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1. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment

Author: Eichiro Ichiishi, Dmitri Beglov, Bernard Maigret, Gyu Rie Lee, Artem B. Mamonov, Shoshana J. Wodak, Jonathan C. Fuller, Dima Kozakov, Jong Young Joung, Petr Popov, Xiaofeng Yu, Keehyoung Joo, João P. G. L. M. Rodrigues, Anna Vangone, Koen M. Visscher, Xiaoqin Zou, Paul A. Bates, Andriy Kryshtafovych, Shourya S. Roy Burman, Daisuke Kihara, Romina Oliva, Efrat Ben-Zeev, Jeffrey J. Gray, Yang Shen, Li C. Xue, Sameer Velankar, Emilie Neveu, Shruthi Viswanath, Dina Schneidman-Duhovny, Juan Esquivel-Rodríguez, Mieczyslaw Torchala, Amit Roy, Alexandre M. J. J. Bonvin, David R. Hall, Tanggis Bohnuud, Xusi Han, David W. Ritchie, Ron Elber, Daisuke Kuroda, Zhiwei Ma, Joan Segura, Carlos A. Del Carpio, Nicholas A. Marze, Jong Yun Kim, Andrej Sali, Petras J. Kundrotas, Ezgi Karaca, Neil J. Bruce, Chaok Seok, Panagiotis L. Kastritis, Shen You Huang, Ilya A. Vakser, Lim Heo, Sanbo Qin, Raphael A. G. Chaleil, Adrien S. J. Melquiond, Miguel Romero-Durana, Anisah W. Ghoorah, Surendra S. Negi, Andrey Tovchigrechko, Françoise Ochsenbein, Narcis Fernandez-Fuentes, Liming Qiu, Miriam Eisenstein, Mehdi Nellen, Marie-Dominique Devignes, Lenna X. Peterson, Jinchao Yu, Minkyung Baek, Brian G. Pierce, Hasup Lee, Toshiyuki Oda, Rebecca C. Wade, Raphael Guerois, Juan Fernández-Recio, Iain H. Moal, Edrisse Chermak, Sergei Grudinin, Sangwoo Park, Ivan Anishchenko, Chengfei Yan, Thom Vreven, Kentaro Tomii, Bing Xia, Hyung Rae Kim, Chiara Pallara, Jooyoung Lee, Kazunori D. Yamada, Xianjin Xu, Kenichiro Imai, Zhiping Weng, Luigi Cavallo, Tyler M. Borrman, Jianlin Cheng, Marc F. Lensink, Huan-Xiang Zhou, Jilong Li, Gydo C. P. van Zundert, Brian Jiménez-García, Tsukasa Nakamura, Scott E. Mottarella, Sandor Vajda, Institut de Recherche Interdisciplinaire [Villeneuve d'Ascq] ( IRI ), Université de Lille, Sciences et Technologies-Université de Lille, Droit et Santé-Centre National de la Recherche Scientifique ( CNRS ), European Molecular Biology Laboratory, European Bioinformatics Institute, Genome Center [UC Davis], University of California at Davis, Research Support Computing [Columbia], University of Missouri-Columbia, Bioinformatics Consortium and Department of Computer Science [Columbia], Department of Bioengineering and Therapeutic Sciences, University of California [San Francisco] ( UCSF ), Department of Pharmaceutical Chemistry, Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, University of California [San Francisco] ( UCSF ) -California Institute for Quantitative Biosciences, GN7 of the National Institute for Bioinformatics (INB) and Biocomputing Unit, Centro Nacional de Biotecnología (CSIC), Institute of Biological, Environmental and Rural Sciences ( IBERS ), Institute for Computational Engineering and Sciences [Austin] ( ICES ), University of Texas at Austin [Austin], Department of Computer Science, Department of Chemistry, Algorithms for Modeling and Simulation of Nanosystems ( NANO-D ), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Laboratoire Jean Kuntzmann ( LJK ), Université Pierre Mendès France - Grenoble 2 ( UPMF ) -Université Joseph Fourier - Grenoble 1 ( UJF ) -Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ) -Université Pierre Mendès France - Grenoble 2 ( UPMF ) -Université Joseph Fourier - Grenoble 1 ( UJF ) -Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ) -Institut National Polytechnique de Grenoble ( INPG ), Moscow Institute of Physics and Technology [Moscow] ( MIPT ), Seoul National University [Seoul], Florida State University [Tallahassee] ( FSU ), Computational Algorithms for Protein Structures and Interactions ( CAPSID ), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Department of Complex Systems, Artificial Intelligence & Robotics ( LORIA - AIS ), Laboratoire Lorrain de Recherche en Informatique et ses Applications ( LORIA ), Institut National de Recherche en Informatique et en Automatique ( Inria ) -Université de Lorraine ( UL ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Université de Lorraine ( UL ) -Centre National de la Recherche Scientifique ( CNRS ) -Laboratoire Lorrain de Recherche en Informatique et ses Applications ( LORIA ), Institut National de Recherche en Informatique et en Automatique ( Inria ) -Université de Lorraine ( UL ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Lorraine ( UL ) -Centre National de la Recherche Scientifique ( CNRS ), University of Mauritius, Biomolecular Modelling Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, G-INCPM, Weizmann Institute of Science, Chemical Research Support [Rehovot], Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch ( UTMB ), Program in Bioinformatics and Integrative Biology [Worcester], University of Massachusetts Medical School [Worcester] ( UMASS ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ), Bijvoet Center for Biomolecular Research [Utrecht], Utrecht University [Utrecht], Dalton Cardiovascular Research Center [Columbia], Department of Computer Science [Columbia], Informatics Intitute, Department of Biochemistry, University of Missouri, UNIVERSITY OF MISSOURI, Toyota Technological Institute at Chicago [Chicago] ( TTIC ), Department of Biological Sciences, Purdue University, Purdue University [West Lafayette], Department of Computer Science [Purdue], Bioinformatics and Computational Biosciences Branch, Rocky Mountain Laboratories, Molecular and Cellular Modeling Group, Heidelberg Institute of Theoretical Studies, Center for Molecular Biology ( ZMBH ), Universität Heidelberg [Heidelberg], Interdisciplinary Center for Scientiﬁc Computing ( IWR ), Department of Molecular Biosciences [Lawrence], University of Kansas [Lawrence] ( KU ), Computational Biology Research Center ( CBRC ), National Institute of Advanced Industrial Science and Technology ( AIST ), Graduate School of Frontier Sciences, The University of Tokyo, Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center - Centro Nacional de Supercomputacion ( BSC - CNS ), Center for In-Silico Protein Science, Korea Institute for Advanced Study ( KIAS ), Center for Advanced Computation, Department of Biomedical Engineering [Boston], Boston University [Boston] ( BU ), Institute of Biological Diversity, International Pacific Institute of Indiana, Drosophila Genetic Resource Center, Kyoto Institute of Technology, International University of Health and Welfare Hospital ( IUHW Hospital ), International University of Health and Welfare Hospital, Department of Chemical and Biomolecular Engineering [Baltimore], Johns Hopkins University ( JHU ), Program in Molecular Biophysics [Baltimore], King Abdullah University of Science and Technology ( KAUST ), University of Naples, J Craig Venter Institute, Structural Biology Research Center, VIB, 1050 Brussels, Belgium, Institut de Recherche Interdisciplinaire [Villeneuve d'Ascq] (IRI), Université de Lille, Sciences et Technologies-Université de Lille, Droit et Santé-Centre National de la Recherche Scientifique (CNRS), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, University of California [Davis] (UC Davis), University of California (UC)-University of California (UC), University of Missouri [Columbia] (Mizzou), University of Missouri System, University of California [San Francisco] (UC San Francisco), Centro Nacional de Biotecnología [Madrid] (CNB-CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Institute of Biological, Environmental and Rural Sciences (IBERS), Institute for Computational Engineering and Sciences [Austin] (ICES), Algorithms for Modeling and Simulation of Nanosystems (NANO-D), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Laboratoire Jean Kuntzmann (LJK ), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Moscow Institute of Physics and Technology [Moscow] (MIPT), Seoul National University [Seoul] (SNU), Florida State University [Tallahassee] (FSU), Computational Algorithms for Protein Structures and Interactions (CAPSID), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Department of Complex Systems, Artificial Intelligence & Robotics (LORIA - AIS), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Biomolecular Modelling Laboratory [London], The Francis Crick Institute [London], Weizmann Institute of Science [Rehovot, Israël], The University of Texas Medical Branch (UTMB), University of Massachusetts Medical School [Worcester] (UMASS), University of Massachusetts System (UMASS)-University of Massachusetts System (UMASS), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Assemblage moléculaire et intégrité du génome (AMIG), Département Biochimie, Biophysique et Biologie Structurale (B3S), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), University of Missouri System-University of Missouri System, Toyota Technological Institute at Chicago [Chicago] (TTIC), Department of Biological Sciences [Lafayette IN], Heidelberg Institute for Theoretical Studies (HITS ), Center for Molecular Biology (ZMBH), Universität Heidelberg [Heidelberg] = Heidelberg University, Interdisciplinary Center for Scientiﬁc Computing (IWR), University of Kansas [Lawrence] (KU), Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), The University of Tokyo (UTokyo), Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), Korea Institute for Advanced Study (KIAS), Boston University [Boston] (BU), International University of Health and Welfare Hospital (IUHW Hospital), Johns Hopkins University (JHU), King Abdullah University of Science and Technology (KAUST), University of Naples Federico II = Università degli studi di Napoli Federico II, J. Craig Venter Institute, VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium], Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Droit et Santé-Université de Lille, Sciences et Technologies, University of California-University of California, University of California [San Francisco] (UCSF), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL), University of Naples Federico II, Barcelona Supercomputing Center, NMR Spectroscopy, and Sub NMR Spectroscopy
Subjects: 0301 basic medicine, Protein Conformation, alpha-Helical, Protein Folding, Computer science, International Cooperation, Amino Acid Motifs, Oligomer state, Homoprotein, DATA-BANK, computer.software_genre, Molecular Docking Simulation, Biochemistry, CAPRI Round 30, DESIGN, Structural Biology, ALIGN, Blind prediction, AFFINITY, Protein interaction, Enginyeria biomèdica [Àrees temàtiques de la UPC], ZDOCK, Oligomer State, computer.file_format, Articles, Protein structure prediction, Proteïnes--Investigació, 3. Good health, WEB SERVER, CASP, Thermodynamics, Data mining, CAPRI, Protein docking, Molecular Biology, Algorithms, INTERFACES, Protein Binding, [ INFO.INFO-MO ] Computer Science [cs]/Modeling and Simulation, Bioinformatics, STRUCTURAL BIOLOGY, Computational biology, Molecular Dynamics Simulation, Article, 03 medical and health sciences, [ INFO.INFO-BI ] Computer Science [cs]/Bioinformatics [q-bio.QM], Heteroprotein, Humans, Protein binding, Macromolecular docking, Protein Interaction Domains and Motifs, Homology modeling, ALGORITHM, Protein-protein docking, Internet, Binding Sites, Models, Statistical, 030102 biochemistry & molecular biology, Bacteria, Sequence Homology, Amino Acid, Computational Biology, Proteins, Protein Data Bank, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Protein Structure, Tertiary, 030104 developmental biology, Structural biology, Docking (molecular), Protein structure, Protein Conformation, beta-Strand, Protein Multimerization, oligomer state, blind prediction, protein interaction, protein docking, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], computer, Software
Abstract: We present the results for CAPRI Round 30, the first joint CASP-CAPRI experiment, which brought together experts from the protein structure prediction and protein–protein docking communities. The Round comprised 25 targets from amongst those submitted for the CASP11 prediction experiment of 2014. The targets included mostly homodimers, a few homotetramers, and two heterodimers, and comprised protein chains that could readily be modeled using templates from the Protein Data Bank. On average 24 CAPRI groups and 7 CASP groups submitted docking predictions for each target, and 12 CAPRI groups per target participated in the CAPRI scoring experiment. In total more than 9500 models were assessed against the 3D structures of the corresponding target complexes. Results show that the prediction of homodimer assemblies by homology modeling techniques and docking calculations is quite successful for targets featuring large enough subunit interfaces to represent stable associations. Targets with ambiguous or inaccurate oligomeric state assignments, often featuring crystal contact-sized interfaces, represented a confounding factor. For those, a much poorer prediction performance was achieved, while nonetheless often providing helpful clues on the correct oligomeric state of the protein. The prediction performance was very poor for genuine tetrameric targets, where the inaccuracy of the homology-built subunit models and the smaller pair-wise interfaces severely limited the ability to derive the correct assembly mode. Our analysis also shows that docking procedures tend to perform better than standard homology modeling techniques and that highly accurate models of the protein components are not always required to identify their association modes with acceptable accuracy. We are most grateful to the PDBe at the European Bioinformatics Institute in Hinxton, UK, for hosting the CAPRI website. Our deepest thanks go to all the structural biologists and to the following structural genomics initiatives: Northeast Structural Genomics Consortium, Joint Center for Structural Genomics, NatPro PSI:Biology, New York Structural Genomics Research Center, Midwest Center for Structural Genomics, Structural Genomics Consortium, for contributing the targets for this joint CASP-CAPRI experiment. MFL acknowledges support from the FRABio FR3688 Research Federation “Structural & Functional Biochemistry of Biomolecular Assemblies.”
Published: 2016
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2. Four principles to establish a universal virus taxonomy

Author: Peter Simmonds, Evelien M. Adriaenssens, F. Murilo Zerbini, Nicola G. A. Abrescia, Pakorn Aiewsakun, Poliane Alfenas-Zerbini, Yiming Bao, Jakub Barylski, Christian Drosten, Siobain Duffy, W. Paul Duprex, Bas E. Dutilh, Santiago F. Elena, Maria Laura García, Sandra Junglen, Aris Katzourakis, Eugene V. Koonin, Mart Krupovic, Jens H. Kuhn, Amy J. Lambert, Elliot J. Lefkowitz, Małgorzata Łobocka, Cédric Lood, Jennifer Mahony, Jan P. Meier-Kolthoff, Arcady R. Mushegian, Hanna M. Oksanen, Minna M. Poranen, Alejandro Reyes-Muñoz, David L. Robertson, Simon Roux, Luisa Rubino, Sead Sabanadzovic, Stuart Siddell, Tim Skern, Donald B. Smith, Matthew B. Sullivan, Nobuhiro Suzuki, Dann Turner, Koenraad Van Doorslaer, Anne-Mieke Vandamme, Arvind Varsani, Nikos Vasilakis, University of Oxford, Quadram Institute Bioscience [Norwich, U.K.] (QIB), Biotechnology and Biological Sciences Research Council (BBSRC), Universidade Federal de Viçosa = Federal University of Viçosa (UFV), Center for Cooperative Research in Biosciences [Derio, Spain], Mahidol University [Bangkok], University of Chinese Academy of Sciences [Beijing] (UCAS), Rutgers, The State University of New Jersey [New Brunswick] (RU), Rutgers University System (Rutgers), Utrecht University [Utrecht], Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], National Institutes of Health [Bethesda] (NIH), Virologie des archées - Archaeal Virology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University College Cork (UCC), MRC - University of Glasgow Centre for Virus Research, Lawrence Berkeley National Laboratory [Berkeley] (LBNL), CNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] (IPSP), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Mississippi State University [Mississippi], Okayama University, University of the West of England [Bristol] (UWE Bristol), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Arizona State University [Tempe] (ASU), The University of Texas Medical Branch (UTMB), European Project: 865694,H2020-EU.1.1. - EXCELLENT SCIENCE - European Research Council (ERC),DiversiPHI(2020), Instituto de Higiene e Medicina Tropical (IHMT), Global Health and Tropical Medicine (GHTM), TB, HIV and opportunistic diseases and pathogens (THOP), Faculty Common Matters (Faculty of Biology and Environmental Sciences), Molecular Principles of Viruses, Molecular and Integrative Biosciences Research Programme, and Molecular and Translational Virology
Subjects: Neuroscience(all), [SDV]Life Sciences [q-bio], principles, R Medicine, Medical and Health Sciences, General Biochemistry, Genetics and Molecular Biology, SDG 3 - Good Health and Well-being, Immunology and Microbiology(all), Humans, Bacteriophages, Phylogeny, Taxonomy, 11832 Microbiology and virology, Agricultural and Veterinary Sciences, General Immunology and Microbiology, Biochemistry, Genetics and Molecular Biology(all), General Neuroscience, universal virus taxonomy, Biodiversity, Biological Sciences, Medical Terminology, Infectious Diseases, 12D8623N#57012320, PDMT2/21/038#56345426, Viruses, 1181 Ecology, evolutionary biology, Metagenomics, Infection, General Agricultural and Biological Sciences, QR355 Virology, Developmental Biology
Abstract: 1759874.Y.B.wassupportedbythe ProfessionalAssociationoftheAllianceof Publisher Copyright: Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. A universal taxonomy of viruses is essential for a comprehensive view of the virus world and for communicating the complicated evolutionary relationships among viruses. However, there are major differences in the conceptualisation and approaches to virus classification and nomenclature among virologists, clinicians, agronomists, and other interested parties. Here, we provide recommendations to guide the construction of a coherent and comprehensive virus taxonomy, based on expert scientific consensus. Firstly, assignments of viruses should be congruent with the best attainable reconstruction of their evolutionary histories, i.e., taxa should be monophyletic. This fundamental principle for classification of viruses is currently included in the International Committee on Taxonomy of Viruses (ICTV) code only for the rank of species. Secondly, phenotypic and ecological properties of viruses may inform, but not override, evolutionary relatedness in the placement of ranks. Thirdly, alternative classifications that consider phenotypic attributes, such as being vector-borne (e.g., “arboviruses”), infecting a certain type of host (e.g., “mycoviruses,” “bacteriophages”) or displaying specific pathogenicity (e.g., “human immunodeficiency viruses”), may serve important clinical and regulatory purposes but often create polyphyletic categories that do not reflect evolutionary relationships. Nevertheless, such classifications ought to be maintained if they serve the needs of specific communities or play a practical clinical or regulatory role. However, they should not be considered or called taxonomies. Finally, while an evolution-based framework enables viruses discovered by metagenomics to be incorporated into the ICTV taxonomy, there are essential requirements for quality control of the sequence data used for these assignments. Combined, these four principles will enable future development and expansion of virus taxonomy as the true evolutionary diversity of viruses becomes apparent. publishersversion published
Published: 2023
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3. INTS13 variants causing a recessive developmental ciliopathy disrupt assembly of the Integrator complex

Author: Lauren G. Mascibroda, Mohammad Shboul, Nathan D. Elrod, Laurence Colleaux, Hanan Hamamy, Kai-Lieh Huang, Natoya Peart, Moirangthem Kiran Singh, Hane Lee, Barry Merriman, Jeanne N. Jodoin, Poojitha Sitaram, Laura A. Lee, Raja Fathalla, Baeth Al-Rawashdeh, Osama Ababneh, Mohammad El-Khateeb, Nathalie Escande-Beillard, Stanley F. Nelson, Yixuan Wu, Liang Tong, Linda J. Kenney, Sudipto Roy, William K. Russell, Jeanne Amiel, Bruno Reversade, Eric J. Wagner, The University of Texas Medical Branch (UTMB), Jordan University of Science and Technology [Irbid, Jordan] (JUST), Marseille medical genetics - Centre de génétique médicale de Marseille (MMG), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Imagine - Institut des maladies génétiques (IMAGINE - U1163), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Hôpital Universitaire de Genève = University Hospitals of Geneva (HUG), University of California [Los Angeles] (UCLA), University of California (UC), Vanderbilt University Medical Center [Nashville], Vanderbilt University [Nashville], National Center for Diabetes, Endocrinology and Genetics, P.O. Box 13165, Amman 11942, Jordan, The University of Jordan (JU), Koç University, Columbia University [New York], Agency for science, technology and research [Singapore] (A*STAR), Reversade, Bruno, Mascibroda, Lauren G., Shboul, Mohammad, Elrod, Nathan D., Colleaux, Laurence, Hamamy, Hanan, Huang, Kai-Lieh, Peart, Natoya, Singh, Moirangthem, Lee, Hane, Merriman, Barry, Jodoin, Jeanne N., Sitaram, Poojitha, Lee, Laura A., Fathalla, Raja, Al-Rawashdeh, Baeth, Ababneh, Osama, El-Khateeb, Mohammad, Escande-Beillard, Nathalie, Nelson, Stanley F., Wu, Yixuan, Tong, Liang, Kenney, Linda J., Roy, Sudipto, Russell, William K., Amiel, Jeanne, Wagner, Eric J., and School of Medicine
Subjects: Multidisciplinary, Molecular biology, Homozygote, General Physics and Astronomy, Cell Cycle Proteins, Diseases, General Chemistry, Orofaciodigital Syndromes, General Biochemistry, Genetics and Molecular Biology, Ciliopathies, Cilia, Humans, Mutation, Orofaciodigital syndromes, RNA, RNA polymerase II, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Genetics, RNA Polymerase II, Carrier Proteins
Abstract: Oral-facial-digital (OFD) syndromes are a heterogeneous group of congenital disorders characterized by malformations of the face and oral cavity, and digit anomalies. Mutations within 12 cilia-related genes have been identified that cause several types of OFD, suggesting that OFDs constitute a subgroup of developmental ciliopathies. Through homozygosity mapping and exome sequencing of two families with variable OFD type 2, we identified distinct germline variants in INTS13, a subunit of the Integrator complex. This multiprotein complex associates with RNA Polymerase II and cleaves nascent RNA to modulate gene expression. We determined that INTS13 utilizes its C-terminus to bind the Integrator cleavage module, which is disrupted by the identified germline variants p.S652L and p.K668Nfs*9. Depletion of INTS13 disrupts ciliogenesis in human cultured cells and causes dysregulation of a broad collection of ciliary genes. Accordingly, its knockdown in Xenopus embryos leads to motile cilia anomalies. Altogether, we show that mutations in INTS13 cause an autosomal recessive ciliopathy, which reveals key interactions between components of the Integrator complex. The integrator complex is required for the synthesis of protein coding and non-coding RNA and contains the protein INTS13. Here, the authors find germline mutations in INTS13 in two families with oral facial digital syndrome and show that the mutation affects the c-terminal domain of the protein and disrupts cilliogenesis., We thank all families for partaking in this study. The authors would also like to thank members of their team for technical assistance and fruitful discussions. This work was supported by the UCLA California Center for Rare Diseases to H.L., S.F.N. and by a grant from the French Ministry of Health to J.A. This work was supported by the National Institutes of Health grant R01-GM134539 (E.J.W.), and the Welch Foundation grant H-1889 to The University of Texas Medical Branch at Galveston (E.J.W.). The UTMB Mass Spectrometry Facility is supported in part by The Cancer Prevention Research Institute of Texas (CPRIT) grant number RP190682 (W.K.R). M.K.S. was supported by CPRIT grant number P71709- B01. M.Singh was supported by CPRT RP200650 and L.J.K. was supported by a Texas STAR award. B.R. is a fellow of the Branco Weiss Foundation, an NRF Investigator, Young EMBO Investigator and recipient of inaugural UIBR funding from the Biomedical Research Council, A*STAR, Singapore.
Published: 2022
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4. Predicting future cognitive decline from non-brain and multimodal brain imaging data in healthy and pathological aging

