Main Menu (Mobile)- Block

Main Menu - Block

janelia7_blocks-janelia7_fake_breadcrumb | block
Koyama Lab / Publications
custom | custom

Filter

facetapi-Q2b17qCsTdECvJIqZJgYMaGsr8vANl1n | block

Associated Lab

facetapi-W9JlIB1X0bjs93n1Alu3wHJQTTgDCBGe | block
facetapi-PV5lg7xuz68EAY8eakJzrcmwtdGEnxR0 | block
facetapi-021SKYQnqXW6ODq5W5dPAFEDBaEJubhN | block
general_search_page-panel_pane_1 | views_panes

252 Publications

Showing 31-40 of 252 results
Your Criteria:
    Sternson Lab
    11/04/15 | Applying the brakes: when to stop eating.
    Betley JN, Sternson SM
    Neuron. 2015 Nov 4;88(3):440-1. doi: 10.1016/j.neuron.2015.10.034

    The nucleus accumbens regulates consummatory behaviors, such as eating. In this issue of Neuron, O'Connor et al. (2015) identify dopamine receptor 1-expressing neurons that project to the lateral hypothalamus as mediating rapid control over feeding behavior.

    View Publication Page
    01/08/15 | Artificial metalloenzymes derived from three-helix bundles.
    Tebo AG, Pecoraro VL
    Current Opinion in Chemical Biology. 01/2015;25C:65 – 70. doi: 10.1016/j.cbpa.2014.12.034

    Three-helix bundles and coiled-coil motifs are well-established de novo designed scaffolds that have been investigated for their metal-binding and catalytic properties. Satisfaction of the primary coordination sphere for a given metal is sufficient to introduce catalytic activity and a given structure may catalyze different reactions dependent on the identity of the incorporated metal. Here we describe recent contributions in the de novo design of metalloenzymes based on three-helix bundles and coiled-coil motifs, focusing on non-heme systems for hydrolytic and redox chemistry.

    View Publication Page
    04/07/15 | Asymmetric formation of coated pits on dorsal and ventral surfaces at the leading edge of motile cells and on protrusions of immobile cells.
    Kural C, Akatay AA, Gaudin R, Chen B, Legant WR, Betzig E, Kirchhausen T
    Molecular Biology of the Cell. 2015 Apr 7;26(11):2044-53. doi: 10.1091/mbc.E15-01-0055

    Clathrin/AP2-coated vesicles are the principal endocytic carriers originating at the plasma membrane. In experiments reported here, we have used spinning disk confocal and lattice light sheet microscopy to study the assembly dynamics of coated pits on the dorsal and ventral membranes of migrating U373 glioblastoma cells stably expressing AP2-EGFP and on lateral protrusions from immobile SUM159 breast carcinoma cells, gene edited to express AP2-EGFP. On U373 cells, coated pits initiated on the dorsal membrane at the front of the lamellipodium, as well as at the approximate boundary between the lamellipodium and lamella, and continued to grow as they were swept back toward the cell body; coated pits were absent from the corresponding ventral membrane. We observed a similar dorsal/ventral asymmetry on membrane protrusions from SUM159 cells. Stationary-coated pits formed and budded on the remainder of the dorsal and ventral surfaces of both types of cells. These observations support a previously proposed model that invokes net membrane deposition at the leading edge due to an imbalance between the endocytic and exocytic membrane flow at the front of a migrating cell.

    View Publication Page
    09/23/15 | Automated cerebellar lobule segmentation with application to cerebellar structural analysis in cerebellar disease.
    Yang Z, Ye C, Bogovic JA, Carass A, Jedynak BM, Ying SH, Prince JL
    NeuroImage. 2015 Sep 23;127:435-44. doi: 10.1016/j.neuroimage.2015.09.032

    The cerebellum plays an important role in both motor control and cognitive function. Cerebellar function is topographically organized and diseases that affect specific parts of the cerebellum are associated with specific patterns of symptoms. Accordingly, delineation and quantification of cerebellar sub-regions from magnetic resonance images are important in the study of cerebellar atrophy and associated functional losses. This paper describes an automated cerebellar lobule segmentation method based on a graph cut segmentation framework. Results from multi-atlas labeling and tissue classification contribute to the region terms in the graph cut energy function and boundary classification contributes to the boundary term in the energy function. A cerebellar parcellation is achieved by minimizing the energy function using the α-expansion technique. The proposed method was evaluated using a leave-one-out cross-validation on 15 subjects including both healthy controls and patients with cerebellar diseases. Based on reported Dice coefficients, the proposed method outperforms two state-of-the-art methods. The proposed method was then applied to 2(j) 77 subjects to study the region-specific cerebellar structural differences in three spinocerebellar ataxia (SCA) genetic subtypes. Quantitative analysis of the lobule volumes show distinct patterns of volume changes associated with different SCA subtypes consistent with known patterns of atrophy in these genetic subtypes.

    View Publication Page
    01/01/13 | Automated long-term tracking and social behavioural phenotyping of animal colonies within a semi-natural environment.
    Weissbrod A, Shapiro A, Vasserman G, Edry L, Dayan M, Yitzhaky A, Hertzberg L, Feinerman O, Kimchi T
    Nature Communications. 2013;4:2018. doi: 10.1038/ncomms3018

    Social behaviour has a key role in animal survival across species, ranging from insects to primates and humans. However, the biological mechanisms driving natural interactions between multiple animals, over long-term periods, are poorly studied and remain elusive. Rigorous and objective quantification of behavioural parameters within a group poses a major challenge as it requires simultaneous monitoring of the positions of several individuals and comprehensive consideration of many complex factors. Automatic tracking and phenotyping of interacting animals could thus overcome the limitations of manual tracking methods. Here we report a broadly applicable system that automatically tracks the locations of multiple, uniquely identified animals, such as mice, within a semi-natural setting. The system combines video and radio frequency identified tracking data to obtain detailed behavioural profiles of both individuals and groups. We demonstrate the usefulness of these data in characterizing individual phenotypes, interactions between pairs and the collective social organization of groups.

