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1,244 results on '"Université d'Auvergne - Clermont-Ferrand I [UdA]"'

1. Dual AAV-mediated gene therapy restores hearing in a DFNB9 mouse model

Author

Omar Akil, Saaid Safieddine, Jacques Boutet de Monvel, Charlotte Calvet, Frank M. Dyka, Ghizlene Lahlou, Sylvie Nouaille, Jean-Pierre Hardelin, Paul Avan, Alice Emptoz, Christine Petit, William W. Hauswirth, Lawrence R. Lustig, University of California [San Francisco] (UC San Francisco), University of California (UC), University of Florida [Gainesville] (UF), Génétique et Physiologie de l'Audition, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), ED 515 - Complexité du vivant, Sorbonne Université (SU), Institut de l'Audition [Paris] (IDA), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Equipe Biophysique Neurosensorielle [Neuro-Dol], Neuro-Dol (Neuro-Dol), Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Neuro-Dol (Neuro-Dol), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Collège de France - Chaire Génétique et physiologie cellulaire, Collège de France (CdF (institution)), Columbia University Medical Center (CUMC), Columbia University [New York], This work was supported by the Hearing Research Incorporation (O.A.), Fondation pour la Recherche Médicale (A.E.), Région Ile de France (DIM Thérapie génique), the European Union Seventh Framework Programme under the Grant Agreement HEALTH-F2-2010-242013 (TREAT RUSH), the French government funds managed by Agence Nationale de la Recherche (EargenCure), and LabEx Lifesenses (ANR-10-BNP Paribas Foundation, FAUN Stiftung, LHW Stiftung, and Mrs. Errera Hoechstetter)., ANR-17-CE18-0027,EARGENCURE,Restauration, par thérapie génique, de l'audition et de l'équilibre chez des souris modèles de surdités et troubles vestibulaires humains(2017), ANR-11-IDEX-0004,SUPER,Sorbonne Universités à Paris pour l'Enseignement et la Recherche(2011), European Project: 242013,EC:FP7:HEALTH,FP7-HEALTH-2009-single-stage,TREATRUSH(2010), University of California [San Francisco] (UCSF), University of California, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), and Chaire Génétique et physiologie cellulaire

Subjects
Medical Sciences, [SDV]Life Sciences [q-bio], Genetic enhancement, Genetic Vectors, Mutant, Mice, Transgenic, Biology, law.invention, Mice, otoferlin, 03 medical and health sciences, 0302 clinical medicine, law, deafness, Complementary DNA, otorhinolaryngologic diseases, DFNB9, Animals, Humans, Coding region, Vector (molecular biology), Gene, 030304 developmental biology, 0303 health sciences, Multidisciplinary, Membrane Proteins, Genetic Therapy, Biological Sciences, Dependovirus, gene therapy, Phenotype, Cell biology, Mice, Inbred C57BL, Disease Models, Animal, Recombinant DNA, dual AAV, 030217 neurology & neurosurgery
Abstract

Significance In humans, inner ear development is completed in utero, with hearing onset at ∼20 weeks of gestation. However, genetic forms of congenital deafness are typically diagnosed during the neonatal period. Gene therapy approaches in animal models should therefore be tested after the period of hearing onset, to determine whether they can reverse an existing deafness phenotype. Here, we used a mouse model of DFNB9, a human deafness form accounting for 2–8% of all cases of congenital genetic deafness. We show that local gene therapy in the mutant mice not only prevents deafness when administered to immature hearing organs, but also durably restores hearing when administered at a mature stage, raising hopes for future gene therapy trials in DFNB9 patients., Autosomal recessive genetic forms (DFNB) account for most cases of profound congenital deafness. Adeno-associated virus (AAV)-based gene therapy is a promising therapeutic option, but is limited by a potentially short therapeutic window and the constrained packaging capacity of the vector. We focus here on the otoferlin gene underlying DFNB9, one of the most frequent genetic forms of congenital deafness. We adopted a dual AAV approach using two different recombinant vectors, one containing the 5′ and the other the 3′ portions of otoferlin cDNA, which exceed the packaging capacity of the AAV when combined. A single delivery of the vector pair into the mature cochlea of Otof−/− mutant mice reconstituted the otoferlin cDNA coding sequence through recombination of the 5′ and 3′ cDNAs, leading to the durable restoration of otoferlin expression in transduced cells and a reversal of the deafness phenotype, raising hopes for future gene therapy trials in DFNB9 patients.

Published
2019

2. Stimulation or inhibition: Leaf microbial decomposition in streams subjected to complex chemical contamination

Author

Joan Artigas, Christophe Portelli, Florence Donnadieu, Frédérique Bonnemoy, Clarisse Mallet, Florent Rossi, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Environmental Engineering, 010504 meteorology & atmospheric sciences, 010501 environmental sciences, Alnus, [SDV.MP.PRO]Life Sciences [q-bio]/Microbiology and Parasitology/Protistology, 01 natural sciences, Pesticide toxicity, Nutrient, Rivers, [CHIM]Chemical Sciences, Environmental Chemistry, Ecosystem, Cities, Waste Management and Disposal, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, 2. Zero hunger, Biomass (ecology), biology, fungi, Agriculture, Forestry, 15. Life on land, Plant litter, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDE.ES]Environmental Sciences/Environmental and Society, Pollution, people.cause_of_death, 6. Clean water, Food web, Plant Leaves, Alnus glutinosa, Biodegradation, Environmental, Microbial population biology, 13. Climate action, Environmental chemistry, Environmental science, France, Seasons, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, people, Water Pollutants, Chemical
Abstract

Leaf litter decomposition is a key mechanism in headwater streams, allowing the transfer of nutrients and energy into the entire food web. However, chemical contamination resulting from human activity may exert a high pressure on the process, possibly threatening the structure of heterotrophic microbial communities and their decomposition abilities. In this study, the rates of microbial Alnus glutinosa (Alnus) leaf decay were assessed in six French watersheds displaying different land use (agricultural, urbanized, forested) and over four seasons (spring, summer, autumn, winter). In addition, for each watershed at each sampling time, both upstream (less-contaminated) and downstream (more-contaminated) sections were monitored. Toxicities (estimated as toxic units) predicted separately for pesticides and pharmaceuticals as well as environmental parameters (including nutrient levels) were related to microbial decay rates corrected for temperature and a range of fungal and bacterial community endpoints, including biomass, structure, and activity (extracellular ligninolytic and cellulolytic enzymatic activities). Results showed that agricultural and urbanized watersheds were more contaminated for nutrients and xenobiotics (higher pesticides and pharmaceuticals predicted toxicity) than forested watersheds. However, Alnus decay rates were higher in agricultural and urbanized watersheds, suggesting compensatory effects of nutrients over xenobiotics. Conversely, fungal biomass in leaves was 2-fold and 1.4-fold smaller in urbanized and agricultural watersheds than in the forested watersheds, respectively, which was mostly related to pesticide toxicity. However, no clear pattern was observed for extracellular enzymatic activities except that β-glucosidase activity positively correlated with Alnus decay rates. Together, these results highlight microbial communities being more efficient for leaf decomposition in polluted watersheds than in less contaminated ones, which is probably explained by changes in microbial community structure. Overall, our study showed that realistic chemical contamination in stream ecosystems may affect the biomass of Alnus-associated microbial communities but that these communities can adapt themselves to xenobiotics and maintain ecosystem functions.

Published
2019

3. Two Metabolomics Phenotypes of Human Hepatocellular Carcinoma in Non-Alcoholic Fatty Liver Disease According to Fibrosis Severity

Author

Robert Sabatier, Natali Abeywickrama Samarakoon, S. Massoulier, Benjamin Buchard, Camille Teilhet, Marie-Paule Vasson, Armando Abergel, Aicha Demidem, Juliette Joubert-Zakeyh, Christelle Reynes, Corinne Blouin, Anne-Sophie Biesse-Martin, CHU Clermont-Ferrand, Unité de Nutrition Humaine (UNH), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Service RMN (UBP-START), Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Image Science for Interventional Techniques (ISIT), Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS)-Clermont Université, Program Canceropole Lyon Auvergne Rhone AlpesOncostarter 'MECASTEN', Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université d'Auvergne - Clermont-Ferrand I (UdA)-Clermont Université-Centre National de la Recherche Scientifique (CNRS), and ROSSI, Sabine

Subjects
Cirrhosis, Endocrinology, Diabetes and Metabolism, lcsh:QR1-502, Biology, Biochemistry, lcsh:Microbiology, Article, 03 medical and health sciences, Liver disease, 0302 clinical medicine, Metabolomics, Fibrosis, medicine, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, neoplasms, Fatty liver, fibrosis, non-alcoholic fatty liver disease, medicine.disease, Phenotype, metabolomics, digestive system diseases, 3. Good health, Glutamine, nuclear magnetic resonance, hepatocarcinoma, 030220 oncology & carcinogenesis, Hepatocellular carcinoma, Cancer research, 030211 gastroenterology & hepatology
Abstract

International audience; Non-Alcoholic Fatty Liver Disease (NAFLD) is considered as the forthcoming predominant cause for hepatocellular carcinoma (HCC). NAFLD-HCC may rise in non-cirrhotic livers in 40 to 50% of patients. The aim of this study was to identify different metabolic pathways of HCC according to fibrosis level (F0F1 vs. F3F4). A non-targeted metabolomics strategy was applied. We analyzed 52 pairs of human HCC and adjacent non-tumoral tissues which included 26 HCC developed in severe fibrosis or cirrhosis (F3F4) and 26 in no or mild fibrosis (F0F1). Tissue extracts were analyzed using 1H-Nuclear Magnetic Resonance spectroscopy. An optimization evolutionary method based on genetic algorithm was used to identify discriminant metabolites. We identified 34 metabolites differentiating the two groups of NAFLD-HCC according to fibrosis level, allowing us to propose two metabolomics phenotypes of NAFLD-HCC. We showed that HCC-F0F1 mainly overexpressed choline derivatives and glutamine, whereas HCC-F3F4 were characterized by a decreased content of monounsaturated fatty acids (FA), an increase of saturated FA and an accumulation of branched amino acids. Comparing HCC-F0F1 and HCC-F3F4, differential expression levels of glucose, choline derivatives and phosphoethanolamine, monounsaturated FA, triacylglycerides were identified as specific signatures. Our metabolomics analysis of HCC tissues revealed for the first time two phenotypes of HCC developed in NAFLD according to fibrosis level. This study highlighted the impact of the underlying liver disease on metabolic reprogramming of the tumor.

Published
2021

4. Trophic conditions influence widespread distribution of Aster-Like nanoparticles within aquatic environments

Author

Télesphore Sime-Ngando, Hermine Billard, Marie Mandart, Maxime Fuster, Jonathan Colombet, Johannes Steiger, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Unité de Nutrition Humaine (UNH), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Géographie Physique et Environnementale (GEOLAB), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Université Clermont Auvergne (UCA)-Institut Sciences de l'Homme et de la Société (IR SHS UNILIM), Université de Limoges (UNILIM)-Université de Limoges (UNILIM)-Centre National de la Recherche Scientifique (CNRS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut Sciences de l'Homme et de la Société (IR SHS UNILIM), Université de Limoges (UNILIM)-Université de Limoges (UNILIM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), and ANR-16-IDEX-0001,CAP 20-25,CAP 20-25(2016)

Subjects
0301 basic medicine, Ecology (disciplines), [SDE.MCG]Environmental Sciences/Global Changes, 030106 microbiology, Soil Science, Distribution (economics), 03 medical and health sciences, Microbial ecology, Rivers, Abundance (ecology), Femtoplankton, 14. Life underwater, Aster (genus), Ecology, Evolution, Behavior and Systematics, Ecosystem, ComputingMilieux_MISCELLANEOUS, Trophic level, Ecology, biology, business.industry, Aquatic ecosystem, Widespread distribution, Aquatic environment, ALNs, [SHS.GEO]Humanities and Social Sciences/Geography, biology.organism_classification, [SDE.ES]Environmental Sciences/Environmental and Society, Geographic distribution, 030104 developmental biology, Prokaryotic Cells, [SDE]Environmental Sciences, Nanoparticles, France, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business
Abstract

International audience; Aster-like nanoparticles (ALNs) are newly described femto-entities. Their ecology (e.g., geographic distribution, spatial dynamic, preferences, forcing factors) is still unknown. Here, we report that these entities, which have largely been ignored until now, can develop or maintain themselves in most aquatic environments in the Loire River catchment, France. We observed a significant influence of the trophic state on ALN ecological distributions. A positive relationship between prokaryotic abundance and ALN (r(2) = 0.72,p < 0.01) has been identified, but its exact nature remains to be clarified. Combined with their ubiquitous distribution and high abundances (up to 7.9 x 10(6) ALNs mL(-1)) recorded in our samples, this probably makes ALNs an overlooked functional component in aquatic ecosystems.

Published
2020

5. Epidemiological investigation for grouped cases of Trichosporon asahii using whole genome and IGS1 sequencing

Author

N. Brieu, B. Sendid, E. Sitterle, Frédéric Gabriel, I. Poilane, D. Moissenet, Christine Aznar, V. Blanc, N. Traversier, M. Sasso, N. Godineau, O. Eloy, Corinne Maufrais, Danièle Maubon, H. Rabérin, C. Lawrence, P. Mariani, P. Cahen, C. Bonnal, B. Bouteille, M. Cornet, F. Moriot, B. Heym, Elisabeth Chachaty, Dominique Toubas, M. Nicolas, Sophie Cassaing, A. Paugam, S. Picot, E. Moalic, Adela Angoulvant, Loïc Favennec, Françoise Dromer, M. Gari‐toussaint, Marc Pihet, Taieb Chouaki, Magalie Pierre Demar, Frédéric Grenouillet, N. Fauchet, L. Collet, Frédéric Dalle, Marie-Elisabeth Bougnoux, Céline Nourrisson, Marie Desnos-Ollivier, O. Faure, Françoise Botterel, C. Nabet, N. Bourgeois, E. Bailly, Dorothée Quinio, Alexandre Alanio, O. Mouquet, S. Brun, S. Bland, Julie Bonhomme, Jean-Pierre Gangneux, Stéphane Ranque, Philippe Poirier, N. Desbois, Florence Persat, Anne-Pauline Bellanger, H. Piarroux, E. Forget, L. Lachaux, V. Bru, Laurence Millon, A. Minoza, C. Kauffman, L. Hasseine, Martine Wallon, A.L. Roux, D. Poisson, S. Bonacorsi, Mycologie moléculaire - Molecular Mycology, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Centre d'Informatique pour la Biologie, Institut Pasteur [Paris], Laboratoire de Parasitologie-Mycologie (CHU d'Angers), Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM)-PRES Université Nantes Angers Le Mans (UNAM), Groupe d'Étude des Interactions Hôte-Pathogène (GEIHP), Université d'Angers (UA), SFR UA 4208 Interactions Cellulaires et Applications Thérapeutiques (ICAT), Laboratoire Hospitalo-Universitaire de Parasitologie-Mycologie, Coordination Régionale de la lutte contre le Virus de L'Immunodéficience Humaine (COREVIH)-Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française]-Université des Antilles (UA), Observatoires Régionaux du Pneumocoque, Partenaires INRAE, Université de Picardie Jules Verne (UPJV), Service de parasitologie et mycologie [CHRU de Besançon], Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Laboratoire de Parasitologie-Mycologie, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), CEA-Direction des Energies (ex-Direction de l'Energie Nucléaire) (CEA-DES (ex-DEN)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Thérapeutique Recombinante Expérimentale (TIMC-IMAG-TheREx ), Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications Grenoble - UMR 5525 (TIMC-IMAG), 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 Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-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 Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Laboratoire de parasitologie [Pointe-à-Pitre], CHU Pointe-à-Pitre/Abymes [Guadeloupe], Ecosystemes Amazoniens et Pathologie Tropicale (EPat), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Guyane (UG), CHU Tenon [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), CHU Sud Saint Pierre [Ile de la Réunion], Centre Hospitalier de Versailles André Mignot (CHV), Hôpital Huriez, CHU Limoges, Hospices Civils de Lyon (HCL), Institut de parasitologie et mycologie médicale, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), Service de Maladies Infectieuses et Tropicales [Fort-de-France, Martinique], CHU Fort de France-CHU de la Martinique [Fort de France]-Hôpital Pierre Zobda-Quitman [CHU de la Martinique], CHU de la Martinique [Fort de France], Hydrosciences Montpellier (HSM), Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Universitaire de Nice (CHU Nice), Matrice extracellulaire et dynamique cellulaire - UMR 7369 (MEDyC), Université de Reims Champagne-Ardenne (URCA)-SFR CAP Santé (Champagne-Ardenne Picardie Santé), Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), Service de Parasitologie-Mycologie [Rennes], Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Hôpital Pontchaillou-CHU Pontchaillou [Rennes], Epidémiosurveillance de protozooses à transmission alimentaire et vectorielle (ESCAPE), Université de Reims Champagne-Ardenne (URCA)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Hôpital Delafontaine, Centre Hospitalier de Saint-Denis [Ile-de-France], Centre Hospitalier Universitaire de Saint-Etienne (CHU de Saint-Etienne), Service de Parasitologie et Mycologie, CHU Toulouse [Toulouse]-Institut Fédératif de Biologie (IFB) - Hôpital Purpan, Hôpital Purpan [Toulouse], CHU Toulouse [Toulouse]-CHU Toulouse [Toulouse]-Hôpital Purpan [Toulouse], CHU Toulouse [Toulouse], Hôpital universitaire Bichat, Hôpital Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Hopital Saint-Louis [AP-HP] (AP-HP), CHU Trousseau [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Institut Curie [Paris], Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP), Laboratoire Chrono-environnement (UMR 6249) (LCE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université de Reims Champagne-Ardenne (URCA)-Université de Reims Champagne-Ardenne (URCA)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Hôpital Pontchaillou-CHU Pontchaillou [Rennes], Centre Hospitalier Universitaire de Saint-Etienne [CHU Saint-Etienne] (CHU ST-E), Service de Parasitologie et Mycologie [CHU Toulouse], Institut Fédératif de Biologie (IFB), Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Pôle Biologie [CHU Toulouse], and Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)

Subjects
0301 basic medicine, Adult, Male, Antifungal Agents, Adolescent, Genotype, Genotyping Techniques, [SDV]Life Sciences [q-bio], 030106 microbiology, Single-nucleotide polymorphism, Dermatology, Trichosporon asahii, Biology, Genome, DNA, Ribosomal, 030207 dermatology & venereal diseases, 03 medical and health sciences, Young Adult, 0302 clinical medicine, Trichosporonosis, medicine, Humans, Child, DNA, Fungal, Mycological Typing Techniques, Genotyping, Phylogeny, ComputingMilieux_MISCELLANEOUS, Aged, Genetics, Voriconazole, Whole genome sequencing, Whole Genome Sequencing, Basidiomycota, Haplotype, Infant, General Medicine, Sequence Analysis, DNA, Middle Aged, medicine.disease, 3. Good health, Infectious Diseases, Child, Preschool, Female, France, Genome, Fungal, medicine.drug
Abstract

BACKGROUND Trichosporonosis is a rare invasive infection in humans mainly due to Trichosporon asahii, and especially recovered from patients having haematological malignancy. Since 2012, IGS1 region sequencing is used as a genotyping method to distinguish isolates, with high frequency of one haplotype worldwide and a geographic specificity for some haplotypes. OBJECTIVES We compared the IGS1 genotyping method and whole genome sequencing (WGS) to study the relationship between clinical isolates involved in two grouped cases in France. METHODS IGS1 sequencing and antifungal susceptibility testing were performed for 54 clinical isolates. Clinical data for 28 isolates included in surveillance programs were analysed. Whole genome was sequenced for 32 clinical isolates and the type strain. RESULTS All isolates were intrinsically resistant to flucytosine, while voriconazole had the most potent in vitro activity. The majority of the isolates was recovered from patients with haematological malignancies (42.86%), with a high proportion of children (

Published
2020

6. Honeybee gut microbiota dysbiosis in pesticide/parasite co-exposures is mainly induced by Nosema ceranae

Author

Frédéric Delbac, Didier Debroas, Anne Moné, Marie Diogon, Laurianne Paris, Hicham El Alaoui, Elodie Peghaire, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), and Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA)

Subjects
Niacinamide, 0106 biological sciences, 0301 basic medicine, Insecticides, [SDV]Life Sciences [q-bio], Zoology, Gut flora, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, Nosema, medicine, Animals, Microbiome, Ecology, Evolution, Behavior and Systematics, Fipronil, ComputingMilieux_MISCELLANEOUS, biology, Biphenyl Compounds, Neonicotinoid, Bees, 15. Life on land, Pesticide, biology.organism_classification, medicine.disease, Nosema ceranae, Fungicides, Industrial, Gastrointestinal Microbiome, 010602 entomology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, 030104 developmental biology, chemistry, Pyrazoles, Dysbiosis, Thiamethoxam
Abstract

Honeybees ensure a key ecosystem service by pollinating many agricultural crops and wild plants. However, in the past few decades, managed bee colonies have been declining in Europe and North America. Researchers have emphasized both parasites and pesticides as the most important factors. Infection by the parasite Nosema ceranae and exposure to pesticides can contribute to gut dysbiosis, impacting the honeybee physiology. Here, we examined and quantified the effects of N. ceranae, the neonicotinoid thiamethoxam, the phenylpyrazole fipronil and the carboxamide boscalid, alone and in combination, on the honeybee gut microbiota. Chronic exposures to fipronil and thiamethoxam alone or combined with N. ceranae infection significantly decreased honeybee survival whereas the fungicide boscalid had no effect on uninfected bees. Interestingly, increased mortality was observed in N. ceranae-infected bees after exposure to boscalid, with synergistic negative effects. Regarding gut microbiota composition, co-exposure to the parasite and each pesticide led to decreased abundance of Alphaproteobacteria, and increased abundance of Gammaproteobacteria. The parasite also induced an increase of bacterial alpha-diversity (species richness). Our findings demonstrated that exposure of honeybees to N. ceranae and/or pesticides play a significant role in colony health and is associated with the establishment of a dysbiotic gut microbiota.