Author: Hebling Vieira, Bruno, Liem, Franziskus, Dadi, Kamalaker, Engemann, Denis A, Gramfort, Alexandre, Bellec, Pierre, Craddock, Richard Cameron, Damoiseaux, Jessica S, Steele, Christopher J, Yarkoni, Tal, Langer, Nicolas, Margulies, Daniel S, Varoquaux, Gael, Universität Zürich [Zürich] = University of Zurich (UZH), Modèles et inférence pour les données de Neuroimagerie (MIND), IFR49 - Neurospin - CEA, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Université du Québec à Montréal = University of Québec in Montréal (UQAM), The University of Texas Medical Branch (UTMB), Wayne State University [Detroit], Concordia University [Montreal], The University of Texas Medical School at Houston, Centre de Recherche de l'Institut du Cerveau et de la Moelle épinière (CRICM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Méthodes computationnelles et mathématiques pour comprendre la société et la santé à partir de données (SODA), Inria Saclay - Ile de France, ANR-20-IADJ-0002,AI-cog,IA pour les sociétés touchées par le vieillissement: des concepts fondamentaux aux outils pratiques pour l'apprentissage cognitif facilité par l'IA(2020), University of Zurich, and Hebling Vieira, Bruno
Subjects: Aging, Neuroimaging, 2717 Geriatrics and Gerontology, [STAT.OT]Statistics [stat]/Other Statistics [stat.ML], 1309 Developmental Biology, 1302 Aging, Activities of Daily Living, Biomarker, Machine learning, Predictive modeling, Cross-validation, Open science, [INFO.INFO-IM]Computer Science [cs]/Medical Imaging, Humans, Cognitive Dysfunction, Aged, Aged, 80 and over, [STAT.AP]Statistics [stat]/Applications [stat.AP], 10093 Institute of Psychology, General Neuroscience, Brain, 2800 General Neuroscience, Middle Aged, Magnetic Resonance Imaging, 2728 Neurology (clinical), Neurology (clinical), Geriatrics and Gerontology, 150 Psychology, Developmental Biology
Abstract: Previous literature has focused on predicting a diagnostic label from structural brain imaging. Since subtle changes in the brain precede a cognitive decline in healthy and pathological aging, our study predicts future decline as a continuous trajectory instead. Here, we tested whether baseline multimodal neuroimaging data improve the prediction of future cognitive decline in healthy and pathological aging. Nonbrain data (demographics, clinical, and neuropsychological scores), structural MRI, and functional connectivity data from OASIS-3 (N = 662; age = 46–96 years) were entered into cross-validated multitarget random forest models to predict future cognitive decline (measured by CDR and MMSE), on average 5.8 years into the future. The analysis was preregistered, and all analysis code is publicly available. Combining non-brain with structural data improved the continuous prediction of future cognitive decline (best test-set performance: R2 = 0.42). Cognitive performance, daily functioning, and subcortical volume drove the performance of our model. Including functional connectivity did not improve predictive accuracy. In the future, the prognosis of age-related cognitive decline may enable earlier and more effective individualized cognitive, pharmacological, and behavioral interventions., Neurobiology of Aging, 118, ISSN:0197-4580, ISSN:1558-1497
Published: 2022
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5. Hepatitis C virus proteins induce lipogenesis and defective triglyceride secretion in transgenic mice

Author: Stanley M. Lemon, Emilie Mérour, Hervé Lerat, Hélène L. Kammoun, Celine Callens, Martin R. Higgs, Jean-Michel Pawlotsky, Fabienne Foufelle, Isabelle Hainault, Institut Mondor de Recherche Biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-IFR10, Centre de Recherche des Cordeliers (CRC (UMR_S 872)), Université Paris Descartes - Paris 5 (UPD5)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institute of Human Infections and Immunity, The University of Texas Medical Branch (UTMB), Service de bactériologie, virologie, hygiène [Mondor], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Institut Mondor de Recherche Biomédicale ( IMRB ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 ( UPEC UP12 ), Centre de Recherche des Cordeliers ( CRC (UMR_S 872) ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), The University of Texas Medical Branch ( UTMB ), Assistance publique - Hôpitaux de Paris (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 ( UPEC UP12 ), Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Guellaen, Georges
Subjects: Male, medicine.medical_specialty, Transgene, Blotting, Western, Mice, Transgenic, Lipids and Lipoproteins: Metabolism, Regulation, and Signaling, Hepacivirus, Biology, Endoplasmic Reticulum, Biochemistry, Mice, Viral Proteins, 03 medical and health sciences, 0302 clinical medicine, Internal medicine, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, medicine, Animals, Humans, Secretion, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, Triglycerides, 030304 developmental biology, Cytopathic effect, 0303 health sciences, Reverse Transcriptase Polymerase Chain Reaction, Lipogenesis, Fatty liver, virus diseases, Lipid metabolism, Cell Biology, medicine.disease, Hepatitis C, Virology, digestive system diseases, 3. Good health, Fatty Liver, Mice, Inbred C57BL, Disease Models, Animal, Endocrinology, Liver, Unfolded protein response, 030211 gastroenterology & hepatology, Steatosis, Sterol Regulatory Element Binding Protein 1
Abstract: This research was originally published in The Journal of Biological Chemistry. © the American Society for Biochemistry and Molecular Biology; International audience; Chronic hepatitis C virus (HCV) infection is associated with altered lipid metabolism and hepatocellular steatosis. Virus-induced steatosis is a cytopathic effect of HCV replication. The goal of this study was to examine the mechanisms underlying HCV-induced lipid metabolic defects in a transgenic mouse model expressing the full HCV protein repertoire at levels corresponding to natural human infection. In this model, expression of the HCV full-length open reading frame was associated with hepatocellular steatosis and reduced plasma triglyceride levels. Triglyceride secretion was impaired, whereas lipogenesis was activated. Increased lipogenic enzyme transcription was observed, resulting from maturational activation and nuclear translocation of sterol regulatory element-binding protein 1c (SREBP1c). However, endoplasmic reticulum (ER) stress markers were expressed at similar levels in both HCV transgenic mice and their wild type counterparts, suggesting that SREBP1c proteolytic cleavage in the presence of HCV proteins was independent of ER stress. In conclusion, transgenic mice expressing the HCV full-length polyprotein at low levels have decreased plasma triglyceride levels and develop hepatocellular steatosis in the same way as HCV-infected patients. In these mice, SREBP1c activation by one or several HCV proteins induces de novo triglyceride synthesis via the lipogenic pathway, in a manner independent of ER stress, whereas triglyceride secretion is simultaneously reduced.
Published: 2009
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6. Behavioural responses of juvenile cuttlefish (Sepia officinalis) to local water movements

Author: Ludovic Dickel, Bernd U. Budelmann, Jean G. Boal, Spogmai Komak, National Resource Center for Cephalopods, The University of Texas Medical Branch (UTMB), Millersville University - Dpt of Biology, EA3211 Physiologie du Comportement des Céphalopodes, Groupe Mémoire et Plasticité comportementale (GMPc), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), The University of Texas Medical Branch ( UTMB ), Groupe Mémoire et Plasticité comportementale ( GMPc ), Université de Caen Normandie ( UNICAEN ), Normandie Université ( NU ) -Normandie Université ( NU ) -Université de Caen Normandie ( UNICAEN ), and Normandie Université ( NU ) -Normandie Université ( NU )
Subjects: Amphibian, Cuttlefish, Cephalopods, [ SDV.BA.ZI ] Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Physiology, Lateral line, Aquatic Science, Oceanography, Lolliguncula brevis, [ SDV.NEU.PC ] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Psychology and behavior, [ SDV.NEU.SC ] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Cognitive Sciences, 03 medical and health sciences, 0302 clinical medicine, biology.animal, Juvenile, 14. Life underwater, Habituation, Sepia, 030304 developmental biology, 0303 health sciences, biology, [SDV.NEU.PC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Psychology and behavior, Water Movements, [SCCO.NEUR]Cognitive science/Neuroscience, [SDV.NEU.SC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Cognitive Sciences, Anatomy, biology.organism_classification, lateral line, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, mechanoreception, hearing, [ SCCO.NEUR ] Cognitive science/Neuroscience, 030217 neurology & neurosurgery
Abstract: International audience; Physiological studies have shown that the epidermal head and arm lines in cephalopods are a mechanoreceptive system that is similar to the fish and amphibian lateral lines (Budelmann BU, Bleckmann H. 1988). A lateral line analogue in cephalopods: Water waves generate microphonic potentials in the epidermal head lines of Sepia officinalis and Lolliguncula brevis. J. Comp. Physiol. A, 164: 1–5. . A lateral line analogue in cephalopods: Water waves generate microphonic potentials in the epidermal head lines of Sepia officinalis and Lolliguncula brevis. J. Comp. Physiol. A 164:1–5.); however, the biological significance of the epidermal lines remains unclear. To test whether cuttlefish show behavioural responses to local water movements, juvenile Sepia officinalis were exposed to local sinusoidal water movements of different frequencies (0.01–1000 Hz) produced by a vibrating sphere. Five behavioural responses were recorded: body pattern changing, moving, burrowing, orienting, and swimming. Cuttlefish responded to a wide range of frequencies (20–600 Hz), but not to all of the frequencies tested within that range. No habituation to repeated stimuli was seen. Results indicate that cuttlefish can detect local water movements (most likely with the epidermal head and arm lines) and are able to integrate that information into behavioural responses.
Published: 2005
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7. The effect of early experience on learning and memory in cuttlefish

Author: Dickel , Ludovic, Boal , Jean Geary, Budelmann , Bernd, EA3211 Physiologie du Comportement des Céphalopodes, Groupe Mémoire et Plasticité comportementale ( GMPc ), Université de Caen Normandie ( UNICAEN ), Normandie Université ( NU ) -Normandie Université ( NU ) -Université de Caen Normandie ( UNICAEN ), Normandie Université ( NU ) -Normandie Université ( NU ), National Resource Center for Cephalopods, The University of Texas Medical Branch ( UTMB ), Groupe Mémoire et Plasticité comportementale (GMPc), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), and The University of Texas Medical Branch (UTMB)
Subjects: [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, [ SDV.NEU.PC ] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Psychology and behavior, [ SDV.NEU.SC ] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Cognitive Sciences, [SDV.NEU.PC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Psychology and behavior, [ SDV.BA.ZI ] Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, [SCCO.NEUR]Cognitive science/Neuroscience, education, [ SCCO.NEUR ] Cognitive science/Neuroscience, [SDV.NEU.SC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Cognitive Sciences, ontogeny of memory, cephalopods, associative learning
Abstract: International audience; The effect of early experience on the growth and ontogeny of memory in cuttlefish (Sepia officinalis) was studied using an associative learning protocol. Five groups of cuttlefish were reared in different conditions (standard conditions, SC; impoverished conditions, IC; enriched conditions, EC; impoverished then enriched conditions, I/EC; enriched then impoverished conditions, E/IC) from birth to the 3rd month of postembryonic life. Acquisition and retention of the learning task were assessed at 1 and 3 months. Growth was slower and maturation of memory abilities occurred later in cuttlefish from Group IC than in cuttlefish from Group EC, with the maturation rate of memory in cuttlefish from Group SC intermediate between these two groups. Retention performances of cuttlefish from Groups I/EC and E/IC indicated that the environment of rearing during the 2nd and/or 3rd months of life was crucial for the development of memory.
Published: 2000
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8. Mutational analysis of Aedes aegypti Dicer 2 provides insights into the biogenesis of antiviral exogenous small interfering RNAs

Author: Rommel J. Gestuveo, Rhys Parry, Laura B. Dickson, Sebastian Lequime, Vattipally B. Sreenu, Matthew J. Arnold, Alexander A. Khromykh, Esther Schnettler, Louis Lambrechts, Margus Varjak, Alain Kohl, MRC - University of Glasgow Centre for Virus Research, University of the Philippines (UP System), University of Queensland [Brisbane], The University of Texas Medical Branch (UTMB), Interactions Virus-Insectes - Insect-Virus Interactions (IVI), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Bernhard Nocht Institute for Tropical Medicine - Bernhard-Nocht-Institut für Tropenmedizin [Hamburg, Germany] (BNITM), A.K. was funded by the UK Medical Research Council (MC_UU_12014/8). R.J.G. was supported by a British Council Newton Fund grant, ID 279705176, under the DOST-Newton PhD Scholarship partnership, the grant is funded by the UK Department for Business, Energy and Industrial Strategy, Philippines Department of Science and Technology-Science Education Institute, and the University of the Philippines Visayas and delivered by the British Council. For further information, please visit www.newtonfund.ac.uk. L.L. was supported by Agence Nationale de la Recherche (grants ANR-16-CE35-0004-01, ANR-17-ERC2-0016-01, and ANR-18-CE35-0003-01) and the French Government’s Investissement d’Avenir program Laboratoire d’Excellence Integrative Biology of Emerging Infectious Diseases (grant ANR-10-LABX-62-IBEID). M.J.A. was funded by the Wellcome Trust Integrated Infection Biology Programme (218518/Z/19Z)., ANR-16-CE35-0004,MOSQUIBIOTA,Contribution de la diversité bactérienne intestinale à la capacité vectorielle d'Aedes aegypti(2016), ANR-17-ERC2-0016,GxG,Base génétique de la spécificité génotype-génotype dans l'interaction naturelle entre un virus et son insecte vecteur(2017), ANR-18-CE35-0003,BAKOUMBA,Dissection de la base génétique d'un phénotype naturel de résistance à la dengue chez le moustique Aedes aegypti(2018), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), and Lequime lab
Subjects: Ribonuclease III, Heredity, Hydrolases, DNA Mutational Analysis, Biochemistry, RNA interference, Sequencing techniques, MESH: Ribonuclease III, Aedes, MESH: RNA, Small Interfering, MESH: Animals, Biology (General), RNA, Small Interfering, MESH: DNA Mutational Analysis, MESH: Alphavirus Infections, RNA sequencing, Genomics, MESH: Aedes, MESH: Semliki forest virus, Small interfering RNA, Enzymes, Nucleic acids, Genetic Mapping, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Genetic interference, MESH: RNA, Viral, Helicases, RNA, Viral, Epigenetics, MESH: Mosquito Vectors, Research Article, QH301-705.5, Nucleases, Immunology, Mosquito Vectors, Microbiology, Ribonucleases, Virology, DNA-binding proteins, Genetics, Animals, Non-coding RNA, Molecular Biology, Alphavirus Infections, Biology and Life Sciences, Proteins, RC581-607, Semliki forest virus, Viral Replication, Gene regulation, Research and analysis methods, Molecular biology techniques, Haplotypes, Enzymology, RNA, Parasitology, Gene expression, Immunologic diseases. Allergy
Abstract: The exogenous small interfering RNA (exo-siRNA) pathway is a key antiviral mechanism in the Aedes aegypti mosquito, a widely distributed vector of human-pathogenic arboviruses. This pathway is induced by virus-derived double-stranded RNAs (dsRNA) that are cleaved by the ribonuclease Dicer 2 (Dcr2) into predominantly 21 nucleotide (nt) virus-derived small interfering RNAs (vsiRNAs). These vsiRNAs are used by the effector protein Argonaute 2 within the RNA-induced silencing complex to cleave target viral RNA. Dcr2 contains several domains crucial for its activities, including helicase and RNase III domains. In Drosophila melanogaster Dcr2, the helicase domain has been associated with binding to dsRNA with blunt-ended termini and a processive siRNA production mechanism, while the platform-PAZ domains bind dsRNA with 3’ overhangs and subsequent distributive siRNA production. Here we analyzed the contributions of the helicase and RNase III domains in Ae. aegypti Dcr2 to antiviral activity and to the exo-siRNA pathway. Conserved amino acids in the helicase and RNase III domains were identified to investigate Dcr2 antiviral activity in an Ae. aegypti-derived Dcr2 knockout cell line by reporter assays and infection with mosquito-borne Semliki Forest virus (Togaviridae, Alphavirus). Functionally relevant amino acids were found to be conserved in haplotype Dcr2 sequences from field-derived Ae. aegypti across different continents. The helicase and RNase III domains were critical for silencing activity and 21 nt vsiRNA production, with RNase III domain activity alone determined to be insufficient for antiviral activity. Analysis of 21 nt vsiRNA sequences (produced by functional Dcr2) to assess the distribution and phasing along the viral genome revealed diverse yet highly consistent vsiRNA pools, with predominantly short or long sequence overlaps including 19 nt overlaps (the latter representing most likely true Dcr2 cleavage products). Combined with the importance of the Dcr2 helicase domain, this suggests that the majority of 21 nt vsiRNAs originate by processive cleavage. This study sheds new light on Ae. aegypti Dcr2 functions and properties in this important arbovirus vector species., Author summary Aedes aegypti mosquitoes that transmit human-pathogenic viruses rely on the exogenous small interfering RNA (exo-siRNA) pathway as part of antiviral responses. This pathway is triggered by virus-derived double-stranded RNA (dsRNA) produced during viral replication that is then cleaved by Dicer 2 (Dcr2) into virus-derived small interfering RNAs (vsiRNAs). These vsiRNAs target viral RNA, leading to suppression of viral replication. The importance of Dcr2 in this pathway has been intensely studied in the Drosophila melanogaster model but is largely lacking in mosquitoes. Here, we have identified conserved and functionally relevant amino acids in the helicase and RNase III domains of Ae. aegypti Dcr2 that are important in its silencing activity and antiviral responses against Semliki Forest virus (SFV). Small RNA sequencing of SFV-infected mosquito cells with functional or mutated Dcr2 gave new insights into the nature and origin of vsiRNAs. The findings of this study, together with the different molecular tools we have previously developed to investigate the exo-siRNA pathway of mosquito cells, have started to uncover important properties of Dcr2 that could be valuable in understanding mosquito-arbovirus interactions and potentially in developing or assisting vector control strategies.
Published: 2022
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9. Pannexin-1 channel opening is critical for COVID-19 pathogenesis

