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1. Samen-Verzeichnis des Botanischen Gartens der Universitãt Greifswald.

Author

Ernst-Moritz-Arndt-Universität Greifswald. Botanischer Garten, Missouri Botanical Garden, Peter H. Raven Library, and Ernst-Moritz-Arndt-Universität Greifswald. Botanischer Garten

Subjects
Botanischer Garten, Catalogs, Catalogs and collections, Ernst-Moritz-Arndt-Universität Greifswald, Germany, Greifswald, Seeds
Published
1893

2. Samen-Verzeichnis des Botanischen Gartens der Universitãt Greifswald.

Author

Ernst-Moritz-Arndt-Universität Greifswald. Botanischer Garten, Missouri Botanical Garden, Peter H. Raven Library, and Ernst-Moritz-Arndt-Universität Greifswald. Botanischer Garten

Subjects
Botanischer Garten, Catalogs, Catalogs and collections, Ernst-Moritz-Arndt-Universität Greifswald, Germany, Greifswald, Seeds

4. Akzeptanz, Identifikation und Engagement: Ansichten und Mitwirkung der Bevölkerung in UNESCO Biosphärenreservaten (AkIdEn)

Author

Geographisches Institut der Universität Zürich (Hrsg.), Institut für Geographie und Geologie der Ernst-Moritz-Arndt Universität Greifswald (Hrsg.), Institut für Landschaftsentwicklung, Erholungs- und Naturschutzplanung, Universität für Bodenkultur Wien (Hrsg.), Koordinationsstelle Parkforschung Schweiz (Hrsg.), Sozialwissenschaftliche Landschaftsforschung an der Eidgenössischen Forschungsanstalt für Wald, Schnee und Landschaft (Hrsg.), Zentrum für Gerontologie der Universität Zürich (Hrsg.), Österreichische Akademie der Wissenschaften (Hrsg.), Geographisches Institut der Universität Zürich (Hrsg.), Institut für Geographie und Geologie der Ernst-Moritz-Arndt Universität Greifswald (Hrsg.), Institut für Landschaftsentwicklung, Erholungs- und Naturschutzplanung, Universität für Bodenkultur Wien (Hrsg.), Koordinationsstelle Parkforschung Schweiz (Hrsg.), Sozialwissenschaftliche Landschaftsforschung an der Eidgenössischen Forschungsanstalt für Wald, Schnee und Landschaft (Hrsg.), Zentrum für Gerontologie der Universität Zürich (Hrsg.), and Österreichische Akademie der Wissenschaften (Hrsg.)

Published
2019
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5. Entwicklung einer Einrichtung zur Konservierung von an Substrate angepasste Mikroorganismenkulturen zur Verbesserung der Biogasausbeute bei vorhersehbarem Substratwechsel : Schlussbericht 'Biogaskulturenpufferspeicher' ; Laufzeit: 01.07.2008 - 30.06.2011

Author

Hochschule Neubrandenburg and Ernst-Moritz-Arndt-Universität Greifswald, Institut Für Hygiene Und Umweltmedizin

Subjects
Zellbiologie, Mechanical engineering, power engineering, Zellkultur, Regenerative Energieformen, alternative Energieformen, Mikroorganismus, In-vitro-Kultur, Biology, Biogasgewinnung
Abstract

Ill., graph. Darst.

Published
2012
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6. Teilprojekt 1 (TP 1): Ermittlung der regionalen Unterschiede in Prävalenz und Inzidenz des Typ 2 Diabetes mellitus und in der Diabetestherapie in Deutschland; Teilprojekt 6 (TP 6): Vergleichbarkeit von Laborergebnissen und die Optimierung der Bestimmung von Laborparametern : Abschlussbericht ; Laufzeit des Vorhabens: TP 1: 04.12.2008 - 30.11.2011; Tp 6: 01.12.2008 - 30.11.2011

Author

Ernst-Moritz-Arndt-Universität Greifswald, Institut Für Community Medicine

Published
2012
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9. Analyse der subzellulären Lokalisation, Orientierung und Interaktion von Proteinen durch Fluoreszenzmikroskopie, topologische Proteomics (Toponomics) und Bioinformatics zur Identifikation von Wirts-Pathogen-Interaktionen von S. aureus, der Resistenztransporter in Trophoblasten, sowie der genomweiten, topologischen Analyse der Oberflächenproteine des Pathogens T. gondii (Vakzinkandidaten) : Schlussbericht ; Laufzeit des Vorhabens: 01.06.2005 - 31.05.2010

Author

Ernst-Moritz-Arndt-Universität Greifswald, Zentrum Für Innovationskompetenz Funktionelle Genomforschung

Subjects
Infektionskrankheiten, parasitäre Krankheiten, Pharmazeutische Technologie, Staphylococcus aureus, Molekularbiologie, Fluoreszenzmikroskopie, Pathogenität, Plasmodium falciparum, Trophoblast, Toxoplasma gondii, Chemical and environmental engineering, Medicine, Biology
Abstract

Ill., graph. Darst.

Published
2010
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10. InnoNet-Verbundprojekt: Torfmooskultivierung auf schwimmfähigen Vegetationsträgern für ein nachhaltiges und umweltfreundliches Torfsubstitut im Erwerbsgartenbau - MOOSFARM, Teilvorhaben: Torfmooskultivierung auf überstauten Hochmoorflächen, Teilvorhaben: Ökonomische Analyse der Torfmooskultivierung : Schlussbericht ; Projektlaufzeit: 01.07.2007 - 30.04.2010

Author

Ernst-Moritz-Arndt-Universität Greifswald, Institut Für Botanik Und Landschaftsökologie

Subjects
Torf, Umweltfreundliche Nutzung natürlicher Ressourcen, Torfmoos (Gattung), Chemical and environmental engineering, Pflanzenproduktion: Allgemeines, Effizienz, Horticulture, Hochmoor
Abstract

Ill., graph. Darst.

Published
2010
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19. Verbundbericht Immuteach - Erstellung eines alltagstauglichen multimedialen Lehr- und Lernsystems für das Fach Immunologie durch Erweiterung und Ausbau von bioTEACH, einer interaktiven Lernsoftware zur Biotechnologie

Author

Ernst-Moritz-Arndt-Universität Greifswald, Institut Für Immunologie Und Transfusionsmedizin

Subjects
Ausbildung, Beruf, Organisationen, E-Learning, Medizinstudium, Computereinsatz in Unterricht und Ausbildung, Immunologie, Medicine, Educational Science
Published
2004
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21. The 2022 Magneto-Optics Roadmap

Author

Alexey Kimel, Anatoly Zvezdin, Sangeeta Sharma, Samuel Shallcross, Nuno de Sousa, Antonio García-Martín, Georgeta Salvan, Jaroslav Hamrle, Ondřej Stejskal, Jeffrey McCord, Silvia Tacchi, Giovanni Carlotti, Pietro Gambardella, Gian Salis, Markus Münzenberg, Martin Schultze, Vasily Temnov, Igor V Bychkov, Leonid N Kotov, Nicolò Maccaferri, Daria Ignatyeva, Vladimir Belotelov, Claire Donnelly, Aurelio Hierro Rodriguez, Iwao Matsuda, Thierry Ruchon, Mauro Fanciulli, Maurizio Sacchi, Chunhui Rita Du, Hailong Wang, N Peter Armitage, Mathias Schubert, Vanya Darakchieva, Bilu Liu, Ziyang Huang, Baofu Ding, Andreas Berger, Paolo Vavassori, Radboud University [Nijmegen], A. M. Prokhorov General Physics Institute (GPI), Russian Academy of Sciences [Moscow] (RAS), Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie (MBI), Donostia International Physics Center (DIPC), University of the Basque Country/Euskal Herriko Unibertsitatea (UPV/EHU), IMN-Instituto de Micro y Nanotecnología (CNM-CSIC), Isaac Newton 8, PTM, 28760 Tres Cantos, Madrid, Spain, Institute of Physics, University of Technology Chemnitz, Chemnitz University of Technology / Technische Universität Chemnitz, Institute of Physics of Charles University, Faculty of Mathematics and Physics, Charles University [Prague] (CU), Institut für Materialwissenschaft Universität Kiel, Università degli Studi di Perugia = University of Perugia (UNIPG), Department of Materials [ETH Zürich] (D-MATL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), IBM Research [Zurich], Institut für Physik [Greifswald], Ernst-Moritz-Arndt-Universität Greifswald, Graz University of Technology [Graz] (TU Graz), Laboratoire des Solides Irradiés (LSI), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Chelyabinsk State University, Syktyvkar State University, Syktywkar State University, Umeå University, Physics and Materials Science Research Unit, University of Luxembourg, University of Luxembourg [Luxembourg], Russian Quantum Center, Faculty of Physics, Lomonosov Moscow State University, Lomonosov Moscow State University (MSU), Max Planck Institute for Chemical Physics of Solids (CPfS), Max-Planck-Gesellschaft, Departamento de Fisica, Universidad de Oviedo, 33006 Oviedo, Spain, Universidad de Oviedo [Oviedo], Nanomaterials and Nanotechnology Research Center (CINN), Universidad de Oviedo [Oviedo]-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Institute for Solid State Physics, The University of Tokyo, Kashiwa 277-8581, Japan, Laboratoire Interactions, Dynamiques et Lasers (ex SPAM) (LIDyl), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Attophysique (ATTO), Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Laboratoire Interactions, Dynamiques et Lasers (ex SPAM) (LIDyl), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique des Matériaux et des Surfaces (LPMS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-CY Cergy Paris Université (CY), Croissance et propriétés de systèmes hybrides en couches minces (INSP-E8), Institut des Nanosciences de Paris (INSP), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Synchrotron SOLEIL (SSOLEIL), Centre National de la Recherche Scientifique (CNRS), University of California [San Diego] (UC San Diego), University of California (UC), Center for Memory and Recording Research, University of California (UC)-University of California (UC), Johns Hopkins University (JHU), University of Nebraska–Lincoln, University of Nebraska System, Department of Physics, Chemistry and Biology, Linköping University, Lund University [Lund], Shenzhen Key Laboratory on Power Battery Safety and Shenzhen Geim Graphene Center, Tsinghua University [Beijing] (THU), Shenzhen Institute of Advanced Technology [Shenzhen] (SIAT), Chinese Academy of Sciences [Beijing] (CAS), CIC NanoGUNE BRTA, Ikerbasque - Basque Foundation for Science, ANR-21-CE30-0037,HELIMAG,Dichroisme hélicoïdal de structures magnétiques(2021), Dutch Research Council, Russian Science Foundation, German Research Foundation, Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Czech Science Foundation, Collaborative Research Centre CRC 1261 (Germany), Ministero dell'Istruzione, dell'Università e della Ricerca, National Centres of Competence in Research (Switzerland), Swiss National Science Foundation, European Commission, Agence Nationale de la Recherche (France), Fonds National de la Recherche Luxembourg, Swedish Research Council, Ministry of Science and Higher Education of the Russian Federation, Max Planck Society, Japan Synchrotron Radiation Research Institute, University of Tokyo, Université Paris-Saclay, Air Force Office of Scientific Research (US), National Science Foundation (US), Energy Frontier Research Centers (US), Swedish Foundation for Strategic Research, Linköping University, and National Natural Science Foundation of China

Subjects
Ultrafast Spectroscopy of Correlated Materials, Acoustics and Ultrasonics, Atom and Molecular Physics and Optics, theoretical description and modelling, magnetic characterization methods, magneto-optical effects, Condensed Matter Physics, magneto-optics, magnetic materials, modern experimental methods, magnetic microscopy, Surfaces, Coatings and Films, Electronic, Optical and Magnetic Materials, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], Atom- och molekylfysik och optik, Den kondenserade materiens fysik
Abstract

Magneto-optical (MO) effects, viz. magnetically induced changes in light intensity or polarization upon reflection from or transmission through a magnetic sample, were discovered over a century and a half ago. Initially they played a crucially relevant role in unveiling the fundamentals of electromagnetism and quantum mechanics. A more broad-based relevance and wide-spread use of MO methods, however, remained quite limited until the 1960s due to a lack of suitable, reliable and easy-to-operate light sources. The advent of Laser technology and the availability of other novel light sources led to an enormous expansion of MO measurement techniques and applications that continues to this day (see section 1). The here-assembled roadmap article is intended to provide a meaningful survey over many of the most relevant recent developments, advances, and emerging research directions in a rather condensed form, so that readers can easily access a significant overview about this very dynamic research field. While light source technology and other experimental developments were crucial in the establishment of today's magneto-optics, progress also relies on an ever-increasing theoretical understanding of MO effects from a quantum mechanical perspective (see section 2), as well as using electromagnetic theory and modelling approaches (see section 3) to enable quantitatively reliable predictions for ever more complex materials, metamaterials, and device geometries. The latest advances in established MO methodologies and especially the utilization of the MO Kerr effect (MOKE) are presented in sections 4 (MOKE spectroscopy), 5 (higher order MOKE effects), 6 (MOKE microscopy), 8 (high sensitivity MOKE), 9 (generalized MO ellipsometry), and 20 (Cotton-Mouton effect in two-dimensional materials). In addition, MO effects are now being investigated and utilized in spectral ranges, to which they originally seemed completely foreign, as those of synchrotron radiation x-rays (see section 14 on three-dimensional magnetic characterization and section 16 on light beams carrying orbital angular momentum) and, very recently, the terahertz (THz) regime (see section 18 on THz MOKE and section 19 on THz ellipsometry for electron paramagnetic resonance detection). Magneto-optics also demonstrates its strength in a unique way when combined with femtosecond laser pulses (see section 10 on ultrafast MOKE and section 15 on magneto-optics using x-ray free electron lasers), facilitating the very active field of time-resolved MO spectroscopy that enables investigations of phenomena like spin relaxation of non-equilibrium photoexcited carriers, transient modifications of ferromagnetic order, and photo-induced dynamic phase transitions, to name a few. Recent progress in nanoscience and nanotechnology, which is intimately linked to the achieved impressive ability to reliably fabricate materials and functional structures at the nanoscale, now enables the exploitation of strongly enhanced MO effects induced by light-matter interaction at the nanoscale (see section 12 on magnetoplasmonics and section 13 on MO metasurfaces). MO effects are also at the very heart of powerful magnetic characterization techniques like Brillouin light scattering and time-resolved pump-probe measurements for the study of spin waves (see section 7), their interactions with acoustic waves (see section 11), and ultra-sensitive magnetic field sensing applications based on nitrogen-vacancy centres in diamond (see section 17)., Despite our best attempt to represent the field of magneto-optics accurately and do justice to all its novel developments and its diversity, the research area is so extensive and active that there remains great latitude in deciding what to include in an article of this sort, which in turn means that some areas might not be adequately represented here. However, we feel that the 20 sections that form this 2022 magneto-optics roadmap article, each written by experts in the field and addressing a specific subject on only two pages, provide an accurate snapshot of where this research field stands today. Correspondingly, it should act as a valuable reference point and guideline for emerging research directions in modern magneto-optics, as well as illustrate the directions this research field might take in the foreseeable future., Journal of Physics D: Applied Physics, 55 (46), ISSN:0022-3727, ISSN:1361-6463

