Author: "Polish Academy of Sciences (PAN)" / Topic: biology - Searchworks@Jio Institute Digital Library Search Results

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282 results on '"Polish Academy of Sciences (PAN)"'

1. Temperature synchronizes temporal variation in laying dates across European hole-nesting passerines

Author: Stefan J. G. Vriend, Vidar Grøtan, Marlène Gamelon, Frank Adriaensen, Markus P. Ahola, Elena Álvarez, Liam D. Bailey, Emilio Barba, Jean‐Charles Bouvier, Malcolm D. Burgess, Andrey Bushuev, Carlos Camacho, David Canal, Anne Charmantier, Ella F. Cole, Camillo Cusimano, Blandine F. Doligez, Szymon M. Drobniak, Anna Dubiec, Marcel Eens, Tapio Eeva, Kjell Einar Erikstad, Peter N. Ferns, Anne E. Goodenough, Ian R. Hartley, Shelley A. Hinsley, Elena Ivankina, Rimvydas Juškaitis, Bart Kempenaers, Anvar B. Kerimov, John Atle Kålås, Claire Lavigne, Agu Leivits, Mark C. Mainwaring, Jesús Martínez‐Padilla, Erik Matthysen, Kees van Oers, Markku Orell, Rianne Pinxten, Tone Kristin Reiertsen, Seppo Rytkönen, Juan Carlos Senar, Ben C. Sheldon, Alberto Sorace, János Török, Emma Vatka, Marcel E. Visser, Bernt‐Erik Sæther, Animal Ecology (AnE), Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Norwegian University of Science and Technology [Trondheim] (NTNU), Norwegian University of Science and Technology (NTNU), Department of Biology [Trondheim] (IBI NTNU), Norwegian University of Science and Technology (NTNU)-Norwegian University of Science and Technology (NTNU), Département écologie évolutive [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), University of Antwerp (UA), Swedish Museum of Natural History (NRM), Unidad de Investigación, Fundación Hospital de Jove, Universitad Politecnica de Valencia, Unité de recherche Plantes et Systèmes de Culture Horticoles (PSH), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Bedfordshire, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), University of Oxford [Oxford], Università degli studi di Palermo - University of Palermo, University of New South Wales [Sydney] (UNSW), Polish Academy of Sciences (PAN), Behavioural Ecology & Ecophysiology Group, University of Turku, High North Research Centre for Climate and the Environment, Norwegian Polar Institute, Centre for Conservation Biology, University of Gloucestershire (Cheltenham, GB), Lancaster University, Centre for Ecology and Hydrology [Wallingford] (CEH), Natural Environment Research Council (NERC), Centre de Recherche en Informatique de Paris 1 (CRI), Université Paris 1 Panthéon-Sorbonne (UP1), Nature Research Centre, Institute of Ecology, Akademijos str. 2, LT-08412, Vilnius, Lithuania., Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Evolutionary Ecology Group, Netherlands Institute of Ecology - NIOO-KNAW (NETHERLANDS), Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València (UV), University of Exeter, Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), University of Oxford, Department of Agriculture and Forest Sciences, Centre National de la Recherche Scientifique (CNRS), Museum and Institute of Zoology, Polska Akademia Nauk = Polish Academy of Sciences (PAN), Department of Biology (Ethology), Cardiff University, University of Gloucestershire [Gloucester], Institute of Ecology of Nature Research Centre, University of Montana, Instituto Pirenaico de Ecologia = Pyrenean Institute of Ecology (IPE), Netherlands Institute of Ecology (NIOO-KNAW), Department of Ecology, University of Oulu, Norwegian Institute for Nature Research (NINA), Museu de Ciències Naturals de Barcelona, and SROPU
Subjects: Ekologi, clutch size, Evolutionary Biology, comparative analysis, Ecology, [SDV]Life Sciences [q-bio], weather, passerines, timing of breeding, phenology, Ecology and Environment, Evolutionsbiologi, spatial synchrony, Chemistry, fledgling number, birds, 1181 Ecology, evolutionary biology, clutch, fitness-related traits, Biology, climate, Ecology, Evolution, Behavior and Systematics
Abstract: Identifying the environmental drivers of variation in fitness-related traits is a central objective in ecology and evolutionary biology. Temporal fluctuations of these environmental drivers are often synchronized at large spatial scales. Yet, whether synchronous environmental conditions can generate spatial synchrony in fitness-related trait values (i.e., correlated temporal trait fluctuations across populations) is poorly understood. Using data from long-term monitored populations of blue tits (Cyanistes caeruleus, n = 31), great tits (Parus major, n = 35), and pied flycatchers (Ficedula hypoleuca, n = 20) across Europe, we assessed the influence of two local climatic variables (mean temperature and mean precipitation in February–May) on spatial synchrony in three fitness-related traits: laying date, clutch size, and fledgling number. We found a high degree of spatial synchrony in laying date but a lower degree in clutch size and fledgling number for each species. Temperature strongly influenced spatial synchrony in laying date for resident blue tits and great tits but not for migratory pied flycatchers. This is a relevant finding in the context of environmental impacts on populations because spatial synchrony in fitness-related trait values among populations may influence fluctuations in vital rates or population abundances. If environmentally induced spatial synchrony in fitness-related traits increases the spatial synchrony in vital rates or population abundances, this will ultimately increase the risk of extinction for populations and species. Assessing how environmental conditions influence spatiotemporal variation in trait values improves our mechanistic understanding of environmental impacts on populations. birds, climate, clutch size, comparative analysis, fitness-related traits, fledgling number, phenology, spatial synchrony, timing of breeding, weather
Published: 2022

2. Is there tree senescence? The fecundity evidence

Author: Catherine A. Gehring, Tong Qiu, Kai Zhu, Richard K. Kobe, María Uriarte, James A. Lutz, Connie J. Clark, S. Joseph Wright, William Farfan-Rios, Sylvain Delzon, Thomas G. Whitham, Robert A. Andrus, Georges Kunstler, John R. Poulsen, Marie-Claire Aravena, Cathryn H. Greenberg, Andreas P. Wion, Ian S. Pearse, Amy V. Whipple, Miranda D. Redmond, Shubhi Sharma, Michał Bogdziewicz, Thomas A. Nagel, James S. Clark, Christopher L. Kilner, Kazuhiko Hoshizaki, Valentin Journé, Jalene M. LaMontagne, Margaret Swift, C. D. Reid, Jonathan Myers, Thomas T. Veblen, Benoît Courbaud, Walter D. Koenig, Kyle C. Rodman, Inés Ibáñez, Rafael Calama, Chase L. Nuñez, C. Lane Scher, Barbara Seget, Mateusz Ledwoń, Łukasz Piechnik, J. Julio Camarero, Qinfeng Guo, Thomas Boivin, Davide Ascoli, Janneke Hille Ris Lambers, Jennifer J. Swenson, Raúl Bonal, Sergio Calderón, Renata Poulton-Kamakura, Jess K. Zimmerman, Giorgio Vacchiano, Magdalena Żywiec, Miles R. Silman, Gregory S. Gilbert, Thomas Caignard, Harald Schmidt Van Marle, Roberta Berretti, Yves Bergeron, Renzo Motta, Nicholas School of the Environment, Duke University [Durham], Universidad de Chile, University of Colorado [Boulder], Department of Agriculture, Forest and Food Sciences, University of Torino, University of Quebec in Abitibi-Temiscamingue (UQAT), Adam Mickiewicz University in Poznań (UAM), Ecologie des Forêts Méditerranéennes (URFM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centro de Investigacion Forestal (INIA-CIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Instituto Pirenaico de Ecologia (IPE), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Laboratoire des EcoSystèmes et des Sociétés en Montagne (UR LESSEM), Missouri Botanical Garden, Northern Arizona University [Flagstaff], University of California [Santa Cruz] (UCSC), University of California, US DEPARTMENT OF AGRICULTURE FOREST SERVICE USA, 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), Eastern Forest Environmental Threat Assessment Center, US Forest Service, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Akita University, University of Michigan [Ann Arbor], University of Michigan System, Michigan State University [East Lansing], Michigan State University System, University of California [Berkeley], DePaul University [Chicago], Polish Academy of Sciences (PAN), Department of Wildland Resources, Utah State University (USU), Washington University in Saint Louis (WUSTL), University of Ljubljana, Max Planck Institute of Animal Behavior, Fort Collins Science Center (FORT), US Geological Survey [Fort Collins], United States Geological Survey [Reston] (USGS)-United States Geological Survey [Reston] (USGS), W. Szafer Institute of Botany, Polska Akademia Nauk = Polish Academy of Sciences (PAN), Department of Forest and Rangeland Stewardship, Colorado State University [Fort Collins] (CSU), University of Wisconsin-Madison, Wake Forest University, Columbia University [New York], Department and Agricultural & Environmental Sciences, (DiSAA), University of Milan, Smithsonian Tropical Research Institute, University of Puerto Rico (UPR), National Science Foundation (NSF) : 1754443, Belmont Forum : 1854976, National Aeronautics and Space Administration (Advanced Information Systems Technology) : 16-0052 AIST18-0063, National Science Foundation (NSF) : DEB-1440409, W. Szafer Institute of Botany of the Polish Academy of Sciences, Foundation for Polish Science : 2019/33/B/NZ8/0134, National Science Foundation (NSF) : DEB 0963447 11222325 LTREB 1754647, Gordon and Betty Moore Foundation, United States Department of Agriculture (USDA)United States Forest Service, and ANR-18-MPGA-0004,FORBIC,Prévision du changement de la biodiversité(2018)
Subjects: 0106 biological sciences, Senescence, Crown architecture, Biology, Forests, 010603 evolutionary biology, 01 natural sciences, Models, Biological, Trees, tree senescence, Tree life history, Models, Regeneration, Tree senescence, Architectural change, Allometric scaling, tree fecundity, Multidisciplinary, Ecology, crown architecture, Crown (botany), Regression analysis, 15. Life on land, Biological Sciences, Fecundity, Biological, Rate of increase, Fertility, Tree fecundity, Tree (set theory), Allometry, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, allometric scaling, 010606 plant biology & botany, tree life history
Abstract: International audience; Despite its importance for forest regeneration, food webs, and human economies, changes in tree fecundity with tree size and age remain largely unknown. The allometric increase with tree diameter assumed in ecological models would substantially overestimate seed contributions from large trees if fecundity eventually declines with size. Current estimates are dominated by overrepresentation of small trees in regression models. We combined global fecundity data, including a substantial representation of large trees. We compared size–fecundity relationships against traditional allometric scaling with diameter and two models based on crown architecture. All allometric models fail to describe the declining rate of increase in fecundity with diameter found for 80% of 597 species in our analysis. The strong evidence of declining fecundity, beyond what can be explained by crown architectural change, is consistent with physiological decline. A downward revision of projected fecundity of large trees can improve the next generation of forest dynamic models.
Published: 2021

3. 1 H -benzo[ d ]imidazole derivatives affect MmpL3 in Mycobacterium tuberculosis

Author: Albertus Viljoen, Dominik Strapagiel, Jakub Pawełczyk, Katarzyna Gobis, Małgorzata Korycka-Machała, Malwina Kawka, Paulina Borówka, Bozena Dziadek, Anna Brzostek, Mickaël Blaise, Laurent Kremer, Jarosław Dziadek, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Mycobacterium Genetics and Physiology Unit, Polska Akademia Nauk = Polish Academy of Sciences (PAN)-Institute for Medical Biology, Dynamique des interactions membranaires normales et pathologiques (DIMNP), Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institute for Medical Biology, and Polska Akademia Nauk = Polish Academy of Sciences (PAN)
Subjects: Pharmacology, 0303 health sciences, Benzimidazole, biology, 030306 microbiology, [SDV]Life Sciences [q-bio], Mutant, SQ109, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, In vitro, 3. Good health, Mycobacterium tuberculosis, Trehalose dimycolate, 03 medical and health sciences, chemistry.chemical_compound, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Biochemistry, chemistry, Arabinogalactan, Pharmacology (medical), Mode of action, 030304 developmental biology
Abstract: International audience; 1H-benzo[d]imidazole derivatives exhibit antitubercular activity in vitro at a nanomolar range of concentrations and are not toxic to human cells, but their mode of action remains unknown. Here, we showed that these compounds are active against intracellular Mycobacterium tuberculosis. To identify their target, we selected drug-resistant M. tuberculosis mutants and then used whole-genome sequenc-ing to unravel mutations in the essential mmpL3 gene, which encodes the integral membrane protein that catalyzes the export of trehalose monomycolate, a precursor of the mycobacterial outer membrane component trehalose dimycolate (TDM), as well as mycolic acids bound to arabinogalactan. The drug-resistant phenotype was also observed in the parental strain overexpressing the mmpL3 alleles carrying the mutations identified in the resistors. However, no cross-resistance was observed between 1H-benzo[d]imidazole derivatives and SQ109, another MmpL3 inhibitor, or other first-line antitubercular drugs. Metabolic labeling and quantitative thin-layer chromatography (TLC) analysis of radiolabeled lipids from M. tuberculosis cultures treated with the benzoimidazoles indicated an inhibition of trehalose dimycolate (TDM) synthesis, as well as reduced levels of mycolylated arabinogalactan, in agreement with the inhibition of MmpL3 activity. Overall, this study emphasizes the pronounced activity of 1H-benzo[d]imidazole derivatives in interfering with mycolic acid metabolism and their potential for therapeutic application in the fight against tuberculosis.
Published: 2019

4. Metabolic and Organelle Morphology Defects in Mice and Human Patients Define Spinocerebellar Ataxia Type 7 as a Mitochondrial Disease

Author: Pawel M. Switonski, Ronald M. Evans, Fanny Mochel, Weiwei Fan, Christopher E. Wall, Chenchen Niu, Chizuru Kinoshita, Farid Ichou, Jacqueline M. Ward, Alysson R. Muotri, Albert R. La Spada, Colleen A. Stoyas, Isaac Adanyeguh, Alexandra Durr, Richard S. Morrison, Bryce L. Sopher, Brett Collins, University of California [San Diego] (UC San Diego), University of California, Duke University [Durham], Institute of Bioorganic Chemistry [Poznań], Polska Akademia Nauk = Polish Academy of Sciences (PAN), Polish Academy of Sciences (PAN), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Institute of cardiometabolism and nutrition (ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), University of Washington [Seattle], Service de Génétique Cytogénétique et Embryologie [CHU Pitié-Salpêtrière], CHU Pitié-Salpêtrière [AP-HP], and Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)
Subjects: 0301 basic medicine, Blood Glucose, Mitochondrial Diseases, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Purkinje cell, Medical Physiology, Nicotinamide adenine dinucleotide, Mitochondrion, Neurodegenerative, chemistry.chemical_compound, Purkinje Cells, Mice, 0302 clinical medicine, spinocerebellar ataxia, Neural Stem Cells, oxidative metabolism, 2.1 Biological and endogenous factors, Aetiology, lcsh:QH301-705.5, Kynurenine, Tryptophan, 3. Good health, Cell biology, Mitochondria, mitochondria, medicine.anatomical_structure, Phenotype, Adipose Tissue, Neurological, Spinocerebellar ataxia, Stem cell, trinucleotide repeat, Ataxin 7, induced pluripotent stem cells, Mitochondrial disease, mouse model, Biology, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Rare Diseases, medicine, Genetics, Animals, Humans, Spinocerebellar Ataxias, Metabolomics, nicotinamide adenine dinucleotide, Organelles, Ataxin-7, Neurosciences, Reproducibility of Results, ataxin-7, medicine.disease, Stem Cell Research, NAD, Brain Disorders, 030104 developmental biology, lcsh:Biology (General), chemistry, biology.protein, NAD+ kinase, Biochemistry and Cell Biology, Peptides, Trinucleotide Repeat Expansion, Energy Metabolism, polyglutamine, 030217 neurology & neurosurgery
Abstract: SUMMARY Spinocerebellar ataxia type 7 (SCA7) is a retinal-cerebellar degenerative disorder caused by CAG-polyglutamine (polyQ) repeat expansions in the ataxin-7 gene. As many SCA7 clinical phenotypes occur in mitochondrial disorders, and magnetic resonance spectroscopy of patients revealed altered energy metabolism, we considered a role for mitochondrial dysfunction. Studies of SCA7 mice uncovered marked impairments in oxygen consumption and respiratory exchange. When we examined cerebellar Purkinje cells in mice, we observed mitochondrial network abnormalities, with enlarged mitochondria upon ultrastructural analysis. We developed stem cell models from patients and created stem cell knockout rescue systems, documenting mitochondrial morphology defects, impaired oxidative metabolism, and reduced expression of nicotinamide adenine dinucleotide (NAD+) production enzymes in SCA7 models. We observed NAD+ reductions in mitochondria of SCA7 patient NPCs using ratiometric fluorescent sensors and documented alterations in tryptophan-kynurenine metabolism in patients. Our results indicate that mitochondrial dysfunction, stemming from decreased NAD+, is a defining feature of SCA7., Graphical Abstract, In Brief Ward et al. document altered metabolism and mitochondrial dysfunction in SCA7 patients, mice, and human stem cell-derived neurons. They link these abnormalities to reduced nicotinamide adenine dinucleotide in specific subcellular compartments. Given the role of mitochondrial impairment in neurodegeneration, their results have therapeutic implications for SCA7 and related neurological disorders.
Published: 2019

5. Effects of interspecific coexistence on laying date and clutch size in two closely related species of hole-nesting birds

Author: Vladimír Remeš, Toni Laaksonen, Frank Adriaensen, Marcel M. Lambrechts, Rianne Pinxten, Tomasz D. Mazgajski, Mariusz Cichoń, Tapio Solonen, Anders Pape Møller, Rimvydas Juškaitis, Blandine Doligez, Anne E. Goodenough, Philipp Heeb, Bernard Leclercq, Marcel Eens, Jordi Camprodon, Shelley A. Hinsley, Alberto Sorace, Sven G. Nilsson, Staffan Jacob, Lars Gustafsson, Ruedi G. Nager, Clotilde Biard, Ana Cláudia Norte, Jan-Åke Nilsson, Andrew G. Gosler, Anna Dubiec, Bruno Massa, Javier Balbontín, Tapio Eeva, Arie J. van Noordwijk, André A. Dhondt, Hugo Robles, Ecologie Systématique et Evolution (ESE), Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Universidad de Sevilla / University of Sevilla, Cornell University [New York], Laboratory of Ornithology, Palacky University Olomouc, Evolutionary Ecology Group, University of Antwerp (UA), Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biodiversity Department, Centre de Ciència i Tecnologia Forestal de Catalunya (CTFC), Institute of Environmental Sciences, Uniwersytet Jagielloński w Krakowie = Jagiellonian University (UJ), Evolution, adaptation et comportement, Département écologie évolutive [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Museum and Institute of Zoology, Polska Akademia Nauk = Polish Academy of Sciences (PAN), Department of Biology (Ethology), Section of Ecology, University of Turku, University of Gloucestershire [Gloucester], Edward Grey Institute of Field Ornithology, University of Oxford, Division of Animal Ecology, Uppsala University, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Station d'écologie théorique et expérimentale (SETE), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-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), Institute of Ecology of Nature Research Centre, Stazione Inanellamento c/o Dipartimento SEN-FIMIZO, Università degli studi di Palermo - University of Palermo, Station Biologique de la Tour du Valat, Animal Ecology, Lund University [Lund], Evolutionary Ecology Group (GIBE), University of A Coruña (UDC), Luontotutkimus Solonen Oy, SROPU, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), 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), 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), DAAA, ONERA, Université Paris Saclay [Meudon], ONERA-Université Paris-Saclay, Universidad de Sevilla, Cornell University, Collège doctoral [Sorbonne universités], Sorbonne Université, Centre Tecnològico Forestal de Catalunya (CTFC), Jagiellonian University [Krakow] (UJ), Université Claude Bernard Lyon 1 - Faculté des sciences et technologies (UCBL FST), Université de Lyon-Université de Lyon, Department of Bioorganic Chemistry Centre of Molecular and Macromolecular Studies Polish Academy of Sciences, Polish Academy of Sciences (PAN), Campus Drie Eiken, University of Gloucestershire (Cheltenham, GB), Institute of Human Sciences, Université Fédérale Toulouse Midi-Pyrénées, Centre for Ecology and Hydrology [Wallingford] (CEH), Natural Environment Research Council (NERC), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Université Fédérale Toulouse Midi-Pyrénées-Centre National d'Études Spatiales [Toulouse] (CNES)-Météo France-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Météo France-Centre National de la Recherche Scientifique (CNRS), University of Glasgow, University of Coimbra [Portugal] (UC), Faculty of Design Sciences [University of Antwerp], ISPRA ROME ITA, 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), Netherlands Institute of Ecology (NIOO-KNAW), Royal Netherlands Academy of Arts and Sciences (KNAW), Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université Paul-Valéry - Montpellier 3 (UPVM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre 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)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Seville, Palacky University, Biogéosciences [UMR 6282] [Dijon] (BGS), 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), Forest Technology Center of Catalonia, Polska Akademia Nauk (PAN), University of Oxford [Oxford], University Basel, Inst Anat, Pestalozzistr, University of Basel (Unibas), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), (Adresse privée), Università di Palermo, Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-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), University of Sevilla, Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (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)-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]), Møller A.P., Balbontín J., Dhondt A.A., Remeš V., Adriaensen F., Biard C., Camprodon J., Cichoń M., Doligez B., Dubiec A., Eens M., Eeva T., Goodenough A.E., Gosler A.G., Gustafsson L., Heeb P., Hinsley S.A., Jacob S., Juškaitis R., Laaksonen T., Leclercq B., Massa B., Mazgajski T.D., Nager R.G., Nilsson J.Å., Nilsson S.G., Norte A.C., Pinxten R., Robles H., Solonen T., Sorace A., van Noordwijk A.J., Lambrechts M.M., and Animal Ecology (AnE)
Subjects: 0106 biological sciences, Avian clutch size, clutch size, nest boxes, Range (biology), media_common.quotation_subject, intraspecific competition, Zoology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, Ecology and Environment, Intraspecific competition, Competition (biology), QH301, Nest, Africa, Northern, Animals, clutch size, density, interspecific competition, intraspecific competition, nest boxes, reaction norm, spatiotemporal variation, Passeriformes, Biology, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, media_common, QL_671, Parus, density, biology, 010604 marine biology & hydrobiology, Reproduction, interspecific competition, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Cyanistes, Interspecific competition, biology.organism_classification, spatiotemporal variation, Europe, Chemistry, Settore AGR/11 - Entomologia Generale E Applicata, reaction norm, international, Animal Science and Zoology, Female, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: Co-existence between great tits Parus major and blue tits Cyanistes caeruleus, \ud but also other hole nesting taxa, constitutes a classic example of species\ud co-occurrence resulting in potential interference and exploitation competition\ud for food and for breeding and roosting sites. However, the spatial and temporal\ud variation in co-existence and its consequences for competition remain poorly\ud understood. 2.We used an extensive database on reproduction in nest boxes by\ud great and blue tits based on 87 study plots across Europe and Northern Africa\ud during 1957-2012 for a total of 19,075 great tit and 16,729 blue tit clutches to \ud assess correlative evidence for a relationship between laying date and clutch\ud size, respectively, and density consistent with effects of intraspecific and\ud interspecific competition. 3.In an initial set of analyses, we statistically\ud controlled for a suite of site specific variables. We found evidence for an\ud effect of intraspecific competition on blue tit laying date (later laying at\ud higher density) and clutch size (smaller clutch size at higher density), but no\ud evidence of significant effects of intraspecific competition in great tits, nor\ud effects of interspecific competition for either species. 4.To further control for\ud site-specific variation caused by a range of potentially confounding variables,\ud we compared means and variances in laying date and clutch size of great and blue \ud tits among three categories of difference in density between the two species. We \ud exploited the fact that means and variances are generally positively correlated. \ud If interspecific competition occurs, we predicted a reduction in mean and an\ud increase in variance in clutch size in great tit and blue tit when density of\ud heterospecifics is higher than the density of conspecifics and for intraspecific \ud competition this reduction would occur when density of conspecifics is higher\ud than the density of heterospecifics. Such comparisons of temporal patterns of\ud means and variances revealed evidence, for both species, consistent with\ud intraspecific competition and to a smaller extent with interspecific competition.\ud 5.These findings suggest that competition associated with reproductive behaviour \ud between blue and great tits is widespread, but also varies across large spatial\ud and temporal scales. This article is protected by copyright.
Published: 2018

6. Toxicity of Food-Grade TiO2 to Commensal Intestinal and Transient Food-Borne Bacteria: New Insights Using Nano-SIMS and Synchrotron UV Fluorescence Imaging

