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92 results on '"Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU )"'

1. Analysis of trapped mosquito excreta as a noninvasive method to reveal biodiversity and arbovirus circulation

Author

Grégory L'Ambert, Mathieu Gendrot, Sébastien Briolant, Agnès Nguyen, Sylvain Pages, Laurent Bosio, Vincent Palomo, Nicolas Gomez, Nicolas Benoit, Hélène Savini, Bruno Pradines, Guillaume André Durand, Isabelle Leparc‐Goffart, Gilda Grard, Albin Fontaine, Entente Interdépartementale pour la démoustication du littoral méditerranéen (EID), Institut de Recherche Biomédicale des Armées [Antenne Marseille] (IRBA), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Biofidal, Université Montpellier 1 (UM1), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Unité des Virus Emergents (UVE), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
Culicidae, Flavivirus, [SDV]Life Sciences [q-bio], Genetics, Animals, Humans, Biodiversity, West Nile virus, Arboviruses, Ecology, Evolution, Behavior and Systematics, Biotechnology
Abstract

Emerging and endemic mosquito-borne viruses can be difficult to detect and monitor because they often cause asymptomatic infections in human or vertebrate animals or cause nonspecific febrile illness with a short recovery waiting period. Some of these pathogens circulate into complex cryptic cycles involving several animal species as reservoir or amplifying hosts. Detection of cases in vertebrate hosts can be complemented by entomological surveillance, but this method is not adapted to low infection rates in mosquito populations that typically occur in low or nonendemic areas. We identified West Nile virus circulation in Camargue, a wetland area in South of France, using a cost-effective xenomonitoring method based on the molecular detection of virus in excreta from trapped mosquitoes. We also succeeded at identifying the mosquito species community on several sampling sites, together with the vertebrate hosts on which they fed prior to being captured using amplicon-based metabarcoding on mosquito excreta without processing any mosquitoes. Mosquito excreta-based virus surveillance can complement standard surveillance methods because it is cost-effective and does not require personnel with a strong background in entomology. This strategy can also be used to noninvasively explore the ecological network underlying arbovirus circulation.

Published
2022

2. Culture and identification of a 'Deltamicron' SARS‐CoV‐2 in a three cases cluster in southern France

Author

Philippe Colson, Pierre‐Edouard Fournier, Jeremy Delerce, Matthieu Million, Marielle Bedotto, Linda Houhamdi, Nouara Yahi, Jeremy Bayette, Anthony Levasseur, Jacques Fantini, Didier Raoult, Bernard La Scola, COMBE, Isabelle, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), Unité de Neurobiologie des canaux Ioniques et de la Synapse (UNIS - Inserm U1072), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)

Subjects
[SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Base Sequence, SARS-CoV-2, COVID-19, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.MHEP.CSC] Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, Infectious Diseases, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Virology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Humans, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, ComputingMilieux_MISCELLANEOUS, [SDV.MP.PAR] Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Phylogeny
Abstract

Multiple SARS-CoV-2 variants have successively, or concommitantly spread worldwide since summer 2020. A few co-infections with different variants were reported and genetic recombinations, common among coronaviruses, were reported or suspected based on co-detection of signature mutations of different variants in a given genome. Here we report three infections in southern France with a Delta 21J/AY.4-Omicron 21K/BA.1 “Deltamicron” recombinant. The hybrid genome harbors signature mutations of the two lineages, supported by a mean sequencing depth of 1,163-1,421 reads and mean nucleotide diversity of 0.1-0.6%. It is composed of the near full-length spike gene (from codons 156-179) of an Omicron 21K/BA.1 variant in a Delta 21J/AY.4 lineage backbone. Importantly, we cultured an isolate of this recombinant and sequenced its genome. It was observed by scanning electron microscopy. As it is misidentified with current variant screening qPCR, we designed and implemented for routine diagnosis a specific duplex qPCR. Finally, structural analysis of the recombinant spike suggested its hybrid content could optimize viral binding to the host cell membrane. These findings prompt further studies of the virological, epidemiological, and clinical features of this recombinant.

Published
2022

3. Habitat mosaic as a driver of the resilience of native species: The case of the assemblage of small mammals from the city of Franceville, Gabon

Author

J. B. Mangombi‐Pambou, O. Fossati‐Gaschignard, N. N'Dilimabaka, O. Banga Mve‐Ella, N. M. Longo Pendy, S. E. Dibakou, O. Mediannikov, F. Fenollar, E. Leroy, M. Bourgarel, Centre International de Recherches Médicales de Franceville (CIRMF), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Université des Sciences et Techniques de Masuku (USTM), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)

Subjects
urban rodents, [SDV]Life Sciences [q-bio], habitat gradient, central African city, Animal Science and Zoology, community composition, landscape heterogeneity, Ecology, Evolution, Behavior and Systematics, introduced rodents
Abstract

International audience; Rodents (Rodentia) are the most abundant and diverse order of mammals, present in all habitats, including urban areas. The traffic linked to globalisation has favoured their involvement in biological invasions that have an impact on local biodiversity, the economy and human health. In Franceville, Gabon, little is known about the rodent community. We therefore studied the composition and distribution of rodents along a gradient highlighting the heterogeneity of the city's landscape. The three habitat types studied showed no difference in small mammal abundance, while the diversity index was higher in the vegetated habitat (SDI = 0.73) compared to the outdoor (SDI = 0.71) and indoor (SDI = 0.45) habitats. Our work shows the importance of vegetal remnants in the city for the maintenance of native species. It also highlights the impact of introduced species on small mammal assemblages and the need for management to reduce the factors of their proliferation.

Published
2023

4. Characteristics of the first 1119 SARS‐CoV‐2 Omicron variant cases, in Marseille, France, November−December 2021

Author

Linda HOUHAMDI, Van Thuan HOANG, Philippe Gautret, Philippe Colson, Pierre-Edouard Fournier, Didier Raoult, Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Microbes évolution phylogénie et infections (MEPHI), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, COVID-19 Vaccines, SARS-CoV-2, COVID-19, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Infectious Diseases, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Virology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Humans, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, France, ComputingMilieux_MISCELLANEOUS
Abstract

One thousand one hundred and nineteen cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant cases have been diagnosed at the Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France, between November 28, 2021, and December 31, 2021. Among the 825 patients with known vaccination status, 383 (46.4%) were vaccinated, of whom 91.9% had received at least two doses of the vaccine. Interestingly, 26.3% of cases developed SARS-CoV-2 infection within 21 days following the last dose of vaccine suggesting possible early production of anti-SARS-CoV-2 facilitating antibodies. Twenty-one patients have been hospitalized, one patient required intensive care, and another patient who received a vaccine booster dose died.

Published
2022

5. Diagnosis and management of rabies encephalitis in two patients in northwest Africa: A case series

Author

Boushab Mohamed Boushab, Hacen Ahmed Benane, Sidi El‐Wafi Ould Baba, Leonardo K. Basco, Kiffa Regional Hospital Assaba, Faculty of Medicine University of Nouakchott Al-Aasriya, WorldWide Antimalarial Resistance Network Falciparum Haematology Study Group, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), Kiffa Regional Hospital Center, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), and Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille)

Subjects
[SDV]Life Sciences [q-bio], General Medicine
Abstract

International audience

Published
2022

6. An absolute radiocarbon chronology for the world heritage site of Sarvestan (SW Iran): A late Sasanian heritage in early Islamic era

Author

Morteza Djamali, Manuela Capano, Nicolas Faucherre, Thibaut Tuna, Alastair Northedge, Alireza Askari-Chaverdi, Edouard Bard, Frédéric Guibal, Elnaz Rashidian, Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), History Department, Shiraz University, Shiraz, Iran, Laboratoire d'Archéologie Médiévale et Moderne en Méditerranée (LA3M), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Université Paris 1 Panthéon-Sorbonne (UP1), Chaire Evolution du climat et de l'océan, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-14-CE35-0026,PaleoPersepolis,The Persepolis Basin (SW Iran): a System Model to investigate Human-Climate-Ecosystem interactions during the Holocene(2014), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), and Collège de France - Chaire Evolution du climat et de l'océan

Subjects
010506 paleontology, Archeology, History, Ancient history, 01 natural sciences, Islamic architecture, law.invention, Late Antiquity, law, Fars, 0601 history and archaeology, Radiocarbon dating, 0105 earth and related environmental sciences, 060102 archaeology, radiocarbon dating, Sasanian architecture, Islam, 06 humanities and the arts, tree rings, Absolute (philosophy), World heritage, [SDE]Environmental Sciences, Chronology
Abstract

International audience; This study presents a new precise radiocarbon chronology for the World Heritage site of Sarvestan (SW Iran). The monument is a key construction in the history of architecture because it is a typical Sasanian construction built during the late Sasanian or early Islamic period. Previous attempts to date the monument have suggested the ages ranging from the middle Sasanian (fifth century CE) to early Abbasid (ninth century CE) era. These age estimations are based on the analysis of architectural plans and techniques, and a few radiocarbon dates with very large age uncertainties. This paper presents the results of a systematic radiocarbon dating of timbers in the walls and charcoals in plaster mortars used in the main dome of the monument. It further applies wiggle matching technique and R_Combine function to substantially reduce the age uncertainties in wood sections. The results indicate that a major construction work was undertaken sometime between 658 and 683 CE, the century of the invasion of Fars by Muslim Arabs. This finding pushes back the age of Sarvestan for two centuries and suggests that the monument was built at the transitional period between Sasanian to Islamic era. Sarvestan would have been an architectural project designed andpossibly initiated during the late Sasanian period but mainly accomplished during the second half of the seventh century CE. It can thus be considered a late Sasanian heritage in early Islamic period. Its construction at a time of political unrest further suggests that some areas of Fars may have benefited from certain socio-political stabilities during the expansion of Islaminto the east at mid- to late seventh century CE

Published
2021

7. How does innovative technology impact nursing in infectious diseases and infection control? A scoping review

Author

Huang, Fanyu, Brouqui, Philippe, Boudjema, Sophia, Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), ANR-15-CE36-0004,MHT,Analyse des facteurs associés à la non-observance a hygiène des mains par enregistrement continue des gestes d'hygiène en situation de soins avec un traceur par radiofréquence associé à un enregistreur de tache au lit du patient.(2015), ANR-10-IAHU-0003,Méditerranée Infection,I.H.U. Méditerranée Infection(2010), and Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)

Subjects
[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, infectious disease, RT1-120, nursing performance, Review Article, Communicable Diseases, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, infection control, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, nursing, Artificial Intelligence, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, quality of care, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, technology, Humans, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Review Articles
Abstract

International audience; AimConsidering the increasing number of emerging infectious diseases, innovative approaches are strongly in demand. Additionally, research in this field has expanded exponentially. Thus, faced with this diverse information, we aim to clarify key concepts and knowledge gaps of technology in nursing and the field of infectious diseases.DesignThis scoping review followed the methodology of scoping review guidance from Arksey and O’Malley.MethodsSix databases were searched systematically (PubMed, Web of Science, IEEE Explore, EBSCOhost, Cochrane Library and Summon). After the removal of duplicates, 532 citations were retrieved and 77 were included in the analysis.ResultsWe identified five major trends in technology for nursing and infectious diseases: artificial intelligence, the Internet of things, information and communications technology, simulation technology and e-learning. Our findings indicate that the most promising trend is the IoT because of the many positive effects validated in most of the reviewed studies.

Published
2021

8. Circulation of enterovirus A71 during 2019–2020, Marseille, France

Author

Aurélie Morand, Christine Zandotti, Géraldine Piorkowski, Léa Luciani, Antoine Nougairède, Aurélie Boutin, Philippe Minodier, Laetitia Ninove, Julie Mazenq, Unité des Virus Emergents (UVE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Service de pédiatrie spécialisée et médecine infantile (neurologie, pneumologie, maladies héréditaires du métabolisme) [Hôpital de la Timone - APHM], Hôpital de la Timone [CHU - APHM] (TIMONE), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Service des urgences pédiatriques, CHU Timone, Service des urgences pédiatriques, CHU Nord AP-HM, and COMBE, Isabelle

Subjects
Acute flaccid paralysis, Genotype, Genome, Viral, medicine.disease_cause, Viral Proteins, 03 medical and health sciences, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Virology, Enterovirus Infections, medicine, Humans, Paralysis, Viral rna, 030212 general & internal medicine, Respiratory samples, Phylogeny, ComputingMilieux_MISCELLANEOUS, Virus classification, Retrospective Studies, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, business.industry, Infant, Newborn, Infant, Enterovirus a71, Enterovirus A, Human, 3. Good health, Treatment Outcome, Infectious Diseases, Child, Preschool, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, RNA, Viral, Enterovirus, 030211 gastroenterology & hepatology, France, business, Paediatric population
Abstract

Enteroviruses A71 (EVs-A71) are known to cause serious neurological infections, especially in the paediatric population. We report here eight cases of EV-A71 infection diagnosed in Marseille over the past two years (seven cases in 2019 and one case in 2020). Only children under 5 years of age were affected, including one case of acute flaccid paralysis. Viral RNA was detected by RT-PCR in peripheral samples for all cases (faeces and upper respiratory samples). Phylogenetic analyses based on VP1 and 2C3C coding regions revealed that all these cases of EV-A71 infection were caused by viruses belonging to the subgenogroup C1 that currently circulates in Europe and that these viruses are genetically closed to other EVs-A71 recently detected in European countries. These data therefore reinforce the usefulness of enterovirus surveillance network and the need of systematic screening for EV-A71 in case of enteroviral infection. This study therefore suggests that the systematic screening for EV-A71 in case of enteroviral infection could provide additional data for enterovirus surveillance networks. This article is protected by copyright. All rights reserved.

Published
2021

9. Host–virus interactions and defense mechanisms for giant viruses

Author

Anthony Levasseur, Nisrine Chelkha, Philippe Colson, Bernard La Scola, Microbes évolution phylogénie et infections (MEPHI), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Virophages, viruses, Biology, Nucleocytoplasmic large DNA viruses, Genome, General Biochemistry, Genetics and Molecular Biology, Virus, 03 medical and health sciences, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, History and Philosophy of Science, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Giant Virus, Gene, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Comparative genomics, Genetics, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, 0303 health sciences, Innate immune system, 030306 microbiology, General Neuroscience, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology
Abstract

Giant viruses, with virions larger than 200 nm and genomes larger than 340 kilobase pairs, modified the now outdated perception of the virosphere. With virions now reported reaching up to 1.5 μm in size and genomes of up to 2.5 Mb encoding components shared with cellular life forms, giant viruses exhibit a complexity similar to microbes, such as bacteria and archaea. Here, we review interactions of giant viruses with their hosts and defense strategies of giant viruses against their hosts and coinfecting microorganisms or virophages. We also searched by comparative genomics for homologies with proteins described or suspected to be involved in defense mechanisms. Our search reveals that natural immunity and apoptosis seem to be crucial components of the host defense against giant virus infection. Conversely, giant viruses possess methods of hijacking host functions to counteract cellular antiviral responses. In addition, giant viruses may encode other unique and complex pathways to manipulate the host machinery and eliminate other competing microorganisms. Notably, giant viruses have evolved defense mechanisms against their virophages and they might trigger defense systems against other viruses through sequence integration. We anticipate that comparative genomics may help identifying genes involved in defense strategies of both giant viruses and their hosts.

