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106 Publications

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    07/12/07 | A genome-wide transgenic RNAi library for conditional gene inactivation in Drosophila.
    Dietzl G, Chen D, Schnorrer F, Su K, Barinova Y, Fellner M, Gasser B, Kinsey K, Oppel S, Scheiblauer S, Couto A, Marra V, Keleman K, Dickson BJ
    Nature. 2007 Jul 12;448(7150):151-6. doi: 10.1038/nature05954

    Forward genetic screens in model organisms have provided important insights into numerous aspects of development, physiology and pathology. With the availability of complete genome sequences and the introduction of RNA-mediated gene interference (RNAi), systematic reverse genetic screens are now also possible. Until now, such genome-wide RNAi screens have mostly been restricted to cultured cells and ubiquitous gene inactivation in Caenorhabditis elegans. This powerful approach has not yet been applied in a tissue-specific manner. Here we report the generation and validation of a genome-wide library of Drosophila melanogaster RNAi transgenes, enabling the conditional inactivation of gene function in specific tissues of the intact organism. Our RNAi transgenes consist of short gene fragments cloned as inverted repeats and expressed using the binary GAL4/UAS system. We generated 22,270 transgenic lines, covering 88% of the predicted protein-coding genes in the Drosophila genome. Molecular and phenotypic assays indicate that the majority of these transgenes are functional. Our transgenic RNAi library thus opens up the prospect of systematically analysing gene functions in any tissue and at any stage of the Drosophila lifespan.

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    07/10/07 | Automatic image analysis for gene expression patterns of fly embryos.
    Peng H, Long F, Zhou J, Leung G, Eisen MB, Myers EW
    BMC Cell Biology. 2007 Jul 10;8(Supplement 1):S7. doi: 10.1007/s12021-010-9090-x

    Staining the mRNA of a gene via in situ hybridization (ISH) during the development of a D. melanogaster embryo delivers the detailed spatio-temporal pattern of expression of the gene. Many biological problems such as the detection of co-expressed genes, co-regulated genes, and transcription factor binding motifs rely heavily on the analyses of these image patterns. The increasing availability of ISH image data motivates the development of automated computational approaches to the analysis of gene expression patterns.

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    07/10/07 | Phenotype clustering of breast epithelial cells in confocal images based on nuclear protein distribution analysis.
    Long F, Peng H, Sudar D, Lelièvre SA, Knowles DW
    BMC Cell Biology. 2007 Jul 10;8 (Suppl 1):S3. doi: 10.1007/s12021-010-9090-x

    The distribution of chromatin-associated proteins plays a key role in directing nuclear function. Previously, we developed an image-based method to quantify the nuclear distributions of proteins and showed that these distributions depended on the phenotype of human mammary epithelial cells. Here we describe a method that creates a hierarchical tree of the given cell phenotypes and calculates the statistical significance between them, based on the clustering analysis of nuclear protein distributions.

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    Svoboda Lab
    07/10/07 | The functional microarchitecture of the mouse barrel cortex.
    Sato TR, Gray NW, Mainen ZF, Svoboda K
    PLoS Biology. 2007 Jul 10;5(7):e189. doi: 10.1371/journal.pbio.0050189

    Cortical maps, consisting of orderly arrangements of functional columns, are a hallmark of the organization of the cerebral cortex. However, the microorganization of cortical maps at the level of single neurons is not known, mainly because of the limitations of available mapping techniques. Here, we used bulk loading of Ca(2+) indicators combined with two-photon microscopy to image the activity of multiple single neurons in layer (L) 2/3 of the mouse barrel cortex in vivo. We developed methods that reliably detect single action potentials in approximately half of the imaged neurons in L2/3. This allowed us to measure the spiking probability following whisker deflection and thus map the whisker selectivity for multiple neurons with known spatial relationships. At the level of neuronal populations, the whisker map varied smoothly across the surface of the cortex, within and between the barrels. However, the whisker selectivity of individual neurons recorded simultaneously differed greatly, even for nearest neighbors. Trial-to-trial correlations between pairs of neurons were high over distances spanning multiple cortical columns. Our data suggest that the response properties of individual neurons are shaped by highly specific subcolumnar circuits and the momentary intrinsic state of the neocortex.

