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158 Publications

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    Riddiford Lab
    04/01/09 | The molecular mechanisms of cuticular melanization: the ecdysone cascade leading to dopa decarboxylase expression in Manduca sexta.
    Hiruma K, Riddiford LM
    Insect Biochemistry and Molecular Biology. 2009 Apr;39(4):245-53. doi: 10.1016/j.ibmb.2009.01.008

    Many insect developmental color changes are known to be regulated by both ecdysone and juvenile hormone. Yet the molecular mechanisms underlying this regulation have not been well understood. This review highlights the hormonal mechanisms involved in the regulation of two key enzymes [dopa decarboxylase (DDC) and phenoloxidase] necessary for insect cuticular melanization, and the molecular action of 20-hydroxyecdysone on various transcription factors leading to DDC expression at the end of a larval molt in Manduca sexta. In addition, the ecdysone cascade found in M. sexta is compared with that of other organisms.

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    03/27/09 | Bead-based mosaicing of single plane illumination microscopy images using geometric local descriptor matching.
    Preibisch S, Saalfeld S, Rohlfing T, Tomancak P
    Medical Imaging 2009: Image Processing. 2009 Mar 27;7259:72592S. doi: 10.1117/12.812612

    Single Plane Illumination Microscopy (SPIM) is an emerging microscopic technique that enables live imaging of large biological specimens in their entirety. By imaging the biological sample from multiple angles, SPIM has the potential to achieve isotropic resolution throughout relatively large biological specimens. For every angle, however, only a shallow section of the specimen is imaged with high resolution, whereas deeper regions appear increasingly blurred. Existing intensity-based registration techniques still struggle to robustly and accurately align images that are characterized by limited overlap and/or heavy blurring. To be able to register such images, we add sub-resolution fluorescent beads to the rigid agarose medium in which the imaged specimen is embedded. For each segmented bead, we store the relative location of its n nearest neighbors in image space as rotation-invariant geometric local descriptors. Corresponding beads between overlapping images are identified by matching these descriptors. The bead correspondences are used to simultaneously estimate the globally optimal transformation for each individual image. The final output image is created by combining all images in an angle-independent output space, using volume injection and local content-based weighting of contributing images. We demonstrate the performance of our approach on data acquired from living embryos of Drosophila and fixed adult C.elegans worms. Bead-based registration outperformed intensity-based registration in terms of computation speed by two orders of magnitude while producing bead registration errors below 1 μm (about 1 pixel). It, therefore, provides an ideal tool for processing of long term time-lapse recordings of embryonic development consisting of hundreds of time points.

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    Grigorieff Lab
    03/20/09 | Pentameric assembly of potassium channel tetramerization domain-containing protein 5.
    Dementieva IS, Tereshko V, McCrossan ZA, Solomaha E, Araki D, Xu C, Grigorieff N, Goldstein SA
    Journal of Molecular Biology. 2009 Mar 20;387(1):175-91. doi: 10.1016/j.jmb.2009.01.030

    We report the X-ray crystal structure of human potassium channel tetramerization domain-containing protein 5 (KCTD5), the first member of the family to be so characterized. Four findings were unexpected. First, the structure reveals assemblies of five subunits while tetramers were anticipated; pentameric stoichiometry is observed also in solution by scanning transmission electron microscopy mass analysis and analytical ultracentrifugation. Second, the same BTB (bric-a-brac, tramtrack, broad complex) domain surface mediates the assembly of five KCTD5 and four voltage-gated K(+) (Kv) channel subunits; four amino acid differences appear crucial. Third, KCTD5 complexes have well-defined N- and C-terminal modules separated by a flexible linker that swivels by approximately 30 degrees; the C-module shows a new fold and is required to bind Golgi reassembly stacking protein 55 with approximately 1 microM affinity, as judged by surface plasmon resonance and ultracentrifugation. Fourth, despite the homology reflected in its name, KCTD5 does not impact the operation of Kv4.2, Kv3.4, Kv2.1, or Kv1.2 channels.

