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139 Publications

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    10/13/08 | Fast monte carlo simulation methods for biological reaction-diffusion systems in solution and on surfaces.
    Kerr RA, Bartol TM, Kaminsky B, Dittrich M, Chang JJ, Baden SB, Sejnowski TJ, Stiles JR
    SIAM Journal on Scientific Computing: A Publication of the Society for Industrial and Applied Mathematics. 2008 Oct 13;30(6):3126. doi: 10.1137/070692017

    Many important physiological processes operate at time and space scales far beyond those accessible to atom-realistic simulations, and yet discrete stochastic rather than continuum methods may best represent finite numbers of molecules interacting in complex cellular spaces. We describe and validate new tools and algorithms developed for a new version of the MCell simulation program (MCell3), which supports generalized Monte Carlo modeling of diffusion and chemical reaction in solution, on surfaces representing membranes, and combinations thereof. A new syntax for describing the spatial directionality of surface reactions is introduced, along with optimizations and algorithms that can substantially reduce computational costs (e.g., event scheduling, variable time and space steps). Examples for simple reactions in simple spaces are validated by comparison to analytic solutions. Thus we show how spatially realistic Monte Carlo simulations of biological systems can be far more cost-effective than often is assumed, and provide a level of accuracy and insight beyond that of continuum methods.

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    Tjian Lab
    10/10/08 | MyoD targets TAF3/TRF3 to activate myogenin transcription.
    Deato MD, Marr MT, Sottero T, Inouye C, Hu P, Tjian R
    Molecular Cell. 2008 Oct 10;32(1):96-105. doi: 10.1073/pnas.1100640108

    Skeletal muscle differentiation requires a cascade of transcriptional events to control the spatial and temporal expression of muscle-specific genes. Until recently, muscle-specific transcription was primarily attributed to prototypic enhancer-binding factors, while the role of core promoter recognition complexes in directing myogenesis remained unknown. Here, we report the development of a purified reconstituted system to analyze the properties of a TAF3/TRF3 complex in directing transcription initiation at the Myogenin promoter. Importantly, this new complex is required to replace the canonical TFIID to recapitulate MyoD-dependent activation of Myogenin. In vitro and cell-based assays identify a domain of TAF3 that mediates coactivator functions targeted by MyoD. Our findings also suggest changes to CRSP/Mediator in terminally differentiated myotubes. This switching of the core promoter recognition complex during myogenesis allows a more balanced division of labor between activators and TAF coactivators, thus providing another strategy to accommodate cell-specific regulation during metazoan development.

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    Tjian Lab
    10/09/08 | The future for Howard Hughes. Interview by Erika Check Hayden.
    Tjian R
    Nature. 2008 Oct 9;455(7214):718. doi: 10.1073/pnas.1100640108
    Tjian Lab
    10/01/08 | Codependent activators direct myoblast-specific MyoD transcription.
    Hu P, Geles KG, Paik J, DePinho RA, Tjian R
    Developmental Cell. 2008 Oct;15(4):534-46. doi: 10.1073/pnas.1100640108

    Although FoxO and Pax proteins represent two important families of transcription factors in determining cell fate, they had not been functionally or physically linked together in mediating regulation of a common target gene during normal cellular transcription programs. Here, we identify MyoD, a key regulator of myogenesis, as a direct target of FoxO3 and Pax3/7 in myoblasts. Our cell-based assays and in vitro studies reveal a tight codependent partnership between FoxO3 and Pax3/7 to coordinately recruit RNA polymerase II and form a preinitiation complex (PIC) to activate MyoD transcription in myoblasts. The role of FoxO3 in regulating muscle differentiation is confirmed in vivo by observed defects in muscle regeneration caused by MyoD downregulation in FoxO3 null mice. These data establish a mutual interdependence and functional link between two families of transcription activators serving as potential signaling sensors and regulators of cell fate commitment in directing tissue specific MyoD transcription.

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    10/01/08 | Design and characterization of a multisource hand-held tandem mass spectrometer.
    Gao L, Sugiarto A, Harper JD, Cooks RG, Ouyang Z
    Analytical Chemistry. 2008 Oct 1;80(19):7198-205. doi: 10.1364/AO.50.001792

    A wireless-controlled miniature rectilinear ion trap mass spectrometer system, total weight with batteries 5.0 kg, consuming less than 35 W of power, and having dimensions of 22 cm in length by 12 cm in width by 18 cm in height, is characterized. The design and construction of the mass spectrometer including mass analyzer, vacuum system, electronics system, and data acquisition and processing systems, is detailed. The mass spectrometer is compatible with various types of ionization sources including a glow discharge electron impact ionization source used in the internal ionization mode, and various atmospheric pressure ionization sources, including electrospray ionization, atmospheric pressure chemical ionization, and desorption electrospray ionization, which are employed for external, atmospheric pressure ionization. These external sources are coupled to the miniature mass spectrometer via a capillary interface that is operated in a discontinuous fashion (discontinuous atmospheric pressure interface) to maximize ion transport. The performance of the mass spectrometer for large and small molecules is characterized. Limits of detection in the parts-per-billion range were obtained for selected compounds examined using both the internal ionization and external ionization modes. Tandem mass spectrometry and fast in situ analysis capabilities are also demonstrated using a variety of compounds and ionization sources. Protein molecules are analyzed as the multiply protonated molecules with mass/charge ratios up to 1500 Da/charge.

