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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. Antioxidant Supplementation Does Not Affect Bone Turnover Markers During 60 Days of 6° Head-Down Tilt Bed Rest: Results from an Exploratory Randomized Controlled Trial

Author: Natalie Baecker, Jean-Pol Frippiat, Katharina Austermann, Peter Stehle, Scott M. Smith, Rolf Fimmers, Martina Heer, Sara R. Zwart, Rheinische Friedrich-Wilhelms-Universität Bonn, The University of Texas Medical Branch (UTMB), Stress, Immunité, Pathogènes (SIMPA), Université de Lorraine (UL), NASA Johnson Space Center (JSC), and NASA
Subjects: Adult, Male, 0301 basic medicine, medicine.medical_specialty, [SDV]Life Sciences [q-bio], medicine.medical_treatment, Medicine (miscellaneous), Parathyroid hormone, 030209 endocrinology & metabolism, Antioxidants, Collagen Type I, Bone resorption, Bone remodeling, Head-Down Tilt, Selenium, Young Adult, 03 medical and health sciences, 0302 clinical medicine, Internal medicine, Fatty Acids, Omega-3, medicine, Humans, Vitamin E, Single-Blind Method, Bone Resorption, 2. Zero hunger, Calcium metabolism, 030109 nutrition & dietetics, Nutrition and Dietetics, biology, business.industry, Polyphenols, Urinary calcium, 3. Good health, Endocrinology, Dietary Supplements, Osteocalcin, biology.protein, Calcium, Bone Remodeling, business, Bed Rest, Biomarkers, Type I collagen
Abstract: International audience; Background Immobilization and related oxidative stress are associated with bone loss. Antioxidants like polyphenols, omega-3 fatty acids, vitamins, and micronutrients may mitigate these negative effects on bone metabolism through scavenging of free radicals. Objectives We hypothesized that antioxidant supplementation during 60 days of 6° head-down tilt bed rest (HDBR) would reduce bone resorption and increase bone formation compared to nonsupplemented controls. Methods This exploratory randomized, controlled, single-blind intervention study conducted in a parallel design included 20 healthy male volunteers (age, 34 ± 8 years; weight, 74 ± 6 kg). The study consisted of a 14-day adaptation phase [baseline data collection (BDC)], followed by 60 days of HDBR and a 14-day recovery period (R). In the antioxidant group, volunteers received an antioxidant cocktail (741 mg/d polyphenols, 2.1 g/d omega-3 fatty acids, 168 mg/d vitamin E, and 80 μg/d selenium) with their daily meals. In the control group, volunteers received no supplement. Based on their body weight, all volunteers received an individually tailored and strictly controlled diet, consistent with DRIs. We analyzed biomarkers of calcium homeostasis, bone formation, and bone resorption during BDC, HDBR, and R, as well as for 30 days after the end of HDBR. Data were analyzed by linear mixed models. Results The antioxidant supplement did not affect serum calcium, parathyroid hormone, urinary C-telopeptide of type I collagen (CTX), urinary N-telopeptide of type I collagen, serum β–C-telopeptide of type I collagen (β-CTX), bone alkaline phosphatase, aminoterminal propeptide of type I collagen, osteocalcin, or urinary calcium excretion. In both groups, typical bed rest–related changes were observed. Conclusions Supplementation of an antioxidant cocktail to a diet matching the DRIs did not affect bone resorption or formation during 60 days of HDBR in healthy young men. This trial was registered at clinicaltrials.gov as NCT03594799.
Published: 2021
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3. Excess all-cause mortality and COVID-19-related mortality:a temporal analysis in 22 countries, from January until August 2020

Author: Oscar Dario Martin Garzon, Fabrizio Stracci, Levan Kandelaki, Jose M. Rodriguez-Llanes, Julia A Critchley, Eva S. Schernhammer, Giuseppe Ambrosio, Neil Mehta, Cathy Bennett, Ourania Kolokotroni, Gleb Denissov, Qian Huang, Lucy Goldsmith, Maider Pagola Ugarte, Inbar Zucker, Jackeline Christiane Pinto Lobato, Petra Klepac, Constantina Constantinou, Alexandros Heraclides, Nolwenn Le Meur, Annalisa Quattrocchi, Kristi Rüütel, Antonio José Leal Costa, Claudia Zimmermann, Ángel Fernández Camporro, Ekaterina Bogatyreva, John Gabel, Pedro Arcos González, Christiana A. Demetriou, Ana Paula Semedo-Aguiar, Ivan Erzen, Laust Hvas Mortensen, Souzana Achilleos, Joan O'Donnell, Nicoletta Nicolaou, Zalman Kaufman, Terje P. Hagen, Shorena Tsiklauri, Gloria Ramírez, Nataliia Pidmurniak, Antonis Polemitis, Olesia Verstiuk, Ngibo Mubeta Fernandes, Ajay Oza, Bo Burström, Andreas Charalambous, University of Cyprus [Nicosia], European Commission - Joint Research Centre [Ispra] (JRC), Deakin University [Burwood], Medizinische Universität Wien = Medical University of Vienna, University of Copenhagen = Københavns Universitet (KU), St George’s University Hospitals, Recherche en Pharmaco-épidémiologie et Recours aux Soins (REPERES), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École des Hautes Études en Santé Publique [EHESP] (EHESP), École des Hautes Études en Santé Publique [EHESP] (EHESP), Département Méthodes quantitatives en santé publique (METIS), Tel Aviv University [Tel Aviv], Università degli Studi di Perugia (UNIPG), University of Oslo (UiO), University of Oviedo, Karolinska Institutet [Stockholm], Bogomolets national medical university, University of South Carolina [Columbia], The University of Texas Medical Branch (UTMB), This work was supported by the University of Nicosia Medical School (internal funding), University of Cyprus [Nicosia] (UCY), University of Copenhagen = Københavns Universitet (UCPH), Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP), Tel Aviv University (TAU), and Università degli Studi di Perugia = University of Perugia (UNIPG)
Subjects: 0301 basic medicine, Coronavirus disease 2019 (COVID-19), Epidemiology, [SDV]Life Sciences [q-bio], Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Northern ireland, 03 medical and health sciences, 0302 clinical medicine, Pandemic, medicine, AcademicSubjects/MED00860, 030212 general & internal medicine, Excess mortality, business.industry, SARS-CoV-2, Mortality rate, pandemic, COVID-19, General Medicine, Seasonality, medicine.disease, mortality, infection control, 3. Good health, 030104 developmental biology, Original Article, business, All cause mortality, Demography
Abstract: This work was supported by the University of Nicosia Medical School (internal funding)., Achilleos S, Quattrocchi A, Gabel J, Heraclides A, Kolokotroni O, Constantinou C, Pagola Ugarte M, Nicolaou N, Rodriguez-Llanes JM, Bennett CM, Bogatyreva E, Schernhammer E, Zimmermann C, Costa AJL, Lobato JCP, Fernandes NM, Semedo-Aguiar AP, Jaramillo Ramirez GI, Martin Garzon OD, Mortensen LH, Critchley JA, Goldsmith LP, Denissov G, Rüütel K, Le Meur N, Kandelaki L, Tsiklauri S, O'Donnell J, Oza A, Kaufman Z, Zucker I, Ambrosio G, Stracci F, Hagen TP, Erzen I, Klepac P, Arcos González P, Fernández Camporro Á, Burström B, Pidmurniak N, Verstiuk O, Huang Q, Mehta NK, Polemitis A, Charalambous A, Demetriou CA.
Published: 2022
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4. Rational design of universal immunotherapy for TfR1-tropic arenaviruses

Author: Thomas W. Geisbert, Vered Padler-Karavani, Sylvain Baize, Hadas Cohen-Dvashi, Ron Amon, Krystle N. Agans, Aliza Borenstein-Katz, Ron Diskin, Robert W. Cross, Mathieu Mateo, Weizmann Institute of Science [Rehovot, Israël], Tel Aviv University (TAU), The University of Texas Medical Branch (UTMB), Biologie des Infections Virales Émergentes - Biology of Emerging Viral Infections (UBIVE), 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)-Institut Pasteur [Paris] (IP), BSL-4 experiments using MACV were supported by the Pasteur-Weizmann joint research program collaborative research grant S-CR18069-02 to M.M. and R.D. BSL-4 operations of the Galveston National Laboratory and Department of Microbiology and Immunology are supported by NIAID/NIH Grant No. UC7AI094660 to T.W.G. The lab of R.D. is supported by research grants from the Enoch Foundation, from the Abramson Family Center for Young Scientists, from Ms. Rudolfine Steindling, and from the I-CORE Program of the Planning and Budgeting Committee and The Israel Science Foundation (grants no. 1775/12 and 682/16)., Tel Aviv University [Tel Aviv], Centre International de Recherche en Infectiologie - UMR (CIRI), 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)-Institut Pasteur [Paris], Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP), and Bodescot, Myriam
Subjects: 0301 basic medicine, New World Arenavirus, Viral protein, medicine.medical_treatment, Science, viruses, General Physics and Astronomy, Transferrin receptor, Biologics, Biology, Antibodies, Viral, medicine.disease_cause, Article, General Biochemistry, Genetics and Molecular Biology, Viral Proteins, 03 medical and health sciences, 0302 clinical medicine, Virology, Receptors, Transferrin, medicine, Arenaviridae Infections, Humans, lcsh:Science, X-ray crystallography, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Multidisciplinary, Transmission (medicine), Rational design, virus diseases, Arenavirus, General Chemistry, Immunotherapy, Antibodies, Neutralizing, Arenaviruses, 3. Good health, Hemorrhagic Fevers, 030104 developmental biology, Drug Design, [SDV.SP.PHARMA] Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, Biological warfare, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.SP.PHARMA]Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, Receptors, Virus, lcsh:Q, 030217 neurology & neurosurgery
Abstract: Certain arenaviruses that circulate in rodent populations can cause life-threatening hemorrhagic fevers when they infect humans. Due to their efficient transmission, arenaviruses pose a severe risk for outbreaks and might be exploited as biological weapons. Effective countermeasures against these viruses are highly desired. Ideally, a single remedy would be effective against many or even all the pathogenic viruses in this family. However, despite the fact that all pathogenic arenaviruses from South America utilize transferrin receptor 1 (TfR1) as a cellular receptor, their viral glycoproteins are highly diversified, impeding efforts to isolate cross-neutralizing antibodies. Here we address this problem using a rational design approach to target TfR1-tropic arenaviruses with high potency and breadth. The pan-reactive molecule is highly effective against all arenaviruses that were tested, offering a universal therapeutic approach. Our design scheme avoids the shortcomings of previous immunoadhesins and can be used to combat other zoonotic pathogens., New World arenaviruses utilize the cellular transferrin receptor 1 (TfR1) to enter host cells. Here, the authors develop a TfR1-mimetic immunoadhesin, Arenacept, that targets viral spike complexes and exerts effective pan-reactive neutralization against pathogenic mammarenaviruses.
Published: 2020
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5. Antiviral activity of oleandrin and a defined extract of Nerium oleander against SARS-CoV-2

