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157 Janelia Publications

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    12/01/20 | Linking axon morphology to gene expression: a strategy for neuronal cell-type classification.
    Winnubst J, Spruston N, Harris JA
    Current Opinion in Neurobiology. 2020 Dec 01;65:70-76. doi: 10.1016/j.conb.2020.10.006

    To study how the brain drives cognition and behavior we need to understand its cellular composition. Advances in single-cell transcriptomics have revolutionized our ability to characterize neuronal diversity. To arrive at meaningful descriptions of cell types, however, gene expression must be linked to structural and functional properties. Axonal projection patterns are an appropriate measure, as they are diverse, change only gradually over time, and they influence and constrain circuit function. Here, we consider how efforts to map transcriptional and morphological diversity in the mouse brain could be linked to generate a modern taxonomy of the mouse brain.

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    11/11/20 | Optimized Vivid-derived Magnets photodimerizers for subcellular optogenetics in mammalian cells.
    Benedetti L, Marvin JS, Falahati H, Guillén-Samander A, Looger LL, De Camilli P
    Elife. 2020 Nov 11;9:. doi: 10.7554/eLife.63230

    Light-inducible dimerization protein modules enable precise temporal and spatial control of biological processes in non-invasive fashion. Among them, Magnets are small modules engineered from the photoreceptor Vivid by orthogonalizing the homodimerization interface into complementary heterodimers. Both Magnets components, which are well-tolerated as protein fusion partners, are photoreceptors requiring simultaneous photoactivation to interact, enabling high spatiotemporal confinement of dimerization with a single-excitation wavelength. However, Magnets require concatemerization for efficient responses and cell preincubation at 28C to be functional. Here we overcome these limitations by engineering an optimized Magnets pair requiring neither concatemerization nor low temperature preincubation. We validated these 'enhanced' Magnets (eMags) by using them to rapidly and reversibly recruit proteins to subcellular organelles, to induce organelle contacts, and to reconstitute OSBP-VAP ER-Golgi tethering implicated in phosphatidylinositol-4-phosphate transport and metabolism. eMags represent a very effective tool to optogenetically manipulate physiological processes over whole cells or in small subcellular volumes.

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    11/06/20 | In vivo optogenetics with stimulus calibration.
    Coddington LT, Dudman JT
    Methods in Molecular Biology. 2020 Nov 06;2188:273-283. doi: 10.1007/978-1-0716-0818-0_14

    Optogenetic reagents allow for depolarization and hyperpolarization of cells with light. This provides unprecedented spatial and temporal resolution to the control of neuronal activity both in vitro and in vivo. In the intact animal this requires strategies to deliver light deep into the highly scattering tissue of the brain. A general approach that we describe here is to implant optical fibers just above brain regions targeted for light delivery. In part due to the fact that expression of optogenetic proteins is accomplished by techniques with inherent variability (e.g., viral expression levels), it also requires strategies to measure and calibrate the effect of stimulation. Here we describe general procedures that allow one to simultaneously stimulate neurons and use photometry with genetically encoded activity indicators to precisely calibrate stimulation.

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    11/05/20 | Hypothesis-driven quantitative fluorescence microscopy - the importance of reverse-thinking in experimental design.
    Wait EC, Reiche MA, Chew T
    Journal of Cell Science. 2020 Nov 05;133(21):. doi: 10.1242/jcs.250027

    One of the challenges in modern fluorescence microscopy is to reconcile the conventional utilization of microscopes as exploratory instruments with their emerging and rapidly expanding role as a quantitative tools. The contribution of microscopy to observational biology will remain enormous owing to the improvements in acquisition speed, imaging depth, resolution and biocompatibility of modern imaging instruments. However, the use of fluorescence microscopy to facilitate the quantitative measurements necessary to challenge hypotheses is a relatively recent concept, made possible by advanced optics, functional imaging probes and rapidly increasing computational power. We argue here that to fully leverage the rapidly evolving application of microscopes in hypothesis-driven biology, we not only need to ensure that images are acquired quantitatively but must also re-evaluate how microscopy-based experiments are designed. In this Opinion, we present a reverse logic that guides the design of quantitative fluorescence microscopy experiments. This unique approach starts from identifying the results that would quantitatively inform the hypothesis and map the process backward to microscope selection. This ensures that the quantitative aspects of testing the hypothesis remain the central focus of the entire experimental design.

