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  • Oxford University Press  (29)
  • Wiley  (4)
  • Wiley-Blackwell  (4)
  • Nature Publishing Group (NPG)
  • 1
    Publication Date: 2014-08-15
    Description: Neurotransmitter-gated ion channels of the Cys-loop receptor family mediate fast neurotransmission throughout the nervous system. The molecular processes of neurotransmitter binding, subsequent opening of the ion channel and ion permeation remain poorly understood. Here we present the X-ray structure of a mammalian Cys-loop receptor, the mouse serotonin 5-HT3 receptor, at 3.5 A resolution. The structure of the proteolysed receptor, made up of two fragments and comprising part of the intracellular domain, was determined in complex with stabilizing nanobodies. The extracellular domain reveals the detailed anatomy of the neurotransmitter binding site capped by a nanobody. The membrane domain delimits an aqueous pore with a 4.6 A constriction. In the intracellular domain, a bundle of five intracellular helices creates a closed vestibule where lateral portals are obstructed by loops. This 5-HT3 receptor structure, revealing part of the intracellular domain, expands the structural basis for understanding the operating mechanism of mammalian Cys-loop receptors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hassaine, Gherici -- Deluz, Cedric -- Grasso, Luigino -- Wyss, Romain -- Tol, Menno B -- Hovius, Ruud -- Graff, Alexandra -- Stahlberg, Henning -- Tomizaki, Takashi -- Desmyter, Aline -- Moreau, Christophe -- Li, Xiao-Dan -- Poitevin, Frederic -- Vogel, Horst -- Nury, Hugues -- England -- Nature. 2014 Aug 21;512(7514):276-81. doi: 10.1038/nature13552. Epub 2014 Aug 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Laboratory of Physical Chemistry of Polymers and Membranes, Ecole Polytechnique Federale de Lausanne, CH-1015 Lausanne, Switzerland [2] [3] Theranyx, 163 Avenue de Luminy, 13288 Marseille, France. ; 1] Laboratory of Physical Chemistry of Polymers and Membranes, Ecole Polytechnique Federale de Lausanne, CH-1015 Lausanne, Switzerland [2]. ; Laboratory of Physical Chemistry of Polymers and Membranes, Ecole Polytechnique Federale de Lausanne, CH-1015 Lausanne, Switzerland. ; Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, CH-4058 Basel, Switzerland. ; Swiss Light Source, Paul Scherrer Institute, CH-5234 Villigen, Switzerland. ; Architecture et Fonction des Macromolecules Biologiques, CNRS UMR 7257 and Universite Aix-Marseille, F-13288 Marseille, France. ; 1] Universite Grenoble Alpes, IBS, F-38000 Grenoble, France [2] CNRS, IBS, F-38000 Grenoble, France [3] CEA, DSV, IBS, F-38000 Grenoble, France. ; Laboratory of Biomolecular Research, Paul Scherrer Institute, CH-5232 Villigen, Switzerland. ; Unite de Dynamique Structurale des Macromolecules, Institut Pasteur, CNRS UMR3528, F-75015 Paris, France. ; 1] Laboratory of Physical Chemistry of Polymers and Membranes, Ecole Polytechnique Federale de Lausanne, CH-1015 Lausanne, Switzerland [2] Universite Grenoble Alpes, IBS, F-38000 Grenoble, France [3] CNRS, IBS, F-38000 Grenoble, France [4] CEA, DSV, IBS, F-38000 Grenoble, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25119048" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Crystallography, X-Ray ; Mice ; Models, Molecular ; Molecular Sequence Data ; Neurotransmitter Agents/metabolism ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Receptors, Serotonin, 5-HT3/*chemistry/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2017-01-10
