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

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

}, doi = {10.64898/2026.02.05.704034}, url = {https://www.biorxiv.org/content/early/2026/02/05/2026.02.05.704034}, author = {Lim, Jing-Xuan and Wei, Ziqiang and Narayan, Sujatha and Zhang, Yan and Hasseman, Jeremy P. and Kolb, Ilya and Zheng, Jihong and Sheikhattar, Alireza and Mi, Xuelong and Zheng, Wei and Yang, Xueying and Beriashvili, Mariam and Fleishman, Greg and Wee, Caroline L. and de Zeeuw, Chris and Yu, Guoqiang and Babadi, Behtash and Rubinov, Mikail and Looger, Loren L. and Bergles, Dwight E. and Fitzgerald, James E. and Ahrens, Misha B.} } @article {70300, title = {BPS2026 - Structural basis of the TOK1 potassium channel from Candida albicans}, journal = {Biophysical Journal}, volume = {125}, year = {2026}, month = {2026 Feb 19}, pages = {194a}, abstract = {

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

}, issn = {0006-3495}, doi = {https://doi.org/10.1016/j.bpj.2025.11.1313}, url = {https://www.sciencedirect.com/science/article/pii/S0006349525020636}, author = {Durocher, Brice and Manville, R{\'\i}an and Yan, Rui and Yu, Zhiheng and Abbott, Geoffrey and Miller. Alexandria N.} } @article {70330, title = {Evolutionary basis of male same-sex sexual behavior by multiple pheromone switches in Drosophila.}, journal = {Curr Biol}, year = {2026}, month = {2026 Mar 20}, abstract = {

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

}, issn = {1879-0445}, doi = {10.1016/j.cub.2026.02.046}, url = {https://doi.org/10.1016/j.cub.2026.02.046}, author = {Ouadah, Youcef and Naragon, Thomas H and Smihula, Hayley and Behrman, Emily L and Khallaf, Mohammed A and Ding, Yun and Stern, David L and Parker, Joseph and Anderson, David J} } @article {70333, title = {Midgestation metabolic constraint in purine metabolism drives distinct strategies for placenta and fetal growth}, journal = {bioRxiv}, year = {2026}, month = {2026 Mar 18}, abstract = {

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

}, doi = {10.64898/2026.03.18.712680}, url = {https://www.biorxiv.org/content/early/2026/03/18/2026.03.18.712680}, author = {Xu, Weizhi and De La Cruz, Nancy and Woods, Andrea and Lokshtanov, Dmitry and Gao, Shihong and Khan, Nawal and Wright, Sylvia and Florian-Rodriguez, Maria E. and McIntire, Donald D. and Duryea, Elaine L and Nelson, David B. and Spong, Catherine Y. and Herrera, Christina L. and Hanna, Jacob H. and Srivatsan, Sanjay and Aguilera-Castrejon, Alejandro and Solmonson, Ashley} } @article {70242, title = {mRNAbow: A versatile gene expression system for multiplexed fluorescent imaging using optimized in vitro transcribed mRNA}, journal = {bioRxiv}, year = {2026}, month = {2026 Jan 02}, abstract = {

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

}, doi = {10.64898/2026.01.02.697412}, url = {https://www.biorxiv.org/content/early/2026/01/02/2026.01.02.697412}, author = {Choi, Heejun and Halanych, Coral and Kasberg, William and Testa, Michael D. and Rubin-Elgressy, Sarah and Nguyen, Phuong and Walpita, Deepika and Tsang, Arthur and Cortes, Dan and Song, Erin Yue and Wu, Haodi and Weissman, Irving L and Espinosa-Medina, Isabel and Satou, Chie and Song, Jia L. and Matus, David Q. and Lippincott-Schwartz, Jennifer} } @article {70287, title = {Orofacial behaviors, not eye movements, govern neural activity in mouse visual cortex}, journal = {bioRxiv}, year = {2026}, month = {2026 Feb 05}, abstract = {

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

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

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

}, doi = {10.64898/2026.01.11.698886}, url = {https://www.biorxiv.org/content/early/2026/01/12/2026.01.11.698886}, author = {Bohic, Manon and Salamone, Paula Celeste and Zuo, Wanhong and Negm, Ahmed and Fulton, Sasha Leilani and Du, Shibin and Jayakumar, Swathi and Keating, Jessica and Soubeyre, Vanessa and Gradwell, Mark Andrew and Upadhyay, Aman and Shorter, Lucero and Kim, Joel and Inoue, Yukiko Ueno and Inoue, Takayoshi and Mensch, Brett and Ye, Jiang-Hong and Peirs, Cedric and Poulen, Gaetan and Lonjon, Nicolas and Vachiery-Lahaye, Florence and Bauchet, Luc and Bourinet, Emmanuel and Olausson, Hakan and Abdus-Saboor, Ishmail and Tao, Yuan-Xiang and Boehme, Rebecca and Abraira, Victoria E.} } @article {70302, title = {Phenotypic CRISPR screens identify NLRX1 as an essential activator of the human mitochondrial permeability transition}, journal = {Proceedings of the National Academy of Sciences}, volume = {123}, year = {2026}, month = {2026 Feb 25}, pages = {e2535298123}, abstract = {

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

}, doi = {10.1073/pnas.2535298123}, url = {https://www.pnas.org/doi/abs/10.1073/pnas.2535298123}, author = {William C. Valinsky and Robert P. Ray and Kathy S. Schaefer and Jonathan B. Grimm and Carla Nicolini and Luke D. Lavis and David E. Clapham} } @article {70285, title = {Whole-brain co-mapping of gene expression and neuronal activity at cellular resolution in behaving zebrafish}, journal = {bioRxiv}, year = {2026}, month = {2026 Feb 10}, abstract = {

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

}, doi = {10.64898/2026.02.07.704095}, url = {https://www.biorxiv.org/content/early/2026/02/10/2026.02.07.704095}, author = {Marquez Legorreta, Emmanuel and Fleishman, Greg M. and Hesselink, Luuk W. and Eddison, Mark and Smeets, Kasper and Stringer, Carsen and Keller, Philipp J. and Narayan, Sujatha and Chen, Alex B. and Mensh, Brett D. and Sternson, Scott M. and Englitz, Bernhard and Tillberg, Paul W. and Ahrens, Misha B.} } @article {70052, title = {Aurora 2.0: A fluorogenic dye library for expanding the capability of protein-adaptive Differential Scanning Fluorimetry (paDSF).}, journal = {SLAS Discov}, year = {2025}, month = {2025 Aug 8}, pages = {100259}, abstract = {

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

}, issn = {2472-5560}, doi = {10.1016/j.slasd.2025.100259}, url = {https://doi.org/10.1016/j.slasd.2025.100259}, author = {Charvat, Annemarie F and Mason-Chalmers, Kayleigh and Grabinska-Rogala, Aneta and Shivakumar, Shloka and Gale-Day, Zachary and Wu, Taiasean and Millbern, Zoe and Grimm, Jonathan and Carroll, Emma C and Nilsson, Peter and Lavis, Luke and Vinueza, Nelson R and Gestwicki, Jason E} } @article {70045, title = {Cdc42 regulates apical membrane fusion via the Rab11a{\textendash}VAMP2 pathway in salivary gland acinar cells}, journal = {bioRxiv}, year = {2025}, month = {2025 Jul 31}, abstract = {

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

}, doi = {10.1101/2025.07.31.667845}, url = {https://www.biorxiv.org/content/early/2025/08/01/2025.07.31.667845}, author = {Shitara, Akiko and Nagase, Haruna and Bleck, Christopher K. E. and Ohno, Yuta and Kataoka, Hideo and Satoh, Keitaro and Kashimata, Masanori} } @article {69749, title = {Cell type-specific driver lines targeting the Drosophila central complex and their use to investigate neuropeptide expression and sleep regulation}, journal = {elife}, year = {2025}, month = {2025 Jan 21}, abstract = {

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

}, doi = {10.7554/elife.104764.2}, url = {http://dx.doi.org/10.7554/eLife.104764.2}, author = {Wolff, Tanya and Eddison, Mark and Chen, Nan and Nern, Aljoscha and Sundaramurthi, Preeti and Sitaraman, Divya and Rubin, Gerald M} } @article {69794, title = {Combining sampling methods with attractor dynamics in spiking models of head-direction systems}, journal = {bioRxiv}, year = {2025}, month = {2025 Feb 26}, abstract = {

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

}, doi = {10.1101/2025.02.25.640158}, url = {https://www.biorxiv.org/content/early/2025/02/26/2025.02.25.640158}, author = {Pjanovic, Vojko and Zavatone-Veth, Jacob A and Masset, Paul and Keemink, Sander W and Nardin, Michele} } @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 {69722, title = {Days-old zebrafish rapidly learn to recognize threatening agents through noradrenergic and forebrain circuits.}, journal = {Curr Biol}, volume = {35}, year = {2025}, month = {12/2024}, pages = {163-176.e4}, abstract = {

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

}, keywords = {Adrenergic Neurons, Animals, Larva, Learning, Predatory Behavior, Prosencephalon, Zebrafish}, issn = {1879-0445}, doi = {10.1016/j.cub.2024.11.057}, author = {Zocchi, Dhruv and Nguyen, Millen and Marquez-Legorreta, Emmanuel and Siwanowicz, Igor and Singh, Chanpreet and Prober, David A and Hillman, Elizabeth M C and Ahrens, Misha B} } @article {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 {70178, title = {ER-to-Golgi trafficking is a nutrient-sensitive checkpoint linking glucose starvation to cell surface remodeling}, journal = {bioRxiv}, year = {2025}, month = {2025 October 31}, abstract = {

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

}, doi = {10.1101/2025.10.31.685804}, url = {https://www.biorxiv.org/content/early/2025/11/01/2025.10.31.685804}, author = {Joo, Joung Hyuck and Kasberg, William and Douglas, Spencer and Udoh, Uwemedimo and Carisey, Alexandre and Messing, James and Wang, Yong-Dong and Narina, Shilpa and Pruett-Miller, Shondra M. and Labelle, Myriam and Lippincott-Schwartz, Jennifer and Chang, Chi-Lun and Kundu, Mondira} } @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 {70200, title = {Form and function of actin impacts actin health and aging}, journal = {bioRxiv}, year = {2025}, month = {2025 Nov 23 }, abstract = {

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

}, doi = {10.1101/2025.11.22.689949}, url = {https://www.biorxiv.org/content/early/2025/11/23/2025.11.22.689949}, author = {Averbukh, Maxim and Nelson, Hunter and Wang, Tiffany and Lange, Caitlin M and Alcala, Athena and Nair, Tripti and Kim, Juri and Suh, Daniella and Vega, Matthew and Gao, Shihong Max and Dutta, Naibedya and Aviles Barahona, Rebecca and Coakley, Aeowynn J and Gerke, Joe A. and Odron, Sofia F. and Clarke, Jacqueline G. and Singh, Navjot and Nickel, Matthew S. and Peterson, Jacob C. and Lam-Truong, Hannah L. and Moaddeli, Darius and Castro Torres, Toni and Oorloff, Maria and Peruch, Melissa and Mehta, Hemal and Thorwald, Max A. and Curran, Sean P. and Wang, Meng C and Johnson, Tyler A. and Crimmins, Eileen M. and Arpawong, Thalida Em and Kumsta, Caroline and Garcia, Gilberto and Higuchi-Sanabria, Ryo} } @article {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 {69833, title = {Glutamate indicators with increased sensitivity and tailored deactivation rates}, journal = {Nat Methods}, year = {2025}, month = {2025 Dec 23}, abstract = {

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

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

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

}, doi = {10.21203/rs.3.rs-6257403/v1}, url = {https://doi.org/10.21203/rs.3.rs-6257403/v1}, author = {Podgorski, Kaspar and Aggarwal, Abhi and Negrean, Adrian and Chen, Yang and Iyer, Rishyashring and Reep, Daniel and Liu, Anyi and Palutla, Anirudh and Xie, Michael and Maclennan, Bryan and Hagihara, Kenta and Kinsey, Lucas and Sun, Julianna and Yao, Pantong and Zheng, Jihong and Tsang, Arthur and Tsegaye, Getahun and Zhang, Yonghai and Patel, Ronak and Hasseman, Jeremy} } @article {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 {68938, title = {Learning produces an orthogonalized state machine in the hippocampus.}, journal = {Nature}, volume = {640}, year = {2025}, month = {2025 February 12}, abstract = {

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

}, doi = {10.1038/s41586-024-08548-w}, url = {https://doi.org/10.1038/s41586-024-08548-w}, author = {Sun, Weinan and Winnubst, Johan and Natrajan, Maanasa and Lai, Chongxi and Kajikawa, Koichiro and Michaelos, Michalis and Gattoni, Rachel and Stringer, Carsen and Flickinger, Daniel and Fitzgerald, James E and Spruston, Nelson} } @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.

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 {69656, title = {Leukocytes use endothelial membrane tunnels to extravasate the vasculature}, journal = {Cell Rep}, year = {2025}, month = {2025 Sep 04}, abstract = {

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

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

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

}, issn = {1548-7105}, doi = {10.1038/s41592-024-02590-2}, url = {https://doi.org/10.1038/s41592-024-02590-2}, author = {Fiore, Antonio and Yu, Guoqiang and Northey, Jason J and Patel, Ronak and Ravenscroft, Thomas A. and Ikegami, Richard and Kolkman, W and Pratik Kumar and Dilan, Tanya L and Ruetten, Virginia M.S. and Ahrens, Misha B and Shroff, Hari and Wang, Shaohe and Weaver, Valarie M and Pedram, Kayvon} } @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 {69994, title = {A multimodal adaptive optical microscope for in vivo imaging from molecules to organisms}, journal = {bioRxiv}, year = {2025}, month = {2025 Jun 16}, abstract = {

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

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

}, doi = {10.1101/2025.06.02.657494}, url = {https://www.biorxiv.org/content/early/2025/06/13/2025.06.02.657494}, author = {Fu, Tian-Ming and Liu, Gaoxiang and Milkie, Daniel E. and Ruan, Xiongtao and G{\"o}rlitz, Frederik and Shi, Yu and Ferro, Valentina and Divekar, Nikita S. and Wang, Wei and York, Harrison M. and Kilic, Velat and Mueller, Matthew and Liang, Yajie and Daugird, Timothy A. and Gacha-Garay, Maria J. and Larkin, Kathryn A. and Adikes, Rebecca C. and Harrison, Nathaniel and Shirazinejad, Cyna and Williams, Samara and Nourse, Jamison L. and Sheu, Shu-Hsien and Gao, Liang and Li, Tongchao and Mondal, Chandrani and Achour, Kemal and Hercule, Wilmene and Stabley, Daniel and Emmerich, Kevin and Dong, Peng and Drubin, David and Liu, Zhe J. and Clapham, David and Mumm, Jeff S. and Koyama, Minoru and Killilea, Alison and Bravo-Cordero, Jose Javier and Keene, C. Dirk and Luo, Liqun and Kirchhausen, Tom and Pathak, Medha M. and Arumugam, Senthil and Nunez, James K. and Gao, Ruixuan and Matus, David Q. and Martin, Benjamin L. and Swinburne, Ian A. and Betzig, Eric and Legant, Wesley R. and Upadhyayula, Srigokul} } @article {70156, title = {Natural evolution of intermale sexual behavior by multiple pheromone switches among Drosophila species}, journal = {bioRxiv}, year = {2025}, month = {2025 Oct 14}, abstract = {

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

}, doi = {10.1101/2025.10.14.682417}, url = {https://www.biorxiv.org/content/early/2025/10/15/2025.10.14.682417}, author = {Ouadah, Youcef and Naragon, Thomas H. and Smihula, Hayley and Behrman, Emily L. and Khallaf, Mohammed A. and Ding, Yun and Stern, David L. and Parker, Joseph and Anderson, David J.} } @article {69774, title = {Neuropixels Opto: Combining high-resolution electrophysiology and optogenetics}, journal = {bioRxiv}, year = {2025}, month = {2025 Feb 06}, abstract = {

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

}, doi = {10.1101/2025.02.04.636286}, url = {https://www.biorxiv.org/content/early/2025/02/06/2025.02.04.636286}, author = {Lakunina, Anna and Socha, Karolina Z and Ladd, Alexander and Bowen, Anna J and Chen, Susu and Colonell, Jennifer and Doshi, Anjal and Karsh, Bill and Krumin, Michael and Kulik, Pavel and Li, Anna and Neutens, Pieter and O{\textquoteright}Callaghan, John and Olsen, Meghan and Putzeys, Jan and Tilmans, Harrie AC and Ye, Zhiwen and Welkenhuysen, Marleen and H{\"a}usser, Michael and Koch, Christof and Ting, Jonathan T. and Neuropixels Opto Consortium and Dutta, Barun and Harris, Timothy D and Steinmetz, Nicholas A and Svoboda, Karel and Siegle, Joshua H and Carandini, Matteo} } @article {70243, title = {The organization of visual pathways in the Drosophila brain}, journal = {bioRxiv}, year = {2025}, month = {2025 Dec 26}, abstract = {

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

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

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

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

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

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

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

}, doi = {10.64898/2025.12.08.692974}, url = {https://www.biorxiv.org/content/early/2025/12/11/2025.12.08.692974}, author = {Nardin, Michele and Wang, Nan and Elziny, Soad and Boyer, Claire and Pjanovic, Vojko and Schuster, Luisa and Boklund, Peter and Lindo, Sarah and Morris, Kendra and Ilanges, Anoj and Voigts, Jakob and Dennis, Emily Jane} } @article {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 {69514, title = {A simplified minimodel of visual cortical neurons}, journal = {Nat Commun}, year = {2025}, month = {2025 Jul 01}, abstract = {

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

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

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

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

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

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

}, keywords = {Animals, Brain, CRISPR-Cas Systems, Mice, Mice, Inbred C57BL, Neurons, Single-Cell Analysis, Synapses}, issn = {2041-1723}, doi = {10.1038/s41467-025-65813-w}, url = {https://doi.org/10.1038/s41467-025-65813-w}, author = {Uchigashima, Motokazu and Iguchi, Risa and Fujii, Kazuma and Shiku, Kaito and Kumar, Pratik and Liu, Xinyi and Isogai, Mari and Hoshino, Chiaki and Abe, Manabu and Nozumi, Motohiro and Okamura, Yosuke and Igarashi, Michihiro and Sakimura, Kenji and Bise, Ryoma and Lavis, Luke D and Mikuni, Takayasu} } @article {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 {69995, title = {Skin health and biological aging.}, journal = {Nat Aging}, year = {2025}, month = {2025 Jun 17}, abstract = {

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

}, issn = {2662-8465}, doi = {10.1038/s43587-025-00901-6}, url = {https://doi.org/10.1038/s43587-025-00901-6}, author = {Furman, David and Auwerx, Johan and Bulteau, Anne-Laure and Church, George and Couturaud, Virginie and Crabbe, Laure and Davies, Kelvin J A and Decottignies, Anabelle and Gladyshev, Vadim N and Kennedy, Brian K and Neretti, Nicola and Nizard, Carine and Pays, Karl and Robinton, Daisy and Sebastiano, Vittorio and Watson, Rachel E B and Wang, Meng C and Woltjen, Knut} } @article {69984, title = {Spatial reasoning via recurrent neural dynamics in mouse retrosplenial cortex}, journal = {Nat Neurosci}, volume = {28}, year = {2025}, month = {2025 Jun 06}, pages = {1293-1299}, abstract = {

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

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

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

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

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

}, doi = {10.1038/s41586-025-09010-1}, url = {https://doi.org/10.1038/s41586-025-09010-1}, author = {Qian, Xuyu and Coleman, Kyle and Jiang, Shunzhou and Kriz, Andrea J. and Marciano, Jack H. and Luo, Chunyu and Cai, Chunhui and Manam, Monica Devi and Caglayan, Emre and Otani, Aoi and Ghosh, Urmi and Shao, Diane D. and Andersen, Rebecca E. and Neil, Jennifer E. and Johnson, Robert and LeFevre, Alexandra and Hecht, Jonathan L. and Miller, Michael B. and Sun, Liang and Stringer, Carsen and Li, Mingyao and Walsh, Christopher A.} } @article {69721, title = {A split-GAL4 driver line resource for Drosophila neuron types}, year = {2025}, month = {01/2025}, doi = {10.7554/elife.98405.3}, url = {http://dx.doi.org/10.7554/eLife.98405.3}, author = {Meissner, Geoffrey W and Vannan, Allison and Jeter, Jennifer and Close, Kari and Depasquale, Gina M and Dorman, Zachary and Forster, Kaitlyn and Beringer, Jaye Anne and Gibney, Theresa V and Hausenfluck, Joanna H and He, Yisheng and Henderson, Kristin and Johnson, Lauren and Johnston, Rebecca M and Ihrke, Gudrun and Iyer, Nirmala and Lazarus, Rachel and Lee, Kelley and Li, Hsing-Hsi and Liaw, Hua-Peng and Melton, Brian and Miller, Scott and Motaher, Reeham and Novak, Alexandra and Ogundeyi, Omotara and Petruncio, Alyson and Price, Jacquelyn and Protopapas, Sophia and Tae, Susana and Taylor, Jennifer and Vorimo, Rebecca and Yarbrough, Brianna and Zeng, Kevin Xiankun and Zugates, Christopher T and Dionne, Heather and Angstadt, Claire and Ashley, Kelly and Cavallaro, Amanda and Dang, Tam and Gonzalez, Guillermo A and Hibbard, Karen L and Huang, Cuizhen and Kao, Jui-Chun and Laverty, Todd and Mercer, Monti and Perez, Brenda and Pitts, Scarlett and Ruiz, Danielle and Vallanadu, Viruthika and Zheng, Grace Zhiyu and Goina, Cristian and Otsuna, Hideo and Rokicki, Konrad and Svirskas, Robert R and Cheong, Han Sj and Dolan, Michael-John and Ehrhardt, Erica and Feng, Kai and El Galfi, Basel and Goldammer, Jens and Huston, Stephen J and Hu, Nan and Ito, Masayoshi and McKellar, Claire and minegishi, ryo and Namiki, Shigehiro and Nern, Aljoscha and Schretter, Catherine E and Sterne, Gabriella R and Venkatasubramanian, Lalanti and Wang, Kaiyu and Wolff, Tanya and Wu, Ming and George, Reed and Malkesman, Oz and Aso, Yoshinori and Card, Gwyneth M and Dickson, Barry J and Korff, Wyatt and Ito, Kei and Truman, James W and Zlatic, Marta and Rubin, Gerald M} } @article {70183, title = {Stability through plasticity: Finding robust memories through representational drift.}, journal = {Proc Natl Acad Sci USA}, volume = {122}, year = {2025}, month = {2025 Nov 11}, pages = {e2500077122}, abstract = {

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

}, keywords = {Humans, Learning, Memory, Models, Neurological, Neuronal Plasticity, Neurons, Synapses}, issn = {1091-6490}, doi = {10.1073/pnas.2500077122}, url = {https://doi.org/10.1073/pnas.2500077122}, author = {Natrajan, Maanasa and Fitzgerald, James E} } @article {70094, title = {Surrogate selection oversamples expanded T cell clonotypes}, journal = {The Annals of Applied Statistics}, volume = {19}, year = {2025}, month = {2025 Sept 01}, pages = {1884 {\textendash} 1907}, abstract = {

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

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

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

}, issn = {1758-535X}, doi = {10.1093/gerona/glaf026}, url = {https://doi.org/10.1093/gerona/glaf026}, author = {Rogina, Blanka and Anderson, Rozalyn and Lebrasseur, Nathan and Curan, Sean and Yousefzadeh, Matthew J and Ghosh, Bhaswati and Duque, Gustavo and Howlett, Susan and Austad, Steven and Demuth, Ilja and Gerstorf, Denis and Korfhage, Justin and Lombard, David B and Abadir, Peter and Christensen, Kaare and Carey, James R and Alberts, Susan C and Campos, Fernando and Palavicini, Juan Pablo and Palmer, Allyson and Bell, Justice and Basisty, Nathan and de Cabo, Rafael and Gomes, Ana and Dixit, Vishwa Deep and Sen, Payel and Baur, Joseph A and Imai, Shin-Ichiro and Li, Xiaoling and Valdez, Gregorio and Orr, Miranda E and Pletcher, Scott and Andersen, Julie and Jones, Leanne and Castillo-Azofeida, David and Bonaguidi, Michael and Suh, Yousin and Duncan, Francesca E and Murray, Anna and Burkewitz, Kristopher and Henne, Mike and Zhou, Kai and Bouhrara, Mustapha and Benjamini, Dan and Kolind, Shannon and Walker, Keenan A and Reiter, David A and Dean Iii, Doug and Gorbunova, Vera and Gladyshev, Vadim N and Palovics, Robert and Niedernhofer, Laura J and Fan, Rong and Bueckle, Andreas D and Hurley, Jennifer and Esser, Karyn A and Kapahi, Pankaj and Sato, Shogo and Jiang, Nisi and Ashiqueali, Sarah A and Diaz, Jose and Mishra, Sidharth Prasad and Ralmundo, Nuno and Banarjee, Reema and Allsopp, Richard and Reynolds, Lindsay M and Zhang, Bohan and Sebastiani, Paola and Monti, Stefano and Schork, Nicholas and Rappaport, Noa} } @article {70091, title = {Synaptic targets of circadian clock neurons influence core clock parameters.}, journal = {Sci Adv}, volume = {11}, year = {2025}, month = {2025 Sep 05}, pages = {eadw4666}, abstract = {

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

}, keywords = {Animals, Circadian Clocks, Circadian Rhythm, Drosophila melanogaster, Drosophila Proteins, Neurons, Neuropeptides, Sleep, Synapses, Tetanus Toxin}, issn = {2375-2548}, doi = {10.1126/sciadv.adw4666}, url = {https://doi.org/10.1126/sciadv.adw4666}, author = {Scholz-Carlson, Eva and Iyer, Aishwarya R and Nern, Aljoscha and Ewer, John and Fernandez, Maria P} } @article {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 {70030, title = {Transforming descending input into motor output: An analysis of the Drosophila Male Adult Nerve Cord connectome}, journal = {eLife}, year = {2025}, month = {2025 Jul 21}, abstract = {

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

}, doi = {10.7554/elife.96084.2}, url = {http://dx.doi.org/10.7554/eLife.96084.2}, author = {Cheong, Han Sj and Eichler, Katharina and St{\"u}rner, Tomke and Asinof, Samuel K and Champion, Andrew S and Marin, Elizabeth C and Oram, Tess B and Sumathipala, Marissa and Venkatasubramanian, Lalanti and Namiki, Shigehiro and Siwanowicz, Igor and Costa, Marta and Berg, Stuart and Jefferis, Gregory Sxe and Card, Gwyneth M} } @article {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 {70133, title = {Ultra-high-density Neuropixels probes improve detection and identification in neuronal recordings.}, journal = {Neuron}, volume = {113}, year = {2025}, month = {2025 Dec 3}, abstract = {

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

bioRxiv preprint: doi.org/10.1101/2023.08.23.554527

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2025.08.030}, url = {https://doi.org/10.1016/j.neuron.2025.08.030}, author = {Ye, Zhiwen and Shelton, Andrew M and Shaker, Jordan R and Boussard, Julien and Colonell, Jennifer and Birman, Daniel and Manavi, Sahar and Chen, Susu and Windolf, Charlie and Hurwitz, Cole and Yu, Han and Namima, Tomoyuki and Pedraja, Federico and Weiss, Shahaf and Raducanu, Bogdan C and Ness, Torbj{\o}rn V and Jia, Xiaoxuan and Mastroberardino, Giulia and Rossi, L Federico and Carandini, Matteo and H{\"a}usser, Michael and Einevoll, Gaute T and Laurent, Gilles and Sawtell, Nathaniel B and Bair, Wyeth and Pasupathy, Anitha and Mora Lopez, Carolina and Dutta, Barundeb and Paninski, Liam and Siegle, Joshua H and Koch, Christof and Olsen, Shawn R and Harris, Timothy D and Steinmetz, Nicholas A} } @article {69790, title = {An updated catalogue of split-GAL4 driver lines for descending neurons in Drosophila melanogaster}, journal = {bioRxiv}, year = {2025}, month = {2025 Feb 24}, abstract = {

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

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

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

}, doi = {10.7554/elife.107450.1}, url = {http://dx.doi.org/10.7554/eLife.107450.1}, author = {Zung, Jessica L and Namiki, Shigehiro and Meissner, Geoffrey W and Cheong, Han Sj and Costa, Marta and Eichler, Katharina and St{\"u}rner, Tomke and Jefferis, Gregory Sxe and Managan, Claire and Korff, Wyatt and Card, Gwyneth M} } @article {69614, title = {Voltage imaging reveals circuit computations in the raphe underlying serotonin-mediated motor vigor learning}, journal = {Neuron}, year = {2025}, month = {2025 Jun 06}, abstract = {

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

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

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

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

}, keywords = {Actins, Animals, Humans, Imaging, Three-Dimensional, Mice, Microscopy, Fluorescence, Microscopy, Polarization, Xylem}, issn = {1091-6490}, doi = {10.1073/pnas.2406679122}, author = {Chandler, Talon and Guo, Min and Su, Yijun and Chen, Jiji and Wu, Yicong and Liu, Junyu and Agashe, Atharva and Fischer, Robert S and Mehta, Shalin B and Kumar, Abhishek and Baskin, Tobias I and Jaumouill{\'e}, Valentin and Liu, Huafeng and Swaminathan, Vinay and Nain, Amrinder S and Oldenbourg, Rudolf and La Riviere, Patrick J and Shroff, Hari} } @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 {69424, title = {Adaptive optical third-harmonic generation microscopy for in vivo imaging of tissues}, journal = {bioRxiv}, year = {2024}, month = {2024 May 05}, abstract = {

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

}, doi = {10.1101/2024.05.02.592275}, url = {https://www.biorxiv.org/content/early/2024/05/05/2024.05.02.592275}, author = {Cristina Rodr{\'\i}guez and Daisong Pan and Ryan G. Natan and Manuel A. Mohr and Max Miao and Xiaoke Chen and Trent R. Northen and John P. Vogel and Na Ji} } @article {69642, title = {All-optical reporting of inhibitory receptor driving force in the nervous system}, journal = {Nat Commun}, volume = {15}, year = {2024}, month = {2024 Oct 16}, pages = {8913}, abstract = {

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

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

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

}, doi = {10.1126/sciadv.adq0791}, url = {https://doi.org/10.1126/sciadv.adq0791}, author = {Taylor B. Updegrove and Thomas Delerue and V. Anantharaman and Hyomoon Cho and Carissa Chan and Thomas Nipper and Hyoyoung Choo-Wosoba and Lisa Jenkins and Lixia Zhang and Yijun Su and Hari Shroff and Jiji Chen and Carole Bewley and L. Aravind and Kumaran S Ramamurthi} } @article {69657, title = {Anti-seizure effects of norepinephrine-induced free fatty acid release.}, journal = {Cell Metab}, year = {2024}, month = {2024 Oct 29}, abstract = {

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

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

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

}, doi = {10.1016/j.cub.2024.07.036}, url = {https://doi.org/10.1016/j.cub.2024.07.036}, author = {Daniel J. Barrero and Sithara S. Wijeratne and Xiaowei Zhao and Grace F. Cunningham and Rui Yan and Christian R. Nelson and Yasuhiro Arimura and Hironori Funabiki and Charles L. Asbury and Zhiheng Yu and Radhika Subramanian and Sue Biggins} } @article {69148, title = {Bridging gaps in traditional research training with iBiology Courses.}, journal = {PLoS Biology}, volume = {22}, year = {2024}, month = {2024 Jan 11}, pages = {e3002458}, abstract = {

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

}, issn = {1545-7885}, doi = {10.1371/journal.pbio.3002458}, author = {Schnoes, Alexandra M and Green, Noah H and Nguyen, Thi A and Vale, Ronald D and Goodwin, Sarah S and Behrman, Shannon L} } @article {69445, title = {Building momentum through networks: Bioimaging across the Americas}, journal = {Journal of Microscopy}, volume = {n/a}, year = {2024}, month = {2024 May 15}, abstract = {

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

}, keywords = {bioimaging networks, BioImaging North America, community-building, imaging scientists, Latin America Bioimaging}, doi = {https://doi.org/10.1111/jmi.13318}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jmi.13318}, author = {De Niz, Mariana and Escobedo Garc{\'\i}a, Rodrigo and Ter{\'a}n Ramirez, Celina and Pakowski, Ysa and Abonza, Yuriney and Bialy, Nikki and Orr, Vanessa L. and Olivera, Andres and Abonza, Victor and Alleva, Karina and Allodi, Silvana and Almeida, Michael F. and Becerril Cuevas, Alexis Ricardo and Bonnet, Frederic and Burgos Solorio, Armando and Chew, Teng-Leong and Chiabrando, Gustavo and Cimini, Beth and Cleret-Buhot, Aur{\'e}lie and Contreras Jim{\'e}nez, Gast{\'o}n and Daza, Laura and De S{\'a}, Vanessa and De Val, Natalia and Delgado-{\'A}lvarez, Diego L. and Eliceiri, Kevin and Fiolka, Reto and Grecco, Hernan and Hanein, Dorit and Hern{\'a}ndez Herrera, Pa{\'u}l and Hockberger, Phil and Hernandez, Haydee O. and Hernandez Guadarrama, Yael and Itano, Michelle and Jacobs, Caron A. and Jim{\'e}nez-Garc{\'\i}a, Luis F. and Jim{\'e}nez Sabinina, Vilma and Kamaid, Andres and Keppler, Antje and Kumar, Abhishek and Lacoste, Judith and Lovy, Alenka and Luby-Phelps, Kate and Mahadevan-Jansen, Anita and Malacrida, Leonel and Mehta, Shalin B. and Miller, Caroline and Miranda, Kildare and Moore, Joshua A. and North, Alison and O{\textquoteright}Toole, Peter and Olivares Urbano, Mariana and Pietrasanta, L{\'\i}a I. and Portugal, Rodrigo V. and Rossi, Andr{\'e}s H. and Sanchez Contreras, Jonathan and Strambio-De-Castilla, Caterina and Soldevila, Gloria and Vale, Bruno and Vazquez, Diana and Wood, Chris and Brown, Claire M. and Guerrero, Adan} } @article {69650, title = {Cell type-specific driver lines targeting the Drosophila central complex and their use to investigate neuropeptide expression and sleep regulation}, journal = {bioRxiv}, year = {2024}, month = {2024 Oct 21}, abstract = {

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

}, doi = {10.1101/2024.10.21.619448}, url = {https://doi.org/10.1101/2024.10.21.619448}, author = {Wolff, Tanya and Eddison, Mark and Chen, Nan and Nern, Aljoscha and Sundaramurthi, Preeti and Sitaraman, Divya and Rubin, Gerald M.} } @article {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 {69138, title = {Connectomic reconstruction predicts visual features used for navigation.}, journal = {Nature}, volume = {634}, year = {2024}, month = {2024 Oct 02}, pages = {181-190}, abstract = {

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

}, doi = {10.1038/s41586-024-07967-z}, url = {https://doi.org/10.1038/s41586-024-07967-z}, author = {Garner, Dustin and Kind, Emil and Yuet Ha Lai, Jennifer and Nern, Aljoscha and Zhao, Arthur and Houghton, Lucy and Sancer, Gizem and Wolff, Tanya and Rubin, Gerald M and Wernet, Mathias F and Kim, Sung Soo} } @article {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 {69706, title = {Days-old zebrafish rapidly learn to recognize threatening agents through noradrenergic and forebrain circuits.}, journal = {Curr Biol}, year = {2024}, month = {2024 Dec 19}, abstract = {

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

}, issn = {1879-0445}, doi = {10.1016/j.cub.2024.11.057}, author = {Zocchi, Dhruv and Nguyen, Millen and Marquez-Legorreta, Emmanuel and Siwanowicz, Igor and Singh, Chanpreet and Prober, David A and Hillman, Elizabeth M C and Ahrens, Misha B} } @article {68919, title = {The density of regulatory information is a major determinant of evolutionary constraint on non-coding DNA in Drosophila}, journal = {Molecular Biology and Evolution}, volume = {41}, year = {2024}, month = {2024 Feb 01}, pages = {msae004}, abstract = {

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

}, doi = {10.1093/molbev/msae004}, url = {https://doi.org/10.1093/molbev/msae004}, author = {Gonzalo Sabar{\'\i}s and Daniela M. Ort{\'\i}z and Ian Laiker and Ignacio Mayansky and Sujay Naik and Giacomo Cavalli and David L. Stern and Ella Preger-Ben Noon and Nicol{\'a}s Frankel} } @article {69154, title = {Failure to mate enhances investment in behaviors that may promote mating reward and impairs the ability to cope with stressors via a subpopulation of Neuropeptide F receptor neurons.}, journal = {PLoS Genetics}, volume = {20}, year = {2024}, month = {2024 Jan 18}, pages = {e1011054}, abstract = {

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

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

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

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

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

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

}, issn = {2212-8778}, doi = {10.1016/j.molmet.2024.102048}, url = {https://doi.org/10.1016/j.molmet.2024.102048}, author = {Wang, Haizhen and Nikain, Cyrus and Fortounas, Konstantinos I and Amengual, Jaime and Tufanli, Ozlem and La Forest, Maxwell and Yu, Yong and Wang, Meng C and Watts, Russell and Lehner, Richard and Qiu, Yunping and Cai, Min and Kurland, Irwin J and Goldberg, Ira J and Rajan, Sujith and Hussain, M Mahmood and Brodsky, Jeffrey L and Fisher, Edward A} } @article {69659, title = {A global dopaminergic learning rate enables adaptive foraging across many options}, journal = {bioRxiv}, year = {2024}, month = {2024 Nov 05}, abstract = {

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

}, doi = {10.1101/2024.11.04.621923}, url = {https://doi.org/10.1101/2024.11.04.621923}, author = {Grima, Laura L and Guo, Yipei and Narayan, Lakshmi and Hermundstad, Ann M and Dudman, Joshua T} } @article {69254, title = {Haploidy-linked cell proliferation defects limit larval growth in Zebrafish}, journal = {Open Biol.}, volume = {14}, year = {2024}, month = {2024 Oct 09}, pages = {240126}, abstract = {

Haploid larvae in non-mammalian vertebrates are lethal, with characteristic organ growth retardation collectively called {\textquoteright}haploid syndrome{\textquoteright}. In contrast to mammals, whose haploid intolerance is attributed to imprinting misregulation, the cellular principle of haploidy-linked defects in non-mammalian vertebrates remains unknown. Here, we investigated cellular defects that disrupt the ontogeny of gynogenetic haploid zebrafish larvae. Unlike diploid control larvae, haploid larvae manifested unscheduled cell death at the organogenesis stage, attributed to haploidy-linked p53 upregulation. Moreover, we found that haploid larvae specifically suffered the gradual aggravation of mitotic spindle monopolarization during 1-3 days post-fertilization, causing spindle assembly checkpoint-mediated mitotic arrest throughout the entire body. High-resolution imaging revealed that this mitotic defect accompanied the haploidy-linked centrosome loss occurring concomitantly with the gradual decrease in larval cell size. Either resolution of mitotic arrest or depletion of p53 partially improved organ growth in haploid larvae. Based on these results, we propose that haploidy-linked mitotic defects and cell death are parts of critical cellular causes shared among vertebrates that limit the larval growth in the haploid state, contributing to an evolutionary constraint on allowable ploidy status in the vertebrate life cycle.

}, doi = {10.1098/rsob.240126}, url = {https://doi.org/10.1098/rsob.240126}, author = {Kan Yaguchi and Daiki Saito and Triveni Menon and Akira Matsura and Takeomi Mizutani and Tomoya Kotani and Sreelaja Nair and Ryota Uehara} } @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 {69383, title = {Hippocampal cholecystokinin-expressing interneurons regulate temporal coding and contextual learning}, journal = {Neuron}, year = {2024}, month = {2024 Apr 17}, abstract = {

Cholecystokinin-expressing interneurons (CCKIs) are hypothesized to shape pyramidal cell-firing patterns and regulate network oscillations and related network state transitions. To directly probe their role in the CA1 region, we silenced their activity using optogenetic and chemogenetic tools in mice. Opto-tagged CCKIs revealed a heterogeneous population, and their optogenetic silencing triggered wide disinhibitory network changes affecting both pyramidal cells and other interneurons. CCKI silencing enhanced pyramidal cell burst firing and altered the temporal coding of place cells: theta phase precession was disrupted, whereas sequence reactivation was enhanced. Chemogenetic CCKI silencing did not alter the acquisition of spatial reference memories on the Morris water maze but enhanced the recall of contextual fear memories and enabled selective recall when similar environments were tested. This work suggests the key involvement of CCKIs in the control of place-cell temporal coding and the formation of contextual memories.

}, issn = {08966273}, doi = {10.1016/j.neuron.2024.03.019}, url = {https://doi.org/10.1016/j.neuron.2024.03.019}, author = {Rangel Guerrero, D{\'a}maris K. and Balueva, Kira and Barayeu, Uladzislau and Baracskay, Peter and Gridchyn, Igor and Nardin, Michele and Roth, Chiara Nina and Wulff, Peer and Csicsvari, Jozsef} } @article {69456, title = {Hue selectivity from recurrent circuitry in Drosophila}, journal = {Nat Neurosci}, year = {2024}, month = {2024 May 16}, abstract = {

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

}, issn = {1546-1726}, doi = {10.1038/s41593-024-01640-4}, author = {Christenson, Matthias P and Sanz Diez, Alvaro and Heath, Sarah L and Saavedra-Weisenhaus, Maia and Adachi, Atsuko and Nern, Aljoscha and Abbott, L F and Behnia, Rudy} } @article {69440, title = {Imaging the extracellular matrix in live tissues and organisms with a glycan-binding fluorophore}, journal = {bioRxiv}, year = {2024}, month = {2024 May 10}, abstract = {

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

}, doi = {10.1101/2024.05.09.593460}, url = {https://www.biorxiv.org/content/early/2024/05/10/2024.05.09.593460}, author = {Fiore, Antonio and Yu, Guoqiang and Northey, Jason J. and Patel, Ronak and Ravenscroft, Thomas A. and Ikegami, Richard and Kolkman, Wiert and Kumar, Pratik and Grimm, Jonathan B. and Dilan, Tanya L. and Ruetten, Virginia M.S. and Ahrens, Misha B. and Shroff, Hari and Lavis, Luke D. and Wang, Shaohe and Weaver, Valerie M. and Pedram, Kayvon} } @article {69643, title = {IRE1α silences dsRNA to prevent taxane-induced pyroptosis in triple-negative breast cancer.}, journal = {Cell}, year = {2024}, month = {2024 Oct 14}, abstract = {

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

}, issn = {1097-4172}, doi = {10.1016/j.cell.2024.09.032}, url = {https://doi.org/10.1016/j.cell.2024.09.032}, author = {Xu, Longyong and Peng, Fanglue and Luo, Qin and Ding, Yao and Yuan, Fei and Zheng, Liting and He, Wei and Zhang, Sophie S and Fu, Xin and Liu, Jin and Mutlu, Ayse Sena and Wang, Shuyue and Nehring, Ralf Bernd and Li, Xingyu and Tang, Qianzi and Li, Catherine and Lv, Xiangdong and Dobrolecki, Lacey E and Zhang, Weijie and Han, Dong and Zhao, Na and Jaehnig, Eric and Wang, Jingyi and Wu, Weiche and Graham, Davis A and Li, Yumei and Chen, Rui and Peng, Weiyi and Chen, Yiwen and Catic, Andre and Zhang, Zhibin and Zhang, Bing and Mustoe, Anthony M and Koong, Albert C and Miles, George and Lewis, Michael T and Wang, Meng C and Rosenberg, Susan M and O{\textquoteright}Malley, Bert W and Westbrook, Thomas F and Xu, Han and Zhang, Xiang H-F and Osborne, C Kent and Li, Jin Billy and Ellis, Matthew J and Rimawi, Mothaffar F and Rosen, Jeffrey M and Chen, Xi} } @article {69703, title = {Ketamine induces plasticity in a norepinephrine-astroglial circuit to promote behavioral perseverance.}, journal = {Neuron}, year = {2024}, month = {2024 Dec 16}, pages = {1-15}, abstract = {

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

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2024.11.011}, url = {https://doi.org/10.1016/j.neuron.2024.11.011}, author = {Duque, Marc and Chen, Alex B and Hsu, Eric and Narayan, Sujatha and Rymbek, Altyn and Begum, Shahinoor and Saher, Gesine and Cohen, Adam E and Olson, David E and Li, Yulong and Prober, David A and Bergles, Dwight E and Fishman, Mark C and Engert, Florian and Ahrens, Misha B} } @article {69632, title = {Maintaining and updating accurate internal representations of continuous variables with a handful of neurons.}, journal = {Nat Neurosci}, year = {2024}, month = {2024 Oct 03}, abstract = {

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

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

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

}, keywords = {Animals, Bone Marrow, Bone Marrow Cells, Hematopoiesis, Hematopoietic Stem Cells, Mice, Stromal Cells}, issn = {2041-1723}, doi = {10.1038/s41467-024-45827-6}, author = {Mertens, Till Fabian and Liebheit, Alina Tabea and Ehl, Johanna and K{\"o}hler, Ralf and Rakhymzhan, Asylkhan and Woehler, Andrew and Katth{\"a}n, Lukas and Ebel, Gernot and Liublin, Wjatscheslaw and Kasapi, Ana and Triantafyllopoulou, Antigoni and Schulz, Tim Julius and Niesner, Raluca Aura and Hauser, Anja Erika} } @article {69545, title = {Mesoscale chromatin confinement facilitates target search of pioneer transcription factors in live cells}, journal = {Nat. Struct. Mol. Biol.}, year = {2024}, month = {2024 Oct 04}, abstract = {

Pioneer transcription factors (PTFs) possess the unique capability to access closed chromatin regions and initiate cell fate changes, yet the underlying mechanisms remain elusive. Here, we characterized the single-molecule dynamics of PTFs targeting chromatin in living cells, revealing a notable {\textquoteright}confined target search{\textquoteright} mechanism. PTFs such as FOXA1, FOXA2, SOX2, OCT4 and KLF4 sampled chromatin more frequently than non-PTF MYC, alternating between fast free diffusion in the nucleus and slower confined diffusion within mesoscale zones. Super-resolved microscopy showed closed chromatin organized as mesoscale nucleosome-dense domains, confining FOXA2 diffusion locally and enriching its binding. We pinpointed specific histone-interacting disordered regions, distinct from DNA-binding domains, crucial for confined target search kinetics and pioneer activity within closed chromatin. Fusion to other factors enhanced pioneer activity. Kinetic simulations suggested that transient confinement could increase target association rate by shortening search time and binding repeatedly. Our findings illuminate how PTFs recognize and exploit closed chromatin organization to access targets, revealing a pivotal aspect of gene regulation.

}, doi = {10.1038/s41594-024-01385-5}, url = {https://www.doi.org/10.1038/s41594-024-01385-5}, author = {Wang, Zuhui and Wang, Bo and Niu, Di and Yin, Chao and Bi, Ying and Cattoglio, Claudia and Loh, Kyle M and Lavis, Luke D and Ge, Hao and Deng, Wulan} } @article {69169, title = {Motion of VAPB molecules reveals ER-mitochondria contact site subdomains.}, journal = {Nature}, volume = {626}, year = {2024}, month = {2024 Jan 24}, pages = {169-176}, abstract = {

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

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

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

}, issn = {1476-4687}, doi = {10.1038/s41586-024-07222-5}, author = {Gorko, Benjamin and Siwanowicz, Igor and Close, Kari and Christoforou, Christina and Hibbard, Karen L and Kabra, Mayank and Lee, Allen and Park, Jin-Yong and Li, Si Ying and Chen, Alex B and Namiki, Shigehiro and Chen, Chenghao and Tuthill, John C and Bock, Davi D and Rouault, Herv{\'e} and Branson, Kristin and Ihrke, Gudrun and Huston, Stephen J} } @article {69511, title = {Near-infrared nanosensors enable optical imaging of oxytocin with selectivity over vasopressin in acute mouse brain slices.}, journal = {Proc Natl Acad Sci U S A}, volume = {121}, year = {2024}, month = {2024 Jun 25}, pages = {e2314795121}, abstract = {

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

}, keywords = {Animals, Brain, Male, Mice, Mice, Inbred C57BL, Nanotubes, Carbon, Optical Imaging, Oxytocin, Receptors, Oxytocin, Spectroscopy, Near-Infrared, Vasopressins}, issn = {1091-6490}, doi = {10.1073/pnas.2314795121}, author = {Mun, Jaewan and Navarro, Nicole and Jeong, Sanghwa and Ouassil, Nicholas and Leem, Esther and Beyene, Abraham G and Landry, Markita P} } @article {69542, title = {Neural circuit basis of placebo pain relief.}, journal = {Nature}, year = {2024}, month = {2024 Jul 24}, abstract = {

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

}, issn = {1476-4687}, doi = {10.1038/s41586-024-07816-z}, author = {Chen, Chong and Niehaus, Jesse K and Dinc, Fatih and Huang, Karen L and Barnette, Alexander L and Tassou, Adrien and Shuster, S Andrew and Wang, Lihua and Lemire, Andrew and Menon, Vilas and Ritola, Kimberly and Hantman, Adam and Zeng, Hongkui and Schnitzer, Mark J and Scherrer, Gr{\'e}gory} } @article {68889, title = {Neuronal wiring diagram of an adult brain.}, journal = {Nature}, volume = {634}, year = {2024}, month = {2024 Oct 02}, pages = {124-138}, abstract = {

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

}, doi = {10.1038/s41586-024-07558-y}, url = {https://doi.org/10.1038/s41586-024-07558-y}, author = {Dorkenwald, Sven and Matsliah, Arie and Sterling, Amy R and Schlegel, Philipp and Yu, Szi-Chieh and McKellar, Claire E and Lin, Albert and Costa, Marta and Eichler, Katharina and Yin, Yijie and Silversmith, Will and Schneider-Mizell, Casey and Jordan, Chris S and Brittain, Derrick and Halageri, Akhilesh and Kuehner, Kai and Ogedengbe, Oluwaseun and Morey, Ryan and Gager, Jay and Kruk, Krzysztof and Perlman, Eric and Yang, Runzhe and Deutsch, David and Bland, Doug and Sorek, Marissa and Lu, Ran and Macrina, Thomas and Lee, Kisuk and Bae, J Alexander and Mu, Shang and Nehoran, Barak and Mitchell, Eric and Popovych, Sergiy and Wu, Jingpeng and Jia, Zhen and Castro, Manuel and Kemnitz, Nico and Ih, Dodam and Bates, Alexander Shakeel and Eckstein, Nils and Funke, Jan and Collman, Forrest and Bock, Davi D and Jefferis, Gregory S X E and Seung, H Sebastian and Murthy, Mala} } @article {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 {69669, title = {ONIX: a unified open-source platform for multimodal neural recording and perturbation during naturalistic behavior.}, journal = {Nat Methods}, year = {2024}, month = {2024 Nov 11}, abstract = {

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

}, issn = {1548-7105}, doi = {10.1038/s41592-024-02521-1}, url = {https://doi.org/10.1038/s41592-024-02521-1}, author = {Newman, Jonathan P and Zhang, Jie and Cuevas-L{\'o}pez, Aar{\'o}n and Miller, Nicholas J and Honda, Takato and van der Goes, Marie-Sophie H and Leighton, Alexandra H and Carvalho, Filipe and Lopes, Gon{\c c}alo and Lakunina, Anna and Siegle, Joshua H and Harnett, Mark T and Wilson, Matthew A and Voigts, Jakob} } @article {69136, title = {Permanent deconstruction of intracellular primary cilia in differentiating granule cell neurons.}, journal = {J Cell Biol.}, volume = {223}, year = {2024}, month = {2024 Aug 13}, pages = {e202404038}, abstract = {

Primary cilia on granule cell neuron progenitors in the developing cerebellum detect sonic hedgehog to facilitate proliferation. Following differentiation, cerebellar granule cells become the most abundant neuronal cell type in the brain. While granule cell cilia are essential during early developmental stages, they become infrequent upon maturation. Here, we provide nanoscopic resolution of cilia in situ using large-scale electron microscopy volumes and immunostaining of mouse cerebella. In many granule cells, we found intracellular cilia, concealed from the external environment. Cilia were disassembled in differentiating granule cell neurons-in a process we call cilia deconstruction-distinct from premitotic cilia resorption in proliferating progenitors. In differentiating granule cells, cilia deconstruction involved unique disassembly intermediates, and, as maturation progressed, mother centriolar docking at the plasma membrane. Unlike ciliated neurons in other brain regions, our results show the deconstruction of concealed cilia in differentiating granule cells, which might prevent mitogenic hedgehog responsiveness. Ciliary deconstruction could be paradigmatic of cilia removal during differentiation in other tissues.

}, doi = {10.1016/j.cub.2024.07.036}, url = {https://doi.org/10.1016/j.cub.2024.07.036 }, author = {Ott, Carolyn M and Constable, Sandii and Nguyen, Tri M and White, Kevin and Lee, Wei-Chung Allen and Lippincott-Schwartz, Jennifer and Mukhopadhyay, Saikat} } @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 {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 {69473, title = {SciJava Ops: An Improved Algorithms Framework for Fiji and Beyond}, journal = {Front. Bioinform.}, volume = {4}, year = {2024}, month = {2024 Sep 26}, abstract = {

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

}, doi = {10.3389/fbinf.2024.1435733}, url = {https://doi.org/10.3389/fbinf.2024.1435733 }, author = {Gabriel J. Selzer and Curtis T. Rueden and Mark C. Hiner and Edward L. Evans III and David Kolb and Marcel Wiedenmann and Christian Birkhold and Tim-Oliver Buchholz and Stefan Helfrich and Brian Northan and Alison Walter and Johannes Schindelin and Tobias Pietzsch and Stephan Saalfeld and Michael R. Berthold and Kevin W. Eliceiri} } @article {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 {69146, title = {Song Torrent: A modular, open-source 96-chamber audio and video recording apparatus with optogenetic activation and inactivation capabilities for Drosophila}, journal = {bioRxiv}, year = {2024}, month = {2024 Jan 10}, abstract = {

Background

Results

Implications

}, doi = {10.1101/2024.01.09.574712}, url = {https://doi.org/10.1101/2024.01.09.574712}, author = {Steve Sawtelle and Lakshmi Narayan and Yun Ding and Elizabeth Kim and Emily L. Behrman and Joshua L. Lillvis and Takashi Kawase and David L. Stern} } @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 {69282, title = {Three-dimensional spatio-angular fluorescence microscopy with a polarized dual-view inverted selective-plane illumination microscope (pol-diSPIM)}, journal = {bioRxiv}, year = {2024}, month = {2024 Mar 12}, abstract = {

Polarized fluorescence microscopy is a valuable tool for measuring molecular orientations, but techniques for recovering three-dimensional orientations and positions of fluorescent ensembles are limited. We report a polarized dual-view light-sheet system for determining the three-dimensional orientations and diffraction-limited positions of ensembles of fluorescent dipoles that label biological structures, and we share a set of visualization, histogram, and profiling tools for interpreting these positions and orientations. We model our samples, their excitation, and their detection using coarse-grained representations we call orientation distribution functions (ODFs). We apply ODFs to create physics-informed models of image formation with spatio-angular point-spread and transfer functions. We use theory and experiment to conclude that light-sheet tilting is a necessary part of our design for recovering all three-dimensional orientations. We use our system to extend known two-dimensional results to three dimensions in FM1-43-labelled giant unilamellar vesicles, fast-scarlet-labelled cellulose in xylem cells, and phalloidin-labelled actin in U2OS cells. Additionally, we observe phalloidin-labelled actin in mouse fibroblasts grown on grids of labelled nanowires and identify correlations between local actin alignment and global cell-scale orientation, indicating cellular coordination across length scales.Competing Interest StatementH.S., A.K., S.M., P.L.R., R.O., Y.W., and T.C. hold US Patent $\#$11428632.

}, doi = {10.1101/2024.03.09.584243}, url = {https://www.biorxiv.org/content/early/2024/03/12/2024.03.09.584243}, author = {Talon Chandler and Min Guo and Yijun Su and Jiji Chen and Yicong Wu and Junyu Liu and Atharva Agashe and Robert S. Fischer and Shalin B. Mehta and Abhishek Kumar and Tobias I. Baskin and Valentin Jamouille and Huafeng Liu and Vinay Swaminathan and Amrinder Nain and Rudolf Oldenbourg and Patrick La Riviere and Hari Shroff} } @article {69350, title = {Ultra-high density electrodes improve detection, yield, and cell type identification in neuronal recordings}, journal = {bioRxiv}, year = {2024}, month = {2024 Apr 10}, abstract = {

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

}, doi = {10.1101/2023.08.23.554527}, url = {https://www.biorxiv.org/content/early/2024/04/10/2023.08.23.554527}, author = {Zhiwen Ye and Andrew M Shelton and Jordan R Shaker and Julien M Boussard and Jennifer Colonell and Daniel Birman and Sahar Manavi and Susu Chen and Charlie Windolf and Cole Hurwitz and Tomoyuki Namima and Frederico Pedraja and Shahaf Weiss and Bogdan Raducanu and Torbj{\o}rn Ness and Xiaoxuan Jia and Giulia Mastroberardino and L. Federico Rossi and Matteo Carandini and Michael Hausser and Gaute T Einevoll and Gilles Laurent and Nathaniel B Sawtell and Wyeth Bair and Anitha Pasupathy and Carolina Mora-Lopez and Barun Dutta and Liam Paninski and Joshua H Siegle and Christof Koch and Shawn R Olsen and Timothy D Harris and Nicholas A Steinmetz} } @inbook {69316, title = {Visualization of Glutamatergic Neurotransmission in Diverse Model Organisms with Genetically Encoded Indicators}, booktitle = {New Technologies for Glutamate Interaction: Neurons and Glia}, volume = {2780}, number = {Neuromethods}, year = {2024}, pages = {3{\textendash}34}, publisher = {Humana}, organization = {Humana}, address = {New York, NY}, abstract = {

Glutamate is the principal excitatory neurotransmitter, and occasionally subserves inhibitory roles, in the vertebrate nervous system. Glutamatergic synapses are dense in the vertebrate brain, at \textasciitilde1/μm3. Glutamate is released from and onto diverse components of the nervous system, including neurons, glia, and other cells. Methods for glutamate detection are critically important for understanding the function of synapses and neural circuits in normal physiology, development, and disease. Here we describe the development, optimization, and deployment of genetically encoded fluorescent glutamate indicators. We review the theoretical considerations governing glutamate sensor properties from first principles of synapse biology, microscopy, and protein structure-function relationships. We provide case studies of the state-of-the-art iGluSnFR glutamate sensor, encompassing design and optimization, mechanism of action, in vivo imaging, data analysis, and future directions. We include detailed protocols for iGluSnFR imaging in common preparations (bacteria, cell culture, and brain slices) and model organisms (worm, fly, fish, rodent).

