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1817 Janelia Publications

Showing 11-20 of 1817 results
10/01/20 | A genetically defined compartmentalized striatal direct pathway for negative reinforcement.
Xiao X, Deng H, Furlan A, Yang T, Zhang X, Hwang G, Tucciarone J, Wu P, He M, Palaniswamy R, Ramakrishnan C, Ritola K, Hantman A, Deisseroth K, Osten P, Huang ZJ, Li B
Cell. 2020 Oct 1;181(1):211. doi: 10.1016/j.cell.2020.08.032

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

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09/30/20 | Structural insight into the ATP-driven exporter of virulent peptide toxins.
Zeytuni N, Dickey SW, Hu J, Chou HT, Worrall LJ, Alexander JA, Carlson ML, Nosella M, Duong F, Yu Z, Otto M, Strynadka NC
Science Advances. 2020 Sep 30;6(40):. doi: 10.1126/sciadv.abb8219

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'-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.

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09/23/20 | Chromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin.
Miron E, Oldenkamp R, Brown JM, Pinto DM, Xu CS, Faria AR, Shaban HA, Rhodes JD, Innocent C, de Ornellas S, Hess HF, Buckle V, Schermelleh L
Science Advances. 2020 Sep 23;6(39):. doi: 10.1126/sciadv.aba8811

Three-dimensional (3D) chromatin organization plays a key role in regulating mammalian genome function; however, many of its physical features at the single-cell level remain underexplored. Here, we use live- and fixed-cell 3D super-resolution and scanning electron microscopy to analyze structural and functional nuclear organization in somatic cells. We identify chains of interlinked ~200- to 300-nm-wide chromatin domains (CDs) composed of aggregated nucleosomes that can overlap with individual topologically associating domains and are distinct from a surrounding RNA-populated interchromatin compartment. High-content mapping uncovers confinement of cohesin and active histone modifications to surfaces and enrichment of repressive modifications toward the core of CDs in both hetero- and euchromatic regions. This nanoscale functional topography is temporarily relaxed in postreplicative chromatin but remarkably persists after ablation of cohesin. Our findings establish CDs as physical and functional modules of mesoscale genome organization.

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09/17/20 | Exploring internal state-coding across the rodent brain.
Sternson SM
Current Opinion in Neurobiology. 2020 Sep 17;65:20-26. doi: 10.1016/j.conb.2020.08.009

The influence of peripheral physiology on goal-directed behavior involves specialized interoceptive sensory neurons that signal internal state to the brain. Here, we review recent progress to examine the impact of these specialized cell types on neurons and circuits throughout the central nervous system. These new approaches are important for understanding how the needs of the body interact and guide goal-directed behaviors.

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09/17/20 | Hindbrain double-negative feedback mediates palatability-guided food and water consumption.
Gong R, Xu S, Hermundstad A, Yu Y, Sternson SM
Cell. 2020 Sep 17;182(6):1589-1605. doi: 10.1016/j.cell.2020.07.031

Hunger and thirst have distinct goals but control similar ingestive behaviors, and little is known about neural processes that are shared between these behavioral states. We identify glutamatergic neurons in the peri-locus coeruleus (periLC neurons) as a polysynaptic convergence node from separate energy-sensitive and hydration-sensitive cell populations. We develop methods for stable hindbrain calcium imaging in free-moving mice, which show that periLC neurons are tuned to ingestive behaviors and respond similarly to food or water consumption. PeriLC neurons are scalably inhibited by palatability and homeostatic need during consumption. Inhibition of periLC neurons is rewarding and increases consumption by enhancing palatability and prolonging ingestion duration. These properties comprise a double-negative feedback relationship that sustains food or water consumption without affecting food- or water-seeking. PeriLC neurons are a hub between hunger and thirst that specifically controls motivation for food and water ingestion, which is a factor that contributes to hedonic overeating and obesity.

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09/17/20 | The mind of a mouse.
Abbott LF, Bock DD, Callaway EM, Denk W, Dulac C, Fairhall AL, Fiete I, Harris KM, Helmstaedter M, Jain V, Kasthuri N, LeCun Y, Lichtman JW, Littlewood PB, Luo L, Maunsell JH, Reid RC, Rosen BR, Rubin GM, Sejnowski TJ, Seung HS, Svoboda K, Tank DW, Tsao D, Van Essen DC
Cell. 2020 Sep 17;182(6):1372-1376. doi: 10.1016/j.cell.2020.08.010

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

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09/15/20 | A comparison of neuronal population dynamics measured with calcium imaging and electrophysiology.
Wei Z, Lin B, Chen T, Daie K, Svoboda K, Druckmann S
PLoS Computational Biology. 2020 Sep 15;16(9):e1008198. doi: 10.1371/journal.pcbi.1008198

Calcium imaging with fluorescent protein sensors is widely used to record activity in neuronal populations. The transform between neural activity and calcium-related fluorescence involves nonlinearities and low-pass filtering, but the effects of the transformation on analyses of neural populations are not well understood. We compared neuronal spikes and fluorescence in matched neural populations in behaving mice. We report multiple discrepancies between analyses performed on the two types of data, including changes in single-neuron selectivity and population decoding. These were only partially resolved by spike inference algorithms applied to fluorescence. To model the relation between spiking and fluorescence we simultaneously recorded spikes and fluorescence from individual neurons. Using these recordings we developed a model transforming spike trains to synthetic-imaging data. The model recapitulated the differences in analyses. Our analysis highlights challenges in relating electrophysiology and imaging data, and suggests forward modeling as an effective way to understand differences between these data.

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09/15/20 | Erasable labeling of neuronal activity using a reversible calcium marker.
Sha F, Abdelfattah AS, Patel R, Schreiter ER
eLife. 2020 Sep 15;9:. doi: 10.7554/eLife.57249

Understanding how the brain encodes and processes information requires the recording of neural activity that underlies different behaviors. Recent efforts in fluorescent protein engineering have succeeded in developing powerful tools for visualizing neural activity, in general by coupling neural activity to different properties of a fluorescent protein scaffold. Here, we take advantage of a previously unexploited class of reversibly switchable fluorescent proteins to engineer a new type of calcium sensor. We introduce rsCaMPARI, a genetically encoded calcium marker engineered from a reversibly switchable fluorescent protein that enables spatiotemporally precise marking, erasing, and remarking of active neuron populations under brief, user-defined time windows of light exposure. rsCaMPARI photoswitching kinetics are modulated by calcium concentration when illuminating with blue light, and the fluorescence can be reset with violet light. We demonstrate the utility of rsCaMPARI for marking and remarking active neuron populations in freely swimming zebrafish.

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09/09/20 | A systematic nomenclature for the Drosophila ventral nerve cord.
Court R, Namiki S, Armstrong JD, Borner J, Card G, Costa M, Dickinson M, Duch C, Korff W, Mann R, Merritt D, Murphey RK, Seeds AM, Shirangi T, Simpson JH, Truman JW, Tuthill JC, Williams DW, Shepherd D
Neuron. 2020 Sep 14;107(6):1071-79. doi: 10.1016/j.neuron.2020.08.005

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.

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09/14/20 | Dense neuronal reconstruction through X-ray holographic nano-tomography.
Kuan AT, Phelps JS, Thomas LA, Nguyen TM, Han J, Chen C, Azevedo AW, Tuthill JC, Funke J, Cloetens P, Pacureanu A, Lee WA
Nature Neuroscience. 2020 Sep 14:. doi: 10.1038/s41593-020-0704-9

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.

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