Author: Isabelle Fourquaux, Jacek Bardowski, Jean-Nicolas Audinot, Matthieu Réfrégiers, Frédéric Jamme, Eric Houdeau, Jasper B. J. Kamphuis, Muriel Thomas, Philippe Langella, Muriel Mercier-Bonin, Esther Lentzen, Christel Cartier, Véronique Robert, Magdalena Kowalczyk, Pauline Talbot, Joanna M. Radziwill-Bienkowska, Institute of Biochemistry and Biophysics, Polish Academy of Science, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, ToxAlim (ToxAlim), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Centre de Microscopie Électronique Appliquée à la Biologie (CMEAB), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Hôpital de Rangueil, CHU Toulouse [Toulouse]-CHU Toulouse [Toulouse], Luxembourg Institute of Science and Technology (LIST), Synchrotron SOLEIL (SSOLEIL), Centre National de la Recherche Scientifique (CNRS), Institute of Biochemistry & Biophysics, Polish Academy of Sciences (PAN), Mercier-Bonin, Muriel, Endocrinologie & Toxicologie de la Barrière Intestinale (ToxAlim-ENTeRisk), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Hôpital de Rangueil, CHU Toulouse [Toulouse]-CHU Toulouse [Toulouse]-Toulouse Réseau Imagerie-Genotoul ( TRI-Genotoul), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Neuro-Gastroentérologie & Nutrition (ToxAlim-NGN), INRA of the 'Nutrition, Chemical Food Safety and Consumer Behaviour' Division (AlimH priority program), Polska Akademia Nauk = Polish Academy of Sciences (PAN), Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: 0301 basic medicine, Microbiology (medical), Streptococcus thermophilus, lcsh:QR1-502, [SDV.TOX.TCA]Life Sciences [q-bio]/Toxicology/Toxicology and food chain, 010501 environmental sciences, Gut flora, medicine.disease_cause, bacterial toxicity, 01 natural sciences, Microbiology, lcsh:Microbiology, 03 medical and health sciences, Lactobacillus rhamnosus, medicine, media_common.cataloged_instance, European union, food-grade TiO2, Escherichia coli, 0105 earth and related environmental sciences, media_common, cellular and subcellular bioimaging, biology, Chemistry, Lactococcus lactis, technology, industry, and agriculture, biology.organism_classification, medicine.disease, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, 030104 developmental biology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, 13. Climate action, food-borne bacteria, intestinal bacteria, Dysbiosis, Bacteria
Abstract: Titanium dioxide (TiO2) is commonly used as a food additive (E171 in the EU) for its whitening and opacifying properties. However, a risk of intestinal barrier disruption, including dysbiosis of the gut microbiota, is increasingly suspected because of the presence of a nano-sized fraction in this additive. We hypothesized that food-grade E171 and Aeroxyde P25 (identical to the NM-105 OECD reference nanomaterial in the European Union Joint Research Centre) interact with both commensal intestinal bacteria and transient food-borne bacteria under non-UV-irradiated conditions. Based on differences in their physicochemical properties, we expect a difference in their respective effects. To test these hypotheses, we chose a panel of eight Gram-positive/Gram-negative bacterial strains, isolated from different biotopes and belonging to the species Escherichia coli, Lactobacillus rhamnosus, Lactococcus lactis (subsp. lactis and cremoris), Streptococcus thermophilus, and Lactobacillus sakei. Bacterial cells were exposed to food-grade E171 vs. P25 in vitro and the interactions were explored with innovative (nano)imaging methods. The ability of bacteria to trap TiO2 was demonstrated using synchrotron UV fluorescence imaging with single cell resolution. Subsequent alterations in the growth profiles were shown, notably for the transient food-borne L. lactis and the commensal intestinal E. coli in contact with food-grade TiO2. However, for both species, the reduction in cell cultivability remained moderate, and the morphological and ultrastructural damages, observed with electron microscopy, were restricted to a small number of cells. E. coli exposed to food-grade TiO2 showed some internalization of TiO2 (7% of cells), observed with high-resolution nano-secondary ion mass spectrometry (Nano-SIMS) chemical imaging. Taken together, these data show that E171 may be trapped by commensal and transient food-borne bacteria within the gut. In return, it may induce some physiological alterations in the most sensitive species, with a putative impact on gut microbiota composition and functioning, especially after chronic exposure.
Published: 2018

7. Rattlesnake Phospholipase A2 Increases CFTR-Chloride Channel Current and Corrects ∆F508CFTR Dysfunction: Impact in Cystic Fibrosis

Author: Harald Herrmann, Naziha Bakouh, Aurélie Hatton, Ariel Roldan, Aiswarya Premchandar, Maciej Ostrowski, Jacques Teulon, Mario Ollero, Gergely L. Lukacs, Iwona Pranke, Frederick Saul, Norbert Odolczyk, Pierre-Jean Corringer, Stéphane Lourdel, Sara Bitam, Isabelle Sermet-Gaudelus, Aleksander Edelman, Christelle Moquereau, Haijin Xu, Nathalie Servel, Michal Dadlez, Gabrielle Planelles, Piotr Zielenkiewicz, Grazyna Faure, Récepteurs Canaux - Channel Receptors, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Canalopathies épithéliales: la mucoviscidose et autres maladies, Institut Necker Enfants-Malades (INEM - UM 111 (UMR 8253 / U1151)), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche des Cordeliers (CRC (UMR_S 872)), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institute of Biochemistry & Biophysics, Polish Academy of Sciences (PAN), Cristallographie (Plateforme) - Crystallography (Platform), German Cancer Research Center - Deutsches Krebsforschungszentrum [Heidelberg] (DKFZ), Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Departments of Physiology, McGill University = Université McGill [Montréal, Canada], Institute of Biochemistry and Biophysics, Polska Akademia Nauk = Polish Academy of Sciences (PAN), This work was supported by French Cystic Fibrosis foundations: Vaincre la mucoviscidose and Mucoviscidose ABCF2, and French National Agency grant, CORCF. The research fellowship of M.K.O. was supported by the project 'Enhancing Educational Potential of Nicolaus Copernicus University in Discipline of Mathematical and Natural Sciences' (project no. POKL.04.0101-00-081/10.). M.D. reports support from National Science Center2014/14/A/NZ1/00306MAESTRO grant., Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Génomique, physiologie et physiopathologie rénales, Université Pierre et Marie Curie - Paris 6 (UPMC)-UMRS 872, Cristallographie (Plate-forme), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Friedrich Alexander University [Erlangen-Nürnberg], McGill University, and Polish Academy of Science
Subjects: Male, 0301 basic medicine, chloride channel, phospholipase A(2), Xenopus, Cystic Fibrosis Transmembrane Conductance Regulator, Cystic fibrosis, cystic fibrosis, Mice, Xenopus laevis, Structural Biology, Cyclic AMP, Sequence Deletion, biology, Chemistry, crotoxin, Phospholipase A2 (EC 3.1.1.4), 3. Good health, Cell biology, Molecular Docking Simulation, Biochemistry, Cyclic nucleotide-binding domain, Chloride channel, Female, Ion Channel Gating, Protein Binding, Snake Venoms, congenital, hereditary, and neonatal diseases and abnormalities, Allosteric modulator, biomolecular interactions, Protein subunit, Allosteric regulation, 03 medical and health sciences, Chloride Channels, Cell Line, Tumor, medicine, Animals, Humans, Molecular Biology, Ion channel, 030102 biochemistry & molecular biology, [SCCO.NEUR]Cognitive science/Neuroscience, Crotalus, medicine.disease, biology.organism_classification, Kinetics, Phospholipases A2, 030104 developmental biology, Mutation, Oocytes, HeLa Cells
Abstract: International audience; Deletion of Phe508 in the nucleotide binding domain (∆F508-NBD1) of the cystic fibrosis transmembrane regulator (CFTR; a cyclic AMP-regulated chloride channel) is the most frequent mutation associated with cystic fibrosis. This mutation affects the maturation and gating of CFTR protein. The search for new high-affinity ligands of CFTR acting as dual modulators (correctors/activators) presents a major challenge in the pharmacology of cystic fibrosis. Snake venoms are a rich source of natural multifunctional proteins, potential binders of ion channels. In this study, we identified the CB subunit of crotoxin from Crotalus durissus terrificus as a new ligand and allosteric modulator of CFTR. We showed that CB interacts with NBD1 of both wild type and ∆F508CFTR and increases their chloride channel currents. The potentiating effect of CB on CFTR activity was demonstrated using electrophysiological techniques in Xenopus laevis oocytes, in CFTR-HeLa cells, and ex vivo in mouse colon tissue. The correcting effect of CB was shown by functional rescue of CFTR activity after 24-h ΔF508CFTR treatments with CB. Moreover, the presence of fully glycosylated CFTR was observed. Molecular docking allowed us to propose a model of the complex involving of the ABCβ and F1-like ATP-binding subdomains of ΔF508-NBD1. Hydrogen-deuterium exchange analysis confirmed stabilization in these regions, also showing allosteric stabilization in two other distal regions. Surface plasmon resonance competition studies showed that CB disrupts the ∆F508CFTR-cytokeratin 8 complex, allowing for the escape of ∆F508CFTR from degradation. Therefore CB, as a dual modulator of ΔF508CFTR, constitutes a template for the development of new anti-CF agents.
Published: 2016

8. Clutch-size variation in Western Palaearctic secondary hole-nesting passerine birds in relation to nest box design

Author: Anne E. Goodenough, Alexis S. Chaine, Martyn J. Stenning, Jacques Blondel, Shelley A. Hinsley, Philipp Heeb, Erkki Korpimäki, Olli J. Loukola, Anne Charmantier, Tore Slagsvold, Eduardo Garcia-del-Rey, Paul Isenmann, Carla S. Pimentel, Aya Goldshtein, Arne Lundberg, Jean Charles Bouvier, Andrew F. Russell, Zihad Bouslama, Ilze Priedniece, Jordi Camprodon, Janne T. Seppänen, Markku Orell, Alexandr Artemyev, Camillo Cusimano, Judith Morales-Fernaz, Peter N. Ferns, Vladimír Remeš, Juan Moreno, Frank Adriaensen, János Török, Xavier Morin, Ian R. Hartley, Ruedi G. Nager, Toni Laaksonen, Marcel M. Lambrechts, Christopher M. Perrins, Tapio Eeva, Rimvydas Juškaitis, Seppo Rytkönen, Luís P. da Silva, Arie J. van Noordwijk, Rianne Pinxten, Hugo Robles, Juan Carlos Senar, Bruno Faivre, Piotr Tryjanowski, Andrew G. Gosler, Tapio Solonen, Arnaud Grégoire, Jerzy Bańbura, Alberto Sorace, Staffan Jacob, Sven G. Nilsson, Heinz Richner, Motti Charter, Clotilde Biard, Blandine Doligez, Wiesaw Walankiewicz, Anders Pape Møller, Claire Doutrelant, Cezary Mitrus, Mikael von Numers, Raivo Mänd, Marcel Eens, Lars Gustafsson, Ana Cláudia Norte, Santiago Merino, Mariusz Cichoń, Mikko Mönkkönen, Esa Lehikoinen, Francesco Cecere, Dorota Czeszczewik, Bernard Leclercq, Antero Järvinen, Anna Dubiec, Wojciech Kania, Jan-Åke Nilsson, Indrikis Krams, Iga Góźdź, Philippe Perret, Marie Claude Quidoz, Mark C. Mainwaring, Jukka T. Forsman, Bruno Massa, Tomasz D. Mazgajski, Emilio Barba, Ecologie Systématique et Evolution (ESE), Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Evolutionary Ecology Group, University of Antwerp (UA), Institute of Biology, Russian Academy of Sciences [Moscow] (RAS), Department of Experimental Zoology & Evolutionary Biology, Łódź University of Technology, Terrestrial Vertebrates Research Unit 'Cavanilles', University of Valencia-Institute of Biodiversity and Evolutionary Biology, Laboratoire Ecologie et évolution, Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), 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), 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), 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), Research Laboratory 'Ecology of Terrestrial and Aquatic Systems', University Badji Mokhtar, Unité de recherche Plantes et Systèmes de Culture Horticoles (PSH), Institut National de la Recherche Agronomique (INRA), Biodiversity Department, Centre de Ciència i Tecnologia Forestal de Catalunya (CTFC), Station d’Ecologie Expérimentale du CNRS à Moulis (SEEM), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), University of Haifa [Haifa], Society for the Protection of Nature, Université de Lausanne (UNIL), Institute of Environmental Sciences, Uniwersytet Jagielloński w Krakowie = Jagiellonian University (UJ), Stazione Inanellamento c/o Dipartimento SEN-FIMIZO, Università di Palermo, Department of Zoology, Siedlce University of Natural Sciences and Humanities, Evolution, adaptation et comportement, Département écologie évolutive [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Museum and Institute of Zoology, Polska Akademia Nauk = Polish Academy of Sciences (PAN), Department of Biology (Ethology), Section of Ecology, University of Turku, Biogéosciences [UMR 6282] [Dijon] (BGS), 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), School of Biosciences [Cardiff], Cardiff University, Department of Biology, University of Oulu, Departamento de Ecología, Universidad de La Laguna [Tenerife - SP] (ULL), Tel Aviv University [Tel Aviv], Department of Natural and Social Sciences, University of Gloucestershire, Edward Grey Institute of Field Ornithology-Institute of Human Sciences, Evolutionary Biology Centre, Uppsala University, Lancaster Environment Centre, Lancaster University, Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, The Lodge, RSPB, Kilpisjarvi Biological Station, Institute of Ecology of Nature Research Centre, Ornithological Station, Polska Akademia Nauk = Polish Academy of Sciences (PAN)-Museum and Institute of Zoology, Institute of Ecology & Earth Sciences, University of Tartu, Departamento de Ecología Evolutiva, Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Museo Nacional de Ciencias Naturales (MNCN), Rzeszow University, Department of Biological and Environmental Science [Jyväskylä Univ] (JYU), University of Jyväskylä (JYU), Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Animal Ecology, Lund University [Lund], Department of Life Sciences, University of Coimbra [Portugal] (UC), Centro de Estudos Florestais, Universidade de Lisboa (ULISBOA)-Instituto Superior de Agronomia, Latvian Fund for Nature, Laboratory of Ornithology, Palacky University Olomouc, Institute of Ecology & Evolution (IEE), University of Bern, Unidad Asociada CSIC de Ecología Evolutiva y de la Conducta, Nat-Museu de Ciències Naturals de Barcelona, Department of Biosciences [Oslo], Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO), Luontotutkimus Solonen Oy, SROPU, School of Life Sciences, University of Sussex, Behavioral Ecology Group, Eötvös Loránd University (ELTE), Institute of Zoology, Poznan University of Life Sciences, Netherlands Institute of Ecology, Netherlands Institute of Ecology - NIOO-KNAW (NETHERLANDS), Environmental and Marine Biology, Åbo Academy University, Study supported by Academy of Finland (Project Number 265859), by the Spanish Research Council-CSIC, by the European Social Fund (programme 'Junta para la Ampliacion de Estudios'), by OTKA (Project Number 75618) and by Fundacion Alfonso Martin Escudero and Xunta de Galicia (Angeles Alvarino program and Plan I2C postdoctoral grant)., Ecologie Systématique et Evolution ( ESE ), Université Paris-Sud - Paris 11 ( UP11 ) -AgroParisTech-Centre National de la Recherche Scientifique ( CNRS ), University of Antwerp ( UA ), Russian Academy of Sciences [Moscow] ( RAS ), Ecologie et évolution, École normale supérieure - Paris ( ENS Paris ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), 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 ), Unité Plantes et Systèmes de Culture Horticoles ( PSH ), Institut National de la Recherche Agronomique ( INRA ), Forest Technology Center of Catalonia, Station d'Ecologie Expérimentale du CNRS, Centre National de la Recherche Scientifique ( CNRS ), University of Lausanne, Jagiellonian University [Krakow] ( UJ ), Laboratoire de Biométrie et Biologie Evolutive ( LBBE ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ), Polska Akademia Nauk ( PAN ), Biogéosciences [Dijon] ( BGS ), 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 ), School of Bioscience, Universidad de la Laguna, Evolution et Diversité Biologique ( EDB ), Institut de Recherche pour le Développement ( IRD ) -Université Paul Sabatier - Toulouse 3 ( UPS ) -Centre National de la Recherche Scientifique ( CNRS ), Polska Akademia Nauk ( PAN ) -Museum and Institute of Zoology, Consejo Superior de Investigaciones Científicas [Spain] ( CSIC ) -Museo Nacional de Ciencias Naturales, Department of Biological and Environmental Sciences, University of Jyväskylä, University of Coimbra [Portugal] ( UC ), Instituto Superior de Agronomia-University of Lisbon, Palacky University, Institute of Ecology & Evolution ( IEE ), Department of Biosciences, University of Oslo ( UiO ), Eötvös Loránd University ( ELTE ), Animal Population Biology, Animal Ecology (AnE), 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), Jagiellonian University [Krakow] (UJ), Polska Akademia Nauk (PAN), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Polska Akademia Nauk (PAN)-Museum and Institute of Zoology, Consejo Superior de Investigaciones Científicas [Spain] (CSIC)-Museo Nacional de Ciencias Naturales (MNCN), Møller, AP, Adriaensen, F, Artemyev, A, Bańbura, J, Barba, E, Biard, C, Blondel, J, Bouslama, Z, Bouvier, JC, Camprodon, J, Cecere, C, Chaine, A, Charmantier, A, Charter, M, Cichoń, M, Cusimano, C, Czeszczewik, D, Doligez, B, Doutrelant, C, Dubiec, A, Eens, M, Eeva, T, Faivre, B, Ferns, PN, Forsman, JT, García-del-Rey, E, Goldshtein, A, Goodenough, AE, Gosler, AG, Góźdź, I, Grégoire, A, Gustafsson, L, Hartley, IR, Heeb, P, Hinsley, SA, Isenmann, P, Jacob, S, Järvinen, A, Juškaitis, R, Kania, W, Korpimäki, E, Krams, I, Laaksonen, T, Leclercq, B, Lehikoinen, E, Loukola, O, Lundberg, A, Mainwaring, MC, Mänd, R, Massa, B, Mazgajski, TD, Merino, S, Mitrus, C, Mönkkönen, M, Morales-Fernaz, J, Moreno, J, Morin, X, Nager, RG, Nilsson, JA, Nilsson, SG, Norte, AC, Orell, M, Perret, P, Perrins, CM, Pimentel, CS, Pinxten, R, Priedniece, I, Quidoz, MC, Remeš, V, Richner, H, Robles, H, Russell, A, Rytkönen, S, Senar, JC, Seppänen, JT, Pascoal da Silva, L, Slagsvold, T, Solonen, T, Sorace, A, Stenning, MJ, Török, J, Tryjanowski, P, van Noordwijk, AJ, von Numers, M, Walankiewicz, W, Lambrechts, MM, École normale supérieure - Paris (ENS-PSL), 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), 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), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Lausanne = University of Lausanne (UNIL), Università degli studi di Palermo - University of Palermo, Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Tel Aviv University (TAU), Museo Nacional de Ciencias Naturales [Madrid] (MNCN), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Universidade de Lisboa = University of Lisbon (ULISBOA)-Instituto Superior de Agronomia [Lisboa] (ISA), Universidade de Lisboa = University of Lisbon (ULISBOA), Museu de Ciències Naturals de Barcelona, European Commission, and Consejo Superior de Investigaciones Científicas (España)
Subjects: 0106 biological sciences, Avian clutch size, Nest box floor area, habitat, Nest boxmaterial, 010603 evolutionary biology, 01 natural sciences, 010605 ornithology, [ SDV.EE ] Life Sciences [q-bio]/Ecology, environment, Nest, biology.animal, nest box material, Nest box, Biology, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Geographic location, Parus, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, Latitude, biology, Ecology, Ecological Modeling, [SDV.BA]Life Sciences [q-bio]/Animal biology, longitude, Cyanistes, Ficedula, nest box floor area, latitude, 15. Life on land, biology.organism_classification, Bird nest, Passerine, Habitat, Chemistry, Settore AGR/11 - Entomologia Generale E Applicata, Longitude, geographic location, international, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Hole nesting, natural holes, nest boxes, reaction norm
Abstract: Møller, A.P. [et al.], Secondary hole-nesting birds that do not construct nest holes themselves and hence regularly breed in nest boxes constitute important model systems for field studies in many biological disciplines with hundreds of scientists and amateurs involved. Those research groups are spread over wide geographic areas that experience considerable variation in environmental conditions, and researchers provide nest boxes of varying designs that may inadvertently introduce spatial and temporal variation in reproductive parameters. We quantified the relationship between mean clutch size and nest box size and material after controlling for a range of environmental variables in four of the most widely used model species in the Western Palaearctic: great tit Parus major, blue tit Cyanistes caeruleus, pied flycatcher Ficedula hypoleuca and collared flycatcher F. albicollis from 365 populations and 79 610 clutches. Nest floor area and nest box material varied non-randomly across latitudes and longitudes, showing that scientists did not adopt a random box design. Clutch size increased with nest floor area in great tits, but not in blue tits and flycatchers. Clutch size of blue tits was larger in wooden than in concrete nest boxes. These findings demonstrate that the size of nest boxes and material used to construct nest boxes can differentially affect clutch size in different species. The findings also suggest that the nest box design may affect not only focal species, but also indirectly other species through the effects of nest box design on productivity and therefore potentially population density and hence interspecific competition. © 2014 The Authors. Methods in Ecology and Evolution © 2014 British Ecological Society., J. Morales by the Spanish Research Council-CSIC and the European Social Fund (programme Junta para la Ampliación de Estudios).
Published: 2014

9. Current Methods in the Molecular Typing of Mycobacterium tuberculosis and Other Mycobacteria

Author: Pawel K. Mazur, Tomasz Jagielski, Jacek Bielecki, Jakko van Ingen, Nalin Rastogi, Jarosław Dziadek, Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw (UW)-University of Warsaw (UW), Department of Medical Microbiology, Radboud University Medical Center [Nijmegen], Institut Pasteur de la Guadeloupe, Réseau International des Instituts Pasteur (RIIP), Mycobacterium Genetics and Physiology Unit, Institute of Medical Biology, Polska Akademia Nauk = Polish Academy of Sciences (PAN)-Polska Akademia Nauk = Polish Academy of Sciences (PAN), Department of Genetics [Stanford], Stanford Medicine, Stanford University-Stanford University, University of Warsaw - University of Warsaw, Radboud University Nijmegen Medical Centre, Réseau International des Instituts Pasteur - Institut Pasteur de la Guadeloupe, Polish Academy of Sciences - Polish Academy of Sciences, Department of Genetics, and Stanford University Medical School
Subjects: Tuberculosis, lcsh:Medicine, Computational biology, Review Article, General Biochemistry, Genetics and Molecular Biology, Mycobacterium tuberculosis, Molecular typing, Tuberculosis diagnosis, medicine, Humans, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), General Immunology and Microbiology, biology, Transmission (medicine), lcsh:R, Strain typing, General Medicine, biology.organism_classification, medicine.disease, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Molecular Typing, lnfectious Diseases and Global Health Radboud Institute for Health Sciences [Radboudumc 4], Immunology, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Mycobacterium species, Mycobacterium
Abstract: In the epidemiology of tuberculosis (TB) and nontuberculous mycobacterial (NTM) diseases, as in all infectious diseases, the key issue is to define the source of infection and to disclose its routes of transmission and dissemination in the environment. For this to be accomplished, the ability of discerning and tracking individualMycobacteriumstrains is of critical importance. Molecular typing methods have greatly improved our understanding of the biology of mycobacteria and provide powerful tools to combat the diseases caused by these pathogens. The utility of various typing methods depends on theMycobacteriumspecies under investigation as well as on the research question. For tuberculosis, different methods have different roles in phylogenetic analyses and person-to-person transmission studies. In NTM diseases, most investigations involve the search for environmental sources or phylogenetic relationships. Here, too, the type of setting determines which methodology is most suitable. Within this review, we summarize currently available molecular methods for strain typing ofM. tuberculosisand some NTM species, most commonly associated with human disease. For the various methods, technical practicalities as well as discriminatory power and accomplishments are reviewed.
Published: 2014

10. The design of artificial nestboxes for the study of secondary hole-nesting birds: A review of methodological inconsistencies and potential biases