Published
2022
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22. Escherichia coliSPFH membrane microdomain proteins HflKC contribute to aminoglycoside and oxidative stress tolerance

Author

Aimee K. Wessel, Yutaka Yoshii, Alexander Reder, Rym Boudjemaa, Magdalena Szczesna, Jean-Michel Betton, Joaquin Bernal-Bayard, Christophe Beloin, Daniel Lopez, Uwe Völker, Jean-Marc Ghigo, Génétique des Biofilms - Genetics of Biofilms, 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), Interfaculty Institute for Genetics and Functional Genomics, Universität Greifswald - University of Greifswald, Abbelight [Cachan, France], Imperial College London, Adaptation au stress et Métabolisme chez les entérobactéries - Stress adaptation and metabolism in enterobacteria (SAMe), Universidad de Sevilla / University of Sevilla, Universidad Autónoma de Madrid (UAM), Ernst-Moritz-Arndt-Universität Greifswald, German Center for Cardiovascular Research (DZHK), Berlin Institute of Health (BIH), This work was supported by EU Horizon 2020 Rafts4Biotech grant 720776 (to JMG, DL, AKW, YY, AR, UV and MS), the French government’s Investissement d’Avenir Program, Laboratoire d’Excellence 'Integrative Biology of Emerging Infectious Diseases' (grant n°ANR-10-LABX-62-IBEID) and the Fondation pour la Recherche Médicale (grant no. DEQ20180339185). This work benefited from the facilities and expertise of Add Photonic BioImaging platform (UTechS PBI, Institut Pasteur). A.K.W. was supported by a Pasteur-Roux-Cantarini postdoctoral and a grant from the Philippe Foundation., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), and European Project: 206568,European Union’s Horizon 2020 research and innovation programme,grant agreement No 720776,R4B(2017)

Subjects
Lipid raft, Flotillin, [SDV]Life Sciences [q-bio], Stress tolerance, Escherichia coli, SPFH proteins, Membrane microdomains, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Abstract

Many eukaryotic membrane-dependent functions are often spatially and temporally regulated by membrane microdomains (FMMs) also known as lipid rafts. These domains are enriched in polyisoprenoid lipids and scaffolding proteins belonging to the Stomatin, Prohibitin, Flotillin, and HflK/C (SPFH) protein superfamily that was also identified in Gram-positive bacteria. By contrast, little is still known about FMMs in Gram-negative bacteria. InEscherichia coliK12, 4 SPFH proteins, YqiK, QmcA, HflK, and HflC, were shown to localize in discrete polar or lateral inner-membrane locations, raising the possibility thatE. coliSPFH proteins could contribute to the assembly of inner-membrane FMMs and the regulation of cellular processes.Here we studied the determinant of the localization of QmcA and HflC and showed that FMM-associated cardiolipin lipid biosynthesis is required for their native localization pattern. Using Biolog phenotypic arrays, we showed that a mutant lacking all SPFH genes displayed increased sensitivity to aminoglycosides and oxidative stress that is due to the absence of HflKC. Our study therefore provides further insights into the contribution of SPFH proteins to stress tolerance inE. coli.IMPORTANCEEukaryotic cells often segregate physiological processes in cholesterol-rich functional membrane micro-domains. These domains are also called lipid rafts and contain proteins of the Stomatin, Prohibitin, Flotillin, and HflK/C (SPFH) superfamily, which are also present in prokaryotes but were mostly studied in Gram-positive bacteria. Here, we showed that the cell localization of the SPFH proteins QmcA and HflKC in the Gram-negative bacteriaE. coliis altered in absence of cardiolipin lipid synthesis. This suggests that cardiolipins contribute toE. colimembrane microdomain assembly. Using a broad phenotypic analysis, we also showed that HflKC contribute toE. colitolerance to aminoglycosides and oxidative stress. Our study, therefore, provides new insights into the cellular processes associated with SPFH proteins inE. coli.

Published
2022
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23. Genome-wide association study of circulating interleukin 6 levels identifies novel loci

Author

Martina Müller-Nurasyid, Jerome I. Rotter, David M. Evans, John P. Kemp, Emelia J. Benjamin, Graciela E. Delgado, Vilmundur Gudnason, Ann Hammarstedt, Panos Deloukas, Aroon D. Hingorani, Riccardo E. Marioni, David Stacey, Jenny van Dongen, Eric Boerwinkle, Joachim Heinrich, Yongmei Liu, S. Goya Wannamethee, Delilah Zabaneh, Braxton D. Mitchell, Marie Standl, Jackie F. Price, Maria G. Stathopoulou, Yoav Ben-Shlomo, Joris Deelen, Eero Kajantie, Mohammadreza Abdollahi, Christie M. Ballantyne, Johan G. Eriksson, Ilkka Seppälä, Elnaz Naderi, Barbara J. Jefferis, Richard W Morris, Nicholas J. Timpson, George Dedoussis, Sirpa Jalkanen, Mika Kivimäki, Perminder S. Sachdev, Diana van Heemst, Melanie Waldenberger, Gaurav Singhal, Elisabeth Thiering, Olli T. Raitakari, Anders Hamsten, Zoltán Kutalik, L. Bain, Eco J. C. de Geus, Tarunveer S. Ahluwalia, Yuri Milaneschi, Hubert Scharnagl, Juan P. Casas, Georg Homuth, Claes Ohlsson, Abbas Dehghan, Nicola J. Armstrong, Behrooz Z. Alizadeh, Terho Lehtimäki, Steve E. Humphries, Naveed Sattar, Bram P. Prins, Peter Rossing, Sophie Visvikis-Siest, Joana A. Revez, Ilja M. Nolte, Stella Trompet, Harold Snieder, Marian Beekman, Diana Marek, Beate St Pourcain, Thorkild I. A. Sørensen, Silvia Naitza, Karen A. Mather, Uwe Völker, Eline Slagboom, Tina Shah, Magdalene C. Jawahar, Jens Baumert, Alexander Teumer, Dorret I. Boomsma, Marcus E. Kleber, Peter Vollenweider, Wolfgang Koenig, Brenda W.J.H. Penninx, Kenneth Rice, Ian J. Deary, Pedro Marques-Vidal, Donna K. Arnett, Eleonora Porcu, Jouke-Jan Hottenga, Maria Sabater-Lleal, Bruce M. Psaty, Matthias Nauck, Dan Mellström, Joel Eriksson, Bernhard T. Baune, Debbie A Lawlor, Catherine Toben, Peter H. Whincup, Toshiko Tanaka, Stavroula Kanoni, Katri Räikkönen, Gonneke Willemsen, Bengt Sennblad, Julian N. Trollor, Yalda Jamshidi, Sarah E. Harris, Jari Lahti, Joshua C. Bis, Peter Durda, Yen Pei C. Chang, Jorgen Engmann, Tom R. Gaunt, Stella Aslibekyan, Anbupalam Thalamuthu, Mary F. Feitosa, Angela Silveira, Tine Jess, Stela McLachlan, J. Wouter Jukema, Chen Lu, Simon P. Mooijaart, Tim D. Spector, Harald Grallert, Winfried März, Alexandros M. Petrelis, Manuel A. R. Ferreira, Meena Kumari, Stochastics, Biological Psychology, APH - Personalized Medicine, APH - Health Behaviors & Chronic Diseases, APH - Mental Health, APH - Methodology, CHARGE Inflammation Working Group, Epidemiology, Tampere University, Department of Clinical Chemistry, Clinical Medicine, Steno Diabetes Center, University of Copenhagen = Københavns Universitet (KU), University of Groningen [Groningen], Murdoch University, University of Alabama at Birmingham [ Birmingham] (UAB), QIMR Berghofer Medical Research Institute, University College of London [London] (UCL), Helmholtz-Zentrum München (HZM), Leiden University Medical Center (LUMC), University of Bristol [Bristol], University of Washington [Seattle], University of Maryland School of Medicine, University of Maryland System, Vrije Universiteit Amsterdam [Amsterdam] (VU), VU University Medical Center [Amsterdam], University of Heidelberg, Medical Faculty, Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne (UNIL), Sahlgrenska Academy at University of Gothenburg [Göteborg], National Institute for Health and Welfare [Helsinki], University of Helsinki, William Harvey Research Institute, Barts and the London Medical School, University of Queensland [Brisbane], School of Public Health [Boston], Boston University [Boston] (BU), MRC Institute of Genetics and Molecular Medicine [Edinburgh] (IGMM), University of Edinburgh-Medical Research Council, University of Edinburgh, Amsterdam UMC, Interactions Gène-Environnement en Physiopathologie Cardio-Vasculaire (IGE-PCV), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lorraine (UL), Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche [Roma] (CNR), Karolinska Institutet [Stockholm], University of Tampere [Finland], Adelaide Medical School [Australia], University of Adelaide, Universität Greifswald - University of Greifswald, University of New South Wales [Sydney] (UNSW), Prince of Wales Hospital, Ludwig-Maximilians-Universität München (LMU), Baylor College of Medicine (BCM), Baylor University, Boston University School of Medicine (BUSM), VA Boston Healthcare System, Harokopio University of Athens, Max planck Institute for Biology of Ageing [Cologne], Larner College of Medicine [University of Vermont, Burlington], University of Vermont [Burlington], Washington University School of Medicine in St. Louis, Washington University in Saint Louis (WUSTL), Interfaculty Institute for Genetics and Functional Genomics, Ernst-Moritz-Arndt-Universität Greifswald, University of Turku, St George's, University of London, Statens Serum Institut [Copenhagen], Medical Faculty [Mannheim], Wake Forest School of Medicine [Winston-Salem], Wake Forest Baptist Medical Center, Centre Hospitalier Universitaire Vaudois [Lausanne] (CHUV), Johannes Gutenberg - Universität Mainz (JGU), Vrije Universiteit Medical Centre (VUMC), British Heart Foundation Glasgow Cardiovascular Research Centre (BHF GCRC), University of Glasgow-NHS Greater Glasgow and Clyde, Medical University Graz, Uppsala Universitet [Uppsala], Max Planck Institute for Psycholinguistics, Max-Planck-Gesellschaft, Donders Institute for Brain, Cognition and Behaviour, Radboud university [Nijmegen], University of Kentucky, Melbourne Medical School [Melbourne], Faculty of Medicine, Dentistry and Health Sciences [Melbourne], University of Melbourne-University of Melbourne, University Hospital Münster - Universitaetsklinikum Muenster [Germany] (UKM), University of Maryland [Baltimore], Queen Mary University of London (QMUL), University of Iceland [Reykjavik], Ludwig Maximilian University [Munich] (LMU), Melbourne School of Population and Global Health [Melbourne], University of Melbourne, Deutsches Herzzentrum München (DHM), German Center for Cardiovascular Research (DZHK), Berlin Institute of Health (BIH), University of Ulm (UUlm), University of Essex, Greifswald University Hospital, Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR), Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), King‘s College London, University of Cambridge [UK] (CAM), Harbor UCLA Medical Center [Torrance, Ca.], Erasmus University Medical Center [Rotterdam] (Erasmus MC), University of Texas Health Science Center, The University of Texas Health Science Center at Houston (UTHealth), Human Genome Sequencing Center [Houston] (HGSC), Baylor University-Baylor University, Psychiatry, Amsterdam Neuroscience - Complex Trait Genetics, Amsterdam Neuroscience - Mood, Anxiety, Psychosis, Stress & Sleep, APH - Digital Health, HUS Children and Adolescents, Lastentautien yksikkö, Children's Hospital, Clinicum, Department of Bacteriology and Immunology, Department of Public Health, Department of Psychology and Logopedics, Research Programs Unit, Johan Eriksson / Principal Investigator, Department of General Practice and Primary Health Care, Doctoral Programme in Human Behaviour, Life Course Epidemiology (LCE), Real World Studies in PharmacoEpidemiology, -Genetics, -Economics and -Therapy (PEGET), and Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI)

Subjects
AcademicSubjects/SCI01140, [SDV]Life Sciences [q-bio], Genome-wide association study, 030204 cardiovascular system & hematology, DISEASE, Pathogenesis, Cohort Studies, 0302 clinical medicine, cytokine, SYSTEMIC-LUPUS-ERYTHEMATOSUS, Association Studies Article, ComputingMilieux_MISCELLANEOUS, Genetics (clinical), Genetics, 0303 health sciences, ARCHITECTURE, CHRONIC INFLAMMATION, 1184 Genetics, developmental biology, physiology, General Medicine, RECEPTOR IL-6R GENE, C-REACTIVE PROTEIN, hla-drb1 gene, 3. Good health, Medical genetics, Medical Genetics, chromosomes, medicine.medical_specialty, SUSCEPTIBILITY LOCI, European Continental Ancestry Group, Locus (genetics), Single-nucleotide polymorphism, Biology, Polymorphism, Single Nucleotide, anti-inflammatory agents, White People, 03 medical and health sciences, medicine, Humans, Genetic Predisposition to Disease, Interleukin 6, Molecular Biology, Medicinsk genetik, 030304 developmental biology, PRODUCE IL-6, Interleukin-6, Chromosome, Receptors, Interleukin-6, RHEUMATOID-ARTHRITIS, Interleukin 1 Receptor Antagonist Protein, Gene Expression Regulation, Genetic Loci, CELLS, biology.protein, 1182 Biochemistry, cell and molecular biology, Human genome, 3111 Biomedicine, Genome-Wide Association Study, HLA-DRB1 Chains, Interleukin-1
Abstract

Interleukin 6 (IL-6) is a multifunctional cytokine with both pro- and anti-inflammatory properties with a heritability estimate of up to 61%. The circulating levels of IL-6 in blood have been associated with an increased risk of complex disease pathogenesis. We conducted a two-staged, discovery and replication meta genome-wide association study (GWAS) of circulating serum IL-6 levels comprising up to 67 428 (ndiscovery = 52 654 and nreplication = 14 774) individuals of European ancestry. The inverse variance fixed effects based discovery meta-analysis, followed by replication led to the identification of two independent loci, IL1F10/IL1RN rs6734238 on chromosome (Chr) 2q14, (Pcombined = 1.8 × 10−11), HLA-DRB1/DRB5 rs660895 on Chr6p21 (Pcombined = 1.5 × 10−10) in the combined meta-analyses of all samples. We also replicated the IL6R rs4537545 locus on Chr1q21 (Pcombined = 1.2 × 10−122). Our study identifies novel loci for circulating IL-6 levels uncovering new immunological and inflammatory pathways that may influence IL-6 pathobiology.

