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57 Publications

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    01/16/04 | Transformation of olfactory representations in the Drosophila antennal lobe.
    Wilson RI, Turner GC, Laurent G
    Science (New York, N.Y.). 2004 Jan 16;303(5656):366-70. doi: 10.1126/science.1090782

    Molecular genetics has revealed a precise stereotypy in the projection of primary olfactory sensory neurons onto secondary neurons. A major challenge is to understand how this mapping translates into odor responses in these second-order neurons. We investigated this question in Drosophila using whole-cell recordings in vivo. We observe that monomolecular odors generally elicit responses in large ensembles of antennal lobe neurons. Comparison of odor-evoked activity from afferents and postsynaptic neurons in the same glomerulus revealed that second-order neurons display broader tuning and more complex responses than their primary afferents. This indicates a major transformation of odor representations, implicating lateral interactions within the antennal lobe.

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    Tjian Lab
    01/13/04 | Myc-interacting protein 1 target gene profile: a link to microtubules, extracellular signal-regulated kinase, and cell growth.
    Ziegelbauer J, Wei J, Tjian R
    Proceedings of the National Academy of Sciences of the United States of America. 2004 Jan 13;101(2):458-63. doi: 10.1073/pnas.1100640108

    To study the role of the transcription factor Myc-interacting protein 1 (MIZ-1) in activating various target genes after induction with the microtubule disrupting agent T113242, we have used small interfering RNA duplexes (siRNAs) to knockdown the expression of MIZ-1. As expected, depletion of MIZ-1 resulted in the inhibition of T113242-dependent activation of the low-density lipoprotein receptor (LDLR) gene in hepatocytes. Cells transfected with MIZ-1 siRNAs also exhibited growth arrest. In addition, inhibition of the extracellular signal-regulated kinase (ERK) pathway inhibited T113242-induced nuclear accumulation of MIZ-1 and activation of LDLR. Gene expression microarray analysis under various induction conditions identified other T113242-activated genes affected by a decrease in MIZ-1 and inhibition of the ERK pathway. We also found that the accumulation of MIZ-1 in the nucleus is influenced by cell-cell contact and/or growth. Taken together, our studies suggest that MIZ-1 regulates a specific set of genes that includes LDLR and that the ERK pathway plays a role in the activation of target promoters by MIZ-1.

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    01/01/04 | Dynamics of leg muscle function in tammar wallabies (M. eugenii) during level versus incline hopping.
    Biewener AA, McGowan C, Card GM, Baudinette RV
    The Journal of Experimental Biology. 2004 Jan;207(Pt 2):211-23

    The goal of our study was to examine whether the in vivo force-length behavior, work and elastic energy savings of distal muscle-tendon units in the legs of tammar wallabies (Macropus eugenii) change during level versus incline hopping. To address this question, we obtained measurements of muscle activation (via electromyography), fascicle strain (via sonomicrometry) and muscle-tendon force (via tendon buckles) from the lateral gastrocnemius (LG) and plantaris (PL) muscles of tammar wallabies trained to hop on a level and an inclined (10 degrees, 17.4% grade) treadmill at two speeds (3.3 m s(-1) and 4.2 m s(-1)). Similar patterns of muscle activation, force and fascicle strain were observed under both level and incline conditions. This also corresponded to similar patterns of limb timing and movement (duty factor, limb contact time and hopping frequency). During both level and incline hopping, the LG and PL exhibited patterns of fascicle stretch and shortening that yielded low levels of net fascicle strain [LG: level, -1.0+/-4.6% (mean +/- S.E.M.) vs incline, 0.6+/-4.5%; PL: level, 0.1+/-1.0% vs incline, 0.4+/-1.6%] and muscle work (LG: level, -8.4+/-8.4 J kg(-1) muscle vs incline, -6.8+/-7.5 J kg(-1) muscle; PL: level, -2.0+/-0.6 J kg(-1) muscle vs incline, -1.4+/-0.7 J kg(-1) muscle). Consequently, neither muscle significantly altered its contractile dynamics to do more work during incline hopping. Whereas electromyographic (EMG) phase, duration and intensity did not differ for the LG, the PL exhibited shorter but more intense periods of activation, together with reduced EMG phase (P<0.01), during incline versus level hopping. Our results indicate that design for spring-like tendon energy savings and economical muscle force generation is key for these two distal muscle-tendon units of the tammar wallaby, and the need to accommodate changes in work associated with level versus incline locomotion is achieved by more proximal muscles of the limb.