    Description: Trimethylation of histone H3K36 is a chromatin mark associated with active gene expression, which has been implicated in coupling transcription with mRNA splicing and DNA damage response. SETD2 is a major H3K36 trimethyltransferase, which has been implicated as a tumor suppressor in mammals. Here, we report the regulation of SETD2 protein stability by the proteasome system, and the identification of SPOP, a key subunit of the CUL3 ubiquitin E3 ligase complex, as a SETD2-interacting protein. We demonstrate that SPOP is critically involved in SETD2 stability control and that the SPOP/CUL3 complex is responsible for SETD2 polyubiquitination both in vivo and in vitro . ChIP-Seq analysis and biochemical experiments demonstrate that modulation of SPOP expression confers differential H3K36me3 on SETD2 target genes, and induce H3K36me3-coupled alternative splicing events. Together, these findings establish a functional connection between oncogenic SPOP and tumor suppressive SETD2 in the dynamic regulation of gene expression on chromatin.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 3
    Electronic Resource
    Electronic Resource
    Chichester [u.a.] : Wiley-Blackwell
    International Journal for Numerical Methods in Engineering 37 (1994), S. 3585-3603 
    ISSN: 0029-5981
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics , Technology
    Notes: In the paper we present a postprocessed type of a posteriori error estimate and a h-version adaptive procedure for the semidiscrete finite element method in dynamic analysis. In space the super-convergent patch recovery technique is used for determining higher-order accurate stresses and, thus, a spatial error estimate. In time a postprocessing technique is developed for obtaining a local error estimate for one step time integration schemes (the HHT-α method). Coupling the error estimate with a mesh generator, a h-version adaptive finite element procedure is presented for two-dimensional dynamic analysis. It updates the spatial mesh and time step automatically so that the discretization errors are controlled within specified tolerances. Numerical studies on different problems are presented for demonstrating the performances of the proposed adaptive procedure.
    Additional Material: 19 Ill.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    Chichester [u.a.] : Wiley-Blackwell
    International Journal for Numerical Methods in Engineering 39 (1996), S. 2131-2152 
    ISSN: 0029-5981
    Keywords: discontinuous Galerkin finite element method ; predictor-multicorrector ; adaptive time integration ; structural dynamics ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics , Technology
    Notes: This paper studies a time-discontinuous Galerkin finite element method for structural dynamic problems, by which both displacements and velocities are approximated as piecewise linear functions in the time domain and may be discontinuous at the discrete time levels. A new iterative solution algorithm which involves only one factorization for each fixed time step size and a few iterations at each step is presented for solving the resulted system of coupled equations. By using the jumps of the displacements and the velocities in the total energy norm as error indicators, an adaptive time-stepping procedure for selecting the proper time step size is described. Numerical examples including both single-DOF and multi-DOF problems are used to illustrate the performance of these algorithms. Comparisons with the exact results and/or the results by the Newmark integration scheme are given. It is shown that the time-discontinuous Galerkin finite element method discussed in this study possesses good accuracy (third order) and stability properties, its numerical implementation is not difficult, and the higher computational cost needed in each time step is compensated by use of a larger time step size.