Published
2020

10. On the small‐scale fractal geometrical structure of a living coral reef barrier

Author

Benjamin Dubarbier, Erik Doerflinger, Raphaël Certain, Frédéric Bouchette, Samuel Meulé, Damien Sous, Bernard Salvat, Gwladys Toulemonde, Laboratoire des Sciences de l'Ingénieur Appliquées à la Mécanique et au génie Electrique (SIAME), Université de Pau et des Pays de l'Adour (UPPA), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Géosciences Montpellier, Institut national des sciences de l'Univers (INSU - CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Modélisation et d'Analyses en géo-environnement et santé - Espace Développement (IMAGES-Espace DEV), UMR 228 Espace-Dev, Espace pour le développement, Institut de Recherche pour le Développement (IRD)-Université de Perpignan Via Domitia (UPVD)-Avignon Université (AU)-Université de La Réunion (UR)-Université de Montpellier (UM)-Université de Guyane (UG)-Université des Antilles (UA)-Institut de Recherche pour le Développement (IRD)-Université de Perpignan Via Domitia (UPVD)-Avignon Université (AU)-Université de La Réunion (UR)-Université de Montpellier (UM)-Université de Guyane (UG)-Université des Antilles (UA), Institut Montpelliérain Alexander Grothendieck (IMAG), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM), Centre National de la Recherche Scientifique (CNRS), Littoral, Environment: MOdels and Numerics (LEMON), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut Montpelliérain Alexander Grothendieck (IMAG), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Hydrosciences Montpellier (HSM), 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)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Environnements et Paléoenvironnements OCéaniques (EPOC), Observatoire aquitain des sciences de l'univers (OASU), Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Excellence CORAIL (LabEX CORAIL), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de La Réunion (UR)-Université de la Polynésie Française (UPF)-Université de la Nouvelle-Calédonie (UNC)-Institut d'écologie et environnement-Université des Antilles (UA), GLADYS, Institut national des sciences de l'Univers (INSU - CNRS)-Université de Montpellier (UM)-Université des Antilles (UA)-Centre National de la Recherche Scientifique (CNRS), Université de Guyane (UG)-Université des Antilles (UA)-Institut de Recherche pour le Développement (IRD)-Université de Perpignan Via Domitia (UPVD)-Avignon Université (AU)-Université de La Réunion (UR)-Université de Montpellier (UM)-Université de Guyane (UG)-Université des Antilles (UA)-Institut de Recherche pour le Développement (IRD)-Université de Perpignan Via Domitia (UPVD)-Avignon Université (AU)-Université de La Réunion (UR)-Université de Montpellier (UM), Littoral, Environnement : Méthodes et Outils Numériques (LEMON), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), Université des Antilles (UA)-Institut d'écologie et environnement-Université de la Nouvelle-Calédonie (UNC)-Université de la Polynésie Française (UPF)-Université de La Réunion (UR)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École des hautes études en sciences sociales (EHESS)-Université des Antilles et de la Guyane (UAG)-Institut de Recherche pour le Développement (IRD)

Subjects
geography, geography.geographical_feature_category, 010504 meteorology & atmospheric sciences, Coral, Geography, Planning and Development, Elevation, Context (language use), Global change, Coral reef, 010502 geochemistry & geophysics, 01 natural sciences, Fractal, Oceanography, Earth and Planetary Sciences (miscellaneous), 14. Life underwater, Scale (map), Reef, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, Geology, 0105 earth and related environmental sciences, Earth-Surface Processes
Abstract

International audience; Topographical complexity of coral reefs is of primary importance for a number of hydrodynamical and ecological processes. The present study is based on a series of high‐resolution seabottom elevation measurements along the Maupiti barrier reef, French Polynesia. Several statistical metrics and spectral analysis are used to characterize the spatial evolution of the coral geometrical structure from the reef crest to the backreef. A consistent fractal‐like power law exists in the spectral density of bottom elevation for length‐scales between 0.1 and 7m while, at larger scale, the reef structure shows a different pattern. Such a fine characterization of the reef geometrical structure provides key elements to reconstruct the reef history, to improve the representation of reef roughness in hydrodynamical models and to monitor the evolution of coral reef systems in the global change context.

Published
2020

11. Zika virus during pregnancy: From maternal exposure to congenital Zika virus syndrome

Author

Alice Panchaud, Gustavo Malinger, Manon Vouga, David Baud, Léo Pomar, Didier Musso, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), and Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)

Subjects
Zika virus, 03 medical and health sciences, 0302 clinical medicine, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, Pregnancy, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Prenatal Diagnosis, Humans, Medicine, Abnormalities, Multiple, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, 030212 general & internal medicine, Pregnancy Complications, Infectious, ComputingMilieux_MISCELLANEOUS, Genetics (clinical), 030304 developmental biology, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, 0303 health sciences, biology, Zika Virus Infection, business.industry, Infant, Newborn, Obstetrics and Gynecology, Zika Virus, Prognosis, medicine.disease, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Virology, 3. Good health, Maternal Exposure, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Microcephaly, Female, business
Abstract

Zika virus (ZIKV), a vector-borne virus similar to dengue virus, was responsible for a global epidemic between 2013 and 2017 and has emerged as a new agent responsible for severe fetopathies. We present a review to describe the risks and complications of maternal and subsequent fetal infection by ZIKV. The risk of ZIKV infection during pregnancy depends on the incidence of the disease, which is highly variable in different affected geographic areas (less than 1% to 75%). Among infected pregnant women, the risk of any adverse fetal/neonatal outcome was estimated at 5% to 42%, with 1% to 4% of fetal loss and 4% to 9% of suspected congenital Zika syndrome (CZS). The estimated rate of maternal-fetal transmission ranges between 7% and 26%, depending on the methodology of the study. Findings associated with CZS are microcephaly (33%-64%), ventriculomegaly (63%-92%), calcifications (71%-92%), malformations of cortical development (79%-82%), anomalies of the corpus callosum (71%-100%) and of the posterior fossa (21%-82%), arthrogryposis (10%-25%), eye abnormalities (25%), and extra-neurologic signs such as intra uterine growth restriction (14%), placentomegaly, transient hepatitis, mild anemia. Infants who present with CZS at birth suffer from motor abnormalities (77%-100%), epilepsy (9%-54%), hearing loss, and neurologic impairments. Prenatal ultrasound with advanced neurosonography and appropriate virological follow-up represent the state-of-the art approach to adequately monitor at-risk pregnancies, in order to diagnose early signs of CZS and to inform parents about the neonatal prognosis.

Published
2019

12. Prevalence ofAnaplasmataceaeandFilariidaespecies in unowned and military dogs in New Caledonia

Author

Didier Raoult, Florence Fenollar, Djamel Tahir, Olivier Cabre, Oleg Mediannikov, Mustapha Dahmani, Bernard Davoust, Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA)

Subjects
Male, 0301 basic medicine, Anaplasma platys, Neorickettsia, 040301 veterinary sciences, Filariidae, Dirofilaria immitis, kennels, Microbiology, 0403 veterinary science, 03 medical and health sciences, Dogs, New Caledonia, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, parasitic diseases, Prevalence, Animals, Helminths, Anaplasma, Dog Diseases, Filarioidea, General Veterinary, biology, Ehrlichia, Ownership, Original Articles, 04 agricultural and veterinary sciences, biology.organism_classification, Anaplasmataceae, Filariasis, 3. Good health, Military Personnel, 030104 developmental biology, Anaplasmataceae Infections, bacteria, Original Article, Female, Wolbachia
Abstract

International audience; Dogs are competent reservoir hosts of several zoonotic agents, including Filariidae nematodes and Anaplasmataceae family bacteria. The latter family unites human and veterinary pathogens (Anaplasma, Ehrlichia and Neorickettsia bacteria) with Wolbachia, some of which are obligatory endosymbionts of pathogenic filarial nematodes. The epidemiology of Anaplasmataceae and Filariidae species infecting dogs living in kennels in New Caledonia was studied. 64 EDTA blood samples were screened for the presence of Anaplasmataceae and filarial nematodes. Molecular study was conducted using primers and probe targeting the of 23S rRNA long fragment of Anaplasmataceae species. Next, all blood sample was screened for the presence of Filariidae species targeting the primers and probe targeting the COI gene, as well as primers targeting the COI and 5S rRNA genes of all filarial worms. Anaplasma platys was identified in 8/64 (12.5, 95% confidence interval [CI]: 4.4-20.6%) and Wolbachia endosymbiont of Dirofilaria immitis in 8/64 (12.5%, CI: 4.4-20.6%). Filariidae species investigation was performed and showed that 11/64 (17.2%, CI: 7.9-26.4%) dogs were infected with D. immitis, whereas, 2/64 (3.1%, CI: 0.0-7.3%) were infected with Acanthocheilonema reconditum. Finally, we checked the occurrence of co-infection between Anaplasmataceae and Filariidae species. Co-occurrence with Wolbachia endosymbiont of D. immitis was observed in seven dogs, one dog was co-infected with A. platys and A. reconditum and another was co-infected with Wolbachia endosymbiont of D. immitis and A. reconditum. These results are the first report of Anaplasmataceae and Filariidae occurring in dogs in New Caledonia.

Published
2018

13. Aspergillus fumigatus in cystic fibrosis: An update on immune interactions and molecular diagnostics in allergic bronchopulmonary aspergillosis

Author

Joana Vitte, Jean-Christophe Dubus, Thomas Romain, Martine Reynaud-Gaubert, Stéphane Ranque, Ania Carsin, Jean-Louis Mege, COMBE, Isabelle, Assistance Publique - Hôpitaux de Marseille (APHM), Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE), Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-Centre National de la Recherche Scientifique (CNRS), and INSB-INSB-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48

Subjects
0301 basic medicine, Pathology, medicine.medical_specialty, Cystic Fibrosis, Immunology, Cystic fibrosis, Aspergillus fumigatus, 03 medical and health sciences, 0302 clinical medicine, Immune system, Fibrosis, medicine, Humans, Immunology and Allergy, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, biology, business.industry, Aspergillosis, Allergic Bronchopulmonary, biology.organism_classification, medicine.disease, Molecular diagnostics, 3. Good health, 030104 developmental biology, 030228 respiratory system, Respiratory failure, Host-Pathogen Interactions, biology.protein, Antibody, Allergic bronchopulmonary aspergillosis, business, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

International audience; A wide spectrum of pathological conditions may result from the interaction of Aspergillus fumigatus and the immune system of its human host. Allergic bronchopulmonary aspergillosis is one of the most severe A.fumigatus-related diseases due to possible evolution toward pleuropulmonary fibrosis and respiratory failure. Allergic bronchopulmonary aspergillosis occurs almost exclusively in cystic fibrosis or asthmatic patients. An estimated 8%-10% of patients with cystic fibrosis experience this condition. The diagnosis of allergic bronchopulmonary aspergillosis relies on criteria first established in 1977. Progress in the understanding of host-pathogen interactions in A.fumigatus and patients with cystic fibrosis and the ongoing validation of novel laboratory tools concur to update and improve the diagnosis of allergic bronchopulmonary aspergillosis.

Published
2017

14. Multitarget selection of catalytic antibodies with β-lactamase activity using phage display

Author

Alain Friboulet, Nancy Chaaya, Srini V. Kaveri, Bérangère Avalle, Bernard Offmann, Narciso Costa, Séverine Padiolleau-Lefèvre, Melody A. Shahsavarian, Didier Boquet, Sébastien Lacroix-Desmazes, Alexandre P. Atkinson, Génie Enzymatique et Cellulaire (GEC), Université de Technologie de Compiègne (UTC)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ingénierie des Anticorps pour la Santé (LIAS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Unité de fonctionnalité et ingénierie de protéines (UFIP), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche des Cordeliers (CRC (UMR_S_1138 / U1138)), École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), École pratique des hautes études (EPHE), Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD), Unité Fonctionnalité et Ingénierie des Protéines (UFIP), Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), and École pratique des hautes études (EPHE)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)

Subjects
Models, Molecular, 0301 basic medicine, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Phage display, Population, Gene Expression, Antibodies, Catalytic, Penicillins, beta-Lactams, Biochemistry, Protein Structure, Secondary, beta-Lactamases, Substrate Specificity, Mice, Structure-Activity Relationship, 03 medical and health sciences, Peptide Library, Catalytic Domain, Escherichia coli, Animals, Protein Interaction Domains and Motifs, Amino Acid Sequence, Cloning, Molecular, Structural motif, education, Molecular Biology, ComputingMilieux_MISCELLANEOUS, chemistry.chemical_classification, education.field_of_study, 030102 biochemistry & molecular biology, biology, Chemistry, Hydrolysis, Active site, Cell Biology, Recombinant Proteins, In vitro, 3. Good health, Kinetics, 030104 developmental biology, Enzyme, Enzyme inhibitor, biology.protein, Immunization, Antibody, Sequence Alignment, Protein Binding, Single-Chain Antibodies
Abstract

β-lactamase enzymes responsible for bacterial resistance to antibiotics are among the most important health threats to the human population today. Understanding the increasingly vast structural motifs responsible for the catalytic mechanism of β-lactamases will help improve the future design of new generation antibiotics and mechanism-based inhibitors of these enzymes. Here we report the construction of a large murine single chain fragment variable (scFv) phage display library of size 2.7 × 109 with extended diversity by combining different mouse models. We have used two molecularly different inhibitors of the R-TEM β-lactamase as targets for selection of catalytic antibodies with β-lactamase activity. This novel methodology has led to the isolation of five antibody fragments, which are all capable of hydrolyzing the β-lactam ring. Structural modeling of the selected scFv has revealed the presence of different motifs in each of the antibody fragments potentially responsible for their catalytic activity. Our results confirm (a) the validity of using our two target inhibitors for the in vitro selection of catalytic antibodies endowed with β-lactamase activity, and (b) the plasticity of the β-lactamase active site responsible for the wide resistance of these enzymes to clinically available inhibitors and antibiotics.

Published
2017

15. Performance of MALDI-TOF MS platforms for fungal identification

Author

Renaud Piarroux, Anne-Cécile Normand, Stéphane Ranque, Carole Cassagne, Coralie L'Ollivier, Aix Marseille Université (AMU), Infections Parasitaires : Transmission, Physiopathologie et Thérapeutiques (IP-TPT), Service de Santé des Armées-Assistance Publique - Hôpitaux de Marseille (APHM)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD), CHU Dijon, Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Service de Santé des Armées, and Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Computer science, Arthrodermataceae, 030106 microbiology, Fungi, Dermatology, General Medicine, Computational biology, MALDI-TOF Mass Spectrometry, Bioinformatics, 03 medical and health sciences, Clinical microbiology, Matrix-assisted laser desorption/ionization, Infectious Diseases, Mycoses, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Yeasts, Humans, Identification (biology)
Abstract

International audience; Matrix-assisted laser desorption/ionisation mass spectrometry (MALDI-TOF MS) is increasingly used by clinical microbiology laboratories to cope with the need for rapid, cost-effective and accurate identification of microorganisms. Several research teams have recently succeed in identifying moulds using MALDI-TOF MS, which was first adapted to bacteria, then to yeast identification. Since 2004, different commercial firms have released several ready-to-use MALDI-TOF MS platforms. This review describes the similarities and differences between the commercially available systems. In two parts, we first describe and compare the preprocessing and identification steps between the platforms and then compare the identification efficacy of yeast, moulds and dermatophytes species.

Published
2016

16. The Ecosystem Approach to Fisheries: Reconciling Conservation and Exploitation

Author

Frédéric Ménard, Sophie Bertrand, Olivier Maury, François Le Loc'h, Florent Renaud, Lynn Shannon, Arnaud Bertrand, Souad Kifani, Marta Coll, Philippe Cury, Yunne-Jai Shin, Philippe Gros, Institut de Recherche pour le Développement (IRD), Institut de Recherche pour le Développement (IRD [France-Sud]), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), 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), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), André Monaco, Patrick Prouzet, 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), Consejo Superior de Investigaciones Científicas [Spain] (CSIC), Institut de Recherche pour le Développement (IRD)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie - UMR5182 (LC), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Humboldt, 0106 biological sciences, Marine conservation, Benguela, Fisheries science, species conservation, 010604 marine biology & hydrobiology, OS, Pelagic zone, 010603 evolutionary biology, 01 natural sciences, Fishery, marine resources exploitation, Marine Strategy Framework Directive, Geography, marine strategy framework directive, Habitat, 13. Climate action, ecosystem approach to fisheries, Marine ecosystem, Ecosystem, 14. Life underwater, Fisheries management, marine ecosystems, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

International audience; Marine fisheries have a direct impact on the resources they exploit but also indirectly affect other species, habitats and the way ecosystems work. Ecosystem approach to fisheries (EAF) is a major aspect for the exploitation of marine resources and conservation of species. An ecosystem is set formed by a community of living beings and their biological, geological, edaphic, hydrological, climatic environment. Organisms are distributed as patches across a wide continuum of spatiotemporal scales. The marine strategy framework directive (MSFD) proposes an ecosystem approach for the assessment of the marine environment. Bottom-up control of predator fish through small pelagic fish has been noticed in the Benguela and Humboldt Current and in Guinea, since several predator fish suffer when their prey stock collapses. The scientific community needs to set up a long-term scientific strategy in order to enhance its ability to provide suitable competences for the ecosystem approach to marine resources.