Author: Geoffroy Lorin de la Grandmaison, Antonio Cibelli, David C. Spray, Juan E. Tichauer, Jean Dubuisson, Arielle Rosenberg, Ross H. Luu, Sandrine Belouzard, Eliana Scemes, Elisabeth Cramer-Bordé, Morgane Bomsel, Djillali Annane, Maximiliano Rovegno, Andrea Cottignies-Calamarte, Silvana Valdebenito, Eliseo A. Eugenin, Calude Capron, [Institut Cochin] Departement Infection, immunité, inflammation, Institut Cochin (IC UM3 (UMR 8104 / U1016)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), The University of Texas Medical Branch (UTMB), New York Medical College (NYMC), Albert Einstein College of Medicine [New York], Pontificia Universidad Católica de Chile (UC), Service de Virologie [CHU Cochin], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Hôpital Ambroise Paré [AP-HP], Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Service des Maladies Infectieuses et Tropicales [CHU Raymond Poincaré], Hôpital Raymond Poincaré [AP-HP], Service médical des soins intensifs [CHU Raymond Poincaré], Université de Versailles Saint-Quentin-en-Yvelines - UFR Sciences de la santé Simone Veil (UVSQ Santé), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Médecine légale, Anatomo-pathologie et Paléopathologie [CHU Raymond Poincaré], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Raymond Poincaré [AP-HP], Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), The authors acknowledge financial support from the National Institutes of Health grant: MH096625/MH128082, The National Institute of Neurological Disorders and Stroke, NS105584, and UTMB internal funding (to E.A.E).Also, funding from the Flash COVID fund from both ANR and Fondation pour la Recherche Medicale (ANR-20-COVI-000 and AO2020- MUCOLUNG-ANR Flash COVID-19 - FRM) was provided to M.B., ANR-20-COVI-0024,MUCOLUNG,Rôle des cellules pulmonaires infectées par le SRAS-CoV-2 et réponse humoral dans l' évolution du COVID-19: de la physiopathologie au test de médicaments candidats dans les modèles de cellules muqueuses(2020), Bomsel, Morgane, and Rôle des cellules pulmonaires infectées par le SRAS-CoV-2 et réponse humoral dans l' évolution du COVID-19: de la physiopathologie au test de médicaments candidats dans les modèles de cellules muqueuses - - MUCOLUNG2020 - ANR-20-COVI-0024 - COVID-19 - VALID
Subjects: Cell biology, Human coronavirus 229E, [SDV.IMM] Life Sciences [q-bio]/Immunology, Science, viruses, Connexin, Endocytosis, medicine.disease_cause, Article, lung, Pathogenesis, 03 medical and health sciences, 0302 clinical medicine, Multiplicity of infection, Virology, medicine, purinergic, education, Furin, Molecular physiology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Coronavirus, 0303 health sciences, education.field_of_study, Multidisciplinary, biology, Chemistry, COVID-19, virus diseases, Pannexin, biology.organism_classification, respiratory tract diseases, 3. Good health, ATP, Allograft inflammatory factor 1, biology.protein, [SDV.IMM]Life Sciences [q-bio]/Immunology, 030217 neurology & neurosurgery
Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rapidly rampaged worldwide, causing a pandemic of coronavirus disease (COVID -19), but the biology of SARS-CoV-2 remains under investigation. We demonstrate that both SARS-CoV-2 spike protein and human coronavirus 229E (hCoV-229E) or its purified S protein, one of the main viruses responsible for the common cold, induce the transient opening of Pannexin-1 (Panx-1) channels in human lung epithelial cells. However, the Panx-1 channel opening induced by SARS-CoV-2 is greater and more prolonged than hCoV-229E/S protein, resulting in an enhanced ATP, PGE2, and IL-1β release. Analysis of lung lavages and tissues indicate that Panx-1 mRNA expression is associated with increased ATP, PGE2, and IL-1β levels. Panx-1 channel opening induced by SARS-CoV-2 spike protein is angiotensin-converting enzyme 2 (ACE-2), endocytosis, and furin dependent. Overall, we demonstrated that Panx-1 channel is a critical contributor to SARS-CoV-2 infection and should be considered as an alternative therapy., Graphical abstract, Cell biology; Molecular physiology; Virology
Published: 2021
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10. Mosquito‐bacteria interactions during larval development trigger metabolic changes with carry‐over effects on adult fitness

Author: Émilie Giraud, Hugo Varet, Rachel Legendre, Odile Sismeiro, Fabien Aubry, Stéphanie Dabo, Laura B. Dickson, Claire Valiente Moro, Louis Lambrechts, Interactions Virus-Insectes - Insect-Virus Interactions (IVI), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Biomics (plateforme technologique), Institut Pasteur [Paris], Biologie des Bactéries pathogènes à Gram-positif - Biology of Gram-Positive Pathogens, The University of Texas Medical Branch (UTMB), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), This work was primarily funded by the Agence Nationale de la Recherche (grant ANR-16-CE35-0004-01). It was also supported by the French Government’s Investissement d’Avenir program Laboratoire d’Excellence Integrative Biology of Emerging Infectious Diseases (grant ANR-10-LABX-62-IBEID to LL), and the City of Paris Emergence(s) program in Biomedical Research (to LL). The Biomics platform was supported by France Génomique (ANR-10-INBS-09-09) and IBISA., ANR-16-CE35-0004,MOSQUIBIOTA,Contribution de la diversité bactérienne intestinale à la capacité vectorielle d'Aedes aegypti(2016), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris] (IP)
Subjects: 0303 health sciences, vector competence, Bacteria, Microbiota, [SDV]Life Sciences [q-bio], 030231 tropical medicine, fungi, gnotobiotic, 03 medical and health sciences, 0302 clinical medicine, Aedes aegypti, Aedes, Larva, Genetics, Animals, triglyceride, transcriptome, Ecosystem, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology
Abstract: International audience; In animals with distinct life stages such as holometabolous insects, adult phenotypic variation is often shaped by the environment of immature stages, including their interactions with microbes colonizing larval habitats. Such carry-over effects were previously observed for several adult traits of the mosquito Aedes aegypti after larval exposure to different bacteria, but the mechanistic underpinnings are unknown. Here, we investigated the molecular changes triggered by gnotobiotic larval exposure to different bacteria in Ae. aegypti. We initially screened a panel of 16 bacterial isolates from natural mosquito breeding sites to determine their ability to influence adult life-history traits. We subsequently focused on four bacterial isolates (belonging to Flavobacterium, Lysobacter, Paenibacillus, and Enterobacteriaceae) with significant carry-over effects on adult survival and found that they were associated with distinct transcriptomic profiles throughout mosquito development. Moreover, we detected carry-over effects at the level of gene expression for the Flavobacterium and Paenibacillus isolates. The most prominent transcriptomic changes in gnotobiotic larvae reflected a profound remodeling of lipid metabolism, which translated into phenotypic differences in lipid storage and starvation resistance at the adult stage. Together, our findings indicate that larval exposure to environmental bacteria trigger substantial physiological changes that impact adult fitness, uncovering a possible mechanism underlying carry-over effects of mosquito-bacteria interactions during larval development.
Published: 2021
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11. Resurgence of Ebola Virus in 2021 in Guinea Suggests a New Paradigm for Outbreaks

Author: Fodé B. Sako, Jacob Camara, Amadou A. Sall, Ariane Düx, Giuditta Annibaldis, Meike Pahlmann, Abdoulaye Toure, Ousmane Faye, Mamadou Condé, Haby Diallo, Steven T. Pullan, Amadou Sidibe, Moriba Povogui, Fara Raymond Koundouno, Christophe Peyrefitte, Liana E. Kafetzopoulou, Alpha Kabinet Keita, Saa L. Millimono, Mandiou Diakite, Ahmadou Doré, Karla Pietro, N'. Faly Magassouba, Fabian H. Leendertz, Nicole Vidal, Stephan Günther, Anke Thielebein, Julia Hinzmann, Dembo Diakite, Ahidjo Ayouba, Cheikh Loucoubar, Kaka Kourouma, Martin Faye, Philippe Lemey, Moussa Moïse Diagne, Mamadou D. Barry, Fodé Y. Soumah, Annick Renevey, Georges Ki-Zerbo, Kékoura Ifono, Andrew Rambaut, Abdoul K. Soumah, Miles W. Carroll, Mamadou S. Bah, Joseph Akoi Bore, Ibrahima Camara, Mamadou S. Sow, Sébastien Calvignac-Spencer, Fodé A. Traore, Sophie Duraffour, Assaïtou Bah, John T. McCrone, Nathalie J. Vielle, Joshua Quick, Noël Tordo, Moussa Baldé, Mamadou Diop, Youssouf Sidibé, Martine Peeters, Madeleine Kourouma, Sakoba Keita, Mamadou B. Keita, Frédéric Le Marcis, Cé D. Saouromou, Anais Legand, Amadou Diallo, Pierre Formenty, Almudena Mari-Saez, Michael R. Wiley, Karifa Kourouma, Eric Delaporte, Barré Soropogui, Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes (TransVIHMI), Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Université Gamal Abdel Nasser de Conakry, Laboratoire des Fièvres Hémorragiques en Guinée, Bernhard Nocht Institute for Tropical Medicine - Bernhard-Nocht-Institut für Tropenmedizin [Hamburg, Germany] (BNITM), Institut Pasteur de Dakar, Réseau International des Instituts Pasteur (RIIP), Robert Koch Institute [Berlin] (RKI), German Center for Infection Research - Partner Site Hamburg-Lübeck-Borstel-Riems, German Centre for Infection Research (DZIF), Centre de Recherche et de Formation en Infectiologie de Guinée [Conakry, Guinée] (CERFIG), Triangle : action, discours, pensée politique et économique (TRIANGLE), École normale supérieure de Lyon (ENS de Lyon)-Université Lumière - Lyon 2 (UL2)-Sciences Po Lyon - Institut d'études politiques de Lyon (IEP Lyon), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Hôpital National Donka, The Wellcome Trust Centre for Human Genetics [Oxford], University of Oxford, Epidemiology of Highly Pathogenic Microorganisms, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), CEA Tech Grand-Est (DGDE), CEA Tech en régions (CEA-TECH-Reg), Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut National de Santé Publique [Conakry, Guinée] (INSP), Ministère de la Santé [Conakry, Guinea], Laboratoire de Physique de l'Atmosphère et de l'Océan Siméon Fongang (LPAO-SF), École Supérieure Polytechnique de Dakar (ESP), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), Public Health England, University of Birmingham [Birmingham], Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), World Health Organization [Geneva], The University of Texas Medical Branch (UTMB), University of Nebraska Medical Center, University of Nebraska System, Institut Pasteur de Guinée, Unité des Virus Emergents (UVE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Recherche Biomédicale des Armées [Antenne Marseille] (IRBA), University of Edinburgh, Division Prévention et Lutte contre la Maladie, Ministère de la Santé et de l’Hygiène Publique, Ecole Nationale Superieure de Lyon, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Infectious and Tropical Diseases Department [Montpellier], Institut de Recherche pour le Développement (IRD)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), Max Planck Institute for Evolutionary Anthropology [Leipzig], Max-Planck-Gesellschaft, ANR-16-IDEX-0006,MUSE,MUSE(2016), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), Centre National de la Recherche Scientifique (CNRS)-Sciences Po Lyon - Institut d'études politiques de Lyon (IEP Lyon), Université de Lyon-Université de Lyon-Université Jean Monnet [Saint-Étienne] (UJM)-Université Lumière - Lyon 2 (UL2)-École normale supérieure - Lyon (ENS Lyon), University of Oxford [Oxford], Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-Centre National de la Recherche Scientifique (CNRS), CEA Tech Alsace Champagne-Ardenne Lorraine, École normale supérieure - Lyon (ENS Lyon)-Université Lumière - Lyon 2 (UL2)-Sciences Po Lyon - Institut d'études politiques de Lyon (IEP Lyon), Université de Lyon-Université de Lyon-Université Jean Monnet [Saint-Étienne] (UJM)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Michel de l'Hospital : laboratoire de recherche en sciences juridiques et politiques (CMH ), and Université Clermont Auvergne (UCA)
Subjects: Male, Zaire ebolavirus, Time Factors, viruses, Disease, Biology, medicine.disease_cause, Disease cluster, Models, Biological, Viral Zoonoses, Virus, Disease Outbreaks, 03 medical and health sciences, Ebola virus, 0302 clinical medicine, medicine, Animals, Humans, Survivors, 030212 general & internal medicine, Clade, Phylogeny, 030304 developmental biology, 0303 health sciences, Multidisciplinary, Transmission (medicine), Guinea-2021, High-Throughput Nucleotide Sequencing, Outbreak, Hemorrhagic Fever, Ebola, [SHS.ANTHRO-SE]Humanities and Social Sciences/Social Anthropology and ethnology, Ebolavirus, Virology, 3. Good health, Democratic Republic of the Congo, Female, Persistent Infection, epidemiology, Guinea, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie
Abstract: Seven years after the declaration of the first epidemic of Ebola virus disease in Guinea, the country faced a new outbreak—between 14 February and 19 June 2021—near the epicentre of the previous epidemic1,2. Here we use next-generation sequencing to generate complete or near-complete genomes of Zaire ebolavirus from samples obtained from 12 different patients. These genomes form a well-supported phylogenetic cluster with genomes from the previous outbreak, which indicates that the new outbreak was not the result of a new spillover event from an animal reservoir. The 2021 lineage shows considerably lower divergence than would be expected during sustained human-to-human transmission, which suggests a persistent infection with reduced replication or a period of latency. The resurgence of Zaire ebolavirus from humans five years after the end of the previous outbreak of Ebola virus disease reinforces the need for long-term medical and social care for patients who survive the disease, to reduce the risk of re-emergence and to prevent further stigmatization. The viral lineage responsible for the February 2021 outbreak of Ebola virus disease in Guinea is nested within a clade that predominantly consists of genomes sampled during the 2013–2016 epidemic, suggesting that the virus might have re-emerged after a long period of latency within a previously infected individual.
Published: 2021
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12. Functional spreading of hyperexcitability induced by human and synthetic intracellular Aβ oligomers

Author: Eduardo J Fernández-Pérez, Christian Peters, Urmi Sengupta, María Paz Espinoza, Luis G. Aguayo, Jerome Epsztein, Nicolas O Riffo-Lepe, Romain Bourboulou, Braulio Muñoz, Caroline Filippi, Rakez Kayed, Denisse Bascuñán, Peter James Morgan, Universidad de Concepción - University of Concepcion [Chile], Institut de Neurobiologie de la Méditerranée [Aix-Marseille Université] (INMED - INSERM U1249), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), George and Cynthia Mitchell Center for Neurodegenerative diseases, The University of Texas Medical Branch (UTMB), University of Texas Medical Branch at Galveston, Universidad de Concepción [Chile], and Institut National de la Santé et de la Recherche Médicale (INSERM)-Aix Marseille Université (AMU)
Subjects: chemistry.chemical_compound, chemistry, nervous system, In vivo, Retrograde signaling, Biophysics, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], AMPA receptor, Hippocampal formation, Beta (finance), Ex vivo, Intracellular, Nitric oxide
Abstract: BackgroundIntracellular amyloid-beta oligomers (iAβo) accumulation and neuronal hyperexcitability are two crucial events at early stages of Alzheimer’s disease (AD). However, to date, no mechanism linking them has been reported.MethodsHere, the effects of human AD brain-derived (h-iAβo) and synthetic (iAβo) peptides on synaptic currents and action potential (AP) firing were investigated in hippocampal neurons in vitro, ex vivo and in vivo.ResultsStarting from 500 pM, iAβo rapidly increased the frequency of synaptic currents and higher concentrations potentiated the AMPA receptor-mediated current. Both effects were PKC-dependent. Parallel recordings of synaptic currents and nitric oxide (NO)-related fluorescence changes indicated that the increased frequency, related to pre-synaptic release, was dependent on a NO-mediated retrograde signaling. Moreover, increased synchronization in NO production was also observed in neurons neighboring those dialyzed with iAβo, indicating that iAβo can increase network excitability at a distance. Current-clamp recordings suggested that iAβo increased neuronal excitability via AMPA-driven synaptic activity without altering membrane intrinsic properties.ConclusionThese results strongly indicate that iAβo causes functional spreading of hyperexcitability through a synaptic-driven mechanism and offer an important neuropathological significance to intracellular species in the initial stages of AD, which include brain hyperexcitability and seizures.
Published: 2020

13. GloPID-R report on chikungunya, o'nyong-nyong and Mayaro virus, part 5: Entomological aspects

Author: Thomas Jaenisch, Anubis Vega-Rúa, Patrícia Brasil, M. G. Rosa-Freitas, Michael A. Drebot, P. Gallian, Sébastien Boyer, Maria Rios, Amadou A. Sall, Laura Pezzi, Anna-Bella Failloux, Angelle Desiree LaBeaud, Lisa F. P. Ng, Michael S. Diamond, Ricardo Lourenço-de-Oliveira, Guilherme S. Ribeiro, Scott C. Weaver, Mariama Dalanda Diallo, Nikos Vasilakis, A. J. Rodriguez-Morales, Alain Kohl, François Simon, Michael P. Busch, André Siqueira, Chantal Reusken, Jan Felix Drexler, Johan Neyts, Graham Simmons, X. de Lamballerie, Marc Lecuit, Unité des Virus Emergents (UVE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), EA Bioscope Corse Méditerranée : Dynamique des infections virales en milieu insulaire, Université Pascal Paoli (UPP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur de Dakar, Réseau International des Instituts Pasteur (RIIP), Fundação Oswaldo Cruz (FIOCRUZ), Institut Pasteur de la Guadeloupe, Agency for science, technology and research [Singapore] (A*STAR), Institut Pasteur du Cambodge, Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], German Centre for Infection Research (DZIF), The University of Texas Medical Branch (UTMB), MRC - University of Glasgow Centre for Virus Research, Arbovirus et Insectes Vecteurs - Arboviruses and Insect Vectors, Institut Pasteur [Paris] (IP), University of California [San Francisco] (UC San Francisco), University of California (UC), Washington University School of Medicine in St. Louis, Washington University in Saint Louis (WUSTL), Public Health Agency of Canada, Etablissement Français du Sang - Alpes-Méditerranée (EFS - Alpes-Méditerranée), Etablissement Français du Sang, Heidelberg University Hospital [Heidelberg], Stanford School of Medicine [Stanford], Stanford Medicine, Stanford University-Stanford University, Biologie des Infections - Biology of Infection, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Descartes - Paris 5 (UPD5), Service des Maladies infectieuses et tropicales [CHU Necker], CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Rega Institute for Medical Research [Leuven, België], National Institute for Public Health and the Environment [Bilthoven] (RIVM), Erasmus University Medical Center [Rotterdam] (Erasmus MC), Universidade Federal da Bahia (UFBA), Instituto Gonçalo Moniz / Gonçalo Moniz Research Centre - Fiocruz Bahia [Salvador, Brésil] (IGM), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), U.S. Food and Drug Administration (FDA), Universidad Tecnológica de Pereira [Colombie] (UTP), Hôpital d'Instruction des Armées Laveran, Service de Santé des Armées, BUISINE, Soline, Virology, Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pascal Paoli (UPP), Institut Pasteur [Paris], University of California [San Francisco] (UCSF), University of California, and Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: 0301 basic medicine, Primates, Research Report, GloPID-R chikungunya, o'nyong-nyong and Mayaro virus Working Group, Aedes albopictus, [SDV]Life Sciences [q-bio], 030106 microbiology, Aedes aegypti, Mosquito Vectors, medicine.disease_cause, 03 medical and health sciences, Aedes, Virology, Anopheles, medicine, Animals, Humans, O'nyong-nyong Virus, Chikungunya, Haemagogus, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Pharmacology, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, biology, Alphavirus Infections, Yellow fever, Outbreak, virus diseases, Central America, biology.organism_classification, medicine.disease, 3. Good health, [SDV] Life Sciences [q-bio], 030104 developmental biology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Infectious disease (medical specialty), Africa, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Enzootic, Chikungunya Fever, Chikungunya virus
Abstract: The GloPID-R (Global Research Collaboration for Infectious Disease Preparedness) chikungunya (CHIKV), o'nyong-nyong (ONNV) and Mayaro virus (MAYV) Working Group has been established to investigate natural history, epidemiology and clinical aspects of infection by these viruses. Here, we present a report dedicated to entomological aspects of CHIKV, ONNV and MAYV. Recent global expansion of chikungunya virus has been possible because CHIKV established a transmission cycle in urban settings using anthropophilic vectors such as Aedes albopictus and Aedes aegypti. MAYV and ONNV have a more limited geographic distribution, being confined to Africa (ONNV) and central-southern America (MAYV). ONNV is probably maintained through an enzootic cycle that has not been characterized yet, with Anopheles species as main vectors and humans as amplification hosts during epidemics. MAYV is transmitted by Haemagogus species in an enzootic cycle using non-human primates as the main amplification and maintenance hosts, and humans becoming sporadically infected when venturing in or nearby forest habitats. Here, we focused on the transmission cycle and natural vectors that sustain circulation of these viruses in their respective locations. The knowledge of the natural ecology of transmission and the capacity of different vectors to transmit these viruses is crucial to understand CHIKV emergence, and to assess the risk that MAYV and ONNV will expand on wide scale using anthropophilic mosquito species not normally considered primary vectors. Finally, the experts identified knowledge gaps and provided adapted recommendations, in order to address future entomological investigations in the right direction. ispartof: ANTIVIRAL RESEARCH vol:174 ispartof: location:Netherlands status: published
Published: 2019
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14. Strengthening the Interaction of the Virology Community with the International Committee on Taxonomy of Viruses (ICTV) by Linking Virus Names and Their Abbreviations to Virus Species