}, isbn = {978-1-0716-3742-5}, doi = {10.1007/978-1-0716-3742-5_1}, url = {https://doi.org/10.1007/978-1-0716-3742-5_1}, author = {Aggarwal, Abhi and Chan, Joyce and Waring, Amelia K. and Negrean, Adrian and Marvin, Jonathan S. and Podgorski, Kaspar and Looger, Loren L.}, editor = {Kukley, Maria} } @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 {68698, title = {3D architecture and a bi-cellular mechanism of touch detection in mechanosensory corpuscle}, journal = {Science Advances}, volume = {9}, year = {2023}, month = {2023 Sep 15}, pages = {eadi4147}, abstract = {

Mechanosensory corpuscles detect transient touch and vibratory signals in the skin of vertebrates, enabling navigation, foraging, and precise manipulation of objects1. The corpuscle core comprises a terminal neurite of a mechanoreceptor afferent, the only known touch-sensing element within corpuscles, surrounded by terminal Schwann cells called lamellar cells (LCs)2{\textendash}4. However, the precise corpuscular ultrastructure, and the role of LCs in touch detection are unknown. Here we used enhanced focused ion beam scanning electron microscopy and electron tomography to reveal the three-dimensional architecture of avian Meissner (Grandry) corpuscle5. We show that corpuscles contain a stack of LCs innervated by two afferents, which form large-area contacts with LCs. LCs form tether-like connections with the afferent membrane and contain dense core vesicles which release their content onto the afferent. Furthermore, by performing simultaneous electrophysiological recordings from both cell types, we show that mechanosensitive LCs use calcium influx to trigger action potential firing in the afferent and thus serve as physiological touch sensors in the skin. Our findings suggest a bi-cellular mechanism of touch detection, which comprises the afferent and LCs, likely enables corpuscles to encode the nuances of tactile stimuli.

}, doi = {10.1126/sciadv.adi4147}, url = {https://doi.org/10.1126/sciadv.adi4147}, author = {Yury A. Nikolaev and Luke H. Ziolkowski and Song Pang and Wei-Ping Li and Viktor V. Feketa and C. Shan Xu and Elena O. Gracheva and Sviatoslav N. Bagriantsev} } @article {68967, title = {All-optical reporting of chloride ion driving force in the nervous system}, journal = {bioRxiv}, year = {2023}, month = {2023 Sep 01}, abstract = {

Ionic driving forces provide the net electromotive force for ion movement across membranes and are therefore a fundamental property of all cells. In the nervous system, chloride driving force (DFCl) determines inhibitory signaling, as fast synaptic inhibition is mediated by chloride-permeable GABAA\ and glycine receptors. Here we present a new tool for all-Optical Reporting of CHloride Ion Driving force (ORCHID). We demonstrate ORCHID{\textquoteright}s ability to provide accurate, high-throughput measurements of resting and dynamic DFCl\ from genetically targeted cell types over a range of timescales. ORCHID confirms theoretical predictions about the biophysical mechanisms that establish DFCl, reveals novel differences in DFCl\ between neurons and astrocytes under different network conditions, and affords the first\ in vivo\ measurements of intact DFCl\ in mouse cortical neurons. This work extends our understanding of chloride homeostasis and inhibitory synaptic transmission and establishes a precedent for utilizing all-optical methods to assess ionic driving force.

}, doi = {10.1101/2023.08.30.555464}, url = {https://doi.org/10.1101/2023.08.30.555464}, author = {Joshua S. Selfe and Teresa J. S. Steyn and Eran F. Shorer and Richard J. Burman and Kira M. D{\"u}sterwald and Ahmed S. Abdelfattah and Eric R. Schreiter and Sarah E. Newey and Colin J. Akerman and Joseph V. Raimondo} } @article {69090, title = {All-optical reporting of inhibitory receptor driving force in the nervous system.}, journal = {bioRxiv}, year = {2023}, month = {2023 Nov 20}, abstract = {

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

}, doi = {10.1101/2023.08.30.555464}, url = {https://doi.org/10.1101/2023.08.30.555464}, author = {Joshua S. Selfe and Teresa J. S. Steyn and Eran F. Shorer and Richard J. Burman and Kira M. D{\"u}sterwald and Ahmed S. Abdelfattah and Eric R. Schreiter and Sarah E. Newey and Colin J. Akerman and Joseph V. Raimondo} } @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 {68964, title = {Brain wiring determinants uncovered by integrating connectomes and transcriptomes.}, journal = {Current Biology}, volume = {33}, year = {2023}, month = {2023 Aug 23}, pages = {3998-3998}, abstract = {

Advances in brain connectomics have demonstrated the extraordinary complexity of neural circuits. Developing neurons encounter the axons and dendrites of many different neuron types and form synapses with only a subset of them. During circuit assembly, neurons express cell-type-specific repertoires comprising many cell adhesion molecules (CAMs) that can mediate interactions between developing neurites. Many CAM families have been shown to contribute to brain wiring in different ways. It has been challenging, however, to identify receptor-ligand pairs directly matching neurons with their synaptic targets. Here, we integrated the synapse-level connectome of the neural circuit with the developmental expression patterns and binding specificities of CAMs on pre- and postsynaptic neurons in the Drosophila visual system. To overcome the complexity of neural circuits, we focus on pairs of genetically related neurons that make differential wiring choices. In the motion detection circuit, closely related subtypes of T4/T5 neurons choose between alternative synaptic targets in adjacent layers of neuropil. This choice correlates with the matching expression in synaptic partners of different receptor-ligand pairs of the Beat and Side families of CAMs. Genetic analysis demonstrated that presynaptic Side-II and postsynaptic Beat-VI restrict synaptic partners to the same layer. Removal of this receptor-ligand pair disrupts layers and leads to inappropriate targeting of presynaptic sites and postsynaptic dendrites. We propose that different Side/Beat receptor-ligand pairs collaborate with other recognition molecules to determine wiring specificities in the fly brain. Combining transcriptomes, connectomes, and protein interactome maps allow unbiased identification of determinants of brain wiring.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2023.08.020}, author = {Yoo, Juyoun and Dombrovski, Mark and Mirshahidi, Parmis and Nern, Aljoscha and LoCascio, Samuel A and Zipursky, S Lawrence and Kurmangaliyev, Yerbol Z} } @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 {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 {69092, title = {Different spectral sensitivities of ON- and OFF-motion pathways enhance the detection of approaching color objects in Drosophila.}, journal = {Nature Communications}, volume = {14}, year = {2023}, month = {2023 Nov 24}, pages = {7693}, abstract = {

Color and motion are used by many species to identify salient objects. They are processed largely independently, but color contributes to motion processing in humans, for example, enabling moving colored objects to be detected when their luminance matches the background. Here, we demonstrate an unexpected, additional contribution of color to motion vision in Drosophila. We show that behavioral ON-motion responses are more sensitive to UV than for OFF-motion, and we identify cellular pathways connecting UV-sensitive R7 photoreceptors to ON and OFF-motion-sensitive T4 and T5 cells, using neurogenetics and calcium imaging. Remarkably, this contribution of color circuitry to motion vision enhances the detection of approaching UV discs, but not green discs with the same chromatic contrast, and we show how this could generalize for systems with ON- and OFF-motion pathways. Our results provide a computational and circuit basis for how color enhances motion vision to favor the detection of saliently colored objects.

}, keywords = {Animals, Drosophila, Humans, Motion Perception, Photoreceptor Cells, Vision, Ocular}, issn = {2041-1723}, doi = {10.1038/s41467-023-43566-8}, author = {Longden, Kit D and Rogers, Edward M and Nern, Aljoscha and Dionne, Heather and Reiser, Michael B} } @article {69111, title = {Different spectral sensitivities of ON- and OFF-motion pathways enhance the detection of approaching color objects in Drosophila.}, journal = {Nature Communications}, volume = {14}, year = {2023}, month = {2023 Nov 24}, pages = {7693}, abstract = {

Color and motion are used by many species to identify salient objects. They are processed largely independently, but color contributes to motion processing in humans, for example, enabling moving colored objects to be detected when their luminance matches the background. Here, we demonstrate an unexpected, additional contribution of color to motion vision in Drosophila. We show that behavioral ON-motion responses are more sensitive to UV than for OFF-motion, and we identify cellular pathways connecting UV-sensitive R7 photoreceptors to ON and OFF-motion-sensitive T4 and T5 cells, using neurogenetics and calcium imaging. Remarkably, this contribution of color circuitry to motion vision enhances the detection of approaching UV discs, but not green discs with the same chromatic contrast, and we show how this could generalize for systems with ON- and OFF-motion pathways. Our results provide a computational and circuit basis for how color enhances motion vision to favor the detection of saliently colored objects.

}, keywords = {Animals, Drosophila, Humans, Motion Perception, Photoreceptor Cells, Vision, Ocular}, issn = {2041-1723}, doi = {10.1038/s41467-023-43566-8}, author = {Longden, Kit D and Rogers, Edward M and Nern, Aljoscha and Dionne, Heather and Reiser, Michael B} } @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 {68715, title = {Extracellular matrix assembly stress initiates Drosophila central nervous system morphogenesis.}, journal = {Developmental Cell}, year = {2023}, month = {2023 Apr 17}, abstract = {

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

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

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

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

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

}, issn = {1476-4687}, doi = {10.1038/s41586-023-05828-9}, author = {Zhang, Yan and Rozsa, Marton and Liang, Yajie and Bushey, Daniel and Wei, Ziqiang and Zheng, Jihong and Reep, Daniel and Broussard, Gerard Joey and Tsang, Arthur and Tsegaye, Getahun and Narayan, Sujatha and Obara, Christopher J and Lim, Jing-Xuan and Patel, Ronak and Zhang, Rongwei and Ahrens, Misha B and Turner, Glenn C and Wang, Samuel S-H and Korff, Wyatt L and Schreiter, Eric R and Svoboda, Karel and Hasseman, Jeremy P and Kolb, Ilya and Looger, Loren L} } @article {69076, title = {High-fidelity 3D live-cell nanoscopy through data-driven enhanced super-resolution radial fluctuation.}, journal = {Nature Methods}, year = {2023}, month = {2023 Nov 13}, abstract = {

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

}, issn = {1548-7105}, doi = {10.1038/s41592-023-02057-w}, author = {Laine, Romain F and Heil, Hannah S and Coelho, Simao and Nixon-Abell, Jonathon and Jimenez, Ang{\'e}lique and Wiesner, Theresa and Mart{\'\i}nez, Dami{\'a}n and Galgani, Tommaso and R{\'e}gnier, Louise and Stubb, Aki and Follain, Gautier and Webster, Samantha and Goyette, Jesse and Dauphin, Aurelien and Salles, Audrey and Culley, Si{\^a}n and Jacquemet, Guillaume and Hajj, Bassam and Leterrier, Christophe and Henriques, Ricardo} } @article {68697, title = {Identifying determinants of synaptic specificity by integrating connectomes and transcriptomes}, journal = {bioRxiv}, year = {2023}, month = {2023 Apr 04}, abstract = {

How do developing neurons select their synaptic partners? To identify molecules matching synaptic partners, we integrated the synapse-level connectome of neural circuits with the developmental expression patterns and binding specificities of cell adhesion molecules (CAMs) on pre- and postsynaptic neurons. We focused on parallel synaptic pathways in the Drosophila visual system, in which closely related neurons form synapses onto closely related target neurons. We show that the choice of synaptic partners correlates with the matching expression of receptor-ligand pairs of Beat and Side proteins of the immunoglobulin superfamily (IgSF) CAMs. Genetic analysis demonstrates that these proteins determine the choice between alternative synaptic targets. Combining transcriptomes, connectomes, and protein interactome maps provides a framework to uncover the molecular logic of synaptic connectivity.

}, doi = {10.1101/2023.04.03.534791}, url = {https://doi.org/10.1101/2023.04.03.534791}, author = {Juyoun Yoo and Mark Dombrovski and Parmis Mirshahidi and Aljoscha Nern and Samuel A. LoCascio and S. Lawrence Zipursky and Yerbol Z. Kurmangaliyev} } @article {69126, title = {Ketamine modulates a norepinephrine-astroglial circuit to persistently suppress futility-induced passivity.}, journal = {bioRxiv}, year = {2023}, month = {2023 Dec 29}, abstract = {

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

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

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

}, keywords = {Animals, Biosensing Techniques, Cells, Cultured, Fluorescence Resonance Energy Transfer, Lactic Acid, Mammals, Mice, Optical Imaging}, issn = {2041-1723}, doi = {10.1038/s41467-023-42230-5}, author = {Nasu, Yusuke and Aggarwal, Abhi and Le, Giang N T and Vo, Camilla Trang and Kambe, Yuki and Wang, Xinxing and Beinlich, Felix R M and Lee, Ashley Bomin and Ram, Tina R and Wang, Fangying and Gorzo, Kelsea A and Kamijo, Yuki and Boisvert, Marc and Nishinami, Suguru and Kawamura, Genki and Ozawa, Takeaki and Toda, Hirofumi and Gordon, Grant R and Ge, Shaoyu and Hirase, Hajime and Nedergaard, Maiken and Paquet, Marie-Eve and Drobizhev, Mikhail and Podgorski, Kaspar and Campbell, Robert E} } @article {68771, title = {Lipid flipping in the omega-3 fatty-acid transporter.}, journal = {Nature Communications}, volume = {14}, year = {2023}, month = {2023 May 08}, pages = {2571}, abstract = {

Mfsd2a is the transporter for docosahexaenoic acid (DHA), an omega-3 fatty acid, across the blood brain barrier (BBB). Defects in Mfsd2a are linked to ailments from behavioral and motor dysfunctions to microcephaly. Mfsd2a transports long-chain unsaturated fatty-acids, including DHA and α-linolenic acid (ALA), that are attached to the zwitterionic lysophosphatidylcholine (LPC) headgroup. Even with the recently determined structures of Mfsd2a, the molecular details of how this transporter performs the energetically unfavorable task of translocating and flipping lysolipids across the lipid bilayer remains unclear. Here, we report five single-particle cryo-EM structures of Danio rerio Mfsd2a (drMfsd2a): in the inward-open conformation in the ligand-free state and displaying lipid-like densities modeled as ALA-LPC at four distinct\ positions. These Mfsd2a snapshots detail the flipping mechanism for lipid-LPC from outer to inner membrane leaflet and release for membrane integration on the cytoplasmic side. These results also map Mfsd2a mutants that disrupt lipid-LPC transport and are associated with disease.

}, keywords = {Biological Transport, Blood-Brain Barrier, Docosahexaenoic Acids, Fatty Acids, Omega-3, Lysophosphatidylcholines, Membrane Transport Proteins, Symporters}, issn = {2041-1723}, doi = {10.1038/s41467-023-37702-7}, author = {Nguyen, Chi and Lei, Hsiang-Ting and Lai, Louis Tung Faat and Gallenito, Marc J and Mu, Xuelang and Matthies, Doreen and Gonen, Tamir} } @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 {68785, title = {Nanoparticle-based targeting of microglia improves the neural regeneration enhancing effects of immunosuppression in the zebrafish retina.}, journal = {Communications Biology}, volume = {6}, year = {2023}, month = {2023 May 18}, pages = {534}, abstract = {

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

}, keywords = {Animals, Dendrimers, Dexamethasone, Immunosuppression Therapy, Mammals, Mice, Microglia, Retina, Zebrafish}, issn = {2399-3642}, doi = {10.1038/s42003-023-04898-9}, author = {Emmerich, Kevin and White, David T and Kambhampati, Siva P and Casado, Grace L and Fu, Tian-Ming and Chunawala, Zeeshaan and Sahoo, Arpan and Nimmagadda, Saumya and Krishnan, Nimisha and Saxena, Meera T and Walker, Steven L and Betzig, Eric and Kannan, Rangaramanujam M and Mumm, Jeff S} } @article {68629, title = {A searchable image resource of Drosophila GAL4-driver expression patterns with single neuron resolution.}, journal = {eLife}, volume = {12}, year = {2023}, month = {2023 Feb 23}, abstract = {

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

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

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

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

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

}, issn = {08966273}, doi = {10.1016/j.neuron.2023.03.009}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0896627323002052}, author = {Abdelfattah, Ahmed S. and Zheng, Jihong and Singh, Amrita and Huang, Yi-Chieh and Reep, Daniel and Tsegaye, Getahun and Tsang, Arthur and Arthur, Benjamin J. and Rehorova, Monika and Olson, Carl V.L. and Shuai, Yichun and Zhang, Lixia and Fu, Tian-Ming and Milkie, Daniel E. and Moya, Maria V. and Weber, Timothy D. and Lemire, Andrew L. and Baker, Christopher A. and Falco, Natalie and Zheng, Qinsi and Grimm, Jonathan B. and Yip, Mighten C. and Walpita, Deepika and Chase, Martin and Campagnola, Luke and Murphy, Gabe J. and Wong, Allan M. and Forest, Craig R. and Mertz, Jerome and Economo, Michael N. and Turner, Glenn C. and Koyama, Minoru and Lin, Bei-Jung and Betzig, Eric and Novak, Ondrej and Lavis, Luke D. and Svoboda, Karel and Korff, Wyatt and Chen, Tsai-Wen and Schreiter, Eric R. and Hasseman, Jeremy P. and Kolb, Ilya} } @article {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 {68999, title = {Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions.}, journal = {Cell Reports}, volume = {42}, year = {2023}, month = {2023 Aug 24}, pages = {113015}, abstract = {

The execution of cognitive functions requires coordinated circuit activity across different brain areas that involves the associated firing of neuronal assemblies. Here, we tested the circuit mechanism behind assembly interactions between the hippocampus and the medial prefrontal cortex (mPFC) of adult rats by recording neuronal populations during a rule-switching task. We identified functionally coupled CA1-mPFC cells that synchronized their activity beyond that expected from common spatial coding or oscillatory firing. When such cell pairs fired together, the mPFC cell strongly phase locked to CA1 theta oscillations and maintained consistent theta firing phases, independent of the theta timing of their CA1 counterpart. These functionally connected CA1-mPFC cells formed interconnected assemblies. While firing together with their CA1 assembly partners, mPFC cells fired along specific theta sequences. Our results suggest that upregulated theta oscillatory firing of mPFC cells can signal transient interactions with specific CA1 assemblies, thus enabling distributed computations.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2023.113015}, author = {Nardin, Michele and Kaefer, Karola and Stella, Federico and Csicsvari, Jozsef} } @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 {68674, title = {Time-resolved correlation of distributed brain activity tracks E-I balance and accounts for diverse scale-free phenomena.}, journal = {Cell Reports}, volume = {42}, year = {2023}, month = {2023 Mar 24}, pages = {112254}, abstract = {

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

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

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

}, doi = {10.1101/2023.06.07.543976}, url = {https://doi.org/10.1101/2023.06.07.543976}, author = {H. S. J. Cheong and K. Eichler and T. Stuerner and S. K. Asinof and A. S. Champion and E. C. Marin and T. B. Oram and M. Sumathipala and L. Venkatasubramanian and S. Namiki and I. Siwanowicz and M. Costa and S. Berg and Janelia FlyEM Project Team and G. S. X. E. Jefferis and G. M. Card} } @article {68968, title = {Ultra-high density electrodes improve detection, yield, and cell type specificity of brain recordings.}, journal = {bioRxiv}, year = {2023}, month = {2023 Aug 25}, abstract = {

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

}, doi = {10.1101/2023.08.23.554527}, author = {Ye, Zhiwen and Shelton, Andrew M and Shaker, Jordan R and Boussard, Julien and Colonell, Jennifer and Manavi, Sahar and Chen, Susu and Windolf, Charlie and Hurwitz, Cole and Namima, Tomoyuki and Pedraja, Federico and Weiss, Shahaf and Raducanu, Bogdan and Ness, Torbj{\o}rn V and Einevoll, Gaute T and Laurent, Gilles and Sawtell, Nathaniel B and Bair, Wyeth and Pasupathy, Anitha and Mora Lopez, Carolina and Dutta, Barun and Paninski, Liam and Siegle, Joshua H and Koch, Christof and Olsen, Shawn R and Harris, Timothy D and Steinmetz, Nicholas A} } @article {68115, title = {Accurate angular integration with only a handful of neurons.}, journal = {bioRxiv}, year = {2022}, month = {2022 May 25}, abstract = {

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

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

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

}, doi = {10.1101/2022.05.04.490675}, author = {J. Cody Herron and Shiqiong Hu and Takashi Watanabe and Ana T. Nogueira and Bei Liu and Megan Kern and Jesse Aaron and Aaron Taylor and Michael Pablo and Teng-Leong Chew and Timothy C. Elston and Klaus M. Hahn} } @article {69715, title = {Best practice standards for circular RNA research}, journal = {Nature Methods}, volume = {19}, year = {2022}, month = {05/2022}, pages = {1208 - 1220}, abstract = {

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

}, issn = {1548-7091}, doi = {10.1038/s41592-022-01487-2}, url = {https://www.nature.com/articles/s41592-022-01487-2https://www.nature.com/articles/s41592-022-01487-2.pdfhttps://www.nature.com/articles/s41592-022-01487-2.pdfhttps://www.nature.com/articles/s41592-022-01487-2}, author = {Nielsen, Anne F. and Bindereif, Albrecht and Bozzoni, Irene and Hanan, Mor and Hansen, Thomas B. and Irimia, Manuel and Kadener, Sebastian and Kristensen, Lasse S. and Legnini, Ivano and Morlando, Mariangela and Jarlstad Olesen, Morten T. and Pasterkamp, R. Jeroen and Preibisch, Stephan and Rajewsky, Nikolaus and Suenkel, Christin and Kjems, J{\o}rgen} } @article {67828, title = {A brainstem integrator for self-localization and positional homeostasis}, journal = {Cell}, volume = {185}, year = {2022}, month = {2022 Dec 22}, pages = {5011-5027.e20}, abstract = {

To accurately track self-location, animals need to integrate their movements through space. In amniotes, representations of self-location have been found in regions such as the hippocampus. It is unknown whether more ancient brain regions contain such representations and by which pathways they may drive locomotion. Fish displaced by water currents must prevent uncontrolled drift to potentially dangerous areas. We found that larval zebrafish track such movements and can later swim back to their earlier location. Whole-brain functional imaging revealed the circuit enabling this process of positional homeostasis. Position-encoding brainstem neurons integrate optic flow, then bias future swimming to correct for past displacements by modulating inferior olive and cerebellar activity. Manipulation of position-encoding or olivary neurons abolished positional homeostasis or evoked behavior as if animals had experienced positional shifts. These results reveal a multiregional hindbrain circuit in vertebrates for optic flow integration, memory of self-location, and its neural pathway to behavior.Competing Interest StatementThe authors have declared no competing interest.

}, doi = {10.1101/2021.11.26.468907}, url = {https://www.biorxiv.org/content/early/2021/11/27/2021.11.26.468907}, author = {Yang, En and Zwart, Maarten F. and Rubinov, Mikail and James, Benjamin and Wei, Ziqiang and Narayan, Sujatha and Vladimirov, Nikita and Mensh, Brett D. and Fitzgerald, James E. and Ahrens, Misha B.} } @article {68502, title = {Channel-independent function of UNC-9/Innexin in spatial arrangement of GABAergic synapses in .}, journal = {eLife}, volume = {11}, year = {2022}, month = {2022 Nov 15}, abstract = {

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

}, keywords = {Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Connexins, Membrane Proteins, Motor Neurons, Synapses}, issn = {2050-084X}, doi = {10.7554/eLife.80555}, author = {Hendi, Ardalan and Niu, Long-Gang and Snow, Andrew William and Ikegami, Richard and Wang, Zhao-Wen and Mizumoto, Kota} } @article {67844, title = {ER proteins decipher the tubulin code to regulate organelle distribution.}, journal = {Nature}, volume = {601}, year = {2022}, month = {2022 Jan 01}, pages = {132-138}, abstract = {

Organelles move along differentially modified microtubules to establish and maintain their proper distributions and functions. However, how cells interpret these post-translational microtubule modification codes to selectively regulate organelle positioning remains largely unknown. The endoplasmic reticulum\ (ER) is an interconnected network of diverse morphologies that extends promiscuously throughout the cytoplasm, forming abundant contacts with other organelles. Dysregulation of endoplasmic reticulum morphology is tightly linked to neurologic disorders and cancer. Here we demonstrate that three membrane-bound endoplasmic reticulum proteins preferentially interact with different microtubule populations, with CLIMP63 binding centrosome microtubules, kinectin (KTN1) binding perinuclear polyglutamylated microtubules, and p180 binding glutamylated microtubules. Knockout of these proteins or manipulation of microtubule populations and glutamylation status results in marked changes in endoplasmic reticulum positioning, leading to similar redistributions of other organelles. During nutrient starvation, cells modulate CLIMP63 protein levels and p180-microtubule binding to bidirectionally move endoplasmic reticulum and lysosomes for proper autophagic responses.

}, issn = {1476-4687}, doi = {10.1038/s41586-021-04204-9}, author = {Zheng, Pengli and Obara, Christopher J and Szczesna, Ewa and Nixon-Abell, Jonathon and Mahalingan, Kishore K and Roll-Mecak, Antonina and Lippincott-Schwartz, Jennifer and Blackstone, Craig} } @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 {67848, title = {Fluorescence activation mechanism and imaging of drug permeation with new sensors for smoking-cessation ligands.}, journal = {eLife}, volume = {11}, year = {2022}, month = {2022 Jan 04}, abstract = {

Nicotinic partial agonists provide an accepted aid for smoking cessation and thus contribute to decreasing tobacco-related disease. Improved drugs constitute a continued area of study. However, there remains no reductionist method to examine the cellular and subcellular pharmacokinetic properties of these compounds in living cells. Here, we developed new intensity-based drug sensing fluorescent reporters ({\textquoteright}iDrugSnFRs{\textquoteright}) for the nicotinic partial agonists dianicline, cytisine, and two cytisine derivatives - 10-fluorocytisine and 9-bromo-10-ethylcytisine. We report the first atomic-scale structures of liganded periplasmic binding protein-based biosensors, accelerating development of iDrugSnFRs and also explaining the activation mechanism. The nicotinic iDrugSnFRs detect their drug partners in solution, as well as at the plasma membrane (PM) and in the endoplasmic reticulum (ER) of cell lines and mouse hippocampal neurons. At the PM, the speed of solution changes limits the growth and decay rates of the fluorescence response in almost all cases. In contrast, we found that rates of membrane crossing differ among these nicotinic drugs by \> 30 fold. The new nicotinic iDrugSnFRs provide insight into the real-time pharmacokinetic properties of nicotinic agonists and provide a methodology whereby iDrugSnFRs can inform both pharmaceutical neuroscience and addiction neuroscience.

}, issn = {2050-084X}, doi = {10.7554/eLife.74648}, author = {Nichols, Aaron L and Blumenfeld, Zack and Fan, ChengCheng and Luebbert, Laura and Blom, Annet Em and Cohen, Bruce N and Marvin, Jonathan S and Borden, Philip M and Kim, Charlene H and Muthusamy, Anand K and Shivange, Amol V and Knox, Hailey J and Campello, Hugo Rego and Wang, Jonathan H and Dougherty, Dennis A and Looger, Loren L and Gallagher, Timothy and Rees, Douglas C and Lester, Henry A} } @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 {68422, title = {Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly.}, journal = {Science}, volume = {375}, year = {2022}, month = {03/2022}, pages = {eabk2432}, abstract = {

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

}, keywords = {Animals, Cell Nucleus, Databases, Genetic, Drosophila melanogaster, Drosophila Proteins, Female, Gene Expression Regulation, Gene Regulatory Networks, Genes, Insect, Male, RNA-Seq, Sex Characteristics, Single-Cell Analysis, Transcription Factors, Transcriptome}, issn = {1095-9203}, doi = {10.1126/science.abk2432}, author = {Li, Hongjie and Janssens, Jasper and De Waegeneer, Maxime and Kolluru, Sai Saroja and Davie, Kristofer and Gardeux, Vincent and Saelens, Wouter and David, Fabrice P A and Brbi{\'c}, Maria and Spanier, Katina and Leskovec, Jure and McLaughlin, Colleen N and Xie, Qijing and Jones, Robert C and Brueckner, Katja and Shim, Jiwon and Tattikota, Sudhir Gopal and Schnorrer, Frank and Rust, Katja and Nystul, Todd G and Carvalho-Santos, Zita and Ribeiro, Carlos and Pal, Soumitra and Mahadevaraju, Sharvani and Przytycka, Teresa M and Allen, Aaron M and Goodwin, Stephen F and Berry, Cameron W and Fuller, Margaret T and White-Cooper, Helen and Matunis, Erika L and DiNardo, Stephen and Galenza, Anthony and O{\textquoteright}Brien, Lucy Erin and Dow, Julian A T and Jasper, Heinrich and Oliver, Brian and Perrimon, Norbert and Deplancke, Bart and Quake, Stephen R and Luo, Liqun and Aerts, Stein and Agarwal, Devika and Ahmed-Braimah, Yasir and Arbeitman, Michelle and Ariss, Majd M and Augsburger, Jordan and Ayush, Kumar and Baker, Catherine C and Banisch, Torsten and Birker, Katja and Bodmer, Rolf and Bolival, Benjamin and Brantley, Susanna E and Brill, Julie A and Brown, Nora C and Buehner, Norene A and Cai, Xiaoyu Tracy and Cardoso-Figueiredo, Rita and Casares, Fernando and Chang, Amy and Clandinin, Thomas R and Crasta, Sheela and Desplan, Claude and Detweiler, Angela M and Dhakan, Darshan B and Don{\`a}, Erika and Engert, Stefanie and Floc{\textquoteright}hlay, Swann and George, Nancy and Gonz{\'a}lez-Segarra, Amanda J and Groves, Andrew K and Gumbin, Samantha and Guo, Yanmeng and Harris, Devon E and Heifetz, Yael and Holtz, Stephen L and Horns, Felix and Hudry, Bruno and Hung, Ruei-Jiun and Jan, Yuh Nung and Jaszczak, Jacob S and Jefferis, Gregory S X E and Karkanias, Jim and Karr, Timothy L and Katheder, Nadja Sandra and Kezos, James and Kim, Anna A and Kim, Seung K and Kockel, Lutz and Konstantinides, Nikolaos and Kornberg, Thomas B and Krause, Henry M and Labott, Andrew Thomas and Laturney, Meghan and Lehmann, Ruth and Leinwand, Sarah and Li, Jiefu and Li, Joshua Shing Shun and Li, Kai and Li, Ke and Li, Liying and Li, Tun and Litovchenko, Maria and Liu, Han-Hsuan and Liu, Yifang and Lu, Tzu-Chiao and Manning, Jonathan and Mase, Anjeli and Matera-Vatnick, Mikaela and Matias, Neuza Reis and McDonough-Goldstein, Caitlin E and McGeever, Aaron and McLachlan, Alex D and Moreno-Roman, Paola and Neff, Norma and Neville, Megan and Ngo, Sang and Nielsen, Tanja and O{\textquoteright}Brien, Caitlin E and Osumi-Sutherland, David and Ozel, Mehmet Neset and Papatheodorou, Irene and Petkovic, Maja and Pilgrim, Clare and Pisco, Angela Oliveira and Reisenman, Carolina and Sanders, Erin Nicole and Dos Santos, Gilberto and Scott, Kristin and Sherlekar, Aparna and Shiu, Philip and Sims, David and Sit, Rene V and Slaidina, Maija and Smith, Harold E and Sterne, Gabriella and Su, Yu-Han and Sutton, Daniel and Tamayo, Marco and Tan, Michelle and Tastekin, Ibrahim and Treiber, Christoph and Vacek, David and Vogler, Georg and Waddell, Scott and Wang, Wanpeng and Wilson, Rachel I and Wolfner, Mariana F and Wong, Yiu-Cheung E and Xie, Anthony and Xu, Jun and Yamamoto, Shinya and Yan, Jia and Yao, Zepeng and Yoda, Kazuki and Zhu, Ruijun and Zinzen, Robert P} } @article {67952, title = {A functionally ordered visual feature map in the Drosophila brain.}, journal = {Neuron}, volume = {110}, year = {2022}, month = {2022 May 18}, pages = {1700}, abstract = {

Topographic maps, the systematic spatial ordering of neurons by response tuning, are common across species. In Drosophila, the lobula columnar (LC) neuron types project from the optic lobe to the central brain, where each forms a glomerulus in a distinct position. However, the advantages of this glomerular arrangement are unclear. Here, we examine the functional and spatial relationships of 10 glomeruli using single-neuron calcium imaging. We discover novel detectors for objects smaller than the lens resolution (LC18) and for complex line motion (LC25). We find that glomeruli are spatially clustered by selectivity for looming versus drifting object motion and ordered by size tuning to form a topographic visual feature map. Furthermore, connectome analysis shows that downstream neurons integrate from sparse subsets of possible glomeruli combinations, which are biased for glomeruli encoding similar features. LC neurons are thus an explicit example of distinct feature detectors topographically organized to facilitate downstream circuit integration.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2022.02.013}, author = {Klapoetke, Nathan C and Nern, Aljoscha and Rogers, Edward M and Rubin, Gerald M and Reiser, Michael B and Card, Gwyneth M} } @article {68414, title = {High-throughput automated methods for classical and operant conditioning of larvae.}, journal = {eLife}, volume = {11}, year = {2022}, month = {2022 Oct 28}, abstract = {

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

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

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

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

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

}, issn = {1999-4915}, doi = {10.3390/v14020177}, author = {Munshi, Sneha and Neupane, Krishna and Ileperuma, Sandaru M and Halma, Matthew T J and Kelly, Jamie A and Halpern, Clarissa F and Dinman, Jonathan D and Loerch, Sarah and Woodside, Michael T} } @article {68420, title = {KIRCD8 T cells suppress pathogenic T cells and are active in autoimmune diseases and COVID-19.}, journal = {Science}, volume = {376}, year = {2022}, month = {04/2022}, pages = {eabi9591}, abstract = {

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

}, keywords = {Animals, Autoimmune Diseases, CD8-Positive T-Lymphocytes, COVID-19, Humans, Mice, Receptors, KIR, T-Lymphocytes, Regulatory}, issn = {1095-9203}, doi = {10.1126/science.abi9591}, author = {Li, Jing and Zaslavsky, Maxim and Su, Yapeng and Guo, Jing and Sikora, Michael J and van Unen, Vincent and Christophersen, Asbj{\o}rn and Chiou, Shin-Heng and Chen, Liang and Li, Jiefu and Ji, Xuhuai and Wilhelmy, Julie and McSween, Alana M and Palanski, Brad A and Mallajosyula, Venkata Vamsee Aditya and Bracey, Nathan A and Dhondalay, Gopal Krishna R and Bhamidipati, Kartik and Pai, Joy and Kipp, Lucas B and Dunn, Jeffrey E and Hauser, Stephen L and Oksenberg, Jorge R and Satpathy, Ansuman T and Robinson, William H and Dekker, Cornelia L and Steinmetz, Lars M and Khosla, Chaitan and Utz, Paul J and Sollid, Ludvig M and Chien, Yueh-Hsiu and Heath, James R and Fernandez-Becker, Nielsen Q and Nadeau, Kari C and Saligrama, Naresha and Davis, Mark M} } @article {68021, title = {Long-term imaging reveals behavioral plasticity during C. elegans dauer exit}, journal = {BMC Biology}, volume = {20}, year = {2022}, month = {2022 Dec 13}, pages = {277}, abstract = {

During their lifetime, animals must adapt their behavior to survive in changing environments. This ability requires the nervous system to adjust through dynamic expression of neurotransmitters and receptors but also through growth, spatial reorganization and connectivity while integrating external stimuli. For instance, despite having a fixed neuronal cell lineage, the nematode\ Caenorhabditis elegans{\textquoteright}\ nervous system remains plastic throughout its development. Here, we focus on a specific example of nervous system plasticity, the\ C. elegans\ dauer exit decision. Under unfavorable conditions, larvae will enter the non-feeding and non-reproductive dauer stage and adapt their behavior to cope with a new environment. Upon improved conditions, this stress resistant developmental stage is actively reversed to resume reproductive development. However, how different environmental stimuli regulate the exit decision mechanism and thereby drive the larva{\textquoteright}s behavioral change is unknown. To fill this gap, we developed a new open hardware method for long-term imaging (12h) of\ C. elegans\ larvae. We identified dauer-specific behavioral motifs and characterized the behavioral trajectory of dauer exit in different environments to identify key decision points. Combining long-term behavioral imaging with transcriptomics, we find that bacterial ingestion triggers a change in neuropeptide gene expression to establish post-dauer behavior. Taken together, we show how a developing nervous system can robustly integrate environmental changes, activate a developmental switch and adapt the organism{\textquoteright}s behavior to a new environment.

}, doi = {10.1186/s12915-022-01471-4}, url = {https://doi.org/10.1186/s12915-022-01471-4}, author = {Friedrich Preusser and Anika Neuschulz and Jan Philipp Junker and Nikolaus Rajewsky and Stephan Preibisch} } @article {68301, title = {Molecular cartography: charting the sea of molecular organization in live synapses with nanoscale precision}, journal = {Biophysical Journal}, volume = {121}, year = {2022}, month = {2022 Feb 01}, pages = {302a}, abstract = {

Understanding live-cell behavior in part requires high precision mapping of molecular species in 3-D dynamic environments. Approaches like single-molecule localization microscopy (SMLM) offer high promise for challenges posed by molecular cartography. Effectively, the precision of these approaches is dependent on the how many photons / second a fluorescent marker is capable of emitting. For this reason, many SRLM experiments are typically done using fluorescent organic dyes (such as Alexa Fluors) in reducing chemical environments which cause some organic dyes to stochastically cycle through dark states, allowing single-molecule localization (e.g. (d)STORM). The need to couple these dyes to antibodies and the harsh reducing conditions makes their application to live cell work problematic. To overcome these limitations, we made use of modifications to Janelia Fluor-based dyes which make them spontaneously cycle through dark states (blink) under physiological imaging conditions. The dyes are spectrally compatible with photo-activatable fluorescent proteins such as mEos and allow for simultaneous 2-color superresolution microscopy. When conjugated to a HaloTag, these artificial dyes can bind genetically encodable targets in live samples, allowing subsequent measurement in a live-cell environment. To correct for nanoscale chromatic aberrations we developed a new machine-learning based approach with reconstruction errors below achievable localization precisions. We show that these methods allow the reconstruction of live synapse surfaces and a variety of the associated molecular machineries with up to 50 nm accuracy in 3 dimensions.

}, issn = {00063495}, doi = {10.1016/j.bpj.2021.11.1246}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0006349521022219}, author = {Nelson, Andrew J. and Zheng, Qinsi and Lavis, Luke D. and Ryan, Timothy A.} } @article {68315, title = {Motion of single molecular tethers reveals dynamic subdomains at ER-mitochondria contact sites}, journal = {bioRxiv}, year = {2022}, month = {2022 Sep 03}, abstract = {

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

}, doi = {10.1101/2022.09.03.505525}, url = {https://doi.org/10.1101/2022.09.03.505525}, author = {Christopher J. Obara and Jonathon Nixon-Abell and Andrew S. Moore and Federica Riccio and David P. Hoffman and Gleb Shtengel and C. Shan Xu and Kathy Schaefer and H. Amalia Pasolli and Jean-Baptiste Masson and Harald F. Hess and Christopher P. Calderon and Craig Blackstone and Jennifer Lippincott-Schwartz} } @article {68413, title = {Muscles that move the retina augment compound eye vision in Drosophila.}, journal = {Nature}, year = {2022}, month = {2022 Oct 26}, abstract = {

Most animals have compound eyes, with tens to thousands of lenses attached rigidly to the exoskeleton. A natural assumption is that all of these species must resort to moving either their head or\ their body to actively change their visual input. However, classic anatomy has revealed that flies have muscles poised to move their retinas under the stable lenses of each compound eye. Here we show that Drosophila use their retinal muscles to smoothly track visual motion, which helps to stabilize the retinal image, and also to perform small saccades when viewing a stationary scene. We show that when the retina moves, visual receptive fields shift accordingly, and that even the smallest retinal saccades activate visual neurons. Using a head-fixed behavioural paradigm, we find that Drosophila perform binocular, vergence movements of their retinas-which could enhance depth perception-when crossing gaps, and impairing the physiology of retinal motor neurons alters gap-crossing trajectories during free behaviour. That flies evolved an ability to actuate their retinas suggests that moving the eye independently of the head is broadly paramount for animals. The similarities of smooth and saccadic movements of the Drosophila retina and the vertebrate eye highlight a notable example of convergent evolution.

}, issn = {1476-4687}, doi = {10.1038/s41586-022-05317-5}, author = {Fenk, Lisa M and Avritzer, Sofia C and Weisman, Jazz L and Nair, Aditya and Randt, Lucas D and Mohren, Thomas L and Siwanowicz, Igor and Maimon, Gaby} } @article {68272, title = {neuPrint: An open access tool for EM connectomics.}, journal = {Frontiers in Neuroinformatics}, volume = {16}, year = {2022}, month = {2022 Jul 20}, pages = {896292}, abstract = {

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

}, issn = {1662-5196}, doi = {10.3389/fninf.2022.896292}, author = {Plaza, Stephen M and Clements, Jody and Dolafi, Tom and Umayam, Lowell and Neubarth, Nicole N and Scheffer, Louis K and Berg, Stuart} } @article {68273, title = {Neural network organization for courtship-song feature detection in Drosophila.}, journal = {Current Biology}, volume = {32}, year = {2022}, month = {2022 Aug 08}, pages = {3317-3333.e7}, abstract = {

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

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

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

}, keywords = {Data Science, Ecosystem, Humans, Metadata, Neurophysiology, Software}, issn = {2050-084X}, doi = {10.7554/eLife.78362}, author = {Rubel, Oliver and Tritt, Andrew and Ly, Ryan and Dichter, Benjamin K and Ghosh, Satrajit and Niu, Lawrence and Baker, Pamela and Soltesz, Ivan and Ng, Lydia and Svoboda, Karel and Frank, Loren and Bouchard, Kristofer E} } @article {68225, title = {Neuronal circuits integrating visual motion information in Drosophila melanogaster.}, journal = {Current Biology}, volume = {32}, year = {2022}, month = {2022 Aug 22}, pages = {3529-3544}, abstract = {

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

}, issn = {1879-0445}, doi = {10.1016/j.cub.2022.06.061}, author = {Shinomiya, Kazunori and Nern, Aljoscha and Meinertzhagen, Ian A and Plaza, Stephen M and Reiser, Michael B} } @article {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 {67930, title = {Online learning for orientation estimation during translation in an insect ring attractor network.}, journal = {Scientific Reports}, volume = {12}, year = {2022}, month = {2022 Feb 25}, pages = {3210}, abstract = {

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

}, issn = {2045-2322}, doi = {10.1038/s41598-022-05798-4}, author = {Robinson, Brian S and Norman-Tenazas, Raphael and Cervantes, Martha and Symonette, Danilo and Johnson, Erik C and Joyce, Justin and Rivlin, Patricia K and Hwang, Grace and Zhang, Kechen and Gray-Roncal, William} } @article {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 {67892, title = {A population of descending neurons that regulates the flight motor of Drosophila.}, journal = {Current Biology}, volume = {32}, year = {2022}, month = {2022 Mar 14}, pages = {1189-1196}, abstract = {

Similar to many insect species, Drosophila melanogaster is capable of maintaining a stable flight trajectory for periods lasting up to several hours. Because aerodynamic torque is roughly proportional to the fifth power of wing length, even small asymmetries in wing size require the maintenance of subtle bilateral differences in flapping motion to maintain a stable path. Flies can even fly straight after losing half of a wing, a feat they accomplish via very large, sustained kinematic changes to both the damaged and intact wings. Thus, the neural network responsible for stable flight must be capable of sustaining fine-scaled control over wing motion across a large dynamic range. In this study, we describe an unusual type of descending neuron (DNg02) that projects directly from visual output regions of the brain to the dorsal flight neuropil of the ventral nerve cord. Unlike many descending neurons, which exist as single bilateral pairs with unique morphology, there is a population of at least 15 DNg02 cell pairs with nearly identical shape. By optogenetically activating different numbers of DNg02 cells, we demonstrate that these neurons regulate wingbeat amplitude over a wide dynamic range via a population code. Using two-photon functional imaging, we show that DNg02 cells are responsive to visual motion during flight in a manner that would make them well suited to continuously regulate bilateral changes in wing kinematics. Collectively, we have identified a critical set of descending neurons that provides the sensitivity and dynamic range required for flight control.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2022.01.008}, author = {Namiki, Shigehiro and Ros, Ivo G and Morrow, Carmen and Rowell, William J and Card, Gwyneth M and Korff, Wyatt and Dickinson, Michael H} } @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 {68370, title = {A proliferative to invasive switch is mediated by srGAP1 downregulation through the activation of TGF-β2 signaling.}, journal = {Cell Reports}, volume = {40}, year = {2022}, month = {2022 Sep 20}, pages = {111358}, abstract = {

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

}, keywords = {Actins, Animals, Cell Line, Tumor, Down-Regulation, Mice, Transforming Growth Factor beta2, Zebrafish}, issn = {2211-1247}, doi = {10.1016/j.celrep.2022.111358}, author = {Mondal, Chandrani and Gacha-Garay, Majo J and Larkin, Kathryn A and Adikes, Rebecca C and Di Martino, Julie S and Chien, Chen-Chi and Fraser, Madison and Eni-Aganga, Ireti and Agullo-Pascual, Esperanza and Cialowicz, Katarzyna and Ozbek, Umut and Naba, Alexandra and Gaitas, Angelo and Fu, Tian-Ming and Upadhyayula, Srigokul and Betzig, Eric and Matus, David Q and Martin, Benjamin L and Bravo-Cordero, Jose Javier} } @article {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 {68278, title = {Selective Serotonin Reuptake Inhibitors Within Cells: Temporal Resolution in Cytoplasm, Endoplasmic Reticulum, and Membrane}, journal = {bioRxiv}, year = {2022}, month = {2022 Aug 12}, abstract = {

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

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

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

}, issn = {1545-7885}, doi = {10.1371/journal.pbio.3001772}, author = {Wu, Sheng-Yi and Wen, Yurong and Serre, Nelson B C and Laursen, Cathrine Charlotte Heiede and Dietz, Andrea Grost{\o}l and Taylor, Brian R and Drobizhev, Mikhail and Molina, Rosana S and Abhi Aggarwal and Rancic, Vladimir and Becker, Michael and Ballanyi, Klaus and Podgorski, Kaspar and Hirase, Hajime and Nedergaard, Maiken and Fendrych, Maty{\'a}{\v s} and Lemieux, M Joanne and Eberl, Daniel F and Kay, Alan R and Campbell, Robert E and Shen, Yi} } @article {68222, title = {Structured sampling of olfactory input by the fly mushroom body.}, journal = {Current Biology}, volume = {32}, year = {2022}, month = {2022 Aug 08}, pages = {3334-3349.e6}, abstract = {

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

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

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

}, issn = {1097-2765}, doi = {https://doi.org/10.1016/j.molcel.2021.11.011}, url = {https://www.sciencedirect.com/science/article/pii/S1097276521009904}, author = {Daoud Sheban and Tom Shani and Roey Maor and Alejandro Aguilera-Castrejon and Nofar Mor and Bernardo Oldak and Merav D. Shmueli and Avital Eisenberg-Lerner and Jonathan Bayerl and Jakob Hebert and Sergey Viukov and Guoyun Chen and Assaf Kacen and Vladislav Krupalnik and Valeriya Chugaeva and Shadi Tarazi and Alejandra Rodr{\'\i}guez-delaRosa and Mirie Zerbib and Adi Ulman and Solaiman Masarwi and Meital Kupervaser and Yishai Levin and Efrat Shema and Yael David and Noa Novershtern and Jacob H. Hanna and Yifat Merbl} } @article {67928, title = {Three Mutations Convert the Selectivity of a Protein Sensor From Nicotinic Agonists to S-Methadone For Use in Cells, Organelles, and Biofluids.}, journal = {Journal of the American Chemical Society}, volume = {144}, year = {2022}, month = {2022 May 18}, abstract = {

We report a reagentless, intensity-based S-methadone fluorescent sensor, iS-methadoneSnFR, consisting of a circularly permuted GFP inserted within the sequence of a mutated bacterial periplasmic binding protein (PBP). We used directed evolution to convert a previously reported nicotine-binding PBP to a selective S-methadone-binding sensor, via three mutations in the PBP{\textquoteright}s second shell and hinge regions. iS-methadoneSnFR displays sensitivity across the pharmacologically relevant range and selectivity against endogenous analytes and other opioids. Robust iS-methadoneSnFR responses in human sweat and saliva and mouse serum enable diagnostic uses. Genetic encoding and imaging in mammalian demonstrated the acid trapping of S-methadone in the Golgi apparatus where opioid receptors can signal. This work shows a straightforward strategy in adapting existing PBPs to serve real-time applications ranging from subcellular to personal pharmacokinetics.

}, doi = {10.1101/2022.02.24.481226}, author = {Anand K. Muthusamy and Charlene H. Kim and Scott C. Virgil and Hailey J. Knox and Jonathan S. Marvin and Aaron L. Nichols and Bruce N. Cohen and Dennis A. Dougherty and Loren L. Looger and Henry A. Lester} } @article {67988, title = {Transverse endoplasmic reticulum expansion in hereditary spastic paraplegia corticospinal axons.}, journal = {Human Molecular Genetics}, year = {2022}, month = {2022 Mar 26}, abstract = {

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

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

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

}, keywords = {Animals, Axons, Disease Models, Animal, Endoplasmic Reticulum, GTP Phosphohydrolases, Humans, Membrane Proteins, Membrane Transport Proteins, Mice, Mice, Knockout, Mutation, Spastic Paraplegia, Hereditary, Spastin}, issn = {1460-2083}, doi = {10.1093/hmg/ddac072}, author = {Zhu, Peng-Peng and Hung, Hui-Fang and Batchenkova, Natalia and Nixon-Abell, Jonathon and Henderson, James and Zheng, Pengli and Renvois{\'e}, Benoit and Pang, Song and Xu, C Shan and Saalfeld, Stephan and Funke, Jan and Xie, Yuxiang and Svara, Fabian and Hess, Harald F and Blackstone, Craig} } @article {68812, title = {A viral toolbox for conditional and transneuronal gene expression in zebrafish}, journal = {eLife}, volume = {11}, year = {2022}, month = {07/2022}, pages = {e77153}, abstract = {

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

}, keywords = {Gene Transfer, Imaging, neuronal circuit, viral vector}, issn = {2050-084X}, doi = {10.7554/eLife.77153}, url = {https://doi.org/10.7554/eLife.77153}, author = {Satou, Chie and Neve, Rachael L and Oyibo, Hassana K and Zmarz, Pawel and Huang, Kuo-Hua and Arn Bouldoires, Estelle and Mori, Takuma and Higashijima, Shin-Ichi and Keller, Georg B and Friedrich, Rainer W}, editor = {Bagnall, Martha W and Stainier, Didier YR and Jin, Lei} } @article {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 {67304, title = {Activity-dependent Golgi satellite formation in dendrites reshapes the neuronal surface glycoproteome}, journal = {bioRxiv}, year = {2021}, month = {05/2021}, abstract = {

Activity-driven changes in the neuronal surface glycoproteome are known to occur with synapse formation, plasticity and related diseases, but their mechanistic basis and significance are unclear. Here, we observed that N-glycans on surface glycoproteins of dendrites shift from immature to mature forms containing sialic acid in response to increased neuronal excitation. In exploring the basis of these N-glycosylation alterations, we discovered they result from the growth and proliferation of Golgi satellites scattered throughout the dendrite. Golgi satellites that formed with neuronal excitation were in close association with ER exit sites and early endosomes and contained glycosylation machinery without the Golgi structural protein, GM130. They functioned as distal glycosylation stations in dendrites, terminally modifying sugars either on newly synthesized glycoproteins passing through the secretory pathway, or on surface glycoproteins taken up from the endocytic pathway. These activities led to major changes in the dendritic surface of excited neurons, impacting binding and uptake of lectins, as well as causing functional changes in neurotransmitter receptors such as nicotinic acetylcholine receptors. Neural activity thus boosts the activity of the dendrite{\textquoteright}s satellite micro-secretory system by redistributing Golgi enzymes involved in glycan modifications into peripheral Golgi satellites. This remodeling of the neuronal surface has potential significance for synaptic plasticity, addiction and disease.Competing Interest StatementThe authors have declared no competing interest.

}, doi = {10.1101/2021.04.06.438745}, url = {https://doi.org/10.1101/2021.04.06.438745}, author = {Govind, Anitha P. and Jeyifous, Okunola and Russell, Theron A. and Yi, Zola and Weigel, Aubrey V. and Ramaprasad, Abhijit and Newell, Luke and Ramos, William and Valbuena, Fernando M. and Casler, Jason C. and Yan, Jing-Zhi and Glick, Benjamin S. and Swanson, Geoffrey T. and Lippincott-Schwartz, Jennifer and Green, William N.} } @article {67733, title = {Activity-dependent Golgi satellite formation in dendrites reshapes the neuronal surface glycoproteome.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Sep 21}, abstract = {

Activity-driven changes in the neuronal surface glycoproteome are known to occur with synapse formation, plasticity and related diseases, but their mechanistic basis and significance are unclear. Here, we observed that -glycans on surface glycoproteins of dendrites shift from immature to mature forms containing sialic acid in response to increased neuronal activation. In exploring the basis of these -glycosylation alterations, we discovered they result from the growth and proliferation of Golgi satellites scattered throughout the dendrite. Golgi satellites that formed during neuronal excitation were in close association with ER exit sites and early endosomes and contained glycosylation machinery without the Golgi structural protein, GM130. They functioned as distal glycosylation stations in dendrites, terminally modifying sugars either on newly synthesized glycoproteins passing through the secretory pathway, or on surface glycoproteins taken up from the endocytic pathway. These activities led to major changes in the dendritic surface of excited neurons, impacting binding and uptake of lectins, as well as causing functional changes in neurotransmitter receptors such as nicotinic acetylcholine receptors. Neural activity thus boosts the activity of the dendrite{\textquoteright}s satellite micro-secretory system by redistributing Golgi enzymes involved in glycan modifications into peripheral Golgi satellites. This remodeling of the neuronal surface has potential significance for synaptic plasticity, addiction and disease.

}, issn = {2050-084X}, doi = {10.7554/eLife.68910}, author = {Govind, Anitha P and Jeyifous, Okunola and Russell, Theron A and Yi, Zola and Weigel, Aubrey V and Ramaprasad, Abhijit and Newell, Luke and Ramos, William and Valbuena, Fernando M and Casler, Jason C and Yan, Jing-Zhi and Glick, Benjamin S and Swanson, Geoffrey T and Lippincott-Schwartz, Jennifer and Green, William N} } @article {67763, title = {An adaptive optics module for deep tissue multiphoton imaging in vivo.}, journal = {Nature Methods}, volume = {18}, year = {2021}, month = {2021 Oct 01}, pages = {1259-1264}, abstract = {

Understanding complex biological systems requires visualizing structures and processes deep within living organisms. We developed a compact adaptive optics module and incorporated it into two- and three-photon fluorescence microscopes, to measure and correct tissue-induced aberrations. We resolved synaptic structures in deep cortical and subcortical areas of the mouse brain, and demonstrated high-resolution imaging of neuronal structures and somatosensory-evoked calcium responses in the mouse spinal cord at great depths in vivo.

}, issn = {1548-7105}, doi = {10.1038/s41592-021-01279-0}, author = {Rodriguez, Cristina and Chen, Anderson and Rivera, Jos{\'e} A and Mohr, Manuel A and Liang, Yajie and Natan, Ryan G and Sun, Wenzhi and Milkie, Daniel E and Bifano, Thomas G and Chen, Xiaoke and Ji, Na} } @article {67298, title = {Adhesion-mediated mechanosignaling forces mitohormesis.}, journal = {Cell Metabolism}, volume = {33}, year = {2021}, month = {2021 July 6}, pages = {1322}, abstract = {

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

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

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

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

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

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

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

}, issn = {1097-4172}, doi = {10.1016/j.cell.2021.09.026}, author = {Liu, Bei and Stone, Orrin J and Pablo, Michael and Herron, J Cody and Nogueira, Ana T and Dagliyan, Onur and Grimm, Jonathan B and Lavis, Luke D and Elston, Timothy C and Hahn, Klaus M} } @article {67696, title = {Campylobacter jejuni Triggers Signaling through Host Cell Focal Adhesions To Inhibit Cell Motility.}, journal = {mBio}, year = {2021}, month = {2021 Aug 24}, pages = {e0149421}, abstract = {

Campylobacter jejuni is a major foodborne pathogen that exploits the focal adhesions of intestinal cells to promote invasion and cause severe gastritis. Focal adhesions are multiprotein complexes involved in bidirectional signaling between the actin cytoskeleton and the extracellular matrix. We investigated the dynamics of focal adhesion structure and function in C. jejuni-infected cells using a comprehensive set of approaches, including confocal microscopy of live and fixed cells, immunoblotting, and superresolution interferometric photoactivated localization microscopy (iPALM). We found that C. jejuni infection of epithelial cells results in increased focal adhesion size and altered topology. These changes resulted in a persistent modulatory effect on the host cell focal adhesion, evidenced by an increase in cell adhesion strength, a decrease in individual cell motility, and a reduction in collective cell migration. We discovered that C. jejuni infection causes an increase in phosphorylation of paxillin and an alteration of paxillin turnover at the focal adhesion, which together represent a potential mechanistic basis for altered cell motility. Finally, we observed that infection of epithelial cells with the C. jejuni wild-type strain in the presence of a protein synthesis inhibitor, a C. jejuni CadF and FlpA fibronectin-binding protein mutant, or a C. jejuni flagellar export mutant blunts paxillin phosphorylation and partially reestablishes individual host cell motility and collective cell migration. These findings provide a potential mechanism for the restricted intestinal repair observed in C. jejuni-infected animals and raise the possibility that bacteria targeting extracellular matrix components can alter cell behavior after binding and internalization by manipulating focal adhesions. Campylobacter jejuni is a major foodborne pathogen that causes severe gastritis. We investigated the dynamics of focal adhesion structure and function in C. jejuni-infected epithelial cells. Focal adhesions act as signaling complexes that connect the extracellular matrix to the intracellular cytoskeleton. The key findings of this study show that C. jejuni changes the structure (size and position), composition, and function of cellular focal adhesions using a combination of virulence factors. Mechanistically, we found that the changes in focal adhesion dynamics are dependent upon the activation of host cell signaling pathways, which affect the assembly and disassembly of cellular proteins from the focal adhesion. To summarize, we have identified a new cellular phenotype in C. jejuni-infected cells that may be responsible for the restricted intestinal repair observed in C. jejuni-infected animals.

}, issn = {2150-7511}, doi = {10.1128/mBio.01494-21}, author = {Klappenbach, Courtney M and Negretti, Nicholas M and Aaron, Jesse and Chew, Teng-Leong and Konkel, Michael E} } @article {67711, title = {Campylobacter jejuni Triggers Signaling through Host Cell Focal Adhesions To Inhibit Cell Motility.}, journal = {mBio}, volume = {12}, year = {2021}, month = {2021 Aug 24}, pages = {e0149421}, abstract = {

Campylobacter jejuni is a major foodborne pathogen that exploits the focal adhesions of intestinal cells to promote invasion and cause severe gastritis. Focal adhesions are multiprotein complexes involved in bidirectional signaling between the actin cytoskeleton and the extracellular matrix. We investigated the dynamics of focal adhesion structure and function in C. jejuni-infected cells using a comprehensive set of approaches, including confocal microscopy of live and fixed cells, immunoblotting, and superresolution interferometric photoactivated localization microscopy (iPALM). We found that C. jejuni infection of epithelial cells results in increased focal adhesion size and altered topology. These changes resulted in a persistent modulatory effect on the host cell focal adhesion, evidenced by an increase in cell adhesion strength, a decrease in individual cell motility, and a reduction in collective cell migration. We discovered that C. jejuni infection causes an increase in phosphorylation of paxillin and an alteration of paxillin turnover at the focal adhesion, which together represent a potential mechanistic basis for altered cell motility. Finally, we observed that infection of epithelial cells with the C. jejuni wild-type strain in the presence of a protein synthesis inhibitor, a C. jejuni CadF and FlpA fibronectin-binding protein mutant, or a C. jejuni flagellar export mutant blunts paxillin phosphorylation and partially reestablishes individual host cell motility and collective cell migration. These findings provide a potential mechanism for the restricted intestinal repair observed in C. jejuni-infected animals and raise the possibility that bacteria targeting extracellular matrix components can alter cell behavior after binding and internalization by manipulating focal adhesions. Campylobacter jejuni is a major foodborne pathogen that causes severe gastritis. We investigated the dynamics of focal adhesion structure and function in C. jejuni-infected epithelial cells. Focal adhesions act as signaling complexes that connect the extracellular matrix to the intracellular cytoskeleton. The key findings of this study show that C. jejuni changes the structure (size and position), composition, and function of cellular focal adhesions using a combination of virulence factors. Mechanistically, we found that the changes in focal adhesion dynamics are dependent upon the activation of host cell signaling pathways, which affect the assembly and disassembly of cellular proteins from the focal adhesion. To summarize, we have identified a new cellular phenotype in C. jejuni-infected cells that may be responsible for the restricted intestinal repair observed in C. jejuni-infected animals.

