Author: "FWF" / Topic: biology - Searchworks@Jio Institute Digital Library Search Results

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101 results on '"FWF"'

1. Digesting the crisis: autophagy and coronaviruses

Author: Katharina Kainz, Maria A. Bauer, Didac Carmona-Gutierrez, Guido Kroemer, Sebastian J. Hofer, Frank Madeo, Andreas Zimmermann, Karl-Franzens-Universität [Graz, Autriche], BioHealth Graz [Graz, Autriche], Centre de Recherche des Cordeliers (CRC (UMR_S_1138 / U1138)), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université de Paris (UP), Plateforme de métabolomique, Direction de la recherche [Gustave Roussy], Institut Gustave Roussy (IGR)-Institut Gustave Roussy (IGR), Cell Biology Platform [Villejuif], Institut Gustave Roussy (IGR), Pôle de biologie, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), Chinese Academy of Medical Sciences [Suzhou, Chine] (CAMS), Karolinska University Hospital [Stockholm], BioTechMed Graz [Graz, Autriche], The authors are grateful to the Austrian Science Fund FWF (SFBLIPOTOX F3007&F3012, W1226, P29203, P29262, P27893) and the Austrian Federal Ministry of Education, Science and Research and the University of Graz for grants 'Unkonventionelle Forschung' and 'flysleep' (BMWFW-80.109/0001-WF/V/3b/2015). The authors also acknowledge the funding of DK Metabolic and Cardiovas-cular Disease (FWF) and the Doctoral College 'Metabolic and Cardiovascular Disease' (FWFW1226) as well as support from NAWI Graz and the BioTechMed-Graz flagship project 'EPIAge'. GK is supported by the Ligue contre le Cancer (équipe labellisée), Agence National de la Recherche (ANR) – Projets blancs, ANR under the frame of E-Rare-2, the ERA-Net for Research on Rare Diseases, AMMICa US23/CNRS UMS3655, Association pour la recherche sur le cancer (ARC), Association 'Le Cancer du Sein, Parlons-en!', Cancéropôle Ile-de-France, Chancelerie des universités de Paris (Legs Poix), Fondation pour la Recherche Médicale (FRM), a donation by Elior, European Research Area Network on Cardiovascular Diseases (ERA-CVD, MINOTAUR), Gustave Roussy Odyssea, the European Union Horizon 2020 Project Oncobiome, Fondation Carrefour, High-end Foreign Expert Program in China (GDW20171100085), Institut National du Cancer (INCa), Inserm (HTE), Institut Universitaire de France, LeDucq Foundation, the LabEx Immuno-Oncology (ANR-18-IDEX-0001), the RHU Torino Lumière, the Seerave Foundation, the SIRIC Stratified Oncology Cell DNA Repair and Tumor Immune Elimination (SOCRATE), and the SIRIC Cancer Research and Personalized Medicine (CARPEM)., Bodescot, Myriam, Karl-Franzens-Universität Graz, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris Cité (UPCité)
Subjects: 0209 industrial biotechnology, Coronavirus disease 2019 (COVID-19), viruses, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), coronavirus, Cellular homeostasis, Inflammation, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, 02 engineering and technology, Biology, medicine.disease_cause, Biochemistry, Genetics and Molecular Biology (miscellaneous), Microbiology, Applied Microbiology and Biotechnology, Viewpoint, 020901 industrial engineering & automation, Immune system, Immunity, Virology, 0202 electrical engineering, electronic engineering, information engineering, Genetics, medicine, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, lcsh:QH301-705.5, Molecular Biology, sars, Coronavirus, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, 020208 electrical & electronic engineering, Autophagy, mers, virophagy, Cell Biology, immunity, 3. Good health, Cell biology, sars-cov-2, covid-19, lcsh:Biology (General), inflammation, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Parasitology, medicine.symptom
Abstract: International audience; Autophagy is a catabolic pathway with multifaceted roles in cellular homeostasis. This process is also involved in the antiviral response at multiple levels, including the direct elimination of intruding viruses (virophagy), the presentation of viral antigens, the fitness of immune cells, and the inhibition of excessive inflammatory reactions. In line with its central role in immunity, viruses have evolved mechanisms to interfere with or to evade the autophagic process, and in some cases, even to harness autophagy or constituents of the autophagic machinery for their replication. Given the devastating consequences of the current COVID-19 pandemic, the question arises whether manipulating autophagy might be an expedient approach to fight the novel coronavirus SARS-CoV-2. In this piece, we provide a short overview of the evidence linking autophagy to coronaviruses and discuss whether such links may provide actionable targets for therapeutic interventions.
Published: 2020
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2. Phytohormone profiles are strongly altered during induction and symptom development of the physiological ripening disorder berry shrivel in grapevine

Author: Michaela Griesser, Petre I. Dobrev, Suriyan Supapvanich, Astrid Forneck, Stefania Savoi, Radomira Vankova, University of Natural Resources and Life Sciences (BOKU), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), King Mongkut’s Institute of Technology Ladkrabang (KMITL), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), Austrian Science Fund (FWF), ASEA-UNINET Ernst Mach Grant, and Austrian Science Fund (FWF) P28966-B29
Subjects: 0106 biological sciences, Ripening regulation, Ethylene, Plant Science, Berry, Biology, Genes, Plant, 01 natural sciences, Veraison, Physiological disorders, 03 medical and health sciences, chemistry.chemical_compound, Metabolomics, Abscission, Plant Growth Regulators, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Vitis, Sugar, 030304 developmental biology, Plant Diseases, 2. Zero hunger, 0303 health sciences, Original Paper, Gene Expression Profiling, food and beverages, Ripening, Plant, General Medicine, Grapevine, Phytohormones, Fruit, Horticulture, Genes, chemistry, Anthocyanin, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: The process of grape berry ripening follows three phases with distinct metabolic processes and complex regulations via phytohormones. The physiological ripening disorder berry shrivel (BS) is characterized by reduced sugar accumulation, low anthocyanin contents, and high acidity in affected berries. The processes leading to BS induction are unknown, but recent transcriptional data on reduced expression of switch genes hint towards a disturbed ripening onset. Herein we investigated the phytohormone composition throughout grape berry ripening in healthy and BS berries in Vitis vinifera L. cultivar Blauer Zweigelt. Thereby we hypothesize that phytohormones are key players for BS induction and suppress the expression of switch genes at veraison. The presented metabolomics and RNAseq data describe two distinct phytohormone profiles in BS berries, differing between pre- and post-veraison with a clear ethylene precursor (aminocyclopropane-1-carboxylic acid, ACC) peak before veraison. Exogenous application of ACC led to BS symptoms, while ethephone application led to berry abscission. During post-veraison, we observed high ABA-glucose ester (ABA-GE) and low indole-3-acetate aspartate (IAA-Asp) and isopentenyladenine (iP) contents in BS berries and the transcriptional induction of several phytohormone pathways. The presented descriptive data provide valuable knowledge to further decipher the role of phytohormones in BS induction and BS symptom development. Electronic supplementary material The online version of this article (10.1007/s11103-020-00980-6) contains supplementary material, which is available to authorized users., Key message Ripening disorder berry shrivel in grapevine leads to distinct phytohormone pattern pre- and post-veraison in grape berries. Electronic supplementary material The online version of this article (10.1007/s11103-020-00980-6) contains supplementary material, which is available to authorized users.
Published: 2020
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3. Serum resistance and phase variation of a nasopharyngeal non-typeable Haemophilus influenzae isolate

Author: Sabine Lichtenegger, Philippe Glaser, Isabelle Bina, Sanel Durakovic, Stefan Schild, Joachim Reidl, Sarah Tutz, Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria, Institute of Molecular Biosciences, Karl-Franzens-Universität [Graz, Autriche], Ecologie et Evolution de la Résistance aux Antibiotiques / Ecology and Evolution of Antibiotics Resistance (EERA), Institut Pasteur [Paris]-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), BioTechMed Graz [Graz, Autriche], Work was supported by the Austrian Science Fund (FWF) ERA-NET FWF I 662-B09 to SL, and JR. Clinical NTHi isolates were donatedby AGES-Graz (Agentur Gesundheit und ErnaehrungssicherheitGmbH/Zentrum fuer lebensmittelbedingte Infektionskrankheiten,Dr. Georg Steindl, AGES Graz) and the Institute for Hygieneand Microbiology (Dr. Thien-Tri Lam, University of Wuerzburg,Germany), University of Graz, Karl-Franzens-Universität Graz, and Institut Pasteur [Paris] (IP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, [SDV]Life Sciences [q-bio], Mutant, Clone (cell biology), medicine.disease_cause, Haemophilus influenzae, MESH: Genotype, chemistry.chemical_compound, MESH: Child, Nasopharynx, MESH: Immune Evasion, Child, education.field_of_study, MESH: Blood Bactericidal Activity, General Medicine, Antigenic Variation, Phenotype, Endocytosis, 3. Good health, MESH: Multilocus Sequence Typing, Infectious Diseases, MESH: Endocytosis, MESH: Glycosyltransferases, MESH: Antigenic Variation, lpsA, Adult, Microbiology (medical), Blood Bactericidal Activity, Genotype, 030106 microbiology, Population, Biology, MESH: Alveolar Epithelial Cells, Microbiology, Cell Line, 03 medical and health sciences, medicine, Humans, education, Immune Evasion, Phase variation, Serum resistance, MESH: Humans, Glycosyltransferases, MESH: Adult, MESH: Haemophilus influenzae, MESH: Nasopharynx, MESH: Cell Line, Sialic acid, 030104 developmental biology, chemistry, Alveolar Epithelial Cells, Multilocus sequence typing, Multilocus Sequence Typing
Abstract: International audience; Haemophilus influenzae harbours a complex array of factors to resist human complement attack. As non-typeable H. influenzae (NTHi) strains do not possess a capsule, their serum resistance mainly depends on other mechanisms including LOS decoration. In this report, we describe the identification of a highly serum resistant, nasopharyngeal isolate (NTHi23) by screening a collection of 77 clinical isolates. For NTHi23, we defined the MLST sequence type 1133, which matches the profile of a previously published invasive NTHi isolate. A detailed genetic analysis revealed that NTHi23 shares several complement evading mechanisms with invasive disease isolates. These mechanisms include the functional expression of a retrograde phospholipid trafficking system and the presumable decoration of the LOS structure with sialic acid. By screening the NTHi23 population for spontaneous decreased serum resistance, we identified a clone, which was about 103-fold more sensitive to complement-mediated killing. Genome-wide analysis of this isolate revealed a phase variation in the N'-terminal region of lpsA, leading to a truncated version of the glycosyltransferase (LpsA). We further showed that a NTHi23 lpsA mutant exhibits a decreased invasion rate into human alveolar basal epithelial cells. Since only a small proportion of the NTHi23 population expressed the serum sensitive phenotype, resulting from lpsA phase-off, we conclude that the nasopharyngeal environment selected for a population expressing the intact and functional glycosyltransferase.
Published: 2017
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4. T-DNA alleles of the receptor kinase THESEUS1 with opposing effects on cell wall integrity signaling

Author: Rodnay Sormani, Herman Höfte, Julia Richter, David Merz, Marie-Theres Hauser, Tobias Eder, Martine Gonneau, Marjolaine Martin, Clara Sánchez-Rodríguez, Kian Hématy, Department of Applied Genetics and Cell Biology, Universität für Bodenkultur Wien [Vienne, Autriche] (BOKU), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, ERL 3559 - Du gène à la graine, Centre National de la Recherche Scientifique (CNRS), Department of Biology, Austrian Science Fund, French National Research Agency [FWF-SFB F3707-B22, ANR-FWF I 1725-B16], and Hauser, Marie-Theres
Subjects: 0301 basic medicine, Physiology, [SDV]Life Sciences [q-bio], Arabidopsis, Cell elongation, Cellulose synthesis, Cell wall integrity signaling, CrRLK1L receptor, Gene silencing, Isoxaben, Plant Science, Lignin, chemistry.chemical_compound, gene silencing, Cell Wall, Gene Expression Regulation, Plant, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Receptor, Genes, Dominant, Genetics, Kinase, cellulose synthesis, Plants, Genetically Modified, Phenotype, Research Papers, 3. Good health, Cell biology, ddc:580, cell wall integrity signaling, Benzamides, Growth and Development, Growth inhibition, Signal Transduction, DNA, Bacterial, Receptors, Cell Surface, Biology, isoxaben, 03 medical and health sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Allele, Cellulose, Gene, Alleles, Arabidopsis Proteins, 030104 developmental biology, Protein kinase domain, chemistry, Seedlings, Botanical sciences, Protein Kinases
Abstract: Antagonistic growth effects of two T-DNA alleles in THESEUS1 correlate with the expression of a predicted functional THE1 protein lacking the kinase domain and antisense transcripts, respectively., Perturbation of cellulose synthesis in plants triggers stress responses, including growth retardation, mediated by the cell wall integrity-sensing receptor-like kinase (RLK) THESEUS1 (THE1). The analysis of two alleles carrying T-DNA insertions at comparable positions has led to conflicting conclusions concerning the impact of THE1 signaling on growth. Here we confirm that, unlike the1-3 and other the1 alleles in which cellular responses to genetic or pharmacological inhibition of cellulose synthesis are attenuated, the1-4 showed enhanced responses, including growth inhibition, ectopic lignification, and stress gene expression. Both the1-3 and the1-4 express a transcript encoding a predicted membrane-associated truncated protein lacking the kinase domain. However, the1-3, in contrast to the1-4, strongly expresses antisense transcripts, which are expected to prevent the expression of the truncated protein as suggested by the genetic interactions between the two alleles. Seedlings overexpressing such a truncated protein react to isoxaben treatment similarly to the1-4 and the full-length THE overexpressor. We conclude that the1-4 is a hypermorphic allele; that THE1 signaling upon cell wall damage has a negative impact on cell expansion; and that caution is required when interpreting the phenotypic effects of T-DNA insertions in RLK genes.
Published: 2017
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5. Common Genetic Polymorphisms within NFκB-Related Genes and the Risk of Developing Invasive Aspergillosis

Author: Carmen Belén Lupiañez, María Teresa Villaescusa, Agostinho Carvalho, Jan Springer, Michaela Lackner, José Manuel Sánchez-Maldonado, Luz María Canet, Cristina Cunha, Juana Segura-Catena, Laura Alcazar-Fuoli, Carlos Solano, Luana Fianchi, Livio Pagano, Leonardo Potenza, José María Aguado, Mario Luppi, Manuel Cuenca-Estrella, Cornelia Lass-Flörl, Hermann Einsele, Lourdes Vázquez, PCRAGA Study Group, Rafael Ríos-Tamayo, Jurgen Loeffler, Manuel Jurado, Juan Sainz, Instituto de Salud Carlos III, Ministerio de Ciencia e Innovación (España), FWF Austrian Science Fund, Fundação para a Ciência e Tecnologia (Portugal), Unión Europea. Fondo Europeo de Desarrollo Regional (FEDER/ERDF), Universidade do Minho, PCRAGA StudyGroup, PCRAGA Study Group, [Lupiañez,CB, Sánchez-Maldonado,JM, Canet,LM, Segura-Catena,J, Ríos-Tamayo,R, Jurado,M, Sainz,J] Genomic Oncology Area, GENYO, Center for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government,Granada, Spain. [Lupiañez,CB, Sainz,J] Hematology Department, Virgen de las Nieves University Hospital, Granada, Spain. [Villaescusa,M, Vázquez,L] Hematology Department, University Hospital of Salamanca, Salamanca, Spain. [Villaescusa,MT] Hematology Department, Jiménez Díaz Foundation, Madrid, Spain. [Carvalho,A, Cunha,C] Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho. 6ICVS/3B's - PT Government Associate Laboratory, Braga, Portugal. [Springer,J, Einsele,H, Loeffler,J] Universitätsklinikum Würzburg, Klinik II, Würzburg, Germany. [Lackner,M, Lass-Flörl,C] Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria. [Alcazar-Fuoli,L: Cuenca-Estrella,M] Mycology Reference Laboratory, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain. [Solano,C] Hematology Department, Clinic University Hospital of Valencia, Valencia, Spain. [Fianchi,L, Pagano,L] Istituto di Ematologia, Università Cattolica del S. Cuore, Rome, Italy. [Potenza,L, Luppi,M] Istituto di Ematologia, Università Cattolica del S. Cuore, Rome, Italy. Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, AOU Policlinico, Modena, Italy. [Aguado,JM] Unit of Infectious Diseases, University Hospital 12 de Octubre, Research Institute of Hospital 12 de Octubre (i+12), Madrid., This study was supported by grants PI12/02688 from Fondo de Investigaciones Sanitarias (Instituto de Salud Carlos III, Madrid, Spain), the ERA-NET PathoGenoMics (03159000A, Ministerio de Ciencia e Innovación PIM2010EPA-00756, Madrid, Spain), the Collaborative Research Center / Transregio 124 FungiNet, the Austrian Science Fundation (FWF I-656-B09), the Fundação para a Ciência e Tecnologia (FCT), cofunded by Programa Operacional Regional do Norte (ON.2—O Novo Norte), the Quadro de Referência Estratégico Nacional (QREN) through the Fundo Europeu de Desenvolvimento Regional (FEDER) and the Projeto Estratégico – LA 26 – 2013–2014 (PEst-C/SAU/LA0026/2013). Agostinho Carvalho and Cristina Cunha were supported by the Fundação para a Ciência e Tecnologia (FCT), Portugal (IF/00735/2014 and SFRH/BPD/96176/2013, respectively).The PCRAGA trial was supported by an unrestricted grant from Pfizer. This study was also supported by Astellas Pharma Inc. and a donation from Consuelo González Moreno, an acute myeloid leukemia survivor., Austrian Science Fund, Fundação para a Ciência e a Tecnologia (Portugal), and European Regional Development Fund
Subjects: 0301 basic medicine, Polimorfismo de nucleótido simple, Medicina Básica [Ciências Médicas], lcsh:QR1-502, Diseases::Bacterial Infections and Mycoses::Mycoses::Hyalohyphomycosis::Aspergillosis [Medical Subject Headings], Genetic Susceptibility, NF kappa B-related genes, lcsh:Microbiology, susceptibility, Diseases::Bacterial Infections and Mycoses::Infection::Opportunistic Infections [Medical Subject Headings], Phenomena and Processes::Genetic Phenomena::Genotype::Haplotypes [Medical Subject Headings], Organisms::Eukaryota::Animals::Chordata::Vertebrates::Mammals::Primates::Haplorhini::Catarrhini::Hominidae::Humans [Medical Subject Headings], Infecciones oportunistas, Invasive Aspergillosis, NFκB-related genes, genetic polymorphisms, interaction, Diseases::Pathological Conditions, Signs and Symptoms::Pathologic Processes::Disease Attributes::Disease Susceptibility [Medical Subject Headings], Genotype, Chemicals and Drugs::Carbohydrates::Glycosides::Nucleotides [Medical Subject Headings], Original Research, Genetics, education.field_of_study, Phenomena and Processes::Genetic Phenomena::Phenotype::Genetic Markers [Medical Subject Headings], Analytical, Diagnostic and Therapeutic Techniques and Equipment::Surgical Procedures, Operative::Transplantation::Cell Transplantation::Stem Cell Transplantation::Hematopoietic Stem Cell Transplantation [Medical Subject Headings], Humanos, 3. Good health, Nucleótidos, Ciências Médicas::Medicina Básica, Haplotipos, Phenomena and Processes::Genetic Phenomena::Genotype [Medical Subject Headings], Trasplante de células madre hematopoyéticas, Microbiology (medical), Marcadores genéticos, nfkb pathway, Population, Single-nucleotide polymorphism, Biology, Microbiology, 03 medical and health sciences, Genetic predisposition, SNP, ddc:610, Allele, education, Phenomena and Processes::Genetic Phenomena::Genetic Variation::Polymorphism, Genetic::Polymorphism, Single Nucleotide [Medical Subject Headings], Science & Technology, Haplotype, Susceptibilidad a enfermedades, Organisms::Eukaryota::Fungi::Mitosporic Fungi::Aspergillus [Medical Subject Headings], Hematologic Diseases, Settore MED/15 - MALATTIE DEL SANGUE, 030104 developmental biology, Aspergilosis, Genetic marker, Invasive Aspergillosis, genetic polymorphisms, susceptibility, NFκB-related genes, interaction, Immunology, Genotipo, Stem Cell Transplantation
Abstract: Invasive Aspergillosis (IA) is an opportunistic infection caused by Aspergillus, a ubiquitously present airborne pathogenic mold. A growing number of studies suggest a major host genetic component in disease susceptibility. Here, we evaluated whether 14 single-nucleotide polymorphisms within NF kappa B1, NF kappa B2, RelA, RelB, Rel, and IRF4 genes influence the risk of IA in a population of 834 high-risk patients (157 IA and 677 non IA) recruited through a collaborative effort involving the aspBlOmics consortium and four European clinical institutions. No significant overall associations between selected SNPs and the risk of IA were found in this large cohort. Although a hematopoietic stem cell transplantation (HSCT)-stratified analysis revealed that carriers of the IRF4(rs12203592T/T) genotype had a six-fold increased risk of developing the infection when compared with those carrying the C allele (ORREC = 6.24, 95%CI 1.25-31.2, P = 0.026), the association of this variant with IA risk did not reach significance at experiment-wide significant threshold. In addition, we found an association of the IRF4(AATC) and IRF4(GGTC) haplotypes (not including the IRF4(rs12203592T/T) risk allele) with a decreased risk of IA but the magnitude of the association was similar to the one observed in the single-SNP analysis, which indicated that the haplotypic effect on IA risk was likely due to the IRF4(rs12203592) SNP Finally, no evidence of significant interactions among the genetic markers tested and the risk of IA was found. These results suggest that the SNPs on the studied genes do not have a clinically relevant impact on the risk of developing IA., This study was supported by grants PI12/02688 from Fond de Investigaciones Sanitarias (Institute de Salud Carlos III, Madrid, Spain), the ERA-NET PathoGenoMics (03159000A; Ministerio de Ciencia e Innovation PIM2010EPA-00756, Madrid, Spain), the Collaborative Research Center / Transregio 124 FungiNet, the Austrian Science Fundation (FWF I-656-B09), the Fundacao para a Ciencia e Tecnologia (FCT), cofundcd by Programa Operacional Regional do Norte (ON.2-O Novo Norte), the Quadro de Referencia Estrategico Nacional (QREN) through the Fundo Europeu de Desenvolvimento Regional (FEDER) and the Projeto Estrategico - LA 26 - 2013-2014 (PEst-C/SAU/LA0026/2013). Agostinho Carvalho and Cristina Cunha were supported by the Fundacao para a e Tecnologia (FCT), Portugal (IF/00735/2014 and SFRH/BPD/96176/2013, respectively). The PCRAGA trial was supported by an unrestricted grant from Pfizer, which had no involvement or control over the collection, analysis, and interpretation of data; the writing of the report; or the decision to submit the paper for publication. This study was also supported by Astellas Pharma Inc. and a donation from Consuelo Gonzalez Moreno, an acute myeloid leukemia survivor., info:eu-repo/semantics/publishedVersion
Published: 2016

6. Of mice, flies--and men? Comparing fungal infection models for large-scale screening efforts

Author: Martin E. A. Richter, Ekkehard Hiller, Bernhard Hube, Lydia Kasper, Sascha Brunke, Dominique Ferrandon, Christophe d'Enfert, Jessica Quintin, Steffen Rupp, Karl Kuchler, Ilse D. Jacobsen, Tobias Schwarzmüller, Department of Microbial Pathogenicity Mechanisms [Jena], Hans Knoell Institute, Center for Sepsis Control & Care, Jena University Hospital, Réponse immunitaire et developpement chez les insectes (RIDI - UPR 9002), Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Escuela de Ciencas Biologicas, Pontificia Universidad Catolica del Ecuador, Research Group Microbial Immunology, Hans Knöll Institute, Jena University Hospital [Jena], Fraunhofer Institute for Interfacial Engineering and Biotechnology (Fraunhofer IGB), Fraunhofer (Fraunhofer-Gesellschaft), Medizinische Universität Wien = Medical University of Vienna, Biologie et Pathogénicité fongiques, Institut Pasteur [Paris]-Institut National de la Recherche Agronomique (INRA), This work was supported via institutional support from CNRS, by the DeutscheForschungsgemeinschaft (DFG) and the Austrian Science Foundation (FWF) via a joint DACH project of the B.H. and K.K. laboratories (DFG HU 528/17-1 and FWF-I-746-B11), and by the German Federal Ministry of Education and Health (BMBF)and the FWF via the ERA-Net Pathogenomics project FunPath (BMBF-FKZ:0313931B and FWF-API-0125). The work of S.B., M.E.R. and B.H. was further supported by the German Federal Ministry of Education and Health (BMBF) Germany via the Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC, FKZ: 01EO1002). Work in the K.K. laboratory was supported by the Austrian Science Foundation FWF by a grant from the Christian Doppler Society., Université de Strasbourg (UNISTRA)-Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Fraunhofer Institute for Interfacial Engineering and Biotechnology (IGB), Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris], Brunke, Sascha, Quintin, Jessica, Pontificia Universidad Católica del Ecuador, Biologie et Pathogénicité fongiques (BPF), Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris] (IP), RIBIERRE, Helene, and Publica
Subjects: MESH: Gene Ontology, Male, [SDV]Life Sciences [q-bio], Mutant, Medicine (miscellaneous), lcsh:Medicine, MESH: Logistic Models, Candida glabrata, MESH: Virulence, medicine.disease_cause, Polymerase Chain Reaction, Mice, Immunology and Microbiology (miscellaneous), [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Animals, Mutant library, Drosophila melanogaster, Alternative infection models, Signature-tagged mutagenesis, Fungal virulence factors, MESH: Candida glabrata, Pathogen, MESH: Organ Specificity, 0303 health sciences, Mutation, Virulence, 3. Good health, [SDV] Life Sciences [q-bio], Organ Specificity, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, lcsh:RB1-214, Research Article, MESH: Mutation, Neuroscience (miscellaneous), Biology, General Biochemistry, Genetics and Molecular Biology, Microbiology, MESH: Drosophila melanogaster, 03 medical and health sciences, MESH: Mycoses, medicine, lcsh:Pathology, Animals, Humans, Drosophila, MESH: Mice, 030304 developmental biology, MESH: Humans, 030306 microbiology, lcsh:R, fungi, MESH: Polymerase Chain Reaction, biology.organism_classification, MESH: Male, Disease Models, Animal, Gene Ontology, Logistic Models, Mycoses, MESH: Disease Models, Animal
Abstract: Studying infectious diseases requires suitable hosts for experimental in vivo infections. Recent years have seen the advent of many alternatives to murine infection models. However, the use of non-mammalian models is still controversial because it is often unclear how well findings from these systems predict virulence potential in humans or other mammals. Here, we compare the commonly used models, fruit fly and mouse (representing invertebrate and mammalian hosts), for their similarities and degree of correlation upon infection with a library of mutants of an important fungal pathogen, the yeast Candida glabrata. Using two indices, for fly survival time and for mouse fungal burden in specific organs, we show a good agreement between the models. We provide a suitable predictive model for estimating the virulence potential of C. glabrata mutants in the mouse from fly survival data. As examples, we found cell wall integrity mutants attenuated in flies, and mutants of a MAP kinase pathway had defective virulence in flies and reduced relative pathogen fitness in mice. In addition, mutants with strongly reduced in vitro growth generally, but not always, had reduced virulence in flies. Overall, we demonstrate that surveying Drosophila survival after infection is a suitable model to predict the outcome of murine infections, especially for severely attenuated C. glabrata mutants. Pre-screening of mutants in an invertebrate Drosophila model can, thus, provide a good estimate of the probability of finding a strain with reduced microbial burden in the mouse host., Summary: Can the fitness of deletion mutants in a murine model be predicted by their virulence in Drosophila melanogaster? For a fungal pathogen, the answer is, mostly, yes.
Published: 2015
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7. Native Wolbachia from Aedes albopictus Blocks Chikungunya Virus Infection In Cellulo