Author: Dennis Rubbenstroth, Thomas Briese, Victoria Wahl, Timothy H. Hyndman, Andrew D. Haddow, Sead Sabanadzovic, Arvind Varsani, Rémi N. Charrel, J. Rodney Brister, Mart Krupovic, Scott C. Weaver, Márcio Roberto Teixeira Nunes, Boris Klempa, A. Desiree LaBeaud, Takahide Sasaya, Jonas Klingström, Norbert Nowotny, Sandra Junglen, Sheli R. Radoshitzky, Susan Payne, Martin H. Groschup, Piet Maes, Ralf Dürrwald, Charles F. Fulhorst, Hideki Ebihara, Francisco Murilo Zerbini, Jens H. Kuhn, Mark D. Stenglein, Charles H. Calisher, Nikos Vasilakis, Andrew M. Kropinski, George Fú Gāo, Colorado State University [Fort Collins] (CSU), Columbia University [New York], National Institutes of Health [Bethesda] (NIH), Unité des Virus Emergents (UVE), Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD)-Institut National de la Santé et de la Recherche Médicale (INSERM), Robert Koch Institute [Berlin] (RKI), Mayo Clinic, The University of Texas Medical Branch (UTMB), Chinese Center for Disease Control and Prevention, Friedrich-Loeffler-Institut (FLI), United States Army (U.S. Army), Murdoch University, Humboldt State University (HSU), Slovak Academy of Science [Bratislava] (SAS), Karolinska Institutet [Stockholm], University of Guelph, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], Stanford School of Medicine [Stanford], Stanford Medicine, Stanford University-Stanford University, Rega Institute for Medical Research [Leuven, België], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Mohammed Bin Rashid University of Medicine and Health Sciences (MBRU), University of Veterinary Medicine [Vienna] (Vetmeduni), Ministry of Health [Brasília, Brazil], Texas A&M University [College Station], Mississippi State University [Mississippi], National Agriculture and Food Research Organization (NARO), Arizona State University [Tempe] (ASU), National Biodefense Analysis and Countermeasures Center [Frederick], U.S. Social Security Administration, Universidade Federal de Vicosa (UFV), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), This work was supported by Battelle Memorial Institute’s prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272200700016I (J.H.K.), by US National Institutes of Health (NIH) grant R24 AI120942 (S.C.W and N.V.), and by the Intramural Research Program of the NIH, National Library of Medicine (J.R.B.). S.S. acknowledges support from Mississippi State University (MSU)—Mississippi Agricultural and Forestry Experiment Station (MAFES) Strategic Research Initiative grants. This work was also funded in part under ContractNo. HSHQDC-15-C-00064 awarded by DHS S&T for the management and operation of the National Biodefense Analysis and Countermeasures Center (NBACC), a federally funded research and development center (V.W.), The authors thank Laura Bollinger, Integrated Research Facility, for critically editing the manuscript. The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of the US Department of Defense or the US Army, of the US Department of Health and Human Services, the Department of Homeland Security (DHS) Science and Technology Directorate (S&T), of the International Committee on Taxonomy of Viruses, or of the institutions and companies affiliated with the authors. In no event shall any of these entities have any responsibility or liability for any use, misuse, inability to use, or reliance upon the information contained herein. The US departments do not endorse any products or commercial services mentioned in this publication, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris] (IP), and Universidade Federal de Viçosa = Federal University of Viçosa (UFV)
Subjects: 0301 basic medicine, Classifica??o / m?todos, International Cooperation, viruses, [SDV]Life Sciences [q-bio], 030106 microbiology, species, virus, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, International Committee on Taxonomy of Viruses, Virus, Points of View, 03 medical and health sciences, taxonomy, Unclassified Viruses, (ICTV), Virology, Genetics, Nomenclature, Ecology, Evolution, Behavior and Systematics, Virus classification, Taxonomy, 2. Zero hunger, Species, Arbovirus, Phylum, Arbovirus / classifica??o, Classification, humanities, 3. Good health, 030104 developmental biology, Taxon, classification, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Mandate, Taxonomy (biology), nomenclature, Terminologia como Assunto
Abstract: This work was supported by Battelle Memorial Institute?s prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272200700016I (J.H.K.), by US National Institutes of Health (NIH) grant R24 AI120942 (S.C.W and N.V.), and by the Intramural Research Program of the NIH, National Library of Medicine (J.R.B.). S.S. acknowledges support from Mississippi State University (MSU)?Mississippi Agricultural and Forestry Experiment Station (MAFES) Strategic Research Initiative grants. This work was also funded in part under ContractNo. HSHQDC-15-C-00064 awarded by DHS S&T for the management and operation of the National Biodefense Analysis and Countermeasures Center (NBACC), a federally funded research and development center (V.W.) Colorado State University. College of Veterinary Medicine and Biomedical Sciences. Department of Microbiology, Immunology and Pathology. Arthropod-borne and Infectious Diseases Laboratory. Fort Collins, CO, USA. Columbia University. Mailman School of Public Health. Center for Infection and Immunity. Department of Epidemiology. New York, NY, USA. National Institutes of Health. National Library of Medicine. National Center for Biotechnology. Bethesda, MD, USA. Universit? Aix-Marseille. Facult? de M?decine. HU M?diterran?e Infection. Unit? des Virus Emergents. Marseille, France. Robert Koch-Institut. Department of Infectious Diseases. Berlin, Germany. Guggenheim Building. Mayo Clinic. Department of Molecular Medicine. Rochester, MN USA. University of Texas Medical Branch. Department of Pathology. Galveston, TX, USA. Chinese Center for Disease Control and Prevention. National Institute for Viral Disease Control and Prevention. Beijing, China. Friedrich-Loeffler-Institut, S?dufer. Institut f?r Virusdiagnostik. Greifswald-Insel Riems, Germany. United States Army Medical Research Institute of Infectious Diseases. Department of Virology. Frederick, MD, USA. Murdoch University. School of Veterinary and Life Sciences. College of Veterinary Medicine. Australia Australia. Humboldt-University Berlin. Berlin Institute of Health. Charit? Universit?tsmedizin Berlin. Institute of Virology. Berlin, Germany / Inhoffenstra?e 7. Deutsches Zentrum f?r Infektionsforschung. Braunschweig, Germany. Slovensk? Akad?mia Vied. Biomedic?nske centrum. Virologick? ?stav. D?bravsk?, Bratislava, Slovakia. Robert Koch-Institut. Department of Infectious Diseases. Berlin, Germany. University of Guelph. Department of Food Sciencen. Guelph, Ontario, Canada / University of Guelph. Department of Pathobiology. Guelph, Ontario, Canada. Institut Pasteur. Departement of Microbiology. Paris, France. Stanford University School of Medicine. Department of Pediatrics. Division of Infectious Diseases. Stanford, CA, USA. KU Leuven. Department of Microbiology, Immunology and Transplantation. Rega Institute. Zoonotic Infectious Diseases unit. Leuven, Belgium. University of Veterinary Medicine Vienna. Department of Pathobiology. Institute of Virology. Veterin?rplatz, Vienna, Austria / Mohammed Bin Rashid University of Medicine and Health Sciences. Department of Basic Medical Sciences. College of Medicine. Dubai, United Arab Emirates. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil. Texas A&M University. Veterinary Medical Sciences Building. College of Veterinary Medicine and Biomedical Sciences. Department of Veterinary Pathobiology. TX, USA. United States Army Medical Research Institute of Infectious Diseases. Molecular and Translational Sciences. Frederick, MD, USA. Friedrich-Loeffler-Institut, S?dufer. Institut f?r Virusdiagnostik. Greifswald-Insel Riems, Germany / Universit?tsklinikum Freiburg. Institut f?r Virologie. Freiburg, Germany. Mississippi State University. Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology. Mississippi State, MS, USA. National Agriculture and Food Research Organization. Department of Planning and Coordination. Ibaraki, Japan. Colorado State University. Department of Microbiology, Immunology and Pathology. Fort Collins, CO, USA. Arizona State University. School of Life Sciences, Center for Evolution and Medicine. The Biodesign Center for Fundamental and Applied Microbiomics. Tempe, AZ, USA. National Biodefense Analysis and Countermeasures Center. Frederick, MD, USA. University of Texas Medical Branch. Institute for Human Infections and Immunity. Department of Microbiology and Immunology. Galveston, TX, USA. Universidade Federal de Vi?osa. Departamento de Fitopatologia/BIOAGRO and National Institute of Science and Technology for Plant-Pest Interactions. Vi?osa, MG, Brazil. University of Texas Medical Branch. Institute for Human Infection and Immunity. Center for Tropical Diseases. Department of Pathology, Center for Biodefense and Emerging Infectious Diseases. Galveston, TX, USA. Integrated Research Facility at Fort Detrick. Frederick, MD, USA. The International Committee on Taxonomy of Viruses (ICTV) is tasked with classifying viruses into taxa (phyla to species) and devising taxon names. Virus names and virus name abbreviations are currently not within the ICTV's official remit and are not regulated by an official entity. Many scientists, medical/veterinary professionals, and regulatory agencies do not address evolutionary questions nor are they concerned with the hierarchical organization of the viral world, and therefore, have limited use for ICTV-devised taxa. Instead, these professionals look to the ICTV as an expert point source that provides the most current taxonomic affiliations of viruses of interests to facilitate document writing. These needs are currently unmet as an ICTV-supported, easily searchable database that includes all published virus names and abbreviations linked to their taxa is not available. In addition, in stark contrast to other biological taxonomic frameworks, virus taxonomy currently permits individual species to have several members. Consequently, confusion emerges among those who are not aware of the difference between taxa and viruses, and because certain well-known viruses cannot be located in ICTV publications or be linked to their species. In addition, the number of duplicate names and abbreviations has increased dramatically in the literature. To solve this conundrum, the ICTV could mandate listing all viruses of established species and all reported unclassified viruses in forthcoming online ICTV Reports and create a searchable webpage using this information. The International Union of Microbiology Societies could also consider changing the mandate of the ICTV to include the nomenclature of all viruses in addition to taxon considerations. With such a mandate expansion, official virus names and virus name abbreviations could be catalogued and virus nomenclature could be standardized. As a result, the ICTV would become an even more useful resource for all stakeholders in virology.
Published: 2019
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15. GloPID-R report on Chikungunya, O'nyong-nyong and Mayaro virus, part I: Biological diagnostics

Author: A. J. Rodriguez-Morales, M. G. Rosa-Freitas, Guilherme S. Ribeiro, Nikos Vasilakis, Lisa F. P. Ng, Mariama Dalanda Diallo, Scott C. Weaver, Patrícia Brasil, Jan Felix Drexler, Johan Neyts, Anna-Bella Failloux, François Simon, Alain Kohl, A. Vega Rua, Maria Rios, Michael P. Busch, Michael S. Diamond, André Siqueira, Michael A. Drebot, P. Gallian, Sébastien Boyer, Ricardo Lourenço-de-Oliveira, Chantal Reusken, Angelle Desiree LaBeaud, Thomas Jaenisch, Marc Lecuit, Laura Pezzi, X. de Lamballerie, Graham Simmons, Amadou A. Sall, Unité des Virus Emergents (UVE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Virologie [UNIV Corse-Inserm] (EA7310), Université Pascal Paoli (UPP)-Institut National de la Santé et de la Recherche Médicale (INSERM), National Institute for Public Health and the Environment [Bilthoven] (RIVM), Erasmus University Medical Center [Rotterdam] (Erasmus MC), The University of Texas Medical Branch (UTMB), Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Humboldt University Of Berlin, Berlin Institute of Health (BIH), German Centre for Infection Research (DZIF), University of California [San Francisco] (UC San Francisco), University of California (UC), Stanford School of Medicine [Stanford], Stanford Medicine, Stanford University-Stanford University, Washington University in Saint Louis (WUSTL), Public Health Agency of Canada, Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP), Universidade Federal da Bahia (UFBA), University of Glasgow, Biologie des Infections - Biology of Infection, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Imagine - Institut des maladies génétiques (IMAGINE - U1163), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Université Paris Descartes - Paris 5 (UPD5), Agency for science, technology and research [Singapore] (A*STAR), Etablissement Français du Sang - Alpes-Méditerranée (EFS - Alpes-Méditerranée), Etablissement Français du Sang, Institut Pasteur du Cambodge, Institut Pasteur de Dakar, Arbovirus et Insectes Vecteurs - Arboviruses and Insect Vectors, Institut Pasteur [Paris] (IP), Heidelberg University Hospital [Heidelberg], Rega Institute for Medical Research [Leuven, België], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), U.S. Food and Drug Administration (FDA), Universidad Tecnológica de Pereira [Colombie] (UTP), Hôpital d'Instruction des Armées Laveran, Service de Santé des Armées, Institut Pasteur de la Guadeloupe, Publication fees were covered by the Global Research Collaboration for Infectious Disease Preparedness (GloPID-R)., Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pascal Paoli (UPP), Humboldt-Universität zu Berlin, University of California [San Francisco] (UCSF), University of California, Fundação Oswaldo Cruz (FIOCRUZ), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris], Virology, Charité - Universitätsmedizin Berlin / Charite - University Medicine Berlin, Humboldt Universität zu Berlin, Stanford University School of Medicine [Stanford], Stanford University [Stanford], Washington University in St Louis, Federal University of Bahia, Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Arbovirus et Insectes Vecteurs, and Rega Institute for Medical Research
Subjects: 0301 basic medicine, medicine.medical_specialty, Genes, Viral, 030106 microbiology, Disease, Alphavirus, Mosquito Vectors, Cross Reactions, medicine.disease_cause, Antibodies, Viral, Communicable Diseases, Emerging, Virus, 03 medical and health sciences, Seroepidemiologic Studies, Virology, O'nyong-nyong, Epidemiology, medicine, Animals, Humans, O'nyong-nyong Virus, Chikungunya, Pathology, Molecular, Diagnostics, Phylogeny, Pharmacology, biology, business.industry, Alphavirus Infections, Outbreak, biology.organism_classification, Mayaro virus, 3. Good health, 030104 developmental biology, Cryoglobulinemia, Infectious disease (medical specialty), Preparedness, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Chikungunya Fever, business, Chikungunya virus
Abstract: The GloPID-R (Global Research Collaboration for Infectious Disease Preparedness) Chikungunya (CHIKV), O'nyong-nyong (ONNV) and Mayaro virus (MAYV) Working Group is investigating the natural history, epidemiology and medical management of infection by these viruses, to identify knowledge gaps and to propose recommendations for direct future investigations and rectification measures. Here, we present the first report dedicated to diagnostic aspects of CHIKV, ONNV and MAYV. Regarding diagnosis of the disease at the acute phase, molecular assays previously described for the three viruses require further evaluation, standardized protocols and the availability of international standards representing the genetic diversity of the viruses. Detection of specific IgM would benefit from further investigations to clarify the extent of cross-reactivity among the three viruses, the sensitivity of the assays, and the possible interfering role of cryoglobulinaemia. Implementation of reference panels and external quality assessments for both molecular and serological assays is necessary. Regarding sero-epidemiological studies, there is no reported high-throughput assay that can distinguish among these different viruses in areas of potential co-circulation. New specific tools and/or improved standardized protocols are needed to enable large-scale epidemiological studies of public health relevance to be performed. Considering the high risk of future CHIKV, MAYV and ONNV outbreaks, the Working Group recommends that a major investigation should be initiated to fill the existing diagnostic gaps. ispartof: ANTIVIRAL RESEARCH vol:166 pages:66-81 ispartof: location:Netherlands status: published
Published: 2019
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16. Meeting the challenge of tick-borne disease control: A proposal for 1000 Ixodes genomes

Author: Timothy J. Kurtti, Karen D. McCoy, Ala E. Tabor, Lesley Bell-Sakyi, Claude Rispe, Manuel Rodriguez Valle, Ulrike G. Munderloh, Benjamin L. Makepeace, Catherine A. Hill, Jyothi Thimmapuram, José de la Fuente, Maria V. Murgia, Saravanan Thangamani, Olivier Plantard, Ben J. Mans, Purdue University [West Lafayette], University of Liverpool, Instituto de Investigación en Recursos Cinegéticos (IREC), University of Minnesota [Twin Cities] (UMN), University of Minnesota System, University of South Africa (UNISA), Evolution of host-microbe communities (MIVEGEC-EVCO), Processus Écologiques et Évolutifs au sein des Communautés (PEEC), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Biologie, Epidémiologie et analyse de risque en Santé Animale (BIOEPAR), Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), University of Queensland [Brisbane], The University of Texas Medical Branch (UTMB), University of Minnesota [Twin Cities], Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), and Institut National de la Recherche Agronomique (INRA)
Subjects: Ixodes ricinus, [SDV]Life Sciences [q-bio], education, 030231 tropical medicine, Tick, Microbiology, Genome, 03 medical and health sciences, 0302 clinical medicine, medicine, Animals, Humans, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Tick-borne disease, biology, Ixodes, Genomics, biology.organism_classification, medicine.disease, Infectious Diseases, Evolutionary biology, Tick-Borne Diseases, Insect Science, Parasitology
Abstract: International audience
Published: 2019
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17. rbFOX1/MBNL1 competition for CCUG RNA repeats binding contributes to myotonic dystrophy type 1/type 2 differences

Author: Frédéric H.-T. Allain, Nicolas Charlet-Berguerand, Frank Ruffenach, John W. Day, Giovanni Meola, Masanori P. Takahashi, Chantal Sellier, Estefanía Cerro-Herreros, Jack Puymirat, Denis Furling, Angeline Gaucherot, Guillaume Bassez, Ruben Artero, Markus Blatter, Beatriz Llamusi, Fernande Freyermuth, Harutoshi Fujimura, Partha S. Sarkar, Bjarne Udd, Benedikt Schoser, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Biomedical Research Institute [Valencia, Spain] (INCLIVA ), Universitat de València (UV), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), The University of Texas Medical Branch (UTMB), Université Laval [Québec] (ULaval), Neurology Department, Tampere University Hospital, University of Helsinki, Stanford University, University of Milan, Università degli Studi di Milano, IRCCS Policlinico San Donato, Institut de Myologie, Centre National de la Recherche Scientifique (CNRS)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Association française contre les myopathies (AFM-Téléthon)-Sorbonne Université (SU), Toneyama National Hospital, Osaka University Graduate School of Medicine, Suita, Ludwig Maximilian University [Munich] (LMU), Medicum, Department of Medical and Clinical Genetics, Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Università degli Studi di Milano = University of Milan (UNIMI), Centre de recherche en Myologie – U974 SU-INSERM, Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Association française contre les myopathies (AFM-Téléthon)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Models, Molecular, Protein Conformation, alpha-Helical, [SDV]Life Sciences [q-bio], General Physics and Astronomy, Gene Expression, RNA-binding protein, Crystallography, X-Ray, chemistry.chemical_compound, MOLECULAR-BASIS, Gene expression, MBNL1, Myotonic Dystrophy, ComputingMilieux_MISCELLANEOUS, Multidisciplinary, CHLORIDE CHANNEL, RNA-Binding Proteins, Recombinant Proteins, 3. Good health, Cell biology, CONGENITAL HEART-DISEASE, Drosophila melanogaster, Thermodynamics, SKELETAL-MUSCLE, RNA Splicing Factors, CUG REPEATS, Protein Binding, musculoskeletal diseases, STEADY-STATE, congenital, hereditary, and neonatal diseases and abnormalities, Science, RBFOX1, Biology, Myotonic dystrophy, Binding, Competitive, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, medicine, Escherichia coli, Animals, Humans, Protein Interaction Domains and Motifs, Binding site, Nucleotide Motifs, Muscle, Skeletal, SPLICING REGULATOR RBFOX2, MUSCLEBLIND PROTEINS, Binding Sites, PRE-MESSENGER-RNA, RNA, General Chemistry, medicine.disease, Disease Models, Animal, Kinetics, 030104 developmental biology, chemistry, TRIPLET REPEAT, Protein Conformation, beta-Strand, 3111 Biomedicine
Abstract: Myotonic dystrophy type 1 and type 2 (DM1, DM2) are caused by expansions of CTG and CCTG repeats, respectively. RNAs containing expanded CUG or CCUG repeats interfere with the metabolism of other RNAs through titration of the Muscleblind-like (MBNL) RNA binding proteins. DM2 follows a more favorable clinical course than DM1, suggesting that specific modifiers may modulate DM severity. Here, we report that the rbFOX1 RNA binding protein binds to expanded CCUG RNA repeats, but not to expanded CUG RNA repeats. Interestingly, rbFOX1 competes with MBNL1 for binding to CCUG expanded repeats and overexpression of rbFOX1 partly releases MBNL1 from sequestration within CCUG RNA foci in DM2 muscle cells. Furthermore, expression of rbFOX1 corrects alternative splicing alterations and rescues muscle atrophy, climbing and flying defects caused by expression of expanded CCUG repeats in a Drosophila model of DM2., Myotonic dystrophy (DM) type 2 is a neuromuscular pathology caused by large expansions of CCTG repeats. Here the authors find that rbFOX1 RNA binding protein binds to CCUG RNA repeats and competes with MBNL1 for the binding to CCUG repeats, releasing MBNL1 from sequestration in DM2 muscle cells.
Published: 2018
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18. i-BLESS is an ultra-sensitive method for detection of DNA double-strand breaks

Author: Benjamin Pardo, Anna Biernacka, Krzysztof Ginalski, Jules Nde, Andrzej Kudlicki, Nicola Crosetto, Magdalena Skrzypczak, Marta Grzelak, Abhishek Mitra, Maga Rowicka, Romain Forey, Yingjie Zhu, Philippe Pasero, Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, 02-089 Warsaw, Poland, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX 77555 USA., Institut de génétique humaine (IGH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), University of Texas Medical Branch at Galveston, The University of Texas Medical Branch (UTMB), and Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17165 Sweden.
Subjects: 0301 basic medicine, Double strand, [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV]Life Sciences [q-bio], Medicine (miscellaneous), Chromosome deletions, High resolution, Cell fate determination, Article, General Biochemistry, Genetics and Molecular Biology, 3. Good health, Cell biology, 03 medical and health sciences, chemistry.chemical_compound, 030104 developmental biology, 0302 clinical medicine, chemistry, lcsh:Biology (General), Agarose, General Agricultural and Biological Sciences, lcsh:QH301-705.5, 030217 neurology & neurosurgery, DNA, Ultra sensitive, Genome stability
Abstract: Maintenance of genome stability is a key issue for cell fate that could be compromised by chromosome deletions and translocations caused by DNA double-strand breaks (DSBs). Thus development of precise and sensitive tools for DSBs labeling is of great importance for understanding mechanisms of DSB formation, their sensing and repair. Until now there has been no high resolution and specific DSB detection technique that would be applicable to any cells regardless of their size. Here, we present i-BLESS, a universal method for direct genome-wide DNA double-strand break labeling in cells immobilized in agarose beads. i-BLESS has three key advantages: it is the only unbiased method applicable to yeast, achieves a sensitivity of one break at a given position in 100,000 cells, and eliminates background noise while still allowing for fixation of samples. The method allows detection of ultra-rare breaks such as those forming spontaneously at G-quadruplexes., Anna Biernacka, Yingjie Zhu et al. present i-BLESS, a universal method for detecting genome-wide DNA double strand breaks, optimized here for yeast. By immobilizing cells on agarose beads, the authors are able to achieve efficient diffusion of reagents and labeling of double strand breaks, including ultra-rare breaks such as those at G-quadruplexes.
Published: 2018
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19. Taxonomy of the order Mononegavirales: update 2018

