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670 results on '"Oregon State University (OSU)"'

1. Oregon State University Teachers Educating All Multilingual Students: Integrating Language Acquisition and Improving Outcomes for English Learner Students

Author: Education Northwest, Oregon State University (OSU), Greenberg Motamedi, Jason, and Vazquez Cano, Manuel
Abstract: Teachers Educating All Multilingual Students (TEAMS) is a teacher professional development program at Oregon State University that culminates in an English for speakers of other languages endorsement and/or a dual language specialization. TEAMS is partially funded through an Office of English Language Acquisition National Professional Development grant from the U.S. Department of Education, and participants receive scholarships to cover tuition. This study explores whether TEAMS professional development had an impact on the academic outcomes of English learner students whose teachers participated in TEAMS. The study authors used a two-step matching procedure to identify a group of comparison teachers in TEAMS school districts who appeared likely to enroll in TEAMS. They then selected a subset of students who had statistically indistinguishable demographic characteristics, program enrollment, and academic achievement from TEAMS students. Due to complications related to the COVID-19 pandemic, reliable assessment data were only available for the academic year 2018/19. The study found that teachers' participation in TEAMS positively impacted English learner students' English language arts assessment outcomes. English language arts testing scores of English learner students taught by TEAMS teachers were 0.348 standard deviations higher than those of comparison students taught by comparison teachers. This difference is statistically significant and of moderate size, representing a 13.6 percentile point increase for an average English learner student. Teachers' participation in TEAMS had no impact on students' English language proficiency outcomes.
Published: 2022

2. Does short food supply chain participation improve farm economic performance? A meta‐analysis

Author: Chiaverina, Pierre, Drogué, Sophie, Jacquet, Florence, Lev, Larry, King, Robert, Montpellier Interdisciplinary center on Sustainable Agri-food systems (Social and nutritional sciences) (UMR MoISA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-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), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Oregon State University (OSU), University of Minnesota System, and This work was financially supported by the French Region Occitanie (# 20007393/ALDOCT – 001034).
Subjects: Meta-analysis, JEL: Q - Agricultural and Natural Resource Economics • Environmental and Ecological Economics/Q.Q1 - Agriculture/Q.Q1.Q13 - Agricultural Markets and Marketing • Cooperatives • Agribusiness, Economics and Econometrics, Farmers, JEL: Q - Agricultural and Natural Resource Economics • Environmental and Ecological Economics/Q.Q1 - Agriculture/Q.Q1.Q14 - Agricultural Finance, Income, [SHS.ECO]Humanities and Social Sciences/Economics and Finance, Economic performance, Short food supply chains, Agronomy and Crop Science
Abstract: International audience; Many researchers, policy makers and food activists view Short Food Supply Chains (SFSC) as attractive levers for improving farm income and the sustainability of farming systems. However, the empirical evidence documenting the association between SFSC participation and farm economic performance has been mixed. In this study, through a meta-analysis using a logistic regression, we identify key factors to explain differences between studies that find better economic performance in SFSC and those that do not. Our meta-analysis consists of 48 studies published in English and French from 2000 to 2022 that examine the economic performance of farms engaged in SFSC. Based on far more empirical evidence than previous reviews, we find that the relationship between SFSC participation and farmer income remains ambiguous. More specifically the findings indicate that the reported effect of SFSC on a farm economic performance varies depending on location and the indicator used to capture the economic performance of farms. Studies conducted in Europe are more likely to report higher farmer income as are studies that use profit satisfaction metrics rather than measures of gross or net income. We also emphasize the need to interpret the reported results cautiously because few are based on causal inference methods. Furthermore, the very few studies that account for selection bias often do so with inadequate corrections.
Published: 2023

3. Towards an integrated ecosystem of R packages for the analysis of population genetic data

Author: Emmanuel Paradis, Hilmar Lapp, Niklaus J. Grünwald, Stéphanie Manel, Thibaut Jombart, Thierry Gosselin, 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 de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Horticultural Crops Research Unit, USDA-ARS : Agricultural Research Service, Department of Botany and Plant Pathology, Oregon State University (OSU), MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), Center for Genomic and Computational Biology (GCB), Duke University, Institut des Sciences de l'Evolution de Montpellier ( ISEM ), Université de Montpellier ( UM ) -Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique ( CNRS ), USDA-ARS, Oregon State University ( OSU ), Centre d’Ecologie Fonctionnelle et Evolutive ( CEFE ), Institut de Recherche pour le Développement ( IRD [France-Sud] ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Montpellier ( UM ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -École pratique des hautes études ( EPHE ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Université Paul-Valéry - Montpellier 3 ( UM3 ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Université Laval [Québec] (ULaval), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), 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)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Subjects: 0301 basic medicine, description allélique, variant call format, [SDV]Life Sciences [q-bio], Population, Biostatistics, Biology, Bioinformatics, 03 medical and health sciences, genetique des populations, Genetics, allelic data, Ecosystem, logiciel r, education, Ecology, Evolution, Behavior and Systematics, Variant Call Format, education.field_of_study, Allelic data, NGS data, [ SDV ] Life Sciences [q-bio], Computational Biology, Genetic data, Data science, Genetics, Population, 030104 developmental biology, Software, Biotechnology
Abstract: International audience; Towards an integrated ecosystem of R packages for the analysis of population genetic data
Published: 2017

4. (2491) Proposal to conserve the name Rhizophagus with a conserved type (Fungi: Glomeromycota: Glomeraceae)

Author: Dirk Redecker, James M. Trappe, Arthur Schüßler, Christopher Walker, David L. Hawksworth, Efrén Cázares, Todd F. Elliott, School of Plant Biology, The University of Western Australia (UWA), Royal Botanic Garden Edinburgh, Department of Forest Ecosystems and Society, Oregon State University (OSU), Pacific Northwest Research Station, USDA Forest Service, SYMPLANTA GmbH & Co, Department of Life Sciences [Trieste], Università degli studi di Trieste, Comparative Plant and Fungal Biology, Royal Botanic Gardens, MycoRoots, Department of Integrative Studies, Warren Wilson College, Agroécologie [Dijon], Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, The University of Western Australia ( UWA ), Oregon State University ( OSU ), Department of Life Sciences, Universita di Trieste, Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté ( UBFC ), and Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)
Subjects: 0301 basic medicine, biology, [ SDV ] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], Plant Science, 15. Life on land, biology.organism_classification, Glomeromycota, 03 medical and health sciences, Rhizophagus (fungus), 030104 developmental biology, Type (biology), Glomeraceae, Botany, Ecology, Evolution, Behavior and Systematics
Abstract: (2491) Proposal to conserve the name Rhizophagus with a conserved type (Fungi: Glomeromycota: Glomeraceae)
Published: 2017

5. Chasing after Non-cyanobacterial Nitrogen Fixation in Marine Pelagic Environments

Author: Pia H. Moisander, Ilana Berman-Frank, Lasse Riemann, Sophie Bonnet, Mar Benavides, Angelicque E. White, University of Massachusetts Dartmouth, Institut méditerranéen d'océanologie ( MIO ), Centre National de la Recherche Scientifique ( CNRS ) -Université de Toulon ( UTLN ) -Aix Marseille Université ( AMU ) -Institut de Recherche pour le Développement ( IRD ), University of Copenhagen ( KU ), Bar-Ilan University [Israël], College of Earth, Ocean and Atmospheric Sciences [Corvallis] ( CEOAS ), Oregon State University ( OSU ), University of Massachusetts [Dartmouth], University of Massachusetts System (UMASS), 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), University of Copenhagen = Københavns Universitet (KU), College of Earth, Ocean and Atmospheric Sciences [Corvallis] (CEOAS), Oregon State University (OSU), 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), and University of Copenhagen = Københavns Universitet (UCPH)
Subjects: 0301 basic medicine, Microbiology (medical), Mesopelagic zone, lcsh:QR1-502, Biology, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Microbiology, lcsh:Microbiology, 03 medical and health sciences, Water column, oxygen minimum zone, Photic zone, mesopelagic, 14. Life underwater, bacteria, DOM, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, [ SDU.STU.OC ] Sciences of the Universe [physics]/Earth Sciences/Oceanography, nifH, Ecology, Nitrogenase, diazotroph, Pelagic zone, nitrogenase, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 030104 developmental biology, 13. Climate action, Aphotic zone, Perspective, Nitrogen fixation, Diazotroph, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, oxygen, minimum zone
Abstract: International audience; Traditionally, cyanobacterial activity in oceanic photic layers was considered responsible for the marine pelagic dinitrogen (N 2) fixation. Other potentially N 2-fixing bacteria and archaea have also been detected in the pelagic water column, however, the activity and importance of these non-cyanobacterial diazotrophs (NCDs) remain poorly constrained. In this perspective we summarize the N 2 fixation rates from recently published studies on photic and aphotic layers that have been attributed to NCD activity via parallel molecular measurements, and discuss the status, challenges, and data gaps in estimating non-cyanobacterial N 2 fixation NCNF in the ocean. Rates attributed to NCNF have generally been near the detection limit thus far (
Published: 2017

6. Plant virus movement proteins originated from jelly-roll capsid proteins

Author: Butkovic, Anamarija, Dolja, Valerian, Koonin, Eugene, Krupovic, Mart, Virologie des archées - Archaeal Virology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Oregon State University (OSU), National Center for Biotechnology Information (NCBI), and ANR-21-CE11-0001,ArcFus,Protéines de classe II de fusion membranaire chez les archées(2021)
Subjects: [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology
Abstract: International audience; Numerous, diverse plant viruses encode movement proteins (MPs) that aid the virus movement through plasmodesmata, the plant intercellular channels. MPs are essential for virus spread and propagation in distal tissues, and several unrelated MPs have been identified. The 30K superfamily of MPs (named after the molecular mass of tobacco mosaic virus MP, the classical model of plant virology) is the largest and most diverse MP variety, represented in 16 virus families, but its evolutionary origin remained obscure. Here, we show that the core structural domain of the 30K MPs is homologous to the jelly-roll domain of the capsid proteins (CPs) of small RNA and DNA viruses, in particular, those infecting plants. The closest similarity was observed between the 30K MPs and the CPs of the viruses in the families Bromoviridae and Geminiviridae . We hypothesize that the MPs evolved via duplication or horizontal acquisition of the CP gene in a virus that infected an ancestor of vascular plants, followed by neofunctionalization of one of the paralogous CPs, potentially through the acquisition of unique N- and C-terminal regions. During the subsequent coevolution of viruses with diversifying vascular plants, the 30K MP genes underwent explosive horizontal spread among emergent RNA and DNA viruses, likely permitting viruses of insects and fungi that coinfected plants to expand their host ranges, molding the contemporary plant virome.
Published: 2023

7. The virome of the last eukaryotic common ancestor and eukaryogenesis

Author: Mart Krupovic, Valerian V. Dolja, Eugene V. Koonin, Virologie des archées - Archaeal Virology, Institut Pasteur [Paris] (IP), Oregon State University (OSU), National Center for Biotechnology Information (NCBI), E.V.K. is supported by funds from the Intramural Research Program of the National Institutes of Health (National Library of Medicine). V.V.D. was partially supported by a National Institutes of Health/National Library of Medicine/National Center for Biotechnology Information Visiting Scientist Fellowship. M.K. was supported by l’Agence Nationale de la Recherche grant ANR-21-CE11-0001-01., ANR-20-CE20-0009,VIROMET,Devoiler le virome des archées methanogenes(2020), and ANR-21-CE11-0001,ArcFus,Protéines de classe II de fusion membranaire chez les archées(2021)
Subjects: Microbiology (medical), Immunology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Genetics, Cell Biology, Applied Microbiology and Biotechnology, Microbiology
Abstract: International audience; All extant eukaryotes descend from the last eukaryotic common ancestor (LECA), which is thought to have featured complex cellular organization. To gain insight into LECA biology and eukaryogenesis-the origin of the eukaryotic cell, which remains poorly understood-we reconstructed the LECA virus repertoire. We compiled an inventory of eukaryotic hosts of all major virus taxa and reconstructed the LECA virome by inferring the origins of these groups of viruses. The origin of the LECA virome can be traced back to a small set of bacterial-not archaeal-viruses. This provenance of the LECA virome is probably due to the bacterial origin of eukaryotic membranes, which is most compatible with two endosymbiosis events in a syntrophic model of eukaryogenesis. In the first endosymbiosis, a bacterial host engulfed an Asgard archaeon, preventing archaeal viruses from entry owing to a lack of archaeal virus receptors on the external membranes.
Published: 2023

8. Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems

Author: Fabien Lombard, Guillaume Bourdin, Stéphane Pesant, Sylvain Agostini, Alberto Baudena, Emilie Boissin, Nicolas Cassar, Megan Clampitt, Pascal Conan, Ophélie Da Silva, Céline Dimier, Eric Douville, Amanda Elineau, Jonathan Fin, J. Michel Flores, Jean François Ghiglione, Benjamin C.C. Hume, Laetitia Jalabert, Seth G. John, Rachel L. Kelly, Ilan Koren, Yajuan Lin, Dominique Marie, Ryan McMinds, Zoé Mériguet, Nicolas Metzl, David A. Paz-García, Maria Luiza Pedrotti, Julie Poulain, Mireille Pujo-Pay, Joséphine Ras, Gilles Reverdin, Sarah Romac, Alice Rouan, Eric Röttinger, Assaf Vardi, Christian R. Voolstra, Clémentine Moulin, Guillaume Iwankow, Bernard Banaigs, Chris Bowler, Colomban de Vargas, Didier Forcioli, Paola Furla, Pierre E. Galand, Eric Gilson, Stéphanie Reynaud, Shinichi Sunagawa, Matthew B. Sullivan, Olivier Thomas, Romain Troublé, Rebecca Vega Thurber, Patrick Wincker, Didier Zoccola, Denis Allemand, Serge Planes, Emmanuel Boss, Gaby Gorsky, 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), Global Oceans Systems Ecology & Evolution - Tara Oceans (GOSEE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Aix Marseille Université (AMU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Université de Toulon (UTLN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche pour le Développement (IRD [France-Nord])-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-European Molecular Biology Laboratory (EMBL)-École Centrale de Nantes (Nantes Univ - ECN), Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Université australe du Chili, Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), University of Maine, European Molecular Biology Laboratory [Hinxton], Shimoda Marine Research Center, Université de Tsukuba = University of Tsukuba, Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Nicholas School of the Environment, Duke University [Durham], 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), Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), 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)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Institut Fédératif de Recherche - Ressources Marines (IFR MARRES), Université Côte d'Azur (UCA), Laboratoire International Associé Réponse des Organismes et Populations face au Stress Environnemental - Université Côte d’Azur - Centre Scientifique de Monaco (LIA ROPSE), Université Côte d’Azur - Centre Scientifique de Monaco, Laboratoire d'Océanographie Microbienne (LOMIC), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), OSU Stations marines (STAMAR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Géochrononologie Traceurs Archéométrie (GEOTRAC), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Cycles biogéochimiques marins : processus et perturbations (CYBIOM), 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), Weizmann Institute of Science [Rehovot, Israël], Universität Konstanz, Department of Earth Sciences [USC Los Angeles], University of Southern California (USC), Station biologique de Roscoff (SBR), Maison de la Modélisation, de la Simulation et des Interactions [Sophia-Antipolis] (MSI), Oregon State University (OSU), Centro de Investigaciones Biologicas del Noroeste [Mexico] (CONACYT-CIBNOR), Consejo Nacional de Ciencia y Tecnología [Mexico] (CONACYT), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Processus et interactions de fine échelle océanique (PROTEO), Tara Ocean Foundation, Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecogéochimie des environnements benthiques (LECOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Centre Scientifique de Monaco (CSM), Ohio State University [Columbus] (OSU), Institute of Microbiology and Swiss Institute of Bioinformatics, Martin Ryan Institute, and National University of Ireland [Galway] (NUI Galway)
Subjects: [SDU]Sciences of the Universe [physics], Ecosystem ecology, Biodiversity
Abstract: The Tara Pacific expedition (2016-2018) sampled coral ecosystems around 32 islands in the Pacific Ocean and the ocean surface waters at 249 locations, resulting in the collection of nearly 58,000 samples. The expedition was designed to systematically study warm coral reefs and included the collection of corals, fish, plankton, and seawater samples for advanced biogeochemical, molecular, and imaging analysis. Here we provide a complete description of the sampling methodology, and we explain how to explore and access the different datasets generated by the expedition. Environmental context data were obtained from taxonomic registries, gazetteers, almanacs, climatologies, operational biogeochemical models, and satellite observations. The quality of the different environmental measures has been validated not only by various quality control steps but also through a global analysis allowing the comparison with known environmental large-scale structures. Such a wide released datasets opens the perspective to address a wide range of scientific questions.
Published: 2023

9. Post-paralysis tyrosine kinase inhibition with masitinib abrogates neuroinflammation and slows disease progression in inherited amyotrophic lateral sclerosis

Author: Olivier Hermine, Emiliano Trias, Patrice Dubreuil, Laura Martínez-Palma, Luis Barbeito, Matthias Guillo, Laurent Gros, Joseph S. Beckman, Joel Babdor, Pablo Díaz-Amarilla, Romina Barreto-Núñez, Patricia Cassina, Sofía Ibarburu, Ivan C. Moura, Thiago Trovati Maciel, Institut Pasteur de Montevideo, Réseau International des Instituts Pasteur ( RIIP ) -Institut Pasteur de Montevideo, Imagine - Institut des maladies génétiques ( IMAGINE - U1163 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Mécanismes cellulaires et moléculaires des désordres hématologiques et implications thérapeutiques, Centre National de la Recherche Scientifique ( CNRS ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), AB Science, Centre de Recherche en Cancérologie de Marseille ( CRCM ), Aix Marseille Université ( AMU ) -Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Instituto de Investigaciones Biologicas Clemente Estable [Montevideo], Departamento de Histologıa y Embriologıa, Facultad de Medicina [Montevideo], Universidad de la República, Linus Pauling Institute, Oregon State University ( OSU ), Centre national de référence des mastocytoses, Institut de Veille Sanitaire (INVS)-CHU Necker - Enfants Malades [AP-HP], Réseau International des Instituts Pasteur (RIIP), Imagine - Institut des maladies génétiques (IMAGINE - U1163), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratory of molecular mechanisms of hematologic disorders and therapeutic implications (ERL 8254 - Equipe Inserm U1163), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Recherche en Cancérologie de Marseille (CRCM), Aix Marseille Université (AMU)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Instituto de Investigaciones Biológicas Clemente Estable [Montevideo] (IIBCE), Oregon State University (OSU), Centre de référence des mastocytoses (CEREMAST), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), and Universidad de la República [Montevideo] (UDELAR)
Subjects: Male, 0301 basic medicine, Pathology, Pyridines, [SDV]Life Sciences [q-bio], Receptor tyrosine kinase, Tyrosine-kinase inhibitor, chemistry.chemical_compound, 0302 clinical medicine, Piperidines, Motor Neurons, Ciencias Médicas y de la Salud, Cell Death, Microglia, biology, General Neuroscience, Masitinib, Neurodegeneration, M-CSF, 3. Good health, medicine.anatomical_structure, Spinal Cord, Neurology, Benzamides, Disease Progression, Encephalitis, Neuroglia, Rats, Transgenic, Tyrosine kinase, medicine.medical_specialty, medicine.drug_class, Immunology, Biotecnología de la Salud, 03 medical and health sciences, Cellular and Molecular Neuroscience, Aberrant glial cells, medicine, Animals, Humans, Paralysis, Protein Kinase Inhibitors, Neuroinflammation, [ SDV ] Life Sciences [q-bio], Superoxide Dismutase, business.industry, Research, Amyotrophic Lateral Sclerosis, medicine.disease, Rats, Disease Models, Animal, Thiazoles, 030104 developmental biology, chemistry, Mutation, biology.protein, Cancer research, ALS, business, 030217 neurology & neurosurgery
Abstract: Background In the SOD1G93A mutant rat model of amyotrophic lateral sclerosis (ALS), neuronal death and rapid paralysis progression are associated with the emergence of activated aberrant glial cells that proliferate in the degenerating spinal cord. Whether pharmacological downregulation of such aberrant glial cells will decrease motor neuron death and prolong survival is unknown. We hypothesized that proliferation of aberrant glial cells is dependent on kinase receptor activation, and therefore, the tyrosine kinase inhibitor masitinib (AB1010) could potentially control neuroinflammation in the rat model of ALS. Methods The cellular effects of pharmacological inhibition of tyrosine kinases with masitinib were analyzed in cell cultures of microglia isolated from aged symptomatic SOD1G93A rats. To determine whether masitinib prevented the appearance of aberrant glial cells or modified post-paralysis survival, the drug was orally administered at 30 mg/kg/day starting after paralysis onset. Results We found that masitinib selectively inhibited the tyrosine kinase receptor colony-stimulating factor 1R (CSF-1R) at nanomolar concentrations. In microglia cultures from symptomatic SOD1G93A spinal cords, masitinib prevented CSF-induced proliferation, cell migration, and the expression of inflammatory mediators. Oral administration of masitinib to SOD1G93A rats starting after paralysis onset decreased the number of aberrant glial cells, microgliosis, and motor neuron pathology in the degenerating spinal cord, relative to vehicle-treated rats. Masitinib treatment initiated 7 days after paralysis onset prolonged post-paralysis survival by 40 %. Conclusions These data show that masitinib is capable of controlling microgliosis and the emergence/expansion of aberrant glial cells, thus providing a strong biological rationale for its use to control neuroinflammation in ALS. Remarkably, masitinib significantly prolonged survival when delivered after paralysis onset, an unprecedented effect in preclinical models of ALS, and therefore appears well-suited for treating ALS. Electronic supplementary material The online version of this article (doi:10.1186/s12974-016-0620-9) contains supplementary material, which is available to authorized users.
Published: 2016