Author: Rick Matos, Divya Mirchandani, Scott C. Weaver, Diana Fernández, Jordi B. Torrelles, Varun Dwivedi, Jennifer Delgado, Nathen E. Bopp, Kenneth S. Plante, Vinay Shivanna, Patricia V. Aguilar, Jun Gyu Park, Luis Martinez-Sobrido, Jessica A. Plante, Paula Pino Tamayo, Robert A. Newman, K. Jagannadha Sastry, The University of Texas Medical Branch (UTMB), World Reference Center for Emerging Viruses and Arboviruses (WRCEVA), Institute for Human Infections and Immunity and Department of Pathology, Texas Biomedical Research Institute [San Antonio, TX], Innovar LLC, Phoenix Biotechnology, Inc., The University of Texas M.D. Anderson Cancer Center [Houston], and This research was supported in part by NIH grant R24 AI120942 to SCW. We thank Natalie Thornburg (Centers 305 for Disease Control and Prevention, Atlanta, GA, USA) and the World Reference Center for Emerging Viruses and Arboviruses for providing the SARS-CoV-2 USA_WA1/2020 isolate. Research was also supported by Phoenix Biotechnology, Inc. Experimental design, conduct of the experiments, and interpretation of the data were the independent products of scientists at University of Texas Medical Branch (Galveston) and Texas Biomedical Research Institute with consulting comments from R. A. Newman, PhD, and K. Jagannadha Sastry, PhD. The authors thank Bev Newman, M.S., R.N. for graphic art support.
Subjects: 0301 basic medicine, Oleandrin, NP, nucleocapsid protein, LDH, lactic dehydrogenase, [SDV]Life Sciences [q-bio], DPI, day post infection, Pharmacology, DMSO, dimethyl sulfoxide, medicine.disease_cause, law.invention, chemistry.chemical_compound, 0302 clinical medicine, HTLV-1, human T-lymphotropic virus, law, Cricetinae, Chlorocebus aethiops, Mab, monoclonal antibody, Antiviral activity, Coronavirus, General Medicine, 3. Good health, HIV, human immunodeficiency virus, Cardenolides, Titer, CPE, cytopathic effect, Reduced infectivity, 030220 oncology & carcinogenesis, BDNF, brain-derived neurotrophic factor, EC50, half maximal effective concentration, Female, Original Article, ATP, adenosine triphosphate, ALT, alanine transaminase, Genome, Viral, RM1-950, Antiviral Agents, Virus, MERS, middle east respiratory syndrome, 03 medical and health sciences, FBS, fetal bovine serum, In vivo, medicine, DPBS, Dulbecco’s phosphate-buffered saline, Animals, Nerium, SARS, severe acute respiratory syndrome, Vero Cells, EC50, ELISA, enzyme-linked immunoassay, ALP, alkaline phosphatase, Plant Extracts, business.industry, SARS-CoV-2, COVID-19, Nrf-2, nuclear factor erythroid 2-related factor 2, Nerium oleander, COVID-19 Drug Treatment, 030104 developmental biology, chemistry, qRT-PCR, real-time quantitative polymerase chain reaction, Vero cell, RNA, ribonucleic acid, H&E, hematoxylin and eosin, BSA, bovine serum albumin, Therapeutics. Pharmacology, business, Phytotherapy, PFU, plaque-forming unit
Abstract: International audience; With continued expansion of the coronavirus disease (COVID-19) pandemic, caused by severe acute respiratory syndrome 2 (SARS-CoV-2), both antiviral drugs as well as effective vaccines are desperately needed to treat patients at high risk of life-threatening disease. Here, we present in vitro evidence for significant inhibition of SARS-CoV-2 by oleandrin and a defined extract of N. oleander (designated as PBI-06150). Using Vero cells, we found that prophylactic (pre-infection) oleandrin (as either the pure compound or as the active principal ingredient in PBI-06150) administration at concentrations as low as 0.05g/ml exhibited potent antiviral activity against SARS-CoV-2, with an 800-fold reduction in virus production, and a 0.1g/ml concentration resulted in a greater than 3000-fold reduction in infectious virus production. The half maximal effective concentration (EC50) values were 11.98ng/ml when virus output was measured at 24h post-infection, and 7.07ng/ml measured at 48h post-infection. Therapeutic (post-infection) treatment up to 24h after SARS-CoV-2 infection of Vero cells also reduced viral titers, with 0.1g/ml and 0.05g/ml concentrations causing greater than 100-fold reduction as measured at 48h, and the 0.05g/ml concentration resulting in a 78-fold reduction. Concentrations of oleandrin up to 10g/ml were well tolerated in Vero cells. We also present in vivo evidence of the safety and efficacy of defined N. oleander extract (PBI-06150), which was administered to golden Syrian hamsters in a preparation containing as high as 130g/ml of oleandrin. In comparison to administration of control vehicle, PBI-06150 provided a statistically significant reduction of the viral titer in the nasal turbinates (nasal conchae). The potent prophylactic and therapeutic antiviral activities demonstrated here, together with initial evidence of its safety and efficacy in a relevant hamster model of COVID-19, support the further development of oleandrin and/or defined extracts containing this molecule for the treatment of SARS-CoV-2 and associated COVID-19 disease and potentially also for reduction of virus spread by persons diagnosed early after infection.
Published: 2021
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6. Zika in the Americas, year 2: What have we learned? What gaps remain? A report from the Global Virus Network

Author: Matthew T. Aliota, Nikos Vasilakis, Edward McSweegan, Leda Bassit, Michael J. Ricciardi, Thomas C. Friedrich, Guilherme S. Ribeiro, Natalia Mercer, Geraldine Schott-Lerner, George R. Saade, Thaddeus G. Golos, Shelton S. Bradrick, Diane E. Griffin, Mariano A. Garcia-Blanco, Lisa F. P. Ng, Pei Yong Shi, Diogo M. Magnani, Bryan Cox, Christina Gavegnano, Marc Lecuit, Chao Shan, Caroline Marrs, Andrew D. Haddow, David I. Watkins, Jorge E. Osorio, Scott C. Weaver, Raymond F. Schinazi, David H. O’Connor, Esper G. Kallas, Shannan L. Rossi, Uriel Kitron, University of Wisconsin-Madison, Emory University [Atlanta, GA], The University of Texas Medical Branch (UTMB), Global Virus Network, University of South Florida [Tampa] (USF), Johns Hopkins Bloomberg School of Public Health [Baltimore], Johns Hopkins University (JHU), U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Universidade de São Paulo = University of São Paulo (USP), 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), CHU Necker - Enfants Malades [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), University of Miami Leonard M. Miller School of Medicine (UMMSM), Agency for science, technology and research [Singapore] (A*STAR), Universidade Federal da Bahia (UFBA), Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP), Work from the authors’ laboratories was funded by in part by U.S. National Institutes of Health grants: R01NS087539-S1 (to DEG), R21AI129607 (to RFS), and R24AI120942, R01AI121452 (to SCW) R01 AI107157-01A1 (to TGG), R01AI116382-01A1S1 (to DHO), U01AI115577 (to NV) and P51 OD011106 (to the WNPRC)., U.S. Army Medical Research Institute of Infectious Diseases, University of São Paulo (USP), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut des Maladies Génétiques Imagine [Paris], Fundação Oswaldo Cruz (FIOCRUZ), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)
Subjects: 0301 basic medicine, Gerontology, medicine.medical_specialty, Asia, Sexual transmission, MALFORMAÇÕES, [SDV]Life Sciences [q-bio], Disease, Antiviral therapy, Nervous System Malformations, Arbovirus, Article, Zika virus, 03 medical and health sciences, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Virology, Drug Discovery, Pandemic, Disease Transmission, Infectious, medicine, Animals, Maternal-fetal transmission, Pharmacology, Vaccines, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, biology, Diagnostic Tests, Routine, Zika Virus Infection, business.industry, Transmission (medicine), Public health, Outbreak, medicine.disease, biology.organism_classification, Infectious Disease Transmission, Vertical, 3. Good health, Congenital manifestations, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, 030104 developmental biology, Family medicine, Africa, Communicable Disease Control, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Americas, business, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: International audience; In response to the outbreak of Zika virus (ZIKV) infection in the Western Hemisphere and the recognition of a causal association with fetal malformations, the Global Virus Network (GVN) assembled an international taskforce of virologists to promote basic research, recommend public health measures and encourage the rapid development of vaccines, antiviral therapies and new diagnostic tests. In this article, taskforce members and other experts review what has been learned about ZIKV-induced disease in humans, its modes of transmission and the cause and nature of associated congenital manifestations. After describing the make-up of the taskforce, we summarize the emergence of ZIKV in the Americas, Africa and Asia, its spread by mosquitoes, and current control measures. We then review the spectrum of primary ZIKV-induced disease in adults and children, sites of persistent infection and sexual transmission, then examine what has been learned about maternal-fetal transmission and the congenital Zika syndrome, including knowledge obtained from studies in laboratory animals. Subsequent sections focus on vaccine development, antiviral therapeutics and new diagnostic tests. After reviewing current understanding of the mechanisms of emergence of Zika virus, we consider the likely future of the pandemic.
Published: 2017
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7. 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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8. Specific Immunologic Countermeasure Protocol for Deep-Space Exploration Missions

Author: George Makedonas, Satish Mehta, Alexander Choukèr, Richard J. Simpson, Gailen Marshall, Jordan S. Orange, Serena Aunon-Chancellor, Scott M. Smith, Sara R. Zwart, Raymond P. Stowe, Martina Heer, Sergey Ponomarev, Alexandra Whitmire, Jean P. Frippiat, Grace L. Douglas, Stephanie S. Krieger, Hernan Lorenzi, Judith-Irina Buchheim, Geoffrey S. Ginsburg, C. Mark Ott, Meghan Downs, Duane Pierson, Natalie Baecker, Clarence Sams, Brian Crucian, JES Tech, University Hospital of the Ludwig-Maximilians University, The University of Arizona Medical Center, University of Arizona, University of Mississippi Medical Center (UMMC), Department of Pediatrics (University of British Columbia), NASA Johnson Space Center (JSC), NASA, The University of Texas Medical Branch (UTMB), Institute of Human Nutrition and Food Science, Rheinische Friedrich-Wilhelms-Universität Bonn, Institute of biomedical problems, Russian Academy of Sciences [Moscow] (RAS), Stress, Immunité, Pathogènes (SIMPA), Université de Lorraine (UL), J. Craig Venter Institute, Duke Center for Applied Genomics and Precision Medicine [Durham, NC, USA], Duke University School of Medicine [Durham, NC, USA], Aerospace Medical Institute, and German Aerospace Center (DLR)
Subjects: 0301 basic medicine, lcsh:Immunologic diseases. Allergy, Opinion, stress management, T-Lymphocytes, Immunology, 03 medical and health sciences, 0302 clinical medicine, Aeronautics, Political science, Herpesvirus reactivation, Agency (sociology), Humans, Immunology and Allergy, Protocol (object-oriented programming), ComputingMilieux_MISCELLANEOUS, Inflammation, Immunity, Cellular, immune countermeasures, immune surveillance, DNA Methylation, Space Flight, Immune surveillance, 3. Good health, 030104 developmental biology, Deep space exploration, Twin Studies as Topic, Space program, [SDV.IMM]Life Sciences [q-bio]/Immunology, space immunology, lcsh:RC581-607, Countermeasure (computer), 030215 immunology
Abstract: German National Space Program [50WB1622]; European Space Agency (ESA)'s Topical Team Stress and Immunity - ESA ELIPS 4 program; European Space Agency (ESA)'s Topical Team Stress and Immunity - ESA SciSpacE program
Published: 2019
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9. GloPID-R report on chikungunya, o'nyong-nyong and Mayaro virus, part 2: Epidemiological distribution of o'nyong-nyong virus