Published
2016

17. Resolution of Viable and Membrane‐Compromised Free Bacteria in Aquatic Environments by Flow Cytometry

Author

Sandra Citterio, Gérald Grégori, Sergio Sgorbati, Michel Denis, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Milano-Bicocca = University of Milano-Bicocca (UNIMIB), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Università degli Studi di Milano-Bicocca [Milano] (UNIMIB), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)

Subjects
DNA, Bacterial, 0301 basic medicine, Biomedical Research, Histology, Diamines, Microbiology, Biochemistry, Flow cytometry, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, medicine, Benzothiazoles, Propidium iodide, Organic Chemicals, Coloring Agents, 030304 developmental biology, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, Bacteriological Techniques, Microbial Viability, Quenching (fluorescence), Bacteria, medicine.diagnostic_test, biology, 030306 microbiology, Cell Membrane, General Medicine, Flow Cytometry, biology.organism_classification, Fluorescence, Medical Laboratory Technology, 030104 developmental biology, Förster resonance energy transfer, Membrane, chemistry, 030220 oncology & carcinogenesis, Quinolines, Nucleic acid, Biophysics, Water Microbiology, NADS, Propidium
Abstract

In aquatic environments, free heterotrophic bacteria play an extremely important role due to their high biomass, wide panel of metabolisms, and ubiquity, as well as the toxicity of certain species. This unit presents a nucleic-acid double-staining protocol (NADS) for flow cytometry that can distinguish fractions of viable, damaged, or membrane-compromised cells within the free-bacterial community. The NADS protocol is based on the simultaneous utilization of two nucleic acid stains-membrane-permeant SYBR Green and membrane-impermeant propidium iodide (PI). The efficiency of the double staining on fresh samples is magnified by the FRET from SYBR Green to PI when both are bound to the nucleic acids. Full quenching of SYBR Green fluorescence by PI identifies cells with a compromised membrane, partial quenching indicates cells with a slightly damaged membrane, and lack of quenching characterizes cells with an intact membrane. Samples do not require any pretreatment and this protocol can be performed almost anywhere. © 2018 by John Wiley & Sons, Inc.

Published
2018

18. Fuzzy species limits in Mediterranean gorgonians (Cnidaria, Octocorallia): inferences on speciation processes

Author

Mauatassem Billah Masmoudi, Anne Haguenauer, Didier Aurelle, Rita Castilho, Lamya Chaoui, Isabelle D. Pivotto, Nur Eda Topçu, Marine Malfant, Márcio A.G. Coelho, Hichem M. Kara, Institut méditerranéen d'océanologie ( MIO ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ), Institut méditerranéen de biodiversité et d'écologie marine et continentale ( IMBE ), Centre National de la Recherche Scientifique ( CNRS ) -Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université ( AMU ) -Université d'Avignon et des Pays de Vaucluse ( UAPV ), Adaptation et diversité en milieu marin ( ADMM ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), Istanbul University, Université Badji Mokhtar - Annaba [Annaba] ( UBMA ), Laboratoire Bioressources Marines, Université Badji Mokhtar de Annaba, Universidade do Algarve, Centre of Marine Sciences ( CCMAR ), University of Algarve [Portugal], State University of New York at Buffalo ( SUNY Buffalo ), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Badji Mokhtar Annaba (UBMA), Universidade do Algarve (UAlg), Centre of Marine Sciences [Faro] (CCMAR), University at Buffalo [SUNY] (SUNY Buffalo), State University of New York (SUNY), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), and Université Badji Mokhtar - Annaba [Annaba] (UBMA)

Subjects
0301 basic medicine, Sympatry, Octocorallia, intron, Evolution, Introgression, ved/biology.organism_classification_rank.species, Insights, Gene flow, Coalescent theory, 03 medical and health sciences, Eunicella singularis, Genetics, 14. Life underwater, Adaptation, Haplotype reconstruction, Molecular Biology, octocorals, hybridization, Ecology, Evolution, Behavior and Systematics, Eunicella, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, Eunicella-singularis, Diversity, biology, Phylogenetic tree, ved/biology, Ecology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Population-genetics, Algal symbiosis, biology.organism_classification, 030104 developmental biology, [ SDV.BID.EVO ] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], speciation, Eunicella cavolini, Animal Science and Zoology, Coral, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ABC
Abstract

The study of the interplay between speciation and hybridization is of primary importance in evolutionary biology. Octocorals are ecologically important species whose shallow phylogenetic relationships often remain to be studied. In the Mediterranean Sea, three congeneric octocorals can be observed in sympatry: Eunicella verrucosa, Eunicella cavolini and Eunicella singularis. They display morphological differences and E.singularis hosts photosynthetic Symbiodinium, contrary to the two other species. Two nuclear sequence markers were used to study speciation and gene flow between these species, through network analysis and Approximate Bayesian Computation (ABC). Shared sequences indicated the possibility of hybridization or incomplete lineage sorting. According to ABC, a scenario of gene flow through secondary contact was the best model to explain these results. At the intraspecific level, neither geographical nor ecological isolation corresponded to distinct genetic lineages in E.cavolini. These results are discussed in the light of the potential role of ecology and genetic incompatibilities in the persistence of species limits. French National Research Agency (ANR) program Adacni (ANR) [ANR-12-ADAP-0016] CNRS Hubert Curien 'Tassili' program [12MDU853] CCMAR Strategic Plan from Fundacao para a Ciencia e a Tecnologia-FCT [PEst-C/MAR/LA0015/2011, FEDER info:eu-repo/semantics/publishedVersion

Published
2017

19. Sporobacter

Author

Grech-Mora, Isabelle, Fardeau, Marie Laure, Garcia, Jean-Louis, Ollivier, Bernard, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Microbiologie et Biotechnologie des Environnements Chauds, Université de la Méditerranée - Aix-Marseille 2-Université de Provence - Aix-Marseille 1, and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)

Subjects
0303 health sciences, 03 medical and health sciences, 030306 microbiology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract

International audience

Published
2015

20. A novel community‐based therapeutic education program for reducing alcohol‐related harms and stigma in people with alcohol use disorders: A quasi‐experimental study ( <scp>ETHER</scp> study)

Author

Tangui Barré, Clémence Ramier, Saskia Antwerpes, Marie Costa, Morgane Bureau, Gwenaelle Maradan, Vincent Di Beo, Christophe Cutarella, Jacques Leloutre, Olivier Riccobono‐Soulier, Sophie Hedoire, Elodie Frot, Fabienne Vernier, Stéphanie Vassas‐Goyard, Sabine Dufort, Camelia Protopopescu, Fabienne Marcellin, Danielle Casanova, Marion Coste, Patrizia Carrieri, Sciences Economiques et Sociales de la Santé & Traitement de l'Information Médicale (SESSTIM - U1252 INSERM - Aix Marseille Univ - UMR 259 IRD), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut des sciences de la santé publique [Marseille] (ISSPAM), Institut de Recherche pour le Développement (IRD), Clinique Saint Barnabé - Ramsay Santé [Marseille] (CSB-RS), Association Addictions France, Aix-Marseille Sciences Economiques (AMSE), École des hautes études en sciences sociales (EHESS)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), ARS PACA (Agence Régionale de Santé de Provence-Alpes Côte d'Azur), ANR-17-EURE-0020,AMSE (EUR),Aix-Marseille School of Economics(2017), and ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011)

Subjects
Health (social science), psychosocial skills, [SDV]Life Sciences [q-bio], Medicine (miscellaneous), France, harm reduction, alcohol use disorder, therapeutic patient education, [SHS]Humanities and Social Sciences
Abstract

International audience; IntroductionAlcohol use disorder (AUD) is associated with a significant disease burden in France, where alcohol use is deeply rooted in culture. However, the treatment gap is large because of several barriers, including stigmatisation and drinkers' apprehension about total abstinence. However, standardised and evidence-based interventions based on controlled-drinking for people with AUD are lacking. We aimed to assess the effectiveness of a novel community-based French therapeutic patient education (TPE) program for people with AUD named Choizitaconso.MethodsA before-after non-randomised quasi-experimental study, named ETHER, was designed and implemented with people living with AUD, over a period of 6 months. The primary outcome was percentage change in the number of alcohol-related harms experienced. Secondary outcomes were percentage changes in psycho-social patient-reported and community-validated outcomes. Participants in the intervention group (n = 34) benefited from the 10-week TPE program Choizitaconso, while the comparison group (n = 58) received standard care. The Kruskall–Wallis and chi-squared or Fisher's exact tests were used to compare before-after changes in variables in both groups. Linear regression models were used to test for the effect of study group on each outcome and to test for the effect of alcohol consumption as a confounder.ResultsAt 6 months, all outcomes but one either remained stable or numerically improved in both groups. Internalised stigma significantly improved in the intervention group (p = 0.026) but not in the comparison group (p = 0.207), with a significant group effect (p = 0.014).Discussion and ConclusionsThis study demonstrates the effectiveness of the Choizitaconso TPE program on community-validated outcomes, especially internalised stigma.

Published
2023

21. Noncontiguous finished genome sequence and description ofRaoultibacter massiliensisgen. nov., sp. nov. andRaoultibacter timonensissp. nov, two new bacterial species isolated from the human gut

Author

Pierre-Edouard Fournier, Fehmida Bibi, Melhem Bilen, Awa Diop, Esam I. Azhar, Maxime Descartes Mbogning Fonkou, Mamadou Beye, Fadi Bittar, Caroline Michelle, Mamadou Lamine Tall, Frédéric Cadoret, Sophie Edouard, Asif Ahmad Jiman-Fatani, Muhammad Yasir, Ziad Daoud, Sory Ibrahima Traore, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), King Abdulaziz University, Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA)

Subjects
DNA, Bacterial, Male, new bacterial species, lcsh:QR1-502, taxonogenomics, Biology, Raoultibacter timonensis, Microbiology, Genome, lcsh:Microbiology, Agar plate, Feces, Young Adult, 03 medical and health sciences, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, Raoultibacter massiliensis, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, human gut microbiota, Genus, RNA, Ribosomal, 16S, Humans, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Phylogeny, 030304 developmental biology, Whole genome sequencing, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, 0303 health sciences, Phylogenetic tree, Strain (chemistry), 030306 microbiology, Genomics, Original Articles, culturomics, 16S ribosomal RNA, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 6. Clean water, Gastrointestinal Microbiome, Actinobacteria, Culturomics, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Original Article, Genome, Bacterial
Abstract

International audience; As part of the culturomics project aiming at describing the human microbiota, we report in this study the description of the new bacterial genus Raoultibacter gen. nov. that includes two new species, that is, R. massiliensis sp. nov. and R. timonensis sp. nov. The R. massiliensis type strain Marseille‐P2849T was isolated from the fecal specimen of a healthy 19‐year‐old Saudi Bedouin, while R. timonensis type strain Marseille‐P3277T was isolated from the feces of an 11‐year‐old pygmy female living in Congo. Strain Marseille‐P2849T exhibited 91.4% 16S rRNA sequence similarity with Gordonibacter urolithinfaciens, its phylogenetic closest neighbor with standing in nomenclature. As well, strain Marseille‐P3277T exhibited 97.96% 16S rRNA similarity with strain Marseille‐P2849T. Both strains were Gram‐positive, motile, nonspore‐forming rod and form transparent microcolonies on blood agar in both anaerobic and microaerophilic atmospheres. The genome sizes of strain Marseille‐P2849T and strain Marseille‐P3277T were 3,657,161 bp and 4,000,215 bp, respectively. Using a taxono‐genomic approach combining the phenotypic, biochemical, and genomic characteristics, we propose the genus Raoultibacter gen. nov., which contains strains Marseille‐P2849T (= CSUR P2849T, = DSM 103407T) and Marseille‐P3277T (=CCUG 70680T, =CSUR P3277T) as type strains of the species R. massiliensis sp. nov., and R. timonensis sp. nov., respectively.

Published
2019

22. Palaeoflood activity and climate change over the last 1400 years recorded by lake sediments in the north-west European Alps

Author

Pierre Sabatier, Bernard Fanget, Edouard Bard, Jean-Jacques Delannoy, Cécile Pignol, Bruno Wilhelm, Emmanuel Chapron, Olivier Magand, Thierry Courp, Fabien Arnaud, Kazuyo Tachikawa, Emmanuel Malet, Environnements, Dynamiques et Territoires de la Montagne (EDYTEM), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), Laboratoire de glaciologie et géophysique de l'environnement (LGGE), Observatoire des Sciences de l'Univers de Grenoble (OSUG), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences de la Terre d'Orléans - UMR7327 (ISTO), Bureau de Recherches Géologiques et Minières (BRGM) (BRGM)-Observatoire des Sciences de l'Univers en région Centre (OSUC), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université d'Orléans (UO)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université d'Orléans (UO)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS), Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Collège de France (CdF)-Institut national des sciences de l'Univers (INSU - CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Grenoble (OSUG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université d'Orléans (UO)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers en région Centre (OSUC), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Bureau de Recherches Géologiques et Minières (BRGM) (BRGM), Chaire Evolution du climat et de l'océan, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Environnements, Dynamiques et Territoires de Montagne (EDYTEM), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS), Collège de France - Chaire Evolution du climat et de l'océan, PSL Research University (PSL)-PSL Research University (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, and PSL Research University (PSL)-PSL Research University (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)

Subjects
010506 paleontology, 010504 meteorology & atmospheric sciences, [SDE.MCG]Environmental Sciences/Global Changes, Climate change, flood frequency, 01 natural sciences, Proxy (climate), flood intensit y, Arts and Humanities (miscellaneous), Earth and Planetary Sciences (miscellaneous), 0105 earth and related environmental sciences, geography, geography.geographical_feature_category, Flood myth, Global warming, Paleontology, Sediment, Glacier, 15. Life on land, Turbidite, climate change, lake sediment, last millennium, 13. Climate action, Climatology, Sedimentary rock, Geology
Abstract

International audience; A high-resolution sedimentological and geochemical study of a high-altitude proglacial lake (Lake Blanc, Aiguilles Rouges, 2352m a.s.l.) revealed 195 turbidites, 190 of which are related to flood events over the last 1400 years. We used the coarsest sediment fraction of each turbidite as a proxy for the intensity of each flood event. Because most flood events at this locality are triggered by localized summer convective precipitation events, the reconstructed sedimentary record reveals changes in the frequency and intensity of such events over the last millennium. Comparisons with other temperature, palaeohydrological and glacier reconstructions in the region suggest that the most intense events occurred during the warmest periods, i.e. during the Medieval Climate Anomaly (AD 800-1300) and the current period of global warming. On a multi-decadal time scale, almost all the flood frequency peaks seem to correspond to warmer periods, whereas multi-centennial variations in flood frequency appear to follow the regional precipitation pattern. Consequently, this new Alpine flood record provides further evidence of a link between climate warming and an increase in the frequency and intensity of flooding on a multidecadal time scale, whereas the centennial variability in flood frequencies is related to regional precipitation patterns.