}, issn = {2150-7511}, doi = {10.1128/mBio.01494-21}, author = {Klappenbach, Courtney M and Negretti, Nicholas M and Aaron, Jesse and Chew, Teng-Leong and Konkel, Michael E} } @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 {67781, title = {Cre-Dependent Anterograde Transsynaptic Labeling and Functional Imaging in Zebrafish Using VSV With Reduced Cytotoxicity.}, journal = {Frontiers in Neuroanatomy}, volume = {15}, year = {2021}, month = {2021 Oct 06}, pages = {758350}, abstract = {

The small size and translucency of larval zebrafish () have made it a unique experimental system to investigate whole-brain neural circuit structure and function. Still, the connectivity patterns between most neuronal types remain mostly unknown. This gap in knowledge underscores the critical need for effective neural circuit mapping tools, especially ones that can integrate structural and functional analyses. To address this, we previously developed a vesicular stomatitis virus (VSV) based approach called Tracer with Restricted Anterograde Spread (TRAS). TRAS utilizes lentivirus to complement replication-incompetent VSV (VSVΔG) to allow restricted (monosynaptic) anterograde labeling from projection neurons to their target cells in the brain. Here, we report the second generation of TRAS (TRAS-M51R), which utilizes a mutant variant of VSVΔG [VSV(M51R)ΔG] with reduced cytotoxicity. Within the primary visual pathway, we found that TRAS-M51R significantly improved long-term viability of transsynaptic labeling (compared to TRAS) while maintaining anterograde spread activity. By using Cre-expressing VSV(M51R)ΔG, TRAS-M51R could selectively label excitatory ( positive) and inhibitory ( positive) retinorecipient neurons. We further show that these labeled excitatory and inhibitory retinorecipient neurons retained neuronal excitability upon visual stimulation at 5-8 days post fertilization (2-5 days post-infection). Together, these findings show that TRAS-M51R is suitable for neural circuit studies that integrate structural connectivity, cell-type identity, and neurophysiology.

}, issn = {1662-5129}, doi = {10.3389/fnana.2021.758350}, author = {Kler, Stanislav and Ma, Manxiu and Narayan, Sujatha and Ahrens, Misha B and Pan, Y Albert} } @article {67721, title = {Electrode pooling can boost the yield of extracellular recordings with switchable silicon probes.}, journal = {Nature Communications}, volume = {12}, year = {2021}, month = {2021 Sep 02}, pages = {5245}, abstract = {

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

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

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

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

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

}, issn = {2050-084X}, doi = {10.7554/eLife.66074}, author = {Arts, Janine Jg and Mahlandt, Eike K and Gr{\"o}nloh, Max and Schimmel, Lilian and Noordstra, Ivar and Gordon, Emma and van Steen, Abraham Ci and Tol, Simon and Walzog, Barbara and van Rijssel, Jos and Nolte, Martijn A and Postma, Marten and Khuon, Satya and Heddleston, John M and Wait, Eric and Chew, Teng Leong and Winter, Mark and Montanez, Eloi and Goedhart, Joachim and van Buul, Jaap D} } @article {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 {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 {67816, title = {A genetically encoded fluorescent biosensor for extracellular L-lactate.}, journal = {Nature Communications}, volume = {12}, year = {2021}, month = {2021 Dec 06}, pages = {7058}, abstract = {

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

}, issn = {2041-1723}, doi = {10.1038/s41467-021-27332-2}, author = {Nasu, Yusuke and Murphy-Royal, Ciaran and Wen, Yurong and Haidey, Jordan N and Molina, Rosana S and Abhi Aggarwal and Zhang, Shuce and Kamijo, Yuki and Paquet, Marie-Eve and Podgorski, Kaspar and Drobizhev, Mikhail and Bains, Jaideep S and Lemieux, M Joanne and Gordon, Grant R and Campbell, Robert E} } @article {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 {67271, title = {Lupus susceptibility region containing CDKN1B rs34330 mechanistically influences expression and function of multiple target genes, also linked to proliferation and apoptosis.}, journal = {Arthritis Rheumatology}, volume = {73}, year = {2021}, month = {2021 Dec 01}, pages = {2303-13}, abstract = {

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

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

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

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

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

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

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

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

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

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

}, issn = {0027-8424}, doi = {10.1073/pnas.1911413116}, url = {https://pnas.org/doi/full/10.1073/pnas.1911413116https://pnas.org/doi/pdf/10.1073/pnas.1911413116http://www.pnas.org/syndication/doi/10.1073/pnas.1911413116}, author = {Northcutt, Adam J. and Kick, Daniel R. and Otopalik, Adriane G. and Goetz, Benjamin M. and Harris, Rayna M. and Santin, Joseph M. and Hofmann, Hans A. and Marder, Eve and Schulz, David J.} } @article {67813, title = {Multiplex Gene Tagging with CRISPR-Cas9 for Live-Cell Microscopy and Application to Study the Role of SARS-CoV-2 Proteins in Autophagy, Mitochondrial Dynamics, and Cell Growth.}, journal = {The CRISPR Journal}, year = {2021}, month = {2021 Nov 30}, abstract = {

The lack of efficient tools to label multiple endogenous targets in cell lines without staining or fixation has limited our ability to track physiological and pathological changes in cells over time via live-cell studies. Here, we outline the FAST-HDR vector system to be used in combination with CRISPR-Cas9 to allow visual live-cell studies of up to three endogenous proteins within the same cell line. Our approach utilizes a novel set of advanced donor plasmids for homology-directed repair and a streamlined workflow optimized for microscopy-based cell screening to create genetically modified cell lines that do not require staining or fixation to accommodate microscopy-based studies. We validated this new methodology by developing two advanced cell lines with three fluorescent-labeled endogenous proteins that support high-content imaging without using antibodies or exogenous staining. We applied this technology to study seven severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2/COVID-19) viral proteins to understand better their effects on autophagy, mitochondrial dynamics, and cell growth. Using these two cell lines, we were able to identify the protein ORF3a successfully as a potent inhibitor of autophagy, inducer of mitochondrial relocalization, and a growth inhibitor, which highlights the effectiveness of live-cell studies using this technology.

}, issn = {2573-1602}, doi = {10.1089/crispr.2021.0041}, author = {Perez-Leal, Oscar and Nixon-Abell, Jonathon and Barrero, Carlos A and Gordon, John C and Oesterling, James and Rico, Mario C} } @article {67241, title = {A perspective on Microscopy Metadata: data provenance and quality control}, journal = {arXiv}, year = {2021}, month = {2021 Apr 26}, abstract = {

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

}, url = {https://arxiv.org/abs/1910.11370}, author = {Maximiliaan Huisman and Mathias Hammer and Alex Rigano and Ulrike Boehm and James J. Chambers and Nathalie Gaudreault and Alison J. North and Jaime A. Pimentel and Damir Sudar and Peter Bajcsy and Claire M. Brown and Alexander D. Corbett and Orestis Faklaris and Judith Lacoste and Alex Laude and Glyn Nelson and Roland Nitschke and David Grunwald and Caterina Strambio-De-Castillia} } @article {68990, title = {Principles of signaling pathway modulation for enhancing human naive pluripotency induction.}, journal = {Cell Stem Cell}, volume = {28}, year = {2021}, month = {09/2021}, pages = {1549-1565.e12}, abstract = {

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

}, keywords = {Animals, Cell Differentiation, Embryo, Mammalian, Humans, Mice, Pluripotent Stem Cells, Signal Transduction, Trophoblasts}, issn = {1875-9777}, doi = {10.1016/j.stem.2021.04.001}, author = {Bayerl, Jonathan and Ayyash, Muneef and Shani, Tom and Manor, Yair Shlomo and Gafni, Ohad and Massarwa, Rada and Kalma, Yael and Aguilera-Castrejon, Alejandro and Zerbib, Mirie and Amir, Hadar and Sheban, Daoud and Geula, Shay and Mor, Nofar and Weinberger, Leehee and Naveh Tassa, Segev and Krupalnik, Vladislav and Oldak, Bernardo and Livnat, Nir and Tarazi, Shadi and Tawil, Shadi and Wildschutz, Emilie and Ashouokhi, Shahd and Lasman, Lior and Rotter, Varda and Hanna, Suhair and Ben-Yosef, Dalit and Novershtern, Noa and Viukov, Sergey and Hanna, Jacob H} } @article {67295, title = {QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy.}, journal = {Nature Methods}, year = {2021}, month = {2021 May 21}, issn = {1548-7105}, doi = {10.1038/s41592-021-01162-y}, author = {Ulrike Boehm and Nelson, Glyn and Brown, Claire M and Bagley, Steve and Bajcsy, Peter and Bischof, Johanna and Dauphin, Aurelien and Dobbie, Ian M and Eriksson, John E and Faklaris, Orestis and Fernandez-Rodriguez, Julia and Ferrand, Alexia and Gelman, Laurent and Gheisari, Ali and Hartmann, Hella and Kukat, Christian and Laude, Alex and Mitkovski, Miso and Munck, Sebastian and North, Alison J and Rasse, Tobias M and Resch-Genger, Ute and Schuetz, Lucas C and Seitz, Arne and Strambio-De-Castillia, Caterina and Swedlow, Jason R and Nitschke, Roland} } @article {66009, title = {QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy}, journal = {Journal of Microscopy}, volume = {284}, year = {2021}, month = {2021 Oct 01}, pages = {56-73}, abstract = {

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

}, url = {https://arxiv.org/abs/2101.09153}, author = {Glyn Nelson and Ulrike Boehm and Steve Bagley and Peter Bajcsy and Johanna Bischof and Claire M Brown and Aurelien Dauphin and Ian M Dobbie and John E Eriksson and Orestis Faklaris and Julia Fernandez-Rodriguez and Alexia Ferrand and Ali Gheisari and Hella Hartmann and Christian Kukat and Alex Laude and Miso Mitkovski and Sebastian Munck and Alison J North and Tobias M Rasse and Ute Resch-Genger and Lucas C Schuetz and Arne Seitz and Caterina Strambio-De-Castillia and Jason R Swedlow and Ioannis Alexopoulos and Karin Aumayr and Sergiy Avilov and Gert-Jan Bakker and Rodrigo R Bammann and Andrea Bassi and Hannes Beckert and Sebastian Beer and Yury Belyaev and Jakob Bierwagen and Konstantin A Birngruber and Manel Bosch and Juergen Breitlow and Lisa A Cameron and Joe Chalfoun and James J Chambers and Chieh-Li Chen and Eduardo Conde-Sousa and Alexander D Corbett and Fabrice P Cordelieres and Elaine Del Nery and Ralf Dietzel and Frank Eismann and Elnaz Fazeli and Andreas Felscher and Hans Fried and Nathalie Gaudreault and Wah Ing Goh and Thomas Guilbert and Roland Hadleigh and Peter Hemmerich and Gerhard A Holst and Michelle S Itano and Claudia B Jaffe and Helena K Jambor and Stuart C Jarvis and Antje Keppler and David Kirchenbuechler and Marcel Kirchner and Norio Kobayashi and Gabriel Krens and Susanne Kunis and Judith Lacoste and Marco Marcell and Gabriel G Martins and Daniel J Metcalf and Claire A Mitchell and Joshua Moore and Tobias Mueller and Michael S Nelson and Stephen Ogg and Shuichi Onami and Alexandra L Palmer and Perrine Paul-Gilloteaux and Jaime A Pimentel and Laure Plantard and Santosh Podder and Elton Rexhepaj and Arnaud Royon and Markku A Saari and Damien Schapman and Vincent Schoonderwoert and Britta Schroth-Diez and Stanley Schwartz and Michael Shaw and Martin Spitaler and Martin T Stoeckl and Damir Sudar and Jeremie Teillon and Stefan Terjung and Roland Thuenauer and Christian D Wilms and Graham D Wright and Roland Nitschke and Laurent Gelman} } @article {65833, title = {Reconstruction of motor control circuits in adult Drosophila using automated transmission electron microscopy}, journal = {Cell}, volume = {184}, year = {2021}, month = {2021 Feb 04}, abstract = {

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

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

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

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

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

}, issn = {2041-1723}, doi = {10.1038/s41467-021-23273-y}, author = {Hiramoto, Atsuki and Jonaitis, Julius and Niki, Sawako and Kohsaka, Hiroshi and Fetter, Richard D and Cardona, Albert and Pulver, Stefan R and Nose, Akinao} } @article {67872, title = {Small-molecule ligands can inhibit -1 programmed ribosomal frameshifting in a broad spectrum of coronaviruses.}, journal = {bioRxiv}, year = {2021}, month = {2021 Aug 06}, abstract = {

Recurrent outbreaks of novel zoonotic coronavirus (CoV) diseases since 2000 have high-lighted the importance of developing therapeutics with broad-spectrum activity against CoVs. Because all CoVs use -1 programmed ribosomal frameshifting (-1 PRF) to control expression of key viral proteins, the frameshift signal in viral mRNA that stimulates -1 PRF provides a promising potential target for such therapeutics. To test the viability of this strategy, we explored a group of 6 small-molecule ligands, evaluating their activity against the frameshift signals from a panel of representative bat CoVs{\textemdash}the most likely source of future zoonoses{\textemdash}as well as SARS-CoV-2 and MERS-CoV. We found that whereas some ligands had notable activity against only a few of the frameshift signals, the serine protease inhibitor nafamostat suppressed -1 PRF significantly in several of them, while having limited to no effect on -1 PRF caused by frameshift signals from other viruses used as negative controls. These results suggest it is possible to find small-molecule ligands that inhibit -1 PRF specifically in a broad spectrum of CoVs, establishing the frameshift signal as a viable target for developing pan-coronaviral therapeutics.

}, doi = {10.1101/2021.08.06.455424}, url = {https://doi.org/10.1101/2021.08.06.455424}, author = {Sneha Munshi and Krishna Neupane and Sandaru M. Ileperuma and Matthew T.J. Halma and Jamie A. Kelly and Clarissa F. Halpern and Jonathan D. Dinman and Sarah Loerch and Michael T. Woodside} } @article {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 {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 {67242, title = {Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model.}, journal = {bioRxiv}, year = {2021}, month = {2021 Apr 28}, abstract = {

Digital light microscopy provides powerful tools for quantitatively probing the real-time dynamics of subcellular structures. While the power of modern microscopy techniques is undeniable, rigorous record-keeping and quality control are required to ensure that imaging data may be properly interpreted\ (quality),\ reproduced\ (reproducibility),\ and used to extract reliable information and scientific knowledge which can be shared for further analysis (value). Keeping notes on microscopy experiments and quality control procedures ought to be straightforward, as the microscope is a machine whose components are defined and the performance measurable. Nevertheless, to this date, no universally adopted community-driven specifications exist that delineate the required information about the microscope hardware and acquisition settings (i.e., microscopy {\textquotedblleft}data provenance{\textquotedblright} metadata) and the minimally accepted calibration metrics (i.e., microscopy quality control metadata) that should be automatically recorded by both commercial microscope manufacturers and customized microscope developers. In the absence of agreed guidelines, it is inherently difficult for scientists to create comprehensive records of imaging experiments and ensure the quality of resulting image data or for manufacturers to incorporate standardized reporting and performance metrics. To add to the confusion, microscopy experiments vary greatly in aim and complexity, ranging from purely descriptive work to complex, quantitative and even sub-resolution studies that require more detailed reporting and quality control measures.

}, doi = {10.1101/2021.04.25.441198v1}, url = {https://www.biorxiv.org/content/10.1101/2021.04.25.441198v1}, author = {Mathias Hammer and Maximiliaan Huisman and Alex Rigano and Ulrike Boehm and James J. Chambers and Nathalie Gaudreault and Alison J. North and Jaime A. Pimentel and Damir Sudar and Peter Bajcsy and Claire M. Brown and Alexander D. Corbett and Orestis Faklaris and Judith Lacoste and Alex Laude and Glyn Nelson and Roland Nitschke and Farzin Farzam and Carlas S. Smith and David Grunwald and Caterina Strambio-De-Castillia} } @article {67812, title = {Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model.}, journal = {Nature Methods}, volume = {18}, year = {2021}, month = {2021 Dec 03}, pages = {1427-1440}, issn = {1548-7105}, doi = {10.1038/s41592-021-01327-9}, author = {Hammer, Mathias and Huisman, Maximiliaan and Rigano, Alessandro and Boehm, Ulrike and Chambers, James J and Gaudreault, Nathalie and North, Alison J and Pimentel, Jaime A and Sudar, Damir and Bajcsy, Peter and Brown, Claire M and Corbett, Alexander D and Faklaris, Orestis and Lacoste, Judith and Laude, Alex and Nelson, Glyn and Nitschke, Roland and Farzam, Farzin and Smith, Carlas S and Grunwald, David and Strambio-De-Castillia, Caterina} } @article {68841, title = {Accelerated EM Connectome Reconstruction using 3D Visualization and Segmentation Graphs}, journal = {bioRxiv}, year = {2020}, month = {2020 Jan 17}, abstract = {

Recent advances in automatic image segmentation and synapse prediction in electron microscopy (EM) datasets of the brain enable more efficient reconstruction of neural connectivity. In these datasets, a single neuron can span thousands of images containing complex tree-like arbors with thousands of synapses. While image segmentation algorithms excel within narrow fields of views, the algorithms sometimes struggle to correctly segment large neurons, which require large context given their size and complexity. Conversely, humans are comparatively good at reasoning with large objects. In this paper, we introduce several semi-automated strategies that combine 3D visualization and machine guidance to accelerate connectome reconstruction. In particular, we introduce a strategy to quickly correct a segmentation through merging and\ cleaving, or splitting a segment along supervoxel boundaries, with both operations driven by affinity scores in the underlying segmentation. We deploy these algorithms as streamlined workflows in a tool called\ Neu3\ and demonstrate superior performance compared to prior work, thus enabling efficient reconstruction of much larger datasets. The insights into proofreading from our work clarify the trade-offs to consider when tuning the parameters of image segmentation algorithms.

}, doi = {10.1101/2020.01.17.909572}, url = {https://doi.org/10.1101/2020.01.17.909572}, author = {Philip M. Hubbard and Stuart Berg and Ting Zhao and Donald J. Olbris and Lowell Umayam and Jeremy Maitin-Shepard and Michal Januszewski and William T. Katz and Erika R. Neace and Stephen M. Plaza} } @article {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 {65797, title = {Brain-wide, scale-wide physiology underlying behavioral flexibility in zebrafish.}, journal = {Current Opinion in Neurobiology}, volume = {64}, year = {2020}, month = {2020 Oct 19}, pages = {151-160}, abstract = {

The brain is tasked with choosing actions that maximize an animal{\textquoteright}s chances of survival and reproduction. These choices must be flexible and informed by the current state of the environment, the needs of the body, and the outcomes of past actions. This information is physiologically encoded and processed across different brain regions on a wide range of spatial scales, from molecules in single synapses to networks of brain areas. Uncovering these spatially distributed neural interactions underlying behavior requires investigations that span a similar range of spatial scales. Larval zebrafish, given their small size, transparency, and ease of genetic access, are a good model organism for such investigations, allowing the use of modern microscopy, molecular biology, and computational techniques. These approaches are yielding new insights into the mechanistic basis of behavioral states, which we review here and compare to related studies in mammalian species.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2020.08.013}, author = {Mu, Yu and Narayan, Sujatha and Mensh, Brett D and Ahrens, Misha B} } @article {65363, title = {Characterization of the Genetic Architecture Underlying Eye Size Variation Within Drosophila melanogaster and Drosophila simulans.}, journal = {Genes|Genomes|Genetics}, volume = {10}, year = {2020}, month = {2020 Mar 01}, pages = {1005-18}, doi = {10.1534/g3.119.400877}, url = {http://g3journal.org/lookup/doi/10.1534/g3.119.400877https://syndication.highwire.org/content/doi/10.1534/g3.119.400877}, author = {Gaspar, Pedro and Arif, Saad and Sumner-Rooney, Lauren and Kittelmann, Maike and Bodey, Andrew J. and Stern, David L. and Nunes, Maria D. S. and McGregor, Alistair P.} } @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 {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 {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 {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 {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 {65282, title = {A genetic, genomic, and computational resource for exploring neural circuit function.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Jan 15}, abstract = {

The anatomy of many neural circuits is being characterized with increasing resolution, but their molecular properties remain mostly unknown. Here, we characterize gene expression patterns in distinct neural cell types of the visual system using genetic lines to access individual cell types, the TAPIN-seq method to measure their transcriptomes, and a probabilistic method to interpret these measurements. We used these tools to build a resource of high-resolution transcriptomes for 100 driver lines covering 67 cell types, available at http://www.opticlobe.com. Combining these transcriptomes with recently reported connectomes helps characterize how information is transmitted and processed across a range of scales, from individual synapses to circuit pathways. We describe examples that include identifying neurotransmitters, including cases of apparent co-release, generating functional hypotheses based on receptor expression, as well as identifying strong commonalities between different cell types.

}, issn = {2050-084X}, doi = {10.7554/eLife.50901}, author = {Davis, Fred P and Nern, Aljoscha and Picard, Serge and Reiser, Michael B and Rubin, Gerald M and Eddy, Sean R and Henry, Gilbert L} } @article {65636, title = {Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells.}, journal = {Science Advances}, volume = {6}, year = {2020}, month = {2020 Jun 17}, pages = {eaaz6699}, abstract = {

Transcriptional bursting is the stochastic activation and inactivation of promoters, contributing to cell-to-cell heterogeneity in gene expression. However, the mechanism underlying the regulation of transcriptional bursting kinetics (burst size and frequency) in mammalian cells remains elusive. In this study, we performed single-cell RNA sequencing to analyze the intrinsic noise and mRNA levels for elucidating the transcriptional bursting kinetics in mouse embryonic stem cells. Informatics analyses and functional assays revealed that transcriptional bursting kinetics was regulated by a combination of promoter- and gene body-binding proteins, including the polycomb repressive complex 2 and transcription elongation factors. Furthermore, large-scale CRISPR-Cas9-based screening identified that the Akt/MAPK signaling pathway regulated bursting kinetics by modulating transcription elongation efficiency. These results uncovered the key molecular mechanisms underlying transcriptional bursting and cell-to-cell gene expression noise in mammalian cells.

}, issn = {2375-2548}, doi = {10.1126/sciadv.aaz6699}, author = {Ochiai, Hiroshi and Hayashi, Tetsutaro and Umeda, Mana and Yoshimura, Mika and Harada, Akihito and Shimizu, Yukiko and Nakano, Kenta and Saitoh, Noriko and Liu, Zhe and Yamamoto, Takashi and Okamura, Tadashi and Ohkawa, Yasuyuki and Kimura, Hiroshi and Nikaido, Itoshi} } @article {65235, title = {In situ structure determination at nanometer resolution using TYGRESS.}, journal = {Nature Methods}, volume = {17}, year = {2020}, month = {2020 Feb 01}, pages = {201-08}, abstract = {

The resolution of subtomogram averages calculated from cryo-electron tomograms (cryo-ET) of crowded cellular environments is often limited owing to signal loss in, and misalignment of, the subtomograms. By contrast, single-particle cryo-electron microscopy (SP-cryo-EM) routinely reaches near-atomic resolution of isolated complexes. We report a method called {\textquoteright}tomography-guided 3D reconstruction of subcellular structures{\textquoteright} (TYGRESS) that is a hybrid of cryo-ET and SP-cryo-EM, and is able to achieve close-to-nanometer resolution of complexes inside crowded cellular environments. TYGRESS combines the advantages of SP-cryo-EM (images with good signal-to-noise ratio and contrast, as well as minimal radiation damage) and subtomogram averaging (three-dimensional alignment of macromolecules in a complex sample). Using TYGRESS, we determined the structure of the intact ciliary axoneme with up to resolution of 12 {\r A}. These results reveal many structural details that were not visible by cryo-ET alone. TYGRESS is generally applicable to cellular complexes that are amenable to subtomogram averaging.

}, issn = {1548-7105}, doi = {10.1038/s41592-019-0651-0}, author = {Song, Kangkang and Shang, Zhiguo and Fu, Xiaofeng and Lou, Xiaochu and Grigorieff, Nikolaus and Nicastro, Daniela} } @article {65581, title = {Live-cell single particle imaging reveals the role of RNA polymerase II in histone H2A.Z eviction.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Apr 27}, abstract = {

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

}, issn = {2050-084X}, doi = {10.7554/eLife.55667}, author = {Ranjan, Anand and Nguyen, Vu Q and Liu, Sheng and Wisniewski, Jan and Kim, Jee Min and Tang, Xiaona and Mizuguchi, Gaku and Elalaoui, Ejlal and Nickels, Timothy J and Jou, Vivian and English, Brian P and Zheng, Qinsi and Luk, Ed and Lavis, Luke D and Lionnet, Timoth{\'e}e and Wu, Carl} } @article {68359, title = {Meissner corpuscles and their spatially intermingled afferents underlie gentle touch perception}, journal = {Science}, volume = {368}, year = {2020}, month = {06/2020}, pages = {eabb2751}, abstract = {

The Meissner corpuscle, a mechanosensory end organ, was discovered more than 165 years ago and has since been found in the glabrous skin of all mammals, including that on human fingertips. Although prominently featured in textbooks, the function of the Meissner corpuscle is unknown. Neubarth et al. generated adult mice without Meissner corpuscles and used them to show that these corpuscles alone mediate behavioral responses to, and perception of, gentle forces (see the Perspective by Marshall and Patapoutian). Each Meissner corpuscle is innervated by two molecularly distinct, yet physiologically similar, mechanosensory neurons. These two neuronal subtypes are developmentally interdependent and their endings are intertwined within the corpuscle. Both Meissner mechanosensory neuron subtypes are homotypically tiled, ensuring uniform and complete coverage of the skin, yet their receptive fields are overlapping and offset with respect to each other. Science, this issue p. eabb2751; see also p. 1311 Light touch perception and fine sensorimotor control arise from spatially overlapping mechanoreceptors of the Meissner corpuscle. Meissner corpuscles are mechanosensory end organs that densely occupy mammalian glabrous skin. We generated mice that selectively lacked Meissner corpuscles and found them to be deficient in both perceiving the gentlest detectable forces acting on glabrous skin and fine sensorimotor control. We found that Meissner corpuscles are innervated by two mechanoreceptor subtypes that exhibit distinct responses to tactile stimuli. The anatomical receptive fields of these two mechanoreceptor subtypes homotypically tile glabrous skin in a manner that is offset with respect to one another. Electron microscopic analysis of the two Meissner afferents within the corpuscle supports a model in which the extent of lamellar cell wrappings of mechanoreceptor endings determines their force sensitivity thresholds and kinetic properties.

}, doi = {10.1126/science.abb2751}, url = {https://www.science.org/doi/abs/10.1126/science.abb2751}, author = {Nicole L. Neubarth and Alan J. Emanuel and Yin Liu and Mark W. Springel and Annie Handler and Qiyu Zhang and Brendan P. Lehnert and Chong Guo and Lauren L. Orefice and Amira Abdelaziz and Michelle M. DeLisle and Michael Iskols and Julia Rhyins and Soo J. Kim and Stuart J. Cattel and Wade Regehr and Christopher D. Harvey and Jan Drugowitsch and David D. Ginty} } @article {65791, title = {The mTORC1/S6K/PDCD4/eIF4A axis determines outcome of mitotic arrest.}, journal = {Cell Reports}, volume = {33}, year = {2020}, month = {2020 Oct 06}, pages = {108230}, abstract = {

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

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2020.108230}, author = {Moustafa-Kamal, Mohamed and Kucharski, Thomas J and El-Assaad, Wissal and Abbas, Yazan M and Gandin, Valentina and Nagar, Bhushan and Pelletier, Jerry and Topisirovic, Ivan and Teodoro, Jose G} } @article {65318, title = {Nicotine exposure and neuronal activity regulate Golgi membrane dispersal and distribution}, journal = {bioRxiv}, year = {2020}, month = {2020 Feb 26}, abstract = {

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

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

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

}, issn = {1948-7193}, doi = {10.1021/acschemneuro.0c00397}, author = {Guthrie, Daryl and Klein Herenbrink, Carmen and Lycas, Matthew and Ku, Therese and Bonifazi, Alessandro and DeVree, Brian and Mathiasen, Signe and Javitch, Jonathan and Grimm, Jonathan B and Lavis, Luke D and Gether, Ulrik and Newman, Amy Hauck} } @article {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 {65847, title = {Spatial readout of visual looming in the central brain of Drosophila.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Nov 18}, abstract = {

Visual systems can exploit spatial correlations in the visual scene by using retinotopy. However, retinotopy is often lost, such as when visual pathways are integrated with other sensory modalities. How is spatial information processed outside of strictly visual brain areas? Here, we focused on visual looming responsive LC6 cells in , a population whose dendrites collectively cover the visual field, but whose axons form a single glomerulus-a structure without obvious retinotopic organization-in the central brain. We identified multiple cell types downstream of LC6 in the glomerulus and found that they more strongly respond to looming in different portions of the visual field, unexpectedly preserving spatial information. Through EM reconstruction of all LC6 synaptic inputs to the glomerulus, we found that LC6 and downstream cell types form circuits within the glomerulus that enable spatial readout of visual features and contralateral suppression-mechanisms that transform visual information for behavioral control.

}, issn = {2050-084X}, doi = {10.7554/eLife.57685}, author = {Morimoto, Mai M and Nern, Aljoscha and Zhao, Arthur and Rogers, Edward M and Wong, Allan and Isaacson, Mathew D and Bock, Davi and Rubin, Gerald M and Reiser, Michael B} } @article {65759, title = {Structural insight into the ATP-driven exporter of virulent peptide toxins.}, journal = {Science Advances}, volume = {6}, year = {2020}, month = {2020 Sep 30}, abstract = {

is a major human pathogen that has acquired alarming broad-spectrum antibiotic resistance. One group of secreted toxins with key roles during infection is the phenol-soluble modulins (PSMs). PSMs are amphipathic, membrane-destructive cytolytic peptides that are exported to the host-cell environment by a designated adenosine 5{\textquoteright}-triphosphate (ATP)-binding cassette (ABC) transporter, the PSM transporter (PmtABCD). Here, we demonstrate that the minimal Pmt unit necessary for PSM export is PmtCD and provide its first atomic characterization by single-particle cryo-EM and x-ray crystallography. We have captured the transporter in the ATP-bound state at near atomic resolution, revealing a type II ABC exporter fold, with an additional cytosolic domain. Comparison to a lower-resolution nucleotide-free map displaying an "open" conformation and putative hydrophobic inner chamber of a size able to accommodate the binding of two PSM peptides provides mechanistic insight and sets the foundation for therapeutic design.

}, issn = {2375-2548}, doi = {10.1126/sciadv.abb8219}, author = {Zeytuni, N and Dickey, S W and Hu, J and Chou, H T and Worrall, L J and Alexander, J A N and Carlson, M L and Nosella, M and Duong, F and Yu, Z and Otto, M and Strynadka, N C J} } @article {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} } @article {65910, title = {An unbiased template of the Drosophila brain and ventral nerve cord.}, journal = {PLoS One}, volume = {15}, year = {2020}, month = {2020 Dec 31}, pages = {e0236495}, abstract = {

The fruit fly Drosophila melanogaster is an important model organism for neuroscience with a wide array of genetic tools that enable the mapping of individual neurons and neural subtypes. Brain templates are essential for comparative biological studies because they enable analyzing many individuals in a common reference space. Several central brain templates exist for Drosophila, but every one is either biased, uses sub-optimal tissue preparation, is imaged at low resolution, or does not account for artifacts. No publicly available Drosophila ventral nerve cord template currently exists. In this work, we created high-resolution templates of the Drosophila brain and ventral nerve cord using the best-available technologies for imaging, artifact correction, stitching, and template construction using groupwise registration. We evaluated our central brain template against the four most competitive, publicly available brain templates and demonstrate that ours enables more accurate registration with fewer local deformations in shorter time.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0236495}, author = {Bogovic, John A and Otsuna, Hideo and Heinrich, Larissa and Ito, Masayoshi and Jeter, Jennifer and Meissner, Geoffrey and Nern, Aljoscha and Colonell, Jennifer and Malkesman, Oz and Ito, Kei and Saalfeld, Stephan} } @article {65297, title = {A versatile vector system for the fast generation of knock-in cell lines with CRISPR.}, journal = {bioRxiv}, year = {2020}, month = {2020 Feb 06}, abstract = {

Until recent advancements in genome editing via CRISPR/Cas9 technology, understanding protein function typically involved artificially overexpressing proteins of interest. Despite that CRISPR/Cas9 has ushered in a new era of possibilities for modifying endogenous genes with labeling tags (knock-in) to more accurately study proteins under physiological conditions, the technique is largely underutilized due to its tedious, multi-step process. Here we outline a homologous recombination system (FAST-HDR) to be used in combination with CRISPR/Cas9 that significantly simplifies and accelerates this process while introducing multiplexing to allow live-cell studies of 3 endogenous proteins within the same cell line. Furthermore, the recombination vectors are assembled in a single reaction that is enhanced for eliminating false positives and reduces the overall creation time for the knockin cell line from\ ~8 weeks to \<15 days. Finally, the system utilizes a modular construction to allow for seamlessly swapping labeling tags to ensure flexibility according to the area under study. We validated this new methodology by developing advanced cell lines with 3 fluorescent-labeled endogenous proteins that support high-content phenotypic drug screening without using antibodies or exogenous staining. Therefore, Fast-HDR cell lines provide a robust alternative for studying multiple proteins of interest in live cells without artificially overexpressing labeled proteins.

}, doi = {10.1101/2020.02.06.927384}, author = {Perez-Leal, Oscar and Nixon-Abell, Jonathon and Barrero, Carlos A. and Gordon, John and Rico, Mario C.} } @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 {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 {65198, title = {A bidirectional network for appetite control in larval zebrafish.}, journal = {Elife}, volume = {8}, year = {2019}, month = {2019 Oct 18}, abstract = {

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

}, issn = {2050-084X}, doi = {10.7554/eLife.43775}, author = {Wee, Caroline Lei and Song, Erin Yue and Johnson, Robert Evan and Ailani, Deepak and Randlett, Owen and Kim, Ji-Yoon and Nikitchenko, Maxim and Bahl, Armin and Yang, Chao-Tsung and Ahrens, Misha B and Kawakami, Koichi and Engert, Florian and Kunes, Sam} } @article {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 {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 {64546, title = {Determining the pharmacokinetics of nicotinic drugs in the endoplasmic reticulum using biosensors.}, journal = {The Journal of General Physiology}, year = {2019}, month = {2019 Feb 04}, abstract = {

Nicotine dependence is thought to arise in part because nicotine permeates into the endoplasmic reticulum (ER), where it binds to nicotinic receptors (nAChRs) and begins an "inside-out" pathway that leads to up-regulation of nAChRs on the plasma membrane. However, the dynamics of nicotine entry into the ER are unquantified. Here, we develop a family of genetically encoded fluorescent biosensors for nicotine, termed iNicSnFRs. The iNicSnFRs are fusions between two proteins: a circularly permutated GFP and a periplasmic choline-/betaine-binding protein engineered to bind nicotine. The biosensors iNicSnFR3a and iNicSnFR3b respond to nicotine by increasing fluorescence at [nicotine] \<1 {\textmu}M, the concentration in the plasma and cerebrospinal fluid of a smoker. We target iNicSnFR3 biosensors either to the plasma membrane or to the ER and measure nicotine kinetics in HeLa, SH-SY5Y, N2a, and HEK293 cell lines, as well as mouse hippocampal neurons and human stem cell-derived dopaminergic neurons. In all cell types, we find that nicotine equilibrates in the ER within 10 s (possibly within 1 s) of extracellular application and leaves as rapidly after removal from the extracellular solution. The [nicotine] in the ER is within twofold of the extracellular value. We use these data to run combined pharmacokinetic and pharmacodynamic simulations of human smoking. In the ER, the inside-out pathway begins when nicotine becomes a stabilizing pharmacological chaperone for some nAChR subtypes, even at concentrations as low as \~{}10 nM. Such concentrations would persist during the 12 h of a typical smoker{\textquoteright}s day, continually activating the inside-out pathway by \>75\%. Reducing nicotine intake by 10-fold decreases activation to \~{}20\%. iNicSnFR3a and iNicSnFR3b also sense the smoking cessation drug varenicline, revealing that varenicline also permeates into the ER within seconds. Our iNicSnFRs enable optical subcellular pharmacokinetics for nicotine and varenicline during an early event in the inside-out pathway.

}, issn = {1540-7748}, doi = {10.1085/jgp.201812201}, author = {Shivange, Amol V and Borden, Philip M and Muthusamy, Anand K and Nichols, Aaron L and Bera, Kallol and Bao, Huan and Bishara, Ishak and Jeon, Janice and Mulcahy, Matthew J and Cohen, Bruce and O{\textquoteright}Riordan, Saidhbhe L and Kim, Charlene and Dougherty, Dennis A and Chapman, Edwin R and Marvin, Jonathan and Looger, Loren and Lester, Henry A} } @article {64783, title = {Determining the pharmacokinetics of nicotinic drugs in the endoplasmic reticulum using biosensors.}, journal = {The Journal of General Physiology}, volume = {151}, year = {2019}, month = {2019 Feb 04}, pages = {738-57}, abstract = {

Nicotine dependence is thought to arise in part because nicotine permeates into the endoplasmic reticulum (ER), where it binds to nicotinic receptors (nAChRs) and begins an "inside-out" pathway that leads to up-regulation of nAChRs on the plasma membrane. However, the dynamics of nicotine entry into the ER are unquantified. Here, we develop a family of genetically encoded fluorescent biosensors for nicotine, termed iNicSnFRs. The iNicSnFRs are fusions between two proteins: a circularly permutated GFP and a periplasmic choline-/betaine-binding protein engineered to bind nicotine. The biosensors iNicSnFR3a and iNicSnFR3b respond to nicotine by increasing fluorescence at [nicotine] \<1 {\textmu}M, the concentration in the plasma and cerebrospinal fluid of a smoker. We target iNicSnFR3 biosensors either to the plasma membrane or to the ER and measure nicotine kinetics in HeLa, SH-SY5Y, N2a, and HEK293 cell lines, as well as mouse hippocampal neurons and human stem cell-derived dopaminergic neurons. In all cell types, we find that nicotine equilibrates in the ER within 10 s (possibly within 1 s) of extracellular application and leaves as rapidly after removal from the extracellular solution. The [nicotine] in the ER is within twofold of the extracellular value. We use these data to run combined pharmacokinetic and pharmacodynamic simulations of human smoking. In the ER, the inside-out pathway begins when nicotine becomes a stabilizing pharmacological chaperone for some nAChR subtypes, even at concentrations as low as \~{}10 nM. Such concentrations would persist during the 12 h of a typical smoker{\textquoteright}s day, continually activating the inside-out pathway by \>75\%. Reducing nicotine intake by 10-fold decreases activation to \~{}20\%. iNicSnFR3a and iNicSnFR3b also sense the smoking cessation drug varenicline, revealing that varenicline also permeates into the ER within seconds. Our iNicSnFRs enable optical subcellular pharmacokinetics for nicotine and varenicline during an early event in the inside-out pathway.

}, issn = {1540-7748}, doi = {10.1085/jgp.201812201}, author = {Shivange, Amol V and Borden, Philip M and Muthusamy, Anand K and Nichols, Aaron L and Bera, Kallol and Bao, Huan and Bishara, Ishak and Jeon, Janice and Mulcahy, Matthew J and Cohen, Bruce and O{\textquoteright}Riordan, Saidhbhe L and Kim, Charlene and Dougherty, Dennis A and Chapman, Edwin R and Marvin, Jonathan and Looger, Loren and Lester, Henry A} } @article {68993, title = {Deterministic Somatic Cell Reprogramming Involves Continuous Transcriptional Changes Governed by Myc and Epigenetic-Driven Modules.}, journal = {Cell Stem Cell}, volume = {24}, year = {2019}, month = {02/2019}, pages = {328-341.e9}, abstract = {

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

}, keywords = {Animals, Cell Lineage, Cellular Reprogramming, Chromatin, Demethylation, Epigenesis, Genetic, Humans, Induced Pluripotent Stem Cells, Kruppel-Like Factor 4, Mice, Protein Binding, Proto-Oncogene Proteins c-myc, RNA, Transfer, Transcription Factors, Transcription, Genetic}, issn = {1875-9777}, doi = {10.1016/j.stem.2018.11.014}, author = {Zviran, Asaf and Mor, Nofar and Rais, Yoach and Gingold, Hila and Peles, Shani and Chomsky, Elad and Viukov, Sergey and Buenrostro, Jason D and Scognamiglio, Roberta and Weinberger, Leehee and Manor, Yair S and Krupalnik, Vladislav and Zerbib, Mirie and Hezroni, Hadas and Jaitin, Diego Adhemar and Larastiaso, David and Gilad, Shlomit and Benjamin, Sima and Gafni, Ohad and Mousa, Awni and Ayyash, Muneef and Sheban, Daoud and Bayerl, Jonathan and Aguilera-Castrejon, Alejandro and Massarwa, Rada and Maza, Itay and Hanna, Suhair and Stelzer, Yonatan and Ulitsky, Igor and Greenleaf, William J and Tanay, Amos and Trumpp, Andreas and Amit, Ido and Pilpel, Yitzhak and Novershtern, Noa and Hanna, Jacob H} } @article {56202, title = {Developmentally arrested precursors of pontine neurons establish an embryonic blueprint of the Drosophila central complex.}, journal = {Current Biology : CB}, volume = {29}, year = {2019}, month = {2019 Jan 15}, pages = {412-25}, abstract = {

Serial electron microscopic analysis shows that the Drosophila brain at hatching possesses a large fraction of developmentally arrested neurons with a small soma, heterochromatin-rich nucleus, and unbranched axon lacking synapses. We digitally reconstructed all 802 "small undifferentiated" (SU) neurons and assigned them to the known brain lineages. By establishing the coordinates and reconstructing trajectories of the SU neuron tracts, we provide a framework of landmarks for the ongoing analyses of the L1 brain circuitry. To address the later fate of SU neurons, we focused on the 54 SU neurons belonging to the DM1-DM4 lineages, which generate all columnar neurons of the central complex. Regarding their topologically ordered projection pattern, these neurons form an embryonic nucleus of the fan-shaped body ("FB pioneers"). Fan-shaped body pioneers survive into the adult stage, where they develop into a specific class of bi-columnar elements, the pontine neurons. Later born, unicolumnar DM1-DM4 neurons fasciculate with the fan-shaped body pioneers. Selective ablation of the fan-shaped body pioneers altered the architecture of the larval fan-shaped body primordium but did not result in gross abnormalities of the trajectories of unicolumnar neurons, indicating that axonal pathfinding of the two systems may be controlled independently. Our comprehensive spatial and developmental analysis of the SU neurons adds to our understanding of the establishment of neuronal circuitry.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2018.12.012}, author = {Andrade, Ingrid V and Riebli, Nadia and Nguyen, Bao-Chau M and Omoto, Jaison J and Cardona, Albert and Hartenstein, Volker} } @article {68755, title = {Extracellular matrix dynamics in cell migration, invasion and tissue morphogenesis}, journal = {International Journal of Experimental Pathology}, volume = {100}, year = {2019}, month = {06/2019}, pages = {144-152}, abstract = {

Summary This review describes how direct visualization of the dynamic interactions of cells with different extracellular matrix microenvironments can provide novel insights into complex biological processes. Recent studies have moved characterization of cell migration and invasion from classical 2D culture systems into 1D and 3D model systems, revealing multiple differences in mechanisms of cell adhesion, migration and signalling{\textemdash}even though cells in 3D can still display prominent focal adhesions. Myosin II restrains cell migration speed in 2D culture but is often essential for effective 3D migration. 3D cell migration modes can switch between lamellipodial, lobopodial and/or amoeboid depending on the local matrix environment. For example, {\textquotedblleft}nuclear piston{\textquotedblright} migration can be switched off by local proteolysis, and proteolytic invadopodia can be induced by a high density of fibrillar matrix. Particularly, complex remodelling of both extracellular matrix and tissues occurs during morphogenesis. Extracellular matrix supports self-assembly of embryonic tissues, but it must also be locally actively remodelled. For example, surprisingly focal remodelling of the basement membrane occurs during branching morphogenesis{\textemdash}numerous tiny perforations generated by proteolysis and actomyosin contractility produce a microscopically porous, flexible basement membrane meshwork for tissue expansion. Cells extend highly active blebs or protrusions towards the surrounding mesenchyme through these perforations. Concurrently, the entire basement membrane undergoes translocation in a direction opposite to bud expansion. Underlying this slowly moving 2D basement membrane translocation are highly dynamic individual cell movements. We conclude this review by describing a variety of exciting research opportunities for discovering novel insights into cell-matrix interactions.

}, keywords = {3D culture, basement membrane remodelling, branching morphogenesis, cell migration, Extracellular Matrix, invasion}, doi = {https://doi.org/10.1111/iep.12329}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/iep.12329}, author = {Yamada, Kenneth M. and Collins, Joshua W. and Cruz Walma, David A. and Doyle, Andrew D. and Morales, Shaimar Gonzalez and Lu, Jiaoyang and Matsumoto, Kazue and Nazari, Shayan S. and Sekiguchi, Rei and Shinsato, Yoshinari and Wang, Shaohe} } @article {65056, title = {A genetically encoded fluorescent sensor for in vivo imaging of GABA.}, journal = {Nature Methods}, volume = {16}, year = {2019}, month = {2019 Jul 15}, pages = {763-770}, abstract = {

Current techniques for monitoring GABA (γ-aminobutyric acid), the primary inhibitory neurotransmitter in vertebrates, cannot follow transients in intact neural circuits. To develop a GABA sensor, we applied the design principles used to create the fluorescent glutamate receptor iGluSnFR. We used a protein derived from a previously unsequenced Pseudomonas fluorescens strain and performed structure-guided mutagenesis and library screening to obtain intensity-based GABA sensing fluorescence reporter (iGABASnFR) variants. iGABASnFR is genetically encoded, detects GABA release evoked by electric stimulation of afferent fibers in acute brain slices and produces readily detectable fluorescence increases in vivo in mice and zebrafish. We applied iGABASnFR to track mitochondrial GABA content and its modulation by an anticonvulsant, swimming-evoked, GABA-mediated transmission in zebrafish cerebellum, GABA release events during interictal spikes and seizures in awake mice, and found that GABA-mediated tone decreases during isoflurane anesthesia.

}, issn = {1548-7105}, doi = {10.1038/s41592-019-0471-2}, author = {Marvin, Jonathan S and Shimoda, Yoshiteru and Magloire, Vincent and Leite, Marco and Kawashima, Takashi and Jensen, Thomas P and Kolb, Ilya and Knott, Erika L and Novak, Ondrej and Podgorski, Kaspar and Leidenheimer, Nancy J and Rusakov, Dmitri A and Ahrens, Misha B and Kullmann, Dimitri M and Looger, Loren L} } @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 {49329, title = {Kilohertz frame-rate two-photon tomography.}, journal = {Nature Methods}, volume = {16}, year = {2019}, month = {2019 Jul 29}, pages = {778-86}, abstract = {

Point-scanning two-photon microscopy enables high-resolution imaging within scattering specimens such as the mammalian brain, but sequential acquisition of voxels fundamentally limits imaging speed. We developed a two-photon imaging technique that scans lines of excitation across a focal plane at multiple angles and uses prior information to recover high-resolution images at over 1.4 billion voxels per second. Using a structural image as a prior for recording neural activity, we imaged visually-evoked and spontaneous glutamate release across hundreds of dendritic spines in mice at depths over 250 microns and frame-rates over 1 kHz. Dendritic glutamate transients in anaesthetized mice are synchronized within spatially-contiguous domains spanning tens of microns at frequencies ranging from 1-100 Hz. We demonstrate high-speed recording of acetylcholine and calcium sensors, 3D single-particle tracking, and imaging in densely-labeled cortex. Our method surpasses limits on the speed of raster-scanned imaging imposed by fluorescence lifetime.

}, doi = {10.1101/357269}, author = {Kazemipour, Abbas and Novak, Ondrej and Flickinger, Daniel and Marvin, Jonathan S and Abdelfattah, Ahmed S and King, J. and Borden, PM and Kim, JJ and Al-Abdullatif, SH and Deal, PE and Miller, EW and Schreiter, ER and Druckmann, S and Svoboda, K and Looger, LL and Podgorski, K} } @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 {69337, title = {Molecular Profiling to Infer Neuronal Cell Identity: Lessons from small ganglia of the Crab Cancer borealis}, journal = {bioRxiv}, year = {2019}, month = {2019 Jul 2}, abstract = {

Understanding circuit organization depends on identification of cell types. Recent advances in transcriptional profiling methods have enabled classification of cell types by their gene expression. While exceptionally powerful and high throughput, the ground-truth validation of these methods is difficult: if cell type is unknown, how does one assess whether a given analysis accurately captures neuronal identity? To shed light on the capabilities and limitations of solely using transcriptional profiling for cell type classification, we performed two forms of transcriptional profiling {\textendash} RNA-seq and quantitative RT-PCR, in single, unambiguously identified neurons from two small crustacean networks: the stomatogastric and cardiac ganglia. We then combined our knowledge of cell type with unbiased clustering analyses and supervised machine learning to determine how accurately functionally-defined neuron types can be classified by expression profile alone. Our results demonstrate that expression profile is able to capture neuronal identity most accurately when combined with multimodal information that allows for post-hoc grouping so analysis can proceed from a supervised perspective. Solely unsupervised clustering can lead to misidentification and an inability to distinguish between two or more cell types. Therefore, our study supports the general utility of cell identification by transcriptional profiling, but adds a caution: it is difficult or impossible to know under what conditions transcriptional profiling alone is capable of assigning cell identity. Only by combining multiple modalities of information such as physiology, morphology or innervation target can neuronal identity be unambiguously determined.SIGNIFICANCE STATEMENT Single cell transcriptional profiling has become a widespread tool in cell identification, particularly in the nervous system, based on the notion that genomic information determines cell identity. However, many cell type classification studies are unconstrained by other cellular attributes (e.g., morphology, physiology). Here, we systematically test how accurately transcriptional profiling can assign cell identity to well-studied anatomically- and functionally-identified neurons in two small neuronal networks. While these neurons clearly possess distinct patterns of gene expression across cell types, their expression profiles are not sufficient to unambiguously confirm their identity. We suggest that true cell identity can only be determined by combining gene expression data with other cellular attributes such as innervation pattern, morphology, or physiology.

}, doi = {10.1101/690388}, url = {https://www.biorxiv.org/content/early/2019/07/02/690388}, author = {Adam J. Northcutt and Daniel R. Kick and Adriane G. Otopalik and Benjamin M. Goetz and Rayna M. Harris and Joseph M. Santin and Hans A. Hofmann and Eve Marder and David J. Schulz} } @article {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 {65206, title = {The organization of the second optic chiasm of the optic lobe.}, journal = {Frontiers in Neural Circuits}, volume = {13}, year = {2019}, month = {2019 Oct 11}, pages = {65}, abstract = {

Visual pathways from the compound eye of an insect relay to four neuropils, successively the lamina, medulla, lobula, and lobula plate in the underlying optic lobe. Among these neuropils, the medulla, lobula, and lobula plate are interconnected by the complex second optic chiasm, through which the anteroposterior axis undergoes an inversion between the medulla and lobula. Given their complex structure, the projection patterns through the second optic chiasm have so far lacked critical analysis. By densely reconstructing axon trajectories using a volumetric scanning electron microscopy (SEM) technique, we reveal the three-dimensional structure of the second optic chiasm of , which comprises interleaving bundles and sheets of axons insulated from each other by glial sheaths. These axon bundles invert their horizontal sequence in passing between the medulla and lobula. Axons connecting the medulla and lobula plate are also bundled together with them but do not decussate the sequence of their horizontal positions. They interleave with sheets of projection neuron axons between the lobula and lobula plate, which also lack decussations. We estimate that approximately 19,500 cells per hemisphere, about two thirds of the optic lobe neurons, contribute to the second chiasm, most being Tm cells, with an estimated additional 2,780 T4 and T5 cells each. The chiasm mostly comprises axons and cell body fibers, but also a few synaptic elements. Based on our anatomical findings, we propose that a chiasmal structure between the neuropils is potentially advantageous for processing complex visual information in parallel. The EM reconstruction shows not only the structure of the chiasm in the adult brain, the previously unreported main topic of our study, but also suggest that the projection patterns of the neurons comprising the chiasm may be determined by the proliferation centers from which the neurons develop. Such a complex wiring pattern could, we suggest, only have arisen in several evolutionary steps.

}, issn = {1662-5110}, doi = {10.3389/fncir.2019.00065}, author = {Shinomiya, Kazunori and Horne, Jane Anne and McLin, Sari and Wiederman, Meagan and Nern, Aljoscha and Plaza, Stephen M and Meinertzhagen, Ian A} } @article {66014, title = {Physical Principles of Membrane Shape Regulation by the Glycocalyx}, journal = {Cell}, volume = {177}, year = {2019}, month = {Jan-06-2019}, pages = {1757 - 1770.e21}, abstract = {

Cells bend their plasma membranes into highly curved forms to interact with the local environment, but how shape generation is regulated is not fully resolved. Here, we report a synergy between shape-generating processes in the cell interior and the external organization and composition of the cell-surface\ glycocalyx.\ Mucinbiopolymers\ and long-chain\ polysaccharides\ within the glycocalyx can generate entropic forces that favor or disfavor the projection of spherical and finger-like extensions from the cell surface. A polymer brush model of the glycocalyx successfully predicts the effects of polymer size and cell-surface density on membrane morphologies. Specific glycocalyx compositions can also induce plasma membrane instabilities to generate more exotic undulating and pearled\ membrane structures\ and drive secretion of extracellular vesicles. Together, our results suggest a fundamental role for the glycocalyx in regulating curved membrane features that serve in communication between cells and with the\ extracellular matrix.

}, issn = {00928674}, doi = {10.1016/j.cell.2019.04.017}, url = {https://www.sciencedirect.com/science/article/pii/S0092867419304039?via\%3Dihub}, author = {Shurer, Carolyn R. and Kuo, Joe Chin-Hun and Roberts, LaDeidra Mon{\'e}t and Gandhi, Jay G. and Colville, Marshall J. and Enoki, Thais A. and Pan, Hao and Su, Jin and Noble, Jade M. and Hollander, Michael J. and O{\textquoteright}Donnell, John P. and Yin, Rose and Pedram, Kayvon and M{\"o}ckl, Leonhard and Kourkoutis, Lena F. and Moerner, W.E. and Bertozzi, Carolyn R. and Feigenson, Gerald W. and Reesink, Heidi L. and Paszek, Matthew J.} } @article {64935, title = {Quantitative in vivo imaging of neuronal glucose concentrations with a genetically encoded fluorescence lifetime sensor.}, journal = {Journal of Neuroscience Research}, volume = {97}, year = {2019}, month = {2019 Aug 01}, pages = {946-60}, abstract = {

Glucose is an essential source of energy for the brain. Recently, the development of genetically encoded fluorescent biosensors has allowed real time visualization of glucose dynamics from individual neurons and astrocytes. A major difficulty for this approach, even for ratiometric sensors, is the lack of a practical method to convert such measurements into actual concentrations in ex vivo brain tissue or in vivo. Fluorescence lifetime imaging provides a strategy to overcome this. In a previous study, we reported the lifetime glucose sensor iGlucoSnFR-TS (then called SweetieTS) for monitoring changes in neuronal glucose levels in response to stimulation. This genetically encoded sensor was generated by combining the Thermus thermophilus glucose-binding protein with a circularly permuted variant of the monomeric fluorescent protein T-Sapphire. Here, we provide more details on iGlucoSnFR-TS design and characterization, as well as pH and temperature sensitivities. For accurate estimation of glucose concentrations, the sensor must be calibrated at the same temperature as the experiments. We find that when the extracellular glucose concentration is in the range 2-10\ mM, the intracellular glucose concentration in hippocampal neurons from acute brain slices is ~20\% of the nominal external glucose concentration (~0.4-2\ mM). We also measured the cytosolic neuronal glucose concentration in vivo, finding a range of ~0.7-2.5\ mM in cortical neurons from awake mice.

}, issn = {1097-4547}, doi = {10.1002/jnr.24433}, author = {D{\'\i}az-Garc{\'\i}a, Carlos Manlio and Lahmann, Carolina and Mart{\'\i}nez-Fran{\c c}ois, Juan Ram{\'o}n and Li, Binsen and Koveal, Dorothy and Nathwani, Nidhi and Rahman, Mahia and Keller, Jacob P and Marvin, Jonathan S and Looger, Loren L and Yellen, Gary} } @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 {65025, title = {Regulation of plasma membrane nanodomains of the water channel aquaporin-3 revealed by fixed and live photoactivated localization microscopy.}, journal = {Nano Letters}, volume = {19}, year = {2019}, month = {2019 Feb 13}, pages = {699-707}, abstract = {

Several aquaporin (AQP) water channels are short-term regulated by the messenger cyclic adenosine monophosphate (cAMP), including AQP3. Bulk measurements show that cAMP can change diffusive properties of AQP3; however, it remains unknown how elevated cAMP affects AQP3 organization at the nanoscale. Here we analyzed AQP3 nano-organization following cAMP stimulation using photoactivated localization microscopy (PALM) of fixed cells combined with pair correlation analysis. Moreover, in live cells, we combined PALM acquisitions of single fluorophores with single-particle tracking (spt-PALM). These analyses revealed that AQP3 tends to cluster and that the diffusive mobility is confined to nanodomains with radii of \~{}150 nm. This domain size increases by \~{}30\% upon elevation of cAMP, which, however, is not accompanied by a significant increase in the confined diffusion coefficient. This regulation of AQP3 organization at the nanoscale may be important for understanding the mechanisms of water AQP3-mediated water transport across plasma membranes.

}, keywords = {Animals, Aquaporin 3, Cell Membrane, Cyclic AMP, Diffusion, Dogs, Epithelial Cells, Madin Darby Canine Kidney Cells, Microscopy, Fluorescence, Photochemical Processes}, issn = {1530-6992}, doi = {10.1021/acs.nanolett.8b03721}, author = {Arnspang, Eva C and Sengupta, Prabuddha and Mortensen, Kim I and Jensen, Helene H and Hahn, Ute and Jensen, Eva B V and Lippincott-Schwartz, Jennifer and Nejsum, Lene N} } @article {65159, title = {A repeated molecular architecture across thalamic pathways.}, journal = {Nature Neuroscience}, volume = {22}, year = {2019}, month = {2019 Sep 16}, pages = {1925-35}, abstract = {

The thalamus is the central communication hub of the forebrain and provides the cerebral cortex with inputs from sensory organs, subcortical systems and the cortex itself. Multiple thalamic regions send convergent information to each cortical region, but the organizational logic of thalamic projections has remained elusive. Through comprehensive transcriptional analyses of retrogradely labeled thalamic neurons in adult mice, we identify three major profiles of thalamic pathways. These profiles exist along a continuum that is repeated across all major projection systems, such as those for vision, motor control and cognition. The largest component of gene expression variation in the mouse thalamus is topographically organized, with features conserved in humans. Transcriptional differences between these thalamic neuronal identities are tied to cellular features that are critical for function, such as axonal morphology and membrane properties. Molecular profiling therefore reveals covariation in the properties of thalamic pathways serving all major input modalities and output targets, thus establishing a molecular framework for understanding the thalamus.

