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7 Janelia Publications

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    12/19/13 | The structure and evolution of cis-regulatory regions: the shavenbaby story.
    Stern DL, Frankel N
    Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 2013 Dec 19;368(1632):20130028. doi: 10.1098/rstb.2013.0028

    In this paper, we provide a historical account of the contribution of a single line of research to our current understanding of the structure of cis-regulatory regions and the genetic basis for morphological evolution. We revisit the experiments that shed light on the evolution of larval cuticular patterns within the genus Drosophila and the evolution and structure of the shavenbaby gene. We describe the experiments that led to the discovery that multiple genetic changes in the cis-regulatory region of shavenbaby caused the loss of dorsal cuticular hairs (quaternary trichomes) in first instar larvae of Drosophila sechellia. We also discuss the experiments that showed that the convergent loss of quaternary trichomes in D. sechellia and Drosophila ezoana was generated by parallel genetic changes in orthologous enhancers of shavenbaby. We discuss the observation that multiple shavenbaby enhancers drive overlapping patterns of expression in the embryo and that these apparently redundant enhancers ensure robust shavenbaby expression and trichome morphogenesis under stressful conditions. All together, these data, collected over 13 years, provide a fundamental case study in the fields of gene regulation and morphological evolution, and highlight the importance of prolonged, detailed studies of single genes.

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    Spruston LabMenon Lab
    12/18/13 | Balanced synaptic impact via distance-dependent synapse distribution and complementary expression of AMPARs and NMDARs in hippocampal dendrites.
    Menon V, Musial TF, Liu A, Katz Y, Kath WL, Spruston N, Nicholson DA
    Neuron. 2013 Dec 18;80:1451-63. doi: 10.1016/j.neuron.2013.09.027

    Neuronal computation involves the integration of synaptic inputs that are often distributed over expansive dendritic trees, suggesting the need for compensatory mechanisms that enable spatially disparate synapses to influence neuronal output. In hippocampal CA1 pyramidal neurons, such mechanisms have indeed been reported, which normalize either the ability of distributed synapses to drive action potential initiation in the axon or their ability to drive dendritic spiking locally. Here we report that these mechanisms can coexist, through an elegant combination of distance-dependent regulation of synapse number and synaptic expression of AMPA and NMDA receptors. Together, these complementary gradients allow individual dendrites in both the apical and basal dendritic trees of hippocampal neurons to operate as facile computational subunits capable of supporting both global integration in the soma/axon and local integration in the dendrite.

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    Magee Lab
    12/18/13 | Variable dendritic integration in hippocampal CA3 pyramidal neurons.
    Makara JK, Magee JC
    Neuron. 2013 Dec 18;80(6):1438-50. doi: 10.1016/j.neuron.2013.10.033

    The hippocampal CA3 region is essential for pattern completion and generation of sharp-wave ripples. During these operations, coordinated activation of ensembles of CA3 pyramidal neurons produces spatiotemporally structured input patterns arriving onto dendrites of recurrently connected CA3 neurons. To understand how such input patterns are translated into specific output patterns, we characterized dendritic integration in CA3 pyramidal cells using two-photon imaging and glutamate uncaging. We found that thin dendrites of CA3 pyramidal neurons integrate synchronous synaptic input in a highly supralinear fashion. The amplification was primarily mediated by NMDA receptor activation and was present over a relatively broad range of spatiotemporal input patterns. The decay of voltage responses, temporal summation, and action potential output was regulated in a compartmentalized fashion mainly by a G-protein-activated inwardly rectifying K(+) current. Our results suggest that plastic dendritic integrative mechanisms may support ensemble behavior in pyramidal neurons of the hippocampal circuitry.