Author: Kang Seuk Choi, Nikos Vasilakis, Claudio Verdugo, Janusz T. Paweska, Thomas Briese, Víctor Manuel Neira Ramírez, Andrew J. Bennett, Masayuki Horie, Charles H. Calisher, Robert Kityo, Anthony R. Fooks, Martin Schwemmle, Sunil K. Mor, Nidia G. Aréchiga Ceballos, Timothy H. Hyndman, Ayato Takada, Yíngyún Caì, Robert A. Lamb, Alexander Bukreyev, Paul A. Rota, Tony L. Goldberg, Lin-Fa Wang, Benhur Lee, Kartik Chandran, Hideki Ebihara, Michael R. Wiley, Ralf G. Dietzgen, Anna E. Whitfield, Mark D. Stenglein, Piet Maes, Andrew J. Easton, Jean L. Patterson, Valerian V. Dolja, Olga Dolnik, Eugene V. Koonin, James F. X. Wellehan, Ralf Dürrwald, Peter L. Collins, Qisheng Song, Susan Payne, Jonathan S. Towner, Sina Bavari, Sonia Vázquez-Morón, Pierre Formenty, Sophie J. Smither, Keizō Tomonaga, Leslie L. Domier, Dàohóng Jiāng, Gael Kurath, Robert B. Tesh, Sergey V. Netesov, Elodie Ghedin, Andrea Maisner, Denise A. Marston, Cristine Campos Lawson, Elke Mühlberger, Christopher F. Basler, Conrad M. Freuling, Yǒng Zhèn Zhāng, Dennis Rubbenstroth, Peter J. Walker, Gōngyín Yè, David Wang, Ron A. M. Fouchier, Gustavo Palacios, Gary P. Kobinger, Yuri I. Wolf, Timothy Song, Hideki Kondō, Mart Krupovic, Karla Prieto, David M. Stone, Luciano M. Thomazelli, Colin A. Chapman, Ashley C. Banyard, Jens H. Kuhn, Stuart G. Siddell, Noël Tordo, John M. Dye, Terry Fei Fan Ng, Charles Y. Chiu, Kim R. Blasdell, Bertus K. Rima, Victoria Wahl, Eric M. Leroy, Gaya K. Amarasinghe, Juan Emilio Echevarría, Norbert Nowotny, Roger Hewson, Thomas Müller, Viktor E. Volchkov, Washington University School of Medicine (WUSM), University of Washington [Seattle], Laboratorio de Rabia, Instituto de Diagnóstico y Referencias Epidemiológicos, Animal and Plant Health Agency [Weybridge] (APHA), Georgia State University, University System of Georgia (USG), U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), School of Veterinary Medicine, Department of Pathobiological Sciences, University of Wisconsin-Madison-Influenza Research Institute, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Columbia Mailman School of Public Health, Columbia University [New York], The University of Texas Medical Branch (UTMB), Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, College of Veterinary Medicine and Biomedical Sciences, Colorado State University [Fort Collins] (CSU), Albert Einstein College of Medicine [New York], Department of Anthropology [Montréal], McGill University = Université McGill [Montréal, Canada], Wildlife Conservation Society (WCS), Primate Research Institute, Kyoto University, University of California [San Francisco] (UC San Francisco), University of California (UC), Avian Disease Research Division, Animal and Plant Quarantine Agency, National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland [Brisbane], Department of Botany and Plant Pathology, Oregon State University (OSU), Center for Genome Research and Biocomputing, Philipps Universität Marburg = Philipps University of Marburg, University of Chicago, IDT Biologika, School of Life Sciences, University of Warwick [Coventry], Department of Biochemistry and Molecular Biology, University of Rochester [USA], Institute of Health Carlos III, Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Department of Viroscience [Rotterdam, The Netherlands], Erasmus University Medical Center [Rotterdam] (Erasmus MC), Institute of Molecular Virology and Cell Biology, Federal Research Institute for Animal Health - Friedrich-Loeffler-Institut, Center for Genomics and Systems Biology, Department of Biology [New York], New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU)-New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU), Public Health England [Salisbury] (PHE), Kagoshima University, Murdoch University, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University [Wuhan] (HZAU), Makerere University [Kampala, Ouganda] (MAK), Research Centre in Infectious Diseases, CHUL Research Centre and Department of Microbiology and Immunology, Université Laval [Québec] (ULaval)-Faculty of Medicine, Institute of Plant Science and Resources, Okayama University, National Center for Biotechnology Information (NCBI), Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), US Geological Survey [Seattle], United States Geological Survey [Reston] (USGS), Northwestern University [Evanston], Icahn School of Medicine at Mount Sinai [New York] (MSSM), Centre International de Recherches Médicales de Franceville (CIRMF), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Neuromuscular Diagnostic Laboratory, University of Minnesota [Twin Cities] (UMN), University of Minnesota System-University of Minnesota System, Boston University School of Medicine (BUSM), Boston University [Boston] (BU), Universidad de Chile = University of Chile [Santiago] (UCHILE), Novosibirsk State University (NSU), Department of Medicine [San Francisco], University of California (UC)-University of California (UC), University of Veterinary Medicine [Vienna] (Vetmeduni), Mohammed Bin Rashid University of Medicine and Health Sciences (MBRU), Texas Biomedical Research Institute [San Antonio, TX], National Institute for Communicable Diseases [Johannesburg] (NICD), Queen's University [Belfast] (QUB), National Center for Immunization and Respiratory Diseases, CDC, Centers for Disease Control and Prevention (CDC), University of Freiburg [Freiburg], University of Bristol [Bristol], Defence Science and Technology Laboratory (Dstl), Ministry of Defence (UK) (MOD), University of Missouri [Columbia] (Mizzou), University of Missouri System, Department of Microbiology, Immunology and Pathology, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Hokkaido University [Sapporo, Japan], Universidade de São Paulo - USP (BRAZIL), Institute for Virus Research, Stratégies antivirales, Institut Pasteur de Guinée, Réseau International des Instituts Pasteur (RIIP), Viral Special Pathogens Branch, Centers for Disease Control and Prevention-WHO Collaborative Centre for Viral Hemorrhagic Fevers, Facultad de Ciencias Veterinarias [Buenos Aires], Universidad de Buenos Aires [Buenos Aires] (UBA), Bases moléculaires de la pathogénicité virale – Molecular Basis of Viral Pathogenicity (BMPV), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), National Biodefense Analysis and Countermeasures Center [Frederick], U.S. Social Security Administration, CSIRO Health & Biosecurity, Department of Agriculture, Fisheries and Forestry, Ecoscience Precinct, GPO Box 267, Brisbane, Duke-NUS Medical School [Singapore], University of Florida [Gainesville] (UF), University of Nebraska Medical Center, University of Nebraska System, Kansas State University, State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences (CAAS), State Key Laboratory for Infectious Disease prevention and Control, Beijing Institute of Technology (BIT), Army Medical Research Institute of Infectious Diseases [USA] (USAMRIID), Albert Einstein College of Medicine, McGill University, Kyoto University [Kyoto], University of California [San Francisco] (UCSF), University of California, Queensland Alliance for Agriculture and Food Innovation, University of Queensland (UQ), Philipps University of Marburg, Warwick University, Public Health England [Porton Down, Salisbury], Huazhong Agricultural University, Makerere University (MAK), Faculty of Medicine-Laval University [Québec], Okayama University [Okayama], Institut Pasteur [Paris], Centre International de Recherches Médicales de Franceville, University of Minnesota [Twin Cities], Universidad de Chile, University of California-University of California, Texas Biomedical Research Institute [San Antonio, Texas], National Institute for Communicable Diseases (NICD), Centre for Experimental Medicine [Queen’s University of Belfast], University of Bristol (School of Cellular and Molecular Medicine), University of Missouri [Columbia], Hokkaido University, Bases moléculaires de la pathogénicité virale – Molecular Basis of Viral Pathogenicity, Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Duke NUS Medical School, University of Florida [Gainesville], and Virology
Subjects: 0301 basic medicine, Order Mononegavirales, 040301 veterinary sciences, Mononegavirales Infections, 04 agricultural and veterinary sciences, General Medicine, Biology, Data science, Virology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Article, 0403 veterinary science, 03 medical and health sciences, 030104 developmental biology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Humans, Animals, [SDV.IMM]Life Sciences [q-bio]/Immunology, Taxonomy (biology), Mononegavirales, Phylogeny
Abstract: International audience; In 2018, the order Mononegavirales was expanded by inclusion of 1 new genus and 12 novel species. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV) and summarizes additional taxonomic proposals that may affect the order in the near future.
Published: 2018
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20. Zika, Chikungunya, and Other Emerging Vector-Borne Viral Diseases

Author: Scott C. Weaver, Caroline Charlier, Nikos Vasilakis, Marc Lecuit, The University of Texas Medical Branch (UTMB), Biologie des Infections - Biology of Infection, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Descartes - Paris 5 (UPD5), CHU Necker - Enfants Malades [AP-HP], Institut des Maladies Génétiques Imagine [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)
Subjects: 0301 basic medicine, chikungunya, viruses, 030231 tropical medicine, mosquito, Aedes aegypti, Mosquito Vectors, Biology, medicine.disease_cause, Arbovirus, Communicable Diseases, Emerging, General Biochemistry, Genetics and Molecular Biology, Article, Dengue fever, yellow fever, 03 medical and health sciences, 0302 clinical medicine, Zika, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, medicine, Animals, Humans, Chikungunya, Rift Valley fever, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Zika Virus Infection, Yellow fever, virus diseases, General Medicine, Japanese encephalitis, medicine.disease, biology.organism_classification, Virology, dengue, 3. Good health, 030104 developmental biology, arbovirus, Virus Diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Enzootic, Chikungunya Fever, Arboviruses, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: International audience; Arthropod-borne viruses (arboviruses) have a long history of emerging to infect humans, but during recent decades, they have been spreading more widely and affecting larger populations. This is due to several factors, including increased air travel and uncontrolled mosquito vector populations. Emergence can involve simple spillover from enzootic (wildlife) cycles, as in the case of West Nile virus accompanying geographic expansion into the Americas; secondary amplification in domesticated animals, as seen with Japanese encephalitis, Venezuelan equine encephalitis, and Rift Valley fever viruses; and urbanization, in which humans become the amplification hosts and peridomestic mosquitoes, mainly Aedes aegypti, mediate human-to-human transmission. Dengue, yellow fever, chikungunya, and Zika viruses have undergone such urban emergence. We focus mainly on the latter two, which are recent arrivals in the Western Hemisphere. We also discuss a few other viruses with the potential to emerge through all of these mechanisms.
Published: 2018
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21. Dual Inhibition of EGFR and c-Src by Cetuximab and Dasatinib Combined with FOLFOX Chemotherapy in Patients with Metastatic Colorectal Cancer

Author: Alain R. Thierry, Christine Megerdichian Parseghian, Ji Yuan Wu, Kanwal Pratap Singh Raghav, Feng Tian, Laura Henderson, Nila U. Parikh, Anastasia D. Katsiampoura, Marc Ychou, Scott Kopetz, Zhi-Qin Jiang, David G. Menter, Gary E. Gallick, Cathy Eng, David R. Fogelman, Robert A. Wolff, Michael J. Overman, Arvind Dasari, Brice Pastor, The University of Texas M.D. Anderson Cancer Center [Houston], The University of Texas Medical Branch (UTMB), Tsinghua University [Beijing] (THU), Institut de Recherche en Cancérologie de Montpellier (IRCM - U1194 Inserm - UM), and CRLCC Val d'Aurelle - Paul Lamarque-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)
Subjects: 0301 basic medicine, Oncology, Adult, Male, Cancer Research, medicine.medical_specialty, Maximum Tolerated Dose, Organoplatinum Compounds, Colorectal cancer, medicine.medical_treatment, Dasatinib, Leucovorin, Cetuximab, [SDV.CAN]Life Sciences [q-bio]/Cancer, medicine.disease_cause, Disease-Free Survival, Article, CSK Tyrosine-Protein Kinase, Proto-Oncogene Proteins p21(ras), 03 medical and health sciences, 0302 clinical medicine, FOLFOX, Internal medicine, Antineoplastic Combined Chemotherapy Protocols, Medicine, Humans, Aged, Chemotherapy, business.industry, Cancer, Middle Aged, medicine.disease, digestive system diseases, 3. Good health, ErbB Receptors, 030104 developmental biology, src-Family Kinases, 030220 oncology & carcinogenesis, Female, KRAS, Fluorouracil, business, Colorectal Neoplasms, MESH: Colorectal Neoplasms, medicine.drug, Proto-oncogene tyrosine-protein kinase Src
Abstract: Purpose: Aberrant activation of the intracellular tyrosine kinase Src has been implicated as a mechanism of acquired chemotherapy resistance in metastatic colorectal cancer (mCRC). Here, the oral tyrosine kinase Src inhibitor, dasatinib, was investigated in combination with FOLFOX and cetuximab. Experimental Design: We performed a phase IB/II study of 77 patients with previously treated mCRC. Primary objectives were to determine the maximum tolerated dose, dose-limiting toxicities (DLT), pharmacodynamics, and efficacy. Using a 3 + 3 design, patients received FOLFOX6 with cetuximab and escalating doses of dasatinib (100, 150, 200 mg daily), followed by a 12-patient expansion cohort at 150 mg. Phase II studies evaluated FOLFOX plus dasatinib 100 mg in KRAS c12/13mut patients or in combination with cetuximab if KRAS c12/13WT. FAK and paxillin were utilized as surrogate blood biomarkers of Src inhibition, and paired biopsies of liver metastases were obtained in patients in the expansion cohort. Results: In phase IB, the DLTs were grade 3/4 fatigue (20%) and neutropenia (23%). In phase II, grade 3/4 fatigue (23%) and pleural effusions (11%) were present. Response rates were 20% (6 of 30) in the phase IB escalation and expansion cohort and 13% (3 of 24) and 0% (0 of 23) in the KRAS c12/13WT and mutant cohorts of phase II, respectively. Median progression-free survival was 4.6, 2.3, and 2.3 months, respectively. There was no evidence of Src inhibition based on surrogate blood biomarkers or paired tumor biopsies. Conclusions: The combination of dasatinib plus FOLFOX with or without cetuximab showed only modest clinical activity in refractory colorectal cancer. This appears to be primarily due to a failure to fully inhibit Src at the achievable doses of dasatinib. The combination of dasatinib plus FOLFOX with or without cetuximab did not show meaningful clinical activity in refractory colorectal cancer due to failure to fully inhibit Src. Clin Cancer Res; 23(15); 4146–54. ©2017 AACR.
Published: 2017
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22. Implementation of Objective PASC-Derived Taxon Demarcation Criteria for Official Classification of Filoviruses

Author: Janusz T. Paweska, Elke Mühlberger, Jonathan S. Towner, Sina Bavari, Kartik Chandran, Eric M. Leroy, Gary P. Kobinger, Ayato Takada, Olga Dolnik, Gaya K. Amarasinghe, Roger Hewson, Victoria Wahl-Jensen, Sophie J. Smither, Christopher F. Basler, Jean L. Patterson, Viktor E. Volchkov, Jens H. Kuhn, Pierre Formenty, Hideki Ebihara, Sergey V. Netesov, John M. Dye, Alexander Bukreyev, Yīmíng Bào, Beijing Institute of Genomics, Chinese Academy of Sciences [Beijing] (CAS)-China Graduate University of the Chinese Academy of Sciences, Department of Pathology and Immunology, Washington University School of Medicine, Georgia State University, University System of Georgia (USG), Army Medical Research Institute of Infectious Diseases [USA] (USAMRIID), The University of Texas Medical Branch (UTMB), Albert Einstein College of Medicine, Philipps University of Marburg, Department of Biochemistry and Molecular Biology, University of Rochester [USA], Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Public Health England [Porton Down, Salisbury], Département de Biochimie et Microbiologie, Université Laval, Centre International de Recherches Médicales de Franceville (CIRMF), Centre International de Recherches Médicales de Franceville, National Emerging Infectious Diseases Laboratories (NEIDL), Boston University [Boston] (BU), Novosibirsk State University (NSU), Texas Biomedical Research Institute [San Antonio, Texas], National Institute for Communicable Diseases (NICD), Defence Science and Technology Laboratory (Dstl), Ministry of Defence (UK) (MOD), Hokkaido University, Viral Special Pathogens Branch, Centers for Disease Control and Prevention-WHO Collaborative Centre for Viral Hemorrhagic Fevers, Bases moléculaires de la pathogénicité virale – Molecular Basis of Viral Pathogenicity, Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), National Biodefense Analysis and Countermeasures Center [Frederick], U.S. Social Security Administration, Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Beijing Genomics Institute [Shenzhen] (BGI), Albert Einstein College of Medicine [New York], Public Health England [Salisbury] (PHE), Université Laval [Québec] (ULaval), Texas Biomedical Research Institute [San Antonio, TX], National Institute for Communicable Diseases [Johannesburg] (NICD), Hokkaido University [Sapporo, Japan], Bases moléculaires de la pathogénicité virale – Molecular Basis of Viral Pathogenicity (BMPV), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Philipps Universität Marburg = Philipps University of Marburg, Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Letter, marburgvirus, lcsh:QR1-502, lcsh:Microbiology, ICTV, Genus, Software Design, RefSeq, Viral, virus classification, Phylogeny, Genome, Ebolavirus, Cuevavirus, Infectious Diseases, GenBank, Ebola, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.IMM]Life Sciences [q-bio]/Immunology, Databases, Nucleic Acid, cuevavirus, Sequence Analysis, Algorithms, filovirus, 030106 microbiology, Genome, Viral, Biology, virus taxonomy, 03 medical and health sciences, Databases, Type (biology), Species Specificity, Virology, ebolavirus, Virus classification, Whole genome sequencing, Base Sequence, Nucleic Acid, Whole Genome Sequencing, Genetic Variation, Sequence Analysis, DNA, DNA, biology.organism_classification, Filoviridae, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 030104 developmental biology, Taxon, Marburgvirus, Evolutionary biology, Mononegavirales
Abstract: The mononegaviral family Filoviridae has eight members assigned to three genera and seven species. Until now, genus and species demarcation were based on arbitrarily chosen filovirus genome sequence divergence values (approximate to 50% for genera, approximate to 30% for species) and arbitrarily chosen phenotypic virus or virion characteristics. Here we report filovirus genome sequence-based taxon demarcation criteria using the publicly accessible PAirwise Sequencing Comparison (PASC) tool of the US National Center for Biotechnology Information (Bethesda, MD, USA). Comparison of all available filovirus genomes in GenBank using PASC revealed optimal genus demarcation at the 55-58% sequence diversity threshold range for genera and at the 23-36% sequence diversity threshold range for species. Because these thresholds do not change the current official filovirus classification, these values are now implemented as filovirus taxon demarcation criteria that may solely be used for filovirus classification in case additional data are absent. A near-complete, coding-complete, or complete filovirus genome sequence will now be required to allow official classification of any novel "filovirus." Classification of filoviruses into existing taxa or determining the need for novel taxa is now straightforward and could even become automated using a presented algorithm/flowchart rooted in RefSeq (type) sequences.
Published: 2017
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23. Consensus statement: Virus taxonomy in the age of metagenomics

