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187 Janelia Publications

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    05/17/17 | A map of anticipatory activity in mouse motor cortex.
    Chen T, Li N, Daie K, Svoboda K
    Neuron. 2017 May 17;94(4):866-879.e4. doi: 10.1016/j.neuron.2017.05.005

    Activity in the mouse anterior lateral motor cortex (ALM) instructs directional movements, often seconds before movement initiation. It is unknown whether this preparatory activity is localized to ALM or widely distributed within motor cortex. Here we imaged activity across motor cortex while mice performed a whisker-based object localization task with a delayed, directional licking response. During tactile sensation and the delay epoch, object location was represented in motor cortex areas that are medial and posterior relative to ALM, including vibrissal motor cortex. Preparatory activity appeared first in deep layers of ALM, seconds before the behavioral response, and remained localized to ALM until the behavioral response. Later, widely distributed neurons represented the outcome of the trial. Cortical area was more predictive of neuronal selectivity than laminar location or axonal projection target. Motor cortex therefore represents sensory, motor, and outcome information in a spatially organized manner.

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    05/17/17 | Integrating Results across Methodologies Is Essential for Producing Robust Neuronal Taxonomies.
    Cembrowski MS, Spruston N
    Neuron. 2017 May 17;94(4):747-751.e1. doi: 10.1016/j.neuron.2017.04.023

    Elucidating the diversity and spatial organization of cell types in the brain is an essential goal of neuroscience, with many emerging technologies helping to advance this endeavor. Using a new in situ hybridization method that can measure the expression of hundreds of genes in a given mouse brain section (amplified seqFISH), Shah et al. (2016) describe a spatial organization of hippocampal cell types that differs from previous reports. In seeking to understand this discrepancy, we find that many of the barcoded genes used by seqFISH to characterize this spatial organization, when cross-validated by other sensitive methodologies, exhibit negligible expression in the hippocampus. Additionally, the results of Shah et al. (2016) do not recapitulate canonical cellular hierarchies and improperly classify major neuronal cell types. We suggest that, when describing the spatial organization of brain regions, cross-validation using multiple techniques should be used to yield robust and informative cellular classification. This Matters Arising paper is in response to Shah et al. (2016), published in Neuron. See also the response by Shah et al. (2017), published in this issue.

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    05/17/17 | Unraveling cell-to-cell signaling networks with chemical biology.
    Gartner ZJ, Prescher JA, Lavis LD
    Nature Chemical Biology. 2017 May 17;13(6):564-568. doi: 10.1038/nchembio.2391
    05/13/17 | Enhanced FIB-SEM systems for large-volume 3D imaging.
    Xu CS, Hayworth KJ, Lu Z, Grob P, Hassan AM, García-Cerdán JG, Niyogi KK, Nogales E, Weinberg RJ, Hess HF
    eLife. 2017 May 13;6:. doi: 10.7554/eLife.25916

    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) µm(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.

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    05/12/17 | CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface.
    Liu Y, Pan J, Jenni S, Raymond DD, Caradonna T, Do KT, Schmidt AG, Harrison SC, Grigorieff N
    Journal of Molecular Biology. 2017 May 12;429(12):1829-39. doi: 10.1016/j.jmb.2017.05.011

    Structure-based vaccine design depends on extensive structural analyses of antigen-antibody complexes. Single-particle electron cryomicroscopy (cryoEM) can circumvent some of the problems of x-ray crystallography as a pipeline for obtaining the required structures. We have examined the potential of single-particle cryoEM for determining the structure of influenza-virus hemagglutinin (HA):single-chain Fv (scFv) complexes, by studying a complex we failed to crystallize in pursuing an extended project of the human immune response to influenza vaccines. The result shows that a combination of cryoEM and molecular modeling can yield details of the antigen:antibody interface, although small variation in the twist of the rod-like HA trimer limited the overall resolution to about 4.5Å. Comparison of principal 3D classes suggests ways to modify the HA trimer to overcome this limitation. A closely related antibody from the same donor did yield crystals when bound with the same HA, giving us an independent validation of the cryoEM results The two structures also augment our understanding of receptor-binding site recognition by antibodies that neutralize a wide range of influenza-virus variants.

