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2. The Immune Epitope Database and Analysis Resource

Author

Sette, A., Bui, H. H., Sidney, J., Bourne, P., Buus, S., Fleri, W., Kubo, R., Lund, O., Nemazee, D., Ponomarenko, J. V., Sathiamurthy, M., Stewart, S., Way, S., Wilson, S. S., Peters, B., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael, editor, Rajapakse, Jagath C., editor, Wong, Limsoon, editor, and Acharya, Raj, editor

Published
2006
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3. The HPV Induced Cancer Resource (THInCR): a Suite of Tools for Investigating HPV-Dependent Human Carcinogenesis.

Author

Salnikov M, Gameiro SF, Zeng PYF, Barrett JW, Nichols AC, and Mymryk JS

Subjects
Carcinogenesis genetics, Humans, Papillomaviridae genetics, RNA, Messenger, Squamous Cell Carcinoma of Head and Neck, Head and Neck Neoplasms genetics, MicroRNAs genetics, Papillomavirus Infections complications, Papillomavirus Infections pathology
Abstract

Human papillomaviruses (HPVs) are highly infectious and cause the most common sexually transmitted viral infections. They induce hyperproliferation of squamous epithelial tissue, often forming warts. Virally encoded proteins reprogram gene expression and cell growth to create an optimal environment for viral replication. In addition to their normal roles in infection, functional alterations induced by viral proteins establish conditions that frequently contribute to human carcinogenesis. In fact, ~5% of human cancers are caused by HPVs, with virtually all cervical squamous cell carcinomas (CESC) and an increasing number of head and neck squamous cell carcinomas (HNSC) attributed to HPV infection. The Cancer Genome Atlas (TCGA) molecularly characterized thousands of primary human cancer samples in many cancer types, including CESC and HNSC, and created a comprehensive atlas of genomic, epigenomic, and transcriptomic data. This publicly available genome-wide information provides an unprecedented opportunity to expand the knowledge of the role that HPV plays in human carcinogenesis. While many tools exist to mine these data, few, if any, focus on the comparison of HPV-positive cancers with their HPV-negative counterparts or adjacent normal control tissue. We have constructed a suite of web-based tools, The HPV Induced Cancer Resource (THInCR), to utilize TCGA data for research related to HPV-induced CESC and HNSC. These tools allow investigators to gain greater biological and medical insights by exploring the impacts of HPV on cellular gene expression (mRNA and microRNA), altered gene methylation, and associations with patient survival and immune landscape features. These tools are accessible at https://thincr.ca/. IMPORTANCE The suite of analytical tools of THInCR provides the opportunity to investigate the roles that candidate target genes identified in cell lines or other model systems contribute to in actual HPV-dependent human cancers and is based on large-scale TCGA data sets. Expression of target genes, including both mRNA and microRNA, can be correlated with HPV gene expression, epigenetic changes in DNA methylation, patient survival, and numerous immune features, like leukocyte infiltration, interferon gamma response, T cell response, etc. Data from these analyses may immediately provide evidence to validate in vitro observations, reveal insights into mechanisms of virus-mediated alterations in cell growth, behavior, gene expression, and innate and adaptive immunity and may help hypothesis generation for further investigations.

Published
2022
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4. Brucella spp. of amphibians comprise genomically diverse motile strains competent for replication in macrophages and survival in mammalian hosts

Author

Al Dahouk, Sascha, Koehler, Stephan, Occhialini, Alessandra, Jimenez de Bagues, Maria Pilar, Hammerl, Jens Andre, Eisenberg, Tobias, Vergnaud, Gilles, Cloeckaert, Axel, Zygmunt, Michel S., Whatmore, Adrian M., Melzer, Falk, Drees, Kevin P., Foster, Jeffrey T., Wattam, Alice R., Scholz, Holger C., Al Dahouk, Sascha, Koehler, Stephan, Occhialini, Alessandra, Jimenez de Bagues, Maria Pilar, Hammerl, Jens Andre, Eisenberg, Tobias, Vergnaud, Gilles, Cloeckaert, Axel, Zygmunt, Michel S., Whatmore, Adrian M., Melzer, Falk, Drees, Kevin P., Foster, Jeffrey T., Wattam, Alice R., and Scholz, Holger C.