Author: Simmonds, Peter, Adams, Mike J., Benkő, Mária, Breitbart, Mya, Brister, J. Rodney, Carstens, Eric B., Davison, Andrew J., Delwart, Eric, Gorbalenya, Alexander E., Harrach, Balázs, Hull, Roger, King, Andrew M.Q., Koonin, Eugene V., Krupovic, Mart, Kuhn, Jens H., Lefkowitz, Elliot J., Nibert, Max L., Orton, Richard, Roossinck, Marilyn J., Sabanadzovic, Sead, Sullivan, Matthew B., Suttle, Curtis A., Tesh, Robert B., van der Vlugt, René A., Varsani, Arvind, Zerbini, F Murilo, University of Oxford [Oxford], University of Hertfordshire [Hatfield] (UH), Hungarian Academy of Sciences (MTA), College of Marine Science [St Petersburg, FL], University of South Florida [Tampa] (USF), National Center for Biotechnology Information (NCBI), Queen's University [Kingston, Canada], University of Glasgow, Blood Systems Research Institute, University of California [San Francisco] (UCSF), University of California-University of California, Leiden University Medical Center (LUMC), Lomonosov Moscow State University (MSU), John Innes Centre [Norwich], Institute for Animal Health, the Pirbright Institute, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), University of Alabama at Birmingham [ Birmingham] (UAB), Harvard Medical School [Boston] (HMS), Pennsylvania State University (Penn State), Penn State System, Mississippi State University [Mississippi], Ohio State University [Columbus] (OSU), Department of Earth, Ocean and Atmospheric Sciences [Vancouver] (UBC EOAS), University of British Columbia (UBC), Canadian Institute for Advanced Research (CIFAR), The University of Texas Medical Branch (UTMB), Wageningen University and Research [Wageningen] (WUR), Arizona State University [Tempe] (ASU), Universidade Federal de Vicosa (UFV), The workshop and discussions were funded by the Wellcome Trust (grant WT108418AIA). The work of A.E.G. was partially supported by the European Union's Horizon 2020 research and innovation programme (under grant agreement number 653316, the European Virus Archive goes Global, EVAg). R.A.v.d.V. was partly supported by the EU Cooperation in Science and Technology (COST) programme (action FA1407). S.S. acknowledges partial financial support from Mississippi State University (MSU)–Mississippi Agricultural and Forestry Experiment Station (MAFES) Strategic Research Initiative grants. The work of E.D. was supported by the US National Heart, Lung, and Blood Institute (NHLBI, grant R01 HL105770). Research by J.R.B. and E.V.K. was supported, in part, by the Intramural Research Program of the US National Institutes of Health (NIH), US National Library of Medicine. M.Breitbart was supported through the Assembling the Tree of Life Programme of the US National Science Foundation (grant DEB-1239976). M.B.S. was supported by an award from the Gordon and Betty Moore Foundation (number 3790). The involvement of J.H.K. was supported, in part, through the prime contract of the Battelle Memorial Institute with the US National Institute of Allergy and Infectious Diseases (NIAID) under contract number HHSN272200700016I. A subcontractor to the Battelle Memorial Institute who carried out this work is J.H.K., who is an employee of Tunnell Government Services, Inc. The views and conclusions that are contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of the US Department of Health and Human Services or of the institutions and companies that are affiliated with the authors., The authors thank the members of the International Committee on Taxonomy of Viruses (ICTV) Executive Committee who did not attend (A. Kropinski, R. Harrison, H. Sanfaçon, A. Mushegian, N. Knowles and S. Siddell) for thoughtful comments and discussion, and S. Roux from the Department of Microbiology at Ohio State University, USA, for the preparation of figure 1., University of Oxford, University of California [San Francisco] (UC San Francisco), University of California (UC)-University of California (UC), Universiteit Leiden, Biotechnology and Biological Sciences Research Council (BBSRC), The Pirbright Institute, Institut Pasteur [Paris] (IP), and Universidade Federal de Viçosa = Federal University of Viçosa (UFV)
Subjects: Base Sequence, Laboratory of Virology, High-Throughput Nucleotide Sequencing, MESH: Base Sequence, PE&RC, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Laboratorium voor Virologie, MESH: Viruses, Biointeractions and Plant Health, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Life Science, Metagenomics, MESH: Metagenomics, MESH: High-Throughput Nucleotide Sequencing
Abstract: Comment in:A sea change for virology. [Nat Rev Microbiol. 2017]; International audience; The number and diversity of viral sequences that are identified in metagenomic data far exceeds that of experimentally characterized virus isolates. In a recent workshop, a panel of experts discussed the proposal that, with appropriate quality control, viruses that are known only from metagenomic data can, and should be, incorporated into the official classification scheme of the International Committee on Taxonomy of Viruses (ICTV). Although a taxonomy that is based on metagenomic sequence data alone represents a substantial departure from the traditional reliance on phenotypic properties, the development of a robust framework for sequence-based virus taxonomy is indispensable for the comprehensive characterization of the global virome. In this Consensus Statement article, we consider the rationale for why metagenomic sequence data should, and how it can, be incorporated into the ICTV taxonomy, and present proposals that have been endorsed by the Executive Committee of the ICTV.
Published: 2017
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24. Taxonomy of the order Mononegavirales: update 2016

Author: Ralf Dürrwald, Krisztián Bányai, Robert A. Lamb, Hideki Kondo, Alexander Bukreyev, Anna N. Clawson, Calogero Terregino, Robert B. Tesh, Andrew J. Easton, Andrea Maisner, Paul A. Rota, Gael Kurath, Kartik Chandran, Charles H. Calisher, Ralf G. Dietzgen, Janusz T. Paweska, Szilvia Marton, Dennis Rubbenstroth, Masayuki Horie, Juliana Freitas-Astúa, Bertus K. Rima, Jonathan S. Towner, Viktor E. Volchkov, Eric M. Leroy, David M. Stone, Susan Payne, Kwok-Yung Yuen, Hideki Ebihara, Lin-Fa Wang, Lìjiāng Liú, C. Li, Nikos Vasilakis, Olga Dolnik, Gaya K. Amarasinghe, Gary P. Kobinger, Jean L. Patterson, Sergio Lenardon, Xian Dan Lin, Leslie L. Domier, Mang Shi, Pierre Formenty, Ben Longdon, Anna E. Whitfield, Sina Bavari, Timothy H. Hyndman, Martin Verbeek, E. W. Kitajima, Elke Mühlberger, Peter J. Walker, Ayato Takada, Mark D. Stenglein, François Xavier Briand, David Wang, Elodie Ghedin, Jiāsēn Chéng, Keizo Tomonaga, Norbert Nowotny, Roger Hewson, Noël Tordo, Jun Hua Tian, Nicolás Bejerman, John M. Dye, Christopher F. Basler, Yong-Zhen Zhang, Kim R. Blasdell, Yanping Fu, Sophie J. Smither, Richard E. Randall, Jens H. Kuhn, Jiǎtāo Xiè, Victoria Wahl-Jensen, Thierry Wetzel, Martin Schwemmle, Michael M. Goodin, John A. Walsh, Thomas Briese, Yīmíng Bào, Peter L. Collins, Dàohóng Jiāng, Sergey V. Netesov, Ron A. M. Fouchier, Szilvia L. Farkas, Claudio L. Afonso, US Department of Agriculture, Washington University School of Medicine (WUSM), University of Washington [Seattle], Centre for Agricultural Research [Budapest] (ATK), Hungarian Academy of Sciences (MTA), National Center for Biotechnology Information (NCBI), Georgia State University, University System of Georgia (USG), Army Medical Research Institute of Infectious Diseases [USA] (USAMRIID), Instituto Nacional de Tecnología Agropecuaria, Universidad Nacional de la Patagonia Austral (UNPA), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Laboratoire de Ploufragan-Plouzané-Niort [ANSES], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Columbia Mailman School of Public Health, The University of Texas Medical Branch (UTMB), Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University System, Albert Einstein College of Medicine [New York], Huazhong Agricultural University, Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Queensland Alliance for Agriculture and Food Innovation - Centre for Animal Science, University of Queensland [Brisbane], Philipps University of Marburg, University of Illinois [Chicago] (UIC), University of Illinois System, IDT Biologika, School of Life Sciences, Warwick University, Laboratory of Persistent Viral Diseases, LABOKLIN, Embrapa Cassava and Fruits, Brazilian Agricultural Research Corporation (Embrapa), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Department of Viroscience [Rotterdam, The Netherlands], Erasmus University Medical Center [Rotterdam] (Erasmus MC), Center for Genomics and Systems Biology, Department of Biology [New York], New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU)-New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU), Department of Plant Pathology, University of Kentucky, University of Kentucky, Public Health England [Salisbury] (PHE), Kagoshima University, School of Veterinary and Life Sciences [Murdoch], Murdoch University, State Key Laboratory of Agricultural Microbiology, Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), Universidade de São Paulo (USP), Research Centre in Infectious Diseases, CHUL Research Centre and Department of Microbiology and Immunology, Université Laval [Québec] (ULaval)-Faculty of Medicine, Institute of Plant Science and Resources, Okayama University, US Geological Survey [Seattle], United States Geological Survey [Reston] (USGS), Northwestern University [Evanston], Centre International de Recherches Médicales de Franceville (CIRMF), State Key Laboratory for Infectious Disease prevention and Control, Beijing Institute of Technology (BIT), Wēnzhōu Center for Disease Control and Prevention, Department of Genetics University of Cambridge, University of Cambridge [UK] (CAM), Boston University School of Medicine (BUSM), Boston University [Boston] (BU), Novosibirsk State University (NSU), University of Veterinary Medicine [Vienna] (Vetmeduni), Mohammed Bin Rashid University of Medicine and Health Sciences (MBRU), Texas Biomedical Research Institute [San Antonio, TX], College of Veterinary Medicine and Biomedical Sciences, National Institute for Communicable Diseases [Johannesburg] (NICD), Biomedical Sciences Research Complex [St Andrews, Scotland] (BSRC), University of St Andrews [Scotland], Queen's University [Belfast] (QUB), National Center for Immunization and Respiratory Diseases, CDC, Centers for Disease Control and Prevention (CDC), University of Freiburg [Freiburg], Chinese Center for Disease Control and Prevention, Defence Science and Technology Laboratory (Dstl), Ministry of Defence (UK) (MOD), Department of Microbiology, Immunology and Pathology, Colorado State University [Fort Collins] (CSU), Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Hokkaido University [Sapporo, Japan], Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Wǔhàn Center for Disease Control and Prevention, Institute for Virus Research, Kyoto University [Kyoto], Stratégies antivirales, Institut Pasteur [Paris], Institut Pasteur de Guinée, Réseau International des Instituts Pasteur (RIIP), Viral Special Pathogens Branch, Centers for Disease Control and Prevention-WHO Collaborative Centre for Viral Hemorrhagic Fevers, Wageningen University and Research [Wageningen] (WUR), Bases moléculaires de la pathogénicité virale – Molecular Basis of Viral Pathogenicity (BMPV), Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), National Biodefense Analysis and Countermeasures Center [Frederick], U.S. Social Security Administration, CSIRO Health & Biosecurity, Departments of Molecular Microbiology and Pathology & Immunology, Department of Agriculture, Fisheries and Forestry, Ecoscience Precinct, GPO Box 267, Brisbane, Duke-NUS Medical School [Singapore], Kansas State University, State Key Laboratory of Emerging Infectious Diseases & Department of Microbiology, The University of Hong Kong (HKU)-Li Ka Shing Faculty of Medicine, State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong (HKU), French Agency for Food, Environmental and Occupational Health & Safety (Anses) - Veterinary epidemiology, Albert Einstein College of Medicine, Public Health England [Porton Down, Salisbury], Faculty of Medicine-Laval University [Québec], Okayama University [Okayama], Centre International de Recherches Médicales de Franceville, Texas Biomedical Research Institute [San Antonio, Texas], A&M University, National Institute for Communicable Diseases (NICD), Centre for Experimental Medicine [Queen’s University of Belfast], Hokkaido University, Istituto Zooprofilattico Sperimentale delle Venezie [Padova], Wageningen University and Research Centre [Wageningen] (WUR), Bases moléculaires de la pathogénicité virale – Molecular Basis of Viral Pathogenicity, Duke NUS Medical School, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Columbia University [New York], Huazhong Agricultural University [Wuhan] (HZAU), Philipps Universität Marburg = Philipps University of Marburg, University of Warwick [Coventry], University of Kentucky (UK), Universidade de São Paulo = University of São Paulo (USP), Kyoto University, Institut Pasteur [Paris] (IP), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Virology, and Biomedical Sciences Research Complex
Subjects: 0301 basic medicine, 030106 microbiology, Zoology, Genome, Viral, Article, 03 medical and health sciences, Genus, Phylogenetics, Virology, Crustavirus, Life Science, Viral, Mononegavirales, Phylogeny, Order Mononegavirales, QR355, Genome, biology, Entomology & Disease Management, General Medicine, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Pneumoviridae, Subfamily Pneumovirinae, MONONEGAVIRALES, 030104 developmental biology, Evolutionary biology, Wildlife Ecology and Conservation, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.IMM]Life Sciences [q-bio]/Immunology, Taxonomy (biology), RA, RC
Abstract: International audience; In 2016, the order Mononegavirales was emended through the addition of two new families (Mymonaviridae and Sunviridae), the elevation of the paramyxoviral subfamily Pneumovirinae to family status (Pneumoviridae), the addition of five free-floating genera (Anphevirus, Arlivirus, Chengtivirus, Crustavirus, and Wastrivirus), and several other changes at the genus and species levels. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).
Published: 2016
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25. Data publication with the structural biology data grid supports live analysis

Author: Emil F. Pai, Qing R. Fan, Yousif Shamoo, Kevin D. Corbett, Dominika Borek, Tom Kirchhausen, James S. Fraser, Elizabeth Ransey, Stephanie M. Socias, Peter A. Meyer, Enrico Di Cera, Oleg V. Tsodikov, Jason S. McLellan, C. S. Raman, James Withrow, Mercè Crosas, Karen S. Anderson, Carlo Petosa, Filipe R. N. C. Maia, Gabrielle Rudenko, Yorgo Modis, Peng Gong, Walter J. Chazin, Zongchao Jia, Zbyszek Otwinowski, Adrian R. Ferré-D'Amaré, Yunsun Nam, Stephen C. Harrison, Sirano Dhe-Paganon, Joseph Schlessinger, Catherine L. Drennan, Kenneth D. Westover, Holger Sondermann, Richard H. G. Baxter, Marc Kvansakul, Ekaterina E. Heldwein, J. Christopher Fromme, Sean Crosson, Michael K. Rosen, Antonina Roll-Mecak, Robert J. Keenan, Tamir Gonen, Andrew C. Kruse, Ian Foster, Kanagalaghatta R. Rajashankar, Titus J. Boggon, Ming Lei, K. Christopher Garcia, Alexandre M. J. J. Bonvin, Michael S. Cosgrove, Amedeo Caflisch, Michael J. Eck, Brandt F. Eichman, Thomas U. Schwartz, Chung-I Chang, Rachelle Gaudet, Yizhi Jane Tao, Emily C. Tjon, Pedro Pereira, Jason Key, David B. Neau, Stephen C. Blacklow, Kay Diederichs, Hao Wu, Tom A. Rapoport, Alejandro Buschiazzo, Tom J. Brett, Piotr Sliz, Chris Botka, Niraj H. Tolia, Department of Biological Chemistry and Molecular Pharmacology [Boston] (DBCMP), Harvard Medical School [Boston] (HMS), Laboratory of molecular and structural microbiology, Institut Pasteur de Montevideo, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Shanghai Institutes for Biological Sciences (Institute of Biochemistry and Cell Biology), Chinese Academy of Sciences [Beijing] (CAS), NE-CAT and department of chemistry and chemical biology [Argonne], Cornell University, Departments of pharmacology and molecular biophysics and biochemistry [New Haven], Yale University School of Medicine, Department of Chemistry and Molecular Biophysics & Biochemistry [New Haven], Yale University [New Haven], Bijovet center [Utrecht], Utrecht University [Utrecht], Department of Biophysics and Biochemistry [Dallas], University of Texas Southwestern Medical Center [Dallas], Department of Internal Medicine [St Louis], Washington University School of Medicine, Department of Biochemistry [Zurich], University of Zürich [Zürich] (UZH), Institute of Biological Chemistry (IBC Sinica), Academia Sinica, Departments of biochemistry and chemistry [Nashville], Vanderbilt University [Nashville], Ludwig Institute for Cancer Research, University of California [San Diego] (UC San Diego), University of California, SUNY Upstate Medical University, State University of New York (SUNY), University of Chicago, Dana-Farber Cancer Institute [Boston], Saint Louis University School of Medicine [St Louis], Massachusetts Institute of Technology (MIT), Department of Biological Chemistry and Molecular Pharmacology (DBCMP), Columbia University [New York], National Heart, Lung, and Blood Institute [Bethesda] (NHLBI), Weill Institute for Cell and Molecular Biology, Howard Hughes Medical Institute [Stanford], Stanford University School of Medicine [CA, USA], Harvard University [Cambridge], Wuhan Institute of Virology, Howard Hughes Medical Institute [Boston], Tufts University School of Medicine [Boston], Queen's University [Kingston], La Trobe University [Melbourne], Geisel School of Medicine at Dartmouth, University of Cambridge [UK] (CAM), University of Texas at Dallas [Richardson] (UT Dallas), Campbell Family Institute for Breast Cancer Research, University Health Network, University of Toronto, Instituto de Biologia Molecular e Celular (IBMC), Institut de biologie structurale (IBS - UMR 5075), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS), University of Maryland [Baltimore County] (UMBC), University of Maryland System, National Institute of Neurological Disorders and Stroke [Bethesda] (NINDS), National Institutes of Health [Bethesda] (NIH), Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch (UTMB), Rice University [Houston], University of Washington School of Medicine, University of Kentucky, Boston Children's Hospital, Department of Computer Science, University of Chicago, University of California [San Francisco] (UCSF), Uppsala University, Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Howard Hughes Medical Institute [Ashburn], Fachbereich Biologie, University of Konstanz, Institute for Quantitative Social Sciences, Development of the Structural Biology Data Grid is funded by The Leona M. and Harry B. Helmsley Charitable Trust 2016PG-BRI002 to PS and MC. Development of citation workflows is supported NSF 1448069 (to PS). DAA is being developed as a pilot project of the National Data Service, with additional funds to support storage and technology development, including NIH P41 GM103403 (NE-CAT) and 1S10RR028832 (HMS) and DOE DE-AC02-06CH11357, NIH 1U54EB020406-01, Big Data for Discovery Science Center, and NIST 60NANB15D077 (Globus Project), Massachusetts Institute of Technology. Department of Biology, Massachusetts Institute of Technology. Department of Chemistry, Drennan, Catherine L., Schwartz, Thomas, Sub NMR Spectroscopy, NMR Spectroscopy, Instituto de Investigação e Inovação em Saúde, Molecular and structural microbiology / Microbiología Molecular y Estructural [Montevideo], Cornell University [New York], Universität Zürich [Zürich] = University of Zurich (UZH), Howard Hughes Medical Institute (HHMI), Queen's University [Kingston, Canada], Institut de biologie structurale (IBS - UMR 5075 ), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), University of Zurich, Sliz, Piotr, Yale School of Medicine [New Haven, Connecticut] (YSM), University of California (UC), Harvard University, Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), University of Kentucky (UK), University of California [San Francisco] (UC San Francisco), Harrison, Seamus Conor [0000-0003-1480-1143], Modis, Yorgo [0000-0002-6084-0429], and Apollo - University of Cambridge Repository
Subjects: 0301 basic medicine, Chemistry(all), Experiences, General Physics and Astronomy, computer.software_genre, Crystallography, X-Ray, Biochemistry, Software, Structural Biology, Databases, Genetic, Structure models, Macromolecular crystallography, media_common, Strukturbiologi, Uncategorized, Multidisciplinary, Crystallography, Data grid, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Publications, X-ray scattering, 1.5 Resources and infrastructure (underpinning), 3100 General Physics and Astronomy, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Networking and Information Technology R&D, Networking and Information Technology R&D (NITRD), The Internet, Data mining, Macromolecular Substances, media_common.quotation_subject, Science, 610 Medicine & health, 1600 General Chemistry, Biology, Physics and Astronomy(all), General Biochemistry, Genetics and Molecular Biology, Article, Synchrotron, 03 medical and health sciences, Databases, Genetic, Underpinning research, 1300 General Biochemistry, Genetics and Molecular Biology, ddc:570, 10019 Department of Biochemistry, Quality (business), Internet, business.industry, Biochemistry, Genetics and Molecular Biology(all), Data quality, Experimental data, General Chemistry, Data science, 030104 developmental biology, Data access, Protein data-bank, Paradigm shift, X-Ray, 570 Life sciences, biology, Resolution, business, computer, Department of Biochemistry, Genetics and Molecular Biology(all)
Abstract: Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. It is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis., The validation and analysis of X-ray crystallographic data is essential for reproducibility and the development of crystallographic methods. Here, the authors describe a repository for crystallographic datasets and demonstrate some of the ways it could serve the crystallographic community.
Published: 2016
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26. The Global Virus Network: Challenging chikungunya

Author: Matthew B. Frieman, Scott C. Weaver, Marc Lecuit, Edward McSweegan, Sharon Hrynkow, Thomas E. Morrison, Global Virus Network, The University of Texas Medical Branch (UTMB), Biologie des Infections - Biology of Infection, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Descartes - Paris 5 (UPD5), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Service des Maladies infectieuses et tropicales [CHU Necker], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), University of Maryland School of Medicine, University of Maryland System, University of Colorado [Denver], Université Paris Descartes - Paris 5 (UPD5)-CHU Necker - Enfants Malades [AP-HP]-Institut des Maladies Génétiques Imagine [Paris], Institut des Maladies Génétiques Imagine [Paris], University of South Florida [Tampa] (USF), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)
Subjects: Resource (biology), International Cooperation, education, Public policy, Global Virus Network, Global Health, medicine.disease_cause, Article, Disease Outbreaks, West africa, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Virology, Global health, Humans, Medicine, Chikungunya, health care economics and organizations, Pharmacology, Western hemisphere, Arbovirus, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, business.industry, Task force, Public relations, Emerging virus, 3. Good health, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Vector-borne, Communicable Disease Control, Epidemiological Monitoring, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Chikungunya Fever, business, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: International audience; The recent spread of chikungunya virus to the Western Hemisphere, together with the ongoing Ebola epidemic in West Africa, have highlighted the importance of international collaboration in the detection and management of disease outbreaks. In response to this need, the Global Virus Network (GVN) was formed in 2011. The GVN is a coalition of leading medical virologists in 34 affiliated laboratories in 24 countries, who collaborate to share their resources and expertise. The GVN supports research, promotes training for young scientists, serves as a technical resource for governments, businesses and international organizations, facilitates international scientific cooperation, and advocates for funding and evidence-based public policies. In response to the spread of chikungunya, the GVN formed a task force to identify research gaps and opportunities, including models of infection and disease, candidate vaccines and antivirals, epidemiology and vector control measures. Its members also serve as authoritative sources of information for the public, press, and policy-makers. This article forms part of a symposium in Antiviral Research on "Chikungunya discovers the New World".
Published: 2015
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27. Chikungunya Virus and the Global Spread of a Mosquito-Borne Disease