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    11/04/20 | Metabolic determinants of cellular fitness dependent on mitochondrial reactive oxygen species.
    Kong H, Reczek CR, McElroy GS, Steinert EM, Wang T, Sabatini DM, Chandel NS
    Science Advances. 2020 Nov 04;6(45):. doi: 10.1126/sciadv.abb7272

    Mitochondria-derived reactive oxygen species (mROS) are required for the survival, proliferation, and metastasis of cancer cells. The mechanism by which mitochondrial metabolism regulates mROS levels to support cancer cells is not fully understood. To address this, we conducted a metabolism-focused CRISPR-Cas9 genetic screen and uncovered that loss of genes encoding subunits of mitochondrial complex I was deleterious in the presence of the mitochondria-targeted antioxidant mito-vitamin E (MVE). Genetic or pharmacologic inhibition of mitochondrial complex I in combination with the mitochondria-targeted antioxidants, MVE or MitoTEMPO, induced a robust integrated stress response (ISR) and markedly diminished cell survival and proliferation in vitro. This was not observed following inhibition of mitochondrial complex III. Administration of MitoTEMPO in combination with the mitochondrial complex I inhibitor phenformin decreased the leukemic burden in a mouse model of T cell acute lymphoblastic leukemia. Thus, mitochondrial complex I is a dominant metabolic determinant of mROS-dependent cellular fitness.

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    11/03/20 | Cell types and neuronal circuitry underlying female aggression in .
    Schretter CE, Aso Y, Robie AA, Dreher M, Dolan M, Chen N, Ito M, Yang T, Parekh R, Branson KM, Rubin GM
    eLife. 2020 Nov 03;9:. doi: 10.7554/eLife.58942

    Aggressive social interactions are used to compete for limited resources and are regulated by complex sensory cues and the organism's internal state. While both sexes exhibit aggression, its neuronal underpinnings are understudied in females. Here, we identify a population of sexually dimorphic aIPg neurons in the adult central brain whose optogenetic activation increased, and genetic inactivation reduced, female aggression. Analysis of GAL4 lines identified in an unbiased screen for increased female chasing behavior revealed the involvement of another sexually dimorphic neuron, pC1d, and implicated aIPg and pC1d neurons as core nodes regulating female aggression. Connectomic analysis demonstrated that aIPg neurons and pC1d are interconnected and suggest that aIPg neurons may exert part of their effect by gating the flow of visual information to descending neurons. Our work reveals important regulatory components of the neuronal circuitry that underlies female aggressive social interactions and provides tools for their manipulation.

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    11/01/20 | A community for Black chemists.
    Beyene AG, Panescu P
    Nature Chemistry. 2020 Nov 01;12(11):988-989. doi: 10.1038/s41557-020-00572-3
    10/29/20 | The Statistical Structure of the Hippocampal Code for Space as a Function of Time, Context, and Value.
    Lee JS, Briguglio JJ, Cohen JD, Romani S, Lee AK
    Cell. 2020 Oct 29;183(3):620-35. doi: 10.1016/j.cell.2020.09.024

    Hippocampal activity represents many behaviorally important variables, including context, an animal's location within a given environmental context, time, and reward. Using longitudinal calcium imaging in mice, multiple large virtual environments, and differing reward contingencies, we derived a unified probabilistic model of CA1 representations centered on a single feature-the field propensity. Each cell's propensity governs how many place fields it has per unit space, predicts its reward-related activity, and is preserved across distinct environments and over months. Propensity is broadly distributed-with many low, and some very high, propensity cells-and thus strongly shapes hippocampal representations. This results in a range of spatial codes, from sparse to dense. Propensity varied ∼10-fold between adjacent cells in salt-and-pepper fashion, indicating substantial functional differences within a presumed cell type. Intracellular recordings linked propensity to cell excitability. The stability of each cell's propensity across conditions suggests this fundamental property has anatomical, transcriptional, and/or developmental origins.

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    10/23/20 | A post-invasion role for type III effector TarP in modulating the dynamics and organization of host cell focal adhesions.
    Pedrosa AT, Murphy KN, Nogueira AT, Brinkworth AJ, Thwaites TR, Aaron J, Chew T, Carabeo RA
    Journal of Biological Chemistry. 2020 Oct 23;295(43):14763-14779. doi: 10.1074/jbc.RA120.015219

    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.

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    Cardona LabZlatic Lab
    10/20/20 | Comparative Connectomics Reveals How Partner Identity, Location, and Activity Specify Synaptic Connectivity in Drosophila.
    Valdes-Aleman J, Fetter RD, Sales EC, Heckman EL, Venkatasubramanian L, Doe CQ, Landgraf M, Cardona A, Zlatic M
    Neuron. 2020 Oct 20:. doi: 10.1016/j.neuron.2020.10.004

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

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