Author: Jean Charles Bouvier, Martyn J. Stenning, Caren B. Cooper, Chan Ryul Park, Christopher M. Perrins, Tapio Eeva, Marcel M. Lambrechts, Beat Naef-Daenzer, Emilio Barba, Bengt Silverin, Henrik G. Smith, Arie J. van Noordwijk, L. Scott Johnson, Jordi Camprodon, Anders Pape Møller, Charles F. Thompson, Paulo E. Llambías, Anne E. Goodenough, Oskars Keišs, Bruno Faivre, Jaime Potti, Jan Ke Nilsson, Francisco Atiénzar, Nadia Ziane, Jerzy Bańbura, Alberto Sorace, Tore Slagsvold, Daniel R. Ardia, Arnaud Grégoire, Simon C. Griffith, Lars Gustafsson, Frank Adriaensen, János Török, Marcel Eens, Markku Orell, Alexandr Artemyev, Heinz Richner, Jan Pinowski, Andrew G. Gosler, Ian R. K. Stewart, Vladimír Remeš, Juan Moreno, Jiri Porkert, Seppo Rytkönen, Tomasz D. Mazgajski, David W. Winkler, Bruno Massa, Russell D. Dawson, Ken A. Otter, Ming Tang Shiao, László Zsolt Garamszegi, Piotr Tryjanowski, Wojciech Kania, Mark C. Mainwaring, Raivo Mänd, Ana Cláudia Norte, Animal Ecology (AnE), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-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), Evolutionary Ecology Group, University of Antwerp (UA), Department of Biology, Franklin & Marshall College, Institute of Biology, Russian Academy of Sciences [Moscow] (RAS), Terrestrial Vertebrates Research Unit 'Cavanilles', University of Valencia-Institute of Biodiversity and Evolutionary Biology, Department of Experimental Zoology & Evolutionary Biology, Łódź University of Technology, Unité de recherche Plantes et Systèmes de Culture Horticoles (PSH), Institut National de la Recherche Agronomique (INRA), Biodiversity Department, Forest Technology Center of Catalonia, Cornell Laboratory of Ornithology, Cornell University, Ecosystem Science and Management Program, University of Northern British Columbia (UNBC), Department of Biology (Ethology), Section of Ecology, University of Turku, Biogéosciences [UMR 6282] [Dijon] (BGS), 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), Department of Evolutionary Ecology, Estacion Biologica de Donana, Department of Natural and Social Sciences, University of Gloucestershire, Department of Zoology, Edward Grey Institute of Field Ornithology-Institute of Human Sciences, Department of Brain, Behaviour and Evolution, Macquarie University, Evolutionary Biology Centre, Uppsala University, Towson University [Towson, MD, United States], University of Maryland System-University of Maryland System, Ornithological Station, Polska Akademia Nauk (PAN)-Museum and Institute of Zoology, Laboratory of Ornithology, University of Latvia (LU), Ecologia del Comportamiento Animal, Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Lancaster Environment Centre, Lancaster University, University of Tartu, Stazione Inanellamento c/o Dipartimento SEN-FIMIZO, Università di Palermo, Museum and Institute of Zoology, Polska Akademia Nauk (PAN), Ecologie Systématique et Evolution (ESE), Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Center for Advanced Study, Departamento de Ecología Evolutiva, Consejo Superior de Investigaciones Científicas [Spain] (CSIC)-Museo Nacional de Ciencias Naturales (MNCN), Swiss Ornithological Institute, Animal Ecology, Lund University [Lund], Department of Life Sciences, University of Coimbra [Portugal] (UC), University of Oulu, Warm-temperate Forest Research Center, Korea Forest Research Institute, Center of Ecological Research, Palacky University, Institute of Ecology & Evolution (IEE), University of Bern, Wildlife laboratory, National Taiwan University [Taiwan] (NTU), University of Gothenburg (GU), Department of Biosciences [Oslo], Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO), School of Life Sciences, University of Sussex, University of Kentucky, Behavior, Ecology, Evolution, and Systematics Section, Illinois State University, Behavioural Ecology Group, Eötvös Loránd University (ELTE), Institute of Zoology, Poznan University of Life Sciences, Netherlands Institute of Ecology, Laboratory of Ornithology and Department of Ecology & Evolutionary Biology, Laboratoire d'Ecophysiologie animale, Département de Biologie, Lambrechts, M M, Adriaensen, F, Ardia, D R, Artemyev, A V, Atiénzar, F, Bańbura, J, Barba, E, Bouvier, J-C, Camprodon, J, Cooper, C B, Dawson, R D, Eens, M, Eeva, T, Faivre, B, Garamszegi, L Z, Goodenough, A E, Gosler, A G, Grégoire, A, Griffith, S C, Gustafsson, L, Johnson, L S, Kania, W, Keišs, O, Llambias, P E, Mainwaring, M C, Mänd, R, Massa, B, Mazgajski, T D, Møller, A P, Moreno, J, Naef-Daenzer, B, Nilsson, J-C, Norte, A C, Orell, M, Otter, K A, Park, Ch R, Perrins, Ch M, Pinowski, J, Porkert, J, Potti, J, Remes, V, Richner, H, Rytkönen, S, Shiao, M-T, Silverin, B, Slagsvold, T, Smith, H G, Sorace, A, Stenning, M J, Stewart, I, Thompson, Ch F, Török, J, Tryjanowski, P, van Noordwijk, A J, Winkler, D W, Ziane, N, 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 Ciència i Tecnologia Forestal de Catalunya (CTFC), Cornell University [New York], University of Northern British Columbia [Prince George] (UNBC), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Polska Akademia Nauk = Polish Academy of Sciences (PAN)-Museum and Institute of Zoology, Polska Akademia Nauk = Polish Academy of Sciences (PAN), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Museo Nacional de Ciencias Naturales (MNCN), Palacky University Olomouc, Centre d’Ecologie Fonctionnelle et Evolutive ( CEFE ), Université Paul-Valéry - Montpellier 3 ( UM3 ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -École pratique des hautes études ( EPHE ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -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 ), University of Antwerp ( UA ), Russian Academy of Sciences [Moscow] ( RAS ), Unité de recherche Plantes et Systèmes de Culture Horticoles ( PSH ), Institut National de la Recherche Agronomique ( INRA ), University of Northern British Columbia ( UNBC ), Biogéosciences [Dijon] ( BGS ), 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 ), Polska Akademia Nauk ( PAN ) -Museum and Institute of Zoology, University of Latvia ( LU ), Consejo Nacional de Investigaciones Científicas y Técnicas ( CONICET ), Polska Akademia Nauk ( PAN ), Ecologie Systématique et Evolution ( ESE ), Université Paris-Sud - Paris 11 ( UP11 ) -AgroParisTech-Centre National de la Recherche Scientifique ( CNRS ), Consejo Superior de Investigaciones Científicas [Spain] ( CSIC ) -Museo Nacional de Ciencias Naturales, University of Coimbra [Portugal] ( UC ), Institute of Ecology & Evolution ( IEE ), National Taiwan University [Taiwan] ( NTU ), University of Gothenburg ( GU ), Department of Biosciences, University of Oslo ( UiO ), Eötvös Loránd University ( ELTE ), and Cornell University Museum of Vertebrates
Subjects: PASSERINES, 0106 biological sciences, Nest-box, design, measures, PARUS, SECONDARY CAVITY-NESTING BIRDS, Otras Ciencias Biológicas, NEST SITES, FLYCATCHER, Ficedula, 010603 evolutionary biology, 01 natural sciences, [ SDV.EE ] Life Sciences [q-bio]/Ecology, environment, 010605 ornithology, methods, field experiments, Ciencias Biológicas, nestboxes, tit, Cyanistes, Research based, Statistics, NESTBOXES, FIELD EXPERIMENTS, Nest box, Biological sciences, Biology, secondary cavity-nesting birds, FICEDULA, Parus, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, biology, Ecology, nest sites, passerines, biology.organism_classification, 3. Good health, TIT, Settore AGR/11 - Entomologia Generale E Applicata, CYANISTES, flycatcher, METHODS, Nesting (computing), Animal Science and Zoology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, CIENCIAS NATURALES Y EXACTAS
Abstract: The widespread use of artificial nestboxes has led to significant advances in our knowledge of the ecology, behaviour and physiology of cavity nesting birds, especially small passerines. Nestboxes have made it easier to perform routine monitoring and experimental manipulation of eggs or nestlings, and also repeatedly to capture, identify and manipulate the parents. However, when comparing results across study sites the use of nestboxes may also introduce a potentially significant confounding variable in the form of differences in nestbox design amongst studies, such as their physical dimensions, placement height, and the way in which they are constructed and maintained. However, the use of nestboxes may also introduce an unconsidered and potentially significant confounding variable due to differences in nestbox design amongst studies, such as their physical dimensions, placement height, and the way in which they are constructed and maintained. Here we review to what extent the characteristics of artificial nestboxes (e.g. size, shape, construction material, colour) are documented in the 'methods' sections of publications involving hole-nesting passerine birds using natural or excavated cavities or artificial nestboxes for reproduction and roosting. Despite explicit previous recommendations that authors describe in detail the characteristics of the nestboxes used, we found that the description of nestbox characteristics in most recent publications remains poor and insufficient. We therefore list the types of descriptive data that should be included in the methods sections of relevant manuscripts and justify this by discussing how variation in nestbox characteristics can affect or confound conclusions from nestbox studies. We also propose several recommendations to improve the reliability and usefulness of research based on long-term studies of any secondary hole-nesting species using artificial nestboxes for breeding or roosting.
Published: 2010

11. The structure of a DnaA/HobA complex from Helicobacter pylori provides insight into regulation of DNA replication in bacteria

Author: Marie-Françoise Noirot-Gros, Laurent Terradot, Ganesh Natrajan, Ulrike Kapp, Anna Zawilak-Pawlik, European Synchroton Radiation Facility [Grenoble] (ESRF), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut of Mathematics - Polish Academy of Sciences (PAN), Polska Akademia Nauk = Polish Academy of Sciences (PAN), and We thank members of the MX group at ESRF for help during data collection and the Partnership for Structural biology (PSB) for support. We also thank G. Waksman, J. Timmins, and G. Leonard for critical comments on the manuscript. This work was supported by the ESRF 'In House Research' program. Support was provided by the Foundation for Polish Science ( to A.Z.P.) and by a grant from Iceland, Lichtenstein, and Norway through the EEA Financial Mechanism ( to F.N.P.) and the Ministry of Science and Higher Education ( project N N301 029334).
Subjects: DNA Replication, DNA, Bacterial, [SDV]Life Sciences [q-bio], genetic processes, Replication Origin, Plasma protein binding, Biology, Pre-replication complex, Crystallography, X-Ray, DNA-binding protein, 03 medical and health sciences, Bacterial Proteins, Binding site, replication regulators, DiaA, dnaB helicase, 030304 developmental biology, X-ray crystallography, Genetics, 0303 health sciences, Multidisciplinary, Binding Sites, Helicobacter pylori, 030306 microbiology, Mutagenesis, DNA replication, Biological Sciences, DnaA, Cell biology, isothermal titration calorimetry, DNA-Binding Proteins, health occupations, bacteria, Protein Multimerization, Protein Binding
Abstract: Bacterial DNA replication requires DnaA, an AAA+ ATPase that initiates replication at a specific chromosome region, oriC , and is regulated by species-specific regulators that directly bind DnaA. HobA is a DnaA binding protein, recently identified as an essential regulator of DNA replication in Helicobacter pylori . We report the crystal structure of HobA in complex with domains I and II of DnaA (DnaA I–II ) from H. pylori , the first structure of DnaA bound to one of its regulators. Biochemical characterization of the complex formed shows that a tetramer of HobA binds four DnaA I–II molecules, and that DnaA I–II is unable to oligomerize by itself. Mutagenesis and protein–protein interaction studies demonstrate that some of the residues located at the HobA-DnaA I–II interface in the structure are necessary for complex formation. Introduction of selected mutations into H. pylori shows that the disruption of the interaction between HobA and DnaA is lethal for the bacteria. Remarkably, the DnaA binding site of HobA is conserved in DiaA from Escherichia coli , suggesting that the structure of the HobA/DnaA complex represents a model for DnaA regulation in other Gram-negative bacteria. Our data, together with those from other studies, indicate that HobA could play a crucial scaffolding role during the initiation of replication in H. pylori by organizing the first step of DnaA oligomerization and attachment to oriC .
Published: 2009

12. Rsp5p ubiquitin ligase and the transcriptional activators Spt23p and Mga2p are involved in co-regulation of biosynthesis of end products of the mevalonate pathway and triacylglycerol in yeast Saccharomyces cerevisiae

Author: Thierry Ferreira, Thierry Bergès, Teresa Zołądek, Anna Szkopinska, Pawel Kaliszewski, Ewa Świeżewska, Department of lipid Biochemistry, Polska Akademia Nauk = Polish Academy of Sciences (PAN)-Institute of Biochemistry and Biophysics, Physiologie Moléculaire du Transport des Sucres chez les Végétaux (PhyMoTS), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Institute of Biochemistry and Biophysics, and Polska Akademia Nauk = Polish Academy of Sciences (PAN)
Subjects: MESH: Dimethylallyltranstransferase, Ubiquinone, MESH: Ergosterol, MESH: Endosomal Sorting Complexes Required for Transport, chemistry.chemical_compound, MESH: Saccharomyces cerevisiae Proteins, Dolichols, Ergosterol, MESH: Ubiquinone, Overproduction, MESH: Dolichol, MESH: Lipid Metabolism, 0303 health sciences, biology, 030302 biochemistry & molecular biology, Ubiquitin-Protein Ligase Complexes, MESH: Transcription Factors, MESH: Mevalonic Acid, MESH: Saccharomyces cerevisiae, Ubiquitin ligase, Sterols, Biochemistry, lipids (amino acids, peptides, and proteins), MESH: Biosynthetic Pathways, Mevalonate pathway, MESH: Membrane Proteins, MESH: Triglycerides, Saccharomyces cerevisiae Proteins, MESH: Mutation, MESH: Trans-Activators, Saccharomyces cerevisiae, Mevalonic Acid, MESH: Cytoplasmic Granules, MESH: Transformation, Genetic, MESH: Alkyl and Aryl Transferases, Cytoplasmic Granules, 03 medical and health sciences, Transformation, Genetic, Biosynthesis, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Molecular Biology, Triglycerides, 030304 developmental biology, Alkyl and Aryl Transferases, Endosomal Sorting Complexes Required for Transport, Membrane Proteins, Lipid metabolism, MESH: Ubiquitin-Protein Ligase Complexes, Cell Biology, biology.organism_classification, Dimethylallyltranstransferase, Lipid Metabolism, Yeast, Biosynthetic Pathways, chemistry, MESH: Sterols, Mutation, biology.protein, Trans-Activators, Transcription Factors
Abstract: International audience; Rsp5p, a yeast S. cerevisiae ubiquitin ligase, is essential for regulation of unsaturated fatty acid synthesis via activation of the transcriptional activators Spt23p and Mga2p. Here we show that the conditional mutant rsp5-19 produces decreased levels of the end products of mevalonate pathway, such as ergosterol, ubiquinone and of dolichols, especially those with 19-24 isoprene units. The mechanism of Rsp5p involvement in the control of these lipid synthesis pathways was addressed by overproduction of Rsp5p-independent Spt23p or Mga2p. Expression of constitutively active forms of these transactivators resulted in excess production of ergosterol, but did not restore a wild-type level of dolichols. Moreover, synthesis of long chain dolichols was decreased in the wild-type and a rsp5-19 background. Finally, overproduction of active Spt23p or Mga2p was accompanied by the appearance of large lipid particles in the wild-type and rsp5-19 strains as observed by Nile Red staining, due to accumulation of unsaturated triacylglycerol. Thus, we conclude that Rsp5p, Spt23p and Mga2p may participate in the control of the homeostasis of lipids and lipid particles.
Published: 2008

13. The 100K-chaperone protein from Adenovirus serotype 2 (subgroup C) assists in trimerization and nuclear localization of hexons from subgroups C and B adenoviruses

Author: S. Myhre, Rob W.H. Ruigrok, Leif Lindholm, Pierre Boulanger, Saw See Hong, Laure Franqueville, Ewa Szolajska, Guy Schoehn, Jadwiga Chroboczek, Virologie et pathogenèse virale (VPV), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Institute of Biochemistry and Biophysics, Polska Akademia Nauk = Polish Academy of Sciences (PAN), Institut de biologie structurale (IBS - UMR 5075 ), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de virologie moléculaire et structurale (LVMS), Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), Department of Medical Microbiology and Immunology [Göteborg], University of Gothenburg (GU), Got-A-Gene AB, Stena Center 1B, E.S. was supported by fellowships from the EMBO, FEBS and FRM (Fondation pour la Recherche Médicale), successively. We are indebted to J.-P. Andrieu for the N-terminal amino acid analysis and to B. Dublet for mass spectrometry. We are indebted to Dr Felipe Andrade (Department of Immunology and Rheumatology, Instituto Nacional de Ciencias Medicas y Nutricion 'Salvador Zubiran', Mexico City, Mexico) for the gift of anti-100K polyclonal antibody and to Professor Willie Russell (University of St. Andrews, Scotland) for the anti-hexon monoclonal antibody 4C3. This work was supported, in part, by grants from VLM (French Foundation for Cystic Fibrosis, Contract no. TG-0402), and AFM (Association Française contre les Myopathies, Contracts no. D09481A/S00634 and D10902A/S00634)., Virologie et Pathologie Humaine (VirPath), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Got-a-Gene AB, Department of Microbiology and Immunology, Laboratoire de Virologie Moléculaire et Structurale, FRE 2854 CNRS/UJF, c/o EMBL BP 181, 38042 Grenoble Cedex 9, France, Polska Akademia Nauk = Polish Academy of Sciences (PAN)-Sciences, FRE 2854 CNRS/UJF, Laboratoire de Virologie-Moleculaire et Structurale, Stena Center, EMBO, FEBS and FRM (Fondation pour la Recherche Me´dicale), successively. We are indebted to J.-P. Andrieu for the N-terminal amino acid analysis and to B. Dublet for mass spectrometry.We are indebted to Dr Felipe Andrade (Department of Immunology and Rheumatology, Instituto Nacional de Ciencias Medicas y Nutricion 'Salvador Zubiran', Mexico City, Mexico) for the gift of anti- 100K polyclonal antibody and to Professor Willie Russell (University of St. Andrews, Scotland) for the anti-hexon monoclonal antibody 4C3. This work was supported, in part, by grants from VLM (French Foundation for Cystic Fibrosis, Contract no. TG-0402), and AFM (Association Franc¸aise contre les Myopathies, Contracts no. D09481A/ S00634 and D10902A/S00634)., Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Scaffold protein, Insecta, Time Factors, viruses, Viral/chemistry/metabolism, Inclusion bodies, law.invention, Structural Biology, law, Hexon protein, OCIS 000.1430, Antigens, Viral, Cells, Cultured, ComputingMilieux_MISCELLANEOUS, 0303 health sciences, Cultured, biology, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], 030302 biochemistry & molecular biology, virus diseases, Recombinant Proteins, Insects, Biochemistry, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Recombinant DNA, Recombinant Proteins/chemistry/metabolism, Capsid Proteins/chemistry/*metabolism, Cells, Adenoviridae/chemistry/classification/*metabolism/ultrastructure, Adenoviridae, 03 medical and health sciences, Capsid, Humans, Animals, Molecular Chaperones/chemistry/*metabolism, Antigens, Molecular Biology, 030304 developmental biology, Capsomere, Capsid/chemistry/ultrastructure, Molecular biology, eye diseases, Molecular Weight, stomatognathic diseases, Cytoplasm, Chaperone (protein), biology.protein, Capsid Proteins, Nuclear localization sequence, Molecular Chaperones
Abstract: Recombinant hexons from subgroup C adenoviruses (Ad2 and Ad5) and from a member of subgroup B (Ad3) adenoviruses have been expressed in insect cells. When expressed alone, all three hexons were found to be insoluble and accumulated as inclusion bodies in the cytoplasm. However, co-expression of recombinant Ad2, Ad5 or Ad3 hexon with Ad2 L4-100K protein resulted in the formation of soluble trimeric hexons. EM analysis of hexons revealed that they were indistinguishable from native hexon capsomers isolated from Ad2-infected human cells, or released from partially disrupted adenovirions. This suggests that 100K acts as a chaperone for hexon folding and self-assembly into capsomer in insect cells. Since 100K protein assists in the trimerization of subgroup C hexon, and of subgroup B hexon protein, it implies that it functions in a manner that is both homo- and heterotypic. During the course of recombinant protein expression, the 100K protein was found in association with hexon monomers and trimers within the cytoplasm. In the nucleus, however, 100K was found in complexes with hexon trimers exclusively. EM observation of purified 100K protein samples showed a dumb-bell-shaped molecule compatible with a monomeric protein. EM analysis of hexon-100K protein complexes showed that interaction of hexon with the 100K protein occurred via one of the globular domains of the 100K protein molecule. Our data confirm the role of the 100K protein as a scaffold protein for hexon, and provide evidence suggesting its function in hexon nuclear import in insect cells.
Published: 2005

14. Phylogeography of a widespread Palaearctic forest bird species: The White‐backed Woodpecker (Aves, Picidae)

Author: Jean-Marc Pons, Hans Winkler, Antonia Ettwein, Giorgio Chiozzi, Łukasz Kajtoch, David Campión, Tomasz D. Mazgajski, Jérôme Fuchs, Marko Raković, Jean-Louis Grangé, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Swiss Ornithological Institute, and Polish Academy of Sciences (PAN)
Subjects: 0106 biological sciences, 0301 basic medicine, education.field_of_study, biology, [SDV]Life Sciences [q-bio], Biogeography, Population, Zoology, Dendrocopos leucotos, 15. Life on land, Woodpecker, Subspecies, Dendrocopos, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Phylogeography, 030104 developmental biology, Refugium (population biology), Genetics, Animal Science and Zoology, education, Molecular Biology, Ecology, Evolution, Behavior and Systematics
Abstract: International audience; We use multilocus molecular data and species distribution modelling to investigate the phylogenetics and the phylogeography of the White‐backed Woodpecker (Dendrocopos leucotos), a bird species widely distributed over the entire Palaearctic. Our phylogenetic results reveal three well‐supported clades within D. leucotos: the Chinese endemic subspecies (tangi, insularis), the northerly distributed subspecies (leucotos, uralensis) and the four poorly genetically differentiated Japanese subspecies (subcirris, stejnegeri, namiyei, owstoni), and the south‐western Palaearctic lilfordi subspecies. According to our results, the Amami Woodpecker, endemic to Amami Oshima Island (Ryukyu archipelago, Japan) sometimes treated as full species Dendrocopos owstoni, does not deserve a species‐level status. Based on the mitochondrial phylogeographic results, the Japanese archipelago was recently colonized only once by D. leucotos from eastern Eurasia. Our results suggest a split between the leucotos and lilfordi lineages that dates back to mid‐Pleistocene (around 0.6 Mya) with likely no gene flow between these two subspecies since then. Our results thus do not support a phylogeographic pattern in which Central Europe and Northern Europe were recolonized from one or several southern glacial refugia where lilfordi populations persisted through several Pleistocene glacial periods. Spatial variation in mitochondrial diversity across leucotos/uralensis populations and niche ecological modelling suggest a possible eastward population expansion from a unique glacial refugium likely located in Central Europe. Molecular species delimitation methods, gene flow analyses and differences in adult and juvenile plumage indicate that the lilfordi subspecies may warrant to be ranked as a valid phylogenetic species. Further studies are nevertheless needed in the Balkans, where leucotos and lilfordi came recently into contact to measure the effectiveness of reproductive barriers and gene flow.
Published: 2020

15. Alcohol intoxication resistance and alcohol dehydrogenase levels differ between the honeybee castes

Author: Laura Pardyak, Karolina Kuszewska, Daniel Stec, Krzysztof Miler, Alicja Kamińska, Institute of Systematics and Evolution of Animals, Polska Akademia Nauk = Polish Academy of Sciences (PAN), and Uniwersytet Jagielloński w Krakowie = Jagiellonian University (UJ)
Subjects: 0301 basic medicine, alcoholism, Age differences, Physiology, Alcohol, honeybee, Biology, medicine.disease, tolerance effect, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, 03 medical and health sciences, chemistry.chemical_compound, 030104 developmental biology, 0302 clinical medicine, Alcohol intoxication, intoxication, chemistry, Insect Science, medicine, biology.protein, ethanol, 030217 neurology & neurosurgery, Alcohol dehydrogenase
Abstract: Various animal models are used in the study of alcoholism, with the honeybee (Apis mellifera L.) among them. Here, we tested the hypothesis that foragers show higher intoxication resistance to alcohol than nurses, an issue thus far not investigated. To this end, we measured the latency to full sedation when exposed to alcohol in foragers, nurses and reverted nurses. In addition, we measured alcohol dehydrogenase (ADH) levels in these worker castes. Caste status was confirmed by comparison of the size of their hypopharyngeal glands. We detected high intoxication resistance to alcohol and presence of ADH in foragers. In nurses, we detected significantly lower intoxication resistance to alcohol and no ADH. These between-caste differences cannot be explained by the age difference between castes as in reverted nurses, characterized by similar age to foragers, we detected an intermediate intoxication resistance to alcohol and no ADH. Our results suggest possible natural exposure to alcohol in different castes of workers. As such, we further develop the honeybee as a model in alcoholism-related research and open new research avenues.
Published: 2020