Published
2020

7. Detection of changes in the circadian rhythm of cattle in relation to disease, stress, and reproductive events

Author

Isabelle Veissier, Alice de Boyer des Roches, Romain Lardy, Marie-Madeleine Mialon, Karen Helle Sloth, Mathieu Silberberg, Nicolas Wagner, Dorothée Ledoux, Laboratoire d'Informatique, de Modélisation et d'optimisation des Systèmes (LIMOS), SIGMA Clermont (SIGMA Clermont)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Ecole Nationale Supérieure des Mines de St Etienne-Centre National de la Recherche Scientifique (CNRS)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), GEA Farm Technologies GmbH, French National Research Agency (ANR)16-IDEX-0001 CAP 20-25INRAE (Phase division) Universite Clermont Auvergne (SPI doctorate school) European CommissionEuropean Commission Joint Research Centre311825, Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-SIGMA Clermont (SIGMA Clermont)-Ecole Nationale Supérieure des Mines de St Etienne (ENSM ST-ETIENNE)-Centre National de la Recherche Scientifique (CNRS), and VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[SDV]Life Sciences [q-bio], Ice calving, Physiology, Disease, Biology, Models, Biological, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Rhythm, Estrus, Stress, Physiological, Stress (linguistics), Animals, Circadian rhythm, Molecular Biology, 030304 developmental biology, Monitoring, Physiologic, 2. Zero hunger, Estrous cycle, 0303 health sciences, Chronobiology, Fourier Analysis, 030302 biochemistry & molecular biology, Circadian Rhythm, Lameness, Cattle, Female
Abstract

International audience; Disease and stress can disrupt the circadian rhythm of activity in animals. Sensor technologies can automatically detect variations in daily activity, but it remains difficult to detect exactly when the circadian rhythm disruption starts. Here we report a mathematical Fourier-Based Approximation with Thresholding (FBAT) method designed to detect changes in the circadian activity rhythm of cows whatever the cause of change (typically disease, stress, oestrus). We used data from an indoor positioning system that provides the time per hour spent by each cow resting, in alleys, or eating. We calculated the hourly activity level of each cow by attributing a weight to each activity. We considered 36-h time series and used Fourier transform to model the variations in activity during the first and last 24 h of these 36-h series. We then compared the Euclidian distance between the two models against a given threshold above which we considered that rhythm had changed. We tested the method on four datasets (giving a cumulative total of ~120000 cow*days) that included disease episodes (acidosis, lameness, mastitis or other infectious diseases), reproductive events (oestrus or calving) and external stimuli that can stress animals (e.g. relocation). The method obtained over 80% recall of normal days and detected 95% of abnormal rhythms due to health or reproductive events. FBAT could be implemented in precision livestock farming system monitoring tools to alert caretakers to individual animals needing specific care. The FBAT method also has the potential to detect anomalies in humans to guide healthcare intervention or in wild animals to detect disturbances. We anticipate that chronobiological studies could apply FBAT to help relate circadian rhythm anomalies to specific events.

Published
2020

8. A Similar Secretome Disturbance as a Hallmark of Non-pathogenic Botrytis cinerea ATMT-Mutants?

Author

Mathias Choquer, Adeline Simon, Lucie Chandat, Nathalie Poussereau, François Villalba, Pascal Bally, Cindy Dieryckx, Sophie Kaiser, Julia Schumacher, Guillaume Morgant, Jean-William Dupuy, Marie-Pascale Latorse, Eytham Souibgui, Christophe Bruel, Amélie de Vallée, Muriel Viaud, Elise Loisel, Géraldine Mey, Christine Rascle, Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), 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), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Génomique fonctionnelle des champignons pathogènes des plantes (FungiPath), Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Génomique fonctionnelle des Champignons Phytopathogènes (GFCP), Bayer Cropscience, Ingénierie des Matériaux Polymères (IMP), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet [Saint-Étienne] (UJM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon, BIOlogie et GEstion des Risques en agriculture (BIOGER), Bernstein Center for Computational Neuroscience [Berlin], Humboldt-Universität zu Berlin, ANR-08-KBBE-0003,BotBank,Creation of a mapped database of Botrytis cinerea T-DNA and transposon transformants allowing pathogenic development and plant defence studies(2008), Institut National de la Recherche Agronomique (INRA)-Université d'Auvergne - Clermont-Ferrand I (UdA), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet [Saint-Étienne] (UJM)-Centre National de la Recherche Scientifique (CNRS), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Humboldt Universität zu Berlin, 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), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet - Saint-Étienne (UJM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Humboldt University Of Berlin, and Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Recherche Agronomique (INRA)

Subjects
Microbiology (medical), Agrobacterium, [SDV]Life Sciences [q-bio], Mutant, lcsh:QR1-502, Virulence, Microbiology, lcsh:Microbiology, Insertional mutagenesis, 03 medical and health sciences, Botrytis cinerea, transcriptomics, pathogenicity, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Agrobacterium tumefaciens-mediated transformation, Pathogen, secretomics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Original Research, 0303 health sciences, biology, 030306 microbiology, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Secretomics, biology.organism_classification, Lytic cycle
Abstract

The gray mold fungus Botrytis cinerea is a necrotrophic pathogen able to infect hundreds of host plants, including high-value crops such as grapevine, strawberry and tomato. In order to decipher its infectious strategy, a library of 2,144 mutants was generated by random insertional mutagenesis using Agrobacterium tumefaciens-mediated transformation (ATMT). Twelve mutants exhibiting total loss of virulence toward different host plants were chosen for detailed analyses. Their molecular characterization revealed a single T-DNA insertion in different loci. Using a proteomics approach, the secretome of four of these strains was compared to that of the parental strain and a common profile of reduced lytic enzymes was recorded. Significant variations in this profile, notably deficiencies in the secretion of proteases and hemicellulases, were observed and validated by biochemical tests. They were also a hallmark of the remaining eight non-pathogenic strains, suggesting the importance of these secreted proteins in the infection process. In the twelve non-pathogenic mutants, the differentiation of infection cushions was also impaired, suggesting a link between the penetration structures and the secretion of proteins involved in the virulence of the pathogen.

Published
2019

9. A mimetic nesting association between a timid social wasp and an aggressive arboreal ant

Author

James M. Carpenter, Jérôme Orivel, Alain Dejean, Bruno Corbara, Pablo Servigne, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Ecologie des forêts de Guyane (ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université des Antilles et de la Guyane (UAG)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Department of Physics and Astronomy [Leicester], University of Leicester, Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Investissement d'Avenir grant : ANR-10-LABX-25-01, Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Arboreal locomotion, Wasps, Ant-wasp interactions, Biology, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Nesting Behavior, Trees, Nest, Animals, Mimicry, Nest site selection, Symbiosis, ComputingMilieux_MISCELLANEOUS, Army ant, General Immunology and Microbiology, Ants, Ecology, Host (biology), Protopolybia emortualis, Dolichoderus bidens, General Medicine, Commensalism, biology.organism_classification, French Guiana, Aggression, 010602 entomology, Polistinae, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, General Agricultural and Biological Sciences
Abstract

International audience; In French Guiana, the arboreal nests of the swarm-founding social wasp Protopolybia emortualis (Polistinae) are generally found near those of the arboreal dolichoderine ant Dolichoderus bidens. These wasp nests are typically protected by an envelope, which in turn is covered by an additional carton 'shelter' with structure resembling the D. bidens nests. A few wasps constantly guard their nest to keep D. bidens workers from approaching. When alarmed by a strong disturbance, the ants invade the host tree foliage whereas the wasps retreat into their nest. Notably, there is no chemical convergence in the cuticular profiles of the wasps and ants sharing a tree. The aggressiveness of D. bidens likely protects the wasps from army ant raids, but the ants do not benefit from the presence of the wasps; therefore, this relationship corresponds to a kind of commensalism. (C) 2018 Academie des sciences. Published by Elsevier Masson SAS. All rights reserved.

Published
2018

10. Histoplasma capsulatum bone and joint infection

Author

Olivier Lortholary, L Epelboin, Mathilde Gaume, Philippe Anract, Frédérique Larousserie, D Archambeau, Dominique Salmon, L Marie-Hardy, A. Paugam, Christian Roux, R. Gauzit, M Lavielle, P Leclerc, L. Eyrolle, Laboratoire Pierre Aigrain (LPA), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Fédération de recherche du Département de physique de l'Ecole Normale Supérieure - ENS Paris (FRDPENS), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Informatique, de Modélisation et d'optimisation des Systèmes (LIMOS), SIGMA Clermont (SIGMA Clermont)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Ecole Nationale Supérieure des Mines de St Etienne-Centre National de la Recherche Scientifique (CNRS)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Ecosystemes Amazoniens et Pathologie Tropicale (EPat), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Guyane (UG), Université de Guyane (UG), Fédération de recherche du Département de physique de l'Ecole Normale Supérieure - ENS Paris (FRDPENS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-SIGMA Clermont (SIGMA Clermont)-Ecole Nationale Supérieure des Mines de St Etienne (ENSM ST-ETIENNE)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, biology, business.industry, Bone and joint fungal infection, 030106 microbiology, Infection ostéo-articulaire fongique Keywords: Histoplasma capsulatum, biology.organism_classification, Histoplasma capsulatum, Microbiology, 03 medical and health sciences, 0302 clinical medicine, Infectious Diseases, [SDV.MHEP.RSOA]Life Sciences [q-bio]/Human health and pathology/Rhumatology and musculoskeletal system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Medicine, 030212 general & internal medicine, Infection ostéo-articulaire fongique, business, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2017

11. TERT promoter status and gene copy number gains: effect on TERT expression and association with prognosis in breast cancer

Author

Lauren Veronese, Catherine Abrial, Philippe Vago, Andrei Tchirkov, Yves-Jean Bignon, Frédérique Penault-Llorca, Maud Privat, Mathilde Gay-Bellile, Fabrice Kwiatkowski, Marie-Mélanie Dauplat, Patricia Combes, Eleonore Eymard-Pierre, Marie-Ange Mouret-Reynier, Anne Cayre, Privat, Maud, Equipe de recherche sur les traitements individualisés des cancers (ERTICa), Université d'Auvergne - Clermont-Ferrand I (UdA), Imagerie Moléculaire et Stratégies Théranostiques (IMoST), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Thérapie ciblée combinatoire en Onco-Hématologie (EA3846), Génétique, Reproduction et Développement (GReD), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Centre Jean Perrin [Clermont-Ferrand] (UNICANCER/CJP), UNICANCER, Service d'anatomo-pathologie, UNICANCER-UNICANCER, Etude Métabolique des Molécules Marquées, Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Département d'Oncogénétique, Histologie Embryologie Cytogénétique, Université d'Auvergne - Clermont-Ferrand I (UdA)-Faculté de Médecine, and 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)

Subjects
0301 basic medicine, Telomerase, Regulator, TERT gene copy number gains, [SDV.CAN]Life Sciences [q-bio]/Cancer, [SDV.GEN.GH] Life Sciences [q-bio]/Genetics/Human genetics, Biology, [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Bioinformatics, 03 medical and health sciences, breast cancer, 0302 clinical medicine, Breast cancer, [SDV.CAN] Life Sciences [q-bio]/Cancer, Downregulation and upregulation, medicine, Telomerase reverse transcriptase, Copy-number variation, Gene, MYC overexpression, Oncogene, TERT promoter mutation and polymorphism, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, medicine.disease, 030104 developmental biology, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Oncology, 030220 oncology & carcinogenesis, Cancer research, prognosis, Research Paper
Abstract

International audience; Upregulation of the telomerase reverse transcriptase (TERT) gene in human cancers leads to telomerase activation, which contributes to the growth advantage and survival of tumor cells. Molecular mechanisms of TERT upregulation are complex, tumor-specific and can be clinically relevant. To investigate these mechanisms in breast cancer, we sequenced the TERT promoter, evaluated TERT copy number changes and assessed the expression of the MYC oncogene, a known transcriptional TERT regulator, in two breast cancer cohorts comprising a total of 122 patients. No activating TERT promoter mutations were found, suggesting that this mutational mechanism is not likely to be involved in TERT upregulation in breast cancer. The T349C promoter polymorphism found in up to 50% of cases was not correlated with TERT expression, but T349C carriers had significantly shorter disease-free survival. TERT gains (15-25% of cases) were strongly correlated with increased TERT mRNA expression and worse patient prognosis in terms of disease-free and overall survival. Particularly aggressive breast cancers were characterized by an association of TERT gains with MYC overexpression. These results evidence a significant effect of gene copy number gain on the level of TERT expression and provide a new insight into the clinical significance of TERT and MYC upregulation in breast cancer.

Published
2017

12. P-gp expression levels in the erythrocytes of brown trout: a new tool for aquatic sentinel biomarker development

Author

Emeline Valton, Marie-Laure Bayle, Bruno Combourieu, Christian Amblard, Ivan Wawrzyniak, Mahchid Bamdad, François Desmolles, Frédérique Penault-Llorca, Fabrice Kwiatkowski, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Synthèse et étude de systèmes à intêret biologique (SEESIB), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Service Central d'Analyse (SCA), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), service de recherche clinique, Centre Jean Perrin [Clermont-Ferrand] (UNICANCER/CJP), UNICANCER-UNICANCER, UNICANCER, Imagerie Moléculaire et Stratégies Théranostiques (IMoST), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Laboratoire Biochimie Médicale (UMR 384), Institut National de la Santé et de la Recherche Médicale (INSERM), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Trout, Health, Toxicology and Mutagenesis, Clinical Biochemistry, Gene Expression, [SDV.CAN]Life Sciences [q-bio]/Cancer, 010501 environmental sciences, Biology, 01 natural sciences, Biochemistry, 03 medical and health sciences, chemistry.chemical_compound, Brown trout, brown trout, Rivers, Detoxification, Water Pollution, Chemical, Animals, ATP Binding Cassette Transporter, Subfamily B, Member 1, Polycyclic Aromatic Hydrocarbons, 0105 earth and related environmental sciences, Pesticide Residues, river pollution, Biomarker, Blood, 030104 developmental biology, chemistry, 13. Climate action, Cell culture, Environmental chemistry, erythrocytes, P-gp, biomarker, Xenobiotic, River pollution, Biomarkers, Environmental Monitoring
Abstract

P-glycoprotein (P-gp) is a ubiquitous membrane detoxification pump involved in cellular defence against xenobiotics. Blood is a hub for the trade and transport of physiological molecules and xenobiotics. Our recent studies have highlighted the expression of a 140-kDa P-gp in brown trout erythrocytes in primary cell culture and its dose-dependent response to Benzo[a]pyrene pollutant.The purpose of this study was focused on using P-gp expression in brown trout erythrocytes as a biomarker for detecting the degree of river pollution.abcb1 gene and P-gp expression level were analysed by reverse transcriptase-PCR and Western blot, in the erythrocytes of brown trouts. The latter were collected in upstream and downstream of four rivers in which 17 polycyclic aromatic hydrocarbons and 348 varieties of pesticides micro-residues were analysed by liquid chromatography and mass spectrometry.The abcb1 gene and the 140-kDa P-gp were not expressed in trout erythrocytes from uncontaminated river. In contrast, they are clearly expressed in contaminated rivers, in correlation with the river pollution degree and the nature of the pollutants.This biological tool may offer considerable advantages since it provides an effective response to the increasing need for an early biomarker.

Published
2017

13. Genomics and metagenomics of trimethylamine-utilizing Archaea in the human gut microbiome

Author

Jean-François Brugère, Guillaume Borrel, Angela McCann, Paul W. O'Toole, Marta C Neto, Denise B. Lynch, Jennifer Deane, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Microbiologie Environnement Digestif Santé (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Science Foundation Ireland through a Principal Investigator award, CSET award, FHRI award by the Department of Agriculture, Fisheries and Marine of the Government of Ireland, Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), and Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])

Subjects
Male, 0301 basic medicine, 030106 microbiology, Genomics, digestive system, Microbiology, Genome, Feces, Methylamines, 03 medical and health sciences, Microbial ecology, Phylogenetics, Animals, Humans, Microbiome, Phylogeny, Ecology, Evolution, Behavior and Systematics, Aged, Aged, 80 and over, 2. Zero hunger, Genetics, biology, Microbiota, Gastrointestinal Microbiome, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Archaea, Gastrointestinal Tract, Metagenomics, Metagenome, Female, Original Article, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract

International audience; The biological significance of Archaea in the human gut microbiota is largely unclear. We recently reported genomic and biochemical analyses of the Methanomassiliicoccales, a novel order of methanogenic Archaea dwelling in soil and the animal digestive tract. We now show that these Methanomassiliicoccales are present in published microbiome data sets from eight countries. They are represented by five Operational Taxonomic Units present in at least four cohorts and phylogenetically distributed into two clades. Genes for utilizing trimethylamine (TMA), a bacterial precursor to an atherosclerogenic human metabolite, were present in four of the six novel Methanomassiliicoccales genomes assembled from ELDERMET metagenomes. In addition to increased microbiota TMA production capacity in long-term residential care subjects, abundance of TMA-utilizing Methanomassiliicoccales correlated positively with bacterial gene count for TMA production and negatively with fecal TMA concentrations. The two large Methanomassiliicoccales clades have opposite correlations with host health status in the ELDERMET cohort and putative distinct genomic signatures for gut adaptation.

Published
2017

14. Tetraspanin 8 is a novel regulator of ILK-driven β1 integrin adhesion and signaling in invasive melanoma cells

Author

Clement Robert, Arnaud de la Fouchardière, Nicolas Gadot, Manale El Kharbili, Emmanuelle Danty-Berger, Shoukat Dedhar, Laetitia Barbollat-Boutrand, Paul C. McDonald, François Le Naour, Ingrid Masse, Tiffany Witkowski, Françoise Degoul, Odile Berthier-Vergnes, Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, University of Colorado, University of Colorado [Boulder], Imagerie Moléculaire et Thérapie Vectorisée (IMTV), ITMO ' Technologies pour la Santé '-Cancéropôle CLARA-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université d'Auvergne - Clermont-Ferrand I (UdA), Cardiovasculaire, métabolisme, diabétologie et nutrition (CarMeN), Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National de la Recherche Agronomique (INRA), Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Léon Bérard [Lyon], British Columbia Cancer Agency, Microenvironnement et Physiopathologie de la Differenciation, Université Paris-Sud - Paris 11 (UP11)-Institut National de la Santé et de la Recherche Médicale (INSERM), Physiopathologie et traitement des maladies du foie, Université Paris-Sud - Paris 11 (UP11)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM), Ligue Nationale Contre le Cancer (Comites de l'Ardeche et de la Savoie), Ligue Nationale de Recherche Contre le Cancer (Comite de Savoie) : ARC fundation, Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Cancéropôle CLARA-ITMO ' Technologies pour la Santé ', Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), and Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
0301 basic medicine, Male, endocrine system, integrin, Tetraspanins, Integrin, Blotting, Western, Transplantation, Heterologous, Mice, Nude, [SDV.CAN]Life Sciences [q-bio]/Cancer, Protein Serine-Threonine Kinases, 03 medical and health sciences, Tetraspanin, Cell Movement, Cell Line, Tumor, medicine, melanoma, Cell Adhesion, Animals, Humans, Neoplasm Invasiveness, Phosphorylation, Cell adhesion, Protein kinase B, Microscopy, Confocal, biology, Melanoma, Integrin beta1, TSPAN8, medicine.disease, tetraspanin 8, matrix, 3. Good health, Gene Expression Regulation, Neoplastic, 030104 developmental biology, Oncology, Tumor progression, embryonic structures, Mutation, Cancer research, biology.protein, Ectopic expression, RNA Interference, ILK, Proto-Oncogene Proteins c-akt, Research Paper, Signal Transduction
Abstract

// Manale El Kharbili 1, 2, 3, 4 , Clement Robert 1, 2, 3 , Tiffany Witkowski 5, 6 , Emmanuelle Danty-Berger 7 , Laetitia Barbollat-Boutrand 1, 2, 3 , Ingrid Masse 1, 2, 3 , Nicolas Gadot 8 , Arnaud de la Fouchardiere 9 , Paul C. McDonald 10 , Shoukat Dedhar 10 , Francois Le Naour 11, 12 , Francoise Degoul 5, 6 , Odile Berthier-Vergnes 1, 2, 3 1 Universite de Lyon, Lyon, France 2 Universite Lyon 1, Lyon, France 3 CNRS, UMR5534, Centre de Genetique et de Physiologie Moleculaire et Cellulaire, Villeurbanne, France 4 Current address: Department of Dermatology, University of Colorado, Aurora, Colorado, USA 5 Clermont Universite, Universite d’Auvergne, Imagerie Moleculaire et Therapie Vectorisee, Clermont-Ferrand, France 6 Inserm, U990, Clermont-Ferrand, France 7 Laboratoire CarMeN (INSERM 1060, INRA1397, INSA), Universite Lyon 1, Lyon, France 8 Universite Lyon 1, Federation de Recherche Sante Lyon-Est, ANIPATH, Faculte Laennec, Lyon, France 9 Departement de Biopathologie, Centre Leon Berard, Lyon, France 10 Department of Integrative Oncology, British Columbia Cancer Research Center, Vancouver, Canada 11 INSERM U602, Villejuif, France 12 Current address: INSERM U1193, Hopital Paul Brousse, Villejuif, France Correspondence to: Odile Berthier-Vergnes, email: odile.berthier-vergnes@univ-lyon1.fr Keywords: melanoma, matrix, integrin, tetraspanin 8, ILK Received: November 09, 2016 Accepted: January 09, 2017 Published: February 04, 2017 ABSTRACT Melanoma is well known for its propensity for lethal metastasis and resistance to most current therapies. Tumor progression and drug resistance depend to a large extent on the interplay between tumor cells and the surrounding matrix. We previously identified Tetraspanin 8 (Tspan8) as a critical mediator of melanoma invasion, whose expression is absent in healthy skin. The present study investigated whether Tspan8 may influence cell-matrix anchorage and regulate downstream molecular pathways leading to an aggressive behavior. Using silencing and ectopic expression strategies, we showed that Tspan8-mediated invasion of melanoma cells resulted from defects in cell-matrix anchorage by interacting with β1 integrins and by interfering with their clustering, without affecting their surface or global expression levels. These effects were associated with impaired phosphorylation of integrin-linked kinase (ILK) and its downstream target Akt-S473, but not FAK. Specific blockade of Akt or ILK activity strongly affected cell-matrix adhesion. Moreover, expression of a dominant-negative form of ILK reduced β 1 integrin clustering and cell-matrix adhesion. Finally, we observed a tumor-promoting effect of Tspan8 in vivo and a mutually exclusive expression pattern between Tspan8 and phosphorylated ILK in melanoma xenografts and human melanocytic lesions. Altogether, the in vitro, in vivo and in situ data highlight a novel regulatory role for Tspan8 in melanoma progression by modulating cell-matrix interactions through β1 integrin-ILK axis and establish Tspan8 as a negative regulator of ILK activity. These findings emphasize the importance of targeting Tspan8 as a means of switching from low- to firm-adhesive states, mandatory to prevent tumor dissemination.