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    10/01/08 | Interfacial structures of acidic and basic aqueous solutions.
    Tian C, Ji N, Waychunas GA, Shen YR
    Journal of the American Chemical Society. 2008 Oct 1;130:13033-9. doi: 10.1021/ja8021297

    Phase-sensitive sum-frequency vibrational spectroscopy was used to study water/vapor interfaces of HCl, HI, and NaOH solutions. The measured imaginary part of the surface spectral responses provided direct characterization of OH stretch vibrations and information about net polar orientations of water species contributing to different regions of the spectrum. We found clear evidence that hydronium ions prefer to emerge at interfaces. Their OH stretches contribute to the "ice-like" band in the spectrum. Their charges create a positive surface field that tends to reorient water molecules more loosely bonded to the topmost water layer with oxygen toward the interface, and thus enhances significantly the "liquid-like" band in the spectrum. Iodine ions in solution also like to appear at the interface and alter the positive surface field by forming a narrow double-charge layer with hydronium ions. In NaOH solution, the observed weak change of the "liquid-like" band and disappearance of the "ice-like" band in the spectrum indicates that OH(-) ions must also have excess at the interface. How they are incorporated in the interfacial water structure is, however, not clear.

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    Eddy/Rivas Lab
    09/19/08 | Probabilistic phylogenetic inference with insertions and deletions.
    Rivas E, Sean R. Eddy
    PLoS Computational Biology. 2008 Sep 19;4(9):e1000172. doi: 10.1371/journal.pcbi.1000172

    A fundamental task in sequence analysis is to calculate the probability of a multiple alignment given a phylogenetic tree relating the sequences and an evolutionary model describing how sequences change over time. However, the most widely used phylogenetic models only account for residue substitution events. We describe a probabilistic model of a multiple sequence alignment that accounts for insertion and deletion events in addition to substitutions, given a phylogenetic tree, using a rate matrix augmented by the gap character. Starting from a continuous Markov process, we construct a non-reversible generative (birth-death) evolutionary model for insertions and deletions. The model assumes that insertion and deletion events occur one residue at a time. We apply this model to phylogenetic tree inference by extending the program dnaml in phylip. Using standard benchmarking methods on simulated data and a new "concordance test" benchmark on real ribosomal RNA alignments, we show that the extended program dnamlepsilon improves accuracy relative to the usual approach of ignoring gaps, while retaining the computational efficiency of the Felsenstein peeling algorithm.

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    Gonen Lab
    09/10/08 | Noncanonical binding of calmodulin to aquaporin-0: implications for channel regulation.
    Reichow SL, Gonen T
    Structure. 2008 Sep 10;16(9):1389-98. doi: 10.1016/j.str.2008.06.011

    Aquaporins (AQPs) are a family of ubiquitous membrane channels that conduct water across cell membranes. AQPs form homotetramers containing four functional and independent water pores. Aquaporin-0 (AQP0) is expressed in the eye lens, where its water permeability is regulated by calmodulin (CaM). Here we use a combination of biochemical methods and NMR spectroscopy to probe the interaction between AQP0 and CaM. We show that CaM binds the AQP0 C-terminal domain in a calcium-dependent manner. We demonstrate that only two CaM molecules bind a single AQP0 tetramer in a noncanonical fashion, suggesting a form of cooperativity between AQP0 monomers. Based on these results, we derive a structural model of the AQP0/CaM complex, which suggests CaM may be inhibitory to channel permeability by capping the vestibules of two monomers within the AQP0 tetramer. Finally, phosphorylation within AQP0's CaM binding domain inhibits the AQP0/CaM interaction, suggesting a temporal regulatory mechanism for complex formation.

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    09/09/08 | Visually mediated motor planning in the escape response of Drosophila.
    Card G, Dickinson MH
    Current Biology. 2008 Sep 9;18(17):1300-7. doi: 10.1016/j.cub.2008.07.094

    A key feature of reactive behaviors is the ability to spatially localize a salient stimulus and act accordingly. Such sensory-motor transformations must be particularly fast and well tuned in escape behaviors, in which both the speed and accuracy of the evasive response determine whether an animal successfully avoids predation [1]. We studied the escape behavior of the fruit fly, Drosophila, and found that flies can use visual information to plan a jump directly away from a looming threat. This is surprising, given the architecture of the pathway thought to mediate escape [2, 3]. Using high-speed videography, we found that approximately 200 ms before takeoff, flies begin a series of postural adjustments that determine the direction of their escape. These movements position their center of mass so that leg extension will push them away from the expanding visual stimulus. These preflight movements are not the result of a simple feed-forward motor program because their magnitude and direction depend on the flies’ initial postural state. Furthermore, flies plan a takeoff direction even in instances when they choose not to jump. This sophisticated motor program is evidence for a form of rapid, visually mediated motor planning in a genetically accessible model organism.

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    Kainmueller Lab
    09/07/08 | Model-based autosegmentation of the central brain of the honeybee, Apis mellifera, using active statistical shape models.
    Singer J, Lienhard M, Seim H, Kainmueller D, Kuss A, Lamecker H, Zachow S, Menzel R, Rybak J
    Neuroinformatics 2008. 2008 Sep 07:. doi: 10.3389/conf.neuro.11.2008.01.064

    The Honeybee Brain Atlas serves as 3D database and communicative platform to accumulate structural data, i.e. reconstructed neurons, derived from confocal scans (Brandt et al., 2005) ( (1). Transforming neurons into the atlas requires manual segmentation of neuropils within confocal images, a time-consuming task requiring expertise in identifying biological structures which can result in different outcomes from various segmenters.

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