10. A global synthesis of high-resolution stable isotope data from benthic foraminifera of the last deglaciation

Author: Juan Muglia, Stefan Mulitza, Janne Repschläger, Andreas Schmittner, Lester Lembke-Jene, Lorraine Lisiecki, Alan Mix, Rajeev Saraswat, Elizabeth Sikes, Claire Waelbroeck, Julia Gottschalk, Jörg Lippold, David Lund, Gema Martinez-Mendez, Elisabeth Michel, Francesco Muschitiello, Sushant Naik, Yusuke Okazaki, Lowell Stott, Antje Voelker, Ning Zhao, Muglia, Juan [0000-0002-6968-7723], Lembke-Jene, Lester [0000-0002-6873-8533], Michel, Elisabeth [0000-0001-7810-8888], Okazaki, Yusuke [0000-0002-2406-3466], Zhao, Ning [0000-0002-1936-8978], Apollo - University of Cambridge Repository, Voelker, Antje [0000-0001-6465-6023], Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, Max Planck Institute for Chemistry (MPIC), Max-Planck-Gesellschaft, College of Earth, Ocean and Atmospheric Sciences [Corvallis] (CEOAS), Oregon State University (OSU), Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Department of Earth Science [Santa Barbara), University of California [Santa Barbara] (UC Santa Barbara), University of California (UC)-University of California (UC), CSIR National Institute of Oceanography [India] (NIO), Department of Marine and Coastal Sciences [New Brunswick], School of Environmental and Biological Sciences [New Brunswick], Rutgers, The State University of New Jersey [New Brunswick] (RU), Rutgers University System (Rutgers)-Rutgers University System (Rutgers)-Rutgers, The State University of New Jersey [New Brunswick] (RU), Rutgers University System (Rutgers)-Rutgers University System (Rutgers), 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), Institute of Geosciences [Kiel], Christian-Albrechts-Universität zu Kiel (CAU), Heidelberg University, Department of Marine Sciences, University of Connecticut (UCONN), Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Carl Von Ossietzky Universität Oldenburg = Carl von Ossietzky University of Oldenburg (OFFIS), Paléocéanographie (PALEOCEAN), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Department of Geography [Cambridge, UK], University of Cambridge [UK] (CAM), Kyushu University, Department of Earth Sciences [USC Los Angeles], University of Southern California (USC), Instituto Português de Investigação do Mar e da Atmosfera (IPMA), and State Key Laboratory of Estuarine and Coastal Research
Subjects: Statistics and Probability, Oxygen, Carbon Isotopes, [SDU]Sciences of the Universe [physics], Seawater, Foraminifera, Library and Information Sciences, Statistics, Probability and Uncertainty, Carbon, Computer Science Applications, Education, Information Systems
Abstract: Acknowledgements: J.M. acknowledges funding from Conicet and FONCyT (PICT-2019-04147), Argentina, NSF’s Marine Geology and Geophysics and Chemical Oceanography Program (grants 1634719 and 1924215), USA, and the Past Global Changes (PAGES) project through its Data Stewardship Scholarship program. This study was undertaken by OC3, a working group of the PAGES project. R.S. acknowledges the financial support from the Council of Scientific and Industrial Research, Government of India. L.L.J. acknowledges funding by the German BMBF through grant no. 03F0785A NOPAWAC., Funder: Consejo Nacional de Investigaciones Científicas y Técnicas (National Scientific and Technical Research Council); doi: https://doi.org/10.13039/501100002923, Funder: Past Global Changes (PAGES); doi: https://doi.org/10.13039/100010439, We present the first version of the Ocean Circulation and Carbon Cycling (OC3) working group database, of oxygen and carbon stable isotope ratios from benthic foraminifera in deep ocean sediment cores from the Last Glacial Maximum (LGM, 23-19 ky) to the Holocene (
Published: 2023
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11. Crystal structure of the effector AvrLm4-7 of Leptosphaeria maculans reveals insights into its translocation into plant cells and recognition by resistance proteins

Author: Audrey Labarde, Karine Blondeau, Marie-Hélène Balesdent, Benedicte Ollivier, Shiv D. Kale, Guillaume Daverdin, Noureddine Lazar, Danielle H Y Choi, Marc Graille, Brett M. Tyler, Isabelle Fudal, Francoise Blaise, Herman van Tilbeurgh, Juliette Linglin, Thierry Rouxel, Fonction et Architecture des Assemblages Macromoléculaires (FAAM), Département Biochimie, Biophysique et Biologie Structurale (B3S), Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), BIOlogie et GEstion des Risques en agriculture (BIOGER), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Virginia Tech [Blacksburg], Center for Genome Research and Biocomputing, Oregon State University (OSU), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), AgroParisTech-Institut National de la Recherche Agronomique (INRA), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), National Science Foundation (NSF) IOS-0924861, ANR-14-CE19-0019,StructuraLEP,Caractérisation structurale et fonctionnelle d'effecteurs de L. maculans et de leurs interactants(2014), Fonction et Architecture des Assemblages Macromoléculaires ( FAAM ), Département Biochimie, Biophysique et Biologie Structurale ( B3S ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ), BIOlogie GEstion des Risques en agriculture - Champignons Pathogènes des Plantes ( BIOGER-CPP ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Virginia Tech, University of Virginia [Charlottesville], and Oregon State University ( OSU )
Subjects: 0106 biological sciences, [SDV]Life Sciences [q-bio], Nicotiana benthamiana, Plant Science, 3D structure, 01 natural sciences, Pichia pastoris, Fungal Proteins, 03 medical and health sciences, Protein structure, Leptosphaeria maculans, Ascomycota, Genetics, avirulence protein, plant cell translocation, Gene, 030304 developmental biology, Plant Diseases, chemistry.chemical_classification, 0303 health sciences, biology, [ SDV ] Life Sciences [q-bio], Virulence, Effector, C-terminus, Brassica napus, Cell Biology, biology.organism_classification, Amino acid, effector, Biochemistry, chemistry, plant disease resistance, 010606 plant biology & botany
Abstract: International audience; The avirulence gene AvrLm4-7 of Leptosphaeria maculans, the causal agent of stem canker in Brassica napus (oilseed rape), confers a dual specificity of recognition by two resistance genes (Rlm4 and Rlm7) and is strongly involved in fungal fitness. In order to elucidate the biological function of AvrLm4-7 and understand the specificity of recognition by Rlm4 and Rlm7, the AvrLm4-7 protein was produced in Pichia pastoris and its crystal structure was determined. It revealed the presence of four disulfide bridges, but no close structural analogs could be identified. A short stretch of amino acids in the C terminus of the protein, (R/N)(Y/F)(R/S)E(F/W), was well-conserved among AvrLm4-7 homologs. Loss of recognition of AvrLm4-7 by Rlm4 is caused by the mutation of a single glycine to an arginine residue located in a loop of the protein. Loss of recognition by Rlm7 is governed by more complex mutational patterns, including gene loss or drastic modifications of the protein structure. Three point mutations altered residues in the well-conserved C-terminal motif or close to the glycine involved in Rlm4-mediated recognition, resulting in the loss of Rlm7-mediated recognition. Transient expression in Nicotiana benthamiana (tobacco) and particle bombardment experiments on leaves from oilseed rape suggested that AvrLm4-7 interacts with its cognate R proteins inside the plant cell, and can be translocated into plant cells in the absence of the pathogen. Translocation of AvrLm4-7 into oilseed rape leaves is likely to require the (R/N)(Y/F)(R/S)E(F/W) motif as well as an RAWG motif located in a nearby loop that together form a positively charged region.
Published: 2015

12. DNA hypomethylation of the host tree impairs interaction with mutualistic ectomycorrhizal fungus

Author: Julien Vigneaud, Annegret Kohler, Mamadou Dia Sow, Alain Delaunay, Laure Fauchery, Frederic Guinet, Christian Daviaud, Kerrie W. Barry, Keykhosrow Keymanesh, Jenifer Johnson, Vasanth Singan, Igor Grigoriev, Régis Fichot, Daniel Conde, Mariano Perales, Jörg Tost, Francis M. Martin, Isabel Allona, Steven H. Strauss, Claire Veneault‐Fourrey, Stéphane Maury, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Université d'Orléans (UO)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de Recherche en Génomique Humaine (CNRGH), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Oregon State University (OSU), Conseil Régional Région Centre Val de Loire, Department of Energy (US), Kohler, Annegret, Sow, Mamadou Dia, Delaunay, Alain, Fauchery, Laure, Barry, Kerrie W., Keymanesh, Keykhosrow, Singan, Vasanth, Grigoriev, Igor, Fichot, Régis, Conde, Daniel, Perales, Mariano, Tost, Jörg, Martin, Francis M., Allona, Isabel, Strauss, Steven H., Veneault-Fourrey, Claire, and Maury, Stéphane 0000-0003-0481-0847]
Subjects: DNA METHYLATION 1, corrhizas, DNA demethylatione, Mycorrhizas, poplar, Physiology, [SDV]Life Sciences [q-bio], Plant Science, DEMETER, Laccaria bicolormy, Laccaria bicolor, pigenetic
Abstract: 17 Pág., Ectomycorrhizas are an intrinsic component of tree nutrition and responses to environmental variations. How epigenetic mechanisms might regulate these mutualistic interactions is unknown. By manipulating the level of expression of the chromatin remodeler DECREASE IN DNA METHYLATION 1 (DDM1) and two demethylases DEMETER-LIKE (DML) in Populus tremula × Populus alba lines, we examined how host DNA methylation modulates multiple parameters of the responses to root colonization with the mutualistic fungus Laccaria bicolor. We compared the ectomycorrhizas formed between transgenic and wild-type (WT) trees and analyzed their methylomes and transcriptomes. The poplar lines displaying lower mycorrhiza formation rate corresponded to hypomethylated overexpressing DML or RNAi-ddm1 lines. We found 86 genes and 288 transposable elements (TEs) differentially methylated between WT and hypomethylated lines (common to both OX-dml and RNAi-ddm1) and 120 genes/1441 TEs in the fungal genome suggesting a host-induced remodeling of the fungal methylome. Hypomethylated poplar lines displayed 205 differentially expressed genes (cis and trans effects) in common with 17 being differentially methylated (cis). Our findings suggest a central role of host and fungal DNA methylation in the ability to form ectomycorrhizas including not only poplar genes involved in root initiation, ethylene and jasmonate-mediated pathways, and immune response but also terpenoid metabolism., MDS and JV received PhD grants from the MRES and Conseil Régional Région Centre Val de Loire, respectively. The LBLGC and the LEE/CNRGH benefit from the support of the ANR EPITREE (ANR-17-CE32-0009-01, https://www6.inrae.fr/epitree-project_eng/) to SM and JT. We thank RTP3E CNRS and IHPE for the access to the bioinformatic platform (http://galaxy.univ-perp.fr/, Christian Chaparro, France). CVF, AK, FM, FG, and LF benefit from the support of the Genomic Science Program (project ‘Plant-Microbe Interface’), US Department of Energy, Office of Science, Biological and Environmental Research under the contract DE-AC05-00OR22725 and the Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE; grant ANR-11-LABX-0002-01). The work (proposal: 10.46936/10.25585/60001022) conducted by the US Department of Energy JGI (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the US Department of Energy operated under Contract no. DE-AC02-05CH11231.
Published: 2023

13. Heat flow and thermal regime in the Guaymas Basin, Gulf of California: Estimates of conductive and advective heat transport

Author: Neumann, Florian, Negrete-Aranda, Raquel, Harris, Robert, Contreras, Juan, Galerne, Christophe, Peña-Salinas, Manet, Spelz, Ronald, Teske, Andreas, Lizarralde, Daniel, Höfig, Tobias, Aiello, Ivano, Ash, Janine, Bojanova, Diana, Buatier, Martine, Edgcomb, Virginia, Gontharet, Swanne, Heuer, Verena, Jiang, Shijun, Kars, Myriam A.C., Kim, Ji‐hoon, Koornneef, Louise M.T., Marsaglia, Kathleen, Meyer, Nicolette, Morono, Yuki, Pastor, Lucie, Pérez Cruz, Ligia, Ran, Lihua, Riboulleau, Armelle, Sarao, John, Schubert, Florian, Singh, S. Khogenkumar, Stock, Joann, Toffin, Laurent M.A.A., Xie, Wei, Yamanaka, Toshiro, Zhuang, Guangchao, Centro de Investigacion Cientifica y de Education Superior de Ensenada [Mexico] (CICESE), College of Earth, Ocean and Atmospheric Sciences [Corvallis] (CEOAS), Oregon State University (OSU), Universität Bremen, Universidad Autónoma de Baja California (UABC), University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC), Woods Hole Oceanographic Institution (WHOI), International Ocean Discovery Program, Laboratoire Chrono-environnement (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Cycles biogéochimiques marins : processus et perturbations (CYBIOM), 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), Center for Marine Environmental Sciences [Bremen] (MARUM), Geological Sciences, Florida State University [Tallahassee] (FSU), Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Laboratoire Environnement Profond (LEP), Etudes des Ecosystèmes Profonds (EEP), and Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)
Subjects: Guyamas Basin, [SDE]Environmental Sciences, IODP Expedition 385, Geology, Heat Flow, Heat Transfer
Abstract: Heat flow is estimated at eight sites drilled during the International Ocean Discovery Program Expedition 385 into the Guaymas Basin, Gulf of California. The expedition sought to understand the thermal regime of the basin and heat transfer between off-axis sills intruding the organic-rich sediments of the Guaymas Basin, and the basin floor. The distinct sedimentation rates, active tectonics, and magmatism makes the basin interesting for scientific discoveries. Results show sedimentation corrected heat flow values range 119-221 mW/m2 in the basin and 257-1003 mW/m2 at the site of a young sill intrusion, denominated Ringvent. Thermal analysis shows that heat in the Guaymas Basin is being dissipated by conduction for plate ages >0.2 Ma, whereas younger plate ages are in a state of transient cooling by both conduction and advection. Drilling sites show that Ringvent is an active sill being cooled down slowly by circulating fluids with discharge velocities 10–200 mm/yr. Possible recharge sites are located ~1 km away from the sill's border. Modeling of the heat output at Ringvent indicates a sill thickness of ~240 m. A simple order-of-magnitude model predicts that relatively small amounts of magma are needed to account for the elevated heat flow in non-volcanic, sediment-filled rifts like the central and northern Gulf of California in which heating of the upper crust is achieved via advection by sill emplacement and hydrothermal circulation. Multiple timescales of cooling control the crustal, chemical and biological evolution of the Guaymas Basin. Here we recognize at least four timescales: the time interval between intrusions (~103 yr), the thermal relaxation time of sills (~104 yr), the characteristic cooling time of the sediments (~105 yr), and the cooling of the entire crust at geologic timescales.
Published: 2023

14. Isotopic measurements in water vapor, precipitation, and seawater during EUREC4A

Author: Adriana Bailey, Franziska Aemisegger, Leonie Villiger, Sebastian A. Los, Gilles Reverdin, Estefanía Quiñones Meléndez, Claudia Acquistapace, Dariusz B. Baranowski, Tobias Böck, Sandrine Bony, Tobias Bordsdorff, Derek Coffman, Simon P. de Szoeke, Christopher J. Diekmann, Marina Dütsch, Benjamin Ertl, Joseph Galewsky, Dean Henze, Przemyslaw Makuch, David Noone, Patricia K. Quinn, Michael Rösch, Andreas Schneider, Matthias Schneider, Sabrina Speich, Bjorn Stevens, Elizabeth Thompson, National Center for Atmospheric Research [Boulder] (NCAR), Institute for Atmospheric and Climate Science [Zürich] (IAC), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Department of Earth and Planetary Sciences [Albuquerque] (EPS), The University of New Mexico [Albuquerque], 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), College of Earth, Ocean and Atmospheric Sciences [Corvallis] (CEOAS), Oregon State University (OSU), Institute for Geophysics and Meteorology [Köln] (IGM), University of Cologne, Institute of Geophysics [Warsaw], Polska Akademia Nauk = Polish Academy of Sciences (PAN), Laboratoire de Météorologie Dynamique (UMR 8539) (LMD), Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-École des Ponts ParisTech (ENPC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département des Géosciences - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), SRON Netherlands Institute for Space Research (SRON), NOAA Pacific Marine Environmental Laboratory [Newport] (PMEL), National Oceanic and Atmospheric Administration (NOAA), Institute of Meteorology and Climate Research, Karlsruhe Institute of Technology (KIT), Department of Meteorology and Geophysics [Vienna], Universität Wien, Department of Earth and Space Sciences [Seattle], University of Washington [Seattle], Steinbuch Centre for Computing [Karlsruhe] (SCC), Karlsruher Institut für Technologie (KIT), Institute of Oceanology, Polish Academy of Sciences (IO-PAN), Department of Physics [Auckland], University of Auckland [Auckland], Department of Environmental Systems Science [ETH Zürich] (D-USYS), Finnish Meteorological Institute (FMI), Max Planck Institute for Meteorology (MPI-M), Max-Planck-Gesellschaft, NOAA Physical Sciences Laboratory (PSL), European Project: 817578,TRIATLAS(2019), European Project: 694768,EUREC4A, and European Project: 256961,EC:FP7:ERC,ERC-2010-StG_20091028,MUSICA(2011)
Subjects: Earth sciences, [SDU]Sciences of the Universe [physics], ddc:550, General Earth and Planetary Sciences
Abstract: In early 2020, an international team set out to investigate trade-wind cumulus clouds and their coupling to the large-scale circulation through the field campaign EUREC4A: ElUcidating the RolE of Clouds-Circulation Coupling in ClimAte. Focused on the western tropical Atlantic near Barbados, EUREC4A deployed a number of innovative observational strategies, including a large network of water isotopic measurements collectively known as EUREC4A-iso, to study the tropical shallow convective environment. The goal of the isotopic measurements was to elucidate processes that regulate the hydroclimate state – for example, by identifying moisture sources, quantifying mixing between atmospheric layers, characterizing the microphysics that influence the formation and persistence of clouds and precipitation, and providing an extra constraint in the evaluation of numerical simulations. During the field experiment, researchers deployed seven water vapor isotopic analyzers on two aircraft, on three ships, and at the Barbados Cloud Observatory (BCO). Precipitation was collected for isotopic analysis at the BCO and from aboard four ships. In addition, three ships collected seawater for isotopic analysis. All told, the in situ data span the period 5 January–22 February 2020 and cover the approximate area 6 to 16∘ N and 50 to 60∘ W, with water vapor isotope ratios measured from a few meters above sea level to the mid-free troposphere and seawater samples spanning the ocean surface to several kilometers depth. This paper describes the full EUREC4A isotopic in situ data collection – providing extensive information about sampling strategies and data uncertainties – and also guides readers to complementary remotely sensed water vapor isotope ratios. All field data have been made publicly available even if they are affected by known biases, as is the case for high-altitude aircraft measurements, one of the two BCO ground-based water vapor time series, and select rain and seawater samples from the ships. Publication of these data reflects a desire to promote dialogue around improving water isotope measurement strategies for the future. The remaining, high-quality data create unprecedented opportunities to close water isotopic budgets and evaluate water fluxes and their influence on cloudiness in the trade-wind environment. The full list of dataset DOIs and notes on data quality flags are provided in Table 3 of Sect. 5 (“Data availability”).
Published: 2023

