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1885 Janelia Publications

Showing 1781-1790 of 1885 results
09/01/09 | A 3D digital atlas of C. elegans and its application to single-cell analyses.
Long F, Peng H, Liu X, Kim SK, Myers E
Nature Methods. 2009 Sep;6:667-72. doi: 10.1007/s12021-010-9090-x

We built a digital nuclear atlas of the newly hatched, first larval stage (L1) of the wild-type hermaphrodite of Caenorhabditis elegans at single-cell resolution from confocal image stacks of 15 individual worms. The atlas quantifies the stereotypy of nuclear locations and provides other statistics on the spatial patterns of the 357 nuclei that could be faithfully segmented and annotated out of the 558 present at this developmental stage. We then developed an automated approach to assign cell names to each nucleus in a three-dimensional image of an L1 worm. We achieved 86% accuracy in identifying the 357 nuclei automatically. This computational method will allow high-throughput single-cell analyses of the post-embryonic worm, such as gene expression analysis, or ablation or stimulation of cells under computer control in a high-throughput functional screen.

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09/01/09 | Experience-dependent structural synaptic plasticity in the mammalian brain.
Holtmaat A, Svoboda K
Nature Reviews Neuroscience. 2009 Sep;10(9):647-58. doi: 10.1038/nrn2699

Synaptic plasticity in adult neural circuits may involve the strengthening or weakening of existing synapses as well as structural plasticity, including synapse formation and elimination. Indeed, long-term in vivo imaging studies are beginning to reveal the structural dynamics of neocortical neurons in the normal and injured adult brain. Although the overall cell-specific morphology of axons and dendrites, as well as of a subpopulation of small synaptic structures, are remarkably stable, there is increasing evidence that experience-dependent plasticity of specific circuits in the somatosensory and visual cortex involves cell type-specific structural plasticity: some boutons and dendritic spines appear and disappear, accompanied by synapse formation and elimination, respectively. This Review focuses on recent evidence for such structural forms of synaptic plasticity in the mammalian cortex and outlines open questions.

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08/01/09 | A Drosophila resource of transgenic RNAi lines for neurogenetics.
Ni J, Liu L, Binari R, Hardy R, Shim H, Cavallaro A, Booker M, Pfeiffer BD, Markstein M, Wang H, Villalta C, Laverty TR, Perkins LA, Perrimon N
Genetics. 2009 Aug;182(4):1089-100. doi: 10.1534/genetics.109.103630

Conditional expression of hairpin constructs in Drosophila is a powerful method to disrupt the activity of single genes with a spatial and temporal resolution that is impossible, or exceedingly difficult, using classical genetic methods. We previously described a method (Ni et al. 2008) whereby RNAi constructs are targeted into the genome by the phiC31-mediated integration approach using Vermilion-AttB-Loxp-Intron-UAS-MCS (VALIUM), a vector that contains vermilion as a selectable marker, an attB sequence to allow for phiC31-targeted integration at genomic attP landing sites, two pentamers of UAS, the hsp70 core promoter, a multiple cloning site, and two introns. As the level of gene activity knockdown associated with transgenic RNAi depends on the level of expression of the hairpin constructs, we generated a number of derivatives of our initial vector, called the "VALIUM" series, to improve the efficiency of the method. Here, we report the results from the systematic analysis of these derivatives and characterize VALIUM10 as the most optimal vector of this series. A critical feature of VALIUM10 is the presence of gypsy insulator sequences that boost dramatically the level of knockdown. We document the efficacy of VALIUM as a vector to analyze the phenotype of genes expressed in the nervous system and have generated a library of 2282 constructs targeting 2043 genes that will be particularly useful for studies of the nervous system as they target, in particular, transcription factors, ion channels, and transporters.

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08/01/09 | New genetic tools for cell lineage analysis in Drosophila.
Lee T
Nature Methods. 2009 Aug;6(8):566-8. doi: 10.1038/nmeth0809-566

Real-time lineage tracing in flies gets a boost with three techniques to specifically label a progenitor’s daughter cells.

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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
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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