16. Repeated hormonal induction of spermiation affects the stress but not the immune response in pikeperch (Sander lucioperca)

Author: Zoltán Bokor, Gergely Bernáth, Pascal Fontaine, Syaghalirwa N. M. Mandiki, Imen Ben Ammar, Daniel Żarski, Ákos Horváth, Katarzyna Palińska-Żarska, Sébastien Baekelandt, Patrick Kestemont, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences (PAN), Biologie environnementale et évolutive (URBE), Département de Biologie, Université de Namur [Namur] (UNamur)-Université de Namur [Namur] (UNamur), Szent István University, University of Warmia and Mazury [Olsztyn], Unité de Recherches Animal et Fonctionnalités des Produits Animaux (URAFPA), and Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Male, 0301 basic medicine, endocrine system, Sperm quality, hCG, sGnRHa, Aquatic Science, Biology, Chorionic Gonadotropin, Human chorionic gonadotropin, Gonadotropin-Releasing Hormone, Andrology, 03 medical and health sciences, Immune system, Stress, Physiological, Animals, Environmental Chemistry, Endocrine system, Percids, Spermatogenesis, Testosterone, Innate immune system, Immunity, 04 agricultural and veterinary sciences, General Medicine, Sperm, 3. Good health, Semen Analysis, 030104 developmental biology, Perches, [SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies, Sperm Motility, 040102 fisheries, 0401 agriculture, forestry, and fisheries, Hormone
Abstract: Hormonal induction of spermiation, previously reported to be immunogenic in fishes, is a common hatchery practice in pikeperch, Sander lucioperca. The aim of the present study was to investigate the effects of repeated induction of spermiation in pikeperch, following application of either human chorionic gonadotropin (hCG) or salmon gonadoliberine analogue (sGnRHa) on sperm quality indices as well as on immune and stress response. Mature males of pikeperch (n = 7 per group) were stimulated twice with five days between injections of either hCG (hCG; 500 IU kg−1), sGnRHa (sGnRHa; 50 μg kg−1) or NaCl (control group; 1 ml kg−1) to assess spermatozoa motility with a computer-assisted sperm analysis (CASA) system. During second sampling, blood plasma was sampled for humoral innate immune (peroxidase and lysozyme activities, ACH50), stress (cortisol, glucose) and endocrine (testosterone) markers. In addition, the head kidney was dissected to assay the expression of several immune genes (such as il1, c3, hamp, tnf-α and lys genes). The results indicate that hormonal treatment significantly increased sperm production. Sperm sampled after the hormonal treatment maintained its quality throughout the study, regardless of the sampling time. However, it appears that the application of hCG induced elevated cortisol and glucose plasma levels compared to the control group. Almost all immune markers, except the relative expression of hepcidin (hamp gene), were unaffected by the two hormones applied. The results showed that the induction treatment of spermiation processes in pikeperch resulted in an important physiological stress response for which the intensity varied according to the hormonal agent used. However, this stress response (more profound following application of hCG) was weakly associated with innate immune functions. On the other hand, a significant negative correlation between the expression of several important immune markers (peroxidase activity, relative expression of c3 and il1 genes) and sperm quality indices indicates significant involvement of immune status on sperm quality. The results obtained shed light on immune-system-induced modifications to sperm quality. The data presented here highlight the need for careful revision of broodstock management and selection practices where welfare status as well as individual predispositions of fish to cope with the stress should be taken under the consideration.
Published: 2020

17. Promotion through external magnetic field of osteogenic differentiation potential in adipose‐derived mesenchymal stem cells: Design of polyurethane/poly(lactic) acid sponges doped with iron oxide nanoparticles

Author: Michael Roecken, Michalina Alicka, Krzysztof Marycz, Katarzyna Kornicka-Garbowska, Rafal J. Wiglusz, Joanna Polnar, Anna Lis-Bartos, Jean-Marie Nedelec, Institut de Chimie de Clermont-Ferrand - Clermont Auvergne (ICCF), Sigma CLERMONT (Sigma CLERMONT)-Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), Wroclaw University of Environmental and Life Sciences, AGH University of Science and Technology [Krakow, PL] (AGH UST), Institute of Low Temperature and Structure Research [Polish Academy of Sciences], Polska Akademia Nauk = Polish Academy of Sciences (PAN), Justus Liebig University Giessen, Institut de Chimie de Clermont-Ferrand (ICCF), SIGMA Clermont (SIGMA Clermont)-Institut de Chimie du CNRS (INC)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Institute of Low Temperature and Structure Research, Polish Academy of Sciences, Wroclaw, and Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-SIGMA Clermont (SIGMA Clermont)
Subjects: Male, Materials science, Polyesters, Polyurethanes, Biomedical Engineering, 02 engineering and technology, Regenerative medicine, Bone morphogenetic protein 2, Biomaterials, Mice, 03 medical and health sciences, Thermoplastic polyurethane, chemistry.chemical_compound, Osteogenesis, Animals, [CHIM]Chemical Sciences, Osteopontin, Magnetite Nanoparticles, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, biology, Mesenchymal stem cell, technology, industry, and agriculture, Biomaterial, Cell Differentiation, Mesenchymal Stem Cells, [CHIM.MATE]Chemical Sciences/Material chemistry, equipment and supplies, 021001 nanoscience & nanotechnology, 3. Good health, Lactic acid, Magnetic Fields, Adipose Tissue, chemistry, Biophysics, biology.protein, Female, lipids (amino acids, peptides, and proteins), 0210 nano-technology, Iron oxide nanoparticles
Abstract: International audience; Recently, iron oxide nanoparticles (IONPs) have gathered special attention in regenerative medicine. Owing to their magnetic and bioactive properties, IONPs are utilized in the fabrication of novel biomaterials. Yet, there was no report regarding thermoplastic polyurethane (TPU) and poly(lactic acid) (PLA) polymer doped with IONPs on osteogenic differentiation of mesenchymal stem cells. Thus the objectives of presented study was to: (a) fabricate magnetic TPU + PLA sponges doped with iron (III) oxide Fe2O3 nanoparticles; (b) investigate the effects of biomaterial and its exposition to static magnetic field (MF) on osteogenic differentiation, proliferation, and apoptosis in adipose‐derived mesenchymal stem cells (ASCs). TPU + PLA sponges were prepared using solvent casting technique while incorporation of the Fe2O3 nanoparticles was performed with solution cast method. RT‐PCR was applied to evaluate expression of osteogenic‐related genes and integrin's in cells cultured on fabricated materials with or without the stimulation of static MF. MF stimulation enhanced the expression of osteopontin and collagen type I while decreased expression of bone morphogenetic protein 2 in tested magnetic materials—TPU + PLA/1% Fe2O3 and TPU + PLA/5% Fe2O3. Therefore, TPU + PLA sponges doped with IONPs and exposure to MF resulted in improved osteogenic differentiation of ASC.
Published: 2020

18. Toward next-generation primate neuroscience: A collaboration-based strategic plan for integrative neuroimaging

Author: David C. Van Essen, Caspar M. Schwiedrzik, Takuro Ikeda, Shaomin Zhang, Marcello G. P. Rosa, Ning Liu, Aidan Murphy, Li Min Chen, Pinglei Bao, Julia Lehman, Yuki Hori, Pengcheng Li, Julien Vezoli, Peter H. Rudebeck, Yao Meng, Julian 'Bene' Ramirez, Pierre Pouget, Guillermo Gallardo, Rogier B. Mars, Charles E. Schroeder, Minqing Jiang, Steve Frey, Michael P. Milham, Mohammad Hadi Aarabi, Pascal Belin, Patrick Friedrich, Bichan Wu, Hector Figueroa, Ye He, Charles L. Wilson, Melanie Wilke, Eunha Baeg, Fadila Hadj-Bouziane, Danny Garside, Marco Pagani, Ting-Yat Wong, Igor Kagan, Abdelhadi Essamlali, Bharat B. Biswal, Wasana Ediri Arachchi, Julio Villalon, Zheng Wang, Kacie Dougherty, Neo Sunhang Shi, Luciano Simone, Roberto Toro, Benjamin Jung, Masaki Fukunaga, Zhanguang Zuo, Loïc Magrou, Xiaowei Song, Kadharbatcha S. Saleem, Michele A. Basso, Eduardo A. Garza-Villarreal, Chihiro Yokoyama, Aaron Tanenbaum, Brian E. Russ, Alexandre Rosa Franco, Alison R. Weiss, Isabel Restrepo, Alan C. Evans, Lixia Gao, Nobuyuki Kimura, Augix Guohua Xu, Piotr Majka, Colline Poirier, Justine Cléry, Bassem Hiba, Alessandro Gozzi, Xiaojie Wang, Nick Upright, Stan Colcombe, Yang Gao, Won Mok Shim, Eduardo Rojas Hortelano, Takuya Hayashi, Anna S. Mitchell, Andrew F. Rossi, Itamar Kahn, Jorge Jaramillo, Henry C. Evrard, Xin Yumeng, Gregory Kiar, Sean Froudist-Walsh, Elise Roger, Roberto A. Gulli, Yufan Wang, Damien A. Fair, Yuguang Zhao, Stephen J. Sawiak, Boris C. Bernhardt, Ulysse Klatzmann, Ashkan Alvand, Kep Kee Loh, David Schaeffer, Virginie Sivan, Daniel S. Margulies, Carly M. Drzewiecki, Tomoko Sakai, Ting Xu, Cirong Liu, Essa Yacoub, Theresa M. Desrochers, Seok-Jun Hong, Sethu Boopathy, Reza Azadi, Lu Yuheng, Aarit Ahuja, Zhifeng Liang, Elena Borra, Fernanda Ponce, Robert Dahnke, Julien Sein, Li Deying, Jitendra Sharma, A.J. Mitchell, Roger Little, Luqi Cheng, Du Xiao, Choong-Wan Woo, Xinhui Li, Chris Petkov, Ruiliang Bai, D Zaldivar, Sheyla Mejia, Haidong D. Lu, Nikoloz Sirmpilatze, Diego Emanuel Ortuzar Martinez, Suzanne N. Haber, Catherine Elorette, Yue Cui, Michael Hawrylycz, Jerome Sallet, Wim Vanduffel, Daniel R. Glen, Ralph Adolphs, Dongrong Xu, Simon Clavagnier, Rakshit Dadarwal, Marzio Gerbella, Hannah Doyle, Ningrong Ye, Xiaojin Liu, Xinyu Liu, Quansheng He, Christopher R. Madan, Vikas Pareek, James Cavanaugh, Sze Chai Kwok, Zhang Ying, Sam Vickery, Xiaoguang Tian, Zhou Xufeng, Bevil R. Conway, Mark Postans, Wei-an Sheng, Gianfranco Chavez, Rober Boshra, Yuki Kikuchi, Michael Ortiz-Rios, Céline Amiez, Felix Hoffstaedter, Elizabeth A. Buffalo, Amy Howard, Hsin-Yi Lai, Marianne Duyck, Samy Rima, Froesel Mathilda, Towela Mvula, Guilherme Freches, Alfonso Fajardo, Maria de la Iglesia-Vaya, Ana Rita Ribeiro Gomes, Xiongjie Yu, Afonso C. Silva, Andrew S. Fox, Long Cao, Anna W. Roe, Meizhen Qian, David Meunier, Erika Raven, Nicola Palomero-Gallagher, Jordy Tasserie, Joonas A. Autio, Francois Chouinard-Decorte, Hank P. Jedema, Shasha Yue, Xinjian Li, Xiaodong Chen, Kathleen Rockland, Satoka Hashimoto Fujimoto, Amiez Celine, Melina Cordeau, Olivier Coulon, Ravi S. Menon, Sandra Gonzalez Torrecilla, Bjørg Elisabeth Kilavik, Adam Messinger, Hecheng Jin, Steven Giavasis, Pierce Perkins, Conor Liston, Yujie Hou, Jakob Seidlitz, Kelly Shen, Yvonne Bennett, Franck Lamberton, Maxime Gaudet-Trafit, Suliann Ben Hamed, Chris Klink, Sabine Kastner, Lucas R. Trambaiolli, Lucija Jankovic-Rapan, Atsushi Fujimoto, Nadira Yusif Rodriguez, Maeva Gacoin, Amir Shmuel, Katja Heuer, Austin K. Behel, Susann Boretius, Paul A. Taylor, Child Mind Institute, Institute of Neurosciences and Psychology [Glasgow], University of Glasgow, Institut des sciences cognitives Marc Jeannerod - Centre de neuroscience cognitive - UMR5229 (ISC-MJ), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), University of Tübingen, Oregon Health and Science University [Portland] (OHSU), New York University [New York] (NYU), NYU System (NYU), Princeton Neuroscience Institute [Princeton], Consortium, PRIMatE Data and Resource Exchange (PRIME-DRE) Global Collaboration Workshop and, Institut des sciences cognitives Marc Jeannerod - Centre de neuroscience cognitive - UMR5229 (CNC), Nathan S. Kline Institute for Psychiatric Research (NKI), New York State Office of Mental Health, Institut de Neurosciences de la Timone (INT), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Nencki Institute of Experimental Biology, Polska Akademia Nauk = Polish Academy of Sciences (PAN), Monash University [Clayton], Wellcome Trust Centre for Integrative Neuroimaging (WIN - FMRIB), University of Oxford, Donders Institute for Brain, Cognition and Behaviour, Radboud University [Nijmegen], National Institute of Mental Health (NIMH), Newcastle University [Newcastle], McConnell Brain Imaging Centre (MNI), Montreal Neurological Institute and Hospital, McGill University = Université McGill [Montréal, Canada]-McGill University = Université McGill [Montréal, Canada], Laboratorium voor Neuro- en Psychofysiologie, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), and Washington University in Saint Louis (WUSTL)
Subjects: Strategic planning, 0303 health sciences, Open science, biology, Action, intention, and motor control, Resource exchange, [SCCO.NEUR]Cognitive science/Neuroscience, Neuroscience(all), General Neuroscience, Nonhuman primate, 03 medical and health sciences, 0302 clinical medicine, Neuroimaging, biology.animal, Primate, Beacon - Precision Imaging, ddc:610, Psychology, Neuroscience, ComputingMilieux_MISCELLANEOUS, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract: Contains fulltext : 239574.pdf (Publisher’s version ) (Closed access) Open science initiatives are creating opportunities to increase research coordination and impact in nonhuman primate (NHP) imaging. The PRIMatE Data and Resource Exchange community recently developed a collaboration-based strategic plan to advance NHP imaging as an integrative approach for multiscale neuroscience. 5 p.
Published: 2022

19. Bird populations most exposed to climate change are less sensitive to climatic variation

Author: Liam D. Bailey, Martijn van de Pol, Frank Adriaensen, Aneta Arct, Emilio Barba, Paul E. Bellamy, Suzanne Bonamour, Jean-Charles Bouvier, Malcolm D. Burgess, Anne Charmantier, Camillo Cusimano, Blandine Doligez, Szymon M. Drobniak, Anna Dubiec, Marcel Eens, Tapio Eeva, Peter N. Ferns, Anne E. Goodenough, Ian R. Hartley, Shelley A. Hinsley, Elena Ivankina, Rimvydas Juškaitis, Bart Kempenaers, Anvar B. Kerimov, Claire Lavigne, Agu Leivits, Mark C. Mainwaring, Erik Matthysen, Jan-Åke Nilsson, Markku Orell, Seppo Rytkönen, Juan Carlos Senar, Ben C. Sheldon, Alberto Sorace, Martyn J. Stenning, János Török, Kees van Oers, Emma Vatka, Stefan J. G. Vriend, Marcel E. Visser, Netherlands Institute of Ecology (NIOO-KNAW), University of Antwerp (UA), AGH University of Science and Technology [Krakow, PL] (AGH UST), Universitad Politecnica de Valencia, University of Bedfordshire, Centre d'Ecologie et des Sciences de la COnservation (CESCO), Muséum national d'Histoire naturelle (MNHN)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Unité de recherche Plantes et Systèmes de Culture Horticoles (PSH), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Università degli studi di Palermo - University of Palermo, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), University of New South Wales [Sydney] (UNSW), Institute of Computer Science [Warszawa], Polska Akademia Nauk = Polish Academy of Sciences (PAN), University of Turku, Cardiff University, Russian Science Foundation (RSF) 20-44-01005Ministry of Economy and Competitivity, Spanish Research Council CGL-2020 PID2020-114907GB-C21National Research, Development & Innovation Office (NRDIO) - Hungary K-115970Australian Research Council DE180100202Polish National Science Centre 2020/39/B/NZ8/012742015/18/E/NZ8/00505, European Project: 337365,EC:FP7:ERC,ERC-2013-StG,SHE(2014), Organismal and Evolutionary Biology Research Programme, Animal Ecology (AnE), van de Pol, Martijn, Adriaensen, Frank, Arct, Aneta, Barba, Emilio, Bellamy, Paul E., Bonamour, Suzanne, Bouvier, Jean-Charles, Burgess, Malcolm D., Charmantier, Anne, Cusimano, Camillo, Doligez, Blandine, Drobniak, Szymon M., Dubiec, Anna, Eens, Marcel, Eeva, Tapio, Ferns, Peter N., Goodenough, Anne E., Hartley, Ian R., Hinsley, Shelley A., Ivankina, Elena, Juškaitis, Rimvydas, Kempenaers, Bart, Kerimov, Anvar B., Lavigne, Claire, Leivits, Agu, Mainwaring, Mark C., Matthysen, Erik, Nilsson, Jan-Åke, Orell, Markku, Rytkönen, Seppo, Senar, Juan Carlos, Sheldon, Ben C., Sorace, Alberto, Stenning, Martyn J., Török, János, van Oers, Kees, Vatka, Emma, Vriend, Stefan J.G., and Visser, Marcel E.
Subjects: General Chemistry, Climate Change [MeSH], Animal behaviour, Seasons [MeSH], Multidisciplinary, Phenology, Animals [MeSH], Songbirds [MeSH], Temperature [MeSH], Passeriformes [MeSH], General Biochemistry, Genetics and Molecular Biology, General Physics and Astronomy, Climate Change, phenology, Ecology and Environment, Songbirds, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Animals, Passeriformes, Biology, 1172 Environmental sciences, QL_671, QH, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Temperature, birds, 1181 Ecology, evolutionary biology, Seasons, sense organs, [SDV.EE.BIO]Life Sciences [q-bio]/Ecology, environment/Bioclimatology, Zoology, Engineering sciences. Technology
Abstract: Includes phenological and climate data used for analysis of article titled 'Bird populations most exposed to climate change are less sensitive to climatic variation' (Nature Communications). Each data file is described below, with a description of all columns. - baileyetal_phenology_data.csv: Primary data used as the basis for all analysis. Column name Description Pop_ID Unique population ID. Species Species ID. Can be either GT (great tit/Parus major) or BT (blue tit/Cyanistes caeruleus). Sample_year Calendar year in which laying date was recorded. Mean Mean laying date (April days). SE Standard error of mean laying date (April days). Min Minimum observed laying date (April days). Count Total number of first nests laying date records for this population/species/year combination. Date Starting date used sliding window analysis (dd/mm/yyyy). SE_calc Inverse of standard error (1/SE), used to weight statistical models. Temp Mean temperature (oC) within population specific temperaturewindow - Pop_info.csv:Information about each study location where data were collected. Column name Description Site_Name Full name of study site Pop_ID Unique population ID Habitat_Type Either deciduous dominant (DEC), evergreen dominant (EVE), or mixed (MIX). Latitude Latitudinal coordinates of study site Longitude Longitudinal coordinates of study site Latitude_new_temp Latitudinal coordinates used to extract data from ECA&D gridded dataset. In most cases this will be identical to column Latitude; however, in 4 cases (Sagunto, Cardiff, Barcelona, Askainen) latitude is shifted slightly to overlap with the gridded dataset. Longitude_new_temp Longitudinal coordinates used to extract data from ECA&D gridded dataset. In most cases this will be identical to column Longitude; however, in 4 cases (Sagunto, Cardiff, Barcelona, Askainen) longitude is shifted slightly to overlap with the gridded dataset. -Sicily_temp_data.csv:Temperature data from study population in Sicily used to fit temperature window. Column name Description Year Year of temperature data collection Month Month of temperature data collection Day Day of temperature data collection Temperature Mean daily temperature (oC) -Vlieland_temp_data_old.csv: Temperature data used to determine temperature windows for Vlieland, Netherlands (1954 - 2016). Column name Description STN KNMI station number Date Date of weather data (dd/mm/yyyy) Mean Daily mean temperature (oC) Min Daily minimum temperature (oC) Max Daily maximum temperature (oC) -Vlieland_temp_data_new.csv: Temperature data used to determine temperature windows for Vlieland, Netherlands (1996 - 2017). Column name Description Station_no KNMI station number Date Date of weather data (yyyymmdd) Mean Daily mean temperature (oC) Min Daily minimum temperature (oC) Max Daily maximum temperature (oC) -slidingwin_results.rar:Compressed file containing results of sliding time window analysis for all population/species combinations. Each population/species combination has three corresponding files: - PopID_Sp.RDS: Results of sliding time window analysis. - PopID_Sp_rand.RDS: Results of randomization procedure to deal with issues of multiple testing. - PopID_Sp_SEM.RDS: Results of structural equation model used to apply detrending to analysis.
Published: 2022

20. Recognition of post-learning alteration of hippocampal ripples by convolutional neural network differs in the wild-type and AD mice

Author: Bartosz Jura, Sheng-Yi Hsu, Pierre Meyrand, Feng-Sheng Tsai, Tiaza Bem, Mau-Hsiang Shih, China Medical University Hospital [Taichung], Polish Academy of Sciences (PAN), Uniwersytet Jagielloński w Krakowie = Jagiellonian University (UJ), Physiopathologie de la Plasticité Neuronale (Neurocentre Magendie - U1215 Inserm), Université de Bordeaux (UB)-Institut François Magendie-Institut National de la Santé et de la Recherche Médicale (INSERM), Neurocentre Magendie : Physiopathologie de la Plasticité Neuronale (U1215 Inserm - UB), and Meyrand, Pierre
Subjects: Science, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Mice, Transgenic, Hippocampal formation, Biology, Convolutional neural network, Hippocampus, Article, Learning and memory, 03 medical and health sciences, Amyloid beta-Protein Precursor, Mice, 0302 clinical medicine, Deep Learning, Alzheimer Disease, Memory, Machine learning, Neural Pathways, Animals, Learning, 10. No inequality, 030304 developmental biology, 0303 health sciences, Multidisciplinary, Wild type, [SDV.NEU.NB] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Brain Waves, Disease Models, Animal, Reference memory, Medicine, Neuroscience, 030217 neurology & neurosurgery
Abstract: Evidence indicates that sharp-wave ripples (SWRs) are primary network events supporting memory processes. However, some studies demonstrate that even after disruption of awake SWRs the animal can still learn spatial task or that SWRs may be not necessary to establish a cognitive map of the environment. Moreover, we have found recently that despite a deficit of sleep SWRs the APP/PS1 mice, a model of Alzheimer’s disease, show undisturbed spatial reference memory. Searching for a learning-related alteration of SWRs that could account for the efficiency of memory in these mice we use convolutional neural networks (CNN) to discriminate pre- and post-learning 256 ms samples of LFP signals, containing individual SWRs. We found that the fraction of samples that were correctly recognized by CNN in majority of discrimination sessions was equal to ~ 50% in the wild-type (WT) and only 14% in APP/PS1 mice. Moreover, removing signals generated in a close vicinity of SWRs significantly diminished the number of such highly recognizable samples in the WT but not in APP/PS1 group. These results indicate that in WT animals a large subset of SWRs and signals generated in their proximity may contain learning-related information whereas such information seem to be limited in the AD mice.
Published: 2021

21. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: Update of taxonomy changes in 2021