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    03/15/09 | Variable phase retarder made of a dielectric elastomer actuator.
    Beck M, Fiolka R, Stemmer A
    Optics Letters. 2009 Mar 15;34(6):803-5

    We present a polymeric optical phase retarder that is electrically tunable by a dielectric elastomer actuator. The soft material device affords a large tuning range (14pi at lambda=488 nm) combined with high accuracy in optical path length and low drift rate (8.3 nm/min). Furthermore, the phase retarder is not sensitive to polarization, introduces a wavefront distortion141 kW/cm2). We show the dynamics for periodic phase modulation and demonstrate a simple drive technique for fast phase stepping. The polymer-based device is inexpensive, easy to fabricate, and its design can be adapted to specific applications.

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    03/11/09 | Loss of sensitivity in an analog neural circuit.
    Borghuis BG, Sterling P, Smith RG
    The Journal of Neuroscience: The Official Journal of the Society for Neuroscience. 2009 Mar 11;29:3045-58. doi: 10.1523/JNEUROSCI.5071-08.2009

    A low-contrast spot that activates just one ganglion cell in the retina is detected in the spike train of the cell with about the same sensitivity as it is detected behaviorally. This is consistent with Barlow’s proposal that the ganglion cell and later stages of spiking neurons transfer information essentially without loss. Yet, when losses of sensitivity by all preneural factors are accounted for, predicted sensitivity near threshold is considerably greater than behavioral sensitivity, implying that somewhere in the brain information is lost. We hypothesized that the losses occur mainly in the retina, where graded signals are processed by analog circuits that transfer information at high rates and low metabolic cost. To test this, we constructed a model that included all preneural losses for an in vitro mammalian retina, and evaluated the model to predict sensitivity at the cone output. Recording graded responses postsynaptic to the cones (from the type A horizontal cell) and comparing to predicted preneural sensitivity, we found substantial loss of sensitivity (4.2-fold) across the first visual synapse. Recording spike responses from brisk-transient ganglion cells stimulated with the same spot, we found a similar loss (3.5-fold) across the second synapse. The total retinal loss approximated the known overall loss, supporting the hypothesis that from stimulus to perception, most loss near threshold is retinal.

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    03/11/09 | Synaptic depolarization is more effective than back-propagating action potentials during induction of associative long-term potentiation in hippocampal pyramidal neurons.
    Hardie J, Spruston N
    The Journal of Neuroscience: The Official Journal of the Society for Neuroscience. 2009 Mar 11;29:3233-41. doi: 10.1523/JNEUROSCI.6000-08.2009

    Long-term potentiation (LTP) requires postsynaptic depolarization that can result from EPSPs paired with action potentials or larger EPSPs that trigger dendritic spikes. We explored the relative contribution of these sources of depolarization to LTP induction during synaptically driven action potential firing in hippocampal CA1 pyramidal neurons. Pairing of a weak test input with a strong input resulted in large LTP (approximately 75% increase) when the weak and strong inputs were both located in the apical dendrites. This form of LTP did not require somatic action potentials. When the strong input was located in the basal dendrites, the resulting LTP was smaller (< or =25% increase). Pairing the test input with somatically evoked action potentials mimicked this form of LTP. Thus, back-propagating action potentials may contribute to modest LTP, but local synaptic depolarization and/or dendritic spikes mediate a stronger form of LTP that requires spatial proximity of the associated synaptic inputs.

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    03/10/09 | Mimicking the folding pathway to improve homology-free protein structure prediction.
    DeBartolo J, Colubri A, Jha AK, Fitzgerald JE, Freed KF, Sosnick TR
    Proceedings of the National Academy of Sciences of the United States of America. 2009 Mar 10;106(10):3734-9. doi: 10.1073/pnas.0811363106

    Since the demonstration that the sequence of a protein encodes its structure, the prediction of structure from sequence remains an outstanding problem that impacts numerous scientific disciplines, including many genome projects. By iteratively fixing secondary structure assignments of residues during Monte Carlo simulations of folding, our coarse-grained model without information concerning homology or explicit side chains can outperform current homology-based secondary structure prediction methods for many proteins. The computationally rapid algorithm using only single (phi,psi) dihedral angle moves also generates tertiary structures of accuracy comparable with existing all-atom methods for many small proteins, particularly those with low homology. Hence, given appropriate search strategies and scoring functions, reduced representations can be used for accurately predicting secondary structure and providing 3D structures, thereby increasing the size of proteins approachable by homology-free methods and the accuracy of template methods that depend on a high-quality input secondary structure.

