon shaft). Each dosage requires 3.375 Ws of electrical power making the device additionally compatible with state-of-the-art wireless headstages. A dosage precision of 0.25 {\textpm} 0.01 μL was determined in vitro before in vivo tests were carried out in awake rats. No passive leakage from the loaded devices into the brain could be detected using methylene blue dye. Finally, the device was used to investigate the effects of the NMDA-receptor antagonist 3-((R)-2-Carboxypiperazin-4-yl)-propyl-1-phosphonic acid, (R)-CPP, administered directly into the prefrontal cortex of rats during performance on a task to assess visual attention and impulsivity. In agreement with previous findings using conventional tethered infusion systems, acute (R)-CPP administration produced a marked increase in impulsivity.

}, keywords = {Animals, Attention, Brain, Drug Delivery Systems, Equipment Design, Impulsive Behavior, Microinjections, Piperazines, Rats, Receptors, N-Methyl-D-Aspartate}, issn = {1572-8781}, doi = {10.1007/s10544-012-9659-2}, author = {Spieth, Sven and Schumacher, Axel and Holtzman, Tahl and Rich, P Dylan and Theobald, David E and Dalley, Jeffrey W and Nouna, Rachid and Messner, Stephan and Zengerle, Roland} } @proceedings {46791, title = {Introduction to ImgLib2}, year = {2012}, month = {2012 Oct 24}, address = {Mondorf-les-Bains, Luxembourg}, author = {Preibisch, Stephan and Pietzsch, Tobias and Myers, Eugene and Tomancak, Pavel and Saalfeld, Stephan} } @article {46048, title = {The mechanisms of repetitive spike generation in an axonless retinal interneuron.}, journal = {Cell Reports}, volume = {1}, year = {2012}, month = {2012 Feb 23}, pages = {155-66}, abstract = {

Several types of retinal interneurons exhibit spikes but lack axons. One such neuron is the AII amacrine cell, in which spikes recorded at the soma exhibit small amplitudes (\<10 mV) and broad time courses (\>5 ms). Here, we used electrophysiological recordings and computational analysis to examine the mechanisms underlying this atypical spiking. We found that somatic spikes likely represent large, brief action potential-like events initiated in a single, electrotonically distal dendritic compartment. In this same compartment, spiking undergoes slow modulation, likely by an M-type K conductance. The structural correlate of this compartment is a thin neurite that extends from the primary dendritic tree: local application of TTX to this neurite, or excision of it, eliminates spiking. Thus, the physiology of the axonless AII is much more complex than would be anticipated from morphological descriptions and somatic recordings; in particular, the AII possesses a single dendritic structure that controls its firing pattern.

}, keywords = {Action Potentials, Amacrine Cells, Animals, Axons, Female, Interneurons, Ion Channel Gating, Mice, Mice, Inbred C57BL, Models, Neurological, Potassium Channels, Retina, Time Factors}, issn = {2211-1247}, doi = {10.1016/j.celrep.2011.12.006}, author = {Cembrowski, Mark S and Logan, Stephen M and Tian, Miao and Jia, Li and Li, Wei and Kath, William L and Riecke, Hermann and Singer, Joshua H} } @article {4761, title = {Multiple dynamic representations in the motor cortex during sensorimotor learning.}, journal = {Nature}, volume = {484}, year = {2012}, month = {2012 Apr 26}, pages = {473-8}, abstract = {

The mechanisms linking sensation and action during learning are poorly understood. Layer 2/3 neurons in the motor cortex might participate in sensorimotor integration and learning; they receive input from sensory cortex and excite deep layer neurons, which control movement. Here we imaged activity in the same set of layer 2/3 neurons in the motor cortex over weeks, while mice learned to detect objects with their whiskers and report detection with licking. Spatially intermingled neurons represented sensory (touch) and motor behaviours (whisker movements and licking). With learning, the population-level representation of task-related licking strengthened. In trained mice, population-level representations were redundant and stable, despite dynamism of single-neuron representations. The activity of a subpopulation of neurons was consistent with touch driving licking behaviour. Our results suggest that ensembles of motor cortex neurons couple sensory input to multiple, related motor programs during learning.

}, issn = {1476-4687}, doi = {10.1038/nature11039}, author = {Huber, D and Gutnisky, D A and Peron, S and O{\textquoteright}Connor, D H and Wiegert, J S and Tian, L and Oertner, T G and Looger, LL and Svoboda, K} } @article {5153, title = {The Ndc80 kinetochore complex directly modulates microtubule dynamics.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, year = {2012}, month = {2012 Aug 20}, pages = {16113-8}, abstract = {

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

}, issn = {1091-6490}, doi = {10.1073/pnas.1209615109}, author = {Umbreit, Neil T and Gestaut, Daniel R and Tien, Jerry F and Vollmar, Breanna S and Gonen, Tamir and Asbury, Charles L and Davis, Trisha N} } @article {5710, title = {Network resets in medial prefrontal cortex mark the onset of behavioral uncertainty.}, journal = {Science}, volume = {338}, year = {2012}, month = {2012 Oct 5}, pages = {135-9}, abstract = {

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

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

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

}, keywords = {Animals, Calcium, Calcium Signaling, Molecular Imaging, Neurons}, issn = {1875-7855}, doi = {10.1016/B978-0-444-59426-6.00005-7}, author = {Tian, Lin and Akerboom, Jasper and Schreiter, Eric R and Looger, Loren L} } @article {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 {5329, title = {Optogenetic analysis of a nociceptor neuron and network reveals ion channels acting downstream of primary sensors.}, journal = {Current Biology}, volume = {22}, year = {2012}, month = {2012 May 8}, pages = {743-52}, abstract = {

Nociception generally evokes rapid withdrawal behavior in order to protect the tissue from harmful insults. Most nociceptive neurons responding to mechanical insults display highly branched dendrites, an anatomy shared by Caenorhabditis elegans FLP and PVD neurons, which mediate harsh touch responses. Although several primary molecular nociceptive sensors have been characterized, less is known about modulation and amplification of noxious signals within nociceptor neurons. First, we analyzed the FLP/PVD network by optogenetics and studied integration of signals from these cells in downstream interneurons. Second, we investigated which genes modulate PVD function, based on prior single-neuron mRNA profiling of PVD.

}, keywords = {Ion Channels, Neurons}, issn = {1879-0445}, doi = {10.1016/j.cub.2012.02.066}, author = {Husson, Steven J and Costa, Wagner Steuer and Wabnig, Sebastian and Stirman, Jeffrey N and Watson, Joseph D and Spencer, W Clay and Akerboom, Jasper and Looger, Loren L and Treinin, Millet and Miller, David M and Lu, Hang and Gottschalk, Alexander} } @article {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 {4898, title = {Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy.}, journal = {Nature Methods}, volume = {9}, year = {2012}, month = {2012 Jun 3}, pages = {755-63}, abstract = {

Live imaging of large biological specimens is fundamentally limited by the short optical penetration depth of light microscopes. To maximize physical coverage, we developed the SiMView technology framework for high-speed in vivo imaging, which records multiple views of the specimen simultaneously. SiMView consists of a light-sheet microscope with four synchronized optical arms, real-time electronics for long-term sCMOS-based image acquisition at 175 million voxels per second, and computational modules for high-throughput image registration, segmentation, tracking and real-time management of the terabytes of multiview data recorded per specimen. We developed one-photon and multiphoton SiMView implementations and recorded cellular dynamics in entire Drosophila melanogaster embryos with 30-s temporal resolution throughout development. We furthermore performed high-resolution long-term imaging of the developing nervous system and followed neuroblast cell lineages in vivo. SiMView data sets provide quantitative morphological information even for fast global processes and enable accurate automated cell tracking in the entire early embryo.

High-resolution movies in the Digital Embryo repository
Nature News: "Fruitfly development, cell by cell" by Lauren Gravitz
Nature Methods Technology Feature: "Faster frames, clearer pictures" by Monya Baker
Andor Insight Awards: Life Sciences Winner

}, issn = {1548-7105}, doi = {10.1038/nmeth.2062}, author = {Tomer, Raju and Khairy, Khaled and Amat, Fernando and Keller, Philipp J} } @article {4594, title = {Regulation of neuronal input transformations by tunable dendritic inhibition.}, journal = {Nature Neuroscience}, volume = {15}, year = {2012}, month = {2012 Jan 15}, pages = {423-30}, abstract = {

Transforming synaptic input into action potential output is a fundamental function of neurons. The pattern of action potential output from principal cells of the mammalian hippocampus encodes spatial and nonspatial information, but the cellular and circuit mechanisms by which neurons transform their synaptic input into a given output are unknown. Using a combination of optical activation and cell type-specific pharmacogenetic silencing in vitro, we found that dendritic inhibition is the primary regulator of input-output transformations in mouse hippocampal CA1 pyramidal cells, and acts by gating the dendritic electrogenesis driving burst spiking. Dendrite-targeting interneurons are themselves modulated by interneurons targeting pyramidal cell somata, providing a synaptic substrate for tuning pyramidal cell output through interactions in the local inhibitory network. These results provide evidence for a division of labor in cortical circuits, where distinct computational functions are implemented by subtypes of local inhibitory neurons.

}, issn = {1546-1726}, doi = {10.1038/nn.3024}, author = {Lovett-Barron, Matthew and Turi, Gergely F and Kaifosh, Patrick and Lee, Peter H and Bolze, Fr{\'e}d{\'e}ric and Sun, Xiao-Hua and Nicoud, Jean-Fran\c cois and Zemelman, Boris V and Sternson, Scott M and Losonczy, Attila} } @article {6515, title = {A resource for manipulating gene expression and analyzing cis-regulatory modules in the Drosophila CNS.}, journal = {Cell Reports}, volume = {2}, year = {2012}, month = {2012 Oct 25}, pages = {1002-13}, abstract = {

Here, we describe the embryonic central nervous system expression of 5,000 GAL4 lines made using molecularly defined cis-regulatory DNA inserted into a single attP genomic location. We document and annotate the patterns in early embryos when neurogenesis is at its peak, and in older embryos where there is maximal neuronal diversity and the first neural circuits are established. We note expression in other tissues, such as the lateral body wall (muscle, sensory neurons, and trachea) and viscera. Companion papers report on the adult brain and larval imaginal discs, and the integrated data sets\ are available online (http://www.janelia.org/gal4-gen1). This collection of embryonically expressed GAL4 lines will be valuable for determining neuronal morphology and function. The 1,862 lines expressed in small subsets of neurons (\<20/segment) will be especially valuable for characterizing\ interneuronal diversity and function, because although interneurons comprise the majority of all central nervous system neurons, their gene expression profile and function remain virtually unexplored.

}, keywords = {Animals, Central Nervous System, Databases, Drosophila, Drosophila Proteins, Embryo, Factual, Female, Gene Expression, Genes, Genetically Modified, Internet, Male, Nonmammalian, Regulatory Elements, Reporter, Transcription Factors, Transcriptional}, issn = {2211-1247}, doi = {10.1016/j.celrep.2012.09.009}, author = {Manning, Laurina and Heckscher, Ellie S and Purice, Maria D and Roberts, Jourdain and Bennett, Alysha L and Kroll, Jason R and Pollard, Jill L and Strader, Marie E and Lupton, Josh R and Dyukareva, Anna V and Doan, Phuong Nam and Bauer, David M and Wilbur, Allison N and Tanner, Stephanie and Kelly, Jimmy J and Lai, Sen-Lin and Tran, Khoa D and Kohwi, Minoree and Laverty, Todd R and Pearson, Joseph C and Crews, Stephen T and Rubin, Gerald M and Doe, Chris Q} } @article {5160, title = {Selective esterase-ester pair for targeting small molecules with cellular specificity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, year = {2012}, month = {2012 Mar 27}, pages = {4756-61}, abstract = {

Small molecules are important tools to measure and modulate intracellular signaling pathways. A longstanding limitation for using chemical compounds in complex tissues has been the inability to target bioactive small molecules to a specific cell class. Here, we describe a generalizable esterase-ester pair capable of targeted delivery of small molecules to living cells and tissue with cellular specificity. We used fluorogenic molecules to rapidly identify a small ester masking motif that is stable to endogenous esterases, but is efficiently removed by an exogenous esterase. This strategy allows facile targeting of dyes and drugs in complex biological environments to label specific cell types, illuminate gap junction connectivity, and pharmacologically perturb distinct subsets of cells. We expect this approach to have general utility for the specific delivery of many small molecules to defined cellular populations.

}, keywords = {Animals, Astrocytes, Biocatalysis, Cell Survival, Cells, Coculture Techniques, Esterases, Esters, Fluorescence, Fluorescent Dyes, Gap Junctions, Hela Cells, Hippocampus, Humans, Hydrolysis, Mice, Microscopy, Neurons, Organ Specificity, Permeability, Rats, Small Molecule Libraries}, issn = {1091-6490}, doi = {10.1073/pnas.1111943109}, author = {Tian, Lin and Yang, Yunlei and Wysocki, Laura M and Arnold, Alma C and Hu, Amy and Ravichandran, Balaji and Sternson, Scott M and Looger, Loren L and Lavis, Luke D} } @article {68361, title = {Sexually Dimorphic BDNF Signaling Directs Sensory Innervation of the Mammary Gland}, journal = {Science}, volume = {338}, year = {2012}, month = {12/2012}, pages = {1357-1360}, abstract = {

Male and female mice differ in the neuronal patterns that serve the mammary glands. Yin Liu et al. (p. 1357) now describe how gonadal hormones drive development of distinct male and female sensory innervations. Although both male and female mammary glands develop their sensory innervation similarly in early embryogenesis, once the androgens take effect, the developmental trajectories diverge. By birth, the rich network of sensory neurons present in the female is absent in the male. Androgens cause a switch from expression of the full-length neurotrophin receptor TrkB to its truncated form, TrkB.T1, both of which are expressed on the neurons. In males, truncated TrkB.T1 sequesters brain-derived neurotrophic factor (BDNF) from further activity, whereas in females, full-length TrkB binds BDNF and supports neuronal development. Androgen-driven changes in receptor expression disrupt a neuronal signaling pathway and de-innervation. How neural circuits associated with sexually dimorphic organs are differentially assembled during development is unclear. Here, we report a sexually dimorphic pattern of mouse mammary gland sensory innervation and the mechanism of its formation. Brain-derived neurotrophic factor (BDNF), emanating from mammary mesenchyme and signaling through its receptor TrkB on sensory axons, is required for establishing mammary gland sensory innervation of both sexes at early developmental stages. Subsequently, in males, androgens promote mammary mesenchymal expression of a truncated form of TrkB, which prevents BDNF-TrkB signaling in sensory axons and leads to a rapid loss of mammary gland innervation independent of neuronal apoptosis. Thus, sex hormone regulation of a neurotrophic factor signal directs sexually dimorphic axonal growth and maintenance, resulting in generation of a sex-specific neural circuit.

}, doi = {10.1126/science.1228258}, url = {https://www.science.org/doi/abs/10.1126/science.1228258}, author = {Yin Liu and Michael Rutlin and Siyi Huang and Colleen A. Barrick and Fan Wang and Kevin R. Jones and Lino Tessarollo and David D. Ginty} } @article {67279, title = {Simplified models for LHC new physics searches}, journal = {Journal of Physics G: Nuclear and Particle Physics}, volume = {39}, year = {2012}, month = {Jan-10-2012}, pages = {105005}, abstract = {

This document proposes a collection of simplified models relevant to the design of new-physics searches at the Large Hadron Collider (LHC) and the characterization of their results. Both ATLAS and CMS have already presented some results in terms of simplified models, and we encourage them to continue and expand this effort, which supplements both signature-based results and benchmark model interpretations. A simplified model is defined by an effective Lagrangian describing the interactions of a small number of new particles. Simplified models can equally well be described by a small number of masses and cross-sections. These parameters are directly related to collider physics observables, making simplified models a particularly effective framework for evaluating searches and a useful starting point for characterizing positive signals of new physics. This document serves as an official summary of the results from the {\textquoteright}Topologies for Early LHC Searches{\textquoteright} workshop, held at SLAC in September of 2010, the purpose of which was to develop a set of representative models that can be used to cover all relevant phase space in experimental searches. Particular emphasis is placed on searches relevant for the first ~50{\textendash}500 pb-1\ of data and those motivated by supersymmetric models. This note largely summarizes material posted at\ http://lhcnewphysics.org/, which includes simplified model definitions, Monte Carlo material, and supporting contacts within the theory community. We also comment on future developments that may be useful as more data is gathered and analyzed by the experiments.

}, issn = {0954-3899}, doi = {10.1088/0954-3899/39/10/105005}, url = {https://iopscience.iop.org/article/10.1088/0954-3899/39/10/105005}, author = {Alves, Daniele and Arkani-Hamed, Nima and Arora, Sanjay and Bai, Yang and Baumgart, Matthew and Berger, Joshua and Buckley, Matthew and Butler, Bart and Chang, Spencer and Cheng, Hsin-Chia and Cheung, Clifford and Chivukula, R Sekhar and Cho, Won Sang and Cotta, Randy and D{\textquoteright}Alfonso, Mariarosaria and Hedri, Sonia El and Essig, Rouven and Evans, Jared A and Fitzpatrick, Liam and Fox, Patrick and Franceschini, Roberto and Freitas, Ayres and Gainer, James S and Gershtein, Yuri and Gray, Richard and Gregoire, Thomas and Gripaios, Ben and Gunion, Jack and Han, Tao and Haas, Andy and Hansson, Per and Hewett, JoAnne and Hits, Dmitry and Hubisz, Jay and Izaguirre, Eder and Kaplan, Jared and Katz, Emanuel and Kilic, Can and Kim, Hyung-Do and Kitano, Ryuichiro and Koay, Sue Ann and Ko, Pyungwon and Krohn, David and Kuflik, Eric and Lewis, Ian and Lisanti, Mariangela and Liu, Tao and Liu, Zhen and Lu, Ran and Luty, Markus and Meade, Patrick and Morrissey, David and Mrenna, Stephen and Nojiri, Mihoko and Okui, Takemichi and Padhi, Sanjay and Papucci, Michele and Park, Michael and Park, Myeonghun and Perelstein, Maxim and Peskin, Michael and Phalen, Daniel and Rehermann, Keith and Rentala, Vikram and Roy, Tuhin and Ruderman, Joshua T and Sanz, Veronica and Schmaltz, Martin and Schnetzer, Stephen and Schuster, Philip and Schwaller, Pedro and Schwartz, Matthew D and Schwartzman, Ariel and Shao, Jing and Shelton, Jessie and Shih, David and Shu, Jing and Silverstein, Daniel and Simmons, Elizabeth and Somalwar, Sunil and Spannowsky, Michael and Spethmann, Christian and Strassler, Matthew and Su, Shufang and Tait, Tim and Thomas, Brooks and Thomas, Scott and Toro, Natalia and Volansky, Tomer and Wacker, Jay and Waltenberger, Wolfgang and Yavin, Itay and Yu, Felix and Zhao, Yue and Zurek, Kathryn} } @article {46725, title = {Single-mRNA counting using fluorescent in situ hybridization in budding yeast.}, journal = {Nature Protocols}, volume = {7}, year = {2012}, month = {2012 Feb 2}, pages = {408-19}, abstract = {

Fluorescent in situ hybridization (FISH) allows the quantification of single mRNAs in budding yeast using fluorescently labeled single-stranded DNA probes, a wide-field epifluorescence microscope and a spot-detection algorithm. Fixed yeast cells are attached to coverslips and hybridized with a mixture of FISH probes, each conjugated to several fluorescent dyes. Images of cells are acquired in 3D and maximally projected for single-molecule analysis. Diffraction-limited labeled mRNAs are observed as bright fluorescent spots and can be quantified using a spot-detection algorithm. FISH preserves the spatial distribution of cellular RNA distribution within the cell and the stochastic fluctuations in individual cells that can lead to phenotypic differences within a clonal population. This information, however, is lost if the RNA content is measured on a population of cells by using reverse transcriptase PCR, microarrays or high-throughput sequencing. The FISH procedure and image acquisition described here can be completed in 3 d.

}, keywords = {Algorithms, Antisense Elements (Genetics), In Situ Hybridization, Fluorescence, RNA, Fungal, RNA, Messenger, Saccharomyces cerevisiae}, issn = {1750-2799}, doi = {10.1038/nprot.2011.451}, author = {Trcek, Tatjana and Chao, Jeffrey A and Larson, Daniel R and Park, Hye Yoon and Zenklusen, Daniel and Shenoy, Shailesh M and Singer, Robert H} } @article {6300, title = {A subset of dopamine neurons signals reward for odour memory in Drosophila.}, journal = {Nature}, volume = {488}, year = {2012}, month = {2012 Aug 23}, pages = {512-6}, abstract = {

Animals approach stimuli that predict a pleasant outcome. After the paired presentation of an odour and a reward, Drosophila melanogaster can develop a conditioned approach towards that odour. Despite recent advances in understanding the neural circuits for associative memory and appetitive motivation, the cellular mechanisms for reward processing in the fly brain are unknown. Here we show that a group of dopamine neurons in the protocerebral anterior medial (PAM) cluster signals sugar reward by transient activation and inactivation of target neurons in intact behaving flies. These dopamine neurons are selectively required for the reinforcing property of, but not a reflexive response to, the sugar stimulus. In vivo calcium imaging revealed that these neurons are activated by sugar ingestion and the activation is increased on starvation. The output sites of the PAM neurons are mainly localized to the medial lobes of the mushroom bodies (MBs), where appetitive olfactory associative memory is formed. We therefore propose that the PAM cluster neurons endow a positive predictive value to the odour in the MBs. Dopamine in insects is known to mediate aversive reinforcement signals. Our results highlight the cellular specificity underlying the various roles of dopamine and the importance of spatially segregated local circuits within the MBs.

}, keywords = {Animals, Appetitive Behavior, Calcium Signaling, Dendrites, Dopamine, Dopaminergic Neurons, Drosophila melanogaster, Memory, Mushroom Bodies, Odors, Reward, Smell}, issn = {1476-4687}, doi = {10.1038/nature11304}, author = {Liu, Chang and Placais, Pierre-Yves and Yamagata, Nobuhiro and Pfeiffer, Barret D and Aso, Yoshinori and Friedrich, Anja B and Siwanowicz, Igor and Rubin, Gerald M and Preat, Thomas and Tanimoto, Hiromu} } @article {4892, title = {Superpenetration optical microscopy by iterative multiphoton adaptive compensation technique.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, year = {2012}, month = {2012 May 29}, pages = {8434-9}, abstract = {

Biological tissues are rarely transparent, presenting major challenges for deep tissue optical microscopy. The achievable imaging depth is fundamentally limited by wavefront distortions caused by aberration and random scattering. Here, we report an iterative wavefront compensation technique that takes advantage of the nonlinearity of multiphoton signals to determine and compensate for these distortions and to focus light inside deep tissues. Different from conventional adaptive optics methods, this technique can rapidly measure highly complicated wavefront distortions encountered in deep tissue imaging and provide compensations for not only aberration but random scattering. The technique is tested with a variety of highly heterogeneous biological samples including mouse brain tissue, skull, and lymph nodes. We show that high quality three-dimensional imaging can be realized at depths beyond the reach of conventional multiphoton microscopy and adaptive optics methods, albeit over restricted distances for a given correction. Moreover, the required laser excitation power can be greatly reduced in deep tissues, deviating from the power requirement of ballistic light excitation and thus significantly reducing photo damage to the biological tissue.

}, issn = {1091-6490}, doi = {10.1073/pnas.1119590109}, author = {Tang, Jianyong and Germain, Ronald N and Cui, Meng} } @article {43051, title = {Tandem fluorescent protein timers for in vivo analysis of protein dynamics.}, journal = {Nature Biotechnology}, volume = {30}, year = {2012}, month = {2012 Jun 24}, pages = {708-14}, abstract = {

The functional state of a cell is largely determined by the spatiotemporal organization of its proteome. Technologies exist for measuring particular aspects of protein turnover and localization, but comprehensive analysis of protein dynamics across different scales is possible only by combining several methods. Here we describe tandem fluorescent protein timers (tFTs), fusions of two single-color fluorescent proteins that mature with different kinetics, which we use to analyze protein turnover and mobility in living cells. We fuse tFTs to proteins in yeast to study the longevity, segregation and inheritance of cellular components and the mobility of proteins between subcellular compartments; to measure protein degradation kinetics without the need for time-course measurements; and to conduct high-throughput screens for regulators of protein turnover. Our experiments reveal the stable nature and asymmetric inheritance of nuclear pore complexes and identify regulators of N-end rule{\textendash}mediated protein degradation.

}, keywords = {Green Fluorescent Proteins, High-Throughput Screening Assays, Kinetics, Nuclear Pore, Protein Stability, Proteins, Proteolysis, Saccharomyces cerevisiae, Subcellular Fractions}, issn = {1546-1696}, doi = {10.1038/nbt.2281}, author = {Khmelinskii, Anton and Keller, Philipp J and Bartosik, Anna and Meurer, Matthias and Barry, Joseph D and Mardin, Balca R and Kaufmann, Andreas and Trautmann, Susanne and Wachsmuth, Malte and Pereira, Gislene and Huber, Wolfgang and Schiebel, Elmar and Knop, Michael} } @article {6301, title = {A toolbox of Cre-dependent optogenetic transgenic mice for light-induced activation and silencing.}, journal = {Nature Neuroscience}, volume = {15}, year = {2012}, month = {2012 May}, pages = {793-802}, abstract = {

Cell type-specific expression of optogenetic molecules allows temporally precise manipulation of targeted neuronal activity. Here we present a toolbox of four knock-in mouse lines engineered for strong, Cre-dependent expression of channelrhodopsins ChR2-tdTomato and ChR2-EYFP, halorhodopsin eNpHR3.0 and archaerhodopsin Arch-ER2. All four transgenes mediated Cre-dependent, robust activation or silencing of cortical pyramidal neurons in vitro and in vivo upon light stimulation, with ChR2-EYFP and Arch-ER2 demonstrating light sensitivity approaching that of in utero or virally transduced neurons. We further show specific photoactivation of parvalbumin-positive interneurons in behaving ChR2-EYFP reporter mice. The robust, consistent and inducible nature of our ChR2 mice represents a significant advance over previous lines, and the Arch-ER2 and eNpHR3.0 mice are to our knowledge the first demonstration of successful conditional transgenic optogenetic silencing. When combined with the hundreds of available Cre driver lines, this optimized toolbox of reporter mice will enable widespread investigations of neural circuit function with unprecedented reliability and accuracy.

}, keywords = {Action Potentials, Animals, Archaeal Proteins, Brain, Electroporation, Halorhodopsins, Integrases, Light, Luminescent Proteins, Mice, Neurogenesis, Neurons, Optics and Photonics, Proteins, Rhodopsin, Transgenic, Wakefulness}, issn = {1546-1726}, doi = {10.1038/nn.3078}, author = {Madisen, Linda and Mao, Tianyi and Koch, Henner and Zhuo, Jia-min and Berenyi, Antal and Fujisawa, Shigeyoshi and Hsu, Yun-Wei A and Garcia, Alfredo J and Gu, Xuan and Zanella, Sebastien and Kidney, Jolene and Gu, Hong and Mao, Yimei and Hooks, Bryan M and Boyden, Edward S and Buzs{\'a}ki, Gy{\"o}rgy and Ramirez, Jan Marino and Jones, Allan R and Svoboda, Karel and Han, Xue and Turner, Eric E and Zeng, Hongkui} } @article {5684, title = {TrakEM2 software for neural circuit reconstruction.}, journal = {PLoS One}, volume = {7}, year = {2012}, month = {2012}, pages = {e38011}, abstract = {

A key challenge in neuroscience is the expeditious reconstruction of neuronal circuits. For model systems such as Drosophila and C. elegans, the limiting step is no longer the acquisition of imagery but the extraction of the circuit from images. For this purpose, we designed a software application, TrakEM2, that addresses the systematic reconstruction of neuronal circuits from large electron microscopical and optical image volumes. We address the challenges of image volume composition from individual, deformed images; of the reconstruction of neuronal arbors and annotation of synapses with fast manual and semi-automatic methods; and the management of large collections of both images and annotations. The output is a neural circuit of 3d arbors and synapses, encoded in NeuroML and other formats, ready for analysis.

}, keywords = {Animals, Models, Nerve Net, Neuroimaging, Neurological, Neurons, Software, Synapses, Synaptic Transmission}, issn = {1932-6203}, doi = {10.1371/journal.pone.0038011}, author = {Cardona, Albert and Saalfeld, Stephan and Schindelin, Johannes and Arganda-Carreras, Ignacio and Preibisch, Stephan and Longair, Mark and Tomancak, Pavel and Hartenstein, Volker and Douglas, Rodney J} } @article {46785, title = {TrakEM2 software for neural circuit reconstruction.}, journal = {PLoS One}, volume = {7}, year = {2012}, month = {2012}, pages = {e38011}, abstract = {

A key challenge in neuroscience is the expeditious reconstruction of neuronal circuits. For model systems such as Drosophila and C. elegans, the limiting step is no longer the acquisition of imagery but the extraction of the circuit from images. For this purpose, we designed a software application, TrakEM2, that addresses the systematic reconstruction of neuronal circuits from large electron microscopical and optical image volumes. We address the challenges of image volume composition from individual, deformed images; of the reconstruction of neuronal arbors and annotation of synapses with fast manual and semi-automatic methods; and the management of large collections of both images and annotations. The output is a neural circuit of 3d arbors and synapses, encoded in NeuroML and other formats, ready for analysis.

}, keywords = {Animals, Models, Neurological, Nerve Net, Neuroimaging, Neurons, Software, Synapses, Synaptic Transmission}, issn = {1932-6203}, doi = {10.1371/journal.pone.0038011}, author = {Cardona, Albert and Saalfeld, Stephan and Schindelin, Johannes and Arganda-Carreras, Ignacio and Preibisch, Stephan and Longair, Mark and Tomancak, Pavel and Hartenstein, Volker and Douglas, Rodney J} } @article {6518, title = {Transcription initiation by human RNA polymerase II visualized at single-molecule resolution.}, journal = {Genes \& Development}, volume = {26}, year = {2012}, month = {2012 Aug 1}, pages = {1691-702}, abstract = {

Forty years of classical biochemical analysis have identified the molecular players involved in initiation of transcription by eukaryotic RNA polymerase II (Pol II) and largely assigned their functions. However, a dynamic picture of Pol II transcription initiation and an understanding of the mechanisms of its regulation have remained elusive due in part to inherent limitations of conventional ensemble biochemistry. Here we have begun to dissect promoter-specific transcription initiation directed by a reconstituted human Pol II system at single-molecule resolution using fluorescence video-microscopy. We detected several stochastic rounds of human Pol II transcription from individual DNA templates, observed attenuation of transcription by promoter mutations, observed enhancement of transcription by activator Sp1, and correlated the transcription signals with real-time interactions of holo-TFIID molecules at individual DNA templates. This integrated single-molecule methodology should be applicable to studying other complex biological processes.

}, keywords = {Fluorescence, Genetic, Humans, Microscopy, Molecular Imaging, Mutation, Promoter Regions, RNA Polymerase II, Sp1 Transcription Factor, Transcription, Transcription Factor TFIID, Video}, issn = {1549-5477}, doi = {10.1101/gad.194936.112}, author = {Revyakin, Andrey and Zhang, Zhengjian and Coleman, Robert A and Li, Yan and Inouye, Carla and Lucas, Julian K and Park, Sang-Ryul and Chu, Steven and Tjian, Robert} } @article {68820, title = {Transcriptional signature of accessory cells in the lateral line, using the Tnk1bp1:EGFP transgenic zebrafish line}, journal = {BMC developmental biology}, volume = {12}, year = {2012}, month = {01/2012}, pages = {6}, abstract = {

Background:\ Because of the structural and molecular similarities between the two systems, the lateral line, a fish and amphibian specific sensory organ, has been widely used in zebrafish as a model to study the development/biology of neuroepithelia of the inner ear. Both organs have hair cells, which are the mechanoreceptor cells, and supporting cells providing other functions to the epithelium. In most vertebrates (excluding mammals), supporting cells comprise a pool of progenitors that replace damaged or dead hair cells. However, the lack of regenerative capacity in mammals is the single leading cause for acquired hearing disorders in humans.

Results:\ In an effort to understand the regenerative process of hair cells in fish, we characterized and cloned an egfp transgenic stable fish line that trapped tnks1bp1, a highly conserved gene that has been implicated in the maintenance of telomeres{\textquoteright} length. We then used this Tg(tnks1bp1:EGFP) line in a FACsorting strategy combined with microarrays to identify new molecular markers for supporting cells.

Conclusions:\ We present a Tg(tnks1bp1:EGFP) stable transgenic line, which we used to establish a transcriptional profile of supporting cells in the zebrafish lateral line. Therefore we are providing a new set of markers specific for supporting cells as well as candidates for functional analysis of this important cell type. This will prove to be a valuable tool for the study of regeneration in the lateral line of zebrafish in particular and for regeneration of neuroepithelia in general.

}, doi = {10.1186/1471-213X-12-6}, author = {Behra, Martine and Gallardo, Viviana and Bradsher, John and Torrado, Aranza and Elkahloun, Abdel and Idol, Jennifer and Sheehy, Jessica and Zonies, Seth and Xu, Lisha and Shaw, Kenna and Satou, Chie and Higashijima, Shin-Ichi and Weinstein, Brant and Burgess, Shawn} } @article {46731, title = {Transgenic expression of ZBP1 in neurons suppresses cocaine-associated conditioning.}, journal = {Learning \& Memory}, volume = {19}, year = {2012}, month = {2012 Feb}, pages = {35-42}, abstract = {

To directly address whether regulating mRNA localization can influence animal behavior, we created transgenic mice that conditionally express Zipcode Binding Protein 1 (ZBP1) in a subset of neurons in the brain. ZBP1 is an RNA-binding protein that regulates the localization, as well as translation and stability of target mRNAs in the cytoplasm. We took advantage of the absence of ZBP1 expression in the mature brain to examine the effect of expressing ZBP1 on animal behavior. We constructed a transgene conditionally expressing a GFP-ZBP1 fusion protein in a subset of forebrain neurons and compared cocaine-cued place conditioning in these mice versus noninduced littermates. Transgenic ZBP1 expression resulted in impaired place conditioning relative to nonexpressing littermates, and acutely repressing expression of the transgene restored normal cocaine conditioning. To gain insight into the molecular changes that accounted for this change in behavior, we identified mRNAs that specifically immunoprecipitated with transgenic ZBP1 protein from the brains of these mice. These data suggest that RNA-binding proteins can be used as a tool to identify the post-transcriptional regulation of gene expression in the establishment and function of neural circuits involved in addiction behaviors.

}, keywords = {Animals, Brain, Cocaine, Conditioning (Psychology), Cues, DNA-Binding Proteins, Dopamine Uptake Inhibitors, Doxycycline, Gene Expression Regulation, Green Fluorescent Proteins, Immunoprecipitation, Male, Mice, Mice, Transgenic, Microarray Analysis, Neurons, RNA, Messenger, RNA-Binding Proteins}, issn = {1549-5485}, doi = {10.1101/lm.024471.111}, author = {Lapidus, Kyle A B and Nwokafor, Chiso and Scott, Daniel and Baroni, Timothy E and Tenenbaum, Scott A and Hiroi, Noboru and Singer, Robert H and Czaplinski, Kevin} } @article {4973, title = {Transvection is common throughout the Drosophila genome.}, journal = {Genetics}, volume = {191}, year = {2012}, month = {2012 May 29}, pages = {1129-41}, abstract = {

Higher-order genome organization plays an important role in transcriptional regulation. In Drosophila, somatic pairing of homologous chromosomes can lead to transvection, by which the regulatory region of a gene can influence transcription in trans. We observe transvection between transgenes inserted at commonly used phiC31 integration sites in the Drosophila genome. When two transgenes that carry endogenous regulatory elements driving the expression of either LexA or GAL4 are inserted at the same integration site and paired, the enhancer of one transgene can drive or repress expression of the paired transgene. These transvection effects depend on compatibility between regulatory elements and are often restricted to a subset of cell types within a given expression pattern. We further show that activated UAS-transgenes can also drive transcription in trans. We discuss the implication of these findings for 1) understanding the molecular mechanisms that underlie transvection and 2) the design of experiments that utilize site-specific integration.

}, issn = {1943-2631}, doi = {10.1534/genetics.112.140475}, author = {Mellert, David J and Truman, James W} } @article {4598, title = {Triggering a cell shape change by exploiting preexisting actomyosin contractions.}, journal = {Science}, volume = {335}, year = {2012}, month = {2012 Mar 9}, pages = {1232-5}, abstract = {

Apical constriction changes cell shapes, driving critical morphogenetic events, including gastrulation in diverse organisms and neural tube closure in vertebrates. Apical constriction is thought to be triggered by contraction of apical actomyosin networks. We found that apical actomyosin contractions began before cell shape changes in both Caenorhabitis elegans and Drosophila. In C. elegans, actomyosin networks were initially dynamic, contracting and generating cortical tension without substantial shrinking of apical surfaces. Apical cell-cell contact zones and actomyosin only later moved increasingly in concert, with no detectable change in actomyosin dynamics or cortical tension. Thus, apical constriction appears to be triggered not by a change in cortical tension, but by dynamic linking of apical cell-cell contact zones to an already contractile apical cortex.

}, issn = {1095-9203}, doi = {10.1126/science.1217869}, author = {Roh-Johnson, Minna and Shemer, Gidi and Higgins, Christopher D and McClellan, Joseph H and Werts, Adam D and Tulu, U Serdar and Gao, Liang and Betzig, Eric and Kiehart, Daniel P and Goldstein, Bob} } @article {6302, title = {Ultrabithorax confers spatial identity in a context-specific manner in the Drosophila postembryonic ventral nervous system.}, journal = {Neural Development}, volume = {7}, year = {2012}, month = {2012 Sep 11}, pages = {31}, abstract = {

BACKGROUND: In holometabolous insects such as Drosophila melanogaster, neuroblasts produce an initial population of diverse neurons during embryogenesis and a much larger set of adult-specific neurons during larval life. In the ventral CNS, many of these secondary neuronal lineages differ significantly from one body segment to another, suggesting a role for anteroposterior patterning genes. RESULTS: Here we systematically characterize the expression pattern and function of the Hox gene Ultrabithorax (Ubx) in all 25 postembryonic lineages. We find that Ubx is expressed in a segment-, lineage-, and hemilineage-specific manner in the thoracic and anterior abdominal segments. When Ubx is removed from neuroblasts via mitotic recombination, neurons in these segments exhibit the morphologies and survival patterns of their anterior thoracic counterparts. Conversely, when Ubx is ectopically expressed in anterior thoracic segments, neurons exhibit complementary posterior transformation phenotypes. CONCLUSION: Our findings demonstrate that Ubx plays a critical role in conferring segment-appropriate morphology and survival on individual neurons in the adult-specific ventral CNS. Moreover, while always conferring spatial identity in some sense, Ubx has been co-opted during evolution for distinct and even opposite functions in different neuronal hemilineages.

}, keywords = {Animals, Cell Death, Developmental, Drosophila, Drosophila melanogaster, Drosophila Proteins, Gene Expression Regulation, Genetically Modified, Homeodomain Proteins, Larva, Nervous System, Transcription Factors}, issn = {1749-8104}, doi = {10.1186/1749-8104-7-31}, author = {Marin, Elizabeth C and Dry, Katie E and Alaimo, Danielle R and Rudd, Kirstin T and Cillo, Anthony R and Clenshaw, Michael E and Negre, Nicolas and White, Kevin P and Truman, James W} } @article {46722, title = {An unbiased analysis method to quantify mRNA localization reveals its correlation with cell motility.}, journal = {Cell Reports}, volume = {1}, year = {2012}, month = {2012 Feb 23}, pages = {179-84}, abstract = {

Localization of mRNA is a critical mechanism used by a large fraction of transcripts to restrict its translation to specific cellular regions. Although current high-resolution imaging techniques provide ample information, the analysis methods for localization have either been qualitative or employed quantification in nonrandomly selected regions of interest. Here, we describe an analytical method for objective quantification of mRNA localization using a combination of two characteristics of its molecular distribution, polarization and dispersion. The validity of the method is demonstrated using single-molecule FISH images of budding yeast and fibroblasts. Live-cell analysis of endogenous β-actin mRNA in mouse fibroblasts reveals that mRNA polarization has a half-life of ~16 min and is cross-correlated with directed cell migration. This novel approach provides insights into the dynamic regulation of mRNA localization and its physiological roles.

}, keywords = {Actins, Animals, Cell Movement, Chick Embryo, Computer Simulation, Embryo, Mammalian, Fibroblasts, Green Fluorescent Proteins, Imaging, Three-Dimensional, In Situ Hybridization, Mice, Monte Carlo Method, RNA Transport, RNA, Messenger, Saccharomyces cerevisiae}, issn = {2211-1247}, doi = {10.1016/j.celrep.2011.12.009}, author = {Park, Hye Yoon and Trcek, Tatjana and Wells, Amber L and Chao, Jeffrey A and Singer, Robert H} } @article {4486, title = {Use of a Drosophila genome-wide conserved sequence database to identify functionally related cis-regulatory enhancers.}, journal = {Developmental Dynamics: An Official Publication of the American Association of Anatomists}, volume = {241}, year = {2012}, month = {2012 Jan}, pages = {169-89}, abstract = {

Phylogenetic footprinting has revealed that cis-regulatory enhancers consist of conserved DNA sequence clusters (CSCs). Currently, there is no systematic approach for enhancer discovery and analysis that takes full-advantage of the sequence information within enhancer CSCs.

}, issn = {1097-0177}, doi = {10.1002/dvdy.22728}, author = {Brody, Thomas and Yavatkar, Amarendra S and Kuzin, Alexander and Kundu, Mukta and Tyson, Leonard J and Ross, Jermaine and Lin, Tzu-Yang and Lee, Chi-Hon and Awasaki, Takeshi and Lee, Tzumin and Odenwald, Ward F} } @article {4629, title = {Using translational enhancers to increase transgene expression in Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, year = {2012}, month = {2012 Apr 9}, pages = {6626-31}, abstract = {

The ability to specify the expression levels of exogenous genes inserted in the genomes of transgenic animals is critical for the success of a wide variety of experimental manipulations. Protein production can be regulated at the level of transcription, mRNA transport, mRNA half-life, or translation efficiency. In this report, we show that several well-characterized sequence elements derived from plant and insect viruses are able to function in Drosophila to increase the apparent translational efficiency of mRNAs by as much as 20-fold. These increases render expression levels sufficient for genetic constructs previously requiring multiple copies to be effective in single copy, including constructs expressing the temperature-sensitive inactivator of neuronal function Shibire(ts1), and for the use of cytoplasmic GFP to image the fine processes of neurons.

}, issn = {1091-6490}, doi = {10.1073/pnas.1204520109}, author = {Pfeiffer, Barret D and Truman, James W and Rubin, Gerald M} } @article {46346, title = {β-secretase cleavage of the fly amyloid precursor protein is required for glial survival.}, journal = {Journal of Neuroscience}, volume = {32}, year = {2012}, month = {2012 Nov 14}, pages = {16181-92}, abstract = {

β-secretase (or BACE1) is the key enzyme in the production of β-amyloid (Aβ), which accumulates in the senile plaques characteristic for Alzheimer{\textquoteright}s disease. Consequently, the lack of BACE1 prevents β-processing of the amyloid precursor protein and Aβ production, which made it a promising target for drug development. However, the loss of BACE1 is also detrimental, leading to myelination defects and altered neuronal activity, functions that have been associated with the cleavage of Neuregulin and a voltage-gated sodium channel subunit. Here we show that the Drosophila ortholog of BACE, dBACE, is required for glial survival. Cell-specific knockdown experiments reveal that this is a non-cell autonomous function, as a knockdown of dBACE in photoreceptor neurons leads to progressive degeneration of glia in their target zone, the lamina. Interestingly, this phenotype is suppressed by the loss of the fly amyloid precursor protein (APPL), whereas a secretion-deficient form of APPL enhances the degeneration. This shows that full-length APPL in neurons promotes the death of neighboring glial cells and that β-processing of APPL is needed to prevent glial death. These results therefore not only demonstrate a novel function for an APP protein in glia, but they also show this function specifically requires regulation by β-cleavage.

}, keywords = {Amyloid beta-Protein Precursor, Amyloid Precursor Protein Secretases, Animals, Axons, Blotting, Western, Cell Death, Cell Movement, Cell Survival, Drosophila, Immunohistochemistry, Microscopy, Electron, Neuregulins, Neuroglia, Polymerase Chain Reaction, Retina, RNA, RNA Interference, Vacuoles}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0228-12.2012}, author = {Bolkan, Bonnie J and Triphan, Tilman and Kretzschmar, Doris} } @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 {5311, title = {The BTB/POZ zinc finger protein Broad-Z3 promotes dendritic outgrowth during metamorphic remodeling of the peripheral stretch receptor dbd.}, journal = {Neural Development}, volume = {6}, year = {2011}, month = {2011 Dec 12}, pages = {39}, abstract = {

Various members of the family of BTB/POZ zinc-finger transcription factors influence patterns of dendritic branching. One such member, Broad, is notable because its BrZ3 isoform is widely expressed in Drosophila in immature neurons around the time of arbor outgrowth. We used the metamorphic remodeling of an identified sensory neuron, the dorsal bipolar dendrite sensory neuron (dbd), to examine the effects of BrZ3 expression on the extent and pattern of dendrite growth during metamorphosis.

}, keywords = {Animals, Biological, Dendrites, Drosophila, Drosophila Proteins, Growth Cones, Mechanoreceptors, Metamorphosis, Neurons, Transcription Factors, Zinc Fingers}, issn = {1749-8104}, doi = {10.1186/1749-8104-6-39}, author = {Scott, Janet A and Williams, Darren W and Truman, James W} } @article {47221, title = {Cellular-resolution population imaging reveals robust sparse coding in the Drosophila mushroom body.}, journal = {The Journal of Neuroscience : the official journal of the Society for Neuroscience}, volume = {31}, year = {2011}, month = {2011 Aug 17}, pages = {11772-85}, abstract = {

Sensory stimuli are represented in the brain by the activity of populations of neurons. In most biological systems, studying population coding is challenging since only a tiny proportion of cells can be recorded simultaneously. Here we used two-photon imaging to record neural activity in the relatively simple Drosophila mushroom body (MB), an area involved in olfactory learning and memory. Using the highly sensitive calcium indicator GCaMP3, we simultaneously monitored the activity of \>100 MB neurons in vivo (\~{}5\% of the total population). The MB is thought to encode odors in sparse patterns of activity, but the code has yet to be explored either on a population level or with a wide variety of stimuli. We therefore imaged responses to odors chosen to evaluate the robustness of sparse representations. Different odors activated distinct patterns of MB neurons; however, we found no evidence for spatial organization of neurons by either response probability or odor tuning within the cell body layer. The degree of sparseness was consistent across a wide range of stimuli, from monomolecular odors to artificial blends and even complex natural smells. Sparseness was mainly invariant across concentrations, largely because of the influence of recent odor experience. Finally, in contrast to sensory processing in other systems, no response features distinguished natural stimuli from monomolecular odors. Our results indicate that the fundamental feature of odor processing in the MB is to create sparse stimulus representations in a format that facilitates arbitrary associations between odor and punishment or reward.

}, keywords = {Animals, Animals, Genetically Modified, Diagnostic Imaging, Drosophila, Microscopy, Fluorescence, Multiphoton, Mushroom Bodies, Odors, Olfactory Pathways, Olfactory Receptor Neurons, Random Allocation, Smell}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.1099-11.2011}, author = {Honegger, Kyle S and Campbell, Robert A A and Turner, Glenn C} } @article {4070, title = {A computational statistics approach for estimating the spatial range of morphogen gradients.}, journal = {Development}, volume = {138}, year = {2011}, month = {2011 Nov}, pages = {4867-74}, abstract = {

A crucial issue in studies of morphogen gradients relates to their range: the distance over which they can act as direct regulators of cell signaling, gene expression and cell differentiation. To address this, we present a straightforward statistical framework that can be used in multiple developmental systems. We illustrate the developed approach by providing a point estimate and confidence interval for the spatial range of the graded distribution of nuclear Dorsal, a transcription factor that controls the dorsoventral pattern of the Drosophila embryo.

}, issn = {1477-9129}, doi = {10.1242/dev.071571}, author = {Kanodia, Jitendra S and Kim, Yoosik and Tomer, Raju and Khan, Zia and Chung, Kwanghun and Storey, John D and Lu, Hang and Keller, Philipp J and Shvartsman, Stansilas Y} } @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 {2384, title = {Core promoter recognition complex changes accompany liver development.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, year = {2011}, month = {2011 Mar 8}, pages = {3906-11}, abstract = {

Recent studies of several key developmental transitions have brought into question the long held view of the basal transcriptional apparatus as ubiquitous and invariant. In an effort to better understand the role of core promoter recognition and coactivator complex switching in cellular differentiation, we have examined changes in transcription factor IID (TFIID) and cofactor required for Sp1 activation/Mediator during mouse liver development. Here we show that the differentiation of fetal liver progenitors to adult hepatocytes involves a wholesale depletion of canonical cofactor required for Sp1 activation/Mediator and TFIID complexes at both the RNA and protein level, and that this alteration likely involves silencing of transcription factor promoters as well as protein degradation. It will be intriguing for future studies to determine if a novel and as yet unknown core promoter recognition complex takes the place of TFIID in adult hepatocytes and to uncover the mechanisms that down-regulate TFIID during this critical developmental transition.

}, issn = {1091-6490}, doi = {10.1073/pnas.1100640108}, author = {D{\textquoteright}Alessio, Joseph A and Ng, Raymond and Willenbring, Holger and Tjian, Robert} } @article {46050, title = {Distinct functions of kainate receptors in the brain are determined by the auxiliary subunit Neto1.}, journal = {Nature Neuroscience}, volume = {14}, year = {2011}, month = {2011 Jul}, pages = {866-73}, abstract = {

Ionotropic glutamate receptors principally mediate fast excitatory transmission in the brain. Among the three classes of ionotropic glutamate receptors, kainate receptors (KARs) have a unique brain distribution, which has been historically defined by (3)H-radiolabeled kainate binding. Compared with recombinant KARs expressed in heterologous cells, synaptic KARs exhibit characteristically slow rise-time and decay kinetics. However, the mechanisms responsible for these distinct KAR properties remain unclear. We found that both the high-affinity binding pattern in the mouse brain and the channel properties of native KARs are determined by the KAR auxiliary subunit Neto1. Through modulation of agonist binding affinity and off-kinetics of KARs, but not trafficking of KARs, Neto1 determined both the KAR high-affinity binding pattern and the distinctively slow kinetics of postsynaptic KARs. By regulating KAR excitatory postsynaptic current kinetics, Neto1 can control synaptic temporal summation, spike generation and fidelity.

}, keywords = {Animals, Animals, Newborn, Biophysical Phenomena, Biophysics, CA1 Region, Hippocampal, Cell Line, Transformed, Cerebellum, Dizocilpine Maleate, Dose-Response Relationship, Drug, Drug Interactions, Electric Stimulation, Excitatory Amino Acid Agonists, Excitatory Amino Acid Antagonists, Excitatory Postsynaptic Potentials, Gene Expression Regulation, Green Fluorescent Proteins, Guanylate Kinase, Humans, Immunoprecipitation, In Vitro Techniques, Intracellular Signaling Peptides and Proteins, Kainic Acid, Lipoproteins, LDL, Membrane Potentials, Membrane Proteins, Mice, Mice, Knockout, Neurons, Patch-Clamp Techniques, Presynaptic Terminals, Protein Binding, Protein Subunits, Receptors, Kainic Acid, Synaptophysin, Transfection, Tritium}, issn = {1546-1726}, doi = {10.1038/nn.2837}, author = {Straub, Christoph and Hunt, David L and Yamasaki, Miwako and Kim, Kwang S and Watanabe, Masahiko and Castillo, Pablo E and Tomita, Susumu} } @article {4525, title = {Drosophila tao controls mushroom body development and ethanol-stimulated behavior through par-1.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {31}, year = {2011}, month = {2011 Jan 19}, pages = {1139-48}, abstract = {

In both mammalian and insect models of ethanol-induced behavior, low doses of ethanol stimulate locomotion. However, the mechanisms of the stimulant effects of ethanol on the CNS are mostly unknown. We have identified tao, encoding a serine-threonine kinase of the Ste20 family, as a gene necessary for ethanol-induced locomotor hyperactivity in Drosophila. Mutations in tao also affect behavioral responses to cocaine and nicotine, making flies resistant to the effects of both drugs. We show that tao function is required during the development of the adult nervous system and that tao mutations cause defects in the development of central brain structures, including the mushroom body. Silencing of a subset of mushroom body neurons is sufficient to reduce ethanol-induced hyperactivity, revealing the mushroom body as an important locus mediating the stimulant effects of ethanol. We also show that mutations in par-1 suppress both the mushroom body morphology and behavioral phenotypes of tao mutations and that the phosphorylation state of the microtubule-binding protein Tau can be altered by RNA interference knockdown of tao, suggesting that tao and par-1 act in a pathway to control microtubule dynamics during neural development.