Author: Patrick Potier, Florence-Hélène Tran, Vincent Raquin, Yoann Saucereau, Patrick Mavingui, Claire Valiente Moro, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Processus Infectieux en Milieu Insulaire Tropical (PIMIT), Centre National de la Recherche Scientifique (CNRS)-IRD-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de La Réunion (UR), Cyclotron Réunion Océan Indien (CYROI), Université de La Réunion (UR)-Centre Hospitalier Universitaire de La Réunion (CHU La Réunion), Agence Nationale de la Recherche (ANR) [ANR-2010-BLAN-170101], Fondation pour la Recherche et la Biodiversite (FRB) [FRBCD-AOOI-07-12], Action Concertee InterPasteurienne (ACIP) [A-10-2009], ERA-Net BiodivERsA network, ANR France [ANR-13-EBID-0007-01], FWF Austria [FWF I-1437], DFG Germany [DFG KL 2087/6-1], Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IRD-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), and Univ, Réunion
Subjects: Aedes albopictus, viruses, Host cells, lcsh:Medicine, Dengue virus, Biology, Virus Replication, medicine.disease_cause, Mosquitoes, Virus, Microbiology, Aedes, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, parasitic diseases, medicine, Viral replication, Animals, Humans, Chikungunya, Symbiosis, lcsh:Science, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Pathogen, Multidisciplinary, lcsh:R, fungi, Correction, virus diseases, biochemical phenomena, metabolism, and nutrition, Arboviral infection, biology.organism_classification, Virology, Phenotype, 3. Good health, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [SDV.BA.ZI] Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Chikungunya Fever, Wolbachia, lcsh:Q, Chikungunya infection, Chikungunya virus, Arboviruses, Research Article
Abstract: International audience; Wolbachia, a widespread endosymbiont of terrestrial arthropods, can protect its host against viral and parasitic infections, a phenotype called "pathogen blocking". However, in some cases Wolbachia may have no effect or even enhance pathogen infection, depending on the host-Wolbachia-pathogen combination. The tiger mosquito Aedes albopictus is naturally infected by two strains of Wolbachia, wAlbA and wAlbB, and is a competent vector for different arboviruses such as dengue virus (DENV) and Chikungunya virus (CHIKV). Interestingly, it was shown in some cases that Ae. albopictus native Wolbachia strains are able to inhibit DENV transmission by limiting viral replication in salivary glands, but no such impact was measured on CHIKV replication in vivo. To better understand the Wolbachia/CHIKV/Ae. albopictus interaction, we generated a cellular model using Ae. albopictus derived C6/36 cells that we infected with the wAlbB strain. Our results indicate that CHIKV infection is negatively impacted at both RNA replication and virus assembly/secretion steps in presence of wAlbB. Using FISH, we observed CHIKV and wAlbB in the same mosquito cells, indicating that the virus is still able to enter the cell in the presence of the bacterium. Further work is needed to decipher molecular pathways involved in Wolbachia-CHIKV interaction at the cellular level, but this cellular model can be a useful tool to study the mechanism behind virus blocking phenotype induced by Wolbachia. More broadly, this underlines that despite Wolbachia antiviral potential other complex interactions occur in vivo to determine mosquito vector competence in Ae. albopictus.
Published: 2015
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8. Biochemical characterization of the major N-acetylmuramidase from Lactobacillus buchneri

Author: Christian Obinger, Christina Schäffer, Julia Anzengruber, Paul Messner, Monika Debreczeny, Jos Vanderleyden, Marie-Pierre Chapot-Chartier, Ingmar Claes, Stefan Hofbauer, Pascal Courtin, Universität für Bodenkultur Wien [Vienne, Autriche] (BOKU), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Catholique de Louvain = Catholic University of Louvain (UCL), Department of Chemistry, Univ Bodenkultur Wien, Dept Chem, A-1190 Vienna, Austria, Partenaires INRAE, Univ Bodenkultur Wien, NanoGlycobiol Unit, Dept Nano Biotechnol, A-1190 Vienna, Austria, Austrian Science Fund, FWF [P21954-B20, P24305-B20], PhD programme 'BioToP - Biomolecular Technology of Proteins' (Austrian Science Fund, FWF) [W1224], Hochschuljubilaumsstiftung der Stadt Wien [H-2442/2012], INRA (France), and Region Ile de France
Subjects: Glycoside Hydrolases, biology, Peptidoglycan, biology.organism_classification, Microbiology, Protein Structure, Secondary, Article, Bacterial cell structure, Cell wall, Lactobacillus, Protein Transport, chemistry.chemical_compound, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Bacterial Proteins, Lactobacillus rhamnosus, chemistry, Biochemistry, Cell Wall, Enzyme Stability, Hydrolase, Glycoside hydrolase, Lactobacillus buchneri
Abstract: Bacterial cell wall hydrolases are essential for peptidoglycan remodelling in regard to bacterial cell growth and division. In this study, peptidoglycan hydrolases (PGHs) of differentLactobacillus buchneristrains were investigated. First, the genome sequence ofL. buchneriCD034 andL. buchneriNRRL B-30929 was analysedin silicofor the presence of PGHs. Of 23 putative PGHs with different predicted hydrolytic specificities, the glycosyl hydrolase family 25 domain-containing homologuesLbGH25B andLbGH25N fromL. buchneriCD034 and NRRL B-30929, respectively, were selected and characterized in detail. Zymogram analysis confirmed hydrolysing activity on bacterial cell walls for both enzymes. Subsequent reversed-phase HPLC and MALDI-TOF MS analysis of the peptidoglycan breakdown products fromL. buchneristrains CD034 and NRRL B-30929, and fromLactobacillus rhamnosusGG, which served as a reference, revealed thatLbGH25B andLbGH25N haveN-acetylmuramidase activity. Both enzymes were identified as cell wall-associated proteins by means of immunofluorescence microscopy and cellular fractionation, as well as by the ability of purified recombinantLbGH25B andLbGH25N to bind toL. buchnericell wallsin vitro. Moreover, similar secondary structures mainly composed of β-sheets and nearly identical thermal stabilities withTmvalues around 49 °C were found for the twoN-acetylmuramidases by far-UV circular dichroism spectroscopy. The functional and structural data obtained are discussed and compared to related PGHs. In this study, a majorN-acetylmuramidase fromL. buchneriwas characterized in detail for the first time.
Published: 2014
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9. Contribution of above- and below-ground plant traits to the structure and function of grassland soil microbial communities

Author: Catherine Baxendale, Nicolas Legay, Jean-Christophe Clément, Maxime Dumont, Cindy Arnoldi, Karl Grigulis, Thomas Pommier, Ute Krainer, Sandra Lavorel, F. Poly, Eva-Maria Kastl, Michael Schloter, Michael Bahn, Richard D. Bardgett, Laboratoire d'Ecologie Alpine ( LECA ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Université Savoie Mont Blanc ( USMB [Université de Savoie] [Université de Chambéry] ) -Centre National de la Recherche Scientifique ( CNRS ), Lancaster Environment Centre, Lancaster University, Ecology, University of Innsbruck, University of Innsbruck, Helmholtz-Zentrum München ( HZM ), Faculty of Life Sciences [Manchester], University of Manchester [Manchester], Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Laboratoire d'Ecologie Alpine (LECA), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Helmholtz-Zentrum München (HZM), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), ERA-Net BiodivERsA project VITAL (ANR-08-BDVA-008), ANR, FWF, NERC, BMBF, Austrian Science Fund (FWF) (I 242-B17), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)
Subjects: 0106 biological sciences, leaf traits, soil microbial community, Plant Science, Plant Roots, 01 natural sciences, Soil, Abundance (ecology), bacteria, Soil Microbiology, 2. Zero hunger, Abiotic component, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Ecology, Community structure, food and beverages, Biodiversity, 04 agricultural and veterinary sciences, Plants, nitrite oxidizers, Grassland, Nitrification, Phenotype, Denitrification, Oxidation-Reduction, Soil microbiology, Nitrogen, Biology, 010603 evolutionary biology, [ SDV.EE ] Life Sciences [q-bio]/Ecology, environment, nitrite reducers, Botany, Ecosystem, Relative species abundance, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, plant functional traits, denitrifiers, Plant community, Original Articles, Plant Components, Aerial, 15. Life on land, Archaea, Ammonia-oxidizing archaea, root traits, Microbial population biology, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, nutrient availability, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Aims: Abiotic properties of soil are known to be major drivers of the microbial community within it. Our understanding of how soil microbial properties are related to the functional structure and diversity of plant communities, however, is limited and largely restricted to above-ground plant traits, with the role of below-ground traits being poorly understood. This study investigated the relative contributions of soil abiotic properties and plant traits, both above-ground and below-ground, to variations in microbial processes involved in grassland nitrogen turnover. Methods In mountain grasslands distributed across three European sites, a correlative approach was used to examine the role of a large range of plant functional traits and soil abiotic factors on microbial variables, including gene abundance of nitrifiers and denitrifiers and their potential activities. Key Results Direct effects of soil abiotic parameters were found to have the most significant influence on the microbial groups investigated. Indirect pathways via plant functional traits contributed substantially to explaining the relative abundance of fungi and bacteria and gene abundances of the investigated microbial communities, while they explained little of the variance in microbial activities. Gene abundances of nitrifiers and denitrifiers were most strongly related to below-ground plant traits, suggesting that they were the most relevant traits for explaining variation in community structure and abundances of soil microbes involved in nitrification and denitrification. Conclusions The results suggest that consideration of plant traits, and especially below-ground traits, increases our ability to describe variation in the abundances and the functional characteristics of microbial communities in grassland soils.
Published: 2014
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10. The CRE1 carbon catabolite repressor of the fungus Trichoderma reesei: a master regulator of carbon assimilation

Author: Erzsébet Fekete, Lukas Hartl, Irina S. Druzhinina, Stéphane Le Crom, Lea Atanasova, Bernhard Seiboth, Erzsébet Sándor, Thomas Portnoy, Antoine Margeot, Levente Karaffa, Rita Linke, Christian P. Kubicek, BMC, Ed., IFP Energies nouvelles (IFPEN), GenomiqueENS (Genomique ENS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Austrian Center of Industrial Biotechnology [Vienna, Austria] (Institute of Chemical Engineering), Vienna University of Technology (TU Wien), Research Area Gene Technology and Applied Biochemistry [Vienna, Austria] (Institute of Chemical Engineering), Biochemical Engineering Department [Debrecen, Hungary] (Faculty of Science & Technology), University of Debrecen Egyetem [Debrecen], Plant Protection Department [Debrecen, Hungary] (Faculty of Agriculture and Food Sciences & Environmental Management), This work was supported by grants from the Austrian Science Foundation (FWF P-19143 and FWF P-19421) to CPK and BS, respectively. Work by SLC was supported by the Infrastructures en Biologie Santé et Agronomie (IBISA). TP is recipient of a Fondation Tuck Enerbio PhD. Fellowship. Work by LK, EF and ES was supported by the Hungarian Scientific Research Fund (OTKA, K67667) and the National Office for Research and Technology (NKTH, A2-2006-0017). EF is supported by a Bolyai János Research Scholarship (BO/00519/09/8)., Plateforme Génomique de l'IBENS, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), University of Debrecen, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Catabolite repression, Biológiai tudományok, Gene Knockout Techniques, MESH: Protein Structure, Tertiary, Természettudományok, Hypocrea, Transcription (biology), MESH: Up-Regulation, Trichoderma reesei, MESH: Gene Knockout Techniques, 2. Zero hunger, Genetics, 0303 health sciences, biology, Up-Regulation, Cell biology, MESH: Glucose, Phenotype, MESH: Repressor Proteins, Hypocreales, MESH: Genome, Fungal, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MESH: Fungal Proteins, Genome, Fungal, Research Article, Biotechnology, MESH: Mutation, lcsh:QH426-470, lcsh:Biotechnology, Repressor, MESH: Carbon, MESH: Hypocreales, MESH: Phenotype, Chromatin remodeling, Fungal Proteins, 03 medical and health sciences, Mediator, lcsh:TP248.13-248.65, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Gene, 030304 developmental biology, Binding Sites, 030306 microbiology, biology.organism_classification, Carbon, Protein Structure, Tertiary, Repressor Proteins, lcsh:Genetics, Glucose, MESH: Binding Sites, Mutation
Abstract: Background The identification and characterization of the transcriptional regulatory networks governing the physiology and adaptation of microbial cells is a key step in understanding their behaviour. One such wide-domain regulatory circuit, essential to all cells, is carbon catabolite repression (CCR): it allows the cell to prefer some carbon sources, whose assimilation is of high nutritional value, over less profitable ones. In lower multicellular fungi, the C2H2 zinc finger CreA/CRE1 protein has been shown to act as the transcriptional repressor in this process. However, the complete list of its gene targets is not known. Results Here, we deciphered the CRE1 regulatory range in the model cellulose and hemicellulose-degrading fungus Trichoderma reesei (anamorph of Hypocrea jecorina) by profiling transcription in a wild-type and a delta-cre1 mutant strain on glucose at constant growth rates known to repress and de-repress CCR-affected genes. Analysis of genome-wide microarrays reveals 2.8% of transcripts whose expression was regulated in at least one of the four experimental conditions: 47.3% of which were repressed by CRE1, whereas 29.0% were actually induced by CRE1, and 17.2% only affected by the growth rate but CRE1 independent. Among CRE1 repressed transcripts, genes encoding unknown proteins and transport proteins were overrepresented. In addition, we found CRE1-repression of nitrogenous substances uptake, components of chromatin remodeling and the transcriptional mediator complex, as well as developmental processes. Conclusions Our study provides the first global insight into the molecular physiological response of a multicellular fungus to carbon catabolite regulation and identifies several not yet known targets in a growth-controlled environment.
Published: 2011
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11. Endothelial sprouting, proliferation, or senescence: tipping the balance from physiology to pathology

Author: Mühleder, Severin, Fernández-Chacón, Macarena, Garcia-Gonzalez, Irene, Benedito, Rui, FWF Austrian Science Fund, Fundación La Caixa, European Research Council, Centro Nacional de Investigaciones Cardiovasculares Carlos III (España), Ministerio de Economía, Industria y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), and Fundación ProCNIC
Subjects: Senescence, Aging, Cell cycle checkpoint, Vascular differentiation, Angiogenesis, Endothelial cells, medicine.medical_treatment, Neovascularization, Physiologic, Review, Disease, Biology, Cell-cycle arrest, Regenerative medicine, 03 medical and health sciences, Cellular and Molecular Neuroscience, 0302 clinical medicine, Cell Movement, Neoplasms, medicine, Humans, Molecular Biology, Cell Proliferation, 030304 developmental biology, Feedback, Physiological, Pharmacology, 0303 health sciences, Neovascularization, Pathologic, Cell growth, Growth factor, Endothelial Cells, Cell Biology, Cell biology, Cardiovascular Diseases, 030220 oncology & carcinogenesis, Malformations, Molecular Medicine, Signal transduction, Sprouting, Signal Transduction
Abstract: Therapeutic modulation of vascular cell proliferation and migration is essential for the effective inhibition of angiogenesis in cancer or its induction in cardiovascular disease. The general view is that an increase in vascular growth factor levels or mitogenic stimulation is beneficial for angiogenesis, since it leads to an increase in both endothelial proliferation and sprouting. However, several recent studies showed that an increase in mitogenic stimuli can also lead to the arrest of angiogenesis. This is due to the existence of intrinsic signaling feedback loops and cell cycle checkpoints that work in synchrony to maintain a balance between endothelial proliferation and sprouting. This balance is tightly and effectively regulated during tissue growth and is often deregulated or impaired in disease. Most therapeutic strategies used so far to promote vascular growth simply increase mitogenic stimuli, without taking into account its deleterious effects on this balance and on vascular cells. Here, we review the main findings on the mechanisms controlling physiological vascular sprouting, proliferation, and senescence and how those mechanisms are often deregulated in acquired or congenital cardiovascular disease leading to a diverse range of pathologies. We also discuss alternative approaches to increase the effectiveness of pro-angiogenic therapies in cardiovascular regenerative medicine. Severin Mühleder was funded by the Austrian Science Fund (FWF) project J4358. Macarena Fernández-Chacón and Irene Garcia-Gonzalez were supported by PhD fellowships from Fundación La Caixa (CX_E-2015-01 and CX-SO-16-1, respectively). Rui Benedito was funded by the European Research Council (ERC-2014-StG—638028), the Centro Nacional de Investigaciones Cardiovasculares (CNIC), and by the Ministerio de Economia, Industria y Competitividad (MEIC: SAF2013-44329-P, SAF2017-89299-P, and RYC-2013-13209). The CNIC is supported by the Ministerio de Ciencia, Innovación y Universidades (MCNU) and the Pro CNIC Foundation, and is a Severo Ochoa Center of Excellence (SEV-2015-0505). Sí
Published: 2020
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12. The metabolomic signature of extreme longevity: naked mole rats versus mice

Author: Frank Madeo, Sylvère Durand, Deborah Lefevre, Mélanie Viltard, Christine Leroy, Maria Perez-Lanzon, Guido Kroemer, Gérard Friedlander, Fanny Aprahamian, Gestionnaire, Hal Sorbonne Université, Fondation pour la Recherche en Physiologie [Brussels, Belgium], Institut Gustave Roussy (IGR), Centre de Recherche des Cordeliers (CRC (UMR_S_1138 / U1138)), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Université Paris Cité (UPCité), Université Paris-Saclay, AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), Institut Necker Enfants-Malades (INEM - UM 111 (UMR 8253 / U1151)), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Karl-Franzens-Universität Graz, Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), University of Science & Technology of China [Suzhou], Karolinska Institutet [Stockholm], Karolinska University Hospital [Stockholm], Plateforme de métabolomique, Direction de la recherche [Gustave Roussy], Institut Gustave Roussy (IGR)-Institut Gustave Roussy (IGR), GK is supported by the Ligue contre le Cancer (équipe labellisée), Agence National de la Recherche (ANR) – Projets blancs, ANR under the frame of E-Rare-2, the ERA-Net for Research on Rare Diseases, Association pour la Recherche sur le Cancer (ARC), Cancéropôle Ile-de-France, Chancelerie des universités de Paris (Legs Poix), Fondation pour la Recherche Médicale (FRM), a donation by Elior, European Research Area Network on Cardiovascular Diseases (ERA-CVD, MINOTAUR), Gustave Roussy Odyssea, the European Union Horizon 2020 Project Oncobiome, Fondation Carrefour, High-end Foreign Expert Program in China (GDW20171100085 and GDW20181100051), Institut National du Cancer (INCa), Inserm (HTE), Institut Universitaire de France, LeDucq Foundation, the LabEx Immuno-Oncology (ANR-18-IDEX-0001), the RHU Torino Lumière, the Seerave Foundation, the SIRIC Stratified Oncology Cell DNA Repair and Tumor Immune Elimination (SOCRATE), and the SIRIC Cancer Research and Personalized Medicine (CARPEM). F.M. is grateful to the Austrian Science Fund FWF (SFB LIPOTOX F3007 & F3012, W1226, P29203, P29262, P27893, P 31727 and the Austrian Federal Ministry of Education, Science and Research and the University of Graz for grants 'Unkonventionelle Forschung-InterFast' and 'flysleep' (BMWFW 80.109/0001-WF/V/3b/2015) as well as the field of excellence program BioHealth. We acknowledge support from NAWI Graz and the BioTechMed-Graz flagship project 'EPIAge'. M.V. is grateful to the Ecole Nationale Vétérinaire d’Alfort (EnvA) and the Association De Prévoyance Santé (ADPS) partners of Allianz, for their invaluable help in establishing and funding the animal facility. M.P.L. is supported by Fondation pour la Recherche Médicale (FRM FDT201904008383)., Université de Paris (UP), and Karl-Franzens-Universität [Graz, Autriche]
Subjects: autophagy, Aging, Rodent, [SDV.MHEP.PHY] Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], medicine.medical_treatment, media_common.quotation_subject, Longevity, 03 medical and health sciences, chemistry.chemical_compound, Mice, 0302 clinical medicine, Metabolomics, Species Specificity, biology.animal, spermidine, [SDV.MHEP.PHY]Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], medicine, Metabolome, microbiota, Animals, 030304 developmental biology, media_common, meta-organism, 0303 health sciences, biology, Vitamin E, Mole Rats, catabolism, Laboratory mouse, Cell Biology, Rats, Spermidine, Metabolic pathway, antioxidants, Biochemistry, chemistry, 030220 oncology & carcinogenesis, Priority Research Paper
Abstract: International audience; The naked mole-rat (Heterocephalus glaber) is characterized by a more than tenfold higher life expectancy compared to another rodent species of the same size, namely, the laboratory mouse (Mus musculus). We used mass spectrometric metabolomics to analyze circulating plasma metabolites in both species at different ages. Interspecies differences were much more pronounced than age-associated alterations in the metabolome. Such interspecies divergences affected multiple metabolic pathways involving amino, bile and fatty acids as well as monosaccharides and nucleotides. The most intriguing metabolites were those that had previously been linked to pro-health and antiaging effects in mice and that were significantly increased in the long-lived rodent compared to its short-lived counterpart. This pattern applies to α-tocopherol (also known as vitamin E) and polyamines (in particular cadaverine, N8-acetylspermidine and N1,N8-diacetylspermidine), all of which were more abundant in naked mole-rats than in mice. Moreover, the age-associated decline in spermidine and N1-acetylspermidine levels observed in mice did not occur, or is even reversed (in the case of N1-acetylspermidine) in naked mole-rats. In short, the present metabolomics analysis provides a series of testable hypotheses to explain the exceptional longevity of naked mole-rats.
Published: 2019
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13. Using electrical resistivity tomography to detect wetwood and estimate moisture content in silver fir (Abies alba Mill.)

Author: L. Martin, Stefan Mayr, Eric Badel, Hervé Cochard, Laboratoire de Physique et Physiologie Intégratives de l’Arbre en environnement Fluctuant (PIAF), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Leopold Franzens Universität Innsbruck - University of Innsbruck, Austrian Science Fund (FWF)P32203, European Project: ERDF, and University of Innsbruck
Subjects: Moisture content, 040101 forestry, 0106 biological sciences, Ecology, biology, Forestry, Soil science, 04 agricultural and veterinary sciences, 15. Life on land, biology.organism_classification, 01 natural sciences, Wetwood, Abies alba, Electrical resistivity and conductivity, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 0401 agriculture, forestry, and fisheries, Environmental science, Electrical resistivity tomography, Nondestructive testing, Water content, 010606 plant biology & botany
Abstract: International audience; Key message: Using several experimental approaches, we have demonstrated that electrical resistivity tomography (ERT) is a reliable nondestructive tool for estimating the moisture content of heartwood in situ. ERT measurements show that water pockets in heartwood (wetwood) are present in a large majority (90%) of silver fir (Abies alba Mill.) trunks. Context: For wood professionals, the presence of wetwood in wood logs leads to an increase in costs, especially during the drying process. Assessing these internal properties in situ with a nondestructive method will provide reliable information for improved management of respective forests. Aims: The objective of this study was to evaluate the efficiency of the electrical resistivity tomography (ERT) tool to detect wetwood in standing trees and to estimate the mean moisture content (MC) of silver fir trunks. Methods: The study was carried out in 3 forests located in the region "Massif Central" in France. We selected 58 silver fir trees, visually healthy and without visible default. Each tree has been subject to regular ERT measurements for more than a year. At the same time, one to three cores were taken from each tree in order to measure the actual MC of the wood. Results: 90% of the silver fir trees showed the presence of wetwood in their heartwood. Our results showed a significant correlation between the mean heartwood MC measured on cores and the mean electrical resistivity (ER) obtained with ERT. Conclusion: (i) The presence of wetwood occurs in a high proportion of the silver fir trees studied, and (ii) ERT can be used to estimate the average MC of the heartwood of standing trees. However, the data provided by ERT vary seasonally and do not allow the precise location of wetwood.
Published: 2021
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14. Associations between specific IgE sensitization to 26 respiratory allergen molecules and HLA class II alleles in the EGEA cohort

Author: Raphaël Vernet, Valérie Siroux, Florence Demenais, Jean Bousquet, Christian Lupinek, Hubert Gheerbrant, Christophe Pison, Winfried F. Pickl, Alicia Guillien, Rachel Nadif, Emmanuelle Bouzigon, Rudolf Valenta, Isabelle Pin, Institute for Advanced Biosciences / Institut pour l'Avancée des Biosciences (Grenoble) (IAB), Centre Hospitalier Universitaire [Grenoble] (CHU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Etablissement français du sang - Auvergne-Rhône-Alpes (EFS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Service de pneumologie [Grenoble], Centre Hospitalier Universitaire [Grenoble] (CHU), Toxicité environnementale, cibles thérapeutiques, signalisation cellulaire (T3S - UMR_S 1124), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Medizinische Universität Wien = Medical University of Vienna, Laboratory of Fundamental and Applied Bioenergetics = Laboratoire de bioénergétique fondamentale et appliquée (LBFA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA), Centre de recherche en épidémiologie et santé des populations (CESP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Hôpital Arnaud de Villeneuve [CHRU Montpellier], Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), University of Vienna [Vienna], NRC Institute of immunology FMBA, Moscow Russian federation, Sechenov First Moscow State Medical University, The study was supported in part by ANR-19-CE36-0005-01 NIRVANA, Inserm Aviesan Itmo santé publique, the Scientific committee 'AGIR for chronic diseases,' grant F4605 of the Austrian Science Fund (FWF), by a grant from the Country of Lower Austria and by the Megagrant of the Government of the Russian Federation, grant number 14.W03.31.0024 to RV, and by the European Commission's Seventh Framework Program MeDALL under grant agreement no. 261357. Genotyping was supported grant from the European Commission (No. LSHB-CT-2006-018996-GABRIEL)., ANR-19-CE36-0005,NIRVANA,Facteurs génomiques impliqués dans l'effet des allergènes et virus respiratoires sur l'asthme(2019), European Project: 261357, BARBAGALLO, Maïlys, Facteurs génomiques impliqués dans l'effet des allergènes et virus respiratoires sur l'asthme - - NIRVANA2019 - ANR-19-CE36-0005 - AAPG2019 - VALID, the European Commission's Seventh Framework Program MeDALL under grant agreement no. - 261357 - INCOMING, Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Contre les MAladies Chroniques pour un VIeillissement Actif en Languedoc-Roussillon (MACVIA-LR), Université Montpellier 1 (UM1)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Hospitalier Universitaire de Nîmes (CHU Nîmes)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-European Innovation Partnership on Active and Healthy Ageing Reference Site (EIP on AHA), and Commission Européenne-Commission Européenne-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO)
Subjects: Allergy, genetic epidemiology, [SDV.IMM] Life Sciences [q-bio]/Immunology, Immunology, Population, [SDV.GEN] Life Sciences [q-bio]/Genetics, Human leukocyte antigen, Biology, medicine.disease_cause, Immunoglobulin E, specific IgE, [SDV.MHEP.PSR]Life Sciences [q-bio]/Human health and pathology/Pulmonology and respiratory tract, 03 medical and health sciences, 0302 clinical medicine, Allergen, Hypersensitivity, medicine, Humans, Immunology and Allergy, education, Alleles, Sensitization, 030304 developmental biology, 0303 health sciences, education.field_of_study, Timothy-grass, [SDV.GEN]Life Sciences [q-bio]/Genetics, HLA class-II genes, Allergens, medicine.disease, biology.organism_classification, 3. Good health, medicine.anatomical_structure, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Phleum, MeDALL allergen-chip, respiratory allergen, biology.protein, [SDV.MHEP.PSR] Life Sciences [q-bio]/Human health and pathology/Pulmonology and respiratory tract, Population study, [SDV.IMM]Life Sciences [q-bio]/Immunology, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, 030215 immunology
Abstract: International audience; Background: Allergy, the most frequent immune disorder affecting 30% of the world's population, is the consequence of immunoglobin E (IgE) sensitization to allergens. Among the genetic factors suspected to be involved in allergy, the HLA class-II genomic region is a strong candidate.Objective: To assess the association between HLA class-II alleles and specific IgE (sIgE) sensitization to a large number of respiratory allergen molecules.Methods: The analysis relied on 927 participants of the EGEA cohort, including 497 asthmatics. The study focuses on 26 aeroallergens recognized by sIgE in at least 5% of the study population (determined with the MEDALL chip with sIgE ≥ 0.3 ISU) and 23 imputed HLA class-II alleles. For each sIgE sensitization and HLA class-II allele, we fitted a logistic regression model accounting for familial dependence and adjusted for gender, age, and genetic principal components. p-values were corrected for multiple comparisons (False Discovery Rate).Results: Most of the 19 statistically significant associations observed regard pollen allergens (mugwort Art v 1, olive tree Ole e 1, timothy grass Phl p 2, Phl p 5 and plantain Pla l 1), three were mold allergen (Alternaria Alt a 1), and a single one regards house dust mite allergen (Der p 7). No association was observed with pet allergens. The strongest associations were found with mugwort Art v 1 (OR = 5.42 (95%CI, 3.30; 8.88), 4.14 (2.65; 6.47), 3.16 (1.88; 5.31) with DQB1*05:01, DQA1*01:01 and DRB1*01:01, respectively).Conclusion: Our results support the important role of HLA class-II alleles as immune response genes predisposing their carriers for sensitization to various major pollen allergens.
Published: 2021
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15. The many bits of positional information