Published
2013

23. The distribution of coastal fish <scp>eDNA</scp> sequences in the Anthropocene

Author

Laetitia Mathon, Virginie Marques, Stéphanie Manel, Camille Albouy, Marco Andrello, Emilie Boulanger, Julie Deter, Régis Hocdé, Fabien Leprieur, Tom B. Letessier, Nicolas Loiseau, Eva Maire, Alice Valentini, Laurent Vigliola, Florian Baletaud, Sandra Bessudo, Tony Dejean, Nadia Faure, Pierre‐Edouard Guerin, Meret Jucker, Jean‐Baptiste Juhel, Kadarusman, Andrea Polanco F., Laurent Pouyaud, Dario Schwörer, Kirsten F. Thompson, Marc Troussellier, Hagi Yulia Sugeha, Laure Velez, Xiaowei Zhang, Wenjun Zhong, Loïc Pellissier, David Mouillot, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Dynamique et durabilité des écosystèmes : de la source à l’océan (DECOD), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institute for the Study of the Anthropic Impacts and the Sustainability in the Marine Environment (IAS), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Andromède Océanologie, Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut de Recherche pour le Développement (IRD [France-Ouest]), Zoological Society of London - ZSL (UNITED KINGDOM), The University of Western Australia (UWA), Lancaster Environment Centre, Lancaster University, SPYGEN [Le Bourget-du-Lac], Ecologie marine tropicale dans les Océans Pacifique et Indien (ENTROPIE [Réunion]), Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS), Ecologie marine tropicale des océans Pacifique et Indien (ENTROPIE [Nouvelle-Calédonie]), Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Ifremer - Nouvelle-Calédonie, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de la Nouvelle-Calédonie (UNC), Fundación Malpelo y Otros Ecosistemas Marinos, Institute of Terrestrial Ecosystems (ITES), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Politeknik Kelautan dan Perikanan Sorong (POLTEK), Programa de Biodiversidad y Ecosistemas Marino, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), University of Exeter, Greenpeace Research Laboratories, Ecosystèmes lagunaires : organisation biologique et fonctionnement (ECOLAG), Université Montpellier 2 - Sciences et Techniques (UM2)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS), Universitas Indonesia (UI ), Centre of Chemical Safety and Risks, School of the Environment, Nanjing University, Nanjing University (NJU), and Swiss Federal Institute for Forest, Snow and Landscape Research WSL

Subjects
α- and β-diversity, Global and Planetary Change, Ecology, coastal fish communities, environmental factors, [SDE.MCG]Environmental Sciences/Global Changes, socio-economic factors, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, environmental DNA, Ecology, Evolution, Behavior and Systematics
Abstract

Aim Coastal fishes have a fundamental role in marine ecosystem functioning and contributions to people, but face increasing threats due to climate change, habitat degradation and overexploitation. The extent to which human pressures are impacting coastal fish biodiversity in comparison with geographic and environmental factors at large spatial scale is still under scrutiny. Here, we took advantage of environmental DNA (eDNA) metabarcoding to investigate the relationship between fish biodiversity, including taxonomic and genetic components, and environmental but also socio-economic factors. Location Tropical, temperate and polar coastal areas. Time period Present day. Major taxa studied Marine fishes. Methods We analysed fish eDNA in 263 stations (samples) in 68 sites distributed across polar, temperate and tropical regions. We modelled the effect of environmental, geographic and socio-economic factors on α- and β-diversity. We then computed the partial effect of each factor on several fish biodiversity components using taxonomic molecular units (MOTU) and genetic sequences. We also investigated the relationship between fish genetic α- and β-diversity measured from our barcodes, and phylogenetic but also functional diversity. Results We show that fish eDNA MOTU and sequence α- and β-diversity have the strongest correlation with environmental factors on coastal ecosystems worldwide. However, our models also reveal a negative correlation between biodiversity and human dependence on marine ecosystems. In areas with high dependence, diversity of all fish, cryptobenthic fish and large fish MOTUs declined steeply. Finally, we show that a sequence diversity index, accounting for genetic distance between pairs of MOTUs, within and between communities, is a reliable proxy of phylogenetic and functional diversity. Main conclusions Together, our results demonstrate that short eDNA sequences can be used to assess climate and direct human impacts on marine biodiversity at large scale in the Anthropocene and can further be extended to investigate biodiversity in its phylogenetic and functional dimensions.

Published
2023

24. Optical imaging of mesopelagic particles indicates deep carbon flux beneath a natural iron-fertilized bloom in the Southern Ocean

Author

Marc Picheral, Thomas W. Trull, Marie-Paule Jouandet, Lars Stemmann, Stéphane Blain, Lionel Guidi, Friederike Ebersbach, Ecologie Marine et BIOdiversité (EMBIO), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Antarctic Climate and Ecosystems Cooperative Research Centre (ACE-CRC), Division of Marine and Atmospheric Research (CSIRO), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Department of Oceanography [Honolulu], University of Hawai‘i [Mānoa] (UHM), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Observatoire océanologique de Banyuls (OOB), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, 010504 meteorology & atmospheric sciences, Mesopelagic zone, 010604 marine biology & hydrobiology, Aquatic Science, Spring bloom, Plankton, Oceanography, 01 natural sciences, Phytoplankton, Seawater, 14. Life underwater, Particle size, Bloom, Equivalent spherical diameter, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, Geology, 0105 earth and related environmental sciences
Abstract

We recorded vertical profiles of size distributions of particles (ranging from 0.052 to several mm in equivalent spherical diameter) in the natural iron-fertilized bloom southeast of Kerguelen Island (Southern Ocean) and in surrounding high-nutrient, low-chlorophyll (HNLC) waters with an Under Water Video Profiler during the Kerguelen Ocean and Plateau Compared Study cruise (Jan-Feb 2005). Total particle numerical abundance and total particle volume (TPV) in the 0-200-m layer were respectively 3-fold and 20-fold higher in the bloom, and integrated TPV was correlated to integrated chlorophyll concentration. The difference persisted well into the ocean interior with a 10-fold higher TPV at 400-m depth beneath the natural iron-fertilized bloom. Below 400 m, increases in TPV values at the bloom stations reflect the suspension of bottom sediments. Bloom waters had a greater proportion of large particles from the surface to 400 m and also exhibited an increase of this proportion with depth compared to HNLC waters. Multiple visits to the bloom reference Sta. A3, suggest preferential removal of large particles as the bloom declined. Comparing our particle abundance size spectra with those observed previously in polyacrylamide gel-filled sediment traps allows us to estimate mesopelagic particle sinking rates. These results suggest that particles sink faster in the HNLC waters than beneath the bloom. The fact that sinking speeds were not a simple monotonic function of particle size and varied spatially highlights the need to go beyond parameterizations of sinking rate as a function of size alone.

Published
2011

25. Automatic recognition of flow cytometric phytoplankton functional groups using convolutional neural networks

Author

Robin Fuchs, Melilotus Thyssen, Véronique Creach, Mathilde Dugenne, Lloyd Izard, Marie Latimier, Arnaud Louchart, Pierre Marrec, Machteld Rijkeboer, Gérald Grégori, Denys Pommeret, Institut de Mathématiques de Marseille (I2M), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Centre for Environment, Fisheries and Aquaculture Science [Lowestoft] (CEFAS), University of Hawaii, Processus et interactions de fine échelle océanique (PROTEO), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Dynamiques des Écosystèmes Côtiers (DYNECO), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Stazione Zoologica Anton Dohrn (SZN), Graduate School of Oceanography [Narragansett], University of Rhode Island (URI), Laboratoire de Sciences Actuarielle et Financière (SAF), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, and European Project: 1166-39417,FEDER

Subjects
[SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Ocean Engineering, ComputingMilieux_MISCELLANEOUS
Abstract

The variability of phytoplankton distribution has been unraveled by high-frequency measurements. Such a resolution can be approached by automated pulse-shape recording flow cytometry (AFCM) operating at hourly sampling resolution. AFCM records morphological and physiological traits as single-cell optical pulse shapes that can be used to classify cells into phytoplankton functional groups (PFGs). However, the associated manual post-processing of the data coupled with the increasing size and number of datasets is time-consuming and error-prone. Machine learning models are increasingly used to run automatic classification. Yet, most of the existing methods either present a long training process, need to manually design features from the raw optical pulse shapes, or are dedicated to images only. In this study, we present a convolutional neural network (CNN) to classify several PFGs using AFCM pulse shapes. The uncertainties of manual classification were first estimated by comparing experts' recognition of six PFGs. Consensual particles from the manual PFG classification were used to train and validate the CNN. The CNN obtained competitive performances compared to other models used in the literature and remained robust across several sampling areas, and instrumental hardware and settings. Finally, we assessed the ability of this classifier to predict phytoplankton counts at a Mediterranean coastal station and from a cruise in the South-West Indian Ocean, providing a comparison with the manual classification over 3-month periods and a 2h frequency. These promising results strengthen the near real-time observation of PFGs, especially required with the increasing use of AFCM in monitoring research programs.

Published
2022

26. Barium and molybdenum records in bivalve shells: Geochemical proxies for phytoplankton dynamics in coastal environments?

Author

Severine Jacquet, Laurent Chauvaud, Christophe Pécheyran, David Amouroux, Jacques Clavier, Stéphane L'Helguen, Aurélie Barats, Julien Thébault, Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Programme ERC Lascaux, Institut de recherche en droit privé (IRDP), Université de Nantes - UFR Droit et Sciences Politiques (UFR DSP), Université de Nantes (UN)-Université de Nantes (UN)-Université de Nantes - UFR Droit et Sciences Politiques (UFR DSP), Université de Nantes (UN)-Université de Nantes (UN), Laboratoire de Chimie Analytique Bio-Inorganique et Environnement (LCABIE), Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Radiochimie et des Sciences Analytiques et Environnement (LRSAE/EA 1175), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), This study was supported by the IRD, the Région Bretagne, the French Programme National Environnement Côtier, and the French Ministry of Research's Actions Concertées Incitatives—Jeunes Chercheurs program (ACI-PECTEN)., Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Nice Sophia Antipolis (1965 - 2019) (UNS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), and Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Pau et des Pays de l'Adour (UPPA)

Subjects
0106 biological sciences, 010504 meteorology & atmospheric sciences, [SDE.MCG]Environmental Sciences/Global Changes, chemistry.chemical_element, Mineralogy, Aquatic Science, Oceanography, Nitrate reductase, 01 natural sciences, chemistry.chemical_compound, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Nitrate, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, Phytoplankton, 14. Life underwater, 0105 earth and related environmental sciences, Calcite, biology, 010604 marine biology & hydrobiology, Barium, Plankton, Bivalvia, biology.organism_classification, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Diatom, chemistry, 13. Climate action, [SDE]Environmental Sciences, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Geology
Abstract

International audience; Barium:calcium and molybdenum:calcium ratios were investigated in shells of the tropical scallop Comptopallium radula. Three juvenile specimens were harvested alive in the southwest lagoon of New Caledonia after a 1-year hydrological survey. Calcite samples representing a few hours of biomineralization were laser-ablated along the maximal growth axis and analyzed for Ba and Mo content using an inductively coupled plasma mass spectrometer. Absolute dates of shell precipitation assigned on the basis of periodic formation of shell growth patterns led to the accurate reconstruction of ontogenetic variations of elemental ratios with subweekly resolution. Inter-individual variability of Ba:Ca and Mo:Ca time series was low, indicating an environmental control on the incorporation of these elements within shells. Both profiles were characterized by a background level punctuated by sharp peaks. The ingestion of diatoms enriched in Ba (adsorbed on iron oxyhydroxides associated with the frustules) is the most likely cause of the formation of Ba:Ca peaks. Some contribution of diatom-associated barite is also possible. In every instance, Ba:Ca would possibly be a proxy for the timing and magnitude of diatom blooms. Among all the theories that could be advanced to explain the occurrence of Mo:Ca peaks, the most plausible appears to be the ingestion of phytoplankton cells grown upon NO3- and therefore containing high levels of Mo required for the activity of nitrate reductase. If this is so, then Mo:Ca could be a new proxy for nitrate uptake by phytoplankton in coastal ecosystems, helping to reconstruct the balance between new and regenerated production in paleoenvironments.

Published
2009

27. Correcting for heterogeneity and non‐comparability bias in multicenter clinical trials with a rescaled random‐effect excess hazard model

Author

Juste A. Goungounga, Nathalie Grafféo, Hadrien Charvat, Roch Giorgi, Sciences Economiques et Sociales de la Santé & Traitement de l'Information Médicale (SESSTIM - U1252 INSERM - Aix Marseille Univ - UMR 259 IRD), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Registre Bourguignon des Cancers Digestifs, Lipides - Nutrition - Cancer (U866) (LNC), Université de Bourgogne (UB)-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-Ecole Nationale Supérieure de Biologie Appliquée à la Nutrition et à l'Alimentation de Dijon (ENSBANA)-Université de Bourgogne (UB)-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-Ecole Nationale Supérieure de Biologie Appliquée à la Nutrition et à l'Alimentation de Dijon (ENSBANA)-Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Centre de Recherches sur l'Action Politique en Europe (ARENES), Université de Rennes (UR)-Institut d'Études Politiques [IEP] - Rennes-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Centre National de la Recherche Scientifique (CNRS), Recherche sur les services et le management en santé (RSMS), Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR), École des Hautes Études en Santé Publique [EHESP] (EHESP), Département Méthodes quantitatives en santé publique (METIS), Observatoire régional de la santé Provence-Alpes-Côte d'Azur [Marseille] (ORS PACA), Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC), Juntendo University Hospital [Tokyo], Assistance Publique - Hôpitaux de Marseille (APHM), Canceropple Provence-Alpes-Cpte d'Azur, Institut National Du Cancer, Conseil Regional Provence-Alpes-Cpte d'Azur, Canceropple PACA, Conseil Regional PACA, and Internationale

Subjects
Statistics and Probability, Net survival, Life tables, [SDV.CAN]Life Sciences [q-bio]/Cancer, General Medicine, Heterogeneity, Statistics, Probability and Uncertainty, Excess hazard model, Cancer
Abstract

International audience; In the presence of competing causes of event occurrence (e.g., death), the interest might not only be in the overall survival but also in the so-called net survival, that is, the hypothetical survival that would be observed if the disease under study were the only possible cause of death. Net survival estimation is commonly based on the excess hazard approach in which the hazard rate of individuals is assumed to be the sum of a disease-specific and expected hazard rate, supposed to be correctly approximated by the mortality rates obtained from general population life tables. However, this assumption might not be realistic if the study participants are not comparable with the general population. Also, the hierarchical structure of the data can induces a correlation between the outcomes of individuals coming from the same clusters (e.g., hospital, registry). We proposed an excess hazard model that corrects simultaneously for these two sources of bias, instead of dealing with them independently as before. We assessed the performance of this new model and compared it with three similar models, using extensive simulation study, as well as an application to breast cancer data from a multicenter clinical trial. The new model performed better than the others in terms of bias, root mean square error, and empirical coverage rate. The proposed approach might be useful to account simultaneously for the hierarchical structure of the data and the non-comparability bias in studies such as long-term multicenter clinical trials, when there is interest in the estimation of net survival.