}, keywords = {Analysis of Variance, Animal, Animals, Behavior, Biological, Blotting, Drosophila, Drosophila Proteins, Ethanol, Hyperkinesis, Immunohistochemistry, Metamorphosis, Motor Activity, Mushroom Bodies, Neurons, Protein-Serine-Threonine Kinases, Western}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4416-10.2011}, author = {King, Ian and Tsai, Linus T-Y and Pflanz, Ralf and Voigt, Aaron and Lee, Seongsoo and J{\"a}ckle, Herbert and Lu, Bingwei and Heberlein, Ulrike} } @article {4389, title = {Facile and general synthesis of photoactivatable xanthene dyes.}, journal = {Angewandte Chemie}, volume = {50}, year = {2011}, month = {2011 Nov 18}, pages = {11206-9}, abstract = {

Despite the apparent simplicity of the xanthene fluorophores, the preparation of caged derivatives with free carboxy groups remains a synthetic challenge. A straightforward and flexible strategy for preparing rhodamine and fluorescein derivatives was developed using reduced, {\textquotedblleft}leuco{\textquotedblright} intermediates.

}, issn = {1521-3773}, doi = {10.1002/anie.201104571}, author = {Wysocki, Laura M and Grimm, Jonathan B and Tkachuk, Ariana N and Brown, Timothy A and Betzig, Eric and Lavis, Luke D} } @article {3359, title = {Functional dissection of the neural substrates for sexual behaviors in Drosophila melanogaster.}, journal = {Genetics}, volume = {189}, year = {2011}, month = {2011 Jun 24}, pages = {195-211}, abstract = {

The male-specific Fruitless proteins (Fru(M)) act to establish the potential for male courtship behavior in Drosophila melanogaster and are expressed in small groups of neurons throughout the nervous system. We screened \ 1000 GAL4 lines, using assays for general courtship, male-male interactions, and male fertility to determine the phenotypes resulting from the GAL4 driven inhibition of Fru(M) expression in subsets of these neurons. A battery of secondary assays showed that the phenotypic classes of GAL4 lines could be divided into subgroups based on additional neurobiological and behavioral criteria. For example, in some lines restoration of Fru(M) expression in cholinergic neurons restores fertility or reduces male-male courtship. Persistent chains of males courting each other in some lines results from males courting both sexes indiscriminately whereas in other lines this phenotype result from apparent habituation deficits. Inhibition of ectopic Fru(M) expression in females, in populations of neurons where Fru(M) is necessary for male fertility, can rescue female infertility. To identify the neurons responsible for some of the observed behavioral alterations, we determined the overlap between the identified GAL4 lines and endogenous Fru(M) expression in lines with fertility defects. The GAL4 lines causing fertility defects generally had widespread overlap with Fru(M) expression in many regions of the nervous system suggesting likely redundant Fru(M)-expressing neuronal pathways capable of conferring male fertility. From associations between the screened behaviors, we propose a functional model for courtship initiation.

}, issn = {1943-2631}, doi = {10.1534/genetics.111.129940}, author = {Meissner, Geoffrey W and Manoli, Devanand S and Chavez, Jose F and Knapp, Jon-Michael and Lin, Tasha L and Stevens, Robin J and Mellert, David J and Tran, David H and Baker, Bruce S} } @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 {47222, title = {Heterotypic gap junctions between two neurons in the drosophila brain are critical for memory.}, journal = {Current Biology : CB}, volume = {21}, year = {2011}, month = {2011 May 24}, pages = {848-54}, abstract = {

Gap junctions play an important role in the regulation of neuronal metabolism and homeostasis by serving as connections that enable small molecules to pass between cells and synchronize activity between cells. Although recent studies have linked gap junctions to memory formation, it remains unclear how they contribute to this process. Gap junctions are hexameric hemichannels formed from the connexin and pannexin gene families in chordates and the innexin (inx) gene family in invertebrates. Here we show that two modulatory neurons, the anterior paired lateral (APL) neuron and the dorsal paired medial (DPM) neuron, form heterotypic gap junctions within the mushroom body (MB), a learning and memory center in the Drosophila brain. Using RNA interference-mediated knockdowns of inx7 and inx6 in the APL and DPM neurons, respectively, we found that flies showed normal olfactory associative learning and intact anesthesia-resistant memory (ARM) but failed to form anesthesia-sensitive memory (ASM). Our results reveal that the heterotypic gap junctions between the APL and DPM neurons are an essential part of the MB circuitry for memory formation, potentially constituting a recurrent neural network to stabilize ASM.

}, keywords = {Anesthesia, Animals, Animals, Genetically Modified, Connexins, Drosophila, Drosophila Proteins, Gap Junctions, Memory, Mushroom Bodies, Neurons, RNA Interference, Smell}, issn = {1879-0445}, doi = {10.1016/j.cub.2011.02.041}, author = {Wu, Chia-Lin and Shih, Meng-Fu Maxwell and Lai, Jason Sih-Yu and Yang, Hsun-Ti and Turner, Glenn C and Chen, Linyi and Chiang, Ann-Shyn} } @article {3930, title = {Imaging light responses of targeted neuron populations in the rodent retina.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {31}, year = {2011}, month = {2011 Feb 23}, pages = {2855-67}, abstract = {

Decoding the wiring diagram of the retina requires simultaneous observation of activity in identified neuron populations. Available recording methods are limited in their scope: electrodes can access only a small fraction of neurons at once, whereas synthetic fluorescent indicator dyes label tissue indiscriminately. Here, we describe a method for studying retinal circuitry at cellular and subcellular levels combining two-photon microscopy and a genetically encoded calcium indicator. Using specific viral and promoter constructs to drive expression of GCaMP3, we labeled all five major neuron classes in the adult mouse retina. Stimulus-evoked GCaMP3 responses as imaged by two-photon microscopy permitted functional cell type annotation. Fluorescence responses were similar to those measured with the small molecule dye OGB-1. Fluorescence intensity correlated linearly with spike rates \>10 spikes/s, and a significant change in fluorescence always reflected a significant change in spike firing rate. GCaMP3 expression had no apparent effect on neuronal function. Imaging at subcellular resolution showed compartment-specific calcium dynamics in multiple identified cell types.

}, keywords = {Action Potentials, Animals, Female, Inbred C57BL, Male, Mice, Neurons, Ocular, Organ Culture Techniques, Retina, Vision, Voltage-Sensitive Dye Imaging}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.6064-10.2011}, author = {Borghuis, Bart G and Tian, Lin and Xu, Ying and Nikonov, Sergei S and Vardi, Noga and Zemelman, Boris V and Looger, Loren L} } @article {46300, title = {Intracellular dynamics of virtual place cells.}, journal = {Neural Computation}, volume = {23}, year = {2011}, month = {2011 Mar}, pages = {651-5}, abstract = {

The pattern of spikes recorded from place cells in the rodent hippocampus is strongly modulated by both the spatial location in the environment and the theta rhythm. The phases of the spikes in the theta cycle advance during movement through the place field. Recently intracellular recordings from hippocampal neurons (Harvey, Collman, Dombeck, \& Tank, 2009 ) showed an increase in the amplitude of membrane potential oscillations inside the place field, which was interpreted as evidence that an intracellular mechanism caused phase precession. Here we show that an existing network model of the hippocampus (Tsodyks, Skaggs, Sejnowski, \& McNaughton, 1996 ) can equally reproduce this and other aspects of the intracellular recordings, which suggests that new experiments are needed to distinguish the contributions of intracellular and network mechanisms to phase precession.

}, issn = {1530-888X}, doi = {10.1162/NECO_a_00087}, author = {Romani, Sandro and Sejnowski, Terrence J and Tsodyks, Misha} } @article {4326, title = {Large-scale automated histology in the pursuit of connectomes.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {31}, year = {2011}, month = {2011 Nov 9}, pages = {16125-38}, abstract = {

How does the brain compute? Answering this question necessitates neuronal connectomes, annotated graphs of all synaptic connections within defined brain areas. Further, understanding the energetics of the brain{\textquoteright}s computations requires vascular graphs. The assembly of a connectome requires sensitive hardware tools to measure neuronal and neurovascular features in all three dimensions, as well as software and machine learning for data analysis and visualization. We present the state of the art on the reconstruction of circuits and vasculature that link brain anatomy and function. Analysis at the scale of tens of nanometers yields connections between identified neurons, while analysis at the micrometer scale yields probabilistic rules of connection between neurons and exact vascular connectivity.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4077-11.2011}, author = {Kleinfeld, David and Bharioke, Arjun and Blinder, Pablo and Bock, Davi D and Briggman, Kevin L and Chklovskii, Dmitri B and Denk, Winfried and Helmstaedter, Moritz and Kaufhold, John P and Lee, Wei-Chung Allen and Meyer, Hanno S and Micheva, Kristina D and Oberlaender, Marcel and Prohaska, Steffen and Reid, R Clay and Smith, Stephen J and Takemura, Shinya and Tsai, Philbert S and Sakmann, Bert} } @proceedings {46351, title = {Learning to Agglomerate Superpixel Hierarchies}, volume = {24}, year = {2011}, month = {12/2011}, publisher = {MIT Press}, address = {Granada, Spain}, abstract = {

An agglomerative clustering algorithm merges the most similar pair of clusters at every iteration. The function that evaluates similarity is traditionally hand- designed, but there has been recent interest in supervised or semisupervised settings in which ground-truth clustered data is available for training. Here we show how to train a similarity function by regarding it as the action-value function of a reinforcement learning problem. We apply this general method to segment images by clustering superpixels, an application that we call Learning to Agglomerate Superpixel Hierarchies (LASH). When applied to a challenging dataset of brain images from serial electron microscopy, LASH dramatically improved segmentation accuracy when clustering supervoxels generated by state of the boundary detection algorithms. The naive strategy of directly training only supervoxel similarities and applying single linkage clustering produced less improvement.

}, author = {Viren Jain and Srinivas C. Turaga and K Briggman and Moritz N. Helmstaedter and Winfried Denk and H. S. Seung} } @article {3846, title = {Learning to agglomerate superpixel hierarchies.}, journal = {Neural Information Processing Systems}, volume = {24}, year = {2011}, month = {2011}, pages = {648-56}, abstract = {

An agglomerative clustering algorithm merges the most similar pair of clusters at every iteration. The function that evaluates similarity is traditionally handdesigned, but there has been recent interest in supervised or semisupervised settings in which ground-truth clustered data is available for training. Here we show how to train a similarity function by regarding it as the action-value function of a reinforcement learning problem. We apply this general method to segment images by clustering superpixels, an application that we call Learning to Agglomerate Superpixel Hierarchies (LASH). When applied to a challenging dataset of brain images from serial electron microscopy, LASH dramatically improved segmentation accuracy when clustering supervoxels generated by state of the boundary detection algorithms. The naive strategy of directly training only supervoxel similarities and applying single linkage clustering produced less improvement.

}, author = {Jain, Viren and Turaga, Srinivas and Briggman, Kevin and Helmstaedter, Moritz N. and Denk, Winfried and Seung, Sebastian} } @article {46612, title = {Lmo genes regulate behavioral responses to ethanol in Drosophila melanogaster and the mouse.}, journal = {Alcoholism, Clinical and Experimental Research}, volume = {35}, year = {2011}, month = {2011 Sep}, pages = {1600-6}, abstract = {

BACKGROUND: Previous work from our laboratory demonstrated a role for the Drosophila Lim-only (dLmo) gene in regulating behavioral responses to cocaine. Herein, we examined whether dLmo influences the flies{\textquoteright} sensitivity to ethanol{\textquoteright}s sedating effects. We also investigated whether 1 of the mammalian homologs of dLmo, Lmo3, is involved in behavioral responses to ethanol in mice.

METHODS: To examine dLmo function in ethanol-induced sedation, mutant flies with reduced or increased dLmo expression were tested using the loss of righting (LOR) assay. To determine whether mouse Lmo3 regulates behavioral responses to ethanol, we generated transgenic mice expressing a short-hairpin RNA targeting Lmo3 for RNA interference-mediated knockdown by lentiviral infection of single cell embryos. Adult founder mice, expressing varying amounts of Lmo3 in the brain, were tested using ethanol loss-of-righting-reflex (LORR) and 2-bottle choice ethanol consumption assays.

RESULTS: We found that in flies, reduced dLmo activity increased sensitivity to ethanol-induced sedation, whereas increased expression of dLmo led to increased resistance to ethanol-induced sedation. In mice, reduced levels of Lmo3 were correlated with increased sedation time in the LORR test and decreased ethanol consumption in the 2-bottle choice protocol.

CONCLUSIONS: These data describe a novel and conserved role for Lmo genes in flies and mice in behavioral responses to ethanol. These studies also demonstrate the feasibility of rapidly translating findings from invertebrate systems to mammalian models of alcohol abuse by combining RNA interference in transgenic mice and behavioral testing.

}, keywords = {Adaptor Proteins, Signal Transducing, Animals, Behavior, Animal, Brain, Central Nervous System Depressants, Disease Models, Animal, Drosophila melanogaster, Drosophila Proteins, Ethanol, Female, Genotype, Green Fluorescent Proteins, Homeodomain Proteins, Hypnotics and Sedatives, LIM Domain Proteins, Male, Mice, Mice, Inbred C57BL, Mice, Transgenic, RNA, Small Interfering}, issn = {1530-0277}, doi = {10.1111/j.1530-0277.2011.01506.x}, author = {Lasek, Amy W and Giorgetti, Francesco and Berger, Karen H and Tayor, Stacy and Heberlein, Ulrike} } @article {5291, title = {Mushroom body efferent neurons responsible for aversive olfactory memory retrieval in Drosophila.}, journal = {Nature Neuroscience}, volume = {14}, year = {2011}, month = {2011 Jun 19}, pages = {903-10}, abstract = {

Aversive olfactory memory is formed in the mushroom bodies in Drosophila melanogaster. Memory retrieval requires mushroom body output, but the manner in which a memory trace in the mushroom body drives conditioned avoidance of a learned odor remains unknown. To identify neurons that are involved in olfactory memory retrieval, we performed an anatomical and functional screen of defined sets of mushroom body output neurons. We found that MB-V2 neurons were essential for retrieval of both short- and long-lasting memory, but not for memory formation or memory consolidation. MB-V2 neurons are cholinergic efferent neurons that project from the mushroom body vertical lobes to the middle superiormedial protocerebrum and the lateral horn. Notably, the odor response of MB-V2 neurons was modified after conditioning. As the lateral horn has been implicated in innate responses to repellent odorants, we propose that MB-V2 neurons recruit the olfactory pathway involved in innate odor avoidance during memory retrieval.

}, keywords = {Afferent Pathways, Analysis of Variance, Animal, Animals, Antigens, Avoidance Learning, Behavior, Biological, CD8, Choline O-Acetyltransferase, Conditioning (Psychology), Drosophila melanogaster, Drosophila Proteins, Gene Expression Regulation, Genetically Modified, Glutamate Decarboxylase, Green Fluorescent Proteins, Memory, Mental Recall, Models, Motor Neurons, Mushroom Bodies, Odors, Olfactory Pathways, Short-Term, Smell, Synapsins, Temperature, Time Factors, Transcription Factors, Tyrosine 3-Monooxygenase, Vesicular Glutamate Transport Proteins}, issn = {1546-1726}, doi = {10.1038/nn.2846}, author = {S{\'e}journ{\'e}, Julien and Placais, Pierre-Yves and Aso, Yoshinori and Siwanowicz, Igor and Trannoy, S{\'e}verine and Thoma, Vladimiros and Tedjakumala, Stevanus R and Rubin, Gerald M and Tch{\'e}nio, Paul and Ito, Kei and Isabel, Guillaume and Tanimoto, Hiromu and Preat, Thomas} } @article {3867, title = {Neural correlates of illusory motion perception in Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, year = {2011}, month = {2011 Jun 7}, pages = {9685-90}, abstract = {

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

}, keywords = {Algorithms, Animals, Dendrites, Drosophila melanogaster, Female, Humans, Male, Models, Motion, Motion Perception, Neural Pathways, Neurological, Neurons, Time Factors}, issn = {1091-6490}, doi = {10.1073/pnas.1100062108}, author = {Tuthill, John C and Chiappe, M Eugenia and Reiser, Michael B} } @article {3602, title = {Phase resolved interferometric spectral modulation (PRISM) for ultrafast pulse measurement and compression.}, journal = {Optics Express}, volume = {19}, year = {2011}, month = {2011 Jul 4}, pages = {12961-8}, abstract = {

We show through experiments and simulations that parallel phase modulation, a technique developed in the field of adaptive optics, can be employed to quickly determine the spectral phase profile of ultrafast laser pulses and to perform phase compensation as well as pulse shaping. Different from many existing ultrafast pulse measurement methods, the technique reported here requires no spectrum measurements of nonlinear signals. Instead, the power of nonlinear signals is used directly to quickly measure the spectral phase, a convenient feature for applications such as two-photon fluorescence microscopy. The method is found to work with both smooth and even completely random distortions. The experimental results are verified with MIIPS measurements.

}, issn = {1094-4087}, doi = {10.1364/OE.19.012961}, author = {Wu, Tsai-Wei and Tang, Jianyong and Hajj, Bassam and Cui, Meng} } @article {47673, title = {Principles and current strategies for targeting autophagy for cancer treatment.}, journal = {Clinical cancer research : an official journal of the American Association for Cancer Research}, volume = {17}, year = {2011}, month = {2011 Feb 15}, pages = {654-66}, abstract = {

Autophagy is an evolutionarily conserved, intracellular self-defense mechanism in which organelles and proteins are sequestered into autophagic vesicles that are subsequently degraded through fusion with lysosomes. Cells, thereby, prevent the toxic accumulation of damaged or unnecessary components, but also recycle these components to sustain metabolic homoeostasis. Heightened autophagy is a mechanism of resistance for cancer cells faced with metabolic and therapeutic stress, revealing opportunities for exploitation as a therapeutic target in cancer. We summarize recent developments in the field of autophagy and cancer and build upon the results presented at the Cancer Therapy Evaluation Program (CTEP) Early Drug Development meeting in March 2010. Herein, we describe our current understanding of the core components of the autophagy machinery and the functional relevance of autophagy within the tumor microenvironment, and we outline how this knowledge has informed preclinical investigations combining the autophagy inhibitor hydroxychloroquine (HCQ) with chemotherapy, targeted therapy, and immunotherapy. Finally, we describe ongoing clinical trials involving HCQ as a first generation autophagy inhibitor, as well as strategies for the development of novel, more potent, and specific inhibitors of autophagy.

}, keywords = {Animals, Antineoplastic Agents, Autophagy, Clinical Trials, Phase III as Topic, Combined Modality Therapy, Cytoplasmic Vesicles, Humans, Hydroxychloroquine, Immune Tolerance, Immunotherapy, Inflammation, Metabolic Networks and Pathways, Molecular Targeted Therapy, Neoplasms, Proteasome Endopeptidase Complex, Signal Transduction}, issn = {1078-0432}, doi = {10.1158/1078-0432.CCR-10-2634}, author = {Amaravadi, Ravi K and Lippincott-Schwartz, Jennifer and Yin, Xiao-Ming and Weiss, William A and Takebe, Naoko and Timmer, William and DiPaola, Robert S and Lotze, Michael T and White, Eileen} } @article {5383, title = {Probing tension and dynamics in actomyosin mediated cell shape change.}, journal = {Molecular Biology of the Cell}, volume = {22}, year = {2011}, month = {2011}, author = {Higgins, C. D. and Tulu, U. S. and Gao, L. and Betzig, E and Kiehart, D. P. and Goldstein, B.} } @article {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 {3684, title = {Shedding light on the system: studying embryonic development with light sheet microscopy.}, journal = {Current Opinion in Genetics and Development}, volume = {21}, year = {2011}, month = {2011 Aug}, pages = {558-65}, abstract = {

Light sheet-based fluorescence microscopy (LSFM) is emerging as a powerful imaging technique for the life sciences. LSFM provides an exceptionally high imaging speed, high signal-to-noise ratio, low level of photo-bleaching and good optical penetration depth. This unique combination of capabilities makes light sheet-based microscopes highly suitable for live imaging applications. There is an outstanding potential in applying this technology to the quantitative study of embryonic development. Here, we provide an overview of the different basic implementations of LSFM, review recent technical advances in the field and highlight applications in the context of embryonic development. We conclude with a discussion of promising future directions.

}, issn = {1879-0380}, doi = {10.1016/j.gde.2011.07.003}, author = {Tomer, Raju and Khairy, Khaled and Keller, Philipp J} } @article {46734, title = {Single-molecule mRNA decay measurements reveal promoter- regulated mRNA stability in yeast.}, journal = {Cell}, volume = {147}, year = {2011}, month = {2011 Dec 23}, pages = {1484-97}, abstract = {

Messenger RNA decay measurements are typically performed on a population of cells. However, this approach cannot reveal sufficient complexity to provide information on mechanisms that may regulate mRNA degradation, possibly on short timescales. To address this deficiency, we measured cell cycle-regulated decay in single yeast cells using single-molecule FISH. We found that two genes responsible for mitotic progression, SWI5 and CLB2, exhibit a mitosis-dependent mRNA stability switch. Their transcripts are stable until mitosis, when a precipitous decay eliminates the mRNA complement, preventing carryover into the next cycle. Remarkably, the specificity and timing of decay is entirely regulated by their promoter, independent of specific cis mRNA sequences. The mitotic exit network protein Dbf2p binds to SWI5 and CLB2 mRNAs cotranscriptionally and regulates their decay. This work reveals the promoter-dependent control of mRNA stability, a regulatory mechanism that could be employed by a variety of mRNAs and organisms.

}, keywords = {Cell Cycle, Cell Cycle Proteins, Cyclin B, Gene Expression Regulation, Fungal, In Situ Hybridization, Fluorescence, Kinetics, Promoter Regions, Genetic, Protein-Serine-Threonine Kinases, RNA Stability, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Transcription Factors, Transcription, Genetic}, issn = {1097-4172}, doi = {10.1016/j.cell.2011.11.051}, author = {Trcek, Tatjana and Larson, Daniel R and Mold{\'o}n, Alberto and Query, Charles C and Singer, Robert H} } @article {5307, title = {Sub-nuclear compartmentalization of core promoter factors and target genes.}, journal = {Cell Cycle}, volume = {10}, year = {2011}, month = {2011 Aug 1}, pages = {2405-6}, issn = {1551-4005}, author = {Yao, Jie and Tjian, Robert} } @article {2385, title = {Subnuclear segregation of genes and core promoter factors in myogenesis. (With commentary)}, journal = {Genes \& Development}, volume = {25}, year = {2011}, month = {2011 Mar 15}, pages = {569-80}, abstract = {

Recent findings implicate alternate core promoter recognition complexes in regulating cellular differentiation. Here we report a spatial segregation of the alternative core factor TAF3, but not canonical TFIID subunits, away from the nuclear periphery, where the key myogenic gene MyoD is preferentially localized in myoblasts. This segregation is correlated with the differential occupancy of TAF3 versus TFIID at the MyoD promoter. Loss of this segregation by modulating either the intranuclear location of the MyoD gene or TAF3 protein leads to altered TAF3 occupancy at the MyoD promoter. Intriguingly, in differentiated myotubes, the MyoD gene is repositioned to the nuclear interior, where TAF3 resides. The specific high-affinity recognition of H3K4Me3 by the TAF3 PHD (plant homeodomain) finger appears to be required for the sequestration of TAF3 to the nuclear interior. We suggest that intranuclear sequestration of core transcription components and their target genes provides an additional mechanism for promoter selectivity during differentiation.

Commentary: Jie Yao in Bob Tijan{\textquoteright}s lab used a combination of confocal microscopy and dual label PALM in thin sections cut from resin-embedded cells to show that certain core transcription components and their target genes are spatially segregated in myoblasts, but not in differentiated myotubes, suggesting that such spatial segregation may play a role in guiding cellular differentiation.

}, issn = {1549-5477}, doi = {10.1073/pnas.1100640108}, author = {Yao, Jie and Fetter, Richard D and Hu, Ping and Betzig, Eric and Tjian, Robert} } @article {4469, title = {Superresolution fluorescence imaging of mitochondrial nucleoids reveals their spatial range, limits, and membrane interaction.}, journal = {Molecular and Cellular Biology}, volume = {31}, year = {2011}, month = {2011 Dec}, pages = {4994-5010}, abstract = {

A fundamental objective in molecular biology is to understand how DNA is organized in concert with various proteins, RNA, and biological membranes. Mitochondria maintain and express their own DNA (mtDNA), which is arranged within structures called nucleoids. Their functions, dimensions, composition, and precise locations relative to other mitochondrial structures are poorly defined. Superresolution fluorescence microscopy techniques that exceed the previous limits of imaging within the small and highly compartmentalized mitochondria have been recently developed. We have improved and employed both two- and three-dimensional applications of photoactivated localization microscopy (PALM and iPALM, respectively) to visualize the core dimensions and relative locations of mitochondrial nucleoids at an unprecedented resolution. PALM reveals that nucleoids differ greatly in size and shape. Three-dimensional volumetric analysis indicates that, on average, the mtDNA within ellipsoidal nucleoids is extraordinarily condensed. Two-color PALM shows that the freely diffusible mitochondrial matrix protein is largely excluded from the nucleoid. In contrast, nucleoids are closely associated with the inner membrane and often appear to be wrapped around cristae or crista-like inner membrane invaginations. Determinations revealing high packing density, separation from the matrix, and tight association with the inner membrane underscore the role of mechanisms that regulate access to mtDNA and that remain largely unknown.

}, keywords = {3T3 Cells, Animals, Confocal, DNA, Fluorescence, Mice, Microscopy, Mitochondria, Mitochondrial, Mitochondrial Proteins, Plasmids, Sequence Alignment, Sequence Analysis}, issn = {1098-5549}, doi = {10.1128/MCB.05694-11}, url = {http://mcb.asm.org/content/31/24/4994.short}, author = {Brown, Timothy A and Tkachuk, Ariana N and Shtengel, Gleb and Kopek, Benjamin G and Bogenhagen, Daniel F and Hess, Harald F and Clayton, David A} } @article {4327, title = {Wiring economy and volume exclusion determine neuronal placement in the Drosophila brain.}, journal = {Current Biology}, volume = {21}, year = {2011}, month = {2011 Dec}, pages = {2000-5}, abstract = {

Wiring economy has successfully explained the individual placement of neurons in simple nervous systems like that of Caenorhabditis elegans [1-3] and the locations of coarser structures like cortical areas in complex vertebrate brains [4]. However, it remains unclear whether wiring economy can explain the placement of individual neurons in brains larger than that of C.\ elegans. Indeed, given the greater number of neuronal interconnections in larger brains, simply minimizing the length of connections results in unrealistic configurations, with multiple neurons occupying the same position in space. Avoiding such configurations, or volume exclusion, repels neurons from each other, thus counteracting wiring economy. Here we test whether wiring economy together with volume exclusion can explain the placement of neurons in a module of the Drosophila melanogaster brain known as lamina cartridge [5-13]. We used newly developed techniques for semiautomated reconstruction from serial electron microscopy (EM) [14] to obtain the shapes of neurons, the location of synapses, and the resultant synaptic connectivity. We show that wiring length minimization and volume exclusion together can explain the structure of the lamina microcircuit. Therefore, even in brains larger than that of C.\ elegans, at least for some circuits, optimization can play an important role in individual neuron placement.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2011.10.022}, author = {Rivera-Alba, Marta and Vitaladevuni, Shiv N. and Mischenko, Yuriy and Lu, Zhiyuan and Takemura, Shin-ya and Scheffer, Lou and Meinertzhagen, Ian and Chklovskii, Dmitri and Polavieja, Gonzalo} } @article {2686, title = {Appetitive and aversive visual learning in freely moving Drosophila.}, journal = {Frontiers in Behavioral Neuroscience}, volume = {4}, year = {2010}, month = {2010 Mar 9}, pages = {10}, abstract = {

To compare appetitive and aversive visual memories of the fruit fly Drosophila melanogaster, we developed a new paradigm for classical conditioning. Adult flies are trained en masse to differentially associate one of two visual conditioned stimuli (CS) (blue and green light as CS) with an appetitive or aversive chemical substance (unconditioned stimulus or US). In a test phase, flies are given a choice between the paired and the unpaired visual stimuli. Associative memory is measured based on altered visual preference in the test. If a group of flies has, for example, received a sugar reward with green light in the training, they show a significantly higher preference for the green stimulus during the test than another group of flies having received the same reward with blue light. We demonstrate critical parameters for the formation of visual appetitive memory, such as training repetition, order of reinforcement, starvation, and individual conditioning. Furthermore, we show that formic acid can act as an aversive chemical reinforcer, yielding weak, yet significant, aversive memory. These results provide a basis for future investigations into the cellular and molecular mechanisms underlying visual memory and perception in Drosophila.

}, issn = {1662-5153}, doi = {10.3389/fnbeh.2010.00010}, author = {Schnaitmann, Christopher and Vogt, Katrin and Triphan, Tilman and Tanimoto, Hiromu} } @article {1160, title = {Approaches toward super-resolution fluorescence imaging of mitochondrial proteins using PALM.}, journal = {Methods}, volume = {51}, year = {2010}, month = {2010 Aug}, pages = {458-63}, abstract = {

Mitochondria are difficult targets for microscopy because of their small size and highly compartmentalized, membranous interior. Super-resolution fluorescence microscopy methods have recently been developed that exceed the historical limits of optical imaging. Here we outline considerations and techniques in preparing to image the relative location of mitochondrial proteins using photoactivated localization microscopy (PALM). PALM and similar methods have the capacity to dramatically increase our ability to image proteins within mitochondria, and to expand our knowledge of the location of macromolecules beyond the current limits of immunoEM.

}, keywords = {Animals, Cryoultramicrotomy, Fluorescence, Freeze Substitution, Genetic, Luminescent Proteins, Mice, Microscopy, Mitochondria, Mitochondrial Proteins, NIH 3T3 Cells, Plastic Embedding, Promoter Regions, Recombinant Fusion Proteins, Transfection}, issn = {1095-9130}, doi = {10.1016/j.ymeth.2010.01.001}, author = {Brown, Timothy A and Fetter, Richard D and Tkachuk, Ariana N and Clayton, David A} } @article {5690, title = {As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets.}, journal = {Bioinformatics}, volume = {26}, year = {2010}, month = {2010 Jun 15}, pages = {i57-63}, abstract = {

Tiled serial section Transmission Electron Microscopy (ssTEM) is increasingly used to describe high-resolution anatomy of large biological specimens. In particular in neurobiology, TEM is indispensable for analysis of synaptic connectivity in the brain. Registration of ssTEM image mosaics has to recover the 3D continuity and geometrical properties of the specimen in presence of various distortions that are applied to the tissue during sectioning, staining and imaging. These include staining artifacts, mechanical deformation, missing sections and the fact that structures may appear dissimilar in consecutive sections.

}, keywords = {Animals, Databases, Drosophila, Electron, Factual, Imaging, Microscopy, Three-Dimensional, Transmission}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btq219}, author = {Saalfeld, Stephan and Cardona, Albert and Hartenstein, Volker and Tomancak, Pavel.} } @conference {3858, title = {Boundary learning by optimization with topological constraints.}, booktitle = {IEEE Conference on Computer Vision and Pattern Recognition}, year = {2010}, month = {2010}, abstract = {

Recent studies have shown that machine learning can improve the accuracy of detecting object boundaries in images. In the standard approach, a boundary detector is trained by minimizing its pixel-level disagreement with human boundary tracings. This naive metric is problematic because it is overly sensitive to boundary locations. This problem is solved by metrics provided with the Berkeley Segmentation Dataset, but these can be insensitive to topological differences, such as gaps in boundaries. Furthermore, the Berkeley metrics have not been useful as cost functions for supervised learning. Using concepts from digital topology, we propose a new metric called the warping error that tolerates disagreements over boundary location, penalizes topological disagreements, and can be used directly as a cost function for learning boundary detection, in a method that we call Boundary Learning by Optimization with Topological Constraints (BLOTC). We trained boundary detectors on electron microscopic images of neurons, using both BLOTC and standard training. BLOTC produced substantially better performance on a 1.2 million pixel test set, as measured by both the warping error and the Rand index evaluated on segmentations generated from the boundary labelings. We also find our approach yields significantly better segmentation performance than either gPb-OWT-UCM or multiscale normalized cut, as well as Boosted Edge Learning trained directly on our data.

}, author = {Jain, Viren and Bollmann, Benjamin and Richardson, Mark and Berger, Daniel R. and Helmstaedter, Moritz N. and Briggman, Kevin L and Denk, Winfried and Bowden, Jared B. and Mendenhall, John M. and Abraham, Wickliffe C. and Harris, Kristen M and Kasthuri, Narayanan and Hayworth, Ken J. and Schalek, Richard and Tapia, Juan Carlos and Lichtman, Jeff W. and Seung, Hyunjune Sebastian} } @article {46301, title = {Continuous attractors with morphed/correlated maps.}, journal = {PLoS Computational Biology}, volume = {6}, year = {2010}, month = {2010 Aug 5}, pages = {e1000869}, abstract = {

Continuous attractor networks are used to model the storage and representation of analog quantities, such as position of a visual stimulus. The storage of multiple continuous attractors in the same network has previously been studied in the context of self-position coding. Several uncorrelated maps of environments are stored in the synaptic connections, and a position in a given environment is represented by a localized pattern of neural activity in the corresponding map, driven by a spatially tuned input. Here we analyze networks storing a pair of correlated maps, or a morph sequence between two uncorrelated maps. We find a novel state in which the network activity is simultaneously localized in both maps. In this state, a fixed cue presented to the network does not determine uniquely the location of the bump, i.e. the response is unreliable, with neurons not always responding when their preferred input is present. When the tuned input varies smoothly in time, the neuronal responses become reliable and selective for the environment: the subset of neurons responsive to a moving input in one map changes almost completely in the other map. This form of remapping is a non-trivial transformation between the tuned input to the network and the resulting tuning curves of the neurons. The new state of the network could be related to the formation of direction selectivity in one-dimensional environments and hippocampal remapping. The applicability of the model is not confined to self-position representations; we show an instance of the network solving a simple delayed discrimination task.

}, keywords = {Animals, Computer Simulation, Discrimination (Psychology), Hippocampus, Models, Biological, Neural Networks (Computer), Numerical Analysis, Computer-Assisted}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1000869}, author = {Romani, Sandro and Tsodyks, Misha} } @article {3844, title = {Convolutional networks can learn to generate affinity graphs for image segmentation.}, journal = {Neural Computation}, volume = {22}, year = {2010}, month = {2010 Feb}, pages = {511-38}, abstract = {

Many image segmentation algorithms first generate an affinity graph and then partition it. We present a machine learning approach to computing an affinity graph using a convolutional network (CN) trained using ground truth provided by human experts. The CN affinity graph can be paired with any standard partitioning algorithm and improves segmentation accuracy significantly compared to standard hand-designed affinity functions. We apply our algorithm to the challenging 3D segmentation problem of reconstructing neuronal processes from volumetric electron microscopy (EM) and show that we are able to learn a good affinity graph directly from the raw EM images. Further, we show that our affinity graph improves the segmentation accuracy of both simple and sophisticated graph partitioning algorithms. In contrast to previous work, we do not rely on prior knowledge in the form of hand-designed image features or image preprocessing. Thus, we expect our algorithm to generalize effectively to arbitrary image types.

}, keywords = {Algorithms, Artificial Intelligence, Automated, Computer-Assisted, Electron, Image Processing, Mathematical Computing, Mathematical Concepts, Mathematics, Microscopy, Neural Networks (Computer), Pattern Recognition}, issn = {1530-888X}, doi = {10.1162/neco.2009.10-08-881}, author = {Turaga, Srinivas C and Murray, Joseph F and Jain, Viren and Roth, Fabian and Helmstaedter, Moritz and Briggman, Kevin and Denk, Winfried and Seung, Hyunjune Sebastian} } @article {3636, title = {Cooperation of the Dam1 and Ndc80 kinetochore complexes enhances microtubule coupling and is regulated by aurora B.}, journal = {The Journal of Cell Biology}, volume = {189}, year = {2010}, month = {2010 May 17}, pages = {713-23}, abstract = {

The coupling of kinetochores to dynamic spindle microtubules is crucial for chromosome positioning and segregation, error correction, and cell cycle progression. How these fundamental attachments are made and persist under tensile forces from the spindle remain important questions. As microtubule-binding elements, the budding yeast Ndc80 and Dam1 kinetochore complexes are essential and not redundant, but their distinct contributions are unknown. In this study, we show that the Dam1 complex is a processivity factor for the Ndc80 complex, enhancing the ability of the Ndc80 complex to form load-bearing attachments to and track with dynamic microtubule tips in vitro. Moreover, the interaction between the Ndc80 and Dam1 complexes is abolished when the Dam1 complex is phosphorylated by the yeast aurora B kinase Ipl1. This provides evidence for a mechanism by which aurora B resets aberrant kinetochore-microtubule attachments. We propose that the action of the Dam1 complex as a processivity factor in kinetochore-microtubule attachment is regulated by conserved signals for error correction.

}, keywords = {Cell Cycle Proteins, Green Fluorescent Proteins, Kinetochores, Microtubule-Associated Proteins, Microtubules, Mitotic Spindle Apparatus, Nuclear Proteins, Protein-Serine-Threonine Kinases, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins}, issn = {1540-8140}, doi = {10.1083/jcb.200910142}, author = {Tien, Jerry F and Umbreit, Neil T and Gestaut, Daniel R and Franck, Andrew D and Cooper, Jeremy and Wordeman, Linda and Gonen, Tamir and Asbury, Charles L and Davis, Trisha N} } @article {1449, title = {Cortical representations of olfactory input by trans-synaptic tracing.}, journal = {Nature}, volume = {472}, year = {2010}, month = {2010 Dec 22}, pages = {191-6}, abstract = {

In the mouse, each class of olfactory receptor neurons expressing a given odorant receptor has convergent axonal projections to two specific glomeruli in the olfactory bulb, thereby creating an odour map. However, it is unclear how this map is represented in the olfactory cortex. Here we combine rabies-virus-dependent retrograde mono-trans-synaptic labelling with genetics to control the location, number and type of {\textquoteright}starter{\textquoteright} cortical neurons, from which we trace their presynaptic neurons. We find that individual cortical neurons receive input from multiple mitral cells representing broadly distributed glomeruli. Different cortical areas represent the olfactory bulb input differently. For example, the cortical amygdala preferentially receives dorsal olfactory bulb input, whereas the piriform cortex samples the whole olfactory bulb without obvious bias. These differences probably reflect different functions of these cortical areas in mediating innate odour preference or associative memory. The trans-synaptic labelling method described here should be widely applicable to mapping connections throughout the mouse nervous system.

}, issn = {1476-4687}, doi = {10.1038/nature09714}, author = {Miyamichi, Kazunari and Amat, Fernando and Moussavi, Farshid and Wang, Chen and Wickersham, Ian and Wall, Nicholas R and Taniguchi, Hiroki and Tasic, Bosiljka and Huang, Z Josh and He, Zhigang and Callaway, Edward M and Horowitz, Mark A and Luo, Liqun} } @article {6386, title = {Droplet confinement and fluorescence measurement of single molecules.}, journal = {Methods in Enzymology}, volume = {472}, year = {2010}, month = {2010}, pages = {61-88}, abstract = {

We describe a method for molecular confinement and single-fluorophore sensitive measurement in aqueous nanodroplets in oil. The sequestration of individual molecules in droplets has become a useful tool in genomics and molecular evolution. Similarly, the use of single fluorophores, or pairs of fluorophores, to study biomolecular interactions and structural dynamics is now common. Most often these single-fluorophore sensitive measurements are performed on molecules that are surface attached. Confinement via surface attachment permits molecules to be located and studied for a prolonged period of time. For molecules that denature on surfaces, for interactions that are transient or out-of-equilibrium, or to observe the dynamic equilibrium of freely diffusing reagents, surface attachment may not be an option. In these cases, droplet confinement presents an alternative method for molecular confinement. Here, we describe this method as used in single-fluorophore sensitive measurement and discuss its advantages, limitations, and future prospects.

}, keywords = {Diffusion, Electrochemical Techniques, Emulsions, Fluorescence, Fluorescent Dyes, Microfluidics, Nanostructures, Oils, Optical Tweezers, Spectrometry, Water}, issn = {1557-7988}, doi = {10.1016/S0076-6879(10)72015-2}, author = {Goldner, Lori S and Jofre, Ana M and Tang, Jianyong} } @article {3634, title = {An engineered DNA-binding protein self-assembles metallic nanostructures.}, journal = {Chembiochem: A European Journal of Chemical Biology}, volume = {11}, year = {2010}, month = {2010 Oct 18}, pages = {2108-12}, abstract = {

The golden age of DNA: We describe a strategy for engineering bifunctional proteins that simultaneously associate with metals and DNA to create self-assembled nanostructures. A DNA binding protein engineered with a gold binding peptide arranges colloidal gold particles along a DNA guide by virtue of its introduced peptide motif. These self-assembled complexes represent a step toward constructing nanoarchitectures with potential in nanoelectronic and photonic devices.

}, keywords = {Amino Acid Sequence, DNA, DNA Helicases, Escherichia coli Proteins, Gold, Nanostructures, Nucleic Acid Conformation, Peptide Library, Peptides, Protein Binding, Protein Engineering, Single-Stranded}, issn = {1439-7633}, doi = {10.1002/cbic.201000407}, author = {Hall Sedlak, Ruth and Hnilova, Marketa and Gachelet, Eliora and Przybyla, Laralynne and Dranow, David and Gonen, Tamir and Sarikaya, Mehmet and Tamerler, Candan and Traxler, Beth} } @article {2326, title = {Error tolerant indexing and alignment of short reads with covering template families.}, journal = {Journal of Computational Biology: A Journal of Computational Molecular Cell Biology}, volume = {17}, year = {2010}, month = {2010 Oct}, pages = {1397-1411}, abstract = {

The rapid adoption of high-throughput next generation sequence data in biological research is presenting a major challenge for sequence alignment tools{\textemdash}specifically, the efficient alignment of vast amounts of short reads to large references in the presence of differences arising from sequencing errors and biological sequence variations. To address this challenge, we developed a short read aligner for high-throughput sequencer data that is tolerant of errors or mutations of all types{\textemdash}namely, substitutions, deletions, and insertions. The aligner utilizes a multi-stage approach in which template-based indexing is used to identify candidate regions for alignment with dynamic programming. A template is a pair of gapped seeds, with one used with the read and one used with the reference. In this article, we focus on the development of template families that yield error-tolerant indexing up to a given error-budget. A general algorithm for finding those families is presented, and a recursive construction that creates families with higher error tolerance from ones with a lower error tolerance is developed.

}, keywords = {Algorithms, Base Sequence, DNA, Genetic, Molecular Sequence Data, Sequence Alignment, Sequence Analysis, Software, Templates}, issn = {1557-8666}, doi = {10.1089/cmb.2010.0005}, author = {Giladi, Eldar and Healy, John and Myers, Gene and Hart, Chris and Kapranov, Philipp and Lipson, Doron and Roels, Steve and Thayer, Edward and Letovsky, Stan} } @article {4369, title = {Filtering of visual information in the tectum by an identified neural circuit.}, journal = {Science}, volume = {330}, year = {2010}, month = {2010 Oct 29}, pages = {669-73}, abstract = {

The optic tectum of zebrafish is involved in behavioral responses that require the detection of small objects. The superficial layers of the tectal neuropil receive input from retinal axons, while its deeper layers convey the processed information to premotor areas. Imaging with a genetically encoded calcium indicator revealed that the deep layers, as well as the dendrites of single tectal neurons, are preferentially activated by small visual stimuli. This spatial filtering relies on GABAergic interneurons (using the neurotransmitter γ-aminobutyric acid) that are located in the superficial input layer and respond only to large visual stimuli. Photo-ablation of these cells with KillerRed, or silencing of their synaptic transmission, eliminates the size tuning of deeper layers and impairs the capture of prey.

}, keywords = {Animals, Axons, Bicuculline, Dendrites, GABA Antagonists, gamma-Aminobutyric Acid, Genetically Modified, Interneurons, Neural Inhibition, Neurons, Neuropil, Nonmammalian, Optic Lobe, Photic Stimulation, Retina, Retinal Neurons, Synaptic Transmission, Visual Pathways, Visual Perception, Zebrafish}, issn = {1095-9203}, doi = {10.1126/science.1192949}, author = {Del Bene, Filippo and Wyart, Claire and Robles, Estuardo and Tran, Amanda and Looger, Loren and Scott, Ethan K and Isacoff, Ehud Y and Baier, Herwig} } @article {3931, title = {Functional imaging of hippocampal place cells at cellular resolution during virtual navigation.}, journal = {Nature Neuroscience}, volume = {13}, year = {2010}, month = {2010 Nov}, pages = {1433-40}, abstract = {

Spatial navigation is often used as a behavioral task in studies of the neuronal circuits that underlie cognition, learning and memory in rodents. The combination of in vivo microscopy with genetically encoded indicators has provided an important new tool for studying neuronal circuits, but has been technically difficult to apply during navigation. Here we describe methods for imaging the activity of neurons in the CA1 region of the hippocampus with subcellular resolution in behaving mice. Neurons that expressed the genetically encoded calcium indicator GCaMP3 were imaged through a chronic hippocampal window. Head-restrained mice performed spatial behaviors in a setup combining a virtual reality system and a custom-built two-photon microscope. We optically identified populations of place cells and determined the correlation between the location of their place fields in the virtual environment and their anatomical location in the local circuit. The combination of virtual reality and high-resolution functional imaging should allow a new generation of studies to investigate neuronal circuit dynamics during behavior.

}, keywords = {Action Potentials, Animals, Calcium, Cerebral Cortex, Computer-Assisted, Dendrites, Genetic, Hippocampus, Image Processing, Inbred C57BL, Male, Membrane Potentials, Mice, Neurons, Nonlinear Dynamics, Patch-Clamp Techniques, Space Perception, Spatial Behavior, Synapsins, Transduction, User-Computer Interface}, issn = {1546-1726}, doi = {10.1038/nn.2648}, author = {Dombeck, Daniel A and Harvey, Christopher D and Tian, Lin and Looger, Loren L and Tank, David W} } @article {46410, title = {The heparin-binding domain of HB-EGF mediates localization to sites of cell-cell contact and prevents HB-EGF proteolytic release.}, journal = {Journal of Cell Science}, volume = {123}, year = {2010}, month = {2010 Jul 1}, pages = {2308-18}, abstract = {

Heparin-binding EGF-like growth factor (HB-EGF) is a ligand for EGF receptor (EGFR) and possesses the ability to signal in juxtacrine, autocrine and/or paracrine mode, with these alternatives being governed by the degree of proteolytic release of the ligand. Although the spatial range of diffusion of released HB-EGF is restricted by binding heparan-sulfate proteoglycans (HSPGs) in the extracellular matrix and/or cellular glycocalyx, ascertaining mechanisms governing non-released HB-EGF localization is also important for understanding its effects. We have employed a new method for independently tracking the localization of the extracellular EGF-like domain of HB-EGF and the cytoplasmic C-terminus. A striking observation was the absence of the HB-EGF transmembrane pro-form from the leading edge of COS-7 cells in a wound-closure assay; instead, this protein localized in regions of cell-cell contact. A battery of detailed experiments found that this localization derives from a trans interaction between extracellular HSPGs and the HB-EGF heparin-binding domain, and that disruption of this interaction leads to increased release of soluble ligand and a switch in cell phenotype from juxtacrine-induced growth inhibition to autocrine-induced proliferation. Our results indicate that extracellular HSPGs serve to sequester the transmembrane pro-form of HB-EGF at the point of cell-cell contact, and that this plays a role in governing the balance between juxtacrine versus autocrine and paracrine signaling.

}, keywords = {Amino Acid Sequence, Amphiregulin, Animals, Cell Communication, Cell Proliferation, Cercopithecus aethiops, COS Cells, EGF Family of Proteins, Glycoproteins, Heparan Sulfate Proteoglycans, Heparin, Heparin-binding EGF-like Growth Factor, Intercellular Junctions, Intercellular Signaling Peptides and Proteins, Mice, Molecular Sequence Data, Mutation, Peptides, Protein Precursors, Protein Structure, Tertiary}, issn = {1477-9137}, doi = {10.1242/jcs.058321}, author = {Prince, Robin N and Schreiter, Eric R and Zou, Peng and Wiley, H Steven and Ting, Alice Y and Lee, Richard T and Lauffenburger, Douglas A} } @article {5687, title = {An integrated micro- and macroarchitectural analysis of the Drosophila brain by computer-assisted serial section electron microscopy.}, journal = {PLoS Biology}, volume = {8}, year = {2010}, month = {2010}, abstract = {

The analysis of microcircuitry (the connectivity at the level of individual neuronal processes and synapses), which is indispensable for our understanding of brain function, is based on serial transmission electron microscopy (TEM) or one of its modern variants. Due to technical limitations, most previous studies that used serial TEM recorded relatively small stacks of individual neurons. As a result, our knowledge of microcircuitry in any nervous system is very limited. We applied the software package TrakEM2 to reconstruct neuronal microcircuitry from TEM sections of a small brain, the early larval brain of Drosophila melanogaster. TrakEM2 enables us to embed the analysis of the TEM image volumes at the microcircuit level into a light microscopically derived neuro-anatomical framework, by registering confocal stacks containing sparsely labeled neural structures with the TEM image volume. We imaged two sets of serial TEM sections of the Drosophila first instar larval brain neuropile and one ventral nerve cord segment, and here report our first results pertaining to Drosophila brain microcircuitry. Terminal neurites fall into a small number of generic classes termed globular, varicose, axiform, and dendritiform. Globular and varicose neurites have large diameter segments that carry almost exclusively presynaptic sites. Dendritiform neurites are thin, highly branched processes that are almost exclusively postsynaptic. Due to the high branching density of dendritiform fibers and the fact that synapses are polyadic, neurites are highly interconnected even within small neuropile volumes. We describe the network motifs most frequently encountered in the Drosophila neuropile. Our study introduces an approach towards a comprehensive anatomical reconstruction of neuronal microcircuitry and delivers microcircuitry comparisons between vertebrate and insect neuropile.

}, keywords = {Animals, Brain, Computer-Assisted, Drosophila melanogaster, Electron, Humans, Image Processing, Imaging, Microscopy, Neurons, Neuropil, Software, Synapses, Three-Dimensional, Transmission}, issn = {1545-7885}, doi = {10.1371/journal.pbio.1000502}, author = {Cardona, Albert and Saalfeld, Stephan and Preibisch, Stephan and Schmid, Benjamin and Cheng, Anchi and Pulokas, Jim and Tomancak, Pavel and Hartenstein, Volker.} } @proceedings {46792, title = {Into ImgLib{\textemdash}Generic image processing in Java}, year = {2010}, month = {2012 Oct 27}, address = {Mondorf-les-Bains, Luxembourg}, abstract = {

The purpose of ImgLib, a Generic Java Image Processing Library, is to provide an abstract framework enabling Java developers to design and implement data processing algorithms without having to consider dimensionality, type of data (e. g. byte, float, complex float), or strategies for data access (e. g. linear arrays, cells, paged cells). This kind of programming has significant advantages over the classical way. An algorithm written once for a certain class of Type will potentially run on any compatible Type, even if it does not exist yet. Same applies for data access strategies and the number of dimensions.
We achieve this abstraction by accessing data through Iterators and Type interfaces. Iterators guarantee efficient traversal through pixels depending on whether random coordinate access is required or just all pixels have to be visited once, whether real or integer coordinates are accessed, whether coordinates outside of image boundaries are accessed or not. Type interfaces define the supported operators on pixel values (like basic algebra) and hide the underlying basic type from algorithm implementation.

}, author = {Preibisch, Stephan and Tomancak, Pavel and Saalfeld, Stephan} } @article {5367, title = {Lineage-based connectivity map of the Drosophila brain.}, journal = {Journal of Neurogenetics}, volume = {24}, year = {2010}, month = {2010}, pages = {79}, author = {Hartenstein, Volker and Pereanu, Wayne and Truman, Jim and Cardona, Albert} } @article {3843, title = {Machines that learn to segment images: a crucial technology for connectomics.}, journal = {Current Opinion in Neurobiology}, volume = {20}, year = {2010}, month = {2010 Oct}, pages = {653-66}, abstract = {

Connections between neurons can be found by checking whether synapses exist at points of contact, which in turn are determined by neural shapes. Finding these shapes is a special case of image segmentation, which is laborious for humans and would ideally be performed by computers. New metrics properly quantify the performance of a computer algorithm using its disagreement with {\textquoteright}true{\textquoteright} segmentations of example images. New machine learning methods search for segmentation algorithms that minimize such metrics. These advances have reduced computer errors dramatically. It should now be faster for a human to correct the remaining errors than to segment an image manually. Further reductions in human effort are expected, and crucial for finding connectomes more complex than that of Caenorhabditis elegans.