Author: Thomas Gregor, Gašper Tkačik, Institute of Science and Technology [Austria] (IST Austria), Department of Physics, Princeton University (DPPU), Princeton University, Physique des fonctions biologiques / Physics of Biological Functions, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), This work was supported in part by the National Science Foundation, through the Center for the Physics of Biological Function (PHY-1734030), by the National Institutes of Health (R01GM097275) and by the Fonds zur Förderung der wissenschaftlichen Forschung (FWF P28844)., Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV.IB.IMA]Life Sciences [q-bio]/Bioengineering/Imaging, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Information Theory, Subject (philosophy), MESH: Biological Evolution, Review, Space (commercial competition), Biology, Information theory, Models, Biological, 03 medical and health sciences, Lewis Wolpert, 0302 clinical medicine, Developmental biology, Animals, Humans, MESH: Animals, Molecular Biology, Body Patterning, 030304 developmental biology, Cognitive science, 0303 health sciences, MESH: Humans, Interpretation (philosophy), Perspective (graphical), MESH: Models, Biological, MESH: Information Theory, [SDV.BDD.MOR]Life Sciences [q-bio]/Development Biology/Morphogenesis, Drosophila embryo, Biological Evolution, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Field (geography), Focus (linguistics), Variable (computer science), Pattern formation, Shannon information, 030217 neurology & neurosurgery, MESH: Body Patterning
Abstract: Half a century after Lewis Wolpert's seminal conceptual advance on how cellular fates distribute in space, we provide a brief historical perspective on how the concept of positional information emerged and influenced the field of developmental biology and beyond. We focus on a modern interpretation of this concept in terms of information theory, largely centered on its application to cell specification in the early Drosophila embryo. We argue that a true physical variable (position) is encoded in local concentrations of patterning molecules, that this mapping is stochastic, and that the processes by which positions and corresponding cell fates are determined based on these concentrations need to take such stochasticity into account. With this approach, we shift the focus from biological mechanisms, molecules, genes and pathways to quantitative systems-level questions: where does positional information reside, how it is transformed and accessed during development, and what fundamental limits it is subject to?
Published: 2021
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16. Developmental roles of Auxin Binding Protein 1 in Arabidopsis thaliana

Author: Markéta Pernisová, Zlata Pavlovičová, Zuzana Gelová, Matouš Glanc, Teva Vernoux, Jaroslav Michalko, Marta Zwiewka, Tongda Xu, Michelle Gallei, Jiří Friml, Géraldine Brunoud, Lukas Hoermayer, Inge Verstraeten, Jakub Hajný, Matyáš Fendrych, Xixi Zhang, Milada Čovanová, Robert Hauschild, Lanxin Li, Huibin Han, Reproduction et développement des plantes (RDP), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), European Research Council (ERC)742985Austrian Science Fund (FWF)I 3630-B25DOC Fellowship of the Austrian Academy of SciencesEuropean Structural and Investment Funds, Operational Programme Research, Development and EducationCZ.02.2.69/0.0/0.0/17_050/0008496Grant Agency of the Czech RepublicGA 20-20860YMEYS CRCZ.02.1.01/0.0/0.0/16_019/0000738, and École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL)
Subjects: 0106 biological sciences, 0301 basic medicine, Mutant, Regulator, Arabidopsis, Receptors, Cell Surface, Plant Science, Biology, Real-Time Polymerase Chain Reaction, 01 natural sciences, Plant Roots, 03 medical and health sciences, Plant Growth Regulators, Auxin, Gene Expression Regulation, Plant, Genetics, Arabidopsis thaliana, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Plant Proteins, chemistry.chemical_classification, Bolting, Microscopy, Confocal, Indoleacetic Acids, Arabidopsis Proteins, Protoplasts, Lateral root, fungi, AUXIN BINDING PROTEIN 1 (ABP1)AuxinPlant developmentAuxin signaling, food and beverages, General Medicine, biology.organism_classification, Hypocotyl, Cell biology, 030104 developmental biology, chemistry, Agronomy and Crop Science, Intracellular, Function (biology), 010606 plant biology & botany
Abstract: International audience; Auxin is a major plant growth regulator, but current models on auxin perception and signaling cannot explain the whole plethora of auxin effects, in particular those associated with rapid responses. A possible candidate for a component of additional auxin perception mechanisms is the AUXIN BINDING PROTEIN 1 (ABP1), whose function in planta remains unclear. Here we combined expression analysis with gain-and loss-of-function approaches to analyze the role of ABP1 in plant development. ABP1 shows a broad expression largely overlapping with, but not regulated by, transcriptional auxin response activity. Furthermore, ABP1 activity is not essential for the transcriptional auxin signaling. Genetic in planta analysis revealed that abp1 loss-of-function mutants show largely normal development with minor defects in bolting. On the other hand, ABP1 gain-of-function alleles show a broad range of growth and developmental defects, including root and hypocotyl growth and bending, lateral root and leaf development, bolting, as well as response to heat stress. At the cellular level, ABP1 gain-of-function leads to impaired auxin effect on PIN polar distribution and affects BFA-sensitive PIN intracellular aggregation. The gain-of-function analysis suggests a broad, but still mechanistically unclear involvement of ABP1 in plant development, possibly masked in abp1 loss-of-function mutants by a functional redundancy.
Published: 2021
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17. Role of Polycomb in the control of transposable elements

Author: Sandra Duharcourt, Angélique Déléris, Frédéric Berger, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Institut Jacques Monod (IJM (UMR_7592)), Université de Paris (UP)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), This work was supported by Centre National de la Recherche Scientifique, the LABEX Who Am I? (ANR-11-LABX-0071, ANR-11-IDEX-0005-02), the Agence Nationale de la Recherche (ANR-18-CE12-0005-04, ANR-19-CE12-0015-01 to S.D., ANR-19-CE12-0033-01 to A.D.), and theAustrian Science Fund (FWF grants P30802, P32054, and TAI304 to F.B.), ANR-11-LABX-0071,WHO AM I,Determinants de l'Identité : de la molécule à l'individu(2011), ANR-11-IDEX-0005,USPC,Université Sorbonne Paris Cité(2011), ANR-18-CE12-0005,LaMarque,Transitions évolutives dans la reconnaissance du 'soi' génomique: petits ARN, facteurs spécifiques de séquence et méthylation de l'ADN(2018), ANR-19-CE12-0015,POLYCHROME,Complexe Polycomb chez la paramécie: interaction avec la machinerie des petits ARN et spécificité de substrats(2019), and ANR-19-CE12-0033,COMPTES,COopération, COmpensation, COmpétition: interactions complexes entre Méthylation de l'ADN et Polycomb dans le contrôle des Eléments Transposables d'ArabidopsiS(2019)
Subjects: Transposable element, Heterochromatin, Mutant, Polycomb-Group Proteins, macromolecular substances, Histones, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Animals, Humans, Gene, 030304 developmental biology, 0303 health sciences, biology, Polycomb Repressive Complex 2, DNA Methylation, Histone, chemistry, Evolutionary biology, DNA methylation, DNA Transposable Elements, biology.protein, PRC2, 030217 neurology & neurosurgery, DNA
Abstract: It is generally considered that Polycomb Repressive Complex (PRC)2 deposits the histone mark H3K27me3 on silent protein-coding genes, while transposable elements are repressed by DNA and/or H3K9 methylation. Yet, there is increasing evidence that PRC2 also targets and even silences transposable elements in representatives of several distantly related eukaryotic lineages. In plants and animals, H3K27me3 is present on transposable elements in mutants and specific cell types devoid of DNA methylation. In this Opinion, we summarize the experimental evidence for this phenomenon across the eukaryotic kingdom, and discuss its functional and evolutionary significance. We hypothesize that an ancestral role of Polycomb group (PcG) proteins was to silence transposable elements.
Published: 2021
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18. The discovery, distribution, and diversity of DNA viruses associated with Drosophila melanogaster in Europe

Author: Omar Rota-Stabelli, Kelsey A. Coffman, Marija Tanasković, Cristina P. Vieira, Andrea J. Betancourt, Gregory F. Albery, Amanda Glaser-Schmitt, Martin Kapun, Catherine Montchamp-Moreau, Thomas Flatt, Iryna Kozeretska, Clément Gilbert, Svitlana Serga, Mads Fristrup Schou, Aleksandra Patenkovic, Katarina Eric, Josefa González, Marta Pascual, Michael G. Ritchie, Paola Bellosta, Darren J. Obbard, Megan A. Wallace, Dorcas J. Orengo, Marija Savic Veselinovic, Eva Puerma, Jorge Vieira, Marina Stamenkovic-Radak, Banu Sebnem Onder, Eliza Argyridou, Jessica K. Abbott, Maaria Kankare, Mihailo Jelić, Sanjana Ravindran, Sonja Grath, John Parsch, Hervé Colinet, Volker Loeschcke, Fabian Staubach, Lino Ometto, University of Edinburgh, University of Georgia [USA], Evolution, génomes, comportement et écologie (EGCE), Institut de Recherche pour le Développement (IRD)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Georgetown University [Washington] (GU), Lund University [Lund], Université de Rennes (UR), Centre National de la Recherche Scientifique (CNRS), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), 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), Université de Fribourg = University of Fribourg (UNIFR), Consejo Superior de Investigaciones Científicas [Spain] (CSIC), University of Freiburg [Freiburg], M.W. was supported by the UK Natural Environmental Research Council through the E3 doctoral training programme (NE/L002558/1), and S.R. was supported by Wellcome Trust PhD programme (108905/Z/15/Z). A.B. received funding from BBSRC (grant number BB/P00685X/1). T.F. received funding from Swiss National Science Foundation (grant numbers 31003A-182262, PP00P3_165836, and PP00P3_133641/1). C.G. received funding from Agence Nationale de la Recherche (grant number ANR-15-CE32-0011-01). J.G. received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (H2020-ERC-2014-CoG-647900) and from the Fundación Española para la Ciencia y la Tecnologia-Ministerio de Economía y Competitividad (FCT-15-10187). S.G. received funding from Deutsche Forschungsgemeinschaft (grant number GR 4495/2). M.K. received funding from Academy of Finland projects (268214 and 322980). M.K. received funding from Austrian Science Fund (FWF, grant number P32275). V.L. received funding from Danish Research council for natural Sciences (FNU, grant number 4002-00113B). B.S.O. received funding from the Scientific and Technological Research Council of Turkey (TUBITAK, grant number 214Z238). J.P. received funding from Deutsche Forschungsgemeinschaft (grant number PA 903/8). M.S.-R., M.S.V., and M.J. received funding from the Ministry of Education, Science and Technological Development of the Republic of Serbia (grant number 451-03-68/2020-14/200178). F.S. received funding from Deutsche Forschungsgemeinschaft (grant number STA1154/4-1, Projektnummer 408908608). M.T., A.P., and K.E. received funding from the Ministry of Education, Science and Technological Development of the Republic of Serbia (grant number 451-03-68/2020-14/200007). The DrosEU consortium has been funded by a Special Topics Network (STN) grant by the European Society of Evolutionary Biology (ESEB)., ANR-15-CE32-0011,TransVir,Mécanismes et fréquence des transferts horizontaux de matériel génétique entre animaux et virus(2015), European Project: 647900,H2020,ERC-2014-CoG,DROSADAPTATION(2016), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES), 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), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), University of Fribourg, Natural Environment Research Council (UK), Wellcome Trust, Biotechnology and Biological Sciences Research Council (UK), Swiss National Science Foundation, Agence Nationale de la Recherche (France), European Commission, European Research Council, Fundación Española para la Ciencia y la Tecnología, Ministerio de Economía y Competitividad (España), German Research Foundation, Academy of Finland, Austrian Science Fund, Danish Research Council, The Scientific and Technological Research Council of Turkey, Ministry of Education, Science and Technological Development (Serbia), European Society for Evolutionary Biology, University of St Andrews. School of Biology, University of St Andrews. Centre for Biological Diversity, University of St Andrews. Institute of Behavioural and Neural Sciences, and University of St Andrews. St Andrews Bioinformatics Unit
Subjects: Galbut virus, virukset, [SDV]Life Sciences [q-bio], viruses, densovirus, Nudivirus, 0302 clinical medicine, Drosòfila, DNA virus, health care economics and organizations, Genetics, 0303 health sciences, biology, AcademicSubjects/SCI02285, 3. Good health, Drosophila, Drosophila melanogaster, galbut virus, QR355 Virology, Research Article, adintovirus, Virus ADN, Filamentous virus, mahlakärpäset, Settore BIO/18 - GENETICA, Microbiology, Virus, 03 medical and health sciences, Virology, Drosophilidae, bidnavirus, nudivirus, Densovirus, Human virome, AcademicSubjects/MED00860, 030304 developmental biology, MCC, QR355, denosovirus, Bidnavirus, Endogenous viral element, fungi, Adintovirus, AcademicSubjects/SCI01130, DAS, RNA virus, biology.organism_classification, AC, filamentous virus, endogenous viral element, DNA viruses, 030217 neurology & neurosurgery
Abstract: Drosophila melanogaster is an important model for antiviral immunity in arthropods, but very few DNA viruses have been described from the family Drosophilidae. This deficiency limits our opportunity to use natural host-pathogen combinations in experimental studies, and may bias our understanding of the Drosophila virome. Here, we report fourteen DNA viruses detected in a metagenomic analysis of 6668 pool-sequenced Drosophila, sampled from forty-seven European locations between 2014 and 2016. These include three new nudiviruses, a new and divergent entomopoxvirus, a virus related to Leptopilina boulardi filamentous virus, and a virus related to Musca domestica salivary gland hypertrophy virus. We also find an endogenous genomic copy of galbut virus, a double-stranded RNA partitivirus, segregating at very low frequency. Remarkably, we find that Drosophila Vesanto virus, a small DNA virus previously described as a bidnavirus, may be composed of up to twelve segments and thus represent a new lineage of segmented DNA viruses. Two of the DNA viruses, Drosophila Kallithea nudivirus and Drosophila Vesanto virus are relatively common, found in 2 per cent or more of wild flies. The others are rare, with many likely to be represented by a single infected fly. We find that virus prevalence in Europe reflects the prevalence seen in publicly available datasets, with Drosophila Kallithea nudivirus and Drosophila Vesanto virus the only ones commonly detectable in public data from wild-caught flies and large population cages, and the other viruses being rare or absent. These analyses suggest that DNA viruses are at lower prevalence than RNA viruses in D.melanogaster, and may be less likely to persist in laboratory cultures. Our findings go some way to redressing an earlier bias toward RNA virus studies in Drosophila, and lay the foundation needed to harness the power of Drosophila as a model system for the study of DNA viruses., M.W. was supported by the UK Natural Environmental Research Council through the E3 doctoral training programme (NE/L002558/1), and S.R. was supported by Wellcome Trust PhD programme (108905/Z/15/Z). A.B. received funding from BBSRC (grant number BB/P00685X/1). T.F. received funding from Swiss National Science Foundation (grant numbers 31003A-182262, PP00P3_165836, and PP00P3_133641/1). C.G. received funding from Agence Nationale de la Recherche (grant number ANR-15-CE32-0011-01). J.G. received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (H2020-ERC-2014-CoG-647900) and from the Fundación Española para la Ciencia y la Tecnologia-Ministerio de Economía y Competitividad (FCT-15-10187). S.G. received funding from Deutsche Forschungsgemeinschaft (grant number GR 4495/2). M.K. received funding from Academy of Finland projects (268214 and 322980). M.K. received funding from Austrian Science Fund (FWF; grant number P32275). V.L. received funding from Danish Research council for natural Sciences (FNU; grant number 4002-00113B). B.S.O. received funding from the Scientific and Technological Research Council of Turkey (TUBITAK; grant number 214Z238). J.P. received funding from Deutsche Forschungsgemeinschaft (grant number PA 903/8). M.S.-R., M.S.V., and M.J. received funding from the Ministry of Education, Science and Technological Development of the Republic of Serbia (grant number 451-03-68/2020-14/200178). F.S. received funding from Deutsche Forschungsgemeinschaft (grant number STA1154/4-1; Projektnummer 408908608). M.T., A.P., and K.E. received funding from the Ministry of Education, Science and Technological Development of the Republic of Serbia (grant number 451-03-68/2020-14/200007). The DrosEU consortium has been funded by a Special Topics Network (STN) grant by the European Society of Evolutionary Biology (ESEB).
Published: 2021
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19. Ustilago maydis effector Jsi1 interacts with Topless corepressor, hijacking plant jasmonate/ethylene signaling

Author: Simon Uhse, Ivo Feussner, Khong-Sam Chia, Michael Borg, Armin Djamei, Indira Saado, Krzysztof Zienkiewicz, Yohann Petit-Houdenot, Luz Mayela Soto-Jiménez, Joana Marques, Martin Alejandro Darino, Ruben Betz, János Bindics, David Aleksza, Austrian Academy of Sciences (OeAW), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), University of Natural Resources and Life Sciences (BOKU), Institute of Molecular Biotechnology (IMBA), Goettingen Center for Molecular Biosciences (GZMB ), Univ Gottingen, Albrecht von Haller Inst, Dept Plant Biochem, BIOlogie et GEstion des Risques en agriculture (BIOGER), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of East Anglia [Norwich] (UEA), University of Bonn, Austrian Science Fund (FWF) I 3033-B22P27818-B22, Austrian Academy of Sciences, German Research Foundation (DFG) INST 186/822-1, European Project, Universität für Bodenkultur Wien = University of Natural Resources and Life [Vienne, Autriche] (BOKU), and Universität Bonn = University of Bonn
Subjects: 0106 biological sciences, 0301 basic medicine, Topless, Physiology, Ustilago, [SDV]Life Sciences [q-bio], Ustilago maydis, Plant Science, Cyclopentanes, jasmonate/ethylene (JA/ET) signaling, 01 natural sciences, Zea mays, Transcriptome, Fungal Proteins, 03 medical and health sciences, Ascomycota, ethylene (JA, Jasmonate, Oxylipins, Psychological repression, Transcription factor, Plant Diseases, biology, Full Paper, Effector, Basidiomycota, Research, fungi, food and beverages, ET) signaling, Ethylenes, Full Papers, biology.organism_classification, jasmonate, Cell biology, Jsi1, 030104 developmental biology, Signal transduction, EAR motif, ethylene response factor, Corepressor, Co-Repressor Proteins, 010606 plant biology & botany
Abstract: early access; International audience; Ustilago maydis is the causal agent of maize smut disease. During the colonization process, the fungus secretes effector proteins that suppress immune responses and redirect the host metabolism in favor of the pathogen. As effectors play a critical role during plant colonization, their identification and functional characterization are essential to understanding biotrophy and disease.Using biochemical, molecular, and transcriptomic techniques, we performed a functional characterization of the U. maydis effector Jasmonate/Ethylene signaling inducer 1 (Jsi1).Jsi1 interacts with several members of the plant corepressor family Topless/Topless related (TPL/TPR). Jsi1 expression in Zea mays and Arabidopsis thaliana leads to transcriptional induction of the ethylene response factor (ERF) branch of the jasmonate/ethylene (JA/ET) signaling pathway. In A. thaliana, activation of the ERF branch leads to biotrophic susceptibility. Jsi1 likely activates the ERF branch via an EAR (ET-responsive element binding-factor-associated amphiphilic repression) motif, which resembles EAR motifs from plant ERF transcription factors, that interacts with TPL/TPR proteins.EAR-motif-containing effector candidates were identified from different fungal species, including Magnaporthe oryzae, Sporisorium scitamineum, and Sporisorium reilianum. Interaction between plant TPL proteins and these effector candidates from biotrophic and hemibiotrophic fungi indicates the convergent evolution of effectors modulating the TPL/TPR corepressor hub.
Published: 2021

20. Air pollution and IgE sensitization in 4 European birth cohorts—the MeDALL project

Author: Magnus Wickman, Alet H. Wijga, Andrea von Berg, Gerard H. Koppelman, Inger Kull, Erik Melén, Anna Bergström, Tamara Schikowski, Judith M. Vonk, Dietrich Berdel, Joachim Heinrich, Marianne van Hage, Josep M. Antó, Christian Lupinek, Jean Bousquet, Olena Gruzieva, Rudolf Valenta, Iana Markevych, E. Thiering, Ulrike Gehring, Hicran Altug, Marie Standl, Vieillissement et Maladies chroniques : approches épidémiologique et de santé publique (VIMA), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut National de la Santé et de la Recherche Médicale (INSERM), 211250, 261357 POIR.04.04.00-1763/18-00 Mead Johnson Nutrition Scottish Environment Protection Agency, SEPA European Commission, EC European Research Council, ERC: 757919 Svenska Forskningsrådet Formas Fundacja na rzecz Nauki Polskiej, FNP Austrian Science Fund, FWF: F4605 Hjärt-Lungfonden Karolinska Institutet, KI Vetenskapsrådet, VR Institut Universitaire de France, IUF: FKZ 20462296 Seventh Framework Programme, FP7 Ludwig-Maximilians-Universität München, LMU Forskningsrådet om Hälsa, Arbetsliv och Välfärd, FORTE: 2017-01146 European Regional Development Fund, FEDER Government Council on Grants, Russian Federation Bundesministerium für Bildung, Wissenschaft, Forschung und Technologie, BMBWF Helmholtz Zentrum München, The research leading to these results has received funding from the European Community's Seventh Framework Program under grant agreement numbers: 211250 (European Study of Cohorts for Air Pollution Effects [ESCAPE]), and 261357 (Mechanisms of the Development of ALLergy [MeDALL]). Children, Allergy, Milieu, Stockholm, Epidemiology (BAMSE) was supported by The Swedish Research Council, The Swedish Heart-Lung Foundation, Region Stockholm (ALF project, and database maintenance), the Strategic Research Programme in Epidemiology at Karolinska Institutet, the Swedish Research Council Formas and the Swedish Environment Protection Agency, the Swedish Asthma and Allergy Research Foundation, the Cancer and Allergy Foundation. E.M. is supported by a grant from the European Research Council (grant agreement 757919, TRIBAL). O.G. is supported by the Swedish Research Council for Health, Working Life and Welfare (FORTE 2017-01146). R.V. is supported the by Austrian Science Fund (grant F4605) and is a recipient of a Megagrant of the Government of the Russian Federation (grant 14.W03.31.0024). The Prevention and Incidence of Asthma and Mite Allergy (PIAMA) study was supported by project grants from The Netherlands Organization for Health Research and Development, The Netherlands Organization for Scientific Research, The Netherlands Asthma Fund, The Netherlands Ministry of Spatial Planning, Housing, and the Environment, and The Netherlands Ministry of Health, Welfare, and Sport. U.G. was supported by a Grant of The Netherlands Organization for Scientific Research. The German Infant Study on the Influence of Nutrition Intervention PLUS Environmental and Genetic Influences on Allergy Development (GINIplus) study was mainly supported for the first 3 years of the Federal Ministry for Education, Science, Research and Technology (interventional arm) and Helmholtz Zentrum Munich (formerly GSF) (observational arm). The 4-year, 6-year, 10-year, and 15-year follow-up examinations of the GINIplus study were covered from the respective budgets of the 5 study centers (Helmholtz Zentrum Munich [formerly GSF], Research Institute at Marien-Hospital Wesel, LMU Munich, TU Munich), and from year 6 onward it was also supported with funding from from IUF-Leibniz Research Institute for Environmental Medicine at the University of D?sseldorf and by a grant from the Federal Ministry for Environment (IUF D?sseldorf [grant FKZ 20462296]). Furthermore, the 15-year follow-up examination of the GINIplus study was supported by the Commission of the European Communities, the Seventh Framework Program MeDALL project, and by the companies Mead Johnson and Nestl?. The Influences of Lifestyle-Related Factors on the Human Immune System and Development of Allergies in Childhood (LISA) study was mainly supported by grants from the Federal Ministry for Education, Science, Research and Technology and also from Helmholtz Zentrum Munich (formerly GSF), the Helmholtz Centre for Environmental Research-UFZ, Leipzig, the Research Institute at Marien-Hospital Wesel, Pediatric Practice, and Bad Honnef for the first 2 years. The 4-year, 6-year, 10-year, and 15-year follow-up examinations of the LISA study were covered from the respective budgets of the involved partners (Helmholtz Zentrum Munich [formerly GSF], the Helmholtz Centre for Environmental Research-UFZ, Leipzig, the Research Institute at Marien-Hospital Wesel, Pediatric Practice, Bad Honnef, and IUF?Leibniz-Research Institute for Environmental Medicine at the University of D?sseldorf) and also by a grant from the Federal Ministry for Environment (IUF D?sseldorf [grant FKZ 20462296]). Furthermore, the 15-year follow-up examination of the LISA study was supported by the Commission of the European Communities, the Seventh Framework Program: MeDALL project. I.M. is supported by a grant from the NeuroSmog: Determining the Impact of Air Pollution on the Developing Brain (grant POIR.04.04.00-1763/18-00) which is implemented as part of the TEAM-NET programme of the Foundation for Polish Science and cofinanced with funding from European Union resources obtained from the European Regional Development Fund under the Smart Growth Operational Programme., The research leading to these results has received funding from the European Community’s Seventh Framework Program under grant agreement numbers: 211250 (European Study of Cohorts for Air Pollution Effects [ESCAPE]), and 261357 (Mechanisms of the Development of ALLergy [MeDALL]). Children, Allergy, Milieu, Stockholm, Epidemiology (BAMSE) was supported by The Swedish Research Council, The Swedish Heart-Lung Foundation, Region Stockholm (ALF project, and database maintenance), the Strategic Research Programme in Epidemiology at Karolinska Institutet, the Swedish Research Council Formas and the Swedish Environment Protection Agency, the Swedish Asthma and Allergy Research Foundation, the Cancer and Allergy Foundation . E.M. is supported by a grant from the European Research Council (grant agreement 757919 , TRIBAL). O.G. is supported by the Swedish Research Council for Health, Working Life and Welfare (FORTE 2017-01146 ). R.V. is supported the by Austrian Science Fund (grant F4605) and is a recipient of a Megagrant of the Government of the Russian Federation (grant 14.W03.31.0024). The Prevention and Incidence of Asthma and Mite Allergy (PIAMA) study was supported by project grants from The Netherlands Organization for Health Research and Development, and The Netherlands Ministry of Health, Welfare, and Sport. U.G. was supported by a Grant of The Netherlands Organization for Scientific Research. The German Infant Study on the Influence of Nutrition Intervention PLUS Environmental and Genetic Influences on Allergy Development (GINIplus) study was mainly supported for the first 3 years of the Federal Ministry for Education, Science, Research and Technology (interventional arm) and Helmholtz Zentrum Munich (formerly GSF) (observational arm). The 4-year, 6-year, 10-year, and 15-year follow-up examinations of the GINIplus study were covered from the respective budgets of the 5 study centers (Helmholtz Zentrum Munich [formerly GSF], Research Institute at Marien-Hospital Wesel, LMU Munich, TU Munich), and from year 6 onward it was also supported with funding from from IUF-Leibniz Research Institute for Environmental Medicine at the University of Düsseldorf and by a grant from the Federal Ministry for Environment (IUF Düsseldorf [grant FKZ 20462296]). Furthermore, the 15-year follow-up examination of the GINIplus study was supported by the Commission of the European Communities, the Seventh Framework Program MeDALL project , and by the companies Mead Johnson and Nestlé. The Influences of Lifestyle-Related Factors on the Human Immune System and Development of Allergies in Childhood (LISA) study was mainly supported by grants from the Federal Ministry for Education, Science, Research and Technology and also from Helmholtz Zentrum Munich (formerly GSF), the Helmholtz Centre for Environmental Research-UFZ, Leipzig, the Research Institute at Marien-Hospital Wesel, Pediatric Practice, and Bad Honnef for the first 2 years. The 4-year, 6-year, 10-year, and 15-year follow-up examinations of the LISA study were covered from the respective budgets of the involved partners (Helmholtz Zentrum Munich [formerly GSF], the Helmholtz Centre for Environmental Research-UFZ, Leipzig, the Research Institute at Marien-Hospital Wesel, Pediatric Practice, Bad Honnef, and IUF–Leibniz-Research Institute for Environmental Medicine at the University of Düsseldorf) and also by a grant from the Federal Ministry for Environment (IUF Düsseldorf [grant FKZ 20462296]). Furthermore, the 15-year follow-up examination of the LISA study was supported by the Commission of the European Communities, the Seventh Framework Program: MeDALL project . I.M. is supported by a grant from the NeuroSmog: Determining the Impact of Air Pollution on the Developing Brain (grant POIR.04.04.00-1763/18-00 ) which is implemented as part of the TEAM-NET programme of the Foundation for Polish Science and cofinanced with funding from European Union resources obtained from the European Regional Development Fund under the Smart Growth Operational Programme., and Groningen Research Institute for Asthma and COPD (GRIAC)
Subjects: Male, Allergy, Respiratory Medicine and Allergy, [SDV]Life Sciences [q-bio], air pollution, 010501 environmental sciences, Immunoglobulin E, medicine.disease_cause, 01 natural sciences, sensitization, Cohort Studies, Allergic sensitization, 0302 clinical medicine, Allergen, Fel d 1, Immunology and Allergy, Medicine, Child, Sensitization, Lungmedicin och allergi, Timothy-grass, biology, cohort, Allergen extract, 3. Good health, Europe, medicine.anatomical_structure, Child, Preschool, Female, IgE, allergen, Adolescent, Immunology, Arbetsmedicin och miljömedicin, 03 medical and health sciences, children, Hypersensitivity, Humans, 0105 earth and related environmental sciences, business.industry, Infant, Newborn, Infant, Occupational Health and Environmental Health, medicine.disease, biology.organism_classification, meta-analysis, 030228 respiratory system, 13. Climate action, biology.protein, Air Pollution, Children, Cohort, Ige, Meta-analysis, business
Abstract: Background: Whether long-term exposure air to pollution has effects on allergic sensitization is controversial. Objective: Our aim was to investigate associations of air pollution exposure at birth and at the time of later biosampling with IgE sensitization against common food and inhalant allergens, or specific allergen molecules, in children aged up to 16 years. Methods: A total of 6163 children from 4 European birth cohorts participating in the Mechanisms of the Development of ALLergy [MeDALL] consortium were included in this meta-analysis of the following studies: Children, Allergy, Milieu, Stockholm, Epidemiology (BAMSE) (Sweden), Influences of Lifestyle-Related Factors on the Human Immune System and Development of Allergies in Childhood (LISA)/German Infant Study on the Influence of Nutrition Intervention PLUS Environmental and Genetic Influences on Allergy Development (GINIplus) (Germany), and Prevention and Incidence of Asthma and Mite Allergy (PIAMA) (The Netherlands). The following indicators were modeled by land use regression: individual residential outdoor levels of particulate matter with aerodynamic diameters less than 2.5 μm, less than 10 μm, and between 2.5 and 10 μm; PM2.5 absorbance (a measurement of the blackness of PM2.5 filters); and nitrogen oxides levels. Blood samples drawn at ages 4 to 6 (n = 5989), 8 to 10 (n = 6603), and 15 to 16 (n = 5825) years were analyzed for IgE sensitization to allergen extracts by ImmunoCAP. Additionally, IgE against 132 allergen molecules was measured by using the MedALL microarray chip (n = 1021). Results: Air pollution was not consistently associated with IgE sensitization to any common allergen extract up to age 16 years. However, allergen-specific analyses suggested increased risks of sensitization to birch (odds ratio [OR] = 1.12 [95% CI = 1.01-1.25] per 10-μg/m3 increase in NO2 exposure). In a subpopulation with microarray data, IgE to the major timothy grass allergen Phleum pratense 1 (Phl p 1) and the cat allergen Felis domesticus 1 (Fel d 1) greater than 3.5 Immuno Solid-phase Allergen Chip standardized units for detection of IgE antibodies were related to PM2.5 exposure at birth (OR = 3.33 [95% CI = 1.40-7.94] and OR = 4.98 [95% CI = 1.59-15.60], respectively, per 5-μg/m3 increase in exposure). Conclusion: Air pollution exposure does not seem to increase the overall risk of allergic sensitization; however, sensitization to birch as well as grass pollen Phl p 1 and cat Fel d 1 allergen molecules may be related to specific pollutants. The research leading to these results has received funding from the European Community’s Seventh Framework Program under grant agreement numbers: 211250 (European Study of Cohorts for Air Pollution Effects [ESCAPE]), and 261357 (Mechanisms of the Development of ALLergy [MeDALL]). Children, Allergy, Milieu, Stockholm, Epidemiology (BAMSE) was supported by The Swedish Research Council, The Swedish Heart-Lung Foundation, Region Stockholm (ALF project, and database maintenance), the Strategic Research Programme in Epidemiology at Karolinska Institutet, the Swedish Research Council Formas and the Swedish Environment Protection Agency, the Swedish Asthma and Allergy Research Foundation, the Cancer and Allergy Foundation. E.M. is supported by a grant from the European Research Council (grant agreement 757919, TRIBAL). O.G. is supported by the Swedish Research Council for Health, Working Life and Welfare (FORTE 2017-01146).
Published: 2021
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21. Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors