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    Looger LabSchreiter Lab
    03/06/09 | Crystal structures of the GCaMP calcium sensor reveal the mechanism of fluorescence signal change and aid rational design.
    Akerboom J, Rivera JD, Guilbe MM, Malavé EC, Hernandez HH, Tian L, Hires SA, Marvin JS, Looger LL, Schreiter ER
    The Journal of Biological Chemistry. 2009 Mar 6;284:6455-64. doi: 10.1074/jbc.M807657200

    The genetically encoded calcium indicator GCaMP2 shows promise for neural network activity imaging, but is currently limited by low signal-to-noise ratio. We describe x-ray crystal structures as well as solution biophysical and spectroscopic characterization of GCaMP2 in the calcium-free dark state, and in two calcium-bound bright states: a monomeric form that dominates at intracellular concentrations observed during imaging experiments and an unexpected domain-swapped dimer with decreased fluorescence. This series of structures provides insight into the mechanism of Ca2+-induced fluorescence change. Upon calcium binding, the calmodulin (CaM) domain wraps around the M13 peptide, creating a new domain interface between CaM and the circularly permuted enhanced green fluorescent protein domain. Residues from CaM alter the chemical environment of the circularly permuted enhanced green fluorescent protein chromophore and, together with flexible inter-domain linkers, block solvent access to the chromophore. Guided by the crystal structures, we engineered a series of GCaMP2 point mutants to probe the mechanism of GCaMP2 function and characterized one mutant with significantly improved signal-to-noise. The mutation is located at a domain interface and its effect on sensor function could not have been predicted in the absence of structural data.

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    Hess LabFetter Lab
    03/03/09 | Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure.
    Shtengel G, Galbraith JA, Galbraith CG, Lippincott-Schwartz J, Gillette JM, Manley S, Sougrat R, Waterman CM, Kanchanawong P, Davidson MW, Fetter RD, Hess HF
    Proceedings of the National Academy of Sciences of the United States of America. 2009 Mar 3;106:3125-30. doi: 10.1073/pnas.0813131106

    Understanding molecular-scale architecture of cells requires determination of 3D locations of specific proteins with accuracy matching their nanometer-length scale. Existing electron and light microscopy techniques are limited either in molecular specificity or resolution. Here, we introduce interferometric photoactivated localization microscopy (iPALM), the combination of photoactivated localization microscopy with single-photon, simultaneous multiphase interferometry that provides sub-20-nm 3D protein localization with optimal molecular specificity. We demonstrate measurement of the 25-nm microtubule diameter, resolve the dorsal and ventral plasma membranes, and visualize the arrangement of integrin receptors within endoplasmic reticulum and adhesion complexes, 3D protein organization previously resolved only by electron microscopy. iPALM thus closes the gap between electron tomography and light microscopy, enabling both molecular specification and resolution of cellular nanoarchitecture.

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    Svoboda Lab
    03/01/09 | A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale.
    Bohland JW, Wu C, Barbas H, Bokil H, Bota M, Breiter HC, Cline HT, Doyle JC, Freed PJ, Greenspan RJ, Haber SN, Hawrylycz M, Herrera DG, Hilgetag CC, Huang ZJ, Jones A, Jones EG, Karten HJ, Kleinfeld D, Kötter R, Lester HA, Lin JM, Mensh BD, Mikula S, Panksepp J, Price JL, Safdieh J, Saper CB, Schiff ND, Schmahmann JD, Stillman BW, Svoboda K, Swanson LW, Toga AW, Van Essen DC, Watson JD, Mitra PP
    PLoS Computational Biology. 2009 Mar;5(3):e1000334. doi: 10.1371/journal.pcbi.1000334

    In this era of complete genomes, our knowledge of neuroanatomical circuitry remains surprisingly sparse. Such knowledge is critical, however, for both basic and clinical research into brain function. Here we advocate for a concerted effort to fill this gap, through systematic, experimental mapping of neural circuits at a mesoscopic scale of resolution suitable for comprehensive, brainwide coverage, using injections of tracers or viral vectors. We detail the scientific and medical rationale and briefly review existing knowledge and experimental techniques. We define a set of desiderata, including brainwide coverage; validated and extensible experimental techniques suitable for standardization and automation; centralized, open-access data repository; compatibility with existing resources; and tractability with current informatics technology. We discuss a hypothetical but tractable plan for mouse, additional efforts for the macaque, and technique development for human. We estimate that the mouse connectivity project could be completed within five years with a comparatively modest budget.

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