Published
2017

15. The degree of processing of foods which are most widely consumed by the French elderly population is associated with satiety and glycemic potentials and nutrient profiles

Author

Gilles Feron, Valentina A. Andreeva, Hélène Labouré, Anthony Fardet, Caroline Méjean, Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Equipe 3: EREN- Equipe de Recherche en Epidémiologie Nutritionnelle (CRESS - U1153), Institut National de la Recherche Agronomique (INRA)-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Université Paris 13 (UP13)-Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), Institut National de la Recherche Agronomique (INRA)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Recherche Agronomique (INRA)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Centre des Sciences du Goût et de l'Alimentation [Dijon] (CSGA), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Clermont Université-Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Recherche Agronomique (INRA), Université Paris 13 (UP13)-Institut National de la Recherche Agronomique (INRA)-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), Unité de Nutrition Humaine ( UNH ), Clermont Université-Université d'Auvergne - Clermont-Ferrand I ( UdA ) -Institut National de la Recherche Agronomique ( INRA ), UMR 1125 Epidémiologie Nutritionnelle, Institut National de la Recherche Agronomique ( INRA ) -Conservatoire National des Arts et Métiers [CNAM] ( CNAM ) -Institut National de la Santé et de la Recherche Médicale ( Inserm ) -Alimentation Humaine ( ALIM.H ) -Université Paris 13 ( UP13 ) -Epidémiologie Nutritionnelle ( UREN ), Centre des Sciences du Goût et de l'Alimentation [Dijon] ( CSGA ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Equipe 3: EREN- Equipe de Recherche en Epidémiologie Nutritionnelle ( CRESS - U1153 ), Université Paris 13 ( UP13 ) -Institut National de la Recherche Agronomique ( INRA ) -Conservatoire National des Arts et Métiers [CNAM] ( CNAM ) -Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité ( CRESS (U1153 / UMR_A 1125) ), Institut National de la Recherche Agronomique ( INRA ) -Université Sorbonne Paris Cité ( USPC ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Institut National de la Recherche Agronomique ( INRA ) -Université Sorbonne Paris Cité ( USPC ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Université Paris 13 (UP13)-Institut National de la Recherche Agronomique (INRA)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), and HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153))

Subjects
Male, 0301 basic medicine, Food Handling, [ SDV.AEN ] Life Sciences [q-bio]/Food and Nutrition, Population, Satiation, Biology, Alimentation, Nutrient density, Eating, 03 medical and health sciences, Nutrient, Humans, Food science, education, Aged, Glycemic, Aged, 80 and over, 2. Zero hunger, education.field_of_study, 030109 nutrition & dietetics, business.industry, personnes âgées, digestive, oral, and skin physiology, Feeding Behavior, General Medicine, Food Analysis, 3. Good health, Glycemic index, Glycemic Index, Food processing, Female, France, Analysis of variance, business, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Nutritive Value, Food Science
Abstract

This study has been financially supported by the French National Research Agency-ANR (AlimaSSenS project No. 14-CE20-0003-01). The NutriNet-Sante is supported by the French Ministry of Health (DGS), the French Institute for Health Surveillance (InVS), the National Institute for Prevention and Health Education (INPES), the Foundation for Medical Research (FRM), the National Institute for Health and Medical Research (INSERM), the National Institute for Agricultural Research (INRA), the National Conservatory of Arts and Crafts (CNAM), and the University of Paris 13; International audience; Food processing impacts both food structure and nutritional density. The effect of food structure on satiety and glycemic potentials is well recognized. However, the association between processing, satiety and glycemic potentials and nutrient profiles has not been much studied, especially in the diets of the elderly. Therefore, this study aimed at exploring relations between the level of food processing, consumption and nutrient profiles and satiety and glycemic potentials among 6686 French elderly people (≥65 years). Dietary assessment was realized through a web-based 24 h dietary record tool. Among a total of 2688 foods, 280 generic foods were aggregated based on a consumption threshold of at least 5% by the population. The satiety potential was calculated using the Fullness Factor equation, and the glycemic potential using the glycemic index and the glucose glycemic equivalent. Foods and dishes were ranked according to an adapted international NOVA classification as raw/minimally-processed (G1), processed (G2) and ultra-processed (G3). ANOVA and correlation analyses showed that the more food is processed, the lower its satiety potential and nutrient density and the higher its glycemic impact, especially when comparing G1 and G3. Besides, the foods consumed in the greatest quantity daily tend to be the most satiating, and ultra-processed foods were among the less frequently consumed both in terms of percentage and daily quantity (around two-fold difference between minimally- and ultra-processed foods). In conclusion, because it is partly related to health food potential, the degree of processing, especially for ultra-processed products, should be taken into consideration more when evaluating consumption profiles of different populations.

Published
2017

16. Strategies used by bacterial pathogens to cross the blood–brain barrier

Author

Xavier Nassif, Sandrine Bourdoulous, Mathieu Coureuil, Loic Le Guennec, Laboratoire d'Informatique, de Modélisation et d'optimisation des Systèmes (LIMOS), SIGMA Clermont (SIGMA Clermont)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Ecole Nationale Supérieure des Mines de St Etienne-Centre National de la Recherche Scientifique (CNRS)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), U1002, Pathogénie des infections systémiques (UMR_S 570), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-SIGMA Clermont (SIGMA Clermont)-Ecole Nationale Supérieure des Mines de St Etienne (ENSM ST-ETIENNE)-Centre National de la Recherche Scientifique (CNRS), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Sigma CLERMONT (Sigma CLERMONT)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure des Mines de St Etienne

Subjects
Virulence Factors, [SDV]Life Sciences [q-bio], Immunology, Biology, Neisseria meningitidis, medicine.disease_cause, Blood–brain barrier, Microbiology, 03 medical and health sciences, Virology, Streptococcus pneumoniae, medicine, Animals, Humans, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Inflammation, 0303 health sciences, Bacteria, 030306 microbiology, Streptococcus, Meninges, Brain, Endothelial Cells, Pathogenic bacteria, Biological Transport, medicine.disease, biology.organism_classification, 3. Good health, medicine.anatomical_structure, Blood-Brain Barrier, Meningitis
Abstract

The skull, spine, meninges, and cellular barriers at the blood-brain and the blood-cerebrospinal fluid interfaces well protect the brain and meningeal spaces against microbial invasion. However, once in the bloodstream, a range of pathogenic bacteria is able to reach the brain and cause meningitis. Despite advances in antibacterial therapy, bacterial meningitis remains one of the most important infectious diseases worldwide. The most common causative bacteria in children and adults are Streptococcus pneumoniae and Neisseria meningitidis associated with high morbidity and mortality, while among neonates, most cases of bacterial meningitis are due to group B Streptococcus and Escherichia coli. Here we summarise our current knowledge on the strategies used by these bacterial pathogens to survive in the bloodstream, to colonise the brain vasculature and to cross the blood-brain barrier.

Published
2019

17. Hormonal and spatial control of SUMOylation in the human and mouse adrenal cortex

Author

T. Dumontet, Antoine Martinez, Bruno Ragazzon, Anne-Marie Lefrançois-Martinez, Jean-Christophe Pointud, Nathanaëlle Montanier, Jérôme Bertherat, Igor Tauveron, Florence Roucher-Boulez, Isabelle Sahut-Barnola, Annabel Berthon, Damien Dufour, Pierre Val, Cyril Djari, M. Batisse-Lignier, Institut Cochin (IC UM3 (UMR 8104 / U1016)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS), Interactions génétiques et cellulaires au cours de la différenciation, Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Génétique, Reproduction et Développement (GReD), 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), Service d’endocrinologie diabétologie et maladies métaboliques, CHU Clermont-Ferrand, CHU Lyon, Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Génétique, Reproduction et Développement (GReD ), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Service d’Endocrinologie Diabète et Maladies Métaboliques [CHU Clermont-Ferrand], Pôle RHEUNNIRS [CHU Clermont-Ferrand], CHU Gabriel Montpied [Clermont-Ferrand], CHU Clermont-Ferrand-CHU Clermont-Ferrand-CHU Gabriel Montpied [Clermont-Ferrand], CHU Clermont-Ferrand-CHU Clermont-Ferrand, Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Clermont-Ferrand, Centre de référence des maladies rares de la surrénale ( CHU Cochin [AP-HP]), Hôpital Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Génétique, Reproduction et Développement - Clermont Auvergne (GReD), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Clermont Université, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), ANR-16-IDEX-0001,CAP 20-25,CAP 20-25(2016), and Clermont Université-Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Recherche Agronomique (INRA)

Subjects
0301 basic medicine, MESH: Neoplasm Proteins, MESH: Signal Transduction, MESH: beta Catenin, SUMO protein, MESH: Adrenal Cortex Neoplasms, Biochemistry, MESH: Mice, Knockout, Dexamethasone, MESH: Zona Fasciculata, Mice, 0302 clinical medicine, Cortex (anatomy), PKA, MESH: Animals, Cycloheximide, MESH: Cycloheximide, Wnt Signaling Pathway, beta Catenin, ComputingMilieux_MISCELLANEOUS, Mice, Knockout, Adrenal cortex, MESH: Sumoylation, MESH: Wnt Signaling Pathway, [SDV.MHEP.EM]Life Sciences [q-bio]/Human health and pathology/Endocrinology and metabolism, PIAS3.β-catenin, Cell biology, Neoplasm Proteins, medicine.anatomical_structure, MESH: Dexamethasone, Dactinomycin, Female, Zona Glomerulosa, Signal transduction, Biotechnology, Endocrine gland, Signal Transduction, MESH: Colforsin, MESH: Cell Line, Tumor, MESH: Mice, Transgenic, MESH: Zona Glomerulosa, MESH: Delayed-Action Preparations, Repressor, Mice, Transgenic, [SDV.CAN]Life Sciences [q-bio]/Cancer, MESH: Cyclic AMP-Dependent Protein Kinases, Biology, 03 medical and health sciences, MESH: Carney Complex, Adrenocorticotropic Hormone, Cell Line, Tumor, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, medicine, Animals, Humans, mouse models, Carney Complex, Molecular Biology, Psychological repression, MESH: Mice, MESH: Adrenocorticotropic Hormone, MESH: Humans, Colforsin, Sumoylation, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, endocrine diseases, Cyclic AMP-Dependent Protein Kinases, Adrenal Cortex Neoplasms, MESH: Dactinomycin, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, 030104 developmental biology, SENP1/2, [SDV.BDD.EO]Life Sciences [q-bio]/Development Biology/Embryology and Organogenesis, Delayed-Action Preparations, MESH: Protein Processing, Post-Translational, Adrenal Cortex, MESH: Adrenal Cortex, Zona Fasciculata, Protein Processing, Post-Translational, MESH: Female, 030217 neurology & neurosurgery, Homeostasis
Abstract

SUMOylation is a highly conserved and dynamic post-translational mechanism primarily affecting nuclear programs for adapting organisms to stressful challenges. Alteration of SUMOylation cycles leads to severe developmental and homeostatic defects and malignancy, but signals coordinating SUMOylation are still unidentified. The adrenal cortex is a zonated endocrine gland that controls body homeostasis and stress response. Here, we show that in human and in mouse adrenals, SUMOylation follows a decreasing centripetal gradient that mirrors cortical differentiation flow and delimits highly and weakly SUMOylated steroidogenic compartments, overlapping glomerulosa, and fasciculata zones. Activation of PKA signaling by acute hormonal treatment, mouse genetic engineering, or in Carney complex results in repression of small ubiquitin-like modifier (SUMO) conjugation in the inner cortex by coordinating expression of SUMO pathway inducers and repressors. Conversely, genetic activation of canonical wingless-related integration site signaling maintains high SUMOylation potential in the outer neoplastic cortex. Thus, SUMOylation is tightly regulated by signaling pathways that orchestrate adrenal zonation and diseases.-Dumontet, T., Sahut-Barnola, I., Dufour, D., Lefrancois-Martinez, A.-M., Berthon, A., Montanier, N., Ragazzon, B., Djari, C., Pointud, J.-C., Roucher-Boulez, F., Batisse-Lignier, M., Tauveron, I., Bertherat, J., Val, P., Martinez, A. Hormonal and spatial control of SUMOylation in the human and mouse adrenal cortex.

Published
2019

18. A Pediococcus strain to rescue honeybees by decreasing Nosema ceranae- and pesticide-induced adverse effects

Author

Didier Debroas, Frédérique Chaucheyras-Durand, Elodie Peghaire, Frédéric Delbac, Anne Moné, Hicham El Alaoui, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Microbiologie Environnement Digestif Santé (MEDIS), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Lallemand Animal Nutrition, Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), and INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])

Subjects
Insecticides, Health, Toxicology and Mutagenesis, [SDV]Life Sciences [q-bio], Honeybee, [SDV.BID]Life Sciences [q-bio]/Biodiversity, law.invention, Microbiology, 03 medical and health sciences, Probiotic, chemistry.chemical_compound, Nosema, law, Immunity, Animals, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Pediococcus, Pesticides, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, biology, 030306 microbiology, Probiotics, Pediococcus acidilactici, General Medicine, Pesticide, Bees, biology.organism_classification, Nosema ceranae, 3. Good health, Fungicide, chemistry, Thiamethoxam, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Agronomy and Crop Science
Abstract

International audience; Honeybees ensure a key ecosystemic service by pollinating many agricultural crops and wild plants. However, since few decades, managed bee colonies have declined worldwide. This phenomenon is considered to be multifactorial, with a strong emphasis on both parasites and pesticides. Infection by the parasite Nosema ceranae and exposure to pesticides can contribute to adverse effects, resulting in a perturbation of the honeybee physiology. We thus hypothesized that probiotic treatment could be promising to treat or prevent these disturbances. The aim of this study was to evaluate the effects of probiotics on N. ceranae-infected and intoxicated honeybees (by the insecticide thiamethoxam and the fungicide boscalid). For this purpose, experiments were conducted with five probiotics. Among them, Pediococcus acidilactici (PA) showed the best protective effect against the parasite and pesticides. PA significantly improved the infected honeybee lifespan as prophylactic and curative treatments (respectively 2.3 fold and 1.7 fold). Furthermore, the exposure to pesticides induced an increase of honeybee mortality compared with the control group (p < .001) that was restored by the PA treatment. Despite its beneficial effect on honeybee lifespan, the PA administration did not induce changes in the gut bacterial communities (neither in abundance or diversity). N. ceranae and the pesticides were shown to deregulate genes involved in honeybee development (vitellogenin), immunity (serine protease 40, defensin) and detoxification system (glutathione peroxidase-like 2, catalase), and these effects were corrected by the PA treatment. This study highlights the promising use of PA to protect honeybees from both pathogens and pesticides.

Published
2019

19. Draft Genome Sequence of Tubulinosema ratisbonensis , a Microsporidian Species Infecting the Model Organism Drosophila melanogaster

Author

Adrien Franchet, Ivan Wawrzyniak, Sebastian Niehus, Christine Gaspin, Caroline Belser, Karine Labadie, Arnaud Couloux, Frédéric Delbac, Valérie Polonais, Eric Peyretaillade, Dominique Ferrandon, Matthieu Reichstadt, Abdel Belkorchia, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Institut für Virologie, Philipps University, Unité de Biométrie et Intelligence Artificielle, Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-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), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-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)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), EA CIDAM - Auvergne IFR Santé, Université d'Auvergne - Clermont-Ferrand I (UdA), Modèles Insectes de l'Immunité Innée (M3I), Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Moné, Anne, Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Institut de Biologie François JACOB (JACOB), 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 Paris-Saclay, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherches sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), and Université d'Auvergne (Clermont Ferrand 1) (UdA)

Subjects
Transposable element, [SDV]Life Sciences [q-bio], ved/biology.organism_classification_rank.species, ORGANIZATION, ANNOTATION, 03 medical and health sciences, 0302 clinical medicine, Immunology and Microbiology (miscellaneous), Tubulinosema ratisbonensis, Genetic model, Genetics, Melanogaster, Model organism, Molecular Biology, Gene, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Whole genome sequencing, 0303 health sciences, biology, ved/biology, Genome Sequences, biology.organism_classification, [SDV] Life Sciences [q-bio], Drosophila melanogaster, 030217 neurology & neurosurgery
Abstract

We present the draft genome sequence of Tubulinosema ratisbonensis, a microsporidium species infecting Drosophila melanogaster. A total of 3,013 protein-encoding genes and an array of transposable elements were identified. This work represents a necessary step to develop a novel model of host-parasite relationships using the highly tractable genetic model D. melanogaster.

Published
2019

20. Evaluation of the performance of existing mathematical models predicting enteric methane emissions from ruminants:Animal categories and dietary mitigation strategies

Author

Peter J. Moate, Mark McGee, Cécile Martin, Zhongtang Yu, Jan Dijkstra, Angela Schwarm, Nico Peiren, K. J. Shingfield, Mmichael Kreuzer, Alexander N. Hristov, A.L.F. Hellwing, André Bannink, Ermias Kebreab, Maguy Eugène, Peter Lund, Les A. Crompton, Ali R. Bayat, Martin Riis Weisbjerg, Christopher K. Reynolds, Xinran Li, David R. Yáñez-Ruiz, Mohammed Benaouda, Unité Mixte de Recherches sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA), Animal Science, Universita degli Studi di Padova, Departement of Animal Science, Aarhus University [Aarhus], Estacion Experimental del Zaidin-CSIC, Centre for Dairy Research, Shool of Agriculture, Animal Science, University of Reading (UOR), Animal Nutrition Group, Animal Science, Wageningen University, Livestock Research, Animal Science, Department of Animal and Aquacultural Sciences, Animal Science, Norwegian University of Life Sciences (NMBU), Institute of Agricultural Sciences, Ecole Polytechnique Fédérale de Zurich, Department of Animal Science, McGill University, Veterinary Science, Queen's University [Belfast] (QUB), Biology, SAMS, Ministry of Food, Agriculture and Livestock (Turkey), University of California, National Institute of Food and Agriculture (US), DSM Nutritional Products, Pennsylvania Soybean Board, Ministry of Economic Affairs (The Netherlands), Agence Nationale de la Recherche (France), Department of Agriculture, Food and Marine (Ireland), Academy of Finland, European Commission, Northeast Sustainable Agriculture Research and Education (US), PMI, Ministry of Agriculture, Nature and Food Quality (The Netherlands), University of New Hampshire, Federal Office for Agriculture (Switzerland), Department for Environment, Food & Rural Affairs (UK), Scottish Government, Global Research Alliance on Agricultural Greenhouse Gases, CSIC - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), German Research Foundation, Swedish Infrastructure for Ecosystem Science, Fondo Regional de Tecnología Agropecuaria, Comisión Nacional de Investigación Científica y Tecnológica (Chile), Fondo Nacional de Desarrollo Científico y Tecnológico (Chile), Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Image Science for Interventional Techniques (ISIT), Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS)-Clermont Université, University of California [Davis] (UC Davis), University of California-University of California, Pennsylvania State University (Penn State), Penn State System, Ohio State University [Columbus] (OSU), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Wageningen University and Research [Wageningen] (WUR), Department of Animal and Aquacultural Sciences, Department of Animal Sciences, University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Agriculture Victoria (AgriBio), Animal Production Research, Agrifood Research Finland, McGill University = Université McGill [Montréal, Canada], Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Université d'Auvergne - Clermont-Ferrand I (UdA)-Clermont Université-Centre National de la Recherche Scientifique (CNRS), University of California (UC)-University of California (UC), and Università degli Studi di Padova = University of Padua (Unipd)

Subjects
model evaluation, dietary strategy, Animal Nutrition, 030309 nutrition & dietetics, Ruminant, [SDV]Life Sciences [q-bio], atténuation, Forage, methane emission, ruminant, Beef cattle, Enteric methane, 03 medical and health sciences, Animal science, Fodder, Dry matter, méthane, Animal nutrition, hedging, Model evaluation, Dairy cattle, Mathematics, 2. Zero hunger, 0303 health sciences, biology, Dietary strategy, 0402 animal and dairy science, 04 agricultural and veterinary sciences, 15. Life on land, biology.organism_classification, 040201 dairy & animal science, Diervoeding, 13. Climate action, marsh gas, Methane emission, WIAS, Animal Science and Zoology, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, performance
Abstract

The objective of this study was to evaluate the performance of existing models predicting enteric methane (CH) emissions, using a large database (3183 individual data from 103 in vivo studies on dairy and beef cattle, sheep and goats fed diets from different countries). The impacts of dietary strategies to reduce CH emissions, and of diet quality (described by organic matter digestibility (dOM) and neutral-detergent fiber digestibility (dNDF)) on model performance were assessed by animal category. The models were first assessed based on the root mean square prediction error (RMSPE) to standard deviation of observed values ratio (RSR) to account for differences in data between models and then on the RMSPE. For dairy cattle, the CH (g/d) predicting model based on feeding level (dry matter intake (DMI)/body weight (BW)), energy digestibility (dGE) and ether extract (EE) had the smallest RSR (0.66) for all diets, as well as for the high-EE diets (RSR = 0.73). For mitigation strategies based on lowering NDF or improving dOM, the same model (RSR = 0.48 to 0.60) and the model using DMI and neutral- and acid-detergent fiber intakes (RSR = 0.53) had the smallest RSR, respectively. For diets with high starch (STA), the model based on nitrogen, ADF and STA intake presented the smallest RSR (0.84). For beef cattle, all evaluated models performed moderately compared with the models of dairy cattle. The smallest RSR (0.83) was obtained using variables of energy intake, BW, forage content and dietary fat, and also for the high-EE and the low-NDF diets (RSR = 0.84 to 0.86). The IPCC Tier 2 models performed better when dietary STA, dOM or dNDF were high. For sheep and goats, the smallest RSR was observed from a model for sheep based on dGE intake (RSR = 0.61). Both IPCC models had low predictive ability when dietary EE, NDF, dOM and dNDF varied (RSR = 0.57 to 1.31 in dairy, and 0.65 to 1.24 in beef cattle). The performance of models depends mostly on explanatory variables and not on the type of data (individual vs. treatment means) used in their development or evaluation. Some empirical models give satisfactory prediction error compared with the error associated with measurement methods. For better prediction, models should include feed intake, digestibility and additional information on dietary concentrations of EE and structural and nonstructural carbohydrates to account for different dietary mitigating strategies., This study is part of the Joint Programming Initiative on Agriculture, Food Security and Climate Change (FACCE-JPI)’s “GLOBAL NETWORK” project and the “Feeding and Nutrition Network” (http://animalscience.psu.edu/fnn) of the Livestock Research Group within the Global Research Alliance for Agricultural Greenhouse Gases (www.globalresearchalliance.org). Authors gratefully acknowledge funding for this project from: USDA National Institute of Food and Agriculture (Grant no. 2014-67003-21979) University of California, Davis Sesnon Endowed Chair Program, USDA, and Austin Eugene Lyons Fellowship (University of California, Davis); Funding from USDA National Institute of Food and Agriculture Federal Appropriations under Project PEN 04539 and Accession number 1000803, DSM Nutritional Products (Basel, Switzerland), Pennsylvania Soybean Board (Harrisburg, PA, USA), Northeast Sustainable Agriculture Research and Education (Burlington, VT, USA), and PMI Nutritional Additives (Shoreview, MN, USA); the Ministry of Economic Affairs (the Netherlands; project BO-20-007-006; Global Research Alliance on Agricultural Greenhouse Gases), the Product Board Animal Feed (Zoetermeer, the Netherlands) and the Dutch Dairy Board (Zoetermeer, the Netherlands); The Cofund for Monitoring & Mitigation of Greenhouse Gases from Agri- and Silvi-culture (FACCE ERA-GAS)’s project Capturing Effects of Diet on Emissions from Ruminant Systems and the Dutch Ministry of Agriculture, Nature and Food Quality (AF-EU-18010 & BO-4400159-01); USDA National Institute of Food and Agriculture (Hatch Multistate NC-1042 Project Number NH00616-R; Project Accession Number 1001855) and the New Hampshire Agricultural Experiment Station (Durham, NH); French National Research Agency through the FACCE-JPI program (ANR-13-JFAC-0003-01); the Department of Agriculture, Food and the Marine, Ireland Agricultural GHG Research Initiative for Ireland (AGRI-I) project; Academy of Finland (No. 281337), Helsinki, Finland; Swiss Federal Office of Agriculture, Berne, Switzerland; the Department for Environment, Food and Rural Affairs (Defra; UK); Defra, the Scottish Government, DARD, and the Welsh Government as part of the UK’s Agricultural GHG Research Platform projects (www.ghgplatform.org.uk); INIA (Spain, project MIT01-GLOBALNET-EEZ); German Federal Ministry of Food and Agriculture (BMBL) through the Federal Office for Agriculture and Food (BLE); Swedish Infrastructure for Ecosystem Science (SITES) at Röbäcksdalen Research Station; Comisión Nacional de Investigación Científica y Tecnológica, Fondo Nacional de Desarrollo Científico y Tecnológico (Grant Nos. 11110410 and 1151355) and Fondo Regional de Tecnología Agropecuaria (FTG/RF-1028-RG); European Commission through SMEthane (FP7-SME-262270).