}, keywords = {Algorithms, Animals, Artificial Intelligence, Computer-Assisted, Electron, Humans, Image Processing, Microscopy, Nanotechnology, Neurobiology}, issn = {1873-6882}, doi = {10.1016/j.conb.2010.07.004}, author = {Jain, Viren and Seung, Hyunjune Sebastian and Turaga, Srinivas C} } @article {2290, title = {Malaria severity and human nitric oxide synthase type 2 (NOS2) promoter haplotypes.}, journal = {Human Genetics}, volume = {127}, year = {2010}, month = {2010 Feb}, pages = {163-82}, abstract = {

Nitric oxide (NO) mediates host resistance to severe malaria and other infectious diseases. NO production and mononuclear cell expression of the NO producing enzyme-inducible nitric oxide synthase (NOS2) have been associated with protection from severe falciparum malaria. The purpose of this study was to identify single nucleotide polymorphisms (SNPs) and haplotypes in the NOS2 promoter, to identify associations of these haplotypes with malaria severity and to test the effects of these polymorphisms on promoter activity. We identified 34 SNPs in the proximal 7.3 kb region of the NOS2 promoter and inferred NOS2 promoter haplotypes based on genotyping 24 of these SNPs in a population of Tanzanian children with and without cerebral malaria. We identified 71 haplotypes; 24 of these haplotypes comprised 82\% of the alleles. We determined whether NOS2 promoter haplotypes were associated with malaria severity in two groups of subjects from Dar es Salaam (N = 185 and N = 250) and in an inception cohort of children from Muheza-Tanga, Tanzania (N = 883). We did not find consistent associations of NOS2 promoter haplotypes with malaria severity or malarial anemia, although interpretation of these results was potentially limited by the sample size of each group. Furthermore, cytokine-induced NOS2 promoter activity determined using luciferase reporter constructs containing the proximal 7.3 kb region of the NOS2 promoter and the G-954C or C-1173T SNPs did not differ from NOS2 promoter constructs that lacked these polymorphisms. Taken together, these studies suggest that the relationship between NOS2 promoter polymorphisms and malaria severity is more complex than previously described.

}, keywords = {Alleles, Base Sequence, Cell Line, Child, DNA, Gene Frequency, Genetic, Genetic Heterogeneity, Genotype, Haplotypes, Humans, Infant, Kenya, Linkage Disequilibrium, Malaria, Molecular Sequence Data, Mutation, Nitric Oxide Synthase Type II, Nucleic Acid, Polymorphism, Preschool, Promoter Regions, Sequence Analysis, Sequence Homology, Severity of Illness Index, Single Nucleotide, Tanzania, Tumor}, issn = {1432-1203}, doi = {10.1007/s00439-009-0753-3}, author = {Levesque, Marc C and Hobbs, Maurine R and O{\textquoteright}Loughlin, Charles W and Chancellor, Jennifer A and Chen, Youwei and Tkachuk, Ariana N and Booth, Jennifer and Patch, Kistie B and Allgood, Sallie and Pole, Ann R and Fernandez, Carolyn A and Mwaikambo, Esther D and Mutabingwa, Theonest K and Fried, Michal and Sorensen, Bess and Duffy, Patrick E and Granger, Donald L and Anstey, Nicholas M and Weinberg, J Brice} } @article {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 {47227, title = {The mushroom body (Quick guide.)}, journal = {Current Biology : CB}, volume = {20}, year = {2010}, month = {2010 Jan 12}, pages = {R11-2}, doi = {10.1016/j.cub.2009.10.031}, author = {Campbell, Robert A A and Turner, Glenn C} } @article {1575, title = {Near-isotropic 3D optical nanoscopy with photon-limited chromophores.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, year = {2010}, month = {2010 Jun 1}, pages = {10068-73}, abstract = {

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

}, keywords = {Animals, Base Sequence, Dendrites, DNA Primers, Escherichia coli K12, Escherichia coli Proteins, Fluorescence, Imaging, Luminescent Proteins, Microscopy, Nanotechnology, Optical Devices, Photons, Rats, Recombinant Fusion Proteins, Sprague-Dawley, Three-Dimensional}, issn = {1091-6490}, doi = {10.1073/pnas.1004899107}, author = {Tang, Jianyong and Akerboom, Jasper and Vaziri, Alipasha and Looger, Loren L and Shank, Charles V} } @article {2386, title = {A new focus on plant sciences.}, journal = {Science}, volume = {330}, year = {2010}, month = {2010 Nov 19}, pages = {1021}, keywords = {Agriculture, Botany, Financing, Government, Plants, Research Support as Topic, United States}, issn = {1095-9203}, doi = {10.1073/pnas.1100640108}, author = {McCormick, Steven J and Tjian, Robert} } @article {4253, title = {The Pfam protein families database.}, journal = {Nucleic Acids Research}, volume = {38}, year = {2010}, month = {2010 Jan}, pages = {D211-22}, abstract = {

Pfam is a widely used database of protein families and domains. This article describes a set of major updates that we have implemented in the latest release (version 24.0). The most important change is that we now use HMMER3, the latest version of the popular profile hidden Markov model package. This software is approximately 100 times faster than HMMER2 and is more sensitive due to the routine use of the forward algorithm. The move to HMMER3 has necessitated numerous changes to Pfam that are described in detail. Pfam release 24.0 contains 11,912 families, of which a large number have been significantly updated during the past two years. Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/).

}, keywords = {Amino Acid, Amino Acid Sequence, Animals, Archaeal, Computational Biology, Databases, Fungal, Genome, Humans, Information Storage and Retrieval, Internet, Molecular Sequence Data, Nucleic Acid, Protein, Protein Structure, Sequence Alignment, Sequence Homology, Software, Tertiary}, issn = {1362-4962}, doi = {10.1093/nar/gkp985}, author = {Finn, Robert D and Mistry, Jaina and Tate, John and Coggill, Penny and Heger, Andreas and Pollington, Joanne E and Gavin, O Luke and Gunasekaran, Prasad and Ceric, Goran and Forslund, Kristoffer and Holm, Liisa and Sonnhammer, Erik L L and Eddy, Sean R. and Bateman, Alex} } @article {68824, title = {Proneural gene-linked neurogenesis in zebrafish cerebellum}, journal = {Developmental Biology}, volume = {343}, year = {2010}, month = {07/2010}, pages = {1-17}, abstract = {

In mammals, cerebellar neurons are categorized as glutamatergic or GABAergic, and are derived from progenitors that express the proneural genes atoh1 or ptf1a, respectively. In zebrafish, three atoh1 genes, atoh1a, atoh1b, and atoh1c, are expressed in overlapping but distinct expression domains in the upper rhombic lip (URL): ptf1a is expressed exclusively in the ventricular zone (VZ). Using transgenic lines expressing fluorescent proteins under the control of the regulatory elements of atoh1a and ptf1a, we traced the lineages of the cerebellar neurons. The atoh1+ progenitors gave rise not only to granule cells but also to neurons of the anteroventral rhombencephalon. The ptf1a+ progenitors generated Purkinje cells. The olig2+ eurydendroid cells, which are glutamatergic, were derived mostly from ptf1a+ progenitors in the VZ but some originated from the atoh1+ progenitors in the URL. In the adult cerebellum, atoh1a, atoh1b, and atoh1c are expressed in the molecular layer of the valvula cerebelli and of the medial corpus cerebelli, and ptf1a was detected in the VZ. The proneural gene expression patterns coincided with the sites of proliferating neuronal progenitors in the adult cerebellum. Our data indicate that proneural gene-linked neurogenesis is evolutionarily conserved in the cerebellum among vertebrates, and that the continuously generated neurons help remodel neural circuits in the adult zebrafish cerebellum.

}, keywords = {Adult neurogenesis, Cerebellum, GABAergic neuron, Glutamatergic neuron, Hindbrain, Proneural gene, Zebrafish}, issn = {0012-1606}, doi = {https://doi.org/10.1016/j.ydbio.2010.03.024}, url = {https://www.sciencedirect.com/science/article/pii/S0012160610002071}, author = {Shuichi Kani and Young-Ki Bae and Takashi Shimizu and Koji Tanabe and Chie Satou and Michael J. Parsons and Ethan Scott and Shin-ichi Higashijima and Masahiko Hibi} } @article {3637, title = {The prototypical H+/galactose symporter GalP assembles into functional trimers.}, journal = {Journal of Molecular Biology}, volume = {396}, year = {2010}, month = {2010 Feb 26}, pages = {593-601}, abstract = {

Glucose is a primary source of energy for human cells. Glucose transporters form specialized membrane channels for the transport of sugars into and out of cells. Galactose permease (GalP) is the closest bacterial homolog of human facilitated glucose transporters. Here, we report the functional reconstitution and 2D crystallization of GalP. Single particle electron microscopy analysis of purified GalP shows that the protein assembles as an oligomer with three distinct densities. Reconstitution assays yield 2D GalP crystals that exhibit a hexagonal array having p3 symmetry. The projection structure of GalP at 18 A resolution shows that the protein is trimeric. Each monomer in the trimer forms its own channel, but an additional cavity (10 approximately 15 A in diameter) is apparent at the 3-fold axis of the oligomer. We show that the crystalline GalP is able to selectively bind substrate, suggesting that the trimeric form is biologically active.

}, keywords = {Calcium-Binding Proteins, Computer-Assisted, Crystallization, Electron, Escherichia coli, Escherichia coli Proteins, Galactose, Image Processing, Microscopy, Monosaccharide Transport Proteins, Periplasmic Binding Proteins, Protein Binding, Protein Multimerization, Protein Structure, Quaternary}, issn = {1089-8638}, doi = {10.1016/j.jmb.2009.12.010}, author = {Zheng, Hongjin and Taraska, Justin and Merz, Alexey J and Gonen, Tamir} } @article {987, title = {Refinement of tools for targeted gene expression in Drosophila.}, journal = {Genetics}, volume = {186}, year = {2010}, month = {2010 Oct}, pages = {735-55}, abstract = {

A wide variety of biological experiments rely on the ability to express an exogenous gene in a transgenic animal at a defined level and in a spatially and temporally controlled pattern. We describe major improvements of the methods available for achieving this objective in Drosophila melanogaster. We have systematically varied core promoters, UTRs, operator sequences, and transcriptional activating domains used to direct gene expression with the GAL4, LexA, and Split GAL4 transcription factors and the GAL80 transcriptional repressor. The use of site-specific integration allowed us to make quantitative comparisons between different constructs inserted at the same genomic location. We also characterized a set of PhiC31 integration sites for their ability to support transgene expression of both drivers and responders in the nervous system. The increased strength and reliability of these optimized reagents overcome many of the previous limitations of these methods and will facilitate genetic manipulations of greater complexity and sophistication.

}, issn = {1943-2631}, doi = {10.1534/genetics.110.119917}, author = {Pfeiffer, Barret D and Ngo, Teri-T B and Hibbard, Karen L and Murphy, Christine and Jenett, Arnim and Truman, James W and Rubin, Gerald M} } @article {2494, title = {A role for juvenile hormone in the prepupal development of Drosophila melanogaster.}, journal = {Development}, volume = {137}, year = {2010}, month = {2010 Apr}, pages = {1117-26}, abstract = {

To elucidate the role of juvenile hormone (JH) in metamorphosis of Drosophila melanogaster, the corpora allata cells, which produce JH, were killed using the cell death gene grim. These allatectomized (CAX) larvae were smaller at pupariation and died at head eversion. They showed premature ecdysone receptor B1 (EcR-B1) in the photoreceptors and in the optic lobe, downregulation of proliferation in the optic lobe, and separation of R7 from R8 in the medulla during the prepupal period. All of these effects of allatectomy were reversed by feeding third instar larvae on a diet containing the JH mimic (JHM) pyriproxifen or by application of JH III or JHM at the onset of wandering. Eye and optic lobe development in the Methoprene-tolerant (Met)-null mutant mimicked that of CAX prepupae, but the mutant formed viable adults, which had marked abnormalities in the organization of their optic lobe neuropils. Feeding Met(27) larvae on the JHM diet did not rescue the premature EcR-B1 expression or the downregulation of proliferation but did partially rescue the premature separation of R7, suggesting that other pathways besides Met might be involved in mediating the response to JH. Selective expression of Met RNAi in the photoreceptors caused their premature expression of EcR-B1 and the separation of R7 and R8, but driving Met RNAi in lamina neurons led only to the precocious appearance of EcR-B1 in the lamina. Thus, the lack of JH and its receptor Met causes a heterochronic shift in the development of the visual system that is likely to result from some cells {\textquoteright}misinterpreting{\textquoteright} the ecdysteroid peaks that drive metamorphosis.

}, keywords = {Animals, Basic Helix-Loop-Helix Transcription Factors, Biological, Corpora Allata, Diet, Drosophila melanogaster, Drosophila Proteins, Invertebrate, Juvenile Hormones, Larva, Metamorphosis, Neurons, Nonmammalian, Optic Lobe, Photoreceptor Cells, Pyridines, Receptors, Recombinant Fusion Proteins, RNA Interference, Steroid}, issn = {1477-9129}, doi = {10.1242/dev.037218}, author = {Riddiford, Lynn M and Truman, James W and Mirth, Christen K and Shen, Yu-Chi} } @article {2439, title = {Role of Notch signaling in establishing the hemilineages of secondary neurons in Drosophila melanogaster.}, journal = {Development}, volume = {137}, year = {2010}, month = {2010 Jan}, pages = {53-61}, abstract = {

The secondary neurons generated in the thoracic central nervous system of Drosophila arise from a hemisegmental set of 25 neuronal stem cells, the neuroblasts (NBs). Each NB undergoes repeated asymmetric divisions to produce a series of smaller ganglion mother cells (GMCs), which typically divide once to form two daughter neurons. We find that the two daughters of the GMC consistently have distinct fates. Using both loss-of-function and gain-of-function approaches, we examined the role of Notch signaling in establishing neuronal fates within all of the thoracic secondary lineages. In all cases, the {\textquoteright}A{\textquoteright} (Notch(ON)) sibling assumes one fate and the {\textquoteright}B{\textquoteright} (Notch(OFF)) sibling assumes another, and this relationship holds throughout the neurogenic period, resulting in two major neuronal classes: the A and B hemilineages. Apparent monotypic lineages typically result from the death of one sibling throughout the lineage, resulting in a single, surviving hemilineage. Projection neurons are predominantly from the B hemilineages, whereas local interneurons are typically from A hemilineages. Although sibling fate is dependent on Notch signaling, it is not necessarily dependent on numb, a gene classically involved in biasing Notch activation. When Numb was removed at the start of larval neurogenesis, both A and B hemilineages were still generated, but by the start of the third larval instar, the removal of Numb resulted in all neurons assuming the A fate. The need for Numb to direct Notch signaling correlated with a decrease in NB cell cycle time and may be a means for coping with multiple sibling pairs simultaneously undergoing fate decisions.

}, keywords = {Animals, Cell Lineage, Central Nervous System, Drosophila melanogaster, Drosophila Proteins, Immunohistochemistry, Neurons, Notch, Receptors, Signal Transduction, Stem Cells, Thorax}, issn = {1477-9129}, doi = {10.1242/dev.041749}, author = {Truman, James W and Moats, Wanda and Altman, Janet and Marin, Elizabeth C and Williams, Darren W} } @article {5371, title = {Serial-section EM derived synaptic circuits in the fly{\textquoteright}s visual system: the medulla opens up.}, journal = {Journal of Neurogenetics}, volume = {24}, year = {2010}, month = {2010}, pages = {9}, author = {Meinertzhagen, I. A. and Takemura, S and Vitaladevuni, S. and Lu, Z. and Scheffer, L. and Chklovskii, D.B.} } @article {2768, title = {Snapshot Image Mapping Spectrometer (IMS) with high sampling density for hyperspectral microscopy.}, journal = {Optics Express}, volume = {18}, year = {2010}, month = {2010 Jul 5}, pages = {14330-44}, abstract = {

A snapshot Image Mapping Spectrometer (IMS) with high sampling density is developed for hyperspectral microscopy, measuring a datacube of dimensions 285 x 285 x 60 (x, y, lambda). The spatial resolution is approximately 0.45 microm with a FOV of 100 x 100 microm(2). The measured spectrum is from 450 nm to 650 nm and is sampled by 60 spectral channels with average sampling interval approximately 3.3 nm. The channel{\textquoteright}s spectral resolution is approximately 8nm. The spectral imaging results demonstrate the potential of the IMS for real-time cellular fluorescence imaging.

}, keywords = {Animals, Cattle, Cell Nucleus, Endothelial Cells, Fluorescence, Imaging, Microscopy, Pulmonary Artery, Spectrum Analysis, Staining and Labeling, Three-Dimensional}, issn = {1094-4087}, doi = {10.1364/AO.50.001792}, author = {Gao, Liang and Kester, Robert T and Hagen, Nathan and Tkaczyk, Tomasz S} } @article {46161, title = {Software for bead-based registration of selective plane illumination microscopy data.}, journal = {Nature Methods}, volume = {7}, year = {2010}, month = {2010 Jun}, pages = {418-9}, keywords = {Animals, Caenorhabditis elegans, Drosophila melanogaster, Imaging, Three-Dimensional, Lighting, Microscopy, Software}, issn = {1548-7105}, doi = {10.1038/nmeth0610-418}, author = {Preibisch, Stephan and Saalfeld, Stephan and Schindelin, Johannes and Tomancak, Pavel} } @article {6509, title = {Toward the second generation of optogenetic tools.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {30}, year = {2010}, month = {2010 Nov 10}, pages = {14998-5004}, abstract = {

This mini-symposium aims to provide an integrated perspective on recent developments in optogenetics. Research in this emerging field combines optical methods with targeted expression of genetically encoded, protein-based probes to achieve experimental manipulation and measurement of neural systems with superior temporal and spatial resolution. The essential components of the optogenetic toolbox consist of two kinds of molecular devices: actuators and reporters, which respectively enable light-mediated control or monitoring of molecular processes. The first generation of genetically encoded calcium reporters, fluorescent proteins, and neural activators has already had a great impact on neuroscience. Now, a second generation of voltage reporters, neural silencers, and functionally extended fluorescent proteins hold great promise for continuing this revolution. In this review, we will evaluate and highlight the limitations of presently available optogenic tools and discuss where these technologies and their applications are headed in the future.

}, keywords = {Fluorescent Dyes, Genetic Engineering, Neurosciences}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4190-10.2010}, author = {Kn{\"o}pfel, Thomas and Lin, Michael Z and Levskaya, Anselm and Tian, Lin and Lin, John Y and Boyden, Edward S} } @article {4284, title = {Two-photon single-cell optogenetic control of neuronal activity by sculpted light.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, year = {2010}, month = {2010 Jun 29}, pages = {11981-6}, abstract = {

Recent advances in optogenetic techniques have generated new tools for controlling neuronal activity, with a wide range of neuroscience applications. The most commonly used approach has been the optical activation of the light-gated ion channel channelrhodopsin-2 (ChR2). However, targeted single-cell-level optogenetic activation with temporal precessions comparable to the spike timing remained challenging. Here we report fast (\< or = 1 ms), selective, and targeted control of neuronal activity with single-cell resolution in hippocampal slices. Using temporally focused laser pulses (TEFO) for which the axial beam profile can be controlled independently of its lateral distribution, large numbers of channels on individual neurons can be excited simultaneously, leading to strong (up to 15 mV) and fast (\< or = 1 ms) depolarizations. Furthermore, we demonstrated selective activation of cellular compartments, such as dendrites and large presynaptic terminals, at depths up to 150 microm. The demonstrated spatiotemporal resolution and the selectivity provided by TEFO allow manipulation of neuronal activity, with a large number of applications in studies of neuronal microcircuit function in vitro and in vivo.

}, keywords = {Action Potentials, Animals, Cell Line, Dendrites, Electrophysiological Phenomena, Hippocampus, Humans, Lasers, Mice, Nerve Tissue Proteins, Neurons, Optical Phenomena, Patch-Clamp Techniques, Photic Stimulation, Photons, Presynaptic Terminals, Rats, Recombinant Fusion Proteins, Rhodopsin, Sprague-Dawley, Transgenic}, issn = {1091-6490}, doi = {10.1073/pnas.1006620107}, author = {Andrasfalvy, Bertalan K and Zemelman, Boris V and Tang, Jianyong and Vaziri, Alipasha} } @article {2387, title = {Unexpected roles for core promoter recognition factors in cell-type-specific transcription and gene regulation.}, journal = {Nature Reviews. Genetics}, volume = {11}, year = {2010}, month = {2010 Aug}, pages = {549-58}, abstract = {

The eukaryotic core promoter recognition complex was generally thought to play an essential but passive role in the regulation of gene expression. However, recent evidence now indicates that core promoter recognition complexes together with {\textquoteright}non-prototypical{\textquoteright} subunits may have a vital regulatory function in driving cell-specific programmes of transcription during development. Furthermore, new roles for components of these complexes have been identified beyond development; for example, in mediating interactions with chromatin and in maintaining active gene expression across cell divisions.

}, keywords = {Animals, Cell Differentiation, DNA, Embryonic Development, Female, Genetic, Germ Cells, Humans, Male, Promoter Regions, RNA Polymerase II, Transcription, Transcription Factors, Transcriptional Activation}, issn = {1471-0064}, doi = {10.1073/pnas.1100640108}, author = {Goodrich, James A and Tjian, Robert} } @article {2685, title = {Visual targeting of motor actions in climbing Drosophila.}, journal = {Current Biology}, volume = {20}, year = {2010}, month = {2010 Apr 13}, pages = {663-8}, abstract = {

Drosophila melanogaster flies cross surmountable gaps in their walkway of widths exceeding their body length with an astounding maneuver but avoid attempts at insurmountable gaps by visual width estimation. Different mutant lines affect specific aspects of this maneuver, indicating a high complexity and modularity of the underlying motor control. Here we report on two mutants, ocelliless(1) and tay bridge(1), that, although making a correct decision to climb, fail dramatically in aiming at the right direction. Both mutants show structural defects in the protocerebral bridge, a central complex neuropil formed like a handlebar spanning the brain hemispheres. The bridge has been implicated in step-length control in walking flies and celestial E-vector orientation in locusts. In rescue experiments using tay bridge(1) flies, the integrity of the bridge was reestablished, concomitantly leading to a significant improvement of their orientation at the gap. Although producing directional scatter, their attempts were clearly aimed at the landing site. However, this partial rescue was lost in these flies at a reduced-visibility landing site. We therefore conclude that the protocerebral bridge is an essential part of a visual targeting network that transmits directional clues to the motor output via a known projection system.

}, keywords = {Animals, Biological, Brain, Drosophila melanogaster, Genes, Genetically Modified, Insect, Models, Motor Activity, Mutation, Visual Perception}, issn = {1879-0445}, doi = {10.1016/j.cub.2010.02.055}, author = {Triphan, Tilman and Poeck, Burkhard and Neuser, Kirsa and Strauss, Roland} } @article {2792, title = {[Analysis on acupuncture literature in Science Citation Index (SCI) periodicals in 2007].}, journal = {Zhongguo Zhen Jiu = Chinese Acupuncture \& Moxibustion}, volume = {29}, year = {2009}, month = {2009 Jun}, pages = {504-7}, abstract = {

To grasp the international developing tendency of acupuncture research and provide some references for promoting acupuncture and moxibustion internationalization process, the articles about acupuncture in Science Citation Index (SCI) periodicals in 2007 were retrieved by adopting the retrieval tactics on line in combination with database searching. Results indicate that 257 articles about acupuncture had been retrived from the SCI Web databases. These articles were published in 125 journals respectively, most of which were Euramerican journals. Among these journals, the impact factor of the Journal of the American Medical Association (JAMA), 25. 547, is the highest one. It is shown that the impact factors of the SCI periodicals, in which acupuncture articles embodied are increased, the quality of these articles are improved obviously and the types of the articles are various in 2007, but there is obvious difference in the results of these studies due to the difference of experimental methods, the subjects of these experiments and acupuncture manipulations. Therefore, standardization of many problems arising from the researches on acupuncture is extremely imminent.

}, keywords = {Acupuncture, Acupuncture Therapy, Journal Impact Factor, Periodicals as Topic, Publications, Reference Standards}, issn = {0255-2930}, doi = {10.1364/AO.50.001792}, author = {Gao, Liang and Tian, Li-xin and Guo, Yi} } @proceedings {46793, title = {Bead-based mosaicing of single plane illumination microscopy images using geometric local descriptor matching.}, volume = {7259}, year = {2009}, month = {2009 Mar 27}, pages = {72592S}, publisher = {SPIE}, address = {Lake Buena Vista, FL}, abstract = {

Single Plane Illumination Microscopy (SPIM) is an emerging microscopic technique that enables live imaging of large biological specimens in their entirety. By imaging the biological sample from multiple angles, SPIM has the potential to achieve isotropic resolution throughout relatively large biological specimens. For every angle, however, only a shallow section of the specimen is imaged with high resolution, whereas deeper regions appear increasingly blurred. Existing intensity-based registration techniques still struggle to robustly and accurately align images that are characterized by limited overlap and/or heavy blurring. To be able to register such images, we add sub-resolution fluorescent beads to the rigid agarose medium in which the imaged specimen is embedded. For each segmented bead, we store the relative location of its n nearest neighbors in image space as rotation-invariant geometric local descriptors. Corresponding beads between overlapping images are identified by matching these descriptors. The bead correspondences are used to simultaneously estimate the globally optimal transformation for each individual image. The final output image is created by combining all images in an angle-independent output space, using volume injection and local content-based weighting of contributing images. We demonstrate the performance of our approach on data acquired from living embryos of Drosophila and fixed adult C.elegans worms. Bead-based registration outperformed intensity-based registration in terms of computation speed by two orders of magnitude while producing bead registration errors below 1 μm (about 1 pixel). It, therefore, provides an ideal tool for processing of long term time-lapse recordings of embryonic development consisting of hundreds of time points.

}, doi = {10.1117/12.812612}, author = {Preibisch, Stephan and Saalfeld, Stephan and Rohlfing, Torsten and Tomancak, Pavel} } @article {5817, title = {CATMAID: collaborative annotation toolkit for massive amounts of image data.}, journal = {Bioinformatics}, volume = {25}, year = {2009}, month = {2009 Aug 1}, pages = {1984-6}, abstract = {

SUMMARY: High-resolution, three-dimensional (3D) imaging of large biological specimens generates massive image datasets that are difficult to navigate, annotate and share effectively. Inspired by online mapping applications like GoogleMaps, we developed a decentralized web interface that allows seamless navigation of arbitrarily large image stacks. Our interface provides means for online, collaborative annotation of the biological image data and seamless sharing of regions of interest by bookmarking. The CATMAID interface enables synchronized navigation through multiple registered datasets even at vastly different scales such as in comparisons between optical and electron microscopy. AVAILABILITY: http://fly.mpi-cbg.de/catmaid.

}, keywords = {Algorithms, Computational Biology, Computer Graphics, Database Management Systems, Databases, Factual, Imaging, Information Storage and Retrieval, Software, Three-Dimensional}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btp266}, author = {Saalfeld, Stephan and Cardona, Albert and Hartenstein, Volker and Tomancak, Pavel} } @article {1555, title = {Crystal structures of the GCaMP calcium sensor reveal the mechanism of fluorescence signal change and aid rational design.}, journal = {The Journal of Biological Chemistry}, volume = {284}, year = {2009}, month = {2009 Mar 6}, pages = {6455-64}, abstract = {

The genetically encoded calcium indicator GCaMP2 shows promise for neural network activity imaging, but is currently limited by low signal-to-noise ratio. We describe x-ray crystal structures as well as solution biophysical and spectroscopic characterization of GCaMP2 in the calcium-free dark state, and in two calcium-bound bright states: a monomeric form that dominates at intracellular concentrations observed during imaging experiments and an unexpected domain-swapped dimer with decreased fluorescence. This series of structures provides insight into the mechanism of Ca2+-induced fluorescence change. Upon calcium binding, the calmodulin (CaM) domain wraps around the M13 peptide, creating a new domain interface between CaM and the circularly permuted enhanced green fluorescent protein domain. Residues from CaM alter the chemical environment of the circularly permuted enhanced green fluorescent protein chromophore and, together with flexible inter-domain linkers, block solvent access to the chromophore. Guided by the crystal structures, we engineered a series of GCaMP2 point mutants to probe the mechanism of GCaMP2 function and characterized one mutant with significantly improved signal-to-noise. The mutation is located at a domain interface and its effect on sensor function could not have been predicted in the absence of structural data.

}, keywords = {Animals, Calcium, Calcium-Binding Proteins, Crystallography, Fluorescent Dyes, Green Fluorescent Proteins, Models, Molecular, Peptides, Protein Binding, Protein Structure, Recombinant Fusion Proteins, Structure-Activity Relationship, Tertiary, X-Ray}, issn = {0021-9258}, doi = {10.1074/jbc.M807657200}, author = {Akerboom, Jasper and Rivera, Jonathan D V{\'e}lez and Guilbe, Mar{\'\i}a M Rodr{\'\i}guez and Malav{\'e}, Elisa C Alfaro and Hernandez, Hector H and Tian, Lin and Hires, S Andrew and Marvin, Jonathan S and Looger, Loren L and Schreiter, Eric R} } @article {6499, title = {Development of an implanted intramuscular EMG-triggered FES system for ambulation after incomplete spinal cord injury.}, journal = {Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society.}, volume = {2009}, year = {2009}, month = {2009}, pages = {6793-7}, abstract = {

Ambulation after spinal cord injury is possible with the aid of neuroprosthesis employing functional electrical stimulation (FES). Individuals with incomplete spinal cord injury (iSCI) retain partial volitional control of muscles below the level of injury, necessitating careful integration of FES with intact voluntary motor function for efficient walking. In this study, the intramuscular electromyogram (iEMG) was used to detect the intent to step and trigger FES-assisted walking in a volunteer with iSCI via an implanted neuroprosthesis consisting of two channels of bipolar iEMG signal acquisition and 12 independent channels of stimulation. The detection was performed with two types of classifiers- a threshold-based classifier that compared the running mean of the iEMG with a discrimination threshold to generate the trigger and a pattern recognition classifier that compared the time-history of the iEMG with a specified template of activity to generate the trigger whenever the cross-correlation coefficient exceeded a discrimination threshold. The pattern recognition classifier generally outperformed the threshold-based classifier, particularly with respect to minimizing False Positive triggers. The overall True Positive rates for the threshold-based classifier were 61.6\% and 87.2\% for the right and left steps with overall False Positive rates of 38.4\% and 33.3\%. The overall True Positive rates for the left and right step with the pattern recognition classifier were 57.2\% and 93.3\% and the overall False Positive rates were 11.9\% and 24.4\%. The subject showed no preference for either the threshold or pattern recognition-based classifier as determined by the Usability Rating Scale (URS) score collected after each trial and both the classifiers were perceived as moderately easy to use.

}, keywords = {Automated, Electric Stimulation, Electrodes, Electromyography, Humans, Implanted, Male, Muscles, Pattern Recognition, Recovery of Function, Spinal Cord Injuries, Walking}, issn = {1557-170X}, doi = {10.1109/IEMBS.2009.5333980}, author = {Dutta, Anirban and Kobetic, Rudi and Triolo, Ronald} } @article {46623, title = {Drosophila, a genetic model system to study cocaine-related behaviors: a review with focus on LIM-only proteins.}, journal = {Neuropharmacology}, volume = {56 Suppl 1}, year = {2009}, month = {2009}, pages = {97-106}, abstract = {

In the last decade, the fruit fly Drosophila melanogaster, highly accessible to genetic, behavioral and molecular analyses, has been introduced as a novel model organism to help decipher the complex genetic, neurochemical, and neuroanatomical underpinnings of behaviors induced by drugs of abuse. Here we review these data, focusing specifically on cocaine-related behaviors. Several of cocaine{\textquoteright}s most characteristic properties have been recapitulated in Drosophila. First, cocaine induces motor behaviors in flies that are remarkably similar to those observed in mammals. Second, repeated cocaine administration induces behavioral sensitization a form of behavioral plasticity believed to underlie certain aspects of addiction. Third, a key role for dopaminergic systems in mediating cocaine{\textquoteright}s effects has been demonstrated through both pharmacological and genetic methods. Finally, and most importantly, unbiased genetic screens, feasible because of the simplicity and scale with which flies can be manipulated in the laboratory, have identified several novel genes and pathways whose role in cocaine behaviors had not been anticipated. Many of these genes and pathways have been validated in mammalian models of drug addiction. We focus in this review on the role of LIM-only proteins in cocaine-induced behaviors.

}, keywords = {Animals, Animals, Genetically Modified, Behavior, Animal, Cocaine, Cocaine-Related Disorders, Disease Models, Animal, Dopamine Uptake Inhibitors, Drosophila melanogaster, Drosophila Proteins, Homeodomain Proteins, Models, Genetic}, issn = {0028-3908}, doi = {10.1016/j.neuropharm.2008.07.023}, author = {Heberlein, Ulrike and Tsai, Linus T-Y and Kapfhamer, David and Lasek, Amy W} } @article {5692, title = {Drosophila brain development: closing the gap between a macroarchitectural and microarchitectural approach.}, journal = {Cold Spring Harbor Symposia on Quantitative Biology}, volume = {74}, year = {2009}, month = {2009}, pages = {235-48}, abstract = {

Neurobiologists address neural structure, development, and function at the level of "macrocircuits" (how different brain compartments are interconnected; what overall pattern of activity they produce) and at the level of "microcircuits" (how connectivity and physiology of individual neurons and their processes within a compartment determine the functional output of this compartment). Work in our lab aims at reconstructing the developing Drosophila brain at both levels. Macrocircuits can be approached conveniently by reconstructing the pattern of brain lineages, which form groups of neurons whose projections form cohesive fascicles interconnecting the compartments of the larval and adult brain. The reconstruction of microcircuits requires serial section electron microscopy, due to the small size of terminal neuronal processes and their synaptic contacts. Because of the amount of labor that traditionally comes with this approach, very little is known about microcircuitry in brains across the animal kingdom. Many of the problems of serial electron microscopy reconstruction are now solvable with digital image recording and specialized software for both image acquisition and postprocessing. In this chapter, we introduce our efforts to reconstruct the small Drosophila larval brain and discuss our results in light of the published data on neuropile ultrastructure in other animal taxa.

}, keywords = {Animals, Brain, Cell Lineage, Drosophila, Electron, Genetically Modified, Imaging, Larva, Mice, Microscopy, Models, Nerve Net, Neurites, Neurological, Neuropil, Phylogeny, Species Specificity, Synapses, Three-Dimensional, Transmission}, issn = {1943-4456}, doi = {10.1101/sqb.2009.74.037}, author = {Cardona, A and Saalfeld, S and Tomancak, P and Hartenstein, V.} } @article {2496, title = {The ecdysone receptor controls the post-critical weight switch to nutrition-independent differentiation in Drosophila wing imaginal discs.}, journal = {Development}, volume = {136}, year = {2009}, month = {2009 Jul}, pages = {2345-53}, abstract = {

In holometabolous insects, a species-specific size, known as critical weight, needs to be reached for metamorphosis to be initiated in the absence of further nutritional input. Previously, we found that reaching critical weight depends on the insulin-dependent growth of the prothoracic glands (PGs) in Drosophila larvae. Because the PGs produce the molting hormone ecdysone, we hypothesized that ecdysone signaling switches the larva to a nutrition-independent mode of development post-critical weight. Wing discs from pre-critical weight larvae [5 hours after third instar ecdysis (AL3E)] fed on sucrose alone showed suppressed Wingless (WG), Cut (CT) and Senseless (SENS) expression. Post-critical weight, a sucrose-only diet no longer suppressed the expression of these proteins. Feeding larvae that exhibit enhanced insulin signaling in their PGs at 5 hours AL3E on sucrose alone produced wing discs with precocious WG, CT and SENS expression. In addition, knocking down the Ecdysone receptor (EcR) selectively in the discs also promoted premature WG, CUT and SENS expression in the wing discs of sucrose-fed pre-critical weight larvae. EcR is involved in gene activation when ecdysone is present, and gene repression in its absence. Thus, knocking down EcR derepresses genes that are normally repressed by unliganded EcR, thereby allowing wing patterning to progress. In addition, knocking down EcR in the wing discs caused precocious expression of the ecdysone-responsive gene broad. These results suggest that post-critical weight, EcR signaling switches wing discs to a nutrition-independent mode of development via derepression.

}, keywords = {Animals, Body Patterning, Cell Differentiation, Developmental, Drosophila, Drosophila Proteins, Gene Expression Regulation, Genes, Genetically Modified, Homeodomain Proteins, Insect, Insulin, Nuclear Proteins, Receptors, Signal Transduction, Steroid, Sucrose, Transcription Factors, Wing, Wnt1 Protein}, issn = {0950-1991}, doi = {10.1242/dev.032672}, author = {Mirth, Christen K and Truman, James W and Riddiford, Lynn M} } @article {2905, title = {Electro-optical imaging microscopy of dye-doped artificial lipidic membranes.}, journal = {Biophysical Journal}, volume = {97}, year = {2009}, month = {2009 Dec 2}, pages = {2913-21}, abstract = {

Artificial lipidic bilayers are widely used as a model for the lipid matrix in biological cell membranes. We use the Pockels electro-optical effect to investigate the properties of an artificial lipidic membrane doped with nonlinear molecules in the outer layer. We report here what is believed to be the first electro-optical Pockels signal and image from such a membrane. The electro-optical dephasing distribution within the membrane is imaged and the signal is shown to be linear as a function of the applied voltage. A theoretical analysis taking into account the statistical orientation distribution of the inserted dye molecules allows us to estimate the doped membrane nonlinearity. Ongoing extensions of this work to living cell membranes are discussed.

}, keywords = {Artificial, Cell Membrane, Coloring Agents, Lipid Bilayers, Membrane Potentials, Membranes, Microfluidic Analytical Techniques, Microscopy, Molecular Imaging, Optical Processes, Phosphatidylcholines, Potentiometry, Pyridinium Compounds}, issn = {1542-0086}, doi = {10.1016/j.bpj.2009.08.055}, author = {Hajj, Bassam and De Reguardati, Sophie and Hugonin, Lo\"{\i}c and Le Pioufle, Bruno and Osaki, Toshihisa and Suzuki, Hiroaki and Takeuchi, Shoji and Mojzisova, Halina and Chauvat, Dominique and Zyss, Joseph} } @article {2344, title = {Enemy avoidance task: a novel behavioral paradigm for assessing spatial avoidance of a moving subject.}, journal = {Journal of Neuroscience Methods}, volume = {180}, year = {2009}, month = {2009 May 30}, pages = {29-33}, abstract = {

Navigation with respect to moving goals represents a useful ability in the everyday life of animals. We have developed a novel behavioral paradigm, "enemy avoidance task", in which a laboratory rat (subject) was trained to avoid another rat (enemy), while searching for small pasta pellets dispensed onto an experimental arena. Whenever the distance between the two animals was smaller than 25 cm, the subject was given a mild electric footshock. The results have shown that rats are capable of avoiding another rat while exploring an environment. Therefore, the enemy avoidance task can be used in electrophysiological, lesion or neuropharmacological studies exploring neuronal substrate coding for egocentric and allocentric positions of an observed animal.

}, keywords = {Animal, Animals, Avoidance Learning, Behavior, Behavioral Sciences, Exploratory Behavior, Fear, Long-Evans, Male, Memory, Motor Activity, Movement, Neuropsychological Tests, Neuropsychology, Orientation, Psychomotor Performance, Rats, Space Perception}, issn = {1872-678X}, doi = {10.1523/JNEUROSCI.3773-10.2011}, author = {Telensky, Petr and Svoboda, Jan and Pastalkova, Eva and Blahna, Karel and Bures, Jan and Stuchlik, Ales} } @article {4411, title = {Evolution of the tan locus contributed to pigment loss in Drosophila santomea: a response to Matute et al.}, journal = {Cell}, volume = {139}, year = {2009}, month = {2009 Dec 11}, pages = {1189-96}, abstract = {

We have shown previously that the loss of abdominal pigmentation in D. santomea relative to its sister species D. yakuba resulted, in part, from cis-regulatory mutations at the tan locus. Matute et al. claim, based solely upon extrapolation from genetic crosses of D. santomea and D. melanogaster, a much more divergent species, that at least four X chromosome regions but not tan are responsible for pigmentation differences. Here, we provide additional evidence from introgressions of D. yakuba genes into D. santomea that support a causative role for tan in the loss of pigmentation and present analyses that contradict Matute et al.{\textquoteright}s claims. We discuss how the choice of parental species and other factors affect the ability to identify loci responsible for species divergence, and we affirm that all of our previously reported results and conclusions stand.

}, keywords = {Animals, Chimera, Chromosomal Proteins, DNA-Binding Proteins, Drosophila, Drosophila Proteins, Evolution, Molecular, Non-Histone, Pigmentation, Species Specificity, X Chromosome}, issn = {1097-4172}, doi = {10.1016/j.cell.2009.11.004}, author = {Rebeiz, Mark and Ramos-Womack, Margarita and Jeong, Sangyun and Andolfatto, Peter and Werner, Thomas and True, John and Stern, David L and Carroll, Sean B} } @article {2442, title = {Fine-tuning of secondary arbor development: the effects of the ecdysone receptor on the adult neuronal lineages of the Drosophila thoracic CNS.}, journal = {Development}, volume = {136}, year = {2009}, month = {2009 Oct}, pages = {3247-56}, abstract = {

The adult central nervous system (CNS) of Drosophila is largely composed of relatively homogenous neuronal classes born during larval life. These adult-specific neuron lineages send out initial projections and then arrest development until metamorphosis, when intense sprouting occurs to establish the massive synaptic connections necessary for the behavior and function of the adult fly. In this study, we identified and characterized specific lineages in the adult CNS and described their secondary branch patterns. Because prior studies show that the outgrowth of incumbent remodeling neurons in the CNS is highly dependent on the ecdysone pathway, we investigated the role of ecdysone in the development of the adult-specific neuronal lineages using a dominant-negative construct of the ecdysone receptor (EcR-DN). When EcR-DN was expressed in clones of the adult-specific lineages, neuroblasts persisted longer, but we saw no alteration in the initial projections of the lineages. Defects were observed in secondary arbors of adult neurons, including clumping and cohesion of fine branches, misrouting, smaller arbors and some defasciculation. The defects varied across the multiple neuron lineages in both appearance and severity. These results indicate that the ecdysone receptor complex influences the fine-tuning of connectivity between neuronal circuits, in conjunction with other factors driving outgrowth and synaptic partnering.

}, keywords = {Animals, Central Nervous System, Developmental, Drosophila, Drosophila Proteins, Ecdysone, Gene Expression Regulation, Genes, Genetically Modified, Insect, Interneurons, Motor Neurons, Neurogenesis, Receptors, Signal Transduction, Steroid}, issn = {1477-9129}, doi = {10.1242/dev.039859}, author = {Brown, Heather L D and Truman, James W} } @article {68816, title = {Functional Role of a Specialized Class of Spinal Commissural Inhibitory Neurons during Fast Escapes in Zebrafish}, journal = {Journal of Neuroscience}, volume = {29}, year = {2009}, month = {05/2009}, pages = {6780{\textendash}6793}, abstract = {

In teleost fish, the Mauthner (M) cell, a large reticulospinal neuron in the brainstem, triggers escape behavior. Spinal commissural inhibitory interneurons that are electrotonically excited by the M-axon have been identified, but the behavioral roles of these neurons have not yet been addressed. Here, we studied these neurons, named CoLo (commissural local), in larval zebrafish using an enhancer-trap line in which the entire population of CoLos was visualized by green fluorescent protein. CoLos were present at one cell per hemi-segment. Electrophysiological recordings showed that an M-spike evoked a spike in CoLos via electrotonic transmission and that CoLos made monosynaptic inhibitory connections onto contralateral primary motoneurons, consistent with the results in adult goldfish. We further showed that CoLos were active only during escapes. We examined the behavioral roles of CoLos by investigating escape behaviors in CoLo-ablated larvae. The results showed that the escape behaviors evoked by sound/vibration stimuli were often impaired with a reduced initial bend of the body, indicating that CoLos play important roles in initiating escapes. We obtained several lines of evidence that strongly suggested that the impaired escapes occurred during bilateral activation of the M-cells: in normal larvae, CoLo-mediated inhibitory circuits enable animals to perform escapes even in these occasions by silencing the output of the slightly delayed firing of the second M-cell. This study illustrates (1) a clear example of the behavioral role of a specialized class of interneurons and (2) the capacity of the spinal circuits to filter descending commands and thereby produce the appropriate behavior.

}, issn = {0270-6474}, doi = {10.1523/JNEUROSCI.0801-09.2009}, url = {https://www.jneurosci.org/content/29/21/6780}, author = {Chie Satou and Yukiko Kimura and Tsunehiko Kohashi and Kazuki Horikawa and Hiroyuki Takeda and Yoichi Oda and Shin-ichi Higashijima} } @article {46786, title = {Globally optimal stitching of tiled 3D microscopic image acquisitions.}, journal = {Bioinformatics}, volume = {25}, year = {2009}, month = {2009 Jun 1}, pages = {1463-5}, abstract = {

MOTIVATION: Modern anatomical and developmental studies often require high-resolution imaging of large specimens in three dimensions (3D). Confocal microscopy produces high-resolution 3D images, but is limited by a relatively small field of view compared with the size of large biological specimens. Therefore, motorized stages that move the sample are used to create a tiled scan of the whole specimen. The physical coordinates provided by the microscope stage are not precise enough to allow direct reconstruction (Stitching) of the whole image from individual image stacks.

RESULTS: To optimally stitch a large collection of 3D confocal images, we developed a method that, based on the Fourier Shift Theorem, computes all possible translations between pairs of 3D images, yielding the best overlap in terms of the cross-correlation measure and subsequently finds the globally optimal configuration of the whole group of 3D images. This method avoids the propagation of errors by consecutive registration steps. Additionally, to compensate the brightness differences between tiles, we apply a smooth, non-linear intensity transition between the overlapping images. Our stitching approach is fast, works on 2D and 3D images, and for small image sets does not require prior knowledge about the tile configuration.

AVAILABILITY: The implementation of this method is available as an ImageJ plugin distributed as a part of the Fiji project (Fiji is just ImageJ: http://pacific.mpi-cbg.de/).

}, keywords = {Animals, Drosophila, Imaging, Three-Dimensional, Larva, Microscopy, Confocal}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btp184}, author = {Preibisch, Stephan and Saalfeld, Stephan and Tomancak, Pavel} } @article {5237, title = {Hydrogen peroxide stimulates activity and alters behavior in Drosophila melanogaster.}, journal = {PLoS One}, volume = {4}, year = {2009}, month = {2009 Oct 28}, pages = {e7580}, abstract = {

Circadian rhythms in animals are regulated at the level of individual cells and by systemic signaling to coordinate the activities of multiple tissues. The circadian pacemakers have several physiological outputs, including daily locomotor rhythms. Several redox-active compounds have been found to function in regulation of circadian rhythms in cells, however, how particular compounds might be involved in regulating specific animal behaviors remains largely unknown. Here the effects of hydrogen peroxide on Drosophila movement were analyzed using a recently developed three-dimensional real-time multiple fly tracking assay. Both hydrogen peroxide feeding and direct injection of hydrogen peroxide caused increased adult fly locomotor activity. Continuous treatment with hydrogen peroxide also suppressed daily locomotor rhythms. Conditional over-expression of the hydrogen peroxide-producing enzyme superoxide dismutase (SOD) also increased fly activity and altered the patterns of locomotor activity across days and weeks. The real-time fly tracking system allowed for detailed analysis of the effects of these manipulations on behavior. For example, both hydrogen peroxide feeding and SOD over-expression increased all fly motion parameters, however, hydrogen peroxide feeding caused relatively more erratic movement, whereas SOD over-expression produced relatively faster-moving flies. Taken together, the data demonstrate that hydrogen peroxide has dramatic effects on fly movement and daily locomotor rhythms, and implicate hydrogen peroxide in the normal control of these processes.

}, keywords = {Animal, Animals, Behavior, Biological, Crosses, Drosophila melanogaster, Flight, Fluorescence, Genetic, Genetically Modified, Hydrogen Peroxide, Microscopy, Models, Movement, Oxidants, Oxidation-Reduction, Seasons, Superoxide Dismutase, Time Factors}, issn = {1932-6203}, doi = {10.1371/journal.pone.0007580}, author = {Grover, Dhruv and Ford, Daniel and Brown, Christopher and Hoe, Nicholas and Erdem, Aysen and Tavar{\'e}, Simon and Tower, John} } @article {1646, title = {Imaging neural activity in worms, flies and mice with improved GCaMP calcium indicators.}, journal = {Nature Methods}, volume = {6}, year = {2009}, month = {2009 Dec}, pages = {875-81}, abstract = {

Genetically encoded calcium indicators (GECIs) can be used to image activity in defined neuronal populations. However, current GECIs produce inferior signals compared to synthetic indicators and recording electrodes, precluding detection of low firing rates. We developed a single-wavelength GCaMP2-based GECI (GCaMP3), with increased baseline fluorescence (3-fold), increased dynamic range (3-fold) and higher affinity for calcium (1.3-fold). We detected GCaMP3 fluorescence changes triggered by single action potentials in pyramidal cell dendrites, with signal-to-noise ratio and photostability substantially better than those of GCaMP2, D3cpVenus and TN-XXL. In Caenorhabditis elegans chemosensory neurons and the Drosophila melanogaster antennal lobe, sensory stimulation-evoked fluorescence responses were significantly enhanced with GCaMP3 (4-6-fold). In somatosensory and motor cortical neurons in the intact mouse, GCaMP3 detected calcium transients with amplitudes linearly dependent on action potential number. Long-term imaging in the motor cortex of behaving mice revealed large fluorescence changes in imaged neurons over months.

}, keywords = {Animals, Brain, Caenorhabditis elegans, Calcium, Cell Line, Drosophila melanogaster, Fluorescence Resonance Energy Transfer, Humans, Mice, Neurons}, issn = {1548-7105}, doi = {10.1038/nmeth.1398}, author = {Tian, Lin and Hires, S Andrew and Mao, Tianyi and Huber, Daniel and Chiappe, M Eugenia and Chalasani, Sreekanth H and Petreanu, Leopoldo and Akerboom, Jasper and McKinney, Sean A and Schreiter, Eric R and Bargmann, Cornelia I and Jayaraman, Vivek and Svoboda, Karel and Looger, Loren L} } @article {2390, title = {Imaging transcription in living cells.}, journal = {Annual Review of Biophysics}, volume = {38}, year = {2009}, month = {2009 Feb 3}, pages = {173-96}, abstract = {

The advent of new technologies for the imaging of living cells has made it possible to determine the properties of transcription, the kinetics of polymerase movement, the association of transcription factors, and the progression of the polymerase on the gene. We report here the current state of the field and the progress necessary to achieve a more complete understanding of the various steps in transcription. Our Consortium is dedicated to developing and implementing the technology to further this understanding.

}, keywords = {Computer-Assisted, Fluorescence, Gene Expression Profiling, Image Interpretation, Microscopy, Transcription Factors, Transcriptional Activation}, issn = {1936-122X}, doi = {10.1073/pnas.1100640108}, author = {Darzacq, Xavier and Yao, Jie and Larson, Daniel R and Causse, Sebastien Z and Bosanac, Lana and de Turris, Valeria and Ruda, Vera M and Lionnet, Timoth{\'e}e and Zenklusen, Daniel and Guglielmi, Benjamin and Tjian, Robert and Singer, Robert H} } @article {6360, title = {Knockdown of parhyale ultrabithorax recapitulates evolutionary changes in crustacean appendage morphology.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, year = {2009}, month = {2009 Aug 18}, pages = {13892-6}, abstract = {

Crustaceans possess remarkably diverse appendages, both between segments of a single individual as well as between species. Previous studies in a wide range of crustaceans have demonstrated a correlation between the anterior expression boundary of the homeotic (Hox) gene Ultrabithorax (Ubx) and the location and number of specialized thoracic feeding appendages, called maxillipeds. Given that Hox genes regulate regional identity in organisms as diverse as mice and flies, these observations in crustaceans led to the hypothesis that Ubx expression regulates the number of maxillipeds and that evolutionary changes in Ubx expression have generated various aspects of crustacean appendage diversity. Specifically, evolutionary changes in the expression boundary of Ubx have resulted in crustacean species with either 0, 1, 2, or 3 pairs of thoracic maxillipeds. Here we test this hypothesis by altering the expression of Ubx in Parhyale hawaiensis, a crustacean that normally possesses a single pair of maxillipeds. By reducing Ubx expression, we can generate Parhyale with additional maxillipeds in a pattern reminiscent of that seen in other crustacean species, and these morphological alterations are maintained as the animals molt and mature. These results provide critical evidence supporting the proposition that changes in Ubx expression have played a role in generating crustacean appendage diversity and lend general insights into the mechanisms of morphological evolution.