    View Publication Page
    Chklovskii LabFlyEM
    08/06/15 | Automatic adaptation to fast input changes in a time-invariant neural circuit.
    Bharioke A, Chklovskii DB
    PLoS Computational Biology. 2015 Aug 6;11(8):e1004315. doi: 10.1371/journal.pcbi.1004315
    Grigorieff Lab
    11/01/15 | Automatic estimation and correction of anisotropic magnification distortion in electron microscopes.
    Grant T, Grigorieff N
    Journal of Structural Biology. 2015 Nov;192(2):204-8. doi: 10.1016/j.jsb.2015.08.006

    We demonstrate a significant anisotropic magnification distortion, found on an FEI Titan Krios microscope and affecting magnifications commonly used for data acquisition on a Gatan K2 Summit detector. We describe a program (mag_distortion_estimate) to automatically estimate anisotropic magnification distortion from a set of images of a standard gold shadowed diffraction grating. We also describe a program (mag_distortion_correct) to correct for the estimated distortion in collected images. We demonstrate that the distortion present on the Titan Krios microscope limits the resolution of a set of rotavirus VP6 images to ∼7 Å, which increases to ∼3 Å following estimation and correction of the distortion. We also use a 70S ribosome sample to demonstrate that in addition to affecting resolution, magnification distortion can also interfere with the classification of heterogeneous data.

    View Publication Page
    Darshan Lab
    03/24/15 | Basal ganglia: songbird models
    Leblois A, Darshan R
    Encyclopedia of Computational Neuroscience:356-61

    Songbirds produce complex vocalizations, a behavior that depends on the ability of juveniles to imitate the song of an adult. Song learning relies on a specialized basal ganglia-thalamocortical loop. Several computational models have examined the role of this circuit in song learning, shedding light on the neurobiological mechanisms underlying sensorimotor learning.

    View Publication Page
    02/09/15 | Behavioral and biological effects of chronic S18986, a positive AMPA receptor modulator, during aging.
    Bloss EB, Hunter RG, Waters EM, Munoz C, Bernard K, McEwen BS
    Exp Neurol. 2008 Mar;210(1):109-17. doi: 10.1016/j.expneurol.2007.10.007

    AMPA receptors are a major subtype of ionotropic receptors that respond to glutamate. Positive allosteric modulators of AMPA receptors selectively enhance fast excitatory neurotransmission in the brain and increase overall neuronal excitability. In addition to enhancing cognitive performance, S18986 (Servier, France) and other AMPA receptor modulators have also been shown to be neuroprotective. A particularly relevant context for AMPAR modulator studies is during aging because of increased neuronal vulnerability. It is currently unknown if chronic AMPAR modulator treatment can alter the course of brain aging, a process characterized by impairment of cognitive function, reduced neuronal excitability, and increased inflammation in the brain. We examined the behavioral and some relevant CNS effects of chronic S18986 in rats from 14 to 18 months of age. Here we show that chronic, oral administration of S18986 increases locomotor activity and performance in a spatial memory task in aged rodents. In addition, chronic S18986 treatment retards the decline of forebrain cholinergic neurons by roughly 37% and midbrain dopaminergic neurons by as much as 43% during aging and attenuates the age-related increase in the expression of a microglial marker in the hippocampus. These results provide a framework for further studies of the potentially beneficial effects of AMPAR modulators on brain aging.

    View Publication Page
    05/14/15 | Behavioral responses to a repetitive visual threat stimulus express a persistent state of defensive arousal in Drosophila
    Gibson WT, Gonzalez CR, Fernandez C, Ramasamy L, Tabachnik T, Du RR, Felsen PD, Maire MM, Perona P, Anderson DJ
    Current Biology. 2015 May 14;25(11):1401-15. doi: 10.1016/j.cub.2015.03.058

    The neural circuit mechanisms underlying emotion states remain poorly understood. Drosophila offers powerful genetic approaches for dissecting neural circuit function, but whether flies exhibit emotion-like behaviors has not been clear. We recently proposed that model organisms may express internal states displaying “emotion primitives,” which are general characteristics common to different emotions, rather than specific anthropomorphic emotions such as “fear” or “anxiety.” These emotion primitives include scalability, persistence, valence, and generalization to multiple contexts. Here, we have applied this approach to determine whether flies’ defensive responses to moving overhead translational stimuli (“shadows”) are purely reflexive or may express underlying emotion states. We describe a new behavioral assay in which flies confined in an enclosed arena are repeatedly exposed to an overhead translational stimulus. Repetitive stimuli promoted graded (scalable) and persistent increases in locomotor velocity and hopping, and occasional freezing. The stimulus also dispersed feeding flies from a food resource, suggesting both negative valence and context generalization. Strikingly, there was a significant delay before the flies returned to the food following stimulus-induced dispersal, suggestive of a slowly decaying internal defensive state. The length of this delay was increased when more stimuli were delivered for initial dispersal. These responses can be mathematically modeled by assuming an internal state that behaves as a leaky integrator of stimulus exposure. Our results suggest that flies’ responses to repetitive visual threat stimuli express an internal state exhibiting canonical emotion primitives, possibly analogous to fear in mammals. The mechanistic basis of this state can now be investigated in a genetically tractable insect species.

    View Publication Page