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6 Publications

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    Tjian Lab
    06/04/04 | Structure and function of CRSP/Med2; a promoter-selective transcriptional coactivator complex.
    Taatjes DJ, Tjian R
    Molecular Cell. 2004 Jun 4;14(5):675-83. doi: 10.1073/pnas.1100640108

    The multi-subunit, human CRSP coactivator-also known as Mediator (Med)-regulates transcription by mediating signals between enhancer-bound factors (activators) and the core transcriptional machinery. Interestingly, different activators are known to bind distinct subunits within the CRSP/Med complex. We have isolated a stable, endogenous CRSP/Med complex (CRSP/Med2) that specifically lacks both the Med220 and the Med70 subunits. The three-dimensional structure of CRSP/Med2 was determined to 31 A resolution using electron microscopy and single-particle reconstruction techniques. Despite lacking both Med220 and Med70, CRSP/Med2 displays potent, activator-dependent transcriptional coactivator function in response to VP16, Sp1, and Sp1/SREBP-1a in vitro using chromatin templates. However, CRSP/Med2 is unable to potentiate activated transcription from a vitamin D receptor-responsive promoter, which requires interaction with Med220 for coactivator recruitment, whereas VDR-directed activation by CRSP/Med occurs normally. Thus, it appears that CRSP/Med may be regulated by a combinatorial assembly mechanism that allows promoter-selective function upon exchange of specific coactivator targets.

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    06/02/04 | Ssn6-Tup1 requires the ISW2 complex to position nucleosomes in Saccharomyces cerevisiae.
    Zhang Z, Reese JC
    The EMBO Journal. 2004 Jun 2;23(11):2246-57. doi: 10.1038/sj.emboj.7600227

    The Imitation SWItch (ISWI) chromatin remodeling factors have been implicated in nucleosome positioning. In vitro, they can mobilize nucleosomes bi-directionally, making it difficult to envision how they can establish precise translational positioning of nucleosomes in vivo. It has been proposed that they require other cellular factors to do so, but none has been identified thus far. Here, we demonstrate that both ISW2 and TUP1 are required to position nucleosomes across the entire coding sequence of the DNA damage-inducible gene RNR3. The chromatin structure downstream of the URS is indistinguishable in Deltaisw2 and Deltatup1 mutants, and the crosslinking of Tup1 and Isw2 to RNR3 is independent of each other, indicating that both complexes are required to maintain repressive chromatin structure. Furthermore, Tup1 repressed RNR3 and blocked preinitiation complex formation in the Deltaisw2 mutant, even though nucleosome positioning was completely disrupted over the promoter and ORF. Our study has revealed a novel collaboration between two nucleosome-positioning activities in vivo, and suggests that disruption of nucleosome positioning is insufficient to cause a high level of transcription.

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    06/01/04 | A Bayesian morphometry algorithm.
    Herskovits EH, Peng H, Davatzikos C
    IEEE Transactions on Medical Imaging. 2004 Jun;23(6):723-37. doi: 10.1007/s12021-010-9090-x

    Most methods for structure-function analysis of the brain in medical images are usually based on voxel-wise statistical tests performed on registered magnetic resonance (MR) images across subjects. A major drawback of such methods is the inability to accurately locate regions that manifest nonlinear associations with clinical variables. In this paper, we propose Bayesian morphological analysis methods, based on a Bayesian-network representation, for the analysis of MR brain images. First, we describe how Bayesian networks (BNs) can represent probabilistic associations among voxels and clinical (function) variables. Second, we present a model-selection framework, which generates a BN that captures structure-function relationships from MR brain images and function variables. We demonstrate our methods in the context of determining associations between regional brain atrophy (as demonstrated on MR images of the brain), and functional deficits. We employ two data sets for this evaluation: the first contains MR images of 11 subjects, where associations between regional atrophy and a functional deficit are almost linear; the second data set contains MR images of the ventricles of 84 subjects, where the structure-function association is nonlinear. Our methods successfully identify voxel-wise morphological changes that are associated with functional deficits in both data sets, whereas standard statistical analysis (i.e., t-test and paired t-test) fails in the nonlinear-association case.