Published
2023

28. Stepping up to genome scan allows stock differentiation in the worldwide distributed blue shark Prionace glauca

Author

Natacha Nikolic, Floriaan Devloo‐Delva, Diane Bailleul, Ekaterina Noskova, Clément Rougeux, Chrystelle Delord, Philippe Borsa, Cathy Liautard‐Haag, Mohamad Hassan, Amandine D. Marie, Pierre Feutry, Peter Grewe, Campbell Davies, Jessica Farley, Daniel Fernando, Sebastian Biton‐Porsmoguer, François Poisson, Denham Parker, Agostino Leone, Jorden Aulich, Matt Lansdell, Francis Marsac, Sophie Arnaud‐Haond, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), 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)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Ecologie Comportementale et Biologie des Populations de Poissons (ECOBIOP), Université de Pau et des Pays de l'Adour (UPPA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Agence de Recherche pour la Biodiversité à La Réunion (ARBRE), CSIRO Environment, University of Tasmania [Hobart, Australia] (UTAS), ITMO University [Russia], Laboratoire d'Excellence CORAIL (LabEX CORAIL), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de La Réunion (UR)-Université de la Polynésie Française (UPF)-Université de la Nouvelle-Calédonie (UNC)-Institut d'écologie et environnement-Université des Antilles (UA), Ecologie marine tropicale dans les Océans Pacifique et Indien (ENTROPIE [Réunion]), Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS), University of Calgary, Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie]), Tishreen University, CSIRO Agriculture and Food (CSIRO), CSIRO Marine and Atmosphere Research [Hobart], Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Linnaeus University, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Office français de la biodiversité (OFB), Department of Forestry, Fisheries and the Environment, Department of Biological Sciences, University of Cape Town, Cape Town, South Africa, This work is part of the PSTBS-IO project supported by funding from CSIRO Oceans and Atmosphere, AZTI Tecnalia, Institut de recherche pour le développement (IRD) and Research Institute for Tuna Fisheries (RITF), and financial assistance of the European Union (GCP/INT/233/EC – Population structure of IOTC species in the Indian Ocean), and POPSIZE project supported by FEAMP (2014– 2020 UE No. 508/2014), Nikolic, Natacha, Devloo-Delva, Floriaan, Bailleul, Diane, Noskova, Ekaterina, Rougeux, Clément, Delord, Chrystelle, Borsa, Philippe, Liautard-Haag, Cathy, Hassan, Mohamad, Marie, Amandine D, Feutry, Pierre, Grewe, Peter, Davies, Campbell, Farley, Jessica, Fernando, Daniel, Biton-Porsmoguer, Sebastian, Poisson, Françoi, Parker, Denham, Leone, Agostino, Aulich, Jorden, Lansdell, Matt, Marsac, Franci, and Arnaud-Haond, Sophie

Subjects
genome scans, [SDE.MCG]Environmental Sciences/Global Changes, Genetics, population genetics, stock differentiation and assessment, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, bycatch, pelagic, Ecology, Evolution, Behavior and Systematics, blue shark, SNPs
Abstract

The blue shark Prionace glauca is a top predator with one of the widest geographic distributions of any shark species, yet classified as critically endangered in the Mediterranean Sea, and Near Threatened globally. Previous genetic studies did not reject the null hypothesis of a single global population across the worldwide species range. Blue shark situation was proposed as a possible archetype of the ‘grey zone of population differentiation’, coined to designate cases where population structure may be too recent or too faint to be detected using a limited set of markers. Here, blue shark samples collected throughout its global range were sequenced using a specific ddRAD method (DArTseq; Georges et al. 2018), which recovered 37,655 genome-wide single nucleotide polymorphisms (SNPs). Two main groups emerged, with Mediterranean Sea and Northern Atlantic samples significantly differentiated from the Indo-west Pacific samples. Significant pairwise FST values indicated further genetic differentiation within the Atlantic Ocean, and between the Atlantic Ocean and the Mediterranean Sea. Reconstruction of recent demographic history suggested the divergence between northern and southern oceanic populations emerged about 500 generations ago and revealed a drastic reduction in effective population size from a large ancestral population. Our results illustrate the power of high-density genome scans to detect population structure and reconstruct demographic history in highly migratory marine species. As the management of the blue shark fishery, either as target or as bycatch, does not account for this delineation, we strongly recommend that the results presented here be considered in future stock assessment and management plans.

Published
2023

29. Use of scanning electron microscopy and energy dispersive X‐ray for urine analysis: A preliminary investigation

Author

Abdourahamane Yacouba, Sara Bellali, Gabriel Haddad, Noelle Mavros, Anthony Fontanini, Grégory Dubourg, Jean‐Christophe Lagier, Didier Raoult, Jacques Bou Khalil, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), and Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille)

Subjects
Medical Laboratory Technology, Histology, [SDV]Life Sciences [q-bio], Anatomy, Instrumentation
Abstract

International audience

Published
2023

30. Towards a framework for assessment and management of cumulative human impacts on marine food webs

Author

Pierre Lejeune, Paolo Guidetti, Loïc Michel, Gérard Pergent, Monica Montefalcone, Sylvie Gobert, Salvatrice Vizzini, Maria-Christina Gambi, Charles-François Boudouresque, Marta Coll, Pablo Sanchez-Jerez, Hugh P. Possingham, Christine Pergent-Martini, Arnaud Abadie, Maria Sini, Sylvaine Giakoumi, Fiorenza Micheli, Branko Velimirov, Stelios Katsanevakis, Benjamin S. Halpern, Laboratoire d'Océanologie - Centre MARE, Université de Liège, Department of Marine Sciences [Aegean], University of the Aegean, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Hellenic Centre for Marine Research (HCMR), Department of Earth, Environmental and Life Sciences (DISTAV), Università degli studi di Genova = University of Genoa (UniGe), Fédération de recherche Environnement et Société (FRES 3041), Université Pascal Paoli (UPP), 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), Ecosystèmes Côtiers Marins et Réponses aux Stress (ECOMERS), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), Hopkins Marine Station [Stanford], Stanford University, The Ecology Centre, University of Queensland [Brisbane], Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Universita degli studi di Genova, 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), Université Nice Sophia Antipolis (... - 2019) (UNS), Universidad de Alicante. Departamento de Ciencias del Mar y Biología Aplicada, Biología Marina, Giakoumi, S, Halpern, BS, Michel, LN, Gobert, S, Sini, M, Boudouresque, CF, Gambi, MC, Katsanevakis, S, Lejeune, P, Montefalcone, M, Pergent, G, Pergent-Martini, C, Sanchez-Jerez, P, Velimirov, B, Vizzini, S, Abadie, A, Coll, M, Guidetti, P, Micheli, F, and Possingham, HP

Subjects
seagrass, Biodiversity & Conservation, vulnerability, 05 Environmental Sciences, Vulnerability, THREATS, Expert knowledge elicitation, Food chain, ecosystem-based management, conservation actions, ecosystem-based management, expert knowledge elicitation, multiple threats, seagrass, vulnerability, ECOSYSTEM-BASED MANAGEMENT, Water Pollution, Chemical, Zoología, ComputingMilieux_MISCELLANEOUS, Trophic level, elicitation, Alismatales, Acciones de conservación, biology, Ecology, multiple threats, Seagra, Environmental resource management, conservation actions, obtencion de conocimiento de expertos, Ecosystem-based management, Food web, acciones de conservación, Seagrass, obtención de conocimiento de expertos, Biodiversity Conservation, Conservation action, Alismatidae, Know-how, Life Sciences & Biomedicine, acciones de conservacion, Amenazas múltiples, Multiple threat, Settore BIO/07 - Ecologia, Conservation of Natural Resources, Food Chain, Fisheries, Environmental Sciences & Ecology, Manejo con base en los ecosistemas, amenazas múltiples, Pastos marinos, expert knowledge, OCEAN, expert knowledge elicitation, Mediterranean Sea, Humans, Ecosystem, Obtención de conocimiento de expertos, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation, Science & Technology, business.industry, manejo con base en los ecosistemas, vulnerabilidad, pastos marinos, 15. Life on land, 06 Biological Sciences, biology.organism_classification, 13. Climate action, amenazas multiples, 07 Agricultural And Veterinary Sciences, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, Vulnerabilidad, Environmental Sciences
Abstract

Effective ecosystem-based management requires understanding ecosystem responses to multiple human threats, rather than focusing on single threats. To understand ecosystem responses to anthropogenic threats holistically, it is necessary to know how threats affect different components within ecosystems and ultimately alter ecosystem functioning. We used a case study of a Mediterranean seagrass (Posidonia oceanica) food web and expert knowledge elicitation in an application of the initial steps of a framework for assessment of cumulative human impacts on food webs. We produced a conceptual seagrass food web model, determined the main trophic relationships, identified the main threats to the food web components, and assessed the components’ vulnerability to those threats. Some threats had high (e.g., coastal infrastructure) or low impacts (e.g., agricultural runoff) on all food web components, whereas others (e.g., introduced carnivores) had very different impacts on each component. Partitioning the ecosystem into its components enabled us to identify threats previously overlooked and to reevaluate the importance of threats commonly perceived as major. By incorporating this understanding of system vulnerability with data on changes in the state of each threat (e.g., decreasing domestic pollution and increasing fishing) into a food web model, managers may be better able to estimate and predict cumulative human impacts on ecosystems and to prioritize conservation actions. El manejo efectivo con base en los ecosistemas requiere entender la respuesta de los ecosistemas a múltiples amenazas humanas en lugar de enfocarse en amenazas individuales. Para entender holísticamente la respuesta de los ecosistemas a las múltiples amenazas antropogénicas es necesario saber cómo estas amenazas afectan a los diferentes componentes dentro de los ecosistemas y cómo alteran finalmente el funcionamiento de los ecosistemas. Usamos el estudio de caso de la red alimenticia del pasto marino del Mediterráneo (Posidonia oceanica) y la obtención de conocimiento de expertos en una aplicación de los pasos iniciales de un método para la evaluación de los impactos humanos acumulativos sobre las redes alimenticias. Produjimos un modelo de red alimenticia de pastos marinos, determinamos las principales relaciones tróficas, identificamos a las principales amenazas para los componentes de la red y evaluamos la vulnerabilidad de los componentes a esas amenazas. Algunas amenazas tuvieron impactos altos (p. ej.: infraestructura costera) o bajos (p. ej.: escorrentía agrícola) sobre todos los componentes de la red, mientras que otros (p. ej.: carnívoros introducidos) tuvieron impactos muy diferentes sobre cada componente. Partir al ecosistema en sus componentes nos permitió identificar amenazas no vistas previamente y reevaluar la importancia de las amenazas percibidas comúnmente como mayores. Al incorporar este entendimiento de la vulnerabilidad del sistema con datos sobre los cambios en el estado de cada amenaza (p. ej.: disminución de la contaminación doméstica e incremento de la pesca) al modelo de red alimenticia, los manejadores pueden ser capaces de estimar y predecir de mejor manera los impactos humanos acumulativos sobre los ecosistemas y priorizar las acciones de conservación. This work is a contribution of the project “NETMED” co-financed by the Greek State and the European Social Fund. Workshop funding was provided by ARC CEED-University of Queensland, the University of Liège, and STARESO. M.C. was supported by EC Marie Curie CIG grant to BIOWEB. This paper contributes to MARE publications (no. 282).

Published
2014

31. Shifts in growth light optima among diatom species support their succession during the spring bloom in the Arctic

Author

Dany Croteau, Thomas Lacour, Nicolas Schiffrine, Philippe‐Israël Morin, Marie‐Hélène Forget, Flavienne Bruyant, Joannie Ferland, Augustin Lafond, Douglas A. Campbell, Jean‐Éric Tremblay, Marcel Babin, Johann Lavaud, Institut de biologie physico-chimique (IBPC (FR_550)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Takuvik Joint International Laboratory ULAVAL-CNRS, Université Laval [Québec] (ULaval)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Physiologie des Microalgues (PHYSALG), Physiologie et Toxines des Microalgues Toxiques et Nuisibles (PHYTOX), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut des Sciences de la MER de Rimouski (ISMER), Université du Québec à Rimouski (UQAR), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Mount Allison University, Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Ecology, ecophysiology, photoacclimation, photoadaptation, seasonal species succession, Plant Science, diatoms, spring bloom, Arctic Ocean, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, primary production
Abstract

1. Diatoms of the Arctic Ocean annually experience extreme changes of light environment linked to photoperiodic cycles and seasonal variations of the snow and sea-ice cover extent and thickness which attenuate light penetration in the water column. Arctic diatom communities exploit this complex seasonal dynamic through a well-documented species succession during spring, beginning in sea-ice and culminating in massive phytoplankton blooms underneath sea-ice and in the marginal ice zone. The pattern of diatom taxa sequentially dominating this succession is relatively well conserved interannually, and taxonomic shifts seem to align with habitat transitions. 2. To understand whether differential photoadaptation strategies among diatom taxa explain these recurring succession sequences, we coupled lab experiments with field work in Baffin Bay at 67.5°N. Based on field data, we selected five diatom species typical of different ecological niches and measured their growth rates under light intensity ranges representative of their natural habitats. To characterize their photoacclimative responses, we sampled pigments and total particulate carbon, and conducted 14C-uptake photosynthesis response curves and variable fluorescence measurements. 3. We documented a gradient in species respective light intensity for maximal growth suggesting divergent light response plasticity, which for the most part align with species sequential dominance. Other photophysiological parameters supported this ecophysiological framing, although contrasts were always clear only between succession endmembers, Nitzschia frigida and Chaetoceros neogracilis. To validate that these photoacclimative responses are representative of in situ dynamics, we compared them to the chlorophyll a-specific light-limited slope (α*) and saturated rate of photosynthesis (P*M), monitored in Baffin Bay on sea-ice and planktonic communities. This complementary approach confirmed that unusual responses in α* and P*M as a function of light history intensity are similar between sentinel sympagic species N. frigida and natural ice-core communities. While no light-history-dependent trends were observed in planktonic communities, their α* and P*M values were in the range of measurements from our monospecific cultures. 4. Synthesis. Our results suggest that Arctic diatoms species photoadaptation strategy is tuned to the light environment of the habitats in which they dominate and indeed drives the seasonal taxonomic succession.

Published
2022

32. The Famenin fall and other ordinary chondrites intermediate between H and L groups

Author

Hamed Pourkhorsandi, Jérôme Gattacceca, Pierre Rochette, Thomas Smith, Lydie Bonal, Massimo D’Orazio, Bertrand Devouard, Corinne Sonzogni, Vinciane Debaille, Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université libre de Bruxelles (ULB), Institute of Geology and Geophysics [Beijing] (IGG), Chinese Academy of Sciences [Beijing] (CAS), Institut de Planétologie et d'Astrophysique de Grenoble (IPAG), Centre National d'Études Spatiales [Toulouse] (CNES)-Observatoire des Sciences de l'Univers de Grenoble (OSUG ), Institut national des sciences de l'Univers (INSU - CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Météo-France -Institut national des sciences de l'Univers (INSU - CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Météo-France, Dipartimento di Scienze della Terra [Pisa], and University of Pisa - Università di Pisa

Subjects
[SDU.STU.PL]Sciences of the Universe [physics]/Earth Sciences/Planetology, Geophysics, classification, Space and Planetary Science, Fall, HL, Intermediate chondrite, ordinary chondrites
Abstract

International audience; The Famenin meteorite fell around 08:30 a.m. local time (GMT+4.5) on June 27, 2015 on the roof of a house in Famenin, a town in NW Iran. A single 640 g stone was recovered, shattered into several pieces upon impact. The shape of the impact hole and the relative position of the recovered meteorites indicate a N-NW fall direction. Famenin is an ordinary chondrite (OC) with well-preserved chondrules of various types, (Fe,Ni) metal, troilite, phosphate, and chromite. The organic matter systematics and the olivine and low-Ca compositional distributions (percent mean deviations 18% and 31%, respectively) indicate it is a type 3.4/3.8 chondrite. Considering the average chemical compositions of olivine (Fa17.5±4.7) and low-Ca pyroxene (Fs16.8±7.5), average Co content of the kamacite (5.6 mg g−1), and Cu/Ni and Ga/Ni ratios, Famenin should be classified as an H chondrite. However, saturation magnetization is 26.0 Am2 kg−1, indicating a bulk metal content similar to L chondrites. Similarly, the whole-rock Ni and Co contents (13073 and 540 µg g−1, respectively), and average chondrule diameter (550 µm) are closer to typical values for L chondrites than H chondrites. The (Fe,Ni) metal modal abundance (5 vol%), magnetic susceptibility, and possibly whole-rock oxygen isotopic composition indicate intermediate properties between H and L chondrites. Noble gas composition and cosmic-ray exposure ages of Famenin and El Médano 195 (another intermediate OC) shows their gas-rich character and an older ejection age from their parent body than those for the majority of H and L chondrites. Famenin, together with similar intermediate OCs, increases the diversity of this meteorite clan and suggests the existence of a separate OC group with a composition broadly intermediate between H and L groups for which a different designation (HL) is proposed. OCs likely originate from more than three parent bodies (H, L, and LL) as traditionally proposed.