Abstract

Twenty-one small Gram-negative motile coccobacilli were isolated from 15 systemically diseased African bullfrogs (Pyxicephalus edulis), and were initially identified as Ochrobactrum anthropi by standard microbiological identification systems. Phylogenetic reconstructions using combined molecular analyses and comparative whole genome analysis of the most diverse of the bullfrog strains verified affiliation with the genus Brucella and placed the isolates in a cluster containing B. inopinata and the other non-classical Brucella species but also revealed significant genetic differences within the group. Four representative but molecularly and phenotypically diverse strains were used for in vitro and in vivo infection experiments. All readily multiplied in macrophage-like murine J774-cells, and their overall intramacrophagic growth rate was comparable to that of B. inopinata BO1 and slightly higher than that of B. microti CCM 4915. In the BALB/c murine model of infection these strains replicated in both spleen and liver, but were less efficient than B. suis 1330. Some strains survived in the mammalian host for up to 12 weeks. The heterogeneity of these novel strains hampers a single species description but their phenotypic and genetic features suggest that they represent an evolutionary link between a soil-associated ancestor and the mammalian host-adapted pathogenic Brucella species.

Published
2017
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5. Scientific Reports

Author

Al Dahouk, Sascha, Köhler, Stephan, Occhialini, Alessandra, Jiménez de Bagüés, María Pilar, Hammerl, Jens Andre, Eisenberg, Tobias, Vergnaud, Gilles, Cloeckaert, Axel, Zygmunt, Michel, Whatmore, Adrian, Melzer, Falk, Drees, Kevin, Foster, Jeffrey, Wattam, Alice, Scholz, Holger, Department of Biological Safety, Bundesinstitut für Risikobewertung - Federal Institute for Risk Assessment (BfR), Institut de Recherche en Infectiologie de Montpellier (IRIM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Unidad de Producción y Sanidad Animal, Centro de Investigación y Tecnología Agroalimentaria, Instituto Agroalimentario de Aragón, University of Zaragoza - Universidad de Zaragoza [Zaragoza], Landesbetrieb Hessisches Landeslabor, Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Infectiologie Animale et Santé Publique - IASP (Nouzilly, France), Institut National de la Recherche Agronomique (INRA), German National Reference Laboratory for Animal Brucellosis, Federal Research Institute for Animal Health - Friedrich-Loeffler-Institut, Northern Arizona University [Flagstaff], Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre d’études d’Agents Pathogènes et Biotechologies pour la Santé (CPBS), Université Paris Sud (Paris 11), Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université Paris-Saclay, Animal and Plant Health Agency (APHA), Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire (UNH), Biocomplexity Institute of Virginia Tech [Blacksburg], Virginia Tech [Blacksburg], Bundeswehr Institute of Microbiology, Federal funds from National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services HHSN272201400027C, Spanish grant INIA-RTA2013-00065-C02-01, Federal Institute for Risk Assessment, Germany 1329-485, Food and Rural Affairs at German Federal Institute SE0314 SE0316, Department of Environment, Federal Ministry of Food and Agriculture 47-003 1322-503 1322-619, Hessian Ministry of Environment, Climate Change, Agriculture and Consumer Protection, French DGA (Direction Generale de l'Armement) via the MicroType project ANR-14-ASMA-0002-02, European Defence Agency (EDA), Université de Montpellier (UM), UR Infectiologie animale et Santé publique (UR IASP), Bundeswehr Institute of Microbiology, Department of Bacteriology, Munich, Germany, RWTH Aachen University, Centro de Investigacion y Tecnologia Agroalimentaria de Aragon (CITA), 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), Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), Animal and Plant Health Agency [Addlestone, UK] (APHA), Friedrich-Loeffler-Institut (FLI), German Center for Infection Research, Partnersite Munich (DZIF), Rheinisch-Westfälische Technische Hochschule Aachen University (RWTH), Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), and Institut National de la Recherche Agronomique (INRA)-Université de Tours