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    01/01/04 | Joint MRI bias removal using entropy minimization across images.
    Learned-Miller E, Ahammad P
    Neural Information Processing Systems Conference. 2004:

    The correction of bias in magnetic resonance images is an important problem in medical image processing. Most previous approaches have used a maximum likelihood method to increase the likelihood of the pixels in a single image by adaptively estimating a correction to the unknown image bias field. The pixel likelihoods are defined either in terms of a pre-existing tissue model, or non-parametrically in terms of the image’s own pixel values. In both cases, the specific location of a pixel in the image is not used to calculate the likelihoods. We suggest a new approach in which we simultaneously eliminate the bias from a set of images of the same anatomy, but from different patients. We use the statistics from the same location across different images, rather than within an image, to eliminate bias fields from all of the images simultaneously. The method builds a multi-resolution non-parametric tissue model conditioned on image location while eliminating the bias fields associated with the original image set. We present experiments on both synthetic and real MR data sets, and present comparisons with other methods.

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    01/01/04 | Mapping of microbial pathways through constrained mapping of orthologous genes.
    Olman V, Peng H, Su Z, Xu Y
    Proceedings / IEEE Computational Systems Bioinformatics Conference, CSB. IEEE Computational Systems Bioinformatics Conference. 2004:363-70. doi: 10.1007/s12021-010-9090-x

    We present a novel computer algorithm for mapping biological pathways from one prokaryotic genome to another. The algorithm maps genes in a known pathway to their homologous genes (if any) in a target genome that is most consistent with (a) predicted orthologous gene relationship, (b) predicted operon structures, and (c) predicted co-regulation relationship of operons. Mathematically, we have formulated this problem as a constrained minimum spanning tree problem (called a Steiner network problem), and demonstrated that this formulation has the desired property through applications. We have solved this mapping problem using a combinatorial optimization algorithm, with guaranteed global optimality. We have implemented this algorithm as a computer program, called PMAP. Our test results on pathway mapping are highly encouraging – we have mapped a number of pathways of H. influenzae, B. subtilis, H. pylori, and M. tuberculosis to E. coli using P-MAP, whose homologous pathways in E coli. are known and hence the mapping accuracy could be checked. We have then mapped known E. coli pathways in the EcoCyc database to the newly sequenced organism Synechococcus sp WH8102, and predicted 158 Synechococcus pathways. Detailed analyses on the predicted pathways indicate that P-MAP’s mapping results are consistent with our general knowledge about (local) pathways. We believe that P-MAP will be a useful tool for microbial genome annotation projects and inference of individual microbial pathways.

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    01/01/04 | Maps in the brain: what can we learn from them?
    Chklovskii DB, Koulakov AA
    Annual Review of Neuroscience. 2004;27:369-92. doi: 10.1016/j.tins.2005.05.006

    In mammalian visual cortex, neurons are organized according to their functional properties into multiple maps such as retinotopic, ocular dominance, orientation preference, direction of motion, and others. What determines the organization of cortical maps? We argue that cortical maps reflect neuronal connectivity in intracortical circuits. Because connecting distant neurons requires costly wiring (i.e., axons and dendrites), there is an evolutionary pressure to place connected neurons as close to each other as possible. Then, cortical maps may be viewed as solutions that minimize wiring cost for given intracortical connectivity. These solutions can help us in inferring intracortical connectivity and, ultimately, in understanding the function of the visual system.

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    01/01/04 | Prospects in aphid genetics
    DL Stern , JC Simon , CA Dedryver , C Rispe , M Hullé
    Aphids in a new millennium. Proceedings of the Sixth International Symposium on Aphids. 09/2004:

    This paper identifies the prospects of using aphid species as ideal genetic model systems for the study of evolutionary developmental biology and genetic control of polyphenisms. The advantages and disadvantages of using aphids as genetic model organisms are discussed.

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