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161 Publications

Showing 31-40 of 161 results
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    Gonen Lab
    10/01/10 | Structure of the cholera toxin secretion channel in its closed state.
    Reichow SL, Korotkov KV, Hol WG, Gonen T
    Nature Structural & Molecular Biology. 2010 Oct;17(10):1226-32. doi: 10.1038/nsmb.1910

    The type II secretion system (T2SS) is a macromolecular complex spanning the inner and outer membranes of Gram-negative bacteria. Remarkably, the T2SS secretes folded proteins, including multimeric assemblies such as cholera toxin and heat-labile enterotoxin from Vibrio cholerae and enterotoxigenic Escherichia coli, respectively. The major outer membrane T2SS protein is the ’secretin’ GspD. Cryo-EM reconstruction of the V. cholerae secretin at 19-Å resolution reveals a dodecameric structure reminiscent of a barrel, with a large channel at its center that contains a closed periplasmic gate. The GspD periplasmic domain forms a vestibule with a conserved constriction, and it binds to a pentameric exoprotein and to the trimeric tip of the T2SS pseudopilus. By combining our results with structures of the cholera toxin and T2SS pseudopilus tip, we provide a structural basis for a possible secretion mechanism of the T2SS.

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    10/01/10 | The long road: peering into live cells.
    Lippincott-Schwartz J
    Nature cell biology. 2010 Oct;12(10):918. doi: 10.1038/ncb1010-918
    09/28/10 | Cellular organization of the neural circuit that drives Drosophila courtship behavior.
    Yu JY, Kanai MI, Demir E, Jefferis GS, Dickson BJ
    Current Biology. 2010 Sep 28;20(18):1602-14. doi: 10.1016/j.cub.2010.08.025

    BACKGROUND: Courtship behavior in Drosophila has been causally linked to the activity of the heterogeneous set of \~{}1500 neurons that express the sex-specific transcripts of the fruitless (fru) gene, but we currently lack an appreciation of the cellular diversity within this population, the extent to which these cells are sexually dimorphic, and how they might be organized into functional circuits. RESULTS: We used genetic methods to define 100 distinct classes of fru neuron, which we compiled into a digital 3D atlas at cellular resolution. We determined the polarity of many of these neurons and computed their likely patterns of connectivity, thereby assembling them into a neural circuit that extends from sensory input to motor output. The cellular organization of this circuit reveals neuronal pathways in the brain that are likely to integrate multiple sensory cues from other flies and to issue descending control signals to motor circuits in the thoracic ganglia. We identified 11 anatomical dimorphisms within this circuit: neurons that are male specific, are more numerous in males than females, or have distinct arborization patterns in males and females. CONCLUSIONS: The cellular organization of the fru circuit suggests how multiple distinct sensory cues are integrated in the fly’s brain to drive sex-specific courtship behavior. We propose that sensory processing and motor control are mediated through circuits that are largely similar in males and females. Sex-specific behavior may instead arise through dimorphic circuits in the brain and nerve cord that differentially couple sensory input to motor output.

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    09/27/10 | Starved cells use mitochondria for autophagosome biogenesis.
    Rambold AS, Lippincott-Schwartz J
    Cell cycle (Georgetown, Tex.). 2010 Sep 15;9(18):3633-4. doi: 10.4161/cc.9.18.13170
    Kainmueller Lab
    09/24/10 | Improving deformable surface meshes through omni-directional displacements and MRFs.
    Kainmueller D, Lamecker H, Seim H, Zachow S, Hege HC
    Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention. 2010;13(Pt 1):227-34

    Deformable surface models are often represented as triangular meshes in image segmentation applications. For a fast and easily regularized deformation onto the target object boundary, the vertices of the mesh are commonly moved along line segments (typically surface normals). However, in case of high mesh curvature, these lines may intersect with the target boundary at "non-corresponding" positions, or even not at all. Consequently, certain deformations cannot be achieved. We propose an approach that allows each vertex to move not only along a line segment, but within a surrounding sphere. We achieve globally regularized deformations via Markov Random Field optimization. We demonstrate the potential of our approach with experiments on synthetic data, as well as an evaluation on 2 x 106 coronoid processes of the mandible in Cone-Beam CTs, and 56 coccyxes (tailbones) in low-resolution CTs.

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    Kainmueller Lab
    09/24/10 | Model-based auto-segmentation of knee bones and cartilage in MRI data.
    Seim H, Kainmueller D, Lamecker H, Bindernagel M, Malinowski J, Zachow S
    Medical Image Analysis for the Clinic - A Grand Challenge, MICCAI 2010, the 13th International Conference on Medical Image Computing and Computer Assisted Intervention. 2010 Sep 24:

    We present a method for fully automatic segmentation of the bones and cartilages of the human knee from MRI data. Based on statistical shape models and graph-based optimization, first the femoral and tibial bone surfaces are reconstructed. Starting from the bone sur- faces the cartilages are segmented simultaneously with a multi object technique using prior knowledge on the variation of cartilage thickness. We validate our method on 40 clinical MRI datasets acquired before knee replacement. 