Author: Boulos Chalhoub, Andrew Katz, David Goodstein, Virginia S. Tartaglio, Rubén Sancho, Shengqiang Shu, Vasanth R. Singan, Scott J. Lee, Joel Martin, John H. Doonan, Jerry Jenkins, Sean P. Gordon, Daniel S. Rokhsar, Angelika Czedik-Eysenberg, Luis A. J. Mur, Eugene Goltsman, Kerrie Barry, Samuel P. Hazen, John P. Vogel, Bruno Contreras-Moreira, Antonio Díaz-Pérez, Christopher Plott, Robert Hasterok, Joshua J. Levy, Adam M. Session, Elzbieta Wolny, Jeremy Schmutz, Joanna Lusinska, Armin Djamei, Pilar Catalán, Vinh Ha Dinh-Thi, Candida Nibau, Amy Cartwright, Department of Energy (US), Universidad de Zaragoza, Ministerio de Economía y Competitividad (España), Gobierno de Aragón, National Science Centre (Poland), Leverhulme Trust, European Commission, Austrian Academy of Sciences, Contreras-Moreira, Bruno [0000-0002-5462-907X], Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), United States Department of Energy (DOE)DE-AC02-05CH11231University of Zaragoza FP00006675United States Department of Energy (DOE)FP00006675503504United States Department of Energy (DOE) Spanish Ministry of Economy and Competitiveness CGL2016-79790-PBioflora grant - Spanish Aragon Government A01-17European Social Fund (ESF) National Science Centre, PolandDEC-2012/04/A/NZ3/00572DEC-2014/14/M/NZ2/00519Leverhulme Trust10754European Research Council (ERC)GA335691Austrian Science Fund (FWF)P27429-B22P27818-B22I 3033-B22Austrian Academy of Science (OEAW), and Contreras-Moreira, Bruno
Subjects: 0106 biological sciences, 0301 basic medicine, Performance, General Physics and Astronomy, Retrotransposon, 01 natural sciences, Genome, Divergence, [SPI]Engineering Sciences [physics], Distachyon, Mechanisms, Fractionation, lcsh:Science, Phylogeny, Diversity, Multidisciplinary, food and beverages, Single Nucleotide, Genomics, Polyploidy in plants, Ploidy, Genome, Plant, Biotechnology, Brachypodium, Genome evolution, Retroelements, Evolution, Science, Biology, Chloroplast, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, Chromosomes, Chromosomes, Plant, Article, Ancient, Evolution, Molecular, Polyploidy, 03 medical and health sciences, Polyploid, Genetic, Species Specificity, Genetics, Polymorphism, Genome, Chloroplast, Gene, Hybridization, Consequences, Alignment, Comparative genomics, Human Genome, fungi, Individuals, Molecular, General Chemistry, Plant, Diploidy, 030104 developmental biology, Natural variation in plants, Evolutionary biology, Hybridization, Genetic, lcsh:Q, 010606 plant biology & botany
Abstract: 16 Pags.- 8 Figs. This article is licensed under a Creative Commons Attribution 4.0 International License., Our understanding of polyploid genome evolution is constrained because we cannot know the exact founders of a particular polyploid. To differentiate between founder effects and post polyploidization evolution, we use a pan-genomic approach to study the allotetraploid Brachypodium hybridum and its diploid progenitors. Comparative analysis suggests that most B. hybridum whole gene presence/absence variation is part of the standing variation in its diploid progenitors. Analysis of nuclear single nucleotide variants, plastomes and k-mers associated with retrotransposons reveals two independent origins for B. hybridum, ~1.4 and ~0.14 million years ago. Examination of gene expression in the younger B. hybridum lineage reveals no bias in overall subgenome expression. Our results are consistent with a gradual accumulation of genomic changes after polyploidization and a lack of subgenome expression dominance. Significantly, if we did not use a pan-genomic approach, we would grossly overestimate the number of genomic changes attributable to post polyploidization evolution., The work conducted by the US DOE Joint Genome Institute is supported by the Office of Science of the US Department of Energy under Contract no. DE-AC02-05CH11231 and User Agreement No. FP00006675 between the University of Zaragoza (User) and the DOE (Community Science Program 503504 proposal); S.J. was supported by the DOE Office of Science Graduate Student Research Program; P.C., B.C.-M., A.D.P., and R.S. were supported by a Spanish Ministry of Economy and Competitiveness grant CGL2016-79790-P; P.C., A.D.P., and R.S. were supported by a Bioflora A01-17 grant co-funded by the Spanish Aragon Government and the European Social Fund. R.H., E.W., and J.L. were supported by the National Science Centre Poland (grants DEC-2012/04/A/NZ3/00572 and DEC-2014/14/M/NZ2/00519). J.H.D. and C.N. were supported by Leverhulme Trust (grant no. 10754). A.C.E. and A.D. were supported by the European Research Council under the European Union’s Seventh Framework Program (FP7/2007-2013)/ERC grant agreement no [GA335691 “Effectomics”], the Austrian Science Fund (FWF): [P27429-B22, P27818-B22, I 3033-B22], and the Austrian Academy of Science (OEAW).
Published: 2020
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22. SYNERGISTIC ON AUXIN AND CYTOKININ 1 positively regulates growth and attenuates soil pathogen resistance

Author: Hana Semerádová, Grégory Mouille, Freia Benade, Rishikesh Bhalearo, Ladislav Dokládal, Andrej Hurný, Jutta Ludwig-Müller, Krisztina Ötvös, András Gorzsás, Ingo Heilmann, Geert De Jaeger, Irene Stenzel, Thomas Rauter, Juan Carlos Montesinos, Jérôme Duclercq, Candela Cuesta, Marçal Gallemí, Eva Sýkorová, Eva Benková, Geert Persiau, Julien Sechet, Nicola Cavallari, Institute of Science and Technology, Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo [Oviedo], Bioresources Unit, Center for Health & Bioresources, Austrian Institute of Technology [Vienna] (AIT)-Austrian Institute of Technology [Vienna] (AIT), Ecologie et Dynamique des Systèmes Anthropisés - UMR CNRS 7058 (EDYSAN), Centre National de la Recherche Scientifique (CNRS)-Université de Picardie Jules Verne (UPJV), Institute of Biophysics, Institute of Biophysics of the Czech Academy of Sciences (IBP / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk Memorial Cancer Institute (RECAMO)-Masaryk Memorial Cancer Institute (RECAMO), Molecular Biology and Biochemistry, Gottfried Schatz Research Center, University of Graz-University of Graz, Department of Cellular Biochemistry, Institute for Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg-Martin-Luther-University Halle-Wittenberg, Department of Plant Biotechnology and Bioinformatics, Universiteit Gent = Ghent University [Belgium] (UGENT), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Institut für Botanik [Dresden], Technische Universität Dresden = Dresden University of Technology (TU Dresden), Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Department of Chemistry, Umeå University, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Austrian Science Fund (FWF)FWF01_I1774SGerman Research Foundation (DFG)He3424/6-1People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant 291734European Commission609398Scientific Service Units of IST-Austria Saclay Plant Sciences-SPS ANR-17-EUR-0007, Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), and Karl-Franzens-Universität [Graz, Autriche]-Karl-Franzens-Universität [Graz, Autriche]
Subjects: 0106 biological sciences, 0301 basic medicine, Cytokinins, Arabidopsis, Vesicular Transport Proteins, Regulator, Golgi Apparatus, General Physics and Astronomy, PUTATIVE METHYLTRANSFERASE, Plasmodiophorida, Plant Roots, 01 natural sciences, Soil, chemistry.chemical_compound, APICAL HOOK, Arabidopsis-thaliana, Plant Growth Regulators, Gene Expression Regulation, Plant, Protein trafficking in plants, Auxin, heterocyclic compounds, lcsh:Science, Disease Resistance, 2. Zero hunger, chemistry.chemical_classification, Regulation of gene expression, Abiotic component, Secretory Pathway, Multidisciplinary, Cell wall, PLANT DEVELOPMENT, food and beverages, Plants, Genetically Modified, Cell biology, B Response Regulators, Cytokinin, PLASMODIOPHORA-BRASSICAE, CYTOKININ RECEPTOR, Chinese-cabbage, Science, Cytokinin Receptor, Plant Development, Genetics and Molecular Biology, Box Protein Tir1, Endosomes, Biology, BOX PROTEIN TIR1, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Putative Methyltransferase, Apical Hook, Biotic, Secretory pathway, Indoleacetic Acids, Arabidopsis Proteins, Gene Expression Profiling, fungi, Botany, Membrane Proteins, Biology and Life Sciences, B RESPONSE REGULATORS, Botanik, General Chemistry, Gene expression profiling, POLLEN-TUBE GROWTH, 030104 developmental biology, chemistry, General Biochemistry, ARABIDOPSIS-THALIANA, Pollen-tube Growth, lcsh:Q, [INFO.INFO-ET]Computer Science [cs]/Emerging Technologies [cs.ET], CHINESE-CABBAGE, Plasmodiophora-brassicae, Transcriptome, 010606 plant biology & botany, Hormone
Abstract: Plants as non-mobile organisms constantly integrate varying environmental signals to flexibly adapt their growth and development. Local fluctuations in water and nutrient availability, sudden changes in temperature or other abiotic and biotic stresses can trigger changes in the growth of plant organs. Multiple mutually interconnected hormonal signaling cascades act as essential endogenous translators of these exogenous signals in the adaptive responses of plants. Although the molecular backbones of hormone transduction pathways have been identified, the mechanisms underlying their interactions are largely unknown. Here, using genome wide transcriptome profiling we identify an auxin and cytokinin cross-talk component; SYNERGISTIC ON AUXIN AND CYTOKININ 1 (SYAC1), whose expression in roots is strictly dependent on both of these hormonal pathways. We show that SYAC1 is a regulator of secretory pathway, whose enhanced activity interferes with deposition of cell wall components and can fine-tune organ growth and sensitivity to soil pathogens., Cytokinin and auxin are two major hormonal regulators of plant growth. Here the authors identify SYAC1, a gene that is synergistically activated by the two hormones being applied together, and show that it is required for normal growth while negatively impacting pathogen resistance.
Published: 2020
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23. Grand Challenges in Infectious Diseases: Are We Prepared for Worst-Case Scenarios?

Author: Karl Kuchler, Axel Cloeckaert, Infectiologie et Santé Publique (UMR ISP), Université de Tours (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Max Perutz Labs, University of Vienna [Vienna], Austrian Science Fund (FWF) (SFB070-P08 Chromatin FWF-P25333-B22 ChromFunVir FWF-P-31712), United States Department of Health & Human Services National Institutes of Health (NIH) -USA (NIH-R01AI124499), ANR-14-ASMA-0002,MicroType,Surveillance planétaire d'agents infectieux : kits de typage et banque de données(2014), European Project: 602125,EC:FP7:HEALTH,FP7-HEALTH-2013-INNOVATION-1,FUNGITECT(2014), European Project: 606786,EC:FP7:PEOPLE,FP7-PEOPLE-2013-ITN,IMRESFUN(2013), and Université de Tours-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Microbiology (medical), 2019-20 coronavirus outbreak, Coronavirus disease 2019 (COVID-19), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), [SDV]Life Sciences [q-bio], lcsh:QR1-502, antimicrobial multidrug resistance, Biology, infectious diseases, Microbiology, lcsh:Microbiology, 03 medical and health sciences, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, host-pathogen interactions, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Grand Challenges, 0303 health sciences, COVID-19, vaccines, Virology, mortality, 3. Good health, polymicrobial disease, Research strategies, 030220 oncology & carcinogenesis, research strategies, Specialty Grand Challenge
Abstract: International audience
Published: 2020
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24. Parasitic Chytrids Upgrade and Convey Primary Produced Carbon During Inedible Algae Proliferation

Author: Matthias Pilecky, Silke Van den Wyngaert, Martin J. Kainz, Robert Ptacnik, Stefanie Danner, Thomas Rohrlack, Serena Rasconi, Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Austrian Science Fund (FWF)P 30419-B29
Subjects: 0301 basic medicine, Cyanobacteria, Food Chain, [SDV]Life Sciences [q-bio], parasitic chytrids, Biology, Microbiology, fatty acids, 03 medical and health sciences, Algae, Phytoplankton, Organic matter, 14. Life underwater, Trophic level, Isotope analysis, chemistry.chemical_classification, Diatoms, Ecology, fungi, 030108 mycology & parasitology, biology.organism_classification, Plankton, Food web, 030104 developmental biology, Chytridiomycota, chemistry, 13. Climate action, Trophic transfer, Essential nutrient, Streptophyta, compound-specific isotope analysis
Abstract: International audience; Microbial parasites have only recently been included in planktonic food web studies, but their functional role in conveying dietary energy still remains to be elucidated. Parasitic fungi (chytrids) infecting phytoplankton may constitute an alternative trophic link and promote organic matter transfer through the production of dissemination zoospores. Particularly, during proliferation of inedible or toxic algal species, such as large Cyanobacteria fostered by global warming, parasites can constitute an alternative trophic link providing essential dietary nutrients that support somatic growth and reproduction of consumers. Using phytoplankton-parasites associations grown under laboratory controlled conditions we assessed the fatty acids and biochemical composition of species with different nutritional quality and followed the metabolic pathway from the algal host and their parasites zoospores using compound specific stable isotope analysis. This study demonstrated that chytrids are trophic upgraders able to retain essential nutrients that can be transferred to upper trophic levels both in terms of organic matter quantity and nutritional quality. Through the production of zoospores, nutritionally important long-chain polyunsaturated fatty acids that can be consequently assimilated by consumers. We conclude that parasitism at the base of aquatic food webs may represent a crucial trophic link for dietary nutrients and essential biomolecules alternative to herbivory or bacterivory, which can be particularly crucial during the proliferation of inedible or nutritionally inadequate algal species fostered by climate change.
Published: 2020
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25. Global quantitative synthesis of ecosystem functioning across climatic zones and ecosystem types

Author: Chelsea J. Little, Florian Altermatt, Isabelle Gounand, Eric Harvey, University of Zurich, Hickler, Thomas, Gounand, Isabelle, Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Evolutionary Biology and Environmental Studies, Universität Zürich [Zürich] = University of Zurich (UZH), Department of Aquatic Ecology, Swiss Federal Insitute of Aquatic Science and Technology [Dübendorf] (EAWAG), Universitat Zurich Austrian Science Fund (FWF)PP00P3_150698PP00P3_179089, and Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, productivity, [SDV]Life Sciences [q-bio], 2306 Global and Planetary Change, meta, 010603 evolutionary biology, 01 natural sciences, Freshwater ecosystem, 10127 Institute of Evolutionary Biology and Environmental Studies, metabolic theory of ecology, multifunctionality, carbon cycle, Marine ecosystem, Ecosystem, 14. Life underwater, climate, Ecology, Evolution, Behavior and Systematics, global change, ecosystem, Global and Planetary Change, Biomass (ecology), decomposition, Ecology, 010604 marine biology & hydrobiology, meta‐ecosystem, Primary production, 15. Life on land, 1105 Ecology, Evolution, Behavior and Systematics, Productivity (ecology), 13. Climate action, ecosystem functioning, Environmental science, 570 Life sciences, biology, 590 Animals (Zoology), Terrestrial ecosystem, Ecosystem respiration, 2303 Ecology, primary production
Abstract: Aim Providing a quantitative overview of ecosystem functioning in a three‐dimensional space defined by ecosystem stocks, fluxes and rates, across major ecosystem types and climatic zones. Location Global. Time period 1966–2019. Major taxa studied Ecosystem‐level measurements (all organism types). Methods We conducted a global quantitative synthesis of a wide range of ecosystem variables related to carbon stocks and fluxes. We gathered a total of 4,479 values from 1,223 individual sites (unique geographical coordinates) reported in the literature (604 studies), covering ecosystem variables including biomass and detritus stocks, gross primary production, ecosystem respiration, detritus decomposition and carbon uptake rates, across eight major aquatic and terrestrial ecosystem types and five broad climatic zones (arctic, boreal, temperate, arid and tropical). We analysed the relationships among variables emerging from the comparisons of stocks, fluxes and rates across ecosystem types and climates. Results Within our three‐dimensional functioning space, average ecosystems align along a gradient from fast rates–low fluxes and stocks (freshwater and pelagic marine ecosystems) to low rates–high fluxes and stocks (forests), a gradient that we hypothesize results mainly from variation in primary producer characteristics. Moreover, fluxes and rates decrease from warm to colder climates, consistent with the metabolic theory of ecology. However, the strength of climatic effects differs among variables and ecosystem types, resulting, for instance, in opposing effects on net ecosystem production between terrestrial and freshwater ecosystems (positive versus negative effects). Main conclusions This large‐scale synthesis provides a first quantified cross‐ecosystem and cross‐climate comparison of multivariate ecosystem functioning. This gives a basis for a mechanistic understanding of the interdependency of different aspects of ecosystem functioning and their sensitivity to global change. To anticipate responses to change at the ecosystem level, further work should investigate potential feedbacks between ecosystem variables at finer scales, which involves site‐level quantifications of multivariate functioning and theoretical developments.
Published: 2020
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26. Aspergillus-Pseudomonas interaction, relevant to competition in airways

Author: Paolo Visca, Gabriele Sass, Karl V. Clemons, Shajia R Ansari, John C. Penner, Eric Déziel, David A. Stevens, Hasan Nazik, Hemi Shah, Hubertus Haas, Anna-Maria Dietl, Marie-Christine Groleau, California Institute for Medical Research (CIMR), Stanford School of Medicine [Stanford], Stanford Medicine, Stanford University-Stanford University, Istanbul University, Institut Armand Frappier (INRS-IAF), Institut National de la Recherche Scientifique [Québec] (INRS)-Réseau International des Instituts Pasteur (RIIP), Innsbruck Medical University [Austria] (IMU), Roma Tre University, These studies were partially supported by a gift from John Flatley, CIMR no. 3770 and by a grant from the Child Health Research Institute, Stanford Transdisciplinary Initiatives Program, CIMR no. 3777. This work was partially supported by the Austrian Science Fund/Infect-ERA program (FWF grant I1616/Infect-ERA project AspMetNet to HH). A-M.D. is an associate student of the HOROS doctoral program (W1253), The authors thank Marife Martinez for excellent technical support, Sass, Gabriele, Nazik, Hasan, Penner, John, Shah, Hemi, Ansari, Shajia R, Clemons, Karl V, Groleau, Marie-Christine, Dietl, Anna-Maria, Visca, Paolo, Haas, Hubertu, Déziel, Eric, and Stevens, David A
Subjects: MESH: Aspergillus fumigatus/growth & development, Siderophore, MESH: Respiratory Tract Infections/pathology, medicine.disease_cause, Aspergillus fumigatus, cystic fibrosis, chemistry.chemical_compound, skin and connective tissue diseases, Respiratory Tract Infections, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, MESH: Oligopeptides/metabolism, 0303 health sciences, Pyoverdine, biology, pyoverdine, MESH: Pseudomonas aeruginosa/growth & development, Pseudomonas, MESH: Pseudomonas aeruginosa/genetics, General Medicine, 3. Good health, Infectious Diseases, Pseudomonas aeruginosa, Oligopeptides, MESH: Mutation, Virulence Factors, Virulence, MESH: Aspergillosis/microbiology, Microbiology, microbial interaction, 03 medical and health sciences, MESH: Respiratory Tract Infections/microbiology, MESH: Virulence Factors/genetics, medicine, Aspergillosis, Humans, Pseudomonas Infections, MESH: Pseudomonas Infections/microbiology, cystic fibrosi, 030304 developmental biology, MESH: Aspergillosis/pathology, MESH: Humans, MESH: Oligopeptides/genetics, 030306 microbiology, MESH: Pseudomonas Infections/pathology, Biofilm, MESH: Virulence Factors/metabolism, biochemical phenomena, metabolism, and nutrition, bacterial infections and mycoses, biology.organism_classification, MESH: Microbial Interactions, Quorum sensing, chemistry, Mutation, Aspergillus fumigatu, Microbial Interactions
Abstract: International audience; In airways of immunocompromised patients and individuals with cystic fibrosis, Pseudomonas aeruginosa and Aspergillus fumigatus are the most common opportunistic bacterial and fungal pathogens. Both pathogens form biofilms and cause acute and chronic illnesses. Previous studies revealed that P. aeruginosa is able to inhibit A. fumigatus biofilms in vitro. While numerous P. aeruginosa molecules have been shown to affect A. fumigatus, there never has been a systematic approach to define the principal causative agent. We studied 24 P. aeruginosa mutants, with deletions in genes important for virulence, iron acquisition, or quorum sensing, for their ability to interfere with A. fumigatus biofilms. Cells, planktonic or biofilm culture filtrates of four P. aeruginosa mutants, pvdD-pchE-, pvdD-, lasR-rhlR-, and lasR-, inhibited A. fumigatus biofilm metabolism or planktonic A. fumigatus growth significantly less than P. aeruginosa wild type. The common defect of these four mutants was a lack in the production of the P. aeruginosa siderophore pyoverdine. Pure pyoverdine affected A. fumigatus biofilm metabolism, and restored inhibition by the above mutants. In lungs from cystic fibrosis patients, pyoverdine production and antifungal activity correlated. The key inhibitory mechanism for pyoverdine was iron-chelation and denial of iron to A. fumigatus. Further experiments revealed a counteracting, self-protective mechanism by A. fumigatus, based on A. fumigatus siderophore production.
Published: 2019
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27. The host-associated archaeome

Author: Simonetta Gribaldo, Christine Moissl-Eichinger, Jean-François Brugère, Ruth A. Schmitz, Guillaume Borrel, Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Christian-Albrechts University of Kiel, Medical University Graz, Funding given by the Austrian Science Fund (FWF) to C.M.-E. (Project IDs P 30796 and P 32697) is highly appreciated, as is the funding from the German Science Foundation (DFG) given to R.A.S. (SCHM1052/11-1/2). The French National Agency for Research is gratefully acknowledged for funding to G.B. and S.G. (Grants ArchEvol ANR-16-CE02-0005-01 and Methevol ANR-19-CE02-0005-01), and we acknowledge a grant to J.-F.B. from Hub Innovergne (‘Investissements d’Avenir’ 16-IDEX-0001 CAP 20–25)., ANR-16-CE02-0005,Arch-Evol,Approches phylogenomiques pour étudier l'origine et évolution des Archées(2016), ANR-19-CE02-0005,METHEVOL,Caractérisation de nouveaux acteurs et des transitions évolutives dans le métabolisme du méthane, un métabolisme clef dans l'évolution du domaine Archaea(2019), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Thaumarchaeota, Disease, Microbiology, 03 medical and health sciences, Phylogenetics, Animals, Humans, Microbiome, Phylogeny, 0303 health sciences, General Immunology and Microbiology, biology, 030306 microbiology, Host (biology), Microbiota, Gastrointestinal Microbiome, 15. Life on land, Plants, biology.organism_classification, Archaea, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Evolutionary biology, Euryarchaeota
Abstract: Host-associated microbial communities have an important role in shaping the health and fitness of plants and animals. Most studies have focused on the bacterial, fungal or viral communities, but often the archaeal component has been neglected. The archaeal community, the so-called archaeome, is now increasingly recognized as an important component of host-associated microbiomes. It is composed of various lineages, including mainly Methanobacteriales and Methanomassiliicoccales (Euryarchaeota), as well as representatives of the Thaumarchaeota. Host–archaeome interactions have mostly been delineated from methanogenic archaea in the gastrointestinal tract, where they contribute to substantial methane production and are potentially also involved in disease-relevant processes. In this Review, we discuss the diversity and potential roles of the archaea associated with protists, plants and animals. We also present the current understanding of the archaeome in humans, the specific adaptations involved in interaction with the resident microbial community as well as with the host, and the roles of the archaeome in both health and disease. The archaeal community, the archaeome, is now increasingly recognized as an important component of host-associated microbiomes. In this Review, Moissl-Eichinger and colleagues discuss the diversity and potential roles of the archaea associated with protists, plants and animals, highlighting the potential roles of archaea in human health and disease.
Published: 2020
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28. Management versus site effects on the abundance of nitrifiers and denitrifiers in European mountain grasslands