Author: M. G. Rosa-Freitas, Sébastien Boyer, A. J. Rodriguez-Morales, Jan Felix Drexler, Thomas Jaenisch, Patrícia Brasil, Johan Neyts, François Simon, Anna-Bella Failloux, de Lamballerie X, Lisa F. P. Ng, Michael A. Drebot, Pierre Gallian, Guilherme S. Ribeiro, Maria Rios, Amadou A. Sall, Chantal Reusken, Marc Lecuit, Scott C. Weaver, Michael P. Busch, Nikos Vasilakis, André Siqueira, A. Vega Rua, Angelle Desiree LaBeaud, Mawlouth Diallo, Michael S. Diamond, Alain Kohl, Ricardo Lourenço-de-Oliveira, Laura Pezzi, Graham Simmons, 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), Stanford School of Medicine [Stanford], Stanford Medicine, Stanford University-Stanford University, National Institute for Public Health and the Environment [Bilthoven] (RIVM), Erasmus University Medical Center [Rotterdam] (Erasmus MC), Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Humboldt University Of Berlin, Berlin Institute of Health (BIH), The University of Texas Medical Branch (UTMB), Institut Pasteur de Dakar, Réseau International des Instituts Pasteur (RIIP), Hôpital d'Instruction des Armées Laveran, Service de Santé des Armées, Heidelberg University Hospital [Heidelberg], Etablissement Français du Sang - Alpes-Méditerranée (EFS - Alpes-Méditerranée), Etablissement Français du Sang, Arbovirus et Insectes Vecteurs - Arboviruses and Insect Vectors, Institut Pasteur [Paris] (IP), Institut Pasteur du Cambodge, Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), University of California [San Francisco] (UC San Francisco), University of California (UC), Washington University in Saint Louis (WUSTL), Public Health Agency of Canada, MRC - University of Glasgow Centre for Virus Research, Université Paris Descartes - Paris 5 (UPD5), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), 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 (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Agency for science, technology and research [Singapore] (A*STAR), Universidade Federal da Bahia (UFBA), U.S. Food and Drug Administration (FDA), Universidad Tecnológica de Pereira [Colombie] (UTP), 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, Institut Pasteur [Paris], Fundação Oswaldo Cruz (FIOCRUZ), University of California [San Francisco] (UCSF), University of California, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Virology, and DEMESLAY GOUGAM, MARIE
Subjects: 0301 basic medicine, GloPID-R chikungunya, o'nyong-nyong and Mayaro virus Working Group, Genes, Viral, Iron, 030106 microbiology, Prevalence, Alphavirus, medicine.disease_cause, Disease Outbreaks, 03 medical and health sciences, Seroepidemiologic Studies, Virology, Environmental health, medicine, Seroprevalence, Animals, Humans, O'nyong-nyong Virus, Serologic Tests, Chikungunya, Phylogeny, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Pharmacology, Molecular epidemiology, Alphavirus Infections, Outbreak, 3. Good health, 030104 developmental biology, Geography, Infectious disease (medical specialty), [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Africa, 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 identify gaps of knowledge about the natural history, epidemiology and medical management of infection by these viruses, and to provide adapted recommendations for future investigations. Here, we present a report dedicated to ONNV epidemiological distribution. Two large-scale ONNV outbreaks have been identified in Africa in the last 60 years, interspersed with sporadic serosurveys and case reports of returning travelers. The assessment of the real scale of ONNV circulation in Africa remains a difficult task and surveillance studies are necessary to fill this gap. The identification of ONNV etiology is made complicated by the absence of multiplex tools in co-circulation areas and that of reference standards, as well as the high cross-reactivity with related pathogens observed in serological tests, in particular with CHIKV. This is a specific obstacle for seroprevalence studies, that necessitate an improvement of serological tools to provide robust results. The scarcity of existent genetic data currently limits molecular epidemiology studies. ONNV epidemiology would also benefit from reinforced entomological and environmental surveillance. Finally, the natural history of the disease deserves to be further investigated, with a specific attention paid to long-term complications. Considering our incomplete knowledge on ONNV distribution, GloPID-R CHIKV, ONNV and MAYV experts recommend that a major effort should be done to fill existing gaps. ispartof: ANTIVIRAL RESEARCH vol:172 ispartof: location:Netherlands status: published
Published: 2019
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10. 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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11. 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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12. NLRP3 inflammasome activation drives tau pathology

Author: Shuangshuang Zhang, David Blum, Ana Vieira-Saecker, Carmen Venegas, Rakez Kayed, Hannah Scheiblich, Douglas T. Golenbock, Maximilian Merten, Shadi Albasset, Susanne V. Schmidt, Eicke Latz, Luc Buée, Frederic Brosseron, Sabine Opitz, Angelika Griep, Francesco Santarelli, Christina Ising, James Stunden, Róisín M. McManus, Michael T. Heneka, Dario Tejera, Stephanie Schwartz, Blum, David, Centre de recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centers for Disease Control and Prevention [Atlanta] (CDC), Centers for Disease Control and Prevention, Institute of Innate Immunity, Bonn, Department of Neurology, The University of Texas Medical Branch (UTMB), Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer - U837 (JPArc), Université Lille Nord de France (COMUE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille, Rheinische Friedrich-Wilhelms-Universität Bonn, Centre de recherche en Biologie Cellulaire (CRBM), Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer - U1172 Inserm - U837 (JPArc), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Lille Nord de France (COMUE)-Université de Lille
Subjects: 0301 basic medicine, Inflammasomes, metabolism [NLR Family, Pyrin Domain-Containing 3 Protein], physiopathology [Protein Aggregation, Pathological], Protein aggregation, genetics [Gene Expression Regulation], Mice, 0302 clinical medicine, genetics [Inflammasomes], Phosphorylation, Multidisciplinary, Microglia, integumentary system, Chemistry, Kinase, Caspase 1, Neurodegeneration, pathology [Microglia], Inflammasome, medicine.anatomical_structure, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], ddc:500, medicine.drug, tau Proteins, Protein Aggregation, Pathological, Article, 03 medical and health sciences, Alzheimer Disease, mental disorders, NLR Family, Pyrin Domain-Containing 3 Protein, medicine, Animals, Humans, [SDV.NEU] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Neuroinflammation, genetics [NLR Family, Pyrin Domain-Containing 3 Protein], Amyloid beta-Peptides, Cyclin-dependent kinase 5, [SCCO.NEUR]Cognitive science/Neuroscience, [SCCO.NEUR] Cognitive science/Neuroscience, Cyclin-Dependent Kinase 5, medicine.disease, metabolism [tau Proteins], Mice, Inbred C57BL, genetics [tau Proteins], 030104 developmental biology, Gene Expression Regulation, metabolism [Cyclin-Dependent Kinase 5], Neuroscience, metabolism [Inflammasomes], 030217 neurology & neurosurgery
Abstract: International audience; Alzheimer's disease is characterized by the accumulation of amyloid-beta in plaques, aggregation of hyperphosphorylated tau in neurofibrillary tangles and neuroinflammation, together resulting in neurodegeneration and cognitive decline1. The NLRP3 inflammasome assembles inside of microglia on activation, leading to increased cleavage and activity of caspase-1 and downstream interleukin-1β release2. Although the NLRP3 inflammasome has been shown to be essential for the development and progression of amyloid-beta pathology in mice3, the precise effect on tau pathology remains unknown. Here we show that loss of NLRP3 inflammasome function reduced tau hyperphosphorylation and aggregation by regulating tau kinases and phosphatases. Tau activated the NLRP3 inflammasome and intracerebral injection of fibrillar amyloid-beta-containing brain homogenates induced tau pathology in an NLRP3-dependent manner. These data identify an important role of microglia and NLRP3 inflammasome activation in the pathogenesis of tauopathies and support the amyloid-cascade hypothesis in Alzheimer's disease, demonstrating that neurofibrillary tangles develop downstream of amyloid-beta-induced microglial activation.
Published: 2019
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13. Discovery of a Small Molecule Inhibitor of Human Adenovirus Capable of Preventing Escape from the Endosome

Author: Haiying Chen, Jerónimo Pachón, Judith Berastegui-Cabrera, Javier Sánchez-Céspedes, Marta Carretero-Ledesma, Eric A. Wold, Jimin Xu, Jia Zhou, Yu Xue, Universidad de Sevilla. Departamento de Medicina, [Xu,J, Chen,H, Xue,Y, Wold,EA, Zhou,J] Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX, USA. [Berastegui-Cabrera,J, Carretero-Ledesma,M, Pachón,J, Sánchez-Céspedes,J] Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío, CSIC, University of Seville, Seville, Spain. [Pachón,J] Department of Medicine, University of Seville, Seville, Spain., and This work was partially supported by the UTMB Technology Commercialization Program, the John D. Stobo, M. D. Distinguished Chair Endowment Fund (to JZ) and John Sealy Memorial Endowment Fund at UTMB, Plan Nacional de I + D + i 2013–2016 and Instituto de Salud Carlos III, Subdirección General de Redes y Centros de Investigación Cooperativa, Ministerio de Economía, Industria y Competitividad, Spanish Network for Research in Infectious Diseases (REIPI RD16/0016/0009), cofinanced by the European Development Regional Fund 'A way to achieve Europe', Operative program Intelligent Growth 20142020, the Instituto de Salud Carlos III, Proyectos de Investigación en Salud (PI15/00489) and Proyectos de Desarrollo Tecnológico en Salud (DTS17/00130), the Spanish Adenovirus Network (AdenoNet, BIO2015/68990-REDT), and the program 'Nicolás Monardes' (C-0059-2018) Servicio Andaluz de Salud, Junta de Andalucía. E.A.W. is supported by the National Institutes of Health (NIH) National Research Service Award (NRSA) F31 DA04551.
Subjects: entry inhibition, 0301 basic medicine, Salicylamide, Virus Replication, Chemicals and Drugs::Chemical Actions and Uses::Pharmacologic Actions::Therapeutic Uses::Anti-Infective Agents::Antiviral Agents [Medical Subject Headings], Organisms::Eukaryota::Animals::Chordata::Vertebrates::Mammals::Primates::Haplorhini::Catarrhini::Hominidae::Humans [Medical Subject Headings], lcsh:Chemistry, Chemicals and Drugs::Chemical Actions and Uses::Specialty Uses of Chemicals::Laboratory Chemicals::Small Molecule Libraries [Medical Subject Headings], Drug Discovery, Salicylamides, Antivíricos, lcsh:QH301-705.5, Spectroscopy, Niclosamide, Infecciones, Chemistry, virus diseases, adenovirus, General Medicine, Chemicals and Drugs::Organic Chemicals::Amides::Anilides::Salicylanilides::Niclosamide [Medical Subject Headings], Small molecule, Virus, Computer Science Applications, Organisms::Viruses::DNA Viruses::Adenoviridae::Mastadenovirus::Adenoviruses, Human [Medical Subject Headings], Anatomy::Cells::Cells, Cultured::Cell Line::Cell Line, Transformed::HEK293 Cells [Medical Subject Headings], Lytic cycle, Phenomena and Processes::Microbiological Phenomena::Virus Physiological Phenomena::Virus Physiological Processes::Virus Internalization [Medical Subject Headings], salicylamide derivatives, Niclosamida, medicine.drug, Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Drug Discovery [Medical Subject Headings], medicine.drug_class, Endosome, Chemicals and Drugs::Organic Chemicals::Amides::Salicylamides [Medical Subject Headings], 030106 microbiology, Endosomes, Antiviral Agents, Endosomas, Article, Catalysis, Adenoviridae, Small Molecule Libraries, antiviral agent, Inorganic Chemistry, Inhibitory Concentration 50, 03 medical and health sciences, Anatomy::Cells::Cellular Structures::Intracellular Space::Cytoplasm::Cytoplasmic Structures::Organelles::Cytoplasmic Vesicles::Transport Vesicles::Endosomes [Medical Subject Headings], Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Toxicity Tests::Inhibitory Concentration 50 [Medical Subject Headings], medicine, Humans, Physical and Theoretical Chemistry, Molecular Biology, Adenoviruses, Human, Organic Chemistry, Virus Internalization, Virology, eye diseases, Phenomena and Processes::Microbiological Phenomena::Microbiological Processes::Virus Physiological Processes::Viral Tropism [Medical Subject Headings], Viral Tropism, Phenomena and Processes::Microbiological Phenomena::Microbiological Processes::Virus Physiological Processes::Virus Replication [Medical Subject Headings], HEK293 Cells, 030104 developmental biology, lcsh:Biology (General), lcsh:QD1-999, A549 Cells, Tissue tropism, Antiviral drug
Abstract: Human adenoviruses (HAdVs) display a wide range of tissue tropism and can cause an array of symptoms from mild respiratory illnesses to disseminated and life-threatening infections in immunocompromised individuals. However, no antiviral drug has been approved specifically for the treatment of HAdV infections. Herein, we report our continued efforts to optimize salicylamide derivatives and discover compound 16 (JMX0493) as a potent inhibitor of HAdV infection. Compound 16 displays submicromolar IC50 values, a higher selectivity index (SI &gt, 100) and 2.5-fold virus yield reduction compared to our hit compound niclosamide. Moreover, unlike niclosamide, our mechanistic studies suggest that the antiviral activity of compound 16 against HAdV is achieved through the inhibition of viral particle escape from the endosome, which bars subsequent uncoating and the presentation of lytic protein VI.
Published: 2021
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14. Changes in the Transmission Dynamic of Chikungunya Virus in Southeastern Senegal