15. The global virome: How much diversity and how many independent origins?

Author: Eugene V. Koonin, Mart Krupovic, Valerian V. Dolja, National Center for Biotechnology Information (NCBI), Virologie des archées - Archaeal Virology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Oregon State University (OSU), and Eugene V. Koonin is supported by the funds of the Intramural Research Program of the National Institutes of Health of the USA. Valerian V. Dolja was partially supported by NIH/NLM/NCBI Visiting Scientist Fellowship.
Subjects: [SDV]Life Sciences [q-bio], Microbiology, Ecology, Evolution, Behavior and Systematics
Abstract: International audience; Viruses are considered to be the most abundant biological entities on earth. They also display striking genetic diversity as emphatically demonstrated by the recent advances of metagenomics and metatranscriptomics. But what are the limits of this diversity, that is, how many virus species in the earth virome? By combining the available estimates of the number of prokaryote species with those of the virome size, we obtain back-of-the-envelope estimates of the total number of distinct virus species, which come out astronomically large, from about 10^7 to about 10^9 . The route of virus origins apparently involved non-viral replicators capturing and exapting various cellular proteins to become virus capsid subunits. How many times in the history of life has this happened? In other words, how many realms of viruses, the highest rank taxa that are supposed to be monophyletic, comprise the global virome? We argue that viruses emerged on a number (even if far from astronomical) independent occasions, so the number of realms will considerably increase from the current 6, by splitting some of the current realms, giving the realm status to some of the currently unclassified groups of viruses and discovery of new distinct groups.
Published: 2023

16. Editorial: Microplastics in water and potential impacts on human health

Author: Trevisan, Rafael, Brander, Susanne, Coffin, Scott, 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), Université de Brest (UBO), Coastal Oregon Marine Experimental Station, Oregon State University (OSU), California State Water Resources Control Board, and La National Science Foundation Growing Convergence Research Big Idea award number 1935028 (to SB)
Subjects: [SDV.EE]Life Sciences [q-bio]/Ecology, environment, plastic pollution, microplastics, sources of contamination, drinking water, toxicity, human health, nanoplastics, Water Science and Technology
Abstract: International audience
Published: 2022

17. Divergent post-breeding spatial habitat use of Laysan and black-footed albatross

Author: Fredrick Dallas Jordan, Scott A. Shaffer, Melinda G. Conners, Julia E. F. Stepanuk, Morgan E. Gilmour, Corey A. Clatterbuck, Elliott L. Hazen, Daniel M. Palacios, Yann Tremblay, Michelle Antolos, David G. Foley, Steven J. Bograd, Daniel P. Costa, Lesley H. Thorne, Stony Brook University [SUNY] (SBU), State University of New York (SUNY), San Jose State University [San Jose] (SJSU), Ocean Sciences Department, University of California [Santa Cruz] (UC Santa Cruz), University of California (UC)-University of California (UC), NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA), Joint Institute for Marine and Atmospheric Research (JIMAR), University of Hawai‘i [Mānoa] (UHM), 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), Oregon State University (OSU), Southwest Fisheries Science Center (SWFSC), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA), University of California (UC), School of Marine and Atmospheric Sciences [Stony Brook] (SoMAS), and State University of New York (SUNY)-State University of New York (SUNY)
Subjects: Overlap, Post-breeding, loggers, Ecology, [SDE.MCG]Environmental Sciences/Global Changes, spatial ecology, post-breeding, Segregation, habitat, Distribution, Loggers, segregation, Movement ecology, Habitat, distribution, movement ecology, Spatial ecology, overlap, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Ecology, Evolution, Behavior and Systematics
Abstract: Understanding the at-sea movements of wide-ranging seabird species throughout their annual cycle is essential for their conservation and management. Habitat use and resource partitioning of Laysan (Phoebastria immutabilis) and black-footed (Phoebastria nigripes) albatross are well-described during the breeding period but are less understood during the post-breeding period, which represents ~40% of their annual cycle. Resource partitioning may be reduced during post-breeding, when birds are not constrained to return to the nest site regularly and can disperse to reduce competitive pressure. We assessed the degree of spatial segregation in the post-breeding distributions of Laysan (n = 82) and black-footed albatrosses (n = 61) using geolocator tags between 2008 and 2012 from two large breeding colonies in the Northwestern Hawaiian Islands, Midway Atoll, and Tern Island. We characterized the species-and colony-specific foraging and focal distributions (represented by the 95 and 50th density contours, respectively) and quantified segregation in at-sea habitat use between species and colonies. Laysan and black-footed albatross showed consistent and significant at-sea segregation in focal areas across colonies, indicating that resource partitioning persists during post-breeding. Within breeding colonies, segregation of foraging areas between the two species was more evident for birds breeding at Tern Island. Spatial segregation decreased as the post-breeding season progressed, when spatial distributions of both species became more dispersed. In contrast to studies conducted on breeding Laysan and black-footed albatross, we found that sea surface temperature distinguished post-breeding habitats of black-footed albatrosses between colonies, with black-footed albatrosses from Midway Atoll occurring in cooler waters (3.6°C cooler on average). Our results reveal marked at-sea segregation between Laysan and black-footed albatross breeding at two colonies during a critical but understudied phase in their annual cycle. The observed variation in species-environment relationships underscores the importance of sampling multiple colonies and temporal periods to more thoroughly understand the spatial distributions of pelagic seabirds.
Published: 2022

18. Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

Author: Dirk Redecker, Johannes Z. Groenewald, B. Stielow, Ibai Olariaga, Wendy A. Untereiner, Steven D. Leavitt, Scott Federhen, Samantha C. Karunarathna, Pedro W. Crous, Katerina Fliegerova, Jianping Xu, Ana Crespo, M. Teresa Telleria, Soili Stenroos, Martha J. Powell, Sajeewa S. N. Maharachchikumbura, Gianluigi Cardinali, Laszlo Irinyi, Hiran A. Ariyawansa, Javier Diéguez Uribeondo, Andrew M. Minnis, Paul M. Kirk, Zai-Wei Ge, Duong Vu, Richard C. Hamelin, Conrad L. Schoch, Jian-Kui Liu, Wieland Meyer, Kevin D. Hyde, Csaba Vágvölgyi, Bryn T. M. Dentinger, Ning Zhang, Dhanushka Udayanga, Tamás Petkovits, Qing Cai, Cletus P. Kurtzman, Raquel Pino-Bodas, Jie Chen, Michael Weiß, Karl-Henrik Larsson, Leho Tedersoo, María P. Martín, Peter M. Letcher, Gábor M. Kovács, Liang-Dong Guo, Kazuaki Tanaka, Bhushan Shrestha, Andrew N. Miller, Krishna V. Subbarao, Nicolas Feau, Urmas Kõljalg, Huzefa A. Raja, D. Jean Lodge, Karen K. Nakasone, Jean-Marc Moncalvo, Nalin N. Wijayawardene, Sung-Oui Suh, Cécile Gueidan, Teun Boekhout, Wen Ying Zhuang, Marieka Gryzenhout, Jullie M. Sarmiento-Ramírez, Bart Buyck, H. Thorsten Lumbsch, Marizeth Groenewald, Seung-Beom Hong, Keith A. Seifert, Peter R. Johnston, Janet Jennifer Luangsa-ard, Barbara Robbertse, Kessy Abarenkov, Dimuthu S. Manamgoda, Z. Wilhelm de Beer, Pradeep K. Divakar, Tuula Niskanen, Patrik Inderbitzin, M. Catherine Aime, Bevan S. Weir, Sarah Hambleton, Zhu L. Yang, R. Henrik Nilsson, Kare Liimatainen, Cobus M. Visagie, Krisztina Krizsán, Michael J. Wingfield, Ulrike Damm, Gareth W. Griffith, Donald M. Walker, Tamás Papp, Vincent Robert, Miguel A. García, Valérie Hofstetter, Martin I. Bidartondo, Karen Hansen, Margarita Dueñas, Jos Houbraken, Karen W. Hughes, Kerstin Voigt, Giuseppina Mulè, Martin Grube, Ekaphan Kraichak, National Center for Biotechnology Information (NCBI), National Institutes of Health (NIH), NLM, National Institutes of Health, CBS-KNAW Fungal Biodiversity Centre, Department of Pharmaceutical Sciences – Microbiology, Università degli Studi di Perugia (UNIPG), Molecular Mycology Research Laboratory, University of Sydney, Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School-Westmead Hospital, The Westmead Institute for Medical Research, Faculty of Biological and Environmental Sciences [Helsinki], University of Helsinki, Ecology and Evolutionary Biology, University of Tennessee System, Illinois Natural History Survey, University of Illinois System-University of Illinois System, Mycology Section, Jodrell Laboratory, Royal Botanic Gardens, University of Tartu, Department of Botany and Plant Pathology, Oregon State University (OSU), Institute of Excellence in Fungal Research and School of Science, Mae Fah Luang University [Thaïlande] (MFU), Imperial College London, 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)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Chinese Academy of Sciences [Beijing] (CAS), School of Science, Departamento de Biologia Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Museum of Natural History Görlitz, Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria (UPSpace), Real Jardin Botanico (RJB), Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia (UBC), Czech Academy of Sciences [Prague] (CAS), Department of Biology, Northern Arizona University [Flagstaff], Aberystwyth University, Institute of Plant Sciences, Karl Franzens University, Department of Plant Sciences, University of California, Plant Industry, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences [Changchun Branch] (CAS), Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food [Ottawa] (AAFC), Department of Botany, National University of Ireland [Galway] (NUI Galway), Département de recherche en Protection des végétaux grandes cultures et vigne/Viticulture et oenologie, Agroscope, Korean Agricultural Culture Collection, National Academy of Agricultural Science, Davis Department of Plant Pathology, Manaaki Whenua – Landcare Research [Lincoln], Institute of Biology, Department of Plant Anatomy, Eötvös Loránd University (ELTE), Plant Protection Institute [Budapest] (ATK NOVI), Centre for Agricultural Research [Budapest] (ATK), Hungarian Academy of Sciences (MTA)-Hungarian Academy of Sciences (MTA), Science and Education, Field Museum, Department of Microbiology [Szeged], University of Szeged [Szeged], Bacterial Foodborne Pathogens and Mycology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research (NCAUR), United States Department of Agriculture (USDA)-United States Department of Agriculture (USDA), The Natural History Museum [London] (NHM), Department of Biological Sciences, The Open University [Milton Keynes] (OU), Plant Biology, Department of Biosciences, Forest Service, United States Department of Agriculture, Biotec - National Center for Genetic Engineering and Biotechnology, Department of Medical Microbiology and Immunology [Göteborg], University of Gothenburg (GU), Department of Natural History, Royal Ontario Museum, Department of Ecology Evolutionary Biology, University of Toronto, Institute of Sciences of Food Production (ISPA), Consiglio Nazionale delle Ricerche (CNR), Northern Research Station, U.S. Forest Service, Center for Forest Mycology Research (CFMR), Botany Unit, Finnish Museum of Natural History, Finnish Museum of Natural History (LUOMUS), University of Helsinki-University of Helsinki, Department of Chemistry and Biochemistry, University of California [Los Angeles] (UCLA), University of California-University of California, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institute of Life Science and Biotechnology, Sungkyunkwan University [Suwon] (SKKU), Mycology and Botany Program, American Type Culture Collection (ATCC), Faculty of Agriculture and Life Science, University of Maribor, Natural History Museum, University of Kansas [Lawrence] (KU), University of California [Davis] (UC Davis), Jena Microbial Resource Collection, Leibniz Institute for Natural Product Research and Infection Biology (Hans Knoell Institute), Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], Department of Natural Sciences, University of Findlay, Institute of Evolution and Ecology, Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, McMaster University, Kunming Institute of Botany [CAS] (KIB), Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey [New Brunswick] (RU), Rutgers University System (Rutgers)-Rutgers University System (Rutgers), National Center for Biotechnology Information, National Library of Medicine, Schoch, Conrad L., Département Systématique et Evolution, Muséum national d'Histoire naturelle (MNHN), Chinese Academy of Sciences, Kunming Institute of Botany, Universidad Complutense de Madrid [Madrid] (UCM), Czech Academy of Sciences [Prague] (ASCR), Landcare Research, United States Department of Agriculture - USDA (USA)-United States Department of Agriculture - USDA (USA), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Friedrich-Schiller-Universität Jena, Eberhard Karls Universität Tübingen, National Center for Biotechnology Information ( NCBI ), National Institutes of Health ( NIH ), Università degli Studi di Perugia, Westmead Institute for Medical Research, Department of Biological and Environmental Sciences, University of Tennessee, Oregon State University ( OSU ), Mae Fah Luang University [Thaïlande] ( MFU ), Muséum National d’Histoire Naturelle ( MNHN ), Universidad Complutense de Madrid [Madrid] ( UCM ), Forestry and Agricultural Biotechnology Institute ( FABI ), University of Pretoria ( UPSpace ), Real Jardin Botanico ( RJB ), University of British Columbia ( UBC ), Czech Academy of Sciences [Prague] ( ASCR ), Commonwealth Scientific and Industrial Research Organisation [Canberra] ( CSIRO ), Chinese Academy of Sciences [Changchun Branch] ( CAS ), Agriculture and Agri-Food Canada ( AAFC ), National University of Ireland [Galway] ( NUI Galway ), Eotvos Lorand University, Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences [Budapest], National Center for Agricultural Utilization Research, The Open University [Milton Keynes] ( OU ), University of Gothenburg ( GU ), Institute of Sciences of Food Production, Center for Forest Mycology Research ( CFMR ), Botanical Museum, Finnish Museum of Natural History, University of California at Los Angeles [Los Angeles] ( UCLA ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté ( UBFC ), Sungkyunkwan University, American Type Culture Collection ( ATCC ), University of Kansas [Lawrence] ( KU ), University of California Davis, Leibniz Institute for Natural Product Research and Infection Biology, Rutgers University (State University of New Jersey), Università degli Studi di Perugia = University of Perugia (UNIPG), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-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), University of Pretoria [South Africa], University of California (UC), Agriculture and Agri-Food (AAFC), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, and University of California (UC)-University of California (UC)
Subjects: [SDV]Life Sciences [q-bio], sequence analyses, ribosomal dna, Intergenic region, 0807 Library And Information Studies, Databases, Genetic, RefSeq, Cluster Analysis, donnée de séquence moléculaire, DNA, Fungal, Genetics, DNA, Intergenic, Genes, Fungal, Molecular Sequence Annotation, Fungi, Sequence Analysis, DNA, Medicine (all), Phylogenetic tree, EPS-4, 3. Good health, internal transcribed spacer, Fungal, Identification (biology), Original Article, General Agricultural and Biological Sciences, Life Sciences & Biomedicine, Sequence Analysis, Information Systems, specimen, life, Sequence analysis, arbuscular mycorrhizal fungi, interspecific hybridization, Computational biology, Biology, General Biochemistry, Genetics and Molecular Biology, DNA sequencing, Databases, Genetic, evolution, Internal transcribed spacer, species complex, Science & Technology, Intergenic, [ SDV ] Life Sciences [q-bio], barcode, 0804 Data Format, DNA, Laboratorium voor Phytopathologie, MATHEMATICAL & COMPUTATIONAL BIOLOGY, référence, Genes, Laboratory of Phytopathology, identification
Abstract: DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Reannotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi., B.R. and C.L.S. acknowledge support from the Intramural Research Program of the National Institutes of Health, National Library of Medicine
Published: 2014

19. Near‐Surface Oceanic Kinetic Energy Distributions From Drifter Observations and Numerical Models

Author: Brian K. Arbic, Shane Elipot, Jonathan M. Brasch, Dimitris Menemenlis, Aurélien L. Ponte, Jay F. Shriver, Xiaolong Yu, Edward D. Zaron, Matthew H. Alford, Maarten C. Buijsman, Ryan Abernathey, Daniel Garcia, Lingxiao Guan, Paige E. Martin, Arin D. Nelson, University of Michigan [Ann Arbor], University of Michigan System, University of Miami, California Institute of Technology (CALTECH), Laboratoire d'Océanographie Physique et Spatiale (LOPS), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Océan Dynamique Observations Analyse (ODYSSEY), Université de Bretagne Occidentale - UFR Sciences et Techniques (UBO UFR ST), Université de Brest (UBO)-Université de Brest (UBO)-Université de Rennes (UR)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Naval Research Laboratory (NRL), Oregon State University (OSU), University of California [San Diego] (UC San Diego), University of California (UC), University of Southern Mississippi (USM), Columbia University [New York], and University of Rhode Island (URI)
Subjects: Geophysics, near-inertial motions, Space and Planetary Science, Geochemistry and Petrology, numerical ocean models, tides, Earth and Planetary Sciences (miscellaneous), drifters, eddies, Oceanography, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, currents
Abstract: The geographical variability, frequency content, and vertical structure of near-surface oceanic kinetic energy (KE) are important for air-sea interaction, marine ecosystems, operational oceanography, pollutant tracking, and interpreting remotely sensed velocity measurements. Here, KE in high-resolution global simulations (HYbrid Coordinate Ocean Model; HYCOM, and Massachusetts Institute of Technology general circulation model; MITgcm), at the sea surface (0 m) and at 15 m, are compared with KE from undrogued and drogued surface drifters, respectively. Global maps and zonal averages are computed for low-frequency (
Published: 2022

20. Physiological and Nutritional Roles of PPAR across Species

Author: Massimo Bionaz, Stéphane Mandard, Gary J. Hausman, Juan J. Loor, Department of Animal and Rangeland Sciences, Oregon State University ( OSU ), Animal and Dairy Science Department, University of Georgia, Department of Animal Sciences & Division of Nutritional Sciences, University of Illinois at Urbana-Champaign [Urbana], 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 ), Mandard, Stéphane, Oregon State University (OSU), University of Georgia [USA], University of Illinois System-University of Illinois System, Lipides - Nutrition - Cancer (U866) (LNC), and 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)
Subjects: medicine.medical_specialty, Article Subject, Animal food, [SDV.MHEP.PHY] Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], Peroxisome proliferator-activated receptor, Adipose tissue, Context (language use), White adipose tissue, Biology, Bioinformatics, Energy homeostasis, 03 medical and health sciences, Internal medicine, Drug Discovery, medicine, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.MHEP.PHY]Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], Pharmacology (medical), [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, lcsh:QH301-705.5, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 2. Zero hunger, chemistry.chemical_classification, [SDV.MHEP.EM] Life Sciences [q-bio]/Human health and pathology/Endocrinology and metabolism, 0303 health sciences, [ SDV.MHEP.PHY ] Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], 0402 animal and dairy science, Lipid metabolism, 04 agricultural and veterinary sciences, [SDV.MHEP.EM]Life Sciences [q-bio]/Human health and pathology/Endocrinology and metabolism, [ SDV.MHEP.EM ] Life Sciences [q-bio]/Human health and pathology/Endocrinology and metabolism, 040201 dairy & animal science, Nutrigenomics, Endocrinology, Editorial, lcsh:Biology (General), chemistry
Abstract: There has been a tremendous amount of information produced on peroxisome proliferator-activated receptors (PPARs). The interest in PPARs was originally driven largely by their role in hypolipidemia and hepatocarcinogenesis, but it soon became evident that they played important roles in the metabolic syndrome and overall health of organisms including regeneration of tissues, differentiation, insulin signaling, overall lipid metabolism, and immune response (reviewed in [1–7]). From a nutritional standpoint, the PPARs are of extreme importance because of their ability to bind and be activated by long-chain fatty acids and their metabolites. Therefore, the PPARs are recognized as ideal candidates for therapeutic use in order to improve metabolism and overall health through diet. At present, there is substantial interest in therapeutic applications tailored to regulate PPARs via synthetic drugs (e.g., [8]), but the exploitation of dietary approaches is not a reality yet. Most of our knowledge on PPARs has been produced by studies carried out in rodents and humans and little from other species, bovine and pig being the most studied among livestock species. The multitude of roles of PPARs and the possibility of regulating them through dietary approaches are also of interest in animal food production. Therefore, a comparative approach to bring together physiological and nutritional roles of PPARs across species appears critical. For this reason, this special issue was dedicated to PPARs interspecies comparisons with a larger emphasis on livestock species compared to animal models or humans. Among the 6 papers published, 3 focused specifically on ruminants and one on chicken. The review from Bionaz et al. assembled all the information pertaining to ruminant PPARs, with emphasis on functions, activation, and potential targets for nutrigenomics approaches to improve animal production and wellbeing. The review underscored that the information about PPARs in ruminants accumulated quickly in the last decade owing to the recognition of their potential importance in those mammalian species. The functional comparison among ruminant, mouse, and human highlighted a similar role of PPAR isotypes on lipid metabolism between species. However, the data highlighted differences in the response to long-chain fatty acids. Monogastrics are more sensitive to unsaturated while ruminants, particularly bovine, are more sensitive to saturated long-chain fatty acids. Based on PPARs data generated in nonruminants and ruminants, they proposed an integrative and dynamic model encompassing the activation (by long-chain fatty acids) of the three PPAR isotypes in order to optimize the adaptation to lactation. Among others, they also reviewed the data supporting a role of PPARγ in controlling milk fat synthesis in ruminants and demonstrated that this feature is not shared by mouse or, likely, other monogastrics. A pivotal role of PPARγ in controlling milk fat synthesis was confirmed by the paper of Shi et al. published in the present special issue. Those authors demonstrated, using a combination of PPARγ specific activator, gene expression, luciferase-PPRE assay, and siRNA techniques, that this nuclear receptor controls the expression of milk fat-related genes also in primary goat mammary epithelial cells. The activation of PPARγ using oral administration of 2,4-thiazolidinedione (TZD) in growing beef bulls was assessed by Arevalo-Turrubiarte et al. The authors aimed to test the effect of PPARγ activation on intramuscular fat (i.e., marbling). They observed a greater amount of TZD in liver of the treated animals, demonstrating an uptake of the drug via oral administration. The TZD treatment had no effect on carcass quality but had a strong effect on the expression of all three PPAR isotypes in liver (all decreased) and in muscle (increase only of PPARα). They observed also an overall increase in cell size and decrease of cellular synthesis in muscle and perirenal adipose tissue, but the opposite was observed in subcutaneous adipose. This effect was explained by higher insulin sensitivity due to the treatment. Activation of PPARγ with oral administration of a TZD in growing pigs also had no significant effect on marbling, but it did increase muscle fiber oxidative capacity regardless of fiber type [9]. As for bovine, the activation of PPARγ in swine may be useful to influence metabolism overall, but more studies are needed to examine this possibility. Takada and Kobayashi provided the first review of the three PPAR isotypes in poultry, particularly in chickens. Interestingly, they also provided a comparison with human PPARs both structurally and functionally. They uncovered several peculiar and unique functions in chicken PPARs and differences between chickens, and human PPARs. These data prompt for more chicken-specific studies in order to exploit the ability of PPARs to control lipid and glucose metabolism in this species. Mandard and Patsouris reviewed recent evidence establishing that PPARs are critical regulators of inflammation in mammals. In the last decade, PPARs have emerged as modulators of inflammatory responses. Therefore, the potential therapeutic usefulness of PPARα and PPARγ activation in the control of obesity and diabetes-induced chronic (low-grade) inflammation has extensively been studied over the last couple of years using rodents. The authors discussed different aspects of the interaction of PPARγ with adipose inflammation. In the light of the recent findings, it has become clear that, besides activating PPARγ in the adipocyte, pharmacological activation of this receptor extends to a much broader range of cell types, such as T regulatory cells, which is likely beneficial in the suppression of obesity-associated inflammation in white adipose tissue, as far as rodents are concerned. The impact of the pharmacological activation of mouse PPARα in the context of obesity-induced hepatic inflammation is also reviewed as well as the potential relevance of PPARβ/δ as a molecular drug target to fight liver inflammation in the case of nonalcoholic fatty liver disease. A growing body of evidence also indicates that PPARs are potent negative regulators of the acute-phase response in different species, ranging from mouse, rat, pig, cattle and humans. The review article by Mandard and Patsouris also expands on the potential beneficial use of PPAR (ant)agonists in the routine of livestock to prevent bacterial-induced excessive inflammatory reaction and associated diseases such as mastitis in dairy cows. PPARα is also known to be critical for energy homeostasis. In line with this, the review paper by Ringseis et al. thoroughly summarizes the implication of PPARα in carnitine homeostasis in no less than six different species including rat, mouse, pig, cattle, chicken, and human. The comparative analysis performed by the authors led them to conclude that PPARα displays a key regulator role in carnitine homeostasis in general. It is the process of cellular carnitine uptake, with the key role of the PPARα target carnitine transporter novel organic cation transporter 2, that is particularly well conserved across the above-mentioned species. All the papers in this special issue emphasized on one hand a similar function of PPARs among species, particularly related to lipid metabolism, but also, and more importantly, accentuated the differences and the species-specific functions and response to agonists. In summary, the analysis of PPARs across species highlighted the following: interspecies conserved functional roles of those nuclear receptors (e.g., regulation of lipid metabolism and inflammation); the potential for therapeutic intervention through nutritional modulation of PPARs in all species in order to prevent diseases and improve animal production; differences between species that prompt for more species-specific studies in order to fully exploit the abovementioned therapeutic roles through nutrition. Massimo Bionaz Gary J. Hausman Juan J. Loor Stephane Mandard
Published: 2013