Published
2021
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25. Management of cavernous sinus meningiomas: Consensus statement on behalf of the EANS skull base section

Author

Marco V. Corniola, Pierre-Hugues Roche, Michaël Bruneau, Luigi M. Cavallo, Roy T. Daniel, Mahmoud Messerer, Sebastien Froelich, Paul A. Gardner, Fred Gentili, Takeshi Kawase, Dimitrios Paraskevopoulos, Jean Régis, Henry W.S. Schroeder, Theodore H. Schwartz, Marc Sindou, Jan F. Cornelius, Marcos Tatagiba, Torstein R. Meling, Laboratoire Traitement du Signal et de l'Image (LTSI), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Pontchaillou [Rennes], Université de Genève = University of Geneva (UNIGE), Aix Marseille Université (AMU), Hôpital Nord [CHU - APHM], Vrije Universiteit Brussel [Bruxelles] (VUB), University of Naples Federico II = Università degli studi di Napoli Federico II, Centre Hospitalier Universitaire Vaudois [Lausanne] (CHUV), Hôpital Lariboisière-Fernand-Widal [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), University of Pittsburgh (PITT), Pennsylvania Commonwealth System of Higher Education (PCSHE), Toronto Western Hospital, Keio University, Barts Health NHS Trust [London, UK], Hôpital de la Timone [CHU - APHM] (TIMONE), Ernst-Moritz-Arndt-Universität Greifswald, Weill Cornell Medicine [Cornell University], Cornell University [New York], Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Université de Lyon, Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf], Universitätsklinikum Tübingen - University Hospital of Tübingen, Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Hôpital Universitaire de Genève = University Hospitals of Geneva (HUG), None, Brussels Heritage Lab, Clinical sciences, Surgical clinical sciences, Neuroprotection & Neuromodulation, Neurosurgery, Weill Cornell Medicine [New York], and Jonchère, Laurent

Subjects
[SDV.IB] Life Sciences [q-bio]/Bioengineering, Microsurgery, Cranial nerves, Radiotherapy, Neurosurgery, Gammaknife, Radiosurgery, Intracranial meningiomas, Pituitary, Gross total resection, Neurosurgery Cavernous sinus Meningioma Microsurgery Gross total resection Cranial nerves Radiosurgery Radiotherapy Pituitary Consensus statement Intracranial meningiomas Gammaknife, Consensus statement, [SDV.IB]Life Sciences [q-bio]/Bioengineering, Neurology. Diseases of the nervous system, Cavernous sinus, RC346-429, Meningioma
Abstract

International audience; INTRODUCTION: The evolution of cavernous sinus meningiomas (CSMs) might be unpredictable and the efficacy of their treatments is challenging due to their indolent evolution, variations and fluctuations of symptoms, heterogeneity of classifications and lack of randomized controlled trials. Here, a dedicated task force provides a consensus statement on the overall management of CSMs. RESEARCH QUESTION: To determine the best overall management of CSMs, depending on their clinical presentation, size, and evolution as well as patient characteristics. MATERIAL AND METHODS: Using the PRISMA 2020 guidelines, we included literature from January 2000 to December 2020. A total of 400 abstracts and 77 titles were kept for full-paper screening. RESULTS: The task force formulated 8 recommendations (Level C evidence). CSMs should be managed by a highly specialized multidisciplinary team. The initial evaluation of patients includes clinical, ophthalmological, endocrinological and radiological assessment. Treatment of CSM should involve experienced skull-base neurosurgeons or neuro-radiosurgeons, radiation oncologists, radiologists, ophthalmologists, and endocrinologists. DISCUSSION AND CONCLUSION: Radiosurgery is preferred as first-line treatment in small, enclosed, pauci-symptomatic lesions/in elderly patients, while large CSMs not amenable to resection or WHO grade II-III are candidates for radiotherapy. Microsurgery is an option in aggressive/rapidly progressing lesions in young patients presenting with oculomotor/visual/endocrinological impairment. Whenever surgery is offered, open cranial approaches are the current standard. There is limited experience reported about endoscopic endonasal approach for CSMs and the main indication is decompression of the cavernous sinus to improve symptoms. Whenever surgery is indicated, the current trend is to offer decompression followed by radiosurgery.

Published
2022
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29. Considering adaptive genetic variation in climate change vulnerability assessment reduces species range loss projections

Author

John B. Taggart, Orly Razgour, Sébastien J. Puechmaille, Michaël Bekaert, Javier Juste, Brenna R. Forester, Antton Alberdi, Stéphanie Manel, Roberto Novella-Fernandez, Carlos F. Ibáñez, University of Bristol [Bristol], University of Southampton, Colorado State University [Fort Collins] (CSU), University of Stirling, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Ernst-Moritz-Arndt-Universität Greifswald, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), University of Copenhagen = Københavns Universitet (UCPH), 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), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), University of Copenhagen = Københavns Universitet (KU), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
0106 biological sciences, Genetic adaptations, Evolution, Range (biology), Climate Change, ecological niche models, Population, Vulnerability, Biology, Models, Biological, 010603 evolutionary biology, 01 natural sciences, Intraspecific competition, 03 medical and health sciences, Ecosystem model, Chiroptera, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Animals, education, Ecosystem, 030304 developmental biology, 0303 health sciences, Adaptive capacity, education.field_of_study, Multidisciplinary, Ecology, Global climate change, Evolutionary rescue, Global warming, global climate change, Genetic Variation, Ecological niche models, Biological Sciences, 15. Life on land, Adaptation, Physiological, genetic adaptations, conservation genomics, 13. Climate action, evolutionary rescue, Conservation genomics, [SDV.EE.BIO]Life Sciences [q-bio]/Ecology, environment/Bioclimatology, Forecasting, Landscape connectivity
Abstract

Significance Forecasts of species vulnerability and extinction risk under future climate change commonly ignore local adaptations despite their importance for determining the potential of populations to respond to future changes. We present an approach to assess the impacts of global climate change on biodiversity that takes into account adaptive genetic variation and evolutionary potential. We show that considering local climatic adaptations reduces range loss projections but increases the potential for competition between species. Our findings suggest that failure to account for within-species variability can result in overestimation of future biodiversity losses. Therefore, it is important to identify the climate-adaptive potential of populations and to increase landscape connectivity between populations to enable the spread of adaptive genetic variation., Local adaptations can determine the potential of populations to respond to environmental changes, yet adaptive genetic variation is commonly ignored in models forecasting species vulnerability and biogeographical shifts under future climate change. Here we integrate genomic and ecological modeling approaches to identify genetic adaptations associated with climate in two cryptic forest bats. We then incorporate this information directly into forecasts of range changes under future climate change and assessment of population persistence through the spread of climate-adaptive genetic variation (evolutionary rescue potential). Considering climate-adaptive potential reduced range loss projections, suggesting that failure to account for intraspecific variability can result in overestimation of future losses. On the other hand, range overlap between species was projected to increase, indicating that interspecific competition is likely to play an important role in limiting species’ future ranges. We show that although evolutionary rescue is possible, it depends on a population’s adaptive capacity and connectivity. Hence, we stress the importance of incorporating genomic data and landscape connectivity in climate change vulnerability assessments and conservation management.

Published
2019
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30. Deciphering myeloid-derived suppressor cells: isolation and markers in humans, mice and non-human primates

Author

Marco A. Cassatella, Anna Bujko, Espen S. Baekkevold, Sven Brandau, Ang Lin, Gosse J. Adema, Patrizia Scapini, Carsten Krieg, Karin Loré, Olivia Marini, Mikael Roussel, Anca Dorhoi, Viktor Umansky, Jeffrey W. Pollard, Luca Cassetta, University of Edinburgh, University of Oslo (UiO), Universitätsklinikum Essen [Universität Duisburg-Essen] (Uniklinik Essen), Università degli studi di Verona = University of Verona (UNIVR), Max Planck Institute for Infection Biology (MPIIB), Max-Planck-Gesellschaft, Ernst-Moritz-Arndt-Universität Greifswald, Medical University of South Carolina [Charleston] (MUSC), Karolinska Institutet [Stockholm], Microenvironment, Cell Differentiation, Immunology and Cancer (MICMAC), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Medizinische Fakultät Mannheim, German Cancer Research Center - Deutsches Krebsforschungszentrum [Heidelberg] (DKFZ), Radboud University Medical Center [Nijmegen], Wellcome Trust [101067/Z/13/Z], Medical Research Council [MR/N022556/1], Dutch cancer Society [KUN2013-6111, 11266], COST (European Cooperation in Science and Technology), COST Action [BM1404], Villa Joep, de STOPHT stichting, China Scholarship Council, Karolinska Institutet, Associazione Italiana per la Ricerca sul Cancro (AIRC) [IG20339], Ministero dell'Istruzione, dell'Universita e della Ricerca [PRIN 2015YYKPNN], Jonchère, Laurent, University of Verona (UNIVR), Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )

Subjects
Cancer Research, Myeloid, Mouse, Neutrophils, Cancer development and immune defence Radboud Institute for Molecular Life Sciences [Radboudumc 2], Human, Mye-EUNITER, Myeloid-derived suppressor cells, Non-human primates, Medizin, DONORS, Cell Separation, Disease, Symposium-in-Writing Paper, ARGINASE, Mice, 0302 clinical medicine, Medicine and Health Sciences, Immunology and Allergy, biology, HUMAN NEUTROPHILS, EXPANSION, CANCER, 3. Good health, medicine.anatomical_structure, Oncology, Antibody, medicine.symptom, EXPRESSION, Primates, BONE-MARROW, Immunology, [SDV.CAN]Life Sciences [q-bio]/Cancer, Inflammation, Context (language use), Immunophenotyping, 03 medical and health sciences, All institutes and research themes of the Radboud University Medical Center, Immune system, [SDV.CAN] Life Sciences [q-bio]/Cancer, medicine, Animals, Humans, Mass cytometry, ACCUMULATION, Myeloid-Derived Suppressor Cells, IMMUNOSUPPRESSIVE ACTIVITY, Biology and Life Sciences, T-CELLS, biology.protein, Myeloid-derived Suppressor Cell, Biomarkers, 030215 immunology
Abstract

International audience; In cancer, infection and inflammation, the immune system's function can be dysregulated. Instead of fighting disease, immune cells may increase pathology and suppress host-protective immune responses. Myeloid cells show high plasticity and adapt to changing conditions and pathological challenges. Despite their relevance in disease pathophysiology, the identity, heterogeneity and biology of myeloid cells is still poorly understood. We will focus on phenotypical and functional markers of one of the key myeloid regulatory subtypes, the myeloid derived suppressor cells (MDSC), in humans, mice and non-human primates. Technical issues regarding the isolation of the cells from tissues and blood, timing and sample handling of MDSC will be detailed. Localization of MDSC in a tissue context is of crucial importance and immunohistochemistry approaches for this purpose are discussed. A minimal antibody panel for MDSC research is provided as part of the Mye-EUNITER COST action. Strategies for the identification of additional markers applying state of the art technologies such as mass cytometry will be highlighted. Such marker sets can be used to study MDSC phenotypes across tissues, diseases as well as species and will be crucial to accelerate MDSC research in health and disease.

Published
2019
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32. Genoscapist: online exploration of quantitative profiles along genomes via interactively customized graphical representations

Author

Cyprien Guérin, Ulrike Mäder, Pierre Nicolas, Sandra Derozier, Université Paris-Saclay, INRAE, BioinfOmics, MIGALE bioinformatics facility (MIGALE), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paris-Saclay, Interfaculty Institute for Genetics and Functional Genomics, and Ernst-Moritz-Arndt-Universität Greifswald

Subjects
Statistics and Probability, 0303 health sciences, Computer science, 030302 biochemistry & molecular biology, [INFO.INFO-WB]Computer Science [cs]/Web, Computational biology, Biochemistry, Genome, Computer Science Applications, Transcriptome, 03 medical and health sciences, Computational Mathematics, Computational Theory and Mathematics, Relevance (information retrieval), [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Molecular Biology, 030304 developmental biology, Reference genome
Abstract

Summary Genoscapist is a tool to design web interfaces generating high-quality images for interactive visualization of hundreds of quantitative profiles along a reference genome together with various annotations. Relevance is demonstrated by deployment of two websites dedicated to large condition-dependent transcriptome datasets available for Bacillus subtilis and Staphylococcus aureus. Availability and implementation Websites and source code freely accessible at https://genoscapist.migale.inrae.fr

Published
2021
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33. Drivers of longitudinal telomere dynamics in a long‐lived bat species, Myotis myotis

Author

Nicole M. Foley, Eric J. Petit, Thomas Brazier, Sébastien J. Puechmaille, Graham M. Hughes, John A. Finarelli, Emma C. Teeling, Frédéric Touzalin, University College Dublin [Dublin] (UCD), Écologie et santé des écosystèmes (ESE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AGROCAMPUS OUEST, 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), Ernst-Moritz-Arndt-Universität Greifswald, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, AGROCAMPUS OUEST, 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
0106 biological sciences, 0301 basic medicine, longitudinal data, Range (biology), Population, bats, Myotis myotis, Biology, Genus Myotis, heritability, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Chiroptera, Genotype, Genetics, telomere length, Animals, Humans, education, Child, Ecology, Evolution, Behavior and Systematics, Telomere Shortening, education.field_of_study, Infant, Newborn, conservation, Infant, Bayes Theorem, Heritability, Telomere, biology.organism_classification, 030104 developmental biology, Cross-Sectional Studies, climate change, Ageing, Evolutionary biology, Child, Preschool, [SDE]Environmental Sciences, France, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

International audience; ge-related telomere shortening is considered a hallmark of the ageing process. However, a recent cross-sectional ageing study of relative telomere length (rTL) in bats failed to detect a relationship between rTL and age in the long-lived genus Myotis (M. myotis and M. bechsteinii), suggesting some other factors are responsible for driving telomere dynamics in these species. Here, we test if longitudinal rTL data show signatures of age-associated telomere attrition in M. myotis and differentiate which intrinsic or extrinsic factors are likely to drive telomere length dynamics. Using quantitative polymerase chain reaction, rTL was measured in 504 samples from a marked population, from Brittany, France, captured between 2013 and 2016. These represent 174 individuals with an age range of 0 to 7+ years. We find no significant relationship between rTL and age (p = .762), but demonstrate that within-individual rTL is highly variable from year to year. To investigate the heritability of rTL, a population pedigree (n = 1744) was constructed from genotype data generated from a 16-microsatellite multiplex, designed from an initial, low-coverage, Illumina genome for M. myotis. Heritability was estimated in a Bayesian, mixed model framework, and showed that little of the observed variance in rTL is heritable (h(2) = 0.01-0.06). Rather, correlations of first differences, correlating yearly changes in telomere length and weather variables, demonstrate that, during the spring transition, average temperature, minimum temperature, rainfall and windspeed correlate with changes in longitudinal telomere dynamics. As such, rTL may represent a useful biomarker to quantify the physiological impact of various environmental stressors in bats.