}, issn = {1546-1726}, doi = {10.1038/s41593-019-0483-3}, author = {Phillips, James W and Schulmann, Anton and Hara, Erina and Winnubst, Johan and Liu, Chenghao and Valakh, Vera and Wang, Lihua and Shields, Brenda C and Korff, Wyatt and Chandrashekar, Jayaram and Lemire, Andrew L and Mensh, Brett and Dudman, Joshua T and Nelson, Sacha B and Hantman, Adam W} } @article {65156, title = {RNA granules hitchhike on lysosomes for long-distance transport, Using annexin A11 as a molecular tether.}, journal = {Cell}, volume = {179}, year = {2019}, month = {2019 Sep 19}, pages = {147-164.e20}, abstract = {

Long-distance RNA transport enables local protein synthesis at metabolically-active sites distant from the nucleus. This process ensures an appropriate spatial organization of proteins, vital to polarized cells such as neurons. Here, we present a mechanism for RNA transport in which RNA granules "hitchhike" on moving lysosomes. In\ vitro biophysical modeling, live-cell microscopy, and unbiased proximity labeling proteomics reveal that annexin A11 (ANXA11), an RNA granule-associated phosphoinositide-binding protein, acts as a molecular tether between RNA granules and lysosomes. ANXA11 possesses an N-terminal low complexity domain, facilitating its phase separation into membraneless RNA granules, and a C-terminal membrane binding domain, enabling interactions with lysosomes. RNA granule transport requires ANXA11, and amyotrophic lateral sclerosis (ALS)-associated mutations in ANXA11 impair RNA granule transport by disrupting their interactions with lysosomes. Thus, ANXA11 mediates neuronal RNA transport by tethering RNA granules to actively-transported lysosomes, performing a critical cellular function that is disrupted in ALS.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2019.08.050}, author = {Liao, Ya-Cheng and Fernandopulle, Michael S and Wang, Guozhen and Choi, Heejun and Hao, Ling and Drerup, Catherine M and Patel, Rajan and Qamar, Seema and Nixon-Abell, Jonathon and Shen, Yi and Meadows, William and Vendruscolo, Michele and Knowles, Tuomas P J and Nelson, Matthew and Czekalska, Magdalena A and Musteikyte, Greta and Gachechiladze, Mariam A and Stephens, Christina A and Pasolli, H Amalia and Forrest, Lucy R and St George-Hyslop, Peter and Lippincott-Schwartz, Jennifer and Ward, Michael E} } @article {65050, title = {State-dependent decoupling of sensory and motor circuits underlies behavioral flexibility in Drosophila.}, journal = {Nature Neuroscience}, volume = {22}, year = {2019}, month = {2019 Jul 01}, pages = {1132-1139}, abstract = {

An approaching predator and self-motion toward an object can generate similar looming patterns on the retina, but these situations demand different rapid responses. How central circuits flexibly process visual cues to activate appropriate, fast motor pathways remains unclear. Here we identify two descending neuron (DN) types that control landing and contribute to visuomotor flexibility in Drosophila. For each, silencing impairs visually evoked landing, activation drives landing, and spike rate determines leg extension amplitude. Critically, visual responses of both DNs are severely attenuated during non-flight periods, effectively decoupling visual stimuli from the landing motor pathway when landing is inappropriate. The flight-dependence mechanism differs between DN types. Octopamine exposure mimics flight effects in one, whereas the other probably receives neuronal feedback from flight motor circuits. Thus, this sensorimotor flexibility arises from distinct mechanisms for gating action-specific descending pathways, such that sensory and motor networks are coupled or decoupled according to the behavioral state.

}, issn = {1546-1726}, doi = {10.1038/s41593-019-0413-4}, author = {Ache, Jan M and Namiki, Shigehiro and Lee, Allen and Branson, Kristin and Card, Gwyneth M} } @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 {65197, title = {Superresolution architecture of cornerstone focal adhesions in human pluripotent stem cells.}, journal = {Nature Communications}, volume = {10}, year = {2019}, month = {2019 Oct 18}, pages = {4756}, abstract = {

While it is clear that key transcriptional programmes are important for maintaining pluripotency, the requirement for cell adhesion to the extracellular matrix remains poorly defined. Human pluripotent stem cells\ (hPSCs) form colonies encircled by an actin ring and large stable cornerstone focal adhesions (FA). Using superresolution two-colour interferometric photo-activated localisation microscopy, we examine the three-dimensional architecture of cornerstone adhesions and report vertical lamination of FA proteins with three main structural features distinct from previously studied focal adhesions: 1) integrin β5 and talin are present at high density, at the edges of cornerstone FA, adjacent to a vertical kank-rich protein wall, 2) vinculin localises higher than previously reported, displaying a head-above-tail orientation, and 3) surprisingly, actin and α-actinin are present in two discrete z-layers. Finally, we report that depletion of kanks diminishes FA patterning, and actin organisation within the colony, indicating a role for kanks in hPSC colony architecture.

}, issn = {2041-1723}, doi = {10.1038/s41467-019-12611-w}, author = {Stubb, Aki and Guzm{\'a}n, Camilo and N{\"a}rv{\"a}, Elisa and Aaron, Jesse and Chew, Teng-Leong and Saari, Markku and Miihkinen, Mitro and Jacquemet, Guillaume and Ivaska, Johanna} } @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 {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 {49520, title = {Brain-wide organization of neuronal activity and convergent sensorimotor transformations in larval zebrafish.}, journal = {Neuron}, volume = {100}, year = {2018}, month = {2018 Nov 21}, pages = {876-890.e5}, abstract = {

Simultaneous recordings of large populations of neurons in behaving animals allow detailed observation of high-dimensional, complex brain activity. However, experimental approaches often focus on singular behavioral paradigms or brain areas. Here, we recorded whole-brain neuronal activity of larval zebrafish presented with a battery of visual stimuli while recording fictive motor output. We identified neurons tuned to each stimulus type and motor output and discovered groups of neurons in the anterior hindbrain that respond to different stimuli eliciting similar behavioral responses. These convergent sensorimotor representations were only weakly correlated to instantaneous motor activity, suggesting that they critically inform, but do not directly generate, behavioral choices. To catalog brain-wide activity beyond explicit sensorimotor processing, we developed an unsupervised clustering technique that organizes neurons into functional groups. These analyses enabled a broad overview of the functional organization of the brain and revealed numerous brain nuclei whose neurons exhibit concerted activity patterns.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2018.09.042}, author = {Chen, Xiuye and Mu, Yu and Hu, Yu and Kuan, Aaron T and Nikitchenko, Maxim and Randlett, Owen and Chen, Alex B and Gavornik, Jeffery P and Sompolinsky, Haim and Engert, Florian and Ahrens, Misha B} } @article {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 {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 {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 {49478, title = {Correlated evolution of two copulatory organs via a single cis-regulatory nucleotide change.}, journal = {Current Biology : CB}, volume = {28}, year = {2018}, month = {2018 Oct 05}, pages = {3450-7}, abstract = {

Diverse traits often covary between species [1-3]. The possibility that a single mutation could contribute to the evolution of several characters between species [3] is rarely investigated as relatively few cases are dissected at the nucleotide level. Drosophila santomea has evolved additional sex comb sensory teeth on its legs and has lost two sensory bristles on its genitalia. We present evidence that a single nucleotide substitution in an enhancer of the scute gene contributes to both changes. The mutation alters a binding site for the Hox protein Abdominal-B in the developing genitalia, leading to bristle loss, and for another factor in the developing leg, leading to bristle gain. Our study suggests that morphological evolution between species can occur through a single nucleotide change affecting several sexually dimorphic traits. VIDEO ABSTRACT.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2018.08.047}, author = {Nagy, Olga and Nuez, Isabelle and Savisaar, Rosina and Peluffo, Alexandre E and Yassin, Amir and Lang, Michael and Stern, David L and Matute, Daniel R and David, Jean R and Courtier-Orgogozo, Virginie} } @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 {49546, title = {Developmental pattern and structural factors of dendritic survival in cerebellar granule cells in vivo.}, journal = {Scientific Reports}, volume = {8}, year = {2018}, month = {2018 Dec 03}, pages = {17561}, abstract = {

Granule cells (GCs) in the cerebellar cortex are important for sparse encoding of afferent sensorimotor information. Modeling studies show that GCs can perform their function most effectively when they have four dendrites. Indeed, mature GCs have four short dendrites on average, each terminating in a claw-like ending that receives both excitatory and inhibitory inputs. Immature GCs, however, have significantly more dendrites-all without claws. How these redundant dendrites are refined during development is largely unclear. Here, we used in vivo time-lapse imaging and immunohistochemistry to study developmental refinement of GC dendritic arbors and its relation to synapse formation. We found that while the formation of dendritic claws stabilized the dendrites, the selection of surviving dendrites was made before claw formation, and longer immature dendrites had a significantly higher chance of survival than shorter dendrites. Using immunohistochemistry, we show that glutamatergic and GABAergic synapses are transiently formed on immature GC dendrites, and the number of GABAergic, but not glutamatergic, synapses correlates with the length of immature dendrites. Together, these results suggest a potential role of transient GABAergic synapses on dendritic selection and show that preselected dendrites are stabilized by the formation of dendritic claws-the site of mature synapses.

}, issn = {2045-2322}, doi = {10.1038/s41598-018-35829-y}, author = {Dhar, Matasha and Hantman, Adam W and Nishiyama, Hiroshi} } @article {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 {49094, title = {Integrative structure and functional anatomy of a nuclear pore complex.}, journal = {Nature}, volume = {555}, year = {2018}, month = {2018 Mar 14}, pages = {475-82}, abstract = {

Nuclear pore complexes play central roles as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm. However, their large size and dynamic nature have impeded a full structural and functional elucidation. Here we determined the structure of the entire 552-protein nuclear pore complex of the yeast Saccharomyces cerevisiae at sub-nanometre precision by satisfying a wide range of data relating to the molecular arrangement of its constituents. The nuclear pore complex incorporates sturdy diagonal columns and connector cables attached to these columns, imbuing the structure with strength and flexibility. These cables also tie together all other elements of the nuclear pore complex, including membrane-interacting regions, outer rings and RNA-processing platforms. Inwardly directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized into distinct functional units. This integrative structure enables us to rationalize the architecture, transport mechanism and evolutionary origins of the nuclear pore complex.

}, issn = {1476-4687}, doi = {10.1038/nature26003}, author = {Kim, Seung Joong and Fernandez-Martinez, Javier and Nudelman, Ilona and Shi, Yi and Zhang, Wenzhu and Raveh, Barak and Herricks, Thurston and Slaughter, Brian D and Hogan, Joanna A and Upla, Paula and Chemmama, Ilan E and Pellarin, Riccardo and Echeverria, Ignacia and Shivaraju, Manjunatha and Chaudhury, Azraa S and Wang, Junjie and Williams, Rosemary and Unruh, Jay R and Greenberg, Charles H and Jacobs, Erica Y and Yu, Zhiheng and de la Cruz, M Jason and Mironska, Roxana and Stokes, David L and Aitchison, John D and Jarrold, Martin F and Gerton, Jennifer L and Ludtke, Steven J and Akey, Christopher W and Chait, Brian T and Sali, Andrej and Rout, Michael P} } @article {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 {49587, title = {Mapping Neurotransmitter Identity in the Whole-Mount Brain Using Multiplex High-Throughput Fluorescence Hybridization.}, journal = {Genetics}, volume = {211}, year = {2018}, month = {2018 Dec 18}, pages = {473-82}, abstract = {

Identifying the neurotransmitters used by specific neurons is a critical step in understanding the function of neural circuits. However, methods for the consistent and efficient detection of neurotransmitter markers remain limited. Fluorescence hybridization (FISH) enables direct labeling of type-specific mRNA in neurons. Recent advances in FISH allow this technique to be carried out in intact tissue samples such as whole-mount brains. Here, we present a FISH platform for high-throughput detection of eight common neurotransmitter phenotypes in brains. We greatly increase FISH throughput by processing samples mounted on coverslips and optimizing fluorophore choice for each probe to facilitate multiplexing. As application examples, we demonstrate cases of neurotransmitter co-expression, reveal neurotransmitter phenotypes of specific cell types and explore the onset of neurotransmitter expression in the developing optic lobe. Beyond neurotransmitter markers, our protocols can in principle be used for large scale FISH detection of any mRNA in whole-mount fly brains.

}, issn = {1943-2631}, doi = {10.1534/genetics.118.301749}, author = {Meissner, Geoffrey W and Nern, Aljoscha and Singer, Robert H and Wong, Allan M and Malkesman, Oz and Long, Xi} } @article {65030, title = {Membrane bending moduli of coexisting liquid phases containing transmembrane peptide.}, journal = {Biophys J}, volume = {114}, year = {2018}, month = {2018 May 08}, pages = {2152-2164}, abstract = {

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

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

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

}, issn = {2041-1723}, doi = {10.1038/s41467-018-05862-6}, author = {Napolitano, Gennaro and Esposito, Alessandra and Choi, Heejun and Matarese, Maria and Benedetti, Valerio and Di Malta, Chiara and Monfregola, Jlenia and Medina, Diego Luis and Lippincott-Schwartz, Jennifer and Ballabio, Andrea} } @article {49529, title = {Neuron-subtype-specific expression, interaction affinities, and specificity determinants of DIP/Dpr cell recognition proteins.}, journal = {Neuron}, volume = {100}, year = {2018}, month = {2018 Nov 12}, pages = {1385-1400}, abstract = {

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

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

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

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

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

}, keywords = {Animals, Cells, Cultured, DNA Helicases, DNA-Binding Proteins, Female, GATA Transcription Factors, Induced Pluripotent Stem Cells, Male, Mi-2 Nucleosome Remodeling and Deacetylase Complex, Mice, Mice, Inbred C57BL, Mice, Inbred CBA, Mice, Knockout, Mice, Transgenic, Transcription Factors}, issn = {1875-9777}, doi = {10.1016/j.stem.2018.07.004}, author = {Mor, Nofar and Rais, Yoach and Sheban, Daoud and Peles, Shani and Aguilera-Castrejon, Alejandro and Zviran, Asaf and Elinger, Dalia and Viukov, Sergey and Geula, Shay and Krupalnik, Vladislav and Zerbib, Mirie and Chomsky, Elad and Lasman, Lior and Shani, Tom and Bayerl, Jonathan and Gafni, Ohad and Hanna, Suhair and Buenrostro, Jason D and Hagai, Tzachi and Masika, Hagit and Vainorius, Gintautas and Bergman, Yehudit and Greenleaf, William J and Esteban, Miguel A and Elling, Ulrich and Levin, Yishai and Massarwa, Rada and Merbl, Yifat and Novershtern, Noa and Hanna, Jacob H} } @article {49366, title = {Optimization of fluorophores for chemical tagging and immunohistochemistry of Drosophila neurons.}, journal = {PLoS One}, volume = {13}, year = {2018}, month = {2018 Aug 15}, pages = {e0200759}, abstract = {

The use of genetically encoded {\textquoteright}self-labeling tags{\textquoteright} with chemical fluorophore ligands enables rapid labeling of specific cells in neural tissue. To improve the chemical tagging of neurons, we synthesized and evaluated new fluorophore ligands based on Cy, Janelia Fluor, Alexa Fluor, and ATTO dyes and tested these with recently improved Drosophila melanogaster transgenes. We found that tissue clearing and mounting in DPX substantially improves signal quality when combined with specific non-cyanine fluorophores. We compared and combined this labeling technique with standard immunohistochemistry in the Drosophila brain.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0200759}, author = {Meissner, Geoffrey W and Grimm, Jonathan B and Johnston, Rebecca M and Sutcliffe, Ben and Ng, Julian and Jefferis, Gregory S X E and Cachero, Sebastian and Lavis, Luke D and Malkesman, Oz} } @article {48976, title = {Optogenetic dissection of descending behavioral control in Drosophila.}, journal = {eLife}, year = {2018}, month = {2018}, pages = {e34275}, abstract = {

In most animals, the brain makes behavioral decisions that are transmitted by descending neurons to the nerve cord circuitry that produces behaviors. In insects, only a few descending neurons have been associated with specific behaviors. To explore how descending neurons control an insect{\textquoteright}s movements, we developed a novel method to systematically assay the behavioral effects of activating individual neurons on freely behaving terrestrial\ D. melanogaster. We calculated a two-dimensional representation of the entire behavior space explored by these flies and we associated descending neurons with specific behaviors by identifying regions of this space that were visited with increased frequency during optogenetic activation. Applying this approach across a large collection of descending neurons, we found that (1) activation of most of the descending neurons drove stereotyped behaviors, (2) in many cases multiple descending neurons activated similar behaviors, and (3) optogenetically-activated behaviors were often dependent on the behavioral state prior to activation.

}, doi = {10.7554/eLife.34275}, author = {Cande, Jessica and Namiki, Shigehiro and Qiu, Jirui and Korff, Wyatt and Card, Gwyneth M and Shaevitz, Joshua W and Stern, David L and Berman, Gordon J} } @article {49049, title = {Physical basis of amyloid fibril polymorphism.}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {2018 Feb 16}, pages = {699}, abstract = {

Polymorphism is a key feature of amyloid fibril structures but it remains challenging to explain these variations for a particular sample. Here, we report electron cryomicroscopy-based reconstructions from different fibril morphologies formed by a peptide fragment from an amyloidogenic immunoglobulin light chain. The observed fibril morphologies vary in the number and cross-sectional arrangement of a structurally conserved building block. A comparison with the theoretically possible constellations reveals the experimentally observed spectrum of fibril morphologies to be governed by opposing sets of forces that primarily arise from the β-sheet twist, as well as peptide-peptide interactions within the fibril cross-section. Our results provide a framework for rationalizing and predicting the structure and polymorphism of cross-β fibrils, and suggest that a small number of physical parameters control the observed fibril architectures.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-03164-5}, author = {Close, William and Neumann, Matthias and Schmidt, Andreas and Hora, Manuel and Annamalai, Karthikeyan and Schmidt, Matthias and Reif, Bernd and Schmidt, Volker and Grigorieff, Nikolaus and F{\"a}ndrich, Marcus} } @article {49233, title = {Reinforcement signaling of punishment versus relief in fruit flies.}, journal = {Learning \& Memory (Cold Spring Harbor, N.Y.)}, volume = {25}, year = {2018}, month = {2018 Jun}, pages = {247-257}, abstract = {

Painful events establish opponent memories: cues that precede pain are remembered negatively, whereas cues that follow pain, thus coinciding with relief are recalled positively. How do individual reinforcement-signaling neurons contribute to this "timing-dependent valence-reversal?" We addressed this question using an optogenetic approach in the fruit fly. Two types of fly dopaminergic neuron, each comprising just one paired cell, indeed established learned avoidance of odors that preceded their photostimulation during training, and learned approach to odors that followed the photostimulation. This is in striking parallel to punishment versus relief memories reinforced by a real noxious event. For only one of these neuron types, both effects were strong enough for further analyses. Notably, interfering with dopamine biosynthesis in these neurons partially impaired the punishing effect, but not the relieving after-effect of their photostimulation. We discuss how this finding constraints existing computational models of punishment versus relief memories and introduce a new model, which also incorporates findings from mammals. Furthermore, whether using dopaminergic neuron photostimulation or a real noxious event, more prolonged punishment led to stronger relief. This parametric feature of relief may also apply to other animals and may explain particular aspects of related behavioral dysfunction in humans.

}, issn = {1549-5485}, doi = {10.1101/lm.047308.118}, author = {K{\"o}nig, Christian and Khalili, Afshin and Ganesan, Mathangi and Nishu, Amrita P and Garza, Alejandra P and Niewalda, Thomas and Gerber, Bertram and Aso, Yoshinori and Yarali, Ayse} } @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 {49221, title = {Single molecule fate of HIV-1 envelope reveals late-stage viral lattice incorporation.}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {2018 May 10}, pages = {1861}, abstract = {

Human immunodeficiency virus type 1 (HIV-1) assembly occurs on the inner leaflet of the host cell plasma membrane, incorporating the essential viral envelope glycoprotein (Env) within a budding lattice of HIV-1 Gag structural proteins. The mechanism by which Env incorporates into viral particles remains poorly understood. To determine the mechanism of recruitment of Env to assembly sites, we interrogate the subviral angular distribution of Env on cell-associated virus using multicolor, three-dimensional (3D) superresolution microscopy. We demonstrate that, in a manner dependent on cell type and on the long cytoplasmic tail of Env, the distribution of Env is biased toward the necks of cell-associated particles. We postulate that this neck-biased distribution is regulated by vesicular retention and steric complementarity of Env during independent Gag lattice formation.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-04220-w}, author = {Buttler, Carmen A and Pezeshkian, Nairi and Fernandez, Melissa V and Aaron, Jesse and Norman, Sofya and Freed, Eric O and Van Engelenburg, Schuyler B} } @article {49418, title = {Speed dependent descending control of freezing behavior in Drosophila melanogaster.}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {2018 Sep 12}, pages = {3697}, abstract = {

The most fundamental choice an animal has to make when it detects a threat is whether to freeze, reducing its chances of being noticed, or to flee to safety. Here we show that Drosophila melanogaster exposed to looming stimuli in a confined arena either freeze or flee. The probability of freezing versus fleeing is modulated by the fly{\textquoteright}s walking speed at the time of threat, demonstrating that freeze/flee decisions depend on behavioral state. We describe a pair of descending neurons crucially implicated in freezing. Genetic silencing of DNp09 descending neurons disrupts freezing yet does not prevent fleeing. Optogenetic activation of both DNp09 neurons induces running and freezing in a state-dependent manner. Our findings establish walking speed as a key factor in defensive response choices and reveal a pair of descending neurons as a critical component in the circuitry mediating selection and execution of freezing or fleeing behaviors.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-05875-1}, author = {Zacarias, Ricardo and Namiki, Shigehiro and Card, Gwyneth M and Vasconcelos, Maria Lu{\'\i}sa and Moita, Marta A} } @article {49584, title = {Stem cells repurpose proliferation to contain a breach in their niche barrier.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Dec 06}, abstract = {

Adult stem cells are responsible for life-long tissue maintenance. They reside in and interact with specialized tissue microenvironments (niches). Using murine hair follicle as a model, we show that when junctional perturbations in the niche disrupt barrier function, adjacent stem cells dramatically change their transcriptome independent of bacterial invasion and become capable of directly signaling to and recruiting immune cells. Additionally, these stem cells elevate cell cycle transcripts which reduce their quiescence threshold, enabling them to selectively proliferate within this microenvironment of immune distress cues. However, rather than mobilizing to fuel new tissue regeneration, these ectopically proliferative stem cells remain within their niche to contain the breach. Together, our findings expose a potential communication relay system that operates from the niche to the stem cells to the immune system and back. The repurposing of proliferation by these stem cells patch the breached barrier, stoke the immune response and restore niche integrity.

}, issn = {2050-084X}, doi = {10.7554/eLife.41661}, author = {Lay, Kenneth and Yuan, Shaopeng and Gur-Cohen, Shiri and Miao, Yuxuan and Han, Tianxiao and Naik, Shruti and Pasolli, H Amalia and Larsen, Samantha B and Fuchs, Elaine} } @article {49006, title = {Sub-{\r a}ngstr{\"o}m cryo-EM structure of a prion protofibril reveals a polar clasp.}, journal = {Nature Structural \& Molecular Biology}, year = {2018}, month = {2018 Jan 15}, abstract = {

The atomic structure of the infectious, protease-resistant, β-sheet-rich and fibrillar mammalian prion remains unknown. Through the cryo-EM method MicroED, we reveal the sub-{\r a}ngstr{\"o}m-resolution structure of a protofibril formed by a wild-type segment from the β2-α2 loop of the bank vole prion protein. The structure of this protofibril reveals a stabilizing network of hydrogen bonds that link polar zippers within a sheet, producing motifs we have named {\textquoteright}polar clasps{\textquoteright}.

}, issn = {1545-9985}, doi = {10.1038/s41594-017-0018-0}, author = {Gallagher-Jones, Marcus and Glynn, Calina and Boyer, David R and Martynowycz, Michael W and Hernandez, Evelyn and Miao, Jennifer and Zee, Chih-Te and Novikova, Irina V and Goldschmidt, Lukasz and McFarlane, Heather T and Helguera, Gustavo F and Evans, James E and Sawaya, Michael R and Cascio, Duilio and Eisenberg, David S and Gonen, Tamir and Rodriguez, Jose A} } @article {64998, title = {Superresolution architecture of pluripotency guarding adhesions.}, journal = {bioRxiv}, year = {2018}, month = {2018 Sep 19}, abstract = {

Human pluripotent stem cells (hPSC) can generate almost all adult cell lineages. While it is clear that key transcriptional programmes are important elements for maintaining pluripotency, the equally essential requirement for cell adhesion to specific extracellular matrix components remains poorly defined. Our recent observation that hPSC colonies form unusually large {\textquotedblleft}cornerstone{\textquotedblright} focal adhesions (FA), distinct from parental somatic cells, that are lost following differentiation, emphasises the potential of these atypical FA as gatekeepers of pluripotency. Here, using nanopatterns, we further demonstrate that physical restriction of adhesion size, in hPSC colonies, is sufficient to trigger differentiation. Using superresolution two-colour interfero-metric photo-activated localization microscopy (iPALM), we examined the three-dimensional architecture of these cornerstone adhesions and report vertical lamination of FA proteins with three main structural peculiarities: 1) integrin β5 and talin are present at high density, at the edges of cornerstone FA, adjacent to a vertical kank-rich protein wall. 2) Vinculin localises higher than expected with respect to the substrata and displays a head-above-tail orientation, and 3) surprisingly, actin and α-actinin are present in two discrete layers, a previously undescribed localisation for these proteins. Finally, we report that depletion of kanks diminishes FA patterning, and actin organisation within the colony, indicating a key role for kanks in hPSC colony architecture.

}, doi = {10.1101/402305}, author = {Aki Stubb and Camilo Guzm{\'a}n and Elisa N{\"a}rv{\"a} and Jesse Aaron and Teng-Leong Chew and Markku Saari and Mitro Miihkinen and Guillaume Jacquemet and Johanna Ivaska} } @article {49220, title = {Synaptic cleft segmentation in non-isotropic volume electron microscopy of the complete Drosophila brain.}, journal = {Medical Image Computing and Computer Assisted Intervention {\textendash} MICCAI 2018}, year = {2018}, month = {2018 Sep 26}, pages = {317-25}, abstract = {

Neural circuit reconstruction at single synapse resolution is increasingly recognized as crucially important to decipher the function of biological nervous systems. Volume electron microscopy in serial transmission or scanning mode has been demonstrated to provide the necessary resolution to segment or trace all neurites and to annotate all synaptic connections.\ 
Automatic annotation of synaptic connections has been done successfully in near isotropic electron microscopy of vertebrate model organisms. Results on non-isotropic data in insect models, however, are not yet on par with human annotation.\ 
We designed a new 3D-U-Net architecture to optimally represent isotropic fields of view in non-isotropic data. We used regression on a signed distance transform of manually annotated synaptic clefts of the CREMI challenge dataset to train this model and observed significant improvement over the state of the art.\ 
We developed open source software for optimized parallel prediction on very large volumetric datasets and applied our model to predict synaptic clefts in a 50 tera-voxels dataset of the complete Drosophila brain. Our model generalizes well to areas far away from where training data was available.

}, doi = {10.1007/978-3-030-00934-2_36}, author = {Heinrich, Larissa and Funke, Jan and Pape, Constantin and Nunez-Iglesias, Juan and Saalfeld, Stephan} } @article {49470, title = {Thy1 transgenic mice expressing the red fluorescent calcium indicator jRGECO1a for neuronal population imaging in vivo.}, journal = {PloS One}, volume = {13}, year = {2018}, month = {2018}, pages = {e0205444}, abstract = {

Calcium imaging is commonly used to measure the neural activity of large groups of neurons in mice. Genetically encoded calcium indicators (GECIs) can be delivered for this purpose using non-invasive genetic methods. Compared to viral gene transfer, transgenic targeting of GECIs provides stable long-term expression and obviates the need for invasive viral injections. Transgenic mice expressing the green GECI GCaMP6 are already widely used. Here we present the generation and characterization of transgenic mice expressing the sensitive red GECI jRGECO1a, driven by the Thy1 promoter. Four transgenic lines with different expression patterns showed sufficiently high expression for cellular in vivo imaging. We used two-photon microscopy to characterize visual responses of individual neurons in the visual cortex in vivo. The signal-to-noise ratio in transgenic mice was comparable to, or better than, mice transduced with adeno-associated virus. In addition, we show that Thy1-jRGECO1a transgenic mice are useful for transcranial population imaging and functional mapping using widefield fluorescence microscopy. We also demonstrate imaging of visual responses in retinal ganglion cells in vitro. Thy1-jRGECO1a transgenic mice are therefore a useful addition to the toolbox for imaging activity in intact neural networks.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0205444}, author = {Dana, Hod and Novak, Ondrej and Guardado-Montesino, Michael and Fransen, James W and Hu, Amy and Borghuis, Bart G and Guo, Caiying and Kim, Douglas S and Svoboda, Karel} } @article {49354, title = {Triggered cell-cell fusion assay for cytoplasmic and organelle intermixing studies.}, journal = {Current Protocols in Cell Biology}, volume = {81}, year = {2018}, month = {2018 Aug 13}, pages = {e61}, abstract = {

Different multicellular organisms undergo cell-cell fusion to form functional syncytia that support specialized functions necessary for proper development and survival. For years, monitoring the structural consequences of this process using live-cell imaging has been challenging due to the unpredictable timing of cell fusion events in tissue systems. Here we present a triggered vesicular stomatitis virus G-protein (VSV-G)-mediated cell-cell fusion assay that can be used to synchronize fusion between cells. This allows the study of cellular changes that occur during cell fusion. The process is induced using a fast wash of low pH isotonic buffer, promoting the fusion of plasma membranes of two or more adjacent cells within seconds. This approach is suitable for studying mixing of small cytoplasmic molecules between fusing cells as well as changes in organelle distribution and dynamics. {\textcopyright} 2018 by John Wiley \& Sons, Inc.

}, issn = {1934-2616}, doi = {10.1002/cpcb.61}, author = {Feliciano, Daniel and Nixon-Abell, Jonathon and Lippincott-Schwartz, Jennifer} } @article {49386, title = {An unbiased template of the Drosophila brain and ventral nerve cord.}, journal = {bioRxiv}, year = {2018}, month = {2018 Jul 25}, abstract = {

The fruit fly Drosophila melanogaster is an important model organism for neuroscience with a wide array of genetic tools that enable the mapping of individuals neurons and neural subtypes. Brain templates are essential for comparative biological studies because they enable analyzing many individuals in a common reference space. Several central brain templates exist for Drosophila, but every one is either biased, uses sub-optimal tissue preparation, is imaged at low resolution, or does not account for artifacts. No publicly available Drosophila ventral nerve cord template currently exists. In this work, we created high-resolution templates of the Drosophila brain and ventral nerve cord using the best-available technologies for imaging, artifact correction, stitching, and template construction using groupwise registration. We evaluated our central brain template against the four most competitive, publicly available brain templates and demonstrate that ours enables more accurate registration with fewer local deformations in shorter time.

}, doi = {10.1101/376384}, author = {Bogovic, John A and Otsuna, Hideo and Heinrich, Larissa and Ito, Masayoshi and Jeter, Jennifer and Meissner, Geoffrey W and Nern, Aljoscha and Colonell, Jennifer and Malkesman, Oz and Saalfeld, Stephan} } @article {49058, title = {VPS4 is a dynamic component of the centrosome that regulates centrosome localization of γ-tubulin, centriolar satellite stability and ciliogenesis.}, journal = {Scientific Reports}, volume = {8}, year = {2018}, month = {2018 Feb 20}, pages = {3353}, abstract = {

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

}, issn = {2045-2322}, doi = {10.1038/s41598-018-21491-x}, author = {Ott, Carolyn and Nachmias, Dikla and Adar, Shai and Jarnik, Michal and Sherman, Shachar and Birnbaum, Ramon Y and Lippincott-Schwartz, Jennifer and Elia, Natalie} } @article {48843, title = {Actin-based protrusions of migrating neutrophils are intrinsically lamellar and facilitate direction changes.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Sep 26}, abstract = {

Leukocytes and other amoeboid cells change shape as they move, forming highly dynamic, actin-filled pseudopods. Although we understand much about the architecture and dynamics of thin lamellipodia made by slow-moving cells on flat surfaces, conventional light microscopy lacks the spatial and temporal resolution required to track complex pseudopods of cells moving in three dimensions. We therefore employed lattice light sheet microscopy to perform three-dimensional, time-lapse imaging of neutrophil-like HL-60 cells crawling through collagen matrices. To analyze three-dimensional pseudopods we: (i) developed fluorescent probe combinations that distinguish cortical actin from dynamic, pseudopod-forming actin networks, and (ii) adapted molecular visualization tools from structural biology to render and analyze complex cell surfaces. Surprisingly, three-dimensional pseudopods turn out to be composed of thin (\<0.75 {\textmu}m), flat sheets that sometimes interleave to form rosettes. Their laminar nature is not templated by an external surface, but likely reflects a linear arrangement of regulatory molecules. Although we find that Arp2/3-dependent pseudopods are dispensable for three-dimensional locomotion, their elimination dramatically decreases the frequency of cell turning, and pseudopod dynamics increase when cells change direction, highlighting the important role pseudopods play in pathfinding.

}, issn = {2050-084X}, doi = {10.7554/eLife.26990}, author = {Fritz-Laylin, Lillian K and Riel-Mehan, Megan and Chen, Bi-Chang and Lord, Samuel J and Goddard, Thomas D and Ferrin, Thomas E and Nicholson-Dykstra, Susan M and Higgs, Henry and Johnson, Graham T and Betzig, Eric and Mullins, R Dyche} } @article {48156, title = {Atomic structures of fibrillar segments of hIAPP suggest tightly mated β-sheets are important for cytotoxicity.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Jan 03}, abstract = {

hIAPP fibrils are associated with Type-II Diabetes, but the link of hIAPP structure to islet cell death remains elusive. Here we observe that hIAPP fibrils are cytotoxic to cultured pancreatic β-cells, leading us to determine the structure and cytotoxicity of protein segments composing the amyloid spine of hIAPP. Using the cryoEM method MicroED, we discover that one segment, 19-29 S20G, forms pairs of β-sheets mated by a dry interface that share structural features with and are similarly cytotoxic to full-length hIAPP fibrils. In contrast, a second segment, 15-25 WT, forms non-toxic labile β-sheets. These segments possess different structures and cytotoxic effects, however, both can seed full-length hIAPP, and cause hIAPP to take on the cytotoxic and structural features of that segment. These results suggest that protein segment structures represent polymorphs of their parent protein and that segment 19-29 S20G may serve as a model for the toxic spine of hIAPP.

}, issn = {2050-084X}, doi = {10.7554/eLife.19273}, author = {Krotee, Pascal and Rodriguez, Jose A and Sawaya, Michael R and Cascio, Duilio and Reyes, Francis E and Shi, Dan and Hattne, Johan and Nannenga, Brent L and Oskarsson, Marie E and Philipp, Stephan and Griner, Sarah and Jiang, Lin and Glabe, Charles G and Westermark, Gunilla T and Gonen, Tamir and Eisenberg, David S} } @article {48982, title = {Behavioral state modulates the ON visual motion pathway of Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, year = {2017}, month = {2017 Dec 18}, pages = {E102-11}, abstract = {

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

}, issn = {1091-6490}, doi = {10.1073/pnas.1703090115}, author = {Strother, James A and Wu, Shiuan-Tze and Rogers, Edward M and Eliason, Jessica L M and Wong, Allan M and Nern, Aljoscha and Reiser, Michael B} } @article {48809, title = {Cohesin can remain associated with chromosomes during DNA replication.}, journal = {Cell Reports}, volume = {20}, year = {2017}, month = {2017 Sep 19}, pages = {2749-55}, abstract = {

To ensure disjunction to opposite poles during anaphase, sister chromatids must be held together following DNA replication. This is mediated by cohesin, which is thought to entrap sister DNAs inside a tripartite ring composed of its Smc and kleisin (Scc1) subunits. How such structures are created during S phase is poorly understood, in particular whether they are derived from complexes that had entrapped DNAs prior to replication. To address this, we used selective photobleaching to determine whether cohesin associated with chromatin in G1 persists in\ situ after replication. We developed a non-fluorescent HaloTag ligand to discriminate the fluorescence recovery signal from labeling of newly synthesized Halo-tagged Scc1 protein (pulse-chase or pcFRAP). In cells where cohesin turnover is inactivated by deletion of WAPL, Scc1 can remain associated with chromatin throughout S phase. These findings suggest that cohesion might be generated by cohesin that is already bound to un-replicated DNA.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2017.08.092}, author = {Rhodes, James D P and Haarhuis, Judith H I and Grimm, Jonathan B and Rowland, Benjamin D and Lavis, Luke D and Nasmyth, Kim A} } @article {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 {48488, title = {Confirmation of five novel susceptibility loci for systemic lupus erythematosus (SLE) and integrated network analysis of 82 SLE susceptibility loci.}, journal = {Human Molecular Genetics}, volume = {26}, year = {2017}, month = {2017 Mar 15}, pages = {1205-1216}, abstract = {

We recently identified ten novel SLE susceptibility loci in Asians and uncovered several additional suggestive loci requiring further validation. This study aimed to replicate five of these suggestive loci in a Han Chinese cohort from Hong Kong, followed by meta-analysis (11,656 cases and 23,968 controls) on previously reported Asian and European populations, and to perform bioinformatic analyses on all 82 reported SLE loci to identify shared regulatory signatures. We performed a battery of analyses for these five loci, as well as joint analyses on all 82 SLE loci. All five loci passed genome-wide significance: MYNN (rs10936599, Pmeta = 1.92 {\texttimes} 10-13, OR = 1.14), ATG16L2 (rs11235604, Pmeta = 8.87 {\texttimes} 10 -12, OR = 0.78), CCL22 (rs223881, Pmeta = 5.87 {\texttimes} 10-16, OR = 0.87), ANKS1A (rs2762340, Pmeta = 4.93 {\texttimes} 10-15, OR = 0.87) and RNASEH2C (rs1308020, Pmeta = 2.96 {\texttimes} 10-19, OR = 0.84) and co-located with annotated gene regulatory elements. The novel loci share genetic signatures with other reported SLE loci, including effects on gene expression, transcription factor binding, and epigenetic characteristics. Most (56\%) of the correlated (r2 \> 0.8) SNPs from the 82 SLE loci were implicated in differential expression (9.81 {\texttimes} 10-198 \< P \< 5 {\texttimes} 10-3) of cis-genes. Transcription factor binding sites for p53, MEF2A and E2F1 were significantly (P \< 0.05) over-represented in SLE loci, consistent with apoptosis playing a critical role in SLE. Enrichment analysis revealed common pathways, gene ontology, protein domains, and cell type-specific expression. In summary, we provide evidence of five novel SLE susceptibility loci. Integrated bioinformatics using all 82 loci revealed that SLE susceptibility loci share many gene regulatory features, suggestive of conserved mechanisms of SLE etiopathogenesis.

}, keywords = {Adaptor Proteins, Signal Transducing, Asian Continental Ancestry Group, Autophagy-Related Proteins, Chemokine CCL22, Gene Expression Regulation, Genetic Predisposition to Disease, Genome-Wide Association Study, Genotype, Humans, Kruppel-Like Transcription Factors, Lupus Erythematosus, Systemic, Polymorphism, Single Nucleotide, Ribonuclease H}, issn = {1460-2083}, doi = {10.1093/hmg/ddx026}, author = {Molineros, Julio E and Yang, Wanling and Zhou, Xu-Jie and Sun, Celi and Okada, Yukinori and Zhang, Huoru and Heng Chua, Kek and Lau, Yu-Lung and Kochi, Yuta and Suzuki, Akari and Yamamoto, Kazuhiko and Ma, Jianyang and Bang, So-Young and Lee, Hye-Soon and Kim, Kwangwoo and Bae, Sang-Cheol and Zhang, Hong and Shen, Nan and Looger, Loren L and Nath, Swapan K} } @article {48419, title = {Defects in ER-endosome contacts impact lysosome function in hereditary spastic paraplegia.}, journal = {The Journal of Cell Biology}, volume = {216}, year = {2017}, month = {2017 Apr 07}, pages = {1337-55}, abstract = {

Contacts between endosomes and the endoplasmic reticulum (ER) promote endosomal tubule fission, but the mechanisms involved and consequences of tubule fission failure are incompletely understood. We found that interaction between the microtubule-severing enzyme spastin and the ESCRT protein IST1 at ER-endosome contacts drives endosomal tubule fission. Failure of fission caused defective sorting of mannose 6-phosphate receptor, with consequently disrupted lysosomal enzyme trafficking and abnormal lysosomal morphology, including in mouse primary neurons and human stem cell-derived neurons. Consistent with a role for ER-mediated endosomal tubule fission in lysosome function, similar lysosomal abnormalities were seen in cellular models lacking the WASH complex component strumpellin or the ER morphogen REEP1. Mutations in spastin, strumpellin, or REEP1 cause hereditary spastic paraplegia (HSP), a disease characterized by axonal degeneration. Our results implicate failure of the ER-endosome contact process in axonopathy and suggest that coupling of ER-mediated endosomal tubule fission to lysosome function links different classes of HSP proteins, previously considered functionally distinct, into a unifying pathway for axonal degeneration.

}, issn = {1540-8140}, doi = {10.1083/jcb.201609033}, author = {Allison, Rachel and Edgar, James R and Pearson, Guy and Rizo, Tania and Newton, Timothy and G{\"u}nther, Sven and Berner, Fiamma and Hague, Jennifer and Connell, James W and Winkler, J{\"u}rgen and Lippincott-Schwartz, Jennifer and Beetz, Christian and Winner, Beate and Reid, Evan} } @article {48648, title = {Desensitized D2 autoreceptors are resistant to trafficking.}, journal = {Scientific Reports}, volume = {7}, year = {2017}, month = {2017 Jun 29}, pages = {4379}, abstract = {

Dendritic release of dopamine activates dopamine D2 autoreceptors, which are inhibitory G protein-coupled receptors (GPCRs), to decrease the excitability of dopamine neurons. This study used tagged D2 receptors to identify the localization and distribution of these receptors in living midbrain dopamine neurons. GFP-tagged D2 receptors were found to be unevenly clustered on the soma and dendrites of dopamine neurons within the substantia nigra pars compacta (SNc). Physiological signaling and desensitization of the tagged receptors were not different from wild type receptors. Unexpectedly, upon desensitization the tagged D2 receptors were not internalized. When tagged D2 receptors were expressed in locus coeruleus neurons, a desensitizing protocol induced significant internalization. Likewise, when tagged {\textmu}-opioid receptors were expressed in dopamine neurons they too were internalized. The distribution and lack of agonist-induced internalization of D2 receptors on dopamine neurons indicate a purposefully regulated localization of these receptors.

}, issn = {2045-2322}, doi = {10.1038/s41598-017-04728-z}, author = {Robinson, Brooks G and Bunzow, James R and Grimm, Jonathan B and Lavis, Luke D and Dudman, Joshua T and Brown, Jennifer and Neve, Kim A and Williams, John T} } @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 {48414, title = {The emergence of directional selectivity in the visual motion pathway of Drosophila.}, journal = {Neuron}, volume = {94}, year = {2017}, month = {2017 Apr 05}, pages = {168-182.e10}, abstract = {

The perception of visual motion is critical for animal navigation, and flies are a prominent model system for exploring this neural computation. In Drosophila, the T4 cells of the medulla are directionally selective and necessary for ON motion behavioral responses. To examine the emergence of directional selectivity, we developed genetic driver lines for the neuron types with the most synapses onto T4 cells. Using calcium imaging, we found that these neuron types are not directionally selective and that selectivity arises in the T4 dendrites. By silencing each input neuron type, we identified which neurons are necessary for T4 directional selectivity and ON motion behavioral responses. We then determined the sign of the connections between these neurons and T4 cells using neuronal photoactivation. Our results indicate a computational architecture for motion detection that is a hybrid of classic theoretical models.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2017.03.010}, author = {Strother, James A and Wu, Shiuan-Tze and Wong, Allan M and Nern, Aljoscha and Rogers, Edward M and Le, Jasmine Q and Rubin, Gerald M and Reiser, Michael B} } @article {48490, title = {Enhanced FIB-SEM systems for large-volume 3D imaging.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 May 13}, abstract = {

Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) can automatically generate 3D images with superior z-axis resolution, yielding data that needs minimal image registration and related post-processing. Obstacles blocking wider adoption of FIB-SEM include slow imaging speed and lack of long-term system stability, which caps the maximum possible acquisition volume. Here we present techniques that accelerate image acquisition while greatly improving FIB-SEM reliability, allowing the system to operate for months and generating continuously imaged volumes \> 10(6) {\textmu}m(3). These volumes are large enough for connectomics, where the excellent z resolution can help in tracing of small neuronal processes and accelerate the tedious and time-consuming human proofreading effort. Even higher resolution can be achieved on smaller volumes. We present example data sets from mammalian neural tissue, Drosophila brain, and Chlamydomonas reinhardtii to illustrate the power of this novel high-resolution technique to address questions in both connectomics and cell biology.

}, issn = {2050-084X}, doi = {10.7554/eLife.25916}, author = {Xu, C Shan and Hayworth, Kenneth J and Lu, Zhiyuan and Grob, Patricia and Hassan, Ahmed M and Garc{\'\i}a-Cerd{\'a}n, Jos{\'e} G and Niyogi, Krishna K and Nogales, Eva and Weinberg, Richard J and Hess, Harald F} } @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} } @article {48600, title = {Feature integration drives probabilistic behavior in the Drosophila escape response.}, journal = {Neuron}, volume = {94}, year = {2017}, month = {2017 Jun 21}, pages = {1190-204}, abstract = {

Animals rely on dedicated sensory circuits to extract and encode environmental features. How individual neurons integrate and translate these features into behavioral responses remains a major question. Here, we identify a visual\ projection neuron\ type that conveys predator approach information to the\ Drosophila\ giant fiber (GF) escape circuit. Genetic removal of this input during looming stimuli reveals that it encodes angular expansion velocity, whereas other input cell type(s) encode angular size. Motor program selection and timing emerge from\ linear\ integration of these two features within the GF. Linear integration improves size detection invariance over prior models and appropriately biases motor selection to rapid,\ GF-mediated\ escapes during fast looms. Our findings suggest\ feature integration, and motor control may occur as simultaneous operations within the same neuron and establish the\ Drosophila\ escape circuit as a model system in which these computations may be further dissected at the circuit level.

}, doi = {10.1016/j.neuron.2017.05.036}, author = {von Reyn, Catherine R and Nern, Aljoscha and Williamson, W Ryan and Breads, Patrick and Wu, Ming and Namiki, Shigehiro and Card, Gwyneth M} } @article {48975, title = {The functional organization of descending sensory-motor pathways in Drosophila.}, journal = {eLife}, year = {2017}, month = {2018 Jun 26}, pages = {e34272}, abstract = {

In most animals, the brain controls the body via a set of descending neurons (DNs) that traverse the neck. DN activity activates, maintains or modulates locomotion and other behaviors. Individual DNs have been well-studied in species from insects to primates, but little is known about overall connectivity patterns across the DN population. We systematically investigated DN anatomy in\ Drosophila melanogaster\ and created over 100 transgenic lines targeting individual cell types. We identified roughly half of all\ Drosophila\ DNs and comprehensively map connectivity between sensory and motor neuropils in the brain and nerve cord, respectively. We find the nerve cord is a layered system of neuropils reflecting the fly{\textquoteright}s capability for two largely independent means of locomotion -- walking and flight -- using distinct sets of appendages. Our results reveal the basic functional map of descending pathways in flies and provide tools for systematic interrogation of neural circuits.

}, doi = {10.7554/eLife.34272}, author = {Namiki, Shigehiro and Dickinson, Michael H and Wong, Allan M and Korff, Wyatt and Card, Gwyneth M} } @article {48698, title = {Genetic and neuronal mechanisms governing the sex-specific interaction between sleep and sexual behaviors in Drosophila.}, journal = {Nature Communications}, volume = {8}, year = {2017}, month = {2017 Jul 28}, pages = {154}, abstract = {

Animals execute one particular behavior among many others in a context-dependent manner, yet the mechanisms underlying such behavioral choice remain poorly understood. Here we studied how two fundamental behaviors, sex and sleep, interact at genetic and neuronal levels in Drosophila. We show that an increased need for sleep inhibits male sexual behavior by decreasing the activity of the male-specific P1 neurons that coexpress the sex determination genes fru (M) and dsx, but does not affect female sexual behavior. Further, we delineate a sex-specific neuronal circuit wherein the P1 neurons encoding increased courtship drive suppressed male sleep by forming mutually excitatory connections with the fru (M) -positive sleep-controlling DN1 neurons. In addition, we find that FRU(M) regulates male courtship and sleep through distinct neural substrates. These studies reveal the genetic and neuronal basis underlying the sex-specific interaction between sleep and sexual behaviors in Drosophila, and provide insights into how competing behaviors are co-regulated.Genes and circuits involved in sleep and sexual arousal have been extensively studied in Drosophila. Here the authors identify the sex determination genes fruitless and doublesex, and a sex-specific P1-DN1 neuronal feedback that governs the interaction between these competing behaviors.

}, issn = {2041-1723}, doi = {10.1038/s41467-017-00087-5}, author = {Chen, Dandan and Sitaraman, Divya and Chen, Nan and Jin, Xin and Han, Caihong and Chen, Jie and Sun, Mengshi and Baker, Bruce S and Nitabach, Michael N and Pan, Yufeng} } @article {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 {48417, title = {Near-infrared fluorescent protein iRFP713 as a reporter protein for optogenetic vectors, a transgenic Cre-reporter rat, and other neuronal studies.}, journal = {Journal of Neuroscience Methods}, volume = {284}, year = {2017}, month = {2017 Apr 02}, pages = {1-14}, abstract = {

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

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

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

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

}, issn = {1872-678X}, doi = {10.1016/j.jneumeth.2017.03.020}, author = {Richie, Christopher T and Whitaker, Leslie R and Whitaker, Keith W and Necarsulmer, Julie and Baldwin, Heather A and Zhang, Yajun and Fortuno, Lowella and Hinkle, Josh J and Koivula, Pyry and Henderson, Mark J and Sun, Wenzhi and Wang, Kai and Smith, Jeffrey C and Pickel, Jim and Ji, Na and Hope, Bruce T and Harvey, Brandon K} } @article {48549, title = {Neural signatures of dynamic stimulus selection in Drosophila.}, journal = {Nature Neuroscience}, volume = {20}, year = {2017}, month = {2017 Jun 12}, pages = {1104-13}, abstract = {

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

}, doi = {10.1038/nn.4581}, author = {Sun, Yi and Nern, Aljoscha and Franconville, Romain and Dana, Hod and Schreiter, Eric R and Looger, Loren L and Svoboda, Karel and Kim, Douglas S and Hermundstad, Ann M and Jayaraman, Vivek} } @article {48642, title = {The Ol1mpiad: concordance of behavioural faculties of stage 1 and stage 3 Drosophila larvae.}, journal = {The Journal of Experimental Biology}, volume = {220}, year = {2017}, month = {2017 Jul 01}, pages = {2452-2475}, abstract = {

Mapping brain function to brain structure is a fundamental task for neuroscience. For such an endeavour, the Drosophila larva is simple enough to be tractable, yet complex enough to be interesting. It features about 10,000 neurons and is capable of various taxes, kineses and Pavlovian conditioning. All its neurons are currently being mapped into a light-microscopical atlas, and Gal4 strains are being generated to experimentally access neurons one at a time. In addition, an electron microscopic reconstruction of its nervous system seems within reach. Notably, this electron microscope-based connectome is being drafted for a stage 1 larva - because stage 1 larvae are much smaller than stage 3 larvae. However, most behaviour analyses have been performed for stage 3 larvae because their larger size makes them easier to handle and observe. It is therefore warranted to either redo the electron microscopic reconstruction for a stage 3 larva or to survey the behavioural faculties of stage 1 larvae. We provide the latter. In a community-based approach we called the Ol1mpiad, we probed stage 1 Drosophila larvae for free locomotion, feeding, responsiveness to substrate vibration, gentle and nociceptive touch, burrowing, olfactory preference and thermotaxis, light avoidance, gustatory choice of various tastants plus odour-taste associative learning, as well as light/dark-electric shock associative learning. Quantitatively, stage 1 larvae show lower scores in most tasks, arguably because of their smaller size and lower speed. Qualitatively, however, stage 1 larvae perform strikingly similar to stage 3 larvae in almost all cases. These results bolster confidence in mapping brain structure and behaviour across developmental stages.

}, issn = {1477-9145}, doi = {10.1242/jeb.156646}, author = {Almeida-Carvalho, Maria J and Berh, Dimitri and Braun, Andreas and Chen, Yi-chun and Eichler, Katharina and Eschbach, Claire and Fritsch, Pauline M J and Gerber, Bertram and Hoyer, Nina and Jiang, Xiaoyi and Kleber, J{\"o}rg and Kl{\"a}mbt, Christian and K{\"o}nig, Christian and Louis, Matthieu and Michels, Birgit and Miroschnikow, Anton and Mirth, Christen and Miura, Daisuke and Niewalda, Thomas and Otto, Nils and Paisios, Emmanouil and Pankratz, Michael J and Petersen, Meike and Ramsperger, Noel and Randel, Nadine and Risse, Benjamin and Saumweber, Timo and Schlegel, Philipp and Schleyer, Michael and Soba, Peter and Sprecher, Simon G and Tanimura, Teiichi and Thum, Andreas S and Toshima, Naoko and Truman, Jim W and Yarali, Ayse and Zlatic, Marta} } @article {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 {48650, title = {Rational engineering of photoconvertible fluorescent proteins for dual-color fluorescence nanoscopy enabled by a triplet-state mechanism of primed conversion.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {56}, year = {2017}, month = {2017 Jun 29}, pages = {11628-33}, abstract = {

Green-to-red photoconvertible fluorescent proteins (pcFPs) are powerful tools for super-resolution localization microscopy and protein tagging. Recently, they have been found to undergo efficient photoconversion not only by the traditional 400-nm illumination but also by an alternative method termed primed conversion, employing dual wavelength illumination with blue and far-red/near-infrared light. Primed conversion has been reported only for Dendra2 and its mechanism has remained elusive. Here, we uncover the molecular mechanism of primed conversion by reporting the intermediate "primed" state to be a triplet dark state formed by intersystem crossing. We show that formation of this state can be influenced by the introduction of serine or threonine at sequence position 69 (Eos notation) and use this knowledge to create "pr"- (for primed convertible) variants of most known green-to-red pcFPs.

}, issn = {1521-3773}, doi = {10.1002/anie.201706121}, author = {Mohr, Manuel Alexander and Kobitski, Andrei Yu and Sabater, Lluc Rullan and Nienhaus, Karin and Obara, Christopher John and Lippincott-Schwartz, Jennifer and Nienhaus, Gerd Ulrich and Pantazis, Periklis} } @article {48435, title = {Stem cell-intrinsic, seven-up-triggered temporal factor gradients diversify intermediate neural progenitors.}, journal = {Current Biology : CB}, volume = {27}, year = {2017}, month = {2017 Apr 10}, pages = {1303-13}, abstract = {

Building a sizable, complex brain requires both cellular expansion and diversification. One mechanism to achieve these goals is production of multiple transiently amplifying intermediate neural progenitors (INPs) from a single neural stem cell. Like mammalian neural stem cells, Drosophila type II neuroblasts utilize INPs to produce neurons and glia. Within a given lineage, the consecutively born INPs produce morphologically distinct progeny, presumably due to differential inheritance of temporal factors. To uncover the underlying temporal fating mechanisms, we profiled type II neuroblasts{\textquoteright} transcriptome across time. Our results reveal opposing temporal gradients of Imp and Syp RNA-binding proteins (descending and ascending, respectively). Maintaining high Imp throughout serial INP production expands the number of neurons and glia with early temporal fate at the expense of cells with late fate. Conversely, precocious upregulation of Syp reduces the number of cells with early fate. Furthermore, we reveal that the transcription factor Seven-up initiates progression of the Imp/Syp gradients. Interestingly, neuroblasts that maintain initial Imp/Syp levels can still yield progeny with a small range of early fates. We therefore propose that the Seven-up-initiated Imp/Syp gradients create coarse temporal windows within type II neuroblasts to pattern INPs, which subsequently undergo fine-tuned subtemporal patterning.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2017.03.047}, author = {Ren, Qingzhong and Yang, Ching-Po and Liu, Zhiyong and Sugino, Ken and Mok, Kent and He, Yisheng and Ito, Masayoshi and Nern, Aljoscha and Otsuna, Hideo and Lee, Tzumin} } @article {48699, title = {Structure and topology around the cleavage site regulate post-translational cleavage of the HIV-1 gp160 signal peptide.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Jul 28}, abstract = {

Like all other secretory proteins, the HIV-1 envelope glycoprotein gp160, is targeted to the endoplasmic reticulum (ER) by its signal peptide during synthesis. Proper gp160 folding in the ER requires core glycosylation, disulfide-bond formation and proline isomerization. Signal-peptide cleavage occurs only late after gp160 chain termination and is dependent on folding of the soluble subunit gp120 to a near-native conformation. We here detail the mechanism by which co-translational signal-peptide cleavage is prevented. Conserved residues from the signal peptide and residues downstream of the canonical cleavage site form an extended alpha-helix in the ER membrane that covers the cleavage site, thus preventing cleavage. A point mutation in the signal peptide breaks the alpha helix allowing co-translational cleavage. We demonstrate that postponed cleavage of gp160 enhances functional folding of the molecule. The change to early cleavage results in decreased viral fitness compared to wild-type HIV.

}, issn = {2050-084X}, doi = {10.7554/eLife.26067}, author = {Snapp, Erik Lee and McCaul, Nicholas and Quandte, Matthias and Cabartova, Zuzana and Bontjer, Ilja and K{\"a}llgren, Carolina and Nilsson, IngMarie and Land, Aafke and von Heijne, Gunnar and Sanders, Rogier W and Braakman, Ineke} } @article {48865, title = {Structure of RNA polymerase bound to ribosomal 30S subunit.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Oct 13}, abstract = {

In bacteria, mRNA transcription and translation are coupled to coordinate optimal gene expression and maintain genome stability. Coupling is thought to involve direct interactions between RNA polymerase (RNAP) and the translational machinery. We present cryo-EM structures of E. coli RNAP core bound to the small ribosomal 30S subunit. The complex is stable under cell-like ionic conditions, consistent with functional interaction between RNAP and the 30S subunit. The RNA exit tunnel of RNAP aligns with the Shine-Dalgarno-binding site of the 30S subunit. Ribosomal protein S1 forms a wall of the tunnel between RNAP and the 30S subunit, consistent with its role in directing mRNAs onto the ribosome. The nucleic-acid-binding cleft of RNAP samples distinct conformations, suggesting different functional states during transcription-translation coupling. The architecture of the 30S{\textbullet}RNAP complex provides a structural basis for co-localization of the transcriptional and translational machineries, and inform future mechanistic studies of coupled transcription and translation.