Author: Scott C. Weaver, Oumar Ndiaye, Abdourahmane Sow, Mawlouth Diallo, Bakary Djilocalisse Sadio, Amadou A. Sall, Ousmane Faye, Anta Tall Dia, Birgit Nikolay, Oumar Faye, Denis Malvy, Jorge Cano, Simon Cauchemez, Arbovirus et Virus de Fièvres Hémorragiques [Dakar, Sénégal], Institut Pasteur de Dakar, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), Team MORPH3EUS (INSERM U1219 - UB - ISPED), Bordeaux population health (BPH), Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM), Modélisation mathématique des maladies infectieuses, 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), London School of Hygiene and Tropical Medicine (LSHTM), Unité d'Entomologie Médicale [Dakar] (UEM), The University of Texas Medical Branch (UTMB), The research was supported by the National Institutes of Health (NIH), Grant Number AI1069145., Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Limouzin, Cécile
Subjects: Male, Rural Population, 0301 basic medicine, Veterinary medicine, lcsh:QR1-502, environmental risk, MESH: Chikungunya Fever, Forests, Antibodies, Viral, medicine.disease_cause, Logistic regression, spatial autocorrelation, Population density, lcsh:Microbiology, law.invention, MESH: Aged, 80 and over, 0302 clinical medicine, MESH: Rural Population, Seroepidemiologic Studies, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], law, MESH: Child, Chikungunya, Child, [MATH.MATH-ST] Mathematics [math]/Statistics [math.ST], Aged, 80 and over, MESH: Aged, MESH: Immunoglobulin G, MESH: Middle Aged, Age Factors, virus diseases, Middle Aged, MESH: Forests, MESH: Mining, MESH: Infant, Senegal, 3. Good health, Infectious Diseases, Transmission (mechanics), MESH: Young Adult, Child, Preschool, Female, Sylvatic cycle, Adult, Adolescent, MESH: Population Density, 030231 tropical medicine, Environment, Biology, Article, Mining, gold mining, Young Adult, 03 medical and health sciences, MESH: Senegal, Virology, medicine, Humans, Seroprevalence, MESH: Environment, Aged, Population Density, MESH: Adolescent, MESH: Age Factors, MESH: Seroepidemiologic Studies, MESH: Humans, MESH: Child, Preschool, Infant, Outbreak, MESH: Adult, Odds ratio, 15. Life on land, MESH: Male, 030104 developmental biology, Immunoglobulin G, Chikungunya Fever, MESH: Female, MESH: Antibodies, Viral
Abstract: In Senegal, chikungunya virus (CHIKV) is maintained in a sylvatic cycle and causes sporadic cases or small outbreaks in rural areas. However, little is known about the influence of the environment on its transmission. To address the question, 120 villages were randomly selected in the Kedougou region of southeastern Senegal. In each selected village, 10 persons by randomly selected household were sampled and tested for specific anti-CHIKV IgG antibodies by ELISA. We investigated the association of CHIKV seroprevalence with environmental variables using logistic regression analysis and the spatial correlation of village seroprevalence based on semivariogram analysis. Fifty-four percent (51%&ndash, 57%) of individuals sampled during the survey tested positive for CHIKV-specific IgG. CHIKV seroprevalence was significantly higher in populations living close to forested areas (Normalized Difference Vegetation Index (NDVI), Odds Ratio (OR) = 1.90 (1.42&ndash, 2.57)), and was negatively associated with population density (OR = 0.76 (0.69&ndash, 0.84)). In contrast, in gold mining sites where population density was &gt, 400 people per km2, seroprevalence peaked significantly among adults (46% (27%&ndash, 67%)) compared to all other individuals (20% (12%&ndash, 31%)). However, traditional gold mining activities significantly modify the transmission dynamic of CHIKV, leading to a potential increase of the risk of human exposition in the region.
Published: 2020
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15. 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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16. Novel Wolbachia strains in Anopheles malaria vectors from Sub-Saharan Africa

Author: James Orsborne, Thomas Walker, Fara Nantenaina Raharimalala, Francis Wat’senga, Kamil Khanipov, Mojca Kristan, Yuriy Fofanov, Yaw A. Afrane, Grant L. Hughes, Emile Z Manzambi, Kalil Keita, Seth R. Irish, Gena G. Lawrence, Eliot Hurn, Denka Camara, Claire L. Jeffries, Janvier Bandibabone, Georgiy Golovko, Shivanand Hegde, Sébastien Boyer, Tarekegn A. Abeku, Yaya Barry, Kirstin Spence, Luciano Michaël Tantely, Abdul Rahim Mohammed, Maria Pimenova, London School of Hygiene and Tropical Medicine (LSHTM), Centers for Disease Control and Prevention [Atlanta] (CDC), Centers for Disease Control and Prevention, The University of Texas Medical Branch (UTMB), Centre de Recherche en Sciences Naturelles [Lwiro, Congo] (CRSN), Unité d'Entomologie Médicale [Antananarivo, Madagascar] (IPM), Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Ministère de la Santé [Conakry, Guinea], Institut National de Recherche Biomédicale [Kinshasa] (INRB), University of Ghana, Malaria Consortium, London, UK, and CLJ and TW were supported by a Wellcome Trust /Royal Society grant awarded to TW (101285): http://www.wellcome.ac.uk
Subjects: 0301 basic medicine, Range (biology), media_common.quotation_subject, Anopheles gambiae, 030231 tropical medicine, malaria, Prevalence, Zoology, Medicine (miscellaneous), Asaia, Insect, Plasmodium, General Biochemistry, Genetics and Molecular Biology, symbols.namesake, 03 medical and health sciences, endosymbionts, 0302 clinical medicine, Anopheles, parasitic diseases, medicine, Parasite hosting, Microbiome, reproductive and urinary physiology, mosquitoes, 030304 developmental biology, media_common, Sanger sequencing, 0303 health sciences, biology, fungi, Articles, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, medicine.disease, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, 030104 developmental biology, symbols, Multilocus sequence typing, bacteria, Wolbachia, Malaria, Research Article
Abstract: Background: Wolbachia, a common insect endosymbiotic bacterium that can influence pathogen transmission and manipulate host reproduction, has historically been considered absent from the Anopheles (An.) genera, but has recently been found in An. gambiae s.l. populations in West Africa. As there are numerous Anopheles species that have the capacity to transmit malaria, we analysed a range of species across five malaria endemic countries to determine Wolbachia prevalence rates, characterise novel Wolbachia strains and determine any correlation between the presence of Plasmodium, Wolbachia and the competing bacterium Asaia. Methods: Anopheles adult mosquitoes were collected from five malaria-endemic countries: Guinea, Democratic Republic of the Congo (DRC), Ghana, Uganda and Madagascar, between 2013 and 2017. Molecular analysis was undertaken using quantitative PCR, Sanger sequencing, Wolbachia multilocus sequence typing (MLST) and high-throughput amplicon sequencing of the bacterial 16S rRNA gene. Results: Novel Wolbachia strains were discovered in five species: An. coluzzii, An. gambiae s.s., An. arabiensis, An. moucheti and An. species A, increasing the number of Anopheles species known to be naturally infected. Variable prevalence rates in different locations were observed and novel strains were phylogenetically diverse, clustering with Wolbachia supergroup B strains. We also provide evidence for resident strain variants within An. species A. Wolbachia is the dominant member of the microbiome in An. moucheti and An. species A but present at lower densities in An. coluzzii. Interestingly, no evidence of Wolbachia/Asaia co-infections was seen and Asaia infection densities were shown to be variable and location dependent. Conclusions: The important discovery of novel Wolbachia strains in Anopheles provides greater insight into the prevalence of resident Wolbachia strains in diverse malaria vectors. Novel Wolbachia strains (particularly high-density strains) are ideal candidate strains for transinfection to create stable infections in other Anopheles mosquito species, which could be used for population replacement or suppression control strategies.
Published: 2018
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17. 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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18. 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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19. Biochemistry and Molecular Biology of Flaviviruses

Author: Mariano A. Garcia-Blanco, K. Reddisiva Prasanth, Nicholas J. Barrows, Kuo-Chieh Liao, Ruben Soto-Acosta, Rafael K. Campos, October M. Sessions, Geraldine Schott-Lerner, Julien Pompon, Shelton S. Bradrick, Shih Chia Yeh, University of Texas Medical Branch at Galveston, Duke University [Durham], Duke-NUS Medical School [Singapore], The University of Texas Medical Branch (UTMB), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), and Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])
Subjects: 0301 basic medicine, Genes, Viral, viruses, RNA-binding protein, Virus Replication, Genome, Virus, Article, Dengue fever, 03 medical and health sciences, medicine, Humans, Gene, Chemistry, Flavivirus, RNA-Binding Proteins, General Chemistry, Japanese encephalitis, biochemical phenomena, metabolism, and nutrition, medicine.disease, Non-coding RNA, Molecular biology, 3. Good health, 030104 developmental biology, Viral replication, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Host-Pathogen Interactions
Abstract: International audience; Flaviviruses, such as dengue, Japanese encephalitis, tick-borne encephalitis, West Nile, yellow fever, and Zika viruses, are critically important human pathogens that sicken a staggeringly high number of humans every year. Most of these pathogens are transmitted by mosquitos, and not surprisingly, as the earth warms and human populations grow and move, their geographic reach is increasing. Flaviviruses are simple RNA–protein machines that carry out protein synthesis, genome replication, and virion packaging in close association with cellular lipid membranes. In this review, we examine the molecular biology of flaviviruses touching on the structure and function of viral components and how these interact with host factors. The latter are functionally divided into pro-viral and antiviral factors, both of which, not surprisingly, include many RNA binding proteins. In the interface between the virus and the hosts we highlight the role of a noncoding RNA produced by flaviviruses to impair antiviral host immune responses. Throughout the review, we highlight areas of intense investigation, or a need for it, and potential targets and tools to consider in the important battle against pathogenic flaviviruses.
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. Chikungunya Outbreak in Kedougou, Southeastern Senegal in 2009-2010