Subjects
phylogénétique, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, [SDV]Life Sciences [q-bio], analysis resource, murine models, Tanzania, Mice, Germany, phénotypage, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), Transmisión de enfermedades, Phylogeny, Mice, Inbred BALB C, amphibians, monocyte-derived macrophages, lipopolysaccharide, comparative sequence, mammifère, genetic diversity, Brucelosis, Biological Evolution, Brucellaceae, bacterial bioinformatics database, melitensis 16m, vole microtus-arvalis, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Liver, Flagella, Host-Pathogen Interactions, Anura, Autre (Sciences du Vivant), [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Biotechnologies, macrophage, Anfibios, brucella spp, Article, Cell Line, Genetic Heterogeneity, Bacterial Proteins, death, Animals, mammals, analyse moléculaire, Mamíferos, Macrophages, amphibien, Gene Expression Regulation, Bacterial, Brucella, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, infection, Producción y sanidad animal, Animals, Zoo, souche bactérienne, Gram-Negative Bacterial Infections, Spleen, Multilocus Sequence Typing
Abstract

Scientific reports 7, 44420 (2017). doi:10.1038/srep44420, Published by Nature Publishing Group, London

Published
2017
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7. Complete Genome and Phylogeny of Puumala Hantavirus Isolates Circulating in France

Author

Mathilde Couteaudier, Noël Tordo, Guillaume Castel, Dominique Pontier, Angelina Plyusnina, Frank Sauvage, Alexander Plyusnin, Jean-Baptiste Pons, Jean-François Cosson, Séverine Murri, Philippe Marianneau, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Ecoevolutionary Dynamics of Infectious Diseases, LabEx ECOFECT, Laboratoire de Lyon, Unité Virologie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Department of Virology [Helsinki], Haartman Institute [Helsinki], Faculty of Medecine [Helsinki], University of Helsinki-University of Helsinki-Faculty of Medecine [Helsinki], University of Helsinki-University of Helsinki, Ecoépidémiologie évolutionniste, Département écologie évolutive [LBBE], Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire d'Alfort (ENVA)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Centre collaborateur de l'OMS Arbovirus et Fièvres Hémorragiques virales - Stratégies antivirales (CC-OMS), Institut Pasteur [Paris], project ECOFECT (ANR-11-LABX-0048, ANR-11-IDEX-0007) - Anses (Afsset grant EST-2007-75) - EU grants FP7-261504 EDENext - FP7- 278976 ANTIGONE, European Project: 261504, 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, École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université de Tours, Unité Virologie, Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Institut Pasteur [Paris] (IP), Medicum, Department of Virology, Castel, Guillaume, Centre de Biologie pour la Gestion des Populations (CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD) - Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro) - Institut national de la recherche agronomique [Montpellier] (INRA Montpellier) - Université de Montpellier (UM) - Institut de Recherche pour le Développement (IRD [France-Sud]), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD) - Institut National de la Recherche Agronomique (INRA) - Institut National de Recherche en Informatique et en Automatique (Inria) - Université de Montpellier (UM) - Centre National de la Recherche Scientifique (CNRS), UR Infectiologie animale et Santé publique (UR IASP), Institut National de la Recherche Agronomique (INRA), Laboratoire de Biométrie et Biologie Evolutive (LBBE), Université Claude Bernard Lyon 1 (UCBL) - Institut National de Recherche en Informatique et en Automatique (Inria) - Centre National de la Recherche Scientifique (CNRS), Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail (ANSES Maisons-Alfort), Haartman Institute, Institut National de la Recherche Agronomique (INRA) - Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12) - Ecole Nationale Vétérinaire d'Alfort - AFSSA, ANR-11-IDEX-0007-02/11-LABX-0048, ECOFECT, Dynamiques eco-évolutives des maladies infectieuses(2011), European Project : 261504, EC:FP7:HEALTH, FP7-HEALTH-2010-single-stage, EDENEXT(2011), and European Project : 278976, EC:FP7:HEALTH, FP7-HEALTH-2011-two-stage, ANTIGONE(2011)