21. RNAi suppression of DNA methylation affects the drought stress response and genome integrity in transgenic poplar

Author: Jose Caius, Sophie Lanciano, Régis Fichot, Sylvie Citerne, Véronique Brunaud, Jörg Tost, Vincent Segura, Steven H. Strauss, Ludivine Soubigou-Taconnat, Stéphane Maury, Alain Delaunay, Isabelle Le Jan, Marie-Claude Lesage-Descauses, Franck Brignolas, Anne-Laure Le Gac, Marie Mirouze, Christoph Grunau, Cristian Chaparro, Hervé Cochard, Christian Daviaud, Mamadou Dia Sow, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Université d'Orléans (UO)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Biologie intégrée pour la valorisation de la diversité des Arbres et de la Forêt (BioForA), Office national des forêts (ONF)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Physique et Physiologie Intégratives de l’Arbre en environnement Fluctuant (PIAF), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Interactions Hôtes-Pathogènes-Environnements (IHPE), Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Oregon State University (OSU), Ministere de la Recherche et Enseignement Superieur, INRAEPI EFPA-2014, RTP3E CNRS grants for mobility, ANR-17-CE32-0009,EPITREE,Impacts évolutif et fonctionnel de variations épigénétiques chez des arbres forestiers.(2017), ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017), ANR-13-JSV6-0002,EXTRACHROM,Contrôle épigénétique des formes extrachromosomiques des éléments transposables chez les plantes.(2013), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Office National des Forêts (ONF)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Perpignan Via Domitia (UPVD), and Ministère de la Recherche et Enseignement SupérieurINRAE PI EFPA-2014RTP3E CNRS grantsIJPB's Plant Observatory technological platformsInfinity English SIRET 82950710200012
Subjects: 0106 biological sciences, Transposable element, Physiology, Meristem, hormone, drought, Plant Science, Biology, 01 natural sciences, Transcriptome, 03 medical and health sciences, shoot apical meristem, Gene Expression Regulation, Plant, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], mobilome, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Epigenetics, Gene, 030304 developmental biology, 0303 health sciences, DNA methylation, [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], epigenetics, fungi, 15. Life on land, ddm1, Droughts, Chromatin, Cell biology, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Populus, Differentially methylated regions, poplar, RNA Interference, 010606 plant biology & botany
Abstract: Trees are long-lived organisms that continuously adapt to their environments, a process in which epigenetic mechanisms are likely to play a key role. Via down regulation of the chromatin remodeler DECREASED IN DNA METHYLATION 1 (DDM1) in poplar (Populus tremula 9 Populus alba) RNAi lines, we examined how DNA methylation coordinates genomic and physiological responses to moderate water deficit.We compared the growth and drought response of two RNAi-ddm1 lines to wild-type (WT) trees under well-watered and water deficit/rewatering conditions, and analyzed their methylomes, transcriptomes, mobilomes and phytohormone contents in the shoot apical meristem. The RNAi-ddm1 lines were more tolerant to drought-induced cavitation but did not differ in height or stem diameter growth. About 5000 differentially methylated regions were consistently detected in both RNAi-ddm1 lines, colocalizing with 910 genes and 89 active transposable elements. Under water deficit conditions, 136 differentially expressed genes were found, including many involved in phytohormone pathways ; changes in phytohormone concentrations were also detected. Finally, the combination of hypomethylation and drought led to the mobility of two transposable elements. Our findings suggest major roles for DNA methylation in regulation of genes involved in hormone-related stress responses, and the maintenance of genome integrity through repression of transposable elements.
Published: 2021

22. Phylogenomics and biogeography of Cunoniaceae (Oxalidales) with complete generic sampling and taxonomic realignments

Author: Olivier Maurin, Yohan Pillon, William J. Baker, Zachary S. Rogers, Helen C. F. Hopkins, Niroshini Epitawalage, Jason C. Bradford, Félix Forest, Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Royal Botanic Gardens, Kew, College of Forestry [Corvallis], Oregon State University (OSU), New Mexico State University, Calleva Foundation, Sackler Trust, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Royal Botanic Gardens [Kew]
Subjects: 0106 biological sciences, Paraphyly, Elaeocarpaceae, Biogeography, Antarctica, Australia, Caldcluvia, Gondwana, Madagascar, relicts, Weinmannia, Plant Science, Tribe (biology), 010603 evolutionary biology, 01 natural sciences, Article, 03 medical and health sciences, Cunoniaceae, Genetics, Vicariance, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Ecology, Evolution, Behavior and Systematics, Research Articles, 030304 developmental biology, 0303 health sciences, biology, Invited Special Article, 15. Life on land, biology.organism_classification, Taxon, Evolutionary biology, Research Article
Abstract: PREMISE: Cunoniaceae are a family of shrubs and trees with 27 genera and ca. 335 species, mostly confined to tropical and wet temperate zones of the southern hemisphere. There are several known issues regarding generic limits, and the family also displays a number of intriguing long- range disjunctions. METHODS: We performed a phylogenomic study using the universal Angiosperms353 probe set for targeted sequence capture. We sampled 37 species covering all genera in the Cunoniaceae, and those in the three closely related families of the crown Oxalidales (Brunelliaceae, Cephalotaceae, and Elaeocarpaceae). We also performed analyses for molecular dating and ancestral area reconstruction. RESULTS: We recovered the topology (Cunoniaceae, (Cephalotaceae, (Brunelliaceae, Elaeocarpaceae))) and a well- resolved genus- level phylogeny of Cunoniaceae with strongly supported clades corresponding to all previously recognized tribes. As previously suspected, the genera Ackama and Weinmannia were recovered as paraphyletic. Australasia was inferred as the likely ancestral area for the family. CONCLUSIONS: The current distribution of Cunoniaceae is best explained by long-distance dispersal with a few possible cases of Australasian–American vicariance events. Extinctions may have been important in determining the mostly Oceanian distribution of this family while some genera in the tribe Cunonieae and in New Caledonia have undergone recent bursts of diversification. New generic diagnoses, 80 new combinations, and one new name are provided for a recircumscribed Ackama (including Spiraeopsis), a much smaller Weinmannia (mostly New World), and a resurrected Pterophylla to accommodate Old World taxa previously in Weinmannia, Note on uploaded file: 5_Cunoniaceae_14gene_dating.tar.gz is the Concatenated matrix of the 14 genes selected using Sortadate for the estimation of divergence times in Cunoniaceae
Published: 2021

23. Phenotypically aberrant astrocytes that promote motoneuron damage in a model of inherited amyotrophic lateral sclerosis

Author: Laura Martínez-Palma, Luis Barbeito, Andrea Cragnolini, Patricia Cassina, Joseph S. Beckman, Silvia Olivera-Bravo, Pablo Díaz-Amarilla, Emiliano Trias, Instituto de Investigaciones Biológicas Clemente Estable [Montevideo] (IIBCE), Institut Pasteur de Montevideo, Réseau International des Instituts Pasteur (RIIP), Facultad de Medicina [Universidad de la Republica, Uruguay], Universidad de la República [Montevideo] (UCUR), Department of Biochemistry and Biophysics, Environmental Health Sciences Center-Oregon State University (OSU), Linus Pauling Institute, Oregon State University (OSU), This work was funded by the program for development of basic sciences (PEDECIBA), Innovation and Research National Agency (ANII) and Institut Pasteur de Montevideo. Partial funding also came from National Institutes of Health National Institute on Environmental Health Sciences Grant P30ES000210, National Institute of Neurological Disorders and Stroke Grant R01NS058628A, and National Center for Complementary and Alternative Medicine Grant NCCAM P01AT002034, and and from the Amyotrophic Lateral Sclerosis Association (to J.B.).
Subjects: Pathology, Connexin, 0302 clinical medicine, MESH: Animals, ASTROCYTE, Amyotrophic lateral sclerosis, MESH: Amyotrophic Lateral Sclerosis, MESH: Superoxide Dismutase, Motor Neurons, 0303 health sciences, education.field_of_study, Multidisciplinary, Glial fibrillary acidic protein, biology, Biological Sciences, 3. Good health, Cell biology, Phenotype, medicine.anatomical_structure, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], CIENCIAS NATURALES Y EXACTAS, MESH: Motor Neurons, Astrocyte, Senescence, medicine.medical_specialty, MESH: Mutation, MESH: Rats, Otras Ciencias Biológicas, SOD1, Population, MESH: Phenotype, Ciencias Biológicas, 03 medical and health sciences, MESH: Cell Proliferation, medicine, Animals, Humans, education, Cell Proliferation, 030304 developmental biology, MESH: Humans, Superoxide Dismutase, Amyotrophic Lateral Sclerosis, fungi, medicine.disease, Rats, MESH: Astrocytes, Disease Models, Animal, nervous system, Astrocytes, Mutation, MOTORNEURON, biology.protein, Astrocytosis, ALS, MESH: Disease Models, Animal, SPINAL CORD, 030217 neurology & neurosurgery
Abstract: Motoneuron loss and reactive astrocytosis are pathological hallmarks of amyotrophic lateral sclerosis (ALS), a paralytic neurodegenerative disease that can be triggered by mutations in Cu-Zn superoxide dismutase (SOD1). Dysfunctional astrocytes contribute to ALS pathogenesis, inducing motoneuron damage and accelerating disease progression. However, it is unknown whether ALS progression is associated with the appearance of a specific astrocytic phenotype with neurotoxic potential. Here, we report the isolation of astrocytes with aberrant phenotype (referred as “AbA cells”) from primary spinal cord cultures of symptomatic rats expressing the SOD1G93A mutation. Isolation was based on AbA cells’ marked proliferative capacity and lack of replicative senescence, which allowed oligoclonal cell expansion for 1 y. AbA cells displayed astrocytic markers including glial fibrillary acidic protein, S100β protein, glutamine synthase, and connexin 43 but lacked glutamate transporter 1 and the glial progenitor marker NG2 glycoprotein. Notably, AbA cells secreted soluble factors that induced motoneuron death with a 10-fold higher potency than neonatal SOD1G93A astrocytes. AbA-like aberrant astrocytes expressing S100β and connexin 43 but lacking NG2 were identified in nearby motoneurons, and their number increased sharply after disease onset. Thus, AbA cells appear to be an as-yet unknown astrocyte population arising during ALS progression with unprecedented proliferative and neurotoxic capacity and may be potential cellular targets for slowing ALS progression. Fil: Diaz Amarilla, Pablo. Instituto de Investigaciones Biológicas "Clemente Estable"; Uruguay Fil: Olivera Bravo, Silvia. Instituto de Investigaciones Biológicas "Clemente Estable"; Uruguay Fil: Trias, Emiliano. Instituto de Investigaciones Biológicas "Clemente Estable"; Uruguay Fil: Cragnolini, Andrea Beatriz. Instituto Pasteur de Montevideo. Laboratorio de Neurodegeneracion; Uruguay. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones Biológicas y Tecnológicas. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Instituto de Investigaciones Biológicas y Tecnológicas; Argentina Fil: Martinez Palma, Laura. Universidad de la República; Uruguay. Instituto de Investigaciones Biológicas "Clemente Estable"; Uruguay Fil: Cassina, Patricia. Universidad de la República; Uruguay Fil: Beckman, Joseph. State University of Oregon; Estados Unidos. Environmental Health Sciences Center; Estados Unidos Fil: Barbeito, Luis. Instituto Pasteur de Montevideo. Laboratorio de Neurodegeneracion; Uruguay. Instituto de Investigaciones Biológicas "Clemente Estable"; Uruguay
Published: 2011

24. The Exomars Climate Sounder (EMCS) Investigation

Author: Forget, F., Schofield, J. T., Kass, D. M., Kleinböhl, A., McCleese, D. J., Allen, M. A., Foote, M. C., Jeganathan, M., Millour, E., Spiga, A., Talagrand, O., Bowles, N., Calcutt, S. B., Irwin, P. G. J., Read, P. L., Lewis, S. R., Fouchet, T., Lefèvre, F., Määttänen, A., Barnes, J. R., Bougher, S. W., Haberle, R. M., Laboratoire de Météorologie Dynamique (UMR 8539) (LMD), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-École des Ponts ParisTech (ENPC)-Centre National de la Recherche Scientifique (CNRS)-Département des Géosciences - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Jet Propulsion Laboratory (JPL), NASA-California Institute of Technology (CALTECH), Department of Atmospheric, Oceanic and Planetary Physics [Oxford] (AOPP), University of Oxford, Department of Physics and Astronomy [Milton Keynes], The Open University [Milton Keynes] (OU), Laboratoire d'études spatiales et d'instrumentation en astrophysique (LESIA), 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 Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), PLANETO - LATMOS, Laboratoire Atmosphères, Milieux, Observations Spatiales (LATMOS), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-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 de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), College of Oceanic and Atmospheric Sciences [Corvallis], Oregon State University (OSU), Department of Atmospheric, Oceanic, and Space Sciences [Ann Arbor] (AOSS), University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, NASA Ames Research Center (ARC), Laboratoire de Météorologie Dynamique (UMR 8539) ( LMD ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -École polytechnique ( X ) -École des Ponts ParisTech ( ENPC ) -Centre National de la Recherche Scientifique ( CNRS ) -Département des Géosciences - ENS Paris, École normale supérieure - Paris ( ENS Paris ) -École normale supérieure - Paris ( ENS Paris ), Jet Propulsion Laboratory ( JPL ), NASA-California Institute of Technology ( CALTECH ), Department of Atmospheric, Oceanic and Planetary Physics [Oxford] ( AOPP ), University of Oxford [Oxford], The Open University [Milton Keynes] ( OU ), Laboratoire d'études spatiales et d'instrumentation en astrophysique ( LESIA ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Observatoire de Paris-Université Paris Diderot - Paris 7 ( UPD7 ) -Centre National de la Recherche Scientifique ( CNRS ), IMPEC - LATMOS, Laboratoire Atmosphères, Milieux, Observations Spatiales ( LATMOS ), Université de Versailles Saint-Quentin-en-Yvelines ( UVSQ ) -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 de Versailles Saint-Quentin-en-Yvelines ( UVSQ ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), Oregon State University ( OSU ), Department of Atmospheric, Oceanic, and Space Sciences [Ann Arbor] ( AOSS ), NASA Ames Research Center ( ARC ), Cardon, Catherine, Département des Géosciences - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École des Ponts ParisTech (ENPC)-École polytechnique (X)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: [PHYS.ASTR.EP] Physics [physics]/Astrophysics [astro-ph]/Earth and Planetary Astrophysics [astro-ph.EP], [ PHYS.ASTR.EP ] Physics [physics]/Astrophysics [astro-ph]/Earth and Planetary Astrophysics [astro-ph.EP], [PHYS.ASTR.EP]Physics [physics]/Astrophysics [astro-ph]/Earth and Planetary Astrophysics [astro-ph.EP], [SDU.ASTR.EP]Sciences of the Universe [physics]/Astrophysics [astro-ph]/Earth and Planetary Astrophysics [astro-ph.EP], [SDU.ASTR.EP] Sciences of the Universe [physics]/Astrophysics [astro-ph]/Earth and Planetary Astrophysics [astro-ph.EP], [ SDU.ASTR.EP ] Sciences of the Universe [physics]/Astrophysics [astro-ph]/Earth and Planetary Astrophysics [astro-ph.EP]
Abstract: The ExoMars Climate Sounder (EMCS) investigation is developed at the Jet Propulsion Laboratory (Principal Investigator J. T. Schofield) in collaboration with an international scientific team from France, the United Kingdom and the USA. EMCS plans to map daily, global, pole-to-pole profiles of temperature, dust, water and CO2 ices, and water vapor from the proposed 2016 ExoMars Trace Gas Orbiter (EMTGO). These profiles are to be assimilated into Mars General Circulation Models (MGCMs) to generate global, interpolated fields of measured and derived parameters such as wind. Sciences objectives of EMCS are to: Enhance understanding of Mars photochemistry by providing daily, global, high vertical resolution fields of atmospheric state, aerosol distribution, and water vapor concentration. EMCS atmospheric state measurements, combined with data assimilation, characterize the transport, sources and sinks of trace gases measured by the proposed EMTGO. The aerosol measurements reveal the heterogeneous photochemical pathways of trace gases. EMCS plans to map water vapor, the key source gas for odd hydrogen, known to be important in Martian photochemistry. Extend the MRO/MCS climatology of high vertical resolution measurements of the lower and middle atmosphere of Mars, with the improved coverage of local time provided by the proposed EMTGO. EMCS will determine the diurnal, seasonal & long-term variability of temperature and aerosol, and its impact on photochemistry. EMCS climatology, combined with earlier data, would relate EMTGO observations to earlier trace gas measurements. Support future Mars missions with measured climatology and near real-time density profile retrievals for landing and aerocapture, in the same way that MRO/MCS supported the Phoenix landing and is supporting the Mars Science Laboratory (MSL) landing. EMCS could be the only instrument in orbit able to support Entry, Descent and Landing (EDL) for the proposed ExoMars 2018 Rover Mission.
Published: 2011