Author: Manfred Weidmann, Cheikh Tidiane Diagne, Abdourahmane Sow, Rubing Chen, Amadou A. Sall, Oumar Ndiaye, Mathilde Guerbois, Scott C. Weaver, Ousmane Faye, Diawo Diallo, Abdourahmane Faye, Cheikh Sadibou Senghor, Youssoupha Ndiaye, Mawlouth Diallo, Bakary Djilocalisse Sadio, Anta Tall Dia, Oumar Faye, Denis Malvy, Kathryn A. Hanley, Douglas M. Watts, Ousmane M. Diop, Arbovirus et Virus de Fièvres Hémorragiques [Dakar, Sénégal], Institut Pasteur de Dakar, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), Bordeaux population health (BPH), Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM), Réseau International des Instituts Pasteur (RIIP), The University of Texas Medical Branch (UTMB), University Medical Center Göttingen (UMG), District sanitaire de Saraya, District sanitaire de Kedougou, University of Texas [El Paso] (UTEP ), New Mexico State University, and The research was funded by the National Institutes of Health (Grant Number 5R01A 1069145).
Subjects: 0301 basic medicine, sylvatic circulation, 030231 tropical medicine, medicine.disease_cause, Chikungunya fever, 03 medical and health sciences, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, medicine, Major Article, Chikungunya, Viral isolation, Aedes, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, School age child, biology, outbreak, business.industry, Outbreak, virus diseases, biology.organism_classification, Senegal, 3. Good health, Kedougou, 030104 developmental biology, Infectious Diseases, Oncology, Ethnology, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business, Chikungunya virus
Abstract: Background In Senegal, Chikungunya virus (CHIKV), which is an emerging mosquito-borne alphavirus, circulates in a sylvatic and urban/domestic cycle and has caused sporadic human cases and epidemics since 1960s. However, the real impact of the CHIKV sylvatic cycle in humans and mechanisms underlying its emergence still remains unknown. Methodology One thousand four hundred nine suspect cases of CHIKV infection, recruited from 5 health facilities located in Kedougou region, south-eastern Senegal, between May 2009 to March 2010, together with 866 serum samples collected from schoolchildren from 4 elementary schools in May and November 2009 from Kedougou were screened for anti-CHIKV immunoglobulin (Ig)M antibodies and, when appropriate, for viral nucleic acid by real-time polymerase chain reaction (rPCR) and virus isolation. In addition, mosquitoes collected in the same area from May 2009 to January 2010 were tested for CHIKV by rPCR and by virus isolation, and 116 monkeys sera collected from March 2010 to May 2010 were tested for anti-CHIKV IgM and neutralizing antibodies. Results The main clinical manifestations of the CHIKV suspect cases were headache, myalgia, and arthralgia. Evidence for CHIKV infection was observed in 1.4% (20 of 1409) of patients among suspect cases. No significant difference was observed among age or sex groups. In addition, 25 (2.9%) students had evidence of CHIKV infection in November 2009. Chikungunya virus was detected in 42 pools of mosquitoes, mainly from Aedes furcifer, and 83% of monkeys sampled were seropositive. Conclusions Our findings further documented that CHIKV is maintained in a sylvatic transmission cycle among monkeys and Aedes mosquitoes in Kedougou, and humans become infected by exposure to the virus in the forest.
Published: 2018
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22. Lactobacillus rhamnosus GG increases cyclooxygenase-2 expression and prostaglandin E2 secretion in colonic myofibroblasts via a MyD88-dependent mechanism during homeostasis

Author: Daniel L. Worthley, Maria C. Urdaci, Philippe Bressollier, Romain Villeger, Rachel Dillard, Don W. Powell, Gabriela Uribe, Irina V. Pinchuk, Timothy C. Wang, The University of Texas Medical Branch (UTMB), Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), Laboratoire de Chimie des Substances Naturelles (LCSN), Université de Limoges (UNILIM)-Génomique, Environnement, Immunité, Santé, Thérapeutique (GEIST FR CNRS 3503), Daniel Guggenheim School of Aerospace Engineering (GA TECH), Georgia Institute of Technology [Atlanta], Chimie et Biologie des Membranes et des Nanoobjets (CBMN), Université de Bordeaux (UB)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne)-Institut National de la Recherche Agronomique (INRA), École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut de Chimie du CNRS (INC)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte - Clermont Auvergne (M2iSH), Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA)-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), and Université Sciences et Technologies - Bordeaux 1-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Stromal cell, Colon, Immunology, Prostaglandin, Administration, Oral, Mice, Transgenic, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Biology, Microbiology, [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity, Article, Dinoprostone, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Downregulation and upregulation, Virology, [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], medicine, Animals, Homeostasis, Humans, Prostaglandin E2, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Myofibroblasts, ComputingMilieux_MISCELLANEOUS, Leukotriene, Innate immune system, Arachidonate 5-Lipoxygenase, Arachidonic Acid, Lacticaseibacillus rhamnosus, Probiotics, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Mice, Inbred C57BL, 030104 developmental biology, Eicosanoid, chemistry, Cyclooxygenase 2, 030220 oncology & carcinogenesis, Myeloid Differentiation Factor 88, Cancer research, Caco-2 Cells, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, medicine.drug
Abstract: Prostaglandin E2 (PGE2 ) plays a critical role in intestinal mucosal tolerance and barrier integrity. Cyclooxygenase-2 (COX-2)-dependent PGE2 production involves mobilisation of arachidonic acid. Lactobacillus rhamnosus GG (LbGG) is one of the most widely used probiotics reported to colonise the colonic mucosa. LbGG contributes to the protection of the small intestine against radiation injury through the repositioning of mucosal COX-2 expressing cells. However, it is unknown if LbGG modulates PGE2 production in the colonic mucosa under homeostasis and the major cellular elements involved in these processes. Colonic epithelial and CD90+ mesenchymal stromal cells, also known as (myo) fibroblasts (CMFs), are abundant innate immune cells in normal colonic mucosa able to produce PGE2 . Herein, we tested the hypothesis that under colonic mucosal homeostasis, LbGG modulates the eicosanoid pathway resulting in increased PGE2 production in both epithelial and stromal cells. Among the five tested human colonic epithelial cell lines, only exposure of Caco-2 to LbGG for 24 hr led to the mobilisation of arachidonic acid with concomitant increase in the components within the leukotriene and COX-2-dependent PGE2 pathways. By contrast, CMFs isolated from the normal human colonic mucosa responded to LbGG with increased expression of COX-2 and PGE2 in the prostaglandin pathway, but not 5-LO in the leukotriene pathway. Oral gavage of C57BL/6 mice for 5 days with LbGG (5 × 108 Colony-Forming Unit (CFU)/dose) increased COX-2 expression in the colonic mucosa. The majority of cells upregulating COX-2 protein expression were located in the colonic lamina propria and colocalised with α-SMA+ cells corresponding to the CMF phenotype. This process was myeloid differentiation factor-88-dependent, because silencing of myeloid differentiation factor-88 expression in CMFs abrogated LbGG-induced upregulation of COX-2 in culture and in vivo. Taken together, our data suggest that LbGG increases release of COX-2-mediated PGE2 , contributing to the maintenance of mucosal homeostasis in the colon and CMFs are among the major contributors to this process.
Published: 2017
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23. 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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24. 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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25. Taxonomy of the order Mononegavirales : update 2017

Author: Andrew J. Easton, Gael Kurath, Jonathan S. Towner, Qi Fang, Calogero Terregino, Noël Tordo, Jean L. Patterson, John H. Werren, John M. Dye, Andrea Maisner, Qisheng Song, Peter J. Walker, Benhur Lee, Pierre Formenty, Richard E. Randall, Ralf Dürrwald, Kim R. Blasdell, Alisa Bochnowski, Bertus K. Rima, Robert A. Lamb, Paul A. Rota, Kartik Chandran, Ralf G. Dietzgen, David M. Stone, Norbert Nowotny, Hideki Kondo, Roger Hewson, Anna E. Whitfield, Janusz T. Paweska, Masayuki Horie, Peter L. Collins, Keizo Tomonaga, Martin Schwemmle, Anthony P. James, Olga Dolnik, Gary P. Kobinger, Beibei Wang, Michael N. Pearson, Nicolás Bejerman, Susan Payne, Ming Li, Jian Hong, Fei Wang, Christopher F. Basler, Robert M. Harding, Jens H. Kuhn, Ron A. M. Fouchier, Charles H. Calisher, Eric M. Leroy, Viktor E. Volchkov, Hideki Ebihara, Lin-Fa Wang, Dàohóng Jiāng, Sina Bavari, Gaya K. Amarasinghe, Ayato Takada, Sergey V. Netesov, Elke Mühlberger, Sophie J. Smither, David Wang, Gongyin Ye, Peter Revill, Martin Beer, Colleen M. Higgins, Yīmíng Bào, Robert B. Tesh, Victoria Wahl-Jensen, Thomas Briese, Zhichao Yan, Dennis Rubbenstroth, Elodie Ghedin, Alexander Bukreyev, Nikos Vasilakis, Virology, Washington University School of Medicine (WUSM), University of Washington [Seattle], National Center for Biotechnology Information (NCBI), Georgia State University, University System of Georgia (USG), Army Medical Research Institute of Infectious Diseases [USA] (USAMRIID), Institute of Diagnostic Virology (IVD), Friedrich-Loeffler-Institut (FLI), 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), Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Columbia Mailman School of Public Health, The University of Texas Medical Branch (UTMB), College of Veterinary Medicine and Biomedical Sciences, Colorado State University [Fort Collins] (CSU), Albert Einstein College of Medicine [New York], 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], Philipps University of Marburg, IDT Biologika, School of Life Sciences, Warwick University, Department of Biochemistry and Molecular Biology, University of Rochester [USA], State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences (CAAS), 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), Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Public Health England [Salisbury] (PHE), Auckland University of Technology (AUT), Infections Virales et Pathologie Comparée - UMR 754 (IVPC), Institut National de la Recherche Agronomique (INRA)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, Kagoshima University, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 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], Icahn School of Medicine at Mount Sinai [New York] (MSSM), Centre International de Recherches Médicales de Franceville (CIRMF), Institute for Applied Ecology New Zealand (AENZ), 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], Texas A&M University System, National Institute for Communicable Diseases [Johannesburg] (NICD), University of Auckland [Auckland], Biomedical Sciences Research Complex [St Andrews, Scotland] (BSRC), University of St Andrews [Scotland], Victorian Infectious Diseases Reference Laboratory, Queen's University [Belfast] (QUB), National Center for Immunization and Respiratory Diseases, CDC, Centers for Disease Control and Prevention (CDC), University of Freiburg [Freiburg], Defence Science and Technology Laboratory (Dstl), Ministry of Defence (UK) (MOD), University of Missouri School of Medicine, University of Missouri System, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Hokkaido University [Sapporo, Japan], Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), 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, Bases moléculaires de la pathogénicité virale – Molecular Basis of Viral Pathogenicity (BMPV), Centre International de Recherche en Infectiologie - UMR (CIRI), 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), National Biodefense Analysis and Countermeasures Center [Frederick], U.S. Social Security Administration, CSIRO Health & Biosecurity, Washington University School of Medicine, Department of Agriculture, Fisheries and Forestry, Ecoscience Precinct, GPO Box 267, Brisbane, Duke-NUS Medical School [Singapore], Department of Biology, Kansas State University, Albert Einstein College of Medicine, Queensland Alliance for Agriculture and Food Innovation, University of Queensland (UQ), Public Health England [Porton Down, Salisbury], Institut National de la Recherche Agronomique (INRA)-École pratique des hautes études (EPHE)-Université Claude Bernard Lyon 1 (UCBL), Faculty of Medicine-Laval University [Québec], Okayama University [Okayama], Centre International de Recherches Médicales de Franceville, Institute for Applied Ecology New Zealand, Texas Biomedical Research Institute [San Antonio, Texas], A&M University, National Institute for Communicable Diseases (NICD), The University of Auckland, Centre for Experimental Medicine [Queen’s University of Belfast], Hokkaido University, Istituto Zooprofilattico Sperimentale delle Venezie, Bases moléculaires de la pathogénicité virale – Molecular Basis of Viral Pathogenicity, 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, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Columbia University [New York], Philipps Universität Marburg = Philipps University of Marburg, University of Warwick [Coventry], Queensland University of Technology [Brisbane] (QUT), Institut National de la Recherche Agronomique (INRA)-École Pratique des Hautes Études (EPHE), Huazhong Agricultural University [Wuhan] (HZAU), Victorian Infectious Diseases Reference Laboratory [Melbourne, Australia] (VIDRL), 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), and Biomedical Sciences Research Complex
Subjects: 0301 basic medicine, 030106 microbiology, Genome, Viral, Article, 03 medical and health sciences, Species Specificity, Genus, Phylogenetics, Virology, Gene Order, Viral, Mononegavirales, Phylogeny, Order Mononegavirales, Genome, biology, General Medicine, Pneumovirus, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 030104 developmental biology, Evolutionary biology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.IMM]Life Sciences [q-bio]/Immunology, Taxonomy (biology)
Abstract: International audience; In 2017, the order Mononegavirales was expanded by the inclusion of a total of 69 novel species. Five new rhabdovirus genera and one new nyamivirus genus were established to harbor 41 of these species, whereas the remaining new species were assigned to already established genera. Furthermore, non-Latinized binomial species names replaced all paramyxovirus and pneumovirus species names, thereby accomplishing application of binomial species names throughout the entire order. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).
Published: 2017
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26. Schizosaccharomyces pombe kinesin-5 switches direction using a steric blocking mechanism