Published
2022

33. The Karla impact structure (Russia) explored by potential‐field investigations

Author

Yoann Quesnel, Natalia S. Bezaeva, Dilyara M. Kuzina, Pierre Rochette, Jérôme Gattacceca, Minoru Uehara, Dmitry D. Badyukov, Bulat M. Nasyrtdinov, Dmitry A. Chareev, Cedric Champollion, Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ural Federal University [Ekaterinburg] (UrFU), Kazan Federal University (KFU), Géosciences Montpellier, and Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Université de Montpellier (UM)

Subjects
Geophysics, Space and Planetary Science, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2022

34. Low rate of <scp>RNAemia</scp> in blood donations collected during the first wave of <scp>COVID</scp> ‐19 in France

Author

Sophie Le Cam, Pierre Gallian, Céline Ricard, Céline Narboux, Valérie Barlet, Claude Maugard, Lisette Hauser, Nadège Brisbarre, Pierre Cappy, Josiane Pillonel, Syria Laperche, Pascal Morel, Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Unité des Virus Emergents (UVE), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
RNAemia, SARS-CoV-2, nucleic acid testing, [SDV]Life Sciences [q-bio], Immunology, COVID-19, Humans, RNA, Viral, blood donors, Immunology and Allergy, Hematology, plasma, Retrospective Studies
Abstract

To investigate the transmission of SARS-CoV-2 via blood, we conducted retrospective molecular screening in blood donated during the first pandemic peak in the two French regions with the highest community transmission.Archived plasma samples randomly selected from donations collected between March 23 and 29, 2020, in Eastern and Northern regions of France were tested for SARS-CoV-2 RNA in minipools of 4 donations (MP4) using the Grifols ProcleixSARS-CoV-2 assay. Reactive MP4 and the four corresponding plasmas were further tested with alternative RT-PCRs and sequencing. Testing for SARS-CoV-2 antibodies and in vitro infectivity in cell culture were also performed.Among the 2818 MP4 (corresponding to 9672 donations) tested for viral RNA, 5 were weakly reactive. Among the 20 plasmas included in these five MP4, one presented low-level reactivity with RT-PCRs and Procleix SARS-CoV-2 and was confirmed on sequencing. The estimated prevalence was 1.03/10,000 (95% CI 0-3.1). The 20 plasmas were antibody nonreactive and none of them showed cytopathic effects in cell culture. When recalled, the index-donor declared having had symptoms compatible with SARS-CoV-2 infection a few days after donation. The two immunocompromised recipients transfused with red blood cells and an inactivated pooled platelet product did not develop COVID-19.Our results indicated a low prevalence of SARS-CoV-2 RNA in the plasma of asymptomatic blood donors during the pandemic peak and no evidence of infectivity in vivo and in vitro. The transfusion risk remains theoretical and does not justify the implementation of SARS-CoV-2 NAT for blood donations.

Published
2022

35. Late Pleistocene glaciation history of the southern Black Forest, Germany: 10 Be cosmic‐ray exposure dating and equilibrium line altitude reconstructions in Sankt Wilhelmer Tal

Author

Felix Martin Hofmann, Frank Preusser, Irene Schimmelpfennig, Laëtitia Léanni, null Aster team (Georges Aumaître, Karim Keddadouche & Fawzi Zaid, University of Freiburg [Freiburg], Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
moraine, Arts and Humanities (miscellaneous), [SDU.STU.CL]Sciences of the Universe [physics]/Earth Sciences/Climatology, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, equilibrium line altitude, glaciation, Earth and Planetary Sciences (miscellaneous), Black Forest, Paleontology, [SDU.STU.GL]Sciences of the Universe [physics]/Earth Sciences/Glaciology, [SDU.STU.GM]Sciences of the Universe [physics]/Earth Sciences/Geomorphology, 10 Be cosmic-ray exposure dating
Abstract

International audience; During the Late Pleistocene, an ice cap temporarily rested on the highest summit of the Black Forest, Feldberg, and on the surrounding region. Moraines inside the last glaciation maximum ice extent document subsequent glacial standstills and/or re-advances, but the chronology of the deglaciation remains largely unknown. In Sankt Wilhelmer Tal, moraines were mapped, and suitable moraine boulders were sampled for 10 Be cosmic ray exposure (CRE) dating. Equilibrium line altitudes (ELAs) during moraine formation were reconstructed to evaluate whether these can be used for local stratigraphical correlations. Geomorphological mapping revealed numerous icemarginal positions in the main valley and in two tributary valleys. CRE ages and ELAs indicate two discrete phases of glacial standstills and/or re-advances by 17-16 ka at the latest and no later than 14 ka, respectively. Differing ELAs across the study area preclude the use of ELAs for local stratigraphical correlations. Recalculated 10 Be CRE ages from other localities in Central Europe indicate similar periods of moraine formation, thus raising the question of a common climatic forcing. Additional sets of CRE ages are needed to answer this question. In addition, future studies should concentrate on determining the age of the last glaciation maximum in the Black Forest.

Published
2022

36. A RUpture‐Based detection method for the Active mesopeLagIc Zone (RUBALIZ): A crucial step toward rigorous carbon budget assessments

Author

Robin Fuchs, Chloé M. J. Baumas, Marc Garel, David Nerini, Frédéric A. C. Le Moigne, Christian Tamburini, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut de Mathématiques de Marseille (I2M), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), This manuscript is a contribution of the APERO project funded by the National Research Agency under the grant APERO [grant number ANR ANR-21-CE01-0027] and by the French LEFE-Cyber program (CNRS, INSU)., and ANR-21-CE01-0027,APERO,Estimer la production, l'export et la reminéralisation de la matière marine biogène : de la surface à l'océan profond(2021)

Subjects
active mesopelagic zone, [SDE.IE]Environmental Sciences/Environmental Engineering, [SDE.MCG]Environmental Sciences/Global Changes, Ocean Engineering, Biological carbon pump, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography
Abstract

International audience; Determining mesopelagic organic carbon budgets is essential to characterize the ocean's role as a carbon dioxide sink. This is because the biological processes observed in the mesopelagic zone are crucial for understanding the biological carbon pump. Yet, field assessments of carbon budgets are often unbalanced with the carbon demand exceeding its supply. This underlines either methodological issues in the budget calculations or incomplete knowledge of the mesopelagic carbon cycling with potentially missing sources. Carbon budgets are built by partitioning the ocean into vertical depth zones. Vertical boundaries are conventionally defined between 200 and 1000 m depth or using various thresholds. Such approaches lack consistent methodology preventing robust comparison of mesopelagic carbon budget from region to region. Here, using a statistical rupture detection method applied to conductivity-temperature-depth (CTD)-cast variables (fluorescence, O 2 concentration, potential temperature, salinity, and density), we aim to provide independent estimates of mesopelagic boundaries. We demonstrate that the so-determined upper boundary is highly correlated with the knee points of the particulate organic carbon (POC) fluxes estimated by a power law and that over 90% of the POC flux attenuation occurs within our method boundaries. The identified zone therefore corresponds to the most active part of the conventional mesopelagic zone and we name it the "active mesopelagic zone" (AMZ). We find that the depths of the mesopelagic zone depend on the region considered. Our results demonstrate that the mesopelagic carbon budget discrepancy can vary up to four folds depending on the boundaries chosen and hence provide novel grounds to reassess existing and future mesopelagic carbon budgets.

Published
2023

37. Bacillus kwashiorkori sp. nov., a new bacterial species isolated from a malnourished child using culturomics

Author

Saber Khelaifia, Caroline Michelle, Didier Raoult, Souleymane Brah, Fadi Bittar, Pierre-Edouard Fournier, Mamadou Beye, Sory Ibrahima Traore, Carine Couderc, El hadji Seck, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-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), and Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)

Subjects
DNA, Bacterial, 0301 basic medicine, 030106 microbiology, Bacillus, taxonogenomics, DNA, Ribosomal, Microbiology, Genome, Feces, 03 medical and health sciences, Cytosol, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, RNA, Ribosomal, 16S, Cluster Analysis, Humans, Bacillus kwashiorkori, genome, Gene, Phylogeny, Original Research, 2. Zero hunger, Genetics, Base Composition, biology, Strain (chemistry), Fatty Acids, Malnutrition, Temperature, Infant, Nucleic Acid Hybridization, Sequence Analysis, DNA, culturomics, biology.organism_classification, 16S ribosomal RNA, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Aerobiosis, Bacterial Typing Techniques, Type species, 030104 developmental biology, Culturomics, Genome, Bacterial, Locomotion, Orthologous Gene
Abstract

International audience; Strain SIT6(T) was isolated from the fecal flora of a severely malnourished child as part of a broad culturomics study aiming to maximize the culture conditions for the in-depth exploration of the human microbiota. An analysis of the 16S rRNA gene sequence showed that strain SIT6(T) shared 94.1% 16S rRNA gene sequence similarity with Bacillus thermoamylovorans DKPT (NR\₀29151), the phylogenetically closest type species. Colonies are creamy white, circular, 4-5 mm in diameter after cultivation at 37 degrees C for 24 hr on 5% sheep blood-enriched Colombia agar. Growth occurs at temperatures in the range of 25-56 degrees C (optimally at 37 degrees C). Strain SIT6(T) is a gram-positive, facultative anaerobic rod and motile by means of peritrichous flagella and sporulating; it is catalase and oxidase positive. The 2,784,637-bp-long genome, composed of 16 contigs, has a G+C content of 35.19%. Of the 2,646 predicted genes, 2,572 were protein-coding genes and 74 were RNAs. The major fatty acids are saturated species (15:0 iso, 16:0 and 17:0 anteiso). Of the 14 detected fatty acids, 11 are saturated, either linear or branched (iso and anteiso). Digital DNA-DNA hybridization (dDDH) estimation and average genomic identity of orthologous gene sequences (AGIOS) of the strain SIT6(T) against genomes of the type strains of related species ranged between 18.6% and 38.3% and between 54.77% and 65.50%, respectively. According to our taxonogenomics results, we propose the creation of Bacillus kwashiorkori sp. nov. that contains the type strain SIT6(T) (=CSUR P2452(T), =DSM 29059(T)).

Published
2017

38. Light noble gas records and cosmic ray exposure histories of recent ordinary chondrite falls

Author

Thomas Smith, Jérôme Gattacceca, Fei Su, Shijie Li, P. M. Ranjith, Régis Braucher, Huaiyu He, Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
Cosmic ray, Noble gas (data page), 010502 geochemistry & geophysics, 01 natural sciences, Astrobiology, [SDU.STU.PL]Sciences of the Universe [physics]/Earth Sciences/Planetology, Geophysics, Space and Planetary Science, 0103 physical sciences, 010303 astronomy & astrophysics, ComputingMilieux_MISCELLANEOUS, Geology, 0105 earth and related environmental sciences, Ordinary chondrite
Abstract

International audience; We measured noble gas concentrations and isotopic ratios (He, Ne, and Ar isotopes) in six recent ordinary chondrite falls: Mangui (L6), Vinales (L6), Ozerki (L6), Tamdakht (H5), Kheneg Ljouad (LL5/6), and Katol (L6). Among them, the three L6 chondrites Mangui, Vinales, and Ozerki fell in only a few months interval; their apparent similar petrographic and mineralogic characteristics might indicate source crater pairing. To test this hypothesis, we have investigated those meteorites for their cosmic ray exposure (CRE) histories, using the cosmogenic noble gases He-3, Ne-21, and Ar-38. We systematically (re)calculated the CRE ages as well as the gas retention ages of these meteorites. The CRE age of the Mangui is, based on noble gases

Published
2021

39. Acoustic seascape partitioning through functional data analysis

Author

Alejandro Ariza, Anne Lebourges‐Dhaussy, David Nerini, Etienne Pauthenet, Gildas Roudaut, Ramilla Assunção, Everton Tosetto, Arnaud Bertrand, 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)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut de Recherche pour le Développement (IRD), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Processus et interactions de fine échelle océanique (PROTEO), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Universidade Federal de Pernambuco [Recife] (UFPE), International Joint Laboratory TAPIOCA (www.tapioca.ird.fr), European Project: 817578,TRIATLAS(2019), and European Project: 734271,PADDLE

Subjects
sound-scattering layers, echoregions, Ecology, soundscape, [SDE.MCG]Environmental Sciences/Global Changes, micronekton, mesopelagic, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Fernando de Noronha, Ecology, Evolution, Behavior and Systematics, biogeography, northeastern Brazil
Abstract

Aim Water column acoustic backscatter is regularly registered during oceanographic surveys, providing valuable information on the composition and distribution of pelagic life in the ocean. We propose an objective approach based on functional data analysis to classify these acoustic seascapes into biogeographical regions. Location Tropical South Atlantic Ocean off northeastern Brazil. Taxon Sound-scattering pelagic fauna detected with acoustic echosounders, principally small fish, crustaceans, squid and diverse gelatinous life-forms. Methods We use acoustic backscatter as a function of depth, simultaneously at three frequencies, to numerically describe the vertical distribution and composition of sound-scattering organisms in the water column. This information is used to classify the acoustic seascape through functional principal component analysis. The analysis routine is tested and illustrated with data collected at 38, 70 and 120 kHz in waters affected by contrasting environmental conditions. Results Acoustic seascape partitioning mirrored the distribution of current systems, fronts and taxonomically based regionalization. The study area was divided between slope-boundary and open-ocean waters, and between spring and fall hydrological regimes. Main Conclusions The acoustic seascape consistency and the spatiotemporal coherence of the regions classified show that the method is efficient at identifying homogeneous and cohesive sound-scattering communities. Comparisons against hydrological and biological regionalization prove that the method is reliable at delineating distinct pelagic ecosystems in a cost-efficient and non-intrusive way.

Published
2022

40. Microscopic observations of SARS‐CoV‐2 like particles in different oral samples

Author

Djamal Brahim Belhaouari, Jean‐Pierre Baudoin, Jean‐Christophe Lagier, Virginie Monnet‐Corti, Bernard La Scola, Angéline Antezack, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Aix-Marseille Université - Faculté d'odontologie (AMU ODONTO), and Aix Marseille Université (AMU)

Subjects
SARS-CoV-2, [SDV]Life Sciences [q-bio], Humans, COVID-19, General Dentistry
Abstract

The emerging coronavirus pneumonia epidemic caused by the SARS-CoV-2 infection has spread rapidly around the world. The main routes of transmission of SARS-CoV-2 are currently recognised as aerosol/droplet inhalation. However, the involvement of the oral cavity in coronavirus disease 2019 (COVID-19) is poorly known. The current data indicates the presence of viral RNA in oral samples, suggesting the implication of saliva in SARS-CoV-2 transmission, however, no direct observation of SARS-CoV-2 particles in different oral samples has been reported. In this study, we investigated whether particles of SARS-CoV-2 were present in oral samples collected from three symptomatic COVID-19 patients. Using scanning electron microscopy (SEM), the correlative strategy of light microscopy and electron microscopy and immunofluorescence staining, we showed the presence of SARS-like particles in RT-qPCR SARS-CoV-2-positive saliva, dental plaque and gingival crevicular fluid (GCF) samples. In the saliva samples, we demonstrated the presence of epithelial oral cells with morphogenetic features of SARS-CoV-2 infected cells. Inside those cells, vacuoles filled with nascent particles were observed, suggesting the potential infection and replication of SARS-CoV-2 in oral tissues. Our results corroborate previous studies and confirm that the oral cavity may be a potential niche for SARS-CoV-2 infection and a potential source of transmission.

Published
2022

41. The contribution of the Weddell Gyre to the lower limb of the global overturning circulation

Author

William J. Jenkins, Jun Dong, Paul R. Holland, Brice Loose, Alberto C. Naveira Garabato, Sinhue Torres-Valdes, Eberhard Fahrbach, Loïc Jullion, Mario Hoppema, Hugh J. Venables, Dorothee C. E. Bakker, Peter J. Brown, Sheldon Bacon, Kevin Speer, Marie-José Messias, Michael P. Meredith, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Nathional Oceanography Centre, University of Southampton, National Oceanography Centre (NOC), British Antarctic Survey (BAS), Natural Environment Research Council (NERC), University of East Anglia [Norwich] (UEA), National Oceanography Centre [Southampton] (NOC), Florida State University [Tallahassee] (FSU), Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), University of Rhode Island, University of Rhode Island (URI), Woods Hole Oceanographic Institution (WHOI), Institut méditerranéen d'océanologie ( MIO ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ), University of Southampton [Southampton], National Oceanographic Centre [Southampton] ( NOC ), British Antarctic Survey ( BAS ), Natural Environment Research Council ( NERC ), University of East Anglia [Norwich] ( UEA ), National Oceanography Centre [Southampton] ( NOC ), Florida State University [Tallahassee] ( FSU ), Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research ( AWI ), Woods Hole Oceanographic Institution ( WHOI ), and Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung ( AWI )

Subjects
Weddell Sea Bottom Water, [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, geography, geography.geographical_feature_category, 010504 meteorology & atmospheric sciences, 010505 oceanography, Oceanography, 01 natural sciences, Geophysics, Antarctic Bottom Water, Shutdown of thermohaline circulation, Space and Planetary Science, Geochemistry and Petrology, Ocean gyre, Downwelling, Climatology, Circumpolar deep water, Earth and Planetary Sciences (miscellaneous), Upwelling, Thermohaline circulation, 14. Life underwater, Geology, 0105 earth and related environmental sciences
Abstract

International audience; The horizontal and vertical circulation of the Weddell Gyre is diagnosed using a box inverse model constructed with recent hydrographic sections and including mobile sea ice and eddy transports. The gyre is found to convey 42 6 8 Sv (1 Sv 5 106 m3 s–1) across the central Weddell Sea and to intensify to 54 6 15 Sv further offshore. This circulation injects 36 6 13 TW of heat from the Antarctic Circumpolar Current to the gyre, and exports 51 6 23 mSv of freshwater, including 13 6 1 mSv as sea ice to the midlati- tude Southern Ocean. The gyre’s overturning circulation has an asymmetric double-cell structure, in which 13 6 4 Sv of Circumpolar Deep Water (CDW) and relatively light Antarctic Bottom Water (AABW) are trans- formed into upper-ocean water masses by midgyre upwelling (at a rate of 2 6 2 Sv) and into denser AABW by downwelling focussed at the western boundary (8 6 2 Sv). The gyre circulation exhibits a substantial throughflow component, by which CDW and AABW enter the gyre from the Indian sector, undergo ventila- tion and densification within the gyre, and are exported to the South Atlantic across the gyre’s northern rim. The relatively modest net production of AABW in the Weddell Gyre (6 6 2 Sv) suggests that the gyre’s prominence in the closure of the lower limb of global oceanic overturning stems largely from the recycling and equatorward export of Indian-sourced AABW.