Author: Michael Bahn, Michael Schloter, Ute Szukics, Richard D. Bardgett, Catherine Baxendale, Nicolas Legay, Jean-Christophe Clément, Karl Grigulis, Sandra Lavorel, Eva-Maria Kastl, Institut für Ökologie, Universität Innsbruck [Innsbruck], Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), Cités, Territoires, Environnement et Sociétés (CITERES), Université de Tours-Centre National de la Recherche Scientifique (CNRS), Helmholtz-Zentrum München (HZM), Lancaster Environment Centre, Lancaster University, School of Earth and Environmental Sciences [Manchester] (SEES), University of Manchester [Manchester], Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de la Recherche Agronomique (INRA), ANR-08-BDVA-0008,VITAL,Services écologiques issus du couplage entre la diversité fonctionnelle des plantes et des microorganismes du sol dans les prairies(2008), Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Centre National de la Recherche Scientifique (CNRS)-Université de Tours (UT), Institut National de la Recherche Agronomique (INRA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), ANR11 INBS-0001AnaEE-Services, ANR ANR-08-BDVA-008 NERC NE/G002258/2, Austrian Science Fund (FWF) I 242-B17, ClimLUC project - ESS-programme of the Austrian Academy of Sciences, National Research Agency, and Centre National de la Recherche Scientifique (CNRS)-Université de Tours
Subjects: mountain grasslands, soil nitrogen cycle, Environmental Engineering, business.product_category, 010504 meteorology & atmospheric sciences, Land management, 010501 environmental sciences, Biology, 01 natural sciences, Grassland, Plough, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Abundance (ecology), Soil pH, Environmental Chemistry, nitrifiers, Organic matter, Transect, Waste Management and Disposal, Water content, 0105 earth and related environmental sciences, 2. Zero hunger, chemistry.chemical_classification, geography, geography.geographical_feature_category, Nitrifiers, Denitrifieis, Land Use Intensity, Mountain Grasslands, Soil Nitrogen Cycle, Ecology, denitrifiers, food and beverages, 15. Life on land, Pollution, chemistry, land use intensity, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business
Abstract: It is well established that the abundances of nitrogen (N) transforming microbes are strongly influenced by land-use intensity in lowland grasslands. However, their responses to management change in less productive and less fertilized mountain grasslands are largely unknown. We studied eight mountain grasslands, positioned along gradients of management intensity in Austria, the UK, and France, which differed in their historical management trajectories. We measured the abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA) as well as nitrite-reducing bacteria using specific marker genes. We found that management affected the abundance of these microbial groups along each transect, though the specific responses differed between sites, due to different management histories and resulting variations in environmental parameters. In Austria, cessation of management caused an increase in nirK and nirS gene abundances. In the UK, intensification of grassland management led to 10-fold increases in the abundances of AOA and AOB and doubling of nirK gene abundance. In France, ploughing of previously mown grassland caused a 20-fold increase in AOA abundance. Across sites the abundance of AOB was most strongly related to soil NO3--N availability, and AOA were favored by higher soil pH. Among the nitrite reducers, nirS abundance correlatedwas most strongly with N parameters, such as soil NO3--N, microbial N. leachate NH4+-N, while the abundance of nirK-denitrifiers was affected by soil total N, organic matter (SOM) and water content. We conclude that alteration of soil environmental conditions is the dominant mechanism by which land management practices influence the abundance of each group of ammonia oxidizers and nitrite reducers. (C) 2018 Elsevier B.V. All rights reserved.
Published: 2019
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29. Madeiran Arabidopsis thaliana reveals ancient long-range colonization and clarifies demography in Eurasia

Author: Maarten Koornneef, Angela M. Hancock, Fabrice Roux, Joachim Hermisson, Andrea Fulgione, Max Planck Institute for Plant Breeding Research (MPIPZ), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Mathematics and BioSciences Group, Faculty of Mathematics [Vienna], University of Vienna [Vienna]-University of Vienna [Vienna], Vienna Graduate School of Population Genetics (Austrian Science Fund, FWF) : DK W1225-B20, Deutsche Forschungsgemeinschaft Research Unit 'Natural selection in structured populations' : FOR 1078, HE 3266 3/2, European Research Council : CVI_ADAPT 638810, Max Planck Society Funding, LABEX TULIP : ANR-10-LABX-41, ANR-11-IDEX-0002-02, European Project: 304301,EC:FP7:PEOPLE,FP7-PEOPLE-2011-CIG,CLIMATE_ADAPTATION(2012), and Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP))
Subjects: 0106 biological sciences, 0301 basic medicine, Arabidopsis thaliana, Population genetics, Admixture, madère, Biology, Relict, 010603 evolutionary biology, 01 natural sciences, Island, 03 medical and health sciences, genetique des populations, Propagule, Effective population size, Genetics, Contact zone, Groep Koornneef, Colonization, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Discoveries, Demography, demography, population genetics, relict, admixture, island, Vegetal Biology, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], eurasie, iles océan pacifique, 030104 developmental biology, Biological dispersal, Selective sweep, Biologie végétale, Founder effect
Abstract: International audience; The study of model organisms on islands may shed light on rare long-range dispersal events, uncover signatures of local evolutionary processes, and inform demographic inference on the mainland. Here, we sequenced the genomes of Arabidopsis thaliana samples from the oceanic island of Madeira. These samples include the most diverged worldwide, likely a result of long isolation on the island. We infer that colonization of Madeira happened between 70 and 85 ka, consistent with a propagule dispersalmodel (of size >= 10), or with an ecological window of opportunity. This represents a clear example of a natural long-range dispersal event in A. thaliana. Long-term effective population size on the island, rather than the founder effect, had the greatest impact on levels of diversity, and rates of coalescence. Our results uncover a selective sweep signature on the ancestral haplotype of a known translocation in Eurasia, as well as the possible importance of the low phosphorous availability in volcanic soils, and altitude, in shaping early adaptations to the island conditions. Madeiran genomes, sheltered from the complexities of continental demography, help illuminate ancient demographic events in Eurasia. Our data support a model in which two separate lineages of A. thaliana, one originating in Africa and the other from the Caucasus expanded and met in Iberia, resulting in a secondary contact zone there. Although previous studies inferred that the westward expansion of A. thaliana coincided with the spread of human agriculture, our results suggest that it happened much earlier (20-40 ka).
Published: 2018
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30. Leaf litter diversity and structure of microbial decomposer communities modulate litter decomposition in aquatic systems

Author: Fabienne Santschi, Eric Harvey, Florian Altermatt, Isabelle Gounand, UMR 7618 IEES-Paris (CNRS, INRA, UPMC, IRD, UPEC), France, Université de Montréal (UdeM), Universität Zürich [Zürich] (UZH), Swiss Federal Insitute of Aquatic Science and Technology [Dübendorf] (EAWAG), University of Zurich, Altermatt, Florian, Institut d'écologie et des sciences de l'environnement de Paris (iEES), Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Universität Zürich [Zürich] = University of Zurich (UZH), Austrian Science Fund (FWF)PP00P3_150698, and Centre National de la Recherche Scientifique (CNRS)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, Alnus glutinosa, biodiversity ecosystem functioning, Fagus sylvatica, Biodiversity, Biology, 010603 evolutionary biology, 01 natural sciences, Decomposer, 10127 Institute of Evolutionary Biology and Environmental Studies, Ecosystem, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, Trophic level, protists, Populus nigraprotists, microcosm experiment, Ecology, 010604 marine biology & hydrobiology, Aquatic ecosystem, 15. Life on land, Plant litter, 1105 Ecology, Evolution, Behavior and Systematics, 13. Climate action, [SDE]Environmental Sciences, Litter, 570 Life sciences, biology, 590 Animals (Zoology), Terrestrial ecosystem, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Quercus robur, Populus nigra
Abstract: Leaf litter decomposition is a major ecosystem process that can link aquatic to terrestrial ecosystems by flows of nutrients. Biodiversity and ecosystem functioning research hypothesizes that the global loss of species leads to impaired decomposition rates and thus to slower recycling of nutrients. Especially in aquatic systems an understanding of diversity effects on litter decomposition is still incomplete. Here we conducted an experiment to test two main factors associated with global species loss that might influence leaf litter decomposition. Firstly, we tested whether mixing different leaf species alters litter decomposition rates compared to decomposition of these species in monoculture. Secondly, we tested the effect of the size structure of a lotic decomposer community on decomposition rates. Overall, leaf litter identity strongly affected decomposition rates, and the observed decomposition rates matched measures of metabolic activity and microbial abundances. While we found some evidence of a positive leaf litter diversity effect on decomposition, this effect was not coherent across all litter combinations and the effect was generally additive and not synergistic. Microbial communities, with a reduced functional and trophic complexity, showed a small but significant overall reduction in decomposition rates compared to communities with the naturally complete functional and trophic complexity, highlighting the importance of a complete microbial community on ecosystem functioning. Our results suggest that top-down diversity effects of the decomposer community on litter decomposition in aquatic systems are of comparable importance as bottom-up diversity effects of primary producers. This article is protected by copyright. All rights reserved.
Published: 2017
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31. Generation and application of river network analogues for use in ecology and evolution

Author: Emanuel A. Fronhofer, Florian Altermatt, Luca Carraro, Andrea Rinaldo, Isabelle Gounand, Enrico Bertuzzo, Reinhard Furrer, Department of Aquatic Ecology, Swiss Federal Insitute of Aquatic Science and Technology [Dübendorf] (EAWAG), University of Ca’ Foscari [Venice, Italy], 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), Universität Zürich [Zürich] = University of Zurich (UZH), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecole Polytechnique Fédérale de Lausanne (EPFL), Austrian Science Fund (FWF)31003A_173074PP00P3_179089, University of Zurich, Carraro, Luca, Altermatt, Florian, Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE)
Subjects: 0106 biological sciences, metacommunity, UFSP13-8 Global Change and Biodiversity, Process (engineering), Computer science, elevation, Distributed computing, diversity patterns, dendritic connectivity, Drainage basin, Metapopulation, biodiversity, dispersal, ecological modeling, landscape, optimal channel network, river networks, spanning trees, 010603 evolutionary biology, 01 natural sciences, 2309 Nature and Landscape Conservation, 10127 Institute of Evolutionary Biology and Environmental Studies, lcsh:QH540-549.5, r package, spatial-patterns, Original Research, metapopulation capacity, geography, Spanning tree, geography.geographical_feature_category, 010604 marine biology & hydrobiology, Aggregate (data warehouse), genetic diversity, dynamics, 15. Life on land, Settore ICAR/02 - Costruzioni Idrauliche e Marittime e Idrologia, 10123 Institute of Mathematics, 1105 Ecology, Evolution, Behavior and Systematics, 10231 Institute for Computational Science, [SDE]Environmental Sciences, Spatial ecology, 570 Life sciences, biology, 590 Animals (Zoology), Evolutionary ecology, lcsh:Ecology, 2303 Ecology
Abstract: Several key processes in freshwater ecology are governed by the connectivity inherent to dendritic river networks. These have extensively been analyzed from a geomorphological and hydrological viewpoint, yet structures classically used in ecological modeling have been poorly representative of the structure of real river basins, often failing to capture well‐known scaling features of natural rivers. Pioneering work identified optimal channel networks (OCNs) as spanning trees reproducing all scaling features characteristic of natural stream networks worldwide. While OCNs have been used to create landscapes for studies on metapopulations, biodiversity, and epidemiology, their generation has not been generally accessible.Given the increasing interest in dendritic riverine networks by ecologists and evolutionary biologists, we here present a method to generate OCNs and, to facilitate its application, we provide the R‐package OCNet. Owing to the stochastic process generating OCNs, multiple network replicas spanning the same surface can be built; this allows performing computational experiments whose results are irrespective of the particular shape of a single river network. The OCN construct also enables the generation of elevational gradients derived from the optimal network configuration, which can constitute three‐dimensional landscapes for spatial studies in both terrestrial and freshwater realms. Moreover, the package provides functions that aggregate OCNs into an arbitrary number of nodes, calculate several descriptors of river networks, and draw relevant network features.We describe the main functionalities of the package and its integration with other R‐packages commonly used in spatial ecology. Moreover, we exemplify the generation of OCNs and discuss an application to a metapopulation model for an invasive riverine species.In conclusion, OCNet provides a powerful tool to generate realistic river network analogues for various applications. It thereby allows the design of spatially realistic studies in increasingly impacted ecosystems and enhances our knowledge on spatial processes in freshwater ecology in general., Recently, research on spatial dynamics in ecology and evolution has bloomed. However, spatial structures used in theoretical and empirical ecological studies are often not representative of realistic landscapes. This is particularly true for river networks, which are of paramount interest to ecologists owing to their wide (but currently severely declining) biodiversity. Indeed, most of ecological work has been neglecting the scaling character of real river networks, despite well‐established knowledge in the fields of geomorphology and hydrology. Here, we present a method to create optimal channel networks (OCNs, i.e., river network analogues reproducing all topographic and scaling features of natural rivers), and the respective R‐package allowing their generation and analysis. We review the theoretical background underlying the OCN concept, present the main package functionalities, discuss possible applications in the realm of ecology and evolution, and detail how the package can be integrated with other popular R‐packages in spatial ecology.
Published: 2020
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32. Using proxies of microbial community‐weighted means traits to explain the cascading effect of management intensity, soil and plant traits on ecosystem resilience in mountain grasslands

Author: Sandra Lavorel, Jean-Christophe Clément, Cindy Arnoldi, Arnaud Foulquier, Gabin Piton, Nicolas Legay, Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Laboratoire de Recherche de l'Ecole Nationale Supérieure du Paysage (LAREP), Ecole Nationale Supérieure Polytechnique de Yaoundé (ENSPY), Université de Yaoundé I-Université de Yaoundé I, Cités, Territoires, Environnement et Sociétés (CITERES), Centre National de la Recherche Scientifique (CNRS)-Université de Tours (UT), Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Austrian Science Fund (FWF) Spanish Government Portuguese Foundation for Science and Technology Swedish Research Council Formas Netherlands Organization for Scientific Research (NWO) French National Research Agency (ANR), Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), Université de Tours-Centre National de la Recherche Scientifique (CNRS), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de la Recherche Agronomique (INRA), and Centre National de la Recherche Scientifique (CNRS)-Université de Tours
Subjects: 0106 biological sciences, media_common.quotation_subject, soil microbial community, Plant Science, drought, Biology, 010603 evolutionary biology, 01 natural sciences, resistance, nitrogen cycling, Ecosystem, Cascading effects, functional traits, Plant traits, Nitrogen cycle, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, media_common, 2. Zero hunger, mountain grassland, Ecology, Resistance (ecology), fungi, food and beverages, 04 agricultural and veterinary sciences, extracellular enzymes, 15. Life on land, stoichiometry, Microbial population biology, 13. Climate action, [SDE]Environmental Sciences, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Psychological resilience, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Weighted arithmetic mean
Abstract: International audience; Trait-based approaches provide a framework to understand the role of functional biodiversity on ecosystem functioning under global change. While plant traits have been reported as potential drivers of soil microbial community composition and resilience, studies directly assessing microbial traits are scarce, limiting our mechanistic understanding of ecosystem functioning. We used microbial biomass and enzyme stoichiometry, and mass-specific enzymes activity as proxies of microbial community-weighted mean (CWM) traits, to infer trade-offs in microbial strategies of resource use with cascading effects on ecosystem resilience. We simulated a drought event on intact plant-soil mesocosms extracted from mountain grasslands along a management intensity gradient. Ecosystem processes and properties related to nitrogen cycling were quantified before, during and after drought to characterize ecosystem resilience. Soil microbial CWM traits and ecosystem resilience to drought were strongly influenced by grassland type. Structural equation modelling revealed a cascading effect from management to ecosystem resilience through modifications in soil nutrients, and plant and microbial CWM traits. Overall, our results depict a shift from high investment in extracellular enzymes in nutrient-poor soils (oligotrophic strategy), to a copiotrophic strategy with low microbial biomass N:P and low investment in extracellular enzymes associated with exploitative plant traits in nutrient-rich soils. Microbial CWM traits responses to management intensity were highly related to ecosystem resilience. Microbial communities with a copiotrophic strategy had lower resistance but higher recovery to drought, while microbial communities with an oligotrophic strategy showed the opposite responses. The unexpected trade-off between plant and microbial resistance suggested that the lower resistance of copiotrophic microbial communities enabled plant resistance to drought. Synthesis. Grassland management has cascading effects on ecosystem resilience through its combined effects on soil nutrients and plant traits propagating to microbial traits and resilience. We suggest that intensification of permanent grassland management and associated increases in soil nutrient availability decreased plant-microbe competition for N under drought through the selection of drought-sensitive microbial communities with a copiotrophic strategy that promoted plant resistance. Including proxies of microbial CWM traits into the functional trait framework will strengthen our understanding of soil ecosystem functioning under global change.
Published: 2020
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33. Infection cushions of Fusarium graminearum are fungal arsenals for wheat infection

Author: Michael Mentges, Ana Lilia Martínez-Rocha, Jörg Bormann, Marc-Henri Lebrun, Anika Glasenapp, Marike Johanne Boenisch, Rasmus John Normand Frandsen, Bernard Henrissat, Ulrich Güldener, Sascha Malz, Wilhelm Schäfer, Martin Münsterkötter, University of Hamburg, Centre National de la Recherche Scientifique (CNRS), Architecture et fonction des macromolécules biologiques (AFMB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Tech Univ Munich, TUM Sch Life Sci Weihenstephan, Dept Bioinformat, Inst Bioinformat & Syst Biol, Sopron Univ, Funct Genom & Bioinformat, BIOlogie et GEstion des Risques en agriculture (BIOGER), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Austrian Science Fund (FWF) F3705/DFGME1682/6-1, German Research Foundation (DFG) BO4098/2-1, Universitat Hamburg, and Tech Univ Denmark, Dept Biotechnol & Biomed
Subjects: 0106 biological sciences, 0301 basic medicine, Fusarium, Hypha, Infection cushion, Soil Science, Virulence, effector proteins, Runner hyphae, Plant Science, Fungus, runner hyphae, 01 natural sciences, Microbiology, 03 medical and health sciences, Fusarium graminearium, RNA-Seq, wheat infection, Secondary metabolism, Molecular Biology, Mycelium, Triticum, Plant Diseases, Plant Proteins, 2. Zero hunger, Appressorium, biology, infection cushion, secondary metabolites, Gene Expression Profiling, Secondary metabolites, food and beverages, Original Articles, biology.organism_classification, Effector proteins, Wheat infection, Reverse genetics, Fusarium graminearum, 030104 developmental biology, [SDE]Environmental Sciences, Original Article, Agronomy and Crop Science, transcriptome, 010606 plant biology & botany
Abstract: Fusarium graminearum is one of the most destructive plant pathogens worldwide, causing fusarium head blight (FHB) on cereals. F. graminearum colonizes wheat plant surfaces with specialized unbranched hyphae called runner hyphae (RH), which develop multicelled complex appressoria called infection cushions (IC). IC generate multiple penetration sites, allowing the fungus to enter the plant cuticle. Complex infection structures are typical for several economically important plant pathogens, yet with unknown molecular basis. In this study, RH and IC formed on the surface of wheat paleae were isolated by laser capture microdissection. RNA‐Seq‐based transcriptomic analyses were performed on RH and IC and compared to mycelium grown in complete medium (MY). Both RH and IC displayed a high number of infection up‐regulated genes (982), encoding, among others, carbohydrate‐active enzymes (CAZymes: 140), putative effectors (PE: 88), or secondary metabolism gene clusters (SMC: 12 of 67 clusters). RH specifically up‐regulated one SMC corresponding to aurofusarin biosynthesis, a broad activity antibiotic. IC specifically up‐regulated 248 genes encoding mostly putative virulence factors such as 7 SMC, including the mycotoxin deoxynivalenol and the newly identified fusaoctaxin A, 33 PE, and 42 CAZymes. Furthermore, we studied selected candidate virulence factors using cellular biology and reverse genetics. Hence, our results demonstrate that IC accumulate an arsenal of proven and putative virulence factors to facilitate the invasion of epidermal cells., Transcriptome analyses on epiphytic runner hyphae (RH) and penetrating infection cushions (IC) of Fusarium graminearum grown on wheat palea compared to in culture‐grown mycelium (MY) reveal that IC are fungal arsenals for infection.
Published: 2020
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34. A fully human anti-BMP6 antibody reduces the need for erythropoietin in rodent models of the anemia of chronic disease

Author: Chiara Volani, Dominik Wolf, Verena Petzer, Stephanie Arndt, Sieghart Sopper, Markus Seifert, Sylvia Berger, Richard Hilbe, Christa Pfeifhofer-Obermair, Natascha Brigo, Alexander Hoffmann, Felix Böhm, Anja K. Bosserhoff, Jonathan Papworth, Lara Valente de Souza, Léon Kautz, Laura von Raffay, Volker Germaschewski, Matthew Wake, Igor Theurl, Luke Bayliss, Cecilia Deantonio, Malte Asshoff, Manfred Nairz, Egon Demetz, Piotr Tymoszuk, Prunelle Perrier, Philipp Grubwieser, Joana Carvalho, Stefanie Dichtl, Guenter Weiss, Department of Internal Medicine, Innsbruck Medical University, Innsbruck, Austria., Med Univ Innsbruck, Dept Internal Med 5, Hematol & Oncol, Innsbruck, Austria, Kymab Ltd, Cambridge, England, Med Univ Innsbruck, Christian Doppler Lab Iron Metab & Anemia Res, Innsbruck, Austria, Univ Med Ctr Regensburg, Dept Dermatol, Regensburg, Germany, Friedrich Alexander Univ Erlangen Nurnberg, Inst Biochem, Emil Fischer Ctr, Erlangen, Germany, Institut de Recherche en Santé Digestive (IRSD ), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Univ Clin Bonn, Internal Med 3, Oncol Oncol Immunooncol & Rheumatol, Bonn, Germany, doctoral college project (W1253 HOROS), Austrian Research Funds (FWF) Project (P 28302), Verein zur Forderung von Forschung und Weiterbildung in Infektiologie und Immunologie, Innsbruck, Christian Doppler Society, Austria, Krebshilfe Tirol project (15024), and Austrian Society of Hematology and Medical Oncology (OeGHO)
Subjects: Darbepoetin alfa, Bone Morphogenetic Protein 6, Ferroportin, Muscle Proteins, Pharmacology, Biochemistry, Mice, Random Allocation, 0302 clinical medicine, Bone Marrow, hemic and lymphatic diseases, Cation Transport Proteins, Erythroid Precursor Cells, 0303 health sciences, biology, Polysaccharides, Bacterial, Antibodies, Monoclonal, [SDV.MHEP.HEM]Life Sciences [q-bio]/Human health and pathology/Hematology, Anemia, Drug Synergism, Hematology, Hep G2 Cells, Recombinant Proteins, 3. Good health, 030220 oncology & carcinogenesis, Erythropoiesis, Cytokines, medicine.drug, Anemia of chronic disease, Iron, Immunology, 03 medical and health sciences, Red Cells, Iron, and Erythropoiesis, Hepcidin, medicine, Animals, Humans, Renal Insufficiency, Chronic, Erythropoietin, 030304 developmental biology, Dose-Response Relationship, Drug, business.industry, Arthritis, Cell Biology, medicine.disease, biology.protein, business
Abstract: Recombinant erythropoietin (EPO) and iron substitution are a standard of care for treatment of anemias associated with chronic inflammation, including anemia of chronic kidney disease. A black box warning for EPO therapy and concerns about negative side effects related to high-dose iron supplementation as well as the significant proportion of patients becoming EPO resistant over time explains the medical need to define novel strategies to ameliorate anemia of chronic disease (ACD). As hepcidin is central to the iron-restrictive phenotype in ACD, therapeutic approaches targeting hepcidin were recently developed. We herein report the therapeutic effects of a fully human anti-BMP6 antibody (KY1070) either as monotherapy or in combination with Darbepoetin alfa on iron metabolism and anemia resolution in 2 different, well-established, and clinically relevant rodent models of ACD. In addition to counteracting hepcidin-driven iron limitation for erythropoiesis, we found that the combination of KY1070 and recombinant human EPO improved the erythroid response compared with either monotherapy in a qualitative and quantitative manner. Consequently, the combination of KY1070 and Darbepoetin alfa resulted in an EPO-sparing effect. Moreover, we found that suppression of hepcidin via KY1070 modulates ferroportin expression on erythroid precursor cells, thereby lowering potentially toxic-free intracellular iron levels and by accelerating erythroid output as reflected by increased maturation of erythrocyte progenitors. In summary, we conclude that treatment of ACD, as a highly complex disease, becomes more effective by a multifactorial therapeutic approach upon mobilization of endogenous iron deposits and stimulation of erythropoiesis.
Published: 2019
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35. Cold acclimation triggers lipidomic and metabolic adjustments in the spotted wing drosophila Drosophila suzukii (Matsumara)

Author: Hervé Colinet, Thomas Enriquez, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), 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), This work has been funded by the SUZUKILL project (The French National Research Agency: ANR-15-CE21-0017 and the Austrian Science Fund, FWF:I 2604-B25)., ANR-15-CE21-0017,Suzukill,Gestion de la tolérance au froid et de la qualité des mouches, Drosophila suzukii, produites en masse pour faciliter la mise en place d'un contrôle biologique par les méthodes de lâchers d'insectes stériles et incompatibles(2015), 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, 0301 basic medicine, Wing, biology, Physiology, Cold tolerance, Cold exposure, homeoviscous adaptation, Homeoviscous adaptation, cold tolerance, 15. Life on land, biology.organism_classification, 01 natural sciences, Cell biology, lipids, 010602 entomology, 03 medical and health sciences, 030104 developmental biology, Physiology (medical), Cold acclimation, metabolic profiles, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Drosophila suzukii, Drosophila, thermal plasticity
Abstract: International audience; Chronic cold exposure is detrimental to chill susceptible insects that may accumulate chill injuries. To cope with deleterious effects of cold temperature, insects employ a variety of physiological strategies and metabolic adjustments, such as production of cryoprotectants, or remodeling of cellular membranes. Cold tolerance is a key element determining the fundamental niche of species. Because Drosophila suzukii is an invasive fruit pest, originating from East Asia, knowledge about its thermal biology is urgently needed. Physiological mechanisms underlying cold tolerance plasticity remain poorly understood in this species. Here, we explored metabolic and lipidomic modifications associated with the acquisition of cold tolerance in D. suzukii using Omics technologies (LC- and GC-MS/MS). In both cold-acclimated males and females, we observed physiological changes consistent with homeoviscous/homeophasic adaptation of membranes: reshuffling of phospholipid headgroups and increasing unsaturation rate of fatty acids. Modification of fatty acids unsaturation were also observed in triacylglycerides, whichwould likely increase accessibility of lipid reserves. At the metabolic level, we observed clear-cut differentiation of metabolic profiles withcold-acclimated metabotypes showing accumulation of several potential cryoprotectants (sugars and amino acids). Metabolic pathwayanalyses indicated a remodeling of various processes, including purine metabolism and aminoacyl tRNA biosynthesis. These data provide alarge-scale characterization of lipid rearrangements and metabolic pathway modifications in D. suzukii in response to cold acclimationand contribute to characterizing the strategies used by this species to modulate cold tolerance.
Published: 2019
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36. Cold acclimation triggers major transcriptional changes in Drosophila suzukii

