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139 Publications

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    03/07/08 | Characterization of vibrational resonances of water-vapor interfaces by phase-sensitive sum-frequency spectroscopy.
    Ji N, Ostroverkhov V, Tian CS, Shen YR
    Physical Review Letters. 2008 Mar 7;100(9):096102

    Phase-sensitive sum-frequency spectroscopy provides correct characterization of vibrational resonances of water-vapor interfaces and allows better identification of interfacial water species contributing to different parts of the spectra. Iodine ions emerging at an interface create a surface field that tends to reorient the more loosely bonded water molecules below the topmost layer.

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    03/01/08 | Coding and non-coding polymorphisms in alcohol dehydrogenase alters protein expression and alcohol-associated erythema.
    Pershing LK, Chen Y, Tkachuk AN, Rausch HL, Petelenz-Rubin K, Corlett JL, Hobbs MR
    The Journal of Investigative Dermatology. 2008 Mar;128(3):616-27. doi: 10.1038/sj.jid.5701105

    Ethanol (EtOH), isopropyl alcohol (IPA), and propylene glycol (PG) increase topical drug delivery, but are sometimes associated with erythema. A potential genetic basis for alcohol-associated erythema was investigated as the function of polymorphisms in coding and non-coding regions of class IB alcohol dehydrogenase (ADHIB) and evaluated for altered gene expression in vitro and metabolic activity in vivo via altered skin blood flow (Doppler velocimeter) and erythema (reflectance colorimeter a*) following topical challenge to 5 M EtOH, IPA, PG, and butanol (ButOH). Promoter polymorphisms G-887A and C-739T and exon G143A form eight ADHIB haplotypes with different frequencies in Caucasians vs Asians and exhibit variable gene expression and metabolic activity. Polymorphisms C-739T and G-887A independently alter gene expression, which is further increased by IPA and PG, but not EtOH or ButOH. EtOH and ButOH increase erythema as a function of skin blood flow. IPA increases skin blood flow without erythema and PG increased erythema with decreased skin blood flow, all as a function of ADHIB haplotype. PG-induced erythema was uniquely associated with tumor necrosis factor-alpha expression. Thus, erythema following alcohol exposure is alcohol type specific, has a pharmacogenetic basis related to ADHIB haplotype and can be functionally evaluated via Doppler velocimetry and reflectance colorimetry in vivo.

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    Cardona Lab
    03/01/08 | Dynamics of zebrafish somitogenesis.
    Schröter C, Herrgen L, Cardona A, Brouhard GJ, Feldman B, Oates AC
    Developmental Dynamics. 2008 Mar;237(3):545-53. doi: 10.1002/dvdy.21458

    Vertebrate somitogenesis is a rhythmically repeated morphogenetic process. The dependence of somitogenesis dynamics on axial position and temperature has not been investigated systematically in any species. Here we use multiple embryo time-lapse imaging to precisely estimate somitogenesis period and somite length under various conditions in the zebrafish embryo. Somites form at a constant period along the trunk, but the period gradually increases in the tail. Somite length varies along the axis in a stereotypical manner, with tail somites decreasing in size. Therefore, our measurements prompt important modifications to the steady-state Clock and Wavefront model: somitogenesis period, somite length, and wavefront velocity all change with axial position. Finally, we show that somitogenesis period changes more than threefold across the standard developmental temperature range, whereas the axial somite length distribution is temperature invariant. This finding indicates that the temperature-induced change in somitogenesis period exactly compensates for altered axial growth.

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    Murphy Lab
    03/01/08 | Signals and noise in an inhibitory interneuron diverge to control activity in nearby retinal ganglion cells.
    Murphy GJ, Rieke F
    Nature Neuroscience. 2008 Mar;11(3):318-26. doi: 10.1038/nn2045

    Information about sensory stimuli is represented by spatiotemporal patterns of neural activity. The complexity of the central nervous system, however, frequently obscures the origin and properties of signals and noise that underlie these activity patterns. We minimized this constraint by examining mechanisms governing correlated activity in mouse retinal ganglion cells (RGCs) under conditions in which light-evoked responses traverse a specific circuit, the rod bipolar pathway. Signals and noise in this circuit produced correlated synaptic input to neighboring On and Off RGCs. Temporal modulation of light intensity did not alter the degree to which noise in the input to nearby RGCs was correlated, and action potential generation in individual RGCs was largely insensitive to differences in network noise generated by dynamic and static light stimuli. Together, these features enable noise in shared circuitry to diminish simultaneous action potential generation in neighboring On and Off RGCs under a variety of conditions.