Author: Carolyn A. Moores, Robert A. Cross, Syeda Rizvi, Mishan Britto, Ottilie von Loeffelholz, Adeline Goulet, Architecture et fonction des macromolécules biologiques (AFMB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de génétique et biologie moléculaire et cellulaire (IGBMC), Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Birkbeck College [University of London], and The University of Texas Medical Branch (UTMB)
Subjects: 0301 basic medicine, Stereochemistry, [SDV]Life Sciences [q-bio], Dynein, Kinesins, Mitosis, bcs, Microtubules, Motor protein, 03 medical and health sciences, Protein Domains, Microtubule, Chromosome Segregation, Schizosaccharomyces, Multidisciplinary, Binding Sites, biology, Microtubule sliding, biology.organism_classification, 030104 developmental biology, PNAS Plus, Schizosaccharomyces pombe, Biophysics, Kinesin, Schizosaccharomyces pombe Proteins, Microtubule-Associated Proteins, Binding domain
Abstract: International audience; Cut7, the sole kinesin-5 in Schizosaccharomyces pombe , is essential for mitosis. Like other yeast kinesin-5 motors, Cut7 can reverse its stepping direction, by mechanisms that are currently unclear. Here we show that for full-length Cut7, the key determinant of stepping direction is the degree of motor crowding on the microtubule lattice, with greater crowding converting the motor from minus end-directed to plus end-directed stepping. To explain how high Cut7 occupancy causes this reversal, we postulate a simple proximity sensing mechanism that operates via steric blocking. We propose that the minus end-directed stepping action of Cut7 is selectively inhibited by collisions with neighbors under crowded conditions, whereas its plus end-directed action, being less space-hungry, is not. In support of this idea, we show that the direction of Cut7-driven microtubule sliding can be reversed by crowding it with non-Cut7 proteins. Thus, crowding by either dynein microtubule binding domain or Klp2, a kinesin-14, converts Cut7 from net minus end-directed to net plus end-directed stepping. Biochemical assays confirm that the Cut7 N terminus increases Cut7 occupancy by binding directly to microtubules. Direct observation by cryoEM reveals that this occupancy-enhancing N-terminal domain is partially ordered. Overall, our data point to a steric blocking mechanism for directional reversal through which collisions of Cut7 motor domains with their neighbors inhibit their minus end-directed stepping action, but not their plus end-directed stepping action. Our model can potentially reconcile a number of previous, apparently conflicting, observations and proposals for the reversal mechanism of yeast kinesins-5.
Published: 2016
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27. 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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28. ISG15 deficiency and increased viral resistance in humans but not mice

Author: Zhi Li, Benhur Lee, Ilhan Tezcan, Payam Tabarsi, Sofija Buta, Nahal Mansouri, Frederic Vigant, Domenico Tortorella, James Duehr, Béatrice Payelle-Brogard, Sandra Pellegrini, Li Qian, Scott D. Speer, Véronique Francois-Newton, Davood Mansouri, Jacob Piehler, Alexander N. Freiberg, Mark Hermann, Thomas J. Gardner, Marisela R. Rodriguez, Ozden Sanal, Tim Wedeking, Adolfo García-Sastre, Coralie F. Daussy, Deborah J. Lenschow, Erminia Rubino, Dusan Bogunovic, Icahn School of Medicine at Mount Sinai [New York] (MSSM), Signalisation des Cytokines, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Osnabrück University, Hacettepe University = Hacettepe Üniversitesi, Shahid Beheshti University of Medical Sciences [Tehran] (SBUMS), Shahid Beheshti University, University of Washington School of Medicine, The University of Texas Medical Branch (UTMB), This was supported in part by NIH grant R00 AI106942-02 to D.B., NIH grant R01 AI101820 to D.T., an American Heart Association pre-doctoral fellowship and a USPHS Institutional Research Training Award T32-AI07647 to T.J.G., NRSA T32 AR07279-30 to M.R.R., NIH grant RO1 A1080672 and Pew Scholar Award to D.J.L., funding by the DFG (SFB 944) to J.P., NIH grant R33 AI102267 to A.N.F. and B.L., CRIP (Center for Research on Influenza Pathogenesis), and NIAID funded Center of Excellence for Influenza Research and Surveillance (contract #HHSN272201400008C) to AGS. Experimental support was provided by the Speed Congenics Facility of the Rheumatic Disease Core Center (P30 AR048335). Work in the Cytokine Signaling Unit was supported by Institut Pasteur, CNRS, INSERM and an Amgen Scholarship to E.R., Çocuk Sağlığı ve Hastalıkları, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Universität Osnabrück - Osnabrück University
Subjects: 0301 basic medicine, Animals, Cell Line, Cytokines/genetics, Cytokines/immunology, Cytokines/metabolism, Female, Gene Expression Regulation, Humans, Interferons/metabolism, Mice, Primary Cell Culture, Ubiquitin Thiolesterase/metabolism, Ubiquitins/genetics, Ubiquitins/immunology, Ubiquitins/metabolism, Virus Diseases/immunology, Science, General Physics and Astronomy, Biology, Viral resistance, Viral infection, General Biochemistry, Genetics and Molecular Biology, Article, MESH: Primary Cell Culture, 03 medical and health sciences, MESH: Ubiquitins, MESH: Animals, MESH: Interferons, MESH: Mice, Ubiquitins, MESH: Cytokines, [SDV.GEN]Life Sciences [q-bio]/Genetics, Multidisciplinary, MESH: Humans, General Chemistry, MESH: Ubiquitin Thiolesterase, ISG15, Virology, MESH: Gene Expression Regulation, 3. Good health, MESH: Cell Line, MESH: Virus Diseases, 030104 developmental biology, Virus Diseases, Immunology, [SDV.IMM]Life Sciences [q-bio]/Immunology, Cytokines, Interferons, MESH: Female, Ubiquitin Thiolesterase
Abstract: ISG15 is an interferon (IFN)-α/β-induced ubiquitin-like protein. It exists as a free molecule, intracellularly and extracellularly, and conjugated to target proteins. Studies in mice have demonstrated a role for Isg15 in antiviral immunity. By contrast, human ISG15 was shown to have critical immune functions, but not in antiviral immunity. Namely, free extracellular ISG15 is crucial in IFN-γ-dependent antimycobacterial immunity, while free intracellular ISG15 is crucial for USP18-mediated downregulation of IFN-α/β signalling. Here we describe ISG15-deficient patients who display no enhanced susceptibility to viruses in vivo, in stark contrast to Isg15-deficient mice. Furthermore, fibroblasts derived from ISG15-deficient patients display enhanced antiviral protection, and expression of ISG15 attenuates viral resistance to WT control levels. The species-specific gain-of-function in antiviral immunity observed in ISG15 deficiency is explained by the requirement of ISG15 to sustain USP18 levels in humans, a mechanism not operating in mice., ISG15 is a ubiquitin-like protein which has important immune-related functions in mice and humans. Here the authors demonstrate that, unlike in mice, human ISG15 stabilizes UPS18 and that ISG15-deficient human cells are more resistant to viral infection.
Published: 2016
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29. 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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30. Whole-Genome Sequencing Analysis from the Chikungunya Virus Caribbean Outbreak Reveals Novel Evolutionary Genomic Elements