Author: Thomas Enriquez, Hervé Colinet, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), 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), ANR-15-CE21-0017, Agence Nationale de la Recherche, FWF I 2604-B25, Austrian Science Fund, ANR-15-CE21-0017,Suzukill,Gestion de la tolérance au froid et de la qualité des mouches, Drosophila suzukii, produites en masse pour faciliter la mise en place d'un contrôle biologique par les méthodes de lâchers d'insectes stériles et incompatibles(2015), 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), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Unité d'Ecologie et de Biogéographie (UEB), Université Catholique de Louvain = Catholic University of Louvain (UCL), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-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), Université de Rennes (UNIV-RENNES)-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), and Briand, Valerie
Subjects: 0106 biological sciences, Thermotolerance, Thermal plasticity, lcsh:QH426-470, Acclimatization, lcsh:Biotechnology, Carbohydrate metabolism, Biology, Cold tolerance, 01 natural sciences, Transcriptome, 03 medical and health sciences, lcsh:TP248.13-248.65, Gene expression, Genetics, Cold acclimation, Animals, Drosophila Proteins, Homeostasis, Genes expression, Drosophila suzukii, Transcriptomics, Gene, Drosophila, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Gene Expression Profiling, fungi, Spotted wing drosophila, biology.organism_classification, Cell biology, Cold Temperature, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, lcsh:Genetics, Gene Expression Regulation, [SDV.IB]Life Sciences [q-bio]/Bioengineering, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 010606 plant biology & botany, Biotechnology, Research Article
Abstract: Background Insects have the capacity to adjust their physiological mechanisms during their lifetime to promote cold tolerance and cope with sublethal thermal conditions, a phenomenon referred to as thermal acclimation. The spotted wing drosophila, Drosophila suzukii, is an invasive fruit pest that, like many other species, enhances its thermotolerance in response to thermal acclimation. However, little is known about the underlying mechanisms of this plastic response. Here, we promoted flies’ cold tolerance by gradually increasing acclimation duration (i.e. pre-exposure from 2 h to 9 days at 10 °C), and then compared transcriptomic responses of cold hardy versus cold susceptible phenotypes using RNA sequencing. Results Cold tolerance of D. suzukii increased with acclimation duration; the longer the acclimation, the higher the cold tolerance. Cold-tolerant flies that were acclimated for 9 days were selected for transcriptomic analyses. RNA sequencing revealed a total of 2908 differentially expressed genes: 1583 were up- and 1325 were downregulated in cold acclimated flies. Functional annotation revealed many enriched GO-terms among which ionic transport across membranes and signaling were highly represented in acclimated flies. Neuronal activity and carbohydrate metabolism were also enriched GO-terms in acclimated flies. Results also revealed many GO-terms related to oogenesis which were underrepresented in acclimated flies. Conclusions Involvement of a large cluster of genes related to ion transport in cold acclimated flies suggests adjustments in the capacity to maintain ion and water homeostasis. These processes are key mechanisms underlying cold tolerance in insects. Down regulation of genes related to oogenesis in cold acclimated females likely reflects that females were conditioned at 10 °C, a temperature that prevents oogenesis. Overall, these results help to understand the molecular underpinnings of cold tolerance acquisition in D. suzukii. These data are of importance considering that the invasive success of D. suzukii in diverse climatic regions relates to its high thermal plasticity. Electronic supplementary material The online version of this article (10.1186/s12864-019-5745-7) contains supplementary material, which is available to authorized users.
Published: 2019
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37. Detecting the macroevolutionary signal of species interactions

Author: Marjorie G. Weber, Scott L. Nuismer, Carlos J. Melián, Daniele Silvestro, Cecilia S. Andreazzi, Ole Seehausen, Blake Matthews, Emma E. Goldberg, Florence Débarre, Seth M. Rudman, Ayana B. Martins, Jonathan P. Drury, Luke J. Harmon, Anita Narwani, Matthew W. Pennell, Swiss Federal Insitute of Aquatic Science and Technology [Dübendorf] (EAWAG), University of Idaho [Moscow, USA], Fundação Oswaldo Cruz (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP), Institut d'écologie et des sciences de l'environnement de Paris (iEES), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA), Durham University, University of Minnesota [Twin Cities] (UMN), University of Minnesota System, Universidade Estadual de Campinas (UNICAMP), University of British Columbia (UBC), University of Pennsylvania [Philadelphia], University of Bern, University of Gothenburg (GU), Michigan State University System, National Science Foundation (NSF)NSF - Directorate for Biological Sciences (BIO)12089121450653, Swedish Research Council2015-04748, Knut & Alice Wallenberg Foundation, Austrian Science Fund (FWF)31003A_15346431003A_163338Z32Z0_166422, ANR-14-ACHN-0003,MOLA,Modélisation mathématique de l'adaptation locale.(2014), Institut d'écologie et des sciences de l'environnement de Paris (IEES (UMR_7618 / UMR_D_242 / UMR_A_1392 / UM_113) ), Institut National de la Recherche Agronomique (INRA)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Department of Fish Ecology and Evolution, Center of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Institute of Zoology, University of Bern, Université de Bern, Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), and Universidade Estadual de Campinas = University of Campinas (UNICAMP)
Subjects: 0106 biological sciences, 0301 basic medicine, Competitive Behavior, trait evolution, Genetic Speciation, [SDV]Life Sciences [q-bio], Diversification (marketing strategy), Macroevolution, Biology, phylogeny, Models, Biological, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Adaptive radiation, Genetic algorithm, Animals, Ecosystem, Ecology, Evolution, Behavior and Systematics, Coevolution, ComputingMilieux_MISCELLANEOUS, macroevolution, species interactions, Extinction, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], extinction, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], 15. Life on land, Complex dynamics, 030104 developmental biology, speciation, Evolutionary biology, coevolution, network, Trait, 570 Life sciences, biology, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; Species interactions lie at the heart of many theories of macroevolution, from adaptive radiation to the Red Queen. Although some theories describe the imprint that interactions will have over long timescales, we are still missing a comprehensive understanding of the effects of interactions on macroevolution. Current research shows strong evidence for the impact of interactions on macroevolutionary patterns of trait evolution and diversification, yet many macroevolutionary studies have only a tenuous relationship to ecological studies of interactions over shorter timescales. We review current research in this area, highlighting approaches that explicitly model species interactions and connect them to broad-scale macroevolutionary patterns. We also suggest that progress has been made by taking an integrative interdisciplinary look at individual clades. We focus on African cichlids as a case study of how this approach can be fruitful. Overall, although the evidence for species interactions shaping macroevolution is strong, further work using integrative and model-based approaches is needed to spur progress towards understanding the complex dynamics that structure communities over time and space.
Published: 2019
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38. Intermicrobial interaction: Aspergillus fumigatus siderophores protect against competition by Pseudomonas aeruginosa

Author: Shajia R Ansari, Eric Déziel, David A. Stevens, Hubertus Haas, Anna-Maria Dietl, Gabriele Sass, California Institute for Medical Research (CIMR), Innsbruck Medical University [Austria] (IMU), Institut Armand Frappier (INRS-IAF), Institut National de la Recherche Scientifique [Québec] (INRS)-Réseau International des Instituts Pasteur (RIIP), Stanford School of Medicine [Stanford], Stanford Medicine, Stanford University-Stanford University, This research was funded by John Flatley (CIMR no. 3770) to D.A.S., Child Health Research Institute, Stanford Transdisciplinary Initiatives Program (CIMR no. 3777) to D.A.S., Austrian Science Fund/Infect-ERA program (FWF grant I1616/Infect-ERA project AspMetNet) to H.H., and HOROS program (W1253) to A.-M.D., and The authors thank Marife Martinez for excellent technical support. The A. fumigatus mutant strain AfΔsidA was kindly provided by M. M. Moore, Department of Biological Sciences, Simon Fraser University, Burnaby, Canada.
Subjects: 0301 basic medicine, Siderophore, Siderophores, Pathology and Laboratory Medicine, medicine.disease_cause, Aspergillus fumigatus, chemistry.chemical_compound, Drug Metabolism, Microbial Physiology, Medicine and Health Sciences, skin and connective tissue diseases, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Fungal Pathogens, Multidisciplinary, Pyoverdine, biology, Chemistry, Microbial Growth and Development, Eukaryota, Pseudomonas Aeruginosa, Bacterial Pathogens, Aspergillus, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Fungal Molds, Medical Microbiology, Celastrol, Engineering and Technology, Medicine, Pathogens, Oligopeptides, Research Article, Heat Treatment, Science, 030106 microbiology, Mycology, Fungus, Microbiology, 03 medical and health sciences, Pseudomonas, Antibiosis, medicine, Pharmacokinetics, Microbial Pathogens, Pharmacology, Bacteria, Pseudomonas aeruginosa, Bacterial Growth, Organisms, Fungi, Wild type, Biofilm, Biology and Life Sciences, Bacteriology, biology.organism_classification, bacterial infections and mycoses, 030104 developmental biology, Manufacturing Processes, Biofilms, Bacterial Biofilms, Developmental Biology
Abstract: International audience; Pseudomonas aeruginosa and Aspergillus fumigatus are pathogens frequently co-inhabiting immunocompromised patient airways, particularly in people with cystic fibrosis. Both microbes depend on the availability of iron, and compete for iron in their microenvironment. We showed previously that the P. aeruginosa siderophore pyoverdine is the main instrument in battling A. fumigatus biofilms, by iron chelation and denial of iron to the fungus. Here we show that A. fumigatus siderophores defend against anti-fungal P. aeruginosa effects. P. aeruginosa supernatants produced in the presence of wildtype A. fumigatus planktonic supernatants (Afsup) showed less activity against A. fumigatus biofilms than P. aeruginosa supernatants without Afsup, despite higher production of pyoverdine by P. aeruginosa. Supernatants of A. fumigatus cultures lacking the sidA gene (AfΔsidA), unable to produce hydroxamate siderophores, were less capable of protecting A. fumigatus biofilms from P. aeruginosa supernatants and pyoverdine. AfΔsidA biofilm was more sensitive towards inhibitory effects of pyoverdine, the iron chelator deferiprone (DFP), or amphothericin B than wildtype A. fumigatus biofilm. Supplementation of sidA-deficient A. fumigatus biofilm with A. fumigatus siderophores restored resistance to pyoverdine. The A. fumigatus siderophore production inhibitor celastrol sensitized wildtype A. fumigatus biofilms towards the anti-fungal activity of DFP. In conclusion, A. fumigatus hydroxamate siderophores play a pivotal role in A. fumigatus competition for iron against P. aeruginosa.
Published: 2019
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39. Cre mRNA Is Not Transferred by EVs from Endothelial and Adipose-Derived Stromal/Stem Cells during Vascular Network Formation

Author: Madhusudhan Reddy Bobbili, Wolfgang Holnthoner, Heinz Redl, Severin Mühleder, Johannes Oesterreicher, Jaana Schneider, Johannes Grillari, Andreas Spittler, Marianne Pultar, Eleni Priglinger, Austrian Research Promotion Agency, and FWF Austrian Science Fund
Subjects: 0301 basic medicine, Cell type, Cell signaling, Stromal cell, Adipose tissue, Cre recombinase, Cell Communication, Biology, Article, Catalysis, lcsh:Chemistry, Inorganic Chemistry, Extracellular Vesicles, 03 medical and health sciences, microRNA, Humans, RNA, Messenger, Physical and Theoretical Chemistry, lcsh:QH301-705.5, Molecular Biology, Spectroscopy, Cre-loxP system, Integrases, 030102 biochemistry & molecular biology, Organic Chemistry, Mesenchymal stem cell, Endothelial Cells, Mesenchymal Stem Cells, General Medicine, Coculture Techniques, endothelial cells, cell–cell communication, Computer Science Applications, Cell biology, MicroRNAs, 030104 developmental biology, lcsh:Biology (General), lcsh:QD1-999, Blood Vessels, Stem cell, extracellular vesicles, coculture
Abstract: Coculture systems employing adipose tissue-derived mesenchymal stromal/stem cells (ASC) and endothelial cells (EC) represent a widely used technique to model vascularization. Within this system, cell-cell communication is crucial for the achievement of functional vascular network formation. Extracellular vesicles (EVs) have recently emerged as key players in cell communication by transferring bioactive molecules between cells. In this study we aimed to address the role of EVs in ASC/EC cocultures by discriminating between cells, which have received functional EV cargo from cells that have not. Therefore, we employed the Cre-loxP system, which is based on donor cells expressing the Cre recombinase, whose mRNA was previously shown to be packaged into EVs and reporter cells containing a construct of floxed dsRed upstream of the eGFP coding sequence. The evaluation of Cre induced color switch in the reporter system via EVs indicated that there is no EV-mediated RNA transmission either between EC themselves or EC and ASC. However, since Cre mRNA was not found present in EVs, it remains unclear if Cre mRNA is generally not packaged into EVs or if EVs are not taken up by the utilized cell types. Our data indicate that this technique may not be applicable to evaluate EV-mediated cell-to-cell communication in an in vitro setting using EC and ASC. Further investigations will require a functional system showing efficient and specific loading of Cre mRNA or protein into EVs. This research was partially funded by the Austrian Research promotion agency. Severin Mühleder was funded by the Austrian Science Fund (FWF). Sí
Published: 2021
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40. KymoRod: a method for automated kinematic analysis of rod-shaped plant organs

Author: Herman Höfte, Renaud Bastien, Marjolaine Martin, David Legland, Alexis Peaucelle, Bruno Moulia, Stéphane Douady, Lucien Fregosi, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), Institut National de la Recherche Agronomique (INRA), Matière et Systèmes Complexes (MSC (UMR_7057)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier (PIAF), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), ANR/FWF grant 'Pectosign', Laboratoire d'Excellence 'Saclay Plant Science', European Project: 267196,EC:FP7:PEOPLE,FP7-PEOPLE-2010-COFUND,AGREENSKILLS(2012), and Matière et Systèmes Complexes (MSC)
Subjects: hypocotyle, 0106 biological sciences, 0301 basic medicine, Scale (ratio), Arabidopsis, Context (language use), Plant Science, Kinematics, analyse d'image, Curvature, Plant Roots, 01 natural sciences, mechano-sensing, 03 medical and health sciences, image analysis, Botany, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Arabidopsis thaliana, Growth rate, hypocotyl, Plant system, cellulose synthesis inhibitor, biology, Arabidopsis Proteins, arabidopsis thaliana, Cell Biology, root, biology.organism_classification, elongation growth, cellulose, cinématique, racine, 030104 developmental biology, kinematics, Biological system, mechanoreceptor, mécanorécepteur, technical advance, 010606 plant biology & botany
Abstract: A major challenge in plant systems biology is the development of robust, predictive multiscale models for organ growth. In this context it is important to bridge the gap between the, rather well-documented molecular scale and the organ scale by providing quantitative methods to study within-organ growth patterns. Here, we describe a simple method for the analysis of the evolution of growth patterns within rod-shaped organs that does not require adding markers at the organ surface. The method allows for the simultaneous analysis of root and hypocotyl growth, provides spatio-temporal information on curvature, growth anisotropy and relative elemental growth rate and can cope with complex organ movements. We demonstrate the performance of the method by documenting previously unsuspected complex growth patterns within the growing hypocotyl of the model species Arabidopsis thaliana during normal growth, after treatment with a growth-inhibiting drug or in a mechano-sensing mutant. The method is freely available as an intuitive and user-friendly Matlab application called KymoRod.
Published: 2016
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41. Spermine and Spermidine Priming against Botrytis cinerea Modulates ROS Dynamics and Metabolism in Arabidopsis

Author: Anis M. Limami, Wim Van den Ende, Henry Christopher Janse van Rensburg, KU Leuven (Laboratory of Molecular Plant Biology), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Agency project Fonds voor Wetenschappelijk Onderzoek (FWO) Vlaanderen (grant number G0F1517N)—Fonds zur Förderung der wissenschaftlichen Forschung (FWF) Austria (grant number I 3231-B25).
Subjects: 0106 biological sciences, 0301 basic medicine, Sucrose, Antifungal Agents, spermine, lcsh:QR1-502, Arabidopsis, Spermine, Nitrate Reductase, 01 natural sciences, Biochemistry, lcsh:Microbiology, chemistry.chemical_compound, Ascorbate Peroxidases, Plant Growth Regulators, Gene Expression Regulation, Plant, Plant Immunity, gamma-Aminobutyric Acid, Disease Resistance, Botrytis cinerea, reactive oxygen species, biology, Chemistry, Catalase, Botrytis, Asparagine, Life Sciences & Biomedicine, Peroxidase, Biochemistry & Molecular Biology, Phenylalanine, polyamines, Fructose, B. cinerea, Nitrate reductase, Article, 03 medical and health sciences, spermidine, mental disorders, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, priming, Molecular Biology, Plant Diseases, amino acids, Science & Technology, fungi, Hydrogen Peroxide, biology.organism_classification, Plant Leaves, Spermidine, Glucose, 030104 developmental biology, sugars, biology.protein, 010606 plant biology & botany
Abstract: Polyamines (PAs) are ubiquitous small aliphatic polycations important for growth, development, and environmental stress responses in plants. Here, we demonstrate that exogenous application of spermine (Spm) and spermidine (Spd) induced cell death at high concentrations, but primed resistance against the necrotrophic fungus Botrytis cinerea in Arabidopsis. At low concentrations, Spm was more effective than Spd. Treatments with higher exogenous Spd and Spm concentrations resulted in a biphasic endogenous PA accumulation. Exogenous Spm induced the accumulation of H2O2 after treatment but also after infection with B. cinerea. Both Spm and Spd induced the activities of catalase, ascorbate peroxidase, and guaiacol peroxidase after treatment but also after infection with B. cinerea. The soluble sugars glucose, fructose, and sucrose accumulated after treatment with high concentrations of PAs, whereas only Spm induced sugar accumulation after infection. Total and active nitrate reductase (NR) activities were inhibited by Spm treatment, whereas Spd inhibited active NR at low concentrations but promoted active NR at high concentrations. Finally, γaminobutyric acid accumulated after treatment and infection in plants treated with high concentrations of Spm. Phenylalanine and asparagine also accumulated after infection in plants treated with a high concentration of Spm. Our data illustrate that Spm and Spd are effective in priming resistance against B. cinerea, opening the door for the development of sustainable alternatives for chemical pesticides. ispartof: BIOMOLECULES vol:11 issue:2 ispartof: location:Switzerland status: published
Published: 2021
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42. Characterization of a DCL2-Insensitive Tomato Bushy Stunt Virus Isolate Infecting Arabidopsis thaliana

Author: Mathieu Erhardt, Christophe Ritzenthaler, Hélène Scheer, Denise Altenbach, Marco Incarbone, Lauriane Kuhn, Patrice Dunoyer, Jean-Michel Hily, Institut de biologie moléculaire des plantes (IBMP), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), and Centre National de la Recherche Scientifique (CNRS)European CommissionEuropean Regional Development Fund (ERDF) in the framework of the INTERREG V Upper Rhine programs VITIFUTUR projectsAustrian Science Fund (FWF)M 2921-B
Subjects: 0106 biological sciences, 0301 basic medicine, Small RNA, Tombusvirus, Arabidopsis, lcsh:QR1-502, 01 natural sciences, lcsh:Microbiology, 03 medical and health sciences, Pathosystem, Tomato bushy stunt virus, Virology, Plant virus, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Arabidopsis thaliana, ComputingMilieux_MISCELLANEOUS, Genetics, biology, fungi, food and beverages, biology.organism_classification, 3. Good health, Tombusviridae, 030104 developmental biology, Infectious Diseases, 010606 plant biology & botany
Abstract: Tomato bushy stunt virus (TBSV), the type member of the genus Tombusvirus in the family Tombusviridae is one of the best studied plant viruses. The TBSV natural and experimental host range covers a wide spectrum of plants including agricultural crops, ornamentals, vegetables and Nicotiana benthamiana. However, Arabidopsis thaliana, the well-established model organism in plant biology, genetics and plant&ndash, microbe interactions is absent from the list of known TBSV host plant species. Most of our recent knowledge of the virus life cycle has emanated from studies in Saccharomyces cerevisiae, a surrogate host for TBSV that lacks crucial plant antiviral mechanisms such as RNA interference (RNAi). Here, we identified and characterized a TBSV isolate able to infect Arabidopsis with high efficiency. We demonstrated by confocal and 3D electron microscopy that in Arabidopsis TBSV-BS3Ng replicates in association with clustered peroxisomes in which numerous spherules are induced. A dsRNA-centered immunoprecipitation analysis allowed the identification of TBSV-associated host components including DRB2 and DRB4, which perfectly localized to replication sites, and NFD2 that accumulated in larger viral factories in which peroxisomes cluster. By challenging knock-out mutants for key RNAi factors, we showed that TBSV-BS3Ng undergoes a non-canonical RNAi defensive reaction. In fact, unlike other RNA viruses described, no 22nt TBSV-derived small RNA are detected in the absence of DCL4, indicating that this virus is DCL2-insensitive. The new Arabidopsis-TBSV-BS3Ng pathosystem should provide a valuable new model for dissecting plant&ndash, virus interactions in complement to Saccharomyces cerevisiae.
Published: 2020
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43. Optimal Decoding of Cellular Identities in a Genetic Network

Author: Eric Wieschaus, William Bialek, Thomas Gregor, Mariela D. Petkova, Gašper Tkačik, Harvard University, Department of Physics, Princeton University (DPPU), Princeton University, Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria), Physique des fonctions biologiques / Physics of Biological Functions, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), This work was supported, in part, by U.S. NIH grants (P50GM071508, R01GM077599, and R01GM097275), U.S. NSF grants (PHY-1607612, CCF-0939370, Center for the Science of Information, PHY–1734030, Center for the Physics of Biological Function), an Austrian Science Fund grant (FWF P28844 to G.T.), and an Howard Hughes Medical Institute International Student Research Fellowship (to M.D.P.)., Harvard University [Cambridge], Institute of Science and Technology [Austria] (IST Austria), and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: Embryo, Nonmammalian, MESH: GTPase-Activating Proteins, 0302 clinical medicine, MESH: Gene Expression Regulation, Developmental, Drosophila Proteins, MESH: Embryonic Development, Gene Regulatory Networks, MESH: Animals, MESH: Models, Genetic, [SDV.BDD]Life Sciences [q-bio]/Development Biology, MESH: Gene Regulatory Networks, 0303 health sciences, cell fate, GTPase-Activating Proteins, Gene Expression Regulation, Developmental, Cell Differentiation, MESH: Transcription Factors, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Drosophila melanogaster, Drosophila, developmental precision, Algorithm, Decoding methods, MESH: Body Patterning, MESH: Cell Differentiation, MESH: Drosophila Proteins, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Genetic network, Embryonic Development, Cell fate determination, Biology, General Biochemistry, Genetics and Molecular Biology, Article, MESH: Drosophila melanogaster, 03 medical and health sciences, Position (vector), genetic networks, Animals, Enhancer, Gap gene, 030304 developmental biology, Body Patterning, Models, Genetic, embryonic patterning, fungi, MESH: Embryo, Nonmammalian, cell specification, Expression (mathematics), optimality, quantitative imaging, 030217 neurology & neurosurgery, Free parameter, Transcription Factors
Abstract: In developing organisms, spatially prescribed cell identities are thought to be determined by the expression levels of multiple genes. Quantitative tests of this idea, however, require a theoretical framework capable of exposing the rules and precision of cell specification over developmental time. Using the gap gene network in the early fly embryo as an example, we use such a framework to show how expression levels of the four gap genes can be jointly decoded into an optimal specification of position with 1% accuracy. The decoder correctly predicts, with no free parameters, the dynamics of pair-rule expression patterns at different developmental time points and in various mutant backgrounds. Precise cellular identities are thus available at the earliest stages of development, contrasting the prevailing view of positional information being slowly refined across successive layers of the patterning network. Our results suggest that developmental enhancers closely approximate a mathematically optimal decoding strategy.
Published: 2019
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44. Evolution and comparative genomics of the most common Trichoderma species

Author: Sabrina Sarrocco, Eva M. Kubicek, Andrei Stecca Steindorff, Igor V. Grigoriev, Bernard Henrissat, Qirong Shen, Alan Kuo, Alexey G. Kopchinskiy, Feng Cai, Giovanni Vannacci, Eliane Ferreira Noronha, Gelsomina Manganiello, Christian P. Kubicek, Jian Zhang, Komal Chenthamara, Irina S. Druzhinina, Riccardo Baroncelli, Vienna University of Technology, United States Department of Energy, Universidade de Brasília (UnB), Seconda Università degli Studi di Napoli = Second University of Naples, Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Department of Biological Sciences, King Abdulaziz University, Nanjing Agricultural University (NAU), Universidad de Salamanca, Department of Agriculture, Food and Environment, University of California [Berkeley] (UC Berkeley), University of California (UC), 2017YFD 0200806, Austrian Science Foundation (FWF) 25613-B20 I-1249, CAPES foundation 99999.001745/2014-00, CNPq 482697/2011-3, 141180/2012-9, Office of Science of the U.S. Department of Energy DE-AC02-05CH11231, Seconda Università degli studi di Napoli, Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Nanjing Agricultural University, University of California [Berkeley], University of California, Kubicek, C. P., Steindorff, A. S., Chenthamara, K., Manganiello, G., Henrissat, B., Zhang, J., Cai, F., Kopchinskiy, A. G., Kubicek, E. M., Kuo, A., Baroncelli, R., Sarrocco, S., Noronha, E. F., Vannacci, G., Shen, Q., Grigoriev, I. V., Druzhinina, I. S., Kubicek C.P., Steindorff A.S., Chenthamara K., Manganiello G., Henrissat B., Zhang J., Cai F., Kopchinskiy A.G., Kubicek E.M., Kuo A., Baroncelli R., Sarrocco S., Noronha E.F., Vannacci G., Shen Q., Grigoriev I.V., and Druzhinina I.S.
Subjects: hypocréales, 0106 biological sciences, enzyme cellulolytique, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Gene loss, Medical and Health Sciences, 01 natural sciences, Genome, Orphan, Biopolymers, Clade, Gene gain, Environmental opportunism, 2. Zero hunger, Trichoderma, 0303 health sciences, biology, Ascomycota, Orphans, Hydrolysis, Reproduction, Gene lo, food and beverages, Genomics, Biological Sciences, Ankyrin domains, CAZymes, Core genome, SSCPs, Fungal, CAZyme, Biotechnology, Research Article, Genome evolution, lcsh:QH426-470, Evolution, Bioinformatics, lcsh:Biotechnology, Hypocreales, Genes, Fungal, Biotechnologies, Evolution, Molecular, Fungal Proteins, 03 medical and health sciences, lcsh:TP248.13-248.65, Information and Computing Sciences, Genetics, analyse génomique, Gene, 030304 developmental biology, Comparative genomics, Human Genome, Molecular, diversité fongique, biology.organism_classification, Carbon, lcsh:Genetics, Genes, Evolutionary biology, Ankyrin domain, Extracellular Space, 010606 plant biology & botany
Abstract: Background The growing importance of the ubiquitous fungal genus Trichoderma (Hypocreales, Ascomycota) requires understanding of its biology and evolution. Many Trichoderma species are used as biofertilizers and biofungicides and T. reesei is the model organism for industrial production of cellulolytic enzymes. In addition, some highly opportunistic species devastate mushroom farms and can become pathogens of humans. A comparative analysis of the first three whole genomes revealed mycoparasitism as the innate feature of Trichoderma. However, the evolution of these traits is not yet understood. Results We selected 12 most commonly occurring Trichoderma species and studied the evolution of their genome sequences. Trichoderma evolved in the time of the Cretaceous-Palaeogene extinction event 66 (±15) mya, but the formation of extant sections (Longibrachiatum, Trichoderma) or clades (Harzianum/Virens) happened in Oligocene. The evolution of the Harzianum clade and section Trichoderma was accompanied by significant gene gain, but the ancestor of section Longibrachiatum experienced rapid gene loss. The highest number of genes gained encoded ankyrins, HET domain proteins and transcription factors. We also identified the Trichoderma core genome, completely curated its annotation, investigated several gene families in detail and compared the results to those of other fungi. Eighty percent of those genes for which a function could be predicted were also found in other fungi, but only 67% of those without a predictable function. Conclusions Our study presents a time scaled pattern of genome evolution in 12 Trichoderma species from three phylogenetically distant clades/sections and a comprehensive analysis of their genes. The data offer insights in the evolution of a mycoparasite towards a generalist. Electronic supplementary material The online version of this article (10.1186/s12864-019-5680-7) contains supplementary material, which is available to authorized users.
Published: 2019
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45. MicroRNAs facilitate skeletal muscle maintenance and metabolic suppression in hibernating brown bears