Published
2014
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42. TAROT: Robotic observatories for gamma-ray bursts and other sources

Author

Alain Klotz, M. Böer, F. Vachier, Observatoire de Haute-Provence (OHP), Institut Pythéas (OSU PYTHEAS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre d'étude spatiale des rayonnements (CESR), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Institut de Mécanique Céleste et de Calcul des Ephémérides (IMCCE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Groupe Astrométrie et Planétologie (GAP), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris

Subjects
Physics, Astrophysics::High Energy Astrophysical Phenomena, Astrophysics::Instrumentation and Methods for Astrophysics, Astronomy, Astronomy and Astrophysics, Astrophysics, Virtual observatory, Supernova, Space and Planetary Science, Astrophysics::Solar and Stellar Astrophysics, Astrophysics::Earth and Planetary Astrophysics, Variable star, [PHYS.ASTR]Physics [physics]/Astrophysics [astro-ph], Gamma-ray burst
Abstract

TAROT (Telescopes a Action Rapide pour les Objets Transitoires) are two robotic observatories designed to observe the early optical counterpart of gamma-ray bursts (GRBs) sources. As GRBs do not occur often, we use TAROT to observe other celestial targets: variable stars, minor-planets, supernovae, etc. In this paper we present the software tools presently used to manage the observations and to process and archive the data. We present also CADOR (Coordination et Analyse des Donnees des Observatoires Robotiques) which will centralize virtual observatory services associated to both TAROT telescopes. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

Published
2008

43. Glacial oscillations during the Bølling–Allerød Interstadial–Younger Dryas transition in the Ruda Valley, Central Pyrenees

Author

Irene Schimmelpfennig, Maria Rosário Fernandes, David Palacios, Julia García-Oteyza, Marc Oliva, Gonçalo Vieira, Dermot Antoniades, Aster Team, José M. Fernández-Fernández, Repositório da Universidade de Lisboa, Universidade de Lisboa = University of Lisbon (ULISBOA), Universitat de Barcelona (UB), Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Université Laval [Québec] (ULaval)

Subjects
Younger Dryas, 010504 meteorology & atmospheric sciences, Bølling–Allerød, 010502 geochemistry & geophysics, 01 natural sciences, Paleontology, Bølling-Allerød, Arts and Humanities (miscellaneous), [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, Cosmic‐ray exposure dating, Earth and Planetary Sciences (miscellaneous), Deglaciation, [SDU.STU.GL]Sciences of the Universe [physics]/Earth Sciences/Glaciology, [SDU.STU.GM]Sciences of the Universe [physics]/Earth Sciences/Geomorphology, Glacial period, Stadial, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, Cosmic-Ray Exposure dating, [SDU.STU.CL]Sciences of the Universe [physics]/Earth Sciences/Climatology, Central Pyrenees, Geology
Abstract

International audience; The Upper Garonne Basin included the largest glacial system in the Pyrenees during the last glacial cycle. Within the long-term glacial retreat during Termination-1 (T-1), glacier fluctuations left geomorphic evidence in the area. However, the chronology of T-1 glacial oscillations on the northern slope of the Central Pyrenees is still poorly constrained. Here, we introduce new geomorphological observations and a 12-sample dataset of 10Be Cosmic-Ray Exposure (CRE) ages from the Ruda Valley. This U-shaped valley, surrounded by peaks exceeding 2800 m a.s.l., includes a sequence of moraines and polished surfaces that enabled to reconstruct the chronology of the last deglaciation. Following the maximum ice extent, warmer conditions prevailing at ~15-14 ka, during the Bølling-Allerød (B-A) Interstadial, favoured glacial retreat in the Ruda Valley. Within the B-A, glaciers experienced two phases of advance/stillstand with moraine formation at 13.5 and 13.0 ka. During the early YD, glacial retreat exposed the highest surfaces of the Saboredo Cirque (~2300-2350 m) at 12.7 ka. Small glaciers persisted only inside the highest cirques (~2470 m), such as in Sendrosa Cirque, with moraines stabilizing at 12.6 ka. The results of this work present the most complete chronology for Pyrenean glacial oscillations from the B-A to the YD.

Published
2021

44. The Late Miocene Biogenic Bloom : A globally distributed but not an ubiquitous event

Author

Quentin PILLOT, Baptiste Suchéras-Marx, Anta-Clarisse Sarr, Clara T Bolton, Yannick Donnadieu, Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and ANR-20-CE49-0002,MioCarb,La transition Mio-Pliocene : mise en place du cycle du carbone moderne(2020)

Subjects
[SDE]Environmental Sciences
Abstract

The Late Miocene Biogenic Bloom (LMBB) is a late Miocene to early Pliocene oceanographic event characterized by high accumulation rates of opal from diatoms and calcite from calcareous nannofossils and planktic foraminifera. This multi-million year event has been recognized in sediment cores from the Pacific, Atlantic and Indian Oceans. The numerous studies discussing the LMBB lead us to believe that this event is omnipresent16in all oceans, although this hypothesis need to be tested. Moreover, the origin of this event is still widely discussed. In this study we aim to provide a comprehensive overview of the geographical and temporal aspects of the LMBB by compiling published ocean drilling (DSDP, ODP and IODP) records of sedimentation rates, CaCO3 and opal and terrigenous accumulation rates that cover the late Miocene and early Pliocene interval. Our data compilation shows that traces of the LMBB are present in many different locations but in a very heterogeneous way, highlighting that the LMBB is not a pervasive event. The compilation in addition shows that the sites where the LMBB is recorded are mainly located in areas with a high productivity regime (i.e. upwelling systems). We suggest that the most likely hypothesis to explain the LMBB is a global increase in upwelling intensity due to an increase in wind strength or an increase in deep water formation, ramping up global thermohaline circulation.

Published
2022

45. Electron ionization mass fragmentation of monounsaturated long‐chain α,ω ‐dicarboxylic acid trimethylsilyl derivatives

Author

Jean‐François Rontani, Claude Aubert, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Traitement du Signal et de l'Image (LTSI), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Pharmacocinétique et Toxicocinétique, and Faculté de Pharmacie

Subjects
Spectrometry, Mass, Electrospray Ionization, Trimethylsilyl Compounds, Mass fragmentation, Organic Chemistry, [CHIM]Chemical Sciences, Electrons, Rapid Communications in Mass Spectrometry, Neutral losses, Gas Chromatography-Mass Spectrometry, Spectroscopy, monounsaturated dicarboxylic acids, TMS derivatives, Analytical Chemistry
Abstract

International audience; RATIONALELong-chain monounsaturated -dicarboxylic acids are important components of the cuticle and suberized cell walls of plants.Identification and quantification of these compounds, which are widespread in environmental samples, can be challenging.METHODSThe EI-MS fragmentation pathways of long-chain monounsaturated -dicarboxylic acid TMS derivatives were investigated. Thesepathways were deduced by low-energy CID-GC-EI-MS/MS and accurate mass measurement.RESULTSLow-energy CID-MS/MS analyses and accurate mass measurement enabled us to elucidate EI-MS fragmentations of long-chainmonounsaturated -dicarboxylic acid TMS derivatives. These fragmentations involves successive losses of neutral molecules of TMSOHand CO initiated by transfer of allylic hydrogen atom to the ionized ester groups, which are thus totally lacking in EI mass spectra of saturatedhomologues.CONCLUSIONSEI-MS fragmentations of long-chain monounsaturated -dicarboxylic acids TMS derivatives exhibit specific fragment ions that can be veryuseful for the quantification in MRM mode of trace amounts of these compounds in environmental samples.

Published
2022

46. Post‐HCV cure self‐reported changes in physical activity, eating behaviours, and fatigue in people living with HIV (ANRS CO13 HEPAVIH)

Author

Marcellin, Fabienne, Di Beo, Vincent, Esterle, Laure, Abgrall, Sophie, Pialoux, Gilles, Barré, Tangui, Wittkop, Linda, Salmon‐ceron, Dominique, Sogni, Philippe, Carrieri, Patrizia, Roustant, F, Platterier, P, Kmiec, I, Traore, L, Lepuil, S, Parlier, S, Sicart‐payssan, V, Bedel, E, Anriamiandrisoa, S, Pomes, C, Mole, M, Bolliot, C, Catalan, P, Mebarki, M, Adda‐lievin, A, Thilbaut, P, Ousidhoum, Y, Makhoukhi, F.Z, Braik, O, Bayoud, R, Gatey, C, Pietri, M.P, Le Baut, V, Ben Rayana, R, Bornarel, D, Chesnel, C, Beniken, D, Pauchard, M, Akel, S, Lions, C, Ivanova, A, Ritleg, A‐s, Debreux, C, Chalal, L, Zelie, J, Hue, H, Soria, A, Cavellec, M, Breau, S, Joulie, A, Fisher, P, Gohier, S, Croisier‐bertin, D, Ogoudjobi, S, Brochier, C, Thoirain‐galvan, V, Le Cam, M, Chalouni, M, Conte, V, Dequae‐merchadou, L, Desvallees, M, Gilbert, C, Gillet, S, Knight, R, Lemboub, T, Michel, L, Mora, M, Protopopescu, C, Roux, P, Tezkratt, S, Ramier, C, Sow, A, Bureau, M, Trimoulet, P, Izopet, J, Serfaty, L, Paradis, V, Spire, B, Valantin, V., Chas, J, Zaegel‐faucher, O, Barange, K, Naqvi, A, Rosenthal, E, Bicart‐see, A, Bouchaud, O, Gervais, A, Lascoux‐combe, C, Goujard, C, Lacombe, K, Duvivier, C, Neau, D, Morlat, P, Bani‐sadr, F, Meyer, L, Boufassa, F, Autran, B, Roque, A.M, Solas, C, Fontaine, H, Costagliola, D, Piroth, L, Simon, A, Zucman, D, Boué, F, Miailhes, P, Billaud, E, Aumaître, H, Rey, D, Peytavin, G, Petrov‐sanchez, V, Levier, A, Usubillaga, R., Terris, B, Tremeaux, P, Katlama, C, Stitou, H, Cacoub, P, Nafissa, S, Benhamou, Y, Charlotte, F, Fourati, S, Poizot‐martin, I, Zaegel, O, Laroche, H, Tamalet, C, Callard, P, Bendjaballah, F, Amiel, C, Le Pendeven, C, Marchou, B, Alric, L, Metivier, S, Selves, J, Larroquette, F, Rio, V, Haudebourg, J, Saint‐paul, M.C, de Monte, A, Giordanengo, V, Partouche, C, Martin, A, Ziol, M, Baazia, Y, Iwaka‐bande, V, Gerber, A, Uzan, M, Garipuy, D, Ferro‐collados, M.J, Nicot, F, Yazdanpanah, Y, Adle‐biassette, H, Alexandre, G, Molina, J.M, Bertheau, P, Chaix, M.L, Delaugerre, C, Maylin, S, Bottero, J, Krause, J, Girard, P.M, Wendum, D, Cervera, P, Adam, J, Viala, C, Vittecocq, D, Quertainmont, Y, Teicher, E, Pallier, C, Lortholary, O, Rouzaud, C, Lourenco, J, Touam, F, Louisin, C, Avettand‐fenoel, V, Gardiennet, E, Mélard, A, Ochoa, A, Blanchard, E, Castet‐lafarie, S, Cazanave, C, Malvy, D, Dupon, M, Dutronc, H, Dauchy, F, Lacaze‐buzy, L, Desclaux, A, Bioulac‐sage, P, Reigadas, S, Lacoste, D, Bonnet, F, Bernard, N, Hessamfar, M, Paccalin, J.F, Martell, C, Pertusa, M.C, Vandenhende, M, Mercié, P, Pistone, T, Receveur, M.C, Méchain, M, Duffau, P, Rivoisy, C, Faure, I, Caldato, S, Bellecave, P, Tumiotto, C, Pellegrin, J.L, Viallard, J.F, Lazzaro, E, Greib, C, Majerholc, C, Brollo, M, Farfour, E, Polo Devoto, J, Kansau, I, Chambrin, V, Pignon, C, Berroukeche, L, Fior, R, Martinez, V, Favier, M, Deback, C, Lévy, Y, Dominguez, S, Lelièvre, J.D, Lascaux, A.S, Melica, G, Raffi, F, Allavena, C, Reliquet, V, Boutoille, D, Biron, C, Lefebvre, M, Hall, N, Bouchez, S, Rodallec, A, Le Guen, L, Hemon, C, Peyramond, D, Chidiac, C, Ader, F, Biron, F, Boibieux, A, Cotte, L, Ferry, T, Perpoint, T, Koffi, J, Zoulim, F, Bailly, F, Lack, P, Maynard, M, Radenne, S, Amiri, M, Valour, F, Augustin‐normand, C, Scholtes, C, Le‐thi, T.T, Chavanet, P, Duong van Huyen, M, Buisson, M, Waldner‐combernoux, A, Mahy, S, Salmon Rousseau, A, Martins, C, Galim, S, Lambert, D, Nguyen, Y, Berger, J.L, Hentzien, M, Brodard, V, Partisani, M, Batard, M.L, Cheneau, C, Priester, M, Bernard‐henry, C, de Mautort, E, Fischer, P, Gantner, P, Fafi‐kremer, S, Sciences Economiques et Sociales de la Santé & Traitement de l'Information Médicale (SESSTIM - U1252 INSERM - Aix Marseille Univ - UMR 259 IRD), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut des sciences de la santé publique [Marseille] (ISSPAM), Team MORPH3EUS (INSERM U1219 - UB - ISPED), Bordeaux population health (BPH), Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM), CIC Bordeaux, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de recherche en épidémiologie et santé des populations (CESP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, AP-HP - Hôpital Antoine Béclère [Clamart], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), CHU Tenon [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), CHU Bordeaux [Bordeaux], Hôpital Cochin [AP-HP], Université Paris Descartes - Paris 5 (UPD5), Physiopathologie du système immunitaire (Inserm U1223), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), ANRS CO13 HEPAVIH Study Group: F Roustant, P Platterier, I Kmiec, L Traore, S Lepuil, S Parlier, V Sicart-Payssan, E Bedel, S Anriamiandrisoa, C Pomes, M Mole, C Bolliot, P Catalan, M Mebarki, A Adda-Lievin, P Thilbaut, Y Ousidhoum, F Z Makhoukhi, O Braik, R Bayoud, C Gatey, M P Pietri, V Le Baut, R Ben Rayana, D Bornarel, C Chesnel, D Beniken, M Pauchard, S Akel, C Lions, A Ivanova, A-S Ritleg, C Debreux, L Chalal, J Zelie, H Hue, A Soria, M Cavellec, S Breau, A Joulie, P Fisher, S Gohier, D Croisier-Bertin, S Ogoudjobi, C Brochier, V Thoirain-Galvan, M Le Cam, M Chalouni, V Conte, L Dequae-Merchadou, M Desvallees, C Gilbert, S Gillet, R Knight, T Lemboub, L Michel, M Mora, C Protopopescu, P Roux, S Tezkratt, C Ramier, A Sow, M Bureau, P Trimoulet, J Izopet, L Serfaty, V Paradis, B Spire, Valantin, J Chas, O Zaegel-Faucher, K Barange, A Naqvi, E Rosenthal, A Bicart-See, O Bouchaud, A Gervais, C Lascoux-Combe, C Goujard, K Lacombe, C Duvivier, D Neau, P Morlat, F Bani-Sadr, L Meyer, F Boufassa, B Autran, A M Roque, C Solas, H Fontaine, D Costagliola, L Piroth, A Simon, D Zucman, F Boué, P Miailhes, E Billaud, H Aumaître, D Rey, G Peytavin, V Petrov-Sanchez, A Levier, R Usubillaga, B Terris, P Tremeaux, C Katlama, H Stitou, P Cacoub, S Nafissa, Y Benhamou, F Charlotte, S Fourati, I Poizot-Martin, O Zaegel, H Laroche, C Tamalet, P Callard, F Bendjaballah, C Amiel, C Le Pendeven, B Marchou, L Alric, S Metivier, J Selves, F Larroquette, V Rio, J Haudebourg, M C Saint-Paul, A De Monte, V Giordanengo, C Partouche, A Martin, M Ziol, Y Baazia, V Iwaka-Bande, A Gerber, M Uzan, D Garipuy, M J Ferro-Collados, J Selves, F Nicot, Y Yazdanpanah, H Adle-Biassette, G Alexandre, J M Molina, P Bertheau, M L Chaix, C Delaugerre, S Maylin, J Bottero, J Krause, P M Girard, D Wendum, P Cervera, J Adam, C Viala, D Vittecocq, Y Quertainmont, E Teicher, C Pallier, O Lortholary, C Rouzaud, J Lourenco, F Touam, C Louisin, V Avettand-Fenoel, E Gardiennet, A Mélard, A Ochoa, E Blanchard, S Castet-Lafarie, C Cazanave, D Malvy, M Dupon, H Dutronc, F Dauchy, L Lacaze-Buzy, A Desclaux, P Bioulac-Sage, S Reigadas, D Lacoste, F Bonnet, N Bernard, M Hessamfar, J F Paccalin, C Martell, M C Pertusa, M Vandenhende, P Mercié, D Malvy, T Pistone, M C Receveur, M Méchain, P Duffau, C Rivoisy, I Faure, S Caldato, P Bioulac-Sage, S Reigadas, P Bellecave, C Tumiotto, J L Pellegrin, J F Viallard, E Lazzaro, C Greib, P Bioulac-Sage, S Reigadas, C Majerholc, M Brollo, E Farfour, J Polo Devoto, I Kansau, V Chambrin, C Pignon, L Berroukeche, R Fior, V Martinez, M Favier, C Deback, Y Lévy, S Dominguez, J D Lelièvre, A S Lascaux, G Melica, F Raffi, C Allavena, V Reliquet, D Boutoille, C Biron, M Lefebvre, N Hall, S Bouchez, A Rodallec, L Le Guen, C Hemon, D Peyramond, C Chidiac, F Ader, F Biron, A Boibieux, L Cotte, T Ferry, T Perpoint, J Koffi, F Zoulim, F Bailly, P Lack, M Maynard, S Radenne, M Amiri, F Valour, J Koffi, F Zoulim, F Bailly, P Lack, M Maynard, S Radenne, C Augustin-Normand, C Scholtes, T T Le-Thi, P Chavanet, M Duong Van Huyen, M Buisson, A Waldner-Combernoux, S Mahy, A Salmon Rousseau, C Martins, S Galim, D Lambert, Y Nguyen, J L Berger, M Hentzien, V Brodard, M Partisani, M L Batard, C Cheneau, M Priester, C Bernard-Henry, E de Mautort, P Fischer, P Gantner, S Fafi-Kremer, Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris], Statistics In System biology and Translational Medicine (SISTM), Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)- Bordeaux population health (BPH), and Malbec, Odile