25. The Exomars Climate Sounder (EMCS) Investigation

Author: Schofield, J. T., Kass, D. M., Kleinböhl, A., Mccleese, D. J., Allen, M. A., Foote, M. C., Jeganathan, M., Forget, François, Spiga, A., Talagrand, O., Lefèvre, Franck, Määttänen, Anni, Fouchet, T., Bowles, N., Calcutt, S. B., J. Irwin, P. G., Read, P. L., Lewis, S. R., Barnes, Jeffrey R., Bougher, S. W., Haberle, R. M., Jet Propulsion Laboratory (JPL), NASA-California Institute of Technology (CALTECH), Laboratoire de Météorologie Dynamique (UMR 8539) (LMD), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-École des Ponts ParisTech (ENPC)-Centre National de la Recherche Scientifique (CNRS)-Département des Géosciences - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Institut Pierre-Simon-Laplace (IPSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Pierre et Marie Curie - Paris 6 (UPMC)-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)-Centre National de la Recherche Scientifique (CNRS), PLANETO - LATMOS, Laboratoire Atmosphères, Milieux, Observations Spatiales (LATMOS), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-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 de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'études spatiales et d'instrumentation en astrophysique (LESIA), 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 Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Department of Atmospheric, Oceanic and Planetary Physics [Oxford] (AOPP), University of Oxford, Department of Physics and Astronomy [Milton Keynes], The Open University [Milton Keynes] (OU), College of Oceanic and Atmospheric Sciences [Corvallis], Oregon State University (OSU), Department of Atmospheric, Oceanic, and Space Sciences [Ann Arbor] (AOSS), University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, NASA Ames Research Center (ARC), Cardon, Catherine, Département des Géosciences - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École des Ponts ParisTech (ENPC)-École polytechnique (X)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), University of Oxford [Oxford], Jet Propulsion Laboratory ( JPL ), NASA-California Institute of Technology ( CALTECH ), Laboratoire de Météorologie Dynamique (UMR 8539) ( LMD ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -École polytechnique ( X ) -École des Ponts ParisTech ( ENPC ) -Centre National de la Recherche Scientifique ( CNRS ) -Département des Géosciences - ENS Paris, École normale supérieure - Paris ( ENS Paris ) -École normale supérieure - Paris ( ENS Paris ), Institut Pierre-Simon-Laplace ( IPSL ), École normale supérieure - Paris ( ENS Paris ) -Université de Versailles Saint-Quentin-en-Yvelines ( UVSQ ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National d'Etudes Spatiales ( CNES ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), IMPEC - LATMOS, Laboratoire Atmosphères, Milieux, Observations Spatiales ( LATMOS ), Université de Versailles Saint-Quentin-en-Yvelines ( UVSQ ) -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 de Versailles Saint-Quentin-en-Yvelines ( UVSQ ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire d'études spatiales et d'instrumentation en astrophysique ( LESIA ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Observatoire de Paris-Université Paris Diderot - Paris 7 ( UPD7 ) -Centre National de la Recherche Scientifique ( CNRS ), Department of Atmospheric, Oceanic and Planetary Physics [Oxford] ( AOPP ), The Open University [Milton Keynes] ( OU ), Oregon State University ( OSU ), Department of Atmospheric, Oceanic, and Space Sciences [Ann Arbor] ( AOSS ), and NASA Ames Research Center ( ARC )
Subjects: [PHYS.ASTR.EP] Physics [physics]/Astrophysics [astro-ph]/Earth and Planetary Astrophysics [astro-ph.EP], [ PHYS.ASTR.EP ] Physics [physics]/Astrophysics [astro-ph]/Earth and Planetary Astrophysics [astro-ph.EP], [PHYS.ASTR.EP]Physics [physics]/Astrophysics [astro-ph]/Earth and Planetary Astrophysics [astro-ph.EP], [SDU.ASTR.EP]Sciences of the Universe [physics]/Astrophysics [astro-ph]/Earth and Planetary Astrophysics [astro-ph.EP], [SDU.ASTR.EP] Sciences of the Universe [physics]/Astrophysics [astro-ph]/Earth and Planetary Astrophysics [astro-ph.EP], [ SDU.ASTR.EP ] Sciences of the Universe [physics]/Astrophysics [astro-ph]/Earth and Planetary Astrophysics [astro-ph.EP]
Abstract: International audience; The ExoMars Climate Sounder (EMCS) investi- gation plans to map daily, global, pole-to-pole pro- files of temperature, dust, water and CO2 ices, and water vapor from the proposed 2016 ExoMars Trace Gas Orbiter (EMTGO). The measurements cover all local times, adding a new dimension to data pre- viously obtained from sun-synchronous spacecraft. These profiles are to be assimilated into Mars Gen- eral Circulation Models (MGCMs) to generate glob- al, interpolated fields of measured and derived pa- rameters such as wind.
Published: 2011

26. Predator-derived bioregions in the Southern Ocean: Characteristics, drivers and representation in marine protected areas

Author: Ryan R. Reisinger, Cassandra M. Brooks, Ben Raymond, Jennifer J. Freer, Cédric Cotté, José C. Xavier, Philip N. Trathan, Horst Bornemann, Jean-Benoit Charrassin, Daniel P. Costa, Bruno Danis, Luis Hückstädt, Ian D. Jonsen, Mary-Anne Lea, Leigh Torres, Anton Van de Putte, Simon Wotherspoon, Ari S. Friedlaender, Yan Ropert-Coudert, Mark Hindell, School of Ocean and Earth Science [UK], University of Southampton, Department of Environmental Studies [Boulder, CO, United States], University of Colorado [Boulder], Australian Antarctic Division, Department of Agriculture [Australia], Australian Antarctic Division, Kingston, Tasmania, 7050, Australia, British Antarctic Survey NERC [UK], 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), Marine and Environmental Sciences Centre (MARE UC), Universidade de Coimbra [Coimbra], Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Institute of Marine Sciences, University of California (UC), Centre for Ecology and Conservation, University of Exeter, Institute for Marine and Antarctic Studies [Hobart] (IMAS), University of Tasmania [Hobart, Australia] (UTAS), Marine Mammal Institute, Oregon State University (OSU), Marine Biology Lab, Université libre de Bruxelles (ULB), Institute for Marine Sciences [California, USA], University of California [Santa Cruz] (UC Santa Cruz), University of California (UC)-University of California (UC), Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), and La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: ISLAND, Science & Technology, Ecology, Biodiversity & Conservation, CONSERVATION, Subantarctic, MPAS, Environmental Sciences & Ecology, Conservation, Management, MPA, Biogeography, [SDE]Environmental Sciences, Biodiversity Conservation, Antarctica, Life Sciences & Biomedicine, Ecology, Evolution, Behavior and Systematics, Environmental Sciences, PRIORITIES, Nature and Landscape Conservation
Abstract: International audience; Multiple initiatives have called for large-scale representative networks of marine protected areas (MPAs). MPAs should be ecologically representative to be effective, but in large, remote regions this can be difficult to quantify and assess. We present a novel bioregionalization for the Southern Ocean, which uses the modelled circumpolar habitat importance of 17 marine bird and mammal species. The habitat-use of these predators indicates biodiversity patterns that require representation in Southern Ocean conservation and management planning. In the predator habitat importance predictions, we identified 17 statistical clusters, falling into four larger groups. We characterized and contrasted these clusters based on their predator, prey and oceanographic characteristics. Under the existing Southern Ocean MPA network, some clusters fall short of 10 % representation, yet others meet or exceed these targets. Implementation of currently proposed MPAs can in some cases contribute to meeting even 30 % spatial coverage conservation targets. However, the effectiveness of mixed-use versus no-take MPAs should be taken into consideration, since some clusters are not adequately represented by no-take MPAs. These results, combined with previous studies in the Southern Ocean, can help inform the continued design, implementation, and evaluation of a representative system of MPAs for Southern Ocean conservation and management.
Published: 2022

27. The logic of virus evolution

Author: Eugene V. Koonin, Valerian V. Dolja, Mart Krupovic, National Center for Biotechnology Information (NCBI), Oregon State University (OSU), Virologie des archées - Archaeal Virology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), E.V.K. is supported by the Intramural Research Program of the National Institutes of Health of the USA (National Library of Medicine). M.K. was supported by l’Agence Nationale de la Recherche grant ANR-21-CE11-0001-01. V.V.D. was partially supported by an NIH/NLM/NCBI Visiting Scientist Fellowship., and ANR-21-CE11-0001,ArcFus,Protéines de classe II de fusion membranaire chez les archées(2021)
Subjects: virus evolution, Genes, Viral, Logic, Microbiology, Biological Evolution, origins of viruses, Evolution, Molecular, Virology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Viruses, exaptation, Parasitology, Capsid Proteins, virus structure, Virus Physiological Phenomena
Abstract: International audience; Viruses are obligate intracellular parasites. Despite their dependence on host cells, viruses are evolutionarily autonomous, with their own genomes and evolutionary trajectories locked in arms races with the hosts. Here, we discuss a simple functional logic to explain virus macroevolution that appears to define the course of virus evolution. A small core of virus hallmark genes that are responsible for genome replication apparently descended from primordial replicators, whereas most virus genes, starting with those encoding capsid proteins, were subsequently acquired from hosts. The oldest of these acquisitions antedate the last universal cellular ancestor (LUCA). Host gene capture followed two major routes: convergent recruitment of genes with functions that directly benefit virus reproduction and exaptation when host proteins are repurposed for unique virus functions. These forms of host protein recruitment by viruses result in different levels of similarity between virus and host homologs, with the exapted ones often changing beyond easy recognition.
Published: 2022

28. Reasons for Embargoing Academic Publications in Institutional Repositories. Case Study of Theses and Dissertations

Author: Rasuli, Behrooz, Schöpfel, Joachim, Boock, Michael, van Wyk, Brenda, Iranian Research Institute for Information Science and Technology (IRANDOC), Iranian Research Institute for Information Science and Technology, Groupe d'Études et de Recherche Interdisciplinaire en Information et COmmunication - ULR 4073 (GERIICO ), Université de Lille, Oregon State University (OSU), and University of Pretoria [South Africa]
Subjects: [SHS.INFO]Humanities and Social Sciences/Library and information sciences
Abstract: International audience
Published: 2022

29. Potential error in density profile measurements for wood composites

Author: Lauri Rautkari, Frederick A. Kamke, Mark Hughes, Forest Products Technology, Helsinki University of Technology ( TKK ), Department of Forest Products Technology, Department of Wood Science and Engineering, Oregon State University ( OSU ), TKK Helsinki University of Technology (TKK), and Oregon State University (OSU)
Subjects: 040101 forestry, 0106 biological sciences, Absolute density, Materials science, Composite number, Forestry, 04 agricultural and veterinary sciences, 01 natural sciences, 010608 biotechnology, Attenuation factor, Physical Sciences, Calibration, 0401 agriculture, forestry, and fisheries, Gravimetric analysis, Maximum density, General Materials Science, Densitometer, Composite material, Densitometry
Abstract: International audience; The vertical density profile of wood-based composites is often measured using X-ray densitometry. During preliminary studies, in which the density profiles of wood composites with discrete layers of varying density were measured, it was observed that the absolute density values of the layers were incorrect when compared to gravimetric measurements of the individual layers. This is due the recommended calibration process of the X-ray densitometer, which uses the overall density of the composite to determine the X-ray attenuation factor. The severity of the error increases with the difference between minimum and maximum density in the profile.
Published: 2010

30. K-N-MOMDPs: Towards Interpretable Solutions for Adaptive Management

Author: Ferrer-Mestres, Jonathan, Dietterich, Thomas, Buffet, Olivier, Chadès, Iadine, CSIRO Land and Water Division, CSIRO Land and Water, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO)-Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Oregon State University (OSU), Lifelong Autonomy and interaction skills for Robots in a Sensing ENvironment (LARSEN), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Department of Complex Systems, Artificial Intelligence & Robotics (LORIA - AIS), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), and Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)
Subjects: adaptive managment, interpretabillity, General Medicine, POMDP, MOMDP, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI]
Abstract: International audience; In biodiversity conservation, adaptive management (AM) is the principal tool for decision making under uncertainty. AM problems are planning problems that can be modelled using Mixed Observability MDPs (MOMDPs). MOMDPs tackle decision problems where state variables are completely or partially observable. Unfortunately, MOMDP solutions (policy graphs) are too complex to be interpreted by human decision-makers. Here, we provide algorithms to solve K-N-MOMDPs, where K represents the maximum number of fully observable states and N represents the maximum number of alpha-vectors. Our algorithms calculate compact and more interpretable policy graphs from existing MOMDP models and solutions. We apply these algorithms to two computational sustainability applications: optimal release of bio-control agents to prevent dengue epidemics and conservation of the threatened bird species Gouldian finch. The methods dramatically reduce the number of states and alpha-vectors in MOMDP problems without significantly reducing their quality. The resulting policies have small policy graphs (4-6 nodes) that can be easily interpreted by human decision-makers.
Published: 2021

31. Interpreting and reporting 40Ar/39Ar geochronologic data

Author: E.L. Matchan, Andrew T. Calvert, Courtney J. Sprain, Morgan Ganerod, Margarita López-Martínez, Jörg A. Pfänder, Huaiyu He, Barbara A. Cohen, Nancy Joyce, Brent D. Turrin, Paulo M. Vasconcelos, Allen J. Schaen, Hua-Ning Qiu, William S. Cassata, Darren F. Mark, Jan R. Wijbrans, C. M. Mercer, Jeffrey A. Benowitz, David Phillips, Osamu Ishizuka, Paul R. Renne, Brian R. Jicha, Hervé Guillou, Tiffany A. Rivera, Sidney R. Hemming, Pieter Vermeesch, Fred Jourdan, Simon P. Kelley, Kip V. Hodges, Jake Ross, Klaudia F. Kuiper, Brad S. Singer, Mark E. Stelten, Sébastien Nomade, Matthew T. Heizler, Adán Ramirez, Elizabeth M. Niespolo, Laura E. Webb, Leah E. Morgan, Willis E. Hames, Anthony A. P. Koppers, Earth Sciences, University of Wisconsin-Madison, Arizona State University [Tempe] (ASU), University College of London [London] (UCL), United States Geological Survey (USGS), NASA Goddard Space Flight Center (GSFC), University of Melbourne, Westminster College, Curtin University [Perth], Planning and Transport Research Centre (PATREC), Lamont-Doherty Earth Observatory (LDEO), Columbia University [New York], University of Edinburgh, Lawrence Livermore National Laboratory (LLNL), New Mexico Institute of Mining and Technology [New Mexico Tech] (NMT), University of Southern Queensland (USQ), University of Alaska [Fairbanks] (UAF), Oregon State University (OSU), Scottish Universities Environmental Research Centre (SUERC), University of Glasgow-University of Edinburgh, Berkeley Geochronology Center (BGC), University of Florida [Gainesville] (UF), Auburn University (AU), VU University Amsterdam, Rutgers, The State University of New Jersey [New Brunswick] (RU), Rutgers University System (Rutgers), University of St Andrews [Scotland], Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Paléocéanographie (PALEOCEAN), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), University of Vermont [Burlington], Geological Survey of Canada [Ottawa] (GSC Central & Northern Canada), Geological Survey of Canada - Office (GSC), Natural Resources Canada (NRCan)-Natural Resources Canada (NRCan), Geological Survey of Norway (NGU), National Institute of Advanced Industrial Science and Technology (AIST), Chinese Academy of Sciences [Beijing] (CAS), Servicio Nacional de Geologia y Mineria (SERNAGEOMIN ), Institut für Geologie [Freiberg], Technishe Universität Bergakademie Freiberg (TU Bergakademie Freiberg), Departamento de Geologia CICESE, Centro de Investigacion Cientifica y de Education Superior de Ensenada [Mexico] (CICESE), China University of Geosciences [Wuhan] (CUG), Vrije universiteit = Free university of Amsterdam [Amsterdam] (VU), Vrije Universiteit Amsterdam [Amsterdam] (VU), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), and Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 010504 meteorology & atmospheric sciences, Interoperability, Geology, Single sample, 010502 geochemistry & geophysics, 01 natural sciences, Data science, Variety (cybernetics), Metadata, Set (abstract data type), Salient, Range (statistics), [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences
Abstract: The 40Ar/39Ar dating method is among the most versatile of geochronometers, having the potential to date a broad variety of K-bearing materials spanning from the time of Earth’s formation into the historical realm. Measurements using modern noble-gas mass spectrometers are now producing 40Ar/39Ar dates with analytical uncertainties of ~0.1%, thereby providing precise time constraints for a wide range of geologic and extraterrestrial processes. Analyses of increasingly smaller subsamples have revealed age dispersion in many materials, including some minerals used as neutron fluence monitors. Accordingly, interpretive strategies are evolving to address observed dispersion in dates from a single sample. Moreover, inferring a geologically meaningful “age” from a measured “date” or set of dates is dependent on the geological problem being addressed and the salient assumptions associated with each set of data. We highlight requirements for collateral information that will better constrain the interpretation of 40Ar/39Ar data sets, including those associated with single-crystal fusion analyses, incremental heating experiments, and in situ analyses of microsampled domains. To ensure the utility and viability of published results, we emphasize previous recommendations for reporting 40Ar/39Ar data and the related essential metadata, with the amendment that data conform to evolving standards of being findable, accessible, interoperable, and reusable (FAIR) by both humans and computers. Our examples provide guidance for the presentation and interpretation of 40Ar/39Ar dates to maximize their interdisciplinary usage, reproducibility, and longevity.
Published: 2021

32. Changes in biochemical and hemocyte parameters of the Pacific oysters Crassostrea gigas fed T-Iso supplemented with lipid emulsions rich in eicosapentaenoic acid

Author: Jeanne Moal, Maryse Delaporte, Jean-Francois Samain, Philippe Soudant, Fu-lin Chu, Chris Langdon, Christophe Lambert, Physiologie et Ecophysiologie des Mollusques Marins ( PE2M ), Université de Caen Normandie ( UNICAEN ), Normandie Université ( NU ) -Normandie Université ( NU ) -Institut Français de Recherche pour l'Exploitation de la Mer ( IFREMER ) -Centre National de la Recherche Scientifique ( CNRS ), Virginia Institute of Marine Science, College of William and Mary, Coastal Oregon Marine Experimental Station, Oregon State University ( OSU ), 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 ) -Université de Brest ( UBO ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD ) -Université de Brest ( UBO ) -Centre National de la Recherche Scientifique ( CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), Institut Français de Recherche pour l'Exploitation de la Mer ( IFREMER ), Physiologie et Ecophysiologie des Mollusques Marins (PE2M), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS), Virginia Institute of Marine Science (VIMS), Oregon State University (OSU), 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), and Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)
Subjects: Oyster, Bivalves, animal structures, Hemocytes, Immunology, 5n 3 [Eicosapentaenoic acid 20], Aquatic Science, [ SDE ] Environmental Sciences, 03 medical and health sciences, Dry weight, biology.animal, 14. Life underwater, Food science, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, biology, fungi, Fatty acid, food and beverages, 04 agricultural and veterinary sciences, Bivalvia, biology.organism_classification, Eicosapentaenoic acid, Eicosapentaenoic acid (20:5n-3), Ostreidae, chemistry, Biochemistry, [SDE]Environmental Sciences, Crassostrea gigas, 040102 fisheries, 0401 agriculture, forestry, and fisheries, Crassostrea, Polyunsaturated fatty acids, Polyunsaturated fatty acid
Abstract: The aim of this study was to assess the effect of dietary eicosapentaenoic acid (20:5n-3) on hemocyte parameters such as hemocyte concentration, phagocytosis, and non-stimulated reactive oxygen species (ROS) production in Pacific oysters Crassostrea gigas, as well on proximate biochemical and fatty acid compositions. One-year-old oysters (C. gigas) were fed T-Isochrysis aff. galbana(T-Iso), which is low in 20:5n-3, either alone or with supplements of a lipid emulsion rich in 20:5n-3 at 1%, 10% or 50% (dry weight of the algal ration) for up to 7 weeks. Changes in gill fatty acid composition demonstrated that the lipid emulsion was well ingested by oysters during the dietary conditioning. Biochemical analysis indicated that oysters fed supplements of 50% and, to a lesser extent, 10% lipid emulsions had a higher total lipid content compared with oysters fed other diets, suggesting a more advanced reproductive status for the oysters fed high doses of lipid emulsion. Moreover, some oysters in these two treatment groups spawned during the last three weeks of the seven-week feeding experiment. Lipid supplements had a significant influence on hemocyte concentration, phagocytic index and non-stimulated hemocyte ROS production. After 4 weeks, highest hemocyte concentrations were found in oysters fed on a supplement of 50% lipid emulsion compared with those fed on other diets but the hemocytes derived from these oysters had the lowest short-term phagocytic index. After 7 weeks of dietary conditioning, the ROS production in non-stimulated hemocytes of oysters fed 10% and 50% lipid emulsion declined. These results suggested that 20:5n-3, and perhaps its eicosanoid metabolites, affected oyster hemocyte functions; however, the reproductive status of oysters may also have interfered with the 20:5n-3 dietary effect. (c) 2007 Elsevier B.V. All rights reserved.
Published: 2007

