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  • 2010-2014  (4)
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  • 1
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    X-ray structure of the mouse serotonin 5-HT3 receptor (2014)
    Nature Publishing Group (NPG)
    Details
    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
    Published by Nature Publishing Group (NPG)
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  • 2
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    Whole transcriptome analysis of the coral Acropora millepora reveals complex responses to CO2-driven acidification during the initiation of calcification (2012)
    PANGAEA
    In:  Supplement to: Moya, Aurélie; Huisman, L; Ball, E E; Hayward, D C; Grasso, L C; Chua, C M; Woo, H N; Gattuso, Jean-Pierre; Forêt, S; Miller, David J (2012): Whole transcriptome analysis of the coral Acropora millepora reveals complex responses to CO2-driven acidification during the initiation of calcification. Molecular Ecology, 21(10), 2440-2454, https://doi.org/10.1111/j.1365-294X.2012.05554.x
    Details
    Publication Date: 2024-03-15
    Description: The impact of ocean acidification (OA) on coral calcification, a subject of intense current interest, is poorly understood in part because of the presence of symbionts in adult corals. Early life history stages of Acropora spp. provide an opportunity to study the effects of elevated CO(2) on coral calcification without the complication of symbiont metabolism. Therefore, we used the Illumina RNAseq approach to study the effects of acute exposure to elevated CO(2) on gene expression in primary polyps of Acropora millepora, using as reference a novel comprehensive transcriptome assembly developed for this study. Gene ontology analysis of this whole transcriptome data set indicated that CO(2) -driven acidification strongly suppressed metabolism but enhanced extracellular organic matrix synthesis, whereas targeted analyses revealed complex effects on genes implicated in calcification. Unexpectedly, expression of most ion transport proteins was unaffected, while many membrane-associated or secreted carbonic anhydrases were expressed at lower levels. The most dramatic effect of CO(2) -driven acidification, however, was on genes encoding candidate and known components of the skeletal organic matrix that controls CaCO(3) deposition. The skeletal organic matrix effects included elevated expression of adult-type galaxins and some secreted acidic proteins, but down-regulation of other galaxins, secreted acidic proteins, SCRiPs and other coral-specific genes, suggesting specialized roles for the members of these protein families and complex impacts of OA on mineral deposition. This study is the first exhaustive exploration of the transcriptomic response of a scleractinian coral to acidification and provides an unbiased perspective on its effects during the early stages of calcification.
    Keywords: Acropora millepora; Alkalinity, total; Alkalinity, total, standard deviation; Animalia; Aragonite saturation state; Aragonite saturation state, standard deviation; Benthic animals; Benthos; Bicarbonate ion; Calcite saturation state; Calculated using CO2SYS; Calculated using seacarb after Nisumaa et al. (2010); Carbon, inorganic, dissolved; Carbonate ion; Carbonate system computation flag; Carbon dioxide; Cnidaria; Coast and continental shelf; Containers and aquaria (20-1000 L or 〈 1 m**2); Fugacity of carbon dioxide (water) at sea surface temperature (wet air); Gene expression; Gene expression, fold change, relative; Gene expression (incl. proteomics); Gene name; Genetic sequence; Identification; Laboratory experiment; OA-ICC; Ocean Acidification International Coordination Centre; Partial pressure of carbon dioxide, standard deviation; Partial pressure of carbon dioxide (water) at sea surface temperature (wet air); pH; pH, standard deviation; Potentiometric; Replicates; Salinity; Single species; South Pacific; Species; Temperature, water; Temperature, water, standard deviation; Treatment; Tropical
    Type: Dataset
    Format: text/tab-separated-values, 2489 data points
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  • 3
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    Hybrid variational-ensemble assimilation of lightning observations in a mesoscale model (2014)
    Copernicus
    Details
    Publication Date: 2014-05-13
    Description: Lightning measurements from the Geostationary Lightning Mapper (GLM) that will be aboard the Goestationary Operational Environmental Satellite – R Series will bring new information that can have the potential for improving the initialization of numerical weather prediction models by assisting in the detection of clouds and convection through data assimilation. In this study we focus on investigating the utility of lightning observations in mesoscale and regional applications suitable for current operational environments, in which convection cannot be explicitly resolved. Therefore, we examine the impact of lightning observations on storm environment. Preliminary steps in developing a lightning data assimilation capability suitable for mesoscale modeling are presented in this paper. World Wide Lightning Location Network (WWLLN) data was utilized as a proxy for GLM measurements and was assimilated with the Maximum Likelihood Ensemble Filter, interfaced with the Nonhydrostatic Mesoscale Model core of the Weather Research and Forecasting system (WRF-NMM). In order to test this methodology, regional data assimilation experiments were conducted. Results indicate that lightning data assimilation had a positive impact on the following: information content, influencing several dynamical variables in the model (e.g., moisture, temperature, and winds), improving initial conditions, and partially improving WRF-NMM forecasts during several data assimilation cycles.
    Electronic ISSN: 2198-5634
    Topics: Geosciences , Physics
    Published by Copernicus on behalf of European Geosciences Union.
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  • 4
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    Development of a hybrid variational-ensemble data assimilation technique for observed lightning tested in a mesoscale model (2014)
    Copernicus
    Details
    Publication Date: 2014-10-10
    Description: Lightning measurements from the Geostationary Lightning Mapper (GLM) that will be aboard the Geostationary Operational Environmental Satellite – R Series will bring new information that can have the potential for improving the initialization of numerical weather prediction models by assisting in the detection of clouds and convection through data assimilation. In this study we focus on investigating the utility of lightning observations in mesoscale and regional applications suitable for current operational environments, in which convection cannot be explicitly resolved. Therefore, we examine the impact of lightning observations on storm environment. Preliminary steps in developing a lightning data assimilation capability suitable for mesoscale modeling are presented in this paper. World Wide Lightning Location Network (WWLLN) data was utilized as a proxy for GLM measurements and was assimilated with the Maximum Likelihood Ensemble Filter, interfaced with the Nonhydrostatic Mesoscale Model core of the Weather Research and Forecasting system (WRF-NMM). In order to test this methodology, regional data assimilation experiments were conducted. Results indicate that lightning data assimilation had a positive impact on the following: information content, influencing several dynamical variables in the model (e.g., moisture, temperature, and winds), and improving initial conditions during several data assimilation cycles. However, the 6 h forecast after the assimilation did not show a clear improvement in terms of root mean square (RMS) errors.
    Print ISSN: 1023-5809
    Electronic ISSN: 1607-7946
    Topics: Geosciences , Physics
    Published by Copernicus on behalf of European Geosciences Union.
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