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190 Publications

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    Svoboda Lab
    09/01/11 | a compendium of resources fostering the continuous development of automated neuronal reconstruction.
    Gillette TA, Brown KM, Svoboda K, Liu Y, Ascoli GA
    Neuroinformatics. 2011 Sep;9(2-3):303-4. doi: 10.1007/s12021-011-9104-3

    Concomitant with the publication of this Special Issue of Neuroinformatics, a substantially updated version of the DIADEM web site has been released at This web site was originally designed to host the challenge for automating the digital reconstruction of axonal and dendritic morphology (hence the DIADEM acronym). This post-competition version features additional content for continued use as the access point for DIADEM-related material. From the very beginning, one of the spirits of DIADEM has been to share data and resources with the neuroscience research community at large. The resources available from or linked to the DIADEM website constitute a substantial scientific legacy of the 2009/2010 competition. The new content includes finalist algorithms, image stack data, gold standard reconstructions, an updated DIADEM metric, and a retrospective on the competition in text and images.

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    Eddy/Rivas Lab
    09/01/11 | Exploiting Oxytricha trifallax nanochromosomes to screen for non-coding RNA genes.
    Jung S, Swart EC, Minx PJ, Magrini V, Mardis ER, Landweber LF, Eddy SR
    Nucleic Acids Research. 2011 Sep 1;39:7529-47. doi: 10.1093/nar/gkr501

    We took advantage of the unusual genomic organization of the ciliate Oxytricha trifallax to screen for eukaryotic non-coding RNA (ncRNA) genes. Ciliates have two types of nuclei: a germ line micronucleus that is usually transcriptionally inactive, and a somatic macronucleus that contains a reduced, fragmented and rearranged genome that expresses all genes required for growth and asexual reproduction. In some ciliates including Oxytricha, the macronuclear genome is particularly extreme, consisting of thousands of tiny ’nanochromosomes’, each of which usually contains only a single gene. Because the organism itself identifies and isolates most of its genes on single-gene nanochromosomes, nanochromosome structure could facilitate the discovery of unusual genes or gene classes, such as ncRNA genes. Using a draft Oxytricha genome assembly and a custom-written protein-coding genefinding program, we identified a subset of nanochromosomes that lack any detectable protein-coding gene, thereby strongly enriching for nanochromosomes that carry ncRNA genes. We found only a small proportion of non-coding nanochromosomes, suggesting that Oxytricha has few independent ncRNA genes besides homologs of already known RNAs. Other than new members of known ncRNA classes including C/D and H/ACA snoRNAs, our screen identified one new family of small RNA genes, named the Arisong RNAs, which share some of the features of small nuclear RNAs.

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    09/01/11 | Lmo genes regulate behavioral responses to ethanol in Drosophila melanogaster and the mouse.
    Lasek AW, Giorgetti F, Berger KH, Tayor S, Heberlein U
    Alcoholism, Clinical and Experimental Research. 2011 Sep;35(9):1600-6. doi: 10.1111/j.1530-0277.2011.01506.x

    BACKGROUND: Previous work from our laboratory demonstrated a role for the Drosophila Lim-only (dLmo) gene in regulating behavioral responses to cocaine. Herein, we examined whether dLmo influences the flies' sensitivity to ethanol's sedating effects. We also investigated whether 1 of the mammalian homologs of dLmo, Lmo3, is involved in behavioral responses to ethanol in mice.

    METHODS: To examine dLmo function in ethanol-induced sedation, mutant flies with reduced or increased dLmo expression were tested using the loss of righting (LOR) assay. To determine whether mouse Lmo3 regulates behavioral responses to ethanol, we generated transgenic mice expressing a short-hairpin RNA targeting Lmo3 for RNA interference-mediated knockdown by lentiviral infection of single cell embryos. Adult founder mice, expressing varying amounts of Lmo3 in the brain, were tested using ethanol loss-of-righting-reflex (LORR) and 2-bottle choice ethanol consumption assays.

    RESULTS: We found that in flies, reduced dLmo activity increased sensitivity to ethanol-induced sedation, whereas increased expression of dLmo led to increased resistance to ethanol-induced sedation. In mice, reduced levels of Lmo3 were correlated with increased sedation time in the LORR test and decreased ethanol consumption in the 2-bottle choice protocol.

    CONCLUSIONS: These data describe a novel and conserved role for Lmo genes in flies and mice in behavioral responses to ethanol. These studies also demonstrate the feasibility of rapidly translating findings from invertebrate systems to mammalian models of alcohol abuse by combining RNA interference in transgenic mice and behavioral testing.