}, keywords = {Animals, Base Sequence, Biological, Biological Evolution, Cloning, Crustacea, Electron, Extremities, Gene Expression Regulation, Genes, Genetic Techniques, Homeobox, Homeodomain Proteins, In Situ Hybridization, Microscopy, Models, Molecular, Molecular Sequence Data, RNA, Scanning, Small Interfering}, issn = {1091-6490}, doi = {10.1073/pnas.0903105106}, author = {Liubicich, Danielle M and Serano, Julia M and Pavlopoulos, Anastasios and Kontarakis, Zacharias and Protas, Meredith E and Kwan, Elaine and Chatterjee, Sandip and Tran, Khoa D and Averof, Michalis and Patel, Nipam H} } @article {4280, title = {Lessons from a compartmental model of a Drosophila neuron.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {29}, year = {2009}, month = {2009 Sep 30}, pages = {12033-4}, abstract = {

Although the vinegar fly, Drosophila melanogaster, has been a biological model organism for over a century, its emergence as a model system for the study of neurophysiology is comparatively recent. The primary reason for this is that the vinegar fly and its neurons are tiny; up until 5 years ago, it was prohibitively difficult to record intracellularly from individual neurons in the intact Drosophila brain (Wilson et al., 2004). Today, fly electrophysiologists can genetically label neurons with GFP and reliably record from many (but not all) neurons in the fruit fly brain. Using genetic tools to drive expression of fluorescent calcium indicators, light-sensitive ion channels, or cell activity suppressors, we are beginning to understand how the external environment is represented with electrical potentials in Drosophila neurons (for review, see Olsen and Wilson, 2008).

}, keywords = {Animals, Drosophila melanogaster, Humans, Models, Neurological, Neurons}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3348-09.2009}, author = {Tuthill, John C} } @proceedings {46329, title = {Maximin affinity learning of image segmentation}, volume = {22}, year = {2009}, publisher = {MIT Press}, abstract = {

Images can be segmented by first using a classifier to predict an affinity graph that reflects the degree to which image pixels must be grouped together and then partitioning the graph to yield a segmentation. Machine learning has been applied to the affinity classifier to produce affinity graphs that are good in the sense of minimizing edge misclassification rates. However, this error measure is only indirectly related to the quality of segmentations produced by ultimately partitioning the affinity graph. We present the first machine learning algorithm for training a classifier to produce affinity graphs that are good in the sense of producing segmentations that directly minimize the Rand index, a well known segmentation performance measure. The Rand index measures segmentation performance by quantifying the classification of the connectivity of image pixel pairs after segmentation. By using the simple graph partitioning algorithm of finding the connected components of the thresholded affinity graph, we are able to train an affinity classifier to directly minimize the Rand index of segmentations resulting from the graph partitioning. Our learning algorithm corresponds to the learning of maximin affinities between image pixel pairs, which are predictive of the pixel-pair connectivity.

}, author = {Srinivas C. Turaga and Kevin Briggman and Moritz N. Helmstaedter and Winfried Denk and Sebastian Seung} } @article {2687, title = {Neurotoxic effects induced by the Drosophila amyloid-beta peptide suggest a conserved toxic function.}, journal = {Neurobiology of Disease}, volume = {33}, year = {2009}, month = {2009 Feb}, pages = {274-81}, abstract = {

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

}, keywords = {Aging, Amino Acid Sequence, Amyloid, Amyloid beta-Protein Precursor, Amyloid Precursor Protein Secretases, Animal, Animals, Apoptosis, Behavior, Blotting, Brain, Cell Surface, Drosophila melanogaster, Drosophila Proteins, Electron, Gene Expression, Immunohistochemistry, Light, Membrane Proteins, Microscopy, Molecular Sequence Data, Nerve Degeneration, Nerve Tissue Proteins, Neurons, Peptide Fragments, Protease Nexins, Receptors, Western}, issn = {1095-953X}, doi = {10.1016/j.nbd.2008.10.014}, author = {Carmine-Simmen, Katia and Proctor, Thomas and Tsch{\"a}pe, Jakob and Poeck, Burkhard and Triphan, Tilman and Strauss, Roland and Kretzschmar, Doris} } @article {2849, title = {A novel mechanism of antagonism between ATP-dependent chromatin remodeling complexes regulates RNR3 expression.}, journal = {Molecular and Cellular Biology}, volume = {29}, year = {2009}, month = {2009 Jun}, pages = {3255-65}, abstract = {

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

}, keywords = {Adenosine Triphosphatases, Adenosine Triphosphate, Base Sequence, Chromatin, Chromatin Assembly and Disassembly, DNA, Fungal, Gene Expression, Genes, Genetic, Multiprotein Complexes, Mutation, Nucleosomes, Promoter Regions, Ribonucleoside Diphosphate Reductase, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Transcription Factors}, issn = {1098-5549}, doi = {10.1128/MCB.01741-08}, author = {Tomar, Raghuvir S and Psathas, James N and Zhang, Hesheng and Zhang, Zhengjian and Reese, Joseph C} } @article {47226, title = {Olfactory information processing in Drosophila.}, journal = {Current Biology : CB}, volume = {19}, year = {2009}, month = {2009 Aug 25}, pages = {R700-13}, abstract = {

In both insect and vertebrate olfactory systems only two synapses separate the sensory periphery from brain areas required for memory formation and the organisation of behaviour. In the\ Drosophila\ olfactory system, which is anatomically very similar to its vertebrate counterpart, there has been substantial recent progress in understanding the flow of information from experiments using\ molecular genetic, electrophysiological and optical imaging techniques. In this review, we shall focus on how olfactory information is processed and transformed in order to extract behaviourally relevant information. We follow the progress from olfactory receptor neurons, through the first processing area, the antennal lobe, to higher olfactory centres. We address both the underlying anatomy and mechanisms that govern the transformation of neural activity. We emphasise our emerging understanding of how different elementary computations, including signal averaging, gain control, decorrelation and integration, may be mapped onto different circuit elements.

}, doi = {10.1016/j.cub.2009.06.026}, author = {Masse, Nicolas Y and Turner, Glenn C and Jeffers, Gregory SXE} } @article {1097, title = {Onconase cytotoxicity relies on the distribution of its positive charge.}, journal = {The FEBS Journal}, volume = {276}, year = {2009}, month = {2009 Jul}, pages = {3846-57}, abstract = {

Onconase (ONC) is a member of the ribonuclease A superfamily that is toxic to cancer cells in vitro and in vivo. ONC is now in Phase IIIb clinical trials for the treatment of malignant mesothelioma. Internalization of ONC to the cytosol of cancer cells is essential for its cytotoxic activity, despite the apparent absence of a cell-surface receptor protein. Endocytosis and cytotoxicity do, however, appear to correlate with the net positive charge of ribonucleases. To dissect the contribution made by the endogenous arginine and lysine residues of ONC to its cytotoxicity, 22 variants were created in which cationic residues were replaced with alanine. Variants with the same net charge (+2 to +5) as well as equivalent catalytic activity and conformational stability were found to exhibit large (\> 10-fold) differences in toxicity for the cells of a human leukemia line. In addition, a more cationic ONC variant could be either much more or much less cytotoxic than a less cationic variant, again depending on the distribution of its cationic residues. The endocytosis of variants with widely divergent cytotoxic activity was quantified by flow cytometry using a small-molecule fluorogenic label, and was found to vary by twofold or less. This small difference in endocytosis did not account for the large difference in cytotoxicity, implicating the distribution of cationic residues as being critical for lipid-bilayer translocation subsequent to endocytosis. This finding has fundamental implications for understanding the interaction of ribonucleases and other proteins with mammalian cells.

}, keywords = {Amino Acid Sequence, Animals, Antineoplastic Agents, Cations, Cell Line, Cell Proliferation, Endocytosis, Genetic Variation, Humans, Models, Molecular, Molecular Sequence Data, Protein Structure, Rana pipiens, Ribonucleases, Sequence Alignment, Tertiary, Tumor}, issn = {1742-4658}, doi = {10.1111/j.1742-4658.2009.07098.x}, author = {Turcotte, Rebecca F and Lavis, Luke D and Raines, Ronald T} } @article {3914, title = {Pathway interactions and synaptic plasticity in the dendritic tuft regions of CA1 pyramidal neurons.}, journal = {Neuron}, volume = {62}, year = {2009}, month = {2009 Apr 16}, pages = {102-11}, abstract = {

Input comparison is thought to occur in many neuronal circuits, including the hippocampus, where functionally important interactions between the Schaffer collateral and perforant pathways have been hypothesized. We investigated this idea using multisite, whole-cell recordings and Ca2+ imaging and found that properly timed, repetitive stimulation of both pathways results in the generation of large plateau potentials in distal dendrites of CA1 pyramidal neurons. These dendritic plateau potentials produce widespread Ca2+ influx, large after-depolarizations, burst firing output, and long-term potentiation of perforant path synapses. Plateau duration is directly related to the strength and temporal overlap of pathway activation and involves back-propagating action potentials and both NMDA receptors and voltage-gated Ca2+ channels. Thus, the occurrence of highly correlated SC and PP input to CA1 is signaled by a dramatic change in output mode and an increase in input efficacy, all induced by a large plateau potential in the distal dendrites of CA1 pyramidal neurons.

}, keywords = {Anesthetics, Animals, Biophysics, Calcium, Calcium Channel Blockers, Dendrites, Electric Stimulation, Excitatory Amino Acid Antagonists, Hippocampus, Inhibitory Postsynaptic Potentials, Local, Long-Term Potentiation, Membrane Potentials, Neural Pathways, Neuronal Plasticity, Newborn, Patch-Clamp Techniques, Pyramidal Cells, Rats, Spider Venoms, Sprague-Dawley, Synapses, Tetrodotoxin}, issn = {1097-4199}, doi = {10.1016/j.neuron.2009.03.007}, author = {Takahashi, Hiroto and Magee, Jeffrey C} } @article {6341, title = {Pentameric assembly of potassium channel tetramerization domain-containing protein 5.}, journal = {Journal of Molecular Biology}, volume = {387}, year = {2009}, month = {2009 Mar 20}, pages = {175-91}, abstract = {

We report the X-ray crystal structure of human potassium channel tetramerization domain-containing protein 5 (KCTD5), the first member of the family to be so characterized. Four findings were unexpected. First, the structure reveals assemblies of five subunits while tetramers were anticipated; pentameric stoichiometry is observed also in solution by scanning transmission electron microscopy mass analysis and analytical ultracentrifugation. Second, the same BTB (bric-a-brac, tramtrack, broad complex) domain surface mediates the assembly of five KCTD5 and four voltage-gated K(+) (Kv) channel subunits; four amino acid differences appear crucial. Third, KCTD5 complexes have well-defined N- and C-terminal modules separated by a flexible linker that swivels by approximately 30 degrees; the C-module shows a new fold and is required to bind Golgi reassembly stacking protein 55 with approximately 1 microM affinity, as judged by surface plasmon resonance and ultracentrifugation. Fourth, despite the homology reflected in its name, KCTD5 does not impact the operation of Kv4.2, Kv3.4, Kv2.1, or Kv1.2 channels.

}, keywords = {Amino Acid, Amino Acid Sequence, Biopolymers, Crystallography, Humans, Models, Molecular, Molecular Sequence Data, Potassium Channels, Protein Conformation, Sequence Homology, Static Electricity, Surface Plasmon Resonance, X-Ray}, issn = {1089-8638}, doi = {10.1016/j.jmb.2009.01.030}, author = {Dementieva, Irina S and Tereshko, Valentina and McCrossan, Zoe A and Solomaha, Elena and Araki, Daniel and Xu, Chen and Grigorieff, Nikolaus and Goldstein, Steve A N} } @article {6491, title = {A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale.}, journal = {PLoS Computational Biology}, volume = {5}, year = {2009}, month = {2009 Mar}, pages = {e1000334}, abstract = {

In this era of complete genomes, our knowledge of neuroanatomical circuitry remains surprisingly sparse. Such knowledge is critical, however, for both basic and clinical research into brain function. Here we advocate for a concerted effort to fill this gap, through systematic, experimental mapping of neural circuits at a mesoscopic scale of resolution suitable for comprehensive, brainwide coverage, using injections of tracers or viral vectors. We detail the scientific and medical rationale and briefly review existing knowledge and experimental techniques. We define a set of desiderata, including brainwide coverage; validated and extensible experimental techniques suitable for standardization and automation; centralized, open-access data repository; compatibility with existing resources; and tractability with current informatics technology. We discuss a hypothetical but tractable plan for mouse, additional efforts for the macaque, and technique development for human. We estimate that the mouse connectivity project could be completed within five years with a comparatively modest budget.

}, keywords = {Animals, Brain, Databases, Factual, Humans, Macaca, Mice, Models, Nerve Net, Neuroanatomy, Neurological, Research Design}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1000334}, author = {Bohland, Jason W and Wu, Caizhi and Barbas, Helen and Bokil, Hemant and Bota, Mihail and Breiter, Hans C and Cline, Hollis T and Doyle, John C and Freed, Peter J and Greenspan, Ralph J and Haber, Suzanne N and Hawrylycz, Michael and Herrera, Daniel G and Hilgetag, Claus C and Huang, Z Josh and Jones, Allan and Jones, Edward G and Karten, Harvey J and Kleinfeld, David and K{\"o}tter, Rolf and Lester, Henry A and Lin, John M and Mensh, Brett D and Mikula, Shawn and Panksepp, Jaak and Price, Joseph L and Safdieh, Joseph and Saper, Clifford B and Schiff, Nicholas D and Schmahmann, Jeremy D and Stillman, Bruce W and Svoboda, Karel and Swanson, Larry W and Toga, Arthur W and Van Essen, David C and Watson, James D and Mitra, Partha P} } @article {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 {2388, title = {Shifting players and paradigms in cell-specific transcription.}, journal = {Molecular Cell}, volume = {36}, year = {2009}, month = {2009 Dec 25}, pages = {924-31}, abstract = {

Historically, developmental-stage- and tissue-specific patterns of gene expression were assumed to be determined primarily by DNA regulatory sequences and their associated activators, while the general transcription machinery including core promoter recognition complexes, coactivators, and chromatin modifiers was held to be invariant. New evidence suggests that significant changes in these general transcription factors including TFIID, BAF, and Mediator may facilitate global changes in cell-type-specific transcription.

}, keywords = {Animals, Developmental, Gene Expression Regulation, Genetic, Mediator Complex, Models, Molecular, Promoter Regions, Protein Isoforms, TATA Box Binding Protein-Like Proteins, Tissue Distribution, Transcription, Transcription Factor TFIID}, issn = {1097-4164}, doi = {10.1073/pnas.1100640108}, author = {D{\textquoteright}Alessio, Joseph A and Wright, Kevin J and Tjian, Robert} } @article {2389, title = {Structures of three distinct activator-TFIID complexes.}, journal = {Genes \& Development}, volume = {23}, year = {2009}, month = {2009 Jul 1}, pages = {1510-21}, abstract = {

Sequence-specific DNA-binding activators, key regulators of gene expression, stimulate transcription in part by targeting the core promoter recognition TFIID complex and aiding in its recruitment to promoter DNA. Although it has been established that activators can interact with multiple components of TFIID, it is unknown whether common or distinct surfaces within TFIID are targeted by activators and what changes if any in the structure of TFIID may occur upon binding activators. As a first step toward structurally dissecting activator/TFIID interactions, we determined the three-dimensional structures of TFIID bound to three distinct activators (i.e., the tumor suppressor p53 protein, glutamine-rich Sp1 and the oncoprotein c-Jun) and compared their structures as determined by electron microscopy and single-particle reconstruction. By a combination of EM and biochemical mapping analysis, our results uncover distinct contact regions within TFIID bound by each activator. Unlike the coactivator CRSP/Mediator complex that undergoes drastic and global structural changes upon activator binding, instead, a rather confined set of local conserved structural changes were observed when each activator binds holo-TFIID. These results suggest that activator contact may induce unique structural features of TFIID, thus providing nanoscale information on activator-dependent TFIID assembly and transcription initiation.

}, keywords = {Hela Cells, Humans, Imaging, Immunoglobulins, Models, Molecular, Protein Binding, Protein Multimerization, Protein Structure, Proto-Oncogene Proteins c-jun, Quaternary, TATA-Binding Protein Associated Factors, Three-Dimensional, Transcription Factor TFIID, Tumor Suppressor Protein p53}, issn = {1549-5477}, doi = {10.1073/pnas.1100640108}, author = {Liu, Wei-Li and Coleman, Robert A and Ma, Elizabeth and Grob, Patricia and Yang, Joyce L and Zhang, Yixi and Dailey, Gina and Nogales, Eva and Tjian, Robert} } @article {6132, title = {Synaptic activity-responsive element in the Arc/Arg3.1 promoter essential for synapse-to-nucleus signaling in activated neurons.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, year = {2009}, month = {2009 Jan 6}, pages = {316-21}, abstract = {

The neuronal immediate early gene Arc/Arg-3.1 is widely used as one of the most reliable molecular markers for intense synaptic activity in vivo. However, the cis-acting elements responsible for such stringent activity dependence have not been firmly identified. Here we combined luciferase reporter assays in cultured cortical neurons and comparative genome mapping to identify the critical synaptic activity-responsive elements (SARE) of the Arc/Arg-3.1 gene. A major SARE was found as a unique approximately 100-bp element located at \>5 kb upstream of the Arc/Arg-3.1 transcription initiation site in the mouse genome. This single element, when positioned immediately upstream of a minimal promoter, was necessary and sufficient to replicate crucial properties of endogenous Arc/Arg-3.1{\textquoteright}s transcriptional regulation, including rapid onset of transcription triggered by synaptic activity and low basal expression during synaptic inactivity. We identified the major determinants of SARE as a unique cluster of neuronal activity-dependent cis-regulatory elements consisting of closely localized binding sites for CREB, MEF2, and SRF. Consistently, a SARE reporter could readily trace and mark an ensemble of cells that have experienced intense activity in the recent past in vivo. Taken together, our work uncovers a novel transcriptional mechanism by which a critical 100-bp element, SARE, mediates a predominant component of the synapse-to-nucleus signaling in ensembles of Arc/Arg-3.1-positive activated neurons.

}, keywords = {Animals, Binding Sites, Cell Nucleus, Cyclic AMP Response Element-Binding Protein, Cytoskeletal Proteins, Gene Expression Regulation, Genetic, Genomics, Mice, Myogenic Regulatory Factors, Nerve Tissue Proteins, Neurons, Nucleic Acid, Promoter Regions, Regulatory Sequences, Serum Response Factor, Signal Transduction, Synapses}, issn = {1091-6490}, doi = {10.1073/pnas.0806518106}, author = {Kawashima, Takashi and Okuno, Hiroyuki and Nonaka, Mio and Adachi-Morishima, Aki and Kyo, Nan and Okamura, Michiko and Takemoto-Kimura, Sayaka and Worley, Paul F and Bito, Haruhiko} } @article {2495, title = {Temporal patterns of broad isoform expression during the development of neuronal lineages in Drosophila.}, journal = {Neural Development}, volume = {4}, year = {2009}, month = {2009 Nov 2}, pages = {39}, abstract = {

During the development of the central nervous system (CNS) of Drosophila, neuronal stem cells, the neuroblasts (NBs), first generate a set of highly diverse neurons, the primary neurons that mature to control larval behavior, and then more homogeneous sets of neurons that show delayed maturation and are primarily used in the adult. These latter, {\textquoteright}secondary{\textquoteright} neurons show a complex pattern of expression of broad, which encodes a transcription factor usually associated with metamorphosis, where it acts as a key regulator in the transitions from larva and pupa.

}, keywords = {Animals, Biological, Drosophila, Drosophila Proteins, Genetically Modified, Interneurons, Metamorphosis, Motor Neurons, Mushroom Bodies, Neurites, Neurons, Newborn, Nonmammalian, Optic Lobe, Protein Isoforms, Thorax, Time Factors, Transcription Factors}, issn = {1749-8104}, doi = {10.1186/1749-8104-4-39}, author = {Zhou, Baohua and Williams, Darren W and Altman, Janet and Riddiford, Lynn M and Truman, James W} } @article {5357, title = {Three dimensional super resolution fluorescence imaging of single bacterial cells by stereo photoactivated localization microscopy.}, journal = {Microscopy and Microanalysis}, volume = {15}, year = {2009}, month = {2009 July 26}, pages = {564-5}, doi = {10.1017/S1431927609095737}, author = {Tang, Jianyong and Vaziri, Alipasha and Akerboom, Jasper P. and Looger, Loren and Shank, Charles V} } @article {5363, title = {Three-dimensional nanoscopy of biological samples.}, journal = {2009 Conference on Lasers and Electro-Optics and Quantum Electronics and Laser Science Conference (CLEO/QELS 2009), Vols. 1-5}, volume = {1-5}, year = {2009}, month = {2009 Jun 5}, pages = {147-8}, abstract = {

We have demonstrated super-resolution imaging of protein distributions in cells at depth at multiple layers with a lateral localization precision better than 50 nm. The approach is based on combining photoactivated localization microscopy with temporal focusing.

}, author = {Vaziri, Alipasha and Tang, Jianyong and Shroff, Hari and Shank, Charles V} } @article {5359, title = {Three-dimensional super-resolution imaging of thick biological samples.}, journal = {Microscopy and Microanalysis}, volume = {15}, year = {2009}, month = {2009 Jul 26}, pages = {36-7}, doi = {10.1017/S1431927609092368}, author = {Vaziri, A. and Tang, J. and Shroff, H. and Shank, C.} } @article {2391, title = {Wnt signaling targets ETO coactivation domain of TAF4/TFIID in vivo.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, year = {2009}, month = {2009 Jan 6}, pages = {55-60}, abstract = {

Understanding the diverse activities of the multisubunit core promoter recognition complex TFIID in vivo requires knowledge of how individual subunits contribute to overall functions of this TATA box-binding protein (TBP)/TBP-associated factor (TAF) complex. By generating altered holo-TFIID complexes in Drosophila we identify the ETO domain of TAF4 as a coactivator domain likely targeted by Pygopus, a protein that is required for Wingless-induced transcription of naked cuticle. These results establish a coactivator function of TAF4 and provide a strategy to dissect mechanisms of TFIID function in vivo.

}, keywords = {Animals, Binding Sites, Cell Line, Drosophila, Drosophila Proteins, Humans, Intracellular Signaling Peptides and Proteins, Larva, Multiprotein Complexes, Proto-Oncogene Proteins, Signal Transduction, TATA-Binding Protein Associated Factors, Transcription Factor TFIID, Transcription Factors, Tumor, Wnt Proteins}, issn = {1091-6490}, doi = {10.1073/pnas.1100640108}, author = {Wright, Kevin J and Tjian, Robert} } @article {2689, title = {Analysis of a spatial orientation memory in Drosophila.}, journal = {Nature}, volume = {453}, year = {2008}, month = {2008 Jun 26}, pages = {1244-7}, abstract = {

Flexible goal-driven orientation requires that the position of a target be stored, especially in case the target moves out of sight. The capability to retain, recall and integrate such positional information into guiding behaviour has been summarized under the term spatial working memory. This kind of memory contains specific details of the presence that are not necessarily part of a long-term memory. Neurophysiological studies in primates indicate that sustained activity of neurons encodes the sensory information even though the object is no longer present. Furthermore they suggest that dopamine transmits the respective input to the prefrontal cortex, and simultaneous suppression by GABA spatially restricts this neuronal activity. Here we show that Drosophila melanogaster possesses a similar spatial memory during locomotion. Using a new detour setup, we show that flies can remember the position of an object for several seconds after it has been removed from their environment. In this setup, flies are temporarily lured away from the direction towards their hidden target, yet they are thereafter able to aim for their former target. Furthermore, we find that the GABAergic (stainable with antibodies against GABA) ring neurons of the ellipsoid body in the central brain are necessary and their plasticity is sufficient for a functional spatial orientation memory in flies. We also find that the protein kinase S6KII (ignorant) is required in a distinct subset of ring neurons to display this memory. Conditional expression of S6KII in these neurons only in adults can restore the loss of the orientation memory of the ignorant mutant. The S6KII signalling pathway therefore seems to be acutely required in the ring neurons for spatial orientation memory in flies.

}, keywords = {90-kDa, Animals, Drosophila melanogaster, gamma-Aminobutyric Acid, Locomotion, Memory, Models, Neurological, Neurons, Orientation, Ribosomal Protein S6 Kinases, Signal Transduction, Space Perception}, issn = {1476-4687}, doi = {10.1038/nature07003}, author = {Neuser, Kirsa and Triphan, Tilman and Mronz, Markus and Poeck, Burkhard and Strauss, Roland} } @proceedings {46794, title = {Automatic landmark correspondence detection for ImageJ.}, year = {2008}, month = {2008 Nov 7}, address = {Luxembourg}, abstract = {

Landmark correspondences can be used for various tasks in image processing such as image alignment, reconstruction of panoramic photographs, object recognition and simultaneous localization and mapping for mobile robots. The computer vision community knows several techniques for extracting and pairwise associating such landmarks using distinctive invariant local image features. Two very successful methods are the Scale Invariant Feature Transform (SIFT)1 and Multi-Scale Oriented Patches (MOPS).2
We implemented these methods in the Java programming language3 for seamless use in ImageJ.4 We use it for fully automatic registration of gigantic serial section Transmission Electron Microscopy (TEM) mosaics. Using automatically detected landmark correspondences, the registration of large image mosaics simplifies to globally minimizing the displacement of corresponding points.
We present here an introduction to automatic landmark correspondence detection and demonstrate our implementation for ImageJ. We demonstrate the application of the plug-in on diverse image data.

}, author = {Saalfeld, Stephan and Tomancak, Pavel} } @article {1732, title = {Characterization of vibrational resonances of water-vapor interfaces by phase-sensitive sum-frequency spectroscopy.}, journal = {Physical Review Letters}, volume = {100}, year = {2008}, month = {2008 Mar 7}, pages = {096102}, abstract = {

Phase-sensitive sum-frequency spectroscopy provides correct characterization of vibrational resonances of water-vapor interfaces and allows better identification of interfacial water species contributing to different parts of the spectra. Iodine ions emerging at an interface create a surface field that tends to reorient the more loosely bonded water molecules below the topmost layer.

}, keywords = {Hydrogen Bonding, Models, Molecular, Spectrum Analysis, Surface Properties, Volatilization, Water}, issn = {0031-9007}, author = {Ji, N and Ostroverkhov, V and Tian, C S and Shen, Y R} } @article {2392, title = {Codependent activators direct myoblast-specific MyoD transcription.}, journal = {Developmental Cell}, volume = {15}, year = {2008}, month = {2008 Oct}, pages = {534-46}, abstract = {

Although FoxO and Pax proteins represent two important families of transcription factors in determining cell fate, they had not been functionally or physically linked together in mediating regulation of a common target gene during normal cellular transcription programs. Here, we identify MyoD, a key regulator of myogenesis, as a direct target of FoxO3 and Pax3/7 in myoblasts. Our cell-based assays and in vitro studies reveal a tight codependent partnership between FoxO3 and Pax3/7 to coordinately recruit RNA polymerase II and form a preinitiation complex (PIC) to activate MyoD transcription in myoblasts. The role of FoxO3 in regulating muscle differentiation is confirmed in vivo by observed defects in muscle regeneration caused by MyoD downregulation in FoxO3 null mice. These data establish a mutual interdependence and functional link between two families of transcription activators serving as potential signaling sensors and regulators of cell fate commitment in directing tissue specific MyoD transcription.

}, keywords = {Animals, Cell Line, Forkhead Transcription Factors, Genetic, Immunohistochemistry, Knockout, Mice, Myoblasts, MyoD Protein, Paired Box Transcription Factors, RNA, RNA Interference, Small Interfering, Trans-Activators, Transcription, Transfection}, issn = {1878-1551}, doi = {10.1073/pnas.1100640108}, author = {Hu, Ping and Geles, Kenneth G and Paik, Ji-Hye and DePinho, Ronald A and Tjian, Robert} } @article {2291, title = {Coding and non-coding polymorphisms in alcohol dehydrogenase alters protein expression and alcohol-associated erythema.}, journal = {The Journal of Investigative Dermatology}, volume = {128}, year = {2008}, month = {2008 Mar}, pages = {616-27}, abstract = {

Ethanol (EtOH), isopropyl alcohol (IPA), and propylene glycol (PG) increase topical drug delivery, but are sometimes associated with erythema. A potential genetic basis for alcohol-associated erythema was investigated as the function of polymorphisms in coding and non-coding regions of class IB alcohol dehydrogenase (ADHIB) and evaluated for altered gene expression in vitro and metabolic activity in vivo via altered skin blood flow (Doppler velocimeter) and erythema (reflectance colorimeter a*) following topical challenge to 5 M EtOH, IPA, PG, and butanol (ButOH). Promoter polymorphisms G-887A and C-739T and exon G143A form eight ADHIB haplotypes with different frequencies in Caucasians vs Asians and exhibit variable gene expression and metabolic activity. Polymorphisms C-739T and G-887A independently alter gene expression, which is further increased by IPA and PG, but not EtOH or ButOH. EtOH and ButOH increase erythema as a function of skin blood flow. IPA increases skin blood flow without erythema and PG increased erythema with decreased skin blood flow, all as a function of ADHIB haplotype. PG-induced erythema was uniquely associated with tumor necrosis factor-alpha expression. Thus, erythema following alcohol exposure is alcohol type specific, has a pharmacogenetic basis related to ADHIB haplotype and can be functionally evaluated via Doppler velocimetry and reflectance colorimetry in vivo.

}, keywords = {Administration, Adolescent, Adult, Aged, Alcohol Dehydrogenase, Alcohols, Asian Continental Ancestry Group, Enzymologic, Erythema, European Continental Ancestry Group, Female, Gene Expression Regulation, Gene Frequency, Genetic, Haplotypes, Humans, Laser-Doppler Flowmetry, Male, Middle Aged, Patch Tests, Polymorphism, Promoter Regions, Single Nucleotide, Skin, Topical}, issn = {1523-1747}, doi = {10.1038/sj.jid.5701105}, author = {Pershing, Lynn K and Chen, Yuexian and Tkachuk, Ariana N and Rausch, Holly L and Petelenz-Rubin, Kasia and Corlett, Judy L and Hobbs, Maurine R} } @article {2396, title = {ES cell pluripotency and germ-layer formation require the SWI/SNF chromatin remodeling component BAF250a.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, year = {2008}, month = {2008 May 6}, pages = {6656-61}, abstract = {

ATP-dependent chromatin remodeling complexes are a notable group of epigenetic modifiers that use the energy of ATP hydrolysis to change the structure of chromatin, thereby altering its accessibility to nuclear factors. BAF250a (ARID1a) is a unique and defining subunit of the BAF chromatin remodeling complex with the potential to facilitate chromosome alterations critical during development. Our studies show that ablation of BAF250a in early mouse embryos results in developmental arrest (about embryonic day 6.5) and absence of the mesodermal layer, indicating its critical role in early germ-layer formation. Moreover, BAF250a deficiency compromises ES cell pluripotency, severely inhibits self-renewal, and promotes differentiation into primitive endoderm-like cells under normal feeder-free culture conditions. Interestingly, this phenotype can be partially rescued by the presence of embryonic fibroblast cells. DNA microarray, immunostaining, and RNA analyses revealed that BAF250a-mediated chromatin remodeling contributes to the proper expression of numerous genes involved in ES cell self-renewal, including Sox2, Utf1, and Oct4. Furthermore, the pluripotency defects in BAF250a mutant ES cells appear to be cell lineage-specific. For example, embryoid body-based analyses demonstrated that BAF250a-ablated stem cells are defective in differentiating into fully functional mesoderm-derived cardiomyocytes and adipocytes but are capable of differentiating into ectoderm-derived neurons. Our results suggest that BAF250a is a key component of the gene regulatory machinery in ES cells controlling self-renewal, differentiation, and cell lineage decisions.

}, keywords = {Adipocytes, Animals, Cardiac, Cell Differentiation, Cell Line, Cell Lineage, Cell Proliferation, Chromatin Assembly and Disassembly, Chromosomal Proteins, Developmental, DNA-Binding Proteins, Embryo, Embryonic Development, Embryonic Stem Cells, Female, Genes, Germ Layers, Knockout, Male, Mammalian, Mice, Muscle, Myocytes, Non-Histone, Nuclear Proteins, Pluripotent Stem Cells, Skeletal, Transcription Factors}, issn = {1091-6490}, doi = {10.1073/pnas.1100640108}, author = {Gao, Xiaolin and Tate, Peri and Hu, Ping and Tjian, Robert and Skarnes, William C and Wang, Zhong} } @article {46624, title = {Ethanol sensitivity and tolerance in long-term memory mutants of Drosophila melanogaster.}, journal = {Alcoholism, Clinical and Experimental Research}, volume = {32}, year = {2008}, month = {2008 May}, pages = {895-908}, abstract = {

BACKGROUND: It has become increasingly clear that molecular and neural mechanisms underlying learning and memory and drug addiction are largely shared. To confirm and extend these findings, we analyzed ethanol-responsive behaviors of a collection of Drosophila long-term memory mutants.

METHODS: For each mutant, sensitivity to the acute uncoordinating effects of ethanol was quantified using the inebriometer. Additionally, 2 distinct forms of ethanol tolerance were measured: rapid tolerance, which develops in response to a single brief exposure to a high concentration of ethanol vapor; and chronic tolerance, which develops following a sustained low-level exposure.

RESULTS: Several mutants were identified with altered sensitivity, rapid or chronic tolerance, while a number of mutants exhibited multiple defects.

CONCLUSIONS: The corresponding genes in these mutants represent areas of potential overlap between learning and memory and behavioral responses to alcohol. These genes also define components shared between different ethanol behavioral responses.

}, keywords = {Animals, Behavior, Animal, Drosophila melanogaster, Drug Tolerance, Ethanol, Learning, Memory}, issn = {1530-0277}, doi = {10.1111/j.1530-0277.2008.00659.x}, author = {Berger, Karen H and Kong, Eric C and Dubnau, Josh and Tully, Tim and Moore, Monica S and Heberlein, Ulrike} } @proceedings {46795, title = {Fast stitching of large 3d biological datasets.}, year = {2008}, month = {2008 Nov 7}, address = {Luxembourg}, abstract = {

In order to study anatomy of organisms with high-resolution there is an increasing demand to image large specimen in three dimensions (3D). Confocal microscopy is able to produce high-resolution 3D images, but these are limited by its relatively small field of view compared to the size of large biological specimens. To overcome this drawback, motorized stages moving the sample are used to create a tiled scan of the whole specimen. The physical coordinates provided by the microscope stage are not precise enough to allow reconstruction ({\textquotedblright}Stitching{\textquotedblright}) of the whole image from individual image stacks.
We developed an algorithm, as well as an ImageJ plug-in, based on the Fourier Shift Theorem that computes all possible translations (x, y, z) between two 3D images at once, yielding the best overlap in terms of the cross correlation measure. Apart from the obvious gain in computation time it has the advantage that it cannot be trapped in local minima as it simply computes all possible solutions. Computing the overlap between two adjacent image stacks is fast (12 seconds for two 512x512x89 images on a Intel {\textregistered} Core2Duo with 2.2GHz) making it suitable for real time use, i.e. computing the output image during acquisition of the individual image stacks.
To compensate the possible shading- and brightness differences we apply a smooth linear intensity transition between the overlapping stacks. Additionally we extended the to generic 3D registration using gradient based rotation detection on top of the phase correlation method. We demonstrate the performance of our 3D stitching plug-in on several tiled confocal images and show an example of its application for 3D registration.

}, author = {Preibisch, Stephan and Saalfeld, Stephan and Tomancak, Pavel} } @article {2394, title = {The future for Howard Hughes. Interview by Erika Check Hayden.}, journal = {Nature}, volume = {455}, year = {2008}, month = {2008 Oct 9}, pages = {718}, keywords = {Academies and Institutes, Creativeness, Disease, Humans, Internationality, Maryland, Molecular Biology, Research, Research Personnel}, issn = {1476-4687}, doi = {10.1073/pnas.1100640108}, author = {Tjian, Robert} } @article {3932, title = {Genetically encoded fluorescent sensors for studying healthy and diseased nervous systems.}, journal = {Drug Discovery Today. Disease Models}, volume = {5}, year = {2008}, month = {2008}, pages = {27-35}, abstract = {

Neurons and glia are functionally organized into circuits and higher-order structures via synaptic connectivity, well-orchestrated molecular signaling, and activity-dependent refinement. Such organization allows the precise information processing required for complex behaviors. Disruption of nervous systems by genetic deficiency or events such as trauma or environmental exposure may produce a diseased state in which certain aspects of inter-neuron signaling are impaired. Optical imaging techniques allow the direct visualization of individual neurons in a circuit environment. Imaging probes specific for given biomolecules may help elucidate their contribution to proper circuit function. Genetically encoded sensors can visualize trafficking of particular molecules in defined neuronal populations, non-invasively in intact brain or reduced preparations. Sensor analysis in healthy and diseased brains may reveal important differences and shed light on the development and progression of nervous system disorders. We review the field of genetically encoded sensors for molecules and cellular events, and their potential applicability to the study of nervous system disease.

}, issn = {1740-6757}, doi = {10.1016/j.ddmod.2008.07.003}, author = {Tian, Lin and Looger, Loren L} } @article {1731, title = {Interfacial structures of acidic and basic aqueous solutions.}, journal = {Journal of the American Chemical Society}, volume = {130}, year = {2008}, month = {2008 Oct 1}, pages = {13033-9}, abstract = {

Phase-sensitive sum-frequency vibrational spectroscopy was used to study water/vapor interfaces of HCl, HI, and NaOH solutions. The measured imaginary part of the surface spectral responses provided direct characterization of OH stretch vibrations and information about net polar orientations of water species contributing to different regions of the spectrum. We found clear evidence that hydronium ions prefer to emerge at interfaces. Their OH stretches contribute to the "ice-like" band in the spectrum. Their charges create a positive surface field that tends to reorient water molecules more loosely bonded to the topmost water layer with oxygen toward the interface, and thus enhances significantly the "liquid-like" band in the spectrum. Iodine ions in solution also like to appear at the interface and alter the positive surface field by forming a narrow double-charge layer with hydronium ions. In NaOH solution, the observed weak change of the "liquid-like" band and disappearance of the "ice-like" band in the spectrum indicates that OH(-) ions must also have excess at the interface. How they are incorporated in the interfacial water structure is, however, not clear.

}, issn = {1520-5126}, doi = {10.1021/ja8021297}, author = {Tian, Chuanshan and Ji, Na and Waychunas, Glenn A and Shen, Y Ron} } @article {2688, title = {Locomotor control by the central complex in Drosophila-an analysis of the tay bridge mutant.}, journal = {Developmental Neurobiology}, volume = {68}, year = {2008}, month = {2008 Jul}, pages = {1046-58}, abstract = {

Several aspects of locomotor control have been ascribed to the central complex of the insect brain; however, the role of distinct substructures of this complex is not well known. The tay bridge1 (tay1) mutant of Drosophila melanogaster was originally isolated on the basis of reduced walking speed and activity. In addition, tay1 is defective in the compensation of rotatory stimuli during walking and histologically, tay1 causes a mid-sagittal constriction of the protocerebral bridge, a constituent of the central complex. Cloning of the tay gene revealed that it encodes a novel protein with no significant homology to any known protein. To associate the behavioral phenotypes with the anatomical defect in the protocerebral bridge, we used different driver lines to express the tay cDNA in various neuronal subpopulations of the central brain in tay1-mutant flies. These experiments showed an association of the aberrant walking speed and activity with the structural defect in the protocerebral bridge. In contrast, the compensation of rotatory stimuli during walking was rescued without a restoration of the protocerebral bridge. The results of our differential rescue approach are supported by neuronal silencing experiments using conditional tetanus toxin expression in the same subset of neurons. These findings show for the first time that the walking speed and activity is controlled by different substructures of the central brain than the compensatory locomotion for rotatory stimuli.

}, keywords = {Amino Acid Sequence, Animal, Animals, Behavior, Brain, Cell Line, Drosophila melanogaster, Drosophila Proteins, Genetic Vectors, Locomotion, Male, Motor Activity, Mushroom Bodies, Mutation, Neurons, Phenotype, Photic Stimulation, Polymerase Chain Reaction, Transformed}, issn = {1932-8451}, doi = {10.1002/dneu.20643}, author = {Poeck, Burkhard and Triphan, Tilman and Neuser, Kirsa and Strauss, Roland} } @article {5225, title = {Multilayer three-dimensional super resolution imaging of thick biological samples.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, year = {2008}, month = {2008 Dec 23}, pages = {20221-6}, abstract = {

Recent advances in optical microscopy have enabled biological imaging beyond the diffraction limit at nanometer resolution. A general feature of most of the techniques based on photoactivated localization microscopy (PALM) or stochastic optical reconstruction microscopy (STORM) has been the use of thin biological samples in combination with total internal reflection, thus limiting the imaging depth to a fraction of an optical wavelength. However, to study whole cells or organelles that are typically up to 15 microm deep into the cell, the extension of these methods to a three-dimensional (3D) super resolution technique is required. Here, we report an advance in optical microscopy that enables imaging of protein distributions in cells with a lateral localization precision better than 50 nm at multiple imaging planes deep in biological samples. The approach is based on combining the lateral super resolution provided by PALM with two-photon temporal focusing that provides optical sectioning. We have generated super-resolution images over an axial range of approximately 10 microm in both mitochondrially labeled fixed cells, and in the membranes of living S2 Drosophila cells.

}, keywords = {Animals, Cell Line, Cells, Humans, Imaging, Microscopy, Mitochondria, Organelles, Three-Dimensional}, issn = {1091-6490}, doi = {10.1073/pnas.0810636105}, author = {Vaziri, Alipasha and Tang, Jianyong and Shroff, Hari and Shank, Charles V} } @article {2393, title = {MyoD targets TAF3/TRF3 to activate myogenin transcription.}, journal = {Molecular Cell}, volume = {32}, year = {2008}, month = {2008 Oct 10}, pages = {96-105}, abstract = {

Skeletal muscle differentiation requires a cascade of transcriptional events to control the spatial and temporal expression of muscle-specific genes. Until recently, muscle-specific transcription was primarily attributed to prototypic enhancer-binding factors, while the role of core promoter recognition complexes in directing myogenesis remained unknown. Here, we report the development of a purified reconstituted system to analyze the properties of a TAF3/TRF3 complex in directing transcription initiation at the Myogenin promoter. Importantly, this new complex is required to replace the canonical TFIID to recapitulate MyoD-dependent activation of Myogenin. In vitro and cell-based assays identify a domain of TAF3 that mediates coactivator functions targeted by MyoD. Our findings also suggest changes to CRSP/Mediator in terminally differentiated myotubes. This switching of the core promoter recognition complex during myogenesis allows a more balanced division of labor between activators and TAF coactivators, thus providing another strategy to accommodate cell-specific regulation during metazoan development.

}, keywords = {Animals, Cell Line, Genetic, Homeodomain Proteins, Mice, Multiprotein Complexes, Muscle Fibers, MyoD Protein, Myogenin, Promoter Regions, Protein Structure, Protein Subunits, Recombinant Proteins, Skeletal, TATA Box Binding Protein-Like Proteins, Tertiary, Trans-Activators, Transcription Factor TFIID, Transcription Initiation Site, Transcriptional Activation}, issn = {1097-4164}, doi = {10.1073/pnas.1100640108}, author = {Deato, Maria Divina E and Marr, Michael T and Sottero, Theo and Inouye, Carla and Hu, Ping and Tjian, Robert} } @article {1161, title = {Native R-loops persist throughout the mouse mitochondrial DNA genome.}, journal = {The Journal of Biological Chemistry}, volume = {283}, year = {2008}, month = {2008 Dec 26}, pages = {36743-51}, abstract = {

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

}, keywords = {Alleles, Animals, Atomic Force, Blotting, DNA, DNA Primers, Electrophoresis, Gel, Genetic, Genome, Mice, Microscopy, Mitochondrial, Models, Northern, Nucleic Acid Conformation, Protein Conformation, RNA, RNA Probes, Two-Dimensional}, issn = {0021-9258}, doi = {10.1016/j.ymeth.2010.01.001}, author = {Brown, Timothy A and Tkachuk, Ariana N and Clayton, David A} } @article {2397, title = {The nucleosome remodeling factor (NURF) regulates genes involved in Drosophila innate immunity.}, journal = {Developmental Biology}, volume = {316}, year = {2008}, month = {2008 Apr 15}, pages = {538-47}, abstract = {

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

}, keywords = {Animals, Chromosomal Proteins, DNA-Binding Proteins, Drosophila, Drosophila Proteins, Gene Expression Profiling, Gene Expression Regulation, Genetic, Genome, Immunity, Innate, Non-Histone, Oligonucleotide Array Sequence Analysis, Phenotype, Recombinant Proteins, Reverse Transcriptase Polymerase Chain Reaction, RNA, Signal Transduction, Transcription}, issn = {1095-564X}, doi = {10.1073/pnas.1100640108}, author = {Kwon, So Yeon and Xiao, Hua and Glover, Bradley P and Tjian, Robert and Wu, Carl and Badenhorst, Paul} } @article {47223, title = {Olfactory representations by Drosophila mushroom body neurons.}, journal = {Journal of Neurophysiology}, volume = {99}, year = {2008}, month = {2008 Feb}, pages = {734-46}, abstract = {

Learning and memory has been studied extensively in Drosophila using behavioral, molecular, and genetic approaches. These studies have identified the mushroom body as essential for the formation and retrieval of olfactory memories. We investigated odor responses of the principal neurons of the mushroom body, the Kenyon cells (KCs), in Drosophila using whole cell recordings in vivo. KC responses to odors were highly selective and, thus sparse, compared with those of their direct inputs, the antennal lobe projection neurons (PNs). We examined the mechanisms that might underlie this transformation and identified at least three contributing factors: excitatory synaptic potentials (from PNs) decay rapidly, curtailing temporal integration, PN convergence onto individual KCs is low ( approximately 10 PNs per KC on average), and KC firing thresholds are high. Sparse activity is thought to be useful in structures involved in memory in part because sparseness tends to reduce representation overlaps. By comparing activity patterns evoked by the same odors across olfactory receptor neurons and across KCs, we show that representations of different odors do indeed become less correlated as they progress through the olfactory system.

}, keywords = {Anesthetics, Local, Animals, Brain Mapping, Drosophila, Electric Stimulation, Excitatory Postsynaptic Potentials, Membrane Potentials, Mushroom Bodies, Nerve Net, Neurons, Afferent, Odors, Olfactory Pathways, Patch-Clamp Techniques, Spectrum Analysis, Tetrodotoxin}, issn = {0022-3077}, doi = {10.1152/jn.01283.2007}, author = {Turner, Glenn C and Bazhenov, Maxim and Laurent, Gilles} } @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 {4367, title = {Reporting neural activity with genetically encoded calcium indicators.}, journal = {Brain Cell Biology}, volume = {36}, year = {2008}, month = {2008 Aug 6}, pages = {69-86}, abstract = {

Genetically encoded calcium indicators (GECIs), based on recombinant fluorescent proteins, have been engineered to observe calcium transients in living cells and organisms. Through observation of calcium, these indicators also report neural activity. We review progress in GECI construction and application, particularly toward in vivo monitoring of sparse action potentials (APs). We summarize the extrinsic and intrinsic factors that influence GECI performance. A simple model of GECI response to AP firing demonstrates the relative significance of these factors. We recommend a standardized protocol for evaluating GECIs in a physiologically relevant context. A potential method of simultaneous optical control and recording of neuronal circuits is presented.

}, keywords = {Action Potentials, Animals, Calcium Signaling, Confocal, Electrophysiology, Luminescent Proteins, Microscopy, Neurons, Signal Transduction}, issn = {1559-7113}, doi = {10.1007/s11068-008-9029-4}, author = {Hires, S Andrew and Tian, Lin and Looger, Loren L} } @article {2505, title = {The role of Broad in the development of Tribolium castaneum: implications for the evolution of the holometabolous insect pupa.}, journal = {Development (Cambridge, England)}, volume = {135}, year = {2008}, month = {2008 Feb}, pages = {569-77}, abstract = {

The evolution of complete metamorphosis in insects is a key innovation that has led to the successful diversification of holometabolous insects, yet the origin of the pupa remains an enigma. Here, we analyzed the expression of the pupal specifier gene broad (br), and the effect on br of isoform-specific, double-stranded RNA-mediated silencing, in a basal holometabolous insect, the beetle Tribolium castaneum. All five isoforms are weakly expressed during the penultimate instar and highly expressed during the prepupal period of the final instar. Application of hydroprene, a juvenile hormone analog, during the penultimate instar caused a repeat of the penultimate br expression patterns, and the formation of supernumerary larvae. Use of dsRNA against the br core region, or against a pair of either the br-Z2 or br-Z3 isoform with the br-Z1 or br-Z4 isoform, produced mobile animals with well-differentiated adult-like appendages, but which retained larval-like urogomphi and epidermis. Disruption of either the br-Z2 or the br-Z3 isoform caused the formation of shorter wings. Disruption of both br-Z1 and br-Z4 caused the appearance of pupal traits in the adults, but disruption of br-Z5 had no morphological effect. Our findings show that the br isoform functions are broadly conserved within the Holometabola and suggest that evolution of br isoform expression may have played an important role in the evolution of the pupa in holometabolous insects.

}, keywords = {Animals, Biological Evolution, Developmental, Double-Stranded, Fatty Acids, Gene Expression Profiling, Gene Expression Regulation, Genes, Insect, Insect Proteins, Larva, Phenotype, Protein Isoforms, Pupa, RNA, RNA Interference, Tribolium, Unsaturated}, issn = {0950-1991}, doi = {10.1242/dev.015263}, author = {Suzuki, Yuichiro and Truman, James W and Riddiford, Lynn M} } @article {1492, title = {Shape registration by optimally coding shapes.}, journal = {IEEE Transactions on Information Technology in Biomedicine : A Publication of the IEEE Engineering in Medicine and Biology Society}, volume = {12}, year = {2008}, month = {2008 Sep}, pages = {627-35}, abstract = {

This paper formulates shape registration as an optimal coding problem. It employs a set of landmarks to establish the correspondence between shapes, and assumes that the best correspondence can be achieved when the polygons formed by the landmarks optimally code all the shape contours, i.e., obtain their minimum description length (MDL). This is different from previous MDL-based shape registration methods, which code the landmark locations. In this paper, each contour is discretized to be a set of points to make the coding feasible, and a number of strategies are adopted to tackle the difficult optimization problem involved. The resulting algorithm, called CAP, is able to yield statistical shape model with better quality in terms of model generalization error, which is demonstrated on both synthetic and biomedical shapes.

}, keywords = {Algorithms, Artificial Intelligence, Automated, Computer-Assisted, Image Enhancement, Image Interpretation, Pattern Recognition, Reproducibility of Results, Sensitivity and Specificity}, issn = {1558-0032}, doi = {10.1109/TITB.2008.920798}, author = {Jiang, Yifeng and Xie, Jun and Tsui, Hung-Tat} } @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 {2399, title = {Structural changes in TAF4b-TFIID correlate with promoter selectivity.}, journal = {Molecular Cell}, volume = {29}, year = {2008}, month = {2008 Jan 18}, pages = {81-91}, abstract = {

Proper ovarian development requires the cell type-specific transcription factor TAF4b, a subunit of the core promoter recognition complex TFIID. We present the 35 A structure of a cell type-specific core promoter recognition complex containing TAF4b and TAF4 (4b/4-IID), which is responsible for directing transcriptional synergy between c-Jun and Sp1 at a TAF4b target promoter. As a first step toward correlating potential structure/function relationships of the prototypic TFIID versus 4b/4-IID, we have compared their 3D structures by electron microscopy and single-particle reconstruction. These studies reveal that TAF4b incorporation into TFIID induces an open conformation at the lobe involved in TFIIA and putative activator interactions. Importantly, this open conformation correlates with differential activator-dependent transcription and promoter recognition by 4b/4-IID. By combining functional and structural analysis, we find that distinct localized structural changes in a megadalton macromolecular assembly can significantly alter its activity and lead to a TAF4b-induced reprogramming of promoter specificity.