}, issn = {2050-084X}, doi = {10.7554/eLife.28560}, author = {Demo, Gabriel and Rasouly, Aviram and Vasilyev, Nikita and Svetlov, Vladimir and Loveland, Anna B and Diaz-Avalos, Ruben and Grigorieff, Nikolaus and Nudler, Evgeny and Korostelev, Andrei A} } @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 {48985, title = {A topographic axis of transcriptional identity in thalamus.}, journal = {bioRxiv}, year = {2017}, month = {2017 Dec 31}, pages = {241315}, abstract = {

A fundamental goal in neuroscience is to uncover common principles by which different modalities of information are processed. In the mammalian brain, thalamus acts as the essential hub for forebrain circuits handling inputs from sensory, motor, limbic, and cognitive pathways. Whether thalamus imposes common transformations on each of these modalities is unknown. Molecular characterization offers a principled approach to revealing the organization of thalamus. Using near-comprehensive and projection-specific transcriptomic sequencing, we found that almost all thalamic nuclei fit into one of three profiles. These profiles lie on a single axis of genetic variance which is aligned with the mediolateral spatial axis of thalamus. Genes defining this axis of variance include receptors and ion channels, providing a systematic diversification of input/output transformations across the topography of thalamus. Single cell transcriptional profiling revealed graded heterogeneity within individual thalamic nuclei, demonstrating that a spectrum of cell types and potentially diverse input/output transforms exist within a given thalamic nucleus. Together, our data argue for an archetypal organization of pathways serving diverse input modalities, and provides a comprehensive organizational scheme for thalamus.

}, doi = {10.1101/241315}, author = {Phillips, James W and Schulman, Anton and Hara, Erina and Liu, Chenghao and Shields, Brenda C and Korff, Wyatt and Lemire, Andrew and Dudman, Joshua T and Nelson, Sacha B and Hantman, Adam W} } @article {48934, title = {Ultra-selective looming detection from radial motion opponency.}, journal = {Nature}, volume = {551}, year = {2017}, month = {2017 Nov 08}, pages = {237-241}, abstract = {

Nervous systems combine lower-level sensory signals to detect higher-order stimulus features critical to survival, such as the visual looming motion created by an imminent collision or approaching predator. Looming-sensitive neurons have been identified in diverse animal species. Different large-scale visual features such as looming often share local cues, which means loom-detecting neurons face the challenge of rejecting confounding stimuli. Here we report the discovery of an ultra-selective looming detecting neuron, lobula plate/lobula columnar, type II (LPLC2) in Drosophila, and show how its selectivity is established by radial motion opponency. In the fly visual system, directionally selective small-field neurons called T4 and T5 form a spatial map in the lobula plate, where they each terminate in one of four retinotopic layers, such that each layer responds to motion in a different cardinal direction. Single-cell anatomical analysis reveals that each arm of the LPLC2 cross-shaped primary dendrites ramifies in one of these layers and extends along that layer{\textquoteright}s preferred motion direction. In vivo calcium imaging demonstrates that, as their shape predicts, individual LPLC2 neurons respond strongly to outward motion emanating from the centre of the neuron{\textquoteright}s receptive field. Each dendritic arm also receives local inhibitory inputs directionally selective for inward motion opposing the excitation. This radial motion opponency generates a balance of excitation and inhibition that makes LPLC2 non-responsive to related patterns of motion such as contraction, wide-field rotation or luminance change. As a population, LPLC2 neurons densely cover visual space and terminate onto the giant fibre descending neurons, which drive the jump muscle motor neuron to trigger an escape take off. Our findings provide a mechanistic description of the selective feature detection that flies use to discern and escape looming threats.

}, issn = {1476-4687}, doi = {10.1038/nature24626}, author = {Klapoetke, Nathan C and Nern, Aljoscha and Peek, Martin Y and Rogers, Edward M and Breads, Patrick and Rubin, Gerald M and Reiser, Michael B and Card, Gwyneth M} } @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 {47380, title = {Brain-wide mapping of neural activity controlling zebrafish exploratory locomotion.}, journal = {eLife}, year = {2016}, month = {2016 Mar 22}, abstract = {

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

}, doi = {10.7554/eLife.12741}, url = {http://dx.doi.org/10.7554/eLife.12741}, author = {Dunn, Timothy W. and Mu, Yu and Narayan, Sujatha and Randlett, Owen and Naumann, Eva A. and Yang, Chao-Tsung and Schier, Alexander F. and Freeman, Jeremy and Engert, Florian and Ahrens, Misha B.} } @article {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 {47324, title = {A circuit mechanism for the propagation of waves of muscle contraction in Drosophila.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Feb 18}, abstract = {

Animals move by adaptively coordinating the sequential activation of muscles. The circuit mechanisms underlying coordinated locomotion are poorly understood. Here, we report on a novel circuit for propagation of waves of muscle contraction, using the peristaltic locomotion of Drosophila larvae as a model system. We found an intersegmental chain of synaptically connected neurons, alternating excitatory and inhibitory, necessary for wave propagation and active in phase with the wave. The excitatory neurons (A27h) are premotor and necessary only for forward locomotion, and are modulated by stretch receptors and descending inputs. The inhibitory neurons (GDL) are necessary for both forward and backward locomotion, suggestive of different yet coupled central pattern generators, and its inhibition is necessary for wave propagation. The circuit structure and functional imaging indicated that the commands to contract one segment promote the relaxation of the next segment, revealing a mechanism for wave propagation in peristaltic locomotion.

}, issn = {2050-084X}, doi = {10.7554/eLife.13253}, author = {Fushiki, Akira and Zwart, Maarten F and Kohsaka, Hiroshi and Fetter, Richard D and Cardona, Albert and Nose, Akinao} } @article {65008, title = {A circuit motif in the zebrafish hindbrain for a two alternative behavioral choice to turn left or right.}, journal = {Elife}, volume = {5}, year = {2016}, month = {2016 08 09}, abstract = {

Animals collect sensory information from the world and make adaptive choices about how to respond to it. Here, we reveal a network motif in the brain for one of the most fundamental behavioral choices made by bilaterally symmetric animals: whether to respond to a sensory stimulus by moving to the left or to the right. We define network connectivity in the hindbrain important for the lateralized escape behavior of zebrafish and then test the role of neurons by using laser ablations and behavioral studies. Key inhibitory neurons in the circuit lie in a column of morphologically similar cells that is one of a series of such columns that form a developmental and functional ground plan for building hindbrain networks. Repetition within the columns of the network motif we defined may therefore lie at the foundation of other lateralized behavioral choices.

}, keywords = {Action Potentials, Animals, Animals, Genetically Modified, Behavior, Animal, Choice Behavior, Laser Therapy, Locomotion, Neural Pathways, Neurons, Patch-Clamp Techniques, Perception, Rhombencephalon, Zebrafish}, issn = {2050-084X}, doi = {10.7554/eLife.16808}, author = {Koyama, Minoru and Minale, Francesca and Shum, Jennifer and Nishimura, Nozomi and Schaffer, Chris B and Fetcho, Joseph R} } @article {47422, title = {The collection of MicroED data for macromolecular crystallography.}, journal = {Nature Protocols}, volume = {11}, year = {2016}, month = {2016 May}, pages = {895-904}, abstract = {

The formation of large, well-ordered crystals for crystallographic experiments remains a crucial bottleneck to the structural understanding of many important biological systems. To help alleviate this problem in crystallography, we have developed the MicroED method for the collection of electron diffraction data from 3D microcrystals and nanocrystals of radiation-sensitive biological material. In this approach, liquid solutions containing protein microcrystals are deposited on carbon-coated electron microscopy grids and are vitrified by plunging them into liquid ethane. MicroED data are collected for each selected crystal using cryo-electron microscopy, in which the crystal is diffracted using very few electrons as the stage is continuously rotated. This protocol gives advice on how to identify microcrystals by light microscopy or by negative-stain electron microscopy in samples obtained from standard protein crystallization experiments. The protocol also includes information about custom-designed equipment for controlling crystal rotation and software for recording experimental parameters in diffraction image metadata. Identifying microcrystals, preparing samples and setting up the microscope for diffraction data collection take approximately half an hour for each step. Screening microcrystals for quality diffraction takes roughly an hour, and the collection of a single data set is \~{}10 min in duration. Complete data sets and resulting high-resolution structures can be obtained from a single crystal or by merging data from multiple crystals.

}, issn = {1750-2799}, doi = {10.1038/nprot.2016.046}, author = {Shi, Dan and Nannenga, Brent L and de la Cruz, M Jason and Liu, Jinyang and Sawtelle, Steven and Calero, Guillermo and Reyes, Francis E and Hattne, Johan and Gonen, Tamir} } @article {47563, title = {Complicating connectomes: Electrical coupling creates parallel pathways and degenerate circuit mechanisms.}, journal = {Developmental Neurobiology}, year = {2016}, month = {2016 Jun 17}, abstract = {

Electrical coupling in circuits can produce non-intuitive circuit dynamics, as seen in both experimental work from the crustacean stomatogastric ganglion and in computational models inspired by the connectivity in this preparation. Ambiguities in interpreting the results of electrophysiological recordings can arise if sets of pre- or postsynaptic neurons are electrically coupled, or if the electrical coupling exhibits some specificity (e.g. rectifying, or voltage-dependent). Even in small circuits, electrical coupling can produce parallel pathways that can allow information to travel by monosynaptic and/or polysynaptic pathways. Consequently, similar changes in circuit dynamics can arise from entirely different underlying mechanisms. When neurons are coupled both chemically and electrically, modifying the relative strengths of the two interactions provides a mechanism for flexibility in circuit outputs. This, together with neuromodulation of gap junctions and coupled neurons is important both in developing and adult circuits. This article is protected by copyright. All rights reserved.

}, issn = {1932-846X}, doi = {10.1002/dneu.22410}, author = {Marder, Eve and Gutierrez, Gabrielle and Nusbaum, Michael P} } @article {47559, title = {Complicating connectomes: Electrical coupling creates parallel pathways and degenerate circuit mechanisms.}, journal = {Developmental Neurobiology}, year = {2016}, month = {2016 Jun 17}, abstract = {

Electrical coupling in circuits can produce non-intuitive circuit dynamics, as seen in both experimental work from the crustacean stomatogastric ganglion and in computational models inspired by the connectivity in this preparation. Ambiguities in interpreting the results of electrophysiological recordings can arise if sets of pre- or postsynaptic neurons are electrically coupled, or if the electrical coupling exhibits some specificity (e.g. rectifying, or voltage-dependent). Even in small circuits, electrical coupling can produce parallel pathways that can allow information to travel by monosynaptic and/or polysynaptic pathways. Consequently, similar changes in circuit dynamics can arise from entirely different underlying mechanisms. When neurons are coupled both chemically and electrically, modifying the relative strengths of the two interactions provides a mechanism for flexibility in circuit outputs. This, together with neuromodulation of gap junctions and coupled neurons is important both in developing and adult circuits. This article is protected by copyright. All rights reserved.

}, issn = {1932-846X}, doi = {10.1002/dneu.22410}, author = {Marder, Eve and Gutierrez, Gabrielle and Nusbaum, Michael P} } @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 {47562, title = {Design of a hyperstable 60-subunit protein icosahedron.}, journal = {Nature}, year = {2016}, month = {2016 Jun 15}, abstract = {

The icosahedron is the largest of the Platonic solids, and icosahedral protein structures are widely used in biological systems for packaging and transport. There has been considerable interest in repurposing such structures for applications ranging from targeted delivery to multivalent immunogen presentation. The ability to design proteins that self-assemble into precisely specified, highly ordered icosahedral structures would open the door to a new generation of protein containers with properties custom-tailored to specific applications. Here we describe the computational design of a 25-nanometre icosahedral nanocage that self-assembles from trimeric protein building blocks. The designed protein was produced in Escherichia coli, and found by electron microscopy to assemble into a homogenous population of icosahedral particles nearly identical to the design model. The particles are stable in 6.7 molar guanidine hydrochloride at up to 80 degrees Celsius, and undergo extremely abrupt, but reversible, disassembly between 2 molar and 2.25 molar guanidinium thiocyanate. The icosahedron is robust to genetic fusions: one or two copies of green fluorescent protein (GFP) can be fused to each of the 60 subunits to create highly fluorescent {\textquoteright}standard candles{\textquoteright} for use in light microscopy, and a designed protein pentamer can be placed in the centre of each of the 20 pentameric faces to modulate the size of the entrance/exit channels of the cage. Such robust and customizable nanocages should have considerable utility in targeted drug delivery, vaccine design and synthetic biology.

}, issn = {1476-4687}, doi = {10.1038/nature18010}, author = {Hsia, Yang and Bale, Jacob B and Gonen, Shane and Shi, Dan and Sheffler, William and Fong, Kimberly K and Nattermann, Una and Xu, Chunfu and Huang, Po-Ssu and Ravichandran, Rashmi and Yi, Sue and Davis, Trisha N and Gonen, Tamir and King, Neil P and Baker, David} } @article {48206, title = {Developmentally programmed germ cell remodelling by endodermal cell cannibalism.}, journal = {Nature Cell Biology}, volume = {18}, year = {2016}, month = {2016 Dec}, pages = {1302-10}, abstract = {

Primordial germ cells (PGCs) in many species associate intimately with endodermal cells, but the significance of such interactions is largely unexplored. Here, we show that Caenorhabditis elegans PGCs form lobes that are removed and digested by endodermal cells, dramatically altering PGC size and mitochondrial content. We demonstrate that endodermal cells do not scavenge lobes PGCs shed, but rather, actively remove lobes from the cell body. CED-10 (Rac)-induced actin, DYN-1 (dynamin) and LST-4 (SNX9) transiently surround lobe necks and are required within endodermal cells for lobe scission, suggesting that scission occurs through a mechanism resembling vesicle endocytosis. These findings reveal an unexpected role for endoderm in altering the contents of embryonic PGCs, and define a form of developmentally programmed cell remodelling involving intercellular cannibalism. Active roles for engulfing cells have been proposed in several neuronal remodelling events, suggesting that intercellular cannibalism may be a more widespread method used to shape cells than previously thought.

}, issn = {1476-4679}, doi = {10.1038/ncb3439}, author = {Abdu, Yusuff and Maniscalco, Chelsea and Heddleston, John M and Chew, Teng-Leong and Nance, Jeremy} } @article {47412, title = {Epigenomic landscapes of retinal rods and cones.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Mar 07}, abstract = {

Rod and cone photoreceptors are highly similar in many respects but they have important functional and molecular differences. Here, we investigate genome-wide patterns of DNA methylation and chromatin accessibility in mouse rods and cones and correlate differences in these features with gene expression, histone marks, transcription factor binding, and DNA sequence motifs. Loss of NR2E3 in rods shifts their epigenomes to a more cone-like state. The data further reveal wide differences in DNA methylation between retinal photoreceptors and brain neurons. Surprisingly, we also find a substantial fraction of DNA hypo-methylated regions in adult rods that are not in active chromatin. Many of these regions exhibit hallmarks of regulatory regions that were active earlier in neuronal development, suggesting that these regions could remain undermethylated due to the highly compact chromatin in mature rods. This work defines the epigenomic landscapes of rods and cones, revealing features relevant to photoreceptor development and function.

}, issn = {2050-084X}, doi = {10.7554/eLife.11613}, author = {Mo, Alisa and Luo, Chongyuan and Davis, Fred P and Mukamel, Eran A and Henry, Gilbert L and Nery, Joseph R and Urich, Mark A and Picard, Serge and Lister, Ryan and Eddy, Sean R and Beer, Michael A and Ecker, Joseph R and Nathans, Jeremy} } @article {47768, title = {Flight of the dragonflies and damselflies.}, journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences}, volume = {371}, year = {2016}, month = {2016 Sep 26}, abstract = {

This work is a synthesis of our current understanding of the mechanics, aerodynamics and visually mediated control of dragonfly and damselfly flight, with the addition of new experimental and computational data in several key areas. These are: the diversity of dragonfly wing morphologies, the aerodynamics of gliding flight, force generation in flapping flight, aerodynamic efficiency, comparative flight performance and pursuit strategies during predatory and territorial flights. New data are set in context by brief reviews covering anatomy at several scales, insect aerodynamics, neuromechanics and behaviour. We achieve a new perspective by means of a diverse range of techniques, including laser-line mapping of wing topographies, computational fluid dynamics simulations of finely detailed wing geometries, quantitative imaging using particle image velocimetry of on-wing and wake flow patterns, classical aerodynamic theory, photography in the field, infrared motion capture and multi-camera optical tracking of free flight trajectories in laboratory environments. Our comprehensive approach enables a novel synthesis of datasets and subfields that integrates many aspects of flight from the neurobiology of the compound eye, through the aeromechanical interface with the surrounding fluid, to flight performance under cruising and higher-energy behavioural modes.This article is part of the themed issue {\textquoteright}Moving in a moving medium: new perspectives on flight{\textquoteright}.

}, issn = {1471-2970}, doi = {10.1098/rstb.2015.0389}, author = {Bomphrey, Richard J and Nakata, Toshiyuki and Henningsson, Per and Lin, Huai-Ti} } @article {48386, title = {From Whole-Brain Data to Functional Circuit Models: The Zebrafish Optomotor Response.}, journal = {Cell}, volume = {167}, year = {2016}, month = {2016 11 03}, pages = {947-960.e20}, abstract = {

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

}, keywords = {Animals, Brain, Feedback, Sensory, Neural Pathways, Neuroimaging, Neurons, Swimming, Visual Perception, Zebrafish}, issn = {1097-4172}, doi = {10.1016/j.cell.2016.10.019}, author = {Naumann, Eva A and Fitzgerald, James E and Dunn, Timothy W and Rihel, Jason and Sompolinsky, Haim and Engert, Florian} } @article {47547, title = {GFP-aequorin protein sensor for ex~vivo and in~vivo imaging of Ca(2+) dynamics in high-Ca(2+) organelles.}, journal = {Cell Chemical Biology}, year = {2016}, month = {2016 Jun 1}, abstract = {

Proper functioning of organelles such as the ER or the Golgi apparatus requires luminal accumulation of Ca(2+) at high concentrations. Here we describe a\ ratiometric low-affinity Ca(2+) sensor of the GFP-aequorin protein (GAP) family optimized for measurements in high-Ca(2+) concentration environments. Transgenic animals expressing the ER-targeted sensor allowed monitoring of Ca(2+) signals inside the organelle. The use of the sensor was demonstrated under three experimental paradigms: (1) ER Ca(2+) oscillations in cultured astrocytes, (2) ex\ vivo functional mapping of cholinergic receptors triggering ER Ca(2+) release in acute hippocampal slices from transgenic mice, and (3) in\ vivo sarcoplasmic reticulum Ca(2+) dynamics in the muscle of transgenic flies. Our results provide proof of the suitability of the new biosensors to monitor Ca(2+) dynamics inside intracellular organelles under physiological conditions and open an avenue to explore complex Ca(2+) signaling in animal models of health and disease.

}, issn = {2451-9456}, doi = {10.1016/j.chembiol.2016.05.010}, author = {Navas-Navarro, Paloma and Rojo-Ruiz, Jonathan and Rodriguez-Prados, Macarena and Ganfornina, Mar{\'\i}a Dolores and Looger, Loren L and Alonso, Mar{\'\i}a Teresa and Garc{\'\i}a-Sancho, Javier} } @article {47348, title = {High-density genotyping of immune-related loci identifies new SLE risk variants in individuals with Asian ancestry.}, journal = {Nature Genetics}, volume = {48}, year = {2016}, month = {2016 Mar}, pages = {323-30}, abstract = {

Systemic lupus erythematosus (SLE) has a strong but incompletely understood genetic architecture. We conducted an association study with replication in 4,478 SLE cases and 12,656 controls from six East Asian cohorts to identify new SLE susceptibility loci and better localize known loci. We identified ten new loci and confirmed 20 known loci with genome-wide significance. Among the new loci, the most significant locus was GTF2IRD1-GTF2I at 7q11.23 (rs73366469, Pmeta = 3.75 {\texttimes} 10(-117), odds ratio (OR) = 2.38), followed by DEF6, IL12B, TCF7, TERT, CD226, PCNXL3, RASGRP1, SYNGR1 and SIGLEC6. We identified the most likely functional variants at each locus by analyzing epigenetic marks and gene expression data. Ten candidate variants are known to alter gene expression in cis or in trans. Enrichment analysis highlights the importance of these loci in B cell and T cell biology. The new loci, together with previously known loci, increase the explained heritability of SLE to 24\%. The new loci share functional and ontological characteristics with previously reported loci and are possible drug targets for SLE therapeutics.

}, issn = {1546-1718}, doi = {10.1038/ng.3496}, author = {Sun, Celi and Molineros, Julio E and Looger, Loren L and Zhou, Xu-Jie and Kim, Kwangwoo and Okada, Yukinori and Ma, Jianyang and Qi, Yuan-Yuan and Kim-Howard, Xana and Motghare, Prasenjeet and Bhattarai, Krishna and Adler, Adam and Bang, So-Young and Lee, Hye-Soon and Kim, Tae-Hwan and Kang, Young Mo and Suh, Chang-Hee and Chung, Won Tae and Park, Yong-Beom and Choe, Jung-Yoon and Shim, Seung Cheol and Kochi, Yuta and Suzuki, Akari and Kubo, Michiaki and Sumida, Takayuki and Yamamoto, Kazuhiko and Lee, Shin-Seok and Kim, Young Jin and Han, Bok-Ghee and Dozmorov, Mikhail and Kaufman, Kenneth M and Wren, Jonathan D and Harley, John B and Shen, Nan and Chua, Kek Heng and Zhang, Hong and Bae, Sang-Cheol and Nath, Swapan K} } @article {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 {47969, title = {Increased spatiotemporal resolution reveals highly dynamic dense tubular matrices in the peripheral ER.}, journal = {Science (New York, N.Y.)}, volume = {354}, year = {2016}, month = {2016 Oct 28}, pages = {433-46}, abstract = {

The endoplasmic reticulum (ER) is an expansive, membrane-enclosed organelle that plays crucial roles in numerous cellular functions. We used emerging superresolution imaging technologies to clarify the morphology and dynamics of the peripheral ER, which contacts and modulates most other intracellular organelles. Peripheral components of the ER have classically been described as comprising both tubules and flat sheets. We show that this system consists almost exclusively of tubules at varying densities, including structures that we term ER matrices. Conventional optical imaging technologies had led to misidentification of these structures as sheets because of the dense clustering of tubular junctions and a previously uncharacterized rapid form of ER motion. The existence of ER matrices explains previous confounding evidence that had indicated the occurrence of ER {\textquotedblleft}sheet{\textquotedblright} proliferation after overexpression of tubular junction{\textendash}forming proteins.

}, doi = {10.1126/science.aaf3928}, author = {Nixon-Abell, Jonathon and Obara, Christopher J and Weigel, Aubrey V and Li, Dong and Legant, Wesley R and Xu, CShan and Pasolli, H Amalia and Harvey, Kirsten and Hess, Harald F and Betzig, Eric and Blackstone, Craig and Lippincott-Schwartz, Jennifer} } @article {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 {47283, title = {Neural circuits underlying visually evoked escapes in larval zebrafish.}, journal = {Neuron}, volume = {89}, year = {2016}, month = {2016 Feb 3}, pages = {613-628}, abstract = {

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

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.12.021}, author = {Dunn, Timothy W and Gebhardt, Christoph and Naumann, Eva A and Riegler, Clemens and Ahrens, Misha B and Engert, Florian and Del Bene, Filippo} } @article {48069, title = {RNA-binding profiles of Drosophila CPEB proteins Orb and Orb2.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, year = {2016}, month = {2016 Oct 24}, abstract = {

Localized protein translation is critical in many biological contexts, particularly in highly polarized cells, such as neurons, to regulate gene expression in a spatiotemporal manner. The cytoplasmic polyadenylation element-binding (CPEB) family of RNA-binding proteins has emerged as a key regulator of mRNA transport and local translation required for early embryonic development, synaptic plasticity, and long-term memory (LTM). Drosophila Orb and Orb2 are single members of the CPEB1 and CPEB2 subfamilies of the CPEB proteins, respectively. At present, the identity of the mRNA targets they regulate is not fully known, and the binding specificity of the CPEB2 subfamily is a matter of debate. Using transcriptome-wide UV cross-linking and immunoprecipitation, we define the mRNA-binding sites and targets of Drosophila CPEBs. Both Orb and Orb2 bind linear cytoplasmic polyadenylation element-like sequences in the 3{\textquoteright} UTRs of largely overlapping target mRNAs, with Orb2 potentially having a broader specificity. Both proteins use their RNA-recognition motifs but not the Zinc-finger region for RNA binding. A subset of Orb2 targets is translationally regulated in cultured S2 cells and fly head extracts. Moreover, pan-neuronal RNAi knockdown of these targets suggests that a number of these targets are involved in LTM. Our results provide a comprehensive list of mRNA targets of the two CPEB proteins in Drosophila, thus providing insights into local protein synthesis involved in various biological processes, including LTM.

}, issn = {1091-6490}, doi = {10.1073/pnas.1603715113}, author = {Stepien, Barbara Krystyna and Oppitz, Cornelia and Gerlach, Daniel and Dag, Ugur and Novatchkova, Maria and Kr{\"u}ttner, Sebastian and Stark, Alexander and Keleman, Krystyna} } @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 {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 {47990, title = {Single-cell coding of sensory, spatial and numerical magnitudes in primate prefrontal, premotor and cingulate motor cortices.}, journal = {Experimental Brain Research}, volume = {234}, year = {2016}, month = {2016 Jan}, pages = {241-54}, abstract = {

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

}, keywords = {Animals, Gyrus Cinguli, Judgment, Macaca mulatta, Male, Mathematical Concepts, Motor Cortex, Neurons, Patch-Clamp Techniques, Pattern Recognition, Visual, Prefrontal Cortex, Space Perception}, issn = {1432-1106}, doi = {10.1007/s00221-015-4449-8}, author = {Eiselt, Anne-Kathrin and Nieder, Andreas} } @article {47709, title = {Super-resolution spectroscopic microscopy via photon localization.}, journal = {Nature Communications}, volume = {7}, year = {2016}, month = {2016 Jul 25}, pages = {12290}, abstract = {

Traditional photon localization microscopy analyses only the spatial distributions of photons emitted by individual molecules to reconstruct super-resolution optical images. Unfortunately, however, the highly valuable spectroscopic information from these photons have been overlooked. Here we report a spectroscopic photon localization microscopy that is capable of capturing the inherent spectroscopic signatures of photons from individual stochastic radiation events. Spectroscopic photon localization microscopy achieved higher spatial resolution than traditional photon localization microscopy through spectral discrimination to identify the photons emitted from individual molecules. As a result, we resolved two fluorescent molecules, which were 15 nm apart, with the corresponding spatial resolution of 10 nm-a four-fold improvement over photon localization microscopy. Using spectroscopic photon localization microscopy, we further demonstrated simultaneous multi-colour super-resolution imaging of microtubules and mitochondria in COS-7 cells and showed that background autofluorescence can be identified through its distinct emission spectra.

}, issn = {2041-1723}, doi = {10.1038/ncomms12290}, author = {Dong, Biqin and Almassalha, Luay and Urban, Ben E and Nguyen, The-Quyen and Khuon, Satya and Chew, Teng-Leong and Backman, Vadim and Sun, Cheng and Zhang, Hao F} } @article {47913, title = {A timecourse analysis of systemic and gonadal effects of temperature on sexual development of the red-eared slider turtle Trachemys scripta elegans.}, journal = {Developmental Biology}, volume = {420}, year = {2016}, month = {2016 Dec 1 }, pages = {166-77}, abstract = {

Temperature dependent sex determination (TSD) is the process by which the environmental temperature experienced during embryogenesis influences the sex of an organism, as in the red-eared slider turtle Trachemys scripta elegans. In accord with current paradigms of vertebrate sex determination, temperature is believed to exert its effects on sexual development in T. scripta entirely within the middle third of development, when the gonad is forming. However, whether temperature regulates the transcriptome in T. scripta early embryos in a manner that could influence secondary sex characteristics or establish a pro-male or pro-female environment has not been investigated. In addition, apart from a handful of candidate genes, very little is known about potential similarities between the expression cascade during TSD and the genetic cascade that drives mammalian sex determination. Here, we conducted an unbiased transcriptome-wide analysis of the effects of male- and female-promoting temperatures on the turtle embryo prior to gonad formation, and on the gonad during the temperature sensitive period. We found sexually dimorphic expression reflecting differences in steroidogenic enzymes and brain development prior to gonad formation. Within the gonad, we mapped a cascade of differential expression similar to the genetic cascade established in mammals. Using a Hidden Markov Model based clustering approach, we identified groups of genes that show heterochronic shifts between M. musculus and T. scripta. We propose a model in which multiple factors influenced by temperature accumulate during early gonadogenesis, and converge on the antagonistic regulation of aromatase to canalize sex determination near the end of the temperature sensitive window of development.

}, issn = {1095-564X}, doi = {10.1016/j.ydbio.2016.09.018}, author = {Czerwinski, Michael and Natarajan, Anirudh and Barske, Lindsey and Looger, Loren L and Capel, Blanche} } @article {48136, title = {Visual projection neurons in the Drosophila lobula link feature detection to distinct behavioral programs.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Dec 28}, abstract = {

Visual projection neurons (VPNs) provide an anatomical connection between early visual processing and higher brain regions. Here we characterize lobula columnar (LC) cells, a class of Drosophila VPNs that project to distinct central brain structures called optic glomeruli. We anatomically describe 22 different LC types and show that, for several types, optogenetic activation in freely moving flies evokes specific behaviors. The activation phenotypes of two LC types closely resemble natural avoidance behaviors triggered by a visual loom. In vivo two-photon calcium imaging reveals that these LC types respond to looming stimuli, while another type does not, but instead responds to the motion of a small object. Activation of LC neurons on only one side of the brain can result in attractive or aversive turning behaviors depending on the cell type. Our results indicate that LC neurons convey information on the presence and location of visual features relevant for specific behaviors.

}, issn = {2050-084X}, doi = {10.7554/eLife.21022}, author = {Wu, Ming and Nern, Aljoscha and Williamson, W Ryan and Morimoto, Mai M and Reiser, Michael B and Card, Gwyneth M and Rubin, Gerald M} } @article {47895, title = {Canonical genetic signatures of the adult human brain.}, journal = {Nature neuroscience}, volume = {18}, year = {2015}, month = {2015 Dec}, pages = {1832-44}, abstract = {

The structure and function of the human brain are highly stereotyped, implying a conserved molecular program responsible for its development, cellular structure and function. We applied a correlation-based metric called differential stability to assess reproducibility of gene expression patterning across 132 structures in six individual brains, revealing mesoscale genetic organization. The genes with the highest differential stability are highly biologically relevant, with enrichment for brain-related annotations, disease associations, drug targets and literature citations. Using genes with high differential stability, we identified 32 anatomically diverse and reproducible gene expression signatures, which represent distinct cell types, intracellular components and/or associations with neurodevelopmental and neurodegenerative disorders. Genes in neuron-associated compared to non-neuronal networks showed higher preservation between human and mouse; however, many diversely patterned genes displayed marked shifts in regulation between species. Finally, highly consistent transcriptional architecture in neocortex is correlated with resting state functional connectivity, suggesting a link between conserved gene expression and functionally relevant circuitry.

}, keywords = {Adult, Animals, Brain, Gene Regulatory Networks, Humans, Mice, Nerve Net, Transcriptome}, issn = {1546-1726}, doi = {10.1038/nn.4171}, author = {Hawrylycz, Michael and Miller, Jeremy A and Menon, Vilas and Feng, David and Dolbeare, Tim and Guillozet-Bongaarts, Angela L and Jegga, Anil G and Aronow, Bruce J and Lee, Chang-Kyu and Bernard, Amy and Glasser, Matthew F and Dierker, Donna L and Menche, J{\"o}rg and Szafer, Aaron and Collman, Forrest and Grange, Pascal and Berman, Kenneth A and Mihalas, Stefan and Yao, Zizhen and Stewart, Lance and Barab{\'a}si, Albert-L{\'a}szl{\'o} and Schulkin, Jay and Phillips, John and Ng, Lydia and Dang, Chinh and Haynor, David R and Jones, Allan and Van Essen, David C and Koch, Christof and Lein, Ed} } @article {47214, title = {Control of sleep by dopaminergic inputs to the Drosophila mushroom body.}, journal = {Frontiers in Neural Circuits}, volume = {9}, year = {2015}, month = {2015 Nov 09}, pages = {73}, abstract = {

The Drosophila mushroom body (MB) is an associative learning network that is important for the control of sleep. We have recently identified particular intrinsic MB Kenyon cell (KC) classes that regulate sleep through synaptic activation of particular MB output neurons (MBONs) whose axons convey sleep control signals out of the MB to downstream target regions. Specifically, we found that sleep-promoting KCs increase sleep by preferentially activating cholinergic sleep-promoting MBONs, while wake-promoting KCs decrease sleep by preferentially activating glutamatergic wake-promoting MBONs. Here we use a combination of genetic and physiological approaches to identify wake-promoting dopaminergic neurons (DANs) that innervate the MB, and show that they activate wake-promoting MBONs. These studies reveal a dopaminergic sleep control mechanism that likely operates by modulation of KC-MBON microcircuits.

}, issn = {1662-5110}, doi = {10.3389/fncir.2015.00073}, author = {Sitaraman, Divya and Aso, Yoshinori and Rubin, Gerald M and Nitabach, Michael N} } @article {46528, title = {Dynamics of ionic shifts in cortical spreading depression.}, journal = {Cerebral Cortex}, volume = {25}, year = {2015}, month = {2015 Apr 2}, pages = {4469-76}, abstract = {

Cortical spreading depression is a slowly propagating wave of near-complete depolarization of brain cells followed by temporary suppression of neuronal activity. Accumulating evidence indicates that cortical spreading depression underlies the migraine aura and that similar waves promote tissue damage in stroke, trauma, and hemorrhage. Cortical spreading depression is characterized by neuronal swelling, profound elevation of extracellular potassium and glutamate, multiphasic blood flow changes, and drop in tissue oxygen tension. The slow speed of the cortical spreading depression wave implies that it is mediated by diffusion of a chemical substance, yet the identity of this substance and the pathway it follows are unknown. Intercellular spread between gap junction-coupled neurons or glial cells and interstitial diffusion of K(+) or glutamate have been proposed. Here we use extracellular direct current potential recordings, K(+)-sensitive microelectrodes, and 2-photon imaging with ultrasensitive Ca(2+) and glutamate fluorescent probes to elucidate the spatiotemporal dynamics of ionic shifts associated with the propagation of cortical spreading depression in the visual cortex of adult living mice. Our data argue against intercellular spread of Ca(2+) carrying the cortical spreading depression wavefront and are in favor of interstitial K(+) diffusion, rather than glutamate diffusion, as the leading event in cortical spreading depression.

}, issn = {1460-2199}, doi = {10.1093/cercor/bhv054}, author = {Enger, Rune and Tang, Wannan and Vindedal, Gry Fluge and Jensen, Vidar and Johannes Helm, P and Sprengel, Rolf and Looger, Loren L and Nagelhus, Erlend A} } @article {46852, title = {Epigenomic signatures of neuronal diversity in the mammalian brain.}, journal = {Neuron}, volume = {86}, year = {2015}, month = {2015 Jun 17}, pages = {1369-1384}, abstract = {

Neuronal diversity is essential for mammalian brain function but poses a challenge to molecular profiling. To address the need for tools that facilitate cell-type-specific epigenomic studies, we developed the first\ affinity purification approach to isolate nuclei from genetically defined cell types in a mammal. We\ combine this technique with next-generation sequencing to show that three subtypes of neocortical neurons have highly distinctive epigenomic landscapes. Over 200,000 regions differ in chromatin accessibility and DNA methylation signatures characteristic of gene regulatory regions. By footprinting and motif analyses, these regions are predicted to bind distinct cohorts of neuron subtype-specific transcription factors. Neuronal epigenomes reflect both past and present gene expression, with DNA hyper-methylation at developmentally critical genes appearing as a novel epigenomic signature in mature neurons. Taken together, our findings link the functional and transcriptional complexity of neurons to their underlying epigenomic diversity.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.05.018}, author = {Mo, Alisa and Mukamel, Eran A and Davis, Fred P and Luo, Chongyuan and Henry, Gilbert L and Picard, Serge and Urich, Mark A and Nery, Joseph R and Sejnowski, Terrence J and Lister, Ryan and Eddy, Sean R and Ecker, Joseph R and Nathans, Jeremy} } @article {46818, title = {Female mice ultrasonically interact with males during courtship displays.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 May 28}, pages = {e06203}, abstract = {

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

}, issn = {2050-084X}, doi = {10.7554/eLife.06203}, author = {Neunuebel, Joshua P and Taylor, Adam L and Arthur, Ben J and Egnor, Se Roian} } @article {68481, title = {From intracellular signaling to population oscillations: bridging size- and time-scales in collective behavior.}, journal = {Mol Syst Biol}, volume = {11}, year = {2015}, month = {01/2015}, pages = {779}, abstract = {

Collective behavior in cellular populations is coordinated by biochemical signaling networks within individual cells. Connecting the dynamics of these intracellular networks to the population phenomena they control poses a considerable challenge because of network complexity and our limited knowledge of kinetic parameters. However, from physical systems, we know that behavioral changes in the individual constituents of a collectively behaving system occur in a limited number of well-defined classes, and these can be described using simple models. Here, we apply such an approach to the emergence of collective oscillations in cellular populations of the social amoeba Dictyostelium discoideum. Through direct tests of our model with quantitative in vivo measurements of single-cell and population signaling dynamics, we show how a simple model can effectively describe a complex molecular signaling network at multiple size and temporal scales. The model predicts novel noise-driven single-cell and population-level signaling phenomena that we then experimentally observe. Our results suggest that like physical systems, collective behavior in biology may be universal and described using simple mathematical models.

}, keywords = {Dictyostelium, Gene Expression Regulation, Image Processing, Computer-Assisted, Microfluidic Analytical Techniques, Molecular Dynamics Simulation, Signal Transduction}, issn = {1744-4292}, doi = {10.15252/msb.20145352}, author = {Sgro, Allyson E and Schwab, David J and Noorbakhsh, Javad and Mestler, Troy and Mehta, Pankaj and Gregor, Thomas} } @article {46267, title = {A general method to improve fluorophores for live-cell and single-molecule microscopy.}, journal = {Nature Methods}, volume = {12}, year = {2015}, month = {2015 Jan 19}, pages = {244-50}, abstract = {

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

}, issn = {1548-7105}, doi = {10.1038/nmeth.3256}, author = {Grimm, Jonathan B and English, Brian P and Chen, Jiji and Slaughter, Joel P and Zhang, Zhengjian and Revyakin, Andrey and Patel, Ronak and Macklin, John J and Normanno, Davide and Singer, Robert H and Lionnet, Timoth{\'e}e and Lavis, Luke D} } @article {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 {47896, title = {Genome engineering of isogenic human ES cells to model autism disorders.}, journal = {Nucleic acids research}, volume = {43}, year = {2015}, month = {2015 May 26}, pages = {e65}, abstract = {

Isogenic pluripotent stem cells are critical tools for studying human neurological diseases by allowing one to study the effects of a mutation in a fixed genetic background. Of particular interest are the spectrum of autism disorders, some of which are monogenic such as Timothy syndrome (TS); others are multigenic such as the microdeletion and microduplication syndromes of the 16p11.2 chromosomal locus. Here, we report engineered human embryonic stem cell (hESC) lines for modeling these two disorders using locus-specific endonucleases to increase the efficiency of homology-directed repair (HDR). We developed a system to: (1) computationally identify unique transcription activator-like effector nuclease (TALEN) binding sites in the genome using a new software program, TALENSeek, (2) assemble the TALEN genes by combining golden gate cloning with modified constructs from the FLASH protocol, and (3) test the TALEN pairs in an amplification-based HDR assay that is more sensitive than the typical non-homologous end joining assay. We applied these methods to identify, construct, and test TALENs that were used with HDR donors in hESCs to generate an isogenic TS cell line in a scarless manner and to model the 16p11.2 copy number disorder without modifying genomic loci with high sequence similarity.

}, keywords = {Autistic Disorder, Binding Sites, Cell Engineering, Cell Line, Child Development Disorders, Pervasive, Deoxyribonucleases, Embryonic Stem Cells, Gene Targeting, Genome, Human, Humans, Long QT Syndrome, Models, Genetic, Recombinational DNA Repair, Software, Syndactyly}, issn = {1362-4962}, doi = {10.1093/nar/gkv164}, author = {Martinez, Refugio A and Stein, Jason L and Krostag, Anne-Rachel F and Nelson, Angelique M and Marken, John S and Menon, Vilas and May, Ryan C and Yao, Zizhen and Kaykas, Ajamete and Geschwind, Daniel H and Grimley, Joshua 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 {47084, title = {Green-to-red photoconversion of GCaMP.}, journal = {PLoS One}, volume = {10}, year = {2015}, month = {2015 Sep 18}, pages = {e0138127}, abstract = {

Genetically encoded calcium indicators (GECIs) permit imaging intracellular calcium transients. Among GECIs, the GFP-based GCaMPs are the most widely used because of their high sensitivity and rapid response to changes in intracellular calcium concentrations. Here we report that the fluorescence of GCaMPs-including GCaMP3, GCaMP5 and GCaMP6-can be converted from green to red following exposure to blue-green light (450-500 nm). This photoconversion occurs in both insect and mammalian cells and is enhanced in a low oxygen environment. The red fluorescent GCaMPs retained calcium responsiveness, albeit with reduced sensitivity. We identified several amino acid residues in GCaMP important for photoconversion and generated a GCaMP variant with increased photoconversion efficiency in cell culture. This light-induced spectral shift allows the ready labeling of specific, targeted sets of GCaMP-expressing cells for functional imaging in the red channel. Together, these findings indicate the potential for greater utility of existing GCaMP reagents, including transgenic animals.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0138127}, author = {Ai, Minrong and Mills, Holly and Kanai, Makoto and Lai, Jason and Deng, Jingjing and Schreiter, Eric and Looger, Loren and Neubert, Thomas and Suh, Greg} } @article {47128, title = {A higher order visual neuron tuned to the spatial amplitude spectra of natural scenes.}, journal = {Nature Communications}, volume = {6}, year = {2015}, month = {2015 Oct 06}, pages = {8522}, abstract = {

Animal sensory systems are optimally adapted to those features typically encountered in natural surrounds, thus allowing neurons with limited bandwidth to encode challengingly large input ranges. Natural scenes are not random, and peripheral visual systems in vertebrates and insects have evolved to respond efficiently to their typical spatial statistics. The mammalian visual cortex is also tuned to natural spatial statistics, but less is known about coding in higher order neurons in insects. To redress this we here record intracellularly from a higher order visual neuron in the hoverfly. We show that the cSIFE neuron, which is inhibited by stationary images, is maximally inhibited when the slope constant of the amplitude spectrum is close to the mean in natural scenes. The behavioural optomotor response is also strongest to images with naturalistic image statistics. Our results thus reveal a close coupling between the inherent statistics of natural scenes and higher order visual processing in insects.

}, issn = {2041-1723}, doi = {10.1038/ncomms9522}, author = {Dyakova, Olga and Lee, Yu-Jen and Longden, Kit D and Kiselev, Valerij G and Nordstr{\"o}m, Karin} } @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 {46522, title = {Identification of genes that promote or inhibit olfactory memory formation in Drosophila.}, journal = {Genetics}, volume = {199}, year = {2015}, month = {2015 Apr}, pages = {1173-82}, abstract = {

Genetic screens in Drosophila melanogaster and other organisms have been pursued to filter the genome for genetic functions important for memory formation. Such screens have employed primarily chemical or transposon-mediated mutagenesis and have identified numerous mutants including classical memory mutants, dunce and rutabaga. Here, we report the results of a large screen using panneuronal RNAi expression to identify additional genes critical for memory formation. We identified \>500 genes that compromise memory when inhibited (low hits), either by disrupting the development and normal function of the adult animal or by participating in the neurophysiological mechanisms underlying memory formation. We also identified \>40 genes that enhance memory when inhibited (high hits). The dunce gene was identified as one of the low hits and further experiments were performed to map the effects of the dunce RNAi to the α/β and γ mushroom body neurons. Additional behavioral experiments suggest that dunce knockdown in the mushroom body neurons impairs memory without significantly affecting acquisition. We also characterized one high hit, sickie, to show that RNAi knockdown of this gene enhances memory through effects in dopaminergic neurons without apparent effects on acquisition. These studies further our understanding of two genes involved in memory formation, provide a valuable list of genes that impair memory that may be important for understanding the neurophysiology of memory or neurodevelopmental disorders, and offer a new resource of memory suppressor genes that will aid in understanding restraint mechanisms employed by the brain to optimize resources.

}, issn = {1943-2631}, doi = {10.1534/genetics.114.173575}, author = {Walkinshaw, Erica and Gai, Yunchao and Farkas, Caitlin and Richter, Daniel and Nicholas, Eric and Keleman, Krystyna and Davis, Ronald L} } @article {47037, title = {Identification of inhibitory premotor interneurons activated at a late phase in a motor cycle during Drosophila larval locomotion.}, journal = {PLoS One}, volume = {10}, year = {2015}, month = {2015 Sep 03}, pages = {e0136660}, abstract = {

Rhythmic motor patterns underlying many types of locomotion are thought to be produced by central pattern generators (CPGs). Our knowledge of how CPG networks generate motor patterns in complex nervous systems remains incomplete, despite decades of work in a variety of model organisms. Substrate borne locomotion in Drosophila larvae is driven by waves of muscular contraction that propagate through multiple body segments. We use the motor circuitry underlying crawling in larval Drosophila as a model to try to understand how segmentally coordinated rhythmic motor patterns are generated. Whereas muscles, motoneurons and sensory neurons have been well investigated in this system, far less is known about the identities and function of interneurons. Our recent study identified a class of glutamatergic premotor interneurons, PMSIs (period-positive median segmental interneurons), that regulate the speed of locomotion. Here, we report on the identification of a distinct class of glutamatergic premotor interneurons called Glutamatergic Ventro-Lateral Interneurons (GVLIs). We used calcium imaging to search for interneurons that show rhythmic activity and identified GVLIs as interneurons showing wave-like activity during peristalsis. Paired GVLIs were present in each abdominal segment A1-A7 and locally extended an axon towards a dorsal neuropile region, where they formed GRASP-positive putative synaptic contacts with motoneurons. The interneurons expressed vesicular glutamate transporter (vGluT) and thus likely secrete glutamate, a neurotransmitter known to inhibit motoneurons. These anatomical results suggest that GVLIs are premotor interneurons that locally inhibit motoneurons in the same segment. Consistent with this, optogenetic activation of GVLIs with the red-shifted channelrhodopsin, CsChrimson ceased ongoing peristalsis in crawling larvae. Simultaneous calcium imaging of the activity of GVLIs and motoneurons showed that GVLIs{\textquoteright} wave-like activity lagged behind that of motoneurons by several segments. Thus, GVLIs are activated when the front of a forward motor wave reaches the second or third anterior segment. We propose that GVLIs are part of the feedback inhibition system that terminates motor activity once the front of the motor wave proceeds to anterior segments.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0136660}, author = {Itakura, Yuki and Kohsaka, Hiroshi and Ohyama, Tomoko and Zlatic, Marta and Pulver, Stefan R and Nose, Akinao} } @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 {48830, title = {Learning enhances sensory and multiple non-sensory representations in primary visual cortex.}, journal = {Neuron}, volume = {86}, year = {2015}, month = {2015 Jun 17}, pages = {1478-90}, abstract = {

We determined how learning modifies neural representations in primary visual cortex (V1) during acquisition of a visually guided behavioral task. We imaged the activity of the same layer 2/3 neuronal populations as mice learned to discriminate two visual patterns while running through a virtual corridor, where one pattern was rewarded. Improvements in behavioral performance were closely associated with increasingly distinguishable population-level representations of task-relevant stimuli, as a result of stabilization of existing and recruitment of new neurons selective for these stimuli. These effects correlated with the appearance of multiple task-dependent signals during learning: those that increased neuronal selectivity across the population when expert animals engaged in the task, and those reflecting anticipation or behavioral choices specifically in neuronal subsets preferring the rewarded stimulus. Therefore, learning engages diverse mechanisms that modify sensory and non-sensory representations in V1 to adjust its processing to task requirements and the behavioral relevance of visual stimuli.

}, keywords = {Animals, Calcium, Discrimination (Psychology), Female, Learning, Luminescent Proteins, Male, Mice, Mice, Inbred C57BL, Mice, Transgenic, Models, Neurological, Neurons, Nonlinear Dynamics, Optogenetics, Photic Stimulation, Sensory Receptor Cells, User-Computer Interface, Vision, Ocular, Visual Cortex}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.05.037}, author = {Poort, Jasper and Khan, Adil G and Pachitariu, Marius and Nemri, Abdellatif and Orsolic, Ivana and Krupic, Julija and Bauza, Marius and Sahani, Maneesh and Keller, Georg B and Mrsic-Flogel, Thomas D and Hofer, Sonja B} } @article {47238, title = {A major locus controls a genital shape difference involved in reproductive isolation between Drosophila yakuba and Drosophila santomea.}, journal = {G3 (Bethesda, Md.)}, volume = {5}, year = {2015}, month = {2015 Oct 28}, pages = {2893-901}, abstract = {

Rapid evolution of genitalia shape, a widespread phenomenon in animals with internal fertilization, offers the opportunity to dissect the genetic architecture of morphological evolution linked to sexual selection and speciation. Most quantitative trait loci (QTL) mapping studies of genitalia divergence have focused on Drosophila melanogaster and its three most closely related species, D. simulans, D. mauritiana, and D. sechellia, and have suggested that the genetic basis of genitalia evolution involves many loci. We report the first genetic study of male genitalia evolution between D. yakuba and D. santomea, two species of the D. melanogaster species subgroup. We focus on male ventral branches, which harm females during interspecific copulation. Using landmark-based geometric morphometrics, we characterized shape variation in parental species, F1 hybrids, and backcross progeny and show that the main axis of shape variation within the backcross population matches the interspecific variation between parental species. For genotyping, we developed a new molecular method to perform multiplexed shotgun genotyping (MSG), which allowed us to prepare genomic DNA libraries from 365 backcross individuals in a few days using little DNA. We detected only three QTL, one of which spans 2.7 Mb and exhibits a highly significant effect on shape variation that can be linked to the harmfulness of the ventral branches. We conclude that the genetic architecture of genitalia morphology divergence may not always be as complex as suggested by previous studies.

}, issn = {2160-1836}, doi = {10.1534/g3.115.023481}, author = {Peluffo, Alexandre E and Nuez, Isabelle and Debat, Vincent and Savisaar, Rosina and Stern, David L and Orgogozo, Virginie} } @article {46326, title = {Mapping social behavior-induced brain activation at cellular resolution in the mouse.}, journal = {Cell Reports}, volume = {10}, year = {2015}, month = {2015 Jan 13}, pages = {292-305}, abstract = {

Understanding how brain activation mediates behaviors is a central goal of systems neuroscience. Here, we apply an automated method for mapping brain activation in the mouse in order to probe how sex-specific social behaviors are represented in the male brain. Our method uses the immediate-early-gene c-fos, a marker of neuronal activation, visualized by serial two-photon tomography: the c-fos-GFP+ neurons are computationally detected, their distribution is registered to a reference brain and a brain atlas, and their numbers are analyzed by statistical tests. Our results reveal distinct and shared female and male interaction-evoked patterns of male brain activation representing sex discrimination and social recognition. We also identify brain regions whose degree of activity correlates to specific features of social behaviors and estimate the total numbers and the densities of activated neurons per brain areas. Our study opens the door to automated screening of behavior-evoked brain activation in the mouse.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2014.12.014}, author = {Kim, Yongsoo and Venkataraju, Kannan Umadevi and Pradhan, Kith and Mende, Carolin and Taranda, Julian and Turaga, Srinivas C and Arganda-Carreras, Ignacio and Ng, Lydia and Hawrylycz, Michael J and Rockland, Kathleen S and Seung, H Sebastian and Osten, Pavel} } @article {46881, title = {MicroED data collection and processing.}, journal = {Acta Crystallographica Section A: Foundations \& Advances}, volume = {71}, year = {2015}, month = {2015 Jul 01}, pages = {353-60}, abstract = {

MicroED, a method at the intersection of X-ray crystallography and electron cryo-microscopy, has rapidly progressed by exploiting advances in both fields and has already been successfully employed to determine the atomic structures of several proteins from sub-micron-sized, three-dimensional crystals. A major limiting factor in X-ray crystallography is the requirement for large and well ordered crystals. By permitting electron diffraction patterns to be collected from much smaller crystals, or even single well ordered domains of large crystals composed of several small mosaic blocks, MicroED has the potential to overcome the limiting size requirement and enable structural studies on difficult-to-crystallize samples. This communication details the steps for sample preparation, data collection and reduction necessary to obtain refined, high-resolution, three-dimensional models by MicroED, and presents some of its unique challenges.

}, issn = {2053-2733}, doi = {10.1107/S2053273315010669}, author = {Hattne, Johan and Reyes, Francis E and Nannenga, Brent L and Shi, Dan and de la Cruz, M Jason and Leslie, Andrew G W and Gonen, Tamir} } @article {68480, title = {Modeling oscillations and spiral waves in Dictyostelium populations.}, journal = {Phys Rev E Stat Nonlin Soft Matter Phys}, volume = {91}, year = {2015}, month = {06/2015}, pages = {062711}, abstract = {

Unicellular organisms exhibit elaborate collective behaviors in response to environmental cues. These behaviors are controlled by complex biochemical networks within individual cells and coordinated through cell-to-cell communication. Describing these behaviors requires new mathematical models that can bridge scales-from biochemical networks within individual cells to spatially structured cellular populations. Here we present a family of "multiscale" models for the emergence of spiral waves in the social amoeba Dictyostelium discoideum. Our models exploit new experimental advances that allow for the direct measurement and manipulation of the small signaling molecule cyclic adenosine monophosphate (cAMP) used by Dictyostelium cells to coordinate behavior in cellular populations. Inspired by recent experiments, we model the Dictyostelium signaling network as an excitable system coupled to various preprocessing modules. We use this family of models to study spatially unstructured populations of "fixed" cells by constructing phase diagrams that relate the properties of population-level oscillations to parameters in the underlying biochemical network. We then briefly discuss an extension of our model that includes spatial structure and show how this naturally gives rise to spiral waves. Our models exhibit a wide range of novel phenomena. including a density-dependent frequency change, bistability, and dynamic death due to slow cAMP dynamics. Our modeling approach provides a powerful tool for bridging scales in modeling of Dictyostelium populations.

}, keywords = {Cyclic AMP, Dictyostelium, Extracellular Space, Kinetics, Models, Biological, Signal Transduction}, issn = {1550-2376}, doi = {10.1103/PhysRevE.91.062711}, author = {Noorbakhsh, Javad and Schwab, David J and Sgro, Allyson E and Gregor, Thomas and Mehta, Pankaj} } @article {46527, title = {Myosin 18A coassembles with nonmuscle myosin 2 to form mixed bipolar filaments.}, journal = {Current Biology}, volume = {25}, year = {2015}, month = {2015 Mar 30}, pages = {942-8}, abstract = {

Class-18 myosins are most closely related to conventional class-2 nonmuscle myosins (NM2). Surprisingly, the purified head domains of Drosophila, mouse, and human myosin 18A (M18A) lack actin-activated ATPase activity and the ability to translocate actin filaments, suggesting that the functions of M18A in\ vivo do not depend on intrinsic motor activity. M18A has the longest coiled coil of any myosin outside of the class-2 myosins, suggesting that it might form bipolar filaments similar to conventional myosins. To address this possibility, we expressed and purified full-length mouse M18A using the baculovirus/Sf9 system. M18A did not form large bipolar filaments under any of the conditions tested. Instead, M18A formed an \~{}65-nm-long bipolar structure with two heads at each end. Importantly, when NM2 was polymerized in the presence of M18A, the two myosins formed mixed bipolar filaments, as evidenced by cosedimentation, electron microscopy, and single-molecule imaging. Moreover, super-resolution imaging of NM2 and M18A using fluorescently tagged proteins and immunostaining of endogenous proteins showed that NM2 and M18A are present together within individual filaments inside living cells. Together, our in\ vitro and live-cell imaging data argue strongly that M18A coassembles with NM2 into mixed bipolar filaments. M18A could regulate the biophysical properties of these filaments and, by virtue of its extra N- and C-terminal domains, determine the localization and/or molecular interactions of the filaments. Given the numerous, fundamental cellular and developmental roles attributed to NM2, our results have far-reaching biological implications.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2015.02.012}, author = {Billington, Neil and Beach, Jordan R and Heissler, Sarah M and Remmert, Kirsten and Guzik-Lendrum, Stephanie and Nagy, Attila and Takagi, Yasuharu and Shao, Lin and Li, Dong and Yang, Yi and Zhang, Yingfan and Barzik, Melanie and Betzig, Eric and Hammer, John A and Sellers, James R} } @article {68448, title = {NAD$^{+}$/NADH metabolism and NAD$^{+}$-dependent enzymes in cell death and ischemic brain injury: current advances and therapeutic implications.}, journal = {Curr Med Chem}, volume = {22}, year = {2015}, month = {2015}, pages = {1239-47}, abstract = {

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

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

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

}, doi = {10.1016/j.cell.2015.06.035}, author = {Mauss, Alex S and Pankova, Katarina and Arenz, Alexander and Nern, Aljoscha and Rubin, Gerald M and Borst, Alexander} } @article {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 {46745, title = {Optimized tools for multicolor stochastic labeling reveal diverse stereotyped cell arrangements in the fly visual system.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, year = {2015}, month = {2015 May 11}, pages = {E2967-76}, abstract = {

We describe the development and application of methods for high-throughput neuroanatomy in Drosophila using light microscopy. These tools enable efficient multicolor stochastic labeling of neurons at both low and high densities. Expression of multiple membrane-targeted and distinct epitope-tagged proteins is controlled both by a transcriptional driver and by stochastic, recombinase-mediated excision of transcription-terminating cassettes. This MultiColor FlpOut (MCFO) approach can be used to reveal cell shapes and relative cell positions and to track the progeny of precursor cells through development. Using two different recombinases, the number of cells labeled and the number of color combinations observed in those cells can be controlled separately. We demonstrate the utility of MCFO in a detailed study of diversity and variability of Distal medulla (Dm) neurons, multicolumnar local interneurons in the adult visual system. Similar to many brain regions, the medulla has a repetitive columnar structure that supports parallel information processing together with orthogonal layers of cell processes that enable communication between columns. We find that, within a medulla layer, processes of the cells of a given Dm neuron type form distinct patterns that reflect both the morphology of individual cells and the relative positions of their arbors. These stereotyped cell arrangements differ between cell types and can even differ for the processes of the same cell type in different medulla layers. This unexpected diversity of coverage patterns provides multiple independent ways of integrating visual information across the retinotopic columns and implies the existence of multiple developmental mechanisms that generate these distinct patterns.

}, issn = {1091-6490}, doi = {10.1073/pnas.1506763112}, author = {Nern, Aljoscha and Pfeiffer, Barret D and Rubin, Gerald M} } @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 {46883, title = {Probing the target search of DNA-binding proteins in mammalian cells using TetR as model searcher.}, journal = {Nature Communications}, volume = {6}, year = {2015}, month = {2015 Jul 7}, pages = {7357}, abstract = {

Many cellular functions rely on DNA-binding proteins finding and associating to specific sites in the genome. Yet the mechanisms underlying the target search remain poorly understood, especially in the case of the highly organized mammalian cell nucleus. Using as a model Tet repressors (TetRs) searching for a multi-array locus, we quantitatively analyse the search process in human cells with single-molecule tracking and single-cell protein-DNA association measurements. We find that TetRs explore the nucleus and reach their target by 3D diffusion interspersed with transient interactions with non-cognate sites, consistent with the facilitated diffusion model. Remarkably, nonspecific binding times are broadly distributed, underlining a lack of clear delimitation between specific and nonspecific interactions. However, the search kinetics is not determined by diffusive transport but by the low association rate to nonspecific sites. Altogether, our results provide a comprehensive view of the recruitment dynamics of proteins at specific loci in mammalian cells.