33. Recruitment of Tat to heterochromatin protein HP1 via interaction with CTIP2 inhibits human immunodeficiency virus type 1 replication in microglial cells

Author: Olivier Rohr, Céline Marban, Sylvette Chasserot-Golaz, Mark Leid, Dorina Avram, Evelyne Schaeffer, Dominique Lecestre, Dominique Aunis, univOAK, Archive ouverte, Physiopathologie du système nerveux., Université Louis Pasteur - Strasbourg I-IFR37-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Louis Pasteur - Strasbourg I, Neurotransmission et sécrétion neuroendocrine (NSN), Centre National de la Recherche Scientifique (CNRS), Laboratory of Molecular Pharmacology [Corvallis, OR, USA] (Department of Pharmaceutical Sciences), Oregon State University (OSU)-College of Pharmacy [Corvallis, OR, USA]-Environmental Health Sciences Center [Corvallis, OR, USA], K01 AR002194, and College of Pharmacy [Corvallis, OR, USA]-Oregon State University (OSU)-Environmental Health Sciences Center [Corvallis, OR, USA]
Subjects: Receptors, Steroid, Chromosomal Proteins, Non-Histone, Immunology, Green Fluorescent Proteins, Replication, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Virus Replication, Microbiology, DNA-binding protein, 03 medical and health sciences, Transactivation, Transcription (biology), Virology, Animals, Humans, Transcription factor, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, Cells, Cultured, 030304 developmental biology, 0303 health sciences, COUP Transcription Factor I, 030302 biochemistry & molecular biology, Molecular biology, Chromatin, 3. Good health, DNA-Binding Proteins, Luminescent Proteins, COUP Transcription Factors, Viral replication, Chromobox Protein Homolog 5, Insect Science, Gene Products, tat, HIV-1, Heterochromatin protein 1, tat Gene Products, Human Immunodeficiency Virus, Microglia, Chickens, Nuclear localization sequence, Gene Deletion, Transcription Factors
Abstract: The Tat protein of human immunodeficiency virus type 1 (HIV-1) plays a key role as inducer of viral gene expression. We report that Tat function can be potently inhibited in human microglial cells by the recently described nuclear receptor cofactor chicken ovalbumin upstream promoter transcription factor-interacting protein 2 (CTIP2). Overexpression of CTIP2 leads to repression of HIV-1 replication, as a result of inhibition of Tat-mediated transactivation. In contrast, the related CTIP1 was unable to affect Tat function and viral replication. Using confocal microscopy to visualize Tat subcellular distribution in the presence of the CTIPs, we found that overexpression of CTIP2, and not of CTIP1, leads to disruption of Tat nuclear localization and recruitment of Tat within CTIP2-induced nuclear ball-like structures. In addition, our studies demonstrate that CTIP2 colocalizes and associates with the heterochromatin-associated protein HP1α. The CTIP2 protein harbors two Tat and HP1 interaction interfaces, the 145-434 and the 717-813 domains. CTIP2 and HP1α associate with Tat to form a three-protein complex in which the 145-434 CTIP2 domain interacts with the N-terminal region of Tat, while the 717-813 domain binds to HP1. The importance of this Tat binding interface and of Tat subnuclear relocation was confirmed by analysis of CTIP2 deletion mutants. Our findings suggest that inhibition of HIV-1 expression by CTIP2 correlates with recruitment of Tat within CTIP2-induced structures and relocalization within inactive regions of the chromatin via formation of the Tat-CTIP2-HP1α complex. These data highlight a new mechanism of Tat inactivation through subnuclear relocalization that may ultimately lead to inhibition of viral pathogenesis.
Published: 2003

34. Mere end lugtesans - COVID-19 er associeret med svær påvirkning af lugtesansen, smagssansen og mundfølelsen

Author: Parma, Valentina, Ohla, Kathrin, Veldhuizen, Maria G, Niv, Masha Y, Kelly, Christine E, Bakke, Alyssa J, Cooper, Keiland W, Bouysset, Cédric, Pirastu, Nicola, Dibattista, Michele, Kaur, Rishemjit, Liuzza, Marco Tullio, Pepino, Marta Y, Schöpf, Veronika, Pereda-Loth, Veronica, Olsson, Shannon B, Gerkin, Richard C, Rohlfs Domínguez, Paloma, Albayay, Javier, Farruggia, Michael C, Bhutani, Surabhi, Fjaeldstad, Alexander W, Kumar, Ritesh, Menini, Anna, Bensafi, Moustafa, Sandell, Mari, Konstantinidis, Iordanis, Di Pizio, Antonella, Genovese, Federica, Öztürk, Lina, Thomas-Danguin, Thierry, Frasnelli, Johannes, Boesveldt, Sanne, Saatci, Özlem, Saraiva, Luis R, Lin, Cailu, Golebiowski, Jérôme, Hwang, Liang-Dar, Ozdener, Mehmet Hakan, Guàrdia, Maria Dolors, Laudamiel, Christophe, Ritchie, Marina, Havlícek, Jan, Pierron, Denis, Roura, Eugeni, Navarro, Marta, Nolden, Alissa A, Lim, Juyun, Whitcroft, Katherine L, Colquitt, Lauren R, Ferdenzi, Camille, Brindha, Evelyn V, Altundag, Aytug, Macchi, Alberto, Nunez-Parra, Alexia, Patel, Zara M, Fiorucci, Sébastien, Philpott, Carl M, Smith, Barry C, Lundström, Johan N, Mucignat, Carla, Parker, Jane K, van den Brink, Mirjam, Schmuker, Michael, Fischmeister, Florian Ph S, Heinbockel, Thomas, Shields, Vonnie D C, Faraji, Farhoud, Santamaría, Enrique, Fredborg, William E A, Morini, Gabriella, Olofsson, Jonas K, Jalessi, Maryam, Karni, Noam, D’Errico, Anna, Alizadeh, Rafieh, Pellegrino, Robert, Meyer, Pablo, Huart, Caroline, Chen, Ben, Soler, Graciela M, Alwashahi, Mohammed K, Welge-Lüssen, Antje, Freiherr, Jessica, de Groot, Jasper H B, Klein, Hadar, Okamoto, Masako, Singh, Preet Bano, Hsieh, Julien W, Abdulrahman, Olagunju, Dalton, Pamela, Yan, Carol H, Voznessenskaya, Vera V, Chen, Jingguo, Sell, Elizabeth A, Walsh-Messinger, Julie, Archer, Nicholas S, Koyama, Sachiko, Deary, Vincent, Roberts, S Craig, Yanık, Hüseyin, Albayrak, Samet, Nováková, Lenka Martinec, Croijmans, Ilja, Mazal, Patricia Portillo, Moein, Shima T, Margulis, Eitan, Mignot, Coralie, Mariño, Sajidxa, Georgiev, Dejan, Kaushik, Pavan K, Malnic, Bettina, Wang, Hong, Seyed-Allaei, Shima, Yoluk, Nur, Razzaghi-Asl, Sara, Justice, Jeb M, Restrepo, Diego, Reed, Danielle R, Hummel, Thomas, Munger, Steven D, Hayes, John E, Indústries Alimentàries, Qualitat i Tecnologia Alimentària, Tecnologia Alimentària, Temple University [Philadelphia], Pennsylvania Commonwealth System of Higher Education (PCSHE), Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association, Mersin University, The Hebrew University of Jerusalem (HUJ), AbScent, Pennsylvania State University (Penn State), Penn State System, University of California [Irvine] (UC Irvine), University of California (UC), Université Côte d'Azur (UCA), University of Edinburgh, Università degli studi di Bari Aldo Moro = University of Bari Aldo Moro (UNIBA), Central Scientific Instruments Organisation (CSIR), Università degli Studi 'Magna Graecia' di Catanzaro = University of Catanzaro (UMG), University of Illinois at Urbana-Champaign [Urbana], University of Illinois System, Medizinische Universität Wien = Medical University of Vienna, Groupement scientifique de Biologie et de Medecine Spatiale (GSBMS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National d'Études Spatiales [Toulouse] (CNES), Tata Institute for Fundamental Research (TIFR), Arizona State University [Tempe] (ASU), Universidad de Extremadura - University of Extremadura (UEX), Università degli Studi di Padova = University of Padua (Unipd), Yale School of Medicine [New Haven, Connecticut] (YSM), San Diego State University (SDSU), Aarhus University [Aarhus], University of Hertfordshire [Hatfield] (UH), Scuola Internazionale Superiore di Studi Avanzati / International School for Advanced Studies (SISSA / ISAS), Neurosciences Sensorielles Comportement Cognition, Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, University of Turku, Aristotle University of Thessaloniki, Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Monell Chemical Senses Center, Centre des Sciences du Goût et de l'Alimentation [Dijon] (CSGA), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Bourgogne Franche-Comté [COMUE] (UBFC), Université de Montréal (UdeM), Wageningen University and Research Centre (WUR), Medical Science University, Sidra Medicine [Doha, Qatar], Institut de Chimie de Nice (ICN), 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)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), University of Southern Queensland (USQ), Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology (IRTA), DreamAir Llc, Charles University [Prague] (CU), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), University of Massachusetts System (UMASS), Oregon State University (OSU), Ear Institute, UCL, Lyon Neuroscience Research center, Karunya University, Biruni University, Assi Sette Llaghi Varese, Stanford School of Medicine [Stanford], Stanford Medicine, Stanford University-Stanford University, University of East Anglia [Norwich] (UEA), California Department of Food and Agriculture (CDFA), Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Maastricht University [Maastricht], Institute for Biology - Neurobiology, Freie Universität Berlin, Karl-Franzens-Universität Graz, Howard University College of Medicine, Towson University, University of California [San Diego] (UC San Diego), Proteomics, Center for Applied Medical Research (CIMA), Stockholm University, University of Gastronomic Sciences, Iran University of Medical Sciences, Goethe Universität Frankfurt, University of Tennessee, IBM T.J. Watson Research Center, Université libre de Bruxelles (ULB), Guangzhou Medical University, Buenos Aires University and GEOG (Grupo de Estudio de Olfato y Gusto), Sultan Qaboos University (SQU), Federal University of Technology of Akure (FUTA), A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences [Moscow] (RAS), Hospital of Xi'an Jiaotong University, University of Pennsylvania, University of Dayton, CSIRO Agriculture and Food (CSIRO), Indiana University [Bloomington], Indiana University System, University of Northumbria at Newcastle [United Kingdom], University of Stirling, Middle East Technical University [Ankara] (METU), Utrecht University [Utrecht], Instituto Universitario del Hospital Italiano [Buenos Aires, Argentina], Institute for Research in Fundamental Sciences [Tehran] (IPM), Hebrew University of Jerusalem, Technische Universität Dresden = Dresden University of Technology (TU Dresden), Terrazas del Club Hipico, University Medical Centre Ljubljana [Ljubljana, Slovenia] (UMCL), Tata Institute of Fundamental Research [Bangalore], Universidade de São Paulo = University of São Paulo (USP), University of Florida [Gainesville] (UF), University of Colorado Anschutz [Aurora], Center for Smell and Taste, Department of Food Science, Pennsylvania State University., Julien, Sabine, Tıp Fakültesi, UCL - SSS/IONS/NEUR - Clinical Neuroscience, UCL - (SLuc) Service d'oto-rhino-laryngologie, Department of Food and Nutrition, Senses and Food, Research Center Jülich, University of California [Irvine] (UCI), University of California, Università degli studi di Bari Aldo Moro (UNIBA), Università degli Studi 'Magna Graecia' di Catanzaro [Catanzaro, Italie] (UMG), University of Extremadura, University of Padova, Yale University School of Medicine, Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, University of Helsinki, Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Institute of Agrifood Research and Technology (IRTA), Universita degli Studi di Padova, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Karl-Franzens-Universität [Graz, Autriche], University of California San Diego Health, University of Brussels, University of Pennsylvania [Philadelphia], Tata Institute of Fundamental Research, University of São Paulo (USP), UCL - SSS/IONS - Institute of NeuroScience, FSE Campus Venlo, and RS: FSE UCV
Subjects: Male, Taste, Physiology, Smagstab, Audiology, AcademicSubjects/SCI01180, Settore BIO/09 - Fisiologia, Behavioral Neuroscience, chemistry.chemical_compound, Olfaction Disorders, Taste Disorders, 0302 clinical medicine, RATINGS, Hyposmia, Surveys and Questionnaires, CHEMOSENSITIVITY, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Viral, PALADAR, 030223 otorhinolaryngology, Sensory Science and Eating Behaviour, media_common, TASTE, US NATIONAL-HEALTH, [SDV.IDA] Life Sciences [q-bio]/Food engineering, Middle Aged, Biological Sciences, 16. Peace & justice, Sensory Systems, 3. Good health, Smell, GCCR Group Author, ddc:540, Smell loss, Female, Original Article, medicine.symptom, Corrigendum, Coronavirus Infections, olfaction, Adult, somatosensation, medicine.medical_specialty, 663/664, Coronavirus disease 2019 (COVID-19), OLFACTORY DISORDERS, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), media_common.quotation_subject, Pneumonia, Viral, head and neck surgery, Aged, Betacoronavirus, COVID-19, Humans, Pandemics, SARS-CoV-2, Self Report, Somatosensory Disorders, Young Adult, Anosmia, Sensory system, Olfaction, 03 medical and health sciences, Chemesthesis, Physiology (medical), Perception, medicine, Neurology & Neurosurgery, Behaviour Change and Well-being, business.industry, R-PACKAGE, 3112 Neurosciences, Pneumonia, Parosmia, COMPONENT, Smagssans, [SDV.AEN] Life Sciences [q-bio]/Food and Nutrition, Sensoriek en eetgedrag, chemistry, Lugtetab, business, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, 030217 neurology & neurosurgery, Lugtesans
Abstract: Correction: Chemical Senses, Volume 46, 2021, bjab050, https://doi.org/10.1093/chemse/bjab050 Published: 08 December 2021 Recent anecdotal and scientific reports have provided evidence of a link between COVID-19 and chemosensory impairments, such as anosmia. However, these reports have downplayed or failed to distinguish potential effects on taste, ignored chemesthesis, and generally lacked quantitative measurements. Here, we report the development, implementation, and initial results of a multilingual, international questionnaire to assess self-reported quantity and quality of perception in 3 distinct chemosensory modalities (smell, taste, and chemesthesis) before and during COVID-19. In the first 11 days after questionnaire launch, 4039 participants (2913 women, 1118 men, and 8 others, aged 19-79) reported a COVID-19 diagnosis either via laboratory tests or clinical assessment. Importantly, smell, taste, and chemesthetic function were each significantly reduced compared to their status before the disease. Difference scores (maximum possible change +/- 100) revealed a mean reduction of smell (-79.7 +/- 28.7, mean +/- standard deviation), taste (-69.0 +/- 32.6), and chemesthetic (-37.3 +/- 36.2) function during COVID-19. Qualitative changes in olfactory ability (parosmia and phantosmia) were relatively rare and correlated with smell loss. Importantly, perceived nasal obstruction did not account for smell loss. Furthermore, chemosensory impairments were similar between participants in the laboratory test and clinical assessment groups. These results show that COVID-19-associated chemosensory impairment is not limited to smell but also affects taste and chemesthesis.The multimodal impact of COVID-19 and the lack of perceived nasal obstruction suggest that severe acute respiratory syndrome coronavirus strain 2 (SARS-CoV-2) infection may disrupt sensory-neural mechanisms.
Published: 2020

35. Deep Roots and Splendid Boughs of the Global Plant Virome

Author: Valerian V. Dolja, Mart Krupovic, Eugene V. Koonin, Department of Botany and Plant Pathology, Oregon State University (OSU), Center for Genome Research and Biocomputing, Virologie des archées - Archaeal Virology, Institut Pasteur [Paris], National Library of Medicine (NLM), National Institutes of Health [Bethesda] (NIH)-National Center for Biotechnology Information (NCBI), and Institut Pasteur [Paris] (IP)
Subjects: 0301 basic medicine, 030106 microbiology, Plant Science, Biology, virus taxonomy, phylogeny, Plant Viruses, 03 medical and health sciences, plant virus, Phylogenetics, Plant virus, RNA Viruses, Human virome, Coevolution, Virus classification, virus evolution, virome, fungi, food and beverages, Plants, 030104 developmental biology, Evolutionary biology, Viral evolution, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Taxonomy (biology), Mobile genetic elements
Abstract: International audience; Land plants host a vast and diverse virome that is dominated by RNA viruses, with major additional contributions from reverse-transcribing and single-stranded (ss) DNA viruses. Here, we introduce the recently adopted comprehensive taxonomy of viruses based on phylogenomic analyses, as applied to the plant virome. We further trace the evolutionary ancestry of distinct plant virus lineages to primordial genetic mobile elements. We discuss the growing evidence of the pivotal role of horizontal virus transfer from invertebrates to plants during the terrestrialization of these organisms, which was enabled by the evolution of close ecological associations between these diverse organisms. It is our hope that the emerging big picture of the formation and global architecture of the plant virome will be of broad interest to plant biologists and virologists alike and will stimulate ever deeper inquiry into the fascinating field of virus-plant coevolution.
Published: 2020

36. The LUCA and its complex virome

Author: Mart Krupovic, Valerian V. Dolja, Eugene V. Koonin, Virologie des archées - Archaeal Virology, Institut Pasteur [Paris], Department of Botany and Plant Pathology, Oregon State University (OSU), National Library of Medicine (NLM), National Institutes of Health [Bethesda] (NIH)-National Center for Biotechnology Information (NCBI), E.V.K. is supported by the funds of the Intramural Research Program of the National Institutes of Health of the USA. M.K. was supported by l’Agence Nationale de la Recherche grant ANR-17-CE15-0005-01., ANR-17-CE15-0005,ENVIRA,Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées(2017), and Institut Pasteur [Paris] (IP)
Subjects: Evolution, [SDV]Life Sciences [q-bio], Population, Genome, Viral, Biology, Microbiology, Genome, Evolution, Molecular, Viral Proteins, 03 medical and health sciences, Virology, Three-domain system, Human virome, education, Gene, Ancestor, 0303 health sciences, education.field_of_study, Bacteria, General Immunology and Microbiology, Virome, 030306 microbiology, Archaea, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Infectious Diseases, Evolutionary biology, Viral evolution, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Capsid Proteins, Mobile genetic elements
Abstract: The last universal cellular ancestor (LUCA) is the most recent population of organisms from which all cellular life on Earth descends. The reconstruction of the genome and phenotype of the LUCA is a major challenge in evolutionary biology. Given that all life forms are associated with viruses and/or other mobile genetic elements, there is no doubt that the LUCA was a host to viruses. Here, by projecting back in time using the extant distribution of viruses across the two primary domains of life, bacteria and archaea, and tracing the evolutionary histories of some key virus genes, we attempt a reconstruction of the LUCA virome. Even a conservative version of this reconstruction suggests a remarkably complex virome that already included the main groups of extant viruses of bacteria and archaea. We further present evidence of extensive virus evolution antedating the LUCA. The presence of a highly complex virome implies the substantial genomic and pan-genomic complexity of the LUCA itself. The last universal cellular ancestor (LUCA) is the most recent population of organisms from which all cellular life on Earth descends. In this Perspective article, Krupovic, Dolja and Koonin analyse the extant distribution of viruses across the two primary domains of life to infer the LUCA virome.
Published: 2020

37. Recession discharge from compartmentalized bedrock hillslopes

Author: Clément Roques, David E. Rupp, Jean-Raynald de Dreuzy, Laurent Longuevergne, Elizabeth R. Jachens, Gordon Grant, Luc Aquilina, John S. Selker, Université de Neuchâtel (UNINE), Géosciences Rennes (GR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Oregon State University (OSU), US Department of Agriculture, National Science Foundation (grant no. 1551483)., and European Project: CHIST-ERA-19-CES-006
Subjects: General Earth and Planetary Sciences, [SDU.STU.HY]Sciences of the Universe [physics]/Earth Sciences/Hydrology, General Environmental Science
Abstract: We used numerical modelling to explore the role of the vertical compartmentalization of hillslopes on groundwater flow and recession discharge. We found that, when hydraulic properties are vertically compartmentalized, streamflow recession behaviour may strongly deviate from what is predicted by groundwater theory that considers the drainage of shallow reservoirs with homogeneous properties. We further identified the hillslope configurations for which the homogeneous theory derived from the Boussinesq solution approximately holds and, conversely, for those for which it does not. By comparing the modelled recession discharge Q and the groundwater table dynamics, we identified the critical hydrogeological conditions controlling the emergence of strong deviations. The three main controls are (i) the contribution of a deep aquifer connected to the stream, (ii) the heterogeneity in hydraulic properties, and (iii) the slope of the interface between a shallow permeable compartment and deep bedrock one with lower hydraulic properties. Our results confirm that a correct physical interpretation of the recession discharge exponent b from the classical equation -dQ/dt=aQb, and its temporal progression, requires knowledge of the structural configuration and heterogeneity of the aquifer.
Published: 2022

38. Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition

Author: Caroline Belser, Julie Poulain, Karine Labadie, Frederick Gavory, Adriana Alberti, Julie Guy, Quentin Carradec, Corinne Cruaud, Corinne da Silva, Stefan Engelen, Paul Mielle, Aude Perdereau, Gaelle Samson, Shahinaz Gas, Genoscope Technical Team, Voolstra, Christian R., Galand, Pierre E., Michel Flores, J., Benjamin Cc Hume, Gabriela Perna, Maren Ziegler, Hans-Joachim Ruscheweyh, Emilie Boissin, Sarah Romac, Guillaume Bourdin, Guillaume Iwankow, Clémentine Moulin, Paz García, David A., Sylvain Agostini, Bernard Banaigs, Emmanuel Boss, Chris Bowler, Colomban de Vargas, Éric Douville, Didier Forcioli, Paola Furla, Éric Gilson, Fabien Lombard, Stephane Pesant, Stéphanie Reynaud, Shinichi Sunagawa, Olivier Thomas, Romain Troublé, Rebecca Vega Thurber, Didier Zoccola, Claude Scarpelli, Krame Jacoby, E., Oliveira, Pedro H., Jean-Marc Aury, Denis Allemand, Serge Planes, Patrick Wincker, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Centre National de Recherche en Génomique Humaine (CNRGH), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Universität Konstanz, Laboratoire d'Ecogéochimie des environnements benthiques (LECOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Weizmann Institute of Science [Rehovot, Israël], Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), Department of Biology [ETH Zürich] (D-BIOL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-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), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), University of Maine, Tara Expéditions, Centro de Investigaciones Biologicas del Noroeste [Mexico] (CONACYT-CIBNOR), Consejo Nacional de Ciencia y Tecnología [Mexico] (CONACYT), Université de Tsukuba = University of Tsukuba, 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), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Géochrononologie Traceurs Archéométrie (GEOTRAC), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), 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)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Université Côte d'Azur (UCA), 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), European Molecular Biology Laboratory (EMBL), Centre Scientifique de Monaco (CSM), National University of Ireland [Galway] (NUI Galway), Oregon State University (OSU), Menguy, Caroline, Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), and 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)
Subjects: FOS: Biological sciences, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Quantitative Biology - Quantitative Methods, Quantitative Methods (q-bio.QM), [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: Coral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic interactions established within a complex holobiont, i.e. the multipartite assemblages comprising the host coral organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses. Tara Pacific is an ambitious project built upon the experience of previous Tara Oceans expeditions, and leveraging state-of-the-art sequencing technologies and analyses to dissect the biodiversity and biocomplexity of the coral holobiont screened across most archipelagos spread throughout the entire Pacific Ocean. Here we detail the Tara Pacific workflow for multi-omics data generation, from sample handling to nucleotide sequence data generation and deposition. This unique multidimensional framework also includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reef dynamics and their fate in the Anthropocene.
Published: 2022
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39. Les scientifiques mettent en garde contre les menaces qui pèsent sur les montagnes

Author: Dirk S. Schmeller, Davnah Urbach, Kieran Bates, Jordi Catalan, Dan Cogălniceanu, Matthew C. Fisher, Jan Friesen, Leopold Füreder, Veronika Gaube, Marilen Haver, Dean Jacobsen, Gael Le Roux, Yu-Pin Lin, Adeline Loyau, Oliver Machate, Andreas Mayer, Ignacio Palomo, Christoph Plutzar, Hugo Sentenac, Ruben Sommaruga, Rocco Tiberti, William J. Ripple, Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), Laboratoire Ecologie Fonctionnelle et Environnement (LEFE), Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-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 National Polytechnique (Toulouse) (Toulouse INP), University of Bern, Imperial College London, CSIC-UAB, CREAF, Universitat Autònoma de Barcelona (UAB), Ovidius University of Constanta, Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), Ecology, University of Innsbruck, Leopold Franzens Universität Innsbruck - University of Innsbruck, University of Natural Resources and Life Sciences Vienna, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Department of Biology [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Centre National de la Recherche Scientifique (CNRS), National Taiwan University [Taiwan] (NTU), Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Institut des Géosciences de l’Environnement (IGE), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Universität für Bodenkultur Wien = University of Natural Resources and Life [Vienne, Autriche] (BOKU), Università degli Studi di Pavia = University of Pavia (UNIPV), Oregon State University (OSU), and ANR-19-MPGA-0009,PORTAL,Pathways for Transformation in the Alps(2019)
Subjects: Conservation of Natural Resources, Environmental Engineering, Water, environmental health, Biodiversity, 580 Plants (Botany), sustainable development goals, Pollution, Carbon, climate change, Animals, Humans, Environmental Chemistry, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Waste Management and Disposal, Ecosystem, policy
Abstract: International audience; Mountains are an essential component of the global life-support system. They are characterized by a rugged, heterogenous landscape with rapidly changing environmental conditions providing myriad ecological niches over relatively small spatial scales. Although montane species are well adapted to life at extremes, they are highly vulnerable to human derived ecosystem threats. Here we build on the manifesto 'World Scientists' Warning to Humanity', issued by the Alliance of World Scientists, to outline the major threats to mountain ecosystems. We highlight climate change as the greatest threat to mountain ecosystems, which are more impacted than their lowland counterparts. We further discuss the cascade of "knock-on" effects of climate change such as increased UV radiation, altered hydrological cycles, and altered pollution profiles; highlighting the biological and socioeconomic consequences. Finally, we present how intensified use of mountains leads to overexploitation and abstraction of water, driving changes in carbon stock, reducing biodiversity, and impacting ecosystem functioning. These perturbations can provide opportunities for invasive species, parasites and pathogens to colonize these fragile habitats, driving further changes and losses of micro-and macrobiodiversity, as well further impacting ecosystem services. Ultimately, imbalances in the normal functioning of mountain ecosystems will lead to changes in vital biological, biochemical, and chemical processes, critically reducing ecosystem health with widespread repercussions for animal and human wellbeing. Developing tools in species/habitat conservation and future restoration is therefore essential if we are to effectively mitigate against the declining health of mountains.
Published: 2022
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40. Ocean Integration: The Needs and Challenges of Effective Coordination Within the Ocean Observing System

Author: Adèle Révelard, Joaquín Tintoré, Jacques Verron, Pierre Bahurel, John A. Barth, Mathieu Belbéoch, Jérôme Benveniste, Pascal Bonnefond, Eric P. Chassignet, Sophie Cravatte, Fraser Davidson, Brad deYoung, Michelle Heupel, Emma Heslop, Cora Hörstmann, Johannes Karstensen, Pierre Yves Le Traon, Miguel Marques, Craig McLean, Raul Medina, Theresa Paluszkiewicz, Ananda Pascual, Jay Pearlman, George Petihakis, Nadia Pinardi, Sylvie Pouliquen, Ralph Rayner, Iian Shepherd, Janet Sprintall, Toste Tanhua, Pierre Testor, Jukka Seppälä, John Siddorn, Soeren Thomsen, Luis Valdés, Martin Visbeck, Anya M. Waite, Francisco Werner, John Wilkin, Ben Williams, Suomen ympäristökeskus, The Finnish Environment Institute, SOCIB Balearic Islands Coastal Ocean Observing and Forecasting System, OceanNext, Mercator Océan, Société Civile CNRS Ifremer IRD Météo-France SHOM, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), College of Earth, Ocean and Atmospheric Sciences [Corvallis] (CEOAS), Oregon State University (OSU), OceanOPS, ESA Centre for Earth Observation (ESRIN), Agence Spatiale Européenne = European Space Agency (ESA), Systèmes de Référence Temps Espace (SYRTE), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Center for Ocean-Atmospheric Prediction Studies (COAPS), Florida State University [Tallahassee] (FSU), Laboratoire d'études en Géophysique et océanographie spatiales (LEGOS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Fisheries and Oceans Canada (DFO), Department of Physics and Physical Oceanography, Memorial University of Newfoundland = Université Memorial de Terre-Neuve [St. John's, Canada] (MUN), Variabilité de l'Océan et de la Glace de mer (VOG), 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), European Union’s Horizon 2020 Research and Innovation Programme under grant agreement No. 862626, project EuroSea (Improving and Integrating European Ocean Observing and Forecasting Systems for Sustainable Use of the Oceans), Revelard A., Tintore J., Verron J., Bahurel P., Barth J.A., Belbeoch M., Benveniste J., Bonnefond P., Chassignet E.P., Cravatte S., Davidson F., deYoung B., Heupel M., Heslop E., Horstmann C., Karstensen J., Le Traon P.Y., Marques M., McLean C., Medina R., Paluszkiewicz T., Pascual A., Pearlman J., Petihakis G., Pinardi N., Pouliquen S., Rayner R., Shepherd I., Sprintall J., Tanhua T., Testor P., Seppala J., Siddorn J., Thomsen S., Valdes L., Visbeck M., Waite A.M., Werner F., Wilkin J., Williams B., and European Commission
Subjects: 0106 biological sciences, coordination, 010504 meteorology & atmospheric sciences, koordinointi, Science, [PHYS.PHYS.PHYS-GEO-PH]Physics [physics]/Physics [physics]/Geophysics [physics.geo-ph], Ocean Engineering, integration, Aquatic Science, QH1-199.5, Oceanography, 01 natural sciences, ympäristön tila, interdisciplinarity, 14. Life underwater, seuranta, organizational silos, 0105 earth and related environmental sciences, Water Science and Technology, Global and Planetary Change, ocean observing, monitieteisyys, 010604 marine biology & hydrobiology, kansainvälinen yhteistyö, General. Including nature conservation, geographical distribution, integraatio, ocean governance and management, collaboration, 13. Climate action, merentutkimus, tieteidenvälisyys, GC Oceanography, tiedontuotanto, meret, ocean science culture
Abstract: Understanding and sustainably managing complex environments such as marine ecosystems benefits from an integrated approach to ensure that information about all relevant components and their interactions at multiple and nested spatiotemporal scales are considered. This information is based on a wide range of ocean observations using different systems and approaches. An integrated approach thus requires effective collaboration between areas of expertise in order to improve coordination at each step of the ocean observing value chain, from the design and deployment of multi-platform observations to their analysis and the delivery of products, sometimes through data assimilation in numerical models. Despite significant advances over the last two decades in more cooperation across the ocean observing activities, this integrated approach has not yet been fully realized. The ocean observing system still suffers from organizational silos due to independent and often disconnected initiatives, the strong and sometimes destructive competition across disciplines and among scientists, and the absence of a well-established overall governance framework. Here, we address the need for enhanced organizational integration among all the actors of ocean observing, focusing on the occidental systems. We advocate for a major evolution in the way we collaborate, calling for transformative scientific, cultural, behavioral, and management changes. This is timely because we now have the scientific and technical capabilities as well as urgent societal and political drivers. The ambition of the United Nations Decade of Ocean Science for Sustainable Development (2021–2030) and the various efforts to grow a sustainable ocean economy and effective ocean protection efforts all require a more integrated approach to ocean observing. After analyzing the barriers that currently prevent this full integration within the occidental systems, we suggest nine approaches for breaking down the silos and promoting better coordination and sharing. These recommendations are related to the organizational framework, the ocean science culture, the system of recognition and rewards, the data management system, the ocean governance structure, and the ocean observing drivers and funding. These reflections are intended to provide food for thought for further dialogue between all parties involved and trigger concrete actions to foster a real transformational change in ocean observing., This work was supported by the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement No. 862626, project EuroSea (Improving and Integrating European Ocean Observing and Forecasting Systems for Sustainable Use of the Oceans).
Published: 2022

41. Guidance for the diagnosis and treatment of hypolipidemia disorders

Author: Cindy Bredefeld, M. Mahmood Hussain, Maurizio Averna, Dennis D. Black, Mitchell F. Brin, John R. Burnett, Sybil Charrière, Charlotte Cuerq, Nicholas O. Davidson, Richard J. Deckelbaum, Ira J. Goldberg, Esther Granot, Robert A. Hegele, Shun Ishibashi, Wahida Karmally, Emile Levy, Philippe Moulin, Hiroaki Okazaki, Pierre Poinsot, Daniel J. Rader, Manabu Takahashi, Patrizia Tarugi, Maret G. Traber, Mathilde Di Filippo, Noel Peretti, Long Island University, Brooklyn (LIU Brooklyn), New York University Langone Medical Center (NYU Langone Medical Center), NYU System (NYU), Dipartimento Universitario di Promozione della Salute, Materno Infantile, Medicina Interna e Specialistica di Eccellenza 'G. D'Alessandro' [Palerme, Italie] (PROMISE), Università degli studi di Palermo - University of Palermo, Le Bonheur Children's Hospital [Memphis, TN, USA] (LBCH), The University of Tennessee Health Science Center [Memphis] (UTHSC), University of California [Irvine] (UC Irvine), University of California (UC), The University of Western Australia (UWA), Cardiovasculaire, métabolisme, diabétologie et nutrition (CarMeN), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Hospices Civils de Lyon (HCL), Washington University School of Medicine [Saint Louis, MO], Columbia University Irving Medical Center (CUIMC), New York University School of Medicine (NYU Grossman School of Medicine), Hadassah Hebrew University Medical Center [Jerusalem], Kaplan Medical Center [Rehovot, Israel], University of Western Ontario (UWO), Jichi Medical University [Tochigi-Ken, Japan], Centre de recherche du CHU Sainte-Justine / Research Center of the Sainte-Justine University Hospital [Montreal, Canada], Université de Montréal (UdeM)-CHU Sainte Justine [Montréal], The University of Tokyo (UTokyo), Hôpital Femme Mère Enfant [CHU - HCL] (HFME), University of Pennsylvania, Università degli Studi di Modena e Reggio Emilia = University of Modena and Reggio Emilia (UNIMORE), Oregon State University (OSU), and CarMeN, laboratoire
Subjects: Nutrition and Dietetics, [SDV.BA] Life Sciences [q-bio]/Animal biology, Endocrinology, Diabetes and Metabolism, Lipoproteins, Abetalipoproteinemia/diagnosis/genetics/therapy, [SDV.BA]Life Sciences [q-bio]/Animal biology, Homozygote, Chylomicron retention disease, Hypobetalipoproteinemias/diagnosis/genetics/therapy, Vitamins, Lipids, Abetalipoproteinemia, Familial hypocholesterolemia, Fat-soluble vitamins, Cholesterol, Lipid Metabolism Disorders, Internal Medicine, Humans, Cardiology and Cardiovascular Medicine, Hypobetalipoproteinemia, Triglycerides
Abstract: The Abetalipoproteinemia and Related Disorders Foundation was established in 2019 to provide guidance and support for the life-long management of inherited hypocholesterolemia disorders. Our mission is "to improve the lives of individuals and families affected by abetalipoproteinemia and related disorders". This review explains the molecular mechanisms behind the monogenic hypobetalipoproteinemia disorders and details their specific pathophysiology, clinical presentation and management throughout the lifespan. In this review, we focus on abetalipoproteinemia, homozygous hypobetalipoproteinemia and chylomicron retention disease; rare genetic conditions that manifest early in life and cause severe complications without appropriate treatment. Absent to low plasma lipid levels, in particular cholesterol and triglyceride, along with malabsorption of fat and fat-soluble vitamins are characteristic features of these diseases. We summarize the genetic basis of these disorders, provide guidance in their diagnosis and suggest treatment regimens including high dose fat-soluble vitamins as therapeutics. A section on preconception counseling and other special considerations pertaining to pregnancy is included. This information may be useful for patients, caregivers, physicians and insurance agencies involved in the management and support of affected individuals.
Published: 2022

42. Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs

Author: Benjamin D. Lee, Uri Neri, Simon Roux, Yuri I. Wolf, Antonio Pedro Camargo, Mart Krupovic, Peter Simmonds, Nikos Kyrpides, Uri Gophna, Valerian V. Dolja, Eugene V. Koonin, National Center for Biotechnology Information (NCBI), University of Oxford, Tel Aviv University (TAU), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Virologie des archées - Archaeal Virology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Oregon State University (OSU), B.D.L. was supported by a fellowship from the National Institutes of Health Oxford-Cambridge Scholars Program. Y.I.W. and E.V.K. are supported through the Intramural Research Program of the US National Institutes of Health (National Library of Medicine). U.G. and U.N. are supported by the European Research Council (ERC-AdG 787514). U.N. is partially supported by a fellowship from the Edmond J. Safra Center for Bioinformatics at Tel Aviv University. V.V.D. was partially supported by NIH/NLM/NCBI Visiting Scientist Fellowship. The work of the US Department of Energy Joint Genome Institute (S.R., N.K., and all JGI co-authors), a DOE Office of Science User Facility, is supported by the Office of Science of the US Department of Energy under contract no. DE-AC02-05CH11231. M.K. was supported by l’Agence Nationale de la Recherche grants ANR-20-CE20-009-02 and ANR-21-CE11-0001-01., ANR-20-CE20-0009,VIROMET,Devoiler le virome des archées methanogenes(2020), and ANR-21-CE11-0001,ArcFus,Protéines de classe II de fusion membranaire chez les archées(2021)
Subjects: [SDV]Life Sciences [q-bio], General Biochemistry, Genetics and Molecular Biology
Abstract: International audience; Viroids and viroid-like covalently closed circular (ccc) RNAs are minimal replicators that typically encode no proteins and hijack cellular enzymes for replication. The extent and diversity of viroid-like agents are poorly understood. We developed a computational pipeline to identify viroid-like cccRNAs and applied it to 5,131 metatranscriptomes and 1,344 plant transcriptomes. The search yielded 11,378 viroid-like cccRNAs spanning 4,409 species-level clusters, a 5-fold increase compared to the previously identified viroid-like elements. Within this diverse collection, we discovered numerous putative viroids, satellite RNAs, retrozymes, and ribozy-like viruses. Diverse ribozyme combinations and unusual ribozymes within the cccRNAs were identified. Self-cleaving ribozymes were identified in ambiviruses, some mito-like viruses and capsid-encoding satellite virus-like cccRNAs. The broad presence of viroid-like cccRNAs in diverse transcriptomes and ecosystems implies that their host range is far broader than currently known, and matches to CRISPR spacers suggest that some cccRNAs replicate in prokaryotes.
Published: 2023

43. Reliability-based topology optimization under random-field material model

Author: Pham, Trung, Hoyle, Christopher, Department of Aerospace Engineering [Ann Arbor], University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, and Oregon State University (OSU)
Subjects: 90-08, Optimization and Control (math.OC), Structural reliability, Continuum topology optimization, Karhunen−Loève expansion, FOS: Mathematics, Material uncertainties, Stochastic response surface, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC], Mathematics - Optimization and Control, [SPI.MECA.GEME]Engineering Sciences [physics]/Mechanics [physics.med-ph]/Mechanical engineering [physics.class-ph]
Abstract: This paper presents an algorithm for reliability-based topology optimization of linear elastic continua under random-field material model. The modelling random field is discretized into a small number of random variables, and then the interested output is estimated by a stochastic response surface. A single-loop inverse-reliability algorithm is applied to reduce computational cost of reliability analysis. Two common benchmark problems in literature are used for demonstration purposes. Different values of target reliability and ranges of Young's modulus are considered to investigate their effects on resulting optimized topologies. Lastly, Monte Carlo simulation tests the proposed algorithm for correctness and accuracy.
Published: 2021

44. Robust reliability-based topology optimization under random-field material model

Author: Pham, Trung, Hoyle, Christopher, Department of Aerospace Engineering [Ann Arbor], University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, and Oregon State University (OSU)
Subjects: 90-08, Optimization and Control (math.OC), FOS: Mathematics, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC], Mathematics - Optimization and Control, [SPI.MECA.GEME]Engineering Sciences [physics]/Mechanics [physics.med-ph]/Mechanical engineering [physics.class-ph]
Abstract: This paper proposes an algorithm to find robust reliability-based topology optimized designs under a random-field material model. The initial design domain is made of linear elastic material whose property, i.e., Young's modulus, is modeled by a random field. To facilitate computation, the Karhunen-Lo\`eve expansion discretizes the modeling random field into a small number of random variables. Robustness is achieved by optimizing a weighted sum of mean and standard deviation of a quantity of interest, while reliability is employed through a probabilistic constraint. The Smolyak-type sparse grid and the stochastic response surface method are applied to reduce computational cost. Furthermore, an efficient inverse-reliability algorithm is utilized to decouple the double-loop structure of reliability analysis. The proposed algorithm is tested on two common benchmark problems in literature. Finally, Monte Carlo simulation is used to validate the claimed robustness and reliability of optimized designs., Comment: arXiv admin note: text overlap with arXiv:2112.14802
Published: 2021