}, keywords = {B-Lymphocytes, Cell Line, Computer-Assisted, Electron, Genetic, Hela Cells, Humans, Image Processing, Imaging, Microscopy, Models, Molecular, Organ Specificity, Promoter Regions, Protein Conformation, Protein Interaction Mapping, Proto-Oncogene Proteins c-jun, Sp1 Transcription Factor, Structure-Activity Relationship, TATA-Binding Protein Associated Factors, Three-Dimensional, Transcription Factor TFIIA, Transcription Factor TFIID, Transcriptional Activation, Tumor}, issn = {1097-2765}, doi = {10.1073/pnas.1100640108}, author = {Liu, Wei-Li and Coleman, Robert A and Grob, Patricia and King, David S and Florens, Laurence and Washburn, Michael P and Geles, Kenneth G and Yang, Joyce L and Ramey, Vincent and Nogales, Eva and Tjian, Robert} } @article {1581, title = {Structural insight into substrate binding and catalysis of a novel 2-keto-3-deoxy-D-arabinonate dehydratase illustrates common mechanistic features of the FAH superfamily.}, journal = {Journal of Molecular Biology}, volume = {379}, year = {2008}, month = {2008 May 30}, pages = {357-71}, abstract = {

The archaeon Sulfolobus solfataricus converts d-arabinose to 2-oxoglutarate by an enzyme set consisting of two dehydrogenases and two dehydratases. The third step of the pathway is catalyzed by a novel 2-keto-3-deoxy-D-arabinonate dehydratase (KdaD). In this study, the crystal structure of the enzyme has been solved to 2.1 A resolution. The enzyme forms an oval-shaped ring of four subunits, each consisting of an N-terminal domain with a four-stranded beta-sheet flanked by two alpha-helices, and a C-terminal catalytic domain with a fumarylacetoacetate hydrolase (FAH) fold. Crystal structures of complexes of the enzyme with magnesium or calcium ions and either a substrate analog 2-oxobutyrate, or the aldehyde enzyme product 2,5-dioxopentanoate revealed that the divalent metal ion in the active site is coordinated octahedrally by three conserved carboxylate residues, a water molecule, and both the carboxylate and the oxo groups of the substrate molecule. An enzymatic mechanism for base-catalyzed dehydration is proposed on the basis of the binding mode of the substrate to the metal ion, which suggests that the enzyme enhances the acidity of the protons alpha to the carbonyl group, facilitating their abstraction by glutamate 114. A comprehensive structural comparison of members of the FAH superfamily is presented and their evolution is discussed, providing a basis for functional investigations of this largely unexplored protein superfamily.

}, keywords = {Amino Acid Sequence, Animals, Archaeal Proteins, Binding Sites, Catalysis, Crystallography, Humans, Hydro-Lyases, Hydrolases, Magnesium, Models, Molecular, Molecular Sequence Data, Molecular Structure, Protein Binding, Protein Structure, Protein Subunits, Quaternary, Secondary, Sequence Alignment, Substrate Specificity, Sulfolobus solfataricus, Tertiary, X-Ray}, issn = {1089-8638}, doi = {10.1016/j.jmb.2008.03.064}, author = {Brouns, Stan J J and Barends, Thomas R M and Worm, Petra and Akerboom, Jasper and Turnbull, Andrew P and Salmon, Laurent and van der Oost, John} } @article {2395, title = {TBP, Mot1, and NC2 establish a regulatory circuit that controls DPE-dependent versus TATA-dependent transcription.}, journal = {Genes \& Development}, volume = {22}, year = {2008}, month = {2008 Sep 1}, pages = {2353-8}, abstract = {

The RNA polymerase II core promoter is a structurally and functionally diverse transcriptional module. RNAi depletion and overexpression experiments revealed a genetic circuit that controls the balance of transcription from two core promoter motifs, the TATA box and the downstream core promoter element (DPE). In this circuit, TBP activates TATA-dependent transcription and represses DPE-dependent transcription, whereas Mot1 and NC2 block TBP function and thus repress TATA-dependent transcription and activate DPE-dependent transcription. This regulatory circuit is likely to be one means by which biological networks can transmit transcriptional signals, such as those from DPE-specific and TATA-specific enhancers, via distinct pathways.

}, keywords = {Animals, Cells, Cultured, Drosophila, Drosophila Proteins, Enhancer Elements, Gene Expression Regulation, Genetic, Promoter Regions, RNA Polymerase II, TATA Box, TATA-Box Binding Protein, Transcription, Transcription Factors}, issn = {0890-9369}, doi = {10.1073/pnas.1100640108}, author = {Hsu, Jer-Yuan and Juven-Gershon, Tamar and Marr, Michael T and Wright, Kevin J and Tjian, Robert and Kadonaga, James T} } @article {2810, title = {Ambient mass spectrometry with a handheld mass spectrometer at high pressure.}, journal = {Analytical Chemistry}, volume = {79}, year = {2007}, month = {2007 Oct 15}, pages = {7734-9}, abstract = {

The first coupling of atmospheric pressure ionization methods, electrospray ionization (ESI) and desorption electrospray ionization (DESI), to a miniature hand-held mass spectrometer is reported. The instrument employs a rectilinear ion trap (RIT) mass analyzer and is battery-operated, hand-portable, and rugged (total system: 10 kg, 0.014 m(3), 75 W power consumption). The mass spectrometer was fitted with an atmospheric inlet, consisting of a 10 cm x 127 microm inner diameter stainless steel capillary tube which was used to introduce gas into the vacuum chamber at 13 mL/min. The operating pressure was 15 mTorr. Ions, generated by the atmospheric pressure ion source, were directed by the inlet along the axis of the ion trap, entering through an aperture in the dc-biased end plate, which was also operated as an ion gate. ESI and DESI sources were used to generate ions; ESI-MS analysis of an aqueous mixture of drugs yielded detection limits in the low parts-per-billion range. Signal response was linear over more than 3 orders of magnitude. Tandem mass spectrometry experiments were used to identify components of this mixture. ESI was also applied to the analysis of peptides and in this case multiply charged species were observed for compounds of molecular weight up to 1200 Da. Cocaine samples deposited or already present on different surfaces, including currency, were rapidly analyzed in situ by DESI. A geometry-independent version of the DESI ion source was also coupled to the miniature mass spectrometer. These results demonstrate that atmospheric pressure ionization can be implemented on simple portable mass spectrometry systems.

}, keywords = {Alkylation, Calibration, Mass Spectrometry, Molecular Structure, Molecular Weight, Pressure, Proteins, Temperature}, issn = {0003-2700}, doi = {10.1364/AO.50.001792}, author = {Keil, Adam and Talaty, Nari and Janfelt, Christian and Noll, Robert J and Gao, Liang and Ouyang, Zheng and Cooks, R Graham} } @article {1583, title = {Crystal structure and biochemical properties of the D-arabinose dehydrogenase from Sulfolobus solfataricus.}, journal = {Journal of Molecular Biology}, volume = {371}, year = {2007}, month = {2007 Aug 31}, pages = {1249-60}, abstract = {

Sulfolobus solfataricus metabolizes the five-carbon sugar d-arabinose to 2-oxoglutarate by an inducible pathway consisting of dehydrogenases and dehydratases. Here we report the crystal structure and biochemical properties of the first enzyme of this pathway: the d-arabinose dehydrogenase. The AraDH structure was solved to a resolution of 1.80 A by single-wavelength anomalous diffraction and phased using the two endogenous zinc ions per subunit. The structure revealed a catalytic and cofactor binding domain, typically present in mesophilic and thermophilic alcohol dehydrogenases. Cofactor modeling showed the presence of a phosphate binding pocket sequence motif (SRS-X2-H), which is likely to be responsible for the enzyme{\textquoteright}s preference for NADP+. The homo-tetrameric enzyme is specific for d-arabinose, l-fucose, l-galactose and d-ribose, which could be explained by the hydrogen bonding patterns of the C3 and C4 hydroxyl groups observed in substrate docking simulations. The enzyme optimally converts sugars at pH 8.2 and 91 degrees C, and displays a half-life of 42 and 26 min at 85 and 90 degrees C, respectively, indicating that the enzyme is thermostable at physiological operating temperatures of 80 degrees C. The structure represents the first crystal structure of an NADP+-dependent member of the medium-chain dehydrogenase/reductase (MDR) superfamily from Archaea.

}, keywords = {Amino Acid, Amino Acid Sequence, Binding Sites, Carbohydrates, Catalytic Domain, Crystallization, Crystallography, Hydrogen-Ion Concentration, Molecular Conformation, Molecular Sequence Data, Protein Binding, Protein Structure, Quaternary, Sequence Homology, Sugar Alcohol Dehydrogenases, Sulfolobus solfataricus, Temperature, X-Ray}, issn = {0022-2836}, doi = {10.1016/j.jmb.2007.05.097}, author = {Brouns, Stan J J and Turnbull, Andrew P and Willemen, Hanneke L D M and Akerboom, Jasper and van der Oost, John} } @article {2401, title = {Daniel E. Koshland, Jr. 1920-2007.}, journal = {Cell}, volume = {130}, year = {2007}, month = {2007 Aug 24}, pages = {579-80}, keywords = {20th Century, 21st Century, Biochemistry, History, United States}, issn = {0092-8674}, doi = {10.1073/pnas.1100640108}, author = {Tjian, Robert} } @article {6494, title = {Evolution of genes and genomes on the Drosophila phylogeny.}, journal = {Nature}, volume = {450}, year = {2007}, month = {2007 Nov 8}, pages = {203-18}, abstract = {

Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

}, keywords = {Animals, Codon, DNA, DNA Transposable Elements, Drosophila, Drosophila Proteins, Evolution, Gene Order, Genes, Genome, Genomics, Immunity, Insect, Mitochondrial, Molecular, Multigene Family, Phylogeny, Reproduction, RNA, Sequence Alignment, Sequence Analysis, Synteny, Untranslated}, issn = {1476-4687}, doi = {10.1038/nature06341}, author = {Clark, Andrew G and Eisen, Michael B and Smith, Douglas R and Bergman, Casey M and Oliver, Brian and Markow, Therese A and Kaufman, Thomas C and Kellis, Manolis and Gelbart, William and Iyer, Venky N and Pollard, Daniel A and Sackton, Timothy B and Larracuente, Amanda M and Singh, Nadia D and Abad, Jose P and Abt, Dawn N and Adryan, Boris and Aguade, Montserrat and Akashi, Hiroshi and Anderson, Wyatt W and Aquadro, Charles F and Ardell, David H and Arguello, Roman and Artieri, Carlo G and Barbash, Daniel A and Barker, Daniel and Barsanti, Paolo and Batterham, Phil and Batzoglou, Serafim and Begun, Dave and Bhutkar, Arjun and Blanco, Enrico and Bosak, Stephanie A and Bradley, Robert K and Brand, Adrianne D and Brent, Michael R and Brooks, Angela N and Brown, Randall H and Butlin, Roger K and Caggese, Corrado and Calvi, Brian R and Bernardo de Carvalho, A and Caspi, Anat and Castrezana, Sergio and Celniker, Susan E and Chang, Jean L and Chapple, Charles and Chatterji, Sourav and Chinwalla, Asif and Civetta, Alberto and Clifton, Sandra W and Comeron, Josep M and Costello, James C and Coyne, Jerry A and Daub, Jennifer and David, Robert G and Delcher, Arthur L and Delehaunty, Kim and Do, Chuong B and Ebling, Heather and Edwards, Kevin and Eickbush, Thomas and Evans, Jay D and Filipski, Alan and Findeiss, Sven and Freyhult, Eva and Fulton, Lucinda and Fulton, Robert and Garcia, Ana C L and Gardiner, Anastasia and Garfield, David A and Garvin, Barry E and Gibson, Greg and Gilbert, Don and Gnerre, Sante and Godfrey, Jennifer and Good, Robert and Gotea, Valer and Gravely, Brenton and Greenberg, Anthony J and Griffiths-Jones, Sam and Gross, Samuel and Guigo, Roderic and Gustafson, Erik A and Haerty, Wilfried and Hahn, Matthew W and Halligan, Daniel L and Halpern, Aaron L and Halter, Gillian M and Han, Mira V and Heger, Andreas and Hillier, LaDeana and Hinrichs, Angie S and Holmes, Ian and Hoskins, Roger A and Hubisz, Melissa J and Hultmark, Dan and Huntley, Melanie A and Jaffe, David B and Jagadeeshan, Santosh and Jeck, William R and Johnson, Justin and Jones, Corbin D and Jordan, William C and Karpen, Gary H and Kataoka, Eiko and Keightley, Peter D and Kheradpour, Pouya and Kirkness, Ewen F and Koerich, Leonardo B and Kristiansen, Karsten and Kudrna, Dave and Kulathinal, Rob J and Kumar, Sudhir and Kwok, Roberta and Lander, Eric and Langley, Charles H and Lapoint, Richard and Lazzaro, Brian P and Lee, So-Jeong and Levesque, Lisa and Li, Ruiqiang and Lin, Chiao-Feng and Lin, Michael F and Lindblad-Toh, Kerstin and Llopart, Ana and Long, Manyuan and Low, Lloyd and Lozovsky, Elena and Lu, Jian and Luo, Meizhong and Machado, Carlos A and Makalowski, Wojciech and Marzo, Mar and Matsuda, Muneo and Matzkin, Luciano and McAllister, Bryant and McBride, Carolyn S and McKernan, Brendan and McKernan, Kevin and Mendez-Lago, Maria and Minx, Patrick and Mollenhauer, Michael U and Montooth, Kristi and Mount, Stephen M and Mu, Xu and Myers, Eugene and Negre, Barbara and Newfeld, Stuart and Nielsen, Rasmus and Noor, Mohamed A F and O{\textquoteright}Grady, Patrick and Pachter, Lior and Papaceit, Montserrat and Parisi, Matthew J and Parisi, Michael and Parts, Leopold and Pedersen, Jakob S and Pesole, Graziano and Phillippy, Adam M and Ponting, Chris P and Pop, Mihai and Porcelli, Damiano and Powell, Jeffrey R and Prohaska, Sonja and Pruitt, Kim and Puig, Marta and Quesneville, Hadi and Ram, Kristipati Ravi and Rand, David and Rasmussen, Matthew D and Reed, Laura K and Reenan, Robert and Reily, Amy and Remington, Karin A and Rieger, Tania T and Ritchie, Michael G and Robin, Charles and Rogers, Yu-Hui and Rohde, Claudia and Rozas, Julio and Rubenfield, Marc J and Ruiz, Alfredo and Russo, Susan and Salzberg, Steven L and Sanchez-Gracia, Alejandro and Saranga, David J and Sato, Hajime and Schaeffer, Stephen W and Schatz, Michael C and Schlenke, Todd and Schwartz, Russell and Segarra, Carmen and Singh, Rama S and Sirot, Laura and Sirota, Marina and Sisneros, Nicholas B and Smith, Chris D and Smith, Temple F and Spieth, John and Stage, Deborah E and Stark, Alexander and Stephan, Wolfgang and Strausberg, Robert L and Strempel, Sebastian and Sturgill, David and Sutton, Granger and Sutton, Granger G and Tao, Wei and Teichmann, Sarah and Tobari, Yoshiko N and Tomimura, Yoshihiko and Tsolas, Jason M and Valente, Vera L S and Venter, Eli and Venter, J Craig and Vicario, Saverio and Vieira, Filipe G and Vilella, Albert J and Villasante, Alfredo and Walenz, Brian and Wang, Jun and Wasserman, Marvin and Watts, Thomas and Wilson, Derek and Wilson, Richard K and Wing, Rod A and Wolfner, Mariana F and Wong, Alex and Wong, Gane Ka-Shu and Wu, Chung-I and Wu, Gabriel and Yamamoto, Daisuke and Yang, Hsiao-Pei and Yang, Shiaw-Pyng and Yorke, James A and Yoshida, Kiyohito and Zdobnov, Evgeny and Zhang, Peili and Zhang, Yu and Zimin, Aleksey V and Baldwin, Jennifer and Abdouelleil, Amr and Abdulkadir, Jamal and Abebe, Adal and Abera, Brikti and Abreu, Justin and Acer, St Christophe and Aftuck, Lynne and Alexander, Allen and An, Peter and Anderson, Erica and Anderson, Scott and Arachi, Harindra and Azer, Marc and Bachantsang, Pasang and Barry, Andrew and Bayul, Tashi and Berlin, Aaron and Bessette, Daniel and Bloom, Toby and Blye, Jason and Boguslavskiy, Leonid and Bonnet, Claude and Boukhgalter, Boris and Bourzgui, Imane and Brown, Adam and Cahill, Patrick and Channer, Sheridon and Cheshatsang, Yama and Chuda, Lisa and Citroen, Mieke and Collymore, Alville and Cooke, Patrick and Costello, Maura and D{\textquoteright}Aco, Katie and Daza, Riza and De Haan, Georgius and DeGray, Stuart and DeMaso, Christina and Dhargay, Norbu and Dooley, Kimberly and Dooley, Erin and Doricent, Missole and Dorje, Passang and Dorjee, Kunsang and Dupes, Alan and Elong, Richard and Falk, Jill and Farina, Abderrahim and Faro, Susan and Ferguson, Diallo and Fisher, Sheila and Foley, Chelsea D and Franke, Alicia and Friedrich, Dennis and Gadbois, Loryn and Gearin, Gary and Gearin, Christina R and Giannoukos, Georgia and Goode, Tina and Graham, Joseph and Grandbois, Edward and Grewal, Sharleen and Gyaltsen, Kunsang and Hafez, Nabil and Hagos, Birhane and Hall, Jennifer and Henson, Charlotte and Hollinger, Andrew and Honan, Tracey and Huard, Monika D and Hughes, Leanne and Hurhula, Brian and Husby, M Erii and Kamat, Asha and Kanga, Ben and Kashin, Seva and Khazanovich, Dmitry and Kisner, Peter and Lance, Krista and Lara, Marcia and Lee, William and Lennon, Niall and Letendre, Frances and LeVine, Rosie and Lipovsky, Alex and Liu, Xiaohong and Liu, Jinlei and Liu, Shangtao and Lokyitsang, Tashi and Lokyitsang, Yeshi and Lubonja, Rakela and Lui, Annie and MacDonald, Pen and Magnisalis, Vasilia and Maru, Kebede and Matthews, Charles and McCusker, William and McDonough, Susan and Mehta, Teena and Meldrim, James and Meneus, Louis and Mihai, Oana and Mihalev, Atanas and Mihova, Tanya and Mittelman, Rachel and Mlenga, Valentine and Montmayeur, Anna and Mulrain, Leonidas and Navidi, Adam and Naylor, Jerome and Negash, Tamrat and Nguyen, Thu and Nguyen, Nga and Nicol, Robert and Norbu, Choe and Norbu, Nyima and Novod, Nathaniel and O{\textquoteright}Neill, Barry and Osman, Sahal and Markiewicz, Eva and Oyono, Otero L and Patti, Christopher and Phunkhang, Pema and Pierre, Fritz and Priest, Margaret and Raghuraman, Sujaa and Rege, Filip and Reyes, Rebecca and Rise, Cecil and Rogov, Peter and Ross, Keenan and Ryan, Elizabeth and Settipalli, Sampath and Shea, Terry and Sherpa, Ngawang and Shi, Lu and Shih, Diana and Sparrow, Todd and Spaulding, Jessica and Stalker, John and Stange-Thomann, Nicole and Stavropoulos, Sharon and Stone, Catherine and Strader, Christopher and Tesfaye, Senait and Thomson, Talene and Thoulutsang, Yama and Thoulutsang, Dawa and Topham, Kerri and Topping, Ira and Tsamla, Tsamla and Vassiliev, Helen and Vo, Andy and Wangchuk, Tsering and Wangdi, Tsering and Weiand, Michael and Wilkinson, Jane and Wilson, Adam and Yadav, Shailendra and Young, Geneva and Yu, Qing and Zembek, Lisa and Zhong, Danni and Zimmer, Andrew and Zwirko, Zac and Jaffe, David B and Alvarez, Pablo and Brockman, Will and Butler, Jonathan and Chin, CheeWhye and Gnerre, Sante and Grabherr, Manfred and Kleber, Michael and Mauceli, Evan and MacCallum, Iain} } @article {955, title = {Global analysis of patterns of gene expression during Drosophila embryogenesis.}, journal = {Genome Biology}, volume = {8}, year = {2007}, month = {2007 July 23}, pages = {R145}, abstract = {

Cell and tissue specific gene expression is a defining feature of embryonic development in multi-cellular organisms. However, the range of gene expression patterns, the extent of the correlation of expression with function, and the classes of genes whose spatial expression are tightly regulated have been unclear due to the lack of an unbiased, genome-wide survey of gene expression patterns.

}, keywords = {Animals, Drosophila melanogaster, Embryonic Development, Gene Expression Profiling}, issn = {1465-6914}, doi = {10.1186/gb-2007-8-7-r145}, author = {Tomancak, Pavel and Berman, Benjamin P and Beaton, Amy and Weiszmann, Richard and Kwan, Elaine and Hartenstein, Volker and Celniker, Susan E and Rubin, Gerald M} } @article {1582, title = {A global transcriptional regulator in Thermococcus kodakaraensis controls the expression levels of both glycolytic and gluconeogenic enzyme-encoding genes.}, journal = {The Journal of Biological Chemistry}, volume = {282}, year = {2007}, month = {2007 Nov 16}, pages = {33659-70}, abstract = {

We identified a novel regulator, Thermococcales glycolytic regulator (Tgr), functioning as both an activator and a repressor of transcription in the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. Tgr (TK1769) displays similarity (28\% identical) to Pyrococcus furiosus TrmB (PF1743), a transcriptional repressor regulating the trehalose/maltose ATP-binding cassette transporter genes, but is more closely related (67\%) to a TrmB paralog in P. furiosus (PF0124). Growth of a tgr disruption strain (Deltatgr) displayed a significant decrease in growth rate under gluconeogenic conditions compared with the wild-type strain, whereas comparable growth rates were observed under glycolytic conditions. A whole genome microarray analysis revealed that transcript levels of almost all genes related to glycolysis and maltodextrin metabolism were at relatively high levels in the Deltatgr mutant even under gluconeogenic conditions. The Deltatgr mutant also displayed defects in the transcriptional activation of gluconeogenic genes under these conditions, indicating that Tgr functions as both an activator and a repressor. Genes regulated by Tgr contain a previously identified sequence motif, the Thermococcales glycolytic motif (TGM). The TGM was positioned upstream of the Transcription factor B-responsive element (BRE)/TATA sequence in gluconeogenic promoters and downstream of it in glycolytic promoters. Electrophoretic mobility shift assay indicated that recombinant Tgr protein specifically binds to promoter regions containing a TGM. Tgr was released from the DNA when maltotriose was added, suggesting that this sugar is most likely the physiological effector. Our results strongly suggest that Tgr is a global transcriptional regulator that simultaneously controls, in response to sugar availability, both glycolytic and gluconeogenic metabolism in T. kodakaraensis via its direct binding to the TGM.

}, keywords = {Amino Acid, Amino Acid Motifs, Amino Acid Sequence, Escherichia coli, Genetic, Genome, Genotype, Gluconeogenesis, Glycolysis, Molecular Sequence Data, Multienzyme Complexes, NADH, NADPH Oxidoreductases, Oligonucleotide Array Sequence Analysis, Promoter Regions, Pyrococcus furiosus, Recombinant Proteins, Sequence Homology, Thermococcus, Transcription}, issn = {0021-9258}, doi = {10.1074/jbc.M703424200}, author = {Kanai, Tamotsu and Akerboom, Jasper and Takedomi, Shogo and van de Werken, Harmen J G and Blombach, Fabian and van der Oost, John and Murakami, Taira and Atomi, Haruyuki and Imanaka, Tadayuki} } @article {46630, title = {Guidelines on nicotine dose selection for in vivo research.}, journal = {Psychopharmacology (Berl)}, volume = {190}, year = {2007}, month = {2007 Feb}, pages = {269-319}, abstract = {

RATIONALE: This review provides insight for the judicious selection of nicotine dose ranges and routes of administration for in vivo studies. The literature is replete with reports in which a dosaging regimen chosen for a specific nicotine-mediated response was suboptimal for the species used. In many cases, such discrepancies could be attributed to the complex variables comprising species-specific in vivo responses to acute or chronic nicotine exposure.

OBJECTIVES: This review capitalizes on the authors{\textquoteright} collective decades of in vivo nicotine experimentation to clarify the issues and to identify the variables to be considered in choosing a dosaging regimen. Nicotine dose ranges tolerated by humans and their animal models provide guidelines for experiments intended to extrapolate to human tobacco exposure through cigarette smoking or nicotine replacement therapies. Just as important are the nicotine dosaging regimens used to provide a mechanistic framework for acquisition of drug-taking behavior, dependence, tolerance, or withdrawal in animal models.

RESULTS: Seven species are addressed: humans, nonhuman primates, rats, mice, Drosophila, Caenorhabditis elegans, and zebrafish. After an overview on nicotine metabolism, each section focuses on an individual species, addressing issues related to genetic background, age, acute vs chronic exposure, route of administration, and behavioral responses.

CONCLUSIONS: The selected examples of successful dosaging ranges are provided, while emphasizing the necessity of empirically determined dose-response relationships based on the precise parameters and conditions inherent to a specific hypothesis. This review provides a new, experimentally based compilation of species-specific dose selection for studies on the in vivo effects of nicotine.

}, keywords = {Animals, Behavioral Research, Dose-Response Relationship, Drug, Ganglionic Stimulants, Guidelines as Topic, Humans, Models, Biological, Nicotine, Species Specificity}, issn = {0033-3158}, doi = {10.1007/s00213-006-0441-0}, author = {Matta, Shannon G and Balfour, David J and Benowitz, Neal L and Boyd, R Thomas and Buccafusco, Jerry J and Caggiula, Anthony R and Craig, Caroline R and Collins, Allan C and Damaj, M Imad and Donny, Eric C and Gardiner, Phillip S and Grady, Sharon R and Heberlein, Ulrike and Leonard, Sherry S and Levin, Edward D and Lukas, Ronald J and Markou, Athina and Marks, Michael J and McCallum, Sarah E and Parameswaran, Neeraja and Perkins, Kenneth A and Picciotto, Marina R and Quik, Maryka and Rose, Jed E and Rothenfluh, Adrian and Schafer, William R and Stolerman, Ian P and Tyndale, Rachel F and Wehner, Jeanne M and Zirger, Jeffrey M} } @article {4047, title = {HCN1 channels constrain synaptically evoked Ca2+ spikes in distal dendrites of CA1 pyramidal neurons.}, journal = {Neuron}, volume = {56}, year = {2007}, month = {2007 Dec 20}, pages = {1076-89}, abstract = {

HCN1 hyperpolarization-activated cation channels act as an inhibitory constraint of both spatial learning and synaptic integration and long-term plasticity in the distal dendrites of hippocampal CA1 pyramidal neurons. However, as HCN1 channels provide an excitatory current, the mechanism of their inhibitory action remains unclear. Here we report that HCN1 channels also constrain CA1 distal dendritic Ca2+ spikes, which have been implicated in the induction of LTP at distal excitatory synapses. Our experimental and computational results indicate that HCN1 channels provide both an active shunt conductance that decreases the temporal integration of distal EPSPs and a tonic depolarizing current that increases resting inactivation of T-type and N-type voltage-gated Ca2+ channels, which contribute to the Ca2+ spikes. This dual mechanism may provide a general means by which HCN channels regulate dendritic excitability.

}, keywords = {Animals, Calcium, Calcium Channel Blockers, Computer Simulation, Cyclic Nucleotide-Gated Cation Channels, Dendrites, Dose-Response Relationship, Electric Stimulation, Excitatory Amino Acid Antagonists, Excitatory Postsynaptic Potentials, Hippocampus, Knockout, Mice, Newborn, Patch-Clamp Techniques, Potassium Channels, Pyramidal Cells, Pyrimidines, Radiation, Reaction Time, Synapses}, issn = {0896-6273}, doi = {10.1016/j.neuron.2007.11.015}, author = {Tsay, David and Dudman, Joshua T and Siegelbaum, Steven A} } @article {2670, title = {Huntingtin-interacting protein 14, a palmitoyl transferase required for exocytosis and targeting of CSP to synaptic vesicles.}, journal = {The Journal of Cell Biology}, volume = {179}, year = {2007}, month = {2007 Dec 31}, pages = {1481-96}, abstract = {

Posttranslational modification through palmitoylation regulates protein localization and function. In this study, we identify a role for the Drosophila melanogaster palmitoyl transferase Huntingtin-interacting protein 14 (HIP14) in neurotransmitter release. hip14 mutants show exocytic defects at low frequency stimulation and a nearly complete loss of synaptic transmission at higher temperature. Interestingly, two exocytic components known to be palmitoylated, cysteine string protein (CSP) and SNAP25, are severely mislocalized at hip14 mutant synapses. Complementary DNA rescue and localization experiments indicate that HIP14 is required solely in the nervous system and is essential for presynaptic function. Biochemical studies indicate that HIP14 palmitoylates CSP and that CSP is not palmitoylated in hip14 mutants. Furthermore, the hip14 exocytic defects can be suppressed by targeting CSP to synaptic vesicles using a chimeric protein approach. Our data indicate that HIP14 controls neurotransmitter release by regulating the trafficking of CSP to synapses.

}, keywords = {Acyltransferases, Adaptor Proteins, Animals, Drosophila melanogaster, Drosophila Proteins, Exocytosis, Ganglia, Invertebrate, Nerve Tissue Proteins, Nervous System, Neuromuscular Junction, Neurotransmitter Agents, Post-Translational, Protein Processing, Protein Transport, Signal Transducing, Synaptic Transmission, Synaptic Vesicles}, issn = {1540-8140}, doi = {10.1083/jcb.200710061}, author = {Ohyama, Tomoko and Verstreken, Patrik and Ly, Cindy V and Rosenmund, Tanja and Rajan, Akhila and Tien, An-Chi and Haueter, Claire and Schulze, Karen L and Bellen, Hugo J} } @article {6497, title = {Identification of differentially expressed small non-coding RNAs in the legume endosymbiont Sinorhizobium meliloti by comparative genomics.}, journal = {Molecular Microbiology}, volume = {66}, year = {2007}, month = {2007 Dec}, pages = {1080-91}, abstract = {

Bacterial small non-coding RNAs (sRNAs) are being recognized as novel widespread regulators of gene expression in response to environmental signals. Here, we present the first search for sRNA-encoding genes in the nitrogen-fixing endosymbiont Sinorhizobium meliloti, performed by a genome-wide computational analysis of its intergenic regions. Comparative sequence data from eight related alpha-proteobacteria were obtained, and the interspecies pairwise alignments were scored with the programs eQRNA and RNAz as complementary predictive tools to identify conserved and stable secondary structures corresponding to putative non-coding RNAs. Northern experiments confirmed that eight of the predicted loci, selected among the original 32 candidates as most probable sRNA genes, expressed small transcripts. This result supports the combined use of eQRNA and RNAz as a robust strategy to identify novel sRNAs in bacteria. Furthermore, seven of the transcripts accumulated differentially in free-living and symbiotic conditions. Experimental mapping of the 5{\textquoteright}-ends of the detected transcripts revealed that their encoding genes are organized in autonomous transcription units with recognizable promoter and, in most cases, termination signatures. These findings suggest novel regulatory functions for sRNAs related to the interactions of alpha-proteobacteria with their eukaryotic hosts.

}, keywords = {Bacterial, Blotting, Computational Biology, DNA, Double-Stranded, Fabaceae, Genetic, Genome, Intergenic, Northern, Nucleic Acid Conformation, Promoter Regions, RNA, Sinorhizobium meliloti, Transcription, Untranslated}, issn = {0950-382X}, doi = {10.1111/j.1365-2958.2007.05978.x}, author = {del Val, Coral and Rivas, Elena and Torres-Quesada, Omar and Toro, Nicol{\'a}s and Jim{\'e}nez-Zurdo, Jos{\'e} I} } @article {2404, title = {IRES-mediated functional coupling of transcription and translation amplifies insulin receptor feedback.}, journal = {Genes \& Development}, volume = {21}, year = {2007}, month = {2007 Jan 15}, pages = {175-83}, abstract = {

It is generally accepted that the growth rate of an organism is modulated by the availability of nutrients. One common mechanism to control cellular growth is through the global down-regulation of cap-dependent translation by eIF4E-binding proteins (4E-BPs). Here, we report evidence for a novel mechanism that allows eukaryotes to coordinate and selectively couple transcription and translation of target genes in response to a nutrient and growth signaling cascade. The Drosophila insulin-like receptor (dINR) pathway incorporates 4E-BP resistant cellular internal ribosome entry site (IRES) containing mRNAs, to functionally couple transcriptional activation with differential translational control in a cell that is otherwise translationally repressed by 4E-BP. Although examples of cellular IRESs have been previously reported, their critical role mediating a key physiological response has not been well documented. Our studies reveal an integrated transcriptional and translational response mechanism specifically dependent on a cellular IRES that coordinates an essential physiological signal responsible for monitoring nutrient and cell growth conditions.

}, keywords = {5{\textquoteright} Untranslated Regions, Animals, Biological, Drosophila melanogaster, Drosophila Proteins, Eukaryotic Initiation Factor-4E, Feedback, Forkhead Transcription Factors, Gene Expression Regulation, Genetic, Insulin, Models, Phosphorylation, Physiological, Protein Biosynthesis, Receptor, Ribosomes, Signal Transduction, Transcription, Transfection}, issn = {0890-9369}, doi = {10.1073/pnas.1100640108}, author = {Marr, Michael T and D{\textquoteright}Alessio, Joseph A and Puig, Oscar and Tjian, Robert} } @article {2443, title = {Molecular patterning mechanism underlying metamorphosis of the thoracic leg in Manduca sexta.}, journal = {Developmental Biology}, volume = {305}, year = {2007}, month = {2007 May 15}, pages = {539-50}, abstract = {

The tobacco hornworm Manduca sexta, like many holometabolous insects, makes two versions of its thoracic legs. The simple legs of the larva are formed during embryogenesis, but then are transformed into the more complex adult legs at metamorphosis. To elucidate the molecular patterning mechanism underlying this biphasic development, we examined the expression patterns of five genes known to be involved in patterning the proximal-distal axis in insect legs. In the developing larval leg of Manduca, the early patterning genes Distal-less and Extradenticle are already expressed in patterns comparable to the adult legs of other insects. In contrast, Bric-a-brac and dachshund are expressed in patterns similar to transient patterns observed during early stages of leg development in Drosophila. During metamorphosis of the leg, the two genes finally develop mature expression patterns. Our results are consistent with the hypothesis that the larval leg morphology is produced by a transient arrest in the conserved adult leg patterning process in insects. In addition, we find that, during the adult leg development, some cells in the leg express the patterning genes de novo suggesting that the remodeling of the leg involves changes in the patterning gene regulation.

}, keywords = {Animals, Biological, Body Patterning, Extremities, Larva, Manduca, Metamorphosis, Thorax}, issn = {0012-1606}, doi = {10.1016/j.ydbio.2007.02.042}, author = {Tanaka, Kohtaro and Truman, James W} } @article {6443, title = {MRI-based localization of electrophysiological recording sites within the cerebral cortex at single-voxel accuracy.}, journal = {Nature Methods}, volume = {4}, year = {2007}, month = {2007 Feb}, pages = {161-8}, abstract = {

The localization of microelectrode recording sites in the layers of primate cerebral cortex permits the analysis of relationships between recorded neuronal activities and underlying anatomical connections. We present a magnetic resonance imaging method for precise in vivo localization of cortical recording sites. In this method, the susceptibility-induced effect thickens the appearance of the microelectrode and enhances the detectability of the microelectrode tip, which usually occupies less than a few percent of the volume of an image voxel. In a phantom study, the optimized susceptibility-induced effect allowed tip detection with single-voxel accuracy (in-plane resolution, 50 mum). We applied this method to recording microelectrodes inserted into the brains of macaque monkeys, and localized the microelectrode tip at an in-plane resolution of 150 mum within the cortex of 2-3 mm in thickness. Subsequent histological analyses validated the single-voxel accuracy of the in vivo tip localization. This method opens up a way to investigate information flow during cognitive processes in the brain.

}, keywords = {Animal, Animals, Behavior, Cerebral Cortex, Electrophysiology, Imaging, Macaca, Magnetic Resonance Imaging, Microelectrodes, Phantoms}, issn = {1548-7091}, doi = {10.1038/nmeth987}, author = {Matsui, Teppei and Koyano, Kenji W and Koyama, Minoru and Nakahara, Kiyoshi and Takeda, Masaki and Ohashi, Yohei and Naya, Yuji and Miyashita, Yasushi} } @article {4979, title = {Multiple memory traces for olfactory reward learning in Drosophila.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {27}, year = {2007}, month = {2007 Oct 10}, pages = {11132-8}, abstract = {

Physical traces underlying simple memories can be confined to a single group of cells in the brain. In the fly Drosophila melanogaster, the Kenyon cells of the mushroom bodies house traces for both appetitive and aversive odor memories. The adenylate cyclase protein, Rutabaga, has been shown to mediate both traces. Here, we show that, for appetitive learning, another group of cells can additionally accommodate a Rutabaga-dependent memory trace. Localized expression of rutabaga in either projection neurons, the first-order olfactory interneurons, or in Kenyon cells, the second-order interneurons, is sufficient for rescuing the mutant defect in appetitive short-term memory. Thus, appetitive learning may induce multiple memory traces in the first- and second-order olfactory interneurons using the same plasticity mechanism. In contrast, aversive odor memory of rutabaga is rescued selectively in the Kenyon cells, but not in the projection neurons. This difference in the organization of memory traces is consistent with the internal representation of reward and punishment.

}, keywords = {Animals, Drosophila melanogaster, Female, Learning, Male, Nerve Net, Olfactory Pathways, Reward, Smell}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.2712-07.2007}, author = {Thum, Andreas S and Jenett, Arnim and Ito, Kei and Heisenberg, Martin and Tanimoto, Hiromu} } @article {2405, title = {Novel TRF1/BRF target genes revealed by genome-wide analysis of Drosophila Pol III transcription.}, journal = {The EMBO Journal}, volume = {26}, year = {2007}, month = {2007 Jan 10}, pages = {79-89}, abstract = {

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

}, keywords = {Animals, Base Sequence, Binding Sites, Chromatin Immunoprecipitation, Deoxyribonuclease I, DNA Polymerase III, Drosophila melanogaster, Genetic, Genome, Molecular Sequence Data, Oligonucleotide Probes, Protein Binding, RNA, Small Nucleolar, Telomeric Repeat Binding Protein 1, Transcription, Transcription Factor TFIIIB}, issn = {0261-4189}, doi = {10.1073/pnas.1100640108}, author = {Isogai, Yoh and Takada, Shinako and Tjian, Robert and Kele\c s, S{\"u}nd{\"u}z} } @article {67285, title = {Observability of Higgs produced with top quarks and decaying to bottom quarks}, journal = {Journal of Physics G: Nuclear and Particle Physics}, volume = {34}, year = {2007}, month = {04/20027}, pages = {N221 - N250}, abstract = {

The decay,\ , is dominant for a Standard Model Higgs boson in the mass range just above the exclusion limit of 114.4 GeV/c2\ reported by the LEP experiments. Unfortunately, an overwhelming abundance of\ \ events arising from more mundane sources, together with the lack of precision inherent in the reconstruction of the Higgs mass, renders this decay mode\ a priori\ undetectable in the case of direct Higgs production at the LHC. It is therefore of no small interest to investigate whether\ \ can be observed in those cases where the Higgs is produced in association with other massive particles. In this note, the results of a study of Higgs bosons produced in association with top quarks and decaying via\ \ are presented. The study was performed as realistically as possible by employing a full and detailed Monte Carlo simulation of the CMS detector followed by the application of trigger and reconstruction algorithms that were developed for use with real data. Important systematic effects resulting from such sources as the uncertainties in the jet energy scale and the estimated rates for correctly tagging b jets or mistagging non-b jets have been taken into account. The impact of large theoretical uncertainties in the cross sections for\ \ plus\ N\ jets processes due to an absence of next-to-leading order calculations is also considered.

}, issn = {0954-3899}, doi = {10.1088/0954-3899/34/5/N03}, url = {https://iopscience.iop.org/article/10.1088/0954-3899/34/5/N03}, author = {Benedetti, D and Cucciarelli, S and Hill, C and Incandela, J and Koay, S A and Riccardi, C and Santocchia, A and Schmidt, A and Torre, P and Weiser, C} } @article {4251, title = {Rapidly inducible, genetically targeted inactivation of neural and synaptic activity in vivo.}, journal = {Current Opinion in Neurobiology}, volume = {17}, year = {2007}, month = {2007 Oct}, pages = {581-6}, abstract = {

Inducible and reversible perturbation of the activity of selected neurons in vivo is critical to understanding the dynamics of brain circuits. Several genetically encoded systems for rapid inducible neuronal silencing have been developed in the past few years offering an arsenal of tools for in vivo experiments. Some systems are based on ion-channels or pumps, others on G protein coupled receptors, and yet others on modified presynaptic proteins. Inducers range from light to small molecules to peptides. This diversity results in differences in the various parameters that may determine the applicability of each tool to a particular biological question. Although further development would be beneficial, the current silencing tool kit already provides the ability to make specific perturbations of circuit function in behaving animals.

}, keywords = {Animals, Brain, G-Protein-Coupled, Gene Targeting, Neurons, Receptors, Synapses}, issn = {0959-4388}, doi = {10.1016/j.conb.2007.10.002}, author = {Tervo, Dougal and Karpova, Alla Y} } @article {4048, title = {A role for synaptic inputs at distal dendrites: instructive signals for hippocampal long-term plasticity.}, journal = {Neuron}, volume = {56}, year = {2007}, month = {2007 Dec 6}, pages = {866-79}, abstract = {

Synaptic potentials originating at distal dendritic locations are severely attenuated when they reach the soma and, thus, are poor at driving somatic spikes. Nonetheless, distal inputs convey essential information, suggesting that such inputs may be important for compartmentalized dendritic signaling. Here we report a new plasticity rule in which stimulation of distal perforant path inputs to hippocampal CA1 pyramidal neurons induces long-term potentiation at the CA1 proximal Schaffer collateral synapses when the two inputs are paired at a precise interval. This subthreshold form of heterosynaptic plasticity occurs in the absence of somatic spiking but requires activation of both NMDA receptors and IP(3) receptor-dependent release of Ca(2+) from internal stores. Our results suggest that direct sensory information arriving at distal CA1 synapses through the perforant path provide compartmentalized, instructive signals that assess the saliency of mnemonic information propagated through the hippocampal circuit to proximal synapses.

}, keywords = {4, 5-Trisphosphate Receptors, Absorptiometry, AMPA, Animals, Calcium, Computer Simulation, Dendrites, Dendritic Spines, Electrophysiology, Excitatory Postsynaptic Potentials, Hippocampus, Inositol 1, Memory, Mice, Models, N-Methyl-D-Aspartate, Neurological, Neuronal Plasticity, Neurophysiological, Patch-Clamp Techniques, Photon, Pyramidal Cells, Receptors, Recruitment, Signal Transduction, Synapses, Synaptic Transmission}, issn = {0896-6273}, doi = {10.1016/j.neuron.2007.10.020}, author = {Dudman, Joshua T and Tsay, David and Siegelbaum, Steven A} } @proceedings {4528, title = {Supervised learning of image restoration with convolutional networks.}, volume = {2}, year = {2007}, month = {2007 Oct 14}, pages = {1-8}, publisher = {IEEE}, edition = {ICCV}, author = {Jain, Viren and Murray, Joseph F and Roth, Fabian and Turaga, Srinivas and Zhigulin, Valentin and Briggman, Kevin L and Helmstaedter, Moritz N. and Denk, Winfried and Seung, H Sebastian} } @conference {46328, title = {Supervised Learning of Image Restoration with Convolutional Networks}, booktitle = {IEEE 11th International Conference on Computer Vision, 2007. ICCV 2007}, year = {2007}, month = {2007-10}, publisher = {IEEE}, organization = {IEEE}, address = {Rio de Janeiro}, abstract = {

Convolutional networks have achieved a great deal of success in high-level vision problems such as object recognition. Here we show that they can also be used as a general method for low-level image processing. As an example of our approach, convolutional networks are trained using gradient learning to solve the problem of restoring noisy or degraded images. For our training data, we have used electron microscopic images of neural circuitry with ground truth restorations provided by human experts. On this dataset, Markov random field (MRF), conditional random field (CRF), and anisotropic diffusion algorithms perform about the same as simple thresholding, but superior performance is obtained with a convolutional network containing over 34,000 adjustable parameters. When restored by this convolutional network, the images are clean enough to be used for segmentation, whereas the other approaches fail in this respect. We do not believe that convolutional networks are fundamentally superior to MRFs as a representation for image processing algorithms. On the contrary, the two approaches are closely related. But in practice, it is possible to train complex convolutional networks, while even simple MRF models are hindered by problems with Bayesian learning and inference procedures. Our results suggest that high model complexity is the single most important factor for good performance, and this is possible with convolutional networks.

}, isbn = {978-1-4244-1630-1}, doi = {10.1109/ICCV.2007.4408909}, author = {Jain, V. and Murray, J.F. and Roth, F. and Turaga, S. and Zhigulin, V. and Briggman, K.L. and Helmstaedter, M.N. and Denk, W. and Seung, H.S.} } @article {2403, title = {Switching of the core transcription machinery during myogenesis.}, journal = {Genes \& Development}, volume = {21}, year = {2007}, month = {2007 Sep 1}, pages = {2137-49}, abstract = {

Transcriptional mechanisms that govern cellular differentiation typically include sequence-specific DNA-binding proteins and chromatin-modifying activities. These regulatory factors are assumed necessary and sufficient to drive both divergent programs of proliferation and terminal differentiation. By contrast, potential contributions of the basal transcriptional apparatus to orchestrate cell-specific gene expression have been poorly explored. In order to probe alternative mechanisms that control differentiation, we have assessed the fate of the core promoter recognition complex, TFIID, during skeletal myogenesis. Here we report that differentiation of myoblast to myotubes involves the disruption of the canonical holo-TFIID and replacement by a novel TRF3/TAF3 (TBP-related factor 3/TATA-binding protein-associated factor 3) complex. This required switching of core promoter complexes provides organisms a simple yet effective means to selectively turn on one transcriptional program while silencing many others. Although this drastic but parsimonious transcriptional switch had previously escaped our attention, it may represent a more general mechanism for regulating cell type-specific terminal differentiation.

}, keywords = {Animals, Cell Differentiation, Cell Line, Developmental, Gene Expression Regulation, Genetic, Humans, Mice, Models, Muscle, Muscle Development, Muscle Fibers, Myofibrils, Nuclear Proteins, RNA Interference, Skeletal, TATA Box Binding Protein-Like Proteins, Transcription, Transcription Factor TFIID}, issn = {0890-9369}, doi = {10.1073/pnas.1100640108}, author = {Deato, Maria Divina E and Tjian, Robert} } @article {2400, title = {Transcription of histone gene cluster by differential core-promoter factors.}, journal = {Genes \& Development}, volume = {21}, year = {2007}, month = {2007 Nov 15}, pages = {2936-49}, abstract = {

The 100 copies of tandemly arrayed Drosophila linker (H1) and core (H2A/B and H3/H4) histone gene cluster are coordinately regulated during the cell cycle. However, the molecular mechanisms that must allow differential transcription of linker versus core histones prevalent during development remain elusive. Here, we used fluorescence imaging, biochemistry, and genetics to show that TBP (TATA-box-binding protein)-related factor 2 (TRF2) selectively regulates the TATA-less Histone H1 gene promoter, while TBP/TFIID targets core histone transcription. Importantly, TRF2-depleted polytene chromosomes display severe chromosomal structural defects. This selective usage of TRF2 and TBP provides a novel mechanism to differentially direct transcription within the histone cluster. Moreover, genome-wide chromatin immunoprecipitation (ChIP)-on-chip analyses coupled with RNA interference (RNAi)-mediated functional studies revealed that TRF2 targets several classes of TATA-less promoters of \>1000 genes including those driving transcription of essential chromatin organization and protein synthesis genes. Our studies establish that TRF2 promoter recognition complexes play a significantly more central role in governing metazoan transcription than previously appreciated.

}, keywords = {Animals, Base Sequence, Biological, Cells, Chromatin Immunoprecipitation, Chromosomes, Cluster Analysis, Cultured, Drosophila, Firefly, Fluorescence, Genes, Genetic, Histones, Immunohistochemistry, In Situ Hybridization, Insect, Luciferases, Models, Molecular Sequence Data, Multigene Family, Nucleic Acid, Promoter Regions, Reporter, RNA Interference, Sequence Homology, TATA Box Binding Protein-Like Proteins, TATA-Box Binding Protein, Transcription}, issn = {0890-9369}, doi = {10.1073/pnas.1100640108}, author = {Isogai, Yoh and Keles, S{\"u}nd{\"u}z and Prestel, Matthias and Hochheimer, Andreas and Tjian, Robert} } @article {2407, title = {An ARC/Mediator subunit required for SREBP control of cholesterol and lipid homeostasis.}, journal = {Nature}, volume = {442}, year = {2006}, month = {2006 Aug 10}, pages = {700-4}, abstract = {

The sterol regulatory element binding protein (SREBP) family of transcription activators are critical regulators of cholesterol and fatty acid homeostasis. We previously demonstrated that human SREBPs bind the CREB-binding protein (CBP)/p300 acetyltransferase KIX domain and recruit activator-recruited co-factor (ARC)/Mediator co-activator complexes through unknown mechanisms. Here we show that SREBPs use the evolutionarily conserved ARC105 (also called MED15) subunit to activate target genes. Structural analysis of the SREBP-binding domain in ARC105 by NMR revealed a three-helix bundle with marked similarity to the CBP/p300 KIX domain. In contrast to SREBPs, the CREB and c-Myb activators do not bind the ARC105 KIX domain, although they interact with the CBP KIX domain, revealing a surprising specificity among structurally related activator-binding domains. The Caenorhabditis elegans SREBP homologue SBP-1 promotes fatty acid homeostasis by regulating the expression of lipogenic enzymes. We found that, like SBP-1, the C. elegans ARC105 homologue MDT-15 is required for fatty acid homeostasis, and show that both SBP-1 and MDT-15 control transcription of genes governing desaturation of stearic acid to oleic acid. Notably, dietary addition of oleic acid significantly rescued various defects of nematodes targeted with RNA interference against sbp-1 and mdt-15, including impaired intestinal fat storage, infertility, decreased size and slow locomotion, suggesting that regulation of oleic acid levels represents a physiologically critical function of SBP-1 and MDT-15. Taken together, our findings demonstrate that ARC105 is a key effector of SREBP-dependent gene regulation and control of lipid homeostasis in metazoans.

}, keywords = {Amino Acid Sequence, Animals, Biomolecular, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Cholesterol, Homeostasis, Humans, Lipid Metabolism, Mediator Complex, Mice, Models, Molecular, Molecular Sequence Data, Nuclear Magnetic Resonance, Protein Binding, Protein Structure, Sterol Regulatory Element Binding Proteins, Tertiary, Transcription Factors, Transcriptional Activation}, issn = {1476-4687}, doi = {10.1073/pnas.1100640108}, author = {Yang, Fajun and Vought, Bryan W and Satterlee, John S and Walker, Amy K and Jim Sun, Z-Y and Watts, Jennifer L and DeBeaumont, Rosalie and Saito, R Mako and Hyberts, Sven G and Yang, Shaosong and Macol, Christine and Iyer, Lakshmanan and Tjian, Robert and van den Heuvel, Sander and Hart, Anne C and Wagner, Gerhard and N{\"a}{\"a}r, Anders M} } @article {1490, title = {Boundary enhancement and speckle reduction for ultrasound images via salient structure extraction.}, journal = {IEEE Transactions on Bio-Medical Engineering}, volume = {53}, year = {2006}, month = {2006 Nov}, pages = {2300-9}, abstract = {

In this paper, we present an approach for medical ultrasound (US) image enhancement. It is based on a novel perceptual saliency measure which favors smooth, long curves with constant curvature. The perceptual salient boundaries of tissues in US images are enhanced by computing the saliency of directional vectors in the image space, via a local searching algorithm. Our measure is generally determined by curvature changes, intensity gradient and the interaction of neighboring vectors. To restrain speckle noise during the enhancement process, an adaptive speckle suspension term is also combined into the proposed saliency measure. The results obtained on both simulated images and medical US data reveal superior performance of the novel approach over a number of commonly used speckle filters. Applications of US image segmentation show that although the proposed algorithm cannot remove the speckle noise completely and may discard weak anatomical structures in some case, it still provides a considerable gain to US image processing for computer-aided diagnosis.