    Additional Material: 20 Ill.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Chichester : Wiley-Blackwell
    Communications in Numerical Methods in Engineering 9 (1993), S. 273-292 
    ISSN: 1069-8299
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics , Technology
    Notes: A simple a posteriori local error estimator for time discretization in structural dynamic analysis is presented. It is derived from the difference of the solutions between an ordinary integration method (the Newmark scheme) and another higher-order one which assumes that the derivatives of accelerations vary linearly within each time step. It may be obtained directly without resolving new equations, so the additional computational cost is small and the implementation is convenient. Furthermore, it is shown that this error estimator may also be obtained by Taylor expansion or by a post-processing technique. Accordingly, an adaptive time-stepping procedure, which automatically adjusts the time-step size so that the local error at each time step is within a prescribed accuracy, is described. Numerical examples, including two single-DOF problems, a two-DOF problem and a multi-DOF model, are presented. The results show that the presented local error estimator is simple, reliable and accurate.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Chichester : Wiley-Blackwell
    Communications in Numerical Methods in Engineering 10 (1994), S. 313-320 
    ISSN: 1069-8299
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics , Technology
    Notes: In the paper we present a superconvergent patch recovery technique for obtaining higher-order-accurate finite-element solutions and thus a postprocessed type of L2 norm error estimate. Two modifications make our procedure different from the one proposed by Zienkiewicz and Zhu (1992), in which higher-order-accurate derivatives of the finite-element solution at nodes are determined. Firstly, the recovery process is made for element, not for nodes. An ‘element patch’, which represents the union of an element under consideration and the surrounding elements, is introduced. Secondly, the local error estimate is calculated directly from the improved solution for this element. Numerical tests on both 1D and 2D model problems show that this method can provide an asymptotically exact a posteriori L2 norm error estimate if the used element possesses superconvergent points for the solutions.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
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  • 7
    Publication Date: 1992-01-01
    Print ISSN: 0098-8847
    Electronic ISSN: 1096-9845
    Topics: Architecture, Civil Engineering, Surveying
    Published by Wiley
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  • 8
    Publication Date: 2013-06-08
    Description: COHCAP (City of Hope CpG Island Analysis Pipeline) is an algorithm to analyze single-nucleotide resolution DNA methylation data produced by either an Illumina methylation array or targeted bisulfite sequencing. The goal of the COHCAP algorithm is to identify CpG islands that show a consistent pattern of methylation among CpG sites. COHCAP is currently the only DNA methylation package that provides integration with gene expression data to identify a subset of CpG islands that are most likely to regulate downstream gene expression, and it can generate lists of differentially methylated CpG islands with ~50% concordance with gene expression from both cell line data and heterogeneous patient data. For example, this article describes known breast cancer biomarkers (such as estrogen receptor) with a negative correlation between DNA methylation and gene expression. COHCAP also provides visualization for quality control metrics, regions of differential methylation and correlation between methylation and gene expression. This software is freely available at https://sourceforge.net/projects/cohcap/ .
    Keywords: Nucleic acid modification, Computational Methods, Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 9
    Publication Date: 2015-05-09
    Description: Dipolarization fronts (DFs) are believed to play important roles in transferring plasmas, magnetic fluxes and energies in the magnetotail. Using the Cluster observations in 2003, electromagnetic energy conversion at the DFs is investigated by case and statistical studies. The case study indicates strongest energy conversion at the DF. The statistical study shows the similar features that the energy of the fields can be significantly transferred to the plasmas (load, J·E 〉0) at the DFs. These results are consistent with some recent simulations. Examining the electromagnetic fluctuations at the DFs, we suggest that the wave activities around the lower hybrid frequency may play an important role in the energy dissipation.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 10
    Publication Date: 2015-04-23
    Description: We propose a method using the redshift dependence of the Alcock–Paczynski (AP) test and volume effect to measure the cosmic expansion history. The galaxy two-point correlation function as a function of angle, (μ), is measured at different redshifts. Assuming an incorrect cosmological model to convert galaxy redshifts to distances, the shape of (μ) appears anisotropic due to the AP effect, and the amplitude is shifted by the change in comoving volume. Due to the redshift dependence of the AP and volume effect, both the shape and amplitude of (μ) exhibit redshift dependence. Similar to Li et al. ( 2014 ), we find that the redshift-space distortions (RSD) caused by galaxy peculiar velocities, although significantly distorting (μ), exhibit much less redshift evolution compared to the AP and volume effects. By focusing on the redshift dependence of (μ), we can correctly recover the cosmological parameters despite the contamination of RSD. The method is tested by using the Horizon Run 3 N -body simulation, from which we made a series of 1/8-sky mock surveys having eight million physically self-bound haloes and sampled to have roughly a uniform number density in z  = 0–1.5. We find the AP effect results in tight, unbiased constraints on the density parameter and dark energy equation of state, with 68.3% CL intervals m  ~ 0.03 and w  ~ 0.1, and the volume effect leads to much tighter constraints of m  ~ 0.007 and w  ~ 0.035.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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