Author: Kenneth B. Storey, Blandine Chazarin, Sylvain Giroud, Guillemette Gauquelin-Koch, Bryan E. Luu, Jon M. Arnemo, Fabrice Bertile, Etienne Lefai, Jon E. Swenson, Alina L. Evans, Biology, SAMS, MCGill University, Unité de Nutrition Humaine - Clermont Auvergne (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Department of Integrative Biology and Evolution, Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Norwegian University of Life Sciences, Faculty of Environmental Sciences and Natural Resource Management (NMBU), Norvegian Institute for Nature Research, Centre National d’Études Spatiales [Paris] (CNES), Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Forestry & Wildlife Management, Inland Norway University of Applied Sciences - Høgskolen i Innlandet, Wildlife Fish and Environment Studies, Swedish University of Agricultural Sciences (SLU), McGill University = Université McGill [Montréal, Canada], Unité de Nutrition Humaine (UNH), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Department of Wildlife, Fish and Environmental Studies, Centre National D'etudes Spatiales874Natural Sciences and Engineering Research Council of Canada6793Universite de Strasbourg Center National de la Recherche Scientifique Miljodirektoratet Naturvardsverket Svenska Jagareforbundet Austrian Science Fund (FWF) Centre National D'etudes Spatiales, and Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Hibernation, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Physiology, Glucose uptake, Clinical Biochemistry, Inflammation, ubiquitin ligase, noncoding RNA, 03 medical and health sciences, 0302 clinical medicine, Atrophy, Downregulation and upregulation, atrophy, medicine, [SDV.MHEP.PHY]Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], Animals, RNA, Messenger, Muscle, Skeletal, biology, Skeletal muscle, myomiR, Cell Biology, medicine.disease, Muscle atrophy, Mef2a, Cell biology, Ubiquitin ligase, Ursus arctos, MicroRNAs, Muscular Atrophy, 030104 developmental biology, medicine.anatomical_structure, 030220 oncology & carcinogenesis, biology.protein, medicine.symptom, Ursidae, Signal Transduction
Abstract: Early ViewOnline Version of Record before inclusion in an issue; Hibernating brown bears, Ursus arctos, undergo extended periods of inactivity and yet these large hibernators are resilient to muscle disuse atrophy. Physiological characteristics associated with atrophy resistance in bear muscle have been examined (e.g., muscle mechanics, neural activity) but roles for molecular signaling/regulatory mechanisms in the resistance to muscle wasting in bears still require investigation. Using quantitative reverse transcription PCR (RT-qPCR), the present study characterized the responses of 36 microRNAs linked with development, metabolism, and regeneration of skeletal muscle, in the vastus lateralis of brown bears comparing winter hibernating and summer active animals. Relative levels of mRNA of selected genes (mef2a, pax7, id2, prkaa1, and mstn) implicated upstream and downstream of the microRNAs were examined. Results indicated that hibernation elicited a myogenic microRNA, or "myomiR", response via MEF2A-mediated signaling. Upregulation of MEF2A-controlled miR-1 and miR-206 and respective downregulation of pax7 and id2 mRNA are suggestive of responses that promote skeletal muscle maintenance. Increased levels of metabolic microRNAs, such as miR-27, miR-29, and miR-33, may facilitate metabolic suppression during hibernation via mechanisms that decrease glucose uptake and fatty acid oxidation. This study identified myomiR-mediated mechanisms for the promotion of muscle regeneration, suppression of ubiquitin ligases, and resistance to muscle atrophy during hibernation mediated by observed increases in miR-206, miR-221, miR-31, miR-23a, and miR-29b. This was further supported by the downregulation of myomiRs associated with a muscle injury and inflammation (miR-199a and miR-223) during hibernation. The present study provides evidence of myomiR-mediated signaling pathways that are activated during hibernation to maintain skeletal muscle functionality in brown bears.
Published: 2019
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46. Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts

Author: Igor V. Grigoriev, Youzhi Miao, Alexey G. Kopchinskiy, Irina S. Druzhinina, Kurt LaButti, Shadi Pourmehdi, Asaf Salamov, Kamariah Abu Salim, Kerrie Barry, Jian Zhang, Lea Atanasova, Mohammad Javad Rahimi, Bernard Henrissat, Hope Hundley, Qirong Shen, Alan Kuo, Anna Lipzen, Komal Chenthamara, Feng Cai, Christian P. Kubicek, Marica Grujic, Andrea Aerts, Carina Pretzer, Dongqing Yang, Mei Wang, Research Area Biotechnology and Microbiology, Technical University of Vienna [Vienna] (TU WIEN)-Institute of Chemical Engineering, Technische Universität Wien (TU Wien), Laboratoire de Linguistique Formelle (LLF UMR7110), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7), Nanjing Agricultural University, Fac Sci, Environm & Life Sci, University of Brunei Darussalam (Biology Department), Universiti Brunei Darussalam, Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), US Department of Energy Joint Genome Institute, U.S Department of Energy, U.S. Department of Energy (DOE)-U.S. Department of Energy (DOE), Dept Energy Great Lakes Bioenergy Res Ctr, Joint Genome institute, United States Department of Energy, Joint Genome Institute, Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), ANR-17-CE34-0002,EMBRASE,Environnement MicroBiologique et Risque Allergique, Suivi des Enfants à 5 ans(2017), Vienna University of Technology (TU Wien)-Institute of Chemical Engineering, Vienna University of Technology (TU Wien), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Nanjing Agricultural University (NAU), U.S. Department of Energy [Washington] (DOE)-U.S. Department of Energy [Washington] (DOE), Austrian Science Fund (FWF) [P 25613 B20], Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231], National Natural Science Foundation of China [31330069], Chinese Ministry of Science and Technology (973 Program) [2015CB150500], IDEX Aix-Marseille (Grant Microbio-E), Kuala Belalong Field Studies Centre [WWTF-LS13-048], Martin, Francis, Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Druzhinina, Irina S., and Shen, Qirong
Subjects: 0301 basic medicine, Cancer Research, Gene Transfer, genome sequence, phylogenetic analysis, transplant recipient, multiple alignments, dna polymorphism, pythium-ultimum, life-style, web server, evolution, reesei, Fungal genetics, Cell Wall, Scanning, Fungal genomics, Genetics (clinical), Phylogeny, Data Management, 2. Zero hunger, Trichoderma, Fungal protein, Microscopy, Phylogenetic analysis, biology, Ascomycota, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Eukaryota, food and beverages, Basidiomycota, Genomics, Plants, Phylogenetics, Parasite evolution, Host-Pathogen Interactions, Hypocreales, Biotechnology, Research Article, Computer and Information Sciences, Hypha, lcsh:QH426-470, Gene Transfer, Horizontal, Glycoside Hydrolases, Hyphae, Fungus, Mycology, Electron, complex mixtures, Horizontal, Fungal Proteins, 03 medical and health sciences, Botany, Genetics, Evolutionary Systematics, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Taxonomy, Evolutionary Biology, fungi, Organisms, technology, industry, and agriculture, Fungi, Biology and Life Sciences, 15. Life on land, biology.organism_classification, Ascomycetes, lcsh:Genetics, 030104 developmental biology, Microscopy, Electron, Scanning, Parasitology, Fungal evolution, Developmental Biology
Abstract: Unlike most other fungi, molds of the genus Trichoderma (Hypocreales, Ascomycota) are aggressive parasites of other fungi and efficient decomposers of plant biomass. Although nutritional shifts are common among hypocrealean fungi, there are no examples of such broad substrate versatility as that observed in Trichoderma. A phylogenomic analysis of 23 hypocrealean fungi (including nine Trichoderma spp. and the related Escovopsis weberi) revealed that the genus Trichoderma has evolved from an ancestor with limited cellulolytic capability that fed on either fungi or arthropods. The evolutionary analysis of Trichoderma genes encoding plant cell wall-degrading carbohydrate-active enzymes and auxiliary proteins (pcwdCAZome, 122 gene families) based on a gene tree / species tree reconciliation demonstrated that the formation of the genus was accompanied by an unprecedented extent of lateral gene transfer (LGT). Nearly one-half of the genes in Trichoderma pcwdCAZome (41%) were obtained via LGT from plant-associated filamentous fungi belonging to different classes of Ascomycota, while no LGT was observed from other potential donors. In addition to the ability to feed on unrelated fungi (such as Basidiomycota), we also showed that Trichoderma is capable of endoparasitism on a broad range of Ascomycota, including extant LGT donors. This phenomenon was not observed in E. weberi and rarely in other mycoparasitic hypocrealean fungi. Thus, our study suggests that LGT is linked to the ability of Trichoderma to parasitize taxonomically related fungi (up to adelphoparasitism in strict sense). This may have allowed primarily mycotrophic Trichoderma fungi to evolve into decomposers of plant biomass., Author summary Individual fungi rely on particular host organisms or substrates for their nutrition. Therefore, the genomes of fungi feeding on plant biomass necessarily contain genes encoding plant cell wall-degrading enzymes, while animal parasites may depend on proteolytic activity. Molds in the genus Trichoderma (Ascomycota) display a unique nutritional versatility. They can feed on other fungi, attack animals, and degrade plant debris. The later property is so efficient that one species (T. reesei) is commercially used for the production of cellulolytic enzymes required for making biofuels and other industry. In this work, we have investigated the evolution of proteins required for plant cell wall degradation in nine Trichoderma genomes and found an unprecedented number of lateral gene transfer (LGT) events for genes encoding these enzymes. Interestingly, the transfers specifically occurred from Ascomycota molds that feed on plants. We detected no cases of LGT from other fungi (e.g., mushrooms or wood-rotting fungi from Basidiomycota) that are frequent hosts of Trichoderma. Therefore, we propose that LGT may be linked to the ability of Trichoderma to parasitize on related organisms. This is a characteristic ecological trait that distinguishes Trichoderma from other mycoparasitic fungi. In this report, we demonstrate that the lateral transfer of genes may result in a profound nutritional expansion and contribute to the emergence of a generalist capable of feeding on organic matter of any origin.
Published: 2018
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47. Assessing the carcinogenic potential of low-dose exposures to chemical mixtures in the environment: the challenge ahead