}, issn = {2041-1723}, doi = {10.1038/ncomms8357}, author = {Normanno, Davide and Boudarene, Lydia and Dugast-Darzacq, Claire and Chen, Jiji and Richter, Christian and Proux, Florence and B{\'e}nichou, Olivier and Voituriez, Rapha{\"e}l and Darzacq, Xavier and Dahan, Maxime} } @article {47202, title = {Propagation of homeostatic sleep signals by segregated synaptic microcircuits of the Drosophila mushroom body.}, journal = {Current Biology : CB}, volume = {25}, year = {2015}, month = {2015 Nov 16}, pages = {2915-27}, abstract = {

The Drosophila mushroom body (MB) is a key associative memory center that has also been implicated in the control of sleep. However, the identity of MB neurons underlying homeostatic sleep regulation, as well as the types of sleep signals generated by specific classes of MB neurons, has remained poorly understood. We recently identified two MB output neuron (MBON) classes whose axons convey sleep control signals from the MB to converge in the same downstream target region: a cholinergic sleep-promoting MBON class and a glutamatergic wake-promoting MBON class. Here, we deploy a combination of neurogenetic, behavioral, and physiological approaches to identify and mechanistically dissect sleep-controlling circuits of the MB. Our studies reveal the existence of two segregated excitatory synaptic microcircuits that propagate homeostatic sleep information from different populations of intrinsic MB\ "Kenyon cells" (KCs) to specific sleep-regulating MBONs: sleep-promoting KCs increase sleep by preferentially activating the cholinergic MBONs, while wake-promoting KCs decrease sleep by preferentially activating the glutamatergic MBONs. Importantly, activity of the sleep-promoting MB microcircuit is increased by sleep deprivation and is necessary for homeostatic rebound sleep (i.e., the increased sleep that occurs after, and in compensation for, sleep lost during deprivation). These studies reveal for the first time specific functional connections between subsets of KCs and particular MBONs and establish the identity of synaptic microcircuits underlying transmission of homeostatic sleep signals in the MB.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2015.09.017}, author = {Sitaraman, Divya and Aso, Yoshinori and Jin, Xin and Chen, Nan and Felix, Mario and Rubin, Gerald M and Nitabach, Michael N} } @article {46497, title = {Proper migration and axon outgrowth of zebrafish cranial motoneuron subpopulations require the cell adhesion molecule MDGA2A.}, journal = {Biology Open}, volume = {4}, year = {2015}, month = {2015}, pages = {146-54}, abstract = {

The formation of functional neuronal circuits relies on accurate migration and proper axonal outgrowth of neuronal precursors. On the route to their targets migrating cells and growing axons depend on both, directional information from neurotropic cues and adhesive interactions mediated via extracellular matrix molecules or neighbouring cells. The inactivation of guidance cues or the interference with cell adhesion can cause severe defects in neuronal migration and axon guidance. In this study we have analyzed the function of the MAM domain containing glycosylphosphatidylinositol anchor 2A (MDGA2A) protein in zebrafish cranial motoneuron development. MDGA2A is prominently expressed in distinct clusters of cranial motoneurons, especially in the ones of the trigeminal and facial nerves. Analyses of MDGA2A knockdown embryos by light sheet and confocal microscopy revealed impaired migration and aberrant axonal outgrowth of these neurons; suggesting that adhesive interactions mediated by MDGA2A are required for the proper arrangement and outgrowth of cranial motoneuron subtypes.

}, issn = {2046-6390}, doi = {10.1242/bio.20148482}, author = {Ingold, Esther and Vom Berg-Maurer, Colette M and Burckhardt, Christoph J and Lehnherr, Andr{\'e} and Rieder, Philip and Keller, Philipp J and Stelzer, Ernst H and Greber, Urs F and Neuhauss, Stephan C F and Gesemann, Matthias} } @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 {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 {46379, title = {Stimulation-evoked Ca2+ signals in astrocytic processes at hippocampal CA3-CA1 synapses of adult mice are modulated by glutamate and ATP.}, journal = {The Journal of Neuroscience}, volume = {35}, year = {2015}, month = {2015 Feb 18}, pages = {3016-21}, abstract = {

To date, it has been difficult to reveal physiological Ca(2+) events occurring within the fine astrocytic processes of mature animals. The objective of the study was to explore whether neuronal activity evokes astrocytic Ca(2+) signals at glutamatergic synapses of adult mice. We stimulated the Schaffer collateral/commissural fibers in acute hippocampal slices from adult mice transduced with the genetically encoded Ca(2+) indicator GCaMP5E driven by the glial fibrillary acidic protein promoter. Two-photon imaging revealed global stimulation-evoked astrocytic Ca(2+) signals with distinct latencies, rise rates, and amplitudes in fine processes and somata. Specifically, the Ca(2+) signals in the processes were faster and of higher amplitude than those in the somata. A combination of P2 purinergic and group I/II metabotropic glutamate receptor (mGluR) antagonists reduced the amplitude of the Ca(2+) transients by 30-40\% in both astrocytic compartments. Blockage of the mGluRs alone only modestly reduced the magnitude of the stimulation-evoked Ca(2+) signals in processes and failed to affect the somatic Ca(2+) response. Local application of group I or I/II mGluR agonists or adenosine triphosphate (ATP) elicited global astrocytic Ca(2+) signals that mimicked the stimulation-evoked astrocytic Ca(2+) responses. We conclude that stimulation-evoked Ca(2+) signals in astrocytic processes at CA3-CA1 synapses of adult mice (1) differ from those in astrocytic somata and (2) are modulated by glutamate and ATP.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3319-14.2015}, author = {Tang, Wannan and Szokol, Karolina and Jensen, Vidar and Enger, Rune and Trivedi, Chintan A and Hvalby, {\O}ivind and Helm, P Johannes and Looger, Loren L and Sprengel, Rolf and Nagelhus, Erlend A} } @article {47031, title = {Structure of the toxic core of α-synuclein from invisible crystals.}, journal = {Nature}, volume = {525}, year = {2015}, month = {2015 Sep 9}, pages = {486-90}, abstract = {

The protein α-synuclein is the main component of Lewy bodies, the neuron-associated aggregates seen in Parkinson disease and other neurodegenerative pathologies. An 11-residue segment, which we term NACore, appears to be responsible for amyloid formation and cytotoxicity of human α-synuclein. Here we describe crystals of NACore that have dimensions smaller than the wavelength of visible light and thus are invisible by optical microscopy. As the crystals are thousands of times too small for structure determination by synchrotron X-ray diffraction, we use micro-electron diffraction to determine the structure at atomic resolution. The 1.4 {\r A} resolution structure demonstrates that this method can determine previously unknown protein structures and here yields, to our knowledge, the highest resolution achieved by any cryo-electron microscopy method to date. The structure exhibits protofibrils built of pairs of face-to-face β-sheets. X-ray fibre diffraction patterns show the similarity of NACore to toxic fibrils of full-length α-synuclein. The NACore structure, together with that of a second segment, inspires a model for most of the ordered portion of the toxic, full-length α-synuclein fibril, presenting opportunities for the design of inhibitors of α-synuclein fibrils.

}, issn = {1476-4687}, doi = {10.1038/nature15368}, author = {Rodriguez, Jose A and Ivanova, Magdalena I and Sawaya, Michael R and Cascio, Duilio and Reyes, Francis E and Shi, Dan and Sangwan, Smriti and Guenther, Elizabeth L and Johnson, Lisa M and Zhang, Meng and Jiang, Lin and Arbing, Mark A and Nannenga, Brent L and Hattne, Johan and Whitelegge, Julian and Brewster, Aaron S and Messerschmidt, Marc and Boutet, S{\'e}bastien and Sauter, Nicholas K and Gonen, Tamir and Eisenberg, David S} } @article {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 {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 {48388, title = {Whole-brain activity mapping onto a zebrafish brain atlas.}, journal = {Nature methods}, volume = {12}, year = {2015}, month = {2015 Nov}, pages = {1039-46}, abstract = {

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

}, keywords = {Algorithms, Animals, Automation, Behavior, Animal, Brain, Brain Mapping, Calcium, Extracellular Signal-Regulated MAP Kinases, Image Processing, Computer-Assisted, Immunohistochemistry, Microscopy, Confocal, Neurites, Neurons, Phosphorylation, Principal Component Analysis, Reproducibility of Results, Software, Swimming, Zebrafish}, issn = {1548-7105}, doi = {10.1038/nmeth.3581}, author = {Randlett, Owen and Wee, Caroline L and Naumann, Eva A and Nnaemeka, Onyeka and Schoppik, David and Fitzgerald, James E and Portugues, Ruben and Lacoste, Alix M B and Riegler, Clemens and Engert, Florian and Schier, Alexander F} } @article {6935, title = {Allelic heterogeneity in NCF2 associated with systemic lupus erythematosus (SLE) susceptibility across four ethnic populations.}, journal = {Human Molecular Genetics}, volume = {23}, year = {2014}, month = {2014 Mar 15}, pages = {1656-68}, abstract = {

Recent reports have associated NCF2, encoding a core component of the multi-protein NADPH oxidase (NADPHO), with systemic lupus erythematosus (SLE) susceptibility in individuals of European ancestry. To identify ethnicity-specific and -robust variants within NCF2, we assessed 145 SNPs in and around the NCF2 gene in 5325 cases and 21 866 controls of European-American (EA), African-American (AA), Hispanic (HS) and Korean (KR) ancestry. Subsequent imputation, conditional, haplotype and bioinformatic analyses identified seven potentially functional SLE-predisposing variants. Association with non-synonymous rs17849502, previously reported in EA, was detected in EA, HS and AA (P(EA) = 1.01 {\texttimes} 10(-54), PHS = 3.68 {\texttimes} 10(-10), P(AA) = 0.03); synonymous rs17849501 was similarly significant. These SNPs were monomorphic in KR. Novel associations were detected with coding variants at rs35937854 in AA (PAA = 1.49 {\texttimes} 10(-9)), and rs13306575 in HS and KR (P(HS) = 7.04 {\texttimes} 10(-7), P(KR) = 3.30 {\texttimes} 10(-3)). In KR, a 3-SNP haplotype was significantly associated (P = 4.20 {\texttimes} 10(-7)), implying that SLE predisposing variants were tagged. Significant SNP-SNP interaction (P = 0.02) was detected between rs13306575 and rs17849502 in HS, and a dramatically increased risk (OR = 6.55) with a risk allele at each locus. Molecular modeling predicts that these non-synonymous mutations could disrupt NADPHO complex assembly. The risk allele of rs17849501, located in a conserved transcriptional regulatory region, increased reporter gene activity, suggesting in vivo enhancer function. Our results not only establish allelic heterogeneity within NCF2 associated with SLE, but also emphasize the utility of multi-ethnic cohorts to identify predisposing variants explaining additional phenotypic variance ({\textquoteright}missing heritability{\textquoteright}) of complex diseases like SLE.

}, issn = {1460-2083}, doi = {10.1093/hmg/ddt532}, author = {Kim-Howard, Xana and Sun, Celi and Molineros, Julio E and Maiti, Amit K and Chandru, Hema and Adler, Adam and Wiley, Graham B and Kaufman, Kenneth M and Kottyan, Leah and Guthridge, Joel M and Rasmussen, Astrid and Kelly, Jennifer and S{\'a}nchez, Elena and Raj, Prithvi and Li, Quan-Zhen and Bang, So-Young and Lee, Hye-Soon and Kim, Tae-Hwan and Kang, Young Mo and Suh, Chang-Hee and Chung, Won Tae and Park, Yong-Beom and Choe, Jung-Yoon and Shim, Seung Cheol and Lee, Shin-Seok and Han, Bok-Ghee and Olsen, Nancy J and Karp, David R and Moser, Kathy and Pons-Estel, Bernardo A and Wakeland, Edward K and James, Judith A and Harley, John B and Bae, Sang-Cheol and Gaffney, Patrick M and Alarc{\'o}n-Riquelme, Marta and Looger, Loren L and Nath, Swapan K} } @article {6932, title = {Amphotericin forms an extramembranous and fungicidal sterol sponge.}, journal = {Nature Chemical Biology}, volume = {10}, year = {2014}, month = {2014 Mar 30}, pages = {400-6}, abstract = {

For over 50 years, amphotericin has remained the powerful but highly toxic last line of defense in treating life-threatening fungal infections in humans with minimal development of microbial resistance. Understanding how this small molecule kills yeast is thus critical for guiding development of derivatives with an improved therapeutic index and other resistance-refractory antimicrobial agents. In the widely accepted ion channel model for its mechanism of cytocidal action, amphotericin forms aggregates inside lipid bilayers that permeabilize and kill cells. In contrast, we report that amphotericin exists primarily in the form of large, extramembranous aggregates that kill yeast by extracting ergosterol from lipid bilayers. These findings reveal that extraction of a polyfunctional lipid underlies the resistance-refractory antimicrobial action of amphotericin and suggests a roadmap for separating its cytocidal and membrane-permeabilizing activities. This new mechanistic understanding is also guiding development of what are to our knowledge the first derivatives of amphotericin that kill yeast but not human cells.

}, issn = {1552-4469}, doi = {10.1038/nchembio.1496}, author = {Anderson, Thomas M and Clay, Mary C and Cioffi, Alexander G and Diaz, Katrina A and Hisao, Grant S and Tuttle, Marcus D and Nieuwkoop, Andrew J and Comellas, Gemma and Maryum, Nashrah and Wang, Shu and Uno, Brice E and Wildeman, Erin L and Gonen, Tamir and Rienstra, Chad M and Burke, Martin D} } @article {6937, title = {Annotating functional RNAs in genomes using infernal.}, journal = {Methods in Molecular Biology}, volume = {1097}, year = {2014}, month = {2014}, pages = {163-97}, abstract = {

Many different types of functional non-coding RNAs participate in a wide range of important cellular functions but the large majority of these RNAs are not routinely annotated in published genomes. Several programs have been developed for identifying RNAs, including specific tools tailored to a particular RNA family as well as more general ones designed to work for any family. Many of these tools utilize covariance models (CMs), statistical models of the conserved sequence, and structure of an RNA family. In this chapter, as an illustrative example, the Infernal software package and CMs from the Rfam database are used to identify RNAs in the genome of the archaeon Methanobrevibacter ruminantium, uncovering some additional RNAs not present in the genome{\textquoteright}s initial annotation. Analysis of the results and comparison with family-specific methods demonstrate some important strengths and weaknesses of this general approach.

}, issn = {1940-6029}, doi = {10.1007/978-1-62703-709-9_9}, author = {Nawrocki, Eric P} } @article {45098, title = {Automated image-based tracking and its application in ecology.}, journal = {Trends in Ecology and Evolution}, volume = {29}, year = {2014}, month = {2014 Jul}, pages = {417-428}, abstract = {

The behavior of individuals determines the strength and outcome of ecological interactions, which drive population, community, and ecosystem organization. Bio-logging, such as telemetry and animal-borne imaging, provides essential individual viewpoints, tracks, and life histories, but requires capture of individuals and is often impractical to scale. Recent developments in automated image-based tracking offers opportunities to remotely quantify and understand individual behavior at scales and resolutions not previously possible, providing an essential supplement to other tracking methodologies in ecology. Automated image-based tracking should continue to advance the field of ecology by enabling better understanding of the linkages between individual and higher-level ecological processes, via high-throughput quantitative analysis of complex ecological patterns and processes across scales, including analysis of environmental drivers.

}, issn = {1872-8383}, doi = {10.1016/j.tree.2014.05.004}, author = {Dell, Anthony I and Bender, John A and Branson, Kristin and Couzin, Iain D and de Polavieja, Gonzalo G and Noldus, Lucas P J J and P{\'e}rez-Escudero, Alfonso and Perona, Pietro and Straw, Andrew D and Wikelski, Martin and Brose, Ulrich} } @article {6952, title = {Cell-type-based model explaining coexpression patterns of genes in the brain.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, year = {2014}, month = {2014 Apr 8}, pages = {5397-402}, abstract = {

Spatial patterns of gene expression in the vertebrate brain are not independent, as pairs of genes can exhibit complex patterns of coexpression. Two genes may be similarly expressed in one region, but differentially expressed in other regions. These correlations have been studied quantitatively, particularly for the Allen Atlas of the adult mouse brain, but their biological meaning remains obscure. We propose a simple model of the coexpression patterns in terms of spatial distributions of underlying cell types and establish its plausibility using independently measured cell-type-specific transcriptomes. The model allows us to predict the spatial distribution of cell types in the mouse brain.

}, issn = {1091-6490}, doi = {10.1073/pnas.1312098111}, author = {Grange, Pascal and Bohland, Jason W and Okaty, Benjamin W and Sugino, Ken and Bokil, Hemant and Nelson, Sacha B and Ng, Lydia and Hawrylycz, Michael and Mitra, Partha P} } @article {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 {45638, title = {Cell-type-specific repression by methyl-CpG-binding protein 2 is biased toward long genes.}, journal = {Journal of Neuroscience}, volume = {34}, year = {2014}, month = {2014 Sep 17}, pages = {12877-83}, abstract = {

Mutations in methyl-CpG-binding protein 2 (MeCP2) cause Rett syndrome and related autism spectrum disorders (Amir et al., 1999). MeCP2 is believed to be required for proper regulation of brain gene expression, but prior microarray studies in Mecp2 knock-out mice using brain tissue homogenates have revealed only subtle changes in gene expression (Tudor et al., 2002; Nuber et al., 2005; Jordan et al., 2007; Chahrour et al., 2008). Here, by profiling discrete subtypes of neurons we uncovered more dramatic effects of MeCP2 on gene expression, overcoming the "dilution problem" associated with assaying homogenates of complex tissues. The results reveal misregulation of genes involved in neuronal connectivity and communication. Importantly, genes upregulated following loss of MeCP2 are biased toward longer genes but this is not true for downregulated genes, suggesting MeCP2 may selectively repress long genes. Because genes involved in neuronal connectivity and communication, such as cell adhesion and cell-cell signaling genes, are enriched among longer genes, their misregulation following loss of MeCP2 suggests a possible etiology for altered circuit function in Rett syndrome.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.2674-14.2014}, author = {Sugino, Ken and Hempel, Chris M and Okaty, Benjamin W and Arnson, Hannah A and Kato, Saori and Dani, Vardhan S and Nelson, Sacha B} } @article {45181, title = {Combined protein- and nucleic acid-level effects of rs1143679 (R77H), a lupus-predisposing variant within ITGAM.}, journal = {Human Molecular Genetics}, volume = {23}, year = {2014}, month = {2014 Aug 1}, pages = {4161-76}, abstract = {

Integrin alpha M (ITGAM; CD11b) is a component of the macrophage-1 antigen complex, which mediates leukocyte adhesion, migration and phagocytosis as part of the immune system. We previously identified a missense polymorphism, rs1143679 (R77H), strongly associated with systemic lupus erythematosus (SLE). However, the molecular mechanisms of this variant are incompletely understood. A meta-analysis of published and novel data on 28 439 individuals with European, African, Hispanic and Asian ancestries reinforces genetic association between rs1143679 and SLE [Pmeta = 3.60 {\texttimes} 10(-90), odds ratio (OR) = 1.76]. Since rs1143679 is in the most active region of chromatin regulation and transcription factor binding in ITGAM, we quantitated ITGAM RNA and surface protein levels in monocytes from patients with each rs1143679 genotype. We observed that transcript levels significantly decreased for the risk allele ({\textquoteright}A{\textquoteright}) relative to the non-risk allele ({\textquoteright}G{\textquoteright}), in a dose-dependent fashion: ({\textquoteright}AA{\textquoteright} \< {\textquoteright}AG{\textquoteright} \< {\textquoteright}GG{\textquoteright}). CD11b protein levels in patients{\textquoteright} monocytes were directly correlated with RNA levels. Strikingly, heterozygous individuals express much lower (average 10- to 15-fold reduction) amounts of the {\textquoteright}A{\textquoteright} transcript than {\textquoteright}G{\textquoteright} transcript. We found that the non-risk sequence surrounding rs1143679 exhibits transcriptional enhancer activity in vivo and binds to Ku70/80, NFKB1 and EBF1 in vitro, functions that are significantly reduced with the risk allele. Mutant CD11b protein shows significantly reduced binding to fibrinogen and vitronectin, relative to non-risk, both in purified protein and in cellular models. This two-pronged contribution (nucleic acid- and protein-level) of the rs1143679 risk allele to decreasing ITGAM activity provides insight into the molecular mechanisms of its potent association with SLE.

}, issn = {1460-2083}, doi = {10.1093/hmg/ddu106}, author = {Maiti, Amit K and Kim-Howard, Xana and Motghare, Prasenjeet and Pradhan, Vandana and Chua, Kek Heng and Sun, Celi and Arango-Guerrero, Mar{\'\i}a Teresa and Ghosh, Kanjaksha and Niewold, Timothy B and Harley, John B and Anaya, Juan-Manual and Looger, Loren L and Nath, Swapan K} } @article {6883, title = {The developmental control of size in insects.}, journal = {Wiley Interdisciplinary Reviews: Developmental Biology}, volume = {3}, year = {2014}, month = {2014 Jan/Feb}, pages = {113-34}, abstract = {

The mechanisms that control the sizes of a body and its many parts remain among the great puzzles in developmental biology. Why do animals grow to a species-specific body size, and how is the relative growth of their body parts controlled to so they grow to the right size, and in the correct proportion with body size, giving an animal its species-characteristic shape? Control of size must involve mechanisms that somehow assess some aspect of size and are upstream of mechanisms that regulate growth. These mechanisms are now beginning to be understood in the insects, in particular in Manduca sexta and Drosophila melanogaster. The control of size requires control of the rate of growth and control of the cessation of growth. Growth is controlled by genetic and environmental factors. Insulin and ecdysone, their receptors, and intracellular signaling pathways are the principal genetic regulators of growth. The secretion of these growth hormones, in turn, is controlled by complex interactions of other endocrine and molecular mechanisms, by environmental factors such as nutrition, and by the physiological mechanisms that sense body size. Although the general mechanisms of growth regulation appear to be widely shared, the mechanisms that regulate final size can be quite diverse. WIREs Dev Biol 2014, 3:113{\textendash}134. doi: 10.1002/wdev.124

}, issn = {1759-7684}, doi = {10.1002/wdev.124}, author = {Nijhout, H. Frederik and Riddiford, Lynn M and Mirth, Christen and Shingleton, Alexander W and Suzuki, Yuichiro and Callier, Viviane} } @article {45175, title = {Direct observation of ON and OFF pathways in the Drosophila visual system.}, journal = {Current Biology}, volume = {24}, year = {2014}, month = {2014 May 5}, pages = {976-83}, abstract = {

Visual motion perception is critical to many animal behaviors, and flies have emerged as a powerful model system for exploring this fundamental neural computation. Although numerous studies have suggested that fly motion vision is governed by a simple neural circuit [1-3], the implementation of this circuit has remained mysterious for decades. Connectomics and neurogenetics have produced a surge in recent progress, and several studies have shown selectivity for light increments (ON) or decrements (OFF) in key elements associated with this circuit [4-7]. However, related studies have reached disparate conclusions about where this selectivity emerges and whether it plays a major role in motion vision [8-13]. To address these questions, we examined activity in the neuropil thought to be responsible for visual motion detection, the medulla, of Drosophila melanogaster in response to a range of visual stimuli using two-photon calcium imaging. We confirmed that the input neurons of the medulla, the LMCs, are not responsible for light-on and light-off selectivity. We then examined the pan-neural response of medulla neurons and found prominent selectivity for light-on and light-off in layers of the medulla associated with two anatomically derived pathways (L1/L2 associated) [14, 15]. We next examined the activity of prominent interneurons within each pathway (Mi1 and Tm1) and found that these neurons have corresponding selectivity for light-on or light-off. These results provide direct evidence that motion is computed in parallel light-on and light-off pathways, demonstrate that this selectivity emerges in neurons immediately downstream of the LMCs, and specify where crucial elements of motion computation occur.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2014.03.017}, author = {Strother, James A and Nern, Aljoscha and Reiser, Michael B} } @article {48390, title = {Flies and humans share a motion estimation strategy that exploits natural scene statistics.}, journal = {Nature neuroscience}, volume = {17}, year = {2014}, month = {2014 Feb}, pages = {296-303}, abstract = {

Sighted animals extract motion information from visual scenes by processing spatiotemporal patterns of light falling on the retina. The dominant models for motion estimation exploit intensity correlations only between pairs of points in space and time. Moving natural scenes, however, contain more complex correlations. We found that fly and human visual systems encode the combined direction and contrast polarity of moving edges using triple correlations that enhance motion estimation in natural environments. Both species extracted triple correlations with neural substrates tuned for light or dark edges, and sensitivity to specific triple correlations was retained even as light and dark edge motion signals were combined. Thus, both species separately process light and dark image contrasts to capture motion signatures that can improve estimation accuracy. This convergence argues that statistical structures in natural scenes have greatly affected visual processing, driving a common computational strategy over 500 million years of evolution.

}, keywords = {Adaptation, Physiological, Animals, Contrast Sensitivity, Drosophila, Electroencephalography, Evoked Potentials, Visual, Genotype, Humans, Models, Neurological, Motion Perception, Pattern Recognition, Visual, Photic Stimulation, Psychophysics}, issn = {1546-1726}, doi = {10.1038/nn.3600}, author = {Clark, Damon A and Fitzgerald, James E and Ales, Justin M and Gohl, Daryl M and Silies, Marion A and Norcia, Anthony M and Clandinin, Thomas R} } @article {6934, title = {Graph-based active learning of agglomeration (GALA): a Python library to segment 2D and 3D neuroimages}, journal = {Frontiers in Neuroinformatics}, volume = {8}, year = {2014}, month = {2014 Apr 4}, pages = {34}, abstract = {

The aim in high-resolution connectomics is to reconstruct complete neuronal connectivity in a tissue. Currently, the only technology capable of resolving the smallest neuronal processes is electron microscopy (EM). Thus, a common approach to network reconstruction is to perform (error-prone) automatic segmentation of EM images, followed by manual proofreading by experts to fix errors. We have developed an algorithm and software library to not only improve the accuracy of the initial automatic segmentation, but also point out the image coordinates where it is likely to have made errors. Our software, called gala (graph-based active learning of agglomeration), improves the state of the art in agglomerative image segmentation. It is implemented in Python and makes extensive use of the scientific Python stack (numpy, scipy, networkx, scikit-learn, scikit-image, and others). We present here the software architecture of the gala library, and discuss several designs that we consider would be generally useful for other segmentation packages. We also discuss the current limitations of the gala library and how we intend to address them.

}, issn = {1662-5196}, doi = {10.3389/fninf.2014.00034}, author = {Nunez-Iglesias, Juan and Kennedy, Ryan and Plaza, Stephen M and Chakraborty, Anirban and William T. Katz} } @article {45637, title = {High thermodynamic stability of parametrically designed helical bundles.}, journal = {Science}, volume = {346}, year = {2014}, month = {2014 Oct 24}, pages = {481-5}, abstract = {

We describe a procedure for designing proteins with backbones produced by varying the parameters in the Crick coiled coil-generating equations. Combinatorial design calculations identify low-energy sequences for alternative helix supercoil arrangements, and the helices in the lowest-energy arrangements are connected by loop building. We design an antiparallel monomeric untwisted three-helix bundle with 80-residue helices, an antiparallel monomeric right-handed four-helix bundle, and a pentameric parallel left-handed five-helix bundle. The designed proteins are extremely stable (extrapolated ΔGfold \> 60 kilocalories per mole), and their crystal structures are close to those of the design models with nearly identical core packing between the helices. The approach enables the custom design of hyperstable proteins with fine-tuned geometries for a wide range of applications.

}, issn = {1095-9203}, doi = {10.1126/science.1257481}, author = {Huang, Po-Ssu and Oberdorfer, Gustav and Xu, Chunfu and Pei, Xue Y and Nannenga, Brent L and Rogers, Joseph M and DiMaio, Frank and Gonen, Tamir and Luisi, Ben and Baker, David} } @article {47897, title = {A high-resolution spatiotemporal atlas of gene expression of the developing mouse brain.}, journal = {Neuron}, volume = {83}, year = {2014}, month = {2014 Jul 16}, pages = {309-23}, abstract = {

To provide a temporal framework for the genoarchitecture of brain development, we generated in situ hybridization data for embryonic and postnatal mouse brain at seven developmental stages for \~{}2,100 genes, which were processed with an automated informatics pipeline and manually annotated. This resource comprises 434,946 images, seven reference atlases, an ontogenetic ontology, and tools to explore coexpression of genes across neurodevelopment. Gene sets coinciding with developmental phenomena were identified. A temporal shift in the principles governing the molecular organization of the brain was detected, with transient neuromeric, plate-based organization of the brain present at E11.5 and E13.5. Finally, these data provided a transcription factor code that discriminates brain structures and identifies the developmental age of a tissue, providing a foundation for eventual genetic manipulation or tracking of specific brain structures over development. The resource is available as the Allen Developing Mouse Brain Atlas (http://developingmouse.brain-map.org).

}, keywords = {Animals, Brain, Brain Mapping, Gene Expression, Gene Expression Profiling, Gene Expression Regulation, Developmental, Mice}, issn = {1097-4199}, doi = {10.1016/j.neuron.2014.05.033}, author = {Thompson, Carol L and Ng, Lydia and Menon, Vilas and Martinez, Salvador and Lee, Chang-Kyu and Glattfelder, Katie and Sunkin, Susan M and Henry, Alex and Lau, Christopher and Dang, Chinh and Garcia-Lopez, Raquel and Martinez-Ferre, Almudena and Pombero, Ana and Rubenstein, John L R and Wakeman, Wayne B and Hohmann, John and Dee, Nick and Sodt, Andrew J and Young, Rob and Smith, Kimberly and Nguyen, Thuc-Nghi and Kidney, Jolene and Kuan, Leonard and Jeromin, Andreas and Kaykas, Ajamete and Miller, Jeremy and Page, Damon and Orta, Geri and Bernard, Amy and Riley, Zackery and Smith, Simon and Wohnoutka, Paul and Hawrylycz, Michael J and Puelles, Luis and Jones, Allan R} } @article {45860, title = {High-resolution structure determination by continuous-rotation data collection in MicroED.}, journal = {Nature Methods}, volume = {11}, year = {2014}, month = {2014 Sep}, pages = {927-30}, abstract = {

MicroED uses very small three-dimensional protein crystals and electron diffraction for structure determination. We present an improved data collection protocol for MicroED called {\textquoteright}continuous rotation{\textquoteright}. Microcrystals are continuously rotated during data collection, yielding more accurate data. The method enables data processing with the crystallographic software tool MOSFLM, which resulted in improved resolution for the model protein lysozyme. These improvements are paving the way for the broad implementation and application of MicroED in structural biology.

}, keywords = {Algorithms, Databases, Protein, Electrons, Imaging, Three-Dimensional, Information Storage and Retrieval, Lasers, Microscopy, Video, Protein Conformation, Proteins, Rotation, Scattering, Small Angle, X-Ray Diffraction}, issn = {1548-7105}, doi = {10.1038/nmeth.3043}, author = {Nannenga, Brent L and Shi, Dan and Leslie, Andrew G W and Gonen, Tamir} } @article {45186, title = {Large-scale, high-density (up to 512 channels) recording of local circuits in behaving animals.}, journal = {Journal of Neurophysiology}, volume = {111}, year = {2014}, month = {2014 Mar}, pages = {1132-49}, abstract = {

Monitoring representative fractions of neurons from multiple brain circuits in behaving animals is necessary for understanding neuronal computation. Here, we describe a system that allows high-channel-count recordings from a small volume of neuronal tissue using a lightweight signal multiplexing headstage that permits free behavior of small rodents. The system integrates multishank, high-density recording silicon probes, ultraflexible interconnects, and a miniaturized microdrive. These improvements allowed for simultaneous recordings of local field potentials and unit activity from hundreds of sites without confining free movements of the animal. The advantages of large-scale recordings are illustrated by determining the electroanatomic boundaries of layers and regions in the hippocampus and neocortex and constructing a circuit diagram of functional connections among neurons in real anatomic space. These methods will allow the investigation of circuit operations and behavior-dependent interregional interactions for testing hypotheses of neural networks and brain function.

}, issn = {1522-1598}, doi = {10.1152/jn.00785.2013}, author = {Berenyi, Antal and Somogyv{\'a}ri, Zolt{\'a}n and Nagy, Anett J and Roux, Lisa and Long, John D and Fujisawa, Shigeyoshi and Stark, Eran and Leonardo, Anthony and Harris, Timothy D and Buzs{\'a}ki, Gy{\"o}rgy} } @article {6896, title = {Live imaging and quantitative analysis of gastrulation in mouse embryos using light-sheet microscopy and 3D tracking tools.}, journal = {Nature Protocols}, volume = {9}, year = {2014}, month = {2014 Mar}, pages = {575-85}, abstract = {

This protocol describes how to observe gastrulation in living mouse embryos by using light-sheet microscopy and computational tools to analyze the resulting image data at the single-cell level. We describe a series of techniques needed to image the embryos under physiological conditions, including how to hold mouse embryos without agarose embedding, how to transfer embryos without air exposure and how to construct environmental chambers for live imaging by digital scanned light-sheet microscopy (DSLM). Computational tools include manual and semiautomatic tracking programs that are developed for analyzing the large 4D data sets acquired with this system. Note that this protocol does not include details of how to build the light-sheet microscope itself. Time-lapse imaging ends within 12 h, with subsequent tracking analysis requiring 3-6 d. Other than some mouse-handling skills, this protocol requires no advanced skills or knowledge. Light-sheet microscopes are becoming more widely available, and thus the techniques outlined in this paper should be helpful for investigating mouse embryogenesis.

}, issn = {1750-2799}, doi = {10.1038/nprot.2014.035}, author = {Ichikawa, Takehiko and Nakazato, Kenichi and Keller, Philipp J and Kajiura-Kobayashi, Hiroko and Stelzer, Ernst H K and Mochizuki, Atsushi and Nonaka, Shigenori} } @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 {46297, title = {Novel cell-based odorant sensor elements based on insect odorant receptors.}, journal = {Biosensors \& Bioelectronics}, volume = {65C}, year = {2014}, month = {2014 Oct 17}, pages = {287-294}, abstract = {

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

}, issn = {1873-4235}, doi = {10.1016/j.bios.2014.10.026}, author = {Mitsuno, Hidefumi and Sakurai, Takeshi and Namiki, Shigehiro and Mitsuhashi, Hiroyuki and Kanzaki, Ryohei} } @article {45698, title = {Oscillatory activity in the medial prefrontal cortex and nucleus accumbens correlates with impulsivity and reward outcome.}, journal = {PLoS One}, volume = {9}, year = {2014}, month = {2014 Oct 21}, pages = {e111300}, abstract = {

Actions expressed prematurely without regard for their consequences are considered impulsive. Such behaviour is governed by a network of brain regions including the prefrontal cortex (PFC) and nucleus accumbens (NAcb) and is prevalent in disorders including attention deficit hyperactivity disorder (ADHD) and drug addiction. However, little is known of the relationship between neural activity in these regions and specific forms of impulsive behaviour. In the present study we investigated local field potential (LFP) oscillations in distinct sub-regions of the PFC and NAcb on a 5-choice serial reaction time task (5-CSRTT), which measures sustained, spatially-divided visual attention and action restraint. The main findings show that power in gamma frequency (50-60 Hz) LFP oscillations transiently increases in the PFC and NAcb during both the anticipation of a cue signalling the spatial location of a nose-poke response and again following correct responses. Gamma oscillations were coupled to low-frequency delta oscillations in both regions; this coupling strengthened specifically when an error response was made. Theta (7-9 Hz) LFP power in the PFC and NAcb increased during the waiting period and was also related to response outcome. Additionally, both gamma and theta power were significantly affected by upcoming premature responses as rats waited for the visual cue to respond. In a subgroup of rats showing persistently high levels of impulsivity we found that impulsivity was associated with increased error signals following a nose-poke response, as well as reduced signals of previous trial outcome during the waiting period. Collectively, these in-vivo neurophysiological findings further implicate the PFC and NAcb in anticipatory impulsive responses and provide evidence that abnormalities in the encoding of rewarding outcomes may underlie trait-like impulsive behaviour.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0111300}, author = {Donnelly, Nicholas A and Holtzman, Tahl and Rich, P Dylan and Nevado-Holgado, Alejo J and Fernando, Anushka B P and Van Dijck, Gert and Holzhammer, Tobias and Paul, Oliver and Ruther, Patrick and Paulsen, Ole and Robbins, Trevor W and Dalley, Jeffrey W} } @article {6933, title = {Protein structure determination by MicroED.}, journal = {Current Opinion in Structural Biology}, volume = {27C}, year = {2014}, month = {2014 Apr 4}, pages = {24-31}, abstract = {

In this review we discuss the current advances relating to structure determination from protein microcrystals with special emphasis on the newly developed method called MicroED. This method uses a transmission electron cryo-microscope to collect electron diffraction data from extremely small 3-dimensional (3D) crystals. MicroED has been used to solve the 3D structure of the model protein lysozyme to 2.9A resolution. As the method further matures, MicroED promises to offer a unique and widely applicable approach to protein crystallography using nanocrystals.

}, issn = {1879-033X}, doi = {10.1016/j.sbi.2014.03.004}, author = {Nannenga, Brent L and Gonen, Tamir} } @article {46062, title = {Quantifying histone and RNA polymerase II post-translational modification dynamics in mother and daughter cells.}, journal = {Methods}, volume = {70}, year = {2014}, month = {2014 Dec}, pages = {77-88}, abstract = {

Post-translational histone modifications are highly correlated with transcriptional activity, but the relative timing of these marks and their dynamic interplay during gene regulation remains controversial. To shed light on this problem and clarify the connections between histone modifications and transcription, we demonstrate how FabLEM (Fab-based Live Endogenous Modification labeling) can be used to simultaneously track histone H3 Lysine 9 acetylation (H3K9ac) together with RNA polymerase II Serine 2 and Serine 5 phosphorylation (RNAP2 Ser2ph/Ser5ph) in single living cells and their progeny. We provide a detailed description of the FabLEM methodology, including helpful tips for preparing and loading fluorescently conjugated antigen binding fragments (Fab) into cells for optimal results. We also introduce simple procedures for analyzing and visualizing FabLEM data, including color-coded scatterplots to track correlations between modifications through the cell cycle and temporal cross-correlation analysis to dissect modification dynamics. Using these methods, we find significant correlations that span cell generations, with a relatively strong correlation between H3K9ac and Ser5ph that appears to peak a few hours before mitosis and may reflect the bookmarking of genes for efficient re-initiation following mitosis. The techniques we have developed are broadly applicable and should help clarify how histone modifications dynamically contribute to gene regulation.

}, issn = {1095-9130}, doi = {10.1016/j.ymeth.2014.08.002}, author = {Stasevich, Timothy J and Sato, Yuko and Nozaki, Naohito and Kimura, Hiroshi} } @article {45843, title = {Regulation of RNA polymerase II activation by histone acetylation in single living cells.}, journal = {Nature}, volume = {516}, year = {2014}, month = {2014 Dec 11}, pages = {272-5}, abstract = {

In eukaryotic cells, post-translational histone modifications have an important role in gene regulation. Starting with early work on histone acetylation, a variety of residue-specific modifications have now been linked to RNA polymerase II (RNAP2) activity, but it remains unclear if these markers are active regulators of transcription or just passive byproducts. This is because studies have traditionally relied on fixed cell populations, meaning temporal resolution is limited to minutes at best, and correlated factors may not actually be present in the same cell at the same time. Complementary approaches are therefore needed to probe the dynamic interplay of histone modifications and RNAP2 with higher temporal resolution in single living cells. Here we address this problem by developing a system to track residue-specific histone modifications and RNAP2 phosphorylation in living cells by fluorescence microscopy. This increases temporal resolution to the tens-of-seconds range. Our single-cell analysis reveals histone H3 lysine-27 acetylation at a gene locus can alter downstream transcription kinetics by as much as 50\%, affecting two temporally separate events. First acetylation enhances the search kinetics of transcriptional activators, and later the acetylation accelerates the transition of RNAP2 from initiation to elongation. Signatures of the latter can be found genome-wide using chromatin immunoprecipitation followed by sequencing. We argue that this regulation leads to a robust and potentially tunable transcriptional response.

}, issn = {1476-4687}, doi = {10.1038/nature13714}, author = {Stasevich, Timothy J and Hayashi-Takanaka, Yoko and Sato, Yuko and Maehara, Kazumitsu and Ohkawa, Yasuyuki and Sakata-Sogawa, Kumiko and Tokunaga, Makio and Nagase, Takahiro and Nozaki, Naohito and McNally, James G and Kimura, Hiroshi} } @article {6961, title = {Reproductive status, endocrine physiology and chemical signaling in the Neotropical, swarm-founding eusocial wasp, Polybia micans Ducke (Vespidae: Epiponini).}, journal = {The Journal of Experimental Biology}, volume = {217}, year = {2014}, month = {2014 Apr 17}, pages = {2399-410}, abstract = {

In the evolution of caste-based societies in Hymenoptera, the classical insect hormones, juvenile hormone (JH) and ecdysteroids, were co-opted into new functions. Social wasps, which show all levels of sociality and lifestyles, are an ideal group to study such functional changes. Virtually all studies on the physiological mechanisms underlying reproductive division of labor and caste functions in wasps have been done on independent-founding paper wasps, and the majority of these studies have focused on species specially adapted for overwintering. The relatively little studied tropical swarming-founding wasps of the Epiponini (Vespidae) are a diverse group of permanently social wasps, with some species maintaining caste flexibility well into the adult phase. We investigated the behavior, reproductive status, JH and ecdysteroid titers in hemolymph, ecdysteroid content of the ovary and cuticular hydrocarbon (CHC) profiles in the caste-monomorphic, epiponine wasp Polybia micans Ducke. We found that the JH titer was not elevated in competing queens from established multiple-queen nests, but increased in lone queens that lack direct competition. In queenless colonies, JH titers rose transiently in young potential reproductives upon challenge by nestmates, suggesting that JH may prime the ovaries for further development. Ovarian ecdysteroids were very low in workers but higher and correlated with the number of vitellogenic oocytes in the queens. Hemolymph ecdysteroid levels were low and variable in both. Profiles of P. micans CHCs reflected caste, age and reproductive status, but were not tightly linked to either hormone. These findings show a significant divergence in hormone function in swarm-founding wasps compared to independent-founding ones.

}, issn = {1477-9145}, doi = {10.1242/jeb.096750}, author = {Kelstrup, Hans C and Hartfelder, Klaus and Nascimento, Fabio S and Riddiford, Lynn M} } @article {45785, title = {The role of juvenile hormone in dominance behavior, reproduction and cuticular pheromone signaling in the caste-flexible epiponine wasp, Synoeca surinama.}, journal = {Frontiers in Zoology}, volume = {11}, year = {2014}, month = {2014}, pages = {78}, abstract = {

BACKGROUND: The popular view on insect sociality is that of a harmonious division of labor among two morphologically distinct and functionally non-overlapping castes. But this is a highly derived state and not a prerequisite for a functional society. Rather, caste-flexibility is a central feature in many eusocial wasps, where adult females have the potential to become queens or workers, depending on the social environment. In non-swarming paper wasps (e.g., Polistes), prospective queens fight one another to assert their dominance, with losers becoming workers if they remain on the nest. This aggression is fueled by juvenile hormone (JH) and ecdysteroids, major factors involved in caste differentiation in most eusocial insects. We tested whether these hormones have conserved aggression-promoting functions in Synoeca surinama, a caste-flexible swarm-founding wasp (Epiponini) where reproductive competition is high and aggressive displays are common.

RESULTS: We observed the behavioral interactions of S. surinama females in field nests before and after we had removed the egg-laying queen(s). We measured the ovarian reproductive status, hemolymph JH and ecdysteroid titers, ovarian ecdysteroid content, and analyzed the cuticular hydrocarbon (CHC) composition of females engaged in competitive interactions in both queenright and queenless contexts. These data, in combination with hormone manipulation experiments, revealed that neither JH nor ecdysteroids are necessary for the expression of dominance behaviors in S. surinama. Instead, we show that JH likely functions as a gonadotropin and directly modifies the cuticular hydrocarbon blend of young workers to match that of a reproductive. Hemolymph ecdysteroids, in contrast, are not different between queens and workers despite great differences in ovarian ecdysteroid content.

CONCLUSIONS: The endocrine profile of S. surinama shows surprising differences from those of other caste-flexible wasps, although a rise in JH titers in replacement queens is a common theme. Extensive remodeling of hormone functions is also evident in the highly eusocial bees, which has been attributed to the evolution of morphologically defined castes. Our results show that hormones which regulate caste-plasticity can lose these roles even while caste-plasticity is preserved.

}, issn = {1742-9994}, doi = {10.1186/s12983-014-0078-5}, author = {Kelstrup, Hans C and Hartfelder, Klaus and Nascimento, Fabio S and Riddiford, Lynn M} } @article {45552, title = {Structure of catalase determined by MicroED.}, journal = {eLife}, volume = {3}, year = {2014}, month = {2014 Oct 17}, pages = {e03600}, abstract = {

MicroED is a recently developed method that uses electron diffraction for structure determination from very small three-dimensional crystals of biological material. Previously we used a series of still diffraction patterns to determine the structure of lysozyme at 2.9 {\r A} resolution with MicroED (Shi et al., 2013). Here we present the structure of bovine liver catalase determined from a single crystal at 3.2 {\r A} resolution by MicroED. The data were collected by continuous rotation of the sample under constant exposure and were processed and refined using standard programs for X-ray crystallography. The ability of MicroED to determine the structure of bovine liver catalase, a protein that has long resisted atomic analysis by traditional electron crystallography, demonstrates the potential of this method for structure determination.

}, issn = {2050-084X}, doi = {10.7554/eLife.03600}, author = {Nannenga, Brent L and Shi, Dan and Hattne, Johan and Reyes, Francis E and Gonen, Tamir} } @article {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 {46702, title = {The translation elongation factor eEF1A1 couples transcription to translation during heat shock response.}, journal = {eLife}, volume = {3}, year = {2014}, month = {2014 Sep 16}, pages = {e03164}, abstract = {

Translation elongation factor eEF1A has a well-defined role in protein synthesis. In this study, we demonstrate a new role for eEF1A: it participates in the entire process of the heat shock response (HSR) in mammalian cells from transcription through translation. Upon stress, isoform 1 of eEF1A rapidly activates transcription of HSP70 by recruiting the master regulator HSF1 to its promoter. eEF1A1 then associates with elongating RNA polymerase II and the 3{\textquoteright}UTR of HSP70 mRNA, stabilizing it and facilitating its transport from the nucleus to active ribosomes. eEF1A1-depleted cells exhibit severely impaired HSR and compromised thermotolerance. In contrast, tissue-specific isoform 2 of eEF1A does not support HSR. By adjusting transcriptional yield to translational needs, eEF1A1 renders HSR rapid, robust, and highly selective; thus, representing an attractive therapeutic target for numerous conditions associated with disrupted protein homeostasis, ranging from neurodegeneration to cancer.

}, issn = {2050-084X}, doi = {10.7554/eLife.03164}, author = {Vera, Maria and Pani, Bibhusita and Griffiths, Lowri A and Muchardt, Christian and Abbott, Catherine M and Singer, Robert H and Nudler, Evgeny} } @article {46676, title = {Visualization of dynamics of single endogenous mRNA labeled in live mouse.}, journal = {Science}, volume = {343}, year = {2014}, month = {2014 Jan 24}, pages = {422-4}, abstract = {

The transcription and transport of messenger RNA (mRNA) are critical steps in regulating the spatial and temporal components of gene expression, but it has not been possible to observe the dynamics of endogenous mRNA in primary mammalian tissues. We have developed a transgenic mouse in which all β-actin mRNA is fluorescently labeled. We found that β-actin mRNA in primary fibroblasts localizes predominantly by diffusion and trapping as single mRNAs. In cultured neurons and acute brain slices, we found that multiple β-actin mRNAs can assemble together, travel by active transport, and disassemble upon depolarization by potassium chloride. Imaging of brain slices revealed immediate early induction of β-actin transcription after depolarization. Studying endogenous mRNA in live mouse tissues provides insight into its dynamic regulation within the context of the cellular and tissue microenvironment.

}, keywords = {Actins, Animals, Brain, Cells, Cultured, Fibroblasts, Fluorescent Dyes, Mice, Mice, Transgenic, Neuroimaging, Neurons, Protein Biosynthesis, RNA, Messenger, Staining and Labeling}, issn = {1095-9203}, doi = {10.1126/science.1239200}, author = {Park, Hye Yoon and Lim, Hyungsik and Yoon, Young J and Follenzi, Antonia and Nwokafor, Chiso and Lopez-Jones, Melissa and Meng, Xiuhua and Singer, Robert H} } @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 {47642, title = {Accelerating 3B single-molecule super-resolution microscopy with cloud computing.}, journal = {Nature methods}, volume = {10}, year = {2013}, month = {2013 Feb}, pages = {96-7}, keywords = {Computational Biology, Computers, Fluorescent Dyes, Microscopy, Fluorescence, Nanotechnology}, issn = {1548-7105}, doi = {10.1038/nmeth.2335}, author = {Hu, Ying S and Nan, Xiaolin and Sengupta, Prabuddha and Lippincott-Schwartz, Jennifer and Cang, Hu} } @article {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 {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 {6715, title = {Balanced synaptic impact via distance-dependent synapse distribution and complementary expression of AMPARs and NMDARs in hippocampal dendrites.}, journal = {Neuron}, volume = {80}, year = {2013}, month = {2013 Dec 18}, pages = {1451-63}, abstract = {

Neuronal computation involves the integration of synaptic inputs that are often distributed over expansive dendritic trees, suggesting the need for compensatory mechanisms that enable spatially disparate synapses to influence neuronal output. In hippocampal CA1 pyramidal neurons, such mechanisms have indeed been reported, which normalize either the ability of distributed synapses to drive action potential initiation in the axon or their ability to drive dendritic spiking locally. Here we report that these mechanisms can coexist, through an elegant combination of distance-dependent regulation of synapse number and synaptic expression of AMPA and NMDA receptors. Together, these complementary gradients allow individual dendrites in both the apical and basal dendritic trees of hippocampal neurons to operate as facile computational subunits capable of supporting both global integration in the soma/axon and local integration in the dendrite.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2013.09.027}, author = {Menon, Vilas and Musial, Timothy F and Liu, Annie and Katz, Yael and Kath, William L and Spruston, Nelson and Nicholson, Daniel A} } @article {46414, title = {Common genetic variation at the IL1RL1 locus regulates IL-33/ST2 signaling.}, journal = {The Journal of Clinical Investigation}, volume = {123}, year = {2013}, month = {2013 Oct}, pages = {4208-18}, abstract = {

The suppression of tumorigenicity 2/IL-33 (ST2/IL-33) pathway has been implicated in several immune and inflammatory diseases. ST2 is produced as 2 isoforms. The membrane-bound isoform (ST2L) induces an immune response when bound to its ligand, IL-33. The other isoform is a soluble protein (sST2) that is thought to be a decoy receptor for IL-33 signaling. Elevated sST2 levels in serum are associated with an increased risk for cardiovascular disease. We investigated the determinants of sST2 plasma concentrations in 2,991 Framingham Offspring Cohort participants. While clinical and environmental factors explained some variation in sST2 levels, much of the variation in sST2 production was driven by genetic factors. In a genome-wide association study (GWAS), multiple SNPs within IL1RL1 (the gene encoding ST2) demonstrated associations with sST2 concentrations. Five missense variants of IL1RL1 correlated with higher sST2 levels in the GWAS and mapped to the intracellular domain of ST2, which is absent in sST2. In a cell culture model, IL1RL1 missense variants increased sST2 expression by inducing IL-33 expression and enhancing IL-33 responsiveness (via ST2L). Our data suggest that genetic variation in IL1RL1 can result in increased levels of sST2 and alter immune and inflammatory signaling through the ST2/IL-33 pathway.

}, keywords = {Amino Acid Substitution, Female, Gene Expression, Gene Expression Regulation, Genetic Association Studies, HEK293 Cells, Humans, Interleukins, Male, Middle Aged, Models, Molecular, Myelin and Lymphocyte-Associated Proteolipid Proteins, Myeloid Differentiation Factor 88, NF-kappa B, Polymorphism, Single Nucleotide, Promoter Regions, Genetic, Prospective Studies, Protein Structure, Tertiary, Receptors, Cell Surface, Signal Transduction, Transcription Factor AP-1}, issn = {1558-8238}, doi = {10.1172/JCI67119}, author = {Ho, Jennifer E and Chen, Wei-Yu and Chen, Ming-Huei and Larson, Martin G and McCabe, Elizabeth L and Cheng, Susan and Ghorbani, Anahita and Coglianese, Erin and Emilsson, Valur and Johnson, Andrew D and Walter, Stefan and Franceschini, Nora and O{\textquoteright}Donnell, Christopher J and Dehghan, Abbas and Lu, Chen and Levy, Daniel and Newton-Cheh, Christopher and Lin, Honghuang and Felix, Janine F and Schreiter, Eric R and Vasan, Ramachandran S and Januzzi, James L and Lee, Richard T and Wang, Thomas J} } @article {6266, title = {Computational identification of functional RNA homologs in metagenomic data.}, journal = {RNA Biology}, volume = {10}, year = {2013}, month = {2013 Jul 1}, pages = {1170-9}, abstract = {

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

}, issn = {1555-8584}, doi = {10.4161/rna.25038}, author = {Nawrocki, Eric P and Eddy, Sean R.} } @article {6091, title = {Contributions of the 12 neuron classes in the fly lamina to motion vision.}, journal = {Neuron}, volume = {79}, year = {2013}, month = {07/2013}, pages = {128-140}, abstract = {

Motion detection is a fundamental neural computation performed by many sensory systems. In the fly, local motion computation is thought to occur within the first two layers of the visual system, the lamina and medulla. We constructed specific genetic driver lines for each of the 12 neuron classes in the lamina. We then depolarized and hyperpolarized each neuron type and quantified fly behavioral responses to a diverse set of motion stimuli. We found that only a small number of lamina output neurons are essential for motion detection, while most neurons serve to sculpt and enhance these feedforward pathways. Two classes of feedback neurons (C2 and C3), and lamina output neurons (L2 and L4), are required for normal detection of directional motion stimuli. Our results reveal a prominent role for feedback and lateral interactions in motion processing and demonstrate that motion-dependent behaviors rely on contributions from nearly all lamina neuron classes.

}, doi = {http://dx.doi.org/10.1016/j.neuron.2013.05.024}, author = {Tuthill, John C and Nern, Aljoscha and Stephen L. Holtz and Rubin, Gerald M and Reiser, Michael B} } @article {5893, title = {Convergence of pontine and proprioceptive streams onto multimodal cerebellar granule cells.}, journal = {eLife}, volume = {2}, year = {2013}, month = {2013 Feb 26}, pages = {e00400}, abstract = {

Cerebellar granule cells constitute the majority of neurons in the brain and are the primary conveyors of sensory and motor-related mossy fiber information to Purkinje cells. The functional capability of the cerebellum hinges on whether individual granule cells receive mossy fiber inputs from multiple precerebellar nuclei or are instead unimodal; this distinction is unresolved. Using cell-type-specific projection mapping with synaptic resolution, we observed the convergence of separate sensory (upper body proprioceptive) and basilar pontine pathways onto individual granule cells and mapped this convergence across cerebellar cortex. These findings inform the long-standing debate about the multimodality of mammalian granule cells and substantiate their associative capacity predicted in the Marr-Albus theory of cerebellar function. We also provide evidence that the convergent basilar pontine pathways carry corollary discharges from upper body motor cortical areas. Such merging of related corollary and sensory streams is a critical component of circuit models of predictive motor control. DOI:http://dx.doi.org/10.7554/eLife.00400.001.

}, issn = {2050-084X}, doi = {10.7554/eLife.00400}, author = {Huang, Cheng-Chiu and Sugino, Ken and Shima, Yasuyuki and Guo, Caiying and Bai, Suxia and Mensh, Brett D and Nelson, Sacha B and Hantman, Adam W} } @article {46040, title = {Depletion of polysialic acid from neural cell adhesion molecule (PSA-NCAM) increases CA3 dendritic arborization and increases vulnerability to excitotoxicity.}, journal = {Experimental Neurology}, volume = {241}, year = {2013}, month = {2013 Mar}, pages = {5-12}, abstract = {

Chronic immobilization stress (CIS) shortens apical dendritic trees of CA3 pyramidal neurons in the hippocampus of the male rat, and dendritic length may be a determinant of vulnerability to stress. Expression of the polysialylated form of neural cell adhesion molecule (PSA-NCAM) in the hippocampal formation is increased by stress, while PSA removal by Endo-neuraminidase-N (endo-N) is known to cause the mossy fibers to defasciculate and synapse ectopically in their CA3 target area. We show here that enzymatic removal of PSA produced a remarkable expansion of dendritic arbors of CA3 pyramidal neurons, with a lesser effect in CA1. This expansion eclipsed the CIS-induced shortening of CA3 dendrites, with the expanded dendrites of both no-stress-endo-N and CIS-endo-N rats being longer than those in no-stress-control rats and much longer than those in CIS-control rats. As predicted by the hypothesis that endo-N-induced dendritic expansion might increase vulnerability to excitotoxic challenge, systemic injection with kainic acid, showed markedly increased neuronal degeneration, as assessed by fluorojade B histochemistry, in rats that had been treated with endo-N compared to vehicle-treated rats throughout the entire hippocampal formation. PSA removal also exacerbated the CIS-induced reduction in body weight and abolished effects of CIS on NPY and NR2B mRNA levels. These findings support the hypothesis that CA3 arbor plasticity plays a protective role during prolonged stress and clarify the role of PSA-NCAM in stress-induced dendritic plasticity.

}, keywords = {Analysis of Variance, Animals, Body Mass Index, CA3 Region, Hippocampal, Dendrites, Disease Models, Animal, Excitatory Amino Acid Agonists, Fluoresceins, Gene Expression Regulation, Kainic Acid, Male, Metalloendopeptidases, Nerve Degeneration, Neural Cell Adhesion Molecules, Organic Chemicals, Pyramidal Cells, Rats, Rats, Sprague-Dawley, Receptors, N-Methyl-D-Aspartate, Sialic Acids, Silver Staining, Stress, Psychological}, issn = {1090-2430}, doi = {10.1016/j.expneurol.2012.11.028}, author = {McCall, Trudy and Weil, Zachary M and Nacher, Juan and Bloss, Erik B and El Maarouf, Abderrahman and Rutishauser, Urs and McEwen, Bruce S} } @article {6275, title = {A directional tuning map of Drosophila elementary motion detectors.}, journal = {Nature}, volume = {500}, year = {2013}, month = {2013 Aug 8}, pages = {212-6}, abstract = {

The extraction of directional motion information from changing retinal images is one of the earliest and most important processing steps in any visual system. In the fly optic lobe, two parallel processing streams have been anatomically described, leading from two first-order interneurons, L1 and L2, via T4 and T5 cells onto large, wide-field motion-sensitive interneurons of the lobula plate. Therefore, T4 and T5 cells are thought to have a pivotal role in motion processing; however, owing to their small size, it is difficult to obtain electrical recordings of T4 and T5 cells, leaving their visual response properties largely unknown. We circumvent this problem by means of optical recording from these cells in Drosophila, using the genetically encoded calcium indicator GCaMP5 (ref. 2). Here we find that specific subpopulations of T4 and T5 cells are directionally tuned to one of the four cardinal directions; that is, front-to-back, back-to-front, upwards and downwards. Depending on their preferred direction, T4 and T5 cells terminate in specific sublayers of the lobula plate. T4 and T5 functionally segregate with respect to contrast polarity: whereas T4 cells selectively respond to moving brightness increments (ON edges), T5 cells only respond to moving brightness decrements (OFF edges). When the output from T4 or T5 cells is blocked, the responses of postsynaptic lobula plate neurons to moving ON (T4 block) or OFF edges (T5 block) are selectively compromised. The same effects are seen in turning responses of tethered walking flies. Thus, starting with L1 and L2, the visual input is split into separate ON and OFF pathways, and motion along all four cardinal directions is computed separately within each pathway. The output of these eight different motion detectors is then sorted such that ON (T4) and OFF (T5) motion detectors with the same directional tuning converge in the same layer of the lobula plate, jointly providing the input to downstream circuits and motion-driven behaviours.