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    09/01/11 | New tools for the analysis of glial cell biology in Drosophila.
    Awasaki T, Lee T
    Glia. 2011 Sep;59(9):1377-86. doi: 10.1002/glia.21133

    Because of its genetic, molecular, and behavioral tractability, Drosophila has emerged as a powerful model system for studying molecular and cellular mechanisms underlying the development and function of nervous systems. The Drosophila nervous system has fewer neurons and exhibits a lower glia:neuron ratio than is seen in vertebrate nervous systems. Despite the simplicity of the Drosophila nervous system, glial organization in flies is as sophisticated as it is in vertebrates. Furthermore, fly glial cells play vital roles in neural development and behavior. In addition, powerful genetic tools are continuously being created to explore cell function in vivo. In taking advantage of these features, the fly nervous system serves as an excellent model system to study general aspects of glial cell development and function in vivo. In this article, we review and discuss advanced genetic tools that are potentially useful for understanding glial cell biology in Drosophila.

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    09/01/11 | Preparation of cuticles from unhatched first-instar Drosophila larvae.
    Stern DL, Sucena E
    Cold Spring Harb Protoc. 2011 Sep;2011(9):. doi: 10.1101/pdb.prot065532

    The finely sculpted cuticle of Drosophila carries a rich array of morphological details. Thus, cuticle examination has had a central role in the history of genetics. Studies of the Drosophila cuticle have focused mainly on first-instar larvae and adult cuticular morphology. This protocol describes the preparation of cuticles from larvae that have not yet hatched from the egg. It is designed for sampling all eggs laid by one or more females. This can be particularly useful, for example, when a mutation produces embryos that are unable to hatch from the egg.

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    09/01/11 | Proof-editing is the bottleneck of 3D neuron reconstruction: the problem and solutions.
    Peng H, Long F, Zhao T, Myers E
    Neuroinformatics. 2011 Sep;9:103-5. doi: 10.1007/s12021-010-9090-x
    09/01/11 | Tao kinases as coordinators of actin and microtubule dynamics in developing neurons.
    King I, Heberlein U
    Communicative & Integrative Biology. 2011 Sep;4(5):554-6. doi: 10.4161/cib.4.5.16051

    Drosophila tao, encoding a Ste20 family kinase, was identified as a gene involved in ethanol, cocaine and nicotine sensitivity. The behavioral phenotypes appear to be caused by defects in the development of the adult brain. Specifically, Drosophila tao functions to promote axon guidance of mushroom body (MB) neurons. The MB is a large structure in the central brain of the fly whose development and function have been well characterized. tao interacts genetically with mutations in the par-1 gene, also encoding a serine-threonine kinase. Since Par-1 has been implicated in the regulation of microtubule dynamics, this suggests that tao regulates the microtubule cytoskeleton in developing MB neurons. Here we discuss these results in light of previous studies that have proposed that Drosophila tao and its mammalian homologs function as a link between the actin and microtubule cytoskeletons, regulating microtubule stability in response to actin signals.

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    Svoboda Lab
    09/01/11 | The past, present, and future of single neuron reconstruction.
    Svoboda K
    Neuroinformatics. 2011 Sep;9(2-3):97-8. doi: 10.1007/s12021-011-9097-y
    Murphy Lab
    08/24/11 | Electrical synaptic input to ganglion cells underlies differences in the output and absolute sensitivity of parallel retinal circuits.
    Murphy GJ, Rieke F
    The Journal of Neuroscience: The Official Journal of the Society for Neuroscience. 2011 Aug 24;31(34):12218-28. doi: 10.1523/JNEUROSCI.3241-11.2011

    Parallel circuits throughout the CNS exhibit distinct sensitivities and responses to sensory stimuli. Ambiguities in the source and properties of signals elicited by physiological stimuli, however, frequently obscure the mechanisms underlying these distinctions. We found that differences in the degree to which activity in two classes of Off retinal ganglion cell (RGC) encode information about light stimuli near detection threshold were not due to obvious differences in the cells’ intrinsic properties or the chemical synaptic input the cells received; indeed, differences in the cells’ light responses were largely insensitive to block of fast ionotropic glutamate receptors. Instead, the distinct responses of the two types of RGCs likely reflect differences in light-evoked electrical synaptic input. These results highlight a surprising strategy by which the retina differentially processes and routes visual information and provide new insight into the circuits that underlie responses to stimuli near detection threshold.

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    Svoboda LabRubin Lab
    08/23/11 | Multiple new site-specific recombinases for use in manipulating animal genomes.
    Nern A, Pfeiffer BD, Svoboda K, Rubin GM
    Proceedings of the National Academy of Sciences of the United States of America. 2011 Aug 23;108(34):14198-203. doi: 10.1073/pnas.1111704108

    Site-specific recombinases have been used for two decades to manipulate the structure of animal genomes in highly predictable ways and have become major research tools. However, the small number of recombinases demonstrated to have distinct specificities, low toxicity, and sufficient activity to drive reactions to completion in animals has been a limitation. In this report we show that four recombinases derived from yeast-KD, B2, B3, and R-are highly active and nontoxic in Drosophila and that KD, B2, B3, and the widely used FLP recombinase have distinct target specificities. We also show that the KD and B3 recombinases are active in mice.

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