Published
2019

21. Occurrence and ecological determinants of the contamination of floodplain wetlands with Klebsiella pneumoniae and pathogenic or antibiotic-resistant Escherichia coli

Author

Xavier Bertrand, Hélène Masclaux, Charles P. Henriot, Gudrun Bornette, Christophe Loup, Didier Hocquet, Daniel Martak, François Gillet, Quentin Cuenot, Laboratoire Chrono-environnement (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA)

Subjects
0301 basic medicine, Klebsiella, Klebsiella pneumoniae, river, Wetland, 010501 environmental sciences, medicine.disease_cause, 01 natural sciences, Applied Microbiology and Biotechnology, groundwater, Environmental Microbiology, bacteria, genes, pseudomonas-aeruginosa, geography.geographical_feature_category, Ecology, public health, food and beverages, Contamination, 6. Clean water, Anti-Bacterial Agents, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, antibiotic-resistance, hydrological connectivity, France, Research Article, 030106 microbiology, Microbial Sensitivity Tests, Biology, survival, Microbiology, wetlands, 03 medical and health sciences, Antibiotic resistance, Rivers, Drug Resistance, Bacterial, Escherichia coli, medicine, sewage, Humans, Ecosystem, ecological niche, 0105 earth and related environmental sciences, geography, bacterioplankton, pathogens, 15. Life on land, biology.organism_classification, 13. Climate action, water treatment plants, phytoplankton, Bacteria
Abstract

The survival and multiplication of human pathogenic and antibiotic-resistant bacteria in ecosystems is of increasing concern but has been little explored. Wetlands can be contaminated by water fluxes from rivers and may present environmental conditions leading to bacterial survival and multiplication. To test this hypothesis, we sampled 16 wetlands located along three rivers of the Jura Massif, France. The bacterial contamination of the wetland and river waters was measured monthly over a one-year cycle together with the water physico-chemical characteristics. We assessed the abundance of three pathogenic species: Escherichia coli,Klebsiella pneumoniaeand Pseudomonas aeruginosa. The concentrations of E. coli producing extended-spectrum β-lactamase (ESBL E. coli) or belonging to the phylogenetic group B2 (E. coli B2–more pathogenic) were also measured. We found that rivers carried total E. coli, ESBL E. coli, and K. pneumoniae to wetlands. ESBL E. coli poorly survived in wetlands, whereas total E. coli and K. pneumoniae possibly met favourable physico-chemical conditions for survival and multiplication in these habitats. K. pneumoniae peaked in summer in warm and shallow wetlands. Total E. coli and E. coli B2 potentially reached wetlands through sources other than rivers (hillslope groundwater or leaching from contaminated fields)., Hydrological connectivity and ecological conditions may favour the dispersal and survival of human-associated bacteria in rivers and their floodplains.

Published
2019

22. A comment on 'Variability in plant nutrients reduces insect herbivore performance'

Author

Toni Klauschies, Apostolos-Manuel Koussoroplis, Alexander Wacker, David Giron, Sylvain Pincebourde, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Institut de recherche sur la biologie de l'insecte UMR7261 (IRBI), Université de Tours-Centre National de la Recherche Scientifique (CNRS), Universität Potsdam, Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), and University of Potsdam = Universität Potsdam

Subjects
0106 biological sciences, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Herbivore, Ecology, media_common.quotation_subject, fungi, synergy, food and beverages, Insect, Biology, antagoni, 010603 evolutionary biology, 01 natural sciences, antagonism, Nutrient, lcsh:QH540-549.5, covariance, Non-linear averaging, lcsh:Ecology, Antagonism, Ecology, Evolution, Behavior and Systematics, 010606 plant biology & botany, media_common
Abstract

In their recent contribution, Wetzel et al. [Wetzel et al. (2016) Variability in plant nutrients reduces insect herbivore performance. Nature 539: 425-427] predict that variance in the plant nutrient level reduces herbivore performance via the nonlinear averaging effect (named Jensen’s effect by the authors) while variance in the defense level does not. We argue that the study likely underestimates the potential of plant defenses’ variance to cause Jensen’s effects for two reasons. First, this conclusion is based on the finding that the average Jensen’s effect of various defense traits on various herbivores is zero which does not imply that the Jensen’s effect of specific defense traits on specific herbivores is null, just that the effects balance each other globally. Second, the study neglects the nonlinearity effects that may arise from the synergy between nutritive and defense traits or between co-occurring defenses on herbivore performance. Covariance between interacting plant defense traits, or between plant nutritive and defense traits, can affect performance differently than would nutritive or single plant defense variance alone. Overlooking the interactive effects of plant traits and the traits’ covariance could impair the assessment of the true role of plant trait variability on herbivore populations in natural settings.

Published
2019

23. Pejvakin-mediated pexophagy protects auditory hair cells against noise-induced damage

Author

Sedigheh Delmaghani, Christine Petit, Alain Aghaie, Paul Avan, Isabelle Perfettini, Jean Defourny, Génétique et Physiologie de l'Audition, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), ED 515 - Complexité du vivant, Sorbonne Université (SU), Institut de la Vision, Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Equipe Biophysique Neurosensorielle [Neuro-Dol], Neuro-Dol (Neuro-Dol), Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Neuro-Dol (Neuro-Dol), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Collège de France - Chaire Génétique et physiologie cellulaire, Collège de France (CdF (institution)), This work was supported by the Louis-Jeantet Foundation, Fondation Bettencourt Schueller, Fondation Agir pour l’Audition, Humanis Novalis-Taitbout, Réunica-Prévoyance, BNP Paribas, and the French Investissements d’Avenir program (ANR-10-LABX-65, to C.P.)., Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Chaire Génétique et physiologie cellulaire

Subjects
intracochlear viral transduction, pejvakin, [SDV]Life Sciences [q-bio], Peroxisome Proliferation, medicine.disease_cause, Mice, 03 medical and health sciences, 0302 clinical medicine, Hair Cells, Auditory, Macroautophagy, medicine, Animals, LC3B, Receptor, 030304 developmental biology, 0303 health sciences, Multidisciplinary, biology, Chemistry, Autophagy, Proteins, Transfection, Peroxisome, pexophagy, Cell biology, noise-induced hearing loss, PNAS Plus, Hearing Loss, Noise-Induced, Chaperone (protein), biology.protein, Microtubule-Associated Proteins, MAP1LC3B, 030217 neurology & neurosurgery, Oxidative stress
Abstract

International audience; Noise overexposure causes oxidative stress, leading to auditory hair cell damage. Adaptive peroxisome proliferation involving pejvakin, a peroxisome-associated protein from the gasdermin family, has been shown to protect against this harmful oxidative stress. However, the role of pejvakin in peroxisome dynamics and homeostasis remains unclear. Here we show that sound overstimulation induces an early and rapid selective autophagic degradation of peroxisomes (pexophagy) in auditory hair cells from wild-type, but not pejvakin-deficient (Pjvk -/-), mice. Noise overexposure triggers recruitment of the autophagosome-associated protein MAP1LC3B (LC3B; microtubule-associated protein 1 light chain 3β) to peroxisomes in wild-type, but not Pjvk -/-, mice. We also show that pejvakin-LC3B binding involves an LC3-interacting region within the predicted chaperone domain of pejvakin. In transfected cells and in vivo transduced auditory hair cells, cysteine mutagenesis experiments demonstrated the requirement for both C328 and C343, the two cysteine residues closest to the C terminus of pejvakin, for reactive oxygen species-induced pejvakin-LC3B interaction and pexophagy. The viral transduction of auditory hair cells from Pjvk -/- mice in vivo with both Pjvk and Lc3b cDNAs completely restored sound-induced pexophagy, fully prevented the development of oxidative stress, and resulted in normal levels of peroxisome proliferation, whereas Pjvk cDNA alone yielded only a partial correction of the defects. Overall, our results demonstrate that pexophagy plays a key role in noise-induced peroxisome proliferation and identify defective pexophagy as a cause of noise-induced hearing loss. They suggest that pejvakin acts as a redox-activated pexophagy receptor/adaptor, thereby identifying a previously unknown function of gasdermin family proteins.

Published
2019

24. Temporal covariation of epibacterial community and surface metabolome in the Mediterranean seaweed holobiont Taonia atomaria

Author

Ahlem Othmani, Gérald Culioli, Jean-François Briand, Didier Debroas, Benoît Paix, Laboratoire Matériaux Polymères Interfaces Environnement Marin - EA 4323 (MAPIEM), Université de Toulon (UTLN), Laboratoire Microorganismes : Génome et Environnement - Clermont Auvergne (LMGE), Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Electronique, Informatique et Image [UMR6306] (Le2i), Université de Bourgogne (UB)-École Nationale Supérieure d'Arts et Métiers (ENSAM), Arts et Métiers Sciences et Technologies, HESAM Université (HESAM)-HESAM Université (HESAM)-Arts et Métiers Sciences et Technologies, HESAM Université (HESAM)-HESAM Université (HESAM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Arts et Métiers Sciences et Technologies, HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0303 health sciences, biology, 030306 microbiology, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Zoology, Alteromonadaceae, biology.organism_classification, Microbiology, Holobiont, 03 medical and health sciences, Metabolomics, Taxon, Algae, Flammeovirgaceae, [SDE]Environmental Sciences, Metabolome, Mantel test, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract

An integrative multi‐omics approach allowed monthly variations for a year of the surface metabolome and the epibacterial community of the Mediterranean Phaeophyceae Taonia atomaria to be investigated. The LC–MS‐based metabolomics and 16S rDNA metabarcoding data sets were integrated in a multivariate meta‐omics analysis (multi‐block PLS‐DA from the MixOmic DIABLO analysis) showing a strong seasonal covariation (Mantel test: p < 0.01). A network based on positive and negative correlations between the two data sets revealed two clusters of variables, one relative to the ‘spring period’ and a second to the ‘summer period’. The ‘spring period’ cluster was mainly characterized by dipeptides positively correlated with a single bacterial taxon of the Alteromonadaceae family (BD1‐7 clade). Moreover, ‘summer’ dominant epibacterial taxa from the second cluster (including Erythrobacteraceae, Rhodospirillaceae, Oceanospirillaceae and Flammeovirgaceae) showed positive correlations with few metabolites known as macroalgal antifouling defences [e.g. dimethylsulphoniopropionate (DMSP) and proline] which exhibited a key role within the correlation network. Despite a core community that represents a significant part of the total epibacteria, changes in the microbiota structure associated with surface metabolome variations suggested that both environment and algal host shape the bacterial surface microbiota.

Published
2019

25. Akinetes and ancient DNA reveal toxic cyanobacterial recurrences and their potential for resurrection in a 6700-year-old core from a eutrophic lake

Author

Yannick Miras, Delphine Latour, Aude Beauger, Matthieu Dussauze, Benjamin Legrand, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Histoire naturelle de l'Homme préhistorique (HNHP), Muséum national d'Histoire naturelle (MNHN)-Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Géographie Physique et Environnementale (GEOLAB), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Université Clermont Auvergne (UCA)-Institut Sciences de l'Homme et de la Société (IR SHS UNILIM), Université de Limoges (UNILIM)-Université de Limoges (UNILIM)-Centre National de la Recherche Scientifique (CNRS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Laboratoire Microorganismes : Génome et Environnement - Clermont Auvergne (LMGE), Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut Sciences de l'Homme et de la Société (IR SHS UNILIM), Université de Limoges (UNILIM)-Université de Limoges (UNILIM)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université Clermont Auvergne (UCA), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut Sciences de l'Homme et de la Société (IR SHS UNILIM), and Université de Limoges (UNILIM)-Université de Limoges (UNILIM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA)

Subjects
Cyanobacteria, Geologic Sediments, Environmental Engineering, 010504 meteorology & atmospheric sciences, Microcystins, Akinete, Microcystin, 010501 environmental sciences, medicine.disease_cause, 01 natural sciences, Recurrence, Pollen, medicine, Environmental Chemistry, Waste Management and Disposal, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, chemistry.chemical_classification, Nostocales, biology, Cyanobacteria Toxins, Ecology, Water Pollution, Sediment, 15. Life on land, Sedimentation, Eutrophication, biology.organism_classification, Pollution, [SDE.ES]Environmental Sciences/Environmental and Society, 6. Clean water, Lakes, chemistry, Seasons, Environmental Monitoring, Tropanes
Abstract

In order to evaluate the recurrence of toxic cyanobacterial blooms and to determine the survival capabilities of the resistance cells through time, a sedimentary core spanning 6700 years was drilled in the eutrophic Lake Aydat. A multiproxy approach (density, magnetic susceptibility, XRF, pollen and non-pollen palynomorph analyses), was used initially to determine the sedimentation model and the land uses around the lake. Comparison with the akinete count revealed that Nostocales cyanobacteria have been present in Lake Aydat over a six thousand year period. This long-term cyanobacterial recurrence also highlights the past presence of both the anaC and mcyB genes, involved in anatoxin-a and microcystin biosynthesis, respectively, throughout the core. The first appearance of cyanobacteria seems to be linked to the natural damming of the river, while the large increase in akinete density around 1800 cal.yr BP can be correlated with the intensification of human activities (woodland clearance, crop planting, grazing, etc.) in the catchment area of the lake, and marks the beginning of a long period of eutrophication. This first investigation into the viability and germination potential of cyanobacteria over thousands of years reveals the ability of intact akinetes to undergo cell divisions even after 1800 years of sedimentation, which is 10 times longer than previously observed. This exceptional cellular resistance, coupled with the long-term eutrophic conditions of this lake, could partly explain the past and current recurrences of cyanobacterial proliferations.

Published
2019

26. Inhibition of Ca v 3.2 calcium channels: A new target for colonic hypersensitivity associated with low‐grade inflammation

Author

Francina Agosti, Denis Ardid, Frederic A. Carvalho, Laurence Daulhac, Elodie Picard, Alain Eschalier, Emmanuel Bourinet, Christophe Mallet, Neuro-Dol - Clermont Auvergne (Neuro-Dol), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA), Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), LabEx Ion Channel Science and Therapeutics, Pharmacologie fondamentale et clinique de la douleur, Neuro-Dol (Neuro-Dol), Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherches sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-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]), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), ANR-16-IDEX-0001,CAP 20-25,CAP 20-25(2016), and Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
0301 basic medicine, [SDV]Life Sciences [q-bio], Inflammation, Pharmacology, Inflammatory bowel disease, 03 medical and health sciences, 0302 clinical medicine, medicine, Channel blocker, Irritable bowel syndrome, ComputingMilieux_MISCELLANEOUS, biology, Voltage-dependent calcium channel, business.industry, Chronic pain, medicine.disease, 3. Good health, 030104 developmental biology, Ethosuximide, Myeloperoxidase, biology.protein, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], medicine.symptom, business, 030217 neurology & neurosurgery, medicine.drug
Abstract

Background and purpose Abdominal pain associated with low-grade inflammation is frequently encountered in irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD) during remission. Current treatments are not very effective and new therapeutic approaches are needed. The role of CaV 3.2 channels, which are important in other chronic pain contexts, was investigated in a murine model of colonic hypersensitivity (CHS) associated with low-grade inflammation. Experimental approach Low doses of dextran sulfate sodium (DSS; 0.5%) were chronically administered to C57BL/6j mice in drinking water. Their inflammatory state was assessed by systemic and local measures of IL-6, myeloperoxidase, and lipocalin-2 using elisa. Colonic sensitivity was evaluated by the visceromotor responses to colorectal distension. Functional involvement of CaV 3.2 channels was assessed with different pharmacological (TTA-A2, ABT-639, and ethosuximide) and genetic tools. Key results DSS induced low-grade inflammation associated with CHS in mice. Genetic or pharmacological inhibition of CaV 3.2 channels reduced CHS. Cav3.2 channel deletion in primary nociceptive neurons in dorsal root ganglia (CaV 3.2Nav1.8 KO mice) suppressed CHS. Spinal, but not systemic, administration of ABT-639, a peripherally acting T-type channel blocker, reduced CHS. ABT-639 given intrathecally to CaV 3.2Nav1.8 KO mice had no effect, demonstrating involvement of CaV 3.2 channels located presynaptically in afferent fibre terminals. Finally, ethosuximide, which is a T-type channel blocker used clinically, reduced CHS. Conclusions and implications These results suggest that ethosuximide represents a promising drug reposition strategy and that inhibition of CaV 3.2 channels is an attractive therapeutic approach for relieving CHS in IBS or IBD.

Published
2019

27. Immunomodulatory effects of Lactobacillus plantarum on inflammatory response induced by Klebsiella pneumoniae

Author

Damien Balestrino, Bertrand Evrard, Sylvie Miquel, Christiane Forestier, Sophie Garcin, Marjolaine Vareille-Delarbre, Thomas Bertran, Université Clermont Auvergne (UCA), Laboratoire Microorganismes : Génome et Environnement - Clermont Auvergne (LMGE), Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), Unité de Nutrition Humaine - Clermont Auvergne (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), and ANR-16-IDEX-0001,CAP 20-25,CAP 20-25(2016)

Subjects
0301 basic medicine, Chemokine, medicine.medical_treatment, Immunology, Inflammation, Microbiology, Mice, 03 medical and health sciences, 0302 clinical medicine, Immune system, Intestinal mucosa, gut-lung axis, Pneumonia, Bacterial, medicine, Animals, ComputingMilieux_MISCELLANEOUS, Host Response and Inflammation, Innate immune system, biology, Probiotics, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Klebsiella Infections, 3. Good health, Mice, Inbred C57BL, Klebsiella pneumoniae, Interleukin 10, Lactobacillus, 030104 developmental biology, Infectious Diseases, Cytokine, inflammation, biology.protein, [SDV.IMM]Life Sciences [q-bio]/Immunology, Parasitology, Tumor necrosis factor alpha, medicine.symptom, Lactobacillus plantarum, 030215 immunology
Abstract

Some respiratory infections have been associated with dysbiosis of the intestinal microbiota. The underlying mechanism is incompletely understood, but cross talk between the intestinal microbiota and local immune cells could influence the immune response at distal mucosal sites. This has led to the concept of enhancing respiratory defenses by modulating the intestinal microbiota with exogenous supplementation of beneficial strains. In this study, we examined the effect of Lactobacillus plantarum CIRM653 on the inflammatory response induced by the pathogen Klebsiella pneumoniae. Oral administration of L. plantarum CIRM653 to mice subsequently infected by K. pneumoniae via the nasal route (i) reduced the pulmonary inflammation response, with decreased numbers of lung innate immune cells (macrophages and neutrophils) and cytokines (mouse keratinocyte-derived chemokine [KC], interleukin-6 [IL-6], and tumor necrosis factor alpha [TNF-α]) in the bronchoalveolar fluid, and (ii) induced an immunosuppressive Treg response in lungs. In vitro coincubation of L. plantarum CIRM653 and K. pneumoniae with human dendritic cells and peripheral blood mononuclear cells resulted in decreased Th1 (IL-12p70 and interferon gamma [IFN-γ]) and Th17 (IL-23 and IL-17) and increased Treg (IL-10) cytokine levels compared to those observed for K. pneumoniae-infected cells. Neither K. pneumoniae nor L. plantarum CIRM653 had any effect on cytokine production by intestinal epithelial cells in vitro, but the induction of the NF-κB pathway and IL-8 and IL-6 production by K. pneumoniae in airway epithelial cells was significantly reduced when the pathogen was coincubated with L. plantarum CIRM653. The remote IL-10-mediated modulation of the K. pneumoniae inflammatory response by L. plantarum CIRM653 supports the concept of immunomodulation by beneficial bacteria through the gut-lung axis.

Published
2019

28. The Cafa Challenge Reports Improved Protein Function Prediction And New Functional Annotations For Hundreds Of Genes Through Experimental Screens