Published
2020
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34. Online exploration of transcription profiles along B. subtilis and S. aureus

Author

Derozier, Sandra, Nicolas, Pierre, Mäder, Ulrike, Guerin, Cyprien, Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paris-Saclay, INRAE, BioinfOmics, MIGALE bioinformatics facility (MIGALE), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Interfaculty Institute for Genetics and Functional Genomics, Ernst-Moritz-Arndt-Universität Greifswald, and DEROZIER, Sandra

Subjects
[INFO.INFO-WB] Computer Science [cs]/Web, [INFO.INFO-WB]Computer Science [cs]/Web
Abstract

International audience; Genoscapist is a web-tool generating high-quality images for interactive visualization of hundreds of quantitative profiles along a reference genome together with various annotations. Relevance is demonstrated by deployment of two websites dedicated to large condition-dependent transcriptome data sets available for Bacillus subtilis and Staphylococcus aureus. Websites and source code freely accessible at https://

Published
2020

35. Genome-wide association and Mendelian randomisation analysis provide insights into the pathogenesis of heart failure

Author

Shah, Sonia, Henry, Albert, Roselli, Carolina, Lin, Honghuang, Sveinbjornsson, Gardar, Fatemifar, Ghazaleh, Hedman, Asa K, Wilk, Jemma B, Morley, Michael P, Chaffin, Mark D, Helgadottir, Anna, Verweij, Niek, Dehghan, Abbas, Almgren, Peter, Andersson, Charlotte, Aragam, Krishna G, Arnlov, Johan, Backman, Joshua D, Biggs, Mary L, Bloom, Heather L, Brandimarto, Jeffrey, Brown, Michael R, Buckbinder, Leonard, Carey, David J, Chasman, Daniel I, Chen, Xing, Chen, Xu, Chung, Jonathan, Chutkow, William, Cook, James P, Delgado, Graciela E, Denaxas, Spiros, Doney, Alexander S, Doerr, Marcus, Dudley, Samuel C, Dunn, Michael E, Engstrom, Gunnar, Esko, Tonu, Felix, Stephan B, Finan, Chris, Ford, Ian, Ghanbari, Mohsen, Ghasemi, Sahar, Giedraitis, Vilmantas, Giulianini, Franco, Gottdiener, John S, Gross, Stefan, Gudbjartsson, Daniel F, Gutmann, Rebecca, Haggerty, Christopher M, van der Harst, Pim, Hyde, Craig L, Ingelsson, Erik, Jukema, J Wouter, Kavousi, Maryam, Khaw, Kay-Tee, Kleber, Marcus E, Kober, Lars, Koekemoer, Andrea, Langenberg, Claudia, Lind, Lars, Lindgren, Cecilia M, London, Barry, Lotta, Luca A, Lovering, Ruth C, Luan, Jian'an, Magnusson, Patrik, Mahajan, Anubha, Margulies, Kenneth B, Maerz, Winfried, Melander, Olle, Mordi, Ify R, Morgan, Thomas, Morris, Andrew D, Morris, Andrew P, Morrison, Alanna C, Nagle, Michael W, Nelson, Christopher P, Niessner, Alexander, Niiranen, Teemu, O'Donoghue, Michelle L, Owens, Anjali T, Palmer, Colin NA, Parry, Helen M, Perola, Markus, Portilla-Fernandez, Eliana, Psaty, Bruce M, Rice, Kenneth M, Ridker, Paul M, Romaine, Simon PR, Rotter, Jerome I, Salo, Perttu, Salomaa, Veikko, van Setten, Jessica, Shalaby, Alaa A, Smelser, Diane T, Smith, Nicholas L, Stender, Steen, Stott, David J, Svensson, Per, Tammesoo, Mari-Liis, Taylor, Kent D, Teder-Laving, Maris, Teumer, Alexander, Thorgeirsson, Gudmundur, Thorsteinsdottir, Unnur, Torp-Pedersen, Christian, Trompet, Stella, Tyl, Benoit, Uitterlinden, Andre G, Veluchamy, Abirami, Voelker, Uwe, Voors, Adriaan A, Wang, Xiaosong, Wareham, Nicholas J, Waterworth, Dawn, Weeke, Peter E, Weiss, Raul, Wiggins, Kerri L, Xing, Heming, Yerges-Armstrong, Laura M, Yu, Bing, Zannad, Faiez, Zhao, Jing Hua, Hemingway, Harry, Samani, Nilesh J, McMurray, John JV, Yang, Jian, Visscher, Peter M, Newton-Cheh, Christopher, Malarstig, Anders, Holm, Hilma, Lubitz, Steven A, Sattar, Naveed, Holmes, Michael V, Cappola, Thomas P, Asselbergs, Folkert W, Hingorani, Aroon D, Kuchenbaecker, Karoline, Ellinor, Patrick T, Lang, Chim C, Stefansson, Kari, Smith, J Gustav, Vasan, Ramachandran S, Swerdlow, Daniel I, Lumbers, R Thomas, Abecasis, Goncalo, Backman, Joshua, Bai, Xiaodong, Balasubramanian, Suganthi, Banerjee, Nilanjana, Baras, Aris, Barnard, Leland, Beechert, Christina, Blumenfeld, Andrew, Cantor, Michael, Chai, Yating, Coppola, Giovanni, Damask, Amy, Dewey, Frederick, Economides, Aris, Eom, Gisu, Forsythe, Caitlin, Fuller, Erin D, Gu, Zhenhua, Gurski, Lauren, Guzzardo, Paloma M, Habegger, Lukas, Hahn, Young, Hawes, Alicia, van Hout, Cristopher, Jones, Marcus B, Khalid, Shareef, Lattari, Michael, Li, Alexander, Lin, Nan, Liu, Daren, Lopez, Alexander, Manoochehri, Kia, Marchini, Jonathan, Marcketta, Anthony, Maxwell, Evan K, McCarthy, Shane, Mitnaul, Lyndon J, O'Dushlaine, Colm, Overton, John D, Padilla, Maria Sotiropoulos, Paulding, Charles, Penn, John, Pradhan, Manasi, Reid, Jeffrey G, Schleicher, Thomas D, Schurmann, Claudia, Shuldiner, Alan, Staples, Jeffrey C, Sun, Dylan, Toledo, Karina, Ulloa, Ricardo H, Widom, Louis, Wolf, Sarah E, Yadav, Ashish, Ye, Bin, Ctr, Regeneron Genetics, Shah, Sonia [0000-0001-5860-4526], Henry, Albert [0000-0001-7422-2288], Roselli, Carolina [0000-0001-5267-6756], Lin, Honghuang [0000-0003-3043-3942], Chaffin, Mark D. [0000-0002-1234-5562], Helgadottir, Anna [0000-0002-1806-2467], Verweij, Niek [0000-0002-4303-7685], Almgren, Peter [0000-0002-0473-0241], Chen, Xu [0000-0002-7299-3238], Ghanbari, Mohsen [0000-0002-9476-7143], Giedraitis, Vilmantas [0000-0003-3423-2021], Gross, Stefan [0000-0003-4121-7161], Guðbjartsson, Daníel F. [0000-0002-5222-9857], Hyde, Craig L. [0000-0002-6939-287X], Ingelsson, Erik [0000-0003-2256-6972], Jukema, J. Wouter [0000-0002-3246-8359], Kleber, Marcus E. [0000-0003-0663-7275], Koekemoer, Andrea [0000-0001-8222-3547], Langenberg, Claudia [0000-0002-5017-7344], Lindgren, Cecilia M. [0000-0002-4903-9374], Lovering, Ruth C. [0000-0002-9791-0064], Luan, Jian’an [0000-0003-3137-6337], Magnusson, Patrik [0000-0002-7315-7899], Mahajan, Anubha [0000-0001-5585-3420], Mordi, Ify R. [0000-0002-2686-729X], Morris, Andrew D. [0000-0002-1766-0473], Nagle, Michael W. [0000-0002-4677-7582], Nelson, Christopher P. [0000-0001-8025-2897], Palmer, Colin N. A. [0000-0002-6415-6560], Rice, Kenneth M. [0000-0002-3071-7278], Rotter, Jerome I. [0000-0001-7191-1723], Salomaa, Veikko [0000-0001-7563-5324], van Setten, Jessica [0000-0002-4934-7510], Svensson, Per [0000-0003-0372-6272], Taylor, Kent D. [0000-0002-2756-4370], Teder-Laving, Maris [0000-0002-5872-1850], Teumer, Alexander [0000-0002-8309-094X], Tyl, Benoit [0000-0001-5297-8412], Uitterlinden, Andre G. [0000-0002-7276-3387], Völker, Uwe [0000-0002-5689-3448], Wiggins, Kerri L. [0000-0003-2749-1279], Hemingway, Harry [0000-0003-2279-0624], Yang, Jian [0000-0003-2001-2474], Visscher, Peter M. [0000-0002-2143-8760], Lubitz, Steven A. [0000-0002-9599-4866], Sattar, Naveed [0000-0002-1604-2593], Cappola, Thomas P. [0000-0002-9630-7204], Asselbergs, Folkert W. [0000-0002-1692-8669], Kuchenbaecker, Karoline [0000-0001-9726-603X], Ellinor, Patrick T. [0000-0002-2067-0533], Vasan, Ramachandran S. [0000-0001-7357-5970], Lumbers, R. Thomas [0000-0002-9077-4741], Apollo - University of Cambridge Repository, Chaffin, Mark D [0000-0002-1234-5562], Guðbjartsson, Daníel F [0000-0002-5222-9857], Hyde, Craig L [0000-0002-6939-287X], Jukema, J Wouter [0000-0002-3246-8359], Kleber, Marcus E [0000-0003-0663-7275], Lindgren, Cecilia M [0000-0002-4903-9374], Lovering, Ruth C [0000-0002-9791-0064], Luan, Jian'an [0000-0003-3137-6337], Mordi, Ify R [0000-0002-2686-729X], Morris, Andrew D [0000-0002-1766-0473], Nagle, Michael W [0000-0002-4677-7582], Nelson, Christopher P [0000-0001-8025-2897], Palmer, Colin NA [0000-0002-6415-6560], Rice, Kenneth M [0000-0002-3071-7278], Rotter, Jerome I [0000-0001-7191-1723], Taylor, Kent D [0000-0002-2756-4370], Uitterlinden, Andre G [0000-0002-7276-3387], Wiggins, Kerri L [0000-0003-2749-1279], Visscher, Peter M [0000-0002-2143-8760], Lubitz, Steven A [0000-0002-9599-4866], Cappola, Thomas P [0000-0002-9630-7204], Asselbergs, Folkert W [0000-0002-1692-8669], Ellinor, Patrick T [0000-0002-2067-0533], Vasan, Ramachandran S [0000-0001-7357-5970], Lumbers, R Thomas [0000-0002-9077-4741], Palmer, Colin N A [0000-0002-6415-6560], Cardiovascular Centre (CVC), University of Queensland [Brisbane], University College of London [London] (UCL), Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], University Medical Center Groningen [Groningen] (UMCG), Boston University School of Medicine (BUSM), Boston University [Boston] (BU), Framingham Heart Study, National Heart, Lung, and Blood Institute [Bethesda] (NHLBI)-Boston University [Boston] (BU), deCODE genetics [Reykjavik], Karolinska Institutet [Stockholm], Pfizer, University of Pennsylvania [Philadelphia], University of Groningen [Groningen], Imperial College London, Lund University [Lund], Herlev and Gentofte Hospital, Massachusetts General Hospital [Boston], Department of Neurobiology, Care Sciences and Society [Stockholm, Sweden] (Division of Family Medicine), Dalarna University, Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, Department of Biostatistics, University of Washington [Seattle], Emory University School of Medicine, Emory University [Atlanta, GA], The University of Texas Medical School at Houston, Department of Molecular and Functional Genomics, Geisinger, Danville, PA, Brigham and Women's Hospital [Boston], Harvard Medical School [Boston] (HMS), Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY, Novartis Institutes for BioMedical Research (NIBR), University of Liverpool, Universität Heidelberg [Heidelberg], Medizinische Fakultät Mannheim, The Alan Turing Institute, Ninewells Hospital and Medical School [Dundee], Universität Greifswald - University of Greifswald, German Center for Cardiovascular Research (DZHK), Berlin Institute of Health (BIH), University of Minnesota System, Regeneron Pharmaceuticals [Tarrytown], Department of Clinical Sciences, Cardiovascular Epidemiology, Skane University Hospital [Lund], Institute of Genomics [Tartu, Estonia], University of Tartu, Robertson Centre for Biostatistics, University of Glasgow, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, Erasmus University Medical Center [Rotterdam] (Erasmus MC), Uppsala University, Brigham & Women’s Hospital [Boston] (BWH), University of Maryland School of Medicine, University of Maryland System, School of Science and Engineering (Reykjavik University), Carver College of Medicine, University of Iowa, Geisinger Health System [Danville, PA, USA], Durrer Center for Cardiogenetic Research, ICIN-Netherlands Heart Institute, Utrecht, Stanford School of Medicine [Stanford], Stanford Medicine, Stanford University-Stanford University, Stanford Cardiovascular Institute, Uppsala Universitet [Uppsala], Leiden University Medical Center (LUMC), Einthoven Laboratory for Experimental Vascular Medicine (ELEVM - LEIDEN), Department of Public Health and Primary Care, University of Cambridge [UK] (CAM), Rigshospitalet [Copenhagen], Copenhagen University Hospital, Glenfield Hospital, University Hospitals Leicester, MRC Epidemiology Unit, University of Cambridge [UK] (CAM)-Institute of Metabolic Science, Big Data Institute, University of Oxford [Oxford], University of Iowa [Iowa City], The Wellcome Trust Centre for Human Genetics [Oxford], Synlab Academy, Synlab Holding Deutschland GmbH, Mannheim, Medical University Graz, Skane University Hospital [Malmo], Vanderbilt University School of Medicine [Nashville], University of Edinburgh, Université médicale de Vienne, Autriche, National Institute for Health and Welfare [Helsinki], University of Turku, Birmingham Women's and Children's NHS Foundation Trust, Kaiser Permanente, Harbor UCLA Medical Center [Torrance, Ca.], Los Angeles Biomedical Research Institute (LA BioMed), University Medical Center [Utrecht], University of Pittsburgh (PITT), Pennsylvania Commonwealth System of Higher Education (PCSHE), Seattle Epidemiologic Research and Information Center [Seattle], Institute of Cardiovascular and Medical Sciences [Glasgow], University of Glasgow, Department of Cardiology, Södersjukhuset, Stockholm, Estonian Genome and Medicine, Landspitali National University Hospital of Iceland, University of Iceland [Reykjavik], Aalborg University [Denmark] (AAU), Institut de Recherches SERVIER (IRS), Interfaculty Institute for Genetics and Functional Genomics, Ernst-Moritz-Arndt-Universität Greifswald, GlaxoSmithKline, Glaxo Smith Kline, Northeastern Ohio Medical University (NEOMED), Centre d'investigation clinique plurithématique Pierre Drouin [Nancy] (CIC-P), Centre d'investigation clinique [Nancy] (CIC), Université de Lorraine (UL)-Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lorraine (UL)-Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy)-Institut National de la Santé et de la Recherche Médicale (INSERM), Défaillance Cardiovasculaire Aiguë et Chronique (DCAC), Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lorraine (UL), Cardiovascular and Renal Clinical Trialists [Vandoeuvre-les-Nancy] (INI-CRCT), Institut Lorrain du Coeur et des Vaisseaux Louis Mathieu [Nancy], French-Clinical Research Infrastructure Network - F-CRIN [Paris] (Cardiovascular & Renal Clinical Trialists - CRCT ), MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, British Heart Foundation Glasgow Cardiovascular Research Centre (BHF GCRC), University of Glasgow-NHS Greater Glasgow and Clyde, Department of Cardiovascular Sciences [Leicester], University of Leicester, Queensland Brain Institute, Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, University of Dundee, National Heart and Lung Institute [London] (NHLI), Imperial College London-Royal Brompton and Harefield NHS Foundation Trust, Atherosclerosis Risk in Communities Study (ARIC)The Atherosclerosis Risk in Communities Study is carried out as a collaborative study supported by National Heart, Lung, and Blood Institute contracts N01-HC-55015, N01-HC- 55016, N01-HC-55018, N01-HC-55019, N01-HC-55020, N01-HC55021, N01-HC-55022, R01HL087641, R01HL59367, R01HL086694 and RC2 HL102419, National Human Genome Research Institute contract U01HG004402, and National Institutes of Health contract HHSN268200625226C. The authors thank the staff and participants of the ARIC study for their important contributions. Infrastructure was partly supported by Grant Number UL1RR025005, a component of the National Institutes of Health and NIH Roadmap for Medical Research. A systems BIOlogy Study to TAilored Treatment in Chronic Heart Failure (BIOSTAT- CHF)This project was funded by a grant from the European Commission (FP7‐242209‐ BIOSTAT‐CHF, EudraCT 2010–020808–29). Cardiovascular Health Study (CHS) This CHS research was supported by NHLBI contracts HHSN268201200036C, HHSN268200800007C, HHSN268201800001C, HHSN268200960009C, N01HC55222, N01HC85079, N01HC85080, N01HC85081, N01HC85082, N01HC85083, N01HC85086, and NHLBI grants U01HL080295, R01HL087652, R01HL105756, R01HL103612, R01HL120393, and U01HL130114 with additional contribution from the National Institute of Neurological Disorders and Stroke (NINDS). Additional support was provided through R01AG023629 from the National Institute on Aging (NIA). A full list of principal CHS investigators and institutions can be found at CHS-NHLBI.org. The provision of genotyping data was supported in part by the National Center for Advancing Translational Sciences, CTSI grant UL1TR001881, and the National Institute of Diabetes and Digestive and Kidney Disease Diabetes Research Center (DRC) grant DK063491 to the Southern California Diabetes Endocrinology Research Center. deCODE Heart Failure Study (deCODE) We at deCODE thank the women and men of Iceland that have participated in our studies and our colleagues that contributed to data collection and processing. DiscovEHR We acknowledge and thank all participants in Geisinger’s MyCode Community Health Initiative for their support and permission to use their health and genomic information in the DiscovEHR collaboration. This work was supported by the Regeneron Genetics Center and Geisinger. Estonian Genome Center at the University of Tartu (EGCUT) This study was supported by Estonian Research Council Grant IUT20-60, EU, H2020 grant 692145, European Union through the European Regional Development Fund (Project No. 2014-2020.4.01.15-0012) GENTRANSMED. Eplerenone Post-Acute Myocardial Infarction Heart Failure Efficacy and Survival Study (EPHESUS) The EPHESUS was supported by Pfizer, Inc. The European Prospective Investigation of Cancer, Norfolk study (EPIC-Norfolk) The EPIC-Norfolk Study is supported by programme grants from the Medical Research Council UK (G1000143) and Cancer Research UK (C864/A14136) and with additional support from the European Union, Stroke Association, British Heart Foundation, Research into Ageing, Department of Health, The Wellcome Trust and the Food Standards Agency. NJW and CL also acknowledge support from the Medical Research Council, UK (MC_UU_12015/1, MC_PC_13048). We thank all EPIC participants and staff for their contribution to the study, and thank staff from the Technical, Field Epidemiology and Data Functional Group Teams of the Medical Research Council Epidemiology Unit in Cambridge, UK, for carrying out sample preparation, DNA provision and quality control, genotyping and data handling work. Framingham Heart Study (FHS) This work was conducted using data and resources from the Framingham Heart Study (FHS) of the National Heart Lung and Blood Institute and Boston University School of Medicine. The study was supported by the National Heart, Lung and Blood Institute’s Framingham Heart Study (Contract No. N01-HC-25195 and HHSN268201500001I) and its contract with Affymetrix, Inc for genotyping services (Contract No.N02-HL-6-4278). The work was also supported by R01 HL093328, R01 HL105993, and R01 HL71039 (PI: Ramachandran). FINRISK V.S. has been supported by the Finnish Foundation for Cardiovascular Research. Genetics of Diabetes Audit and Research Tayside Scotland GoDARTS) The Wellcome Trust United Kingdom Type 2 Diabetes Case Control Collection (supporting GoDARTS) was funded by the Wellcome Trust (072960/Z/03/Z, 084726/Z/08/Z, 084727/Z/08/Z, 085475/Z/08/Z, 085475/B/08/Z) and as part of the EU IMI-SUMMIT programme. We acknowledge the support of the Health Informatics Centre, University of Dundee, for managing and supplying the anonymized data and NHS Tayside, the original data owner. The Genetic Risk Assessment of Defibrillator Events (GRADE) NIH-NHLBI R01 HL77398 (Genetic Modulators of Sudden Death). S.L. is supported by NIH grant 1R01HL139731 and American Heart Association 18SFRN34250007. The LUdwigshafen RIsk and Cardiovascular Health (LURIC) study We extend our appreciation to the participants of the LURIC study, without their collaboration, this article would not have been written. We thank the LURIC study team who were either temporarily or permanently involved in patient recruitment as well as sample and data handling, in addition to the laboratory staff at the Ludwigshafen General Hospital and the Universities of Freiburg and Ulm, Germany. LURIC has received funding from the 7th Framework Program (RiskyCAD, grant agreement number 305739 and Atheroremo, grant agreement number 201668) of the European Union. Malmö Diet and Cancer Study (MDCS) J. Gustav Smith was supported by grants from the Swedish Heart-Lung Foundation (2016- 0134 and 2016-0315), the Swedish Research Council (2017-02554), the European Research Council (ERC-STG-2015-679242), the Crafoord Foundation, Skåne University Hospital, the Scania county, governmental funding of clinical research within the Swedish National Health Service, a generous donation from the Knut and Alice Wallenberg foundation to the Wallenberg Center for Molecular Medicine in Lund, and funding from the Swedish Research Council (Linnaeus grant Dnr 349-2006-237, Strategic Research Area Exodiab Dnr 2009-1039) and Swedish Foundation for Strategic Research (Dnr IRC15- 0067) to the Lund University Diabetes Center. The Malmo Diet and Cancer Study was made possible by grants from the Swedish Cancer Society, the Swedish Medical Research Council, the Swedish Dairy Association, and the Malmo city council. Penn Heart Failure Study (PHFS) The study was supported by NIH grants (NIH R01L088577 and NIH R01H105993). Prevention of REnal and Vascular ENd-stage Disease (PREVEND) The Prevention of Renal and Vascular Endstage Disease Study (PREVEND) genetics is supported by the Dutch Kidney Foundation (Grant E033), the EU project grant GENECURE (FP-6 LSHM CT 2006 037697), the National Institutes of Health (grant LM010098), the Netherlands organisation for health research and development (NWO VENI grant 916.761.70), and the Dutch Inter University Cardiology Institute Netherlands (ICIN). Niek Verweij was supported by NWO VENI grant 016.186.125. PROspective Study of Pravastatin in the Elderly at Risk for vascular disease (PROSPER)The PROSPER study was supported by an investigator-initiated grant obtained from Bristol- Myers Squibb. Support for genotyping was provided by the seventh framework program of the European commission (grant 223004) and by the Netherlands Genomics Initiative (Netherlands Consortium for Healthy Aging grant 050-060-810). J.W.J. is an Established Clinical Investigator of the Netherlands Heart Foundation (grant 2001 D 032). Study of Health in Pomerania (SHIP) SHIP is part of the Community Medicine Research net of the University of Greifswald, Germany, which is funded by the Federal Ministry of Education and Research (grants no. 01ZZ9603, 01ZZ0103, and 01ZZ0403), the Ministry of Cultural Affairs as well as the Social Ministry of the Federal State of Mecklenburg-West Pomerania, and the network ‘Greifswald Approach to Individualized Medicine (GANI_MED)’ funded by the Federal Ministry of Education and Research (grant 03IS2061A). Genome-wide data have been supported by the Federal Ministry of Education and Research (grant no. 03ZIK012) and a joint grant from Siemens Healthineers, Erlangen, Germany and the Federal State of Mecklenburg- West Pomerania. The University of Greifswald is a member of the Caché Campus program of the InterSystems GmbH. Stabilization of Plaque using Darapladib-Thrombolysis in Myocardial Infarction 52 (SOLID)SOLID-TIMI 52 was funded by GlaxoSmithKline. TwinGene (TwinGene) TwinGene received funding from the Swedish Research Council (M-2005-1112), GenomEUtwin (EU/QLRT-2001-01254, QLG2-CT-2002-01254), NIH DK U01-066134, The Swedish Foundation for Strategic Research (SSF) and the Heart and Lung foundation no. 20070481. TwinGene is part of the Swedish Twin Registry which is managed by Karolinska Institutet and receives funding through the Swedish Research Council (2017–00641). UK Biobank (UKBiobank) This research has been conducted using the UK Biobank Resource under Application Number 15422. This work was supported in part by grants to R.T.L. from the EU/EFPIA Innovative Medicines Initiative 2 Joint Undertaking BigData@Heart grant no. 116074, MRC Proximity to Discovery Award Scheme, the American Heart Association Institute for Precision Mecidine, Pfizer Ltd, the University College London British Heart Foundation Research Accelerator (AA/18/6/34223), and was supported by the National Institute for Health Research University College London Hospitals Biomedical Research Centre. A. H. is supported by the British Heart Foundation Cardiovascular Biomedicine PhD studentship. R.T.L is supported by a UK Research and Innovation Rutherford Fellowship and was previously supported by a National Institutes of Health Research Clinical Lectureship. Uppsala Longitudinal Study of Adult Men (ULSAM) J.Ä. is supported by the Swedish Research Council and the Swedish Heart Lung foundation. C.M.L is supported by the Li Ka Shing Foundation, WT-SSI/John Fell funds and by the NIHR Biomedical Research Centre, Oxford, by Widenlife and NIH (5P50HD028138- 27). Women’s Genome Health Study (WGHS) The WGHS is supported by the National Heart, Lung, and Blood Institute (HL043851 and HL080467, HL099355) and the National Cancer Institute (CA047988 and UM1CA182913), with collaborative scientific support and funding for genotyping provided by Amgen., Epidemiology, Internal Medicine, Læknadeild (HÍ), Faculty of Medicine (UI), Verkfræði- og náttúruvísindasvið (HÍ), School of Engineering and Natural Sciences (UI), Heilbrigðisvísindasvið (HÍ), School of Health Sciences (UI), Háskóli Íslands, and University of Iceland

Subjects
0301 basic medicine, Dánartíðni, Epidemiology, LOCI, 45/43, General Physics and Astronomy, Muscle Proteins, Genome-wide association study, Disease, Coronary Artery Disease, 030204 cardiovascular system & hematology, Bioinformatics, Genome-wide association studies, DISEASE, Ventricular Function, Left, Coronary artery disease, 0302 clinical medicine, Risk Factors, Atrial Fibrillation, IMPUTATION, Medicine, Blóðrásarsjúkdómar, 692/308/174, lcsh:Science, 2. Zero hunger, RISK, Multidisciplinary, Microfilament Proteins, article, Atrial fibrillation, Mendelian Randomization Analysis, CATALOG, 3. Good health, OBESITY, Erfðarannsóknir, Cardiomyopathies, Medical Genetics, Cyclin-Dependent Kinase Inhibitor p21, Science, 631/208/205/2138, Heart failure, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 631/443/592/2727, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, RESOURCE, Humans, Mortality, METAANALYSIS, Genetic association, Medicinsk genetik, Adaptor Proteins, Signal Transducing, Heart Failure, HYPERTENSION, business.industry, Case-control study, Klinisk medicin, 692/699/75/230, General Chemistry, Cardiovascular genetics, medicine.disease, R1, 030104 developmental biology, Case-Control Studies, lcsh:Q, Morbidity, Clinical Medicine, business, Apoptosis Regulatory Proteins, Carrier Proteins, Genome-Wide Association Study
Abstract

Publisher's version (útgefin grein), Heart failure (HF) is a leading cause of morbidity and mortality worldwide. A small proportion of HF cases are attributable to monogenic cardiomyopathies and existing genome-wide association studies (GWAS) have yielded only limited insights, leaving the observed heritability of HF largely unexplained. We report results from a GWAS meta-analysis of HF comprising 47,309 cases and 930,014 controls. Twelve independent variants at 11 genomic loci are associated with HF, all of which demonstrate one or more associations with coronary artery disease (CAD), atrial fibrillation, or reduced left ventricular function, suggesting shared genetic aetiology. Functional analysis of non-CAD-associated loci implicate genes involved in cardiac development (MYOZ1, SYNPO2L), protein homoeostasis (BAG3), and cellular senescence (CDKN1A). Mendelian randomisation analysis supports causal roles for several HF risk factors, and demonstrates CAD-independent effects for atrial fibrillation, body mass index, and hypertension. These findings extend our knowledge of the pathways underlying HF and may inform new therapeutic strategies., We acknowledge the contribution from the EchoGen Consortium.