Subjects
Male, Disease reservoir, [SDV]Life Sciences [q-bio], TULA, lcsh:QR1-502, Sequence Homology, phylogeny, Puumala virus, lcsh:Microbiology, INFECTION, Nephropathia epidemica, Cluster Analysis, biology, Arvicolinae, MAJOR ANTIGENIC DOMAIN, 3. Good health, [SDV] Life Sciences [q-bio], Bank vole, Phylogeography, Infectious Diseases, diversité génétique, ANALYSIS RESOURCE, RNA, Viral, Female, France, Hantavirus, GENETICS, BIOINFORMATICS DATABASE, Molecular Sequence Data, complete genome, Zoology, Genome, Viral, analyse phylogénétique, Article, diversity, Phylogenetics, Virology, Genetic variation, medicine, Animals, Disease Reservoirs, technique elisa, VIRUS NUCLEOCAPSID PROTEIN, STRAINS, Sequence Analysis, DNA, biology.organism_classification, medicine.disease, MOLECULAR EVOLUTION, PATTERNS, campagnol roussatre, 3111 Biomedicine
Abstract

Puumala virus (PUUV) is the agent of nephropathia epidemica (NE), a mild form of hemorrhagic fever with renal syndrome (HFRS) in Europe. NE incidence presents a high spatial variation throughout France, while the geographical distribution of the wild reservoir of PUUV, the bank vole, is rather continuous. A missing piece of the puzzle is the current distribution and the genetic variation of PUUV in France, which has been overlooked until now and remains poorly understood. During a population survey, from 2008 to 2011, bank voles were trapped in eight different forests of France located in areas known to be endemic for NE or in area from where no NE case has been reported until now. Bank voles were tested for immunoglobulin (Ig)G ELISA serology and two seropositive animals for each of three different areas (Ardennes, Jura and Orleans) were then subjected to laboratory analyses in order to sequence the whole S, M and L segments of PUUV. Phylogenetic analyses revealed that French PUUV isolates globally belong to the central European (CE) lineage although isolates from Ardennes are clearly distinct from those in Jura and Orleans, suggesting a different evolutionary history and origin of PUUV introduction in France. Sequence analyses revealed specific amino acid signatures along the N protein, including in PUUV from the Orleans region from where NE in humans has never been reported. The relevance of these mutations in term of pathophysiology is discussed.

Published
2015
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8. The Immune Epitope Database and Analysis Resource

Author

Rajapakse J, Wong L, Acharya R, Sette A, Bui H, Sidney J, Bourne P, Buus S, Fleri W, Kubo R, Lund O, Nemazee D, Julia Ponomarenko, Sathiamurthy M, and Peters B

Subjects
Antibody Epitope, Analysis Resource, Epitope Prediction, Article, Enterprise Architecture, Cell Epitope
Abstract

Epitopes are defined as the molecular structures interacting with specific receptors of the immune system such as antibodies, MHC, and T cell receptor molecules. The Immune Epitope Database and Analysis Resource (IEDB, http://www.immuneepitope.org) is a database specifically devoted to immune epitope data. The database is populated with intrinsic and context-dependent epitope data curated from the scientific literature by immunologists, biochemists, and microbiologists. An analysis resource is linked to the database which hosts various bioinformatics tools to analyze epitope data as well as to predict de novo epitopes. The availability of the IEDB will facilitate the exploration of immunity to infectious diseases, allergies, autoimmune diseases, and cancer. The utility of the IEDB was recently demonstrated through a comprehensive analysis of all current information regarding antibody and T cell epitopes derived from influenza A and determining possible cross-reactivity among H5N1 avian flu and human flu viruses.

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