Author

Heiko Schoof, Ahmet Sureyya Rifaioglu, Ian Sillitoe, Shanfeng Zhu, Marco Carraro, Naihui Zhou, Asa Ben-Hur, Rui Fa, Alice C. McHardy, David W. Ritchie, George Georghiou, Filip Ginter, Haixuan Yang, Alex A. Freitas, Constance J. Jeffery, Tapio Salakoski, Radoslav Davidovic, Huy N Nguyen, Devon Johnson, Yotam Frank, Alexandra J. Lee, Sean D. Mooney, Marco Falda, Marie-Dominique Devignes, Gianfranco Politano, David T. Jones, Silvio C. E. Tosatto, Renzhi Cao, Zihan Zhang, Sabeur Aridhi, Stefano Pascarelli, Vedrana Vidulin, Qizhong Mao, Balint Z. Kacsoh, Patricia C. Babbitt, Giovanni Bosco, Farrokh Mehryary, Florian Boecker, Alfonso E. Romero, Angela D. Wilkins, Saso Dzeroski, Richard Bonneau, Hans Moen, Chengxin Zhang, Prajwal Bhat, Giuliano Grossi, Martti Tolvanen, Matteo Re, Meet Barot, Mohammad R. K. Mofrad, Predrag Radivojac, Stefano Di Carlo, Tatyana Goldberg, Branislava Gemovic, Suyang Dai, Pier Luigi Martelli, Giorgio Valentini, Maxat Kulmanov, Maria Jesus Martin, Claire O'Donovan, Dallas J. Larsen, Alexandre Renaux, Alan Medlar, Jeffrey M. Yunes, Erica Suh, Volkan Atalay, Vladimir Gligorijević, Fran Supek, Elaine Zosa, Wei-Cheng Tseng, Nafiz Hamid, Marco Mesiti, Tunca Doğan, Petri Törönen, Hafeez Ur Rehman, Jose Manuel Rodriguez, Alessandro Petrini, Sayoni Das, Burkhard Rost, Miguel Amezola, Mateo Torres, Jianlin Cheng, Daisuke Kihara, Liisa Holm, Marco Frasca, Steven E. Brenner, Stefano Toppo, Adrian M. Altenhoff, Chenguang Zhao, Daniel B. Roche, Alperen Dalkiran, Alex W. Crocker, Marco Notaro, Iddo Friedberg, Michal Linial, Julian Gough, Damiano Piovesan, Slobodan Vucetic, Natalie Thurlby, Olivier Lichtarge, Jari Björne, Jonas Reeb, Rabie Saidi, Yuxiang Jiang, Christophe Dessimoz, Jie Hou, Ronghui You, Tomislav Šmuc, Paolo Fontana, Michele Berselli, Jia-Ming Chang, Deborah A. Hogan, Larry Davis, Ehsaneddin Asgari, Shuwei Yao, Zheng Wang, Fabio Fabris, Michael L. Tress, Caleb Chandler, Christine A. Orengo, Rengul Cetin Atalay, Castrense Savojardo, Danielle A Brackenridge, Peter W. Rose, Yang Zhang, Dane Jo, Gage S. Black, Shanshan Zhang, Aashish Jain, Liam J. McGuffin, Timothy Bergquist, Peter L. Freddolino, Robert Hoehndorf, Rita Casadio, Da Chen Emily Koo, Mark N. Wass, Hai Fang, Casey S. Greene, Suwisa Kaewphan, Magdalena Antczak, Wen-Hung Liao, Enrico Lavezzo, Neven Sumonja, Ashton Omdahl, José M. Fernández, Ilya Novikov, Jonathan B. Dayton, Feng Zhang, Vladimir Perovic, Cen Wan, Jonathan G. Lees, Kai Hakala, Weidong Tian, Alex Warwick Vesztrocy, Domenico Cozzetto, Nevena Veljkovic, Yi-Wei Liu, Imane Boudellioua, Po-Han Chi, Kimberley A. Lewis, Seyed Ziaeddin Alborzi, Giuseppe Profiti, Alberto Paccanaro, Itamar Borukhov, Alfredo Benso, Indika Kahanda, Rebecca L. Hurto, Bilgisayar Mühendisliği, National Science Foundation (United States), Gordon and Betty Moore Foundation, United States of Department of Health & Human Services, Cystic Fibrosis Foundation, Consejo Nacional de Ciencia y Tecnología (México), Deutsche Forschungsgemeinschaft (Alemania), European Research Council, Ministerio de Ciencia e Innovación (España), Unión Europea, University of Turku (Finlandia), Finlands Akademi (Finlandia), National Natural Science Foundation of China, Nanjing Agricultural University. The Academy of Science. National Key Research & Development Program of China, Ministero dell Istruzione, dell Universita e della Ricerca (Italia), Shanghai Municipal Science and Technology Major Project, Biotechnology and Biological Sciences Research Council (Reino Unido), Extreme Science and Engineering Discovery Environment, Ministry of Education, Science and Technological Development (Serbia), Ministry of Science and Technology, Ministry for Education (Baviera) (Alemania), Yad Hanadiv, University of Milan (Italia), Swiss National Science Foundation, Unión Europea. European Cooperation in Science and Technology (COST), Plataforma ISCIII de Bioinformática (España), Scientific and Technological Research Council of Turkey, Ministry of Education (China), University of Padua (Italia), Mühendislik ve Doğa Bilimleri Fakültesi -- Bilgisayar Mühendisliği Bölümü, Rifaioğlu, Ahmet Süreyya, Zhou N., Jiang Y., Bergquist T.R., Lee A.J., Kacsoh B.Z., Crocker A.W., Lewis K.A., Georghiou G., Nguyen H.N., Hamid M.N., Davis L., Dogan T., Atalay V., Rifaioglu A.S., Dalklran A., Cetin Atalay R., Zhang C., Hurto R.L., Freddolino P.L., Zhang Y., Bhat P., Supek F., Fernandez J.M., Gemovic B., Perovic V.R., Davidovic R.S., Sumonja N., Veljkovic N., Asgari E., Mofrad M.R.K., Profiti G., Savojardo C., Martelli P.L., Casadio R., Boecker F., Schoof H., Kahanda I., Thurlby N., McHardy A.C., Renaux A., Saidi R., Gough J., Freitas A.A., Antczak M., Fabris F., Wass M.N., Hou J., Cheng J., Wang Z., Romero A.E., Paccanaro A., Yang H., Goldberg T., Zhao C., Holm L., Toronen P., Medlar A.J., Zosa E., Borukhov I., Novikov I., Wilkins A., Lichtarge O., Chi P.-H., Tseng W.-C., Linial M., Rose P.W., Dessimoz C., Vidulin V., Dzeroski S., Sillitoe I., Das S., Lees J.G., Jones D.T., Wan C., Cozzetto D., Fa R., Torres M., Warwick Vesztrocy A., Rodriguez J.M., Tress M.L., Frasca M., Notaro M., Grossi G., Petrini A., Re M., Valentini G., Mesiti M., Roche D.B., Reeb J., Ritchie D.W., Aridhi S., Alborzi S.Z., Devignes M.-D., Koo D.C.E., Bonneau R., Gligorijevic V., Barot M., Fang H., Toppo S., Lavezzo E., Falda M., Berselli M., Tosatto S.C.E., Carraro M., Piovesan D., Ur Rehman H., Mao Q., Zhang S., Vucetic S., Black G.S., Jo D., Suh E., Dayton J.B., Larsen D.J., Omdahl A.R., McGuffin L.J., Brackenridge D.A., Babbitt P.C., Yunes J.M., Fontana P., Zhang F., Zhu S., You R., Zhang Z., Dai S., Yao S., Tian W., Cao R., Chandler C., Amezola M., Johnson D., Chang J.-M., Liao W.-H., Liu Y.-W., Pascarelli S., Frank Y., Hoehndorf R., Kulmanov M., Boudellioua I., Politano G., Di Carlo S., Benso A., Hakala K., Ginter F., Mehryary F., Kaewphan S., Bjorne J., Moen H., Tolvanen M.E.E., Salakoski T., Kihara D., Jain A., Smuc T., Altenhoff A., Ben-Hur A., Rost B., Brenner S.E., Orengo C.A., Jeffery C.J., Bosco G., Hogan D.A., Martin M.J., O'Donovan C., Mooney S.D., Greene C.S., Radivojac P., Friedberg I., Faculty of Economic and Social Sciences and Solvay Business School, Faculty of Sciences and Bioengineering Sciences, Faculty of Engineering, Computational genomics, Institute of Biotechnology, Bioinformatics, Genetics, Helsinki Institute of Life Science HiLIFE, Discovery Research Group/Prof. Hannu Toivonen, Iowa State University (ISU), European Bioinformatics Institute, École Polytechnique de Montréal (EPM), Vinča Institute of Nuclear Sciences, University of Belgrade [Belgrade], University of Bologna, Max Planck Institute for Plant Breeding Research (MPIPZ), European Virus Bioinformatics Center [Jena], Université libre de Bruxelles (ULB), Laboratoire d'Informatique, de Modélisation et d'optimisation des Systèmes (LIMOS), SIGMA Clermont (SIGMA Clermont)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Ecole Nationale Supérieure des Mines de St Etienne-Centre National de la Recherche Scientifique (CNRS)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Department of Computer Science, University of Bristol [Bristol], Department of Computer Science [Columbia], University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, Yale School of Public Health (YSPH), Departamento de Geometría y Topología, Universidad de Granada (UGR), Tumor Biology Center, Centre for Nephrology [London, UK], University College of London [London] (UCL), Baylor College of Medicine (BCM), Baylor University, Department of Knowledge Technologies, Structural and Molecular Biology Department, University College London, Queen Mary University of London (QMUL), Spanish National Cancer Research Center (CNIO), Dipartimento di Informatica, Università degli Studi di Milano [Milano] (UNIMI), Dipartimento di Scienze dell'Informazione [Milano], United States Naval Academy, 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), Department of Molecular Medicine, Universita degli Studi di Padova, Centro de Regulación Genómica (CRG), Universitat Pompeu Fabra [Barcelona] (UPF), Physics Department, National Tsing Hua University [Hsinchu] (NTHU), Dipartimento di Automatica e Informatica [Torino] (DAUIN), Politecnico di Torino = Polytechnic of Turin (Polito), University of Turku, Bioinformatics Laboratory, University of Turku-Turku Center for Computer Science, Toyota Technological Institute at Chicago [Chicago] (TTIC), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne (UNIL), Department of Computer Science [Colorado State University], Colorado State University [Fort Collins] (CSU), Centre for Plant Integrative Biology [Nothingham] (CPIB), University of Nottingham, UK (UON), BRICS, Braunschweiger Zentrum für Systembiologie, Rebenring 56,38106 Braunschweig, Germany., University of Bologna/Università di Bologna, Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-SIGMA Clermont (SIGMA Clermont)-Ecole Nationale Supérieure des Mines de St Etienne (ENSM ST-ETIENNE)-Centre National de la Recherche Scientifique (CNRS), Universidad de Granada = University of Granada (UGR), Università degli Studi di Milano = University of Milan (UNIMI), Università degli Studi di Padova = University of Padua (Unipd), and Université de Lausanne = University of Lausanne (UNIL)

Subjects
Library, Male, Identification, Candida-albicans, Protein function prediction, Long-term memory, Biofilm, Critical assessment, Community challenge, Procedures, Genome, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], 0302 clinical medicine, Candida albicans, Molecular genetics, lcsh:QH301-705.5, ComputingMilieux_MISCELLANEOUS, Biological ontology, Settore BIO/11 - BIOLOGIA MOLECOLARE, 0303 health sciences, 318 Medical biotechnology, Biotechnology & applied microbiology, Ontology, Expectation, Genetics & heredity, Plant leaf, ddc, 3. Good health, Drosophila melanogaster, Human experiment, Fungal genome, Pseudomonas aeruginosa, Female, [INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC], Genome, Fungal, BIOINFORMATICS, Long-Term memory, Locomotion, Human, Adult, Memory, Long-Term, lcsh:QH426-470, Bioinformatics, Long term memory, Generation, Bacterial genome, Computational biology, Biology, Article, 03 medical and health sciences, Annotation, Big data, [INFO.INFO-LG]Computer Science [cs]/Machine Learning [cs.LG], Pseudomonas, Genetics, Animals, Humans, Gene, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], Animal, Research, Experimental data, Molecular Sequence Annotation, Cell Biology, Nonhuman, Human genetics, lcsh:Genetics, lcsh:Biology (General), Biofilms, Proteins | Genes | Protein functions, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], 030217 neurology & neurosurgery, Function (biology), Genome, Bacterial
Abstract

Tosatto, Silvio/0000-0003-4525-7793; Zhang, Feng/0000-0003-3447-897X; Gonzalez, Jose Maria Fernandez/0000-0002-4806-5140; Devignes, Marie-Dominique/0000-0002-0399-8713; Wass, Mark/0000-0001-5428-6479; Falda, Marco/0000-0003-2642-519X; Thurlby, Natalie/0000-0002-1007-0286; Zosa, Elaine/0000-0003-2482-0663; Dessimoz, Christophe/0000-0002-2170-853X; Yunes, Jeffrey/0000-0003-1869-3231; Hamid, Md Nafiz/0000-0001-8681-6526; Hoehndorf, Robert/0000-0001-8149-5890; Dogan, Tunca/0000-0002-1298-9763; NOTARO, MARCO/0000-0003-4309-2200; Cozzetto, Domenico/0000-0001-6752-5432; Lewis, Kimberley/0000-0003-3010-8453; Roche, Daniel/0000-0002-9204-1840; Martin, Maria-Jesus/0000-0001-5454-2815; Tress, Michael/0000-0001-9046-6370; Tolvanen, Martti/0000-0003-3434-7646; Cheng, Jianlin/0000-0003-0305-2853; Rose, Peter/0000-0001-9981-9750; Renaux, Alexandre/0000-0002-4339-2791; Kacsoh, Balint/0000-0001-9171-0611; O'Donovan, Claire/0000-0001-8051-7429; Kulmanov, Maxat/0000-0003-1710-1820; Friedberg, Iddo/0000-0002-1789-8000; Zhou, Naihui/0000-0001-6268-6149, WOS: 000498615000001, PubMed ID: 31744546, Background The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Results Here, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory. Conclusion We conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens., National Science FoundationNational Science Foundation (NSF) [DBI1564756, DBI-1458359, DBI-1458390, DMS1614777, CMMI1825941, NSF 1458390]; Gordon and Betty Moore FoundationGordon and Betty Moore Foundation [GBMF 4552]; National Institutes of Health NIGMSUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of General Medical Sciences (NIGMS) [P20 GM113132]; Cystic Fibrosis Foundation [CFRDP STANTO19R0]; BBSRCBiotechnology and Biological Sciences Research Council (BBSRC) [BB/K004131/1, BB/F00964X/1, BB/M025047/1, BB/M015009/1]; Consejo Nacional de Ciencia y Tecnologia Paraguay (CONACyT)Consejo Nacional de Ciencia y Tecnologia (CONACyT) [14-INV-088, PINV15-315]; NSFNational Science Foundation (NSF) [1660648, DBI 1759934, IIS1763246, DBI-1458477, 0965768, DMR-1420073, DBI-1458443]; NIHUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USA [R01GM093123, DP1MH110234, UL1 TR002319, U24 TR002306]; Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy-EXC 2155 "RESIST"German Research Foundation (DFG) [39087428]; National Institutes of HealthUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USA [R01GM123055, R01GM60595, R15GM120650, GM083107, GM116960, AI134678, NIH R35-GM128637, R00-GM097033]; ERCEuropean Research Council (ERC) [StG 757700]; Spanish Ministry of Science, Innovation and Universities [BFU2017-89833-P]; Severo Ochoa award; Centre of Excellence project "BioProspecting of Adriatic Sea"; Croatian Government; European Regional Development FundEuropean Union (EU) [KK.01.1.1.01.0002]; ATT Tieto kayttoon grant; Academy of FinlandAcademy of Finland; University of Turku; CSC-IT Center for Science Ltd.; University of Miami; National Cancer Institute of the National Institutes of HealthUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Cancer Institute (NCI) [U01CA198942]; Helsinki Institute for Life Sciences; Academy of FinlandAcademy of Finland [292589]; National Natural Science Foundation of ChinaNational Natural Science Foundation of China [31671367, 31471245, 91631301, 61872094, 61572139]; National Key Research and Development Program of China [2016YFC1000505, 2017YFC0908402]; Italian Ministry of Education, University and Research (MIUR) PRIN 2017 projectMinistry of Education, Universities and Research (MIUR) [2017483NH8]; Shanghai Municipal Science and Technology Major Project [2017SHZDZX01, 2018SHZDZX01]; UK Biotechnology and Biological Sciences Research CouncilBiotechnology and Biological Sciences Research Council (BBSRC) [BB/N019431/1, BB/L020505/1, BB/L002817/1]; Elsevier; Extreme Science and Engineering Discovery Environment (XSEDE) award [MCB160101, MCB160124]; Ministry of Education, Science and Technological Development of the Republic of Serbia [173001]; Taiwan Ministry of Science and Technology [106-2221-E-004-011-MY2]; Montana State University; Bavarian Ministry for Education; Simons Foundation; NIH NINDSUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of Neurological Disorders & Stroke (NINDS) [1R21NS103831-01]; University of Illinois at Chicago (UIC) Cancer Center award; UIC College of Liberal Arts and Sciences Faculty Award; UIC International Development Award; Yad Hanadiv [9660/2019]; National Institute of General Medical Science of the National Institute of Health [GM066099, GM079656]; Research Supporting Plan (PSR) of University of Milan [PSR2018-DIP-010-MFRAS]; Swiss National Science FoundationSwiss National Science Foundation (SNSF) [150654]; EMBL-European Bioinformatics Institute core funds; CAFA BBSRC [BB/N004876/1]; European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grantEuropean Union (EU) [778247]; COST ActionEuropean Cooperation in Science and Technology (COST) [BM1405]; NIH/NIGMSUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of General Medical Sciences (NIGMS) [R01 GM071749]; National Human Genome Research Institute of the National of Health [U41 HG007234]; INB Grant (ISCIII-SGEFI/ERDF) [PT17/0009/0001]; TUBITAKTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [EEEAG-116E930]; KanSil [2016K121540]; Universita degli Studi di Milano; 111 ProjectMinistry of Education, China - 111 Project [B18015]; key project of Shanghai Science Technology [16JC1420402]; ZJLab; project Ribes Network POR-FESR 3S4H [TOPP-ALFREVE18-01]; PRID/SID of University of Padova [TOPP-SID19-01]; NIGMSUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of General Medical Sciences (NIGMS) [R15GM120650]; King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) [URF/1/3454-01-01, URF/1/3790-01-01]; "the Human Project from Mind, Brain and Learning" of the NCCU Higher Education Sprout Project by the Taiwan Ministry of Education; National Center for High-performance ComputingIstanbul Technical University, The work of IF was funded, in part, by the National Science Foundation award DBI-1458359. The work of CSG and AJL was funded, in part, by the National Science Foundation award DBI-1458390 and GBMF 4552 from the Gordon and Betty Moore Foundation. The work of DAH and KAL was funded, in part, by the National Science Foundation award DBI-1458390, National Institutes of Health NIGMS P20 GM113132, and the Cystic Fibrosis Foundation CFRDP STANTO19R0. The work of AP, HY, AR, and MT was funded by BBSRC grants BB/K004131/1, BB/F00964X/1 and BB/M025047/1, Consejo Nacional de Ciencia y Tecnologia Paraguay (CONACyT) grants 14-INV-088 and PINV15-315, and NSF Advances in BioInformatics grant 1660648. The work of JC was partially supported by an NIH grant (R01GM093123) and two NSF grants (DBI 1759934 and IIS1763246). ACM acknowledges the support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy -EXC 2155 "RESIST" - Project ID 39087428. DK acknowledges the support from the National Institutes of Health (R01GM123055) and the National Science Foundation (DMS1614777, CMMI1825941). PB acknowledges the support from the National Institutes of Health (R01GM60595). GB and BZK acknowledge the support from the National Science Foundation (NSF 1458390) and NIH DP1MH110234. FS was funded by the ERC StG 757700 "HYPER-INSIGHT" and by the Spanish Ministry of Science, Innovation and Universities grant BFU2017-89833-P. FS further acknowledges the funding from the Severo Ochoa award to the IRB Barcelona. TS was funded by the Centre of Excellence project "BioProspecting of Adriatic Sea", co-financed by the Croatian Government and the European Regional Development Fund (KK.01.1.1.01.0002). The work of SK was funded by ATT Tieto kayttoon grant and Academy of Finland. JB and HM acknowledge the support of the University of Turku, the Academy of Finland and CSC -IT Center for Science Ltd. TB and SM were funded by the NIH awards UL1 TR002319 and U24 TR002306. The work of CZ and ZW was funded by the National Institutes of Health R15GM120650 to ZW and start-up funding from the University of Miami to ZW. The work of PWR was supported by the National Cancer Institute of the National Institutes of Health under Award Number U01CA198942. PR acknowledges NSF grant DBI-1458477. PT acknowledges the support from Helsinki Institute for Life Sciences. The work of AJM was funded by the Academy of Finland (No. 292589). The work of FZ and WT was funded by the National Natural Science Foundation of China (31671367, 31471245, 91631301) and the National Key Research and Development Program of China (2016YFC1000505, 2017YFC0908402]. CS acknowledges the support by the Italian Ministry of Education, University and Research (MIUR) PRIN 2017 project 2017483NH8. SZ is supported by the National Natural Science Foundation of China (No. 61872094 and No. 61572139) and Shanghai Municipal Science and Technology Major Project (No. 2017SHZDZX01). PLF and RLH were supported by the National Institutes of Health NIH R35-GM128637 and R00-GM097033. JG, DTJ, CW, DC, and RF were supported by the UK Biotechnology and Biological Sciences Research Council (BB/N019431/1, BB/L020505/1, and BB/L002817/1) and Elsevier. The work of YZ and CZ was funded in part by the National Institutes of Health award GM083107, GM116960, and AI134678; the National Science Foundation award DBI1564756; and the Extreme Science and Engineering Discovery Environment (XSEDE) award MCB160101 and MCB160124.; The work of BG, VP, RD, NS, and NV was funded by the Ministry of Education, Science and Technological Development of the Republic of Serbia, Project No. 173001. The work of YWL, WHL, and JMC was funded by the Taiwan Ministry of Science and Technology (106-2221-E-004-011-MY2). YWL, WHL, and JMC further acknowledge the support from "the Human Project from Mind, Brain and Learning" of the NCCU Higher Education Sprout Project by the Taiwan Ministry of Education and the National Center for High-performance Computing for computer time and facilities. The work of IK and AB was funded by Montana State University and NSF Advances in Biological Informatics program through grant number 0965768. BR, TG, and JR are supported by the Bavarian Ministry for Education through funding to the TUM. The work of RB, VG, MB, and DCEK was supported by the Simons Foundation, NIH NINDS grant number 1R21NS103831-01 and NSF award number DMR-1420073. CJJ acknowledges the funding from a University of Illinois at Chicago (UIC) Cancer Center award, a UIC College of Liberal Arts and Sciences Faculty Award, and a UIC International Development Award. The work of ML was funded by Yad Hanadiv (grant number 9660/2019). The work of OL and IN was funded by the National Institute of General Medical Science of the National Institute of Health through GM066099 and GM079656. Research Supporting Plan (PSR) of University of Milan number PSR2018-DIP-010-MFRAS. AWV acknowledges the funding from the BBSRC (CASE studentship BB/M015009/1). CD acknowledges the support from the Swiss National Science Foundation (150654). CO and MJM are supported by the EMBL-European Bioinformatics Institute core funds and the CAFA BBSRC BB/N004876/1. GG is supported by CAFA BBSRC BB/N004876/1. SCET acknowledges funding from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 778247 (IDPfun) and from COST Action BM1405 (NGP-net). SEB was supported by NIH/NIGMS grant R01 GM071749. The work of MLT, JMR, and JMF was supported by the National Human Genome Research Institute of the National of Health, grant numbers U41 HG007234. The work of JMF and JMR was also supported by INB Grant (PT17/0009/0001 - ISCIII-SGEFI/ERDF). VA acknowledges the funding from TUBITAK EEEAG-116E930. RCA acknowledges the funding from KanSil 2016K121540. GV acknowledges the funding from Universita degli Studi di Milano - Project "Discovering Patterns in Multi-Dimensional Data" and Project "Machine Learning and Big Data Analysis for Bioinformatics". SZ is supported by the National Natural Science Foundation of China (No. 61872094 and No. 61572139) and Shanghai Municipal Science and Technology Major Project (No. 2017SHZDZX01). RY and SY are supported by the 111 Project (NO. B18015), the key project of Shanghai Science & Technology (No. 16JC1420402), Shanghai Municipal Science and Technology Major Project (No. 2018SHZDZX01), and ZJLab. ST was supported by project Ribes Network POR-FESR 3S4H (No. TOPP-ALFREVE18-01) and PRID/SID of University of Padova (No. TOPP-SID19-01). CZ and ZW were supported by the NIGMS grant R15GM120650 to ZW and start-up funding from the University of Miami to ZW. The work of MK and RH was supported by the funding from King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) under Award No. URF/1/3454-01-01 and URF/1/3790-01-01. The work of SDM is funded, in part, by NSF award DBI-1458443.

Published
2019

29. Probiotic and enterohemorrhagic Escherichia coli: An effective strategy against a deadly enemy?

Author

Jonathan Thévenot, Lucie Etienne-Mesmin, Stéphanie Blanquet-Diot, Charlotte Cordonnier, Valérie Livrelli, Monique Alric, CRNH, Concept Ingéniérie et Développement Aliment et Médicament, Université d'Auvergne - Clermont-Ferrand I (UdA), 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), CRNH, Concept Ingéniérie et Developpement Aliment et Medicament, Service Bactériologie, CHU Clermont-Ferrand, Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Recherche Agronomique (INRA), Université d'Auvergne (Clermont Ferrand 1) (UdA), Centre Hospitalier Universitaire de Clermont-Ferrand, and Institut National de la Recherche Agronomique (INRA)-Université d'Auvergne - Clermont-Ferrand I (UdA)

Subjects
0301 basic medicine, [SDV]Life Sciences [q-bio], 030106 microbiology, Virulence, Biology, Bacterial Physiological Phenomena, medicine.disease_cause, Applied Microbiology and Biotechnology, Microbiology, law.invention, 03 medical and health sciences, Probiotic, enterohemorrhagic Escherichia coli, law, Yeasts, Antibiosis, medicine, Global health, Animals, Humans, Probiotic bacteria, Intestinal Mucosa, Escherichia coli, Beneficial effects, Escherichia coli Infections, Bacteria, Foodborne pathogen, Probiotics, General Medicine, 3. Good health, Immunology, Food-borne pathogen, gastrointestinal tract, innovative treatment, probiotic
Abstract

Enterohemorrhagic Escherichia coli (EHEC) are major food-borne pathogens that constitute a serious public health threat. Currently, there is no specific treatment available for EHEC infections in human creating an urgent need for the development of alternative therapeutic strategies. Among them, one of the most promising approaches is the use of probiotic microorganisms. Even if many studies have shown the antagonistic effects of probiotic bacteria or yeast on EHEC survival, virulence, adhesion on intestinal epithelium or pathogen-induced inflammatory responses, mechanisms mediating their beneficial effects remain unclear. This review describes EHEC pathogenesis and novel therapeutic strategies, with a particular emphasis on probiotics. The interests and limits of a probiotic-based approach and the way it might be incorporated into global health strategies against EHEC infections will be discussed.