Author: Marco Vignuzzi, Magnus Fontes, Bryan C. Mounce, Ofer Isakov, Rubing Chen, Gonzalo Moratorio, Antoine Enfissi, Hervé Blanc, Kenneth A. Stapleford, Séverine Matheus, Rasmus Henningsson, Daphna Weissglas-Volkov, Myrielle Dupont-Rouzeyrol, Dominique Rousset, Scott C. Weaver, Noam Shomron, Populations virales et Pathogenèse - Viral Populations and Pathogenesis, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), International Group for Data Analysis (IGDA), Institut Pasteur [Paris] (IP), The University of Texas Medical Branch (UTMB), Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP), Sackler Faculty of Medicine, Tel Aviv University (TAU), Institut Pasteur de Nouvelle-Calédonie, This work was supported by a Institut Pasteur Programme Transversal de Recherche PTR 489 grant, the French Government ’s Investissementd’Avenir program, Laboratoire d ’Excellence' Integrative Biology of Emerging Infectious Diseases ' grant ANR-10-LABX-62-IBEID) and a ' Equipe FRM DEQ20150331759 ' grant from the French Fondation pour la Recherche Médicale (KAS, MV). RC and SCW were supported by National institutes of Health Contract HHSN272201000040I/HHSN27200004/D04, and by the Institute for Human Infections and Immunity at the University of Texas Medical Branch. DWV was supported by the Edmond J. Safra Center for Bioinformatics and the Center for Nanoscience and nanotechnology at Tel-Aviv University., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris], Tel Aviv University [Tel Aviv], Stapleford K.A., Moratorio Gonzalo, Universidad de la República (Uruguay). Facultad de Ciencias. Centro de Investigaciones Nucleares. Instituto Pasteur, Henningsson R., Chen R., Matheus S., Enfissi A., Weissglas-Volkov D., Isakov O., Blanc H., Mounce B.C, Dupont-Rouzeyrol M., Shomron N., Weaver S., Fontes M., Rousset D., Vignuzz M., Calvez, Elodie, and Integrative Biology of Emerging Infectious Diseases - - IBEID2010 - ANR-10-LABX-0062 - LABX - VALID
Subjects: Pathology and Laboratory Medicine, Infographics, Geographical locations, Disease Outbreaks, Togaviridae, MESH: Genetic Variation, Chikungunya, MESH: Phylogeny, Phylogeny, education.field_of_study, MESH: Genomics, virus diseases, Phylogenetic Analysis, Genomics, Virus, 3. Good health, [SDV] Life Sciences [q-bio], [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Caribbean Region, Medical Microbiology, Viral Pathogens, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, MESH: Caribbean Region, lcsh:RC955-962, Alphaviruses, 030106 microbiology, Molecular Sequence Data, Alphavirus, Viral quasispecies, Microbiology, Evolution, Molecular, 03 medical and health sciences, Humans, education, Molecular Biology Techniques, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Microbial Pathogens, Molecular Biology, Caribbean, Molecular Biology Assays and Analysis Techniques, MESH: Humans, MESH: Molecular Sequence Data, Data Visualization, Public Health, Environmental and Occupational Health, Organisms, Outbreak, Chikungunya Infection, Genetic Variation, MESH: Chikungunya virus, lcsh:RA1-1270, Virology, 030104 developmental biology, People and places, Cloning, 0301 basic medicine, RNA viruses, MESH: Sequence Analysis, DNA, Viral Diseases, viruses, [SDV]Life Sciences [q-bio], MESH: Chikungunya Fever, medicine.disease_cause, Medicine and Health Sciences, MESH: Disease Outbreaks, MESH: Evolution, Molecular, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Chikungunya Virus, biology, lcsh:Public aspects of medicine, Infectious Diseases, Viral evolution, Viruses, MESH: Genome, Viral, Pathogens, Martinique, Sequence Analysis, Graphs, Research Article, Computer and Information Sciences, lcsh:Arctic medicine. Tropical medicine, Population, Genome, Viral, Research and Analysis Methods, Viral Evolution, Togaviruses, medicine, Sequencing Techniques, Evolutionary Biology, Biology and life sciences, Sequence Analysis, DNA, biology.organism_classification, Genética, Organismal Evolution, North America, Microbial Evolution, Chikungunya Fever, Sequence Alignment
Abstract: Background Chikungunya virus (CHIKV), an alphavirus and member of the Togaviridae family, is capable of causing severe febrile disease in humans. In December of 2013 the Asian Lineage of CHIKV spread from the Old World to the Americas, spreading rapidly throughout the New World. Given this new emergence in naïve populations we studied the viral genetic diversity present in infected individuals to understand how CHIKV may have evolved during this continuing outbreak. Methodology/Principle Findings We used deep-sequencing technologies coupled with well-established bioinformatics pipelines to characterize the minority variants and diversity present in CHIKV infected individuals from Guadeloupe and Martinique, two islands in the center of the epidemic. We observed changes in the consensus sequence as well as a diverse range of minority variants present at various levels in the population. Furthermore, we found that overall diversity was dramatically reduced after single passages in cell lines. Finally, we constructed an infectious clone from this outbreak and identified a novel 3’ untranslated region (UTR) structure, not previously found in nature, that led to increased replication in insect cells. Conclusions/Significance Here we preformed an intrahost quasispecies analysis of the new CHIKV outbreak in the Caribbean. We identified novel variants present in infected individuals, as well as a new 3’UTR structure, suggesting that CHIKV has rapidly evolved in a short period of time once it entered this naïve population. These studies highlight the need to continue viral diversity surveillance over time as this epidemic evolves in order to understand the evolutionary potential of CHIKV., Author Summary Chikungunya virus is a re-emerging and rapidly spreading arbovirus that has caused several outbreaks in the last decade with the most recent in the Caribbean islands and the Americas beginning in 2013 infecting over 1 million individuals. The ability to monitor such epidemics would be enhanced by characterizing the viral populations that circulate within infected individuals. To do this, we deep-sequenced viral populations from infected individuals and identified minority variants present at high frequencies, as well as the presence of a novel 3’ untranslated genome region (UTR) structure, a key determinant of chikungunya virus infectivity and evolution never before described in nature. Finally, we genetically engineered an infectious clone from this outbreak strain and established that the novel 3’UTR structure increases viral replication in mosquito cells. Taken together these studies highlight the vast diversity of viral populations in infected individuals, reveal potential novel determinants of chikungunya virus biology, and provide an indispensable tool for future studies involved in viral evolution and adaptation.
Published: 2016
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31. Lack of evidence for Zika virus transmission by Culex mosquitoes

Author: Scott C. Weaver, Scott A. Ritchie, Aaron C. Brault, Nikos Vasilakis, Ricardo Lourenço-de-Oliveira, Guilherme S. Ribeiro, Gregory D. Ebel, Laura Beatriz Tauro, Jorge E. Osorio, Gonzalo M. Vazquez-Prokopec, Laura D. Kramer, Christopher M. Roundy, Igor Adolfo Dexheimer Paploski, Uriel Kitron, Ildefonso Fernández-Salas, Sasha R. Azar, Anna-Bella Failloux, The University of Texas Medical Branch (UTMB), Centers for Disease Control and Prevention, Colorado State University [Fort Collins] (CSU), Arbovirus et Insectes Vecteurs - Arboviruses and Insect Vectors, Institut Pasteur [Paris], Centro Regional de Investigación en Salud Pública = Regional Centre of Research in Public Health [Tapachula, Mexique] (CRISP), National Institute of Public Health = Instituto Nacional de Salud Pública [Cuernavaca, Mexique] (INSP), Emory University [Atlanta, GA], Wadsworth Center, New York State Department of Health [Albany], Fundação Oswaldo Cruz (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP), University of Wisconsin-Madison, Universidade Federal da Bahia (UFBA), James Cook University (JCU), Institut Pasteur [Paris] (IP), and Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ)
Subjects: 0301 basic medicine, Epidemiology, Culex, 030231 tropical medicine, Immunology, Microbiology, Zika virus, law.invention, 03 medical and health sciences, 0302 clinical medicine, Aedes, law, Virology, parasitic diseases, Drug Discovery, Animals, Humans, Letter to the Editor, biology, Zika Virus Infection, fungi, Zika Virus, General Medicine, biology.organism_classification, Insect Vectors, 3. Good health, 030104 developmental biology, Infectious Diseases, Transmission (mechanics), [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Parasitology
Abstract: Response to: ‘Lack of evidence for Zika virus transmission by Culex mosquitoes’https://www.nature.com/articles/emi201786doi:10.1038/emi.2017.86; International audience; LETTER TO THE EDITORDear Editor,Since Zika virus (ZIKV) emerged in the Americas, major research efforts have been focused on identifying the mosquito species responsible for transmission. [...]
Published: 2017
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32. Possibility and Challenges of Conversion of Current Virus Species Names to Linnaean Binomials

Author: Sbina Bavari, Susan Payne, Alexander Bukreyev, Arvind Varsani, Víctor Romanowski, Kartik Chandran, Ralf G. Dietzgen, Mark D. Stenglein, Anna N. Clawson, Sead Sabanadzovic, Gael Kurath, Andrea Maisner, Peter J. Walker, Ralf Dürrwald, Juan Carlos de la Torre, Eric M. Leroy, Mária Benko, Keizo Tomonaga, Gary P. Kobinger, Robert A. Lamb, Hideki Kondo, F. Murilo Zerbini, Martin Schwemmle, Robert B. Tesh, Gaya K. Amarasinghe, Andrew J. Easton, Michael J. Buchmeier, Jean-Paul Gonzalez, Anna E. Whitfield, Nikos Vasilakis, Jonathan S. Towner, Pierre Formenty, Jens H. Kuhn, Norbert Nowotny, Roger Hewson, Ayato Takada, Mart Krupovic, Igor S. Lukashevich, David M. Stone, Clarence J. Peters, Sheli R. Radoshitzky, Bertus K. Rima, Janusz T. Paweska, Masayuki Horie, Christopher S. Clegg, Victoria Wahl-Jensen, Christopher F. Basler, Sébastian Emonet, Charles H. Calisher, Lin-Fa Wang, Rémi N. Charrel, Jean L. Patterson, Elodie Ghedin, Dennis Rubbenstroth, Dàohóng Jiāng, Sergey V. Netesov, Hélène Sanfaçon, Thomas S. Postler, Ron A. M. Fouchier, Peter L. Collins, Noël Tordo, Maria S. Salvato, John M. Dye, Arcady Mushegian, Sophie J. Smither, Joseph L. DeRisi, Olga Dolnik, Kim R. Blasdell, Balázs Harrach, Viktor E. Volchkov, Thomas Briese, Andrew M. Kropinski, Columbia University College of Physicians and Surgeons, Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Washington University School of Medicine (WUSM), University of Washington [Seattle], Georgia State University, University System of Georgia (USG), Army Medical Research Institute of Infectious Diseases [USA] (USAMRIID), Institute for Soil Sciences and Agricultural Chemistry (ATK TAKI), Centre for Agricultural Research [Budapest] (ATK), Hungarian Academy of Sciences (MTA)-Hungarian Academy of Sciences (MTA), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Columbia Mailman School of Public Health, University of California [Irvine] (UCI), University of California, The University of Texas Medical Branch (UTMB), College of Veterinary Medicine and Biomedical Sciences, Colorado State University [Fort Collins] (CSU), Albert Einstein College of Medicine [New York], Emergence des Pathologies Virales (EPV), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Les Mandinaux, National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Department of Immunology and Microbial Science, Scripps Research Institute, Department of Medicine [San Francisco], University of California [San Francisco] (UCSF), University of California-University of California, Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland [Brisbane], Philipps University of Marburg, IDT Biologika, School of Life Sciences, Warwick University, Unité de Virologie, Institut de Recherche Biomédicale des Armées (IRBA), 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), Health for Development, Public Health England [Salisbury] (PHE), Kagoshima University, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 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, University of Guelph, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], US Geological Survey [Seattle], United States Geological Survey [Reston] (USGS), Northwestern University [Evanston], Centre International de Recherches Médicales de Franceville (CIRMF), Department of Pharmacology and Toxicology, University of Louisville, Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Infectious Disease, University of Texas at Austin [Austin], 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], Texas A&M University System, National Institute for Communicable Diseases [Johannesburg] (NICD), Queen's University [Belfast] (QUB), Instituto de Biotecnología y Biología Molecular [La Plata] (IBBM), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Facultad de Ciencias Exactas [La Plata], Universidad Nacional de la Plata [Argentine] (UNLP)-Universidad Nacional de la Plata [Argentine] (UNLP), University of Freiburg [Freiburg], Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology [Mstate, USA] (BCH-EPP), Mississippi State University [Mississippi], Summerland Research and Development Centre, Agriculture and Agri-Food [Ottawa] (AAFC), University of Maryland School of Medicine, University of Maryland System, Defence Science and Technology Laboratory (Dstl), Ministry of Defence (UK) (MOD), Department of Microbiology, Immunology and Pathology, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Hokkaido University [Sapporo, Japan], Institute for Virus Research, Kyoto University [Kyoto], 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, Bases moléculaires de la pathogénicité virale – Molecular Basis of Viral Pathogenicity (BMPV), Centre International de Recherche en Infectiologie - UMR (CIRI), 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), 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], Center for Fundamental and Applied Microbiomics, Arizona State University [Tempe] (ASU)-Biodesign Institute, Kansas State University, Departamento de Fitopatologia [Viçosa, Brazil] (BIOAGRO), Universidade Federal de Vicosa (UFV), This work was supported in part through Battelle Memorial Institute’s prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272200700016I. A subcontractor to Battelle Memorial Institute who performed this work is J.H.K., an employee of Tunnell Government Services, Inc. This work was also funded in part under National Institutes of Health (NIH) contract HHSN272201000040I/HHSN27200004/D04 and R24AI120942 (N.V., R.B.T.), and the National Science Foundation (NSF) Individual Research and Development (IR/D) program (A.R.M.)., We thank Laura Bollinger (NIH/NIAID Integrated Research Facility at Fort Detrick, Frederick, MD, USA) for critically editing the manuscript, Andrew J. Davison (MRC – University of Glasgow Centre for Virus Research, Glasgow, UK) and Michael J. Adams (Department of Plant Pathology and Microbiology, Rothamsted Research, Harpenden, Herts, UK) of the ICTV Executive Committee for suggestions on manuscript improvement, and Arya Ariël Kuhn for sustained vocal support and (dia)critical remarks, Albert Einstein College of Medicine, Institut Hospitalier Universitaire Méditerranée Infection (IHU AMU), Queensland Alliance for Agriculture and Food Innovation, University of Queensland (UQ), 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], Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Hokkaido University, Bases moléculaires de la pathogénicité virale – Molecular Basis of Viral Pathogenicity, 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, Departamento de Fitopatologia/BIOAGRO, Virology, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Columbia University [New York], University of California [Irvine] (UC Irvine), University of California (UC), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Institut National de la Santé et de la Recherche Médicale (INSERM), The Scripps Research Institute [La Jolla, San Diego], University of California [San Francisco] (UC San Francisco), University of California (UC)-University of California (UC), Philipps Universität Marburg = Philipps University of Marburg, University of Warwick [Coventry], Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Huazhong Agricultural University [Wuhan] (HZAU), Institut Pasteur [Paris] (IP), Agriculture and Agri-Food (AAFC), Kyoto University, 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), and Universidade Federal de Viçosa = Federal University of Viçosa (UFV)
Subjects: 0301 basic medicine, MESH: Terminology as Topic, media_common.quotation_subject, Biología, 030106 microbiology, Binomials, Zoology, Biology, Points of View, 03 medical and health sciences, Genus, Terminology as Topic, Genetics, MESH: Classification, Epithet, Arenaviridae, Ecology, Evolution, Behavior and Systematics, Virus classification, media_common, Order Mononegavirales, Evolutionary Biology, Virus taxonomy, Classification, MESH: Viruses, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Virus nomenclature, Genealogy, Ictv, International committee on taxonomy of viruses, 030104 developmental biology, Homo sapiens, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.IMM]Life Sciences [q-bio]/Immunology, Mononegavirales
Abstract: Botanical, mycological, zoological, and prokaryotic species names follow the Linnaean format, consisting of an italicized Latinized binomen with a capitalized genus name and a lower case species epithet (e.g., Homo sapiens). Virus species names, however, do not follow a uniform format, and, even when binomial, are not Linnaean in style. In this thought exercise, we attempted toconvert all currently official names ofspecies included in the viru sfamily Arenaviridae and the virus order Mononegavirales to Linnaean binomials, and to identify and address associated challenges and concerns. Surprisingly, this endeavor was not as complicated or time-consuming as even the authors of this article expected when conceiving the experiment., La lista completa de autores que integran el documento puede consultarse en el archivo, Instituto de Biotecnologia y Biologia Molecular
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33. Taxonomy of the family Arenaviridae and the order Bunyavirales: update 2018