Published
2020
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36. Mating type determination within a microsatellite multiplex for the fungal pathogen Pseudogymnoascus destructans, the causative agent of white-nose disease in bats

Author

Nicola M. Fischer, Marcus Fritze, Jeffrey T. Foster, Sébastien J. Puechmaille, Andrea Altewischer, Kevin P. Drees, Serena E. Dool, Ernst-Moritz-Arndt-Universität Greifswald, Northern Arizona University [Flagstaff], Universität Greifswald - University of Greifswald, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226

Subjects
0106 biological sciences, 0301 basic medicine, Mating type, Pseudogymnoascus, food.ingredient, Population, [SDV.BDLR.RA]Life Sciences [q-bio]/Reproductive Biology/Asexual reproduction, Asexual reproduction, Biology, 010603 evolutionary biology, 01 natural sciences, [SDV.BDLR.RS]Life Sciences [q-bio]/Reproductive Biology/Sexual reproduction, 03 medical and health sciences, Geomyces, food, Pseudogymnoascus destructans, Genetics, Mating, education, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, Mating type determination, education.field_of_study, biology.organism_classification, 3. Good health, 030104 developmental biology, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Emerging infectious diseases are a severe conservation threat for a variety of plants and animals. In North America, several bat species are threatened by white-nose disease, which has caused an unprecedented mass mortality of > 6 million bats since 2006. The fungus Pseudogymnoascus (Geomyces) destructans is the causative agent of the disease. Though asexual reproduction is the norm, sexual reproduction is possible as two mating types exist. Sexual reproduction has been implicated in the emergence of virulent strains of fungi but to date no rapid means of mating type characterisation was available for P. destructans. In this study, three mating type-specific primer sets were designed and tested on 80 isolates. The primers were multiplexed with microsatellite loci allowing for rapid and concurrent genotyping and mating type assignment. These markers will have great utility in better understanding and predicting the population dynamics and evolutionary potential of this fungus, including the emergence of virulent strains.

Published
2018
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37. Population level mitogenomics of long-lived bats reveals dynamic heteroplasmy and challenges the Free Radical Theory of Ageing

Author

Nicole M. Foley, Emma C. Teeling, Sébastien J. Puechmaille, David Jebb, Conor V. Whelan, Frédéric Touzalin, University College Dublin [Dublin] (UCD), 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), Ernst-Moritz-Arndt-Universität Greifswald, Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
0301 basic medicine, Aging, Population level, Free Radicals, Longitudinal data, lcsh:Medicine, Myotis myotis, Biology, DNA, Mitochondrial, Article, 03 medical and health sciences, 0302 clinical medicine, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Chiroptera, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Animals, lcsh:Science, Free-radical theory of aging, Multidisciplinary, lcsh:R, High-Throughput Nucleotide Sequencing, biology.organism_classification, Heteroplasmy, 030104 developmental biology, Ageing, Evolutionary biology, Mutation, Metabolic rate, lcsh:Q, 030217 neurology & neurosurgery
Abstract

Bats are the only mammals capable of true, powered flight, which drives an extremely high metabolic rate. The “Free Radical Theory of Ageing” (FTRA) posits that a high metabolic rate causes mitochondrial heteroplasmy and the progressive ageing phenotype. Contrary to this, bats are the longest-lived order of mammals given their small size and high metabolic rate. To investigate if bats exhibit increased mitochondrial heteroplasmy with age, we performed targeted, deep sequencing of mitogenomes and measured point heteroplasmy in wild, long lived Myotis myotis. Blood was sampled from 195 individuals, aged between

Published
2018
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38. Male-biased dispersal and the potential impact of human-induced habitat modifications on the Neotropical batTrachops cirrhosus

Author

Sébastien J. Puechmaille, Tanja K. Halczok, Stefan Dominik Brändel, Rachel A. Page, Gerald Kerth, Victoria Flores, Marco Tschapka, Smithsonian Tropical Research Institute, Ernst-Moritz-Arndt-Universität Greifswald, Universität Ulm - Ulm University [Ulm, Allemagne], and University of Chicago

Subjects
0106 biological sciences, 0301 basic medicine, Neotropics, Mitochondrial DNA, Population genetics, 010603 evolutionary biology, 01 natural sciences, Trachops cirrhosus, Gene flow, 03 medical and health sciences, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, 14. Life underwater, Mating, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation, Panama, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Ecology, biology, population genetics, 15. Life on land, biology.organism_classification, 030104 developmental biology, Habitat, Evolutionary biology, sex-biased dispersal, Biological dispersal, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, gene flow
Abstract

International audience; Gene flow, maintained through natal dispersal and subsequent mating events, is one of the most important processes in both ecology and population genetics. Among mammalian populations, gene flow is strongly affected by a variety of factors, including the species’ ability to disperse, and the composition of the environment which can limit dispersal. Information on dispersal patterns is thus crucial both for conservation management and for understanding the social system of a species. We used 16 polymorphic nuclear microsatellite loci in addition to mitochondrial DNA sequences (1.61 kbp) to analyse the population structure and the sex‐specific pattern of natal dispersal in the frog‐eating fringe‐lipped bat, Trachops cirrhosus, in Central Panama. Our study revealed that—unlike most of the few other investigated Neotropical bats—gene flow in this species is mostly male‐mediated. Nevertheless, distinct genetic clusters occur in both sexes. In particular, the presence of genetic differentiation in the dataset only consisting of the dispersing sex (males) indicates that gene flow is impeded within our study area. Our data are in line with the Panama Canal in connection with the widening of the Río Chagres during the canal construction acting as a recent barrier to gene flow. The sensitivity of T. cirrhosus to human‐induced habitat modifications is further indicated by an extremely low capture success in highly fragmented areas. Taken together, our genetic and capture data provide evidence for this species to be classified as less mobile and thus vulnerable to habitat change, information that is important for conservation management.

Published
2018
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39. Range expansion is associated with increased survival and fecundity in a long-lived bat species

Author

Anne-Laure Besnard, Wigbert Schorcht, Eric J. Petit, Gerald Kerth, Pierre-Loup Jan, Martin Biedermann, Lisa Lehnen, Sébastien J. Puechmaille, P. Le Gouar, Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Ernst-Moritz-Arndt-Universität Greifswald, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), École pratique des hautes études (EPHE), Office National des Forets (ONF), PROCOPE/DAAD programme [57211773], PROCOPE/PHC programme [35454SB], DFG (RESPONSE exchange grant), Deutsche Forschungsgemeinschaft, German Science Foundation DFG, Interessengemeinschaft Fledermausschutz & Forsch, Bad Liebenstein, Nachtaktiv Biologists Bat Res GbR, Erfurt, Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL), 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)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)

Subjects
0106 biological sciences, life history, capture-mark-recapture, Range (biology), media_common.quotation_subject, Rhinolophus hipposideros, Population, Longevity, Population Dynamics, Zoology, Trade-off, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Feces, Chiroptera, Germany, Population growth, Animals, education, Population Growth, range expansion, 030304 developmental biology, General Environmental Science, media_common, trade-off, 0303 health sciences, education.field_of_study, General Immunology and Microbiology, biology, Ecology, Reproduction, General Medicine, DNA, 15. Life on land, Fecundity, biology.organism_classification, Fertility, Habitat, Female, France, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, General Agricultural and Biological Sciences, Animal Distribution
Abstract

The speed and dynamics of range expansions shape species distributions and community composition. Despite the critical impact of population growth rates for range expansion, they are neglected in existing empirical studies, which focus on the investigation of selected life-history traits. Here, we present an approach based on non-invasive genetic capture–mark–recapture data for the estimation of adult survival, fecundity and juvenile survival, which determine population growth. We demonstrate the reliability of our method with simulated data, and use it to investigate life-history changes associated with range expansion in 35 colonies of the bat species Rhinolophus hipposideros . Comparing the demographic parameters inferred for 19 of those colonies which belong to an expanding population with those inferred for the remaining 16 colonies from a non-expanding population reveals that range expansion is associated with higher net reproduction. Juvenile survival was the main driver of the observed reproduction increase in this long-lived bat species with low per capita annual reproductive output. The higher average growth rate in the expanding population was not associated with a trade-off between increased reproduction and survival, suggesting that the observed increase in reproduction stems from a higher resource acquisition in the expanding population. Environmental conditions in the novel habitat hence seem to have an important influence on range expansion dynamics, and warrant further investigation for the management of range expansion in both native and invasive species.

Published
2019
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40. Analytical modelling of Tm-doped tellurite glass including cross-relaxation process

Author

Hazel Hung, Wilfried Blanc, Ali Albalawi, Hrvoje Gebavi, Rolindes Balda, Alexander Quandt, Charlie Brilliant, Maurizio Ferrari, Alessandro Chiasera, Anna Lukowiak, Stefano Taccheo, Wedad Albalawi, European Commission, College of Engineering [Swansea], Swansea University, Caratterizzazione e Sviluppo di Materiali per la Fotonica e l'Optoelecttronica (CSMFO), CNR Istituto di Fotonica e Nanotecnologie [Trento] (IFN), Consiglio Nazionale delle Ricerche [Roma] (CNR)-Consiglio Nazionale delle Ricerche [Roma] (CNR), Rudjer Boskovic Institute [Zagreb], Universidad del Pais Vasco / Euskal Herriko Unibertsitatea [Espagne] (UPV/EHU), Institut de Physique de Nice (INPHYNI), Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Institut für Physik, Ernst-Moritz-Arndt-Universität Greifswald, Institute of Low Temperatures and Structure Research, and Polska Akademia Nauk = Polish Academy of Sciences (PAN)

Subjects
[PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], Materials science, Dopant, Tellurite glass, Organic Chemistry, Doping, tellurite glass, 02 engineering and technology, 010402 general chemistry, 021001 nanoscience & nanotechnology, Population inversion, 01 natural sciences, Cross relaxation, Fluorescence, Molecular physics, Atomic and Molecular Physics, and Optics, 0104 chemical sciences, Electronic, Optical and Magnetic Materials, Inorganic Chemistry, Scientific method, Electrical and Electronic Engineering, Physical and Theoretical Chemistry, 0210 nano-technology, ComputingMilieux_MISCELLANEOUS, Spectroscopy
Abstract

In this paper, we present a comprehensive analytical model of Tm able to take into account direct cross-relaxation process. We show that by using an appropriate set of parameters the model is able to properly fit the first part of the fluorescence decay of Tm-doped tellurite glasses for different dopant concentration values. We also compare the model with a full numerical model to investigate its limitations. We assess the model is a valid tool to fit fluorescence properties but for precisely predicting population inversion is limited to doping level up to about 1%. In fact, we show the reverse cross-relaxation process becomes significant in case of higher doping level., This article is based upon work from H2020 COST Action MP1401 on “Fiber Lasers and Their Applications” supported by COST “(European Cooperation in Science and Technology)”.

Published
2019
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41. Screening and Biosecurity for White-Nose Fungus Pseudogymnoascus destructans (Ascomycota: Pseudeurotiaceae) in Hawai‘i1

Author

Kristina Montoya-Aiona, Violeta Zhelyazkova, Corinna A. Pinzari, Nia Toshkova, Sébastien J. Puechmaille, Frank J. Bonaccorso, Serena E. Dool, Ernst-Moritz-Arndt-Universität Greifswald, National Museum of Natural History, Sofia, Bulgaria (NMNHS), Bulgarian Academy of Sciences (BAS), US Geological Survey [Pasadena], United States Geological Survey [Reston] (USGS), University of Hawai'i [Hilo], Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226

Subjects
0106 biological sciences, pathogen pollution, Fauna, Biosecurity, Fungus, 010603 evolutionary biology, 01 natural sciences, bat conservation, emerging infectious diseases, Cave, Pseudogymnoascus destructans, cave management, Pseudeurotiaceae, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Multidisciplinary, geography.geographical_feature_category, Lasiurus, biology, Ecology, 010604 marine biology & hydrobiology, 15. Life on land, biology.organism_classification, Mass mortality, Geography, white-nose syndrome, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

International audience; Introduced pathogens causing emerging infectious diseases (EIDs) are serious contemporary threats to animal, plant, and ecosystem health. The invasive fungus, Pseudogymnoascus destructans, has established populations of European origin in North America, resulting in mass mortality of several hibernating bat species. Extensive monitoring for this pathogen exists in Europe and North America, but limited screening is taking place elsewhere. We report results from cave surveys on Hawai‘i Island. Substrates in 10 lava-tube caves with elevations up to 3,045 m were swabbed providing samples for screening P. destructans. Interior cave air temperatures spanned temperatures suitable for the growth and survival of P. destructans. Using quantitative PCR, all 85 samples tested were negative for the presence of P. destructans. The biology of the Hawaiian hoary bat (Lasiurus cinereus semotus) in relation to its unusual use of high elevation caves is discussed because these bats could come into contact with P. destructans should it arrive in Hawai‘i. Large numbers of cave enthusiasts visit Hawaiian caves from across the world after having been inside caves elsewhere including areas with P. destructans. Thus, resource managers in Hawai‘i and other remote areas may want to consider the potential for P. destructans to arrive unintentionally via human activities. Biosecurity measures and periodic screening for P. destructans are especially important in Hawai‘i given the presence of high elevation caves with suitable temperatures for its growth. If P. destructans was introduced to Hawaiian caves, it could affect the local fauna but also act as a source population for colonisations elsewhere.