}, keywords = {Algorithms, Automated, Computer-Assisted, Humans, Image Enhancement, Image Interpretation, Pattern Recognition, Reproducibility of Results, Sensitivity and Specificity, Ultrasonography}, issn = {0018-9294}, doi = {10.1109/TBME.2006.878088}, author = {Xie, Jun and Jiang, Yifeng and Tsui, Hung-Tat and Heng, Pheng-Ann} } @article {1773, title = {The cells and logic for mammalian sour taste detection.}, journal = {Nature}, volume = {442}, year = {2006}, month = {2006 Aug 24}, pages = {934-8}, abstract = {

Mammals taste many compounds yet use a sensory palette consisting of only five basic taste modalities: sweet, bitter, sour, salty and umami (the taste of monosodium glutamate). Although this repertoire may seem modest, it provides animals with critical information about the nature and quality of food. Sour taste detection functions as an important sensory input to warn against the ingestion of acidic (for example, spoiled or unripe) food sources. We have used a combination of bioinformatics, genetic and functional studies to identify PKD2L1, a polycystic-kidney-disease-like ion channel, as a candidate mammalian sour taste sensor. In the tongue, PKD2L1 is expressed in a subset of taste receptor cells distinct from those responsible for sweet, bitter and umami taste. To examine the role of PKD2L1-expressing taste cells in vivo, we engineered mice with targeted genetic ablations of selected populations of taste receptor cells. Animals lacking PKD2L1-expressing cells are completely devoid of taste responses to sour stimuli. Notably, responses to all other tastants remained unaffected, proving that the segregation of taste qualities even extends to ionic stimuli. Our results now establish independent cellular substrates for four of the five basic taste modalities, and support a comprehensive labelled-line mode of taste coding at the periphery. Notably, PKD2L1 is also expressed in specific neurons surrounding the central canal of the spinal cord. Here we demonstrate that these PKD2L1-expressing neurons send projections to the central canal, and selectively trigger action potentials in response to decreases in extracellular pH. We propose that these cells correspond to the long-sought components of the cerebrospinal fluid chemosensory system. Taken together, our results suggest a common basis for acid sensing in disparate physiological settings.

}, keywords = {Action Potentials, Animals, Calcium Channels, Cell Surface, Computational Biology, Gene Expression Profiling, Hydrogen-Ion Concentration, Membrane Glycoproteins, Mice, Neurons, Phosphoproteins, Receptors, Spinal Cord, Taste, Tongue, Transgenic}, issn = {1476-4687}, doi = {10.1038/nature05084}, author = {Huang, Angela L and Chen, Xiaoke and Hoon, Mark A and Chandrashekar, Jayaram and Guo, Wei and Tr{\"a}nkner, Dimitri and Ryba, Nicholas J P and Zuker, Charles S} } @article {2411, title = {Cell-type-selective induction of c-jun by TAF4b directs ovarian-specific transcription networks.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, year = {2006}, month = {2006 Feb 21}, pages = {2594-9}, abstract = {

Cell-type-selective expression of the TFIID subunit TAF(II)105 (renamed TAF4b) in the ovary is essential for proper follicle development. Although a multitude of signaling pathways required for folliculogenesis have been identified, downstream transcriptional integrators of these signals remain largely unknown. Here, we show that TAF4b controls the granulosa-cell-specific expression of the proto-oncogene c-jun, and together they regulate transcription of ovary-selective promoters. Instead of using cell-type-specific activators, our findings suggest that the coactivator TAF4b regulates the expression of tissue-specific genes, at least in part, through the cell-type-specific induction of c-jun, a ubiquitous activator. Importantly, the loss of TAF4b in ovarian granulosa cells disrupts cellular morphologies and interactions during follicle growth that likely contribute to the infertility observed in TAF4b-null female mice. These data highlight a mechanism for potentiating tissue-selective functions of the basal transcription machinery and reveal intricate networks of gene expression that orchestrate ovarian-specific functions and cell morphology.

}, keywords = {Animals, Developmental, Female, Gene Expression Regulation, Genetic, Gonadotropins, Granulosa Cells, Horses, Messenger, Mice, Mutant Strains, Ovarian Follicle, Ovary, Promoter Regions, Proto-Oncogene Proteins c-jun, Rats, RNA, TATA-Binding Protein Associated Factors, Transcription, Transcription Factor TFIID, Up-Regulation}, issn = {0027-8424}, doi = {10.1073/pnas.1100640108}, author = {Geles, Kenneth G and Freiman, Richard N and Liu, Wei-Li and Zheng, Shuang and Voronina, Ekaterina and Tjian, Robert} } @article {46353, title = {Cluster analysis and robust use of full-field models for sonar beamforming}, journal = {Journal of Acoustical Society of America }, volume = {120}, year = {2006}, month = {11/2006}, pages = { 2635{\textendash}2647}, type = {Journal Article}, chapter = {2635}, abstract = {

Multipath propagation in shallow water can lead to mismatch losses when single-path replicas are\ usedfor horizontal array\ beamforming.Matched field processing(MFP) seeks to remedy this by\ using\ full-fieldacoustic propagationmodels to predict the multipath arrival structure. Ideally MFP can give source localization in range and depth as well as detection gains but\ robustly\ estimating range and depth is difficult in practice. The approach described here seeks to collapse\ full-field\ replica outputs to bearing which is\ robustly\ estimated while retaining any signal gains provided by the\ full-field\ model.Clusteranalysis\ is\ used\ to group together\ full-field\ replicas with similar responses. This yields a less redundant {\textquotedblleft}sampled field{\textquotedblright} describing a set of representative multipath structures for each bearing. A detection algorithm is introduced that\ uses\ clustering\ to collapse\ beamformer\ outputs to bearing such that signal gains are retained while increases in the noise floor are minimized. Horizontal array data from SWELLEX-96 are\ used\ to demonstrate the detection benefits of sampled field as compared to single-pathbeamforming.

}, issn = {0001-4966}, doi = {10.1121/1.2346128}, author = {Brian Tracey and  Nigel Lee and Srinivas Turaga} } @article {2408, title = {Coactivator cross-talk specifies transcriptional output.}, journal = {Genes \& Development}, volume = {20}, year = {2006}, month = {2006 Jun 1}, pages = {1458-69}, abstract = {

Cells often fine-tune gene expression at the level of transcription to generate the appropriate response to a given environmental or developmental stimulus. Both positive and negative influences on gene expression must be balanced to produce the correct level of mRNA synthesis. To this end, the cell uses several classes of regulatory coactivator complexes including two central players, TFIID and Mediator (MED), in potentiating activated transcription. Both of these complexes integrate activator signals and convey them to the basal apparatus. Interestingly, many promoters require both regulatory complexes, although at first glance they may seem to be redundant. Here we have used RNA interference (RNAi) in Drosophila cells to selectively deplete subunits of the MED and TFIID complexes to dissect the contribution of each of these complexes in modulating activated transcription. We exploited the robust response of the metallothionein genes to heavy metal as a model for transcriptional activation by analyzing direct factor recruitment in both heterogeneous cell populations and at the single-cell level. Intriguingly, we find that MED and TFIID interact functionally to modulate transcriptional response to metal. The metal response element-binding transcription factor-1 (MTF-1) recruits TFIID, which then binds promoter DNA, setting up a "checkpoint complex" for the initiation of transcription that is subsequently activated upon recruitment of the MED complex. The appropriate expression level of the endogenous metallothionein genes is achieved only when the activities of these two coactivators are balanced. Surprisingly, we find that the same activator (MTF-1) requires different coactivator subunits depending on the context of the core promoter. Finally, we find that the stability of multi-subunit coactivator complexes can be compromised by loss of a single subunit, underscoring the potential for combinatorial control of transcription activation.

}, keywords = {Animals, Cells, Chromatin Immunoprecipitation, Cultured, Drosophila, Gene Expression, Genetic, Metallothionein, Models, Polymerase Chain Reaction, Promoter Regions, RNA Interference, Transcription}, issn = {0890-9369}, doi = {10.1073/pnas.1100640108}, author = {Marr, Michael T and Isogai, Yoh and Wright, Kevin J and Tjian, Robert} } @article {2410, title = {Cryo-electron microscopy studies of human TFIID: conformational breathing in the integration of gene regulatory cues.}, journal = {Structure}, volume = {14}, year = {2006}, month = {2006 Mar}, pages = {511-20}, abstract = {

The multisubunit transcription factor TFIID is essential for directing eukaryotic promoter recognition and mediating interactions with activators/cofactors during assembly of the preinitiation complex. Despite its central role in transcription initiation and regulation, structural knowledge of the TFIID complex has so far been largely limited to electron microscopy studies of negatively stained samples. Here, we present a cryo-electron microscopy 3D reconstruction of the large endogenous human TFIID complex. The improved cryopreservation has allowed for a more detailed definition of the structural elements in the complex and for the detection, by an extensive statistical analysis of the data, of a conformational opening and closing of the cavity central to the TFIID architecture. We propose that these density rearrangements in the structure are a likely reflection of the plasticity of the interactions between TFIID and its many partner proteins.

}, keywords = {Cryoelectron Microscopy, Gene Expression Regulation, Genetic, Humans, Protein Binding, Protein Structure, Tertiary, Transcription, Transcription Factor TFIID}, issn = {0969-2126}, doi = {10.1073/pnas.1100640108}, author = {Grob, Patricia and Cruse, Michael J and Inouye, Carla and Peris, Marian and Penczek, Pawel A and Tjian, Robert and Nogales, Eva} } @article {45909, title = {Distance-dependent differences in synapse number and AMPA receptor expression in hippocampal CA1 pyramidal neurons.}, journal = {Neuron}, volume = {50}, year = {2006}, month = {2006 May 4}, pages = {431-42}, abstract = {

The ability of synapses throughout the dendritic tree to influence neuronal output is crucial for information processing in the brain. Synaptic potentials attenuate dramatically, however, as they propagate along dendrites toward the soma. To examine whether excitatory axospinous synapses on CA1 pyramidal neurons compensate for their distance from the soma to counteract such dendritic filtering, we evaluated axospinous synapse number and receptor expression in three progressively distal regions: proximal and distal stratum radiatum (SR), and stratum lacunosum-moleculare (SLM). We found that the proportion of perforated synapses increases as a function of distance from the soma and that their AMPAR, but not NMDAR, expression is highest in distal SR and lowest in SLM. Computational models of pyramidal neurons derived from these results suggest that they arise from the compartment-specific use of conductance scaling in SR and dendritic spikes in SLM to minimize the influence of distance on synaptic efficacy.

}, keywords = {Animals, Cell Polarity, Cell Shape, Crosses, Genetic, Dendritic Spines, Excitatory Postsynaptic Potentials, Glutamic Acid, Hippocampus, Image Cytometry, Immunohistochemistry, Male, Microscopy, Electron, Transmission, Perforant Pathway, Presynaptic Terminals, Pyramidal Cells, Rats, Rats, Inbred BN, Rats, Inbred F344, Receptors, AMPA, Synapses, Synaptic Transmission}, issn = {0896-6273}, doi = {10.1016/j.neuron.2006.03.022}, author = {Nicholson, Daniel A and Trana, Rachel and Katz, Yael and Kath, William L and Spruston, Nelson and Geinisman, Yuri} } @article {5487, title = {Distinct behavioral responses to ethanol are regulated by alternate RhoGAP18B isoforms.}, journal = {Cell}, volume = {127}, year = {2006}, month = {2006 Oct 6}, pages = {199-211}, abstract = {

In most organisms, low ethanol doses induce increased activity, while high doses are sedating. To investigate the underlying mechanisms, we isolated Drosophila mutants with altered ethanol responsiveness. Mutations in white rabbit (whir), disrupting RhoGAP18B, are strongly resistant to the sedating effects of ethanol. This resistance can be suppressed by reducing the levels of Rho1 or Rac, implicating these GTPases in the behavioral response to ethanol. Indeed, expression of constitutively active forms of Rho1 or Rac1 in adult flies results in ethanol resistance similar to that observed in whir mutants. The whir locus produces several transcripts, RA-RD, which are predicted to encode three distinct RhoGAPs that share only the GAP domain. The RC transcript mediates the sedating effects of ethanol, while the RA transcript regulates its stimulant effects. Thus, distinct RhoGAPs, encoded by the same gene, regulate different manifestations of acute ethanol intoxication.

}, keywords = {Animal, Animals, Behavior, Brain, Central Nervous System Depressants, Drosophila melanogaster, Drosophila Proteins, Enzyme Activation, Ethanol, Female, GTPase-Activating Proteins, Humans, Molecular Sequence Data, Motor Activity, Mutation, Protein Isoforms, Rabbits, rho GTP-Binding Proteins, Transgenes}, issn = {0092-8674}, doi = {10.1016/j.cell.2006.09.010}, author = {Rothenfluh, Adrian and Threlkeld, Robert J and Bainton, Roland J and Tsai, Linus T-Y and Lasek, Amy W and Heberlein, Ulrike} } @article {2470, title = {A double-switch system regulates male courtship behavior in male and female Drosophila melanogaster.}, journal = {Nature Genetics}, volume = {38}, year = {2006}, month = {2006 Dec}, pages = {1435-9}, abstract = {

Current models describe male-specific fruitless (fruM) as a genetic {\textquoteright}switch{\textquoteright} regulating sexual behavior in Drosophila melanogaster, and they postulate that female (F) and male (M) doublesex (dsx) products control body sexual morphology. In contradiction to this simple model, we show that dsx, as well as fruM and non-sex-specific retained (retn), affect both male and female sexual behaviors. In females, both retn and dsxF contribute to female receptivity, and both genes act to repress male-like courtship activity in the presence or absence of fruM. In males, consistent with the opposing functions of dsxM and dsxF, dsxM acts as a positive factor for male courtship. retn also acts counter to fruM in the development of the male-specific muscle of Lawrence. Molecularly, retn seems to regulate sexual behavior via a previously described complex that represses zerknullt. Thus, we show that fru and dsx together act as a {\textquoteright}switch{\textquoteright} system regulating behavior in the context of other developmental genes, such as retn.

}, keywords = {Animal, Animals, DNA-Binding Proteins, Drosophila melanogaster, Drosophila Proteins, Female, Gene Expression Regulation, Genes, Homeodomain Proteins, Insect, Male, Mutation, Nerve Tissue Proteins, Nuclear Proteins, Phenotype, Sexual Behavior, Transcription Factors}, issn = {1061-4036}, doi = {10.1038/ng1908}, author = {Shirangi, Troy R and Taylor, Barbara J and McKeown, Michael} } @article {48655, title = {High-speed pollen release in the white mulberry tree, Morus alba L.}, journal = {Sexual Plant Reproduction}, volume = {19}, year = {2006}, month = {2006 Mar}, pages = {19-24}, abstract = {

Anemophilous plants described as catapulting pollen explosively into the air have rarely attracted detailed examination. We investigated floral anthesis in a male mulberry tree with high-speed video and a force probe. The stamen was inflexed within the floral bud. Exposure to dry air initially resulted in a gradual movement of the stamen. This caused fine threads to tear at the stomium, ensuring dehiscence of the anther, and subsequently enabled the anther to slip off a restraining pistillode. The sudden release of stored elastic energy in the spring-like filament drove the stamen to straighten in less than 25\ μs, and reflex the petals to velocities in excess of half the speed of sound. This is the fastest motion yet observed in biology, and approaches the theoretical physical limits for movements in plants.

}, doi = {10.1007/s00497-005-0018-9}, author = {Taylor, Philip E and Card, Gwyneth M and House, James and Dickinson, Michael H and Flagan, Richard C} } @article {46629, title = {Increased ethanol resistance and consumption in Eps8 knockout mice correlates with altered actin dynamics.}, journal = {Cell}, volume = {127}, year = {2006}, month = {2006 Oct 6}, pages = {213-26}, abstract = {

Dynamic modulation of the actin cytoskeleton is critical for synaptic plasticity, abnormalities of which are thought to contribute to mental illness and addiction. Here we report that mice lacking Eps8, a regulator of actin dynamics, are resistant to some acute intoxicating effects of ethanol and show increased ethanol consumption. In the brain, the N-methyl-D-aspartate (NMDA) receptor is a major target of ethanol. We show that Eps8 is localized to postsynaptic structures and is part of the NMDA receptor complex. Moreover, in Eps8 null mice, NMDA receptor currents and their sensitivity to inhibition by ethanol are abnormal. In addition, Eps8 null neurons are resistant to the actin-remodeling activities of NMDA and ethanol. We propose that proper regulation of the actin cytoskeleton is a key determinant of cellular and behavioral responses to ethanol.

}, keywords = {Actins, Adaptor Proteins, Signal Transducing, Alcohol Drinking, Animals, Behavior, Animal, Cells, Cultured, Central Nervous System Depressants, Cerebellum, Cytoskeletal Proteins, Cytoskeleton, Ethanol, Female, Humans, Male, Mice, Mice, Knockout, Neurons, Receptors, N-Methyl-D-Aspartate, Recombinant Proteins, Signal Transduction}, issn = {0092-8674}, doi = {10.1016/j.cell.2006.09.011}, author = {Offenh{\"a}user, Nina and Castelletti, Daniela and Mapelli, Lisa and Soppo, Blanche Ekalle and Regondi, Maria Cristina and Rossi, Paola and D{\textquoteright}Angelo, Egidio and Frassoni, Carolina and Amadeo, Alida and Tocchetti, Arianna and Pozzi, Benedetta and Disanza, Andrea and Guarnieri, Douglas and Betsholtz, Christer and Scita, Giorgio and Heberlein, Ulrike and Di Fiore, Pier Paolo} } @article {2508, title = {Juvenile hormone is required to couple imaginal disc formation with nutrition in insects.}, journal = {Science }, volume = {312}, year = {2006}, month = {2006 Jun 2}, pages = {1385-8}, abstract = {

In starved larvae of the tobacco hornworm moth Manduca sexta, larval and imaginal tissues stop growing, the former because they lack nutrient-dependent signals but the latter because of suppression by juvenile hormone. Without juvenile hormone, imaginal discs form and grow despite severe starvation. This hormone inhibits the intrinsic signaling needed for disc morphogenesis and does so independently of ecdysteroid action. Starvation and juvenile hormone treatments allowed the separation of intrinsic and nutrient-dependent aspects of disc growth and showed that both aspects must occur during the early phases of disc morphogenesis to ensure normal growth leading to typical-sized adults.

}, keywords = {Animal Nutritional Physiological Phenomena, Animals, Ecdysteroids, Juvenile Hormones, Larva, Manduca, Morphogenesis, Pyridines}, issn = {1095-9203}, doi = {10.1126/science.1123652}, author = {Truman, J W and Hiruma, K and Allee, J P and Macwhinnie, S G B and Champlin, D T and Riddiford, L M} } @article {45751, title = {Large-scale gene discovery in the pea aphid Acyrthosiphon pisum (Hemiptera).}, journal = {Genome Biol}, volume = {7}, year = {2006}, month = {2006}, pages = {R21}, abstract = {

Aphids are the leading pests in agricultural crops. A large-scale sequencing of 40,904 ESTs from the pea aphid Acyrthosiphon pisum was carried out to define a catalog of 12,082 unique transcripts. A strong AT bias was found, indicating a compositional shift between Drosophila melanogaster and A. pisum. An in silico profiling analysis characterized 135 transcripts specific to pea-aphid tissues (relating to bacteriocytes and parthenogenetic embryos). This project is the first to address the genetics of the Hemiptera and of a hemimetabolous insect.

}, keywords = {Animals, Aphids, Base Composition, Base Sequence, DNA, DNA, Complementary, Expressed Sequence Tags, Gene Library, Microsatellite Repeats, Peas, Phylogeny, Plant Diseases, Population Density, Transcription, Genetic}, issn = {1465-6914}, doi = {10.1186/gb-2006-7-3-r21}, author = {Sabater-Mu{\~n}oz, Beatriz and Legeai, Fabrice and Rispe, Claude and Bonhomme, Jo{\"e}l and Dearden, Peter and Dossat, Carole and Duclert, Aymeric and Gauthier, Jean-Pierre and Ducray, Dani{\`e}le Giblot and Hunter, Wayne and Dang, Phat and Kambhampati, Srini and Martinez-Torres, David and Cortes, Teresa and Moya, Andr{\`e}s and Nakabachi, Atsushi and Philippe, Cathy and Prunier-Leterme, Nathalie and Rahb{\'e}, Yvan and Simon, Jean-Christophe and Stern, David L and Wincker, Patrick and Tagu, Denis} } @article {2444, title = {Local caspase activity directs engulfment of dendrites during pruning.}, journal = {Nature Neuroscience}, volume = {9}, year = {2006}, month = {2006 Oct}, pages = {1234-6}, abstract = {

Pruning is important for sculpting neural circuits, as it removes excessive or inaccurate projections. Here we show that the removal of sensory neuron dendrites during pruning in Drosophila melanogaster is directed by local caspase activity. Suppressing caspase activity prevented dendrite removal, whereas a global activation of caspases within a neuron caused cell death. A new genetically encoded caspase probe revealed that caspase activity is confined to the degenerating dendrites of pruning neurons.

}, keywords = {Afferent, Analysis of Variance, Animals, Apoptosis, Caspases, Dendrites, Drosophila melanogaster, Drosophila Proteins, Enzyme Activation, Enzyme Inhibitors, Fluorescent Antibody Technique, Ganglia, Genetically Modified, Neurons, Spinal, Time Factors}, issn = {1097-6256}, doi = {10.1038/nn1774}, author = {Williams, Darren W and Kondo, Shu and Krzyzanowska, Agnieszka and Hiromi, Yasushi and Truman, James W} } @article {1691, title = {Nud1p, the yeast homolog of Centriolin, regulates spindle pole body inheritance in meiosis.}, journal = {The EMBO Journal}, volume = {25}, year = {2006}, month = {2006 Aug 23}, pages = {3856-68}, abstract = {

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

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

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

}, keywords = {Animal Nutritional Physiological Phenomena, Animals, Drosophila melanogaster, Drosophila Proteins, Forkhead Transcription Factors, Insulin, Receptor, Signal Transduction}, issn = {1551-4005}, doi = {10.1073/pnas.1100640108}, author = {Puig, Oscar and Tjian, Robert} } @article {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} } @article {1588, title = {Structural insight into gene transcriptional regulation and effector binding by the Lrp/AsnC family.}, journal = {Nucleic Acids Research}, volume = {34}, year = {2006}, month = {2006 Mar 9}, pages = {1439-49}, abstract = {

The Lrp/AsnC family of transcriptional regulatory proteins is found in both archaea and bacteria. Members of the family influence cellular metabolism in both a global (Lrp) and specific (AsnC) manner, often in response to exogenous amino acid effectors. In the present study we have determined both the first bacterial and the highest resolution structures for members of the family. Escherichia coli AsnC is a specific gene regulator whose activity is triggered by asparagine binding. Bacillus subtilis LrpC is a global regulator involved in chromosome condensation. Our AsnC-asparagine structure is the first for a regulator-effector complex and is revealed as an octameric disc. Key ligand recognition residues are identified together with a route for ligand access. The LrpC structure reveals a stable octamer supportive of a topological role in dynamic DNA packaging. The structures yield significant clues to the functionality of Lrp/AsnC-type regulators with respect to ligand binding and oligomerization states as well as to their role in specific and global DNA regulation.

}, keywords = {Amino Acid Sequence, Asparagine, Bacillus subtilis, Bacterial, Bacterial Proteins, Escherichia coli Proteins, Gene Expression Regulation, Genetic, Ligands, Models, Molecular, Molecular Sequence Data, Sequence Alignment, Trans-Activators, Transcription, Transcription Factors}, issn = {1362-4962}, doi = {10.1093/nar/gkl009}, author = {Thaw, Paul and Sedelnikova, Svetlana E and Muranova, Tatyana and Wiese, Sebastian and Ayora, Sylvia and Alonso, Juan C and Brinkman, Arie B and Akerboom, Jasper and van der Oost, John and Rafferty, John B} } @article {2406, title = {TAF4 nucleates a core subcomplex of TFIID and mediates activated transcription from a TATA-less promoter.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, year = {2006}, month = {2006 Aug 15}, pages = {12347-52}, abstract = {

Activator-dependent recruitment of TFIID initiates formation of the transcriptional preinitiation complex. TFIID binds core promoter DNA elements and directs the assembly of other general transcription factors, leading to binding of RNA polymerase II and activation of RNA synthesis. How TATA box-binding protein (TBP) and the TBP-associated factors (TAFs) are assembled into a functional TFIID complex with promoter recognition and coactivator activities in vivo remains unknown. Here, we use RNAi to knock down specific TFIID subunits in Drosophila tissue culture cells to determine which subunits are most critical for maintaining stability of TFIID in vivo. Contrary to expectations, we find that TAF4 rather than TBP or TAF1 plays the most critical role in maintaining stability of the complex. Our analysis also indicates that TAF5, TAF6, TAF9, and TAF12 play key roles in stability of the complex, whereas TBP, TAF1, TAF2, and TAF11 contribute very little to complex stability. Based on our results, we propose that holo-TFIID comprises a stable core subcomplex containing TAF4, TAF5, TAF6, TAF9, and TAF12 decorated with peripheral subunits TAF1, TAF2, TAF11, and TBP. Our initial functional studies indicate a specific and significant role for TAF1 and TAF4 in mediating transcription from a TATA-less, downstream core promoter element (DPE)-containing promoter, whereas a TATA-containing, DPE-less promoter was far less dependent on these subunits. In contrast to both TAF1 and TAF4, RNAi knockdown of TAF5 had little effect on transcription from either class of promoter. These studies significantly alter previous models for the assembly, structure, and function of TFIID.

}, keywords = {Animals, Cell Line, Drosophila melanogaster, Drosophila Proteins, Enzyme Stability, Gene Expression Regulation, Genetic, Humans, Macromolecular Substances, Models, Molecular, Protein Subunits, RNA Interference, TATA Box, TATA-Binding Protein Associated Factors, Transcription, Transcription Factor TFIID}, issn = {0027-8424}, doi = {10.1073/pnas.1100640108}, author = {Wright, Kevin J and Marr, Michael T and Tjian, Robert} } @article {3936, title = {Where to start and when to stop.}, journal = {Nature Structural \& Molecular Biology}, volume = {13}, year = {2006}, month = {2006 Aug}, pages = {668-70}, abstract = {

The activity of a handful of transcription factors, such as mammalian NF-B, Drosophila melanogaster Cubitus interruptus and yeast Spt23 and Mga2, are regulated through partial protein degradation by the proteasome. New data now show that the proteasome activates membrane-bound Spt23 and Mga2 by initiating their proteolysis at an internal site and then degrading the proteins bidirectionally toward both ends of the polypeptide chain, modifying our ideas on how the proteasome degrades targeted substrates.

}, keywords = {Animals, DNA-Binding Proteins, Drosophila Proteins, Membrane Proteins, NF-kappa B, Oncogene Proteins, Proteasome Endopeptidase Complex, Protein Structure, Saccharomyces cerevisiae Proteins, Tertiary, Trans-Activators, Transcription Factors}, issn = {1545-9993}, doi = {10.1038/nsmb0806-668}, author = {Tian, Lin and Matouschek, Andreas} } @article {2448, title = {Cellular mechanisms of dendrite pruning in Drosophila: insights from in vivo time-lapse of remodeling dendritic arborizing sensory neurons.}, journal = {Development}, volume = {132}, year = {2005}, month = {2005 Aug}, pages = {3631-42}, abstract = {

Regressive events that refine exuberant or inaccurate connections are critical in neuronal development. We used multi-photon, time-lapse imaging to examine how dendrites of Drosophila dendritic arborizing (da) sensory neurons are eliminated during early metamorphosis, and how intrinsic and extrinsic cellular mechanisms control this deconstruction. Removal of the larval dendritic arbor involves two mechanisms: local degeneration and branch retraction. In local degeneration, major branch severing events entail focal disruption of the microtubule cytoskeleton, followed by thinning of the disrupted region, severing and fragmentation. Retraction was observed at distal tips of branches and in proximal stumps after severing events. The pruning program of da neuron dendrites is steroid induced; cell-autonomous dominant-negative inhibition of steroid action blocks local degeneration, although retraction events still occur. Our data suggest that steroid-induced changes in the epidermis may contribute to dendritic retraction. Finally, we find that phagocytic blood cells not only engulf neuronal debris but also attack and sever intact branches that show signs of destabilization.

}, keywords = {Abdomen, Afferent, Animals, Biological, Cytoskeleton, Dendrites, Drosophila melanogaster, Fluorescent Dyes, Metamorphosis, Microscopy, Neurons, Phagocytes, Receptors, Steroid, Video}, issn = {0950-1991}, doi = {10.1242/dev.01928}, author = {Williams, Darren W and Truman, James W} } @article {3937, title = {A conserved processing mechanism regulates the activity of transcription factors Cubitus interruptus and NF-kappaB.}, journal = {Nature Structural \& Molecular Biology}, volume = {12}, year = {2005}, month = {2005 Dec}, pages = {1045-53}, abstract = {

The proteasome degrades some proteins, such as transcription factors Cubitus interruptus (Ci) and NF-kappaB, to generate biologically active protein fragments. Here we have identified and characterized the signals in the substrate proteins that cause this processing. The minimum signal consists of a simple sequence preceding a tightly folded domain in the direction of proteasome movement. The strength of the processing signal depends primarily on the complexity of the simple sequence rather than on amino acid identity, the resistance of the folded domain to unraveling by the proteasome and the spacing between the simple sequence and folded domain. We show that two unrelated transcription factors, Ci and NF-kappaB, use this mechanism to undergo partial degradation by the proteasome in vivo. These findings suggest that the mechanism is conserved evolutionarily and that processing signals may be widespread in regulatory proteins.

}, keywords = {Amino Acid Sequence, Animals, Cells, Cultured, DNA-Binding Proteins, Drosophila Proteins, Humans, NF-kappa B p50 Subunit, Proteasome Endopeptidase Complex, Protein Folding, Transcription Factors}, issn = {1545-9993}, doi = {10.1038/nsmb1018}, author = {Tian, Lin and Holmgren, Robert A and Matouschek, Andreas} } @article {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 {1589, title = {Engineering a selectable marker for hyperthermophiles.}, journal = {The Journal of Biological Chemistry}, volume = {280}, year = {2005}, month = {2005 Mar 25}, pages = {11422-31}, abstract = {

Limited thermostability of antibiotic resistance markers has restricted genetic research in the field of extremely thermophilic Archaea and bacteria. In this study, we used directed evolution and selection in the thermophilic bacterium Thermus thermophilus HB27 to find thermostable variants of a bleomycin-binding protein from the mesophilic bacterium Streptoalloteichus hindustanus. In a single selection round, we identified eight clones bearing five types of double mutated genes that provided T. thermophilus transformants with bleomycin resistance at 77 degrees C, while the wild-type gene could only do so up to 65 degrees C. Only six different amino acid positions were altered, three of which were glycine residues. All variant proteins were produced in Escherichia coli and analyzed biochemically for thermal stability and functionality at high temperature. A synthetic mutant resistance gene with low GC content was designed that combined four substitutions. The encoded protein showed up to 17 degrees C increased thermostability and unfolded at 85 degrees C in the absence of bleomycin, whereas in its presence the protein unfolded at 100 degrees C. Despite these highly thermophilic properties, this mutant was still able to function normally at mesophilic temperatures in vivo. The mutant protein was co-crystallized with bleomycin, and the structure of the binary complex was determined to a resolution of 1.5 A. Detailed structural analysis revealed possible molecular mechanisms of thermostabilization and enhanced antibiotic binding, which included the introduction of an intersubunit hydrogen bond network, improved hydrophobic packing of surface indentations, reduction of loop flexibility, and alpha-helix stabilization. The potential applicability of the thermostable selection marker is discussed.

}, keywords = {Amino Acid Sequence, Bacterial, Bacterial Proteins, Biological Markers, Bleomycin, Carrier Proteins, Drug Resistance, Genetic Engineering, Hydrogen Bonding, Hydrophobic and Hydrophilic Interactions, Molecular Sequence Data, Protein Folding, Protein Structure, Secondary, Temperature, Thermus thermophilus}, issn = {0021-9258}, doi = {10.1074/jbc.M413623200}, author = {Brouns, Stan J J and Wu, Hao and Akerboom, Jasper and Turnbull, Andrew P and de Vos, Willem M and van der Oost, John} } @article {2369, title = {How to find decision makers in neural networks.}, journal = {Biological Cybernetics}, volume = {93}, year = {2005}, month = {2005 Dec}, pages = {447-62}, abstract = {

Nervous systems often face the problem of classifying stimuli and making decisions based on these classifications. The neurons involved in these tasks can be characterized as sensory or motor, according to their correlation with sensory stimulus or motor response. In this study we define a third class of neurons responsible for making perceptual decisions. Our mathematical formalism enables the weighting of neuronal units according to their contribution to decision making, thus narrowing the field for more detailed studies of underlying mechanisms. We develop two definitions of a contribution to decision making. The first definition states that decision making activity can be found at the points of emergence for behavioral correlations in the system. The second definition involves the study of propagation of noise in the network. The latter definition is shown to be equivalent to the first one in the cases when they can be compared. Our results suggest a new approach to analyzing decision making networks.

}, keywords = {Animals, Computer Simulation, Decision Making, Electric Stimulation, Humans, Models, Nerve Net, Neural Networks (Computer), Neurological, Neurons, Nonlinear Dynamics, Stochastic Processes}, issn = {0340-1200}, doi = {10.1523/JNEUROSCI.3613-08.2008}, author = {Koulakov, Alexei A and Rinberg, Dmitry A and Tsigankov, Dmitry N} } @article {2412, title = {In vitro analysis of huntingtin-mediated transcriptional repression reveals multiple transcription factor targets.}, journal = {Cell}, volume = {123}, year = {2005}, month = {2005 Dec 29}, pages = {1241-53}, abstract = {

Transcriptional dysregulation has emerged as a potentially important pathogenic mechanism in Huntington{\textquoteright}s disease, a neurodegenerative disorder associated with polyglutamine expansion in the huntingtin (htt) protein. Here, we report the development of a biochemically defined in vitro transcription assay that is responsive to mutant htt. We demonstrate that both gene-specific activator protein Sp1 and selective components of the core transcription apparatus, including TFIID and TFIIF, are direct targets inhibited by mutant htt in a polyglutamine-dependent manner. The RAP30 subunit of TFIIF specifically interacts with mutant htt both in vitro and in vivo to interfere with formation of the RAP30-RAP74 native complex. Importantly, overexpression of RAP30 in cultured primary striatal cells protects neurons from mutant htt-induced cellular toxicity and alleviates the transcriptional inhibition of the dopamine D2 receptor gene by mutant htt. Our results suggest a mutant htt-directed repression mechanism involving multiple specific components of the basal transcription apparatus.

}, keywords = {Animals, Biological Assay, Cell-Free System, Cells, Cercopithecus aethiops, COS Cells, Cultured, Dopamine D2, Down-Regulation, Genetic, Mice, Mutation, Nerve Tissue Proteins, Neurons, Nuclear Proteins, Protein Binding, Protein Subunits, Rats, Receptors, Sp1 Transcription Factor, TFII, Transcription, Transcription Factor TFIID, Transcription Factors}, issn = {0092-8674}, doi = {10.1073/pnas.1100640108}, author = {Zhai, Weiguo and Jeong, Hyunkyung and Cui, Libin and Krainc, Dimitri and Tjian, Robert} } @article {2414, title = {Maintenance of spermatogenesis requires TAF4b, a gonad-specific subunit of TFIID.}, journal = {Genes \& Development}, volume = {19}, year = {2005}, month = {2005 Apr 1}, pages = {794-803}, abstract = {

The establishment and maintenance of spermatogenesis in mammals requires specialized networks of gene expression programs in the testis. The gonad-specific TAF4b component of TFIID (formerly TAF(II)105) is a transcriptional regulator enriched in the mouse testis. Herein we show that TAF4b is required for maintenance of spermatogenesis in the mouse. While young Taf4b-null males are initially fertile, Taf4b-null males become infertile by 3 mo of age and eventually exhibit seminiferous tubules devoid of germ cells. At birth, testes of Taf4b-null males appear histologically normal; however, at post-natal day 3 gonocyte proliferation is impaired and expression of spermatogonial stem cell markers c-Ret, Plzf, and Stra8 is reduced. Together, these data indicate that TAF4b is required for the precise expression of gene products essential for germ cell proliferation and suggest that TAF4b may be required for the regulation of spermatogonial stem cell specification and proliferation that is obligatory for normal spermatogenic maintenance in the adult.

}, keywords = {Aging, Animals, Cell Division, Infertility, Male, Mice, Spermatids, Spermatogenesis, Spermatogonia, TATA-Binding Protein Associated Factors, Testis, Transcription Factor TFIID}, issn = {0890-9369}, doi = {10.1073/pnas.1100640108}, author = {Falender, Allison E and Freiman, Richard N and Geles, Kenneth G and Lo, Kirk C and Hwang, KeumSil and Lamb, Dolores J and Morris, Patricia L and Tjian, Robert and Richards, JoAnne S} } @article {1138, title = {Male-specific fruitless specifies the neural substrates of Drosophila courtship behaviour.}, journal = {Nature}, volume = {436}, year = {2005}, month = {2005 Jul 21}, pages = {395-400}, abstract = {

Robust innate behaviours are attractive systems for genetically dissecting how environmental cues are perceived and integrated to generate complex behaviours. During courtship, Drosophila males engage in a series of innate, stereotyped behaviours that are coordinated by specific sensory cues. However, little is known about the specific neural substrates mediating this complex behavioural programme. Genetic, developmental and behavioural studies have shown that the fruitless (fru) gene encodes a set of male-specific transcription factors (FruM) that act to establish the potential for courtship in Drosophila. FruM proteins are expressed in approximately 2\% of central nervous system neurons, at least one subset of which coordinates the component behaviours of courtship. Here we have inserted the yeast GAL4 gene into the fru locus by homologous recombination and show that (1) FruM is expressed in subsets of all peripheral sensory systems previously implicated in courtship, (2) inhibition of FruM function in olfactory system components reduces olfactory-dependent changes in courtship behaviour, (3) transient inactivation of all FruM-expressing neurons abolishes courtship behaviour, with no other gross changes in general behaviour, and (4) {\textquoteright}masculinization{\textquoteright} of FruM-expressing neurons in females is largely sufficient to confer male courtship behaviour. Together, these data demonstrate that FruM proteins specify the neural substrates of male courtship.

}, keywords = {Animal, Animals, Central Nervous System, Courtship, Developmental, Drosophila melanogaster, Drosophila Proteins, Female, Gene Expression Regulation, Male, Nerve Tissue Proteins, Neurons, Sex Characteristics, Sexual Behavior, Transcription Factors}, issn = {1476-4687}, doi = {10.1038/nature03859}, author = {Manoli, Devanand S and Foss, Margit and Villella, Adriana and Taylor, Barbara J and Hall, Jeffrey C and Baker, Bruce S} } @article {5488, title = {Moody encodes two GPCRs that regulate cocaine behaviors and blood-brain barrier permeability in Drosophila.}, journal = {Cell}, volume = {123}, year = {2005}, month = {2005 Oct 7}, pages = {145-56}, abstract = {

We identified moody in a genetic screen for Drosophila mutants with altered cocaine sensitivity. Hypomorphic mutations in moody cause an increased sensitivity to cocaine and nicotine exposure. In contrast, sensitivity to the acute intoxicating effects of ethanol is reduced. The moody locus encodes two novel GPCRs, Moody-alpha and Moody-beta. While identical in their membrane-spanning domains, the two Moody proteins differ in their long carboxy-terminal domains, which are generated by use of alternative reading frames. Both Moody forms are required for normal cocaine sensitivity, suggesting that they carry out distinct but complementary functions. Moody-alpha and Moody-beta are coexpressed in surface glia that surround the nervous system, where they are actively required to maintain the integrity of the blood-brain barrier in the adult fly. We propose that a Moody-mediated signaling pathway functions in glia to regulate nervous system insulation and drug-related behaviors.

}, keywords = {Alternative Splicing, Animal, Animals, Behavior, Blood-Brain Barrier, Brain, Cocaine, Cocaine-Related Disorders, Disease Models, Dopamine Uptake Inhibitors, Drosophila melanogaster, Drosophila Proteins, Drug Tolerance, G-Protein-Coupled, Male, Motor Activity, Neuroglia, Nicotine, Protein Structure, Receptors, Substance-Related Disorders, Tertiary}, issn = {0092-8674}, doi = {10.1016/j.cell.2005.07.029}, author = {Bainton, Roland J and Tsai, Linus T-Y and Schwabe, Tina and DeSalvo, Michael and Gaul, Ulrike and Heberlein, Ulrike} } @article {46399, title = {Rapid and reversible chemical inactivation of synaptic transmission in genetically targeted neurons.}, journal = {Neuron}, volume = {48}, year = {2005}, month = {2005 Dec 8}, pages = {727-35}, abstract = {

Inducible and reversible silencing of selected neurons in vivo is critical to understanding the structure and dynamics of brain circuits. We have developed Molecules for Inactivation of Synaptic Transmission (MISTs) that can be genetically targeted to allow the reversible inactivation of neurotransmitter release. MISTs consist of modified presynaptic proteins that interfere with the synaptic vesicle cycle when crosslinked by small molecule "dimerizers." MISTs based on the vesicle proteins VAMP2/Synaptobrevin and Synaptophysin induced rapid ( approximately 10 min) and reversible block of synaptic transmission in cultured neurons and brain slices. In transgenic mice expressing MISTs selectively in Purkinje neurons, administration of dimerizer reduced learning and performance of the rotarod behavior. MISTs allow for specific, inducible, and reversible lesions in neuronal circuits and may provide treatment of disorders associated with neuronal hyperactivity.

}, keywords = {Animals, Cells, Cultured, Cross-Linking Reagents, Dimerization, Gene Targeting, In Vitro Techniques, Learning, Mice, Mice, Transgenic, Motor Activity, Neural Inhibition, Neurons, Neurotransmitter Agents, Purkinje Cells, Synaptic Transmission, Synaptic Vesicles, Synaptophysin, Time Factors, Vesicle-Associated Membrane Protein 2}, issn = {0896-6273}, doi = {10.1016/j.neuron.2005.11.015}, author = {Karpova, Alla Y and Tervo, Dougal G R and Gray, Noah W and Svoboda, Karel} } @article {1166, title = {Replication of mitochondrial DNA occurs by strand displacement with alternative light-strand origins, not via a strand-coupled mechanism.}, journal = {Genes \& Development}, volume = {19}, year = {2005}, month = {2005 Oct 15}, pages = {2466-76}, abstract = {

The established strand-displacement model for mammalian mitochondrial DNA (mtDNA) replication has recently been questioned in light of new data using two-dimensional (2D) agarose gel electrophoresis. It has been proposed that a synchronous, strand-coupled mode of replication occurs in tissues, thereby casting doubt on the general validity of the "orthodox," or strand-displacement model. We have examined mtDNA replicative intermediates from mouse liver using atomic force microscopy and 2D agarose gel electrophoresis in order to resolve this issue. The data provide evidence for only the orthodox, strand-displacement mode of replication and reveal the presence of additional, alternative origins of lagging light-strand mtDNA synthesis. The conditions used for 2D agarose gel analysis are favorable for branch migration of asymmetrically replicating nascent strands. These data reconcile the original displacement mode of replication with the data obtained from 2D gel analyses.

}, keywords = {Agar Gel, Animals, Atomic Force, DNA, DNA Replication, Electrophoresis, Mice, Microscopy, Mitochondrial, Replication Origin}, issn = {0890-9369}, doi = {10.1101/gad.1352105}, author = {Brown, Timothy A and Cecconi, Ciro and Tkachuk, Ariana N and Bustamante, Carlos and Clayton, David A} } @article {2447, title = {The role of the prothoracic gland in determining critical weight for metamorphosis in Drosophila melanogaster.}, journal = {Current Biology}, volume = {15}, year = {2005}, month = {2005 Oct 25}, pages = {1796-807}, abstract = {

The timely onset of metamorphosis in holometabolous insects depends on their reaching the appropriate size known as critical weight. Once critical weight is reached, juvenile hormone (JH) titers decline, resulting in the release of prothoracicotropic hormone (PTTH) at the next photoperiod gate and thereby inducing metamorphosis. How individuals determine when they have reached critical weight is unknown. We present evidence that in Drosophila, a component of the ring gland, the prothoracic gland (PG), assesses growth to determine when critical weight has been achieved.

}, keywords = {Animals, Biological, Body Weight, Developmental, Drosophila, Drosophila Proteins, Ecdysteroids, Endocrine Glands, Gene Expression Regulation, Immunoenzyme Techniques, Insect Hormones, Insulin, Larva, Metamorphosis, PTEN Phosphohydrolase}, issn = {0960-9822}, doi = {10.1016/j.cub.2005.09.017}, author = {Mirth, Christen and Truman, James W and Riddiford, Lynn M} } @article {1692, title = {Spore number control and breeding in Saccharomyces cerevisiae: a key role for a self-organizing system.}, journal = {The Journal of Cell Biology}, volume = {171}, year = {2005}, month = {2005 Nov 21}, pages = {627-40}, abstract = {

Spindle pole bodies (SPBs) provide a structural basis for genome inheritance and spore formation during meiosis in yeast. Upon carbon source limitation during sporulation, the number of haploid spores formed per cell is reduced. We show that precise spore number control (SNC) fulfills two functions. SNC maximizes the production of spores (1-4) that are formed by a single cell. This is regulated by the concentration of three structural meiotic SPB components, which is dependent on available amounts of carbon source. Using experiments and computer simulation, we show that the molecular mechanism relies on a self-organizing system, which is able to generate particular patterns (different numbers of spores) in dependency on one single stimulus (gradually increasing amounts of SPB constituents). We also show that SNC enhances intratetrad mating, whereby maximal amounts of germinated spores are able to return to a diploid lifestyle without intermediary mitotic division. This is beneficial for the immediate fitness of the population of postmeiotic cells.

}, keywords = {Biological, Carbon, Centromere, Computer Simulation, Cytoplasm, Dominant, Electron, Fungal, Gene Expression Regulation, Genes, Genetic, Genetic Linkage, Genotype, Green Fluorescent Proteins, Haploidy, Meiosis, Microscopy, Mitotic Spindle Apparatus, Models, Mutation, Open Reading Frames, Plasmids, Recombination, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Software, Spores, Time Factors, Video}, issn = {0021-9525}, doi = {10.1083/jcb.200507168}, author = {Taxis, Christof and Keller, Philipp and Kavagiou, Zaharoula and Jensen, Lars Juhl and Colombelli, Julien and Bork, Peer and Stelzer, Ernst H K and Knop, Michael} } @article {2415, title = {Structural studies of the human PBAF chromatin-remodeling complex.}, journal = {Structure}, volume = {13}, year = {2005}, month = {2005 Feb}, pages = {267-75}, abstract = {

ATP-dependent chromatin remodeling is one of the central processes responsible for imparting fluidity to chromatin and thus regulating DNA transactions. Although knowledge on this process is accumulating rapidly, the basic mechanism (or mechanisms) by which the remodeling complexes alter the structure of a nucleosome is not yet understood. Structural information on these macromolecular machines should aid in interpreting the biochemical and genetic data; to this end, we have determined the structure of the human PBAF ATP-dependent chromatin-remodeling complex preserved in negative stain by electron microscopy and have mapped the nucleosome binding site using two-dimensional (2D) image analysis. PBAF has an overall C-shaped architecture{\textendash}with a larger density to which two smaller knobs are attached{\textendash}surrounding a central cavity; one of these knobs appears to be flexible and occupies different positions in each of the structures determined. The 2D analysis of PBAF:nucleosome complexes indicates that the nucleosome binds in the central cavity.

}, keywords = {Binding Sites, Chromosomal Proteins, Humans, Imaging, Molecular Conformation, Non-Histone, Nucleosomes, Three-Dimensional, Transcription Factors}, issn = {0969-2126}, doi = {10.1073/pnas.1100640108}, author = {Leschziner, Andres E and Lemon, Bryan and Tjian, Robert and Nogales, Eva} } @article {1108, title = {Template-dependent morphogenesis of oriented calcite crystals in the presence of magnesium ions.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {44}, year = {2005}, month = {2005 Apr 15}, pages = {2386-90}, issn = {1433-7851}, doi = {10.1002/anie.200462296}, author = {Han, Yong-Jin and Wysocki, Laura M and Thanawala, Monica S and Siegrist, Theo and Aizenberg, Joanna} } @article {2413, title = {Transcriptional feedback control of insulin receptor by dFOXO/FOXO1.}, journal = {Genes \& Development}, volume = {19}, year = {2005}, month = {2005 Oct 15}, pages = {2435-46}, abstract = {

The insulin signaling pathway, which is conserved in evolution from flies to humans, evolved to allow a fast response to changes in nutrient availability while keeping glucose concentration constant in serum. Here we show that, both in Drosophila and mammals, insulin receptor (InR) represses its own synthesis by a feedback mechanism directed by the transcription factor dFOXO/FOXO1. In Drosophila, dFOXO is responsible for activating transcription of dInR, and nutritional conditions can modulate this effect. Starvation up-regulates mRNA of dInR in wild-type but not dFOXO-deficient flies. Importantly, FOXO1 acts in mammalian cells like its Drosophila counterpart, up-regulating the InR mRNA level upon fasting. Mammalian cells up-regulate the InR mRNA in the absence of serum, conditions that induce the dephosphorylation and activation of FOXO1. Interestingly, insulin is able to reverse this effect. Therefore, dFOXO/FOXO1 acts as an insulin sensor to activate insulin signaling, allowing a fast response to the hormone after each meal. Our results reveal a key feedback control mechanism for dFOXO/FOXO1 in regulating metabolism and insulin signaling.

}, keywords = {Animals, Cell Line, Drosophila, Drosophila Proteins, Evolution, Food Deprivation, Forkhead Transcription Factors, Genetic, Humans, Insulin, Messenger, Mice, Molecular, Receptor Protein-Tyrosine Kinases, RNA, Signal Transduction, Transcription, Up-Regulation}, issn = {0890-9369}, doi = {10.1073/pnas.1100640108}, author = {Puig, Oscar and Tjian, Robert} } @article {1255, title = {Class-specific features of neuronal wiring.}, journal = {Neuron}, volume = {43}, year = {2004}, month = {2004 Jul 22}, pages = {251-9}, abstract = {

Brain function relies on specificity of synaptic connectivity patterns among different classes of neurons. Yet, the substrates of specificity in complex neuropil remain largely unknown. We search for imprints of specificity in the layout of axonal and dendritic arbors from the rat neocortex. An analysis of 3D reconstructions of pairs consisting of pyramidal cells (PCs) and GABAergic interneurons (GIs) revealed that the layout of GI axons is specific. This specificity is manifested in a relatively high tortuosity, small branch length of these axons, and correlations of their trajectories with the positions of postsynaptic neuron dendrites. Axons of PCs show no such specificity, usually taking a relatively straight course through neuropil. However, wiring patterns among PCs hold a large potential for circuit remodeling and specificity through growth and retraction of dendritic spines. Our results define distinct class-specific rules in establishing synaptic connectivity, which could be crucial in formulating a canonical cortical circuit.

}, keywords = {Animals, Axons, Computer-Assisted, Dendrites, gamma-Aminobutyric Acid, Image Processing, Imaging, Interneurons, Neocortex, Neural Pathways, Neurons, Pyramidal Cells, Rats, Synapses, Three-Dimensional, Wistar}, issn = {0896-6273}, doi = {10.1016/j.tins.2005.05.006}, author = {Stepanyants, Armen and Tam{\'a}s, G{\'a}bor and Chklovskii, Dmitri B} } @article {2449, title = {Developmental architecture of adult-specific lineages in the ventral CNS of Drosophila.}, journal = {Development}, volume = {131}, year = {2004}, month = {2004 Oct}, pages = {5167-84}, abstract = {

In Drosophila most thoracic neuroblasts have two neurogenic periods: an initial brief period during embryogenesis and a second prolonged phase during larval growth. This study focuses on the adult-specific neurons that are born primarily during the second phase of neurogenesis. The fasciculated neurites arising from each cluster of adult-specific neurons express the cell-adhesion protein Neurotactin and they make a complex scaffold of neurite bundles within the thoracic neuropils. Using MARCM clones, we identified the 24 lineages that make up the scaffold of a thoracic hemineuromere. Unlike the early-born neurons that are strikingly diverse in both form and function, the adult specific cells in a given lineage are remarkably similar and typically project to only one or two initial targets, which appear to be the bundled neurites from other lineages. Correlated changes in the contacts between the lineages in different segments suggest that these initial contacts have functional significance in terms of future synaptic partners. This paper provides an overall view of the initial connections that eventually lead to the complex connectivity of the bulk of the thoracic neurons.