45. Viruses Defined by the Position of the Virosphere within the Replicator Space

Author: Mart Krupovic, Valerian V. Dolja, Jens H. Kuhn, Eugene V. Koonin, National Center for Biotechnology Information (NCBI), Oregon State University (OSU), Virologie des archées - Archaeal Virology, Institut Pasteur [Paris] (IP), Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH)-National Institutes of Health [Bethesda] (NIH), V.K. is supported by the Intramural Research Program of the National Institutes of Health of the USA (National Library of Medicine). This work was supported in part through Laulima Government Solutions, LLC, prime contract with the U.S. National Institute of Allergy and Infectious Diseases (NIAID) under contract no. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC, under contract no. HHSN272201800013C. M.K. was supported by l’Agence Nationale de la Recherche (grant ANR-20-CE20-0009) and Emergence(s) project MEMREMA from Ville de Paris., and ANR-20-CE20-0009,VIROMET,Devoiler le virome des archées methanogenes(2020)
Subjects: viruses, Virtual space, replicator, virus, Review, Biology, Space (commercial competition), virus taxonomy, Microbiology, Genome, Defective virus, 03 medical and health sciences, virus classification, Molecular Biology, Virus classification, Host protein, virosphere, 030304 developmental biology, perivirosphere, 0303 health sciences, orthovirosphere, 030306 microbiology, mobile genetic element, MGE, DNA Viruses, DNA, Biological Evolution, Infectious Diseases, Evolutionary biology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Viruses, virus definition, Plasmids
Abstract: International audience; Originally, viruses were defined as miniscule infectious agents that passed through filters that retain even the smallest cells. Subsequently, viruses were considered obligate intracellular parasites whose reproduction depends on their cellular hosts for energy supply and molecular building blocks. However, these features are insufficient to unambiguously define viruses as they are broadly understood today. We outline possible approaches to define viruses and explore the boundaries of the virosphere within the virtual space of replicators and the relationships between viruses and other types of replicators. Regardless of how, exactly, viruses are defined, viruses clearly have evolved on many occasions from nonviral replicators, such as plasmids, by recruiting host proteins to become virion components. Conversely, other types of replicators have repeatedly evolved from viruses. Thus, the virosphere is a dynamic entity with extensive evolutionary traffic across its boundaries. We argue that the virosphere proper, here termed orthovirosphere, consists of a distinct variety of replicators that encode structural proteins encasing the replicators' genomes, thereby providing protection and facilitating transmission among hosts. Numerous and diverse replicators, such as virus-derived but capsidless RNA and DNA elements, or defective viruses occupy the zone surrounding the orthovirosphere in the virtual replicator space. We define this zone as the perivirosphere. Although intense debates on the nature of certain replicators that adorn the internal and external boundaries of the virosphere will likely continue, we present an operational definition of virus that recently has been accepted by the International Committee on Taxonomy of Viruses.
Published: 2021

46. From settlers to subspecies: genetic differentiation in Commerson’s dolphins between South America and the Kerguelen Islands

Author: Sebastián Kraft, MJosé Pérez-Alvarez, Carlos Olavarría, Rodrigo Moraga, C. Scott Baker, Debbie Steel, Paul Tixier, Christophe Guinet, Amelia Viricel, Paul Brickle, Marina Costa, Enrique Crespo, Cristian Durante, Rocio Loizaga, Elie Poulin, Instituto de Ecología y Biodiversidad (IEB), Centro de Investigación Eutropia [Chile], Marine Mammal Institute, Oregon State University (OSU), 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), Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), LIttoral ENvironnement et Sociétés (LIENSs), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS), South Atlantic Environmental Research Institute [Falkland Islands] (SAERI), Laboratorio de Mamíferos Marinos, Centro Nacional Patagónico (CENPAT), 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 de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), and Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Cephalorhynchus commersonii, Colonization, Science, Ocean Engineering, mitochondrial DNA, Aquatic Science, QH1-199.5, phylogeography, Oceanography, 010603 evolutionary biology, 01 natural sciences, Divergence, 03 medical and health sciences, 14. Life underwater, 030304 developmental biology, Water Science and Technology, 0303 health sciences, Global and Planetary Change, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], General. Including nature conservation, geographical distribution, Last glacial maximum, colonization, Mitochondrial DNA, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Phylogeography, last glacial maximum, [SDE]Environmental Sciences, divergence
Abstract: Commerson’s dolphins (Cephalorhynchus commersonii) are separated into the subspecies C. c. commersonii, found along southern South America (SA) and the Falkland Islands/Islas Malvinas (FI/IM), and C. c. kerguelenensis, restricted to the subantarctic Kerguelen Islands (KI). Following the dispersal model proposed for the genus, the latter is thought to have originated from SA after a long-distance dispersal event. To evaluate this biogeographic scenario, a distribution-wide, balanced sampling of mitochondrial DNA (mtDNA) control region sequences was designed. New tissue samples from southern Chile, Argentina, FI/IM, and KI were added to published sequences from SA and KI, for a total of 256 samples. Genetic diversity indices, genetic and phylogeographic structure, and migration rates were calculated. One haplotype was shared between subspecies, with which all haplotypes of C. c. kerguelenensis formed a distinct group in the haplotype network. A new haplotype for C. c. kerguelenensis is reported. Differentiation in haplotype frequencies was found among localities within the distribution of C. c. commersonii, yet the phylogeographic signal was only statistically significant between subspecies. Coalescent-based historical gene flow estimations indicated migration between the northern and southern portions of the species’ range in SA as well as between SA and the FI/IM, but not between these and the KI. The net nucleotide divergence between dolphins from SA and the FI/IM was lower than the recommended threshold value suggested for delimiting subspecies, unlike that found between C. c. commersonii and C. c. kerguelenensis. The results are consistent with the model of post-glacial colonization of KI by South American C. commersonii, followed by an ongoing divergence process and subspecies status. Thus, C. c. kerguelenensis may represent the most recent diversification step of Cephalorhynchus, where isolation from their source population is driving a process of incipient speciation.
Published: 2021

47. Calculation and Interpretation of Substrate Assimilation Rates in Microbial Cells Based on Isotopic Composition Data Obtained by nanoSIMS

Author: Polerecky, Lubos, Eichner, Meri, Masuda, Takako, Zavřel, Tomáš, Rabouille, Sophie, Campbell, Douglas A., Halsey, Kimberly, Geochemistry, Bio-, hydro-, and environmental geochemistry, Utrecht University [Utrecht], Institute of Microbiology of the Czech Academy of Sciences (MBU / CAS), Czech Academy of Sciences [Prague] (CAS), 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), Laboratoire d'Océanographie Microbienne (LOMIC), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Mount Allison University, Oregon State University (OSU), Geochemistry, and Bio-, hydro-, and environmental geochemistry
Subjects: Microbiology (medical), [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, storage inclusions, cell growth model, Cell division, 030306 microbiology, Chemistry, Stable-isotope probing, Assimilation (biology), Substrate (marine biology), Microbiology, QR1-502, Interpretation (model theory), Isotopic labeling, Secondary ion mass spectrometry, 03 medical and health sciences, Yield (chemistry), Methods, assimilation rates, Biological system, stable isotope probing, 030304 developmental biology, nanoSIMS
Abstract: International audience; Stable isotope probing (SIP) combined with nano-scale secondary ion mass spectrometry (nanoSIMS) is a powerful approach to quantify assimilation rates of elements such as C and N into individual microbial cells. Here, we use mathematical modeling to investigate how the derived rate estimates depend on the model used to describe substrate assimilation by a cell during a SIP incubation. We show that the most commonly used model, which is based on the simplifying assumptions of linearly increasing biomass of individual cells over time and no cell division, can yield underestimated assimilation rates when compared to rates derived from a model that accounts for cell division. This difference occurs because the isotopic labeling of a dividing cell increases more rapidly over time compared to a non-dividing cell and becomes more pronounced as the labeling increases above a threshold value that depends on the cell cycle stage of the measured cell. Based on the modeling results, we present formulae for estimating assimilation rates in cells and discuss their underlying assumptions, conditions of applicability, and implications for the interpretation of intercellular variability in assimilation rates derived from nanoSIMS data, including the impacts of storage inclusion metabolism. We offer the formulae as a Matlab script to facilitate rapid data evaluation by nanoSIMS users.
Published: 2021

48. Progress in understanding of Indian Ocean circulation, variability, air-sea exchange and impacts on biogeochemistry

Author: H. E. Phillips, A. Tandon, R. Furue, R. Hood, C. C. Ummenhofer, J. A. Benthuysen, V. Menezes, S. Hu, B. Webber, A. Sanchez-Franks, D. Cherian, E. Shroyer, M. Feng, H. Wijesekera, A. Chatterjee, L. Yu, J. Hermes, R. Murtugudde, T. Tozuka, D. Su, A. Singh, L. Centurioni, S. Prakash, J. Wiggert, University of Tasmania [Hobart, Australia] (UTAS), University of Massachusetts [Dartmouth], University of Massachusetts System (UMASS), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), University of Maryland Center for Environmental Science (UMCES), University of Maryland System, Woods Hole Oceanographic Institution (WHOI), University of New South Wales [Sydney] (UNSW), Australian Institute of Marine Science (AIMS), Chinese Academy of Sciences [Beijing] (CAS), University of East Anglia [Norwich] (UEA), National Oceanography Centre [Southampton] (NOC), University of Southampton, National Center for Atmospheric Research [Boulder] (NCAR), Oregon State University (OSU), CSIRO Indian Ocean Marine Research Centre [Australia], The University of Western Australia (UWA), Centre for Southern Hemisphere Oceans Research, Hobart, Tasmania, Australia, Naval Research Laboratory at Stennis Space Center (NRL-SSC), Naval Research Laboratory (NRL), Indian National Centre for Ocean Information Services, South African Environmental Observation Network [Pretoria] (SAEON), University of Maryland [College Park], The University of Tokyo (UTokyo), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), Physical Research Laboratory [Ahmedabad] (PRL), Indian Space Research Organisation (ISRO), University of California [San Diego] (UC San Diego), University of California, University of Southern Mississippi (USM), Indian National Centre for Ocean Information Services (INCOIS), Processus et interactions de fine échelle océanique (PROTEO), 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), and University of California (UC)
Subjects: Water mass, 010504 meteorology & atmospheric sciences, 010505 oceanography, Ocean current, Biogeochemistry, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, Physical oceanography, Monsoon, Deep sea, 01 natural sciences, Boundary current, Environmental sciences, Oceanography, 13. Climate action, Geography. Anthropology. Recreation, Environmental science, GE1-350, 14. Life underwater, Ocean heat content, 0105 earth and related environmental sciences
Abstract: Over the past decade, our understanding of the Indian Ocean has advanced through concerted efforts toward measuring the ocean circulation and air–sea exchanges, detecting changes in water masses, and linking physical processes to ecologically important variables. New circulation pathways and mechanisms have been discovered that control atmospheric and oceanic mean state and variability. This review brings together new understanding of the ocean–atmosphere system in the Indian Ocean since the last comprehensive review, describing the Indian Ocean circulation patterns, air–sea interactions, and climate variability. Coordinated international focus on the Indian Ocean has motivated the application of new technologies to deliver higher-resolution observations and models of Indian Ocean processes. As a result we are discovering the importance of small-scale processes in setting the large-scale gradients and circulation, interactions between physical and biogeochemical processes, interactions between boundary currents and the interior, and interactions between the surface and the deep ocean. A newly discovered regional climate mode in the southeast Indian Ocean, the Ningaloo Niño, has instigated more regional air–sea coupling and marine heatwave research in the global oceans. In the last decade, we have seen rapid warming of the Indian Ocean overlaid with extremes in the form of marine heatwaves. These events have motivated studies that have delivered new insight into the variability in ocean heat content and exchanges in the Indian Ocean and have highlighted the critical role of the Indian Ocean as a clearing house for anthropogenic heat. This synthesis paper reviews the advances in these areas in the last decade.
Published: 2021

49. Bioactive trace metals and their isotopes as paleoproductivity proxies: An assessment using GEOTRACES‐era data

Author: Tristan Horner, Susan Little, Tim Conway, Jesse Farmer, Jennifer Hertzberg, David Janssen, Alastair Lough, Jennifer McKay, Allyson Tessin, Stephen Galer, Sam Jaccard, Francois Lacan, Adina Paytan, Kathrin Wuttig, Clara Bolton, Eva Calvo, Damien Cardinal, Thibault de Garidel-Thoron, Susanne Fietz, Katharine Hendry, Franco Marcantonio, Patrick Rafter, Haojia Ren, Christopher Somes, Jill Sutton, Adi Torfstein, Gisela Winckler, Department of Marine Chemistry and Geochemistry (WHOI), Woods Hole Oceanographic Institution (WHOI), Birkbeck College [University of London], College of Marine Science [St Petersburg, FL], University of South Florida [Tampa] (USF), Department of Geosciences [Princeton], Princeton University, Department of Ocean, Earth and Atmospheric Sciences [Norfolk], Old Dominion University [Norfolk] (ODU), Oeschger Centre for Climate Change Research (OCCR), University of Bern, College of Earth, Ocean and Atmospheric Sciences [Corvallis] (CEOAS), Oregon State University (OSU), Kentucky State University, Max Planck Institute for Chemistry (MPIC), Max-Planck-Gesellschaft, Laboratoire d'études en Géophysique et océanographie spatiales (LEGOS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Institute of Marine Sciences, Long Marine Laboratory, University of California [Santa Cruz] (UCSC), University of California-University of California, Antarctic Climate and Ecosystems Cooperative Research Centre (ACE-CRC), 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), Cycles biogéochimiques marins : processus et perturbations (CYBIOM), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Sorbonne Université (SU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Sorbonne Université (SU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-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 de Paris (UP), National Science Foundation (US), Swiss Academy of Sciences, Natural Environment Research Council (UK), University of South Florida, Max Planck Society, Agencia Estatal de Investigación (España), 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)-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 de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-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)-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 de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), University of California [Santa Cruz] (UC Santa Cruz), University of California (UC)-University of California (UC), 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), GEOTRACES, and PAGES Global Charcoal Database
Subjects: 0106 biological sciences, Atmospheric Science, 010504 meteorology & atmospheric sciences, Geotraces, chemistry.chemical_element, 010502 geochemistry & geophysics, 01 natural sciences, 7. Clean energy, Atmosphere, Paleoceanography, Phytoplankton, marine chemistry, Environmental Chemistry, 14. Life underwater, General Environmental Science, Global and Planetary Change, 0105 earth and related environmental sciences, Isotope, 010604 marine biology & hydrobiology, Biological pump, biogeochemical cycles, Seafloor spreading, Oceanography, chemistry, 13. Climate action, micronutrients, [SDE]Environmental Sciences, paleoceanography, phytoplankton, Environmental science, Carbon, biological pump
Abstract: 86 pages, 33 figures, 2 tables, 1 appendix.-- Data Availability Statement: The majority of the dissolved data were sourced from the GEOTRACES Intermediate Data Products in 2014 (Mawji et al., 2015) and 2017 (Schlitzer et al., 2018), and citations to the primary data sources are given in the caption for each figure. Data sources for Figure 1 are given below. Figure 1: Iron: Conway & John, 2014a (Atlantic); Conway & John, 2015a (Pacific); Abadie et al., 2017 (Southern). Zinc: Conway & John, 2014b (Atlantic); Conway & John, 2015a (Pacific); R. M. Wang et al., 2019 (Southern). Copper: Little et al., 2018 (Atlantic); Takano et al., 2017 (Pacific); Boye et al., 2012 (Southern). Cadmium: Conway and John, 2015b (Atlantic); Conway & John, 2015a (Pacific); Abouchami et al., 2014 (Southern). Molybdenum: Nakagawa et al., 2012 (all basins). Barium: Bates et al., 2017 (Atlantic); Geyman et al., 2019 (Pacific); Hsieh & Henderson, 2017 (Southern). Nickel: Archer et al., 2020 (Atlantic); Takano et al., 2017 (Pacific); R. M. Wang et al., 2019 (Southern). Chromium: Goring-Harford et al., 2018 (Atlantic); Moos & Boyle, 2019 (Pacific); Rickli et al., 2019 (Southern). Silver: Fischer et al., 2018 (Pacific); Boye et al., 2012 (Southern), Phytoplankton productivity and export sequester climatically significant quantities of atmospheric carbon dioxide as particulate organic carbon through a suite of processes termed the biological pump. Constraining how the biological pump operated in the past is important for understanding past atmospheric carbon dioxide concentrations and Earth's climate history. However, reconstructing the history of the biological pump requires proxies. Due to their intimate association with biological processes, several bioactive trace metals and their isotopes are potential proxies for past phytoplankton productivity, including iron, zinc, copper, cadmium, molybdenum, barium, nickel, chromium, and silver. Here, we review the oceanic distributions, driving processes, and depositional archives for these nine metals and their isotopes based on GEOTRACES-era datasets. We offer an assessment of the overall maturity of each isotope system to serve as a proxy for diagnosing aspects of past ocean productivity and identify priorities for future research. This assessment reveals that cadmium, barium, nickel, and chromium isotopes offer the most promise as tracers of paleoproductivity, whereas iron, zinc, copper, and molybdenum do not. Too little is known about silver to make a confident determination. Intriguingly, the trace metals that are least sensitive to productivity may be used to track other aspects of ocean chemistry, such as nutrient sources, particle scavenging, organic complexation, and ocean redox state. These complementary sensitivities suggest new opportunities for combining perspectives from multiple proxies that will ultimately enable painting a more complete picture of marine paleoproductivity, biogeochemical cycles, and Earth's climate history, This contribution grew (and grew) out of a joint workshop between GEOTRACES and Past Global Changes (PAGES) held in Aix-en-Provence in December 2018. The workshop was funded by the U.S. National Science Foundation (NSF) through the GEOTRACES program, the international PAGES project, which received support from the Swiss Academy of Sciences and NSF, and the French program Les Envelopes Fluides et l'Environnement. [...] T. J. Horner acknowledges support from NSF; S. H. Little from the UK Natural Environment Research Council (NE/P018181/1); T. M. Conway from the University of South Florida; and, J. R. Farmer from the Max Planck Society, the Tuttle Fund of the Department of Geosciences of Princeton University, the Grand Challenges Program of the Princeton Environmental Institute, and the Andlinger Center for Energy and the Environment of Princeton University. [...] With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)
Published: 2021

50. A global perspective on the functional responses of stream communities to flow intermittence

Author: Crabot, Julie, Mondy, Cedric P., Usseglio‐Polatera, Philippe, Fritz, Ken M., Wood, Paul J., Greenwood, Michelle J., Bogan, Michael T., Meyer, Elisabeth I., Datry, Thibault, Riverly (Riverly), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Géographie Physique et Environnementale (GEOLAB), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Université Clermont Auvergne (UCA)-Institut Sciences de l'Homme et de la Société (IR SHS UNILIM), Université de Limoges (UNILIM)-Université de Limoges (UNILIM)-Centre National de la Recherche Scientifique (CNRS), Office français de la biodiversité (OFB), Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Terre et Environnement de Lorraine (OTELo), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), United States Environmental Protection Agency [Cincinnati], Loughborough University, National Institute of Water and Atmospheric Research [Christchurch] (NIWA), Oregon State University (OSU), University of Münster, RiverLy - Fonctionnement des hydrosystèmes (RiverLy), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut Sciences de l'Homme et de la Société (IR SHS UNILIM), Université de Limoges (UNILIM)-Université de Limoges (UNILIM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), and Westfälische Wilhelms-Universität Münster = University of Münster (WWU)
Subjects: biodiversity loss, fragmentation, temporary rivers, [SDE]Environmental Sciences, global change, life-history traits
Abstract: International audience; The current erosion of biodiversity is a major concern that threatens the ecological integrity of ecosystems and the ecosystem services they provide. Due to global change, an increasing proportion of river networks are drying and changes from perennial to non-perennial flow regimes represent dramatic ecological shifts with potentially irreversible alterations of community and ecosystem dynamics. However, there is minimal understanding of how biological communities respond functionally to drying. Here, we highlight the taxonomic and functional responses of aquatic macroinvertebrate communities to flow intermittence across river networks from three continents, to test predictions from underlying trait-based conceptual theory. We found a significant breakpoint in the relationship between taxonomic and functional richness, indicating higher functional redundancy at sites with flow intermittence higher than 28%. Multiple strands of evidence, including patterns of alpha and beta diversity and functional group membership, indicated that functional redundancy did not compensate for biodiversity loss associated with increasing intermittence, contrary to received wisdom. A specific set of functional trait modalities, including small body size, short life span and high fecundity, were selected with increasing flow intermittence. These results demonstrate the functional responses of river communities to drying and suggest that ongoing biodiversity reduction due to global change in drying river networks is threatening their functional integrity. These results indicate that such patterns might be common in these ecosystems, even where drying is considered a predictable disturbance. This highlights the need for the conservation of natural drying regimes of intermittent rivers to secure their ecological integrity.
Published: 2021

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