Subjects
0303 health sciences, Hepatology, business.industry, [SDV]Life Sciences [q-bio], Human immunodeficiency virus (HIV), MEDLINE, Physical activity, medicine.disease_cause, 3. Good health, [SDV] Life Sciences [q-bio], 03 medical and health sciences, 0302 clinical medicine, Infectious Diseases, Virology, Medicine, 030211 gastroenterology & hepatology, business, Eating behaviour, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Clinical psychology
Abstract

International audience; No abstract available

Published
2021

47. 10 Be exposure age for sorted polygons in the Sudetes Mountains

Author

Marek Křížek, Zbyněk Engel, Tomáš Uxa, Régis Braucher, David Krause, Charles University [Prague] (CU), Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
Marine isotope stage, 010506 paleontology, 010504 meteorology & atmospheric sciences, [SDE.MCG]Environmental Sciences/Global Changes, Permafrost, 01 natural sciences, cosmogenic-nuclide dating, Quaternary, Paleoclimatology, periglacial environment, [SDU.STU.GM]Sciences of the Universe [physics]/Earth Sciences/Geomorphology, Glacial period, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, 0105 earth and related environmental sciences, Earth-Surface Processes, Patterned ground, [SDU.STU.TE]Sciences of the Universe [physics]/Earth Sciences/Tectonics, geography, geography.geographical_feature_category, Central Europe, Landform, past permafrost, Exposure age, Physical geography, patterned ground, Geology
Abstract

International audience; Patterned-ground landforms represent the most common phenomenon of periglacial environment, and their large sorted forms belong to the few morphological indicators of past permafrost distribution. The relic forms of patterned ground are widespread on high-elevated surfaces in the central European uplands, providing the evidence of regional periglacial conditions in the last glacial period. However, the timing of theselandforms, as well as their potential for paleoclimate reconstructions, has remained unexplored. In this paper, we present 10 Be exposure ages from the large sorted polygons sampled at four sites in the Sudetes Mountains, the highest part of the central European uplands. These results indicate that these landforms started to form at the end of Marine Isotope Stage 3, and the main phase of their formation occurredbetween 30 and 20 ka. This research confirms the hypothesis of sorted patterned-ground formation within the last (Weichselian) glacial stage (110.6 – 11.7 ka) and suggests that earlier-sorted features are not preserved in the Sudetes. The recognized period of enhanced periglacial activity coincides with a prominent cold interval identified earlier in both regional and northern-hemispheric proxy records.Central Europe, cosmogenic-nuclide dating, past permafrost, patterned ground, periglacial environment, Quaternary

Published
2020

48. Biodiversity, climate change, and adaptation in the Mediterranean

Author

Aurelle, D., Thomas, Séverine, Albert, Cécile H., Bally, Marc, Bondeau, Alberte, Boudouresque, Charles-François, Cahill, Abigail E., Carlotti, François, Chenuil, Anne, Cramer, Wolfgang, Davi, Hendrik, Jode, Aurélien De, Ereskovsky, Alexander, Farnet da Silva, Anne Marie, Fernandez, Catherine, Gauquelin, Thierry, Mirleau, Pascal, Monnet, Anne-Christine, Prévosto, Bernard, Rossi, Vincent, Sartoretto, Stéphane, van Wambeke, France, Fady, Bruno, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Aix Marseille Université (AMU), Biology Department, Albion College, Ecologie des Forêts Méditerranéennes (URFM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Gothenburg (GU), Saint Petersburg State University [Saint Petersburg, Russian Federation], Centre d'Ecologie et des Sciences de la COnservation (CESCO), Muséum national d'Histoire naturelle (MNHN)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Risques, Ecosystèmes, Vulnérabilité, Environnement, Résilience (RECOVER), Aix Marseille Université (AMU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Regional Development Fund, Grant/Award Number: 1166-39417, ANR-11-LABX-0061,OTMed,Objectif Terre : Bassin Méditerranéen(2011), and ANR-12-ADAP-0016,ADACNI,Processus adaptatifs chez les cnidaires: étude intégrative de la réponse au stress thermique et au changement climatique, des gènes aux populations(2012)

Subjects
adaptive management, climate change, marineecosystems, [SDE]Environmental Sciences, terrestrial ecosystems, biological adaptation, ZABR, marine ecosystems, Mediterranean, biodiversity
Abstract

International audience; Potential for, and limits to, adaptation to environmental changes are critical for resilience and risk mitigation. The Mediterranean basin is a mosaic of biodiversity-rich ecosystems long affected by human influence, whose resilience is now questioned by climate change. After reviewing the different components of biological adaptation, we present the main characteristics of marine and terrestrial biodiversity in the Mediterranean basin and of the pressures they face. Taking climatic trends into consideration, we discuss the adaptive potential of a range of ecosystems dominated by species without active dispersal. We argue that the high heterogeneity of Mediterranean landscapes and seascapes constitutes a laboratory for the study of adaptation when environmental conditions change rapidly and may provide opportunities for adaptation and adaptability of species and ecosystems. Adaptive management in the Mediterranean can and should harness the nature-based solutions offered by both ecological and evolutionary processes for increasing the resilience of ecosystems to climate change

Published
2022

49. A 6 Ma record of palaeodenudation in the central Himalayas from in situ cosmogenic 10 Be in the Surai section

Author

Charreau, Julien, Lave, Jerome, France-Lanord, Christian, Puchol, Nicolas, Blard, P.H., Pik, Raphaël, Gajurel, Ananta Prasad, Arnold, Maurice, Aumaitre, Georges, Bourles, D.L., Keddadouche, Karim, Centre de Recherches Pétrographiques et Géochimiques (CRPG), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Tribhuvan University, Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Université de Lorraine (UL)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
010504 meteorology & atmospheric sciences, Himalaya, Geochemistry, Sediment, Geology, 15. Life on land, Structural basin, 010502 geochemistry & geophysics, Neogene, 01 natural sciences, Deposition (geology), Sedimentary depositional environment, palaeodenudation rates, Denudation, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, 13. Climate action, [SDU.STU.ST]Sciences of the Universe [physics]/Earth Sciences/Stratigraphy, late Neogene, cosmogenic 10Be, Quaternary, Foreland basin, 0105 earth and related environmental sciences
Abstract

International audience; To better constrain late Neogene denudation of the Himalayas, we analysed in situ 10Be concentrations in 17 Neogene sediment samples of the Surai section (central Nepal) and two modern sediment samples of the Rapti River. We first refined the depositional ages of the Surai section from 36 new paleomagnetic analyses, five 26Al/10Be burial ages, and, based on the Dynamic Time Warping algorithm, 104 automatically calculated likely magnetostratigraphic correlations. We also traced changing sediment sources using major element and Sr‐Nd isotopic data, finding at 4–3 Ma a switch from a large, trans‐Himalayan river to a river draining only the Lesser Himalaya and Siwalik piedmont, increasing the contribution of recycled sediments at that time. 10Be concentrations in Neogene sediments range from (1.00 ± 0.36) to (5.22 ± 0.98) × 103 at g–1 and decrease with stratigraphic age. Based on a flood plain transport model, our refined age model, and assuming a drainage change at 4–3 Ma, we reconstructed 10Be concentrations at the time of deposition. Assuming cosmogenic production rates similar to those of the modern basins, we calculated palaeodenudation rates of 0.9 ± 0.5 to 3.9 ± 2.7 mm a–1 from ca. 6 to 3 Ma in the palaeo‐Karnali basin and 0.6 ± 0.2 to 1.6 ± 0.8 mm a–1 since ca. 3 Ma in the palaeo‐Rapti basin. Given the uncertainties and similar modern values of ~2 mm a–1, the palaeo‐Karnali denudation rates may have been steady at ~1.7 ± 0.3 mm a–1 for the last ca. 6 Ma. A transient acceleration of the denudation in the palaeo‐Rapti basin of ~1.5 mm a–1 since ca. 1.5 Ma was likely due to the reworking of older, 10Be‐depleted Siwalik sediments in the foreland. If true, this steadiness of the denudation rates may suggest that Quaternary glaciations did not largely affect Himalayan denudation.

Published
2020

50. Potential drug–drug interactions associated with drugs currently proposed for COVID‐19 treatment in patients receiving other treatments

Author

Elisabeth Polard, Chantal Barin-Le Guellec, Caroline Solas, Agnès Sommet, Laurence Lagarce, Florian Lemaitre, Matthieu Grégoire, Michel Tod, Béatrice Saint-Salvi, Laure Elens, Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Centre d'Investigation Clinique [Rennes] (CIC), Université de Rennes (UR)-Hôpital Pontchaillou-Institut National de la Santé et de la Recherche Médicale (INSERM), Assistance Publique - Hôpitaux de Marseille (APHM), Unité des Virus Emergents (UVE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Hôpital de la Timone [CHU - APHM] (TIMONE), Centre hospitalier universitaire de Nantes (CHU Nantes), The Enteric Nervous System in gut and brain disorders [U1235] (TENS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN), Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM), Université Catholique de Louvain = Catholic University of Louvain (UCL), Agence nationale de sécurité du médicament et des produits de santé [Saint-Denis] (ANSM), Centre d'Investigation Clinique 1426 (CIC 1426), Institut National de la Santé et de la Recherche Médicale (INSERM)-AP-HP Hôpital universitaire Robert-Debré [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Epidémiologie et analyses en santé publique : risques, maladies chroniques et handicaps (LEASP), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Hôpital de la Croix-Rousse [CHU - HCL], Hospices Civils de Lyon (HCL), Institut des Sciences Pharmaceutiques et Biologiques (ISPB), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, CHU Trousseau [Tours], Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), Ciblage individuel et prévention des risques de traitements immunosupresseurs et de la transplantation (IPPRITT), CHU Limoges-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Génomique, Environnement, Immunité, Santé, Thérapeutique (GEIST), Université de Limoges (UNILIM)-Université de Limoges (UNILIM), UCL - SSS/LDRI - Louvain Drug Research Institute, UCL - SSS/IREC/LTAP - Louvain Centre for Toxicology and Applied Pharmacology, Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Santé et de la Recherche Médicale (INSERM)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université d'Angers (UA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Hôpital Pontchaillou-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Université d'Angers (UA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Jonchère, Laurent

Subjects
Anti-Inflammatory Agents, Antitubercular Agents, Review Article, 030226 pharmacology & pharmacy, Lopinavir, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Drug Interactions, Pharmacology (medical), Anti-Asthmatic Agents, Review Articles, Hypolipidemic Agents, media_common, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Analgesics, education.field_of_study, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, medicine.diagnostic_test, Anti-Bacterial Agents, 3. Good health, Editorial, [SDV.SP.PHARMA] Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Coronavirus Infections, Risk assessment, Interferon beta-1b, Hydroxychloroquine, medicine.drug, Drug, Thyroid Hormones, medicine.medical_specialty, Prescription Drugs, Coronavirus disease 2019 (COVID-19), media_common.quotation_subject, Pneumonia, Viral, Population, MEDLINE, Antineoplastic Agents, Therapeutic drug monitoring, Risk Assessment, Antiviral Agents, Betacoronavirus, 03 medical and health sciences, Pharmacokinetics, medicine, Hypoglycemic Agents, Humans, In patient, education, Intensive care medicine, Adverse effect, Pandemics, Pharmacology, Psychotropic Drugs, SARS-CoV-2, business.industry, Anticoagulants, COVID-19, Outbreak, Cardiovascular Agents, Receptors, Interleukin, COVID-19 Drug Treatment, Clinical trial, Pharmacodynamics, Adverse events, [SDV.SP.PHARMA]Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, business, 030217 neurology & neurosurgery
Abstract

International audience; Patients with COVID-19 are sometimes already being treated for one or more other chronic conditions, especially if they are elderly. Introducing a treatment against COVID-19, either on an outpatient basis or during hospitalization for more severe cases, raises the question of potential drug-drug interactions. Here, we analyzed the potential or proven risk of the co-administration of drugs used for the most common chronic diseases and those currently offered as treatment or undergoing therapeutic trials for COVID-19. Practical recommendations are offered, where possible.

Published
2020

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