Author: Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtboke, Ipek, Brister, J. Rodney, Lood, Cedric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Lobocka, Malgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, Francois, Knezevic, Petar, Lavigne, Rob, Rhee, Sung-Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, Adriaenssens, Evelien M., Sub Bioinformatics, Theoretical Biology and Bioinformatics, UCL - SST/ELI/ELIM - Applied Microbiology, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Virologie des archées - Archaeal Virology, Institut Pasteur [Paris], University of the West of England [Bristol] (UWE Bristol), Institute of Chemical Biology and Fundamental Medicine [Novosibirsk, Russia] (ICBFM SB RAS), Siberian Branch of the Russian Academy of Sciences (SB RAS), University of Melbourne, University of Helsinki, Flinders Accelerator for Microbiome Exploration [Adelaide, Australia], Utrecht University [Utrecht], U.S. Food and Drug Administration (FDA), Universidad de los Andes [Bogota] (UNIANDES), Ohio State University [Columbus] (OSU), Azabu University, Makerere University [Kampala, Ouganda] (MAK), Adam Mickiewicz University in Poznań (UAM), Montana State University (MSU), Wuhan University [China], Universidade Federal de Vicosa (UFV), National Academy of Sciences of Ukraine (NASU), University of Guelph, University of the Sunshine Coast (USC), National Institutes of Health [Bethesda] (NIH), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Indian Council of Medical Research [New Dehli] (ICMR), Beijing University of Chemical Technology, Chinese Academy of Sciences [Beijing] (CAS), Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (DSMZ), George Eliava Institute of Bacteriophages, Microbiology and Virology [Tbilisi, Georgia], University of the Western Cape, Latvian Biomedical Research and Study Centre [Rīga], Tokyo Institute of Technology [Tokyo] (TITECH), University of Jyväskylä (JYU), Cairo University, Polish Academy of Sciences (PAN), Portland State University [Portland] (PSU), University College Cork (UCC), Université Catholique de Louvain = Catholic University of Louvain (UCL), University of Copenhagen = Københavns Universitet (KU), Laboratoire Microorganismes : Génome et Environnement (LMGE), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), University of Novi Sad, Chungbuk National University, University of Oldenburg, Pontificia Universidad Católica de Chile (UC), University of Leicester, Ivane Javakhishvili Tbilisi State University (TSU), Quadram Institute, V.M. was supported by Russian Ministry of Education and Science Project No. 0245-2021-0008, H.M.O. was supported by University of Helsinki funding for FINStruct and Instruct-ERIC research infrastructure, R.A.E. was supported by the National Institute Of Diabetes And Digestive And Kidney Diseases of the National Institutes of Health under Award Number RC2DK116713, B.E.D. was supported by the European Research Council (ERC) Consolidator grant 865694: DiversiPHI, M.B.S. was supported by National Science Foundation Advances in Biological Infrastructure award #1758974, M.Y. acknowledges funding by the Gordon and Betty Moore Foundation grant GBMF9195, S.D. was supported by National Natural Science Foundation of of China grant 32070032, C.L. is supported by the Fonds Wetenschappelijk Onderzoek (1S64718N), L.H. was funded by the Strategic Priority Research Program of the Chinese Academy of Sciences Award XDB42000000,National Natural Science Foundation of China (NSFC) grant 31970170, T.M. was supported by JSPS KAKENHI Grant Numbers 21H02100, 19H04827, 18K14372, and JST JPMJJR2005, and SUMITOMO Fund 200673, MJ is supported by Academy of Finland grants #336518 and #297049 and Jane and Aatos Erkko Foundation, R.K.A. is supported by the Egyptian Academy of Scientific Research and Technology (ASRT) project #3046 (JESOR), M.L. is supported by the statutory funds for the Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, K.M.S. is supported by the US. National Science Foundation (MCB1929273 and MCB2025305), A.N.S. is supported by Wellcome Trust Research Career Development Fellowship (220646/Z/20/Z) and by European Research Council (ERC) grant under the European Union’s Horizon 2020 research and innovation programme (grant agreement 101001684), X.P. is supported by Novo Nordisk Foundation/Hallas-Møller Ascending Investigator Grant (grant number NNF17OC0031154) and the Danish Council for Independent Research/FNU (grant number DFF–0135-00402), S.K.R. was supported by the National Research Foundation of Korea (NRF) grants funded by the Ministry of Science, ICT & Future Planning (2021R1A2C3004015), C.M. acknowledges funding by the Deutsche Forschungsgemeinschaft within the Collaborative Research Center TRR51 Roseobacter (INST 184/170-1), M.M.P. acknowledges funding from the Academy of Finland (grant 331627) and the Sigrid Juselius Foundation, E.M.A. gratefully acknowledges funding by the Biotechnology and Biological Sciences Research Council (BBSRC), this research was funded by the BBSRC Institute Strategic Programme Gut Microbes and Health BB/R012490/1 and its constituent projects BBS/E/F/000PR10353 and BBS/E/F/000PR10356., European Project: 865694,H2020-EU.1.1. - EXCELLENT SCIENCE - European Research Council (ERC),DiversiPHI(2020), European Project: 101001684,ERC-2020-COG,PHAGENET(2021), 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), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Universidade Federal de Viçosa = Federal University of Viçosa (UFV), University of the Western Cape (UWC), University of Copenhagen = Københavns Universitet (UCPH), Biotechnology and Biological Sciences Research Council (BBSRC), Molecular and Integrative Biosciences Research Programme, and Molecular and Translational Virology
Subjects: Archaeal Viruses, Societies, Scientific, virukset, Library science, Biology, bakteriofagit, Executive committee, 03 medical and health sciences, Virology Division News, Virology, viruses, Bacteriophages, 030304 developmental biology, Taxonomy, 11832 Microbiology and virology, 0303 health sciences, Science & Technology, Bacteria, 030306 microbiology, systematiikka (biologia), General Medicine, Archaea, virologia, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Taxonomy (biology), Bacterial virus, Life Sciences & Biomedicine
Abstract: In this article, we – the Bacterial Viruses Subcommittee and the Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) – summarise the results of our activities for the period March 2020 – March 2021. We report the division of the former Bacterial and Archaeal Viruses Subcommittee in two separate Subcommittees, welcome new members, a new Subcommittee Chair and Vice Chair, and give an overview of the new taxa that were proposed in 2020, approved by the Executive Committee and ratified by vote in 2021. In particular, a new realm, three orders, 15 families, 31 subfamilies, 734 genera and 1845 species were newly created or redefined (moved/promoted). Supplementary Information The online version contains supplementary material available at 10.1007/s00705-021-05205-9.
Published: 2021

22. Baseline and stress-induced prolactin and corticosterone concentrations in a species with female offspring desertion – the case of Whiskered Tern Chlidonias hybrida

Author: Agata Banach, Adam Flis, Grzegorz Neubauer, Frédéric Angelier, Mateusz Ledwoń, Institute of Systematics and Evolution of Animals, Polska Akademia Nauk = Polish Academy of Sciences (PAN), Institute of Nature Conservation, Laboratory of Forest Biology [Poland], University of Wrocław [Poland] (UWr), Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), and Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Male, 0106 biological sciences, endocrine system, Offspring, avian physiology brood desertion capture and restraint chicks rearing parental care, Physiology, Captivity, Biology, 010603 evolutionary biology, 01 natural sciences, Nesting Behavior, 010605 ornithology, Charadriiformes, chemistry.chemical_compound, Endocrinology, Stress, Physiological, Corticosterone, Animals, Maternal Behavior, Parental investment, Prolactin, Brood, chemistry, [SDE]Environmental Sciences, Female, Animal Science and Zoology, Paternal care, Hormone
Abstract: International audience; To understand the proximate mechanisms regulating brood desertion, we studied hormonal and behavioural stress responses during the chick-rearing period in adult Whiskered Terns (Chlidonias hybrida), a socially monogamous, semi-precocial species with prolonged post-fledging parental care. In contrast to males, almost all females of this species desert during the chick-rearing and post-fledging periods. Because of the expected link between corticosterone, prolactin and parental investment, we hypothesized that males and females should differ in circulating prolactin and corticosterone concentrations. Baseline hormone concentrations did not differ between males and females. In both sexes, prolactin and corticosterone concentrations decreased and increased in response to acute stress (30 min after capture), respectively. Baseline and stress-induced prolactin concentrations decreased significantly in both sexes with advancing brood age. As expected, males had significantly higher stress-induced prolactin concentrations than females. None of the nine males released after being held in captivity for 24 h deserted, whereas four (29%) of the 14 females kept in captivity for 24 h did so. Altogether, these results suggest that higher prolactin concentrations may be involved in the maintenance of parental care under stress. However, there was no statistically significant difference in stress-induced hormone levels between males, females that deserted and those that returned to the nest after prolonged stress (24 h). Our data indicate that males are probably more resistant to stress as regards the continuation of parental care. The pattern of male and female behavioural and hormonal responses to stress partially predicts their behaviour in terms of natural desertion.
Published: 2021

23. New Cytoplasmic Virus-Like Elements (VLEs) in the Yeast Debaryomyces hansenii

Author: Cécile Neuvéglise, Serge Casaregola, Barbara Żarowska, Xymena Połomska, Joanna Zyzak, Zbigniew Lazar, Department of Biotechnology and Food Microbiology, Wroclaw University of Environmental and Life Sciences, Sciences Pour l'Oenologie (SPO), 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), Ludwik Hirszfeld Institute of Immunology and Experimental therapy (LUDWIK HIRSZFELD INSTITUTE OF IMMUNOLOGY AND EXPERIMENTAL THERAPY), Polska Akademia Nauk = Polish Academy of Sciences (PAN), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), and AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Debaryomyces hansenii, Health, Toxicology and Mutagenesis, killer activity, [SDV]Life Sciences [q-bio], yeast, Toxicology, virus-like elements (VLEs), 03 medical and health sciences, killer toxins, ORFS, Killer yeast, Gene, 030304 developmental biology, Genetics, 0303 health sciences, biology, 030306 microbiology, Yarrowia, Penicillium roqueforti, Deoxyribonuclease, biology.organism_classification, Yeast, linear dsDNA plasmids, Medicine, osmotolerance
Abstract: Yeasts can have additional genetic information in the form of cytoplasmic linear dsDNA molecules called virus-like elements (VLEs). Some of them encode killer toxins. The aim of this work was to investigate the prevalence of such elements in D. hansenii killer yeast deposited in culture collections as well as in strains freshly isolated from blue cheeses. Possible benefits to the host from harboring such VLEs were analyzed. VLEs occurred frequently among fresh D. hansenii isolates (15/60 strains), as opposed to strains obtained from culture collections (0/75 strains). Eight new different systems were identified: four composed of two elements and four of three elements. Full sequences of three new VLE systems obtained by NGS revealed extremely high conservation among the largest molecules in these systems except for one ORF, probably encoding a protein resembling immunity determinant to killer toxins of VLE origin in other yeast species. ORFs that could be potentially involved in killer activity due to similarity to genes encoding proteins with domains of chitin-binding/digesting and deoxyribonuclease NucA/NucB activity, could be distinguished in smaller molecules. However, the discovered VLEs were not involved in the biocontrol of Yarrowia lipolytica and Penicillium roqueforti present in blue cheeses.
Published: 2021

24. Constant darkness negatively affects the outcome of hormonally induced reproduction in cultured Eurasian perch females

Author: Katarzyna Dryl, Daniel Żarski, Sylvain Milla, Pascal Fontaine, Beata Sarosiek, Piotr Gomułka, Lola Toomey, J. Król, Katarzyna Palińska-Żarska, Yannick Ledoré, Polska Akademia Nauk = Polish Academy of Sciences (PAN), Stanislaw Sakowicz Inland Fisheries Institute, Unité de Recherches Animal et Fonctionnalités des Produits Animaux (URAFPA), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Warmia and Mazury [Olsztyn], and European Project: 652831,H2020,H2020-INFRAIA-2014-2015,AQUAEXCEL2020(2015)
Subjects: Ovulation, media_common.quotation_subject, Broodstock, Stress, Acclimatization, SF1-1100, Gonadotropin-Releasing Hormone, Animal science, Controlled reproduction, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Animals, ComputingMilieux_MISCELLANEOUS, media_common, photoperiodism, Perch, biology, Reproduction, Darkness, biology.organism_classification, Eurasian perch, Animal culture, Hormonal stimulation, Perches, Animal Science and Zoology, Female, Gonadotropins, Hormone
Abstract: International audience; This study aimed to assess the effect of constant darkness applied to fish during controlled breeding on reproductive traits in domesticated females of Eurasian perch. Based on the assumption that keeping fish in constant darkness during the reproduction operation may reduce stress, suspected to be responsible for variable spawning effectiveness in this species. Two conditions were assessed (16 h light per day [group 16L] and constant darkness [group 0L], two tank replicates per condition). The reproductive protocol involved a 7-day-long adaptation period for group 0L where photoperiod was reduced by 2.3 h a day down to constant darkness. After the adaptation period, two hormone injections (salmon gonadoliberin analogue) were applied to both groups: priming (10 mu g/kg) and resolving (25 mu g/kg) with a 7-day interval between them. During the study, morphometric indices were recorded and blood, brain, and pituitary samples were collected to assess stress markers and determine hypothalamic-pituitary-gonadal axis functioning via measuring blood plasma hormones, as well as gonadoliberin and gonadotropins (luteinising hormone [LH] and follicle-stimulating hormone [FSH]) transcript abundance (n = 7 for each group at each sampling point). In addition, kinetics of the final oocyte maturation (FOM) process, ovulation rate, and egg quality of each group was monitored (n = 12 for each group). The results indicated that there were no differences in terms of morphometry, FOM kinetics, and most stress indices between groups throughout the experiment, except haematocrit, which increased immediately following the acclimation period in fish kept in darkness. Constant darkness negatively affected plasma levels of 17 alpha,20 beta-dihy droxy-4-pregnen-3-one (DHP) and LH transcript expression at the time of the second hormone injection. This indicated that exposure to constant darkness negatively affected priming of the hormonal dose applied, resulted in the disruption of ovulation, and reduced ovulation rates (50%) for group 0L, as compared to 16L (91%). The findings of this study clearly indicate that constant darkness may have significant deleterious effects on reproductive traits throughout out-of-season induced, hormonally supported, controlled reproduction. Therefore, we advise against the use of constant darkness when managing broodstock reproduction in domesticated Eurasian perch.
Published: 2021

25. Phylogeny and biogeography of the enigmatic ghost lineage Cylindrotomidae (Diptera, Nematocera)

Author: Wiesław Krzemiński, Wiktoria Jordan-Stasiło, Jacek Szwedo, André Nel, Iwona Kania-Kłosok, University of Information Technology and Management in Rzeszow (WSIZ), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), University of Gdańsk (UG), and Polish Academy of Sciences (PAN)
Subjects: 0106 biological sciences, 0301 basic medicine, Evolution, Science, Biogeography, [SDV.BID]Life Sciences [q-bio]/Biodiversity, 010603 evolutionary biology, 01 natural sciences, Article, 03 medical and health sciences, Genus, Phylogenetics, Animals, Clade, Phylogeny, Multidisciplinary, Cylindrotomidae, biology, Diptera, Palaeontology, Paleontology, biology.organism_classification, Crown group, Phylogeography, 030104 developmental biology, Ghost lineage, Sister group, Evolutionary biology, Medicine, Systems biology
Abstract: Ghost lineages have always challenged the understanding of organism evolution. They participate in misinterpretations in phylogenetic, clade dating, biogeographic, and paleoecologic studies. They directly result from fossilization biases and organism biology. The Cylindrotomidae are a perfect example of an unexplained ghost lineage during the Mesozoic, as its sister family Tipulidae is already well diversified during the Cretaceous, while the oldest Cylindrotomidae are Paleogene representatives of the extant genus Cylindrotoma and of the enigmatic fossil genus Cyttaromyia. Here we clarify the phylogenetic position of Cyttaromyia in the stem group of the whole family, suggesting that the crown group of the Cylindrotomidae began to diversify during the Cenozoic, unlike their sister group Tipulidae. We make a comparative analysis of all species in Cyttaromyia, together with the descriptions of the two new species, C. gelhausi sp. nov. and C. freiwaldi sp. nov., and the revision of C. obdurescens. The cylindrotomid biogeography seems to be incongruent with the phylogenetic analysis, the apparently most derived subfamily Stibadocerinae having apparently a ‘Gondwanan’ distribution, with some genera only known from Australia or Chile, while the most inclusive Cylindrotominae are Holarctic.
Published: 2021

26. Legacy of plant-parasitic nematode communities from past ecosystems and shift by recent afforestation

Author: Véronique Edel-Hermann, Nadine Ali, Christian Steinberg, Gilles Granereau, Stéphane Barbier, Cécile Héraud, Elodie Chapuis, David Jimenez, Johannes Tavoillot, Stephan Plas, Elsa Rulliat, Ewa Dmowska, Grażyna Winiszewska, Odile Fossati-Gaschignard, Bernard Martiny, Thierry Mateille, Nadine Gautheron, Department of Plant Protection, Faculty of Agriculture, Tishreen University, Latakia, Syria., Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Fruits et Légumes d'Aquitaine (INVENIO), Museum and Institute of Zoology PAS, Polska Akademia Nauk = Polish Academy of Sciences (PAN), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Laboratoire de la Santé des Végétaux, CONSEIL GENERAL DES LANDES, 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), Office National des Forêts (ONF), Conservatoire Botanique National Sud Atlantique (CBNSA), Nutrition, Métabolisme, Aquaculture (NuMéA), Université de Pau et des Pays de l'Adour (UPPA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Agroécologie [Dijon], 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), This work was part of the SYSBIOTEL project: Integrated management of soil-borne bioagressors in vegetable cropping systems, granted by the French agency Agence Nationale de la Recherche (no ANR-08-STRA-14) and managed by Dr. P. Lucas (INRAE, France). It was also supported by a Master grant from Tishreen University (Latakia, Syrian Arabic Republic) to N.A., ANR-08-STRA-0014,SYSBIOTEL,Gestion intégrée des bioagresseurs telluriques en systèmes de cultures légumiers(2008), Polish Academy of Sciences, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier 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), Invenio, Laboratoire de la santé des végétaux (LSV), and Office national des forêts (ONF)
Subjects: 0106 biological sciences, Peatland, [SDV]Life Sciences [q-bio], 010603 evolutionary biology, 01 natural sciences, Diversity index, Natural ecosystem, Moorland, Afforestation, Ecosystem, QH540-549.5, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation, Plant-parasitic nematodes, Ecology, Land use, biology, 010604 marine biology & hydrobiology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Vegetation, Understory, 15. Life on land, Nematode community, biology.organism_classification, Geography, [SDE]Environmental Sciences, Pine forest, Pinus pinaster, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; Ancient ecological legacies and past land use changes may inform on the present structure of biological communities. However, regions providing such successive ecosystems are scarce. In France, the Landes de Gascogne area provides such ecological shifts since a few ancient moorland, peatland and oak areas prior the afforestation with maritime pine (Pinus pinaster) 160 years ago still remain. Focusing on soil-borne parasites such as plant-parasitic nematodes (PPN), because forests were recently increasingly impacted by the introduction of intensive agriculture, this study is therefore aimed at comparing the diversity and the community patterns of these organisms at different scales (intra- and intersites) and between different successive ecosystems. The understory vegetation as well as the pedoclimatic characterization of the sampled sites were also considered. Common diversity indices were not impacted by this transition from ancient to past ecosystems. Although the most colonizer nematodes prevailed in all the ecosystems, PPN community structures significantly diverged between both ecosystems. In the logged pine forests, the sediment legacy could have primarily impacted the diversity. Moreover, the PPN diversity would mainly respond to the soil hydromorphicity that determined the associated understory vegetation. Consequently, a significant shift in community structure from moorlands to logged pine to logged pine forests was observed, regarding especially high pathogenic species such as Pratylenchus spp. Thus, analyzing PPN community structure highlights the PPN potential risk to consider during the introduction of intensive cropping systems.
Published: 2021

27. MicroRNA expression profile in bovine mammary gland parenchyma infected by coagulase-positive or coagulase-negative staphylococci

Author: Aleksandra Kapusta, Ewelina Kawecka-Grochocka, Tomasz Ząbek, E. Kościuczuk, Magdalena Zalewska, Klaudia Pawlina-Tyszko, Sylwester Marczak, Emilia Bagnicka, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences (PAN), Warsaw University of Life Sciences (SGGW), and University of Warsaw (UW)
Subjects: 0301 basic medicine, Coagulase, Staphylococcus aureus, Mammary gland, Biology, [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity, 03 medical and health sciences, 0302 clinical medicine, Immune system, Mammary Glands, Animal, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], microRNA, Parenchyma, Target gene expression, Escherichia coli, Dairy cattle, Animals, Epigenetics, KEGG, Mastitis, Bovine, Escherichia coli Infections, Inflammation, lcsh:Veterinary medicine, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, General Veterinary, Gene Expression Profiling, MicroRNA, MicroRNA Expression Profile, Staphylococcal Infections, Molecular biology, MicroRNAs, 030104 developmental biology, [SDV.IMM.IA]Life Sciences [q-bio]/Immunology/Adaptive immunology, Tumor progression, 030220 oncology & carcinogenesis, lcsh:SF600-1100, Cattle, Female, Mesophyll Cells, Transcriptome, Research Article
Abstract: MicroRNAs (miRNAs) are short, non-coding RNAs, 21–23 nucleotides in length which are known to regulate biological processes that greatly impact immune system activity. The aim of the study was to compare the miRNA expression in non-infected (H) mammary gland parenchyma samples with that of glands infected with coagulase-positive staphylococci (CoPS) or coagulase-negative staphylococci (CoNS) using next-generation sequencing. The miRNA profile of the parenchyma was found to change during mastitis, with its profile depending on the type of pathogen. Comparing the CoPS and H groups, 256 known and 260 potentially new miRNAs were identified, including 32 that were differentially expressed (p ≤ 0.05), of which 27 were upregulated and 5 downregulated. Comparing the CoNS and H groups, 242 known and 171 new unique miRNAs were identified: 10 were upregulated (p ≤ 0.05), and 2 downregulated (p ≤ 0.05). In addition, comparing CoPS with H and CoNS with H, 5 Kyoto Encyclopedia of Genes and Genomes pathways were identified; in both comparisons, differentially-expressed miRNAs were associated with the bacterial invasion of epithelial cells and focal adhesion pathways. Four gene ontology terms were identified in each comparison, with 2 being common to both immune system processes and signal transduction. Our results indicate that miRNAs, especially miR-99 and miR-182, play an essential role in the epigenetic regulation of a range of cellular processes, including immunological systems bacterial growth in dendritic cells and disease pathogenesis (miR-99), DNA repair and tumor progression (miR-182).
Published: 2021

28. Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring

Author: M. Zupancic, Johannes Rusch, Florian Leese, S. Zlatkovic, A. Stovicek, Romana K. Salis, Jens Boenigk, Jeremy J. Piggott, Tina Elersek, Peeter Nõges, Larissa Frühe, Thorsten Stoeck, Karel Šimek, Sandi Orlić, Adam Petrusek, Agnès Bouchez, David A. Strand, Tadeusz Fleituch, M. Gajdosova, Kristina Cermakova, Jan Pawlowski, Tristan Cordier, Jan Kopecky, Marlen I. Vasquez, Nadine Graupner, Teofana Chonova, Trude Vrålstad, Arne Haegerbaeumer, Kristel Panksep, Ursula Eisendle, Stefano Fazi, A. M. Kelly, Janina Schenk, Marketa Sagova-Mareckova, Czech University of Life Sciences Prague (CZU), Universität Duisburg-Essen [Essen], Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ID-Gene ecodiagnostics [Geneva], University of Geneva [Switzerland], Universität Salzburg, National Institute of Biology [Ljubljana] (NIB), Natl Res Council CNR, Inst Ecosyst Study ISE, Res Unit Pisa, Pisa, Italy, Polish Academy of Sciences (PAN), Technische Universität Kaiserslautern (TU Kaiserslautern), Charles University [Prague] (CU), Universität Bielefeld = Bielefeld University, University of Dublin, Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Estonian University of Life Sciences (EMU), Institut Ruđer Bošković (IRB), Norwegian Veterinary Institute [Oslo], University of Oslo (UiO), Lund University [Lund], Biology Centre of the Czech Academy of Sciences (BIOLOGY CENTRE CAS), Czech Academy of Sciences [Prague] (CAS), and Cyprus University of Technology
Subjects: Environmental Engineering, River ecosystem, Ecology (disciplines), 0208 environmental biotechnology, Fresh Water, 02 engineering and technology, 010501 environmental sciences, Biology, 01 natural sciences, Freshwater ecosystem, Environmental biomarkers, NATURAL SCIENCES, Environmental monitoring, 14. Life underwater, freshwater, Waste Management and Disposal, Ecosystem, 0105 earth and related environmental sciences, Water Science and Technology, Civil and Structural Engineering, Environmental Biomarkers, Ecology, Fresh water, Ecological Modeling, Aquatic ecosystem, Lake ecosystem, Ecological assessment, Pollution, Archaea, 6. Clean water, 020801 environmental engineering, Biological monitoring, 13. Climate action, biomonitoring, [SDE]Environmental Sciences, Biologie, Bioindicator, ecological assessment, microorganisms, freshwater biomonitoring, Biological Monitoring, Environmental Monitoring
Abstract: International audience; Bioindication has become an indispensable part of water quality monitoring in most countries of the world, with the presence and abundance of bioindicator taxa, mostly multicellular eukaryotes, used for biotic indices. In contrast, microbes (bacteria, archaea and protists) are seldom used as bioindicators in routine assessments, although they have been recognized for their importance in environmental processes. Recently, the use of molecular methods has revealed unexpected diversity within known functional groups and novel metabolic pathways that are particularly important in energy and nutrient cycling. In various habitats, microbial communities respond to eutrophication, metals, and natural or anthropogenic organic pollutants through changes in diversity and function. In this review, we evaluated the common trends in these changes, documenting that they have value as bioindicators and can be used not only for monitoring but also for improving our understanding of the major processes in lotic and lentic environments. Current knowledge provides a solid foundation for exploiting microbial taxa, community structures and diversity, as well as functional genes, in novel monitoring programs. These microbial community measures can also be combined into biotic indices, improving the resolution of individual bioindicators. Here, we assess particular molecular approaches complemented by advanced bioinformatic analysis, as these are the most promising with respect to detailed bioindication value. We conclude that microbial community dynamics are a missing link important for our understanding of rapid changes in the structure and function of aquatic ecosystems, and should be addressed in the future environmental monitoring of freshwater ecosystems.
Published: 2021