Author: Thomas Briese, Valerian V. Dolja, Shyi-Dong Yeh, Yīmíng Bào, Marco Marklewitz, Rakesh K. Jain, Thiện Hồ, Ioannis E. Tzanetakis, Yàzhōu Zhèng, Robert R. Martin, Tobiasz Druciarek, Janusz T. Paweska, S. V. Alkhovsky, Li Yang, Bradley S. Schneider, Beatriz Navarro, Nikos Vasilakis, Amethyst Gillis, Eugene V. Koonin, Petrus Jansen van Vuren, Michael J. Buchmeier, Francesco Di Serio, Takahide Sasaya, Wenxing Xu, Clarence J. Peters, Amy J. Lambert, Zuòkūn Yāng, Eric Delwart, Peter J. Walker, Charles H. Calisher, Florian Zirkel, Igor S. Lukashevich, Matthew LeBreton, Zhìqiáng Wú, Jean-Paul J. Gonzalez, Pertteli Salmenperä, Rémi N. Charrel, Márcio Roberto Teixeira Nunes, Liping Wang, Chénxī Zhū, Miranda Gilda Jonson, Juan Carlos de la Torre, Anja Kipar, Nicole Mielke-Ehret, Alan Kemp, Christopher S. Clegg, Nadia Storm, Víctor Romanowski, Guoping Wang, Olli Vapalahti, Jiang Du, Martin Beer, Qi Jin, Giovanni P. Martelli, Michael R. Wiley, Hélène Sanfaçon, Piet Maes, Mart Krupovic, Anne-Lise Haenni, Richard Kormelink, Rose C. Gergerich, Terry Fei Fan Ng, Toufic Elbeaino, Udo Hetzel, Ni Hong, Wanda Markotter, Yuri I. Wolf, Gustavo Palacios, Yanxiang Wang, Michele Digiaro, Connie S. Schmaljohn, Yukio Shirako, Mark D. Stenglein, Patrick L. Di Bello, Jussi Hepojoki, Alma G. Laney, Maria S. Salvato, Hideki Ebihara, Taiyun Wei, Sandra Junglen, Nathan D. Wolfe, Monica Birkhead, H.-P. Mühlbach, Stuart G. Siddell, Christian Drosten, Nikola O. Kondov, Hari Kishan Sudini, Joseph L. DeRisi, Mangala Uppala, Tarja Sironen, Jens H. Kuhn, Yǒng-Zhèn Zhāng, Karen E. Keller, Alexander Plyusnin, Yegor Korzyukov, Xueping Zhou, Il-Ryong Choi, Sheli R. Radoshitzky, Robert B. Tesh, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Gamaleya Research Center, Chinese Academy of Sciences [Beijing] (CAS), Friedrich-Loeffler-Institut (FLI), National Institute for Communicable Diseases [Johannesburg] (NICD), Columbia University [New York], Synopsys Inc., Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food (AAFC), Department of Biology, University of Western Ontario (UWO), Metabiota Inc. [San Francisco], East China Jiaotong University (ECJU), 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 Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Aix Marseille Université (AMU), International Rice Research Institute [Philippines] (IRRI), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Blood Systems Research Institute, University of California [San Francisco] (UC San Francisco), University of California (UC)-University of California (UC), Department of Laboratory Medicine [San Francisco], Universität Bonn = University of Bonn, Laboratory of Virology, Division of Intramural Research [Hamilton], National Institute of Allergy and Infectious Diseases (NIAID) (NIAID), Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), School of Ocean and Earth Sciences (SOES-NOC), University of Southampton, National Center for Biotechnology Information (NCBI), Laboratory of Virology [Wageningen], Wageningen University and Research [Wageningen] (WUR), Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), Mosaic, University of Pretoria [South Africa], Department of Arbovirology and Hemorrhagic Fevers, Instituto Evandro Chagas, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Department of Virology [Helsinki], Haartman Institute [Helsinki], Faculty of Medecine [Helsinki], Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Faculty of Medecine [Helsinki], Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Instituto de Biotecnología y Biología Molecular [La Plata] (IBBM), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Facultad de Ciencias Exactas [La Plata], Universidad Nacional de la Plata [Argentine] (UNLP)-Universidad Nacional de la Plata [Argentine] (UNLP), Pacific Agri-Food Research Center, Divison of Plant Protection, National Agricultural Research Center, National Agricultural Research Center, The University of Texas Medical Branch (UTMB), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), This work was supported in part through Battelle Memorial Institute’s prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272200700016I (J.H.K.). This work was also funded in part by National Institutes of Health (NIH) contract HHSN272201000040I/HHSN27200004/D04 and Grant R24AI120942 (N.V., R.B.T.), intramural funds of the US Department of Health and Human Services to the US National Library of Medicine (E.V.K. and Y.I.W.), and the 100-Talent Program of the Chinese Academy of Sciences, the National Key R&D Program of China (2016YFE0206600) and the International Union of Biological Sciences (Y.B.)., We thank Laura Bollinger (NIH/NIAID Integrated Research Facility at Fort Detrick, Frederick, MD, USA) and F. Murilo Zerbini (BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil) for critically editing the manuscript., National Institute for Communicable Diseases (NICD), Agriculture and Agri-Food [Ottawa] (AAFC), Metabiota Inc., Institut Hospitalier Universitaire Méditerranée Infection (IHU AMU), International Rice Research Institute (IRRI), Consultative Group on International Agricultural Research [CGIAR], University of California [San Francisco] (UCSF), University of California-University of California, Department of Laboratory Medicine, University of Bonn, Wageningen University and Research Centre [Wageningen] (WUR), Institut Pasteur [Paris], Department of Microbiology and Plant Pathology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa, Department of Microbiology and Plant Pathology, Faculty of Natural and Agricultural Sciences, University of Pretoria, U.S. Army Medical Research Institute of Infectious Diseases, University of Helsinki-University of Helsinki-Faculty of Medecine [Helsinki], University of Helsinki-University of Helsinki, Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD)-Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Virology, Doctoral Programme in Clinical Veterinary Medicine, Viral Zoonosis Research Unit, Medicum, University of Helsinki, Veterinary Pathology and Parasitology, Veterinary Biosciences, Doctoral Programme in Drug Research, Doctoral Programme in Food Chain and Health, Veterinary Microbiology and Epidemiology, Olli Pekka Vapalahti / Principal Investigator, Clinicum, and Emerging Infections Research Group
Subjects: 0301 basic medicine, MESH: Arenaviridae Infections/virology, Arenaviridae, [SDV]Life Sciences [q-bio], Biología, Laboratory of Virology, MYCOVIRUSES, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, MESH: Arenaviridae/isolation & purification, ICTV, Bunyavirales / classifica??o, Bunyavirales, MESH: Animals, MESH: Phylogeny, MESH: Arenaviridae/genetics, Phylogeny, General Medicine, humanities, Genealogy, INCLUSION-BODY DISEASE, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, VIRUS, Taxonomy (biology), CIENCIAS NATURALES Y EXACTAS, AFRICA, Classifica??o / m?todos, 030106 microbiology, Family Arenaviridae, ORDER BUNYAVIRALES, FAMILY ARENAVIRIDAE, DIVERGENT, Biology, Bunyaviridae / classifica??o, EMARAVIRUS, Ciencias Biológicas, Laboratorium voor Virologie, 03 medical and health sciences, Virology, Life Science, Animals, Arenaviridae Infections, Humans, Ciencias Exactas, SNAKES, MESH: Arenaviridae Infections/veterinary, Taxonomy, V?rus de RNA / gen?tica, MESH: Humans, IDENTIFICATION, TAXONOMY, Arenaviridae / classifica??o, 030104 developmental biology, DISCOVERY, 3111 Biomedicine, EPS, MESH: Arenaviridae/classification, Infections Humans, Virología
Abstract: In 2018, the family Arenaviridae was expanded by inclusion of 1 new genus and 5 novel species. At the same time, the recently established order Bunyavirales was expanded by 3 species. This article presents the updated taxonomy of the family Arenaviridae and the order Bunyavirales 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., La lista completa de autores que integran el documento puede consultarse en el archivo., Facultad de Ciencias Exactas, Instituto de Biotecnologia y Biologia Molecular
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33 results on '"The University of Texas Medical Branch ( UTMB )"'

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33. Taxonomy of the family Arenaviridae and the order Bunyavirales: update 2018

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