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    12/07/13 | A computational model of flow between the microscale respiratory structures of fish gills.
    Strother JA
    Journal of Theoretical Biology. 2013 Dec 7;338:23-40. doi: 10.1016/j.jtbi.2013.08.015

    The gills of most teleost fishes are covered by plate-like structures, the secondary lamellae, that provide the bulk of the respiratory surface area. Water passing over the secondary lamellae exchanges gases with blood passing through the secondary lamellae, forming a system that has served as a classic model of counter-current exchange. In this study, a computational model of flow around the secondary lamellae is used to examine the hydrodynamic consequences of changes to the lamellar morphology. Consistent with previous studies, the interlamellar distance is found to strongly affect the hydrodynamic resistance of the gills. However, the presence of a small gap between the tips of the secondary lamellae is found to have a similarly strong effect on the hydrodynamic resistance and flow patterns within the gills. The results from this model have been generally formulated, allowing the calculation of the hydrodynamic resistance for measured morphometric parameters. These results provide a new basis for comparing theoretical predictions of the gill resistance with measured values, and provide a general model for examining the diversity gill morphologies observed in teleost fishes.

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    Sternson Lab
    12/05/13 | Parallel, redundant circuit organization for homeostatic control of feeding behavior.
    Betley JN, Cao ZF, Ritola KD, Sternson SM
    Cell. 2013 Dec 5;155(6):1337-50. doi: 10.1016/j.cell.2013.11.002

    Neural circuits for essential natural behaviors are shaped by selective pressure to coordinate reliable execution of flexible goal-directed actions. However, the structural and functional organization of survival-oriented circuits is poorly understood due to exceptionally complex neuroanatomy. This is exemplified by AGRP neurons, which are a molecularly defined population that is sufficient to rapidly coordinate voracious food seeking and consumption behaviors. Here, we use cell-type-specific techniques for neural circuit manipulation and projection-specific anatomical analysis to examine the organization of this critical homeostatic circuit that regulates feeding. We show that AGRP neuronal circuits use a segregated, parallel, and redundant output configuration. AGRP neuron axon projections that target different brain regions originate from distinct subpopulations, several of which are sufficient to independently evoke feeding. The concerted anatomical and functional analysis of AGRP neuron projection populations reveals a constellation of core forebrain nodes, which are part of an extended circuit that mediates feeding behavior.

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    Druckmann Lab
    12/01/13 | Mapping mammalian synaptic connectivity.
    Yook C, Druckmann S, Kim J
    Cellular and Molecular Life Sciences: CMLS. 2013 Dec;70(24):4747-57. doi: 10.1007/s00018-013-1417-y

    Mapping mammalian synaptic connectivity has long been an important goal of neuroscientists since it is considered crucial for explaining human perception and behavior. Yet, despite enormous efforts, the overwhelming complexity of the neural circuitry and the lack of appropriate techniques to unravel it have limited the success of efforts to map connectivity. However, recent technological advances designed to overcome the limitations of conventional methods for connectivity mapping may bring about a turning point. Here, we address the promises and pitfalls of these new mapping technologies.

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    Grigorieff Lab
    12/01/13 | Quantitative characterization of electron detectors for transmission electron microscopy.
    Ruskin RS, Yu Z, Grigorieff N
    Journal of Structural Biology. 2013 Dec;184(3):385-93. doi: 10.1016/j.jsb.2013.10.016

    A new generation of direct electron detectors for transmission electron microscopy (TEM) promises significant improvement over previous detectors in terms of their modulation transfer function (MTF) and detective quantum efficiency (DQE). However, the performance of these new detectors needs to be carefully monitored in order to optimize imaging conditions and check for degradation over time. We have developed an easy-to-use software tool, FindDQE, to measure MTF and DQE of electron detectors using images of a microscope’s built-in beam stop. Using this software, we have determined the DQE curves of four direct electron detectors currently available: the Gatan K2 Summit, the FEI Falcon I and II, and the Direct Electron DE-12, under a variety of total dose and dose rate conditions. We have additionally measured the curves for the Gatan US4000 and TVIPS TemCam-F416 scintillator-based cameras. We compare the results from our new method with published curves.

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