}, keywords = {Animal, Animals, Behavior, Drosophila, Interneurons, Locomotion, Motion Perception, Neurons, Signal Transduction, Visual Pathways}, issn = {1476-4687}, doi = {10.1038/nature12320}, author = {Maisak, Matthew S and Haag, Juergen and Ammer, Georg and Serbe, Etienne and Meier, Matthias and Leonhardt, Aljoscha and Schilling, Tabea and Bahl, Armin and Rubin, Gerald M and Nern, Aljoscha and Dickson, Barry J and Reiff, Dierk F and Hopp, Elisabeth and Borst, Alexander} } @article {6588, title = {Distinct balance of excitation and inhibition in an interareal feedforward and feedback circuit of mouse visual cortex.}, journal = {The Journal of Neuroscience}, volume = {33}, year = {2013}, month = {2013 Oct 30}, pages = {17373-84}, abstract = {

Mouse visual cortex is subdivided into multiple distinct, hierarchically organized areas that are interconnected through feedforward (FF) and feedback (FB) pathways. The principal synaptic targets of FF and FB axons that reciprocally interconnect primary visual cortex (V1) with the higher lateromedial extrastriate area (LM) are pyramidal cells (Pyr) and parvalbumin (PV)-expressing GABAergic interneurons. Recordings in slices of mouse visual cortex have shown that layer 2/3 Pyr cells receive excitatory monosynaptic FF and FB inputs, which are opposed by disynaptic inhibition. Most notably, inhibition is stronger in the FF than FB pathway, suggesting pathway-specific organization of feedforward inhibition (FFI). To explore the hypothesis that this difference is due to diverse pathway-specific strengths of the inputs to PV neurons we have performed subcellular Channelrhodopsin-2-assisted circuit mapping in slices of mouse visual cortex. Whole-cell patch-clamp recordings were obtained from retrobead-labeled FFV1{\textrightarrow}LM- and FBLM{\textrightarrow}V1-projecting Pyr cells, as well as from tdTomato-expressing PV neurons. The results show that the FFV1{\textrightarrow}LM pathway provides on average 3.7-fold stronger depolarizing input to layer 2/3 inhibitory PV neurons than to neighboring excitatory Pyr cells. In the FBLM{\textrightarrow}V1 pathway, depolarizing inputs to layer 2/3 PV neurons and Pyr cells were balanced. Balanced inputs were also found in the FFV1{\textrightarrow}LM pathway to layer 5 PV neurons and Pyr cells, whereas FBLM{\textrightarrow}V1 inputs to layer 5 were biased toward Pyr cells. The findings indicate that FFI in FFV1{\textrightarrow}LM and FBLM{\textrightarrow}V1 circuits are organized in a pathway- and lamina-specific fashion.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.2515-13.2013}, author = {Yang, Weiguo and Carrasquillo, Yarimar and Hooks, Bryan M and Nerbonne, Jeanne M and Burkhalter, Andreas} } @article {6676, title = {Electron microscopy reconstruction of brain structure using sparse representations over learned dictionaries.}, journal = {IEEE Transactions on Medical Imaging}, volume = {32}, year = {2013}, month = {2013 Aug 2}, pages = {2179-88}, abstract = {

A central problem in neuroscience is reconstructing neuronal circuits on the synapse level. Due to a wide range of scales in brain architecture such reconstruction requires imaging that is both high-resolution and high-throughput. Existing electron microscopy (EM) techniques possess required resolution in the lateral plane and either high-throughput or high depth resolution but not both. Here, we exploit recent advances in unsupervised learning and signal processing to obtain high depth-resolution EM images computationally without sacrificing throughput. First, we show that the brain tissue can be represented as a sparse linear combination of localized basis functions that are learned using high-resolution datasets. We then develop compressive sensing-inspired techniques that can reconstruct the brain tissue from very few (typically 5) tomographic views of each section. This enables tracing of neuronal processes and, hence, high throughput reconstruction of neural circuits on the level of individual synapses.

}, issn = {1558-254X}, doi = {10.1109/TMI.2013.2276018}, author = {Hu, Tao and Nunez-Iglesias, Juan and Vitaladevuni, Shiv and Scheffer, Lou and Xu, Shan and Bolorizadeh, Mehdi and Hess, Harald and Fetter, Richard and Chklovskii, Dmitri} } @article {6122, title = {Fine time-course expression analysis identifies cascades of activation and repression and maps a regulator of mammalian sex determination.}, journal = {PLoS Genetics}, volume = {9}, year = {2013}, month = {2013 Jul}, pages = {e1003630}, abstract = {

In vertebrates, primary sex determination refers to the decision within a bipotential organ precursor to differentiate as a testis or ovary. Bifurcation of organ fate begins between embryonic day (E) 11.0{\textendash}E12.0 in mice and likely involves a dynamic transcription network that is poorly understood. To elucidate the first steps of sexual fate specification, we profiled the XX and XY gonad transcriptomes at fine granularity during this period and resolved cascades of gene activation and repression. C57BL/6J (B6) XY gonads showed a consistent \ 5-hour delay in the activation of most male pathway genes and repression of female pathway genes relative to 129S1/SvImJ, which likely explains the sensitivity of the B6 strain to male-to-female sex reversal. Using this fine time course data, we predicted novel regulatory genes underlying expression QTLs (eQTLs) mapped in a previous study. To test predictions, we developed an in vitro gonad primary cell assay and optimized a lentivirus-based shRNA delivery method to silence candidate genes and quantify effects on putative targets. We provide strong evidence that Lmo4 (Lim-domain only 4) is a novel regulator of sex determination upstream of SF1 (Nr5a1), Sox9, Fgf9, and Col9a3. This approach can be readily applied to identify regulatory interactions in other systems.

}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1003630}, author = {Munger, Steven C. and Natarajan, Anirudh and Looger, Loren L and Ohler, Uwe and Capel, Blanche} } @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 {6923, title = {Genetic and neural mechanisms that inhibit Drosophila from mating with other species.}, journal = {Cell}, volume = {154}, year = {2013}, month = {2013 Jul 3}, pages = {89-102}, abstract = {

Genetically hard-wired neural mechanisms must enforce behavioral reproductive isolation because interspecies courtship is rare even in sexually na{\"{\i}ve animals of most species. We find that the chemoreceptor Gr32a inhibits male D. melanogaster from courting diverse fruit fly species. Gr32a recognizes nonvolatile aversive cues present on these reproductively dead-end targets, and activity of Gr32a neurons is necessary and sufficient to inhibit interspecies courtship. Male-specific Fruitless (Fru(M)), a master regulator of courtship, also inhibits interspecies courtship. Gr32a and Fru(M) are not coexpressed, but Fru(M) neurons contact Gr32a neurons, suggesting that these genes influence a shared neural circuit that inhibits interspecies courtship. Gr32a and Fru(M) also suppress within-species intermale courtship, but we show that distinct mechanisms preclude sexual displays toward conspecific males and other species. Although this chemosensory pathway does not inhibit interspecies mating in D. melanogaster females, similar mechanisms appear to inhibit this behavior in many other male drosophilids.

}, keywords = {Animal, Animals, Cell Surface, Courtship, Drosophila, Drosophila melanogaster, Drosophila Proteins, Female, Genetic Speciation, Male, Mating Preference, Nerve Tissue Proteins, Neurons, Receptors, Transcription Factors}, issn = {1097-4172}, doi = {10.1016/j.cell.2013.06.008}, author = {Fan, Pu and Manoli, Devanand S and Ahmed, Osama M and Chen, Yi and Agarwal, Neha and Kwong, Sara and Cai, Allen G and Neitz, Jeffrey and Renslo, Adam and Baker, Bruce S and Shah, Nirao M} } @article {6453, title = {Infernal 1.1: 100-fold faster RNA homology searches.}, journal = {Bioinformatics}, volume = {29}, year = {2013}, month = {2013 Sep 19}, pages = {2933-5}, abstract = {

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

}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btt509}, author = {Nawrocki, Eric P and Eddy, Sean R.} } @article {6073, title = {Live imaging of whole mouse embryos during gastrulation: migration analyses of epiblast and mesodermal cells.}, journal = {PLoS One}, volume = {8}, year = {2013}, month = {2013 Jul 8}, pages = {e64506}, abstract = {

During gastrulation in the mouse embryo, dynamic cell movements including epiblast invagination and mesodermal layer expansion lead to the establishment of the three-layered body plan. The precise details of these movements, however, are sometimes elusive, because of the limitations in live imaging. To overcome this problem, we developed techniques to enable observation of living mouse embryos with digital scanned light sheet microscope (DSLM). The achieved deep and high time-resolution images of GFP-expressing nuclei and following 3D tracking analysis revealed the following findings: (i) Interkinetic nuclear migration (INM) occurs in the epiblast at embryonic day (E)6 and 6.5. (ii) INM-like migration occurs in the E5.5 embryo, when the epiblast is a monolayer and not yet pseudostratified. (iii) Primary driving force for INM at E6.5 is not pressure from neighboring nuclei. (iv) Mesodermal cells migrate not as a sheet but as individual cells without coordination.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0064506}, author = {Ichikawa, Takehiko and Nakazato, Kenichi and Keller, Philipp J and Kajiura-Kobayashi, Hiroko and Stelzer, Ernst H K and Mochizuki, Atsushi and Nonaka, Shigenori} } @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 {6263, title = {Machine learning of hierarchical clustering to segment 2D and 3D images.}, journal = {PLoS One}, volume = {8}, year = {2013}, month = {2013}, pages = {e71715}, abstract = {

We aim to improve segmentation through the use of machine learning tools during region agglomeration. We propose an active learning approach for performing hierarchical agglomerative segmentation from superpixels. Our method combines multiple features at all scales of the agglomerative process, works for data with an arbitrary number of dimensions, and scales to very large datasets. We advocate the use of variation of information to measure segmentation accuracy, particularly in 3D electron microscopy (EM) images of neural tissue, and using this metric demonstrate an improvement over competing algorithms in EM and natural images.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0071715}, author = {Nunez-Iglesias, Juan and Kennedy, Ryan and Toufiq Parag and Shi, Jianbo and Chklovskii, Dmitri B} } @article {6413, title = {Molecular architecture of the ATP-dependent chromatin-remodeling complex SWR1.}, journal = {Cell}, volume = {154}, year = {2013}, month = {2013 Sep 12}, pages = {1220-31}, abstract = {

The ATP-dependent chromatin-remodeling complex SWR1 exchanges a variant histone H2A.Z/H2B dimer\ for a canonical H2A/H2B dimer at nucleosomes flanking histone-depleted regions, such as promoters. This localization of H2A.Z is conserved throughout eukaryotes. SWR1 is a 1 megadalton complex containing 14 different polypeptides, including the AAA+ ATPases Rvb1 and Rvb2. Using electron microscopy, we obtained the three-dimensional structure of SWR1 and mapped its major functional components. Our data show that SWR1 contains a single heterohexameric Rvb1/Rvb2 ring that, together with the catalytic subunit Swr1, brackets two independently assembled multisubunit modules. We also show that SWR1 undergoes a large conformational change upon engaging a limited region of the nucleosome core particle. Our work suggests an important structural role for the Rvbs and a distinct substrate-handling mode by SWR1, thereby providing a structural framework for understanding the complex dimer-exchange reaction.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2013.08.018}, author = {Nguyen, Vu Q and Ranjan, Anand and Stengel, Florian and Wei, Debbie and Aebersold, Ruedi and Wu, Carl and Leschziner, Andres E} } @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} } @article {5883, title = {New technologies in imaging.}, journal = {Molecular Biology of the Cell}, volume = {24}, year = {2013}, month = {2013 Mar}, pages = {669}, abstract = {

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

}, issn = {1939-4586}, doi = {10.1091/mbc.E12-12-0867}, author = {Galbraith, Catherine G and Keller, Philipp J and Nogales, Eva} } @article {48275, title = {Optogenetics through windows on the brain in the nonhuman primate.}, journal = {Journal of neurophysiology}, volume = {110}, year = {2013}, month = {2013 Sep}, pages = {1455-67}, abstract = {

Optogenetics combines optics and genetics to control neuronal activity with cell-type specificity and millisecond temporal precision. Its use in model organisms such as rodents, Drosophila, and Caenorhabditis elegans is now well-established. However, application of this technology in nonhuman primates (NHPs) has been slow to develop. One key challenge has been the delivery of viruses and light to the brain through the thick dura mater of NHPs, which can only be penetrated with large-diameter devices that damage the brain. The opacity of the NHP dura prevents visualization of the underlying cortex, limiting the spatial precision of virus injections, electrophysiological recordings, and photostimulation. Here, we describe a new optogenetics approach in which the native dura is replaced with an optically transparent artificial dura. This artificial dura can be penetrated with fine glass micropipettes, enabling precisely targeted injections of virus into brain tissue with minimal damage to cortex. The expression of optogenetic agents can be monitored visually over time. Most critically, this optical window permits targeted, noninvasive photostimulation and concomitant measurements of neuronal activity via intrinsic signal imaging and electrophysiological recordings. We present results from both anesthetized-paralyzed (optical imaging) and awake-behaving NHPs (electrophysiology). The improvements over current methods made possible by the artificial dura should enable the widespread use of optogenetic tools in NHP research, a key step toward the development of therapies for neuropsychiatric and neurological diseases in humans.

}, keywords = {Animals, Brain, Dura Mater, Gene Transfer Techniques, Haplorhini, Neurosurgical Procedures, Optogenetics}, issn = {1522-1598}, doi = {10.1152/jn.00153.2013}, author = {Ruiz, Octavio and Lustig, Brian R and Nassi, Jonathan J and Cetin, Ali and Reynolds, John H and Albright, Thomas D and Callaway, Edward M and Stoner, Gene R and Roe, Anna W} } @article {5959, title = {Overview of electron crystallography of membrane proteins: crystallization and screening strategies using negative stain electron microscopy.}, journal = {Current Protocols in Protein Science }, volume = {Chapter 17}, year = {2013}, month = {2013 Apr 2}, pages = {Unit 17.15}, abstract = {

Electron cryomicroscopy, or cryoEM, is an emerging technique for studying the three-dimensional structures of proteins and large macromolecular machines. Electron crystallography is a branch of cryoEM in which structures of proteins can be studied at resolutions that rival those achieved by X-ray crystallography. Electron crystallography employs two-dimensional crystals of a membrane protein embedded within a lipid bilayer. The key to a successful electron crystallographic experiment is the crystallization, or reconstitution, of the protein of interest. This unit describes ways in which protein can be expressed, purified, and reconstituted into well-ordered two-dimensional crystals. A protocol is also provided for negative stain electron microscopy as a tool for screening crystallization trials. When large and well-ordered crystals are obtained, the structures of both protein and its surrounding membrane can be determined to atomic resolution.

}, issn = {1934-3663}, doi = {10.1002/0471140864.ps1715s72}, author = {Nannenga, Brent L and Iadanza, Matthew G and Vollmar, Breanna S and Gonen, Tamir} } @article {6526, title = {The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes.}, journal = {PLoS Biology}, volume = {11}, year = {2013}, month = {2013 Jan}, pages = {e1001473}, abstract = {

The macronuclear genome of the ciliate Oxytricha trifallax displays an extreme and unique eukaryotic genome architecture with extensive genomic variation. During sexual genome development, the expressed, somatic macronuclear genome is whittled down to the genic portion of a small fraction (\~{}5\%) of its precursor "silent" germline micronuclear genome by a process of "unscrambling" and fragmentation. The tiny macronuclear "nanochromosomes" typically encode single, protein-coding genes (a small portion, 10\%, encode 2-8 genes), have minimal noncoding regions, and are differentially amplified to an average of \~{}2,000 copies. We report the high-quality genome assembly of \~{}16,000 complete nanochromosomes (\~{}50 Mb haploid genome size) that vary from 469 bp to 66 kb long (mean \~{}3.2 kb) and encode \~{}18,500 genes. Alternative DNA fragmentation processes \~{}10\% of the nanochromosomes into multiple isoforms that usually encode complete genes. Nucleotide diversity in the macronucleus is very high (SNP heterozygosity is \~{}4.0\%), suggesting that Oxytricha trifallax may have one of the largest known effective population sizes of eukaryotes. Comparison to other ciliates with nonscrambled genomes and long macronuclear chromosomes (on the order of 100 kb) suggests several candidate proteins that could be involved in genome rearrangement, including domesticated MULE and IS1595-like DDE transposases. The assembly of the highly fragmented Oxytricha macronuclear genome is the first completed genome with such an unusual architecture. This genome sequence provides tantalizing glimpses into novel molecular biology and evolution. For example, Oxytricha maintains tens of millions of telomeres per cell and has also evolved an intriguing expansion of telomere end-binding proteins. In conjunction with the micronuclear genome in progress, the O. trifallax macronuclear genome will provide an invaluable resource for investigating programmed genome rearrangements, complementing studies of rearrangements arising during evolution and disease.

}, keywords = {Base Sequence, DNA, DNA Copy Number Variations, DNA Fragmentation, Gene Amplification, Gene Rearrangement, Genes, Genetic Variation, Genome, Macronucleus, Messenger, Molecular Sequence Data, Oxytricha, Protein Binding, Protozoan, RNA, Sequence Analysis, Telomere}, issn = {1545-7885}, doi = {10.1371/journal.pbio.1001473}, author = {Swart, Estienne C and Bracht, John R and Magrini, Vincent and Minx, Patrick and Chen, Xiao and Zhou, Yi and Khurana, Jaspreet S and Goldman, Aaron D and Nowacki, Mariusz and Schotanus, Klaas and Jung, Seolkyoung and Fulton, Robert S and Ly, Amy and McGrath, Sean and Haub, Kevin and Wiggins, Jessica L and Storton, Donna and Matese, John C and Parsons, Lance and Chang, Wei-Jen and Bowen, Michael S and Stover, Nicholas A and Jones, Thomas A and Eddy, Sean R. and Herrick, Glenn A and Doak, Thomas G and Wilson, Richard K and Mardis, Elaine R and Landweber, Laura F} } @article {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 {46711, title = {Single cell analysis of RNA-mediated histone H3.3 recruitment to a cytomegalovirus promoter-regulated transcription site.}, journal = {The Journal of Biological Chemistry}, volume = {288}, year = {2013}, month = {2013 Jul 5}, pages = {19882-99}, abstract = {

Unlike the core histones, which are incorporated into nucleosomes concomitant with DNA replication, histone H3.3 is synthesized throughout the cell cycle and utilized for replication-independent (RI) chromatin assembly. The RI incorporation of H3.3 into nucleosomes is highly conserved and occurs at both euchromatin and heterochromatin. However, neither the mechanism of H3.3 recruitment nor its essential function is well understood. Several different chaperones regulate H3.3 assembly at distinct sites. The H3.3 chaperone, Daxx, and the chromatin-remodeling factor, ATRX, are required for H3.3 incorporation and heterochromatic silencing at telomeres, pericentromeres, and the cytomegalovirus (CMV) promoter. By evaluating H3.3 dynamics at a CMV promoter-regulated transcription site in a genetic background in which RI chromatin assembly is blocked, we have been able to decipher the regulatory events upstream of RI nucleosomal deposition. We find that at the activated transcription site, H3.3 accumulates with sense and antisense RNA, suggesting that it is recruited through an RNA-mediated mechanism. Sense and antisense transcription also increases after H3.3 knockdown, suggesting that the RNA signal is amplified when chromatin assembly is blocked and attenuated by nucleosomal deposition. Additionally, we find that H3.3 is still recruited after Daxx knockdown, supporting a chaperone-independent recruitment mechanism. Sequences in the H3.3 N-terminal tail and αN helix mediate both its recruitment to RNA at the activated transcription site and its interaction with double-stranded RNA in vitro. Interestingly, the H3.3 gain-of-function pediatric glioblastoma mutations, G34R and K27M, differentially affect H3.3 affinity in these assays, suggesting that disruption of an RNA-mediated regulatory event could drive malignant transformation.

}, keywords = {Cell Line, Chromatin Assembly and Disassembly, Cytomegalovirus, Histones, Humans, Nucleosomes, Promoter Regions, Genetic, Protein Structure, Secondary, RNA, Viral, Transcription, Genetic}, issn = {1083-351X}, doi = {10.1074/jbc.M113.473181}, author = {Newhart, Alyshia and Rafalska-Metcalf, Ilona U and Yang, Tian and Joo, Lucy M and Powers, Sara Lawrence and Kossenkov, Andrew V and Lopez-Jones, Melissa and Singer, Robert H and Showe, Louise C and Skordalakes, Emmanuel and Janicki, Susan M} } @article {6633, title = {Three-dimensional electron crystallography of protein microcrystals.}, journal = {eLife}, volume = {2}, year = {2013}, month = {2013 Nov 19}, pages = {01345}, abstract = {

We demonstrate that it is feasible to determine high-resolution protein structures by electron crystallography of three-dimensional crystals in an electron cryo-microscope (CryoEM). Lysozyme microcrystals were frozen on an electron microscopy grid, and electron diffraction data collected to 1.7 {\r A} resolution. We developed a data collection protocol to collect a full-tilt series in electron diffraction to atomic resolution. A single tilt series contains up to 90 individual diffraction patterns collected from a single crystal with tilt angle increment of 0.1{\textendash}1{\textdegree} and a total accumulated electron dose less than 10 electrons per angstrom squared. We indexed the data from three crystals and used them for structure determination of lysozyme by molecular replacement followed by crystallographic refinement to 2.9 {\r A} resolution. This proof of principle paves the way for the implementation of a new technique, which we name {\textquoteleft}MicroED{\textquoteright}, that may have wide applicability in structural biology.

}, doi = {10.7554/eLife.01345}, author = {Shi, Dan and Nannenga, Brent L and Iadanza, Matthew G and Gonen, Tamir} } @article {6031, title = {Two-photon calcium imaging during fictive navigation in virtual environments.}, journal = {Frontiers in Neural Circuits}, volume = {7}, year = {2013}, month = {2013 Jun 6}, pages = {104}, abstract = {

A full understanding of nervous system function requires recording from large populations of neurons during naturalistic behaviors. Here we enable paralyzed larval zebrafish to fictively navigate two-dimensional virtual environments while we record optically from many neurons with two-photon imaging. Electrical recordings from motor nerves in the tail are decoded into intended forward swims and turns, which are used to update a virtual environment displayed underneath the fish. Several behavioral features-such as turning responses to whole-field motion and dark avoidance-are well-replicated in this virtual setting. We readily observed neuronal populations in the hindbrain with laterally selective responses that correlated with right or left optomotor behavior. We also observed neurons in the habenula, pallium, and midbrain with response properties specific to environmental features. Beyond single-cell correlations, the classification of network activity in such virtual settings promises to reveal principles of brainwide neural dynamics during behavior.

}, issn = {1662-5110}, doi = {10.3389/fncir.2013.00104 *equal contribution}, author = {Ahrens, Misha B* and Huang, Kuo Hua* and Narayan, Sujatha and Mensh, Brett D and Engert, Florian} } @article {6145, title = {Unsupervised segmentation of noisy electron microscopy images using salient watersheds and region merging.}, journal = {BMC Bioinformatics}, volume = {14}, year = {2013}, month = {2013 Oct 4}, pages = {294}, abstract = {

Background: Segmenting electron microscopy (EM) images of cellular and subcellular processes in the nervous system is a key step in many bioimaging pipelines involving classification and labeling of ultrastructures. However, fully automated techniques to segment images are often susceptible to noise and heterogeneity in EM images (e.g. different histological preparations, different organisms, different brain regions, etc.). Supervised techniques to address this problem are often helpful but require large sets of training data, which are often difficult to obtain in practice, especially across many conditions. Results: We propose a new, principled unsupervised algorithm to segment EM images using a two-step approach: edge detection via salient watersheds following by robust region merging. We performed experiments to gather EM neuroimages of two organisms (mouse and fruit fly) using different histological preparations and generated manually curated ground-truth segmentations. We compared our algorithm against several state-of- the-art unsupervised segmentation algorithms and found superior performance using two standard measures of under-and over-segmentation error. Conclusions: Our algorithm is general and may be applicable to other large-scale segmentation problems for bioimages.

}, issn = {1471-2105}, doi = {10.1186/1471-2105-14-294}, author = {Navlakha, Saket and Ahammad, Parvez and Myers, Eugene W}, editor = {Myers, Eugene W} } @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 {6505, title = {Betamax: towards optimal sampling strategies for high-throughput screens.}, journal = {Journal of Computational Biology: A Journal of Computational Molecular Cell Biology}, volume = {19}, year = {2012}, month = {2012 Jun}, pages = {776-84}, abstract = {

Sample size is a critical component in the design of any high-throughput genetic screening approach. Sample size determination from assumptions or limited data at the planning stages, though standard practice, may at times be unreliable because of the difficulty of a priori modeling of effect sizes and variance. Methods to update the sample size estimate during the course of the study could improve statistical power. In this article, we introduce an approach to estimate the power and update it continuously during the screen. We use this estimate to decide where to sample next to achieve maximum overall statistical power. Finally, in simulations, we demonstrate significant gains in study recall over the naive strategy of equal sample sizes while maintaining the same total number of samples.

}, keywords = {Algorithms, Computer Simulation, Genetic Testing, High-Throughput Screening Assays, Humans, Models, Research Design, Sample Size, Statistical}, issn = {1557-8666}, doi = {10.1089/cmb.2012.0036}, author = {Grover, Dhruv and Nunez-Iglesias, Juan} } @article {65028, title = {Columnar cells necessary for motion responses of wide-field visual interneurons in Drosophila.}, journal = {J Comp Physiol A Neuroethol Sens Neural Behav Physiol}, volume = {198}, year = {2012}, month = {2012 May 01}, pages = {389-95}, abstract = {

Wide-field motion-sensitive neurons in the lobula plate (lobula plate tangential cells, LPTCs) of the fly have been studied for decades. However, it has never been conclusively shown which cells constitute their major presynaptic elements. LPTCs are supposed to be rendered directionally selective by integrating excitatory as well as inhibitory input from many local motion detectors. Based on their stratification in the different layers of the lobula plate, the columnar cells T4 and T5 are likely candidates to provide some of this input. To study their role in motion detection, we performed whole-cell recordings from LPTCs in Drosophila with T4 and T5 cells blocked using two different genetically encoded tools. In these flies, motion responses were abolished, while flicker responses largely remained. We thus demonstrate that T4 and T5 cells indeed represent those columnar cells that provide directionally selective motion information to LPTCs. Contrary to previous assumptions, flicker responses seem to be largely mediated by a third, independent pathway. This work thus represents a further step towards elucidating the complete motion detection circuitry of the fly.

}, keywords = {Animals, Drosophila, Ganglia, Invertebrate, Interneurons, Motion Perception, Nerve Net, Sensory Receptor Cells, Visual Fields, Visual Pathways}, issn = {1432-1351}, doi = {10.1007/s00359-012-0716-3}, author = {Schnell, Bettina and Raghu, Shamprasad Varija and Nern, Aljoscha and Borst, Alexander} } @article {6856, title = {Drosophila CPEB Orb2A mediates memory independent of Its RNA-binding domain.}, journal = {Neuron}, volume = {76}, year = {2012}, month = {2012 Oct 18}, pages = {383-95}, abstract = {

Long-term memory and synaptic plasticity are thought to require the synthesis of new proteins at activated synapses. The CPEB family of RNA binding proteins, including Drosophila Orb2, has been implicated in this process. The precise mechanism by which these molecules regulate memory formation is however poorly understood. We used gene targeting and site-specific transgenesis to specifically modify the endogenous orb2 gene in order to investigate its role in long-term memory formation. We show that the Orb2A and Orb2B isoforms, while both essential, have distinct functions in memory formation. These two isoforms have common glutamine-rich and RNA-binding domains, yet Orb2A uniquely requires the former and Orb2B the latter. We further show that Orb2A induces Orb2 complexes in a manner dependent upon both its glutamine-rich region and neuronal activity. We propose that Orb2B acts as a conventional CPEB to regulate transport and/or translation of specific mRNAs, whereas Orb2A acts in an unconventional manner to form stable Orb2 complexes that are essential for memory to persist.

}, keywords = {Animals, Biogenic Amines, Brain, Cell Line, Chromatography, Courtship, Developmental, Drosophila, Drosophila Proteins, Embryo, Gene Expression Regulation, Genetically Modified, Genotype, Green Fluorescent Proteins, High Pressure Liquid, Immunoelectron, Immunoprecipitation, Larva, Learning, Male, Mass Spectrometry, Memory, Messenger, Microscopy, Mitogen-Activated Protein Kinases, mRNA Cleavage and Polyadenylation Factors, Mushroom Bodies, Mutation, Nonmammalian, Protein Isoforms, Protein Structure, RNA, RNA-Binding Proteins, Tertiary, Transcription Factors}, issn = {1097-4199}, doi = {10.1016/j.neuron.2012.08.028}, author = {Kr{\"u}ttner, Sebastian and Stepien, Barbara and Noordermeer, Jasprina N and Mommaas, Mieke A and Mechtler, Karl and Dickson, Barry J and Keleman, Krystyna} } @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 {4595, title = {An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.}, journal = {The ISME Journal}, volume = {6}, year = {2012}, month = {2012 Mar}, pages = {610-8}, abstract = {

Reference phylogenies are crucial for providing a taxonomic framework for interpretation of marker gene and metagenomic surveys, which continue to reveal novel species at a remarkable rate. Greengenes is a dedicated full-length 16S rRNA gene database that provides users with a curated taxonomy based on de novo tree inference. We developed a {\textquoteright}taxonomy to tree{\textquoteright} approach for transferring group names from an existing taxonomy to a tree topology, and used it to apply the Greengenes, National Center for Biotechnology Information (NCBI) and cyanoDB (Cyanobacteria only) taxonomies to a de novo tree comprising 408 315 sequences. We also incorporated explicit rank information provided by the NCBI taxonomy to group names (by prefixing rank designations) for better user orientation and classification consistency. The resulting merged taxonomy improved the classification of 75\% of the sequences by one or more ranks relative to the original NCBI taxonomy with the most pronounced improvements occurring in under-classified environmental sequences. We also assessed candidate phyla (divisions) currently defined by NCBI and present recommendations for consolidation of 34 redundantly named groups. All intermediate results from the pipeline, which includes tree inference, jackknifing and transfer of a donor taxonomy to a recipient tree (tax2tree) are available for download. The improved Greengenes taxonomy should provide important infrastructure for a wide range of megasequencing projects studying ecosystems on scales ranging from our own bodies (the Human Microbiome Project) to the entire planet (the Earth Microbiome Project). The implementation of the software can be obtained from http://sourceforge.net/projects/tax2tree/.

}, issn = {1751-7370}, doi = {10.1038/ismej.2011.139}, author = {McDonald, Daniel and Price, Morgan N and Goodrich, Julia and Nawrocki, Eric P and Desantis, Todd Z and Probst, Alexander and Andersen, Gary L and Knight, Rob and Hugenholtz, Philip} } @article {65029, title = {An intra-cerebral drug delivery system for freely moving animals.}, journal = {Biomed Microdevices}, volume = {14}, year = {2012}, month = {2012 Oct 01}, pages = {799-809}, abstract = {

Microinfusions of drugs directly into the central nervous system of awake animals represent a widely used means of unravelling brain functions related to behaviour. However, current approaches generally use tethered liquid infusion systems and a syringe pump to deliver drugs into the brain, which often interfere with behaviour. We address this shortfall with a miniaturised electronically-controlled drug delivery system (20 {\texttimes} 17.5 {\texttimes} 5 mm{\textthreesuperior}) designed to be skull-mounted in rats. The device features a micropump connected to two 8-mm-long silicon microprobes with a cross section of 250 {\texttimes} 250 μm{\texttwosuperior} and integrated fluid microchannels. Using an external electronic control unit, the device allows infusion of 16 metered doses (0.25 μL each, 8 per silicon shaft). Each dosage requires 3.375 Ws of electrical power making the device additionally compatible with state-of-the-art wireless headstages. A dosage precision of 0.25 {\textpm} 0.01 μL was determined in vitro before in vivo tests were carried out in awake rats. No passive leakage from the loaded devices into the brain could be detected using methylene blue dye. Finally, the device was used to investigate the effects of the NMDA-receptor antagonist 3-((R)-2-Carboxypiperazin-4-yl)-propyl-1-phosphonic acid, (R)-CPP, administered directly into the prefrontal cortex of rats during performance on a task to assess visual attention and impulsivity. In agreement with previous findings using conventional tethered infusion systems, acute (R)-CPP administration produced a marked increase in impulsivity.

}, keywords = {Animals, Attention, Brain, Drug Delivery Systems, Equipment Design, Impulsive Behavior, Microinjections, Piperazines, Rats, Receptors, N-Methyl-D-Aspartate}, issn = {1572-8781}, doi = {10.1007/s10544-012-9659-2}, author = {Spieth, Sven and Schumacher, Axel and Holtzman, Tahl and Rich, P Dylan and Theobald, David E and Dalley, Jeffrey W and Nouna, Rachid and Messner, Stephan and Zengerle, Roland} } @article {5325, title = {Intra-nuclear mobility and target search mechanisms of transcription factors: a single-molecule perspective on gene expression.}, journal = {Biochimica et Biophysica Acta}, volume = {1819}, year = {2012}, month = {2012 Jun}, pages = {482-93}, abstract = {

Precise expression of specific genes in time and space is at the basis of cellular viability as well as correct development of organisms. Understanding the mechanisms of gene regulation is fundamental and still one of the great challenges for biology. Gene expression is regulated also by specific transcription factors that recognize and bind to specific DNA sequences. Transcription factors dynamics, and especially the way they sample the nucleoplasmic space during the search for their specific target in the genome, are a key aspect for regulation and it has been puzzling researchers for forty years. The scope of this review is to give a state-of-the-art perspective over the intra-nuclear mobility and the target search mechanisms of specific transcription factors at the molecular level. Going through the seminal biochemical experiments that have raised the first questions about target localization and the theoretical grounds concerning target search processes, we describe the most recent experimental achievements and current challenges in understanding transcription factors dynamics and interactions with DNA using in vitro assays as well as in live prokaryotic and eukaryotic cells. This article is part of a Special Issue entitled: Nuclear Transport and RNA Processing.

}, issn = {0006-3002}, doi = {10.1016/j.bbagrm.2012.02.001}, author = {Normanno, Davide and Dahan, Maxime and Darzacq, Xavier} } @conference {6448, title = {Learning hierarchical similarity metrics.}, booktitle = {IEEE Conference on Computer Vision and Pattern Recognition}, year = {2012}, month = {2012}, author = {Verma, N and Mahajan, D and Sellamanickam, S and Nair, V} } @article {46719, title = {Nuclear pore component Nup98 is a potential tumor suppressor and regulates posttranscriptional expression of select p53 target genes.}, journal = {Molecular Cell}, volume = {48}, year = {2012}, month = {2012 Dec 14}, pages = {799-810}, abstract = {

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

}, keywords = {14-3-3 Proteins, 3{\textquoteright} Untranslated Regions, Animals, Antineoplastic Agents, Phytogenic, Apoptosis, Binding Sites, Camptothecin, Carcinoma, Hepatocellular, Cell Aging, Cyclin-Dependent Kinase Inhibitor p21, Exosomes, Gene Expression Regulation, Neoplastic, Hep G2 Cells, Humans, Liver Neoplasms, Male, Mice, Mice, Knockout, Nuclear Pore Complex Proteins, P-Glycoproteins, RNA Interference, RNA Processing, Post-Transcriptional, RNA Stability, RNA, Messenger, Time Factors, Transfection, Tumor Suppressor Protein p53}, issn = {1097-4164}, doi = {10.1016/j.molcel.2012.09.020}, author = {Singer, Stephan and Zhao, Ruiying and Barsotti, Anthony M and Ouwehand, Anette and Fazollahi, Mina and Coutavas, Elias and Breuhahn, Kai and Neumann, Olaf and Longerich, Thomas and Pusterla, Tobias and Powers, Maureen A and Giles, Keith M and Leedman, Peter J and Hess, Jochen and Grunwald, David and Bussemaker, Harmen J and Singer, Robert H and Schirmacher, Peter and Prives, Carol} } @article {6501, title = {Organization and metamorphosis of glia in the Drosophila visual system.}, journal = {The Journal of Comparative Neurology}, volume = {520}, year = {2012}, month = {2012 Jul 1}, pages = {2067-85}, abstract = {

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

}, keywords = {Animals, Biological, Drosophila, Drosophila Proteins, Electron, Eye, Genetically Modified, Green Fluorescent Proteins, Horseradish Peroxidase, Metamorphosis, Microscopy, Neuroglia, Neuropil, Nonmammalian, Optic Chiasm, Optic Lobe, Transmission, Visual Pathways}, issn = {1096-9861}, doi = {10.1002/cne.23071}, author = {Edwards, Tara N and Nuschke, Andrea C and Nern, Aljoscha and Meinertzhagen, Ian A.} } @article {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 {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 {6175, title = {Super-resolution using sparse representations over learned dictionaries: reconstruction of brain structure using electron microscopy.}, journal = {arXiv.org }, year = {2012}, month = {2012 Oct}, abstract = {

A central problem in neuroscience is reconstructing neuronal circuits on the synapse level. Due to a wide range of scales in brain architecture such reconstruction requires imaging that is both high-resolution and high-throughput. Existing electron microscopy (EM) techniques possess required resolution in the lateral plane and either high-throughput or high depth resolution but not both. Here, we exploit recent advances in unsupervised learning and signal processing to obtain high depth-resolution EM images computationally without sacrificing throughput. First, we show that the brain tissue can be represented as a sparse linear combination of localized basis functions that are learned using high-resolution datasets. We then develop compressive sensing-inspired techniques that can reconstruct the brain tissue from very few (typically 5) tomographic views of each section. This enables tracing of neuronal processes and, hence, high throughput reconstruction of neural circuits on the level of individual synapses.

}, author = {Hu, T and Nunez-Iglesias, J and Vitaladevuni, S. and Scheffer, L. and Xu, S and Bolorizadeh, M and Hess, H and Fetter, R and Chklovskii, D} } @article {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 {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 {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 {46736, title = {Cotranscriptional effect of a premature termination codon revealed by live-cell imaging.}, journal = {RNA}, volume = {17}, year = {2011}, month = {2011 Dec}, pages = {2094-107}, abstract = {

Aberrant mRNAs with premature translation termination codons (PTCs) are recognized and eliminated by the nonsense-mediated mRNA decay (NMD) pathway in eukaryotes. We employed a novel live-cell imaging approach to investigate the kinetics of mRNA synthesis and release at the transcription site of PTC-containing (PTC+) and PTC-free (PTC-) immunoglobulin-μ reporter genes. Fluorescence recovery after photobleaching (FRAP) and photoconversion analyses revealed that PTC+ transcripts are specifically retained at the transcription site. Remarkably, the retained PTC+ transcripts are mainly unspliced, and this RNA retention is dependent upon two important NMD factors, UPF1 and SMG6, since their depletion led to the release of the PTC+ transcripts. Finally, ChIP analysis showed a physical association of UPF1 and SMG6 with both the PTC+ and the PTC- reporter genes in vivo. Collectively, our data support a mechanism for regulation of PTC+ transcripts at the transcription site.

}, keywords = {Cell Line, Codon, Nonsense, Cytoplasm, Gene Expression Regulation, Gene Order, Gene Silencing, Humans, Immunoglobulin mu-Chains, In Situ Hybridization, Fluorescence, Nonsense Mediated mRNA Decay, RNA Splicing, RNA, Messenger, Telomerase, Trans-Activators, Transcription, Genetic}, issn = {1469-9001}, doi = {10.1261/rna.02918111}, author = {de Turris, Valeria and Nicholson, Pamela and Orozco, Rodolfo Zamudio and Singer, Robert H and M{\"u}hlemann, Oliver} } @article {6524, title = {A critical role of mitochondrial phosphatase Ptpmt1 in embryogenesis reveals a mitochondrial metabolic stress-induced differentiation checkpoint in embryonic stem cells.}, journal = {Molecular and Cellular Biology}, volume = {31}, year = {2011}, month = {2011 Dec}, pages = {4902-16}, abstract = {

Mitochondria are highly dynamic organelles that play multiple roles in cells. How mitochondria cooperatively modulate embryonic stem (ES) cell function during development is not fully understood. Global disruption of Ptpmt1, a mitochondrial Pten-like phosphatidylinositol phosphate (PIP) phosphatase, resulted in developmental arrest and postimplantation lethality. Ptpmt1(-/-) blastocysts failed to outgrow, and inner-cell-mass cells failed to thrive. Depletion of Ptpmt1 in conditional knockout ES cells decreased proliferation without affecting energy homeostasis or cell survival. Differentiation of Ptpmt1-depleted ES cells was essentially blocked. This was accompanied by upregulation of cyclin-dependent kinase inhibitors and a significant cell cycle delay. Reintroduction of wild-type but not of catalytically deficient Ptpmt1 C132S or truncated Ptpmt1 lacking the mitochondrial localization signal restored the differentiation capabilities of Ptpmt1 knockout ES cells. Intriguingly, Ptpmt1 is specifically important for stem cells, as ablation of Ptpmt1 in differentiated embryonic fibroblasts did not disturb cellular function. Further analyses demonstrated that oxygen consumption of Ptpmt1-depleted cells was decreased, while glycolysis was concomitantly enhanced. In addition, mitochondrial fusion/dynamics were compromised in Ptpmt1 knockout cells due to accumulation of PIPs. These studies, while establishing a crucial role for Ptpmt1 phosphatase in embryogenesis, reveal a mitochondrial metabolic stress-activated checkpoint in the control of ES cell differentiation.

}, keywords = {Alleles, Animals, Apoptosis, Cell Cycle Checkpoints, Cell Differentiation, Cell Proliferation, Cloning, Confocal, Embryonic Development, Embryonic Stem Cells, Fibroblasts, Glycolysis, Immunohistochemistry, In Situ Nick-End Labeling, Knockout, Mice, Microscopy, Mitochondria, Molecular, Phosphatidylinositol Phosphates, Physiological, PTEN Phosphohydrolase, Reactive Oxygen Species, Stress}, issn = {1098-5549}, doi = {10.1128/MCB.05629-11}, author = {Shen, Jinhua and Liu, Xia and Yu, Wen-Mei and Liu, Jie and Nibbelink, Milou Groot and Guo, Caiying and Finkel, Toren and Qu, Cheng-Kui} } @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 {47905, title = {Hallmarks of molecular action of microtubule stabilizing agents: effects of epothilone B, ixabepilone, peloruside A, and laulimalide on microtubule conformation.}, journal = {The Journal of biological chemistry}, volume = {286}, year = {2011}, month = {2011 Apr 1}, pages = {11765-78}, abstract = {

Microtubule stabilizing agents (MSAs) comprise a class of drugs that bind to microtubule (MT) polymers and stabilize them against disassembly. Several of these agents are currently in clinical use as anticancer drugs, whereas others are in various stages of development. Nonetheless, there is insufficient knowledge about the molecular modes of their action. Recent studies from our laboratory utilizing hydrogen-deuterium exchange in combination with mass spectrometry (MS) provide new information on the conformational effects of Taxol and discodermolide on microtubules isolated from chicken erythrocytes (CET). We report here a comprehensive analysis of the effects of epothilone B, ixabepilone (IXEMPRA(TM)), laulimalide, and peloruside A on CET conformation. The results of our comparative hydrogen-deuterium exchange MS studies indicate that all MSAs have significant conformational effects on the C-terminal H12 helix of α-tubulin, which is a likely molecular mechanism for the previously observed modulations of MT interactions with microtubule-associated and motor proteins. More importantly, the major mode of MT stabilization by MSAs is the tightening of the longitudinal interactions between two adjacent αβ-tubulin heterodimers at the interdimer interface. In contrast to previous observations reported with bovine brain tubulin, the lateral interactions between the adjacent protofilaments in CET are particularly strongly stabilized by peloruside A and laulimalide, drugs that bind outside the taxane site. This not only highlights the significance of tubulin isotype composition in modulating drug effects on MT conformation and stability but also provides a potential explanation for the synergy observed when combinations of taxane and alternative site binding drugs are used.

}, keywords = {Animals, Bicyclo Compounds, Heterocyclic, Binding Sites, Brain, Brain Chemistry, Cattle, Epothilones, Lactones, Macrolides, Mass Spectrometry, Microtubules, Nerve Tissue Proteins, Protein Structure, Secondary, Tubulin, Tubulin Modulators}, issn = {1083-351X}, doi = {10.1074/jbc.M110.162214}, author = {Khrapunovich-Baine, Marina and Menon, Vilas and Yang, Chia-Ping Huang and Northcote, Peter T and Miller, John H and Angeletti, Ruth Hogue and Fiser, Andras and Horwitz, Susan Band and Xiao, Hui} } @article {4325, title = {High resolution segmentation of neuronal tissues from low depth-resolution EM imagery.}, journal = {8th International Conference of Energy Minimization Methods in Computer Vision and Pattern Recognition Energy Minimization Methods in Computer Vision and Pattern Recognition}, volume = {6819}, year = {2011}, month = {2011}, pages = {261-72}, abstract = {

The challenge of recovering the topology of massive neuronal circuits can potentially be met by high throughput Electron Microscopy (EM) imagery. Segmenting a 3-dimensional stack of EM images into the individual neurons is difficult, due to the low depth-resolution in existing high-throughput EM technology, such as serial section Transmission EM (ssTEM). In this paper we propose methods for detecting the high resolution locations of membranes from low depth-resolution images. We approach this problem using both a method that learns a discriminative, over-complete dictionary and a kernel SVM. We test this approach on tomographic sections produced in simulations from high resolution Focused Ion Beam (FIB) images and on low depth-resolution images acquired with ssTEM and evaluate our results by comparing it to manual labeling of this data.

}, issn = {978-3-642-23093-6}, author = {Glasner, Daniel and Hu, Tao and Nunez-Iglesias, Juan and Scheffer, Lou and Xu, CS and Hess, Harald and Fetter, Richard and Chklovskii, Dmitri and Basri, Ronen} } @article {68486, title = {A high-throughput method for generating uniform microislands for autaptic neuronal cultures.}, journal = {J Neurosci Methods}, volume = {198}, year = {2011}, month = {06/2011}, pages = {230-5}, abstract = {

Generating microislands of culture substrate on coverslips by spray application of poly-d lysine is a commonly used method for culturing isolated neurons that form self (autaptic) synapses. This preparation has multiple advantages for studying synaptic transmission in isolation; however, generating microislands by spraying produces islands of non-uniform size and thus cultures vary widely in the number of islands containing single neurons. To address these problems, we developed a high-throughput method for reliably generating uniformly shaped microislands of culture substrate. Stamp molds formed of poly(dimethylsiloxane) (PDMS) were fabricated with arrays of circles and used to generate stamps made of 9.2\% agarose. The agarose stamps were capable of loading sufficient poly D-lysine and collagen dissolved in acetic acid to rapidly generate coverslips containing at least 64 microislands per coverslip. When hippocampal neurons were cultured on these coverslips, there were significantly more single-neuron islands per coverslip. We noted that single neurons tended to form one of three distinct neurite-arbor morphologies, which varied with island size and the location of the cell body on the island. To our surprise, the number of synapses per autaptic neuron did not correlate with arbor shape or island size, suggesting that other factors regulate the number of synapses formed by isolated neurons. The stamping method we report can be used to increase the number of single-neuron islands per culture and aid in the rapid visualization of microislands.

}, keywords = {Animals, Cell Communication, Cell Culture Techniques, Cells, Cultured, Dendrites, Hippocampus, Mice, Neurons, Synapses, Synaptic Transmission}, issn = {1872-678X}, doi = {10.1016/j.jneumeth.2011.04.012}, author = {Sgro, Allyson E and Nowak, Amy L and Austin, Naola S and Custer, Kenneth L and Allen, Peter B and Chiu, Daniel T and Bajjalieh, Sandra M} } @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 {2161, title = {Multi-camera real-time three-dimensional tracking of multiple flying animals.}, journal = {Journal of the Royal Society, Interface}, volume = {8}, year = {2011}, month = {2011 Mar 6}, pages = {395-409}, abstract = {

Automated tracking of animal movement allows analyses that would not otherwise be possible by providing great quantities of data. The additional capability of tracking in real time{\textendash}with minimal latency{\textendash}opens up the experimental possibility of manipulating sensory feedback, thus allowing detailed explorations of the neural basis for control of behaviour. Here, we describe a system capable of tracking the three-dimensional position and body orientation of animals such as flies and birds. The system operates with less than 40 ms latency and can track multiple animals simultaneously. To achieve these results, a multi-target tracking algorithm was developed based on the extended Kalman filter and the nearest neighbour standard filter data association algorithm. In one implementation, an 11-camera system is capable of tracking three flies simultaneously at 60 frames per second using a gigabit network of nine standard Intel Pentium 4 and Core 2 Duo computers. This manuscript presents the rationale and details of the algorithms employed and shows three implementations of the system. An experiment was performed using the tracking system to measure the effect of visual contrast on the flight speed of Drosophila melanogaster. At low contrasts, speed is more variable and faster on average than at high contrasts. Thus, the system is already a useful tool to study the neurobiology and behaviour of freely flying animals. If combined with other techniques, such as {\textquoteright}virtual reality{\textquoteright}-type computer graphics or genetic manipulation, the tracking system would offer a powerful new way to investigate the biology of flying animals.

}, issn = {1742-5662}, doi = {10.1098/rsif.2010.0230}, author = {Straw, Andrew D and Branson, Kristin and Neumann, Titus R and Dickinson, Michael H} } @article {3892, title = {Multiple new site-specific recombinases for use in manipulating animal genomes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, year = {2011}, month = {2011 Aug 23}, pages = {14198-203}, abstract = {

Site-specific recombinases have been used for two decades to manipulate the structure of animal genomes in highly predictable ways and have become major research tools. However, the small number of recombinases demonstrated to have distinct specificities, low toxicity, and sufficient activity to drive reactions to completion in animals has been a limitation. In this report we show that four recombinases derived from yeast-KD, B2, B3, and R-are highly active and nontoxic in Drosophila and that KD, B2, B3, and the widely used FLP recombinase have distinct target specificities. We also show that the KD and B3 recombinases are active in mice.

}, issn = {1091-6490}, doi = {10.1073/pnas.1111704108}, author = {Nern, Aljoscha and Pfeiffer, Barret D and Svoboda, Karel and Rubin, Gerald M} } @article {47904, title = {Multi-scale correlation structure of gene expression in the brain.}, journal = {Neural networks : the official journal of the International Neural Network Society}, volume = {24}, year = {2011}, month = {2011 Nov}, pages = {933-42}, abstract = {

The mammalian brain is best understood as a multi-scale hierarchical neural system, in the sense that connection and function occur on multiple scales from micro to macro. Modern genomic-scale expression profiling can provide insight into methodologies that elucidate this architecture. We present a methodology for understanding the relationship of gene expression and neuroanatomy based on correlation between gene expression profiles across tissue samples. A resulting tool, NeuroBlast, can identify networks of genes co-expressed within or across neuroanatomic structures. The method applies to any data modality that can be mapped with sufficient spatial resolution, and provides a computation technique to elucidate neuroanatomy via patterns of gene expression on spatial and temporal scales. In addition, from the perspective of spatial location, we discuss a complementary technique that identifies gene classes that contribute to defining anatomic patterns.

}, keywords = {Algorithms, Animals, Atlases as Topic, Brain, Brain Chemistry, Data Mining, Databases, Genetic, Gene Expression, Mice, Mice, Inbred C57BL, Nerve Tissue Proteins, Tryptophan Hydroxylase}, issn = {1879-2782}, doi = {10.1016/j.neunet.2011.06.012}, author = {Hawrylycz, Mike and Ng, Lydia and Page, Damon and Morris, John and Lau, Chris and Faber, Sky and Faber, Vance and Sunkin, Susan and Menon, Vilas and Lein, Ed and Jones, Allan} } @article {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 {4485, title = {RNIE: genome-wide prediction of bacterial intrinsic terminators.}, journal = {Nucleic Acids Research}, volume = {39}, year = {2011}, month = {2011 Aug}, pages = {5845-52}, abstract = {

Bacterial Rho-independent terminators (RITs) are important genomic landmarks involved in gene regulation and terminating gene expression. In this investigation we present RNIE, a probabilistic approach for predicting RITs. The method is based upon covariance models which have been known for many years to be the most accurate computational tools for predicting homology in structural non-coding RNAs. We show that RNIE has superior performance in model species from a spectrum of bacterial phyla. Further analysis of species where a low number of RITs were predicted revealed a highly conserved structural sequence motif enriched near the genic termini of the pathogenic Actinobacteria, Mycobacterium tuberculosis. This motif, together with classical RITs, account for up to 90\% of all the significantly structured regions from the termini of M. tuberculosis genic elements. The software, predictions and alignments described below are available from http://github.com/ppgardne/RNIE.

}, keywords = {Bacterial, Base Sequence, Conserved Sequence, Genetic, Genome, Genomics, Models, Molecular Sequence Annotation, Mycobacterium tuberculosis, Software, Statistical, Terminator Regions}, issn = {1362-4962}, doi = {10.1093/nar/gkr168}, author = {Gardner, Paul P and Barquist, Lars and Bateman, Alex and Nawrocki, Eric P and Weinberg, Zasha} } @article {65032, title = {Robo-3--mediated repulsive interactions guide R8 axons during Drosophila visual system development.}, journal = {Proc Natl Acad Sci U S A}, volume = {108}, year = {2011}, month = {2011 May 03}, pages = {7571-6}, abstract = {

The formation of neuronal connections requires the precise guidance of developing axons toward their targets. In the Drosophila visual system, photoreceptor neurons (R cells) project from the eye into the brain. These cells are grouped into some 750 clusters comprised of eight photoreceptors or R cells each. R cells fall into three classes: R1 to R6, R7, and R8. Posterior R8 cells are the first to project axons into the brain. How these axons select a specific pathway is not known. Here, we used a microarray-based approach to identify genes expressed in R8 neurons as they extend into the brain. We found that Roundabout-3 (Robo3), an axon-guidance receptor, is expressed specifically and transiently in R8 growth cones. In wild-type animals, posterior-most R8 axons extend along a border of glial cells demarcated by the expression of Slit, the secreted ligand of Robo3. In contrast, robo3 mutant R8 axons extend across this border and fasciculate inappropriately with other axon tracts. We demonstrate that either Robo1 or Robo2 rescues the robo3 mutant phenotype when each is knocked into the endogenous robo3 locus separately, indicating that R8 does not require a function unique to the Robo3 paralog. However, persistent expression of Robo3 in R8 disrupts the layer-specific targeting of R8 growth cones. Thus, the transient cell-specific expression of Robo3 plays a crucial role in establishing neural circuits in the Drosophila visual system by selectively regulating pathway choice for posterior-most R8 growth cones.

}, keywords = {Animals, Axons, Drosophila, Drosophila Proteins, Growth Cones, Image Processing, Computer-Assisted, Immunohistochemistry, Microarray Analysis, Nerve Tissue Proteins, Photoreceptor Cells, Invertebrate, Receptors, Immunologic, Visual Pathways}, issn = {1091-6490}, doi = {10.1073/pnas.1103419108}, author = {Pappu, Kartik S and Morey, Marta and Nern, Aljoscha and Spitzweck, Bettina and Dickson, Barry J and Zipursky, S L} } @article {46412, title = {The structure, molecular dynamics, and energetics of centrin-melittin complex.}, journal = {Proteins}, volume = {79}, year = {2011}, month = {2011 Nov}, pages = {3132-43}, abstract = {

Centrin is a calcium binding protein (CaBP) belonging to the EF-hand superfamily. As with other proteins within this family, centrin is a calcium sensor with multiple biological target proteins. We chose to study Chlamydomonas reinhardtii centrin (Crcen) and its interaction with melittin (MLT) as a model for CaBP complexes due to its amphipathic properties. Our goal was to determine the molecular interactions that lead to centrin-MLT complex formation, their relative stability, and the conformational changes associated with the interaction, when compared to the single components. For this, we determined the thermodynamic parameters that define Crcen-MLT complex formation. Two-dimensional infrared (2D IR) correlation spectroscopy were used to study the amide I{\textquoteright}, I{\textquoteright}*, and side chain bands for (13)C-Crcen, MLT, and the (13)C-Crcen-MLT complex. This approach resulted in the determination of MLT{\textquoteright}s increased helicity, while centrin was stabilized within the complex. Herein we provide the first complete molecular description of centrin-MLT complex formation and the dissociation process. Also, discussed is the first structure of a CaBP-MLT complex by X-ray crystallography, which shows that MLT has a different binding orientation than previously characterized centrin-bound peptides. Finally, all of the experimental results presented herein are consistent with centrin maintaining an extended conformation while interacting with MLT. The molecular implications of these results are: (1) the recognition of hydrophobic contacts as requirements for initial binding, (2) minimum electrostatic interactions within the C-terminal end of the peptide, and (3) van der Waals interactions within MLTs N-terminal end are required for complex formation.

}, keywords = {Calcium-Binding Proteins, Crystallography, X-Ray, Melitten, Molecular Dynamics Simulation, Protein Binding, Protein Conformation, Spectroscopy, Fourier Transform Infrared, Thermodynamics}, issn = {1097-0134}, doi = {10.1002/prot.23142}, author = {Sosa, Liliana Del Valle and Alfaro, Elisa and Santiago, Jorge and Narv{\'a}ez, Daniel and Rosado, Marie Cely and Rodr{\'\i}guez, Aslin and G{\'o}mez, Ana Mar{\'\i}a and Schreiter, Eric R and Pastrana-R{\'\i}os, Belinda} } @article {46737, title = {Variegated gene expression caused by cell-specific long-range DNA interactions.}, journal = {Nature Cell Biology}, volume = {13}, year = {2011}, month = {2011 Aug}, pages = {944-51}, abstract = {

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

}, keywords = {Animals, beta-Globins, DNA, GATA1 Transcription Factor, Gene Expression, In Situ Hybridization, Fluorescence, Kruppel-Like Transcription Factors, Locus Control Region, Mice, Mice, Transgenic, RNA, Messenger, Transcriptional Activation}, issn = {1476-4679}, doi = {10.1038/ncb2278}, author = {Noordermeer, Daan and de Wit, Elzo and Klous, Petra and van de Werken, Harmen and Simonis, Marieke and Lopez-Jones, Melissa and Eussen, Bert and de Klein, Annelies and Singer, Robert H and de Laat, Wouter} } @article {1452, title = {Analysis of the intact surface layer of Caulobacter crescentus by cryo-electron tomography.}, journal = {Journal of Bacteriology}, volume = {192}, year = {2010}, month = {2010 Nov}, pages = {5855-65}, abstract = {

The surface layers (S layers) of those bacteria and archaea that elaborate these crystalline structures have been studied for 40 years. However, most structural analysis has been based on electron microscopy of negatively stained S-layer fragments separated from cells, which can introduce staining artifacts and allow rearrangement of structures prone to self-assemble. We present a quantitative analysis of the structure and organization of the S layer on intact growing cells of the Gram-negative bacterium Caulobacter crescentus using cryo-electron tomography (CET) and statistical image processing. Instead of the expected long-range order, we observed different regions with hexagonally organized subunits exhibiting short-range order and a broad distribution of periodicities. Also, areas of stacked double layers were found, and these increased in extent when the S-layer protein (RsaA) expression level was elevated by addition of multiple rsaA copies. Finally, we combined high-resolution amino acid residue-specific Nanogold labeling and subtomogram averaging of CET volumes to improve our understanding of the correlation between the linear protein sequence and the structure at the 2-nm level of resolution that is presently available. The results support the view that the U-shaped RsaA monomer predicted from negative-stain tomography proceeds from the N terminus at one vertex, corresponding to the axis of 3-fold symmetry, to the C terminus at the opposite vertex, which forms the prominent 6-fold symmetry axis. Such information will help future efforts to analyze subunit interactions and guide selection of internal sites for display of heterologous protein segments.