29. Quo vadis? Historical distribution and impact of climate change on the worldwide distribution of the Australasian fungus Clathrus archeri (Phallales, Basidiomycota)

Author: Marc-André Selosse, Marcin Pietras, Marta Kolanowska, Polish Academy of Sciences (PAN), University of Lódź, University of Gdańsk (UG), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)
Subjects: 0106 biological sciences, 0301 basic medicine, Ecological niche, Ecology, Range (biology), Niche, Climate change, 15. Life on land, Biology, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Agricultural and Biological Sciences (miscellaneous), Invasive species, 03 medical and health sciences, Clathrus archeri, 030104 developmental biology, Habitat, 13. Climate action, Threatened species, [SDE]Environmental Sciences, Ecology, Evolution, Behavior and Systematics
Abstract: Clathrus archeri is a fungus native to Australia and New Zealand that has started to expand into Europe, and it is considered a potentially invasive species. In this study, we examine the historical occurrence, current geographical range and potential future changes in the distribution of C. archeri using worldwide distribution data. Ecological modelling was used to assess the locations of the potential climatic niches of C. archeri within both its native and introduced ranges in the past, present and future. Our study clearly shows that the coverage of suitable habitats of this fungus has decreased since the last glacial maximum, and anthropogenic climate changes are accelerating the process of niche loss. The highest rate of C. archeri range contraction is expected in Australia, where the fungus should be considered a threatened species in the future. Highly valuable habitats will be available in Tasmania and New Zealand. However, a significant expansion rate of C. archeri will still probably be observed in Europe, where the climatic conditions preferred by the fungus will allow its quick expansion northeast into the continent.
Published: 2021

30. Root traits as drivers of plant and ecosystem functioning: current understanding, pitfalls and future research needs

Author: A. Glyn Bengough, Ina C. Meier, Grégoire T. Freschet, Monique Weemstra, Jitka Klimešová, Catherine Picon-Cochard, Sarah E. Hobbie, Agnieszka Bagniewska-Zadworna, Alexandra Weigelt, Louise H. Comas, Elison B. Blancaflor, Martin Lukac, Liesje Mommer, Arthur Gessler, David W. Johnson, Laura Rose, Iván Prieto, Marcin Zadworny, Tao Sun, Ivano Brunner, Nadejda A. Soudzilovskaia, Peter Ryser, Richard D. Bardgett, Catherine Roumet, Nina Wurzburger, Boris Rewald, M. Luke McCormack, Hendrik Poorter, Alexia Stokes, Loïc Pagès, Colleen M. Iversen, Oscar J. Valverde-Barrantes, Michael Scherer-Lorenzen, Gerlinde B. De Deyn, Larry M. York, Johannes A. Postma, Station d'Ecologie Théorique et Expérimentale (SETE), Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier 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), National Center for Cool and Cold Water Aquaculture, ARS-USDA, USDA-ARS : Agricultural Research Service, University of Dundee, The James Hutton Institute, Universität für Bodenkultur Wien = University of Natural Resources and Life [Vienne, Autriche] (BOKU), University of Manchester [Manchester], Wageningen University and Research [Wageningen] (WUR), Institute of Botany of the Czech Academy of Sciences (IB / CAS), Czech Academy of Sciences [Prague] (CAS), University of Reading (UOR), Czech University of Life Sciences Prague (CZU), Center for Tree Science, Hamburg University of Applied Sciences [Hamburg], Georg-August-University = Georg-August-Universität Göttingen, Unité de recherche Plantes et Systèmes de Culture Horticoles (PSH), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association, Macquarie University, Centro de Investigaciones Biológicas (CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), University of Georgia [USA], Polish Academy of Sciences (PAN), Adam Mickiewicz University in Poznań (UAM), Noble Research Institute, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Institute of Terrestrial Ecosystems (ITES), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Department of Anthropology [University of Minnesota], University of Minnesota [Twin Cities] (UMN), University of Minnesota System-University of Minnesota System, University of Minnesota System, Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC, Unité Mixte de Recherche sur l'Ecosystème Prairial - UMR (UREP), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laurentian University, University of Freiburg [Freiburg], Universiteit Leiden, Chinese Academy of Sciences [Beijing] (CAS), Florida International University [Miami] (FIU), Leipzig University, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), 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])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Grant Agency of the Czech Republic 1913103S, Station d'écologie théorique et expérimentale (SETE), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (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), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (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 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), 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), University of Natural Resources and Life Sciences (BOKU), University of Göttingen - Georg-August-Universität Göttingen, and Leiden University
Subjects: 0106 biological sciences, 0301 basic medicine, Root (linguistics), spatial and temporal scales, Physiology, Ecology (disciplines), belowground ecology, Plant Ecology and Nature Conservation, Plant Science, Biology, 01 natural sciences, 03 medical and health sciences, plant functions, Ecosystem, ecosystem properties and processes, environmental gradients, trait covariation, Bodembiologie, Ecology, trait causal relationships, Atmosphere, Biosphere, Research needs, Soil Biology, 15. Life on land, Plants, PE&RC, 030104 developmental biology, Phenotype, root traits, 13. Climate action, [SDE]Environmental Sciences, Trait, Plantenecologie en Natuurbeheer, Terrestrial ecosystem, 010606 plant biology & botany
Abstract: International audience; The effects of plants on the biosphere, atmosphere and geosphere are key determinants of terrestrial ecosystem functioning. However, despite substantial progress made regarding plant belowground components, we are still only beginning to explore the complex relationships between root traits and functions. Drawing on the literature in plant physiology, ecophysiology, ecology, agronomy and soil science, we reviewed 24 aspects of plant and ecosystem functioning and their relationships with a number of root system traits, including aspects of architecture, physiology, morphology, anatomy, chemistry, biomechanics and biotic interactions. Based on this assessment, we critically evaluated the current strengths and gaps in our knowledge, and identify future research challenges in the field of root ecology. Most importantly, we found that belowground traits with the broadest importance in plant and ecosystem functioning are not those most commonly measured. Also, the estimation of trait relative importance for functioning requires us to consider a more comprehensive range of functionally relevant traits from a diverse range of species, across environments and over time series. We also advocate that establishing causal hierarchical links among root traits will provide a hypothesis-based framework to identify the most parsimonious sets of traits with the strongest links on functions, and to link genotypes to plant and ecosystem functioning.
Published: 2021

31. Insights into the structure and morphogenesis of the giant basal spicule of the glass sponge Monorhaphis chuni

Author: Marco Bertolino, Magdalena Łukowiak, Hermann Ehrlich, Sylvie Masse, Konstantin R. Tabachnick, Jane Fromont, Andrzej Pisera, Institute of Paleobiology [Warsaw], Polska Akademia Nauk = Polish Academy of Sciences (PAN), Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), P.P. Shirshov Institute of Oceanology (SIO), Russian Academy of Sciences [Moscow] (RAS), Western Australian Museum (WAM), Technishe Universität Bergakademie Freiberg (TU Bergakademie Freiberg), Adam Mickiewicz University in Poznań (UAM), University of Toronto at Mississauga, Dipartimento di Scienze della Terra dell'Ambiente e della Vita (DISTAV), and Universita degli studi di Genova
Subjects: Spicule, Basal spicule, Morphogenesis, Sclerocytes, 02 engineering and technology, Biology, 03 medical and health sciences, Spicule structure, Sponge spicule, Spicule formation, Apex (mollusc), Monorhaphis chuni, Composite material, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Sclerocyte, 0303 health sciences, Hexactinellid, Research, [SDV.BDD.MOR]Life Sciences [q-bio]/Development Biology/Morphogenesis, 021001 nanoscience & nanotechnology, Microstructure, biology.organism_classification, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Sponge, QL1-991, Animal Science and Zoology, 0210 nano-technology, Zoology
Abstract: Background A basal spicule of the hexactinellid sponge Monorhaphis chuni may reach up to 3 m in length and 10 mm in diameter, an extreme case of large spicule size. Generally, sponge spicules are of scales from micrometers to centimeters. Due to its large size many researchers have described its structure and properties and have proposed it as a model of hexactinellid spicule development. Thorough examination of new material of this basal spicule has revealed numerous inconsistencies between our observations and earlier descriptions. In this work, we present the results of detailed examinations with transmitted light and epifluorescence microscopy, SEM, solid state NMR analysis, FTIR and X-ray analysis and staining of Monorhaphis chuni basal spicules of different sizes, collected from a number of deep sea locations, to better understand its structure and function. Results Three morphologically/structurally different silica layers i.e. plain glassy layer (PG), tuberculate layer (TL) and annular layer (AL), and an axial cylinder (AC) characterize adult spicules. Young, immature spicules display only plain glassy silica layers which dominate the spicule volume. All three layers i.e. PG, TL and AL can substitute for each other along the surface of the spicule, but equally they are superimposed in older parts of the spicules, with AL being the most external and occurring only in the lower part of the spicules and TL being intermediate between AL and PG. The TL, which is composed of several thinner layers, is formed by a progressive folding of its surface but its microstructure is the same as in the PG layer (glassy silica). The AL differs significantly from the PG and TL in being granular and porous in structure. The TL was found to display positive structures (tubercles), not depressions, as earlier suggested. The apparent perforated and non-perforated bands of the AL are an optical artefact. The new layer type that we called the Ripple Mark Layer (RML) was noted, as well as narrow spikes on the AL ridges, both structures not reported earlier. The interface of the TL and AL, where tubercles fit into depressions of the lower surface of the AL, represent tenon and mortise or dovetail joints, making the spicules more stiff/strong and thus less prone to breaking in the lower part. Early stages of the spicule growth are bidirectional, later growth is unidirectional toward the spicule apex. Growth in thickness proceeds by adding new layers. The spicules are composed of well condensed silica, but the outermost AL is characterized by slightly more condensed silica with less water than the rest. Organics permeating the silica are homogeneous and proteinaceous. The external organic net (most probably collagen) enveloping the basal spicule is a structural element that bounds the sponge body together with the spicule, rather than controlling tubercle formation. Growth of various layers may proceed simultaneously in different locations along the spicule and it is sclerosyncytium that controls formation of silica layers. The growth in spicule length is controlled by extension of the top of the axial filament that is not enclosed by silica and is not involved in further silica deposition. No structures that can be related to sclerocytes (as known in Demospongiae) in Monorhaphis were discovered during this study. Conclusions Our studies resulted in a new insight into the structure and growth of the basal Monorhaphis spicules that contradicts earlier results, and permitted us to propose a new model of this spicule’s formation. Due to its unique structure, associated with its function, the basal spicule of Monorhaphis chuni cannot serve as a general model of growth for all hexactinellid spicules.
Published: 2021

32. Revision of the genus Coccidula Kugelann (Coleoptera, Coccinellidae)

Author: Karol Szawaryn, Tomasz Czerwiński, Amir Biranvand, Oldřich Nedvěd, Romain Nattier, Polish Academy of Sciences (PAN), University of South Bohemia, Czech Academy of Sciences [Prague] (CAS), Islamic Azad University Shiraz branch, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)
Subjects: 0106 biological sciences, new synonym, Insecta, Subfamily, Arthropoda, ladybirds, 010607 zoology, Identification key, Zoology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Tribe (biology), 010603 evolutionary biology, 01 natural sciences, taxonomy, Holarctic, Coccinelloidea, Genus, Animalia, morphological revision, Ecology, Evolution, Behavior and Systematics, biology, biology.organism_classification, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Coleoptera, Coccinellinae, QL1-991, Coccinellidae, Coccidula, Animal Science and Zoology, Taxonomy (biology)
Abstract: The genus Coccidula Kugelann includes five species distributed in the Holarctic, with one species in North America and four in Palearctic region. Coccidula belongs to the tribe Coccidulini which historically was treated as a separate subfamily within ladybird beetles, but recent studies confirmed its placement as a tribe within the broadly defined subfamily Coccinellinae. All species are revised and a new synonymy of Lithophilus naviauxi Duverger with C. litophiloides Reitter is proposed. Light and electron microscopy pictures support morphological descriptions. An identification key to all species is also provided.
Published: 2021

33. Integration of MsrB1 and MsrB2 in the Redox Network during the Development of Orthodox and Recalcitrant Acer Seeds

Author: Agnieszka Bagniewska-Zadworna, Pascal Rey, Karolina Bilska, Ewa Marzena Kalemba, Natalia Wojciechowska, Ewelina Stolarska, Polish Academy of Sciences (PAN), Adam Mickiewicz University in Poznań (UAM), Protéines de Protection des Végétaux (PPV), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-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)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-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), National Science Center (Poland) Grant No. 2015/18/E/NZ9/00729, Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Physiology, Clinical Biochemistry, seed maturation, Acer platanoides, Nicotinamide adenine dinucleotide, Protein oxidation, 01 natural sciences, Biochemistry, Redox, Article, 03 medical and health sciences, chemistry.chemical_compound, methionine sulfoxide, Botany, Acer pseudoplatanus, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, glutathione, Molecular Biology, biology, Chemistry, Methionine sulfoxide, lcsh:RM1-950, Cell Biology, 15. Life on land, ascorbate, biology.organism_classification, nicotinamide adenine dinucleotide phosphate, lcsh:Therapeutics. Pharmacology, 030104 developmental biology, methionine sulfoxide reductase, Methionine sulfoxide reductase, NAD+ kinase, 010606 plant biology & botany
Abstract: International audience; Two related tree species, Norway maple (Acer platanoides L.) and sycamore (Acer pseudoplatanus L.), produce desiccation-tolerant (orthodox) and desiccation-sensitive (recalcitrant) seeds, respectively. We compared the seeds of these two species to characterize the developmentally driven changes in the levels of peptide-bound methionine sulfoxide (MetO) and the abundance of methionine sulfoxide reductases (Msrs) B1 and B2, with respect to the cellular redox environment. Protein oxidation at the Met level was dynamic only in Norway maple seeds, and the reduced MsrB2 form was detected only in this species. Cell redox status, characterized by the levels of reduced and oxidized ascorbate, glutathione, and nicotinamide adenine dinucleotide (NAD)/phosphate (NADP), was clearly more reduced in the Norway maple seeds than in the sycamore seeds. Clear correlations between MetO levels, changes in water content and redox status were reported in orthodox Acer seeds. The abundance of Msrs was correlated in both species with redox determinants, mainly ascorbate and glutathione. Our data suggest that MsrB2 is associated with the acquisition of desiccation tolerance and that ascorbate might be involved in the redox pathway enabling the regeneration of Msr via intermediates that are not known yet.
Published: 2020

34. Cepharanthine induces ROS stress in glioma and neuronal cells via modulation of VDAC permeability

Author: Joanna Rossowska, Anna Szewczyk, Mounir Tarek, Jolanta Saczko, Wojciech Szlasa, Karolina Cierluk, Julita Kulbacka, Wroclaw University of Science and Technology, Wroclaw Medical University [Wrocław, Pologne], Polish Academy of Sciences (PAN), Laboratoire de Physique et Chimie Théoriques (LPCT), and Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Voltage-dependent anion channel, Pharmaceutical Science, Mitochondrion, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Cepharanthine, MTT assay, Cytotoxicity, ComputingMethodologies_COMPUTERGRAPHICS, Pharmacology, chemistry.chemical_classification, Reactive oxygen species, VDAC, biology, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Calcium channel, lcsh:RM1-950, ROS, Glioma, 3. Good health, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, lcsh:Therapeutics. Pharmacology, 030104 developmental biology, chemistry, Apoptosis, 030220 oncology & carcinogenesis, Neuronal cells, biology.protein, Biophysics, Original Article
Abstract: Graphical abstract, Cepharanthine (CEP) is a bisbenzylisoquinoline alkaloid. Molecular dynamics studies show that CEP interacts with Voltage-dependent anion channel (VDAC), inducing the voltage-independent channel narrowing. In the new conformation, transport between mitochondria and cytoplasm is altered, which leads to the dose-dependent cytotoxicity. The biological effects of the interaction were investigated on glioblastoma multiforme (SNB-19) and neuronal (PC-12 + NGF) cell lines. The cytotoxic potential of cepharanthine was determined by MTT assay and flow cytometry apoptosis/necrosis studies. T-type calcium channel and VDAC were labelled by the immunocytochemical method. Additionally, fluorescent labelling of reactive oxygen species and mitochondria was performed. Changes in the pore size of VDAC were calculated as well. Molecular dynamics simulations were carried out to examine the interactions of cepharanthine with VDAC. The obtained results prove that cepharanthine enhances the apoptosis in glioma and neuronal cells by the release of reactive oxygen species. Cepharanthine alters the mitochondria-to-cytoplasm transport and thus induces the cytotoxicity with no selectivity.
Published: 2020

35. Functional Divergence of the Arabidopsis Florigen-Interacting bZIP Transcription Factors FD and FDP

Author: Seonghoe Jang, Guillaume Née, Hyonhwa Ohr, Coral Vincent, Maida Romera-Branchat, Pedro Madrigal, Fernando Andrés, Chloé Pocard, Edouard Severing, Rafael Martinez-Gallegos, George Coupland, Madrigal, Pedro [0000-0003-1959-8199], Apollo - University of Cambridge Repository, Max Planck Institute for Plant Breeding Research (MPIPZ), University of Münster, World Vegetable Center Korea Office, Développement Adaptatif du Riz [AGAP] (DAR), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), 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 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), Institute of Plant Genetics (IPG), Polish Academy of Sciences (PAN), University of Cambridge [UK] (CAM), ERC Advanced Grant HyLife, German Research Foundation (DFG) : EXC 2048/1, 390686111, Max Planck Society, Foundation CELLEX, European Project: 237909,EC:FP7:PEOPLE,FP7-PEOPLE-ITN-2008,SYSFLO(2009), Westfälische Wilhelms-Universität Münster = University of Münster (WWU), 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)-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, and 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)
Subjects: 0301 basic medicine, 0106 biological sciences, [SDV]Life Sciences [q-bio], Mutant, Arabidopsis, 01 natural sciences, chemistry.chemical_compound, 0302 clinical medicine, Transcription (biology), Gene Expression Regulation, Plant, Abscisic acid, lcsh:QH301-705.5, Phylogeny, Gene Editing, 0303 health sciences, biology, food and beverages, Plants, Genetically Modified, Cell biology, ChIP-seq, Basic-Leucine Zipper Transcription Factors, ABA, Florigen, FD, Genotype, MADS Domain Proteins, Flowers, FDP, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, FT, florigen, Gene, Transcription factor, 030304 developmental biology, Homeodomain Proteins, flowering, Arabidopsis Proteins, CCAAT-Enhancer-Binding Protein-beta, fungi, 15. Life on land, biology.organism_classification, 030104 developmental biology, chemistry, lcsh:Biology (General), Mutagenesis, bZIPs, CRISPR-Cas Systems, RNA-seq, 030217 neurology & neurosurgery, Functional divergence, Abscisic Acid, Transcription Factors, 010606 plant biology & botany
Abstract: Summary Flowering of many plant species depends on interactions between basic leucine zipper (bZIP) transcription factors and systemically transported florigen proteins. Members of the genus Arabidopsis contain two of these bZIPs, FD and FDP, which we show have largely complementary expression patterns in shoot apices before and during flowering. CRISPR-Cas9-induced null mutants for FDP flower slightly earlier than wild-type, whereas fd mutants are late flowering. Identical G-box sequences are enriched at FD and FDP binding sites, but only FD binds to genes involved in flowering and only fd alters their transcription. However, both proteins bind to genes involved in responses to the phytohormone abscisic acid (ABA), which controls developmental and stress responses. Many of these genes are differentially expressed in both fd and fdp mutant seedlings, which also show reduced ABA sensitivity. Thus, florigen-interacting bZIPs have distinct functions in flowering dependent on their expression patterns and, at earlier stages in development, play common roles in phytohormone signaling., Graphical Abstract, Highlights • FDP is expressed at the shoot apex in a largely discrete pattern to FD • Flowering genes are bound only by FD, whereas other targets are bound by FD and FDP • FD and FDP bind to and regulate genes involved in ABA responses in seedlings • FT overexpressed in the phloem promotes flowering independently of FD and FDP, Florigen activating complex facilitates the response to day length in higher plants and contains a specific class of bZIP transcription factor. Romera-Branchat et al. analyze the two factors of this class in Arabidopsis and find they play distinct functions in flowering control and participate in ABA signaling in early development.
Published: 2020

36. Moonlighting Function of Phytochelatin Synthase1 in Extracellular Defense against Fungal Pathogens

Author: Melisa Lim, Mariola Piślewska-Bednarek, Rene Fuchs, Volker Lipka, Kian Hématy, Paweł Bednarek, Shauna Somerville, Clara Sánchez-Rodríguez, Candice Cherk, Erwin Grill, Paul Schulze-Lefert, Mónica Stein, Antonio Molina, Christine Klapprodt, Carnegie Institution for Science, Department of Plant Biology, Stanford University-Stanford University, Energy Biosciences Institute, University of California [Berkeley], University of California-University of California, Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research (MPIPZ), Institute of Bioorganic Chemistry, Polish Academy of Sciences (PAN), Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Schwann-Schleiden Research Center for Molecular Cell Biology, University Medical Center Göttingen (UMG), Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Lehrstuhl für Botanik, Technische Universtät München, and National Science Foundation (NSF) Carnegie Institution for Science Stanford University Max Planck SocietyFoundation CELLEX German Research Foundation (DFG)SPP1212GR 938LI 1317/2-1Spanish Ministry of Economy and Competitiveness (MINECO) BIO2015-64077-RBIO2012-32910Polish National Science Centre 2012/07/E/NZ2/04098
Subjects: 0106 biological sciences, Protein moonlighting, Physiology, [SDV]Life Sciences [q-bio], Mutant, Arabidopsis, Plant Science, 01 natural sciences, Catalysis, chemistry.chemical_compound, Arabidopsis-thaliana, Ascomycota, Gene Expression Regulation, Plant, Phytochelatins, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Research Articles, Heavy metal detoxification, Glucosinolate Metabolism, biology, Arabidopsis Proteins, Myrosinase, Binding Cassette Transporter, Nonhost Resistance, Tryptophan, Glutathione, Plants, Genetically Modified, biology.organism_classification, Mitochondria, Metabolic pathway, Biochemistry, chemistry, Gamma-glutamylcysteine, Phytochelatin, Pathogens, Tolerance, 010606 plant biology & botany
Abstract: Phytochelatin synthase (PCS) is a key component of heavy metal detoxification in plants. PCS catalyzes both the synthesis of the peptide phytochelatin from glutathione and the degradation of glutathione conjugates via peptidase activity. Here, we describe a role for PCS in disease resistance against plant pathogenic fungi. The pen4 mutant, which is allelic to cadmium insensitive1 (cad1/pcs1) mutants, was recovered from a screen for Arabidopsis mutants with reduced resistance to the nonadapted barley fungal pathogen Blumeria graminis f. sp. hordei. PCS1, which is found in the cytoplasm of cells of healthy plants, translocates upon pathogen attack and colocalizes with the PEN2 myrosinase on the surface of immobilized mitochondria. pcs1 and pen2 mutant plants exhibit similar metabolic defects in the accumulation of pathogen-inducible indole glucosinolate-derived compounds, suggesting that PEN2 and PCS1 act in the same metabolic pathway. The function of PCS1 in this pathway is independent of phytochelatin synthesis and deglycination of glutathione conjugates, as catalytic-site mutants of PCS1 are still functional in indole glucosinolate metabolism. In uncovering a peptidase-independent function for PCS1, we reveal this enzyme to be a moonlighting protein important for plant responses to both biotic and abiotic stresses.
Published: 2020