Published
2016

30. Molecular tools to detect anatoxin-a genes in aquatic ecosystems: Toward a new nested PCR-based method

Author

Benjamin Legrand, Jérôme Lesobre, Jonathan Colombet, Marion Sabart, Delphine Latour, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Cyanobacteria, [SDV]Life Sciences [q-bio], Bacterial Toxins, 030106 microbiology, Fresh Water, Plant Science, Aquatic Science, Polymerase Chain Reaction, Anatoxin-a, 03 medical and health sciences, chemistry.chemical_compound, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Ecosystem, 14. Life underwater, Gene, ComputingMilieux_MISCELLANEOUS, Cyanobacteria Toxins, biology, Anabaena, Ecology, Aquatic ecosystem, Cyanotoxin, biology.organism_classification, 030104 developmental biology, chemistry, Evolutionary biology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Nested polymerase chain reaction, Environmental Monitoring, Tropanes
Abstract

Over the last few decades, cyanobacterial mass occurrence has become a recurrent feature of aquatic ecosystems. This has led to ecosystem exposure and health hazards associated with cyanotoxin production. The neurotoxin anatoxin-a and its homologs can be synthesized by benthic cyanobacterial species in lotic systems, but also by planktonic lacustrine species such as Dolichospermum (also known as Anabaena). However, only a few studies have focused on anatoxin-a occurrence and its biosynthesis genes in freshwater lakes. The initial aim of this study was to evaluate the molecular tools available in the literature to detect anatoxin-a biosynthesis genes in lacustrine environments. Having tested different sets of PCR primers, we found that that some sets of primers, such as anxC, were too specific and did not amplify anatoxin-a biosynthesis genes in all producing strains. On the other hand, some sets of primers, such as atxoa, seemed not to be specific enough, amplifying numerous non-specific bands in environmental samples, especially those from sediments. Furthermore, anaC and anaF amplification exhibited different band intensities during electrophoresis, suggesting a high variation in number of gene copies between samples. As a result, we proposed a new nested PCR-based method which considerably improved the amplification of the anaC gene in our environmental samples, eliminating non-specific bands and weak detections. Using this tool, our study also highlighted that anatoxin-a genes are widely distributed throughout freshwater lakes. This suggests the need for further ecological investigations into anatoxin-a in these ecosystems.

Published
2016

31. Metabolic adaptations to HFHS overfeeding: how whole body and tissues postprandial metabolic flexibility adapt in Yucatan mini-pigs

Author

Annick Bernalier-Donadille, Dominique Dardevet, Sergio Polakof, Estelle Pujos-Guillot, Blandine Comte, Isabelle Savary-Auzeloux, Didier Rémond, Mathieu Rambeau, Unité de Nutrition Humaine (UNH), Clermont Université-Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Recherche Agronomique (INRA), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Microbiologie Environnement Digestif Santé (MEDIS), Institut National de la Recherche Agronomique (INRA)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Clermont Université, and INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])

Subjects
Blood Glucose, 0301 basic medicine, Swine, Transamination, medicine.medical_treatment, Medicine (miscellaneous), Adipose tissue, postprandial, régime riche en saccharose, Urine, métabolisme des lipides, 0302 clinical medicine, Dietary Sucrose, Homeostasis, Insulin, Amino Acids, Phosphorylation, 2. Zero hunger, chemistry.chemical_classification, Nutrition and Dietetics, glyceride metabolism, High-fat–high-sucrose diet, Postprandial Period, Adaptation, Physiological, Cholesterol, Postprandial, Liver, mini-pig, mini porc, Lipogenesis, Swine, Miniature, Female, Leucine, aliment riche en graisse, métabolomique, metabolomic, medicine.medical_specialty, 030209 endocrinology & metabolism, Hyperphagia, Biology, Diet, High-Fat, glucose and lipid metabolism, 03 medical and health sciences, Internal medicine, Metabolome, medicine, Animals, Metabolomics, métabolisme du glucose, Triglycerides, Catabolism, Gluconeogenesis, Lipid Metabolism, Glucose, 030104 developmental biology, Endocrinology, chemistry, Energy Metabolism, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract

The authors acknowledge J. David, C. Prolhac, D. Durand and the personnel of the Animal Facility (C. de L’Homme, B. Cohade) for technical assistance; PurposeIn the present study, we aimed to metabolically characterize the postprandial adaptations of the major tissues involved in energy, lipids and amino acids metabolisms in mini-pigs.MethodMini-pigs were fed on high-fat–high-sucrose (HFHS) diet for 2 months and several tissues explored for metabolic analyses. Further, the urine metabolome was followed over the time to picture the metabolic adaptations occurring at the whole body level following overfeeding.ResultsAfter 2 months of HFHS consumption, mini-pigs displayed an obese phenotype characterized by high circulating insulin, triglycerides and cholesterol levels. At the tissue level, a general (muscle, adipose tissue, intestine) reduction in the capacity to phosphorylate glucose was observed. This was also supported by the enhanced hepatic gluconeogenesis potential, despite the concomitant normoglycaemia, suggesting that the high circulating insulin levels would be enough to maintain glucose homoeostasis. The HFHS feeding also resulted in a reduced capacity of two other pathways: the de novo lipogenesis, and the ranched-chain amino acids transamination. Finally, the follow-up of the urine metabolome over the time allowed determining breaking points in the metabolic trajectory of the animals.ConclusionsSeveral features confirmed the pertinence of the animal model, including increased body weight, adi-posity and porcine obesity index. At the metabolic level,we observed a perturbed glucose and amino acid metabolism, known to be related to the onset of the obesity. The urine metabolome analyses revealed several metabolic pathways potentially involved in the obesity onset, including TCA (citrate, pantothenic acid), amino acids catabolism (cysteine, threonine, leucine).

Published
2016

32. Extracellular magnesium and calcium blockers modulate macrophage activity

Author

Patrycja Libako, Jeanette A.M. Maier, Sara Castiglioni, Andrzej Mazur, Wojciech Nowacki, Department of Immunology, Pathophysiology and Veterinary Preventive Medicine, Wroclaw University of Environmental and Life Sciences, Department of Biomedical and Clinical Sciences, Università degli studi di Milano [Milano], Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Clermont Université, Polish Ministry of Education and Science NN308075234, Università degli Studi di Milano [Milano] (UNIMI), Université d'Auvergne - Clermont-Ferrand I (UdA)-Clermont Université-Institut National de la Recherche Agronomique (INRA), Università degli Studi di Milano = University of Milan (UNIMI), and Clermont Université-Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Recherche Agronomique (INRA)

Subjects
0301 basic medicine, medicine.medical_specialty, Lipopolysaccharide, Clinical Biochemistry, propriété anti-inflammatoire, chemistry.chemical_element, macrophage, 02 engineering and technology, Calcium, Pharmacology, Endocytosis, Biochemistry, Mice, Structure-Activity Relationship, 03 medical and health sciences, chemistry.chemical_compound, Internal medicine, medicine, Extracellular, Animals, Magnesium, magnésium, Molecular Biology, Cells, Cultured, reactive oxygen species, chemistry.chemical_classification, Mice, Inbred BALB C, Reactive oxygen species, calcium, Dose-Response Relationship, Drug, biology, monocyte-derived macrophages, Calcium Channel Blockers, 021001 nanoscience & nanotechnology, cytokines, macrophages, 3. Good health, Ovalbumin, 030104 developmental biology, Endocrinology, Verapamil, chemistry, Cell culture, biology.protein, 0210 nano-technology, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, medicine.drug
Abstract

Magnesium (Mg) possesses anti-inflammatory properties, partly because it antagonizes calcium (Ca) and inhibits L-type Ca channels. Our aim was to determine the effects of different concentrations of extracellular Mg, with or without Ca-channel blockers, in macrophages. A macrophage-like cell line J774.E was cultured in different concentrations of extracellular Mg and exposed to i) the phorbol ester PMA to induce the production of reactive oxygen species ii) lipopolysaccharide to induce the production of pro-inflammatory cytokines, or iii) ovalbumin to study endocytosis. The Ca antagonists verapamil and/or TMB-8 were used to interfere with Ca homeostasis. Different concentrations of extracellular Mg did not impact on endocytosis, while Ca antagonists markedly decreased it. Low extracellular Mg exacerbated, whereas Ca antagonists inhibited, PMA-induced production of free radicals. Ca blockers prevented lipopolysaccharide-induced transcription and release of IL-1β, IL-6 and TNF-α, while extracellular Mg had only a marginal effect. Ca channel inhibitors markedly reduced the activity of J774.E cells, thus underscoring the critical role of Ca in the non-specific immune response, a role which was, in some instances, also modulated by extracellular Mg.

Published
2016

33. Skeletal muscle regeneration and impact of aging and nutrition

Author

Yves Boirie, Carla Domingues-Faria, Nicolas Goncalves-Mendes, Marie-Paule Vasson, Stéphane Walrand, Unité de Nutrition Humaine - Clermont Auvergne (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Clermont Université, Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), Centre Jean Perrin - Centre Régional de Lutte contre le Cancer d'Auvergne, Université d'Auvergne - Clermont-Ferrand I (UdA)-Clermont Université-Institut National de la Recherche Agronomique (INRA), Centre Jean Perrin [Clermont-Ferrand] (UNICANCER/CJP), and UNICANCER

Subjects
0301 basic medicine, Sarcopenia, Aging, Immunosenescence, Muscle Fibers, Skeletal, Nutritional Status, Context (language use), Biology, Biochemistry, 03 medical and health sciences, Immune system, medicine, Humans, Regeneration, Myocyte, Molecular Biology, Nutrition, Regeneration (biology), Immunity, Skeletal muscle, medicine.disease, Cell biology, 030104 developmental biology, medicine.anatomical_structure, Neurology, Muscle, Stem cell, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Biotechnology
Abstract

In press; After skeletal muscle injury a regeneration process takes place to repair muscle. Skeletal muscle recovery is a highly coordinated process involving cross-talk between immune and muscle cells. It is well known that the physiological activities of both immune cells and muscle stem cells decline with advancing age, thereby blunting the capacity of skeletal muscle to regenerate. The age-related reduction in muscle repair efficiency contributes to the development of sarcopenia, one of the most important factors of disability in elderly people. Preserving muscle regeneration capacity may slow the development of this syndrome. In this context, nutrition has drawn much attention: studies have demonstrated that nutrients such as amino acids, n-3 polyunsaturated fatty acids, polyphenols and vitamin D can improve skeletal muscle regeneration by targeting key functions of immune cells, muscle cells or both. Here we review the process of skeletal muscle regeneration with a special focus on the cross-talk between immune and muscle cells. We address the effect of aging on immune and skeletal muscle cells involved in muscle regeneration. Finally, the mechanisms of nutrient action on muscle regeneration are described, showing that quality of nutrition may help to preserve the capacity for skeletal muscle regeneration with age.

Published
2016

34. Trichodysplasia spinulosa: a polyomavirus infection specifically targeting follicular keratinocytes in immunocompromised patients

Author

L Bessenay, Pauline Gaboriaud, Patricia Berthon, Jérôme T. J. Nicol, Antoine Touzé, F. Franck, Mariet C.W. Feltkamp, Michel D'Incan, Jacques Rouanet, François Aubin, CHU Clermont-Ferrand, Imagerie Moléculaire et Thérapie Vectorisée (IMTV), Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Cancéropôle CLARA-ITMO ' Technologies pour la Santé ', Carcinogénèse épithéliale : facteurs prédictifs et pronostiques - UFC (UR 3181) (CEF2P / CARCINO), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Service de Dermatologie, Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Faculte des Sciences Pharmaceutiques, Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), Department of Medical Microbiology, Leiden University Medical Center (LUMC), ProdInra, Migration, ITMO ' Technologies pour la Santé '-Cancéropôle CLARA-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université d'Auvergne - Clermont-Ferrand I (UdA), Carcinogénèse épithéliale : facteurs prédictifs et pronostiques - UFC (EA 3181) (CEF2P / CARCINO), Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Universiteit Leiden-Universiteit Leiden, and Institut National de la Recherche Agronomique (INRA)-Université de Tours

Subjects
Keratinocytes, Male, 0301 basic medicine, Pathology, medicine.medical_specialty, education, Dermatology, Disease, Opportunistic Infections, Biology, law.invention, Immunocompromised Host, 030207 dermatology & venereal diseases, 03 medical and health sciences, 0302 clinical medicine, law, medicine, Humans, Child, Polymerase chain reaction, Polyomavirus Infections, medicine.diagnostic_test, [SDV.MHEP.DERM] Life Sciences [q-bio]/Human health and pathology/Dermatology, Hair follicle, medicine.disease, Trichodysplasia, 3. Good health, 030104 developmental biology, medicine.anatomical_structure, Hair disease, Skin Diseases, Viral, Skin biopsy, Immunology, Hair Diseases, Hair Follicle, [SDV.MHEP.DERM]Life Sciences [q-bio]/Human health and pathology/Dermatology, Immunosuppressive Agents, Immunostaining
Abstract

Summary Trichodysplasia spinulosa (TS) is a rare skin disease, caused by a specific polyomavirus, occurring in immunocompromised patients. The pathophysiological mechanisms of TS are not yet fully understood. By using polymerase chain reaction and skin biopsy immunostaining we report evidence, in a paediatric case, of follicular keratinocytes being the primary target of trichodysplasia spinulosa-associated polyomavirus.

Published
2016

35. Capturing prokaryotic dark matter genomes

Author

Pierre Peyret, Nicolas Parisot, Eric Peyretaillade, Réjane Beugnot, Clémence Defois, Delphine Boucher, Corinne Petit-Biderre, Céline Ribière, Cyrielle Gasc, Conception, Ingénierie et Développement de l'Aliment et du Médicament (CIDAM), Université d'Auvergne - Clermont-Ferrand I (UdA), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Auvergne Regional Council, European Regional Development Fund, program Investissements d'Avenir AMI VALTEX, French 'Ministere de l'Enseignement Superieur et de la Recherche', French 'Direction Generale de l'Armement' (DGA), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA)

Subjects
Single-cell genomics, [SDV]Life Sciences [q-bio], Dark matter, Biology, Microbiology, Genome, Cellular life, 03 medical and health sciences, Genome, Archaeal, Ecosystem, Molecular Biology, ComputingMilieux_MISCELLANEOUS, Complete genome reconstruction, 030304 developmental biology, 0303 health sciences, Bacteria, 030306 microbiology, Ecology, High-Throughput Nucleotide Sequencing, General Medicine, 15. Life on land, Archaea, Prokaryotic Cells, Metagenomics, Evolutionary biology, Single-Cell Analysis, Genome, Bacterial, Function (biology)
Abstract

Prokaryotes are the most diverse and abundant cellular life forms on Earth. Most of them, identified by indirect molecular approaches, belong to microbial dark matter. The advent of metagenomic and single-cell genomic approaches has highlighted the metabolic capabilities of numerous members of this dark matter through genome reconstruction. Thus, linking functions back to the species has revolutionized our understanding of how ecosystem function is sustained by the microbial world. This review will present discoveries acquired through the illumination of prokaryotic dark matter genomes by these innovative approaches.

Published
2015

36. Evaluation of a new multiplex PCR assay (ParaGENIE G-Amoeba Real-Time PCR kit) targeting Giardia intestinalis, Entamoeba histolytica and Entamoeba dispar/Entamoeba moshkovskii from stool specimens: evidence for the limited performances of microscopy-based approach for amoeba species identification

Author

Estelle Cateau, Nathalie Bourgeois, Marie Machouart, Florent Morio, Fakhri Jeddi, M. Gaboyard, Françoise Botterel, Stéphane Valot, Céline Nourrisson, Frédéric Dalle, Christelle Pomares, P. Le Pape, Adrien Laude, Guillaume Desoubeaux, Y. Le Govic, M. Leterrier, Nicolas Argy, Cibles et Médicaments des Infections et de l'Immunité (IICiMed), Université de Nantes - UFR des Sciences Pharmaceutiques et Biologiques, Université de Nantes (UN)-Université de Nantes (UN), Laboratoire de parasitologie mycologie (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Laboratoire d'économie d'Orleans [2008-2011] (LEO), Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS), Université de Tours (UT), Services de Maladies Infectieuses et Tropicales [CHU Bichat], AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Service de Parasitologie-Mycologie [CHRU Nancy], Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Groupe d'Étude des Interactions Hôte-Pathogène (GEIHP), Université d'Angers (UA), Service des Recherches Métallurgiques Appliquées (SRMA), Département des Matériaux pour le Nucléaire (DMN), CEA-Direction des Energies (ex-Direction de l'Energie Nucléaire) (CEA-DES (ex-DEN)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-CEA-Direction des Energies (ex-Direction de l'Energie Nucléaire) (CEA-DES (ex-DEN)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Hôpital Henri Mondor, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Service de pharmacologie clinique et vigilances, Centre régional, de pharmacovigilance et de renseignement sur les médicaments, Hopital de la Milétrie, Poitiers, Microbiologie de l'Eau (MDE), Ecologie et biologie des interactions (EBI), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS)-Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Parasitologie-Mycologie (CHU de Poitiers), Centre hospitalier universitaire de Poitiers (CHU Poitiers), Service de Bactériologie-Hygiène, Institut Pasteur de Tunis, Réseau International des Instituts Pasteur (RIIP), Institut des Sciences Moléculaires (ISM), Université Montesquieu - Bordeaux 4-Université Sciences et Technologies - Bordeaux 1 (UB)-École Nationale Supérieure de Chimie et de Physique de Bordeaux (ENSCPB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Parasitologie-Mycologie (Institut de biologie, CHU de Nantes), Centre hospitalier universitaire de Nantes (CHU Nantes), IICiMed - EA 1155, Université de Nantes (UN)-UFR Sciences et Techniques [Université de Nantes], Université de Nantes (UN)-UFR des Sciences Pharmaceutiques [Université de Nantes], Université de Nantes (UN), Laboratoire d'économie d'Orleans (LEO), Université de Tours, L’UNAM Université, Groupe d’Etude des Interactions Hôte-Pathogène, UPRES EA 3142, CEA-Direction de l'Energie Nucléaire (CEA-DEN), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-CEA-Direction de l'Energie Nucléaire (CEA-DEN), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Statistique, Analyse et Modélisation Multidisciplinaire (SAmos-Marin Mersenne) (SAMM), Université Panthéon-Sorbonne (UP1), Université Montesquieu - Bordeaux 4-Université Sciences et Technologies - Bordeaux 1-École Nationale Supérieure de Chimie et de Physique de Bordeaux (ENSCPB)-Centre National de la Recherche Scientifique (CNRS), Géosciences Paris Sud (GEOPS), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Cibles et médicaments de l'infection, de l'immunité et du cancer (IICiMed), Université Montesquieu - Bordeaux 4-Université Sciences et Technologies - Bordeaux 1-École Nationale Supérieure de Chimie et de Physique de Bordeaux (ENSCPB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), CHU Dijon, Biologie–Pharmacie, Pharmacie Centrale [CHU Nantes] (Pôle hospitalo-universitaire PHU7 - BPPC), Centre méditerranéen de médecine moléculaire (C3M), Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire d'analyse et modélisation de systèmes pour l'aide à la décision (LAMSADE), Université Paris Dauphine-PSL-Centre National de la Recherche Scientifique (CNRS), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Départemental - Hôpital de La Roche-sur-Yon, CHU Montpellier, Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Ademtech S.A., and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA)

Subjects
Giardiasis, 0301 basic medicine, diagnosis, Entamoeba, Feces, Entamoeba dispar/Entamoeba moshkovskii, Giardia intestinalis, 0302 clinical medicine, fluids and secretions, Entamoeba moshkovskii, samples, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Amoeba species, Microscopy, parasitic infections, Entamoebiasis, biology, Entamoeba histolytica, General Medicine, 3. Good health, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Infectious Diseases, Real-time polymerase chain reaction, Stool, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, antigen-detection, Microbiology (medical), food.ingredient, 030231 tropical medicine, 030106 microbiology, Real-Time Polymerase Chain Reaction, [SDV.MP.PRO]Life Sciences [q-bio]/Microbiology and Parasitology/Protistology, Microbiology, Amoeba (genus), 03 medical and health sciences, food, Species Specificity, Multiplex polymerase chain reaction, parasitic diseases, Humans, spp, dispar, Multiplex PCR, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Bacterial adhesin, amebiasis, Giardia lamblia, Multiplex Polymerase Chain Reaction, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

Objectives Besides the potential to identify a wide variety of gastrointestinal parasites, microscopy remains the reference standard in clinical microbiology for amoeba species identification and, especially when coupled with adhesin detection, to discriminate the pathogenic Entamoeba histolytica from its sister but non-pathogenic species Entamoeba dispar / Entamoeba moshkovskii . However, this approach is time-consuming, requires a high-level of expertise that can be jeopardized considering the low prevalence of gastrointestinal parasites in non-endemic countries. Here, we evaluated the CE-IVD-marked multiplex PCR (ParaGENIE G-Amoeba, Ademtech) targeting E. histolytica and E. dispar / E. moshkovskii and Giardia intestinalis . Methods This evaluation was performed blindly on a reference panel of 172 clinical stool samples collected prospectively from 12 laboratories and analysed using a standardized protocol relying on microscopy (and adhesin detection by ELISA for the detection of E. histolytica ) including G. intestinalis ( n = 37), various amoeba species ( n = 55) including E. dispar ( n = 15), E. histolytica ( n = 5), as well as 17 other gastrointestinal parasites ( n = 80), and negative samples ( n = 37). Results This new multiplex PCR assay offers fast and reliable results with appropriate sensitivity and specificity for the detection of G. intestinalis and E. dispar / E. moshkovskii from stools (89.7%/96.9% and 95%/100%, respectively). Detection rate and specificity were greatly improved by the PCR assay, highlighting several samples misidentified by microscopy, including false-negative and false-positive results for both E. dispar/E. moshkovskii and E. histolytica . Conclusion Given the clinical relevance of amoeba species identification, microbiologists should be aware of the limitations of using an algorithm relying on microscopy coupled with adhesin detection by ELISA.

Published
2018

37. Hydrogenotrophic methanogens of the mammalian gut: functionally similar, thermodynamically different - A modelling approach

Author

Rafael Muñoz-Tamayo, Diego P. Morgavi, Nicole Morel-Desrosiers, Milka Popova, Jean-Pierre Morel, Gérard Fonty, Maxence Tillier, Modélisation Systémique Appliquée aux Ruminants (MoSAR), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité Mixte de Recherches sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Thermodynamique des solutions et des polymères (TSP), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, and VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement

Subjects
Methane emissions, 0303 health sciences, Work (thermodynamics), [SDV.BIO]Life Sciences [q-bio]/Biotechnology, biology, 030306 microbiology, Chemistry, Methanogenesis, Kinetic information, Niche, biology.organism_classification, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, [SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies, [INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, Biological system, In vitro growth, Kinetic function, 030304 developmental biology, Archaea
Abstract

Methanogenic archaea occupy a functionally important niche in the gut microbial ecosystem of mammals. Our purpose was to quantitatively characterize the dynamics of methanogenesis by integrating microbiology, thermodynamics and mathematical modelling. For that,in vitrogrowth experiments were performed with pure cultures of key methanogens from the human and ruminant gut, namelyMethanobrevibacter smithii, Methanobrevibacter ruminantiumandMethanobacterium formicium. Microcalorimetric experiments were performed to quantify the methanogenesis heat flux. We constructed an energetic-based mathematical model of methanogenesis. Our model captured efficiently the dynamics of methanogenesis with concordance correlation coefficients of 0.94 for CO2, 0.99 for H2and 0.97 for CH4. Together, experimental data and model enabled us to quantify metabolism kinetics and energetic patterns that were specific and distinct for each species despite their use of analogous methane-producing pathways. Then, we testedin silicothe interactions between these methanogens under anin vivosimulation scenario using a theoretical modelling exercise.In silicosimulations suggest that the classical competitive exclusion principle is inapplicable to gut ecosystems and that kinetic information alone cannot explain gut ecological aspects such as microbial coexistence. We suggest that ecological models of gut ecosystems require the integration of microbial kinetics with nonlinear behaviours related to spatial and temporal variations taking place in mammalian guts. Our work provides novel information on the thermodynamics and dynamics of methanogens. This understanding will be useful to construct new gut models with enhanced prediction capabilities and could have practical applications for promoting gut health in mammals and mitigating ruminant methane emissions.