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    07/06/07 | S-nitrosylation-induced conformational change in blackfin tuna myoglobin.
    Schreiter ER, Rodríguez MM, Weichsel A, Montfort WR, Bonaventura J
    Journal of Biological Chemistry. 2007 Jul 6;282(27):19773-80. doi: 10.1074/jbc.M701363200

    S-nitrosylation is a post-translational protein modification that can alter the function of a variety of proteins. Despite the growing wealth of information that this modification may have important functional consequences, little is known about the structure of the moiety or its effect on protein tertiary structure. Here we report high-resolution x-ray crystal structures of S-nitrosylated and unmodified blackfin tuna myoglobin, which demonstrate that in vitro S-nitrosylation of this protein at the surface-exposed Cys-10 directly causes a reversible conformational change by "wedging" apart a helix and loop. Furthermore, we have demonstrated in solution and in a single crystal that reduction of the S-nitrosylated myoglobin with dithionite results in NO cleavage from the sulfur of Cys-10 and rebinding to the reduced heme iron, showing the reversibility of both the modification and the conformational changes. Finally, we report the 0.95-A structure of ferrous nitrosyl myoglobin, which provides an accurate structural view of the NO coordination geometry in the context of a globin heme pocket.

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    07/01/07 | [Role of Bid protein in the mitochondria and endoplasmic reticulum associated apoptotic pathway].
    Hu J, He D, Gao L, Yang C, Cai Z
    Zhonghua Xue Ye Xue Za Zhi = Zhonghua Xueyexue Zazhi. 2007 Jul;28(7):466-9. doi: 10.1364/AO.50.001792

    To explore the role of Bid protein in the mitochondria and endoplasmic reticulum (ER) associated apoptotic pathway.

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    07/01/07 | Cell type-specific relationships between spiking and [Ca2+]i in neurons of the Xenopus tadpole olfactory bulb.
    Lin B, Chen T, Schild D
    The Journal of Physiology. 2007 Jul 1;582(Pt 1):163-75. doi: 10.1113/jphysiol.2006.125963

    Multi-neuronal recordings with Ca2+ indicator dyes usually relate [Ca2+]i to action potentials (APs) assuming a stereotypical dependency between the two. However, [Ca2+]i affects and is affected by numerous complex mechanisms that differ from cell type to cell type, from cell compartment to cell compartment. Moreover, [Ca2+]i depends on the specific way a cell is activated. Here we investigate, by combining calcium imaging and on-cell patch clamp recordings, the relationship between APs (spiking) and somatic [Ca2+]i in mitral and granule cells of the olfactory bulb in Xenopus laevis tadpoles. Both cell types exhibit ongoing and odour-modulated [Ca2+]i dynamics. In mitral cells, the occurrence of APs in both spontaneous and odour-evoked situations correlates tightly to step-like [Ca2+]i increases. Moreover, odorant-induced suppression of spontaneous firing couples to a decrease in [Ca2+]i. In contrast, granule cells show a substantial number of uncorrelated events such as increases in [Ca2+]i without APs occurring or APs without any effect upon [Ca2+]i. The correlation between spiking and [Ca2+]i is low, possibly due to somatic NMDAR-mediated and subthreshold voltage-activated Ca2+ entries, and thus does not allow a reliable prediction of APs based on calcium imaging. Taken together, our results demonstrate that the relationship between somatic [Ca2+]i and APs can be cell type specific. Taking [Ca2+]i dynamics as an indicator for spiking activity is thus only reliable if the correlation has been established in the system of interest. When [Ca2+]i and APs are precisely correlated, fast calcium imaging is an extremely valuable tool for determining spatiotemporal patterns of APs in neuronal population.