}, keywords = {Amino Acids, Bacterial Proteins, Caulobacter crescentus, Computer-Assisted, Cryoelectron Microscopy, Electron Microscope Tomography, Image Processing, Membrane Glycoproteins, Metal Nanoparticles, Staining and Labeling}, issn = {1098-5530}, doi = {10.1128/JB.00747-10}, author = {Amat, Fernando and Comolli, Luis R and Nomellini, John F and Moussavi, Farshid and Downing, Kenneth H and Smit, John and Horowitz, Mark} } @article {5369, title = {Anatomic analysis of Gal4 expression patterns of the Rubin line collection: the central complex.}, journal = {Journal of Neurogenetics}, volume = {24}, year = {2010}, month = {2010}, pages = {71-2}, chapter = {71}, author = {Jenett, A and Wolff, T and Nern, A. and Pfeiffer, B D and Ngo, T. and Murphy, C. and Long, F. and Peng, H. and Rubin, G M} } @article {4403, title = {A full-length cDNA resource for the pea aphid, acyrthosiphon pisum.}, journal = {Insect Molecular Biology}, volume = {19 Suppl 2}, year = {2010}, month = {2010 Mar}, pages = {23-31}, abstract = {

Large collections of full-length cDNAs are important resources for genome annotation and functional genomics. We report the creation of a collection of 50 599 full-length cDNA clones from the pea aphid, Acyrthosiphon pisum. Sequencing from 5{\textquoteright} and 3{\textquoteright} ends of the clones generated 97 828 high-quality expressed sequence tags, representing approximately 9000 genes. These sequences were imported to AphidBase and are shown to play crucial roles in both automatic gene prediction and manual annotation. Our detailed analyses demonstrated that the full-length cDNAs can further improve gene models and can even identify novel genes that are not included in the current version of the official gene set. This full-length cDNA collection can be utilized for a wide variety of functional studies, serving as a community resource for the study of the functional genomics of the pea aphid.

}, keywords = {3{\textquoteright} Untranslated Regions, 5{\textquoteright} Untranslated Regions, Animals, Aphids, Base Sequence, Complementary, DNA, DNA Primers, Expressed Sequence Tags, Gene Library, Genetic, Genome, Host-Pathogen Interactions, Insect, Models, Peas}, issn = {1365-2583}, doi = {10.1111/j.1365-2583.2009.00946.x}, author = {Shigenobu, S and Richards, S and Cree, A G and Morioka, M and Fukatsu, T and Kudo, T and Miyagishima, S and Gibbs, R A and Stern, D L and Nakabachi, A} } @article {6322, title = {The Ndc80 kinetochore complex forms oligomeric arrays along microtubules.}, journal = {Nature}, volume = {467}, year = {2010}, month = {2010 Oct 14}, pages = {805-10}, abstract = {

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

}, keywords = {Binding Sites, Biological, Cryoelectron Microscopy, Humans, Kinetochores, Microtubules, Mitosis, Models, Molecular, Nuclear Proteins, Protein Conformation, Tubulin}, issn = {1476-4687}, doi = {10.1038/nature09423}, author = {Alushin, Gregory M and Ramey, Vincent H and Pasqualato, Sebastiano and Ball, David A and Grigorieff, Nikolaus and Musacchio, Andrea and Nogales, Eva} } @article {46041, title = {Persistence of coordinated long-term potentiation and dendritic spine enlargement at mature hippocampal CA1 synapses requires N-cadherin.}, journal = {Journal of Neuroscience}, volume = {30}, year = {2010}, month = {2010 Jul 28}, pages = {9984-9}, abstract = {

Persistent changes in spine shape are coupled to long-lasting synaptic plasticity in hippocampus. The molecules that coordinate such persistent structural and functional plasticity are unknown. Here, we generated mice in which the cell adhesion molecule N-cadherin was conditionally ablated from postnatal, excitatory synapses in hippocampus. We applied to adult mice of either sex a combination of whole-cell recording, two-photon microscopy, and spine morphometric analysis to show that postnatal ablation of N-cadherin has profound effects on the stability of coordinated spine enlargement and long-term potentiation (LTP) at mature CA1 synapses, with no effects on baseline spine density or morphology, baseline properties of synaptic neurotransmission, or long-term depression. Thus, N-cadherin couples persistent spine structural modifications with long-lasting synaptic functional modifications associated selectively with LTP, revealing unexpectedly distinct roles at mature synapses in comparison with earlier, broader functions in synapse and spine development.

}, keywords = {Action Potentials, Animals, Biophysics, CA1 Region, Hippocampal, Cadherins, Dendritic Spines, Electric Stimulation, Excitatory Postsynaptic Potentials, In Vitro Techniques, Long-Term Potentiation, Mice, Mice, Inbred C57BL, Mice, Knockout, Microscopy, Immunoelectron, Patch-Clamp Techniques, Pyramidal Cells, Statistics, Nonparametric, Synapses}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.1223-10.2010}, author = {Bozdagi, Ozlem and Wang, Xiao-bin and Nikitczuk, Jessica S and Anderson, Tonya R and Bloss, Erik B and Radice, Glenn L and Zhou, Qiang and Benson, Deanna L and Huntley, George W} } @article {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 {3631, title = {Tension directly stabilizes reconstituted kinetochore-microtubule attachments.}, journal = {Nature}, volume = {468}, year = {2010}, month = {2010 Nov 25}, pages = {576-9}, abstract = {

Kinetochores are macromolecular machines that couple chromosomes to dynamic microtubule tips during cell division, thereby generating force to segregate the chromosomes. Accurate segregation depends on selective stabilization of correct {\textquoteright}bi-oriented{\textquoteright} kinetochore-microtubule attachments, which come under tension as the result of opposing forces exerted by microtubules. Tension is thought to stabilize these bi-oriented attachments indirectly, by suppressing the destabilizing activity of a kinase, Aurora B. However, a complete mechanistic understanding of the role of tension requires reconstitution of kinetochore-microtubule attachments for biochemical and biophysical analyses in vitro. Here we show that native kinetochore particles retaining the majority of kinetochore proteins can be purified from budding yeast and used to reconstitute dynamic microtubule attachments. Individual kinetochore particles maintain load-bearing associations with assembling and disassembling ends of single microtubules for \>30 min, providing a close match to the persistent coupling seen in vivo between budding yeast kinetochores and single microtubules. Moreover, tension increases the lifetimes of the reconstituted attachments directly, through a catch bond-like mechanism that does not require Aurora B. On the basis of these findings, we propose that tension selectively stabilizes proper kinetochore-microtubule attachments in vivo through a combination of direct mechanical stabilization and tension-dependent phosphoregulation.

}, keywords = {Chromosomes, Fungal Proteins, Kinetochores, Microtubules, Saccharomyces cerevisiae}, issn = {1476-4687}, doi = {10.1038/nature09594}, author = {Akiyoshi, Bungo and Sarangapani, Krishna K and Powers, Andrew F and Nelson, Christian R and Reichow, Steve L and Arellano-Santoyo, Hugo and Gonen, Tamir and Ranish, Jeffrey A and Asbury, Charles L and Biggins, Sue} } @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 {46421, title = {Caenorhabditis elegans innexins regulate active zone differentiation.}, journal = {The Journal of Neuroscience}, volume = {29}, year = {2009}, month = {2009 Apr 22}, pages = {5207-17}, abstract = {

In a genetic screen for active zone defective mutants in Caenorhabditis elegans, we isolated a loss-of-function allele of unc-7, a gene encoding an innexin/pannexin family gap junction protein. Innexin UNC-7 regulates the size and distribution of active zones at C. elegans neuromuscular junctions. Loss-of-function mutations in another innexin, UNC-9, cause similar active zone defects as unc-7 mutants. In addition to presumptive gap junction localizations, both UNC-7 and UNC-9 are also localized perisynaptically throughout development and required in presynaptic neurons to regulate active zone differentiation. Our mosaic analyses, electron microscopy, as well as expression studies suggest a novel and likely nonjunctional role of specific innexins in active zone differentiation in addition to gap junction formations.

}, keywords = {Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Cell Differentiation, Connexins, Gap Junctions, Gene Expression Regulation, Developmental, Male, Membrane Proteins, Organisms, Genetically Modified, Presynaptic Terminals}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0637-09.2009}, author = {Yeh, Edward and Kawano, Taizo and Ng, Sharon and Fetter, Richard and Hung, Wesley and Wang, Ying and Zhen, Mei} } @article {2197, title = {The challenges of sequencing by synthesis.}, journal = {Nature Biotechnology}, volume = {27}, year = {2009}, month = {2009 Nov}, pages = {1013-23}, abstract = {

DNA sequencing-by-synthesis (SBS) technology, using a polymerase or ligase enzyme as its core biochemistry, has already been incorporated in several second-generation DNA sequencing systems with significant performance. Notwithstanding the substantial success of these SBS platforms, challenges continue to limit the ability to reduce the cost of sequencing a human genome to $100,000 or less. Achieving dramatically reduced cost with enhanced throughput and quality will require the seamless integration of scientific and technological effort across disciplines within biochemistry, chemistry, physics and engineering. The challenges include sample preparation, surface chemistry, fluorescent labels, optimizing the enzyme-substrate system, optics, instrumentation, understanding tradeoffs of throughput versus accuracy, and read-length/phasing limitations. By framing these challenges in a manner accessible to a broad community of scientists and engineers, we hope to solicit input from the broader research community on means of accelerating the advancement of genome sequencing technology.

}, keywords = {Animals, DNA, Fluorescent Dyes, Humans, Optical Phenomena, Sequence Analysis, Substrate Specificity, Surface Properties}, issn = {1546-1696}, doi = {10.1038/nbt0510-426}, author = {Fuller, Carl W and Middendorf, Lyle R and Benner, Steven A and Church, George M and Harris, Timothy and Huang, Xiaohua and Jovanovich, Stevan B and Nelson, John R and Schloss, Jeffery A and Schwartz, David C and Vezenov, Dmitri V} } @article {48171, title = {Comparison and evaluation of methods for liver segmentation from CT datasets.}, journal = {IEEE transactions on medical imaging}, volume = {28}, year = {2009}, month = {2009 Aug}, pages = {1251-65}, abstract = {

This paper presents a comparison study between 10 automatic and six interactive methods for liver segmentation from contrast-enhanced CT images. It is based on results from the "MICCAI 2007 Grand Challenge" workshop, where 16 teams evaluated their algorithms on a common database. A collection of 20 clinical images with reference segmentations was provided to train and tune algorithms in advance. Participants were also allowed to use additional proprietary training data for that purpose. All teams then had to apply their methods to 10 test datasets and submit the obtained results. Employed algorithms include statistical shape models, atlas registration, level-sets, graph-cuts and rule-based systems. All results were compared to reference segmentations five error measures that highlight different aspects of segmentation accuracy. All measures were combined according to a specific scoring system relating the obtained values to human expert variability. In general, interactive methods reached higher average scores than automatic approaches and featured a better consistency of segmentation quality. However, the best automatic methods (mainly based on statistical shape models with some additional free deformation) could compete well on the majority of test images. The study provides an insight in performance of different segmentation approaches under real-world conditions and highlights achievements and limitations of current image analysis techniques.

}, keywords = {Algorithms, Bayes Theorem, Databases, Factual, Humans, Image Processing, Computer-Assisted, Liver, Tomography, X-Ray Computed}, issn = {1558-254X}, doi = {10.1109/TMI.2009.2013851}, author = {Heimann, Tobias and van Ginneken, Bram and Styner, Martin A and Arzhaeva, Yulia and Aurich, Volker and Bauer, Christian and Beck, Andreas and Becker, Christoph and Beichel, Reinhard and Bekes, Gy{\"o}rgy and Bello, Fernando and Binnig, Gerd and Bischof, Horst and Bornik, Alexander and Cashman, Peter M M and Chi, Ying and Cordova, Andr{\'e}s and Dawant, Benoit M and Fidrich, M{\'a}rta and Furst, Jacob D and Furukawa, Daisuke and Grenacher, Lars and Hornegger, Joachim and Kainm{\"u}ller, Dagmar and Kitney, Richard I and Kobatake, Hidefumi and Lamecker, Hans and Lange, Thomas and Lee, Jeongjin and Lennon, Brian and Li, Rui and Li, Senhu and Meinzer, Hans-Peter and Nemeth, G{\'a}bor and Raicu, Daniela S and Rau, Anne-Mareike and van Rikxoort, Eva M and Rousson, Mika{\"e}l and Rusko, L{\'a}szl{\'o} and Saddi, Kinda A and Schmidt, G{\"u}nter and Seghers, Dieter and Shimizu, Akinobu and Slagmolen, Pieter and Sorantin, Erich and Soza, Grzegorz and Susomboon, Ruchaneewan and Waite, Jonathan M and Wimmer, Andreas and Wolf, Ivo} } @article {4278, title = {A Drosophila resource of transgenic RNAi lines for neurogenetics.}, journal = {Genetics}, volume = {182}, year = {2009}, month = {2009 Aug}, pages = {1089-100}, abstract = {

Conditional expression of hairpin constructs in Drosophila is a powerful method to disrupt the activity of single genes with a spatial and temporal resolution that is impossible, or exceedingly difficult, using classical genetic methods. We previously described a method (Ni et al. 2008) whereby RNAi constructs are targeted into the genome by the phiC31-mediated integration approach using Vermilion-AttB-Loxp-Intron-UAS-MCS (VALIUM), a vector that contains vermilion as a selectable marker, an attB sequence to allow for phiC31-targeted integration at genomic attP landing sites, two pentamers of UAS, the hsp70 core promoter, a multiple cloning site, and two introns. As the level of gene activity knockdown associated with transgenic RNAi depends on the level of expression of the hairpin constructs, we generated a number of derivatives of our initial vector, called the "VALIUM" series, to improve the efficiency of the method. Here, we report the results from the systematic analysis of these derivatives and characterize VALIUM10 as the most optimal vector of this series. A critical feature of VALIUM10 is the presence of gypsy insulator sequences that boost dramatically the level of knockdown. We document the efficacy of VALIUM as a vector to analyze the phenotype of genes expressed in the nervous system and have generated a library of 2282 constructs targeting 2043 genes that will be particularly useful for studies of the nervous system as they target, in particular, transcription factors, ion channels, and transporters.

}, keywords = {Animals, Carrier Proteins, Drosophila, Gene Knockdown Techniques, Ion Channels, Methods, Nervous System, RNA, RNA Interference, Small Interfering, Transcription Factors}, issn = {1943-2631}, doi = {10.1534/genetics.109.103630}, author = {Ni, Jian-Quan and Liu, Lu-Ping and Binari, Richard and Hardy, Robert and Shim, Hye-Seok and Cavallaro, Amanda and Booker, Matthew and Pfeiffer, Barret D and Markstein, Michele and Wang, Hui and Villalta, Christians and Laverty, Todd R and Perkins, Lizabeth A and Perrimon, Norbert} } @article {3913, title = {Fast synaptic subcortical control of hippocampal circuits.}, journal = {Science}, volume = {326}, year = {2009}, month = {2009 Oct 16}, pages = {449-53}, abstract = {

Cortical information processing is under state-dependent control of subcortical neuromodulatory systems. Although this modulatory effect is thought to be mediated mainly by slow nonsynaptic metabotropic receptors, other mechanisms, such as direct synaptic transmission, are possible. Yet, it is currently unknown if any such form of subcortical control exists. Here, we present direct evidence of a strong, spatiotemporally precise excitatory input from an ascending neuromodulatory center. Selective stimulation of serotonergic median raphe neurons produced a rapid activation of hippocampal interneurons. At the network level, this subcortical drive was manifested as a pattern of effective disynaptic GABAergic inhibition that spread throughout the circuit. This form of subcortical network regulation should be incorporated into current concepts of normal and pathological cortical function.

}, keywords = {Afferent, Animals, Electric Stimulation, Excitatory Postsynaptic Potentials, Glutamic Acid, Hippocampus, Inhibitory Postsynaptic Potentials, Interneurons, Mice, Neural Inhibition, Neural Pathways, Neurons, Patch-Clamp Techniques, Photic Stimulation, Raphe Nuclei, Rats, Serotonin, Sprague-Dawley, Synapses, Synaptic Potentials}, issn = {1095-9203}, doi = {10.1126/science.1178307}, author = {Varga, Viktor and Losonczy, Attila and Zemelman, Boris V and Borhegyi, Zsolt and Nyiri, G{\'a}bor and Domonkos, Andor and Hangya, Bal{\'a}zs and Holderith, No{\'e}mi and Magee, Jeffrey C and Freund, Tam{\'a}s F} } @article {2796, title = {In situ SIMS analysis and reactions of surfaces prepared by soft landing of mass-selected cations and anions using an ion trap mass spectrometer.}, journal = {Journal of the American Society for Mass Spectrometry}, volume = {20}, year = {2009}, month = {2009 Jun}, pages = {949-56}, abstract = {

Mass-selected polyatomic cations and anions, produced by electrosonic spray ionization (ESSI), were deposited onto polycrystalline Au or fluorinated self-assembled monolayer (FSAM) surfaces by soft landing (SL), using a rectilinear ion trap (RIT) mass spectrometer. Protonated and deprotonated molecules, as well as intact cations and anions generated from such molecules as peptides, inorganic catalysts, and fluorescent dyes, were soft-landed onto the surfaces. Analysis of the modified surfaces was performed in situ by Cs(+) secondary ion mass spectrometry (SIMS) using the same RIT mass analyzer to characterize the sputtered ions as that used to mass select the primary ions for SL. Soft-landing times as short as 30 s provided surfaces that yielded good quality SIMS spectra. Chemical reactions of the surfaces modified by SL were generated in an attached reaction chamber into which the surface was transferred under vacuum. For example, a surface on which protonated triethanolamine had been soft landed was silylated using vapor-phase chlorotrimethylsilane before being returned still under vacuum to the preparation chamber where SIMS analysis revealed the silyloxy functionalization. SL and vapor-phase reactions are complementary methods of surface modification and in situ surface analysis by SIMS is a simple way to characterize the products produced by either technique.

}, issn = {1879-1123}, doi = {10.1364/AO.50.001792}, author = {Nie, Zongxiu and Li, Guangtao and Goodwin, Michael P and Gao, Liang and Cyriac, Jobin and Cooks, R Graham} } @article {4277, title = {Infernal 1.0: inference of RNA alignments.}, journal = {Bioinformatics}, volume = {25}, year = {2009}, month = {2009 May 15}, pages = {1335-7}, abstract = {

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

}, keywords = {Databases, Nucleic Acid, Nucleic Acid Conformation, RNA, Sequence Alignment, Sequence Analysis, Software}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btp157}, author = {Nawrocki, Eric P and Kolbe, Diana L and Eddy, Sean R.} } @article {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 {4410, title = {Similar patterns of linkage disequilibrium and nucleotide diversity in native and introduced populations of the pea aphid, Acyrthosiphon pisum.}, journal = {BMC Genetics}, volume = {10}, year = {2009}, month = {2009 May 26}, pages = {22}, abstract = {

The pea aphid, Acyrthosiphon pisum, is an emerging genomic model system for studies of polyphenisms, bacterial symbioses, host-plant specialization, and the vectoring of plant viruses. Here we provide estimates of nucleotide diversity and linkage disequilibrium (LD) in native (European) and introduced (United States) populations of the pea aphid. Because introductions can cause population bottlenecks, we hypothesized that U.S. populations harbor lower levels of nucleotide diversity and higher levels of LD than native populations.

}, keywords = {Animals, Aphids, Europe, Genetic Variation, Genetics, INDEL Mutation, Linkage Disequilibrium, North America, Nucleotides, Population}, issn = {1471-2156}, doi = {10.1186/1471-2156-10-22}, author = {Brisson, Jennifer A and Nuzhdin, Sergey V and Stern, David L} } @article {2312, title = {Stochastically gating ion channels enable patterned spike firing through activity-dependent modulation of spike probability.}, journal = {PLoS Computational Biology}, volume = {5}, year = {2009}, month = {2009 Feb}, pages = {e1000290}, abstract = {

The transformation of synaptic input into patterns of spike output is a fundamental operation that is determined by the particular complement of ion channels that a neuron expresses. Although it is well established that individual ion channel proteins make stochastic transitions between conducting and non-conducting states, most models of synaptic integration are deterministic, and relatively little is known about the functional consequences of interactions between stochastically gating ion channels. Here, we show that a model of stellate neurons from layer II of the medial entorhinal cortex implemented with either stochastic or deterministically gating ion channels can reproduce the resting membrane properties of stellate neurons, but only the stochastic version of the model can fully account for perithreshold membrane potential fluctuations and clustered patterns of spike output that are recorded from stellate neurons during depolarized states. We demonstrate that the stochastic model implements an example of a general mechanism for patterning of neuronal output through activity-dependent changes in the probability of spike firing. Unlike deterministic mechanisms that generate spike patterns through slow changes in the state of model parameters, this general stochastic mechanism does not require retention of information beyond the duration of a single spike and its associated afterhyperpolarization. Instead, clustered patterns of spikes emerge in the stochastic model of stellate neurons as a result of a transient increase in firing probability driven by activation of HCN channels during recovery from the spike afterhyperpolarization. Using this model, we infer conditions in which stochastic ion channel gating may influence firing patterns in vivo and predict consequences of modifications of HCN channel function for in vivo firing patterns.

}, keywords = {Action Potentials, Animals, Cyclic Nucleotide-Gated Cation Channels, Entorhinal Cortex, Humans, Ion Channel Gating, Ion Transport, Models, Neural Conduction, Neurological, Potassium Channels, Stochastic Processes, Synaptic Transmission}, issn = {1553-7358}, doi = {10.3389/fnana.2010.00147}, author = {Dudman, Joshua T and Nolan, Matthew F} } @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 {6784, title = {Synapse distribution suggests a two-stage model of dendritic integration in CA1 pyramidal neurons.}, journal = {Neuron}, volume = {63}, year = {2009}, month = {2009 Jul 30}, pages = {171-7}, abstract = {

Competing models have been proposed to explain how neurons integrate the thousands of inputs distributed throughout their dendritic trees. In a simple global integration model, inputs from all locations sum in the axon. In a two-stage integration model, inputs contribute directly to dendritic spikes, and outputs from multiple branches sum in the axon. These two models yield opposite predictions of how synapses at different dendritic locations should be scaled if they are to contribute equally to neuronal output. We used serial-section electron microscopy to reconstruct individual apical oblique dendritic branches of CA1 pyramidal neurons and observe a synapse distribution consistent with the two-stage integration model. Computational modeling suggests that the observed synapse distribution enhances the contribution of each dendritic branch to neuronal output.

}, keywords = {Animals, Dendrites, Electron, Hippocampus, Humans, Microscopy, Models, Neural Networks (Computer), Neural Pathways, Neurological, Neurons, Synapses}, issn = {1097-4199}, doi = {10.1016/j.neuron.2009.06.023}, author = {Katz, Yael and Menon, Vilas and Nicholson, Daniel A and Geinisman, Yuri and Kath, William L and Spruston, Nelson} } @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 {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} } @article {4258, title = {Characterization and subcellular targeting of GCaMP-type genetically-encoded calcium indicators.}, journal = {PLoS One}, volume = {3}, year = {2008}, month = {2008 Mar 19}, pages = {e1796}, abstract = {

Genetically-encoded calcium indicators (GECIs) hold the promise of monitoring [Ca(2+)] in selected populations of neurons and in specific cellular compartments. Relating GECI fluorescence to neuronal activity requires quantitative characterization. We have characterized a promising new genetically-encoded calcium indicator-GCaMP2-in mammalian pyramidal neurons. Fluorescence changes in response to single action potentials (17+/-10\% DeltaF/F [mean+/-SD]) could be detected in some, but not all, neurons. Trains of high-frequency action potentials yielded robust responses (302+/-50\% for trains of 40 action potentials at 83 Hz). Responses were similar in acute brain slices from in utero electroporated mice, indicating that long-term expression did not interfere with GCaMP2 function. Membrane-targeted versions of GCaMP2 did not yield larger signals than their non-targeted counterparts. We further targeted GCaMP2 to dendritic spines to monitor Ca(2+) accumulations evoked by activation of synaptic NMDA receptors. We observed robust DeltaF/F responses (range: 37\%-264\%) to single spine uncaging stimuli that were correlated with NMDA receptor currents measured through a somatic patch pipette. One major drawback of GCaMP2 was its low baseline fluorescence. Our results show that GCaMP2 is improved from the previous versions of GCaMP and may be suited to detect bursts of high-frequency action potentials and synaptic currents in vivo.

}, keywords = {Action Potentials, Animals, Calcium, Hippocampus, Humans, Rats, Subcellular Fractions}, issn = {1932-6203}, doi = {10.1371/journal.pone.0001796}, author = {Mao, Tianyi and O{\textquoteright}Connor, Daniel H and Scheuss, Volker and Nakai, Junichi and Svoboda, Karel} } @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 {2806, title = {Monitoring of toxic compounds in air using a handheld rectilinear ion trap mass spectrometer.}, journal = {Analytical Chemistry}, volume = {80}, year = {2008}, month = {2008 Feb 1}, pages = {734-41}, abstract = {

A miniature, handheld mass spectrometer, based on the rectilinear ion trap mass analyzer, has been applied to air monitoring for traces of toxic compounds. The instrument is battery-operated, hand-portable, and rugged. We anticipate its use in public safety, industrial hygiene, and environmental monitoring. Gaseous samples of nine toxic industrial compounds, phosgene, ethylene oxide, sulfur dioxide, acrylonitrile, cyanogen chloride, hydrogen cyanide, acrolein, formaldehyde, and ethyl parathion, were tested. A sorption trap inlet was constructed to serve as the interface between atmosphere and the vacuum chamber of the mass spectrometer. After selective collection of analytes on the sorbent bed, the sorbent tube was evacuated and then heated to desorb analyte into the instrument. Sampling, detection, identification, and quantitation of all compounds were readily achieved in times of less than 2 min, with detection limits ranging from 800 parts per trillion to 3 parts per million depending on the analyte. For all but one analyte, detection limits were well below (3.5-130 times below) permissible exposure limits. A linear dynamic range of 1-2 orders of magnitude was obtained over the concentration ranges studied (sub-ppbv to ppmv) for all analytes.

}, issn = {0003-2700}, doi = {10.1364/AO.50.001792}, author = {Keil, Adam and Hernandez-Soto, Heriberto and Noll, Robert J and Fico, Miriam and Gao, Liang and Ouyang, Zheng and Cooks, R Graham} } @article {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 {988, title = {Tools for neuroanatomy and neurogenetics in Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, year = {2008}, month = {2008 Jul 15}, pages = {9715-20}, abstract = {

We demonstrate the feasibility of generating thousands of transgenic Drosophila melanogaster lines in which the expression of an exogenous gene is reproducibly directed to distinct small subsets of cells in the adult brain. We expect the expression patterns produced by the collection of 5,000 lines that we are currently generating to encompass all neurons in the brain in a variety of intersecting patterns. Overlapping 3-kb DNA fragments from the flanking noncoding and intronic regions of genes thought to have patterned expression in the adult brain were inserted into a defined genomic location by site-specific recombination. These fragments were then assayed for their ability to function as transcriptional enhancers in conjunction with a synthetic core promoter designed to work with a wide variety of enhancer types. An analysis of 44 fragments from four genes found that \>80\% drive expression patterns in the brain; the observed patterns were, on average, comprised of \<100 cells. Our results suggest that the D. melanogaster genome contains \>50,000 enhancers and that multiple enhancers drive distinct subsets of expression of a gene in each tissue and developmental stage. We expect that these lines will be valuable tools for neuroanatomy as well as for the elucidation of neuronal circuits and information flow in the fly brain.

}, keywords = {Animals, Biomedical Research, Brain, Developmental, Drosophila melanogaster, Enhancer Elements, Gene Expression Regulation, Genes, Genetic, Genetically Modified, Insect, Neurons, Neurosciences, Recombination}, issn = {1091-6490}, doi = {https://doi.org/10.1073/pnas.0803697105}, author = {Pfeiffer, Barret D and Jenett, Arnim and Hammonds, Ann S and Ngo, Teri-T B and Misra, Sima and Murphy, Christine and Scully, Audra and Carlson, Joseph W and Wan, Kenneth H and Laverty, Todd R and Mungall, Chris and Svirskas, Rob and Kadonaga, James T and Doe, Chris Q and Eisen, Michael B and Celniker, Susan E and Rubin, Gerald M} } @article {6516, title = {Vector and parameters for targeted transgenic RNA interference in Drosophila melanogaster.}, journal = {Nature Methods}, volume = {5}, year = {2008}, month = {2008 Jan}, pages = {49-51}, abstract = {

The conditional expression of hairpin constructs in Drosophila melanogaster has emerged in recent years as a method of choice in functional genomic studies. To date, upstream activating site-driven RNA interference constructs have been inserted into the genome randomly using P-element-mediated transformation, which can result in false negatives due to variable expression. To avoid this problem, we have developed a transgenic RNA interference vector based on the phiC31 site-specific integration method.

}, keywords = {Animals, Drosophila melanogaster, Drosophila Proteins, Gene Targeting, Genetic Vectors, RNA Interference}, issn = {1548-7105}, doi = {10.1038/nmeth1146}, author = {Ni, Jian-Quan and Markstein, Michele and Binari, Richard and Pfeiffer, Barret and Liu, Lu-Ping and Villalta, Christians and Booker, Matthew and Perkins, Lizabeth and Perrimon, Norbert} } @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 {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 {4050, title = {HCN1 channels control resting and active integrative properties of stellate cells from layer II of the entorhinal cortex.}, journal = {The Journal of Neuroscience}, volume = {27}, year = {2007}, month = {2007 Nov 14}, pages = {12440-51}, abstract = {

Whereas recent studies have elucidated principles for representation of information within the entorhinal cortex, less is known about the molecular basis for information processing by entorhinal neurons. The HCN1 gene encodes ion channels that mediate hyperpolarization-activated currents (I(h)) that control synaptic integration and influence several forms of learning and memory. We asked whether hyperpolarization-activated, cation nonselective 1 (HCN1) channels control processing of information by stellate cells found within layer II of the entorhinal cortex. Axonal projections from these neurons form a major component of the synaptic input to the dentate gyrus of the hippocampus. To determine whether HCN1 channels control either the resting or the active properties of stellate neurons, we performed whole-cell recordings in horizontal brain slices prepared from adult wild-type and HCN1 knock-out mice. We found that HCN1 channels are required for rapid and full activation of hyperpolarization-activated currents in stellate neurons. HCN1 channels dominate the membrane conductance at rest, are not required for theta frequency (4-12 Hz) membrane potential fluctuations, but suppress low-frequency (\<4 Hz) components of spontaneous and evoked membrane potential activity. During sustained activation of stellate cells sufficient for firing of repeated action potentials, HCN1 channels control the pattern of spike output by promoting recovery of the spike afterhyperpolarization. These data suggest that HCN1 channels expressed by stellate neurons in layer II of the entorhinal cortex are key molecular components in the processing of inputs to the hippocampal dentate gyrus, with distinct integrative roles during resting and active states.

}, keywords = {Action Potentials, Animals, Cyclic Nucleotide-Gated Cation Channels, Dentate Gyrus, Entorhinal Cortex, Female, Ion Channel Gating, Knockout, Male, Membrane Potentials, Memory, Mice, Neural Inhibition, Neural Pathways, Neurons, Organ Culture Techniques, Patch-Clamp Techniques, Potassium Channels, Synaptic Membranes, Synaptic Transmission, Theta Rhythm}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.2358-07.2007}, author = {Nolan, Matthew F and Dudman, Joshua T and Dodson, Paul D and Santoro, Bina} } @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 {1112, title = {A new strategy for the synthesis of benzylic sulfonamides: palladium-catalyzed arylation and sulfonamide metathesis.}, journal = {The Journal of Organic Chemistry}, volume = {72}, year = {2007}, month = {2007 Oct 12}, pages = {8135-8}, abstract = {

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

}, keywords = {Benzyl Compounds, Catalysis, Molecular Structure, Palladium, Sulfonamides}, issn = {0022-3263}, doi = {10.1021/jo701431j}, author = {Grimm, Jonathan B and Katcher, Matthew H and Witter, David J and Northrup, Alan B} } @article {4224, title = {Query-dependent banding (QDB) for faster RNA similarity searches.}, journal = {PLoS Computational Biology}, volume = {3}, year = {2007}, month = {2007 Mar 30}, pages = {e56}, abstract = {

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

}, keywords = {Base Sequence, Database Management Systems, Databases, Genetic, Information Storage and Retrieval, Molecular Sequence Data, Nucleic Acid, RNA, Sequence Alignment, Sequence Analysis, Sequence Homology}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.0030056}, author = {Nawrocki, Eric P and Eddy, Sean R.} } @article {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 {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 {4142, title = {Functional dissection of a neuronal network required for cuticle tanning and wing expansion in Drosophila.}, journal = {The Journal of Neuroscience The Official Journal of the Society for Neuroscience}, volume = {26}, year = {2006}, month = {2006 Jan 11}, pages = {573-84}, abstract = {

A subset of Drosophila neurons that expresses crustacean cardioactive peptide (CCAP) has been shown previously to make the hormone bursicon, which is required for cuticle tanning and wing expansion after eclosion. Here we present evidence that CCAP-expressing neurons (NCCAP) consist of two functionally distinct groups, one of which releases bursicon into the hemolymph and the other of which regulates its release. The first group, which we call NCCAP-c929, includes 14 bursicon-expressing neurons of the abdominal ganglion that lie within the expression pattern of the enhancer-trap line c929-Gal4. We show that suppression of activity within this group blocks bursicon release into the hemolymph together with tanning and wing expansion. The second group, which we call NCCAP-R, consists of NCCAP neurons outside the c929-Gal4 pattern. Because suppression of synaptic transmission and protein kinase A (PKA) activity throughout NCCAP, but not in NCCAP-c929, also blocks tanning and wing expansion, we conclude that neurotransmission and PKA are required in NCCAP-R to regulate bursicon secretion from NCCAP-c929. Enhancement of electrical activity in NCCAP-R by expression of the bacterial sodium channel NaChBac also blocks tanning and wing expansion and leads to depletion of bursicon from central processes. NaChBac expression in NCCAP-c929 is without effect, suggesting that the abdominal bursicon-secreting neurons are likely to be silent until stimulated to release the hormone. Our results suggest that NCCAP form an interacting neuronal network responsible for the regulation and release of bursicon and suggest a model in which PKA-mediated stimulation of inputs to normally quiescent bursicon-expressing neurons activates release of the hormone.

}, keywords = {Animals, Bacterial Proteins, Cyclic AMP-Dependent Protein Kinases, Drosophila melanogaster, Drosophila Proteins, Electroretinography, Ganglia, Gene Targeting, Genetically Modified, Invertebrate, Invertebrate Hormones, Nerve Net, Neurons, Neuropeptides, Phenotype, Pigmentation, Recombinant Fusion Proteins, Shaker Superfamily of Potassium Channels, Sodium Channels, Synaptic Transmission, Wing}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3916-05.2006}, author = {Luan, Haojiang and Lemon, William C and Peabody, Nathan C and Pohl, Jascha B and Zelensky, Paul K and Wang, Ding and Nitabach, Michael N and Holmes, Todd C and White, Benjamin H} } @article {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 {2129, title = {A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor binding profiles.}, journal = {Genome Research}, volume = {16}, year = {2006}, month = {2006 Mar}, pages = {405-13}, abstract = {

An important aspect of understanding a biological pathway is to delineate the transcriptional regulatory mechanisms of the genes involved. Two important tasks are often encountered when studying transcription regulation, i.e., (1) the identification of common transcriptional regulators of a set of coexpressed genes; (2) the identification of genes that are regulated by one or several transcription factors. In this study, a systematic and statistical approach was taken to accomplish these tasks by establishing an integrated model considering all of the promoters and characterized transcription factors (TFs) in the genome. A promoter analysis pipeline (PAP) was developed to implement this approach. PAP was tested using coregulated gene clusters collected from the literature. In most test cases, PAP identified the transcription regulators of the input genes accurately. When compared with chromatin immunoprecipitation experiment data, PAP{\textquoteright}s predictions are consistent with the experimental observations. When PAP was used to analyze one published expression-profiling data set and two novel coregulated gene sets, PAP was able to generate biologically meaningful hypotheses. Therefore, by taking a systematic approach of considering all promoters and characterized TFs in our model, we were able to make more reliable predictions about the regulation of gene expression in mammalian organisms.

}, keywords = {Animals, Cell Proliferation, Cholesterol, Chromatin Immunoprecipitation, Computational Biology, Conserved Sequence, Gene Expression Profiling, Gene Expression Regulation, Genetic, Humans, Mice, Models, Promoter Regions, Protein Binding, Transcription Factors}, issn = {1088-9051}, doi = {10.1002/cbic.201000254}, author = {Chang, Li-Wei and Nagarajan, Rakesh and Magee, Jeffrey A and Milbrandt, Jeffrey and Stormo, Gary D} } @article {1251, title = {Highly nonrandom features of synaptic connectivity in local cortical circuits.}, journal = {PLoS Biology}, volume = {3}, year = {2005}, month = {2005 Mar}, pages = {e68}, abstract = {

How different is local cortical circuitry from a random network? To answer this question, we probed synaptic connections with several hundred simultaneous quadruple whole-cell recordings from layer 5 pyramidal neurons in the rat visual cortex. Analysis of this dataset revealed several nonrandom features in synaptic connectivity. We confirmed previous reports that bidirectional connections are more common than expected in a random network. We found that several highly clustered three-neuron connectivity patterns are overrepresented, suggesting that connections tend to cluster together. We also analyzed synaptic connection strength as defined by the peak excitatory postsynaptic potential amplitude. We found that the distribution of synaptic connection strength differs significantly from the Poisson distribution and can be fitted by a lognormal distribution. Such a distribution has a heavier tail and implies that synaptic weight is concentrated among few synaptic connections. In addition, the strengths of synaptic connections sharing pre- or postsynaptic neurons are correlated, implying that strong connections are even more clustered than the weak ones. Therefore, the local cortical network structure can be viewed as a skeleton of stronger connections in a sea of weaker ones. Such a skeleton is likely to play an important role in network dynamics and should be investigated further.

}, keywords = {Animals, Cell Communication, Neural Pathways, Neuronal Plasticity, Neurons, Rats, Signal Transduction, Synapses, Visual Cortex}, issn = {1545-7885}, doi = {10.1016/j.tins.2005.05.006}, author = {Song, Sen and Sj{\"o}str{\"o}m, Per Jesper and Reigl, Markus and Nelson, Sacha and Chklovskii, Dmitri B} } @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 {6442, title = {Functional magnetic resonance imaging of macaque monkeys performing visually guided saccade tasks: comparison of cortical eye fields with humans.}, journal = {Neuron}, volume = {41}, year = {2004}, month = {2004 Mar 4}, pages = {795-807}, abstract = {

The frontal and parietal eye fields serve as functional landmarks of the primate brain, although their correspondences between humans and macaque monkeys remain unclear. We conducted fMRI at 4.7 T in monkeys performing visually-guided saccade tasks and compared brain activations with those in humans using identical paradigms. Among multiple parietal activations, the dorsal lateral intraparietal area in monkeys and an area in the posterior superior parietal lobule in humans exhibited the highest selectivity to saccade directions. In the frontal cortex, the selectivity was highest at the junction of the precentral and superior frontal sulci in humans and in the frontal eye field (FEF) in monkeys. BOLD activation peaks were also found in premotor areas (BA6) in monkeys, which suggests that the apparent discrepancy in location between putative human FEF (BA6, suggested by imaging studies) and monkey FEF (BA8, identified by microstimulation studies) partly arose from methodological differences.

}, keywords = {Analysis of Variance, Animals, Cerebral Cortex, Female, Humans, Macaca, Magnetic Resonance Imaging, Male, Photic Stimulation, Psychomotor Performance, Rats, Saccades, Species Specificity, Visual Fields}, issn = {0896-6273}, author = {Koyama, Minoru and Hasegawa, Isao and Osada, Takahiro and Adachi, Yusuke and Nakahara, Kiyoshi and Miyashita, Yasushi} } @article {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 {1778, title = {An amino-acid taste receptor.}, journal = {Nature}, volume = {416}, year = {2002}, month = {2002 Mar 14}, pages = {199-202}, abstract = {

The sense of taste provides animals with valuable information about the nature and quality of food. Mammals can recognize and respond to a diverse repertoire of chemical entities, including sugars, salts, acids and a wide range of toxic substances. Several amino acids taste sweet or delicious (umami) to humans, and are attractive to rodents and other animals. This is noteworthy because L-amino acids function as the building blocks of proteins, as biosynthetic precursors of many biologically relevant small molecules, and as metabolic fuel. Thus, having a taste pathway dedicated to their detection probably had significant evolutionary implications. Here we identify and characterize a mammalian amino-acid taste receptor. This receptor, T1R1+3, is a heteromer of the taste-specific T1R1 and T1R3 G-protein-coupled receptors. We demonstrate that T1R1 and T1R3 combine to function as a broadly tuned L-amino-acid sensor responding to most of the 20 standard amino acids, but not to their D-enantiomers or other compounds. We also show that sequence differences in T1R receptors within and between species (human and mouse) can significantly influence the selectivity and specificity of taste responses.

}, keywords = {Alleles, Amino Acids, Animals, Calcium Signaling, Cell Line, Cell Surface, Chorda Tympani Nerve, Dose-Response Relationship, Drug, G-Protein-Coupled, Genetic, Heterotrimeric GTP-Binding Proteins, Humans, Inosine Monophosphate, Mice, Mutation, Polymorphism, Protein Subunits, Receptors, Stereoisomerism, Structure-Activity Relationship, Substrate Specificity, Taste, Taste Buds, Transfection}, issn = {0028-0836}, doi = {10.1038/nature726}, author = {Nelson, Greg and Chandrashekar, Jayaram and Hoon, Mark A and Feng, Luxin and Zhao, Grace and Ryba, Nicholas J P and Zuker, Charles S} } @article {2143, title = {Conditional loss of Nkx3.1 in adult mice induces prostatic intraepithelial neoplasia.}, journal = {Molecular and Cellular Biology}, volume = {22}, year = {2002}, month = {2002 Mar}, pages = {1495-503}, abstract = {

The homeodomain-containing transcription factor NKX3.1 is a putative prostate tumor suppressor that is expressed in a largely prostate-specific and androgen-regulated manner. Loss of NKX3.1 protein expression is common in human prostate carcinomas and prostatic intraepithelial neoplasia (PIN) lesions and correlates with tumor progression. Disruption of the murine Nkx3.1 gene results in defects in prostate branching morphogenesis, secretions, and growth. To more closely mimic the pattern of NKX3.1 loss that occurs in human prostate tumors, we have used Cre- and loxP-mediated recombination to delete the Nkx3.1 gene in the prostates of adult transgenic mice. Conditional deletion of one or both alleles of Nkx3.1 leads to the development of preinvasive lesions that resemble PIN. The pattern of expression of several biomarkers (Ki-67, E-cadherin, and high-molecular-weight cytokeratins) in these PIN lesions resembled that observed in human cases of PIN. Furthermore, PIN foci in mice with conditional deletion of a single Nkx3.1 allele lose expression of the wild-type allele. Our results support the role of NKX3.1 as a prostate tumor suppressor and indicate a role for this gene in tumor initiation.

}, keywords = {Animals, Gene Deletion, Genes, Genetic Predisposition to Disease, Homeodomain Proteins, Homozygote, Hyperplasia, Integrases, Male, Mice, Prostate, Prostatic Intraepithelial Neoplasia, Prostatic Neoplasms, Transcription Factors, Transgenic, Tumor Suppressor, Viral Proteins}, issn = {0270-7306}, doi = {10.1002/cbic.201000254}, author = {Abdulkadir, Sarki A and Magee, Jeffrey A and Peters, Thomas J and Kaleem, Zahid and Naughton, Cathy K and Humphrey, Peter A and Milbrandt, Jeffrey} } @article {1143, title = {A genomic analysis of gene expresson during the Drosophila life cycle.}, journal = {Science}, year = {2002}, month = {2002}, pages = {2270-75}, author = {Baker, B.S. and Arbeitman, M. and Furlong, E. and Imam, F. and Johnson, E. and Null, B.} } @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 {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 {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 {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 {1780, title = {Mammalian sweet taste receptors.}, journal = {Cell}, volume = {106}, year = {2001}, month = {2001 Aug 10}, pages = {381-90}, abstract = {

The sense of taste provides animals with valuable information about the quality and nutritional value of food. Previously, we identified a large family of mammalian taste receptors involved in bitter taste perception (the T2Rs). We now report the characterization of mammalian sweet taste receptors. First, transgenic rescue experiments prove that the Sac locus encodes T1R3, a member of the T1R family of candidate taste receptors. Second, using a heterologous expression system, we demonstrate that T1R2 and T1R3 combine to function as a sweet receptor, recognizing sweet-tasting molecules as diverse as sucrose, saccharin, dulcin, and acesulfame-K. Finally, we present a detailed analysis of the patterns of expression of T1Rs and T2Rs, thus providing a view of the representation of sweet and bitter taste at the periphery.

}, keywords = {Animals, Calcium Signaling, Cell Line, Cell Surface, Chromosomes, Cricetinae, Evolution, G-Protein-Coupled, Gene Expression Profiling, Genetic Complementation Test, Heterotrimeric GTP-Binding Proteins, Human, Humans, Messenger, Mice, Molecular, Molecular Sequence Data, Multigene Family, Pair 4, Phenylurea Compounds, Physical Chromosome Mapping, Receptors, RNA, Saccharin, Substrate Specificity, Sucrose, Sweetening Agents, Taste, Taste Buds, Thiazines, Transgenic}, issn = {0092-8674}, author = {Nelson, G and Hoon, M A and Chandrashekar, J and Zhang, Y and Ryba, N J and Zuker, C S} } @article {2707, title = {The sequence of the human genome.}, journal = {Science}, volume = {291}, year = {2001}, month = {2001 Feb 16}, pages = {1304-51}, abstract = {

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90\% of the genome is in scaffold assemblies of 100,000 bp or more, and 25\% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1\% of the genome is spanned by exons, whereas 24\% is in introns, with 75\% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1\% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

}, keywords = {Algorithms, Animals, Artificial, Bacterial, Chromosome Banding, Chromosome Mapping, Chromosomes, Computational Biology, Consensus Sequence, CpG Islands, Databases, DNA, Evolution, Exons, Factual, Female, Gene Duplication, Genes, Genetic Variation, Genome, Human, Human Genome Project, Humans, Intergenic, Introns, Male, Molecular, Nucleic Acid, Phenotype, Physical Chromosome Mapping, Polymorphism, Proteins, Pseudogenes, Repetitive Sequences, Retroelements, Sequence Analysis, Single Nucleotide, Species Specificity}, issn = {0036-8075}, doi = {10.1126/science.1058040}, author = {Venter, J C and Adams, M D and Myers, E W and Li, P W and Mural, R J and Sutton, G G and Smith, H O and Yandell, M and Evans, C A and Holt, R A and Gocayne, J D and Amanatides, P and Ballew, R M and Huson, D H and Wortman, J R and Zhang, Q and Kodira, C D and Zheng, X H and Chen, L and Skupski, M and Subramanian, G and Thomas, P D and Zhang, J and Gabor Miklos, G L and Nelson, C and Broder, S and Clark, A G and Nadeau, J and McKusick, V A and Zinder, N and Levine, A J and Roberts, R J and Simon, M and Slayman, C and Hunkapiller, M and Bolanos, R and Delcher, A and Dew, I and Fasulo, D and Flanigan, M and Florea, L and Halpern, A and Hannenhalli, S and Kravitz, S and Levy, S and Mobarry, C and Reinert, K and Remington, K and Abu-Threideh, J and Beasley, E and Biddick, K and Bonazzi, V and Brandon, R and Cargill, M and Chandramouliswaran, I and Charlab, R and Chaturvedi, K and Deng, Z and Di Francesco, V and Dunn, P and Eilbeck, K and Evangelista, C and Gabrielian, A E and Gan, W and Ge, W and Gong, F and Gu, Z and Guan, P and Heiman, T J and Higgins, M E and Ji, R R and Ke, Z and Ketchum, K A and Lai, Z and Lei, Y and Li, Z and Li, J and Liang, Y and Lin, X and Lu, F and Merkulov, G V and Milshina, N and Moore, H M and Naik, A K and Narayan, V A and Neelam, B and Nusskern, D and Rusch, D B and Salzberg, S and Shao, W and Shue, B and Sun, J and Wang, Z and Wang, A and Wang, X and Wang, J and Wei, M and Wides, R and Xiao, C and Yan, C and Yao, A and Ye, J and Zhan, M and Zhang, W and Zhang, H and Zhao, Q and Zheng, L and Zhong, F and Zhong, W and Zhu, S and Zhao, S and Gilbert, D and Baumhueter, S and Spier, G and Carter, C and Cravchik, A and Woodage, T and Ali, F and An, H and Awe, A and Baldwin, D and Baden, H and Barnstead, M and Barrow, I and Beeson, K and Busam, D and Carver, A and Center, A and Cheng, M L and Curry, L and Danaher, S and Davenport, L and Desilets, R and Dietz, S and Dodson, K and Doup, L and Ferriera, S and Garg, N and Gluecksmann, A and Hart, B and Haynes, J and Haynes, C and Heiner, C and Hladun, S and Hostin, D and Houck, J and Howland, T and Ibegwam, C and Johnson, J and Kalush, F and Kline, L and Koduru, S and Love, A and Mann, F and May, D and McCawley, S and McIntosh, T and McMullen, I and Moy, M and Moy, L and Murphy, B and Nelson, K and Pfannkoch, C and Pratts, E and Puri, V and Qureshi, H and Reardon, M and Rodriguez, R and Rogers, Y H and Romblad, D and Ruhfel, B and Scott, R and Sitter, C and Smallwood, M and Stewart, E and Strong, R and Suh, E and Thomas, R and Tint, N N and Tse, S and Vech, C and Wang, G and Wetter, J and Williams, S and Williams, M and Windsor, S and Winn-Deen, E and Wolfe, K and Zaveri, J and Zaveri, K and Abril, J F and Guig{\'o}, R and Campbell, M J and Sjolander, K V and Karlak, B and Kejariwal, A and Mi, H and Lazareva, B and Hatton, T and Narechania, A and Diemer, K and Muruganujan, A and Guo, N and Sato, S and Bafna, V and Istrail, S and Lippert, R and Schwartz, R and Walenz, B and Yooseph, S and Allen, D and Basu, A and Baxendale, J and Blick, L and Caminha, M and Carnes-Stine, J and Caulk, P and Chiang, Y H and Coyne, M and Dahlke, C and Mays, A and Dombroski, M and Donnelly, M and Ely, D and Esparham, S and Fosler, C and Gire, H and Glanowski, S and Glasser, K and Glodek, A and Gorokhov, M and Graham, K and Gropman, B and Harris, M and Heil, J and Henderson, S and Hoover, J and Jennings, D and Jordan, C and Jordan, J and Kasha, J and Kagan, L and Kraft, C and Levitsky, A and Lewis, M and Liu, X and Lopez, J and Ma, D and Majoros, W and McDaniel, J and Murphy, S and Newman, M and Nguyen, T and Nguyen, N and Nodell, M and Pan, S and Peck, J and Peterson, M and Rowe, W and Sanders, R and Scott, J and Simpson, M and Smith, T and Sprague, A and Stockwell, T and Turner, R and Venter, E and Wang, M and Wen, M and Wu, D and Wu, M and Xia, A and Zandieh, A and Zhu, X} } @article {958, title = {Comparative genomics of the eukaryotes.}, journal = {Science}, volume = {287}, year = {2000}, month = {2000 Mar 24}, pages = {2204-15}, abstract = {

A comparative analysis of the genomes of Drosophila melanogaster, Caenorhabditis elegans, and Saccharomyces cerevisiae-and the proteins they are predicted to encode-was undertaken in the context of cellular, developmental, and evolutionary processes. The nonredundant protein sets of flies and worms are similar in size and are only twice that of yeast, but different gene families are expanded in each genome, and the multidomain proteins and signaling pathways of the fly and worm are far more complex than those of yeast. The fly has orthologs to 177 of the 289 human disease genes examined and provides the foundation for rapid analysis of some of the basic processes involved in human disease.

}, keywords = {Animals, Apoptosis, Biological Evolution, Caenorhabditis elegans, Cell Adhesion, Cell Cycle, Drosophila melanogaster, Duplicate, Fungal Proteins, Genes, Genetic Diseases, Genetics, Genome, Helminth Proteins, Humans, Immunity, Inborn, Insect Proteins, Medical, Multigene Family, Neoplasms, Protein Structure, Proteome, Saccharomyces cerevisiae, Signal Transduction, Tertiary}, issn = {0036-8075}, doi = {10.1186/gb-2007-8-7-r145}, author = {Rubin, G M and Yandell, M D and Wortman, J R and Gabor Miklos, G L and Nelson, C R and Hariharan, I K and Fortini, M E and Li, P W and Apweiler, R and Fleischmann, W and Cherry, J M and Henikoff, S and Skupski, M P and Misra, S and Ashburner, M and Birney, E and Boguski, M S and Brody, T and Brokstein, P and Celniker, S E and Chervitz, S A and Coates, D and Cravchik, A and Gabrielian, A and Galle, R F and Gelbart, W M and George, R A and Goldstein, L S and Gong, F and Guan, P and Harris, N L and Hay, B A and Hoskins, R A and Li, J and Li, Z and Hynes, R O and Jones, S J and Kuehl, P M and Lemaitre, B and Littleton, J T and Morrison, D K and Mungall, C and O{\textquoteright}Farrell, P H and Pickeral, O K and Shue, C and Vosshall, L B and Zhang, J and Zhao, Q and Zheng, X H and Lewis, S} } @article {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 {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 {2705, title = {A whole-genome assembly of Drosophila.}, journal = {Science}, volume = {287}, year = {2000}, month = {2000 Mar 24}, pages = {2196-204}, abstract = {

We report on the quality of a whole-genome assembly of Drosophila melanogaster and the nature of the computer algorithms that accomplished it. Three independent external data sources essentially agree with and support the assembly{\textquoteright}s sequence and ordering of contigs across the euchromatic portion of the genome. In addition, there are isolated contigs that we believe represent nonrepetitive pockets within the heterochromatin of the centromeres. Comparison with a previously sequenced 2.9- megabase region indicates that sequencing accuracy within nonrepetitive segments is greater than 99. 99\% without manual curation. As such, this initial reconstruction of the Drosophila sequence should be of substantial value to the scientific community.

}, keywords = {Algorithms, Animals, Chromatin, Computational Biology, Contig Mapping, DNA, Drosophila melanogaster, Euchromatin, Genes, Genome, Heterochromatin, Insect, Molecular Sequence Data, Nucleic Acid, Physical Chromosome Mapping, Repetitive Sequences, Sequence Analysis, Sequence Tagged Sites}, issn = {0036-8075}, author = {Myers, E W and Sutton, G G and Delcher, A L and Dew, I M and Fasulo, D P and Flanigan, M J and Kravitz, S A and Mobarry, C M and Reinert, K H and Remington, K A and Anson, E L and Bolanos, R A and Chou, H H and Jordan, C M and Halpern, A L and Lonardi, S and Beasley, E M and Brandon, R C and Chen, L and Dunn, P J and Lai, Z and Liang, Y and Nusskern, D R and Zhan, M and Zhang, Q and Zheng, X and Rubin, G M and Adams, M D and Venter, J C} } @article {962, title = {The Drosophila peanut gene is required for cytokinesis and encodes a protein similar to yeast putative bud neck filament proteins.}, journal = {Cell}, volume = {77}, year = {1994}, month = {1994 May 6}, pages = {371-9}, abstract = {

We have identified a Drosophila gene, peanut (pnut), that is related in sequence to the CDC3, CDC10, CDC11, and CDC12 genes of S. cerevisiae. These genes are required for cytokinesis, and their products are present at the bud neck during cell division. We find that pnut is also required for cytokinesis: in pnut mutants, imaginal tissues fail to proliferate and instead develop clusters of large, multinucleate cells. Pnut protein is localized to the cleavage furrow of dividing cells during cytokinesis and to the intercellular bridge connecting postmitotic daughter cells. In addition to its role in cytokinesis, pnut displays genetic interactions with seven in absentia, a gene required for neuronal fate determination in the compound eye, suggesting that pnut may have pleiotropic functions. Our results suggest that this class of proteins is involved in aspects of cytokinesis that have been conserved between flies and yeast.

}, keywords = {Amino Acid, Amino Acid Sequence, Animals, Base Sequence, Cell Division, Cell Line, Cloning, Complementary, DNA, Drosophila, Drosophila Proteins, Enhancer Elements, Female, Fungal, Fungal Proteins, Gene Library, Genes, Genetic, Insect, Larva, Male, Mice, Microfilament Proteins, Molecular, Molecular Sequence Data, Proteins, Saccharomyces cerevisiae, Sequence Analysis, Sequence Homology}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Neufeld, T P and Rubin, G M} } @article {68294, title = {Visual projection neuron convergence and compensation in developing sensorimotor circuits in the Drosophila optic glomeruli}, month = {2022 Aug 22}, abstract = {

Visual features detected by the early visual system must be combined into higher order representations to guide behavioral decision. Although key developmental mechanisms that enable the separation of visual feature channels in early visual circuits have been discovered, relatively little is known about the mechanisms that underlie their convergence in later stages of visual processing. Here we explore the development of a functionally well-characterized sensorimotor circuit in\ Drosophila melanogaster, the convergence of visual projection neurons (VPNs) onto the dendrites of a large descending neuron called the giant fiber (GF). We find two VPNs encoding different visual features that target the same giant fiber dendrite establish their territories on the dendrite, in part, through sequential axon arrival during development prior to synaptogenesis. Physical occupancy is important to maintain territories, as we find the ablation of one VPN results in expanded dendrite territory of the remaining VPN, and that this compensation enables the GF to remain responsive to ethologically relevant visual stimuli. Our data highlight temporal mechanisms for visual feature convergence and promote the GF circuit, and the\ Drosophila\ optic glomeruli where VPN to GF connectivity resides, as an ideal developmental model for investigating complex wiring programs and plasticity in visual feature convergence.

}, doi = {10.1101/2022.08.20.504653}, url = {https://doi.org/10.1101/2022.08.20.504653}, author = {Brennan W. McFarland and HyoJong Jang and Natalie Smolin and Tanja A. Godenschwege and Aljoscha Nern and Yerbol Z. Kurmangaliyev and Catherine R. von Reyn} }