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    Svoboda Lab
    09/23/10 | Neural activity in barrel cortex underlying vibrissa-based object localization in mice.
    O’Connor DH, Peron SP, Huber D, Svoboda K
    Neuron. 2010 Sep 23;67(6):1048-61. doi: 10.1016/j.neuron.2010.08.026

    Classical studies have related the spiking of selected neocortical neurons to behavior, but little is known about activity sampled from the entire neural population. We recorded from neurons selected independent of spiking, using cell-attached recordings and two-photon calcium imaging, in the barrel cortex of mice performing an object localization task. Spike rates varied across neurons, from silence to >60 Hz. Responses were diverse, with some neurons showing large increases in spike rate when whiskers contacted the object. Nearly half the neurons discriminated object location; a small fraction of neurons discriminated perfectly. More active neurons were more discriminative. Layer (L) 4 and L5 contained the highest fractions of discriminating neurons (\~{}63% and 79%, respectively), but a few L2/3 neurons were also highly discriminating. Approximately 13,000 spikes per activated barrel column were available to mice for decision making. Coding of object location in the barrel cortex is therefore highly redundant.

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    Chklovskii Lab
    09/23/10 | Ultrastructural analysis of hippocampal neuropil from the connectomics perspective.
    Mishchenko Y, Hu T, Spacek J, Mendenhall J, Harris KM, Chklovskii DB
    Neuron. 2010 Sep 23;67(6):1009-20. doi: 10.1371/journal.pcbi.1001066

    Complete reconstructions of vertebrate neuronal circuits on the synaptic level require new approaches. Here, serial section transmission electron microscopy was automated to densely reconstruct four volumes, totaling 670 μm(3), from the rat hippocampus as proving grounds to determine when axo-dendritic proximities predict synapses. First, in contrast with Peters’ rule, the density of axons within reach of dendritic spines did not predict synaptic density along dendrites because the fraction of axons making synapses was variable. Second, an axo-dendritic touch did not predict a synapse; nevertheless, the density of synapses along a hippocampal dendrite appeared to be a universal fraction, 0.2, of the density of touches. Finally, the largest touch between an axonal bouton and spine indicated the site of actual synapses with about 80% precision but would miss about half of all synapses. Thus, it will be difficult to predict synaptic connectivity using data sets missing ultrastructural details that distinguish between axo-dendritic touches and bona fide synapses.

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    09/14/10 | Fast live simultaneous multiwavelength four-dimensional optical microscopy.
    Carlton PM, Boulanger J, Kervrann C, Sibarita J, Salamero J, Gordon-Messer S, Bressan D, Haber JE, Haase S, Shao L, Winoto L, Matsuda A, Kner P, Uzawa S, Gustafsson M, Kam Z, Agard DA, Sedat JW
    Proceedings of the National Academy of Sciences of the United States of America. 2010 Sep 14;107(37):16016-22. doi: 10.1073/pnas.1004037107

    Live fluorescence microscopy has the unique capability to probe dynamic processes, linking molecular components and their localization with function. A key goal of microscopy is to increase spatial and temporal resolution while simultaneously permitting identification of multiple specific components. We demonstrate a new microscope platform, OMX, that enables subsecond, multicolor four-dimensional data acquisition and also provides access to subdiffraction structured illumination imaging. Using this platform to image chromosome movement during a complete yeast cell cycle at one 3D image stack per second reveals an unexpected degree of photosensitivity of fluorophore-containing cells. To avoid perturbation of cell division, excitation levels had to be attenuated between 100 and 10,000× below the level normally used for imaging. We show that an image denoising algorithm that exploits redundancy in the image sequence over space and time allows recovery of biological information from the low light level noisy images while maintaining full cell viability with no fading.

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    09/14/10 | Structural basis of low-affinity nickel binding to the nickel-responsive transcription factor NikR from Escherichia coli.
    Phillips CM, Schreiter ER, Stultz CM, Drennan CL
    Biochemistry. 2010 Sep 14;49(36):7830-8. doi: 10.1021/bi100923j

    Escherichia coli NikR regulates cellular nickel uptake by binding to the nik operon in the presence of nickel and blocking transcription of genes encoding the nickel uptake transporter. NikR has two binding affinities for the nik operon: a nanomolar dissociation constant with stoichiometric nickel and a picomolar dissociation constant with excess nickel [Bloom, S. L., and Zamble, D. B. (2004) Biochemistry 43, 10029-10038; Chivers, P. T., and Sauer, R. T. (2002) Chem. Biol. 9, 1141-1148]. While it is known that the stoichiometric nickel ions bind at the NikR tetrameric interface [Schreiter, E. R., et al. (2003) Nat. Struct. Biol. 10, 794-799; Schreiter, E. R., et al. (2006) Proc. Natl. Acad. Sci. U.S.A. 103, 13676-13681], the binding sites for excess nickel ions have not been fully described. Here we have determined the crystal structure of NikR in the presence of excess nickel to 2.6 A resolution and have obtained nickel anomalous data (1.4845 A) in the presence of excess nickel for both NikR alone and NikR cocrystallized with a 30-nucleotide piece of double-stranded DNA containing the nik operon. These anomalous data show that excess nickel ions do not bind to a single location on NikR but instead reveal a total of 22 possible low-affinity nickel sites on the NikR tetramer. These sites, for which there are six different types, are all on the surface of NikR, and most are found in both the NikR alone and NikR-DNA structures. Using a combination of crystallographic data and molecular dynamics simulations, the nickel sites can be described as preferring octahedral geometry, utilizing one to three protein ligands (typically histidine) and at least two water molecules.

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