Published
2019
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42. Inhibition of Rho Activity Increases Expression of SaeRS-Dependent Virulence Factor Genes in Staphylococcus aureus, Showing a Link between Transcription Termination, Antibiotic Action, and Virulence

Author

Tarek Msadek, Anna Nagel, Hermann Rath, Michel Débarbouillé, Manuela Gesell Salazar, Stephan Michalik, Jan Maarten van Dijl, Tobias Hertlein, Uwe Völker, Ulrike Mäder, Knut Ohlsen, Universität Greifswald - University of Greifswald, Interfaculty Institute for Genetics and Functional Genomics, Ernst-Moritz-Arndt-Universität Greifswald, Biologie des Bactéries pathogènes à Gram-positif, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), University of Würzburg, University of Groningen [Groningen], This work was supported by grants from the Deutsche Forschungsgemeinschaft within the framework of the Research Training Group 1870 'Bacterial respiratory infections—Common and specific mechanisms of pathogen adaptation and immune defence' and the SFB TRR34 as well as CEU project LSHG-CT-2006-037469 (BaSysBio)., European Project: 38901,BASYSBIO, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), University of Groningen, Microbes in Health and Disease (MHD), and Translational Immunology Groningen (TRIGR)

Subjects
0301 basic medicine, antisense transcription, IMMUNE EVASION, Bacteremia, Virulence Factors/biosynthesis, MESH: Virulence, Protein Kinases/genetics, medicine.disease_cause, Virulence factor, RNA-POLYMERASE, SUBINHIBITORY CONCENTRATIONS, Transcription (biology), MESH: Rho Factor, Gene expression, MESH: Staphylococcus aureus, MESH: Animals, MESH: Bacteremia, MESH: Bacterial Proteins, IN-VIVO, MESH: Gene Expression Regulation, Bacterial, MESH: Genetic Complementation Test, Virulence, Anti-Bacterial Agents/metabolism, Bacterial, PANTON-VALENTINE LEUKOCIDIN, SaeRS TCS, MESH: Transcription Factors, Staphylococcal Infections, QR1-502, Anti-Bacterial Agents, Bacteremia/microbiology, MESH: Proteome, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, 2-COMPONENT SYSTEM SAERS, ESCHERICHIA-COLI, Staphylococcus aureus, MESH: Regulon, MYCOBACTERIUM-TUBERCULOSIS, Transcription Termination, Virulence Factors, bicyclomycin, proteome, REGULATORY SYSTEM, 030106 microbiology, MESH: Staphylococcal Infections, Staphylococcus aureus/drug effects, Transcription Factors/genetics, Biology, Microbiology, Regulon, Rho Factor/genetics, BACILLUS-SUBTILIS, Bicyclomycin, 03 medical and health sciences, MESH: Gene Expression Profiling, Bacterial Proteins, Genetic, MESH: Transcription Termination, Genetic, Virology, MESH: Anti-Bacterial Agents, medicine, Proteome/analysis, Animals, MESH: Protein Kinases, MESH: Virulence Factors, Bacterial Proteins/genetics, Animal, Gene Expression Profiling, Genetic Complementation Test, Gene Expression Regulation, Bacterial, Rho Factor, Bacterial adhesin, Staphylococcal Infections/microbiology, Disease Models, Animal, Gene Expression Regulation, MESH: Gene Deletion, Transcription Termination, Genetic, Disease Models, MESH: Disease Models, Animal, Protein Kinases, Gene Deletion, Transcription Factors
Abstract

International audience; Staphylococcus aureus causes various diseases ranging from skin and soft tissue infections to life-threatening infections. Adaptation to the different host niches is controlled by a complex network of transcriptional regulators. Global profiling of condition-dependent transcription revealed adaptation of S. aureus HG001 at the levels of transcription initiation and termination. In particular, deletion of the gene encoding the Rho transcription termination factor triggered a remarkable overall increase in antisense transcription and gene expression changes attributable to indirect regulatory effects. The goal of the present study was a detailed comparative analysis of S. aureus HG001 and its isogenic rho deletion mutant. Proteome analysis revealed significant differences in cellular and extracellular protein profiles, most notably increased amounts of the proteins belonging to the SaeR regulon in the Rho-deficient strain. The SaeRS two-component system acts as a major regulator of virulence gene expression in staphylococci. Higher levels of SaeRS-dependent virulence factors such as adhesins, toxins, and immune evasion proteins in the rho mutant resulted in higher virulence in a murine bacteremia model, which was alleviated in a rho complemented strain. Inhibition of Rho activity by bicyclomycin, a specific inhibitor of Rho activity, also induced the expression of SaeRS-dependent genes, at both the mRNA and protein levels, to the same extent as observed in the rho mutant. Taken together, these findings indicate that activation of the Sae system in the absence of Rho is directly linked to Rho's transcription termination activity and establish a new link between antibiotic action and virulence gene expression in S. aureusIMPORTANCE The major human pathogen Staphylococcus aureus is a widespread commensal bacterium but also the most common cause of nosocomial infections. It adapts to the different host niches through a complex gene regulatory network. We show here that the Rho transcription termination factor, which represses pervasive antisense transcription in various bacteria, including S. aureus, plays a role in controlling SaeRS-dependent virulence gene expression. A Rho-deficient strain produces larger amounts of secreted virulence factors in vitro and shows increased virulence in mice. We also show that treatment of S. aureus with the antibiotic bicyclomycin, which inhibits Rho activity and is effective against Gram-negative bacteria, induces the same changes in the proteome as observed in the Rho-deficient strain. Our results reveal for the first time a link between transcription termination and virulence regulation in S. aureus, which implies a novel mechanism by which an antibiotic can modulate the expression of virulence factors.

Published
2018
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43. Growing old, yet staying young:The role of telomeres in bats' exceptional longevity

Author

Olivier Farcy, Emma C. Teeling, Mike Clarke, Nicole M. Foley, Roger D. Ransome, Gareth Jones, Hugo Rebelo, David Jebb, Joanna Kacprzyk, Conor V. Whelan, Luísa Rodrigues, Sébastien J. Puechmaille, Mary J. O'Connell, Graham M. Hughes, Zixia Huang, Gerald Kerth, Eric J. Petit, Frédéric Touzalin, University College Dublin [Dublin] (UCD), Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Bretagne Vivante, School of Biological Sciences [Bristol], University of Bristol [Bristol], University of Leeds, Ernst-Moritz-Arndt-Universität Greifswald, Universidade do Porto [Porto], Universidade de Lisboa (ULISBOA), Instituto de Conservaçao da natureza e das Florestas, Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Universidade do Porto = University of Porto, Universidade de Lisboa = University of Lisbon (ULISBOA), ERC-2012-StG311000, 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 de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, and Universidade do Porto

Subjects
0301 basic medicine, Telomerase, animal structures, DNA repair, DNA damage, media_common.quotation_subject, Longevity, Myotis myotis, 03 medical and health sciences, 0302 clinical medicine, Species Specificity, Chiroptera, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Genetics, Animals, Selection, Genetic, Gene, Research Articles, media_common, Multidisciplinary, biology, Body Weight, Rhinolophus ferrumequinum, SciAdv r-articles, Telomere, biology.organism_classification, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, 030104 developmental biology, Evolutionary biology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 030217 neurology & neurosurgery, Research Article
Abstract

Telomeres do not shorten with age in longest-lived bats., Understanding aging is a grand challenge in biology. Exceptionally long-lived animals have mechanisms that underpin extreme longevity. Telomeres are protective nucleotide repeats on chromosome tips that shorten with cell division, potentially limiting life span. Bats are the longest-lived mammals for their size, but it is unknown whether their telomeres shorten. Using >60 years of cumulative mark-recapture field data, we show that telomeres shorten with age in Rhinolophus ferrumequinum and Miniopterus schreibersii, but not in the bat genus with greatest longevity, Myotis. As in humans, telomerase is not expressed in Myotis myotis blood or fibroblasts. Selection tests on telomere maintenance genes show that ATM and SETX, which repair and prevent DNA damage, potentially mediate telomere dynamics in Myotis bats. Twenty-one telomere maintenance genes are differentially expressed in Myotis, of which 14 are enriched for DNA repair, and 5 for alternative telomere-lengthening mechanisms. We demonstrate how telomeres, telomerase, and DNA repair genes have contributed to the evolution of exceptional longevity in Myotis bats, advancing our understanding of healthy aging.

Published
2018
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44. Mycobiomes of sympatric Amorphophallus albispathus (Araceae) and Camellia sinensis (Theaceae) – a case study reveals clear tissue preferences and differences in diversity and composition

Author

David G. Würth, Nikki Heherson A. Dagamac, R. Henrik Nilsson, Kevin D. Hyde, Sébastien J. Puechmaille, Mathilde Borg Dahl, Christian Wurzbacher, Serena E. Dool, Michael G. Schöner, Michelle Galla, Abu Bakar Siddique, Kristina Wicke, Martin Unterseher, Caroline R. Schöner, García Roberto Cruz, Annette Teltewskoi, Samantha C. Karunarathna, Lina Herbst, Ernst-Moritz-Arndt-Universität Greifswald, Kunming Institute of Botany [CAS] (KIB), Chinese Academy of Sciences [Beijing] (CAS), University of Gothenburg (GU), and Mae Fah Luang University [Thaïlande] (MFU)

Subjects
0106 biological sciences, 0301 basic medicine, Biogeography, Biodiversity, 01 natural sciences, 03 medical and health sciences, Amorphophallus, Botany, Camellia sinensis, Mycobiome diversity, Internal transcribed spacer, Ecology, Evolution, Behavior and Systematics, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, High-throughput metabarcoding, Abiotic component, biology, Host (biology), fungi, food and beverages, Host specialization, Camellia, 030108 mycology & parasitology, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, Agricultural and Biological Sciences (miscellaneous), Sympatric speciation, Tissue preferences of endophytes, 010606 plant biology & botany, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

International audience; Multiple biotic and abiotic parameters influence the dynamics of individual fungal species and entire communities. Major drivers for tropical plant endophytes are undoubtedly seasonality, local habitat conditions and biogeography. However, host specialization and tissue preferences also contribute to the structuring of endophytic mycobiomes. To elucidate such specializations and preferences, we sampled two commercially important, unrelated plant species, Amorphophallus albispathus and Camellia sinensis (tea plant) simultaneously at close proximity. The mycobiomes of different tissue types were assessed with high-throughput amplicon sequencing of the internal transcribed spacer DNA region. Both plants hosted different fungal communities and varied in α-and β-diversity, despite their neighboring occurrence. However, the fungal assemblages of Amorphophallus leaflets shared taxa with the mycobiomes of tea leaves, thereby suggesting common driving forces for leaf-inhabiting fungi irrespective of host plant identity. The mycobiome composition and diversity of tea leaves was clearly driven by leaf age. We suggest that the very youngest tea leaves are colonized by stochastic processes, while mycobiomes of old leaves are rather similar as the result of progressive succession. The biodiversity of fungi associated with A. albispathus was characterized by a large number of unclassified OTUs (at genus and species level) and by tissue-specific composition.This study is the first cultivation-independent high-throughput assessment of fungal biodiversity of an Amorphophallus species, and additionally expands the knowledge base on fungi associated with tea plants.

Published
2018
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45. Is there a link between aging and microbiome diversity in exceptional mammalian longevity?

Author

Emma C. Teeling, Graham M. Hughes, Sébastien J. Puechmaille, John Leech, Jose V. Lopez, University College Dublin [Dublin] (UCD), University College Cork (UCC), Ernst-Moritz-Arndt-Universität Greifswald, and Nova Southeastern University (NSU)

Subjects
0106 biological sciences, 0301 basic medicine, Aging, Evolution, media_common.quotation_subject, lcsh:Medicine, Gut microbiota, Conservation, Myotis myotis, Comparative biology, Gut flora, 010603 evolutionary biology, 01 natural sciences, Microbiology, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Information, Bats, Proteobacteria, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Juvenile, Microbiome, Organism, media_common, Geography, biology, General Neuroscience, Communities, lcsh:R, Longevity, General Medicine, Fuel, biology.organism_classification, Host phylogeny, Phenotype, Evolutionary Studies, 030104 developmental biology, Metabolism, Flight, Evolutionary biology, Comparative Biology, General Agricultural and Biological Sciences, Zoology, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

A changing microbiome has been linked to biological aging in mice and humans, suggesting a possible role of gut flora in pathogenic aging phenotypes. Many bat species have exceptional longevity given their body size and some can live up to ten times longer than expected with little signs of aging. This study explores the anal microbiome of the exceptionally long-lived Myotis myotis bat, investigating bacterial composition in both adult and juvenile bats to determine if the microbiome changes with age in a wild, long-lived non-model organism, using non-lethal sampling. The anal microbiome was sequenced using metabarcoding in more than 50 individuals, finding no significant difference between the composition of juvenile and adult bats, suggesting that age-related microbial shifts previously observed in other mammals may not be present in Myotis myotis. Functional gene categories, inferred from metabarcoding data, expressed in the M. myotis microbiome were categorized identifying pathways involved in metabolism, DNA repair and oxidative phosphorylation. We highlight an abundance of ‘Proteobacteria’ relative to other mammals, with similar patterns compared to other bat microbiomes. Our results suggest that M. myotis may have a relatively stable, unchanging microbiome playing a role in their extended ‘health spans’ with the advancement of age, and suggest a potential link between microbiome and sustained, powered flight.