37. Re-evaluating the phylogenetic position of the enigmatic early Cambrian deuterostome Yanjiahella

Author: Oldřich Fatka, Przemysław Gorzelak, Samuel Zamora, Imran A. Rahman, Bertrand Lefebvre, Jeffrey R. Thompson, Rich Mooi, Timothy A. M. Ewin, Martina Nohejlová, James Sprinkle, Bruno David, Thomas E. Guensburg, Colin D. Sumrall, Elise Nardin, David F. Wright, Selina R. Cole, Mike Reich, Aaron W. Hunter, Instituto Geológico y Minero de España (IGME), Grupo Aragosaurus-IUCA, University of Zaragoza - Universidad de Zaragoza [Zaragoza], Division of Paleontology (Invertebrates), American Museum of Natural History (AMNH), Department of Paleobiology [Washington], Smithsonian Institution, Department of Invertebrate Zoology & Geology, California Academy of Sciences, Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement [Lyon] (LGL-TPE), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Integrative Research Center, Field Museum of Natural History [Chicago, USA], Institute of Paleobiology [Warsaw], Polska Akademia Nauk = Polish Academy of Sciences (PAN), Muséum national d'Histoire naturelle (MNHN), Department of Earth and Planetary Sciences [Knoxville], The University of Tennessee [Knoxville], Department of Earth Sciences [Cambridge, UK], University of Cambridge [UK] (CAM), School of Earth Sciences [Perth], The University of Western Australia (UWA), Department of Geological Sciences [Austin], Jackson School of Geosciences (JSG), University of Texas at Austin [Austin]-University of Texas at Austin [Austin], Department of Genetics, Evolution and Environment, University College of London [London] (UCL), The Natural History Museum [London] (NHM), Department of Geology and Palaeontology, Faculty of Science, Charles University, Géosciences Environnement Toulouse (GET), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-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), Staatliche Naturwissenschaftliche Sammlungen Bayerns (SNSB), Paleontology and Geobiology, Ludwig-Maximilians-Universität München (LMU), GeoBio-CenterLMU, Czech Geological Survey [Praha], Oxford University Museum of Natural History, University of Oxford [Oxford], Work supported by the Spanish Ministry of Science, Innovation and Universities [grant number CGL2017-87631], cofinanced by the European Regional Development Fund, project 'Aragosaurus: recursos geológicos y paleoambientales' (ref: E18_17R) funded by the Government of Aragón, by Gerstner Scholar and Lerner-Gray postdoctoral fellowships at the American Museum of Natural History (AMNH), by a Kathryn W. Davis postdoctoral fellowship at the AMNH, by a Royal Society Newton International Fellowship. I.A.R. is supported by the Oxford University Museum of Natural History., Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement (LGL-TPE), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), 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), Oxford University Museum of Natural History (OUMNH), University of Oxford, Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon)
Subjects: 0301 basic medicine, Geologic Sediments, China, 010506 paleontology, Science, Starfish, General Physics and Astronomy, 02 engineering and technology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Monophyly, Matters Arising, Chordata, Nonvertebrate, Animals, lcsh:Science, Clade, History, Ancient, Phylogeny, Taxonomy, 030304 developmental biology, 0105 earth and related environmental sciences, Appendage, 0303 health sciences, Multidisciplinary, Deuterostome, Phylogenetic tree, biology, Fossils, Palaeontology, Geology, General Chemistry, 021001 nanoscience & nanotechnology, biology.organism_classification, Biological Evolution, Position (obstetrics), 030104 developmental biology, Taxon, Body plan, Echinoderm, Evolutionary biology, lcsh:Q, Geologi, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, 0210 nano-technology, Echinodermata
Abstract: Recently we documented a bilaterally symmetrical, solitary organism, Yanjiahella biscarpa from the early Cambrian (Fortunian) of China1. We interpreted that Y. biscarpa possessed an echinoderm-like plated theca, a muscular stalk similar to hemichordates and a pair of long, feeding appendages. Our interpretation and our phylogenetic analysis suggest that Y. biscarpa is a stem-echinoderm, which would confirm that echinoderms acquired plates before pentaradial symmetry and that their history is firmly rooted in bilateral forms. Zamora et al.2 however, have criticized our interpretation, arguing against an echinoderm affinity, instead suggesting that the phylogenetic placement of Y. biscarpa is dubious and its significance for understanding deuterostome evolution is uncertain. This criticism2 seems to stem from our interpretation of particular morphological features in Y. biscarpa1 and the perceived lack of echinoderm synapomorphies. Echinoderms possess a calcitic skeleton with a distinctive three-dimensional mesh-like microstructure called stereom, that is considered a major synapomorphy of the Echinodermata3. Zamora et al.2 highlighted the absence of stereom in Y. biscarpa, additionally stating that we had omitted appropriate methods, specifically latex casting, that may confirm the presence of stereom in our specimens. We concede that initially we did not latex cast any specimens of Y. biscarpa, predominantly due to the fragile nature and the associated risk of damaging the specimens in question. In lieu of latex casting we employed Scanning Electron Microscopy (SEM) to investigate the surface and the details of Y. biscarpa specimens. SEM has been extensively used in the past to study stereom microstructure4,5,6 and if such a microstructure was preserved in Y. biscarpa it would have been detected using this technique. Artikeln är ett refereegranskat svar på en publicerad kommentar på en tidigare artikel.
Published: 2020

38. Genomic Footprints of Recovery in the European Bison

Author: Mathieu Gautier, Stanisław Kamiński, Tom Druet, Małgorzata Tokarska, Laurence Flori, Wanda Olech, Kamil Oleński, Amandine R. Bertrand, Druet, Tom, Université de Liège, University of Warmia and Mazury [Olsztyn], Systèmes d'élevage méditerranéens et tropicaux (UMR SELMET), 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), Warsaw University of Life Sciences (SGGW), Polish Academy of Sciences (PAN), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Fonds de la Recherche Scientifique - FNRS : J.0134.16, J.0154.18, University of Warmia and Mazury (Olsztyn, Poland) : 0105-804, 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), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro
Subjects: 0106 biological sciences, 0301 basic medicine, Genotype, [SDV]Life Sciences [q-bio], Population, european bison, ROH, RZooRoH, homozygous-by-descent, inbreeding, recovery, Biology, 010603 evolutionary biology, 01 natural sciences, Polymorphism, Single Nucleotide, 03 medical and health sciences, Data filtering, Genetics, Animals, [INFO]Computer Science [cs], Inbreeding, education, Molecular Biology, Genetics (clinical), education.field_of_study, Extinction, Genome, Bison, Whole Genome Sequencing, Small number, Homozygote, Genetic Variation, Founder Effect, Europe, 030104 developmental biology, Genetics, Population, Evolutionary biology, [SDE]Environmental Sciences, Biotechnology, Founder effect
Abstract: After extinction in the wild in the beginning of the 20th century, the European bison has been successfully recovered in 2 distinct genetic lines from only 12 and 7 captive founders. We here aimed at characterizing the levels of realized inbreeding in these 2 restored lines to provide empirical insights into the genomic footprints left by population recovery from a small number of founders. To that end, we genotyped 183 European bison born over the last 40 years with the Illumina BovineHD beadchip that contained 22 602 informative autosomal single-nucleotide polymorphisms after data filtering. We then identified homozygous-by-descent (HBD) segments and classified them into different age-related classes relying on a model-based approach. As expected, we observed that the strong and recent founder effect experienced by the 2 lines resulted in very high levels of recent inbreeding and in the presence of long HBD tracks (up to 120 Mb). These long HBD tracks were associated with ancestors living approximately from 4 to 32 generations in the past, suggesting that inbreeding accumulated over multiple generations after the bottleneck. The contribution to inbreeding of the most recent groups of ancestors was however found to be decreasing in both lines. In addition, comparison of Lowland individuals born at different time periods showed that the levels of inbreeding tended to stabilize, HBD segments being shorter in animals born more recently which indicates efficient control of inbreeding. Monitoring HBD segment lengths over generations may thus be viewed as a valuable genomic diagnostic tool for populations in conservation or recovery programs.
Published: 2020

39. Successful post-glacial colonization of Europe by single lineage of freshwater amphipod from its Pannonian Plio-Pleistocene diversification hotspot

Author: Hedvig Kriszta Csapó, Tomasz Mamos, Tomasz Rewicz, Paula Krzywoźniak, Michał Grabowski, Karolina Bącela-Spychalska, Mišel Jelić, Rémi Wattier, Institute of Oceanology, Polska Akademia Nauk = Polish Academy of Sciences (PAN), Department of Invertebrate Zoology and Hydrobiology, Łódź University of Technology, Department of Hydrobiology, University of Pecs, Biogéosciences [UMR 6282] [Dijon] (BGS), 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), Zoological Institute, University of Basel (Unibas), Department of Natural Sciences, Varaždin City Museum, Biodiversity Institute of Ontario, Centre for Biodiversity Genomics, University of Guelph, and Work supported by internal funds of the University of Lodz as well as, partly, by the Polish Ministry of Science and Education (Grant No. NN303 579439) and National Science Centre, Poland (Grant No. 2014/15/B/NZ8/00266), internal funds of the UMR-CNRS-Ub-6282 Biogéosciences and the Burgundy Region.
Subjects: 0106 biological sciences, 0301 basic medicine, Evolution, lcsh:Medicine, Zoology, Fresh Water, Biology, 010603 evolutionary biology, 01 natural sciences, Article, 03 medical and health sciences, Species Specificity, Ice age, Animals, Amphipoda, Glacial period, Internal transcribed spacer, lcsh:Science, Genetic diversity, Multidisciplinary, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Ecology, lcsh:R, Plio-Pleistocene, Biological Evolution, Europe, Colonisation, Phylogeography, 030104 developmental biology, Taxon, Haplotypes, Gammarus, lcsh:Q, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: Gammarus roeselii Gervais, 1835 is a morphospecies with a wide distribution range in Europe. The Balkan Peninsula is known as an area of pre-Pleistocene cryptic diversification within this taxon, resulting in at least 13 Molecular Operational Taxonomic Units (MOTUs). The morphospecies diversified there during Neogene and has probably invaded other parts of the continent very recently, in postglacial or even historical times. Thus, the detailed goals of our study were to (1) identify which lineage(s) colonized Central-Western Europe (CWE), (2) determine their possible geographical origin, (3) verify, whether the colonisation was associated with demographic changes. In total, 663 individuals were sequenced for the cytochrome oxidase I (COI) barcoding fragment and 137 individuals for the internal transcribed spacer II (ITS2). We identified two MOTUs in the study area with contrasting Barcode Index Number and haplotype diversities. The Pannonian Basin (PB) appeared to be a potential ice age refugium for the species, while CWE was colonised by a single lineage (also present in PB), displaying low genetic diversity. Our results suggest that G. roeselii is a relatively recent coloniser in CWE, starting demographic expansion around 10 kya.
Published: 2020

40. Evolutionary plasticity of mating-type determination mechanisms in Paramecium aurelia sibling species

Author: Simon Penel, Linda Sperling, Alexey Potekhin, Sebastian Tarcz, Irina Nekrasova, Inessa Grevtseva, Deepankar Pratap Singh, Eric Meyer, Natalia Sawka-Gądek, Olivier Arnaiz, Laurent Duret, Polish Academy of Sciences (PAN), Saint Petersburg State University (SPBU), 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), 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), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), ANR-18-CE12-0005,LaMarque,Transitions évolutives dans la reconnaissance du 'soi' génomique: petits ARN, facteurs spécifiques de séquence et méthylation de l'ADN(2018), SERRE, Marie-Claude, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), École normale supérieure - Paris (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 Paris), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, and 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)
Subjects: AcademicSubjects/SCI01140, 0106 biological sciences, Mating type, Paramecium, [SDV]Life Sciences [q-bio], Gene Expression, Biology, 010603 evolutionary biology, 01 natural sciences, Evolution, Molecular, 03 medical and health sciences, symbols.namesake, Gene duplication, Genetics, Allele, Gene, Alleles, Phylogeny, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Mating type determination, Paramecium aurelia, 0303 health sciences, self-incompatibility systems, programmed genome rearrangements, AcademicSubjects/SCI01130, evolutionary genomics, Membrane Proteins, biology.organism_classification, [SDV] Life Sciences [q-bio], Mendelian inheritance, symbols, Epistasis, ciliates, Research Article
Abstract: The Paramecium aurelia complex, a group of morphologically similar but sexually incompatible sibling species, is a unique example of the evolutionary plasticity of mating-type systems. Each species has two mating types, O (Odd) and E (Even). Although O and E types are homologous in all species, three different modes of determination and inheritance have been described: genetic determination by Mendelian alleles, stochastic developmental determination, and maternally inherited developmental determination. Previous work in three species of the latter kind has revealed the key roles of the E-specific transmembrane protein mtA and its highly specific transcription factor mtB: type O clones are produced by maternally inherited genome rearrangements that inactivate either mtA or mtB during development. Here we show, through transcriptome analyses in five additional species representing the three determination systems, that mtA expression specifies type E in all cases. We further show that the Mendelian system depends on functional and nonfunctional mtA alleles, and identify novel developmental rearrangements in mtA and mtB which now explain all cases of maternally inherited mating-type determination. Epistasis between these genes likely evolved from less specific interactions between paralogs in the P. aurelia common ancestor, after a whole-genome duplication, but the mtB gene was subsequently lost in three P. aurelia species which appear to have returned to an ancestral regulation mechanism. These results suggest a model accounting for evolutionary transitions between determination systems, and highlight the diversity of molecular solutions explored among sibling species to maintain an essential mating-type polymorphism in cell populations.
Published: 2020

41. Diverse responses of common vole (Microtus arvalis) populations to Late Glacial and Early Holocene climate changes – Evidence from ancient DNA

Author: Emmanuel Desclaux, Katarzyna Baca, Xabier Murelaga, Jarosław Wilczyński, Magdalena Krajcarz, Monika Knul, Barbara Miękina, Evelyne Crégut-Bonnoure, Ivan Horáček, Anna Lemanik, Jadranka Mauch Lenardić, Claudio Berto, Karolina Doan, Gloria Cuenca-Bescós, Mateusz Baca, Piroska Pazonyi, Danijela Popović, Juan Manuel López-García, Adam Nadachowski, Alexandru Petculescu, John R. Stewart, Zoran Marković, Sandra Bañuls-Cardona, Institute of Systematics and Evolution of Animals, Polish Academy of Sciences (PAN), Culture et Environnements, Préhistoire, Antiquité, Moyen-Age (CEPAM), Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Travaux et recherches archéologiques sur les cultures, les espaces et les sociétés (TRACES), École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)
Subjects: 010506 paleontology, Archeology, post-glacial recolonization, Younger Dryas, 010504 meteorology & atmospheric sciences, Pleistocene, Climate change, 01 natural sciences, Glacial period, common vole, mtDNA, post-glacial recolonization, ancient DNA, Younger Dryas, Holocene, common vole, ancient DNA, Ecology, Evolution, Behavior and Systematics, Holocene, 0105 earth and related environmental sciences, Global and Planetary Change, biology, mtDNA, Ecology, Geology, Last Glacial Maximum, 15. Life on land, biology.organism_classification, humanities, Ancient DNA, Geography, 13. Climate action, Vole, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology
Abstract: The harsh climatic conditions during the Last Glacial Maximum (LGM) period have been considered the cause of local extinctions and major faunal reorganizations that took place at the end of the Pleistocene. Recent studies have shown, however, that in addition many of these ecological events were associated with abrupt climate changes during the so-called Late Glacial and the Pleistocene/Holocene transition. Here we used ancient DNA to investigate the impact of those changes on common vole (Microtus arvalis) populations in Europe. The common vole is a temperate rodent species widespread in Europe. The genetic diversity of modern populations and the fossil record suggests that the species may have survived cold episodes, like LGM, not only in the traditional Mediterranean glacial refugia but also at higher latitudes in cryptic northern refugia located in Central France, the northern Alps as well as the Carpathians. However, the details of the post-glacial recolonization and the impact of the Late Glacial and Early Holocene climate changes on the evolutionary history of the common vole remains unclear. To address this issue, we analysed mtDNA cytochrome b sequences from more than one hundred common vole specimens from 36 paleontological and archaeological sites scattered across Europe. Our data suggest that populations from the European mid- and high latitudes suffered a local population extinction and contraction as a result of Late Glacial and Early Holocene climate and environmental changes. The recolonization of earlier abandoned areas took place in the Mid- to Late Holocene. In contrast, at low latitudes, in Northern Spain there was a continuity of common vole populations. This indicates different responses of common vole populations to climate and environmental changes across Europe and corroborates the hypothesis that abrupt changes, like those associated with Younger Dryas and the Pleistocene/Holocene transition, had a significant impact on populations at the mid- and high latitudes of Europe.
Published: 2020

42. Carbohydrates stimulated Amaryllidaceae alkaloids biosynthesis in Leucojum aestivum L. plants cultured in RITA ® bioreactor

Author: Edyta Skrzypek, Emilia Morańska, Magdalena Simlat, Marzena Warchoł, Dominique Laurain-Mattar, Rosella Spina, Agata Ptak, Agricultural University of Krakow, Polska Akademia Nauk (PAN), Laboratoire Lorrain de Chimie Moléculaire (L2CM), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), MEAE and MESRI PHC Polonium project, Polska Akademia Nauk = Polish Academy of Sciences (PAN), and Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Leucojum aestivum, Sucrose, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, lcsh:Medicine, Plant Science, Lycorine, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, chemistry.chemical_compound, In vitro, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, [CHIM]Chemical Sciences, Food science, Agricultural Science, Sugar, Amaryllidaceae Alkaloids, 030304 developmental biology, 0303 health sciences, Carbon sources, biology, General Neuroscience, lcsh:R, food and beverages, Fructose, General Medicine, Maltose, Amaryllidaceae, 15. Life on land, biology.organism_classification, chemistry, Galanthamine, General Agricultural and Biological Sciences, Biotechnology, 010606 plant biology & botany
Abstract: BackgroundLeucojum aestivumL. is an important medicinal plant which produces Amaryllidaceae alkaloids, especially galanthamine and lycorine. Research is currently exploring the possibility of producing these alkaloids using biotechnological methods, including in vitro cultures. The biosynthesis of alkaloids may be affected by the types and concentrations of carbohydrate sources used in the medium. In the present investigation we performed such studies on in vitro cultures ofL. aestivumwith a view to obtaining plant material of good quality, characterized, in particular, by a high content of valuable Amaryllidaceae alkaloids.MethodsWe examined the effects of various types of carbohydrate sources—sucrose, glucose, fructose and maltose—at different concentrations (30, 60 and 90 g/L)—on the quality ofL. aestivumplants grown in the RITA®bioreactor. The plants’ quality was assessed by their biomass increments, as well by as analysing photosynthetic pigments, endogenous sugar, phenolics and Amaryllidaceae alkaloid content. We also investigated the effect of sugars on the activity of the antioxidant enzymes catalase (CAT), peroxidase (POD) and superoxide dismutase (SOD).ResultsThe highest biomass increments were observed in plants cultivated in the medium containing 90 g/L sucrose. The highest CAT activity was noted in cultures growing in the medium supplemented with 90 g/L maltose, while the highest POD activity was observed in the presence of 90 g/L fructose and 60 g/L maltose. No differences in SOD activity were observed. Moreover, the sugars did not affect the contents of chlorophyllaand carotenoids, whereas the highest amount of chlorophyllbwas recorded in plants growing in the medium with 60 g/L maltose. No statistically significant differences were observed in the contents of endogenous sugars and phenolics in any in vitro conditions. However, the addition of sugar had a decisive effect on the biosynthesis of the Amaryllidaceae alkaloids. The highest distribution of alkaloids occurred in plants cultured in the medium containing 60 g/L sucrose. Six Amaryllidaceae alkaloids were detected in the plant tissue. The addition of 30 g/L fructose in the medium resulted in the accumulation of five alkaloids, including ismine, which was not identified in other analysed tissues. The highest concentration of galanthamine was observed in plants cultured in the presence of 30 g/L fructose and 60 g/L sucrose (39.2 and 37.5 µg/g of dry weight (DW), respectively). The plants grown in the medium containing 60 g/L sucrose exhibited the highest lycorine content (1048 µg/g of DW).ConclusionsThe type and concentration of sugar used in the medium have an essential influence on the biosynthesis of Amaryllidaceae alkaloids inL. aestivumplants cultured in a RITA®bioreactor. The results point to an interesting approach for commercial production of galanthamine and lycorine.
Published: 2020

43. Assessing the response of forest productivity to climate extremes in Switzerland using model-data fusion

Author: Flurin Babst, Arthur Gessler, Esther Thürig, Werner Eugster, Volodymyr Trotsiuk, Marco Ferretti, Andreas Rigling, Nina Buchmann, Maxime Cailleret, Harald Bugmann, Marcus Schaub, Mana Gharun, Francesco Minunno, David I. Forrester, Florian Hartig, Jonas Stillhard, Andri Baltensweiler, Peter Waldner, Brigitte Rohner, Department of Environmental Systems Science [ETH Zürich] (D-USYS), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Department of Forest Ecology, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague (CZU), University of Regensburg, Risques, Ecosystèmes, Vulnérabilité, Environnement, Résilience (RECOVER), Aix Marseille Université (AMU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), W. Szafer Institute of Botany, Polska Akademia Nauk = Polish Academy of Sciences (PAN), Institute of Agricultural Sciences [Zürich], Institute of Terrestrial Ecosystems (ITES), Department of Forest Sciences [Helsinki], Faculty of Agriculture and Forestry [Helsinki], Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Wiley, University of Helsinki-University of Helsinki, Department of Forest Sciences, Ecosystem processes (INAR Forest Sciences), and Forest Modelling Group
Subjects: 0106 biological sciences, GROSS PRIMARY PRODUCTIVITY, SPECIES INTERACTIONS, 010504 meteorology & atmospheric sciences, Fagus sylvatica, Species distribution, Bayesian inference, carbon cycling, drought, Atmospheric sciences, ecosystem productivity, 01 natural sciences, Primary Research Article, General Environmental Science, 4112 Forestry, Global and Planetary Change, model calibration, Ecology, biology, MULTIPLE DATA STREAMS, Productivity (ecology), 1181 Ecology, evolutionary biology, CARBON-CYCLE, 1171 Geosciences, extreme events, [SDE.MCG]Environmental Sciences/Global Changes, inverse modeling, 010603 evolutionary biology, Carbon cycle, TEMPORAL DYNAMICS, Forest ecology, NET PRIMARY PRODUCTION, Environmental Chemistry, Ecosystem, data assimilation, 1172 Environmental sciences, 0105 earth and related environmental sciences, Picea abies, Primary production, PINUS-SYLVESTRIS, 15. Life on land, biology.organism_classification, Primary Research Articles, BAYESIAN CALIBRATION, Carbon cycling, Data assimilation, Drought, Ecosystem productivity, Extreme events, Inverse modeling, Model calibration, 13. Climate action, Environmental science, CONSTANT FRACTION, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: The response of forest productivity to climate extremes strongly depends on ambient environmental and site conditions. To better understand these relationships at a regional scale, we used nearly 800 observation years from 271 permanent long‐term forest monitoring plots across Switzerland, obtained between 1980 and 2017. We assimilated these data into the 3‐PG forest ecosystem model using Bayesian inference, reducing the bias of model predictions from 14% to 5% for forest stem carbon stocks and from 45% to 9% for stem carbon stock changes. We then estimated the productivity of forests dominated by Picea abies and Fagus sylvatica for the period of 1960–2018, and tested for productivity shifts in response to climate along elevational gradient and in extreme years. Simulated net primary productivity (NPP) decreased with elevation (2.86 ± 0.006 Mg C ha−1 year−1 km−1 for P. abies and 0.93 ± 0.010 Mg C ha−1 year−1 km−1 for F. sylvatica). During warm–dry extremes, simulated NPP for both species increased at higher and decreased at lower elevations, with reductions in NPP of more than 25% for up to 21% of the potential species distribution range in Switzerland. Reduced plant water availability had a stronger effect on NPP than temperature during warm‐dry extremes. Importantly, cold–dry extremes had negative impacts on regional forest NPP comparable to warm–dry extremes. Overall, our calibrated model suggests that the response of forest productivity to climate extremes is more complex than simple shift toward higher elevation. Such robust estimates of NPP are key for increasing our understanding of forests ecosystems carbon dynamics under climate extremes., We assimilated extensive and long‐term monitoring data into the 3‐PG forest ecosystem model to assess how forest productivity responds to climate extremes across environmental gradients in Switzerland. Data assimilation using Bayesian inference significantly improved model predictions. During warm–dry extremes, net primary productivity increased at higher and decreased at lower elevations, with reductions in NPP of more than 25% for one‐fifth of the potential species distribution range in Switzerland.
Published: 2020

44. Monitoring the ecological status of rivers with diatom eDNA metabarcoding: a comparison of taxonomic markers and analytical approaches for the inference of a molecular diatom index