Author: Marc Lecuit, Scott C. Weaver, The University of Texas Medical Branch (UTMB), Global Virus Network, Biologie des Infections - Biology of Infection, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Descartes - Paris 5 (UPD5), CHU Necker - Enfants Malades [AP-HP], Service des Maladies infectieuses et tropicales [CHU Necker], Université Paris Descartes - Paris 5 (UPD5)-CHU Necker - Enfants Malades [AP-HP]-Institut des Maladies Génétiques Imagine [Paris], Institut des Maladies Génétiques Imagine [Paris], We thank Therese Couderc, the members of the Biology of Infection Unit, and the members of the Chikungunya Task Force at Institut Pasteur, and Rose Langsjoen for assistance with graphics., University of South Florida [Tampa] (USF), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)
Subjects: musculoskeletal diseases, myalgia, viruses, [SDV]Life Sciences [q-bio], 030231 tropical medicine, Disease, Alphavirus, MESH: Chikungunya Fever, MESH: Insect Vectors, medicine.disease_cause, Virus, 03 medical and health sciences, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, parasitic diseases, medicine, MESH: Animals, Chikungunya, MESH: Disease Outbreaks, MESH: Travel, 030304 developmental biology, Mosquito-borne disease, 0303 health sciences, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, MESH: Humans, biology, business.industry, virus diseases, MESH: Chikungunya virus, General Medicine, medicine.disease, biology.organism_classification, Virology, Rash, 3. Good health, body regions, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Chikungunya Virus Infection, Immunology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, MESH: Disease Progression, medicine.symptom, business, MESH: Culicidae, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: Comment in Chikungunya Virus Infections. [N Engl J Med. 2015] Chikungunya Virus Infections. [N Engl J Med. 2015] Chikungunya Virus Infections. [N Engl J Med. 2015]; International audience; Chikungunya virus is a mosquito-borne alphavirus; its name comes from a Makonde word describing the bent posture of persons with the severe arthralgia that is a hallmark of chikungunya fever, the disease caused by the virus.1 Chikungunya virus was first isolated after a 1952–1953 epidemic in present-day Tanzania. Outbreaks were subsequently identified in Asia during the 1950s and 1960s [...]
Published: 2015
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28. HS during circulatory shock: Some unresolved questions

Author: McCook, Oscar, Radermacher, Peter, Volani, C., Asfar, Pierre, Ignatius, A., Kemmler, J., Moller, P., Szabo, C., Whiteman, M., Wood, M., Wang, R., Georgieff, M., Wachter, Ulrich, Universitätsklinikum Ulm - University Hospital of Ulm, Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM), The University of Texas Medical Branch (UTMB), University of Exeter Medical School, University of Exeter, Lakehead University, and Univ Angers, Okina
Subjects: [SDV] Life Sciences [q-bio], Cystathionine-γ-lyase, H(2)S, GYY4137, [SDV]Life Sciences [q-bio], NaSH, Cystathione-β-synthase, Na(2)S
Abstract: International audience; Numerous papers have been published on the role of H2S during circulatory shock. Consequently, knowledge about vascular sulfide concentrations may assume major importance, in particular in the context of "acute on chronic disease", i.e., during circulatory shock in animals with pre-existing chronic disease. This review addresses the questions (i) of the "real" sulfide levels during circulatory shock, and (ii) to which extent injury and pre-existing co-morbidity may affect the expression of H2S producing enzymes under these conditions. In the literature there is a huge range on sulfide blood levels during circulatory shock, in part as a result of the different analytical methods used, but also due to the variable of the models and species studied. Clearly, some of the very high levels reported should be questioned in the context of the well-known H2S toxicity. As long as "real" sulfide levels during circulatory shock are unknown and/or undetectable "on line" due to the lack of appropriate techniques, it appears to be premature to correlate the measured blood levels of hydrogen sulfide with the severity of shock or the H2S therapy-related biological outcomes. The available data on the tissue expression of the H2S-releasing enzymes during circulatory shock suggest that a "constitutive" CSE expression may play a crucial role of for the maintenance of organ function, at least in the kidney. The data also indicate that increased CBS and CSE expression, in particular in the lung and the liver, represents an adaptive response to stress states.
Published: 2014
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29. STATE OF THE CLIMATE IN 2011 Special Supplement to the Bulletin of the American Meteorological Society Vol. 93, No. 7, July 2012

Author: Arndt, D. S., Blunden, J., Willett, K. M., Dolman, A. J., Hall, B. D., Thorne, P. W., Gregg, M. C., Newlin, M. L., Xue, Y., Hu, Z., Kumar, A., Banzon, V., Smith, T. M., Rayner, N. A., Jeffries, M. O., Richter-Menge, J., Overland, J., Bhatt, U., Key, J., Liu, Y., Walsh, J., Wang, M., Fogt, R. L., Scambos, T. A., Wovrosh, A. J., Barreira, S., Sanchez-Lugo, A., Renwick, J. A., Thiaw, W. M., Weaver, S. J., Whitewood, R., Phillips, D., Achberger, C., Ackerman, S. A., Ahmed, F. H., Albanil-Encarnacion, A., Alfaro, E. J., Alves, L. M., Allan, R., Amador, J. A., Ambenje, P., Antoine, M. D., Antonov, J., Arevalo, J., Ashik, I., Atheru, Z., Baccini, A., Baez, J., Baringer, M. O., Barriopedro, D. E., Bates, J. J., Becker, A., Behrenfeld, M. J., Bell, G. D., Benedetti, A., Bernhard, G., Berrisford, P., Berry, D. I., Beszczynska-Moeller, A., Bhatt, U. S., Bidegain, M., Bieniek, P., Birkett, C., Bissolli, P., Blake, E. S., Boudet-Rouco, D., Box, J. E., Boyer, T., Braathen, G. O., Brackenridge, G. R., Brohan, P., Bromwich, D. H., Brown, L., Brown, R., Bruhwiler, L., Bulygina, O. N., Burrows, J., Calderon, B., Camargo, S. J., Cappellen, J., Carmack, E., Carrasco, G., Chambers, D. P., Christiansen, H. H., Christy, J., Chung, D., Ciais, P., Coehlo, C. A. S., Colwell, S., Comiso, J., Cretaux, J. F., Crouch, J., Cunningham, S. A., Jeu, R. A. M., Demircan, M., Derksen, C., Diamond, H. J., Dlugokencky, E. J., Dohan, K., Dorigo, W. A., Drozdov, D. S., Duguay, C., Dutton, E., Dutton, G. S., Elkins, J. W., Epstein, H. E., Famiglietti, J. S., Fanton D Andon, O. H., Feely, R. A., Fekete, B. M., Fenimore, C., Fernandez-Prieto, D., Fields, E., Fioletov, V., Folland, C., Foster, M. J., Frajka-Williams, E., Franz, B. A., Frey, K., Frith, S. H., Frolov, I., Frost, G. V., Ganter, C., Garzoli, S., Gitau, W., Gleason, K. L., Gobron, N., Goldenberg, S. B., Goni, G., Gonzalez-Garcia, I., Gonzalez-Rodriguez, N., Good, S. A., Goryl, P., Gottschalck, J., Gouveia, C. M., Griffiths, G. M., Grigoryan, V., Grooss, J. U., Guard, C., Guglielmin, M., Halpert, M. S., Heidinger, A. K., Heikkila, A., Heim, R. R., Hennon, P. A., Hidalgo, H. G., Hilburn, K., Ho, S. P., Hobbs, W. R., Holgate, S., Hook, S. J., Hovsepyan, A., Hu, Z. Z., Hugony, S., Hurst, D. F., Ingvaldsen, R., Itoh, M., Jaimes, E., Jeffries, M., Johns, W. E., Johnsen, B., Johnson, B., Johnson, G. C., Jones, L. T., Jumaux, G., Kabidi, K., Kaiser, J. W., Kang, K. K., Kanzow, T. O., Kao, H. Y., Keller, L. M., Kendon, M., Kennedy, J. J., Kervankiran, S., Khatiwala, S., Kholodov, A. L., Khoshkam, M., Kikuchi, T., Kimberlain, T. B., King, D., Knaff, J. A., Korshunova, N. N., Koskela, T., Kratz, D. P., Krishfield, R., Kruger, A., Kruk, M. C., Lagerloef, G., Lakkala, K., Lammers, R. B., Lander, M. A., Landsea, C. W., Lankhorst, M., Lapinel-Pedroso, B., Lazzara, M. A., Leduc, S., Lefale, P., Leon, G., Leon-Lee, A., Leuliette, E., Levitus, S., L Heureux, M., Lin, II, Liu, H. X., Liu, Y. J., Lobato-Sanchez, R., Locarnini, R., Loeb, N. G., Loeng, H., Long, C. S., Lorrey, A. M., Lumpkin, R., Myhre, C. L., Jing-Jia Luo, Lyman, J. M., Maccallum, S., Macdonald, A. M., Maddux, B. C., Manney, G., Marchenko, S. S., Marengo, J. A., Maritorena, S., Marotzke, J., Marra, J. J., Martinez-Sanchez, O., Maslanik, J., Massom, R. A., Mathis, J. T., Mcbride, C., Mcclain, C. R., Mcgrath, D., Mcgree, S., Mclaughlin, F., Mcvicar, T. R., Mears, C., Meier, W., Meinen, C. S., Menendez, M., Merchant, C., Merrifield, M. A., Miller, L., Mitchum, G. T., Montzka, S. A., Moore, S., Mora, N. P., Morcrette, J. J., Mote, T., Muhle, J., Mullan, A. B., Muller, R., Myhre, C., Nash, E. R., Nerem, R. S., Newman, P. A., Ngari, A., Nishino, S., Njau, L. N., Noetzli, J., Oberman, N. G., Obregon, A., Ogallo, L., Oludhe, C., Oyunjargal, L., Parinussa, R. M., Park, G. H., Parker, D. E., Pasch, R. J., Pascual-Ramirez, R., Pelto, M. S., Penalba, O., Perez-Suarez, R., Perovich, D., Pezza, A. B., Pickart, R., Pinty, B., Pinzon, J., Pitts, M. C., Pour, H. K., Prior, J., Privette, J. L., Proshutinsky, A., Quegan, S., Quintana, J., Rabe, B., Rahimzadeh, F., Rajeevan, M., Rayner, D., Raynolds, M. K., Razuvaev, V. N., Reagan, J., Reid, P., Revadekar, J., Rex, M., Rivera, I. L., Robinson, D. A., Rodell, M., Roderick, M. L., Romanovsky, V. E., Ronchail, J., Rosenlof, K. H., Rudels, B., Sabine, C. L., Santee, M. L., Sawaengphokhai, P., Sayouri, A., Schauer, U., Schemm, J., Schmid, C., Schreck, C., Semiletov, I., Send, U., Sensoy, S., Shakhova, N., Sharp, M., Shiklomanov, N. I., Shimada, K., Shin, J., Siegel, D. A., Simmons, A., Skansi, M., Sokolov, V., Spence, J., Srivastava, A. K., Stackhouse, P. W., Stammerjohn, S., Steele, M., Steffen, K., Steinbrecht, W., Stephenson, T., Stolarski, R. S., Sweet, W., Takahashi, T., Taylor, M. A., Tedesco, M., Thepaut, J. N., Thompson, P., Timmermans, M. L., Tobin, S., Toole, J., Trachte, K., Trewin, B. C., Trigo, R. M., Trotman, A., Tucker, C. J., Ulupinar, Y., Wal, R. S. W., Werf, G. R., Vautard, R., Votaw, G., Wagner, W. W., Wahr, J., Walker, D. A., Wang, C. Z., Wang, J. H., Wang, L., Wang, M. H., Wang, S. H., Wanninkhof, R., Weaver, S., Weber, M., Weingartner, T., Weller, R. A., Wentz, F., Wilber, A. C., Williams, W., Willis, J. K., Wilson, R. C., Wolken, G., Wong, T. M., Woodgate, R., Yamada, R., Yamamoto-Kawai, M., Yoder, J. A., Yu, L. S., Yueh, S., Zhang, L. Y., Zhang, P. Q., Zhao, L., Zhou, X. J., Zimmermann, S., Zubair, L., Laboratoire d'études en Géophysique et océanographie spatiales (LEGOS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), National Oceanic and Atmospheric Administration (NOAA), Lamont-Doherty Earth Observatory (LDEO), Columbia University [New York], Space Technology Center, European Centre for Medium-Range Weather Forecasts (ECMWF), Climate Research Division [Toronto], Environment and Climate Change Canada, Earth and Space Research Institute [Seattle] (ESR), Department of Hydrology and Geo-Environmental Sciences [Amsterdam], Vrije Universiteit Amsterdam [Amsterdam] (VU), Vienna University of Technology (TU Wien), Instituto Dom Luiz, Universidade de Lisboa = University of Lisbon (ULISBOA), NOAA Earth System Research Laboratory (ESRL), Cooperative Institute for Research in Environmental Sciences (CIRES), University of Colorado [Boulder]-National Oceanic and Atmospheric Administration (NOAA), Department of Earth System Science [Irvine] (ESS), University of California [Irvine] (UC Irvine), University of California (UC)-University of California (UC), Jet Propulsion Laboratory (JPL), NASA-California Institute of Technology (CALTECH), University of California Center for Hydrologic Modeling [Irvine] (UCCHM), NOAA Pacific Marine Environmental Laboratory [Seattle] (PMEL), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Extrèmes : Statistiques, Impacts et Régionalisation (ESTIMR), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Department of Physics [Boulder], University of Colorado [Boulder], Istituto Nazionale di Fisica Nucleare [Pisa] (INFN), Istituto Nazionale di Fisica Nucleare (INFN), NOAA Atlantic Oceanographic and Meteorological Laboratory (AOML), University at Albany [SUNY], State University of New York (SUNY), Cooperative Institute for Meteorological Satellite Studies (CIMSS), University of Wisconsin-Madison-NASA-National Oceanic and Atmospheric Administration (NOAA), Peking University [Beijing], National Oceanography Centre [Southampton] (NOC), University of Southampton, NOAA National Environmental Satellite, Data, and Information Service (NESDIS), The University of Texas Medical Branch (UTMB), Institut für Umweltphysik [Bremen] (IUP), Universität Bremen, Department of Meteorology, University of Nairobi (UoN), Climate Prediction and Applications Centre (ICPAC), IGAD, Institute for Environment and Sustainability of the JRC, Partenaires INRAE, Met Office Hadley Centre for Climate Change (MOHC), United Kingdom Met Office [Exeter], Agricultural Information Institute (AII), Chinese Academy of Agricultural Sciences (CAAS), Woods Hole Oceanographic Institution (WHOI), Universitá degli Studi dell’Insubria = University of Insubria [Varese] (Uninsubria), Heilongjiang Institute of Science and Technology, Finnish Meteorological Institute (FMI), Universidad de Costa Rica (UCR), University Corporation for Atmospheric Research (UCAR), NOAA Center for Satellite Applications and Research (STAR), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA), ESRL Global Monitoring Laboratory [Boulder] (GML), Materials and structures Laboratory, Tokyo Institute of Technology [Tokyo] (TITECH), Rosenstiel School of Marine and Atmospheric Science (RSMAS), University of Miami [Coral Gables], Norwegian Radiation and Nuclear Safety Authority, Direction Interrégionale de Météo-France pour l'océan Indien (DIROI), Météo-France, Department of Earth Sciences [Oxford], University of Oxford, NASA Langley Research Center [Hampton] (LaRC), University of Hawai‘i [Mānoa] (UHM), Department of Earth and Space Sciences [Seattle], University of Washington [Seattle], Leibniz-Institut für Meereswissenschaften (IFM-GEOMAR), Scripps Institution of Oceanography (SIO - UC San Diego), University of California [San Diego] (UC San Diego), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Huazhong Agricultural University [Wuhan] (HZAU), NOAA National Weather Service (NWS), Department of Oceanography, Florida State University [Tallahassee] (FSU), Norwegian Institute for Air Research (NILU), Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), NorthWest Research Associates (NWRA), Department of Physics [Socorro], New Mexico Institute of Mining and Technology [New Mexico Tech] (NMT), Ocean and Earth Science [Southampton], University of Southampton-National Oceanography Centre (NOC), Australian Antarctic Division (AAD), Australian Government, Department of the Environment and Energy, Antarctic Climate and Ecosystems Cooperative Research Centre (ACE-CRC), Massachusetts General Hospital [Boston], Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Australian Research Council (ARC), Remote Sensing Systems [Santa Rosa] (RSS), Développement, institutions et analyses de long terme (DIAL), Université Paris Dauphine-PSL, Université Paris sciences et lettres (PSL), NOAA National Marine Fisheries Service (NMFS), University of California (UC), NMR Laboratory, Université de Mons, Université de Mons (UMons), NASA Goddard Space Flight Center (GSFC), Glaciology, Geomorphodynamics and Geochronology, Department of Geography [Zürich], Universität Zürich [Zürich] = University of Zurich (UZH)-Universität Zürich [Zürich] = University of Zurich (UZH), Chemistry Department [Massachusetts Institute of Technology], Massachusetts Institute of Technology (MIT), Nichols College Dudley, ERDC Cold Regions Research and Engineering Laboratory (CRREL), USACE Engineer Research and Development Center (ERDC), European Commission, Space Science and Engineering Center [Madison] (SSEC), University of Wisconsin-Madison, Lausanne University Hospital, Centro de Ciencias do Sistema Terrestre, Instituto Nacional de Pesquisas Espaciais (INPE), University of Sheffield, Hochschule Mannheim - University of Applied Sciences, Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Indian Institute of Tropical Meteorology (IITM), Ministry of Earth Sciences [India], Woods Hole Research Center, Department of Earth and Environment [Boston], Boston University [Boston] (BU), Centre for Australian Weather and Climate Research (CAWCR), Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Génétique et Ecologie des Virus, Génétique des Virus et Pathogénèse des Maladies Virales, Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Botany and Plant Pathology, Oregon State University (OSU), Ctr Ecol & Hydrol, Bangor, Environm Ctr Wales, Biospherical Instruments Inc., Processus de la variabilité climatique tropicale et impacts (PARVATI), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Université Paris Diderot - Paris 7 (UPD7), Instituto Uruguayo de Meteorología, Javier Barrios Amorín 1488, CP 11200, Montevideo, Uruguay, Science Systems and Applications, Inc. [Hampton] (SSAI), National Snow and Ice Data Center (NSIDC), Naval Postgraduate School (NPS), University of California [Berkeley] (UC Berkeley), Centre de physique moléculaire optique et hertzienne (CPMOH), Université Sciences et Technologies - Bordeaux 1 (UB)-Centre National de la Recherche Scientifique (CNRS), CYRIC, Tohoku University [Sendai], The University of Tennessee [Knoxville], Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC, The University Centre in Svalbard (UNIS), Institute of Arctic Alpine Research [University of Colorado Boulder] (INSTAAR), Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Meteorologisches Observatorium Hohenpeißenberg (MOHp), Deutscher Wetterdienst [Offenbach] (DWD), British Antarctic Survey (BAS), Natural Environment Research Council (NERC), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Universidade de Lisboa (ULISBOA), University of California [Irvine] (UCI), University of California-University of California, Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Universitá degli Studi dell’Insubria, University of Costa Rica, Météo France [Sainte-Clotilde], Météo France, University of Oxford [Oxford], Scripps Institution of Oceanography (SIO), Huazhong Agricultural University, University of California, NMR and Molecular Imaging Laboratory [Mons], University of Mons [Belgium] (UMONS), Lausanne University Hospital [Switzerland], Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Diderot - Paris 7 (UPD7), Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Berkeley University of California (UC BERKELEY), Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1, and Institute of Arctic and Alpine Research (INSTAAR)
Subjects: [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography
Abstract: International audience; Large-scale climate patterns influenced temperature and weather patterns around the globe in 2011. In particular, a moderate-to-strong La Nina at the beginning of the year dissipated during boreal spring but reemerged during fall. The phenomenon contributed to historical droughts in East Africa, the southern United States, and northern Mexico, as well the wettest two-year period (2010-11) on record for Australia, particularly remarkable as this follows a decade-long dry period. Precipitation patterns in South America were also influenced by La Nina. Heavy rain in Rio de Janeiro in January triggered the country's worst floods and landslides in Brazil's history. The 2011 combined average temperature across global land and ocean surfaces was the coolest since 2008, but was also among the 15 warmest years on record and above the 1981-2010 average. The global sea surface temperature cooled by 0.1 degrees C from 2010 to 2011, associated with cooling influences of La Nina. Global integrals of upper ocean heat content for 2011 were higher than for all prior years, demonstrating the Earth's dominant role of the oceans in the Earth's energy budget. In the upper atmosphere, tropical stratospheric temperatures were anomalously warm, while polar temperatures were anomalously cold. This led to large springtime stratospheric ozone reductions in polar latitudes in both hemispheres. Ozone concentrations in the Arctic stratosphere during March were the lowest for that period since satellite records began in 1979. An extensive, deep, and persistent ozone hole over the Antarctic in September indicates that the recovery to pre-1980 conditions is proceeding very slowly. Atmospheric carbon dioxide concentrations increased by 2.10 ppm in 2011, and exceeded 390 ppm for the first time since instrumental records began. Other greenhouse gases also continued to rise in concentration and the combined effect now represents a 30% increase in radiative forcing over a 1990 baseline. Most ozone depleting substances continued to fall. The global net ocean carbon dioxide uptake for the 2010 transition period from El Nino to La Nina, the most recent period for which analyzed data are available, was estimated to be 1.30 Pg C yr(-1), almost 12% below the 29-year long-term average. Relative to the long-term trend, global sea level dropped noticeably in mid-2010 and reached a local minimum in 2011. The drop has been linked to the La Nina conditions that prevailed throughout much of 2010-11. Global sea level increased sharply during the second half of 2011. Global tropical cyclone activity during 2011 was well-below average, with a total of 74 storms compared with the 1981-2010 average of 89. Similar to 2010, the North Atlantic was the only basin that experienced above-normal activity. For the first year since the widespread introduction of the Dvorak intensity-estimation method in the 1980s, only three tropical cyclones reached Category 5 intensity level-all in the Northwest Pacific basin. The Arctic continued to warm at about twice the rate compared with lower latitudes. Below-normal summer snowfall, a decreasing trend in surface albedo, and above-average surface and upper air temperatures resulted in a continued pattern of extreme surface melting, and net snow and ice loss on the Greenland ice sheet. Warmer-than-normal temperatures over the Eurasian Arctic in spring resulted in a new record-low June snow cover extent and spring snow cover duration in this region. In the Canadian Arctic, the mass loss from glaciers and ice caps was the greatest since GRACE measurements began in 2002, continuing a negative trend that began in 1987. New record high temperatures occurred at 20 m below the land surface at all permafrost observatories on the North Slope of Alaska, where measurements began in the late 1970s. Arctic sea ice extent in September 2011 was the second-lowest on record, while the extent of old ice (four and five years) reached a new record minimum that was just 19% of normal. On the opposite pole, austral winter and spring temperatures were more than 3 degrees C above normal over much of the Antarctic continent. However, winter temperatures were below normal in the northern Antarctic Peninsula, which continued the downward trend there during the last 15 years. In summer, an all-time record high temperature of -12.3 degrees C was set at the South Pole station on 25 December, exceeding the previous record by more than a full degree. Antarctic sea ice extent anomalies increased steadily through much of the year, from briefly setting a record low in April, to well above average in December. The latter trend reflects the dispersive effects of low pressure on sea ice and the generally cool conditions around the Antarctic perimeter.
Published: 2012
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30. SNMIB/Apollo protects leading-strand telomeres against NHEJ-mediated repair