Published
2018

38. Human intestinal parasites in Mahajanga, Madagascar: The kingdom of the protozoa

Author

Bruno Pereira, Valentin Greigert, Rivo Solotiana Rakotomalala, Milijaona Randrianarivelojosia, Ermanno Candolfi, Julie Brunet, Jean-Louis Razafindrakoto, Alexander W. Pfaff, Ahmed Abou-Bacar, Eugene Morel, Céline Nourrisson, Philippe Poirier, Leila Benarbia, Hôpital pasteur [Colmar], Institut de Parasitologie et de Pathologie Tropicale (IPPTS), Université de Strasbourg (UNISTRA), Laboratoire de Parasitologie et de Mycologie Médicale [Strasbourg], Les Hôpitaux Universitaires de Strasbourg (HUS), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Laboratoire de Parasitologie et Mycologie [CHU Clermont-Ferrand], CHU Gabriel Montpied [Clermont-Ferrand], CHU Clermont-Ferrand-CHU Clermont-Ferrand, Direction de la recherche clinique et de l’innovation [CHU Clermont-Ferrand] (DRCI), CHU Clermont-Ferrand, Unité de Recherche sur le Paludisme [Antananarivo, Madagascar], Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), CHU PZaga [Mahajanga, Madagascar], CHU Mahavoky Atsimo [Mahajanga, Madagascar], Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Male, Rural Population, Veterinary medicine, Urban Population, lcsh:Medicine, 0302 clinical medicine, Intestinal Parasites, MESH: Rural Population, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Genotype, Prevalence, Medicine and Health Sciences, Prospective Studies, Geography, Medical, Intestinal Diseases, Parasitic, Sanitation, lcsh:Science, MESH: Phylogeny, Dientamoeba fragilis, Phylogeny, 2. Zero hunger, Protozoans, education.field_of_study, Multidisciplinary, biology, MESH: Dientamoeba/genetics, Eukaryota, 3. Good health, MESH: Urban Population, Microsporidia, MESH: Intestinal Diseases, Parasitic/diagnosis, Female, MESH: Blastocystis, Research Article, Adult, Dientamoeba Fragilis, MESH: Madagascar/epidemiology, MESH: Protozoan Infections/epidemiology, 030231 tropical medicine, Population, MESH: Intestinal Diseases, Parasitic/epidemiology, 03 medical and health sciences, Population Metrics, Protozoan infection, MESH: Geography, Medical, parasitic diseases, medicine, Madagascar, Parasitic Diseases, MESH: Cities, Helminths, Humans, MESH: Sanitation, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Sex Ratio, Cities, education, Dientamoeba, MESH: Prevalence, Blastocystis, Protozoan Infections, MESH: Humans, Population Biology, MESH: Protozoan Infections/diagnosis, lcsh:R, Organisms, Biology and Life Sciences, MESH: Adult, biology.organism_classification, medicine.disease, Parasitic Protozoans, MESH: Male, MESH: Prospective Studies, 030104 developmental biology, Protozoa, lcsh:Q, Parasitology, Parasitic Intestinal Diseases, MESH: Female
Abstract

International audience; INTRODUCTION: Intestinal parasitic infections are a major public health problem in inter-tropical areas. The aim of our study was to describe the situation in Mahajanga, Madagascar with a particular focus on two protozoa, Dientamoeba fragilis and Blastocystis sp.METHODS: This was a prospective study from February to June 2015. Stool samples from symptomatic hospitalized patients and asymptomatic volunteers were submitted to microscopy and molecular assays in order to detect parasites.RESULTS: A wide panel of intestinal parasites were identified among the 265 included subjects, protozoa being the most prevalent with 72.8% whereas the prevalence of helminths and microsporidia was of 7.9% and 4.5%, respectively. Blastocystis sp. was the most prevalent protozoa (64.5% of the entire cohort) followed by various amoebas (35.5%) and flagellates (27,5%). We only detected subtypes 1, 2 and 3 of Blastocystis sp. Among the patients positive for D. fragilis (9.4%), 23 carried genotype 1 and 1 genotype 2. For the first time, we detected in 4 human stools the DNA of a recently described protozoon, Simplicimonas similis. Interestingly, subjects living in urban areas harbored significantly more different parasitic species than subjects living in rural areas with a correlation between sanitary level of neighborhood and protozoan infection. However, there was no difference in prevalence of digestive symptoms between parasite-free and parasite-infected subjects, except for Giardia intestinalis which had more symptomatic carriers.DISCUSSION: Our study reveals a high overall parasite prevalence, similar to what had been found in 2003 in the same city and to other prevalence studies conducted in Africa. The poor access of the population to sanitary infrastructures may explain this result. Data from our study provide valuable key for sanitation programs and prevention of fecal-related infectious diseases.

Published
2018

39. A strong link between marine microbial community composition and function challenges the idea of functional redundancy

Author

Jean-Christophe Auguet, Corentin Hochart, Didier Debroas, Pierre E. Galand, Olivier Pereira, Laboratoire d'Ecogéochimie des environnements benthiques (LECOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institute of Information and Communication Technologies, Electronics and Applied Mathematics (ICTEAM), Université Catholique de Louvain = Catholic University of Louvain (UCL), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD)

Subjects
0301 basic medicine, Time Factors, [SDV]Life Sciences [q-bio], media_common.quotation_subject, Microbial metabolism, Biology, Microbiology, Article, 03 medical and health sciences, Microbial ecology, Redundancy (engineering), 14. Life underwater, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, media_common, Bacteria, Ecology, Microbiota, 030104 developmental biology, Taxon, Microbial population biology, 13. Climate action, Metagenomics, [SDE]Environmental Sciences, Metagenome, Species richness, Diversity (politics)
Abstract

Marine microbes have tremendous diversity, but a fundamental question remains unanswered: why are there so many microbial species in the sea? The idea of functional redundancy for microbial communities has long been assumed, so that the high level of richness is often explained by the presence of different taxa that are able to conduct the exact same set of metabolic processes and that can readily replace each other. Here, we refute the hypothesis of functional redundancy for marine microbial communities by showing that a shift in the community composition altered the overall functional attributes of communities across different temporal and spatial scales. Our metagenomic monitoring of a coastal northwestern Mediterranean site also revealed that diverse microbial communities harbor a high diversity of potential proteins. Working with all information given by the metagenomes (all reads) rather than relying only on known genes (annotated orthologous genes) was essential for revealing the similarity between taxonomic and functional community compositions. Our finding does not exclude the possibility for a partial redundancy where organisms that share some specific function can coexist when they differ in other ecological requirements. It demonstrates, however, that marine microbial diversity reflects a tremendous diversity of microbial metabolism and highlights the genetic potential yet to be discovered in an ocean of microbes.

Published
2018

40. Clarin-1 gene transfer rescues auditory synaptopathy in model of Usher syndrome

Author

Omar Akil, Didier Dulon, Samantha Papal, Vincent Michel, Paul Avan, Alice Emptoz, Aziz El-Amraoui, Olinda Alegria-Prévot, Sedigheh Delmaghani, Pranav Patni, Lawrence R. Lustig, Christine Petit, Alain Aghaie, Abdelaziz Tlili, Elise Pepermans, Yohan Bouleau, Saaid Safieddine, Margot Tertrais, Matteo Cortese, Philippe F.Y. Vincent, Neurophysiologie de la Synapse Auditive, Université de Bordeaux (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU de Bordeaux Pellegrin [Bordeaux]-Neuroscience Institute, Génétique et Physiologie de l'Audition, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), ED 515 - Complexité du vivant, Université Pierre et Marie Curie - Paris 6 (UPMC), University of California [San Francisco] (UC San Francisco), University of California (UC), Columbia University [New York], Equipe Biophysique Neurosensorielle [Neuro-Dol], Neuro-Dol (Neuro-Dol), Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Neuro-Dol (Neuro-Dol), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Centre National de la Recherche Scientifique (CNRS), Collège de France - Chaire Génétique et physiologie cellulaire, Collège de France (CdF (institution)), SP and MC benefited from fellowships from the Ministry of National Education, Research and Technology of France, and PP from the European Union’s Horizon 2020 Marie Sklodowska-Curie grant 665807. This work was supported by European Research Council (ERC) advanced grant 'Hair bundle' (ERC-2011-AdG 294570), the European Union Seventh Framework Programme under grant agreement HEALTH-F2-2010-242013 (TREATRUSH), the French National Research Agency (ANR) as part of the second 'Investissements d’Avenir' programme (light4deaf, ANR-15-RHUS-0001), ANR-HearInNoise-(ANR-17-CE16-0017), LHW-Stiftung, FAUN Stiftung (Suchert Foundation), LABEX Life-senses (ANR-10-LABX-65), and a grant from the Fondation Pour l’Audition to DD (2015-APA Research Grant)., We thank Jean-Pierre Hardelin and Jacques Boutet de Monvel for critical reading of the manuscript., ANR-15-RHUS-0001,LIGHT4DEAF,ECLAIRER LA SURDITÉ : UNE APPROCHE HOLISTIQUE DU SYNDROME D'USHER(2015), ANR-11-IDEX-0004,SUPER,Sorbonne Universités à Paris pour l'Enseignement et la Recherche(2011), European Project: 294570,EC:FP7:ERC,ERC-2011-ADG_20110310,HAIRBUNDLE(2012), European Project: 242013,EC:FP7:HEALTH,FP7-HEALTH-2009-single-stage,TREATRUSH(2010), Neuroscience Institute-Université de Bordeaux ( UB ) -CHU de Bordeaux Pellegrin [Bordeaux]-Institut National de la Santé et de la Recherche Médicale ( INSERM ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Collège de France ( CdF ) -Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale ( INSERM ), Biologie du fruit et pathologie ( BFP ), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique ( INRA ) -Université Sciences et Technologies - Bordeaux 1, Laboratoire Biochimie et Biologie Moléculaire ( LBBM ), Université Hassan II, Neuro-Dol ( Neuro-Dol ), Université d'Auvergne - Clermont-Ferrand I ( UdA ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université d'Auvergne - Clermont-Ferrand I ( UdA ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Neuro-Dol - Clermont Auvergne ( Neuro-Dol ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université Clermont Auvergne ( UCA ) -Université Clermont Auvergne ( UCA ), Comité Français de la Semoulerie Industrielle ( CFSI ), Génétique et physiologie de l'audition, This work was supported by European Research Council (ERC) advanced grant 'Hair bundle' (ERC-2011-AdG 294570), the European Union Seventh Framework Programme under grant agreement HEALTH-F2-2010-242013 (TREATRUSH), the French National Research Agency (ANR) as part of the second 'Investissements d’Avenir' programme (light4deaf, ANR-15-RHUS-0001), ANR-HearInNoise-(ANR-17-CE16-0017), LHW-Stiftung, FAUN Stiftung (Suchert Foundation), LABEX Life-senses (ANR-10-LABX-65), and a grant from the Fondation Pour l’Audition to DD (2015-APA Research Grant)., ANR-15-RHUS-0001,LIGHT4DEAF,ECLAIRER LA SURDITÉ : UNE APPROCHE HOLISTIQUE DU SYNDROME D'USHER ( 2015 ), ANR-17-CE16-0017,HearInNoise,Surdité d’apparition tardive et progressive: de la physiopathologie à la thérapie ( 2017 ), ANR-11-IDEX-0004-02/10-LABX-0065,LIFESENSES,DES SENS POUR TOUTE LA VIE ( 2011 ), European Project : 294570,EC:FP7:ERC,ERC-2011-ADG_20110310,HAIRBUNDLE ( 2012 ), European Project : 242013,EC:FP7:HEALTH,FP7-HEALTH-2009-single-stage,TREATRUSH ( 2010 ), Neuroscience Institute-Université de Bordeaux (UB)-CHU de Bordeaux Pellegrin [Bordeaux]-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), University of California [San Francisco] (UCSF), University of California, Chaire Génétique et physiologie cellulaire, Oficjalska, Danuta, ECLAIRER LA SURDITÉ : UNE APPROCHE HOLISTIQUE DU SYNDROME D'USHER - - LIGHT4DEAF2015 - ANR-15-RHUS-0001 - RHUS - VALID, Sorbonne Universités à Paris pour l'Enseignement et la Recherche - - SUPER2011 - ANR-11-IDEX-0004 - IDEX - VALID, Assembling the puzzle of the operating auditory hair bundle - HAIRBUNDLE - - EC:FP7:ERC2012-12-01 - 2017-11-30 - 294570 - VALID, and Fighting blindness of Usher syndrome: diagnosis, pathogenesis and retinal treatment (TreatRetUsher) - TREATRUSH - - EC:FP7:HEALTH2010-02-01 - 2014-01-31 - 242013 - VALID

Subjects
0301 basic medicine, Calcium Channels, L-Type, Usher syndrome, PDZ domain, Cell Cycle Proteins, AMPA receptor, Ribbon synapse, Biology, 03 medical and health sciences, Mice, 0302 clinical medicine, Gene therapy, Postsynaptic potential, Hair Cells, Auditory, medicine, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, otorhinolaryngologic diseases, Animals, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Receptors, AMPA, Mice, Knockout, Gene Transfer Techniques, Membrane Proteins, General Medicine, Genetic Therapy, Dependovirus, medicine.disease, Cell biology, Cytoskeletal Proteins, Disease Models, Animal, Calcium channels, 030104 developmental biology, medicine.anatomical_structure, Knockout mouse, Synapses, Synaptopathy, Human medicine, Hair cell, [ SCCO ] Cognitive science, Carrier Proteins, Usher Syndromes, 030217 neurology & neurosurgery, Research Article, Neuroscience
Abstract

Clarin-1, a tetraspan-like membrane protein defective in Usher syndrome type IIIA (USH3A), is essential for hair bundle morphogenesis in auditory hair cells. We report a new synaptic role for clarin-1 in mouse auditory hair cells elucidated by characterization of Clrn1 total (Clrn1(ex4-/-)) and postnatal hair cell-specific conditional (Clrn1(ex4fl/fl) Myo15-Cre(+/-)) knockout mice. Clrn1(ex4-/-) mice were profoundly deaf, whereas Clrn1(ex4fl/fl) Myo15-Cre(+/-) mice displayed progressive increases in hearing thresholds, with, initially, normal otoacoustic emissions and hair bundle morphology. Inner hair cell (IHC) patch-clamp recordings for the 2 mutant mice revealed defective exocytosis and a disorganization of synaptic F-actin and Ca(V)1.3 Ca2+ channels, indicative of a synaptopathy. Postsynaptic defects were also observed, with an abnormally broad distribution of AMPA receptors associated with a loss of afferent dendrites and defective electrically evoked auditory brainstem responses. Protein-protein interaction assays revealed interactions between clarin-1 and the synaptic Ca(V)1.3 Ca2+ channel complex via the Ca-V beta(2) auxiliary subunit and the PDZ domain-containing protein harmonin (defective in Usher syndrome type IC). Cochlear gene therapy in vivo, through adeno-associated virus-mediated Clrn1 transfer into hair cells, prevented the synaptic defects and durably improved hearing in Clrn1(ex4fl/fl) Myo15-Cre(+/-) mice. Our results identify clarin-1 as a key organizer of IHC ribbon synapses, and suggest new treatment possibilities for USH3A patients.

Published
2018

41. Error-prone protein synthesis in parasites with the smallest eukaryotic genome

Author

Mark J. Solomon, Darryl J. Pappin, Arthur Makarenko, James J. Becnel, Catherine Texier, Denis Ostapenko, Dieter Söll, Neil D. Sanscrainte, Sergey Melnikov, Keith Rivera, National Research University of Information Technologies, Mechanics and Optics [St. Petersburg] (ITMO), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Department of Molecular Biophysics and Biochemistry-Yale (DMBB), Yale University [New Haven], and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA)

Subjects
0301 basic medicine, [SDV]Life Sciences [q-bio], 030106 microbiology, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Genome, Amino Acyl-tRNA Synthetases, Fungal Proteins, 03 medical and health sciences, RNA, Transfer, Protein biosynthesis, ComputingMilieux_MISCELLANEOUS, Genetics, Fungal protein, Multidisciplinary, Microsporida, fungi, Protein primary structure, RNA, Fungal, biology.organism_classification, 030104 developmental biology, PNAS Plus, Protein Biosynthesis, Proteome, Eukaryote, Genome, Fungal, Leucine
Abstract

Microsporidia are parasitic fungi-like organisms that invade the interior of living cells and cause chronic disorders in a broad range of animals, including humans. These pathogens have the tiniest known genomes among eukaryotic species, for which they serve as a model for exploring the phenomenon of genome reduction in obligate intracellular parasites. Here we report a case study to show an apparent effect of overall genome reduction on the primary structure and activity of aminoacyl-tRNA synthetases, indispensable cellular proteins required for protein synthesis. We find that most microsporidian synthetases lack regulatory and eukaryote-specific appended domains and have a high degree of sequence variability in tRNA-binding and catalytic domains. In one synthetase, LeuRS, an apparent sequence degeneration annihilates the editing domain, a catalytic center responsible for the accurate selection of leucine for protein synthesis. Unlike accurate LeuRS synthetases from other eukaryotic species, microsporidian LeuRS is error-prone: apart from leucine, it occasionally uses its near-cognate substrates, such as norvaline, isoleucine, valine, and methionine. Mass spectrometry analysis of the microsporidium Vavraia culicis proteome reveals that nearly 6% of leucine residues are erroneously replaced by other amino acids. This remarkably high frequency of mistranslation is not limited to leucine codons and appears to be a general property of protein synthesis in microsporidian parasites. Taken together, our findings reveal that the microsporidian protein synthesis machinery is editing-deficient, and that the proteome of microsporidian parasites is more diverse than would be anticipated based on their genome sequences.

Published
2018

42. Genetic diversity analysis of Blastocystis subtypes from both symptomatic and asymptomatic subjects using a barcoding region from the 18S rRNA gene

Author

Mohammad Reza Zali, Ivan Wawrzyniak, Mohammad Amin Pourhoseingholi, Ali Haghighi, Frédéric Delbac, Hamed Mirjalali, Tahereh Rezaei Riabi, Mohammad Rostami Nejad, Philippe Poirier, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), BRICHEUX, Genevieve, and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Microbiology (medical), Genetic Markers, Male, 030231 tropical medicine, Blastocystis Infections, [SDV.MP.PRO] Life Sciences [q-bio]/Microbiology and Parasitology/Protistology, Microbiology, Asymptomatic, Genetic analysis, [SDV.MP.PRO]Life Sciences [q-bio]/Microbiology and Parasitology/Protistology, 18S ribosomal RNA, 03 medical and health sciences, Feces, 0302 clinical medicine, Gene Frequency, Genetics, medicine, RNA, Ribosomal, 18S, Humans, Genetic variability, Allele, Molecular Biology, Asymptomatic Infections, Ecology, Evolution, Behavior and Systematics, Phylogeny, ComputingMilieux_MISCELLANEOUS, Blastocystis, Genetic diversity, biology, Phylogenetic tree, Genetic Variation, DNA, Protozoan, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, 030104 developmental biology, Infectious Diseases, Female, medicine.symptom, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Abstract

Blastocystis is the most prevalent protozoa found in human stool samples. This study aimed to evaluate genetic diversity among Blastocystis subtypes isolated from both symptomatic and asymptomatic subjects as well as the potential correlation between subtypes and symptoms. A total of 55 Blastocystis-positive isolates were included in this study. A barcoding region of the small subunit rDNA was amplified and genetically assessed using MEGA6 and DnaSP regarding the presence of symptoms. BLAST analyses revealed the presence of 5 different subtypes (ST1, ST2, ST3, ST6 and ST7) among the samples. ST3 was the most prevalent subtype (25/55, 45%) while only one ST7 isolate was detected. Moreover, alleles 4 and 86 for ST1; alleles 9, 11 and 12 for ST2; alleles 31, 34, 36, 37 and 52 for ST3; allele 122 for ST6 and allele 137 for ST7 were detected. No statistically significant association was found between gender and symptoms with certain subtypes. Analysis of the intra-subtype variability in both symptomatic and asymptomatic subjects revealed highest similarity among ST1 isolates while lowest similarity was seen among ST3 isolates. Neutrality indices, Tajima's D and Fu's Fs, were negative but only statistically significant for ST3. Furthermore, highest values of Hd, π and S were observed among ST1, ST2 and ST3 isolated from symptomatic patients indicating high level of diversity among isolates obtained from these subjects. In addition, inter-subtype analysis showed the highest similarity between ST1 and ST2 isolates and the lowest similarity between ST2 and ST7 isolates. This is the first study revealing the presence of both ST6 and ST7 isolates in human from Iran. Phylogenetic analysis did not suggest any significant correlation between clinical manifestations and certain subtypes although genetic analysis showed highest value of diversity and significant neutrality indices among ST3 isolates obtained from symptomatic patients.

Published
2018

43. Plasmids carrying DHA-1 β-lactamases

Author

Frédéric Robin, Claire Hennequin, Viviane Ravet, MEB, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA)

Subjects
0301 basic medicine, Microbiology (medical), Salmonella, Klebsiella pneumoniae, Antibiotic resistance, 030106 microbiology, Microbial Sensitivity Tests, medicine.disease_cause, beta-Lactamases, 03 medical and health sciences, Plasmid, Bacterial Proteins, Drug Resistance, Multiple, Bacterial, medicine, Humans, AmpC, Insertion sequence, Gene, Cephalosporinase, Genetics, biology, General Medicine, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, bacterial infections and mycoses, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Anti-Bacterial Agents, Klebsiella Infections, Multiple drug resistance, Infectious Diseases, Composite transposon, DHA-1, Plasmids
Abstract

International audience; The aim of this review is to provide an update on the plasmids mediating DHA-1 cephalosporinase in Klebsiella pneumoniae. These plasmids have been mainly found in this bacterium but not only. The first was isolated from Salmonella sp. in France in the early 1990s. They are currently reported worldwide. Bla (DHA-1) beta-lactamase gene is usually co-expressed with many other antibiotic resistance genes such as extended-spectrum beta-lactamases (bla (CTX-M) -, bla (SHV) -types), oxacillinases (bla (OXA-1,) bla (OXA-30) ), penicillinases (bla (TEM) -type), carbapenemases (bla (OXA48) , bla (KPC-2) ), aminoglycosides (aacA, aadA, armA), fluoroquinolones (qnrB4, aac6'-1b-cr), and sulfonamide (sul1) resistance genes. Plasmids carrying DHA-1 cephalosporinase have different sizes (22 to 313 kb), belong to diverse groups of incompatibility (R, L/M, FII(k), FIB, A/C2, HI2, HIB), and are self-transferable or not. The multidrug resistance region consists of a mosaic structure composed of resistance genes, insertion sequences, composite transposon, and integrons.