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    07/01/07 | Common genome-wide patterns of transcript accumulation underlying the wing polyphenism and polymorphism in the pea aphid (Acyrthosiphon pisum).
    Brisson JA, Davis GK, Stern DL
    Evol Dev. 2007 Jul-Aug;9(4):338-46. doi: 10.1111/j.1525-142X.2007.00170.x

    The pea aphid, Acyrthosiphon pisum, exhibits several environmentally cued polyphenisms, in which discrete, alternative phenotypes are produced. At low-density, parthenogenetic females produce unwinged female progeny, but at high-density females produce progeny that develop with wings. These alternative phenotypes represent a solution to the competing demands of dispersal and reproduction. Males also develop as either winged or unwinged, but these alternatives are determined by a genetic polymorphism. Winged and unwinged males are morphologically less distinct from each other than winged and unwinged females, possibly because males experience fewer trade-offs between dispersal and reproduction. To assess whether shared physiological differences mirror the shared morphological differences that characterize the wing polyphenism and polymorphism, we used a cDNA microarray representing an estimated 10% of the coding genome (1734 genes) to examine differential transcript accumulation between winged and unwinged females and males. We identified several transcripts that differentially accumulate between winged and unwinged morphs in both sexes, the majority of which are involved in energy production. Unexpectedly, the extent of differential transcript accumulation between winged and unwinged morphs was greater for adult males than for adult females. Together, these results suggest not only that similar physiological differences underlie the polyphenism and polymorphism, but that male morphs, like females, are subject to trade-offs between reproduction and dispersal that are reflected in levels of transcript accumulation and possibly genome-wide patterns of gene regulation. These data also provide a baseline for future studies of the molecular and physiological basis of life-history trade-offs.

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    07/01/07 | Dynamic properties of large-field and small-field optomotor flight responses in Drosophila.
    Duistermars BJ, Reiser MB, Zhu Y, Frye MA
    Journal of Comparative Physiology. A, Neuroethology, Sensory, Neural, and Behavioral Physiology. 2007 Jul;193:787-99. doi: 10.1016/j.cub.2010.06.072

    Optomotor flight control in houseflies shows bandwidth fractionation such that steering responses to an oscillating large-field rotating panorama peak at low frequency, whereas responses to small-field objects peak at high frequency. In fruit flies, steady-state large-field translation generates steering responses that are three times larger than large-field rotation. Here, we examine the optomotor steering reactions to dynamically oscillating visual stimuli consisting of large-field rotation, large-field expansion, and small-field motion. The results show that, like in larger flies, large-field optomotor steering responses peak at low frequency, whereas small-field responses persist under high frequency conditions. However, in fruit flies large-field expansion elicits higher magnitude and tighter phase-locked optomotor responses than rotation throughout the frequency spectrum, which may suggest a further segregation within the large-field pathway. An analysis of wing beat frequency and amplitude reveals that mechanical power output during flight varies according to the spatial organization and motion dynamics of the visual scene. These results suggest that, like in larger flies, the optomotor control system is organized into parallel large-field and small-field pathways, and extends previous analyses to quantify expansion-sensitivity for steering reflexes and flight power output across the frequency spectrum.

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    07/01/07 | Hysteresis phenomena of the intelligent driver model for traffic flow.
    Dahui W, Ziqiang W, Ying F
    Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 2007 Jul;76(1 Pt 2):016105

    We present hysteresis phenomena of the intelligent driver model for traffic flow in a circular one-lane roadway. We show that the microscopic structure of traffic flow is dependent on its initial state by plotting the fraction of congested vehicles over the density, which shows a typical hysteresis loop, and by investigating the trajectories of vehicles on the velocity-over-headway plane. We find that the trajectories of vehicles on the velocity-over-headway plane, which usually show a hysteresis loop, include multiple loops. We also point out the relations between these hysteresis loops and the congested jams or high-density clusters in traffic flow.

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