}, keywords = {Animals, Central Nervous System, Drosophila, Drosophila Proteins, Larva, Membrane Glycoproteins}, issn = {0950-1991}, doi = {10.1242/dev.01371}, author = {Truman, James W and Schuppe, Hansj{\"u}rgen and Shepherd, David and Williams, Darren W} } @article {2417, title = {Distinct conformational states of nuclear receptor-bound CRSP-Med complexes.}, journal = {Nature Structural \& Molecular Biology}, volume = {11}, year = {2004}, month = {2004 Jul}, pages = {664-71}, abstract = {

The human CRSP-Med coactivator complex is targeted by a diverse array of sequence-specific regulatory proteins. Using EM and single-particle reconstruction techniques, we recently completed a structural analysis of CRSP-Med bound to VP16 and SREBP-1a. Notably, these activators induced distinct conformational states upon binding the coactivator. Ostensibly, these different conformational states result from VP16 and SREBP-1a targeting distinct subunits in the CRSP-Med complex. To test this, we conducted a structural analysis of CRSP-Med bound to either thyroid hormone receptor (TR) or vitamin D receptor (VDR), both of which interact with the same subunit (Med220) of CRSP-Med. Structural comparison of TR- and VDR-bound complexes (at a resolution of 29 A) indeed reveals a shared conformational feature that is distinct from other known CRSP- Med structures. Importantly, this nuclear receptor-induced structural shift seems largely dependent on the movement of Med220 within the complex.

}, keywords = {Bacterial Proteins, Binding Sites, Calcitriol, Genetic, Hela Cells, Humans, Protein Binding, Protein Conformation, Receptors, Thyroid Hormone, Trans-Activators, Transcription}, issn = {1545-9993}, doi = {10.1073/pnas.1100640108}, author = {Taatjes, Dylan J and Schneider-Poetsch, Tilman and Tjian, Robert} } @article {5491, title = {Lmo mutants reveal a novel role for circadian pacemaker neurons in cocaine-induced behaviors.}, journal = {PLoS Biology}, volume = {2}, year = {2004}, month = {2004 Dec}, pages = {e408}, abstract = {

Drosophila has been developed recently as a model system to investigate the molecular and neural mechanisms underlying responses to drugs of abuse. Genetic screens for mutants with altered drug-induced behaviors thus provide an unbiased approach to define novel molecules involved in the process. We identified mutations in the Drosophila LIM-only (LMO) gene, encoding a regulator of LIM-homeodomain proteins, in a genetic screen for mutants with altered cocaine sensitivity. Reduced Lmo function increases behavioral responses to cocaine, while Lmo overexpression causes the opposite effect, reduced cocaine responsiveness. Expression of Lmo in the principal Drosophila circadian pacemaker cells, the PDF-expressing ventral lateral neurons (LN(v)s), is sufficient to confer normal cocaine sensitivity. Consistent with a role for Lmo in LN(v)function,Lmomutants also show defects in circadian rhythms of behavior. However, the role for LN(v)s in modulating cocaine responses is separable from their role as pacemaker neurons: ablation or functional silencing of the LN(v)s reduces cocaine sensitivity, while loss of the principal circadian neurotransmitter PDF has no effect. Together, these results reveal a novel role for Lmo in modulating acute cocaine sensitivity and circadian locomotor rhythmicity, and add to growing evidence that these behaviors are regulated by shared molecular mechanisms. The finding that the degree of cocaine responsiveness is controlled by the Drosophila pacemaker neurons provides a neuroanatomical basis for this overlap. We propose that Lmo controls the responsiveness of LN(v)s to cocaine, which in turn regulate the flies{\textquoteright} behavioral sensitivity to the drug.

}, keywords = {Alleles, Animal, Animals, Behavior, Biological, Biological Clocks, Circadian Rhythm, Cocaine, Drosophila melanogaster, Drosophila Proteins, Gene Expression Regulation, Gene Silencing, Genetic, Homeodomain Proteins, Models, Mutation, Neurons, Neuropeptides, Neurotransmitter Agents, Protein Structure, Reverse Transcriptase Polymerase Chain Reaction, Tertiary}, issn = {1545-7885}, doi = {10.1371/journal.pbio.0020408}, author = {Tsai, Linus T-Y and Bainton, Roland J and Blau, Justin and Heberlein, Ulrike} } @article {2420, title = {Myc-interacting protein 1 target gene profile: a link to microtubules, extracellular signal-regulated kinase, and cell growth.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, year = {2004}, month = {2004 Jan 13}, pages = {458-63}, abstract = {

To study the role of the transcription factor Myc-interacting protein 1 (MIZ-1) in activating various target genes after induction with the microtubule disrupting agent T113242, we have used small interfering RNA duplexes (siRNAs) to knockdown the expression of MIZ-1. As expected, depletion of MIZ-1 resulted in the inhibition of T113242-dependent activation of the low-density lipoprotein receptor (LDLR) gene in hepatocytes. Cells transfected with MIZ-1 siRNAs also exhibited growth arrest. In addition, inhibition of the extracellular signal-regulated kinase (ERK) pathway inhibited T113242-induced nuclear accumulation of MIZ-1 and activation of LDLR. Gene expression microarray analysis under various induction conditions identified other T113242-activated genes affected by a decrease in MIZ-1 and inhibition of the ERK pathway. We also found that the accumulation of MIZ-1 in the nucleus is influenced by cell-cell contact and/or growth. Taken together, our studies suggest that MIZ-1 regulates a specific set of genes that includes LDLR and that the ERK pathway plays a role in the activation of target promoters by MIZ-1.

}, keywords = {Cell Division, Cell Line, DNA-Binding Proteins, Flow Cytometry, Fluorescent Antibody Technique, Gene Expression Profiling, Humans, Indirect, Kruppel-Like Transcription Factors, Mitogen-Activated Protein Kinases, RNA Interference, Transcription Factors}, issn = {0027-8424}, doi = {10.1073/pnas.1100640108}, author = {Ziegelbauer, Joseph and Wei, Joyce and Tjian, Robert} } @article {2513, title = {Overexpression of broad: a new insight into its role in the Drosophila prothoracic gland cells.}, journal = {The Journal of Experimental Biology}, volume = {207}, year = {2004}, month = {2004 Mar}, pages = {1151-61}, abstract = {

Insect molting is triggered by ecdysteroids, which are produced in the prothoracic glands (PG). The broad (br) gene is one of the {\textquoteright}early genes{\textquoteright} directly regulated by ecdysteroids. Ectopic expression of the BR-Z3 isoform in early second instar Drosophila larvae (L2) before the rise of the ecdysteroid titer prevented molting to the third instar, but the larvae subsequently formed L2 prepupae after prolonged feeding. When these larvae were fed on diet containing 20-hydroxyecdysone (20E), they formed pharate third instar larvae. The critical weight for normal L3 pupariation of w(1118) larvae was found to be 0.8 mg and that for L2 pupariation was 0.45 mg. We also defined a threshold weight for metamorphosis of 0.3 mg, above which L2 larvae will metamorphose when provided with 20E. BR-Z3 apparently works through the PG cells of the ring gland but not the putative neurosecretory cells that drive ecdysone secretion, because ectopic expression of BR-Z3 specifically in the ring gland caused 53\% of the larvae to become permanent first instar larvae. Driving other BR isoforms in the ring gland prevented larval molting or pupariation to varying degrees. These molting defects were rescued by feeding 20E. Overexpression of each of the BR isoforms caused degeneration of the PG cells but on different time courses, indicating that BR is a signal for the degeneration of the PG cells that normally occurs during the pupal-adult transition.

}, keywords = {Animals, Body Weights and Measures, Drosophila, Drosophila Proteins, Ecdysterone, Exocrine Glands, Gene Expression Regulation, Genetically Modified, Immunohistochemistry, Larva, Molting, Protein Isoforms, Transcription Factors}, issn = {0022-0949}, author = {Zhou, Xiaofeng and Zhou, Baohua and Truman, James W and Riddiford, Lynn M} } @article {2416, title = {Polybromo protein BAF180 functions in mammalian cardiac chamber maturation.}, journal = {Genes \& Development}, volume = {18}, year = {2004}, month = {2004 Dec 15}, pages = {3106-16}, abstract = {

BAF and PBAF are two related mammalian chromatin remodeling complexes essential for gene expression and development. PBAF, but not BAF, is able to potentiate transcriptional activation in vitro mediated by nuclear receptors, such as RXRalpha, VDR, and PPARgamma. Here we show that the ablation of PBAF-specific subunit BAF180 in mouse embryos results in severe hypoplastic ventricle development and trophoblast placental defects, similar to those found in mice lacking RXRalpha and PPARgamma. Embryonic aggregation analyses reveal that in contrast to PPARgamma-deficient mice, the heart defects are likely a direct result of BAF180 ablation, rather than an indirect consequence of trophoblast placental defects. We identified potential target genes for BAF180 in heart development, such as S100A13 as well as retinoic acid (RA)-induced targets RARbeta2 and CRABPII. Importantly, BAF180 is recruited to the promoter of these target genes and BAF180 deficiency affects the RA response for CRABPII and RARbeta2. These studies reveal unique functions of PBAF in cardiac chamber maturation.

}, keywords = {Animals, Cell Aggregation, Chromatin Assembly and Disassembly, Congenital, Developmental, DNA Primers, Gene Expression Regulation, Heart Defects, Immunoprecipitation, In Situ Hybridization, In Situ Nick-End Labeling, Knockout, Mice, Nuclear Proteins, Oligonucleotide Array Sequence Analysis, Placenta, Receptors, Retinoic Acid, Reverse Transcriptase Polymerase Chain Reaction, S100 Proteins, Transcription Factors}, issn = {0890-9369}, doi = {10.1073/pnas.1100640108}, author = {Wang, Zhong and Zhai, Weiguo and Richardson, James A and Olson, Eric N and Meneses, Juanito J and Firpo, Meri T and Kang, Chulho and Skarnes, William C and Tjian, Robert} } @article {2419, title = {Regulatory diversity among metazoan co-activator complexes.}, journal = {Nature Reviews. Molecular Cell Biology}, volume = {5}, year = {2004}, month = {2004 May}, pages = {403-10}, abstract = {

Transcription is a stepwise process that involves many specialized proteins and protein complexes, all of which must work together to express a given gene in a spatially and temporally regulated manner. An integral step in this regulatory process is carried out by large, multisubunit co-activator complexes, which have diverse roles in transcriptional control. Their diversity and large size allows for many potential regulatory inputs, but how is the versatility and specificity of these co-activator complexes determined?

}, keywords = {Animals, DNA-Binding Proteins, Evolution, Gene Expression Regulation, Genetic, Genetic Variation, Humans, Molecular, Promoter Regions, Repressor Proteins, Species Specificity, Transcription, Transcription Factors}, issn = {1471-0072}, doi = {10.1073/pnas.1100640108}, author = {Taatjes, Dylan J and Marr, Michael T and Tjian, Robert} } @proceedings {46354, title = {Statistical clustering applied to adaptive matched field processing}, year = {2004}, author = {BH Tracey and NL Lee and SC Turaga} } @article {2418, title = {Structure and function of CRSP/Med2; a promoter-selective transcriptional coactivator complex.}, journal = {Molecular Cell}, volume = {14}, year = {2004}, month = {2004 Jun 4}, pages = {675-83}, abstract = {

The multi-subunit, human CRSP coactivator-also known as Mediator (Med)-regulates transcription by mediating signals between enhancer-bound factors (activators) and the core transcriptional machinery. Interestingly, different activators are known to bind distinct subunits within the CRSP/Med complex. We have isolated a stable, endogenous CRSP/Med complex (CRSP/Med2) that specifically lacks both the Med220 and the Med70 subunits. The three-dimensional structure of CRSP/Med2 was determined to 31 A resolution using electron microscopy and single-particle reconstruction techniques. Despite lacking both Med220 and Med70, CRSP/Med2 displays potent, activator-dependent transcriptional coactivator function in response to VP16, Sp1, and Sp1/SREBP-1a in vitro using chromatin templates. However, CRSP/Med2 is unable to potentiate activated transcription from a vitamin D receptor-responsive promoter, which requires interaction with Med220 for coactivator recruitment, whereas VDR-directed activation by CRSP/Med occurs normally. Thus, it appears that CRSP/Med may be regulated by a combinatorial assembly mechanism that allows promoter-selective function upon exchange of specific coactivator targets.

}, keywords = {CCAAT-Enhancer-Binding Proteins, DNA-Binding Proteins, Genes, Genetic, Hela Cells, Herpes Simplex Virus Protein Vmw65, Humans, Macromolecular Substances, Promoter Regions, Protein Structure, Protein Subunits, Regulator, Sp1 Transcription Factor, Sterol Regulatory Element Binding Protein 1, Tertiary, Trans-Activators, Transcription Factors, Transcriptional Activation, Vitamin D Response Element}, issn = {1097-2765}, doi = {10.1073/pnas.1100640108}, author = {Taatjes, Dylan J and Tjian, Robert} } @article {1590, title = {The structures of inhibitor complexes of Pyrococcus furiosus phosphoglucose isomerase provide insights into substrate binding and catalysis.}, journal = {Journal of Molecular Biology}, volume = {343}, year = {2004}, month = {2004 Oct 22}, pages = {649-57}, abstract = {

Pyrococcus furiosus phosphoglucose isomerase (PfPGI) is a metal-containing enzyme that catalyses the interconversion of glucose 6-phosphate (G6P) and fructose 6-phosphate (F6P). The recent structure of PfPGI has confirmed the hypothesis that the enzyme belongs to the cupin superfamily and identified the position of the active site. This fold is distinct from the alphabetaalpha sandwich fold commonly seen in phosphoglucose isomerases (PGIs) that are found in bacteria, eukaryotes and some archaea. Whilst the mechanism of the latter family is thought to proceed through a cis-enediol intermediate, analysis of the structure of PfPGI in the presence of inhibitors has led to the suggestion that the mechanism of this enzyme involves the metal-dependent direct transfer of a hydride between C1 and C2 atoms of the substrate. To gain further insight in the reaction mechanism of PfPGI, the structures of the free enzyme and the complexes with the inhibitor, 5-phospho-d-arabinonate (5PAA) in the presence and absence of metal have been determined. Comparison of these structures with those of equivalent complexes of the eukaryotic PGIs reveals similarities at the active site in the disposition of possible catalytic residues. These include the presence of a glutamic acid residue, Glu97 in PfPGI, which occupies the same position relative to the inhibitor as that of the glutamate that is thought to function as the catalytic base in the eukaryal-type PGIs. These similarities suggest that aspects of the catalytic mechanisms of these two structurally unrelated PGIs may be similar and based on an enediol intermediate.

}, keywords = {Archaeal Proteins, Binding Sites, Catalysis, Crystallography, Dimerization, Fructosephosphates, Glucose-6-Phosphate, Glucose-6-Phosphate Isomerase, Manganese, Models, Molecular, Molecular Structure, Pentosephosphates, Protein Binding, Protein Conformation, Pyrococcus furiosus, X-Ray}, issn = {0022-2836}, doi = {10.1016/j.jmb.2004.08.061}, author = {Berrisford, John M and Akerboom, Jasper and Brouns, Stan and Sedelnikova, Svetlana E and Turnbull, Andrew P and van der Oost, John and Salmon, Laurent and Hardr{\'e}, Renaud and Murray, Iain A and Blackburn, G Michael and Rice, David W and Baker, Patrick J} } @article {47224, title = {Transformation of olfactory representations in the Drosophila antennal lobe.}, journal = {Science (New York, N.Y.)}, volume = {303}, year = {2004}, month = {2004 Jan 16}, pages = {366-70}, abstract = {

Molecular genetics has revealed a precise stereotypy in the projection of primary olfactory sensory neurons onto secondary neurons. A major challenge is to understand how this mapping translates into odor responses in these second-order neurons. We investigated this question in Drosophila using whole-cell recordings in vivo. We observe that monomolecular odors generally elicit responses in large ensembles of antennal lobe neurons. Comparison of odor-evoked activity from afferents and postsynaptic neurons in the same glomerulus revealed that second-order neurons display broader tuning and more complex responses than their primary afferents. This indicates a major transformation of odor representations, implicating lateral interactions within the antennal lobe.

}, keywords = {Action Potentials, Animals, Drosophila, Excitatory Postsynaptic Potentials, GABA Antagonists, GABA-A Receptor Antagonists, Nervous System Physiological Phenomena, Neural Inhibition, Neurons, Afferent, Odors, Olfactory Pathways, Olfactory Receptor Neurons, Patch-Clamp Techniques, Picrotoxin, Receptors, GABA-A, Sense Organs, Smell, Synapses}, issn = {1095-9203}, doi = {10.1126/science.1090782}, author = {Wilson, Rachel I and Turner, Glenn C and Laurent, Gilles} } @article {3938, title = {An unstructured initiation site is required for efficient proteasome-mediated degradation.}, journal = {Nature Structural \& Molecular Biology}, volume = {11}, year = {2004}, month = {2004 Sep}, pages = {830-7}, abstract = {

The proteasome is the main ATP-dependent protease in eukaryotic cells and controls the concentration of many regulatory proteins in the cytosol and nucleus. Proteins are targeted to the proteasome by the covalent attachment of polyubiquitin chains. The ubiquitin modification serves as the proteasome recognition element but by itself is not sufficient for efficient degradation of folded proteins. We report that proteolysis of tightly folded proteins is accelerated greatly when an unstructured region is attached to the substrate. The unstructured region serves as the initiation site for degradation and is hydrolyzed first, after which the rest of the protein is digested sequentially. These results identify the initiation site as a novel component of the targeting signal, which is required to engage the proteasome unfolding machinery efficiently. The proteasome degrades a substrate by first binding to its ubiquitin modification and then initiating unfolding at an unstructured region.

}, keywords = {Adenosine Triphosphate, Animals, Bacillus, Binding Sites, Biological, Catalysis, Cell Nucleus, Cysteine Endopeptidases, Cytosol, Electrophoresis, Endopeptidases, Escherichia coli, Genetic, Hydrolysis, Models, Multienzyme Complexes, Polyacrylamide Gel, Promoter Regions, Proteasome Endopeptidase Complex, Protein Binding, Protein Folding, Protein Structure, Rabbits, Temperature, Tertiary, Time Factors, Ubiquitin}, issn = {1545-9993}, doi = {10.1038/nsmb814}, author = {Prakash, Sumit and Tian, Lin and Ratliff, Kevin S and Lehotzky, Rebecca E and Matouschek, Andreas} } @article {2425, title = {Bromodomains mediate an acetyl-histone encoded antisilencing function at heterochromatin boundaries.}, journal = {Molecular Cell}, volume = {11}, year = {2003}, month = {2003 Feb}, pages = {365-76}, abstract = {

Bromodomains bind acetylated histone H4 peptides in vitro. Since many chromatin remodeling complexes and the general transcription factor TFIID contain bromodomains, they may link histone acetylation to increased transcription. Here we show that yeast Bdf1 bromodomains recognize endogenous acetyl-histone H3/H4 as a mechanism for chromatin association in vivo. Surprisingly, deletion of BDF1 or a Bdf1 mutation that abolishes histone binding leads to transcriptional downregulation of genes located at heterochromatin-euchromatin boundaries. Wild-type Bdf1 protein imposes a physical barrier to the spreading of telomere- and mating-locus-proximal SIR proteins. Biochemical experiments indicate that Bdf1 competes with the Sir2 deacetylase for binding to acetylated histone H4. These data suggest an active role for Bdf1 in euchromatin maintenance and antisilencing through a histone tail-encoded boundary function.

}, keywords = {Acetylation, Biological, Down-Regulation, Fungal, Genes, Heterochromatin, Histones, Hydrogen Bonding, Models, Mutation, Protein Binding, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Silent Information Regulator Proteins, Transcription Factor TFIID, Transcription Factors}, issn = {1097-2765}, doi = {10.1073/pnas.1100640108}, author = {Ladurner, Andreas G and Inouye, Carla and Jain, Rajan and Tjian, Robert} } @article {46352, title = {Calculating free energies for diffusion in tight-fitting zeolite-guest systems: Local normal-mode Monte Carlo}, journal = {Journal of Chemical Physics}, volume = {118}, year = {2003}, month = {2003}, type = {Journal Article}, abstract = {

We present an efficient Monte Carlo algorithm for simulating diffusion in tight-fitting host{\textendash}guest systems, based on using zeolitenormal modes. Computational efficiency is gained by sampling framework distortions using normal-mode coordinates, and by exploiting the fact that zeolite distortion energies are well approximated by harmonic estimates. Additional savings are obtained by performing local normal-mode analysis, i.e., only including the motions of zeolite atoms close to the jumping molecule, hence focusing the calculation on zeolite distortions relevant to guest diffusion. We performed normal-mode analysis on various silicalite structures to demonstrate the accuracy of the harmonic approximation. We computed free energy surfaces for benzene in silicalite, finding excellent agreement with previous theoretical studies. Our method is found to be orders-of-magnitude faster than comparable Monte Carlo calculations that use conventional forcefields to quantify zeolite distortion energies. For tight-fitting guests, the efficiency of our new method allows flexible-lattice simulations to converge in less CPU time than that required for fixed-lattice simulations, because of the increased likelihood of jumping through a flexible lattice.

}, issn = {0021-9606}, doi = {10.1063/1.1558033}, author = {Srinivas C. Turaga and Scott M. Auerbach} } @article {2421, title = {Control of cell number by Drosophila FOXO: downstream and feedback regulation of the insulin receptor pathway.}, journal = {Genes \& Development}, volume = {17}, year = {2003}, month = {2003 Aug 15}, pages = {2006-20}, abstract = {

The Drosophila insulin receptor (dInR) regulates cell growth and proliferation through the dPI3K/dAkt pathway, which is conserved in metazoan organisms. Here we report the identification and functional characterization of the Drosophila forkhead-related transcription factor dFOXO, a key component of the insulin signaling cascade. dFOXO is phosphorylated by dAkt upon insulin treatment, leading to cytoplasmic retention and inhibition of its transcriptional activity. Mutant dFOXO lacking dAkt phosphorylation sites no longer responds to insulin inhibition, remains in the nucleus, and is constitutively active. dFOXO activation in S2 cells induces growth arrest and activates two key players of the dInR/dPI3K/dAkt pathway: the translational regulator d4EBP and the dInR itself. Induction of d4EBP likely leads to growth inhibition by dFOXO, whereas activation of dInR provides a novel transcriptionally induced feedback control mechanism. Targeted expression of dFOXO in fly tissues regulates organ size by specifying cell number with no effect on cell size. Our results establish dFOXO as a key transcriptional regulator of the insulin pathway that modulates growth and proliferation.

}, keywords = {Amino Acid, Amino Acid Sequence, Animals, Biological, Cell Count, Cell Division, Cell Nucleus, Chromones, Drosophila, Drosophila Proteins, Enzyme Inhibitors, Feedback, Forkhead Transcription Factors, Gene Expression Regulation, Insect Proteins, Insulin, Models, Molecular Sequence Data, Morpholines, Physiological, Post-Translational, Protein Processing, Protein-Serine-Threonine Kinases, Proto-Oncogene Proteins, Proto-Oncogene Proteins c-akt, Receptor, Recombinant Proteins, Sequence Homology, Signal Transduction, Trans-Activators, Transcription Factors}, issn = {0890-9369}, doi = {10.1073/pnas.1100640108}, author = {Puig, Oscar and Marr, Michael T and Ruhf, M Laure and Tjian, Robert} } @article {1592, title = {Crystal structure of Pyrococcus furiosus phosphoglucose isomerase. Implications for substrate binding and catalysis.}, journal = {The Journal of Biological Chemistry}, volume = {278}, year = {2003}, month = {2003 Aug 29}, pages = {33290-7}, abstract = {

Phosphoglucose isomerase (PGI) catalyzes the reversible isomerization between d-fructose 6-phosphate and d-glucose 6-phosphate as part of the glycolytic pathway. PGI from the Archaea Pyrococcus furiosus (Pfu) was crystallized, and its structure was determined by x-ray diffraction to a 2-A resolution. Structural comparison of this archaeal PGI with the previously solved structures of bacterial and eukaryotic PGIs reveals a completely different structure. Each subunit of the homodimeric Pfu PGI consists of a cupin domain, for which the overall structure is similar to other cupin domain-containing proteins, and includes a conserved transition metal-binding site. Biochemical data on the recombinant enzyme suggests that Fe2+ is bound to Pfu PGI. However, as catalytic activity is not strongly influenced either by the replacement of Fe2+ by a range of transition metals or by the presence or absence of the bound metal ion, we suggest that the metal may not be directly involved in catalysis but rather may be implicated in substrate recognition.

}, keywords = {Amino Acid, Amino Acid Sequence, Binding Sites, Chemical, Crystallography, Dimerization, Fructosephosphates, Glucose-6-Phosphate, Glucose-6-Phosphate Isomerase, Ions, Iron, Metals, Models, Molecular, Molecular Sequence Data, Protein Binding, Protein Conformation, Protein Structure, Pyrococcus furiosus, Secondary, Selenomethionine, Sequence Homology, Substrate Specificity, Temperature, Tertiary, X-Ray, X-Ray Diffraction}, issn = {0021-9258}, doi = {10.1074/jbc.M305170200}, author = {Berrisford, John M and Akerboom, Jasper and Turnbull, Andrew P and de Geus, Daniel and Sedelnikova, Svetlana E and Staton, Ian and McLeod, Cameron W and Verhees, Corn{\'e} H and van der Oost, John and Rice, David W and Baker, Patrick J} } @article {2424, title = {Diversified transcription initiation complexes expand promoter selectivity and tissue-specific gene expression.}, journal = {Genes \& Development}, volume = {17}, year = {2003}, month = {2003 Jun 1}, pages = {1309-20}, keywords = {Animals, Developmental, Drosophila, Drosophila Proteins, Gene Expression Regulation, Genetic, Male, Messenger, Organ Specificity, Promoter Regions, RNA, RNA Polymerase III, Spermatogenesis, TATA Box Binding Protein-Like Proteins, Telomeric Repeat Binding Protein 2, Transcription}, issn = {0890-9369}, doi = {10.1073/pnas.1100640108}, author = {Hochheimer, Andreas and Tjian, Robert} } @article {2322, title = {Dopamine D1 receptors mediate CREB phosphorylation via phosphorylation of the NMDA receptor at Ser897-NR1.}, journal = {Journal of Neurochemistry}, volume = {87}, year = {2003}, month = {2003 Nov}, pages = {922-34}, abstract = {

Addictive drugs such as amphetamine and cocaine stimulate the dopaminergic system, activate dopamine receptors and induce gene expression throughout the striatum. The signal transduction pathway leading from dopamine receptor stimulation at the synapse to gene expression in the nucleus has not been fully elucidated. Here, we present evidence that D1 receptor stimulation leads to phosphorylation of the transcription factor Ca2+ and cyclic AMP response element binding protein (CREB) in the nucleus by means of NMDA receptor-mediated Ca2+ signaling. Stimulation of D1 receptors induces the phosphorylation of Ser897 on the NR1 subunit by protein kinase A (PKA). This phosphorylation event is crucial for D1 receptor-mediated CREB phosphorylation. Dopamine cannot induce CRE-mediated gene expression in neurons transfected with a phosphorylation-deficient NR1 construct. Moreover, stimulation of D1 receptors or increase in cyclic AMP levels leads to an increase in cytosolic Ca2+ in the presence of glutamate, but not in the absence of glutamate, indicating the ability of dopamine and cyclic AMP to facilitate NMDA channel activity. The recruitment of the NMDA receptor signal transduction pathway by D1 receptors may provide a general mechanism for gene regulation that is fundamental for mechanisms of drug addiction and long-term memory.

}, keywords = {Animals, Calcium, Calcium-Calmodulin-Dependent Protein Kinases, Cells, Corpus Striatum, Cultured, Cyclic AMP Response Element-Binding Protein, Cyclic AMP-Dependent Protein Kinases, Dopamine D1, Glutamic Acid, Mutagenesis, N-Methyl-D-Aspartate, Neurons, Phosphorylation, Rats, Receptors, Signal Transduction, Site-Directed, Sprague-Dawley}, issn = {0022-3042}, doi = {10.3389/fnana.2010.00147}, author = {Dudman, Joshua T and Eaton, Molly E and Rajadhyaksha, Anjali and Mac{\'\i}as, Wendy and Taher, Muffadal and Barczak, Amy and Kameyama, Kimihiko and Huganir, Richard and Konradi, Christine} } @article {2514, title = {E74 exhibits stage-specific hormonal regulation in the epidermis of the tobacco hornworm, manduca sexta.}, journal = {Developmental Biology}, volume = {258}, year = {2003}, month = {2003 Jun 1}, pages = {76-90}, abstract = {

The transcription factor E74 is one of the early genes induced by ecdysteroids during metamorphosis of Drosophila melanogaster. Here, we report the cloning and hormonal regulation of E74 from the tobacco hornworm, Manduca sexta (MsE74). MsE74 is 98\% identical to that of D. melanogaster within the DNA-binding ETS domain of the protein. The 5{\textquoteright}-isoform-specific regions of MsE74A and MsE74B share significantly lower sequence similarity (30-40\%). Developmental expression by Northern blot analysis reveals that, during the 5th larval instar, MsE74B expression correlates with pupal commitment on day 3 and is induced to maximal levels within 12h by low levels of 20-hydroxyecdysone (20E) and repressed by physiologically relevant levels of juvenile hormone I (JH I). Immunocytochemical analysis shows that MsE74B appears in the epidermis before the 20E-induced Broad transcription factor that is correlated with pupal commitment (Zhou and Riddiford, 2001). In contrast, MsE74A is expressed late in the larval and the pupal molts when the ecdysteroid titer has declined to low levels and in the adult molt just as the ecdysteroid titer begins to decline. This change in timing during the adult molt appears not to be due to the absence of JH as there was no change during the pupal molt of allatectomized animals. When either 4th or 5th instar larval epidermis was explanted and subjected to hormonal manipulations, MsE74A induction occurred only after exposure to 20E followed by its removal. Thus, MsE74B appears to have a similar role at the onset of metamorphosis in Manduca as it does in Drosophila, whereas MsE74A is regulated differently at pupation in Manduca than at pupariation in Drosophila.

}, keywords = {Amino Acid, Amino Acid Sequence, Animals, Base Sequence, Biological, Cells, Cultured, Developmental, Drosophila, Ecdysterone, Epidermis, Gene Expression Regulation, Genes, Insect, Insect Proteins, Juvenile Hormones, Larva, Manduca, Messenger, Metamorphosis, Molecular Sequence Data, Open Reading Frames, Protein Isoforms, Protein Structure, Pupa, RNA, Sequence Homology, Tertiary, Transcription Factors}, issn = {0012-1606}, author = {Stilwell, Geoffrey E and Nelson, Charles A and Weller, John and Cui, Haiyang and Hiruma, Kiyoshi and Truman, James W and Riddiford, Lynn M} } @article {2321, title = {The hyperpolarization-activated HCN1 channel is important for motor learning and neuronal integration by cerebellar Purkinje cells.}, journal = {Cell}, volume = {115}, year = {2003}, month = {2003 Nov 26}, pages = {551-64}, abstract = {

In contrast to our increasingly detailed understanding of how synaptic plasticity provides a cellular substrate for learning and memory, it is less clear how a neuron{\textquoteright}s voltage-gated ion channels interact with plastic changes in synaptic strength to influence behavior. We find, using generalized and regional knockout mice, that deletion of the HCN1 channel causes profound motor learning and memory deficits in swimming and rotarod tasks. In cerebellar Purkinje cells, which are a key component of the cerebellar circuit for learning of correctly timed movements, HCN1 mediates an inward current that stabilizes the integrative properties of Purkinje cells and ensures that their input-output function is independent of the previous history of their activity. We suggest that this nonsynaptic integrative function of HCN1 is required for accurate decoding of input patterns and thereby enables synaptic plasticity to appropriately influence the performance of motor activity.

}, keywords = {Action Potentials, Afferent Pathways, Animals, Cells, Conditioning (Psychology), Cultured, Cyclic Nucleotide-Gated Cation Channels, Ion Channels, Knockout, Learning, Maze Learning, Mice, Motor Skills, Movement, Nerve Tissue Proteins, Neuronal Plasticity, Potassium Channels, Purkinje Cells, Synapses, Synaptic Transmission}, issn = {0092-8674}, doi = {10.3389/fnana.2010.00147}, author = {Nolan, Matthew F and Malleret, Ga{\"e}l and Lee, Ka Hung and Gibbs, Emma and Dudman, Joshua T and Santoro, Bina and Yin, Deqi and Thompson, Richard F and Siegelbaum, Steven A and Kandel, Eric R and Morozov, Alexei} } @article {2292, title = {Inducible nitric oxide synthase (NOS2) promoter CCTTT repeat polymorphism: relationship to in vivo nitric oxide production/NOS activity in an asymptomatic malaria-endemic population.}, journal = {The American Journal of Tropical Medicine and Hygiene}, volume = {69}, year = {2003}, month = {2003 Dec}, pages = {569-73}, abstract = {

Polymorphisms in the inducible nitric oxide synthase gene (NOS2) promoter have been associated with clinical outcome from malaria. These include a CCTTT repeat (CCTTTn) 2.5 kilobases upstream from the NOS2 transcription start site, and two single nucleotide substitutions: G{\textendash}\>C at position -954 (G-954C), and C{\textendash}\>T at position -1173 (C-1173T). Although hypothesized to influence NO production in vivo, the functional relevance of (CCTTT)n and G-954C is uncertain because disease association studies have yielded inconsistent results. This study found no association between CCTTT repeat number and levels of plasma NO metabolites or peripheral blood mononuclear cell NOS activity in a cohort of asymptomatic malaria-exposed coastal Papua New Guineans 1-60 years old. This suggests that (CCTTT)n does not independently influence NOS2 transcription in vivo. Neither the G-954C nor the C-1173T polymorphisms were identified in this population, indicating the variability and complexity of selection for NOS2 promoter polymorphisms in different malaria-endemic populations.

}, keywords = {Endemic Diseases, Female, Genetic, Genetic Predisposition to Disease, Humans, Malaria, Male, Nitric Oxide, Nitric Oxide Synthase, Nitric Oxide Synthase Type II, Nucleic Acid, Oceanic Ancestry Group, Papua New Guinea, Polymorphism, Promoter Regions, Repetitive Sequences}, issn = {0002-9637}, author = {Boutlis, Craig S and Hobbs, Maurine R and Marsh, Robyn L and Misukonis, Mary A and Tkachuk, Ariana N and Lagog, Moses and Booth, Jennifer and Granger, Donald L and Bockarie, Moses J and Mgone, Charles S and Levesque, Marc C and Weinberg, J Brice and Anstey, Nicholas M} } @article {1591, title = {Purification, crystallization and preliminary crystallographic analysis of phosphoglucose isomerase from the hyperthermophilic archaeon Pyrococcus furiosus.}, journal = {Acta Crystallographica. Section D, Biological Crystallography}, volume = {59}, year = {2003}, month = {2003 Oct 19}, pages = {1822-3}, abstract = {

The glycolytic enzyme phosphoglucose isomerase catalyses the reversible isomerization of glucose 6-phosphate to fructose 6-phosphate. The phosphoglucose isomerase from the hyperthermophilic archaeon Pyrococcus furiosus, which shows no sequence similarity to any known bacterial or eukaryotic phosphoglucose isomerase, has been cloned and overexpressed in Escherichia coli, purified and subsequently crystallized by the hanging-drop method of vapour diffusion using 1.6 M sodium citrate as the precipitant at pH 6.5. Multiple-wavelength anomalous dispersive X-ray data have been collected to a maximum resolution of 1.92 A on a single selenomethionine-incorporated crystal. This crystal belongs to space group C2, with approximate unit-cell parameters a = 84.7

}, keywords = {Crystallization, Crystallography, Escherichia coli, Glucose-6-Phosphate Isomerase, Protein Conformation, Pyrococcus furiosus, Recombinant Proteins, Selenomethionine, X-Ray}, issn = {0907-4449}, author = {Akerboom, Jasper and Turnbull, Andrew P and Hargreaves, David and Fisher, Martin and de Geus, Daniel and Sedelnikova, Svetlana E and Berrisford, John M and Baker, Patrick J and Verhees, Corn{\'e} H and van der Oost, John and Rice, David W} } @article {2426, title = {Regulating the regulators: lysine modifications make their mark.}, journal = {Cell}, volume = {112}, year = {2003}, month = {2003 Jan 10}, pages = {11-7}, abstract = {

Decades of research have uncovered much of the molecular machinery responsible for establishing and maintaining proper gene transcription patterns in eukaryotes. Although the composition of this machinery is largely known, mechanisms regulating its activity by covalent modification are just coming into focus. Here, we review several cases of ubiquitination, sumoylation, and acetylation that link specific covalent modification of the transcriptional apparatus to their regulatory function. We propose that potential cascades of modifications serve as molecular rheostats that fine-tune the control of transcription in diverse organisms.

}, keywords = {Acetylation, Basic-Leucine Zipper Transcription Factors, Cell Nucleus, DNA-Binding Proteins, Gene Expression Regulation, Genetic, Humans, Lysine, Messenger, Models, Promoter Regions, RNA, RNA Polymerase II, Saccharomyces cerevisiae Proteins, Small Ubiquitin-Related Modifier Proteins, Trans-Activators, Transcription, Transcription Factors, Transcriptional Activation, Ubiquitins}, issn = {0092-8674}, doi = {10.1073/pnas.1100640108}, author = {Freiman, Richard N and Tjian, Robert} } @article {4152, title = {Spike sorting in the frequency domain with overlap detection.}, year = {2003}, abstract = {

This paper deals with the problem of extracting the activity of individual neurons from multi-electrode recordings. Important aspects of this work are: 1) the sorting is done in two stages - a statistical model of the spikes from different cells is built and only then are occurrences of these spikes in the data detected by scanning through the original data, 2) the spike sorting is done in the frequency domain, 3) strict statistical tests are applied to determine if and how a spike should be classiffed, 4) the statistical model for detecting overlaping spike events is proposed, 5) slow dynamics of spike shapes are tracked during long experiments. Results from the application of these techniques to data collected from the escape response system of the American cockroach, Periplaneta americana, are presented.

}, author = {Rinberg, D and Bialek, W and Davidowitz, H and Tishby, N} } @article {2423, title = {Targeting genes and transcription factors to segregated nuclear compartments.}, journal = {Current Opinion in Cell Biology}, volume = {15}, year = {2003}, month = {2003 Jun}, pages = {296-303}, abstract = {

With increasingly detailed images of nuclear structures revealed by advanced microscopy, a remarkably compartmentalized cell nucleus has come into focus. Although this complex nuclear organization remains largely unexplored, some progress has been made in deciphering the functional aspects of various subnuclear structures, revealing how this elaborate framework can influence gene activation. Several recent studies have helped illustrate how cells might utilize the nuclear architecture as an additional level of transcriptional control, perhaps by targeting genes and regulatory factors to specific sites within the nucleus that are designated for active RNA synthesis.

}, keywords = {Animals, Cell Nucleus Structures, Gene Expression, Humans, Protein Transport, Transcription Factors}, issn = {0955-0674}, doi = {10.1073/pnas.1100640108}, author = {Isogai, Yoh and Tjian, Robert} } @article {2422, title = {Transcription regulation and animal diversity.}, journal = {Nature}, volume = {424}, year = {2003}, month = {2003 Jul 10}, pages = {147-51}, abstract = {

Whole-genome sequence assemblies are now available for seven different animals, including nematode worms, mice and humans. Comparative genome analyses reveal a surprising constancy in genetic content: vertebrate genomes have only about twice the number of genes that invertebrate genomes have, and the increase is primarily due to the duplication of existing genes rather than the invention of new ones. How, then, has evolutionary diversity arisen? Emerging evidence suggests that organismal complexity arises from progressively more elaborate regulation of gene expression.

}, keywords = {Animals, Chromatin, DNA, Ecosystem, Gene Expression Regulation, Genetic, Humans, Nucleic Acid, Regulatory Sequences, Transcription, Transcription Factors}, issn = {1476-4687}, doi = {10.1073/pnas.1100640108}, author = {Levine, Michael and Tjian, Robert} } @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 {2293, title = {Haemozoin as a marker of placental parasitization.}, journal = {Transactions of the Royal Society of Tropical Medicine and Hygiene}, volume = {96}, year = {2002}, month = {2002 Nov-Dec}, pages = {644-6}, abstract = {

Both Plasmodium vivax and P. falciparum malaria can cause the delivery of low birthweight babies. In this report, we have quantitated haemozoin levels in placentas from women living on the Thai-Burmese border in a region of low transmission for both P. falciparum and P. vivax malaria from June 1995 to January 2000. P. falciparum malaria infections during pregnancy lead to the accumulation of haemozoin (malaria pigment) in the placenta, especially in infections near term and in primigravid pregnancies. Haemozoin concentration was not associated with adverse birth outcomes. Women with P. vivax infections during pregnancy do not have measurable levels of placental haemozoin suggesting that P. vivax-infected erythrocytes do not accumulate in the placenta as much as P. falciparum-infected ones.

}, keywords = {Analysis of Variance, Biological Markers, Falciparum, Female, Hemeproteins, Humans, Infant, Low Birth Weight, Malaria, Newborn, Parasitemia, Parasitic, Placenta, Placenta Diseases, Pregnancy, Pregnancy Complications, Regression Analysis, Vivax}, issn = {0035-9203}, author = {McGready, Rose and Brockman, Alan and Cho, Thein and Levesque, Martin A and Tkachuk, Ariana N and Meshnick, Steven R and Nosten, Fran\c cois} } @article {5492, title = {High-resolution analysis of ethanol-induced locomotor stimulation in Drosophila.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {22}, year = {2002}, month = {2002 Dec 15}, pages = {11035-44}, abstract = {

Understanding how ethanol influences behavior is key to deciphering the mechanisms of ethanol action and alcoholism. In mammals, low doses of ethanol stimulate locomotion, whereas high doses depress it. The acute stimulant effect of ethanol has been proposed to be a manifestation of its rewarding effects. In Drosophila, ethanol exposure transiently potentiates locomotor activity in a biphasic dose- and time-dependent manner. An initial short-lived peak of activity corresponds to an olfactory response to ethanol. A second, longer-lasting period of increased activity coincides with rising internal ethanol concentrations; these closely parallel concentrations that stimulate locomotion in mammals. High-resolution analysis of the walking pattern of individual flies revealed that locomotion consists of bouts of activity; bout structure can be quantified by bout frequency, bout length, and the time spent walking at high speeds. Ethanol exposure induces both dramatic and dynamic changes in bout structure. Mutants with increased ethanol sensitivity show distinct changes in ethanol-induced locomotor behavior, as well as genotype-specific changes in activity bout structure. Thus, the overall effect of ethanol on locomotor behavior in Drosophila is caused by changes in discrete quantifiable parameters of walking pattern. The effects of ethanol on locomotion are comparable in flies and mammals, suggesting that Drosophila is a suitable model system to study the underlying mechanisms.

}, keywords = {Afferent Pathways, Animal, Animals, Automation, Behavior, Cyclic AMP, Dose-Response Relationship, Drosophila, Drug, Ethanol, Kinetics, Locomotion, Male, Mutation, Sensitivity and Specificity}, issn = {1529-2401}, author = {Wolf, Fred W and Rodan, Aylin R and Tsai, Linus T-Y and Heberlein, Ulrike} } @article {2430, title = {Human CRSP interacts with RNA polymerase II CTD and adopts a specific CTD-bound conformation.}, journal = {Genes \& Development}, volume = {16}, year = {2002}, month = {2002 Jun 1}, pages = {1339-44}, abstract = {

Activation of gene transcription in mammalian cells requires several classes of coactivators that participate in different steps of the activation cascade. Using conventional and affinity chromatography, we have isolated a human coactivator complex that interacts directly with the C-terminal domain (CTD) of RNA polymerase II (Pol II). The CTD-binding complex is structurally and functionally indistinguishable from our previously isolated CRSP coactivator complex. The closely related, but transcriptionally inactive, ARC-L complex failed to interact with the CTD, indicating a significant biochemical difference between CRSP and ARC-L that may, in part, explain their functional divergence. Electron microscopy and three-dimensional single-particle reconstruction reveals a conformation for CTD-CRSP that is structurally distinct from unliganded CRSP or CRSP bound to SREBP-1a, but highly similar to CRSP bound to the VP16 activator. Together, our findings suggest that the human CRSP coactivator functions, at least in part, by mediating activator-dependent recruitment of RNA Pol II via the CTD.

}, keywords = {Binding Sites, Chromatin, Electron, Electrophoresis, Genetic, Glutathione Transferase, Hela Cells, Humans, Immunoblotting, Ligands, Microscopy, Models, Molecular, Polyacrylamide Gel, Protein Binding, Protein Conformation, Protein Structure, Recombinant Fusion Proteins, RNA Polymerase II, Tertiary, Trans-Activators, Transcription}, issn = {0890-9369}, doi = {10.1073/pnas.1100640108}, author = {N{\"a}{\"a}r, Anders M and Taatjes, Dylan J and Zhai, Weiguo and Nogales, Eva and Tjian, Robert} } @article {2450, title = {Mutations in the Drosophila glycoprotein hormone receptor, rickets, eliminate neuropeptide-induced tanning and selectively block a stereotyped behavioral program.}, journal = {The Journal of Experimental Biology}, volume = {205}, year = {2002}, month = {2002 Sep}, pages = {2555-65}, abstract = {

Adult insects achieve their final form shortly after adult eclosion by the combined effects of specialized behaviors that generate increased blood pressure, which causes cuticular expansion, and hormones, which plasticize and then tan the cuticle. We examined the molecular mechanisms contributing to these processes in Drosophila by analyzing mutants for the rickets gene. These flies fail to initiate the behavioral and tanning processes that normally follow ecdysis. Sequencing of rickets mutants and STS mapping of deficiencies confirmed that rickets encodes the glycoprotein hormone receptor DLGR2. Although rickets mutants produce and release the insect-tanning hormone bursicon, they do not melanize when injected with extracts containing bursicon. In contrast, mutants do melanize in response to injection of an analog of cyclic AMP, the second messenger for bursicon. Hence, rickets appears to encode a component of the bursicon response pathway, probably the bursicon receptor itself. Mutants also have a behavioral deficit in that they fail to initiate the behavioral program for wing expansion. A set of decapitation experiments utilizing rickets mutants and flies that lack cells containing the neuropeptide eclosion hormone, reveals a multicomponent control to the activation of this behavioral program.

}, keywords = {Animals, Cell Surface, Drosophila, Drosophila Proteins, G-Protein-Coupled, Genes, Insect, Insect Hormones, Invertebrate Hormones, Molting, Mutation, Receptors, Sequence Tagged Sites, Stereotyped Behavior, Wing}, issn = {0022-0949}, author = {Baker, James D and Truman, James W} } @article {2429, title = {Neurodegeneration. A glutamine-rich trail leads to transcription factors.}, journal = {Science }, volume = {296}, year = {2002}, month = {2002 Jun 21}, pages = {2149-50}, keywords = {Animals, Brain, CREB-Binding Protein, DNA-Binding Proteins, Dopamine D2, Gene Expression Regulation, Genetic, Humans, Huntington Disease, Mice, Models, Nerve Tissue Proteins, Neurodegenerative Diseases, Neurons, Nuclear Proteins, Peptides, Promoter Regions, Protein Binding, Protein Structure, Receptors, Sp1 Transcription Factor, TATA-Binding Protein Associated Factors, Tertiary, Trans-Activators, Transcription, Transcription Factor TFIID, Transcription Factors, Trinucleotide Repeat Expansion}, issn = {1095-9203}, doi = {10.1073/pnas.1100640108}, author = {Freiman, Richard N and Tjian, Robert} } @article {2295, title = {A new NOS2 promoter polymorphism associated with increased nitric oxide production and protection from severe malaria in Tanzanian and Kenyan children.}, journal = {Lancet}, volume = {360}, year = {2002}, month = {2002 Nov 9}, pages = {1468-75}, abstract = {

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

}, keywords = {Anemia, Cerebral, Child, DNA, Falciparum, Female, Genetic, Humans, Immunity, Infant, Innate, Kenya, Malaria, Male, Nitric Oxide, Nitric Oxide Synthase, Nitric Oxide Synthase Type II, Parasitemia, Polymorphism, Preschool, Sequence Analysis, Single-Stranded Conformational, Tanzania}, issn = {0140-6736}, doi = {10.1016/S0140-6736(02)11474-7}, author = {Hobbs, Maurine R and Udhayakumar, Venkatachalam and Levesque, Marc C and Booth, Jennifer and Roberts, Jacquelin M and Tkachuk, Ariana N and Pole, Ann and Coon, Hilary and Kariuki, Simon and Nahlen, Bernard L and Mwaikambo, Esther D and Lal, Altaf L and Granger, Donald L and Anstey, Nicholas M and Weinberg, J Brice} } @article {47225, title = {Oscillations and sparsening of odor representations in the mushroom body.}, journal = {Science (New York, N.Y.)}, volume = {297}, year = {2002}, month = {2002 Jul 19}, pages = {359-65}, abstract = {

In the insect olfactory system, oscillatory synchronization is functionally relevant and reflects the coherent activation of dynamic neural assemblies. We examined the role of such oscillatory synchronization in information transfer between networks in this system. The antennal lobe is the obligatory relay for olfactory afferent signals and generates oscillatory output. The mushroom body is responsible for formation and retrieval of olfactory and other memories. The format of odor representations differs significantly across these structures. Whereas representations are dense, dynamic, and seemingly redundant in the antennal lobe, they are sparse and carried by more selective neurons in the mushroom body. This transformation relies on a combination of oscillatory dynamics and intrinsic and circuit properties that act together to selectively filter and synthesize the output from the antennal lobe. These results provide direct support for the functional relevance of correlation codes and shed some light on the role of oscillatory synchronization in sensory networks.

}, keywords = {Action Potentials, Animals, Electric Stimulation, Electrodes, Evoked Potentials, Excitatory Postsynaptic Potentials, Female, gamma-Aminobutyric Acid, Grasshoppers, Interneurons, Male, Mushroom Bodies, Nerve Net, Neural Inhibition, Neurons, Odors, Patch-Clamp Techniques, Picrotoxin, Smell, Synaptic Transmission, Time Factors}, issn = {1095-9203}, doi = {10.1126/science.1070502}, author = {Perez-Orive, Javier and Mazor, Ofer and Turner, Glenn C and Cassenaer, Stijn and Wilson, Rachel I and Laurent, Gilles} } @article {2428, title = {Redundant role of tissue-selective TAF(II)105 in B lymphocytes.}, journal = {Molecular and Cellular Biology}, volume = {22}, year = {2002}, month = {2002 Sep}, pages = {6564-72}, abstract = {

Regulated gene expression is a complex process achieved through the function of multiple protein factors acting in concert at a given promoter. The transcription factor TFIID is a central component of the machinery regulating mRNA synthesis by RNA polymerase II. This large multiprotein complex is composed of the TATA box binding protein (TBP) and several TBP-associated factors (TAF(II)s). The recent discovery of multiple TBP-related factors and tissue-specific TAF(II)s suggests the existence of specialized TFIID complexes that likely play a critical role in regulating transcription in a gene- and tissue-specific manner. The tissue-selective factor TAF(II)105 was originally identified as a component of TFIID derived from a human B-cell line. In this report we demonstrate the specific induction of TAF(II)105 in cultured B cells in response to bacterial lipopolysaccharide (LPS). To examine the in vivo role of TAF(II)105, we have generated TAF(II)105-null mice by homologous recombination. Here we show that B-lymphocyte development is largely unaffected by the absence of TAF(II)105. TAF(II)105-null B cells can proliferate in response to LPS, produce relatively normal levels of resting antibodies, and can mount an immune response by producing antigen-specific antibodies in response to immunization. Taken together, we conclude that the function of TAF(II)105 in B cells is likely redundant with the function of other TAF(II)105-related cellular proteins.

}, keywords = {Animals, B-Lymphocytes, Blotting, Cell Division, Cell Separation, DNA-Binding Proteins, Dose-Response Relationship, Drug, Erythrocytes, Flow Cytometry, Genetic, Immunoglobulin A, Immunoglobulin G, Immunoglobulin M, Lipopolysaccharides, Messenger, Mice, Precipitin Tests, RNA, Spleen, TATA-Binding Protein Associated Factors, Time Factors, Transcription, Transcription Factor TFIID, Transcription Factors, Transcriptional Activation, Western}, issn = {0270-7306}, doi = {10.1073/pnas.1100640108}, author = {Freiman, Richard N and Albright, Shane R and Chu, Leslie E and Zheng, Shuang and Liang, Hong-Erh and Sha, William C and Tjian, Robert} } @article {2431, title = {Structure, function, and activator-induced conformations of the CRSP coactivator.}, journal = {Science}, volume = {295}, year = {2002}, month = {2002 Feb 8}, pages = {1058-62}, abstract = {

The human cofactor complexes ARC (activator-recruited cofactor) and CRSP (cofactor required for Sp1 activation) mediate activator-dependent transcription in vitro. Although these complexes share several common subunits, their structural and functional relationships remain unknown. Here, we report that affinity-purified ARC consists of two distinct multisubunit complexes: a larger complex, denoted ARC-L, and a smaller coactivator, CRSP. Reconstituted in vitro transcription with biochemically separated ARC-L and CRSP reveals differential cofactor functions. The ARC-L complex is transcriptionally inactive, whereas the CRSP complex is highly active. Structural determination by electron microscopy (EM) and three-dimensional reconstruction indicate substantial differences in size and shape between ARC-L and CRSP. Moreover, EM analysis of independently derived CRSP complexes reveals distinct conformations induced by different activators. These results suggest that CRSP may potentiate transcription via specific activator-induced conformational changes.