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    06/01/04 | Biophysical constraints on neuronal branching.
    Shefi O, Harel A, Chklovskii DB, Ben-Jacob E, Ayali A
    Neurocomputing. 2004 Jun;58-60:487-95

    We investigate rules that govern neuronal arborization, speci%cally the local geometry of the

    bifurcation of a neurite into its sub-branches. In the present study we set out to determine

    the relationship between branch diameter and angle. Existing theories are based on minimizing a

    neuronal volume cost function, or, alternatively, on the equilibrium of mechanical tension forces,

    whichdepend on branchdiameters. Our experimental results utilizing two-dimensional cultured

    neural networks partly corroborate both the volume optimization principles and the tension theory.

    Deviation from pure tension forces equilibrium is explained by an additional force exerted by

    the anchoring of the junction to the substrate.

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    Pavlopoulos Lab
    06/01/04 | Efficient transformation of the beetle Tribolium castaneum using the Minos transposable element: quantitative and qualitative analysis of genomic integration events.
    Pavlopoulos A, Berghammer AJ, Averof M, Klingler M
    Genetics. 2004 Jun;167:737-46. doi: 10.1534/genetics.103.023085

    Genetic transformation in insects holds great promise as a tool for genetic manipulation in species of particular scientific, economic, or medical interest. A number of transposable elements have been tested recently as potential vectors for transformation in a range of insects. Minos is one of the most promising elements because it appears to be active in diverse species and has the capacity to carry large inserts. We report here the use of the Minos element as a transformation vector in the red flour beetle Tribolium castaneum (Coleoptera), an important species for comparative developmental and pest management studies. Transgenic G(1) beetles were recovered from 32.4% of fertile G(0)’s injected with a plasmid carrying a 3xP3-EGFP-marked transposon and in vitro synthesized mRNA encoding the Minos transposase. This transformation efficiency is 2.8-fold higher than that observed when using a plasmid helper. Molecular and genetic analyses show that several independent insertions can be recovered from a single injected parent, but that the majority of transformed individuals carry single Minos insertions. These results establish Minos as one of the most efficient vectors for genetic transformation in insects. In combination with piggyBac-based transgenesis, our work allows the introduction of sophisticated multicomponent genetic tools in Tribolium.

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    06/01/04 | Habituation of an odorant-induced startle response in Drosophila.
    Cho W, Heberlein U, Wolf FW
    Genes, Brain, and Behavior. 2004 Jun;3(3):127-37. doi: 10.1111/j.1601-183x.2004.00061.x

    Habituation is a fundamental form of behavioral plasticity that permits organisms to ignore inconsequential stimuli. Here we describe the habituation of a locomotor response to ethanol and other odorants in Drosophila, measured by an automated high-throughput locomotor tracking system. Flies exhibit an immediate and transient startle response upon exposure to a novel odor. Surgical removal of the antennae, the fly's major olfactory organs, abolishes this startle response. With repeated discrete exposures to ethanol vapor, the startle response habituates. Habituation is reversible by a mechanical stimulus and is not due to the accumulation of ethanol in the organism, nor to non-specific mechanisms. Ablation or inactivation of the mushroom bodies, central brain structures involved in olfactory and courtship conditioning, results in decreased olfactory habituation. In addition, olfactory habituation to ethanol generalizes to odorants that activate separate olfactory receptors. Finally, habituation is impaired in rutabaga, an adenylyl cyclase mutant isolated based on a defect in olfactory associative learning. These data demonstrate that olfactory habituation operates, at least in part, through central mechanisms. This novel model of olfactory habituation in freely moving Drosophila provides a scalable method for studying the molecular and neural bases of this simple and ubiquitous form of learning.

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