Published
2018

44. Hygroregulation, a key ability for eusocial insects: Native Western European bees as a case study

Author

Télesphore Sime-Ngando, Francis Fabre, Cátia J. Neves, Andone Estonba, Iris Eouzan, Iratxe Montes, Sylvie Houte, David Biron, Maria Alice Pinto, Jérôme Lesobre, Lionel Garnery, Damien Delalande, Laboratoire Microorganismes : Génome et Environnement - Clermont Auvergne (LMGE), Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), Évolution, génomes, comportement et écologie (EGCE), Université Paris-Sud - Paris 11 (UP11)-IRD-Centre National de la Recherche Scientifique (CNRS), Instituto Politécnico de Bragança, Centro de Investigação de Montanha (CIMO), Laboratoire Evolution, Génomes et Spéciation [Gif-sur-Yvette] (LEGS), Institut de recherche pour le développement [IRD] : UR072-Centre National de la Recherche Scientifique (CNRS), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), Institut National de la Recherche Agronomique (INRA)-Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Department of Genetics, Physical Anthropology and Animal Physiology [Spain] (UPV/EHU), University of the Basque Country [Bragança, Spain], Universidad del Pais Vasco / Euskal Herriko Unibertsitatea [Espagne] (UPV/EHU), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Evolution, génomes, comportement et écologie (EGCE), Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Centro de Investigação de Montanha [Bragança, Portugal] (CIMO), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), and Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
0106 biological sciences, Population, Zoology, Hymenoptera, Biology, Subspecies, 010603 evolutionary biology, 01 natural sciences, Honeybees, 03 medical and health sciences, Nest, education, 030304 developmental biology, 0303 health sciences, education.field_of_study, Larva, humidity, biology.organism_classification, Eusociality, Brood, Pupa, [SDE]Environmental Sciences, hygroregulation, subspecies, Apis mellifera, black bee
Abstract

Sociality has brought many advantages to various hymenoptera species, including their ability of regulating physical factors in their nest (e.g., temperature). Although less studied, humidity is known to be important for egg, larval and pupal development. Two subspecies ofApis melliferaof the M branch, also called black bees, were used as models to test the “hygroregulation hypothesis”, by means of monitoring hygrometry in hives during one year in four conservation centers: two in France (A. m. mellifera) and two in Portugal (A. m. iberiensis). We investigated the ability of both subspecies to regulate the hygrometry daily, but also during the seasons and one complete year. Our data and statistical analysis probed the capacity of the bees to regulate humidity in their hive, regardless of the day, season or subspecies. Furthermore, the study showed that humidity in beehives is very stable even during winter, when brood is absent, and when temperature is known to be less stable in the beehives. These results would support that hygrometry could prevail over temperature in maintaining nest homeostasis, maybe because of a bigger importance of hygrometry for all the population during a year, or because of the ‘imprint’ of the evolutionary history of this hymenopteran lineage.

Published
2018

45. GCN2 contributes to mTORC1 inhibition by leucine deprivation through an ATF4 independent mechanism

Author

Florent Mesclon, Christopher G. Proud, Céline Jousse, Laurent Parry, Anne Catherine Maurin, Valérie Carraro, Julien Averous, Alain Bruhat, Pierre Fafournoux, Sarah Lambert-Langlais, Philippe Pierre, Unité de Nutrition Humaine - Clermont Auvergne (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Centre d'Immunologie de Marseille - Luminy (CIML), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Aix Marseille Université (AMU), Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Institute for Research in Biomedicine, University of Aveiro, South Australian Health and Medical Research Institute [ Adelaide] (SAHMRI), University of Adelaide, Unité de Nutrition Humaine (UNH), Université d'Auvergne - Clermont-Ferrand I (UdA)-Clermont Université-Institut National de la Recherche Agronomique (INRA), Institute for Research in Biomedicine ( iBiMED), Universidade de Aveiro, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia, Institut National de la Recherche Agronomique (INRA) Fondation ARC pour la Recherche sur le CancerIlidio Pinho foundation, Institut National de la Recherche Agronomique (INRA)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Clermont Université, Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of South Australia [Adelaide], Institut National de la Recherche Agronomique (INRA), Fondation ARC pour la Recherche sur le Cancer, Ilidio Pinho foundation, Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), ProdInra, Archive Ouverte, Unité de Nutrition Humaine - Clermont Auvergne ( UNH ), Université Clermont Auvergne ( UCA ) -Institut national de la recherche agronomique [Auvergne/Rhône-Alpes] ( INRA Auvergne/Rhône-Alpes ), U1104, UMR 7280, Centre d'Immunologie de Marseille-Luminy ( CIML ), Aix Marseille Université ( AMU ), Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique ( CNRS ), South Australian Health and Medical Research Institute ( SAHMRI ), and VAFFIDES, Chantal

Subjects
0301 basic medicine, Arginine, [ SDV.AEN ] Life Sciences [q-bio]/Food and Nutrition, Eukaryotic Initiation Factor-2, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Mechanistic Target of Rapamycin Complex 1, Protein Serine-Threonine Kinases, Biology, Activating Transcription Factor 4, Article, Mice, 03 medical and health sciences, Leucine, preinitiation complex, translational control, pathway, mammalian target, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Animals, Food and Nutrition, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Phosphorylation, chemistry.chemical_classification, ATF3, Multidisciplinary, synthèse de protéine, ATF4, Translation (biology), muscle squelettique, Fibroblasts, Embryo, Mammalian, Amino acid, [SDV.AEN] Life Sciences [q-bio]/Food and Nutrition, acide aminé, 030104 developmental biology, voluntary muscle, Biochemistry, chemistry, Alimentation et Nutrition, biological phenomena, cell phenomena, and immunity, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, amino acid, Signal Transduction, expression des gènes
Abstract

It is well known that the GCN2 and mTORC1 signaling pathways are regulated by amino acids and share common functions, in particular the control of translation. The regulation of GCN2 activity by amino acid availability relies on the capacity of GCN2 to sense the increased levels of uncharged tRNAs upon amino acid scarcity. In contrast, despite recent progress in the understanding of the regulation of mTORC1 by amino acids, key aspects of this process remain unsolved. In particular, while leucine is well known to be a potent regulator of mTORC1, the mechanisms by which this amino acid is sensed and control mTORC1 activity are not well defined. Our data establish that GCN2 is involved in the inhibition of mTORC1 upon leucine or arginine deprivation. However, the activation of GCN2 alone is not sufficient to inhibit mTORC1 activity, indicating that leucine and arginine exert regulation via additional mechanisms. While the mechanism by which GCN2 contributes to the initial step of mTORC1 inhibition involves the phosphorylation of eIF2α, we show that it is independent of the downstream transcription factor ATF4. These data point to a novel role for GCN2 and phosphorylation of eIF2α in the control of mTORC1 by certain amino acids.

Published
2018

46. Infection-related ventilator-associated complications in ICU patients colonised with extended-spectrum beta-lactamase-producing Enterobacteriaceae

Author

Laurent Papazian, Michael Darmon, Dany Goldgran-Toledano, Benoit Misset, Elie Azoulay, Sébastien Bailly, Etienne de Montmollin, Laurent Argaud, Hatem Kallel, Guillaume Marcotte, Jean-Ralph Zahar, Bruno Mourvillier, Shidasp Siami, Bertrand Souweine, Carole Schwebel, Jean Reignier, François Barbier, Jean-François Timsit, Clinique de réanimation médicale, Université Joseph Fourier - Grenoble 1 (UJF)-CHU Grenoble-Hôpital Michallon, Hôpital Sainte-Marguerite [CHU - APHM] (Hôpitaux Sud ), Hôpital Saint-Louis, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Diderot - Paris 7 (UPD7), Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française], Hôpital Sud Francilien Corbeil-Essonnes, Hospices Civils de Lyon (HCL), Cardiovasculaire, métabolisme, diabétologie et nutrition (CarMeN), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM), Hôpital Edouard Herriot [CHU - HCL], Service d'anesthésie et réanimation chirurgicale [Nantes], Hôtel-Dieu-Centre hospitalier universitaire de Nantes (CHU Nantes), Service des Urgences et de Réanimation Médicale (Urg - SAINT ETIENNE), Centre Hospitalier Universitaire de Saint-Etienne [CHU Saint-Etienne] (CHU ST-E), Hôpital Avicenne [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Infection, Anti-microbiens, Modélisation, Evolution (IAME (UMR_S_1137 / U1137)), Université Paris 13 (UP13)-Université Paris Diderot - Paris 7 (UPD7)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Service de réanimation médicale et infectieuse, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-AP-HP - Hôpital Bichat - Claude Bernard [Paris], Hôpital Sainte-Marguerite, CHU Marseille, Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Université Paris Diderot - Paris 7 (UPD7), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hospices Civils de Lyon (HCL), Centre Hospitalier Universitaire de Saint-Etienne (CHU de Saint-Etienne), Hôpital avicenne, Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Université Paris 13 (UP13)-Hôpital Avicenne, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris 13 (UP13)-Université Paris Diderot - Paris 7 (UPD7)-Université Sorbonne Paris Cité (USPC), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-AP-HP - Hôpital Bichat - Claude Bernard [Paris]-Université Paris Diderot - Paris 7 (UPD7), Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National de la Recherche Agronomique (INRA), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Université Paris 13 (UP13)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Avicenne, Université Paris Diderot - Paris 7 (UPD7)-AP-HP - Hôpital Bichat - Claude Bernard [Paris]-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP), Université Paris Diderot - Paris 7 (UPD7)-AP-HP - Hôpital Bichat - Claude Bernard [Paris], and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)

Subjects
Male, 0301 basic medicine, Carbapenem, gram-negative bacilli, [SDV]Life Sciences [q-bio], Pneumonia ventilator associated, Critical Care and Intensive Care Medicine, antibiotic-therapy, 0302 clinical medicine, Mechanical ventilation, polycyclic compounds, Prospective Studies, 030212 general & internal medicine, urinary-tract-infections, bacteria, Outcome, biology, Enterobacteriaceae Infections, Ventilator-associated pneumonia, Pneumonia, Ventilator-Associated, Enterobacteriaceae, 3. Good health, Extended-spectrum beta-lactamase, Intensive Care Units, strategies, Carrier State, surveillance, Female, France, medicine.drug, intensive-care units, metaanalysis, Icu patients, medicine.medical_specialty, 030106 microbiology, beta-Lactamases, 03 medical and health sciences, Antibiotic resistance, Internal medicine, Antibiotic therapy, General & Internal Medicine, medicine, Humans, pneumonia, antimicrobial resistance, Aged, business.industry, Gram negative bacilli, biochemical phenomena, metabolism, and nutrition, medicine.disease, biology.organism_classification, bacterial infections and mycoses, Carbapenems, business
Abstract

International audience; Purpose: To investigate the clinical significance of infection-related ventilator-associated complications (IVAC) and their impact on carbapenem consumption in mechanically ventilated (MV) patients colonised with extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBLE). Methods: Inception cohort study from the French prospective multicenter OUTCOMEREA database (17 ICUs, 1997-2015) including all ESBLE carriers (systematic rectal swabbing at admission then weekly and/or urinary or superficial surgical site colonisation) with MV duration \textgreater 48 h and \textgreater= 1 episode of IVAC after carriage documentation. All ICU-acquired infections were microbiologically documented. Results: The 318 enrolled ESBLE carriers (median age 68 years; males 67%; medical admission 68%; imported carriage 53%) experienced a total of 576 IVAC comprising 361 episodes (63%) without documented infection, 124 (21%) related to infections other than ventilator-associated pneumonia (VAP), 73 (13%) related to non-ESBLE VAP and 18 (3%) related to ESBLE VAP. Overall, ESBLE infections accounted for only 43 episodes (7%). Carbapenem exposure within the preceding 3 days was the sole independent predictor of ESBLE infection as the causative event of IVAC, with a protective effect (adjusted odds ratio 0.2, 95% confidence interval 0.05-0.6; P \textless 0.01). Carbapenems were initiated in 9% of IVAC without infection, 15% of IVAC related to non-VAP infections, 42% of IVAC related to non-ESBLE VAP, and 56% of IVAC related to ESBLE VAP (ESBLE VAP versus non-ESBLE VAP: P = 0.43). Conclusions: IVAC in ESBLE carriers mostly reflect noninfectious events but act as a strong driver of empirical carbapenem consumption. ESBLE infections are scarce yet hard to predict, strengthening the need for novel diagnostic approaches and carbapenem-sparing alternatives.

Published
2018

47. Population Structure of Candida parapsilosis: No Genetic Difference Between French and Uruguayan Isolates Using Microsatellite Length Polymorphism

Author

Françoise Dromer, Marie Desnos-Ollivier, Victoria Bórmida, Philippe Poirier, Stéphane Bretagne, Céline Nourrisson, Dinorah Pan, Andrès Puime, Centre National de Référence Mycologie et Antifongiques-Mycologie Moléculaire (CNRMA), Institut Pasteur [Paris], Ministerio de salud publica, Unidad de Parasitologia y Micologia, Montevideo, Uruguay, Universidad de Montevideo, CHU Clermont-Ferrand, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Université Paris Diderot - Paris 7 (UPD7), Laboratoire de Parasitologie-Mycologie [CHU Saint Louis, Paris], Groupe Hospitalier Saint Louis - Lariboisière - Fernand Widal [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), The YEASTS program was supported in part by Institut de Veille Sanitaire/Santé Publique France, and Institut Pasteur. This work was partially supported by grants from the Uruguayan Agency for Innovation and Research (ANII_FSS_2009_1721, ANII_POS_2011_1_3472) and French Embassy in Uruguay/Amsud Pasteur. The funders had no role in study design, data collection, analysis or interpretation of data., Institut Pasteur [Paris] (IP), Centre National de Référence des Mycoses invasives et antifongiques - Mycologie moléculaire (CNRMA), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut national de recherches archéologiques préventives (Inrap), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Service de parasitologie [Mondor], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Mycologie moléculaire, Centre National de Référence Mycoses Invasives et Antifongiques - National Reference Center Invasive Mycoses & Antifungals (CNRMA), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Parasitologie et Mycologie [CHU Clermont-Ferrand], CHU Gabriel Montpied [Clermont-Ferrand], CHU Clermont-Ferrand-CHU Clermont-Ferrand, Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Hôpital Saint-Louis, and Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Université Paris Diderot - Paris 7 (UPD7)

Subjects
0301 basic medicine, Candida parapsilosis, Genotype, Genotyping Techniques, Veterinary (miscellaneous), [SDV]Life Sciences [q-bio], 030106 microbiology, Population, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Population structure, Applied Microbiology and Biotechnology, Microbiology, [SDV.MP.PRO]Life Sciences [q-bio]/Microbiology and Parasitology/Protistology, 03 medical and health sciences, Polymorphism (computer science), Humans, education, Mycological Typing Techniques, Microsatellites genotyping, Genotyping, ComputingMilieux_MISCELLANEOUS, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Genetics, Candida parapsilosis Microsatellites genotyping Azoles resistance Candidemia Population structure, education.field_of_study, Genetic diversity, Molecular Epidemiology, biology, Outbreak, Genetic Variation, Candidemia, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Microsatellite, Uruguay, Azoles resistance, France, Agronomy and Crop Science, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Microsatellite Repeats
Abstract

International audience; Candida parapsilosis is a human commensal yeast, frequently involved in infection worldwide and especially in neonates. It is the second species responsible for bloodstream infections in Uruguay and the third species in France. We were interested in knowing whether the population structure of isolates responsible for candidemia in France and in Uruguay was different. Genotyping methods based on microsatellite length polymorphism (MLP) have been described and are especially used for investigation of local outbreaks. We therefore determined the genotypes of 159 C. parapsilosis isolates recovered from 122 patients (84 French patients from 43 hospitals and 38 Uruguayan patients from 10 hospitals) using three microsatellites markers previously described. Our results confirmed that C. parapsilosis population has a high genetic diversity, clonal inheritance and that majority of patients were infected by a single isolate. But we described recurrent infections due to related or unrelated genotypes resulting from isolates harboring loss or gain of heterozygosity. We also described three cases of coinfections due to unrelated genotypes. We did not uncover geographic specificity but observed two linked genotypes that seem to be associated with voriconazole resistance. Finally, among eight isolates involved in grouped cases, the genotypes were similar in six cases supporting the hypothesis of inter-patient transmission. These results confirmed the usefulness of performing MLP genotyping analysis for grouped cases of C. parapsilosis isolates in order to reinforce preventive hygiene measures.

Published
2018

48. Effects of the gut parasite Nosema ceranae on honey bee physiology and behavior

Author

Laurianne Paris, Marie Diogon, Frédéric Delbac, Hicham El Alaoui, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), and BRICHEUX, Genevieve

Subjects
0301 basic medicine, [SDE.MCG]Environmental Sciences/Global Changes, 030106 microbiology, Foraging, Physiology, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, [SDV.MP.PRO] Life Sciences [q-bio]/Microbiology and Parasitology/Protistology, complex mixtures, [SDV.MP.PRO]Life Sciences [q-bio]/Microbiology and Parasitology/Protistology, 03 medical and health sciences, Nosema, Microsporidiosis, Parasite hosting, Animals, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Behavior, Animal, Host (biology), digestive, oral, and skin physiology, fungi, food and beverages, Midgut, Honey bee, Bees, biology.organism_classification, Nosema ceranae, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Western honey bee, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDE.MCG] Environmental Sciences/Global Changes, 030104 developmental biology, Insect Science, behavior and behavior mechanisms, Pheromone, Female, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

The common and widespread parasite Nosema ceranae is considered a major threat to the Western honey bee at both the individual and colony levels. Several studies demonstrated that infection by this parasite may affect physiology, behavior, and survival of honey bees. N. ceranae infection impairs midgut integrity and alters the energy demand in honey bees. The infection can also significantly suppress the bee immune response and modify pheromone production in worker and queen honey bees leading to precocious foraging. However, the presence of N. ceranae is not systematically associated with colony weakening and honey bee mortality. This variability depends upon parasite or host genetics, nutrition, climate or interactions with other stressors such as environmental contaminants or other parasites.

Published
2018

49. Invasive Infections Caused by Nannizziopsis spp. Molds in Immunocompromised Patients

Author

Christine Jacomet, Charlotte Bothorel, Sophie Cayot, Philippe Poirier, Albane Ledoux-Pilon, Olivier Lesens, Magali Vidal-Roux, Fanny Anthony-Moumouni, Céline Nourrisson, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), CHU Clermont-Ferrand, Service d'Anatomie Pathologique [CHU Clermont-Ferrand], CHU Gabriel Montpied [Clermont-Ferrand], CHU Clermont-Ferrand-CHU Clermont-Ferrand, Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA)

Subjects
0301 basic medicine, Antifungal Agents, Epidemiology, Nannizziopsis, Biopsy, lcsh:Medicine, HIV Infections, invasive fungal infection, emerging disease, ComputingMilieux_MISCELLANEOUS, medicine.diagnostic_test, biology, Dispatch, Middle Aged, 3. Good health, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, immunocompromised patients, Female, Radiology, France, Microbiology (medical), medicine.medical_specialty, Cerebral Abscesses, 030106 microbiology, [SDV.MP.PRO]Life Sciences [q-bio]/Microbiology and Parasitology/Protistology, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Immunocompromised Host, central nervous system fungal infection, molds, medicine, Dermatomycoses, Humans, lcsh:RC109-216, business.industry, Arthrodermataceae, lcsh:R, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 030104 developmental biology, Tomography x ray computed, fungi, business, Tomography, X-Ray Computed, Invasive Infections Caused by Nannizziopsis spp. Molds in Immunocompromised Patients, opportunistic fungal pathogen, Biomarkers, Invasive Fungal Infections, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

We report 2 new cases of invasive infections caused by Nannizziopsis spp. molds in France. Both patients had cerebral abscesses and were immunocompromised. Both patients had recently spent time in Africa.

Published
2018

50. Early Retinal Defects in Fmr1−/y Mice: Toward a Critical Role of Visual Dys-Sensitivity in the Fragile X Syndrome Phenotype?

Author

Olivier Perche, Chloé Felgerolle, Maryvonne Ardourel, Audrey Bazinet, Arnaud Pâris, Rafaëlle Rossignol, Géraldine Meyer-Dilhet, Anne-Laure Mausset-Bonnefont, Betty Hébert, David Laurenceau, Céline Montécot-Dubourg, Arnaud Menuet, Jean-Charles Bizot, Jacques Pichon, Isabelle Ranchon-Cole, Sylvain Briault, Bonnefont, Anne-Laure, Centre Hospitalier Régional d'Orléans (CHRO), Immunologie et Neurogénétique Expérimentales et Moléculaires (INEM), Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS), Institut de Myologie, Université Pierre et Marie Curie - Paris 6 (UPMC)-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)-Centre National de la Recherche Scientifique (CNRS), Laboratoire pluridisciplinaire de recherche en ingénierie des systèmes, mécanique et énergétique (PRISME), Université d'Orléans (UO)-Institut National des Sciences Appliquées - Centre Val de Loire (INSA CVL), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA), Cellules Souches, Plasticité Cellulaire, Médecine Régénératrice et Immunothérapies (IRMB), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), laboratoire de Neurobiologie, Université d'Orléans (UO), Key-Obs, Equipe Biophysique Neurosensorielle [Clermont-Ferrand], Neuro-Dol (Neuro-Dol), Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS)-Université d'Orléans (UO), and Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)

Subjects
0301 basic medicine, congenital, hereditary, and neonatal diseases and abnormalities, vision, Biology, sensorial dys-sensitivity, lcsh:RC321-571, 03 medical and health sciences, chemistry.chemical_compound, Cellular and Molecular Neuroscience, 0302 clinical medicine, peripheral nervous system, medicine, [SDV.NEU] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], lcsh:Neurosciences. Biological psychiatry. Neuropsychiatry, Fmrp, Retina, Retinal, medicine.disease, FMR1, Phenotype, Fragile X syndrome, 030104 developmental biology, Visual cortex, medicine.anatomical_structure, chemistry, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Neuron, Retinal Defect, Neuroscience, 030217 neurology & neurosurgery
Abstract

International audience; Fragile X Syndrome (FXS) is caused by a deficiency in Fragile X Mental Retardation Protein (FMRP) leading to global sensorial abnormalities, among which visual defects represent a critical part. These visual defects are associated with cerebral neuron immaturity especially in the primary visual cortex. However, we recently demonstrated that retinas of adult Fmr1 −/y mice, the FXS murine model, present molecular, cellular and functional alterations. However, no data are currently available on the evolution pattern of such defects. As retinal stimulation through Eye Opening (EO) is a crucial signal for the cerebral visual system maturation, we questioned the precocity of molecular and functional retinal phenotype. To answer this question, we studied the retinal molecular phenotype of Fmr1 −/y mice before EO until adult age and the consequences of the retinal loss of Fmrp on retinal function in young and adult mice. We showed that retinal molecular defects are present before EO and remain stable at adult age, leading to electrophysiological impairments without any underlying structural changes. We underlined that loss of Fmrp leads to a wide range of defects in the retina, settled even before EO. Our work demonstrates a critical role of the sensorial dysfunction in the Fmr1 −/y mice overall phenotype, and provides evidence that altered peripheral perception is a component of the sensory processing defect in FXS conditions.

Published
2018

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