Published
2018
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46. On computing the maximum parsimony score of a phylogenetic network

Author

Celine Scornavacca, Mareike Fischer, Steven Kelk, Leo van Iersel, RS: FSE DACS BMI, DKE Scientific staff, Ernst-Moritz-Arndt-Universität Greifswald, Delft University of Technology (TU Delft), Department of data science and Knowledge Engineering [Maastricht], Maastricht University [Maastricht], Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)

Subjects
General Mathematics, F.2, 0206 medical engineering, G.2, approximability, Inference, 02 engineering and technology, Network topology, parsimony, Combinatorics, 03 medical and health sciences, phylogenetic networks, FOS: Mathematics, Mathematics - Combinatorics, [INFO]Computer Science [cs], Quantitative Biology - Populations and Evolution, Integer programming, 030304 developmental biology, Mathematics, Discrete mathematics, 0303 health sciences, Phylogenetic tree, AMS subject classifications. 68W25, 05C20, 90C27, 92B10, software, Populations and Evolution (q-bio.PE), Phylogenetic network, Tree (graph theory), Maximum parsimony, phylogenetic trees, Tree rearrangement, FOS: Biological sciences, fixed-parameter tractability, Combinatorics (math.CO), [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], complexity, Algorithm, 020602 bioinformatics
Abstract

International audience; Phylogenetic networks are used to display the relationship among different species whose evolution is not treelike, which is the case, for instance, in the presence of hybridization events or horizontal gene transfers. Tree inference methods such as maximum parsimony need to be modified in order to be applicable to networks. In this paper, we discuss two different definitions of maximum parsimony on networks, “hardwired” and “softwired,” and examine the complexity of computing them given a network topology and a character. By exploiting a link with the problem Multiterminal Cut, we show that computing the hardwired parsimony score for 2-state characters is polynomial-time solvable, while for characters with more states this problem becomes NP-hard but is still approximable and fixed parameter tractable in the parsimony score. On the other hand we show that, for the softwired definition, obtaining even weak approximation guarantees is already difficult for binary characters and restricted network topologies, and fixed-parameter tractable algorithms in the parsimony score are unlikely. On the positive side we show that computing the softwired parsimony score is fixed-parameter tractable in the level of the network, a natural parameter describing how tangled reticulate activity is in the network. Finally, we show that both the hardwired and the softwired parsimony scores can be computed efficiently using integer linear programming. The software has been made freely available.

Published
2015
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47. Change in Stripes for Cholesteric Shells via Anchoring in Moderation

Author

Martin F. Haase, Alexandre Darmon, Daeyeon Lee, Lisa Tran, Kathleen J. Stebe, Teresa Lopez-Leon, Ningwei Li, Maxim O. Lavrentovich, Randall D. Kamien, Guillaume Durey, Institut Langevin - Ondes et Images (UMR7587) (IL), Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), UNIROUEN - UFR Santé (UNIROUEN UFR Santé), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Vogelwarte Hiddensee, Zoologisches Institut und Museum, Ernst-Moritz-Arndt-Universität Greifswald, Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Gulliver (UMR 7083), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut Langevin - Ondes et Images, Université Paris Diderot - Paris 7 (UPD7)-ESPCI ParisTech-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Gulliver, ESPCI ParisTech-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)

Subjects
[PHYS]Physics [physics], Materials science, Physics, QC1-999, FOS: Physical sciences, General Physics and Astronomy, Anchoring, 02 engineering and technology, Condensed Matter - Soft Condensed Matter, 021001 nanoscience & nanotechnology, 01 natural sciences, Condensed Matter::Soft Condensed Matter, Chemical physics, Liquid crystal, 0103 physical sciences, Soft Condensed Matter (cond-mat.soft), Molecule, 010306 general physics, 0210 nano-technology, ComputingMilieux_MISCELLANEOUS
Abstract

Chirality, ubiquitous in complex biological systems, can be controlled and quantified in synthetic materials such as cholesteric liquid crystal (CLC) systems. In this work, we study spherical shells of CLC under weak anchoring conditions. We induce anchoring transitions at the inner and outer boundaries using two independent methods: by changing the surfactant concentration or by raising the temperature close to the clearing point. The shell confinement leads to new states and associated surface structures: a state where large stripes on the shell can be filled with smaller, perpendicular sub-stripes, and a focal conic domain (FCD) state, where thin stripes wrap into at least two, topologically required, double spirals. Focusing on the latter state, we use a Landau-de Gennes model of the CLC to simulate its detailed configurations as a function of anchoring strength. By abruptly changing the topological constraints on the shell, we are able to study the interconversion between director defects and pitch defects, a phenomenon usually restricted by the complexity of the cholesteric phase. This work extends the knowledge of cholesteric patterns, structures that not only have potential for use as intricate, self-assembly blueprints but are pervasive in biological systems., 27 pages, 10 figures

Published
2017
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48. Genetic engineering of the branched fatty acid metabolic pathway of Bacillus subtilis for the overproduction of surfactin C14 isoform

Author

Sandrine Auger, Philippe Jacques, Debarun Dhali, Michael Lalk, Vladimir Bidnenko, Joana Sousa, Joachim Niehren, Gabrielle Chataigné, Anthony Arguelles Arias, François Coutte, Cristian Versari, Institut Charles Viollette (ICV) - EA 7394 (ICV), Université d'Artois (UA)-Institut National de la Recherche Agronomique (INRA)-Université du Littoral Côte d'Opale (ULCO)-Institut Supérieur d'Agriculture-Université de Lille, Laboratoire de Procédés Biologiques, Génie Enzymatique et Microbien (ProBioGEM), Université de Lille, Sciences et Technologies-École polytechnique universitaire de Lille (Polytech Lille), Unité de recherche TERRA [Gembloux], Gembloux Agro-Bio Tech [Gembloux], Université de Liège-Université de Liège, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Ernst-Moritz-Arndt-Universität Greifswald, BioComputing, Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Linking Dynamic Data (LINKS), Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), European INTERREG V BioProd project, French National Research Agency (ANR) [ANR-11-EQPX-0037], European Project: 317338,EC:FP7:PEOPLE,FP7-PEOPLE-2012-ITN,AMBER(2013), Centre de Recherche en Informatique, Signal et Automatique de Lille (CRIStAL) - UMR 9189 (CRIStAL), Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Ecole Centrale de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Ecole Centrale de Lille, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre de Recherche en Informatique, Signal et Automatique de Lille (CRIStAL) - UMR 9189 (CRIStAL), Transfrontalière BioEcoAgro - UMR 1158 (BioEcoAgro), Université d'Artois (UA)-Université de Liège-Université de Picardie Jules Verne (UPJV)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-JUNIA (JUNIA), and Université catholique de Lille (UCL)-Université catholique de Lille (UCL)

Subjects
0301 basic medicine, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Operon, [SDV]Life Sciences [q-bio], 030106 microbiology, Branched-chain amino acid, Mutant, Bacillus subtilis, Metabolic networks, Applied Microbiology and Biotechnology, 03 medical and health sciences, chemistry.chemical_compound, chemistry.chemical_classification, biology, Wild type, Fatty acid, General Medicine, biology.organism_classification, Metabolic pathway, chemistry, Biochemistry, Molecular Medicine, lipids (amino acids, peptides, and proteins), Knockout prediction, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Surfactin, Systems biology
Abstract

International audience; Surfactin, a lipopeptide produced by Bacillus subtilis, is one of the most powerful biosurfactants known. This molecule consists of a cyclic heptapeptide linked to a β-hydroxy fatty acid chain. The isomery and the length of the fatty acid (FA) chain are responsible for the surfactin’s activities. In this study, the gene codY, which encode for the global transcriptional regulator and the gene lpdV, located in the bkd operon (lpdV, bkdAA, bkdAB and bkdB genes), which is responsible for the last step of the branched chain amino acid (BCAA) degradation in acyl- CoA were deleted. The influence of these deletions on the quantitative and qualitative surfactin production was analysed. The surfactin production was quantified by RP-HPLC and the surfactin isoforms were characterized using LC-MS-MS and GC-MS analysis. The results obtained in the mutants showed an enhancement of surfactin specific production by a factor of 5.8 for the codY mutant and 1.4 for lpdV mutant. Moreover qualitative analysis of the lpdV mutant reveals that it mainly produced surfactin C14 isoform (2 fold more than the wild type) with linear FA chain. Complete analysis of the extracellular metabolites using 1H quantitative NMR reveals a reduced production of acetoin in this mutant. This work demonstrates for the first time an original approach to overproduce specifically surfactin with C14 FA chain.

Published
2017
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49. Harmonized dataset of ozone profiles from satellite limb and occultation measurements

Author

Viktoria Sofieva, Gabriele Stiller, D. A. Degenstein, Stefan Lossow, N. Kalb, Mark Weber, Erkki Kyrölä, C. Adams, Francis Dalaudier, Niilo Kalakoski, Nicholas D. Lloyd, Robert J. Hargreaves, T. von Clarmann, Chris Roth, Jakub Urban, Johanna Tamminen, Peter F. Bernath, Claus Zehner, Donal P. Murtagh, C. von Savigny, A. Laeng, Adam Bourassa, Nabiz Rahpoe, Alain Hauchecorne, A. Rozanov, M. Van Roozendael, Finnish Meteorological Institute (FMI), Institute of Environmental Physics [Bremen] (IUP), University of Bremen, Institut für Physik [Greifswald], Ernst-Moritz-Arndt-Universität Greifswald, Institute for Meteorology and Climate Research (IMK), Karlsruhe Institute of Technology (KIT), Institute of Space and Atmospheric Studies [Saskatoon] (ISAS), Department of Physics and Engineering Physics [Saskatoon], University of Saskatchewan [Saskatoon] (U of S)-University of Saskatchewan [Saskatoon] (U of S), Department of Chemistry [York, UK], University of York [York, UK], Chalmers University of Technology [Göteborg], STRATO - LATMOS, Laboratoire Atmosphères, Milieux, Observations Spatiales (LATMOS), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Belgian Institute for Space Aeronomy / Institut d'Aéronomie Spatiale de Belgique (BIRA-IASB), European Space Research Institute (ESRIN), Agence Spatiale Européenne = European Space Agency (ESA), and European Space Agency (ESA)

Subjects
NetCDF, [PHYS.PHYS.PHYS-AO-PH]Physics [physics]/Physics [physics]/Atmospheric and Oceanic Physics [physics.ao-ph], lcsh:GE1-350, Data consistency, 010504 meteorology & atmospheric sciences, Meteorology, lcsh:QE1-996.5, Data validation, computer.file_format, 01 natural sciences, Occultation, SCIAMACHY, 010309 optics, lcsh:Geology, Altitude, 13. Climate action, Data quality, 0103 physical sciences, General Earth and Planetary Sciences, Environmental science, Satellite, computer, lcsh:Environmental sciences, 0105 earth and related environmental sciences, Remote sensing
Abstract

In this paper, we present a HARMonized dataset of OZone profiles (HARMOZ) based on limb and occultation measurements from Envisat (GOMOS, MIPAS and SCIAMACHY), Odin (OSIRIS, SMR) and SCISAT (ACE-FTS) satellite instruments. These measurements provide high-vertical-resolution ozone profiles covering the altitude range from the upper troposphere up to the mesosphere in years 2001–2012. HARMOZ has been created in the framework of the European Space Agency Climate Change Initiative project. The harmonized dataset consists of original retrieved ozone profiles from each instrument, which are screened for invalid data by the instrument teams. While the original ozone profiles are presented in different units and on different vertical grids, the harmonized dataset is given on a common pressure grid in netCDF (network common data form)-4 format. The pressure grid corresponds to vertical sampling of ~ 1 km below 20 km and 2–3 km above 20 km. The vertical range of the ozone profiles is specific for each instrument, thus all information contained in the original data is preserved. Provided altitude and temperature profiles allow the representation of ozone profiles in number density or mixing ratio on a pressure or altitude vertical grid. Geolocation, uncertainty estimates and vertical resolution are provided for each profile. For each instrument, optional parameters, which are related to the data quality, are also included. For convenience of users, tables of biases between each pair of instruments for each month, as well as bias uncertainties, are provided. These tables characterize the data consistency and can be used in various bias and drift analyses, which are needed, for instance, for combining several datasets to obtain a long-term climate dataset. This user-friendly dataset can be interesting and useful for various analyses and applications, such as data merging, data validation, assimilation and scientific research. The dataset is available at http://www.esa-ozone-cci.org/?q=node/161 or at doi:10.5270/esa-ozone_cci-limb_occultation_profiles-2001_2012-v_1-201308.

Published
2013
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50. Ultrafast photocurrents at the surface of the three-dimensional topological insulator Bi 2 Se 3

Author

Gregor Mussler, Andrzej Hruban, Martin Wolf, Markus Münzenberg, Lukas Braun, Luca Perfetti, Tobias Kampfrath, Marcin Konczykowski, Thomas Schumann, Fritz-Haber-Institut der Max-Planck-Gesellschaft (FHI), Max Planck Society, PGI-9 and JARA-FIT, Forschungszentrum Ju¨lich, 52425 Ju¨lich, Germany, Institute of Electronic Materials Technology, 01-919 Warsaw, Poland, Laboratoire des Solides Irradiés (LSI), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Institut für Physik [Greifswald], Ernst-Moritz-Arndt-Universität Greifswald, and ANR-13-IS04-0001,IRIDOTI,Dopage par Irradiation des IsolantsTopologiques(2013)

Subjects
Electromagnetic field, Terahertz radiation, Science, General Physics and Astronomy, Physics::Optics, 02 engineering and technology, terahertz spectroscopy, 01 natural sciences, Article, General Biochemistry, Genetics and Molecular Biology, 0103 physical sciences, Light beam, [PHYS.COND]Physics [physics]/Condensed Matter [cond-mat], 010306 general physics, Spin-½, Physics, Multidisciplinary, Condensed matter physics, business.industry, Scattering, General Chemistry, Condensed Matter::Mesoscopic Systems and Quantum Hall Effect, 021001 nanoscience & nanotechnology, topological insulators, Orders of magnitude (time), Topological insulator, Optoelectronics, 0210 nano-technology, business, Ultrashort pulse
Abstract

Three-dimensional topological insulators are fascinating materials with insulating bulk yet metallic surfaces that host highly mobile charge carriers with locked spin and momentum. Remarkably, surface currents with tunable direction and magnitude can be launched with tailored light beams. To better understand the underlying mechanisms, the current dynamics need to be resolved on the timescale of elementary scattering events (∼10 fs). Here, we excite and measure photocurrents in the model topological insulator Bi2Se3 with a time resolution of 20 fs by sampling the concomitantly emitted broadband terahertz (THz) electromagnetic field from 0.3 to 40 THz. Strikingly, the surface current response is dominated by an ultrafast charge transfer along the Se–Bi bonds. In contrast, photon-helicity-dependent photocurrents are found to be orders of magnitude smaller than expected from generation scenarios based on asymmetric depopulation of the Dirac cone. Our findings are of direct relevance for broadband optoelectronic devices based on topological-insulator surface currents., Surface currents in topological insulators can be controlled by light, but the underlying mechanisms are not well understood. Here, Braun et al. report an ultrafast shift photocurrent at the surface of Ca-doped Bi2Se3, whereas injection currents are much smaller than expected from asymmetric depopulation of the Dirac cone.

Published
2016
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