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17 Janelia Publications

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    Cardona LabTruman LabZlatic Lab
    01/29/19 | Neural substrates of Drosophila larval anemotaxis.
    Jovanic T, Winding M, Cardona A, Truman JW, Gershow M, Zlatic M
    Current Biology : CB. 2019 Jan 29;29(4):554-66. doi: 10.1016/j.cub.2019.01.009

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

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    01/25/19 | Probing nicotinic acetylcholine receptor function in mouse brain slices via laser flash photolysis of photoactivatable nicotine.
    Arvin MC, Wokosin DL, Banala S, Lavis LD, Drenan RM
    Journal of Visualized Experiments : JoVE. 2019 Jan 25(143):. doi: 10.3791/58873

    Acetylcholine (ACh) acts through receptors to modulate a variety of neuronal processes, but it has been challenging to link ACh receptor function with subcellular location within cells where this function is carried out. To study the subcellular location of nicotinic ACh receptors (nAChRs) in native brain tissue, an optical method was developed for precise release of nicotine at discrete locations near neuronal membranes during electrophysiological recordings. Patch-clamped neurons in brain slices are filled with dye to visualize their morphology during 2-photon laser scanning microscopy, and nicotine uncaging is executed with a light flash by focusing a 405 nm laser beam near one or more cellular membranes. Cellular current deflections are measured, and a high-resolution three-dimensional (3D) image of the recorded neuron is made to allow reconciliation of nAChR responses with cellular morphology. This method allows for detailed analysis of nAChR functional distribution in complex tissue preparations, promising to enhance the understanding of cholinergic neurotransmission.

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    01/21/19 | A genetically encoded near-infrared fluorescent calcium ion indicator.
    Qian Y, Piatkevich KD, Mc Larney B, Abdelfattah AS, Mehta S, Murdock MH, Gottschalk S, Molina RS, Zhang W, Chen Y, Wu J, Drobizhev M, Hughes TE, Zhang J, Schreiter ER, Shoham S, Razansky D, Boyden ES, Campbell RE
    Nature Methods. 2019 Jan 21;16(2):171-4. doi: 10.1038/s41592-018-0294-6

    We report an intensiometric, near-infrared fluorescent, genetically encoded calcium ion (Ca) indicator (GECI) with excitation and emission maxima at 678 and 704 nm, respectively. This GECI, designated NIR-GECO1, enables imaging of Ca transients in cultured mammalian cells and brain tissue with sensitivity comparable to that of currently available visible-wavelength GECIs. We demonstrate that NIR-GECO1 opens up new vistas for multicolor Ca imaging in combination with other optogenetic indicators and actuators.

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    01/21/19 | Internal models in control, biology and neuroscience.
    Huang J, Isidori A, Marconi L, Mischiati M, Sontag E, Wonham WM
    2018 IEEE Conference on Decision and Control (CDC). 2019 Jan 21:. doi: 10.1109/CDC.2018.8619624

    This tutorial paper deals with the Internal Model Principle (IMP) from different perspectives. The goal is to start from the principle as introduced and commonly used in the control theory and then enlarge the vision to other fields where “internal models” play a role. The biology and neuroscience fields are specifically targeted in the paper. The paper ends by presenting an “abstract” theory of IMP applicable to a large class of systems.

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    01/18/19 | Cortical column and whole-brain imaging with molecular contrast and nanoscale resolution.
    Gao R, Asano SM, Upadhyayula S, Pisarev I, Milkie DE, Liu T, Singh V, Graves AR, Huynh GH, Zhao Y, Bogovic JA, Colonell J, Ott CM, Zugates CT, Tappan S, Rodriguez A, Mosaliganti KR, Sheu S, Pasolli HA, et al
    Science (New York, N.Y.). 2019 Jan 18;363(6424):eaau8302. doi: 10.1126/science.aau8302

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

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    Gonen Lab
    01/18/19 | Structural basis for substrate binding and specificity of a sodium-alanine symporter AgcS.
    Ma J, Lei H, Reyes FE, Sanchez-Martinez S, Sarhan MF, Hattne J, Gonen T
    Proceedings of the National Academy of Sciences of the United States of America. 2019 Jan 18;116(6):2086-90. doi: 10.1073/pnas.1806206116

