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7 Janelia Publications

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    Chklovskii Lab
    07/28/09 | Maximization of the connectivity repertoire as a statistical principle governing the shapes of dendritic arbors.
    Wen Q, Stepanyants A, Elston GN, Grosberg AY, Chklovskii DB
    Proceedings of the National Academy of Sciences of the United States of America. 2009 Jul 28;106(30):12536-41. doi: 10.1371/journal.pcbi.1001066

    The shapes of dendritic arbors are fascinating and important, yet the principles underlying these complex and diverse structures remain unclear. Here, we analyzed basal dendritic arbors of 2,171 pyramidal neurons sampled from mammalian brains and discovered 3 statistical properties: the dendritic arbor size scales with the total dendritic length, the spatial correlation of dendritic branches within an arbor has a universal functional form, and small parts of an arbor are self-similar. We proposed that these properties result from maximizing the repertoire of possible connectivity patterns between dendrites and surrounding axons while keeping the cost of dendrites low. We solved this optimization problem by drawing an analogy with maximization of the entropy for a given energy in statistical physics. The solution is consistent with the above observations and predicts scaling relations that can be tested experimentally. In addition, our theory explains why dendritic branches of pyramidal cells are distributed more sparsely than those of Purkinje cells. Our results represent a step toward a unifying view of the relationship between neuronal morphology and function.

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    07/26/09 | Fast throughput low voltage scanning transmission electron microscope imaging of nano-resolution three dimensional tissue.
    Bolorizadeh M, Hess HF
    Microscopy and Microanalysis. 2009 Jul 26;15:642-3. doi: 10.1017/S1431927609092435
    Looger Lab
    07/26/09 | Three dimensional super resolution fluorescence imaging of single bacterial cells by stereo photoactivated localization microscopy.
    Tang J, Vaziri A, Akerboom JP, Looger L, Shank CV
    Microscopy and Microanalysis. 2009 July 26;15:564-5. doi: 10.1017/S1431927609095737
    07/26/09 | Three-dimensional super-resolution imaging of thick biological samples.
    Vaziri A, Tang J, Shroff H, Shank C
    Microscopy and Microanalysis. 2009 Jul 26;15:36-7. doi: 10.1017/S1431927609092368
    Eddy/Rivas Lab
    07/01/09 | A tool for identification of genes expressed in patterns of interest using the Allen Brain Atlas.
    Davis FP, Eddy SR
    Bioinformatics. 2009 Jul 1;25(13):1647-54. doi: 10.1093/bioinformatics/btp288

    Gene expression patterns can be useful in understanding the structural organization of the brain and the regulatory logic that governs its myriad cell types. A particularly rich source of spatial expression data is the Allen Brain Atlas (ABA), a comprehensive genome-wide in situ hybridization study of the adult mouse brain. Here, we present an open-source program, ALLENMINER, that searches the ABA for genes that are expressed, enriched, patterned or graded in a user-specified region of interest.

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    Truman LabRiddiford Lab
    07/01/09 | The ecdysone receptor controls the post-critical weight switch to nutrition-independent differentiation in Drosophila wing imaginal discs.
    Mirth CK, Truman JW, Riddiford LM
    Development. 2009 Jul;136:2345-53. doi: 10.1242/dev.032672

    In holometabolous insects, a species-specific size, known as critical weight, needs to be reached for metamorphosis to be initiated in the absence of further nutritional input. Previously, we found that reaching critical weight depends on the insulin-dependent growth of the prothoracic glands (PGs) in Drosophila larvae. Because the PGs produce the molting hormone ecdysone, we hypothesized that ecdysone signaling switches the larva to a nutrition-independent mode of development post-critical weight. Wing discs from pre-critical weight larvae [5 hours after third instar ecdysis (AL3E)] fed on sucrose alone showed suppressed Wingless (WG), Cut (CT) and Senseless (SENS) expression. Post-critical weight, a sucrose-only diet no longer suppressed the expression of these proteins. Feeding larvae that exhibit enhanced insulin signaling in their PGs at 5 hours AL3E on sucrose alone produced wing discs with precocious WG, CT and SENS expression. In addition, knocking down the Ecdysone receptor (EcR) selectively in the discs also promoted premature WG, CUT and SENS expression in the wing discs of sucrose-fed pre-critical weight larvae. EcR is involved in gene activation when ecdysone is present, and gene repression in its absence. Thus, knocking down EcR derepresses genes that are normally repressed by unliganded EcR, thereby allowing wing patterning to progress. In addition, knocking down EcR in the wing discs caused precocious expression of the ecdysone-responsive gene broad. These results suggest that post-critical weight, EcR signaling switches wing discs to a nutrition-independent mode of development via derepression.

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    07/01/09 | Twin-spot MARCM to reveal the developmental origin and identity of neurons.
    Yu H, Chen C, Shi L, Huang Y, Lee T
    Nature Neuroscience. 2009 Jul;12(7):947-53. doi: 10.1038/nn.2345

    A comprehensive understanding of the brain requires the analysis of individual neurons. We used twin-spot mosaic analysis with repressible cell markers (twin-spot MARCM) to trace cell lineages at high resolution by independently labeling paired sister clones. We determined patterns of neurogenesis and the influences of lineage on neuron-type specification. Notably, neural progenitors were able to yield intermediate precursors that create one, two or more neurons. Furthermore, neurons acquired stereotyped projections according to their temporal position in various brain sublineages. Twin-spot MARCM also permitted birth dating of mutant clones, enabling us to detect a single temporal fate that required chinmo in a sublineage of six Drosophila central complex neurons. In sum, twin-spot MARCM can reveal the developmental origins of neurons and the mechanisms that underlie cell fate.

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