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    05/12/17 | Visualizing dynamic microvillar search and stabilization during ligand detection by T cells.
    Cai E, Marchuk K, Beemiller P, Beppler C, Rubashkin MG, Weaver VM, Gérard A, Liu T, Chen B, Betzig E, Bartumeus F, Krummel MF
    Science (New York, N.Y.). 2017 May 12;356(6338):. doi: 10.1126/science.aal3118

    During immune surveillance, T cells survey the surface of antigen-presenting cells. In searching for peptide-loaded major histocompatibility complexes (pMHCs), they must solve a classic trade-off between speed and sensitivity. It has long been supposed that microvilli on T cells act as sensory organs to enable search, but their strategy has been unknown. We used lattice light-sheet and quantum dot-enabled synaptic contact mapping microscopy to show that anomalous diffusion and fractal organization of microvilli survey the majority of opposing surfaces within 1 minute. Individual dwell times were long enough to discriminate pMHC half-lives and T cell receptor (TCR) accumulation selectively stabilized microvilli. Stabilization was independent of tyrosine kinase signaling and the actin cytoskeleton, suggesting selection for avid TCR microclusters. This work defines the efficient cellular search process against which ligand detection takes place.

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    05/09/17 | How to make a worm twitch.
    Keller PJ
    Biophysical Journal. 2017 May 09;112(9):1737-1738. doi: 10.1016/j.bpj.2017.03.035
    05/09/17 | Representations of Novelty and Familiarity in a Mushroom Body Compartment.
    Hattori D, Aso Y, Swartz KJ, Rubin GM, Abbott LF, Axel R
    Cell. 2017 May 09;169(5):956-69. doi: 10.1016/j.cell.2017.04.028

    Animals exhibit a behavioral response to novel sensory stimuli about which they have no prior knowledge. We have examined the neural and behavioral correlates of novelty and familiarity in the olfactory system of Drosophila. Novel odors elicit strong activity in output neurons (MBONs) of the α'3 compartment of the mushroom body that is rapidly suppressed upon repeated exposure to the same odor. This transition in neural activity upon familiarization requires odor-evoked activity in the dopaminergic neuron innervating this compartment. Moreover, exposure of a fly to novel odors evokes an alerting response that can also be elicited by optogenetic activation of α'3 MBONs. Silencing these MBONs eliminates the alerting behavior. These data suggest that the α'3 compartment plays a causal role in the behavioral response to novel and familiar stimuli as a consequence of dopamine-mediated plasticity at the Kenyon cell-MBONα'3 synapse.

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    Zlatic LabCardona Lab
    05/09/17 | Semiparametric spectral modeling of the Drosophila connectome.
    Priebe CE, Park Y, Tang M, Athreya A, Lyzinski V, Vogelstein JT, Qin Y, Cocanougher B, Eichler K, Zlatic M, Cardona A
    arXiv. 2017 May 9:1705.03297

    We present semiparametric spectral modeling of the complete larval Drosophila mushroom body connectome. Motivated by a thorough exploratory data analysis of the network via Gaussian mixture modeling (GMM) in the adjacency spectral embedding (ASE) representation space, we introduce the latent structure model (LSM) for network modeling and inference. LSM is a generalization of the stochastic block model (SBM) and a special case of the random dot product graph (RDPG) latent position model, and is amenable to semiparametric GMM in the ASE representation space. The resulting connectome code derived via semiparametric GMM composed with ASE captures latent connectome structure and elucidates biologically relevant neuronal properties.

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    05/05/17 | Detachable glass microelectrodes for recording action potentials in active moving organs.
    Barbic M, Moreno A, Harris TD, Kay MW
    American Journal of Physiology. Heart and Circulatory Physiology. 2017 May 05;312(6):H1248-59. doi: 10.1152/ajpheart.00741.2016

    We describe new detachable floating glass micropipette electrode devices that provide targeted action potential recordings in active moving organs without requiring constant mechanical constraint or pharmacological inhibition of tissue motion. The technology is based on the concept of a glass micropipette electrode that is held firmly during cell targeting and intracellular insertion, after which a 100µg glass microelectrode, a "microdevice", is gently released to remain within the moving organ. The microdevices provide long-term recordings of action potentials, even during millimeter-scale movement of tissue in which the device is embedded. We demonstrate two different glass micropipette electrode holding and detachment designs appropriate for the heart (sharp glass microdevices for cardiac myocytes in rats, guinea pigs and humans) and the brain (patch glass microdevices for neurons in rats). We explain how microdevices enable measurements of multiple cells within a moving organ that are typically difficult with other technologies. Using sharp microdevices, action potential duration (APD) was monitored continuously for 15 minutes in unconstrained perfused hearts during global ischemia-reperfusion, providing beat-to-beat measurements of changes in APD. Action potentials from neurons in the hippocampus of anaesthetized rats were measured with patch microdevices, which provided stable base potentials during long-term recordings. Our results demonstrate that detachable microdevices are an elegant and robust tool to record electrical activity with high temporal resolution and cellular level localization without disturbing the physiological working conditions of the organ.

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