    The amino acid, polyamine, and organocation (APC) superfamily is the second largest superfamily of membrane proteins forming secondary transporters that move a range of organic molecules across the cell membrane. Each transporter in the APC superfamily is specific for a unique subset of substrates, even if they possess a similar structural fold. The mechanism of substrate selectivity remains, by and large, elusive. Here, we report two crystal structures of an APC member from , the alanine or glycine:cation symporter (AgcS), with l- or d-alanine bound. Structural analysis combined with site-directed mutagenesis and functional studies inform on substrate binding, specificity, and modulation of the AgcS family and reveal key structural features that allow this transporter to accommodate glycine and alanine while excluding all other amino acids. Mutation of key residues in the substrate binding site expand the selectivity to include valine and leucine. These studies provide initial insights into substrate selectivity in AgcS symporters.

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    01/17/19 | NWB:N 2.0: An accessible data standard for neurophysiology.
    Rubel O, Tritt A, Dichter B, Braun T, Cain N, Clack NG, Davidson TJ, Dougherty M, Fillion-Rubin J, Graddis N, Grauer M, Kiggins JT, Niu L, Ozturk D, Schroeder W, Soltesz I, Sommer FT, Svoboda K, Ng L, et al
    bioRxiv. 2019 Jan 17:. doi: 10.1101/523035

    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.

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    Bock Lab
    01/16/19 | Regulation of modulatory cell activity across olfactory structures in Drosophila melanogaster.
    Zhang X, Coates K, Dacks A, Gunay C, Lauritzen JS, Li F, Calle-Schuler SA, Bock DD, Gaudry Q
    bioRxiv. 2019 Jan 16:. doi: 10.1101/522177

    All centralized nervous systems possess modulatory neurons that arborize broadly across multiple brain regions. Such modulatory systems are critical for proper sensory, motor, and cognitive processing. How single modulatory neurons integrate into circuits within their target destination remains largely unexplored due to difficulties in both labeling individual cells and imaging across distal parts of the CNS. Here, we take advantage of an identified modulatory neuron in Drosophila that arborizes in multiple olfactory neuropils. We demonstrate that this serotonergic neuron has opposing odor responses in its neurites of the antennal lobe and lateral horn, first and second order olfactory neuropils respectively. Specifically, processes of this neuron in the antennal lobe have responses that are inhibitory and odor-independent, while lateral horn responses are excitatory and odor-specific. The results show that widespread modulatory neurons may not function purely as integrate-and-fire cells, but rather their transmitter release is locally regulated based on neuropil. As nearly all vertebrate and invertebrate neurons are subject to synaptic inputs along their dendro-axonic axis, it is likely that our findings generalize across phylogeny and other broadly-projecting modulatory systems.

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    01/15/19 | An orderly single-trial organization of population dynamics in premotor cortex predicts behavioral variability.
    Wei Z, Inagaki H, Li N, Svoboda K, Druckmann S
    Nature Communications. 2019 Jan 15;10(1):216. doi: 10.1038/s41467-018-08141-6

    Animals are not simple input-output machines. Their responses to even very similar stimuli are variable. A key, long-standing question in neuroscience is to understand the neural correlates of such behavioral variability. To reveal these correlates, behavior and neural population activity must be related to one another on single trials. Such analysis is challenging due to the dynamical nature of brain function (e.g., in decision making), heterogeneity across neurons and limited sampling of the relevant neural population. By analyzing population recordings from mouse frontal cortex in perceptual decision-making tasks, we show that an analysis approach tailored to the coarse grain features of the dynamics is able to reveal previously unrecognized structure in the organization of population activity. This structure is similar on error and correct trials, suggesting dynamics that may be constrained by the underlying circuitry, is able to predict multiple aspects of behavioral variability and reveals long time-scale modulation of population activity.

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    01/15/19 | Characterization of neurite dystrophy after trauma by high speed structured illumination microscopy and lattice light sheet microscopy.
    Phillips JK, Sherman SA, Cotton KY, Heddleston JM, Taylor AB, Finan JD
    Journal of Neuroscience Methods. 2019 Jan 15;312:154-61. doi: 10.1016/j.jneumeth.2018.12.005

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

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

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

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

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

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