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    03/01/08 | Visual pattern memory requires foraging function in the central complex of Drosophila.
    Wang Z, Pan Y, Li W, Jiang H, Chatzimanolis L, Chang J, Gong Z, Liu L
    Learning & Memory. 2008 Mar;15(3):133-42. doi: 10.1101/lm.873008

    The role of the foraging (for) gene, which encodes a cyclic guanosine-3’,5’-monophosphate (cGMP)-dependent protein kinase (PKG), in food-search behavior in Drosophila has been intensively studied. However, its functions in other complex behaviors have not been well-characterized. Here, we show experimentally in Drosophila that the for gene is required in the operant visual learning paradigm. Visual pattern memory was normal in a natural variant rover (for(R)) but was impaired in another natural variant sitter (for(S)), which has a lower PKG level. Memory defects in for(S) flies could be rescued by either constitutive or adult-limited expression of for in the fan-shaped body. Interestingly, we showed that such rescue also occurred when for was expressed in the ellipsoid body. Additionally, expression of for in the fifth layer of the fan-shaped body restored sufficient memory for the pattern parameter "elevation" but not for "contour orientation," whereas expression of for in the ellipsoid body restored sufficient memory for both parameters. Our study defines a Drosophila model for further understanding the role of cGMP-PKG signaling in associative learning/memory and the neural circuit underlying this for-dependent visual pattern memory.

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    02/20/08 | Nonlinearities and contextual influences in auditory cortical responses modeled with multilinear spectrotemporal methods.
    Ahrens MB, Linden JF, Sahani M
    The Journal of Neuroscience. 2008 Feb 20;28(8):1929-42. doi: 10.1523/JNEUROSCI.3377-07.2008

    The relationship between a sound and its neural representation in the auditory cortex remains elusive. Simple measures such as the frequency response area or frequency tuning curve provide little insight into the function of the auditory cortex in complex sound environments. Spectrotemporal receptive field (STRF) models, despite their descriptive potential, perform poorly when used to predict auditory cortical responses, showing that nonlinear features of cortical response functions, which are not captured by STRFs, are functionally important. We introduce a new approach to the description of auditory cortical responses, using multilinear modeling methods. These descriptions simultaneously account for several nonlinearities in the stimulus-response functions of auditory cortical neurons, including adaptation, spectral interactions, and nonlinear sensitivity to sound level. The models reveal multiple inseparabilities in cortical processing of time lag, frequency, and sound level, and suggest functional mechanisms by which auditory cortical neurons are sensitive to stimulus context. By explicitly modeling these contextual influences, the models are able to predict auditory cortical responses more accurately than are STRF models. In addition, they can explain some forms of stimulus dependence in STRFs that were previously poorly understood.

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    02/19/08 | Structural basis of the metal specificity for nickel regulatory protein NikR.
    Phillips CM, Schreiter ER, Guo Y, Wang SC, Zamble DB, Drennan CL
    Biochemistry. 2008 Feb 19;47(7):1938-46. doi: 10.1021/bi702006h

    In the presence of excess nickel, Escherichia coli NikR regulates cellular nickel uptake by suppressing the transcription of the nik operon, which encodes the nickel uptake transporter, NikABCDE. Previously published in vitro studies have shown that NikR is capable of binding a range of divalent transition metal ions in addition to Ni2+, including Co2+, Cu2+, Zn2+, and Cd2+. To understand how the high-affinity nickel binding site of NikR is able to accommodate these other metal ions, and to improve our understanding of NikR's mechanism of binding to DNA, we have determined structures of the metal-binding domain (MBD) of NikR in the apo form and in complex with Cu2+ and Zn2+ ions and compared them with the previously published structures with Ni2+. We observe that Cu2+ ions bind in a manner very similar to that of Ni2+, with a square planar geometry but with longer bond lengths. Crystals grown in the presence of Zn2+ reveal a protein structure similar to that of apo MBD with a disordered alpha3 helix, but with two electron density peaks near the Ni2+ binding site corresponding to two Zn2+ ions. These structural findings along with biochemical data on NikR support a hypothesis that ordering of the alpha3 helix is important for repressor activation.