Author: Sandy Chang, Eric Gilson, Anaïs Poulet, Yung C. Lam, Randy J. Legerski, Peili Gu, Marie Josèphe Giraud-Panis, Shamima Akhter, Susan M. Bailey, Jing Ye, Department of Genetics, The University of Texas Medical Branch (UTMB), Laboratoire de biologie et pathologie des génomes, Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Environmental and Radiological Health Sciences, Colorado State University [Fort Collins] (CSU), Department of Medical Genetics, Centre Hospitalier Universitaire de Nice (CHU Nice), Department of Hematopathology, Ganivet, Agnès, Laboratory of Biology and Pathology of Genomes, and Centre National de la Recherche Scientifique (CNRS)
Subjects: Exonuclease, chromosomes, DNA Repair, DNA damage, Telomere-Binding Proteins, Cell Cycle Proteins, Ataxia Telangiectasia Mutated Proteins, Protein Serine-Threonine Kinases, Biology, Aminopeptidases, Shelterin Complex, Article, General Biochemistry, Genetics and Molecular Biology, Mice, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Dipeptidyl-Peptidases and Tripeptidyl-Peptidases, Molecular Biology, 030304 developmental biology, Mice, Knockout, 0303 health sciences, Nuclease, Tripeptidyl-Peptidase 1, General Immunology and Microbiology, DNA synthesis, Tumor Suppressor Proteins, General Neuroscience, DNA replication, Fibroblasts, Telomere, Embryo, Mammalian, telomeres, Molecular biology, DNA-Binding Proteins, Exodeoxyribonucleases, chemistry, 030220 oncology & carcinogenesis, Knockout mouse, biology.protein, Serine Proteases, DNA
Abstract: Progressive telomere attrition or deficiency of the protective shelterin complex elicits a DNA damage response as a result of a cell's inability to distinguish dysfunctional telomeric ends from DNA double-strand breaks. SNMIB/Apollo is a shelterin-associated protein and a member of the SMN1/PSO2 nuclease family that localizes to telomeres through its interaction with TRF2. Here, we generated SNMIB/Apollo knockout mouse embryo fibroblasts (MEFs) to probe the function of SNMIB/Apollo at mammalian telomeres. SNMIB/Apollo null MEFs exhibit an increased incidence of G2 chromatid-type fusions involving telomeres created by leading-strand DNA synthesis, reflective of a failure to protect these telomeres after DNA replication. Mutations within SNMIB/Apollo's conserved nuclease domain failed to suppress this phenotype, suggesting that its nuclease activity is required to protect leading-strand telomeres. SNMIB/Apollo(-/-)ATM(-/-) MEFs display robust telomere fusions when Trf2 is depleted, indicating that ATM is dispensable for repair of uncapped telomeres in this setting. Our data implicate the 5'-3' exonuclease function of SNM1B/Apollo in the generation of 3' single-stranded overhangs at newly replicated leading-strand telomeres to protect them from engaging the non-homologous end-joining pathway.
Published: 2010

31. Neuro-glial crosstalk in inflammatory bowel disease

Author: L. Van Landeghem, Tor C. Savidge, Michel Neunlist, Arnaud Bourreille, Neunlist, Michel, Neuropathies du système nerveux entérique et pathologies digestives, implication des cellules gliales entériques, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes (UN), Institut des Maladies de l'Appareil Digestif, Université de Nantes (UN), Department of Gastroenterology, and The University of Texas Medical Branch (UTMB)
Subjects: Crohn's disease, business.industry, Inflammation, [SDV.MHEP.HEG]Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, medicine.disease, Inflammatory Bowel Diseases, Ulcerative colitis, Inflammatory bowel disease, Intestinal absorption, Enteric Nervous System, [SDV.MHEP.HEG] Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, Pathogenesis, Intestines, Immune system, Intestinal Absorption, Immunology, Internal Medicine, medicine, Humans, Enteric nervous system, medicine.symptom, business, Neuroglia
Abstract: International audience; Inflammatory bowel disease (IBD) is a multifactorial disease in which environmental, immune and genetic factors are involved in the pathogenesis. Although biological therapies (antibodies anti-tumour necrosis factor-alpha or anti-integrin) have considerably improved the symptoms and quality of life of IBD patients, some drawbacks have emerged limiting their long-term use. In addition, prevention of relapses and treatment of resistant ulcers remains a clinical challenge. In this context, a better understanding of the pathophysiology of IBD and the development of novel therapeutic intervention would benefit from further basic and preclinical research into the role of the cellular microenvironment and the interaction between its cellular constituents. In this context, the role of the enteric nervous system (ENS) in the regulation of the intestinal epithelial barrier (IEB) and the gut immune response has fuelled an increased interest in the last few years. Recent advances, summarized in this review, have highlighted the ENS as playing a key role in the control of IEB functions and gut immune homeostasis, and that alterations of the ENS could be directly associated in the development of IBD and its associated symptoms.
Published: 2008
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32. Beta-catenin/Tcf-4 inhibition after progastrin targeting reduces growth and drives differentiation of intestinal tumors

Author: Julie Pannequin, Arthur Shulkes, André Pèlegrin, Fanny Surrel, Graham S. Baldwin, Pomila Singh, Frédéric Hollande, Nathalie Delaunay, Dominique Joubert, Joanne Ryan, Gérard Lambeau, Christine Pignodel, Philippe Jay, Stéphanie Boireau, Mildred Yim, Jean-François Bourgaux, Jessica Coelho, Michael Buchert, Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Institut de pharmacologie moléculaire et cellulaire (IPMC), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Service d'Hépato Gastroentérologie, Centre Hospitalier Universitaire de Nîmes (CHU Nîmes), Immunociblage des tumeurs et ingénierie des anticorps, Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Neuroscience & Cell Biology, The University of Texas Medical Branch (UTMB), and Service d'Anatomopathologie
Subjects: MESH: Signal Transduction, Small interfering RNA, MESH: Protein Precursors, MESH: Random Allocation, MESH: beta Catenin, Apoptosis, Cell Cycle Proteins, MESH: Gastrins, Mice, Phosphatidylinositol 3-Kinases, Random Allocation, 0302 clinical medicine, Differentiation therapy, MESH: RNA, Small Interfering, MESH: Animals, RNA, Small Interfering, beta Catenin, Regulation of gene expression, 0303 health sciences, MESH: Genes, APC, biology, Gastroenterology, MESH: Transcription Factors, MESH: Gene Expression Regulation, Neoplastic, Gene Expression Regulation, Neoplastic, Cell Transformation, Neoplastic, Adenomatous Polyposis Coli, 030220 oncology & carcinogenesis, Colorectal Neoplasms, TCF Transcription Factors, Transcription Factor 7-Like 2 Protein, Signal Transduction, Adenoma, Transcriptional Activation, Genes, APC, Beta-catenin, MESH: Cell Line, Tumor, Adenomatous polyposis coli, Transplantation, Heterologous, Mice, Nude, [SDV.CAN]Life Sciences [q-bio]/Cancer, 03 medical and health sciences, MESH: Cell Cycle Proteins, Cell Line, Tumor, MESH: Cell Proliferation, Gastrins, MESH: Mice, Nude, Animals, Humans, Protein Precursors, MESH: Transplantation, Heterologous, MESH: Mice, PI3K/AKT/mTOR pathway, Adaptor Proteins, Signal Transducing, Cell Proliferation, 030304 developmental biology, MESH: Adenoma, MESH: Humans, Hepatology, Cell growth, MESH: Apoptosis, MESH: 1-Phosphatidylinositol 3-Kinase, Molecular biology, MESH: Adenomatous Polyposis Coli, Repressor Proteins, MESH: Cell Transformation, Neoplastic, Catenin, Cancer research, biology.protein, MESH: TCF Transcription Factors, MESH: Colorectal Neoplasms, Transcription Factors
Abstract: BACKGROUND & AIMS: Aberrant activation of the beta-catenin/Tcf-4 transcriptional complex represents an initiating event for colorectal carcinogenesis, shifting the balance from differentiation toward proliferation in colonic crypts. Here, we assessed whether endogenous progastrin, encoded by a target gene of this complex, was in turn able to regulate beta-catenin/Tcf-4 activity in adenomatous polyposis coli (APC)-mutated cells, and we analyzed the impact of topical progastrin depletion on intestinal tumor growth in vivo. METHODS: Stable or transient RNA silencing of the GAST gene was induced in human tumor cells and in mice carrying a heterozygous Apc mutation (APCDelta14), which overexpress progastrin but not amidated or glycine-extended gastrin. RESULTS: Depletion of endogenous progastrin production strongly decreased intestinal tumor growth in vivo through a marked inhibition of constitutive beta-catenin/Tcf-4 activity in tumor cells. This effect was mediated by the de novo expression of the inhibitor of beta-catenin and Tcf-4 (ICAT), resulting from a down-regulation of integrin-linked kinase in progastrin-depleted cells. Accordingly, ICAT down-regulation was correlated with progastrin overexpression and Tcf-4 target gene activation in human colorectal tumors, and ICAT repression was detected in the colon epithelium of tumor-prone, progastrin-overexpressing mice. In APCDelta14 mice, small interfering RNA-mediated progastrin depletion not only reduced intestinal tumor size and numbers, but also increased goblet cell lineage differentiation and cell apoptosis in the remaining adenomas. CONCLUSIONS: Thus, depletion of endogenous progastrin inhibits the tumorigenicity of APC-mutated colorectal cancer cells in vivo by promoting ICAT expression, thereby counteracting Tcf-4 activity. Progastrin targeting strategies should provide an exciting prospect for the differentiation therapy of colorectal cancer.
Published: 2007
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33. PPAR-alpha agonism improves whole body and muscle mitochondrial fat oxidation, but does not alter intracellular fat concentrations in burn trauma children

Author: Cree, Melanie, Newcomer, Bradley, Herndon, David, Qian, Ting, Sun, Dayoung, Morio, Béatrice, Zwetsloot, Jennifer, Dohm, Lynis, Fram, Ricki, Aarsland, Asle, Wolfe, Robert, The University of Texas Medical Branch (UTMB), University of Alabama at Birmingham (UAB), Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Clermont Université, Centre de Recherche en Nutrition Humaine, East Carolina University, and ProdInra, Migration
Subjects: [SDV.BA] Life Sciences [q-bio]/Animal biology, [SDV.BA]Life Sciences [q-bio]/Animal biology, PPAR ALPHA, lipids (amino acids, peptides, and proteins)
Abstract: Meeting abstract 738.20; International audience; BACKGROUND: Insulin resistance is often associated with increased levels of intracellular triglycerides, diacylglycerol and decreased fat beta-oxidation. It was unknown if this relationship was present in patients with acute insulin resistance induced by trauma. METHODS: A double blind placebo controlled trial was conducted in 18 children with severe burn injury. Metabolic studies to assess whole body palmitate oxidation and insulin sensitivity, muscle biopsies for mitochondrial palmitate oxidation, diacylglycerol, fatty acyl Co-A and fatty acyl carnitine concentrations, and magnetic resonance spectroscopy for muscle and liver triglycerides were compared before and after two weeks of placebo or PPAR-alpha agonist treatment. RESULTS: Insulin sensitivity and basal whole body palmitate oxidation as measured with an isotope tracer increased significantly (P = 0.003 and P = 0.004, respectively) after PPAR-alpha agonist treatment compared to placebo. Mitochondrial palmitate oxidation rates in muscle samples increased significantly after PPAR-alpha treatment (P = 0.002). However, the concentrations of muscle triglyceride, diacylglycerol, fatty acyl CoA, fatty acyl carnitine, and liver triglycerides did not change with either treatment. PKC-theta activation during hyper-insulinemia decreased significantly following PPAR-alpha treatment. CONCLUSION: PPAR-alpha agonist treatment increases palmitate oxidation and decreases PKC activity along with reduced insulin sensitivity in acute trauma, However, a direct link between these responses cannot be attributed to alterations in intracellular lipid concentrations.
Published: 2007

34. Insulin sensitivity and mitochondrial function are improved in children with burn injury during a randomized controlled trial of fenofibrate

Author: Ting Qian, Asle Aarsland, David N. Herndon, Melanie G. Cree, Béatrice Morio, Arthur P. Sanford, Ricki Y. Fram, Robert R. Wolfe, Jennifer J. Zwetsloot, University of Texas Medical Branch, Partenaires INRAE, East Carolina University, Shriners Hospitals for Children [Boston], Department of Cell Physiology, Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Clermont Université, Centre de Recherche en Nutrition Humaine, Department of Anesthesiology, and The University of Texas Medical Branch (UTMB)
Subjects: Blood Glucose, medicine.medical_specialty, Adolescent, medicine.medical_treatment, Biopsy, [SDV]Life Sciences [q-bio], 03 medical and health sciences, 0302 clinical medicine, Insulin resistance, Double-Blind Method, Fenofibrate, Diabetes mellitus, Intensive care, Internal medicine, medicine, Humans, PPAR alpha, Myocardial infarction, Prospective Studies, Child, Muscle, Skeletal, 030304 developmental biology, Hypolipidemic Agents, 0303 health sciences, Trauma Severity Indices, business.industry, Insulin, 030208 emergency & critical care medicine, Glucose clamp technique, medicine.disease, 3. Good health, Metformin, Mitochondria, Muscle, Endocrinology, Treatment Outcome, Liver, Child, Preschool, Randomized Controlled Trial, Cardiology, Glucose Clamp Technique, Surgery, Animal studies, Insulin Resistance, business, Burns, medicine.drug, Follow-Up Studies
Abstract: Multiple studies have documented hyperglycemia and insulin resistance following trauma, myocardial infarction, stroke, or surgery.1–4 Both are of serious clinical concern, as hyperglycemia is associated with increased morbidity and mortality of critically ill, surgical, and burned patients.3–5 These outcome studies emphasize the importance of better understanding insulin resistance in this large patient population. Pediatric burns provide a unique model for studying acute onset insulin resistance, since the nature of the injury is severe and quantifiable and the timing of onset is exactly known. Further, lean children are much less likely to have preexisting comorbid conditions such as diabetes, or to have been taking medications prior to injury. We have recently demonstrated that mitochondrial oxidative function is impaired in burned children by more than 70% at 1 week postburn.6 A limited number of animal studies have found that mitochondrial genes, protein, and function are also decreased in skeletal muscle, liver, and cardiac muscle following burn injury.7–9 Similar findings were reported from the liver of patients who died after prolonged stays in intensive care for nonsurgical illness.10 In patients with type II diabetes, correlations between mitochondrial function and insulin sensitivity have been documented.11,12 These studies indicate that improving mitochondrial function may be a potential treatment target for improving insulin sensitivity. There are limited proven therapies for treating acute injury-induced insulin resistance. Insulin therapy to prevent hyperglycemia has been shown to reduce mortality and/or morbidity in intensive care patients, patients undergoing surgical procedures and in burns.4,10 However, intensive insulin therapy requires constant vigilance and does not alter the underlying pathology. One study found that metformin decreased muscle loss after burn,13 but other medications that are typically prescribed for treatment of insulin resistance have not been tested in these populations. PPAR-γ agonists, or thioglitazones, have been shown to improve insulin sensitivity in patients with diabetes.14 The mechanism of action apparently involves suppression of peripheral lipolysis and redistribution of triglyceride stores to subcutaneous fat cells.14 However, burned children often have a large amount of their subcutaneous triglyceride stores destroyed or removed, decreasing the availability for redistribution sites. Further, burn patients may be treated with the beta-blocking agent propranolol to reduce myocardial stress, which also suppresses lipolysis.15 Therefore, a PPAR-γ agonist would be anticipated to be redundant in children given propranolol. PPAR-α agonists have been shown in numerous animal studies and a few human studies to improve insulin sensitivity by enhancing mitochondrial function.16–18 We therefore hypothesized that PPAR-α agonism would stimulate mitochondrial function and improve insulin sensitivity in pediatric burn patients.
Published: 2007
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34 results on '"The University of Texas Medical Branch ( UTMB )"'

1. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment

2. Four principles to establish a universal virus taxonomy

3. INTS13 variants causing a recessive developmental ciliopathy disrupt assembly of the Integrator complex

4. Predicting future cognitive decline from non-brain and multimodal brain imaging data in healthy and pathological aging

5. Hepatitis C virus proteins induce lipogenesis and defective triglyceride secretion in transgenic mice

6. Behavioural responses of juvenile cuttlefish (Sepia officinalis) to local water movements

7. The effect of early experience on learning and memory in cuttlefish

8. Mutational analysis of Aedes aegypti Dicer 2 provides insights into the biogenesis of antiviral exogenous small interfering RNAs

9. Pannexin-1 channel opening is critical for COVID-19 pathogenesis

10. Mosquito‐bacteria interactions during larval development trigger metabolic changes with carry‐over effects on adult fitness

11. Resurgence of Ebola Virus in 2021 in Guinea Suggests a New Paradigm for Outbreaks

12. Functional spreading of hyperexcitability induced by human and synthetic intracellular Aβ oligomers

13. GloPID-R report on chikungunya, o'nyong-nyong and Mayaro virus, part 5: Entomological aspects

14. Strengthening the Interaction of the Virology Community with the International Committee on Taxonomy of Viruses (ICTV) by Linking Virus Names and Their Abbreviations to Virus Species

15. GloPID-R report on Chikungunya, O'nyong-nyong and Mayaro virus, part I: Biological diagnostics

16. Meeting the challenge of tick-borne disease control: A proposal for 1000 Ixodes genomes

17. rbFOX1/MBNL1 competition for CCUG RNA repeats binding contributes to myotonic dystrophy type 1/type 2 differences

18. i-BLESS is an ultra-sensitive method for detection of DNA double-strand breaks

19. Taxonomy of the order Mononegavirales: update 2018

20. Zika, Chikungunya, and Other Emerging Vector-Borne Viral Diseases

21. Dual Inhibition of EGFR and c-Src by Cetuximab and Dasatinib Combined with FOLFOX Chemotherapy in Patients with Metastatic Colorectal Cancer

22. Implementation of Objective PASC-Derived Taxon Demarcation Criteria for Official Classification of Filoviruses

23. Consensus statement: Virus taxonomy in the age of metagenomics

24. Taxonomy of the order Mononegavirales: update 2016

25. Data publication with the structural biology data grid supports live analysis

26. The Global Virus Network: Challenging chikungunya

27. Chikungunya Virus and the Global Spread of a Mosquito-Borne Disease

28. HS during circulatory shock: Some unresolved questions

29. STATE OF THE CLIMATE IN 2011 Special Supplement to the Bulletin of the American Meteorological Society Vol. 93, No. 7, July 2012

30. SNMIB/Apollo protects leading-strand telomeres against NHEJ-mediated repair

31. Neuro-glial crosstalk in inflammatory bowel disease

32. Beta-catenin/Tcf-4 inhibition after progastrin targeting reduces growth and drives differentiation of intestinal tumors

33. PPAR-alpha agonism improves whole body and muscle mitochondrial fat oxidation, but does not alter intracellular fat concentrations in burn trauma children

34. Insulin sensitivity and mitochondrial function are improved in children with burn injury during a randomized controlled trial of fenofibrate

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