}, keywords = {CCAAT-Enhancer-Binding Proteins, Chromatin, Computer-Assisted, DNA-Binding Proteins, Electron, Genetic, Hela Cells, Herpes Simplex Virus Protein Vmw65, Humans, Image Processing, Imaging, Macromolecular Substances, Microscopy, Models, Precipitin Tests, Protein Binding, Protein Structure, Protein Subunits, Quaternary, Recombinant Fusion Proteins, Recombinant Proteins, Sterol Regulatory Element Binding Protein 1, Tertiary, Three-Dimensional, Trans-Activators, Transcription, Transcription Factors, Transcriptional Activation}, issn = {1095-9203}, doi = {10.1073/pnas.1100640108}, author = {Taatjes, Dylan J and N{\"a}{\"a}r, Anders M and Andel, Frank and Nogales, Eva and Tjian, Robert} } @article {2427, title = {TRF2 associates with DREF and directs promoter-selective gene expression in Drosophila.}, journal = {Nature}, volume = {420}, year = {2002}, month = {2002 Nov 28}, pages = {439-45}, abstract = {

Drosophila TATA-box-binding protein (TBP)-related factor 2 (TRF2) is a member of a family of TBP-related factors present in metazoan organisms. Recent evidence suggests that TRF2s are required for proper embryonic development and differentiation. However, true target promoters and the mechanisms by which TRF2 operates to control transcription remain elusive. Here we report the antibody affinity purification of a Drosophila TRF2-containing complex that contains components of the nucleosome remodelling factor (NURF) chromatin remodelling complex as well as the DNA replication-related element (DRE)-binding factor DREF. This latter finding led us to potential target genes containing TRF2-responsive promoters. We have used a combination of in vitro and in vivo assays to show that the DREF-containing TRF2 complex directs core promoter recognition of the proliferating cell nuclear antigen (PCNA) gene. We also identified additional TRF2-responsive target genes involved in DNA replication and cell proliferation. These data suggest that TRF2 functions as a core promoter-selectivity factor responsible for coordinating transcription of a subset of genes in Drosophila.

}, keywords = {Animals, Cell Line, Chromatin, Drosophila, Drosophila Proteins, Gene Expression Regulation, Genes, Genetic, Insect, Macromolecular Substances, Nuclease Protection Assays, Oligonucleotide Array Sequence Analysis, Precipitin Tests, Proliferating Cell Nuclear Antigen, Promoter Regions, Protein Binding, RNA Interference, Substrate Specificity, Telomeric Repeat Binding Protein 2, Transcription Factors, Transcription Initiation Site}, issn = {0028-0836}, doi = {10.1073/pnas.1100640108}, author = {Hochheimer, Andreas and Zhou, Sharleen and Zheng, Shuang and Holmes, Michael C and Tjian, Robert} } @article {1142, title = {Are complex behaviors specified by dedicated regularoty genes? Reasoning from Drosophila.}, journal = {Cell}, volume = {105}, year = {2001}, month = {2001 Apr 6}, pages = {13-24}, issn = {0092-8674}, author = {Baker, B.S. and Taylor, B.T. and Hall, Jeffrey C} } @article {1782, title = {Independent anchoring and assembly mechanisms of INAD signaling complexes in Drosophila photoreceptors.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {21}, year = {2001}, month = {2001 Jan 1}, pages = {150-8}, abstract = {

In Drosophila photoreceptors the multivalent PDZ protein INAD organizes the phototransduction cascade into a macromolecular signaling complex containing the effector PLC, the light-activated TRP channels, and a regulatory PKC. Previously, we showed that the subcellular localization of INAD signaling complexes is critical for signaling. Now we have examined how INAD complexes are anchored and assembled in photoreceptor cells. We find that trp mutants, or transgenic flies expressing inaD alleles that disrupt the interaction between INAD and TRP, cause the mislocalization of the entire transduction complex. The INAD-TRP interaction is not required for targeting but rather for anchoring of complexes, because INAD and TRP can be targeted independently of each other. We also show that, in addition to its scaffold role, INAD functions to preassemble transduction complexes. Preassembly of signaling complexes helps to ensure that transduction complexes with the appropriate composition end up in the proper location. This may be a general mechanism used by cells to target different signaling machinery to the pertinent subcellular location.

}, keywords = {Animals, Calcium Channels, Cell Membrane, CHO Cells, Cricetinae, Drosophila, Drosophila Proteins, Eye Proteins, Invertebrate, Macromolecular Substances, Mutagenesis, Mutation, Ocular, Photoreceptor Cells, Precipitin Tests, Protein Kinase C, Protein Structure, Protein Transport, Site-Directed, Tertiary, TRPC Cation Channels, Type C Phospholipases, Vision}, issn = {1529-2401}, author = {Tsunoda, S and Sun, Y and Suzuki, E and Zuker, C} } @article {2296, title = {Malaria enhances expression of CC chemokine receptor 5 on placental macrophages.}, journal = {The Journal of Infectious Diseases}, volume = {183}, year = {2001}, month = {2001 Mar 15}, pages = {967-72}, abstract = {

Malaria and human immunodeficiency virus (HIV) coinfections are common in pregnant women in sub-Saharan Africa. The current study shows that placentas of malaria-infected women contain 3 times as much CC chemokine receptor 5 (CCR5) RNA as placentas of women without malaria. By immunohistochemistry, CCR5(+) maternal macrophages were seen in placentas from malaria-infected women but not in placentas from malaria-uninfected women. In addition, CCR5 also was found on fetal Hofbauer cells in placentas from both groups. Thus, malaria infections increase the potential reservoir for HIV in the placenta by increasing the number of HIV target cells.

}, keywords = {Antigens, CCR5, CD14, CD4, Chemokine, Direct, Female, Fetus, Fluorescent Antibody Technique, HIV Infections, Humans, Immunohistochemistry, Macrophages, Malaria, Messenger, Parasitic, Placenta, Pregnancy, Pregnancy Complications, Receptors, RNA, Transcriptional Activation}, issn = {0022-1899}, doi = {10.1086/319248}, author = {Tkachuk, A N and Moormann, A M and Poore, J A and Rochford, R A and Chensue, S W and Mwapasa, V and Meshnick, S R} } @article {2452, title = {Neural network partitioning by NO and cGMP.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {21}, year = {2001}, month = {2001 Mar 1}, pages = {1610-8}, abstract = {

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

}, keywords = {Animals, Arginine, Brachyura, Citrulline, Cyclic GMP, Digestive System, Enzyme Inhibitors, Fluorescent Dyes, Ganglia, Guanylate Cyclase, Immunohistochemistry, Invertebrate, Isoquinolines, Male, Nerve Net, Neurons, Neurotransmitter Agents, Nitric Oxide, Nitric Oxide Donors, Periodicity, Signal Transduction}, issn = {1529-2401}, author = {Scholz, N L and de Vente, J and Truman, J W and Graubard, K} } @article {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 {2451, title = {Tiling of the body wall by multidendritic sensory neurons in Manduca sexta.}, journal = {The Journal of Comparative Neurology}, volume = {440}, year = {2001}, month = {2001 Nov 19}, pages = {271-83}, abstract = {

A plexus of multidendritic sensory neurons, the dendritic arborization (da) neurons, innervates the epidermis of soft-bodied insects. Previous studies have indicated that the plexus may comprise distinct subtypes of da neurons, which utilize diverse cyclic 3{\textquoteright},5{\textquoteright}-guanosine monophosphate signaling pathways and could serve several functions. Here, we identify three distinct classes of da neurons in Manduca, which we term the alpha, beta, and gamma classes. These three classes differ in their sensory responses, branch complexity, peripheral dendritic fields, and axonal projections. The two identified alpha neurons branch over defined regions of the body wall, which in some cases correspond to specific natural folds of the cuticle. These cells project to an intermediate region of the neuropil and appear to function as proprioceptors. Three beta neurons are characterized by long, sinuous dendritic branches and axons that terminate in the ventral neuropil. The function of this group of neurons is unknown. Four neurons belonging to the gamma class have the most complex peripheral dendrites. A representative gamma neuron responds to forceful touch of the cuticle. Although the dendrites of da neurons of different classes may overlap extensively, cells belonging to the same class show minimal dendritic overlap. As a result, the body wall is independently tiled by the beta and gamma da neurons and partially innervated by the alpha neurons. These properties of the da system likely allow insects to discriminate the quality and location of several types of stimuli acting on the cuticle.

}, keywords = {Afferent, Animals, Central Nervous System, Dendrites, Electrophysiology, Epidermis, Manduca, Neurons, Synaptic Transmission}, issn = {0021-9967}, doi = {10.1002/cne.1385}, author = {Grueber, W B and Graubard, K and Truman, J W} } @article {5495, title = {Dopamine modulates acute responses to cocaine, nicotine and ethanol in Drosophila.}, journal = {Current Biology}, volume = {10}, year = {2000}, month = {2000 Feb 24}, pages = {187-94}, abstract = {

Drugs of abuse have a common property in mammals, which is their ability to facilitate the release of the neurotransmitter and neuromodulator dopamine in specific brain regions involved in reward and motivation. This increase in synaptic dopamine levels is believed to act as a positive reinforcer and to mediate some of the acute responses to drugs. The mechanisms by which dopamine regulates acute drug responses and addiction remain unknown.

}, keywords = {Animal, Animals, Behavior, Cocaine, Dopamine, Drosophila, Ethanol, Male, Nicotine}, issn = {0960-9822}, author = {Bainton, R J and Tsai, L T and Singh, C M and Moore, M S and Neckameyer, W S and Heberlein, U} } @article {46644, title = {Early retinal development in Drosophila.}, journal = {Results and Problems in Cell Differentiation}, volume = {31}, year = {2000}, month = {2000}, pages = {37-50}, keywords = {Animals, Cell Differentiation, Drosophila melanogaster, Retina}, issn = {0080-1844}, author = {Heberlein, U and Treisman, J E} } @article {2453, title = {Ecdysteroid coordinates optic lobe neurogenesis via a nitric oxide signaling pathway.}, journal = {Development}, volume = {127}, year = {2000}, month = {2000 Aug 15}, pages = {3543-51}, abstract = {

Proliferation of neural precursors in the optic lobe of Manduca sexta is controlled by circulating steroids and by local production of nitric oxide (NO). Diaphorase staining, anti-NO synthase (NOS) immunocytochemistry and the NO-indicator, DAF-2, show that cells throughout the optic anlage contain NOS and produce NO. Signaling via NO inhibits proliferation in the anlage. When exposed to low levels of ecdysteroid, NO production is stimulated and proliferation ceases. When steroid levels are increased, NO production begins to decrease within 15 minutes independent of RNA or protein synthesis and cells rapidly resume proliferation. Resumption of proliferation is not due simply to the removal of NO repression though, but also requires an ecdysteroid stimulatory pathway. The consequence of these opposing pathways is a sharpening of the responsiveness to the steroid, thereby facilitating a tight coordination between development of the different elements of the adult visual system.

}, keywords = {Animals, Cell Division, Ecdysterone, Enzyme Inhibitors, Manduca, Neurons, NG-Nitroarginine Methyl Ester, Nitric Oxide, Nitric Oxide Synthase, Nitric Oxide Synthase Type I, Nonmammalian, Optic Lobe, Signal Transduction, Stem Cells}, issn = {0950-1991}, author = {Champlin, D T and Truman, J W} } @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 {2016, title = {Optical imaging of calcium transients in neurons and pharyngeal muscle of C. elegans.}, journal = {Neuron}, volume = {26}, year = {2000}, month = {2000 Jun}, pages = {583-94}, abstract = {

Electrophysiology and optical indicators have been used in vertebrate systems to investigate excitable cell firing and calcium transients, but both techniques have been difficult to apply in organisms with powerful reverse genetics. To overcome this limitation, we expressed cameleon proteins, genetically encoded calcium indicators, in the pharyngeal muscle of the nematode worm Caenorhabditis elegans. In intact transgenic animals expressing cameleons, fluorescence ratio changes accompanied muscular contraction, verifying detection of calcium transients. By comparing the magnitude and duration of calcium influx in wild-type and mutant animals, we were able to determine the effects of calcium channel proteins on pharyngeal calcium transients. We also successfully used cameleons to detect electrically evoked calcium transients in individual C. elegans neurons. This technique therefore should have broad applications in analyzing the regulation of excitable cell activity in genetically tractable organisms.

}, keywords = {Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Calcium, Calcium Channels, Down-Regulation, Electrophysiology, Helminth Proteins, Muscle Proteins, Mutation, Neurons, Optics and Photonics, Pharyngeal Muscles, Protein Isoforms}, issn = {0896-6273}, author = {Kerr, R and Lev-Ram, V and Baird, G and Vincent, P and Tsien, R Y and Schafer, W R} } @article {45925, title = {Resting and active properties of pyramidal neurons in subiculum and CA1 of rat hippocampus.}, journal = {J Neurophysiol}, volume = {84}, year = {2000}, month = {2000 Nov}, pages = {2398-408}, abstract = {

Action potentials are the end product of synaptic integration, a process influenced by resting and active neuronal membrane properties. Diversity in these properties contributes to specialized mechanisms of synaptic integration and action potential firing, which are likely to be of functional significance within neural circuits. In the hippocampus, the majority of subicular pyramidal neurons fire high-frequency bursts of action potentials, whereas CA1 pyramidal neurons exhibit regular spiking behavior when subjected to direct somatic current injection. Using patch-clamp recordings from morphologically identified neurons in hippocampal slices, we analyzed and compared the resting and active membrane properties of pyramidal neurons in the subiculum and CA1 regions of the hippocampus. In response to direct somatic current injection, three subicular firing types were identified (regular spiking, weak bursting, and strong bursting), while all CA1 neurons were regular spiking. Within subiculum strong bursting neurons were found preferentially further away from the CA1 subregion. Input resistance (R(N)), membrane time constant (tau(m)), and depolarizing "sag" in response to hyperpolarizing current pulses were similar in all subicular neurons, while R(N) and tau(m) were significantly larger in CA1 neurons. The first spike of all subicular neurons exhibited similar action potential properties; CA1 action potentials exhibited faster rising rates, greater amplitudes, and wider half-widths than subicular action potentials. Therefore both the resting and active properties of CA1 pyramidal neurons are distinct from those of subicular neurons, which form a related class of neurons, differing in their propensity to burst. We also found that both regular spiking subicular and CA1 neurons could be transformed into a burst firing mode by application of a low concentration of 4-aminopyridine, suggesting that in both hippocampal subfields, firing properties are regulated by a slowly inactivating, D-type potassium current. The ability of all subicular pyramidal neurons to burst strengthens the notion that they form a single neuronal class, sharing a burst generating mechanism that is stronger in some cells than others.

}, keywords = {Action Potentials, Animals, Cell Size, Electric Impedance, Electric Stimulation, Hippocampus, Patch-Clamp Techniques, Periodicity, Pyramidal Cells, Rats, Rats, Wistar, Synapses}, issn = {0022-3077}, author = {Staff, N P and Jung, H Y and Thiagarajan, T and Yao, M and Spruston, N} } @article {2454, title = {The RXR ortholog USP suppresses early metamorphic processes in Drosophila in the absence of ecdysteroids.}, journal = {Development}, volume = {127}, year = {2000}, month = {2000 Mar 15}, pages = {1151-9}, abstract = {

The steroid hormone 20-hydroxyecdysone (20E) initiates metamorphosis in insects by signaling through the ecdysone receptor complex, a heterodimer of the ecdysone receptor (EcR) and ultraspiracle (USP). Analysis of usp mutant clones in the wing disc of Drosophila shows that in the absence of USP, early hormone responsive genes such as EcR, DHR3 and E75B fail to up-regulate in response to 20E, but other genes that are normally expressed later, such as (\&bgr;)-Ftz-F1 and the Z1 isoform of the Broad-Complex (BRC-Z1), are expressed precociously. Sensory neuron formation and axonal outgrowth, two early metamorphic events, also occur prematurely. In vitro experiments with cultured wing discs showed that BRC-Z1 expression and early metamorphic development are rendered steroid-independent in the usp mutant clones. These results are consistent with a model in which these latter processes are induced by a signal arising during the middle of the last larval stage but suppressed by the unliganded EcR/USP complex. Our observations suggest that silencing by the unliganded EcR/USP receptor and the subsequent release of silencing by moderate steroid levels may play an important role in coordinating early phases of steroid driven development.

}, keywords = {Afferent, Animals, Biological, Developmental, DNA-Binding Proteins, Drosophila, Ecdysteroids, Ecdysterone, Female, Gene Expression Regulation, Gene Targeting, Genes, Insect, Male, Metamorphosis, Models, Neurons, Receptors, Signal Transduction, Steroid, Steroids, Transcription Factors, Up-Regulation, Wing}, issn = {0950-1991}, author = {Schubiger, M and Truman, J W} } @article {2455, title = {The origins of insect metamorphosis.}, journal = {Nature}, volume = {401}, year = {1999}, month = {1999 Sep 30}, pages = {447-52}, abstract = {

Insect metamorphosis is a fascinating and highly successful biological adaptation, but there is much uncertainty as to how it evolved. Ancestral insect species did not undergo metamorphosis and there are still some existing species that lack metamorphosis or undergo only partial metamorphosis. Based on endocrine studies and morphological comparisons of the development of insect species with and without metamorphosis, a novel hypothesis for the evolution of metamorphosis is proposed. Changes in the endocrinology of development are central to this hypothesis. The three stages of the ancestral insect species-pronymph, nymph and adult-are proposed to be equivalent to the larva, pupa and adult stages of insects with complete metamorphosis. This proposal has general implications for insect developmental biology.

}, keywords = {Animals, Biological, Biological Evolution, Insect Hormones, Insects, Juvenile Hormones, Metamorphosis, Nymph, Wing}, issn = {0028-0836}, doi = {10.1038/46737}, author = {Truman, J W and Riddiford, L M} } @article {2456, title = {Drosophila EcR-B ecdysone receptor isoforms are required for larval molting and for neuron remodeling during metamorphosis.}, journal = {Development}, volume = {125}, year = {1998}, month = {1998 Jun}, pages = {2053-62}, abstract = {

During the metamorphic reorganization of the insect central nervous system, the steroid hormone 20-hydroxyecdysone induces a wide spectrum of cellular responses including neuronal proliferation, maturation, cell death and the remodeling of larval neurons into their adult forms. In Drosophila, expression of specific ecdysone receptor (EcR) isoforms has been correlated with particular responses, suggesting that different EcR isoforms may govern distinct steroid-induced responses in these cells. We have used imprecise excision of a P element to create EcR deletion mutants that remove the EcR-B promoter and therefore should lack EcR-B1 and EcR-B2 expression but retain EcR-A expression. Most of these EcR-B mutant animals show defects in larval molting, arresting at the boundaries between the three larval stages, while a smaller percentage of EcR-B mutants survive into the early stages of metamorphosis. Remodeling of larval neurons at metamorphosis begins with the pruning back of larval-specific dendrites and occurs as these cells are expressing high levels of EcR-B1 and little EcR-A. This pruning response is blocked in the EcR-B mutants despite the fact that adult-specific neurons, which normally express only EcR-A, can progress in their development. These observations support the hypothesis that different EcR isoforms control cell-type-specific responses during remodeling of the nervous system at metamorphosis.

}, keywords = {Animals, Biological, Drosophila, Genes, Insect, Insertional, Larva, Lethal, Metamorphosis, Molting, Mutagenesis, Nervous System, Neurons, Receptors, Sequence Deletion, Steroid}, issn = {0950-1991}, author = {Schubiger, M and Wade, A A and Carney, G E and Truman, J W and Bender, M} } @article {2457, title = {Ecdysteroids govern two phases of eye development during metamorphosis of the moth, Manduca sexta.}, journal = {Development}, volume = {125}, year = {1998}, month = {1998 Jun}, pages = {2009-18}, abstract = {

The eye primordium of the moth, Manduca sexta, shows two different developmental responses to ecdysteroids depending on the concentration to which it is exposed. Tonic exposure to moderate levels of 20-hydroxyecdysone (20E) or its precursor, ecdysone, are required for progression of the morphogenetic furrow across the primordium. Proliferation, cell-type specification and organization of immature ommatidial clusters occur in conjunction with furrow progression. These events can be reversibly started or stopped in cultured primordia simply by adjusting levels of ecdysteroid to be above or below a critical threshold concentration. In contrast, high levels of 20E cause maturation of the photoreceptors and the support cells that comprise the ommatidia. Ommatidial maturation normally occurs after the furrow has crossed the primordium, but premature exposure to high levels of 20E at any time causes precocious maturation. In such cases, the furrow arrests irreversibly and cells behind the furrow produce a well-formed, but miniature, eye. Precocious and catastrophic metamorphosis occurs throughout such animals, suggesting that ecdysteroids control development of other tissues in a manner similar to the eye. The threshold concentrations of 20E required for furrow progression versus ommatidial maturation differ by about 17-fold. This capacity to regulate distinct phases of development by different concentrations of a single hormone is probably achieved by differential sensitivity of target gene promoters to induction by the hormone-bound receptor(s).

}, keywords = {Amphibians, Animals, Biological, Ecdysone, Ecdysteroids, Ecdysterone, Eye, Gene Expression Regulation, Genes, Insect, Invertebrate, Larva, Manduca, Metamorphosis, Photoreceptor Cells, Pupa, Species Specificity, Steroids, Time Factors}, issn = {0950-1991}, author = {Champlin, D T and Truman, J W} } @article {5496, title = {Ethanol intoxication in Drosophila: genetic and pharmacological evidence for regulation by the cAMP signaling pathway.}, journal = {Cell}, volume = {93}, year = {1998}, month = {1998 Jun 12}, pages = {997-1007}, abstract = {

Upon exposure to ethanol, Drosophila display behaviors that are similar to ethanol intoxication in rodents and humans. Using an inebriometer to measure ethanol-induced loss of postural control, we identified cheapdate, a mutant with enhanced sensitivity to ethanol. Genetic and molecular analyses revealed that cheapdate is an allele of the memory mutant amnesiac. amnesiac has been postulated to encode a neuropeptide that activates the cAMP pathway. Consistent with this, we find that enhanced ethanol sensitivity of cheapdate can be reversed by treatment with agents that increase cAMP levels or PKA activity. Conversely, genetic or pharmacological reduction in PKA activity results in increased sensitivity to ethanol. Taken together, our results provide functional evidence for the involvement of the cAMP signal transduction pathway in the behavioral response to intoxicating levels of ethanol.

}, keywords = {Adenylate Cyclase, Alleles, Amino Acid Sequence, Animal, Animals, Base Sequence, Behavior, Cloning, Cyclic AMP, Cyclic AMP-Dependent Protein Kinases, Drosophila melanogaster, Drosophila Proteins, Enzyme Activation, Enzyme Inhibitors, Ethanol, Forskolin, Genes, Genetic Complementation Test, Genetically Modified, Insect, Male, Messenger, Molecular, Molecular Sequence Data, Mutation, Neuropeptides, RNA, Signal Transduction}, issn = {0092-8674}, author = {Moore, M S and DeZazzo, J and Luk, A Y and Tully, T and Singh, C M and Heberlein, U} } @article {46648, title = {Eye development in Drosophila: formation of the eye field and control of differentiation.}, journal = {Current Topics in Developmental Biology}, volume = {39}, year = {1998}, month = {1998}, pages = {119-58}, keywords = {Animals, Cell Differentiation, Drosophila, Eye, Gene Expression Regulation, Developmental, Larva, Morphogenesis, Mutation, Visual Fields}, issn = {0070-2153}, author = {Treisman, J E and Heberlein, U} } @article {46645, title = {Y do we drink?}, journal = {Cell}, volume = {95}, year = {1998}, month = {1998 Dec 11}, pages = {733-5}, keywords = {Alcohol Drinking, Alcoholic Intoxication, Animals, Ethanol, Feeding Behavior, Humans, Mice, Mice, Mutant Strains, Neuropeptide Y, Rats}, issn = {0092-8674}, author = {Tecott, L H and Heberlein, U} } @article {2458, title = {Disruption of a behavioral sequence by targeted death of peptidergic neurons in Drosophila.}, journal = {Neuron}, volume = {19}, year = {1997}, month = {1997 Oct}, pages = {813-23}, abstract = {

The neuropeptide eclosion hormone (EH) is a key regulator of insect ecdysis. We tested the role of the two EH-producing neurons in Drosophila by using an EH cell-specific enhancer to activate cell death genes reaper and head involution defective to ablate the EH cells. In the EH cell knockout flies, larval and adult ecdyses were disrupted, yet a third of the knockouts emerged as adults, demonstrating that EH has a significant but nonessential role in ecdysis. The EH cell knockouts had discrete behavioral deficits, including slow, uncoordinated eclosion and an insensitivity to ecdysis-triggering hormone. The knockouts lacked the lights-on eclosion response despite having a normal circadian eclosion rhythm. This study represents a novel approach to the dissection of neuropeptide regulation of a complex behavioral program.

}, keywords = {Animals, Cell Death, Circadian Rhythm, Crosses, Darkness, DNA Transposable Elements, Drosophila, Embryo, Genetic, Green Fluorescent Proteins, Insect Hormones, Invertebrate, Larva, Light, Luminescent Proteins, Mutagenesis, Neurons, Neuropeptides, Nonmammalian, Photoreceptor Cells, Recombinant Fusion Proteins}, issn = {0896-6273}, author = {McNabb, S L and Baker, J D and Agapite, J and Steller, H and Riddiford, L M and Truman, J W} } @article {46649, title = {eyelid antagonizes wingless signaling during Drosophila development and has homology to the Bright family of DNA-binding proteins.}, journal = {Genes \& Development}, volume = {11}, year = {1997}, month = {1997 Aug 1}, pages = {1949-62}, abstract = {

In Drosophila, pattern formation at multiple stages of embryonic and imaginal development depends on the same intercellular signaling pathways. We have identified a novel gene, eyelid (eld), which is required for embryonic segmentation, development of the notum and wing margin, and photoreceptor differentiation. In these tissues, eld mutations have effects opposite to those caused by wingless (wg) mutations. eld encodes a widely expressed nuclear protein with a region homologous to a novel family of DNA-binding domains. Based on this homology and on the phenotypic analysis, we suggest that Eld could act as a transcription factor antagonistic to the Wg pathway.

}, keywords = {Amino Acid Sequence, Animals, Body Patterning, Cell Differentiation, Cloning, Molecular, DNA-Binding Proteins, Drosophila, Drosophila Proteins, Gene Expression Regulation, Developmental, Genes, Insect, Molecular Sequence Data, Mutation, Phenotype, Photoreceptor Cells, Invertebrate, Proto-Oncogene Proteins, Recombinant Fusion Proteins, Restriction Mapping, Sequence Homology, Amino Acid, Signal Transduction, Trans-Activators, Transcription Factors, Wing, Wnt1 Protein}, issn = {0890-9369}, author = {Treisman, J E and Luk, A and Rubin, G M and Heberlein, U} } @article {2459, title = {Neuropeptide hierarchies and the activation of sequential motor behaviors in the hawkmoth, Manduca sexta.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {17}, year = {1997}, month = {1997 Jun 1}, pages = {4389-97}, abstract = {

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

}, keywords = {Animal, Animals, Antibody Specificity, Behavior, Calcitonin, Cyclic GMP, Electrophysiology, Ganglia, Insect Hormones, Invertebrate, Larva, Manduca, Molting, Motor Activity, Nervous System, Nervous System Physiological Phenomena, Neuropeptides, Peptide Fragments, Peptides, Sensitivity and Specificity}, issn = {0270-6474}, author = {Gammie, S C and Truman, J W} } @article {1163, title = {Control of male sexual behavior and sexual orientation in Drosophila by the fruitless gene.}, journal = {Cell}, volume = {87}, year = {1996}, month = {1996 Dec 13}, pages = {1079-89}, abstract = {

Sexual orientation and courtship behavior in Drosophila are regulated by fruitless (fru), the first gene in a branch of the sex-determination hierarchy functioning specifically in the central nervous system (CNS). The phenotypes of new fru mutants encompass nearly all aspects of male sexual behavior. Alternative splicing of fru transcripts produces sex-specific proteins belonging to the BTB-ZF family of transcriptional regulators. The sex-specific fru products are produced in only about 500 of the 10(5) neurons that comprise the CNS. The properties of neurons expressing these fru products suggest that fru specifies the fates or activities of neurons that carry out higher order control functions to elicit and coordinate the activities comprising male courtship behavior.

}, issn = {0092-8674}, author = {Baker, B.S. and Ryner, L.C. and Goodwin, S.F. and Castrillon, D.H. and Anand, A and Villella, A and Hall, J.C. and Taylor, B.J. and Wasserman, S.A.} } @article {2460, title = {Nitric oxide-sensitive guanylate cyclase activity is associated with the maturational phase of neuronal development in insects.}, journal = {Development}, volume = {122}, year = {1996}, month = {1996 Dec}, pages = {3949-58}, abstract = {

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

}, keywords = {Afferent, Animals, Cyclic GMP, Dihydrolipoamide Dehydrogenase, Drosophila melanogaster, Grasshoppers, Guanylate Cyclase, Insects, Interneurons, Motor Neurons, Nervous System, Neurons, Nitric Oxide, Nitroprusside, Phylogeny}, issn = {0950-1991}, author = {Truman, J W and de Vente, J and Ball, E E} } @article {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 {1193, title = {Strain-dependent variation in carbon source regulation of nucleus-encoded mitochondrial proteins of Saccharomyces cerevisiae.}, journal = {Journal of Bacteriology}, volume = {177}, year = {1995}, month = {1995 Mar}, pages = {1380-2}, abstract = {

Nuclear genes encoding mitochondrial proteins are regulated by carbon source with significant heterogeneity among four Saccharomyces cerevisiae strains. This strain-dependent variation is seen both in respiratory capacity of the cells and in the expression of beta-galactosidase reporter fusions to the promoters of CYB2, CYC1, CYC3, MnSOD, and RPO41.

}, keywords = {Bacterial Proteins, Base Sequence, beta-Galactosidase, Carbon, Cell Nucleus, Cytochrome b Group, Cytochrome c Group, Ferritins, Fungal, Fungal Proteins, Gene Expression Regulation, Genes, Genetic, Genetic Variation, L-Lactate Dehydrogenase, L-Lactate Dehydrogenase (Cytochrome), Mitochondria, Molecular Sequence Data, Oxygen Consumption, Promoter Regions, Recombinant Fusion Proteins, Reporter, Saccharomyces cerevisiae, Species Specificity, Superoxide Dismutase}, issn = {0021-9193}, author = {Brown, T A and Trumpower, B L} } @article {963, title = {The activities of two Ets-related transcription factors required for Drosophila eye development are modulated by the Ras/MAPK pathway.}, journal = {Cell}, volume = {78}, year = {1994}, month = {1994 Jul 15}, pages = {137-47}, abstract = {

We show that the activities of two Ets-related transcription factors required for normal eye development in Drosophila, pointed and yan, are regulated by the Ras1/MAPK pathway. The pointed gene codes for two related proteins, and we show that one form is a constitutive activator of transcription, while the activity of the other form is stimulated by the Ras1/MAPK pathway. Mutation of the single consensus MAPK phosphorylation site in the second form abrogates this responsiveness. yan is a negative regulator of photoreceptor determination, and genetic data suggest that it acts as an antagonist of Ras1. We demonstrate that yan can repress transcription and that this repression activity is negatively regulated by the Ras1/MAPK signal, most likely through direct phosphorylation of yan by MAPK.

}, keywords = {Animals, Biological, Calcium-Calmodulin-Dependent Protein Kinases, DNA-Binding Proteins, Drosophila, Drosophila Proteins, Extracellular Signal-Regulated MAP Kinases, Eye, Eye Proteins, Gene Expression Regulation, Genes, Genetic, Insect, Invertebrate, Models, Morphogenesis, Nerve Tissue Proteins, Phenotype, Photoreceptor Cells, Proto-Oncogene Proteins, Proto-Oncogene Proteins p21(ras), ras, Repressor Proteins, Signal Transduction, Transcription, Transcription Factors}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {O{\textquoteright}Neill, E M and Rebay, I and Tjian, R and Rubin, G M} } @article {1158, title = {Behavioral and neurobiological implications of sex-determining factors in Drosophila.}, journal = {Developmental. Genetics}, volume = {15}, year = {1994}, month = {1994}, pages = {275-96}, abstract = {

The function of the central nervous system as it controls sex-specific behaviors in Drosophila has been studied with renewed intensity, in the context of genetic factors that influence the development of sexually differentiated aspects of this insect. Three categories of genetic variations that cause anomalies in courtship and mating behaviors are discussed: (1) mutants isolated with regard to courtship defects, of which putatively courtship-specific variants such as the fruitless mutant are a subset; (2) general behavioral and neurological variants (including sensory and learning mutants), whose defects include subnormal reproductive performance; and (3) mutations of genes within the sex-determination regulatory hierarchy of Drosophila, the analysis of which has included studies of reproductive behavior. Recent studies of mutations in two of these categories have provided new insights into the control of neuronally based aspects of sex-specific behavior. The doublesex gene, the final factor acting in the sex-determination hierarchy, had been previously thought to regulate all aspects of sexual differentiation. Yet, it has been recently shown that doublesex does not control at least one neuronally-determined feature of sex-specific anatomy--a muscle in the male{\textquoteright}s abdomen, whose normal development is, however, dependent on the action of fruitless. These considerations prompted us to examine further (and in some cases re-examine) the influences exerted by sex-determination hierarchy genes on behavior. Our results--notably those obtained from assessments of doublesex mutations{\textquoteright} effects on general reproductive actions and on a particular component of the courtship sequence (male "singing" behavior)--lead to the suggestion that there is a previously unrecognized branch within the sex-determination hierarchy, which controls the differentiation of the male- and female- specific phenotypes of Drosophila. This new branch separates from the doublesex-related one immediately before the action of that gene (just after transformer and transformer-2) and appears to control as least some aspects of neuronally determined sexual differentiation of males.

}, issn = {0192-253X}, author = {Baker, B.S. and Taylor, B.J. and Villella. A. and Ryner, L.C. and Hall, J.C.} } @article {2461, title = {Neuropeptide induction of cyclic GMP increases in the insect CNS: resolution at the level of single identifiable neurons.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {14}, year = {1994}, month = {1994 Dec}, pages = {7704-12}, abstract = {

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

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

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

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

}, author = {Betzig, E and Chichester, R J and Lanni, F and Taylor, D L} } @article {2097, title = {Near-field magneto-optics and high density data storage. (With commentary)}, journal = {Applied Physics Letters.}, volume = {61}, year = {1992}, month = {1992}, abstract = {

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

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

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

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

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

}, issn = {0036-8075}, doi = {10.1126/science.257.5067.189}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17794749}, author = {Betzig, E and Trautman, J K} } @article {2563, title = {Polarization contrast in near-field scanning optical microscopy.}, journal = {Applied Optics}, volume = {31}, year = {1992}, month = {1992 Aug 1}, pages = {4563-8}, abstract = {

Recent advances in probe design have led to enhanced resolution (currently as significant as \  12 nm) in optical microscopes based on near-field imaging. We demonstrate that the polarization of emitted and detected light in such microscopes can be manipulated sensitively to generate contrast. We show that the contrast on certain patterns is consistent with a simple interpretation of the requisite boundary conditions, whereas in other cases a more complicated interaction between the probe and the sample is involved. Finally application of the technique to near-filed magneto-optic imaging is demonstrated.

}, issn = {0003-6935}, doi = {10.1364/AO.31.004563}, author = {Betzig, E and Trautman, J K and Weiner, J S and Harris, T D and Wolfe, R} } @article {2564, title = {Breaking the diffraction barrier: optical microscopy on a nanometric scale.}, journal = {Science}, volume = {251}, year = {1991}, month = {1991 Mar 22}, pages = {1468-70}, abstract = {

In near-field scanning optical microscopy, a light source or detector with dimensions less than the wavelength (lambda) is placed in close proximity (lambda/50) to a sample to generate images with resolution better than the diffraction limit. A near-field probe has been developed that yields a resolution of approximately 12 nm ( approximately lambda/43) and signals approximately 10(4)- to 10(6)-fold larger than those reported previously. In addition, image contrast is demonstrated to be highly polarization dependent. With these probes, near-field microscopy appears poised to fulfill its promise by combining the power of optical characterization methods with nanometric spatial resolution.

}, issn = {0036-8075}, doi = {10.1126/science.251.5000.1468}, author = {Betzig, E and Trautman, J K and Harris, T D and Weiner, J S and Kostelak, R L} } @article {2095, title = {Breaking the diffraction barrier: optical microscopy on a nanometric scale. (With commentary)}, journal = {Science}, volume = {251}, year = {1991}, month = {1991 Mar 22}, pages = {1468-70}, abstract = {

In near-field scanning optical microscopy, a light source or detector with dimensions less than the wavelength (lambda) is placed in close proximity (lambda/50) to a sample to generate images with resolution better than the diffraction limit. A near-field probe has been developed that yields a resolution of approximately 12 nm ( approximately lambda/43) and signals approximately 10(4)- to 10(6)-fold larger than those reported previously. In addition, image contrast is demonstrated to be highly polarization dependent. With these probes, near-field microscopy appears poised to fulfill its promise by combining the power of optical characterization methods with nanometric spatial resolution.

Commentary: Introduced the adiabatically tapered single mode fiber probe to near-field scanning optical microscopy which, together with shear force feedback, made the technique a practical reality. Although earlier claims of superresolution via near-field microscopy existed for nearly a decade, this paper was the first to convincingly break Abbe{\textquoteright}s limit with visible light, as demonstrated by reproducibly resolving known, complex nanoscale patterns having features separated by much less than the wavelength. Whereas our fiber probe and shear force technologies were soon widely adopted and key to many novel applications (see above), the earlier methods proved to be technological dead ends, never achieving the results of their original claims. This experience taught me the most valuable lesson of my career: while it{\textquoteright}s bad to bullshit others, it{\textquoteright}s even worse to bullshit yourself. It{\textquoteright}s a lesson sadly unheeded by many current practitioners of superresolution microscopy.

}, issn = {0036-8075}, doi = {10.1126/science.251.5000.1468}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17779440}, author = {Betzig, E and Trautman, J K and Harris, T D and Weiner, J S and Kostelak, R L} } @article {2462, title = {The regulation of transmitter expression in postembryonic lineages in the moth Manduca sexta. II. Role of cell lineage and birth order.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {11}, year = {1991}, month = {1991 Jul}, pages = {1990-7}, abstract = {

The expression of GABA is restricted to the progeny of only six of the 24 identified postembryonic lineages in the thoracic ganglia of the tobacco hornworm, Manduca sexta (Witten and Truman, 1991). It is colocalized with a peptide similar to molluscan small cardioactive peptide B (SCPB) in some of the neurons in two of the six lineages. By combining chemical ablation of the neuroblasts at specific larval stages with birth dating of the progeny, we tested whether the expression of GABA and the SCPB-like peptide was determined strictly by cell lineage or involved cellular interactions among the members of individual clonal groups. Chemical ablation of the six specific neuroblasts that produced the GABA-positive neurons (E, K, M, N, T, and X) or of the two that produced the GABA + SCPB-like-immunoreactive neurons (K, M) prior to the generation of their lineages resulted in the loss of these immunoreactivities. These results suggest that regulation between lineages did not occur. Ablation of the K and M neuroblasts after they had produced a small portion of their lineages had no effect on the expression of GABA, but did affect the pattern of the SCPB-like immunoreactivity. Combining birth-dating techniques with transmitter immunocytochemistry revealed that it was the position in the birth order and not interactions among the clonally related neurons that influenced the peptidergic phenotype. These results suggest that cell lineage is involved in establishing the GABAergic phenotype and that both cell lineage and birth order influence the determination of the peptidergic phenotype.(ABSTRACT TRUNCATED AT 250 WORDS)

}, keywords = {Animals, Cell Communication, Cell Differentiation, gamma-Aminobutyric Acid, Ganglia, Immunohistochemistry, Invertebrate Hormones, Larva, Moths, Nervous System, Neurons, Neuropeptides, Neurotransmitter Agents, Phenotype, Pupa}, issn = {0270-6474}, author = {Witten, J L and Truman, J W} } @article {1195, title = {Isolation and characterization of QCR9, a nuclear gene encoding the 7.3-kDa subunit 9 of the Saccharomyces cerevisiae ubiquinol-cytochrome c oxidoreductase complex. An intron-containing gene with a conserved sequence occurring in the intron of COX4.}, journal = {The Journal of Biological Chemistry}, volume = {265}, year = {1990}, month = {1990 Dec 5}, pages = {20813-21}, abstract = {

A nuclear gene (QCR9) encoding the 7.3-kDa subunit 9 of the mitochondrial cytochrome bc1 complex from Saccharomyces cerevisiae has been isolated from a yeast genomic library by hybridization with a degenerate oligonucleotide corresponding to nine amino acids proximal to the N terminus of purified subunit 9. QCR9 includes a 195-base pair open reading frame capable of encoding a protein of 66 amino acids and having a predicted molecular weight of 7471. The N-terminal methionine of subunit 9 is removed posttranslationally because the N-terminal sequence of the purified protein begins with serine 2. The ATG triplet corresponding to the N-terminal methionine is separated from the open reading frame by an intron. The intron is 213 base pairs long and contains previously reported 5{\textquoteright} donor, 3{\textquoteright} acceptor, and TACTAAC sequences necessary for splicing. The splice junctions, as well as the 5{\textquoteright} end of the message, were confirmed by isolation and sequencing of a cDNA copy of QCR9. In addition, the intron contains a nucleotide sequence in which 15 out of 18 nucleotides are identical with a sequence in the intron of COX4, the nuclear gene encoding cytochrome c oxidase subunit 4. The deduced amino acid sequence of the yeast subunit 9 is 39\% identical with that of a protein of similar molecular weight from beef heart cytochrome bc1 complex. If conservative substitutions are allowed for, the two proteins are 56\% similar. The predicted secondary structure of the 7.3-kDa protein revealed a single possible transmembrane helix, in which the amino acids conserved between beef heart and yeast are asymmetrically arranged along one face of the helix, implying that this domain of the protein is involved in a conserved interaction with another hydrophobic protein of the cytochrome bc1 complex. Two yeast strains, JDP1 and JDP2, were constructed in which QCR9 was deleted. Both strains grew very poorly, or not at all, on nonfermentable carbon sources and exhibited, at most, only 5\% of wild-type ubiquinol-cytochrome c oxidoreductase activity. Optical spectra of mitochondrial membranes from the deletion strains revealed slightly reduced levels of cytochrome b. When JDP1 and JDP2 were complemented with a plasmid carrying QCR9, the resulting yeast grew normally on ethanol/glycerol and exhibited normal cytochrome c reductase activities and optical spectra. These results indicate that QCR9 encodes a 7.3-kDa subunit of the bc1 complex that is required for formation of a fully functional complex.(ABSTRACT TRUNCATED AT 400 WORDS)

}, keywords = {Amino Acid Sequence, Base Sequence, Cell Nucleus, Chromosome Deletion, Cloning, Electron Transport Complex III, Electron Transport Complex IV, Fungal, Genes, Genomic Library, Introns, Macromolecular Substances, Models, Molecular, Molecular Sequence Data, Protein Conformation, Restriction Mapping, Saccharomyces cerevisiae}, issn = {0021-9258}, author = {Phillips, J D and Schmitt, M E and Brown, T A and Beckmann, J D and Trumpower, B L} } @article {2463, title = {Postmetamorphic cell death in the nervous and muscular systems of Drosophila melanogaster.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {10}, year = {1990}, month = {1990 Feb}, pages = {403-1}, abstract = {

Programmed cell death occurs in the nervous and muscular system of newly emerged adult Drosophila melanogaster. Many of the abdominal muscles that were used for eclosion and wing-spreading behavior degenerate by 12 hr after eclosion. Related neurons in the ventral ganglion also die within the first 24 hr. Ligation experiments showed that the muscle breakdown is triggered by a signal from the anterior region, presumably the head, that occurs about 1 hr before adult emergence. The timing of this signal suggests that eclosion hormone may be involved. Although muscle death is triggered prior to ecdysis, it can be delayed, at least temporarily, by forcing the emerging flies to show a prolonged ecdysis behavior. In contrast to the muscles, the death of the neurons is triggered after emergence. The signal for neuronal degeneration is closely correlated with the initiation of wing inflation behavior. Ligation and digging experiments and behavioral manipulations that either blocked or delayed wing expansion behavior had a parallel effect in suppressing or delaying neuronal death.

}, keywords = {Animal, Animals, Behavior, Biological, Cell Survival, Drosophila melanogaster, Female, Ligation, Male, Metamorphosis, Muscles, Nervous System, Neurons}, issn = {0270-6474}, author = {Kimura, K I and Truman, J W} } @article {1194, title = {A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae.}, journal = {Nucleic Acids Research}, volume = {18}, year = {1990}, month = {1990 May 25}, pages = {3091-2}, keywords = {Agar Gel, Electrophoresis, Fungal, Methods, RNA, Saccharomyces cerevisiae}, issn = {0305-1048}, author = {Schmitt, M E and Brown, T A and Trumpower, B L} } @article {974, title = {Localization of the sevenless protein, a putative receptor for positional information, in the eye imaginal disc of Drosophila.}, journal = {Cell}, volume = {51}, year = {1987}, month = {1987 Oct 9}, pages = {143-50}, abstract = {

The Drosophila gene sevenless encodes a putative trans-membrane receptor required for the formation of one particular cell, the R7 photoreceptor, in each ommatidium of the compound eye. Mutations in this gene result in the cell normally destined to form the R7 cell forming a non-neuronal cell type instead. These observations have led to the proposal that the sevenless protein receives at least part of the positional information required for the R7 developmental pathway. We have generated antibodies specific for sevenless and have examined expression of the protein by light and electron microscopy. sevenless protein is present transiently at high levels in at least 9 cells in each developing ommatidium and is detectable several hours before any overt differentiation of R7. The protein is mostly localized at the apices of the cells, in microvilli, but is also found deeper in the tissue where certain cells contact the R8 cell. This finding suggests that R8 expresses a ligand for the sevenless protein.

}, keywords = {Animals, Drosophila melanogaster, Electron, Epithelium, Eye, Eye Proteins, Histocytochemistry, Immunologic Techniques, Insect Hormones, Microscopy, Microvilli, Peptide Fragments, Photoreceptor Cells}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Tomlinson, A and Bowtell, D D and Hafen, E and Rubin, G M} } @article {2464, title = {Postembryonic neurogenesis in the CNS of the tobacco hornworm, Manduca sexta. I. Neuroblast arrays and the fate of their progeny during metamorphosis.}, journal = {The Journal of Comparative Neurology}, volume = {255}, year = {1987}, month = {1987 Jan 22}, pages = {548-59}, abstract = {

The tobacco hornworm Manduca sexta exhibits dramatic changes in its body morphology and behavior as it is transformed from a larva into an adult during metamorphosis. Accompanying these changes is an extensive reorganization of this moth{\textquoteright}s central nervous system (CNS), which involves both the death and remodeling of subsets of larval neurons. We report here that the segmental ganglia of the larvae also contain a stereotyped array of identifiable neuronal stem cells (neuroblasts) that contribute over 2,000 cells to each thoracic ganglion and about 40-80 cells to each abdominal ganglion. The distribution of these neuroblasts varies in a segment specific manner. Dormant neuroblasts are found adjacent to the neuropil in late embryos and early first instar larvae. After the molt to the second instar, these cells enlarge and begin to divide. Through a series of asymmetrical divisions, each neuroblast generates a discrete nest of 10-90 progeny by the end of larval life. These progeny (the imaginal nest cells) are developmentally arrested at an early stage of differentiation and remain so until metamorphosis. At the onset of metamorphosis, a wave of cell death sweeps through the nests, the extent of the death being much greater within the abdominal nests than in the thoracic nests. The surviving imaginal nest cells then differentiate to become functional neurons that are incorporated into the adult CNS.

}, keywords = {Animals, Biological, Cell Division, Central Nervous System, Larva, Lepidoptera, Metamorphosis, Moths, Neurons}, issn = {0021-9967}, doi = {10.1002/cne.902550407}, author = {Booker, R and Truman, J W} } @article {1177, title = {Promoter selection in human mitochondria involves binding of a transcription factor to orientation-independent upstream regulatory elements.}, journal = {Cell}, volume = {50}, year = {1987}, month = {1987 Jul 17}, pages = {247-58}, abstract = {

Selective transcription of human mitochondrial DNA requires a transcription factor (mtTF) in addition to an essentially nonselective RNA polymerase. Partially purified mtTF is able to sequester promoter-containing DNA in preinitiation complexes in the absence of mitochondrial RNA polymerase, suggesting a DNA-binding mechanism for factor activity. Functional domains, required for positive transcriptional regulation by mtTF, are identified within both major promoters of human mtDNA through transcription of mutant promoter templates in a reconstituted in vitro system. These domains are essentially coextensive with DNA sequences protected from nuclease digestion by mtTF-binding. Comparison of the sequences of the two mtTF-responsive elements reveals significant homology only when one sequence is inverted; the binding sites are in opposite orientations with respect to the predominant direction of transcription. Thus mtTF may function bidirectionally, requiring additional protein-DNA interactions to dictate transcriptional polarity. The mtTF-responsive elements are arrayed as direct repeats, separated by approximately 80 bp within the displacement-loop region of human mitochondrial DNA; this arrangement may reflect duplication of an ancestral bidirectional promoter, giving rise to separate, unidirectional promoters for each strand.

}, keywords = {DNA, DNA-Directed RNA Polymerases, Genes, Genetic, Humans, KB Cells, Mitochondria, Mitochondrial, Promoter Regions, Regulator, Templates, Transcription, Transcription Factors}, issn = {0092-8674}, doi = {10.1101/gad.1352105}, author = {Fisher, R P and Topper, J N and Clayton, D A} } @article {2465, title = {Endocrine regulation of the form and function of axonal arbors during insect metamorphosis.}, journal = {The Journal of Neuroscienc : The Official Journal of the Society for Neuroscience}, volume = {6}, year = {1986}, month = {1986 Jan}, pages = {293-9}, abstract = {

By discrete manipulation of the endocrine cues that control insect metamorphosis, it has been possible to examine the mechanisms governing the growth of neural processes during development. During the transition from larva to pupa in the hawkmoth, Manduca sexta, identified sensory neurons reorganize their central projections to evoke a new behavior{\textendash}the gintrap reflex. Topical application of a juvenile hormone analog to the peripheral cell bodies of these sensory neurons during a critical period of development caused them to retain their larval commitment rather than undergo pupal development with the rest of the animal. The sensory neurons retained the larval arborization pattern within the pupal CNS and were unable to evoke the gin-trap reflex. Thus, the hormonal environment of the cell body is critical for controlling growth and synapse formation by distant axonal processes.

}, keywords = {Animal, Animals, Axons, Behavior, Biological, Cobalt, Juvenile Hormones, Larva, Lepidoptera, Metamorphosis, Moths, Neurons}, issn = {0270-6474}, author = {Levine, R B and Truman, J W and Linn, D and Bate, C M} } @article {2466, title = {Dendritic reorganization of an identified motoneuron during metamorphosis of the tobacco hornworm moth.}, journal = {Science}, volume = {192}, year = {1976}, month = {1976 Apr 30}, pages = {477-9}, abstract = {

In the tobacco hornworm, many larval motoneurons become respecified and supply new muscles in the adult. Changes in the morphology of one such neuron were examined through metamorphosis. The dendritic pattern of the adult comes about both by outgrowth from the primary and secondary branches of the larval neuron and by the development of new branches that are unique to the adult.

}, keywords = {Age Factors, Animals, Biological, Cell Differentiation, Dendrites, Larva, Lepidoptera, Male, Metamorphosis, Moths, Motor Neurons, Pupa}, issn = {0036-8075}, author = {Truman, J W and Reiss, S E} } @article {2467, title = {Neuroendocrine control of ecdysis in silkmoths.}, journal = {Science}, volume = {167}, year = {1970}, month = {1970 Mar 20}, pages = {1624-6}, abstract = {

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

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