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    Gonen Lab
    02/15/08 | A conformational switch in bacteriophage p22 portal protein primes genome injection.
    Zheng H, Olia AS, Gonen M, Andrews S, Cingolani G, Gonen T
    Molecular Cell. 2008 Feb 15;29(3):376-83. doi: 10.1016/j.molcel.2007.11.034

    Double-stranded DNA (dsDNA) viruses such as herpesviruses and bacteriophages infect by delivering their genetic material into cells, a task mediated by a DNA channel called "portal protein." We have used electron cryomicroscopy to determine the structure of bacteriophage P22 portal protein in both the procapsid and mature capsid conformations. We find that, just as the viral capsid undergoes major conformational changes during virus maturation, the portal protein switches conformation from a procapsid to a mature phage state upon binding of gp4, the factor that initiates tail assembly. This dramatic conformational change traverses the entire length of the DNA channel, from the outside of the virus to the inner shell, and erects a large dome domain directly above the DNA channel that binds dsDNA inside the capsid. We hypothesize that this conformational change primes dsDNA for injection and directly couples completion of virus morphogenesis to a new cycle of infection.

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    Gonen Lab
    02/15/08 | Polymorphic assemblies and crystalline arrays of lens tetraspanin MP20.
    Gonen T, Hite RK, Cheng Y, Petre BM, Kistler J, Walz T
    Journal of Molecular Biology. 2008 Feb 15;376(2):380-92. doi: 10.1016/j.jmb.2007.09.001

    Members of the tetraspanin superfamily function as transmembrane scaffold proteins that mediate the assembly of membrane proteins into specific signaling complexes. Tetraspanins also interact with each other and concentrate membrane proteins into tetraspanin-enriched microdomains (TEMs). Here we report that lens-specific tetraspanin MP20 can form multiple types of higher-order assemblies and we present crystalline arrays of MP20. When isolated in the absence of divalent cations, MP20 is solubilized predominantly in tetrameric form, whereas the presence of divalent cations during solubilization promotes the association of MP20 tetramers into higher-order species. This effect only occurs when divalent cations are present during solubilization but not when divalent cations are added to solubilized tetrameric MP20, suggesting that other factors may also be involved. When purified MP20 tetramers are reconstituted with native lens lipids in the presence of magnesium, MP20 forms two-dimensional (2D) crystals. A projection map at 18 A resolution calculated from negatively stained 2D crystals showed that the building block of the crystal is an octamer consisting of two tetramers related to each other by 2-fold symmetry. In addition to 2D crystals, reconstitution of MP20 with native lipids also produced a variety of large protein-lipid complexes, and we present three-dimensional (3D) reconstructions of the four most abundant of these complexes in negative stain. The various complexes formed by MP20 most likely reflect the many ways in which tetraspanins can interact with each other to allow formation of TEMs.

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    Fetter Lab
    02/07/08 | GFP Reconstitution Across Synaptic Partners (GRASP) defines cell contacts and synapses in living nervous systems.
    Feinberg EH, Vanhoven MK, Bendesky A, Wang G, Fetter RD, Shen K, Bargmann CI
    Neuron. 2008 Feb 7;57(3):353-63. doi: 10.1016/j.neuron.2007.11.030

    The identification of synaptic partners is challenging in dense nerve bundles, where many processes occupy regions beneath the resolution of conventional light microscopy. To address this difficulty, we have developed GRASP, a system to label membrane contacts and synapses between two cells in living animals. Two complementary fragments of GFP are expressed on different cells, tethered to extracellular domains of transmembrane carrier proteins. When the complementary GFP fragments are fused to ubiquitous transmembrane proteins, GFP fluorescence appears uniformly along membrane contacts between the two cells. When one or both GFP fragments are fused to synaptic transmembrane proteins, GFP fluorescence is tightly localized to synapses. GRASP marks known synaptic contacts in C. elegans, correctly identifies changes in mutants with altered synaptic specificity, and can uncover new information about synaptic locations as confirmed by electron microscopy. GRASP may prove particularly useful for defining connectivity in complex nervous systems.

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