Author: Jan Pawlowski, Arielle Cordonier, Agnès Bouchez, Frédéric Rimet, Tristan Cordier, Julie Guéguen, Laure Apothéloz-Perret-Gentil, Valentin Vasselon, University of Geneva [Switzerland], ID GENE ECODIAGNOSTICS UNIVERSITE DE GENEVE CHE, 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), Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Water Ecology Service, Pôle Écla - écosystèmes lacustres (ECLA), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Office français de la biodiversité (OFB), Institute of Oceanology, Polish Academy of Sciences (IO-PAN), Polska Akademia Nauk = Polish Academy of Sciences (PAN), and European Cross-Border Cooperation Program (Interreg France-Switzerland 2014-2020) Swiss canton (Valais) Swiss canton (Geneva) Swiss canton (Vaud) Swiss National Science Foundation (SNSF)31003A_179125European Union (EU)CA15219
Subjects: 0106 biological sciences, 0301 basic medicine, Index (economics), Inference, NOVEL APPROACHES TO MONITOR ECOSYSTEMS, Biology, aquatic bioindication, 010603 evolutionary biology, 01 natural sciences, 18S ribosomal RNA, diatoms, Machine Learning, 03 medical and health sciences, Rivers, Genetics, DNA Barcoding, Taxonomic, Environmental DNA, Ecology, Evolution, Behavior and Systematics, Quality assessment, Ecology, Special Issue, taxonomy‐free, 15. Life on land, taxonomy&#8208, biology.organism_classification, environmental DNA, 030104 developmental biology, Diatom, biomonitoring, metabarcoding, Reference database, free, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Biomarkers, Ecological Genomics, Environmental Monitoring
Abstract: International audience; Recently, several studies demonstrated the usefulness of diatom eDNA metabarcoding as an alternative to assess the ecological quality of rivers and streams. However, the choice of the taxonomic marker as well as the methodology for data analysis differ between these studies, hampering the comparison of their results and effectiveness. The aim of this study was to compare two taxonomic markers commonly used in diatom metabarcoding and three distinct analytical approaches to infer a molecular diatom index. We used the values of classical morphological diatom index as a benchmark for this comparison. We amplified and sequenced both a fragment of the rbcL gene and the V4 region of the 18S rRNA gene for 112 epilithic samples from Swiss and French rivers. We inferred index values using three analytical approaches: by computing it directly from taxonomically assigned sequences, by calibrating de novo the ecovalues of all metabarcodes, and by using a supervised machine learning algorithm to train predictive models. In general, the values of index obtained using the two "taxonomy-free" approaches, encompassing molecular assignment and machine learning, were closer correlated to the values of the morphological index than the values based on taxonomically assigned sequences. The correlations of the three analytical approaches were higher in the case of rbcL compared to the 18S marker, highlighting the importance of the reference database which is more complete for the rbcL marker. Our study confirms the effectiveness of diatom metabarcoding as an operational tool for rivers ecological quality assessment and shows that the analytical approaches by-passing the taxonomic assignments are particularly efficient when reference databases are incomplete.
Published: 2020

45. Interaction of climate change with effects of conspecific and heterospecific density on reproduction

Author: Møller, Anders Pape, Balbontín, Javier, Dhondt, André A., Adriaensen, Frank, Artemyev, Alexandr, Bańbura, Jerzy, Barba, Emilio, Biard, Clotilde, Blondel, Jacques, Bouvier, Jean-Charles, Camprodon, Jordi, Cecere, Francesco, Charter, Motti, Cichoń, Mariusz, Cusimano, Camillo, Dubiec, Anna, Eens, Marcel, Eeva, Tapio, Ferns, Peter N., Forsman, Jukka T., Goldshtein, Aya, Goodenough, Anne E., Gosler, Andrew G., Gustafsson, Lars, Harnist, Iga, Hartley, Ian R., Heeb, Philipp, Hinsley, Shelley A., Jacob, Staffan, Järvinen, Antero, Juškaitis, Rimvydas, Korpimäki, Erkki, Krams, Indrikis, Laaksonen, Toni, Leclercq, Bernard, Lehikoinen, Esa, Loukola, Olli, Mainwaring, Mark C., Mänd, Raivo, Massa, Bruno, Matthysen, Erik, Mazgajski, Tomasz D., Merino, Santiago, Mitrus, Cezary, Mönkkönen, Mikko, Nager, Ruedi G., Nilsson, Jan-Åke, Nilsson, Sven G., Norte, Ana C., von Numers, Mikael, Orell, Markku, Pimentel, Carla S., Pinxten, Rianne, Priedniece, Ilze, Remeš, Vladimir, Richner, Heinz, Robles Díez, Hugo, Rytkönen, Seppo, Senar, Juan Carlos, Seppänen, Janne T., da Silva, Luís P., Slagsvold, Tore, Solonen, Tapio, Sorace, Alberto, Stenning, Martyn J., Török, János, Tryjanowski, Piotr, van Noordwijk, Arie J., Walankiewicz, Wiesław, Lambrechts, Marcel M., Moller, Anders Pape, Balbontin, Javier, Dhondt, Andre A., Banbura, Jerzy, Cichon, Mariusz, Jarvinen, Antero, Juskaitis, Rimvydas, Korpimaki, Erkki, Mand, Raivo, Monkkonen, Mikko, Nilsson, Jan-ake, Remes, Vladimir, Rytkonen, Seppo, Seppanen, Janne T., da Silva, Luis P., Torok, Janos, Walankiewicz, Wieslaw, Helsinki Institute of Sustainability Science (HELSUS), Organismal and Evolutionary Biology Research Programme, Kilpisjärvi Biological Station, Ecologie Systématique et Evolution (ESE), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Universidad de Sevilla / University of Sevilla, Cornell University [New York], University of Antwerp (UA), Russian Academy of Sciences [Moscow] (RAS), University of Lódź, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier 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), Unité de recherche Plantes et Systèmes de Culture Horticoles (PSH), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre de Ciència i Tecnologia Forestal de Catalunya (CTFC), University of Haifa [Haifa], Uniwersytet Jagielloński w Krakowie = Jagiellonian University (UJ), Stazione Ornitologica di Palermo, Polish Academy of Sciences (PAN), Université de Lyon, University of Turku, School of Biosciences [Cardiff], Cardiff University, University of Oulu, Tel Aviv University (TAU), University of Gloucestershire (Cheltenham, GB), Edward Grey Institute, Department of Zoology, University of Oxford, Uppsala University, Lancaster University, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Centre for Ecology and Hydrology [Wallingford] (CEH), Natural Environment Research Council (NERC), Station d'écologie théorique et expérimentale (SETE), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-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), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Nature Research Centre, Institute of Ecology, Akademijos str. 2, LT-08412, Vilnius, Lithuania., University of Tartu, University of Montana, Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Uniwersytet Wroclawski, University of Jyväskylä (JYU), University of Glasgow, Lund University [Lund], Marine and Environmental Sciences Centre (MARE UC), Universidade de Coimbra [Coimbra], Åbo Akademi University [Turku], Université de Lisbonne, Latvian Fund for Nature, Palacky University Olomouc, University of Bern, University of A Coruña (UDC), Museu de Ciències Naturals de Barcelona, Universidade do Porto = University of Porto, University of Oslo (UiO), Luontotutkimus Solonen Oy, SROPU, University of Sussex, Eötvös Loránd University (ELTE), Poznan University of Life Sciences (Uniwersytet Przyrodniczy w Poznaniu) (PULS), Netherlands Institute of Ecology - NIOO-KNAW (NETHERLANDS), IB KRC RAS no. 0218-2019-0080, Academy of Finland (project 265859), Ministry of Economy and Competitivity, Spanish Research Council: research project CGL-2016-79568-C3-3-P, ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), Animal Ecology (AnE), Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, Universidad de Sevilla, Cavanilles Institute of Biodiversity and Evolutionary Biology, Terrestrial Vertebrates Group, Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (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 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), 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), Tel Aviv University [Tel Aviv], University of Oxford [Oxford], Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (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), University of Helsinki, Universidade do Porto, Russian Academy of Sciences, Academy of Finland, Ministerio de Economía y Competitividad (España), Consejo Superior de Investigaciones Científicas (España), Université Paul-Valéry - Montpellier 3 (UPVM)-École pratique des hautes études (EPHE), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-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)
Subjects: BREEDING SUCCESS, 0106 biological sciences, Avian clutch size, clutch size, Q1, 01 natural sciences, DEPENDENCE, Parus major, sinitiainen, POPULATION, QL_671, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, education.field_of_study, GE, biology, Ecology, Blue tit, tiaiset, Cyanistes, blue tit, Plan_S-Compliant_NO, talitiainen, Spatial heterogeneity, Chemistry, great tit, international, 1181 Ecology, evolutionary biology, lämpötila, laying date, CLUTCH-SIZE, intraspecific competition, Population, HABITAT HETEROGENEITY, PARUS-MAJOR, 010603 evolutionary biology, Ecology and Environment, Intraspecific competition, temperature anomaly, muninta, QH301, BLUE, Cyanistes caeruleus, education, Biology, Ecology, Evolution, Behavior and Systematics, Interspecioc competition, FICEDULA, Parus, QL, pesintä, lisääntymiskäyttäytyminen, BIRDS, 010604 marine biology & hydrobiology, interspecific competition, Ficedula, Interspecific competition, ilmastonmuutokset, biology.organism_classification, 13. Climate action, GREAT TITS
Abstract: We studied the relationship between temperature and the coexistence of great tit Parus major and blue tit Cyanistes caeruleus, breeding in 75 study plots across Europe and North Africa. We expected an advance in laying date and a reduction in clutch size during warmer springs as a general response to climate warming and a delay in laying date and a reduction in clutch size during warmer winters due to density-dependent effects. As expected, as spring temperature increases laying date advances and as winter temperature increases clutch size is reduced in both species. Density of great tit affected the relationship between winter temperature and laying date in great and blue tit. Specifically, as density of great tit increased and temperature in winter increased both species started to reproduce later. Density of blue tit affected the relationship between spring temperature and blue and great tit laying date. Thus, both species start to reproduce earlier with increasing spring temperature as density of blue tit increases, which was not an expected outcome, since we expected that increasing spring temperature should advance laying date, while increasing density should delay it cancelling each other out. Climate warming and its interaction with density affects clutch size of great tits but not of blue tits. As predicted, great tit clutch size is reduced more with density of blue tits as temperature in winter increases. The relationship between spring temperature and density on clutch size of great tits depends on whether the increase is in density of great tit or blue tit. Therefore, an increase in temperature negatively affected the coexistence of blue and great tits differently in both species. Thus, blue tit clutch size was unaffected by the interaction effect of density with temperature, while great tit clutch size was affected in multiple ways by these interactions terms., A. Artemyev acknowledges funding by IB KRC RAS no. 0218-2019-0080 and T. Eeva acknowledges funding by the Academy of Finland (project 265859). This study was funded by research project CGL-2016-79568-C3-3-P (to J. C. Senar), from the Ministry of Economy and Competitivity, Spanish Research Council.
Published: 2020

46. Experimental neoichnology of post-autotomy arm movements of sea lilies and possible evidence of thrashing behaviour in Triassic holocrinids

Author: Przemysław Gorzelak, Tomasz Brachaniec, Dorota Kołbuk, Krzysztof R. Brom, Thomas Saucède, Kazumasa Oguri, Marek Dec, Mariusz A. Salamon, Tatsuo Oji, Institute of Paleobiology [Warsaw], Polska Akademia Nauk = Polish Academy of Sciences (PAN), Faculty of Natural Sciences, University of Silesia in Katowice, University Museum, Nagoya University, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Polish Geological Institute, National Research Institute, Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, and Grants from the National Science Centre (Grant Number UMO-2018/31/B/ST10/00387), the National Science Centre Grant No. 2015/17/N/ST10/03069, the PROM programme 2018/2019 – International scholarship exhange of PhD candidates and academic staff, Project No. POWR.03.03.00-IP.08-00-P13/18, the Nagoya University Grant, the Japan Society of the Promotion of Science (Kakenhi, Grant Number 15K12197).
Subjects: 0106 biological sciences, 010506 paleontology, Range (biology), Movement, Early Triassic, Metacrinus rotundus, Zoology, lcsh:Medicine, 01 natural sciences, Article, Predation, Mesozoic marine revolution, Animals, lcsh:Science, 0105 earth and related environmental sciences, Appendage, Multidisciplinary, biology, Behavior, Animal, Fossils, palaeontology, 010604 marine biology & hydrobiology, lcsh:R, experimental neoichnology, Extremities, palaeoecology, Crinoid, biology.organism_classification, Biological Evolution, Biomechanical Phenomena, Predatory Behavior, Triassic holocrinids, lcsh:Q, sea lilies, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, Autotomy, Echinodermata
Abstract: Echinoderms exhibit remarkable powers of autotomy. For instance, crinoids can shed arm and stalk portions when attacked by predators. In some species, it has been reported that the autotomized arms display vigorous movements, which are thought to divert the attention of predators. This phenomenon, however, has not been well explored. Here we present results of experiments using the shallowest water species of living stalked crinoid (Metacrinus rotundus) collected at 140 m depth. A wide range of movements of detached arms, from sluggish writhing to violent flicks, was observed. Interestingly, autotomized arms produce distinct traces on the sediment surface. They are composed of straight or arched grooves usually arranged in radiating groups and shallow furrows. Similar traces were found associated with detached arms of the oldest (Early Triassic) stem-group isocrinid (Holocrinus). This finding may suggest that the origins of autotomy-related thrashing behaviour in crinoids could be traced back to at least the Early Triassic, underscoring the magnitude of anti-predatory traits that occurred during the Mesozoic Marine Revolution. A new ethological category, autotomichnia, is proposed for the traces produced by thrashing movements of shed appendages.
Published: 2020

47. Enhancing photocatalytic performance and solar absorption by schottky nanodiodes heterojunctions in mechanically resilient palladium coated TiO2/Si nanopillars by atomic layer deposition

Author: Karol Załęski, Katarzyna Siuzdak, Marcin Ziółek, Octavio Graniel, Matthieu Weber, Mikhael Bechelany, Mykola Pavlenko, Igor Iatsunskyi, Philippe Miele, Emerson Coy, Sebastien Balme, Adam Mickiewicz University in Poznań (UAM), Szewalski Institute of Fluid-Flow Machinery [Gdańsk] (IMP), Polska Akademia Nauk = Polish Academy of Sciences (PAN), Institut Européen des membranes (IEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM), Institut Charles Gerhardt Montpellier - Institut de Chimie Moléculaire et des Matériaux de Montpellier (ICGM ICMMM), and Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut de Chimie du CNRS (INC)
Subjects: Materials science, General Chemical Engineering, chemistry.chemical_element, 02 engineering and technology, Electron, 010402 general chemistry, 01 natural sciences, 7. Clean energy, Industrial and Manufacturing Engineering, Atomic layer deposition, Environmental Chemistry, [CHIM]Chemical Sciences, Nanopillar, biology, business.industry, Schottky diode, Heterojunction, General Chemistry, 021001 nanoscience & nanotechnology, biology.organism_classification, 0104 chemical sciences, chemistry, Photocatalysis, Optoelectronics, Nanodiodes, 0210 nano-technology, business, Palladium
Abstract: International audience; The development of highly efficient photocatalytic materials and composites has been one of the main goals in the energy and environmental fields. To this date, however, the efficiency and stability of photocatalytic materials are still very low. This work shows a novel strategy of Pd coated TiO2/Si nanopillars produced by atomic layer deposition with a wide light absorption window. The structures show significantly improved performance due to the synergistic effect of Pd decorated TiO2/Si nanopillars, and the cooperative effect between Hot and Photoexcited electrons and Schottky nanojunctions. The performance of the composites is evaluated, the enhancement mechanism is explained and the advantages of the rational design of these materials are discussed.
Published: 2020
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48. Integrated bio- and carbon-isotope stratigraphy of the Upper Cretaceous Gurpi Formation (Iran): A new reference for the eastern Tethys and its implications for large-scale correlation of stage boundaries

Author: Nicolas Thibault, Amir Mohammad Jamali, Silke Voigt, Anoshiravan Kani, Samira Shahriari, Théophile Cocquerez, Clemens V. Ullmann, Mohammad Javad Razmjooei, Wiesława Radmacher, Emmanuelle Pucéat, Jaume Dinarès-Turell, Department of Geology, Shahid Beheshti University, Department of Geosciences and Natural Resource Management [Copenhagen] (IGN), Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Istituto Nazionale di Geofisica e Vulcanologia - Sezione di Roma (INGV), Istituto Nazionale di Geofisica e Vulcanologia, Biogéosciences [UMR 6282] [Dijon] (BGS), 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), Institute of Geological Sciences, Polish Academy of Sciences (PAN), Exploration Directorate, National Iranian Oil Company, Camborne School of Mines & Environment and Sustainability Institute, University of Exeter, Institute of Geosciences [Frankfurt am Main], Goethe-Universität Frankfurt am Main, Carlsberg Foundation (Carlsbergfondet 2013-01-0425 and CF16-0457)., and Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement
Subjects: 010506 paleontology, Structural basin, 010502 geochemistry & geophysics, 01 natural sciences, Paleontology, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, Stage (stratigraphy), Calcareous nannofossils, 14. Life underwater, 0105 earth and related environmental sciences, biology, Stable isotope ratio, Dinoflagellate cysts, Carbon isotopes, Dinoflagellate, Planktic foraminifera, Plankton, biology.organism_classification, Zagros, Cretaceous, Stratigraphy, 13. Climate action, Isotopes of carbon, Tethyan realm, [SDU.STU.ST]Sciences of the Universe [physics]/Earth Sciences/Stratigraphy, Coniacian–Maastrichtian, Geology
Abstract: 29 pages; International audience; A high-resolution stratigraphic analysis of the Upper Cretaceous Gurpi Formation has been undertaken in the Shahneshin section (Zagros Basin, Iran). New results on calcareous nannofossils, planktic foraminifers, dinoflagellate cysts and high-resolution carbon and oxygen stable isotopes form the basis of a reference section for the eastern Tethys that spans the upper Coniacian to the late Danian. Carbon-isotope correlation to Gubbio, Italy and the NW German chalk allows for the identification of many isotopic events as well as for the definition of new events in the Campanian and Maastrichtian. Our results allow for a review of the accurate position of the Coniacian/Santonian, Santonian/Campanian, and Campanian/Maastrichtian stage boundaries relative to carbon isotopes and plankton bioevents. The reliability of Coniacian to Maastrichtian planktic foraminifer, dinoflagellate cysts and calcareous nannofossil biohorizons is assessed.
Published: 2018

49. Foraging habitats and niche partitioning of European large herbivores during the Holocene – Insights from 3D dental microwear texture analysis

Author: Gildas Merceron, Emilie Berlioz, Daniel Makowiecki, Hervé Bocherens, Anusha Ramdarshan, Rafał Kowalczyk, Giedrė Piličiauskienė, Emilia Hofman-Kamińska, Mammal Research Institute, Polska Akademia Nauk = Polish Academy of Sciences (PAN), Laboratoire de paléontologie, évolution, paléoécosystèmes, paléoprimatologie (PALEVOPRIM ), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Institut für Geologie und Palaeontologie [Tübingen], Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Nicolaus Copernicus University [Toruń], and Vilnius University [Vilnius]
Subjects: 0106 biological sciences, Alces alces, 010506 paleontology, Food habits, Foraging, Cervus elaphus, Ungulates, Oceanography, 010603 evolutionary biology, 01 natural sciences, Deforestation, Bison bonasus, Ecology, Evolution, Behavior and Systematics, Holocene, 0105 earth and related environmental sciences, Earth-Surface Processes, 2. Zero hunger, Herbivore, biology, Ecology, Niche differentiation, Paleontology, 15. Life on land, Aurochs, biology.organism_classification, Bos primigenius, Habitat, Period (geology), [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, Geology
Abstract: International audience; Environmental changes related to forest expansion and later to agricultural development and deforestation during the Holocene in Europe have strongly shaped herbivore distribution and habitat selection, leading to species extinction. In this paper, we examine, through dental microwear textural analysis, the foraging habitats, dietary flexibility and niche partitioning of large herbivores (100 to 1000 kg) including two bovids (European bison Bison bonasus and aurochs Bos primigenius) and two cervids (moose Alces alces and red deer Cervus elaphus). The study focuses on northeast (NE) and south central (SC) Europe during three periods of the Holocene: Neolithic (6500–3500 cal yrs BP), Roman Period and Middle Ages (~2000–450 cal yrs BP) and Recent times (1963–2014). Our study highlights differences in diet between species only in the Neolithic SC Europe. This may have resulted from diversified habitats and dietary niche separation in SC Europe. The absence of differences in NE Europe may suggest more homogeneous habitat conditions in combination with lower densities of large herbivores in forested habitats. Analysis shows that during the Neolithic, in the bison diet there was more herbaceous monocotyledons in SC Europe than in NE Europe. We also found temporal changes in microwear texture variables for the bison in SC Europe suggesting a more herbaceous diet in the Neolithic than during the Roman Period and Middle Ages. However, neither spatial nor temporal differences in microwear texture variables were found in the aurochs. Thus, the diet of the European bison has likely changed, which may indicate a greater plasticity that promoted survival in refuge habitats.
Published: 2018

50. Active benzimidazole derivatives targeting the MmpL3 transporter in Mycobacterium abscessus

Author: Laurent Kremer, Matt D. Johansen, Jarosław Dziadek, Katarzyna Gobis, Alan P. Kozikowski, Mickaël Blaise, Jean-Louis Herrmann, Clément Raynaud, Wassim Daher, Françoise Roquet-Banères, Oluseye K. Onajole, Schistosomiase, paludisme et inflammation, Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille, Droit et Santé, Institut de Recherche en Infectiologie de Montpellier (IRIM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut Mondor de Recherche Biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Infection et inflammation chronique (2I), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Dynamique des interactions membranaires normales et pathologiques (DIMNP), Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre d'économie de la Sorbonne (CES), Centre National de la Recherche Scientifique (CNRS)-Université Panthéon-Sorbonne (UP1), Roosevelt University [Chicago], Starwise Therapeutics LLC [Chicago], Service de Microbiologie [Garches], Hôpital Raymond Poincaré [AP-HP], Polish Academy of Sciences (PAN), Medical University of Gdańsk, Infection et inflammation (2I), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut National de la Santé et de la Recherche Médicale (INSERM), This study was supported by the Association Gregory Lemarchal and Vaincre la Mucoviscidose (RIF20180502320) and by the National Science Centre (Krakow, Poland) on the basis of decision number DEC-2017/25/B/NZ7/00124. MDJ received a post-doctoral fellowship granted by Labex EpiGenMed, an «Investissements d’avenir» program (ANR-10-LABX-12-01)., and Blaise, Mickael
Subjects: 0301 basic medicine, Benzimidazole, [SDV.SP.MED] Life Sciences [q-bio]/Pharmaceutical sciences/Medication, Tuberculosis, medicine.drug_class, [SDV]Life Sciences [q-bio], 030106 microbiology, Antibiotics, Mycobacterium abscessus, benzimidazole, Microbiology, Mycolic acid, Mycobacterium tuberculosis, 03 medical and health sciences, chemistry.chemical_compound, [SDV.SP.MED]Life Sciences [q-bio]/Pharmaceutical sciences/Medication, mycolic acid, medicine, ComputingMilieux_MISCELLANEOUS, chemistry.chemical_classification, biology, therapeutic activity, [SDV.SP]Life Sciences [q-bio]/Pharmaceutical sciences, zebrafish, bacterial infections and mycoses, biology.organism_classification, medicine.disease, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, In vitro, 3. Good health, MmpL3, 030104 developmental biology, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, chemistry, Nontuberculous mycobacteria, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Abstract: International audience; The prevalence of pulmonary infections due to non-tuberculous mycobacteria such as Mycobacterium abscessus, has been increasing and surpassing tuberculosis (TB) in some industrialized countries. Due to intrinsic resistance to most antibiotics that drastically limits conventional chemotherapeutic treatment options, new anti-M. abscessus therapeutics are urgently needed against this emerging pathogen. Extensive screening of a library of benzimidazole derivatives that were previously shown to be active against Mycobacterium tuberculosis led to the identification of a lead compound exhibiting very potent in vitro activity against a wide panel of M. abscessus clinical strains. Designated EJMCh-6, this compound, a 2-(2-cyclohexylethyl)-5,6-dimethyl-1H-benzo[d]imidazole), also exerted a very strong activity against intramacrophage-residing M. abscessus. Moreover, treatment of infected zebrafish embryos with EJMCh-6 correlated with a significantly increased embryo survival and a decrease in the bacterial burden as compared to untreated fish. Insights into the mechanism of action were inferred from the generation of spontaneous benzimidazole-resistant strains and the identification of a large set of missense mutations in MmpL3; the mycolic acid transporter in mycobacteria. Over-expression of the mutated mmpL3 alleles in a susceptible M. abscessus strain was associated with high resistance levels to EJMCh-6 and to other known MmpL3 inhibitors. Mapping the mutations conferring resistance on a MmpL3 three-dimensional homology model defined a potential EJMCh-6-binding cavity. These data emphasize a yet unexploited chemical structure class against M. abscessus with promising translational developments for the treatment of M. abscessus lung diseases.
Published: 2019

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