Author: Dustin G. Brown, Tove Hultman, Judith Weisz, H. Kim Lyerly, Paola A. Marignani, Ann-Karin Olsen, Rabindra Roy, Kim Moorwood, Masoud H. Manjili, Monica Vaccari, Jesse Roman, Hasiah Ab Hamid, Kalan R. Prudhomme, Periyadan K. Krishnakumar, Chenfang Dong, Tiziana Guarnieri, Leandro S. D'Abronzo, Gloria M. Calaf, Amelia K Charles, Emanuela Corsini, Yunus A. Luqmani, Graeme Williams, Louis Vermeulen, Pankaj Vadgama, Sarah N Bay, Véronique Maguer-Satta, Sabine A. S. Langie, Christian C. Naus, Le Jian, Gladys N. Nangami, Lorenzo Memeo, Stephanie C. Casey, Thomas Sanderson, Takemi Otsuki, Nichola Cruickshanks, William H. Bisson, Sudjit Luanpitpong, Jonathan Whitfield, Ahmed Lasfar, Yon Rojanasakul, A. Ivana Scovassi, Shelley A. Harris, Ferdinando Chiaradonna, Richard Ponce-Cusi, Gregory T. Wolf, Valérian Dormoy, Roslida Abd Hamid, Hyun Ho Park, Matilde E. Lleonart, William K. Decker, Maria Romano, Leroy Lowe, Fabio Marongiu, Jan Vondráček, Chiara Mondello, Luc Leyns, Josiah Ochieng, Pratima Nangia-Makker, Edward A. Ratovitski, Zhiwei Hu, Jayadev Raju, Hemad Yasaei, Rafaela Andrade-Vieira, Jordan Woodrick, Hideko Sone, Harini Krishnan, W. Kimryn Rathmell, Andrew Collins, Luoping Zhang, Barry J. Barclay, Amaya Azqueta, Laura Soucek, Marc A. Williams, David O. Carpenter, Roberta Palorini, Rita Nahta, Juan Fernando Martinez-Leal, Firouz Darroudi, Rita Dornetshuber-Fleiss, James E. Klaunig, Elizabeth P. Ryan, Qiang Shawn Cheng, Arthur Berg, Andrew Ward, Gudrun Koppen, Tao Chen, Petr Heneberg, Michael Gilbertson, Amedeo Amedei, Sakina E. Eltom, Ezio Laconi, Joseph Christopher, Hiroshi Kondoh, Neetu Singh, Danielle J Carlin, Marion Chapellier, Michalis V. Karamouzis, Rekha Mehta, Tae-Jin Lee, Annamaria Colacci, Venkata S. Sabbisetti, Mark Wade, Micheline Kirsch-Volders, Patricia Ostrosky-Wegman, Isabelle R. Miousse, Patricia A. Thompson, Philippa D. Darbre, Frederik J. van Schooten, Sofia Pavanello, Igor Koturbash, Binhua P. Zhou, Ranjeet Kumar Sinha, Anna C. Salzberg, Mahara Valverde, Fahd Al-Mulla, Julia Kravchenko, Nicole Kleinstreuer, Carolyn J. Baglole, Menghang Xia, Samira A. Brooks, Amancio Carnero, Gunnar Brunborg, Sandra S. Wise, Daniel C. Koch, John Pierce Wise, Rabeah Al-Temaimi, Laetitia Gonzalez, Lisa J. McCawley, R. Brooks Robey, Gary S. Goldberg, Thierry Massfelder, Linda S M Gulliver, Olugbemiga Ogunkua, Emilio Rojas, Eun-Yi Moon, Lin Li, Silvana Papagerakis, Nik van Larebeke, Adela Lopez de Cerain Salsamendi, Staffan Eriksson, Simona Romano, Dean W. Felsher, Paramita M. Ghosh, Karine A. Cohen-Solal, Paul Dent, Jun Sun, Carmen Blanco-Aparicio, Riccardo Di Fiore, Chia-Wen Hsu, Mahin Khatami, Kannan Badri Narayanan, Francis Martin, Colleen S. Curran, Dale W. Laird, William H. Goodson, Abdul Manaf Ali, Valerie Odero-Marah, Michael J. Gonzalez, Renza Vento, Liang Tzung Lin, Clement G. Yedjou, Hosni Salem, Hsue-Yin Hsu, Zhenbang Chen, Nuzhat Ahmed, Gerard Wagemaker, Sandra Ryeom, Stefano Forte, Debasish Roy, Nancy B. Kuemmerle, Robert C. Castellino, Po Sing Leung, Wilhelm Engström, National Institute of Environmental Health Sciences (US), Research Council of Norway, Ministerio de Economía y Competitividad (España), Instituto de Salud Carlos III, Red Temática de Investigación Cooperativa en Cáncer (España), European Commission, Junta de Andalucía, Ministerio de Educación y Ciencia (España), Ministero dell'Istruzione, dell'Università e della Ricerca, University of Oslo, Regione Emilia Romagna, National Institutes of Health (US), Consejo Nacional de Ciencia y Tecnología (México), Associazione Italiana per la Ricerca sul Cancro, National Research Foundation of Korea, Ministry of Education, Science and Technology (South Korea), Fondo Nacional de Desarrollo Científico y Tecnológico (Chile), Ministry of Education, Culture, Sports, Science and Technology (Japan), Japan Science and Technology Agency, Ministry of Science and Technology (Taiwan), Arkansas Biosciences Institute, Czech Science Foundation, Fundación Fero, Swim Across America, American Cancer Society, Research Foundation - Flanders, Austrian Science Fund, Institut National de la Santé et de la Recherche Médicale (France), Natural Sciences and Engineering Research Council of Canada, Farmacologie en Toxicologie, RS: NUTRIM - R4 - Gene-environment interaction, Goodson, William H, Lowe, Leroy, Carpenter, David O, Gilbertson, Michael, Manaf Ali, Abdul, Lopez de Cerain Salsamendi, Adela, Lasfar, Ahmed, Carnero, Amancio, Azqueta, Amaya, Amedei, Amedeo, Charles, Amelia K, Collins, Andrew R, Ward, Andrew, Salzberg, Anna C, Colacci, Annamaria, Olsen, Ann Karin, Berg, Arthur, Barclay, Barry J, Zhou, Binhua P, Blanco Aparicio, Carmen, Baglole, Carolyn J, Dong, Chenfang, Mondello, Chiara, Hsu, Chia Wen, Naus, Christian C, Yedjou, Clement, Curran, Colleen S, Laird, Dale W, Koch, Daniel C, Carlin, Danielle J, Felsher, Dean W, Roy, Debasish, Brown, Dustin G, Ratovitski, Edward, Ryan, Elizabeth P, Corsini, Emanuela, Rojas, Emilio, Moon, Eun Yi, Laconi, Ezio, Marongiu, Fabio, Al Mulla, Fahd, Chiaradonna, Ferdinando, Darroudi, Firouz, Martin, Francis L, Van Schooten, Frederik J, Goldberg, Gary S, Wagemaker, Gerard, Nangami, Gladys N, Calaf, Gloria M, Williams, Graeme, Wolf, Gregory T, Koppen, Gudrun, Brunborg, Gunnar, Lyerly, H. Kim, Krishnan, Harini, Ab Hamid, Hasiah, Yasaei, Hemad, Sone, Hideko, Kondoh, Hiroshi, Salem, Hosni K, Hsu, Hsue Yin, Park, Hyun Ho, Koturbash, Igor, Miousse, Isabelle R, Scovassi, A. Ivana, Klaunig, James E, Vondráček, Jan, Raju, Jayadev, Roman, Jesse, Wise, John Pierce, Whitfield, Jonathan R, Woodrick, Jordan, Christopher, Joseph A, Ochieng, Josiah, Martinez Leal, Juan Fernando, Weisz, Judith, Kravchenko, Julia, Sun, Jun, Prudhomme, Kalan R, Narayanan, Kannan Badri, Cohen Solal, Karine A, Moorwood, Kim, Gonzalez, Laetitia, Soucek, Laura, Jian, Le, D'Abronzo, Leandro S, Lin, Liang Tzung, Li, Lin, Gulliver, Linda, Mccawley, Lisa J, Memeo, Lorenzo, Vermeulen, Loui, Leyns, Luc, Zhang, Luoping, Valverde, Mahara, Khatami, Mahin, Romano, MARIA FIAMMETTA, Chapellier, Marion, Williams, Marc A, Wade, Mark, Manjili, Masoud H, Lleonart, Matilde E, Xia, Menghang, Gonzalez, Michael J, Karamouzis, Michalis V, Kirsch Volders, Micheline, Vaccari, Monica, Kuemmerle, Nancy B, Singh, Neetu, Cruickshanks, Nichola, Kleinstreuer, Nicole, van Larebeke, Nik, Ahmed, Nuzhat, Ogunkua, Olugbemiga, Krishnakumar, P. K, Vadgama, Pankaj, Marignani, Paola A, Ghosh, Paramita M, Ostrosky Wegman, Patricia, Thompson, Patricia A, Dent, Paul, Heneberg, Petr, Darbre, Philippa, Sing Leung, Po, Nangia Makker, Pratima, Cheng, Qiang Shawn, Robey, R. Brook, Al Temaimi, Rabeah, Roy, Rabindra, Andrade Vieira, Rafaela, Sinha, Ranjeet K, Mehta, Rekha, Vento, Renza, Di Fiore, Riccardo, Ponce Cusi, Richard, Dornetshuber Fleiss, Rita, Nahta, Rita, Castellino, Robert C, Palorini, Roberta, Abd Hamid, Roslida, Langie, Sabine A. S, Eltom, Sakina E, Brooks, Samira A, Ryeom, Sandra, Wise, Sandra S, Bay, Sarah N, Harris, Shelley A, Papagerakis, Silvana, Romano, Simona, Pavanello, Sofia, Eriksson, Staffan, Forte, Stefano, Casey, Stephanie C, Luanpitpong, Sudjit, Lee, Tae Jin, Otsuki, Takemi, Chen, Tao, Massfelder, Thierry, Sanderson, Thoma, Guarnieri, Tiziana, Hultman, Tove, Dormoy, Valérian, Odero Marah, Valerie, Sabbisetti, Venkata, Maguer Satta, Veronique, Rathmell, W. Kimryn, Engström, Wilhelm, Decker, William K, Bisson, William H, Rojanasakul, Yon, Luqmani, Yunu, Chen, Zhenbang, Hu, Zhiwei, Goodson, W., Lowe, L., Carpenter, D., Gilbertson, M., Ali, A., de Cerain Salsamendi, A., Lasfar, A., Carnero, A., Azqueta, A., Amedei, A., Charles, A., Collins, A., Ward, A., Salzberg, A., Colacci, A., Olsen, A., Berg, A., Barclay, B., Zhou, B., Blanco-Aparicio, C., Baglole, C., Dong, C., Mondello, C., Hsu, C., Naus, C., Yedjou, C., Curran, C., Laird, D., Koch, D., Carlin, D., Felsher, D., Roy, D., Brown, D., Ratovitski, E., Ryan, E., Corsini, E., Rojas, E., Moon, E., Laconi, E., Marongiu, F., Al-Mulla, F., Chiaradonna, F., Darroudi, F., Martin, F., Van Schooten, F., Goldberg, G., Wagemaker, G., Nangami, G., Calaf, G., Williams, G., Wolf, G., Koppen, G., Brunborg, G., Kim Lyerly, H., Krishnan, H., Hamid, H., Yasaei, H., Sone, H., Kondoh, H., Salem, H., Hsu, H., Park, H., Koturbash, I., Miousse, I., Ivana Scovassi, A., Klaunig, J., Vondráček, J., Raju, J., Roman, J., Wise, J., Whitfield, J., Woodrick, J., Christopher, J., Ochieng, J., Martinez-Leal, J., Weisz, J., Kravchenko, J., Sun, J., Prudhomme, K., Narayanan, K., Cohen-Solal, K., Moorwood, K., Gonzalez, L., Soucek, L., Jian, L., D'Abronzo, L., Lin, L., Li, L., Gulliver, L., Mccawley, L., Memeo, L., Vermeulen, L., Leyns, L., Zhang, L., Valverde, M., Khatami, M., Romano, M., Chapellier, M., Williams, M., Wade, M., Manjili, M., Lleonart, M., Xia, M., Gonzalez, M., Karamouzis, M., Kirsch-Volders, M., Vaccari, M., Kuemmerle, N., Singh, N., Cruickshanks, N., Kleinstreuer, N., Van Larebeke, N., Ahmed, N., Ogunkua, O., Krishnakumar, P., Vadgama, P., Marignani, P., Ghosh, P., Ostrosky-Wegman, P., Thompson, P., Dent, P., Heneberg, P., Darbre, P., Leung, P., Nangia-Makker, P., Cheng, Q., Brooks Robey, R., Al-Temaimi, R., Roy, R., Andrade-Vieira, R., Sinha, R., Mehta, R., Vento, R., Di Fiore, R., Ponce-Cusi, R., Dornetshuber-Fleiss, R., Nahta, R., Castellino, R., Palorini, R., Hamid, R., Langie, S., Eltom, S., Brooks, S., Ryeom, S., Wise, S., Bay, S., Harris, S., Papagerakis, S., Romano, S., Pavanello, S., Eriksson, S., Forte, S., Casey, S., Luanpitpong, S., Lee, T., Otsuki, T., Chen, T., Massfelder, T., Sanderson, T., Guarnieri, T., Hultman, T., Dormoy, V., Odero-Marah, V., Sabbisetti, V., Maguer-Satta, V., Kimryn Rathmell, W., Engström, W., Decker, W., Bisson, W., Rojanasakul, Y., Luqmani, Y., Chen, Z., Hu, Z., Goodson, W.H., Carpenter, D.O., Ali, A.M., de Cerain Salsamendi, A.L., Charles, A.K., Collins, A.R., Salzberg, A.C., Olsen, A.-K., Barclay, B.J., Zhou, B.P., Baglole, C.J., Hsu, C.-W., Naus, C.C., Curran, C.S., Laird, D.W., Koch, D.C., Carlin, D.J., Felsher, D.W., Brown, D.G., Ryan, E.P., Moon, E.-Y., Martin, F.L., Van Schooten, F.J., Goldberg, G.S., Calaf, G.M., Wolf, G.T., Hamid, H.A., Salem, H.K., Hsu, H.-Y., Park, H.H., Miousse, I.R., Klaunig, J.E., Vondracek, J., Wise, J.P., Whitfield, J.R., Christopher, J.A., Martinez-Leal, J.F., Prudhomme, K.R., Narayanan, K.B., Cohen-Solal, K.A., D'Abronzo, L.S., Lin, L.-T., Mccawley, L.J., Romano, M.F., Williams, M.A., Manjili, M.H., Gonzalez, M.J., Karamouzis, M.V., Kuemmerle, N.B., Krishnakumar, P.K., Marignani, P.A., Ghosh, P.M., Leung, P.S., Cheng, Q.S., Sinha, R.K., Castellino, R.C., Hamid, R.A., Langie, S.A.S., Brooks, S.A., Wise, S.S., Bay, S.N., Harris, S.A., Casey, S.C., Lee, T.-J., Engstrom, W., Decker, W.K., Bisson, W.H., sans affiliation, Centre de Recherche en Cancérologie de Lyon (UNICANCER/CRCL), Centre Léon Bérard [Lyon]-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA), Institut Armand Frappier (INRS-IAF), Institut National de la Recherche Scientifique [Québec] (INRS)-Réseau International des Instituts Pasteur (RIIP), We gratefully acknowledge the support of the National Institute of Health-National Institute of Environmental Health Sciences (NIEHS) conference grant travel support (R13ES023276), Glenn Rice, Office of Research and Development, United States Environmental Protection Agency, Cincinnati, OH, USA also deserves thanks for his thoughtful feedback and inputs on the manuscript, William H.Goodson III was supported by the California Breast Cancer Research Program, Clarence Heller Foundation and California Pacific Medical Center Foundation, Abdul M.Ali would like to acknowledge the financial support of the University of Sultan Zainal Abidin, Malaysia, Ahmed Lasfar was supported by an award from the Rutgers Cancer Institute of New Jersey, Ann-Karin Olsen and Gunnar Brunborg were supported by the Research Council of Norway (RCN) through its Centres of Excellence funding scheme (223268/F50), Amancio Carnero’s lab was supported by grants from the Spanish Ministry of Economy and Competitivity, ISCIII (Fis: PI12/00137, RTICC: RD12/0036/0028) co-funded by FEDER from Regional Development European Funds (European Union), Consejeria de Ciencia e Innovacion (CTS-1848) and Consejeria de Salud of the Junta de Andalucia (PI-0306-2012), Matilde E. Lleonart was supported by a trienal project grant PI12/01104 and by project CP03/00101 for personal support. Amaya Azqueta would like to thank the Ministerio de Educacion y Ciencia (‘Juande la Cierva’ programme, 2009) of the Spanish Government for personal support, Amedeo Amedei was supported by the Italian Ministry of University and Research (2009FZZ4XM_002), and the University of Florence (ex60%2012), Andrew R.Collins was supported by the University of Oslo, Annamaria Colacci was supported by the Emilia-Romagna Region - Project ‘Supersite’ in Italy, Carolyn Baglole was supported by a salary award from the Fonds de recherche du Quebec-Sante (FRQ-S), Chiara Mondello’s laboratory is supported by Fondazione Cariplo in Milan, Italy (grant n. 2011-0370), Christian C.Naus holds a Canada Research Chair, Clement Yedjou was supported by a grant from the National Institutes of Health (NIH-NIMHD grant no. G12MD007581), Daniel C.Koch is supported by the Burroughs Wellcome Fund Postdoctoral Enrichment Award and the Tumor Biology Training grant: NIH T32CA09151, Dean W. Felsher would like to acknowledge the support of United States Department of Health and Human Services, NIH grants (R01 CA170378 PQ22, R01 CA184384, U54 CA149145, U54 CA151459, P50 CA114747 and R21 CA169964), Emilio Rojas would like to thank CONACyT support 152473, Ezio Laconi was supported by AIRC (Italian Association for Cancer Research, grant no. IG 14640) and by the Sardinian Regional Government (RAS), Eun-Yi Moon was supported by grants from the Public Problem-Solving Program (NRF-015M3C8A6A06014500) and Nuclear R&D Program (#2013M2B2A9A03051296 and 2010-0018545) through the National Research Foundation of Korea (NRF) and funded by the Ministry of Education, Science and Technology (MEST) in Korea, Fahd Al-Mulla was supported by the Kuwait Foundation for the Advancement of Sciences (2011-1302-06), Ferdinando Chiaradonna is supported by SysBioNet, a grant for the Italian Roadmap of European Strategy Forum on Research Infrastructures (ESFRI) and by AIRC (Associazione Italiana Ricerca sul Cancro, IG 15364), Francis L.Martin acknowledges funding from Rosemere Cancer Foundation, he also thanks Lancashire Teaching Hospitals NHS trust and the patients who have facilitated the studies he has undertaken over the course of the last 10 years, Gary S.Goldberg would like to acknowledge the support of the New Jersey Health Foundation, Gloria M.Calaf was supported by Fondo Nacional de Ciencia y Tecnología (FONDECYT), Ministerio de Educación de Chile (MINEDUC), Universidad de Tarapacá (UTA), Gudrun Koppen was supported by the Flemish Institute for Technological Research (VITO), Belgium, Hemad Yasaei was supported from a triennial project grant (Strategic Award) from the National Centre for the Replacement, Refinement and Reduction (NC3Rs) of animals in research (NC.K500045.1 and G0800697), Hiroshi Kondoh was supported in part by grants from the Ministry of Education, Culture, Sports, Science, and Technology of Japan, Japan Science and Technology Agency and by JST, CREST, Hsue-Yin Hsu was supported by the Ministry of Science and Technology of Taiwan (NSC93-2314-B-320-006 and NSC94-2314-B-320-002), Hyun Ho Park was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) of the Ministry of Education, Science and Technology (2012R1A2A2A01010870) and a grant from the Korea Healthcare Technology R&D project, Ministry of Health and Welfare, Republic of Korea (HI13C1449), Igor Koturbash is supported by the UAMS/NIH Clinical and Translational Science Award (UL1TR000039 and KL2TR000063) and the Arkansas Biosciences Institute, the major research component of the Arkansas Tobacco Settlement Proceeds Act of 2000, Jan Vondráček acknowledges funding from the Czech Science Foundation (13-07711S), Jesse Roman thanks the NIH for their support (CA116812), John Pierce Wise Sr. and Sandra S.Wise were supported by National Institute of Environmental Health Sciences (ES016893 to J.P.W.) and the Maine Center for Toxicology and Environmental Health, Jonathan Whitfield acknowledges support from the FERO Foundation in Barcelona, Spain, Joseph Christopher is funded by Cancer Research UK and the International Journal of Experimental Pathology, Julia Kravchenko is supported by a philanthropic donation by Fred and Alice Stanback, Jun Sun is supported by a Swim Across America Cancer Research Award, Karine A.Cohen-Solal is supported by a research scholar grant from the American Cancer Society (116683-RSG-09-087-01-TBE), Laetitia Gonzalez received a postdoctoral fellowship from the Fund for Scientific Research–Flanders (FWO-Vlaanderen) and support by an InterUniversity Attraction Pole grant (IAP-P7-07), Laura Soucek is supported by grant #CP10/00656 from the Miguel Servet Research Contract Program and acknowledges support from the FERO Foundation in Barcelona, Spain, Liang-Tzung Lin was supported by funding from the Taipei Medical University (TMU101-AE3-Y19), Linda Gulliver is supported by a Genesis Oncology Trust (NZ) Professional Development Grant, and the Faculty of Medicine, University of Otago, Dunedin, New Zealand, Louis Vermeulen is supported by a Fellowship of the Dutch Cancer Society (KWF, UVA2011-4969) and a grant from the AICR (14–1164), Mahara Valverde would like to thank CONACyT support 153781, Masoud H. Manjili was supported by the office of the Assistant Secretary of Defense for Health Affairs (USA) through the Breast Cancer Research Program under Award No. W81XWH-14-1-0087 Neetu Singh was supported by grant #SR/FT/LS-063/2008 from the Department of Science and Technology, Government of India, Nicole Kleinstreuer is supported by NIEHS contracts (N01-ES 35504 and HHSN27320140003C), P.K. Krishnakumar is supported by the Funding (No. T.K. 11-0629) of King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia, Paola A.Marignani is supported by the Dalhousie Medical Research Foundation, The Beatrice Hunter Cancer Institute and CIHR and the Nova Scotia Lung Association, Paul Dent is the holder of the Universal Inc.Chair in Signal Transduction Research and is supported with funds from PHS grants from the NIH (R01-CA141704, R01-CA150214, R01-DK52825 and R01-CA61774), Petr Heneberg was supported by the Charles University in Prague projects UNCE 204015 and PRVOUK P31/2012, and by the Czech Science Foundation projects P301/12/1686 and 15-03834Y, Po Sing Leung was supported by the Health and Medical Research Fund of Food and Health Bureau, Hong Kong Special Administrative Region, Ref. No: 10110021, Qiang Cheng was supported in part by grant NSF IIS-1218712, R. Brooks Robey is supported by the United States Department of Veterans Affairs, Rabindra Roy was supported by United States Public Health Service Grants (RO1 CA92306, RO1 CA92306-S1 and RO1 CA113447), Rafaela Andrade-Vieira is supported by the Beatrice Hunter Cancer Research Institute and the Nova Scotia Health Research Foundation, Renza Vento was partially funded by European Regional Development Fund, European Territorial Cooperation 2007–13 (CCI 2007 CB 163 PO 037, OP Italia-Malta 2007–13) and grants from the Italian Ministry of Education, University and Research (MIUR) ex-60%, 2007, Riccardo Di Fiore was a recipient of fellowship granted by European Regional Development Fund, European Territorial Cooperation 2007–2013 (CCI 2007 CB 163 PO 037, OP Italia-Malta 2007–2013), Rita Dornetshuber-Fleiss was supported by the Austrian Science Fund (FWF, project number T 451-B18) and the Johanna Mahlke, geb.-Obermann-Stiftung, Roberta Palorini is supported by a SysBioNet fellowship, Roslida Abd Hamid is supported by the Ministry of Education, Malaysia-Exploratory Research Grant Scheme-Project no: ERGS/1-2013/5527165, Sabine A.S.Langie is the beneficiary of a postdoctoral grant from the AXA Research Fund and the Cefic-LRI Innovative Science Award 2013, Sakina Eltom is supported by NIH grant SC1CA153326, Samira A.Brooks was supported by National Research Service Award (T32 ES007126) from the National Institute of Environmental Health Sciences and the HHMI Translational Medicine Fellowship, Sandra Ryeom was supported by The Garrett B. Smith Foundation and the TedDriven Foundation, Thierry Massfelder was supported by the Institut National de la Santé et de la Recherche Médicale INSERM and Université de Strasbourg, Thomas Sanderson is supported by the Canadian Institutes of Health Research (CIHR, MOP-115019), the Natural Sciences and Engineering Council of Canada (NSERC, 313313) and the California Breast Cancer Research Program (CBCRP, 17UB-8703), Tiziana Guarnieri is supported by a grant from Fundamental Oriented Research (RFO) to the Alma Mater Studiorum University of Bologna, Bologna, Italy and thanks the Fondazione Cassa di Risparmio di Bologna and the Fondazione Banca del Monte di Bologna e Ravenna for supporting the Center for Applied Biomedical Research, S.Orsola-Malpighi University Hospital, Bologna, Italy, W.Kimryn Rathmell is supported by the V Foundation for Cancer Research and the American Cancer Society, William K.Decker was supported in part by grant RP110545 from the Cancer Prevention Research Institute of Texas, William H.Bisson was supported with funding from the NIH P30 ES000210, Yon Rojanasakul was supported with NIH grant R01-ES022968, Zhenbang Chen is supported by NIH grants (MD004038, CA163069 and MD007593), Zhiwei Hu is grateful for the grant support from an institutional start-up fund from The Ohio State University College of Medicine and The OSU James Comprehensive Cancer Center (OSUCCC) and a Seed Award from the OSUCCC Translational Therapeutics Program., Sans affiliation, Courcelles, Michel, Goodson, W, Lowe, L, Carpenter, D, Gilbertson, M, Ali, A, de Cerain Salsamendi, A, Lasfar, A, Carnero, A, Azqueta, A, Amedei, A, Charles, A, Collins, A, Ward, A, Salzberg, A, Colacci, A, Olsen, A, Berg, A, Barclay, B, Zhou, B, Blanco Aparicio, C, Baglole, C, Dong, C, Mondello, C, Hsu, C, Naus, C, Yedjou, C, Curran, C, Laird, D, Koch, D, Carlin, D, Felsher, D, Roy, D, Brown, D, Ratovitski, E, Ryan, E, Corsini, E, Rojas, E, Moon, E, Laconi, E, Marongiu, F, Al Mulla, F, Chiaradonna, F, Darroudi, F, Martin, F, Van Schooten, F, Goldberg, G, Wagemaker, G, Nangami, G, Calaf, G, Williams, G, Wolf, G, Koppen, G, Brunborg, G, Kim Lyerly, H, Krishnan, H, Hamid, H, Yasaei, H, Sone, H, Kondoh, H, Salem, H, Hsu, H, Park, H, Koturbash, I, Miousse, I, Ivana Scovassi, A, Klaunig, J, Vondráček, J, Raju, J, Roman, J, Wise, J, Whitfield, J, Woodrick, J, Christopher, J, Ochieng, J, Martinez Leal, J, Weisz, J, Kravchenko, J, Sun, J, Prudhomme, K, Narayanan, K, Cohen Solal, K, Moorwood, K, Gonzalez, L, Soucek, L, Jian, L, D'Abronzo, L, Lin, L, Li, L, Gulliver, L, Mccawley, L, Memeo, L, Vermeulen, L, Leyns, L, Zhang, L, Valverde, M, Khatami, M, Romano, M, Chapellier, M, Williams, M, Wade, M, Manjili, M, Lleonart, M, Xia, M, Gonzalez, M, Karamouzis, M, Kirsch Volders, M, Vaccari, M, Kuemmerle, N, Singh, N, Cruickshanks, N, Kleinstreuer, N, Van Larebeke, N, Ahmed, N, Ogunkua, O, Krishnakumar, P, Vadgama, P, Marignani, P, Ghosh, P, Ostrosky Wegman, P, Thompson, P, Dent, P, Heneberg, P, Darbre, P, Leung, P, Nangia Makker, P, Cheng, Q, Brooks Robey, R, Al Temaimi, R, Roy, R, Andrade Vieira, R, Sinha, R, Mehta, R, Vento, R, Di Fiore, R, Ponce Cusi, R, Dornetshuber Fleiss, R, Nahta, R, Castellino, R, Palorini, R, Hamid, R, Langie, S, Eltom, S, Brooks, S, Ryeom, S, Wise, S, Bay, S, Harris, S, Papagerakis, S, Romano, S, Pavanello, S, Eriksson, S, Forte, S, Casey, S, Luanpitpong, S, Lee, T, Otsuki, T, Chen, T, Massfelder, T, Sanderson, T, Guarnieri, T, Hultman, T, Dormoy, V, Odero Marah, V, Sabbisetti, V, Maguer Satta, V, Kimryn Rathmell, W, Engström, W, Decker, W, Bisson, W, Rojanasakul, Y, Luqmani, Y, Chen, Z, and Hu, Z
Subjects: Cancer Research, Carcinogenesis, [SDV]Life Sciences [q-bio], METHOXYCHLOR-INDUCED ALTERATIONS, Review, Pharmacology, MESH: Carcinogens, Environmental, Carcinogenic synergies, Chemical mixtures, Neoplasms, MESH: Animals, MESH: Neoplasms, Carcinogenesi, Risk assessment, Cancer, ACTIVATED PROTEIN-KINASES, Medicine (all), Low dose, 1. No poverty, Cumulative effects, BREAST-CANCER CELLS, General Medicine, Environmental exposure, MESH: Carcinogenesis, BIO/10 - BIOCHIMICA, EPITHELIAL-MESENCHYMAL TRANSITION, 3. Good health, [SDV] Life Sciences [q-bio], Environmental Carcinogenesis, ESTROGEN-RECEPTOR-ALPHA, Human, MESH: Environmental Exposure, ENDOCRINE-DISRUPTING CHEMICALS, TARGETING TISSUE FACTOR, [SDV.CAN]Life Sciences [q-bio]/Cancer, Biology, Prototypical chemical disruptors, Exposure, [SDV.CAN] Life Sciences [q-bio]/Cancer, Environmental health, medicine, [SDV.EE.SANT] Life Sciences [q-bio]/Ecology, environment/Health, Carcinogen, Environmental carcinogenesis, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, MESH: Humans, Animal, POLYBROMINATED DIPHENYL ETHERS, Environmental Exposure, medicine.disease, MESH: Hazardous Substances, Carcinogens, Environmental, MIGRATION INHIBITORY FACTOR, VASCULAR ENDOTHELIAL-CELLS, Hazardous Substance, Neoplasm
Abstract: Goodson, William H. et al., © The Author 2015. Lifestyle factors are responsible for a considerable portion of cancer incidence worldwide, but credible estimates from the World Health Organization and the International Agency for Research on Cancer (IARC) suggest that the fraction of cancers attributable to toxic environmental exposures is between 7% and 19%. To explore the hypothesis that low-dose exposures to mixtures of chemicals in the environment may be combining to contribute to environmental carcinogenesis, we reviewed 11 hallmark phenotypes of cancer, multiple priority target sites for disruption in each area and prototypical chemical disruptors for all targets, this included dose-response characterizations, evidence of low-dose effects and cross-hallmark effects for all targets and chemicals. In total, 85 examples of chemicals were reviewed for actions on key pathways/ mechanisms related to carcinogenesis. Only 15% (13/85) were found to have evidence of a dose-response threshold, whereas 59% (50/85) exerted low-dose effects. No dose-response information was found for the remaining 26% (22/85). Our analysis suggests that the cumulative effects of individual (non-carcinogenic) chemicals acting on different pathways, and a variety of related systems, organs, tissues and cells could plausibly conspire to produce carcinogenic synergies. Additional basic research on carcinogenesis and research focused on low-dose effects of chemical mixtures needs to be rigorously pursued before the merits of this hypothesis can be further advanced. However, the structure of the World Health Organization International Programme on Chemical Safety 'Mode of Action' framework should be revisited as it has inherent weaknesses that are not fully aligned with our current understanding of cancer biology., We gratefully acknowledge the support of the National Institute of Health-National Institute of Environmental Health Sciences (NIEHS) conference grant travel support (R13ES023276); Glenn Rice, Office of Research and Development, United States Environmental Protection Agency, Cincinnati, OH, USA also deserves thanks for his thoughtful feedback and inputs on the manuscript; William H.Goodson III was supported by the California Breast Cancer Research Program, Clarence Heller Foundation and California Pacific Medical Center Foundation; Abdul M.Ali would like to acknowledge the financial support of the University of Sultan Zainal Abidin, Malaysia; Ahmed Lasfar was supported by an award from the Rutgers Cancer Institute of New Jersey; Ann-Karin Olsen and Gunnar Brunborg were supported by the Research Council of Norway (RCN) through its Centres of Excellence funding scheme (223268/F50), Amancio Carnero’s lab was supported by grants from the Spanish Ministry of Economy and Competitivity, ISCIII (Fis: PI12/00137, RTICC: RD12/0036/0028) co-funded by FEDER from Regional Development European Funds (European Union), Consejeria de Ciencia e Innovacion (CTS-1848) and Consejeria de Salud of the Junta de Andalucia (PI-0306-2012); Matilde E. Lleonart was supported by a trienal project grant PI12/01104 and by project CP03/00101 for personal support. Amaya Azqueta would like to thank the Ministerio de Educacion y Ciencia (‘Juande la Cierva’ programme, 2009) of the Spanish Government for personal support; Amedeo Amedei was supported by the Italian Ministry of University and Research (2009FZZ4XM_002), and the University of Florence (ex60%2012); Andrew R.Collins was supported by the University of Oslo; Annamaria Colacci was supported by the Emilia-Romagna Region - Project ‘Supersite’ in Italy; Carolyn Baglole was supported by a salary award from the Fonds de recherche du Quebec-Sante (FRQ-S); Chiara Mondello’s laboratory is supported by Fondazione Cariplo in Milan, Italy (grant n. 2011-0370); Christian C.Naus holds a Canada Research Chair; Clement Yedjou was supported by a grant from the National Institutes of Health (NIH-NIMHD grant no. G12MD007581); Daniel C.Koch is supported by the Burroughs Wellcome Fund Postdoctoral Enrichment Award and the Tumor Biology Training grant: NIH T32CA09151; Dean W. Felsher would like to acknowledge the support of United States Department of Health and Human Services, NIH grants (R01 CA170378 PQ22, R01 CA184384, U54 CA149145, U54 CA151459, P50 CA114747 and R21 CA169964); Emilio Rojas would like to thank CONACyT support 152473, Ezio Laconi was supported by AIRC (Italian Association for Cancer Research, grant no. IG 14640) and by the Sardinian Regional Government (RAS); Eun-Yi Moon was supported by grants from the Public Problem-Solving Program (NRF-015M3C8A6A06014500) and Nuclear R&D Program (#2013M2B2A9A03051296 and 2010-0018545) through the National Research Foundation of Korea (NRF) and funded by the Ministry of Education, Science and Technology (MEST) in Korea; Fahd Al-Mulla was supported by the Kuwait Foundation for the Advancement of Sciences (2011-1302-06); Ferdinando Chiaradonna is supported by SysBioNet, a grant for the Italian Roadmap of European Strategy Forum on Research Infrastructures (ESFRI) and by AIRC (Associazione Italiana Ricerca sul Cancro; IG 15364); Francis L.Martin acknowledges funding from Rosemere Cancer Foundation; he also thanks Lancashire Teaching Hospitals NHS trust and the patients who have facilitated the studies he has undertaken over the course of the last 10 years; Gary S.Goldberg would like to acknowledge the support of the New Jersey Health Foundation; Gloria M.Calaf was supported by Fondo Nacional de Ciencia y Tecnología (FONDECYT), Ministerio de Educación de Chile (MINEDUC), Universidad de Tarapacá (UTA); Gudrun Koppen was supported by the Flemish Institute for Technological Research (VITO), Belgium; Hemad Yasaei was supported from a triennial project grant (Strategic Award) from the National Centre for the Replacement, Refinement and Reduction (NC3Rs) of animals in research (NC.K500045.1 and G0800697); Hiroshi Kondoh was supported in part by grants from the Ministry of Education, Culture, Sports, Science, and Technology of Japan, Japan Science and Technology Agency and by JST, CREST; Hsue-Yin Hsu was supported by the Ministry of Science and Technology of Taiwan (NSC93-2314-B-320-006 and NSC94-2314-B-320-002); Hyun Ho Park was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) of the Ministry of Education, Science and Technology (2012R1A2A2A01010870) and a grant from the Korea Healthcare Technology R&D project, Ministry of Health and Welfare, Republic of Korea (HI13C1449); Igor Koturbash is supported by the UAMS/NIH Clinical and Translational Science Award (UL1TR000039 and KL2TR000063) and the Arkansas Biosciences Institute, the major research component of the Arkansas Tobacco Settlement Proceeds Act of 2000; Jan Vondráček acknowledges funding from the Czech Science Foundation (13-07711S); Jesse Roman thanks the NIH for their support (CA116812), John Pierce Wise Sr. and Sandra S.Wise were supported by National Institute of Environmental Health Sciences (ES016893 to J.P.W.) and the Maine Center for Toxicology and Environmental Health; Jonathan Whitfield acknowledges support from the FERO Foundation in Barcelona, Spain; Joseph Christopher is funded by Cancer Research UK and the International Journal of Experimental Pathology; Julia Kravchenko is supported by a philanthropic donation by Fred and Alice Stanback; Jun Sun is supported by a Swim Across America Cancer Research Award; Karine A.Cohen-Solal is supported by a research scholar grant from the American Cancer Society (116683-RSG-09-087-01-TBE); Laetitia Gonzalez received a postdoctoral fellowship from the Fund for Scientific Research–Flanders (FWO-Vlaanderen) and support by an InterUniversity Attraction Pole grant (IAP-P7-07); Laura Soucek is supported by grant #CP10/00656 from the Miguel Servet Research Contract Program and acknowledges support from the FERO Foundation in Barcelona, Spain; Liang-Tzung Lin was supported by funding from the Taipei Medical University (TMU101-AE3-Y19); Linda Gulliver is supported by a Genesis Oncology Trust (NZ) Professional Development Grant, and the Faculty of Medicine, University of Otago, Dunedin, New Zealand; Louis Vermeulen is supported by a Fellowship of the Dutch Cancer Society (KWF, UVA2011-4969) and a grant from the AICR (14–1164); Mahara Valverde would like to thank CONACyT support 153781; Masoud H. Manjili was supported by the office of the Assistant Secretary of Defense for Health Affairs (USA) through the Breast Cancer Research Program under Award No. W81XWH-14-1-0087 Neetu Singh was supported by grant #SR/FT/LS-063/2008 from the Department of Science and Technology, Government of India; Nicole Kleinstreuer is supported by NIEHS contracts (N01-ES 35504 and HHSN27320140003C); P.K. Krishnakumar is supported by the Funding (No. T.K. 11-0629) of King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia; Paola A.Marignani is supported by the Dalhousie Medical Research Foundation, The Beatrice Hunter Cancer Institute and CIHR and the Nova Scotia Lung Association; Paul Dent is the holder of the Universal Inc.Chair in Signal Transduction Research and is supported with funds from PHS grants from the NIH (R01-CA141704, R01-CA150214, R01-DK52825 and R01-CA61774); Petr Heneberg was supported by the Charles University in Prague projects UNCE 204015 and PRVOUK P31/2012, and by the Czech Science Foundation projects P301/12/1686 and 15-03834Y; Po Sing Leung was supported by the Health and Medical Research Fund of Food and Health Bureau, Hong Kong Special Administrative Region, Ref. No: 10110021; Qiang Cheng was supported in part by grant NSF IIS-1218712; R. Brooks Robey is supported by the United States Department of Veterans Affairs; Rabindra Roy was supported by United States Public Health Service Grants (RO1 CA92306, RO1 CA92306-S1 and RO1 CA113447); Rafaela Andrade-Vieira is supported by the Beatrice Hunter Cancer Research Institute and the Nova Scotia Health Research Foundation, Renza Vento was partially funded by European Regional Development Fund, European Territorial Cooperation 2007–13 (CCI 2007 CB 163 PO 037, OP Italia-Malta 2007–13) and grants from the Italian Ministry of Education, University and Research (MIUR) ex-60%, 2007; Riccardo Di Fiore was a recipient of fellowship granted by European Regional Development Fund, European Territorial Cooperation 2007–2013 (CCI 2007 CB 163 PO 037, OP Italia-Malta 2007–2013); Rita Dornetshuber-Fleiss was supported by the Austrian Science Fund (FWF, project number T 451-B18) and the Johanna Mahlke, geb.-Obermann-Stiftung; Roberta Palorini is supported by a SysBioNet fellowship; Roslida Abd Hamid is supported by the Ministry of Education, Malaysia-Exploratory Research Grant Scheme-Project no: ERGS/1-2013/5527165; Sabine A.S.Langie is the beneficiary of a postdoctoral grant from the AXA Research Fund and the Cefic-LRI Innovative Science Award 2013; Sakina Eltom is supported by NIH grant SC1CA153326; Samira A.Brooks was supported by National Research Service Award (T32 ES007126) from the National Institute of Environmental Health Sciences and the HHMI Translational Medicine Fellowship; Sandra Ryeom was supported by The Garrett B. Smith Foundation and the TedDriven Foundation; Thierry Massfelder was supported by the Institut National de la Santé et de la Recherche Médicale INSERM and Université de Strasbourg; Thomas Sanderson is supported by the Canadian Institutes of Health Research (CIHR; MOP-115019), the Natural Sciences and Engineering Council of Canada (NSERC; 313313) and the California Breast Cancer Research Program (CBCRP; 17UB-8703); Tiziana Guarnieri is supported by a grant from Fundamental Oriented Research (RFO) to the Alma Mater Studiorum University of Bologna, Bologna, Italy and thanks the Fondazione Cassa di Risparmio di Bologna and the Fondazione Banca del Monte di Bologna e Ravenna for supporting the Center for Applied Biomedical Research, S.Orsola-Malpighi University Hospital, Bologna, Italy; W.Kimryn Rathmell is supported by the V Foundation for Cancer Research and the American Cancer Society; William K.Decker was supported in part by grant RP110545 from the Cancer Prevention Research Institute of Texas; William H.Bisson was supported with funding from the NIH P30 ES000210; Yon Rojanasakul was supported with NIH grant R01-ES022968; Zhenbang Chen is supported by NIH grants (MD004038, CA163069 and MD007593); Zhiwei Hu is grateful for the grant support from an institutional start-up fund from The Ohio State University College of Medicine and The OSU James Comprehensive Cancer Center (OSUCCC) and a Seed Award from the OSUCCC Translational Therapeutics Program.
Published: 2015
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48. Recognizing Patterns: Spatial Analysis of Observed Microbial Colonization on Root Surfaces

Author: Hannes Schmidt, Alexander Höck, Xavier Raynaud, Christina Kaiser, Naoise Nunan, Dagmar Woebken, Thilo Eickhorst, Centre National de la Recherche Scientifique (CNRS), University of Bremen, Institut d'écologie et des sciences de l'environnement de Paris (IEES), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA), University of Vienna [Vienna], Institut d'écologie et des sciences de l'environnement de Paris (iEES), Sorbonne Universités (COMUE), Univ Vienna, Res Network Chem Meets Microbiol, Dept Microbiol & Ecosyst Sci, Div Microbial Ecol, Vienna, Austria, Partenaires INRAE, Marie Curie Intra European Fellowship within the 7th European Community Framework Program [628361], Austrian Science Fund (FWF) [P25700-B20], ERC Starting grant from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program [636928], DAAD [57212076], Amadee Project [FR 11/2016], Amadeus Project [35603ZL], Procope Project [35486YA], European Project: 636928,H2020,ERC-2014-STG,DormantMicrobes(2015), Raynaud, Xavier, and Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Root (linguistics), bacterial colonization, Microorganism, [SDV]Life Sciences [q-bio], 030106 microbiology, microbial ecology, root surface, point process, spatial statistics, image analysis, pattern recognition, wetland rice, Biology, Spatial distribution, Cell wall, 03 medical and health sciences, Nutrient, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Microbial ecology, Botany, Spatial analysis, lcsh:Environmental sciences, ComputingMilieux_MISCELLANEOUS, General Environmental Science, 2. Zero hunger, lcsh:GE1-350, Replicate, 15. Life on land, 030104 developmental biology, [SDE]Environmental Sciences
Abstract: International audience; Root surfaces are major sites of interactions between plants and associated microorganisms. Here, plants and microbes communicate via signaling molecules, compete for nutrients, and release substrates that may have beneficial or harmful effects on each other. Whilst the body of knowledge on the abundance and diversity of microbial communities at root-soil interfaces is now substantial, information on their spatial distribution at the microscale is still scarce. In this study, a standardized method for recognizing and analyzing microbial cell distributions on root surfaces is presented. Fluorescence microscopy was combined with automated image analysis and spatial statistics to explore the distribution of bacterial colonization patterns on rhizoplanes of rice roots. To test and evaluate the presented approach, a gnotobiotic experiment was performed using a potential nitrogen-fixing bacterial strain in combination with roots of wetland rice. The automated analysis procedure resulted in reliable spatial data of bacterial cells colonizing the rhizoplane. Among all replicate roots, the analysis revealed an increasing density of bacterial cells from the root tip to the region of root cell maturation. Moreover, bacterial cells showed significant spatial clustering and tended to be located around plant root cell borders. The quantitative data suggest that the structure of the root surface plays a major role in bacterial colonization patterns. Possible adaptations of the presented approach for future studies are discussed along with potential pitfalls such as inaccurate imaging. Our results demonstrate that standardized recognition and statistical evaluation of microbial colonization on root surfaces holds the potential to increase our understanding of microbial associations with roots and of the underlying ecological interactions.
Published: 2018
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49. Short-term impacts of anthropogenic stressors on Aedes albopictus mosquito vector microbiota

Author: Van Tran Van, Guillaume Minard, Florence-Hélène Tran, Morgane Guégan, Claire Valiente Moro, Audrey Dubost, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), ERA-NET BiodivERsA [ANR-13-EBID-0007–01], [FWF I-1437], [DFG KL 2087/6–1], Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL)
Subjects: 0301 basic medicine, moustique, food.ingredient, Aedes albopictus, Range (biology), Elizabethkingia, Climate, 030106 microbiology, Chryseobacterium, Mosquito Vectors, asian tiger mosquito, Applied Microbiology and Biotechnology, Microbiology, antibiotics, antibiotique, 03 medical and health sciences, food, microbiote, Aedes, antibiotic, microbiota, Animals, Humans, Microbiome, mosquitoes, metataxogenomic, Ecology, biology, Bacteroidetes, temperature, 15. Life on land, biology.organism_classification, Bacteroidales, Anti-Bacterial Agents, 030104 developmental biology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, 13. Climate action, Vector (epidemiology), Dysbiosis, Wolbachia, Flavobacteriaceae
Abstract: Recent studies have highlighted the potential role of microbiota in the biology of the Aedes albopictus mosquito vector. This species is highly anthropogenic and exhibits marked ecological plasticity, with a resulting high potential to colonize a wide range of habitats-including anthropized areas-under various climatic conditions. We put forward the hypothesis that climate and anthropogenic activities, such as the use of antibiotics in agriculture and human medicine, might affect the mosquito-associated bacterial community. We thus studied the additive impact of a temperature decrease and antibiotic ingestion on the temporal dynamics of Ae. albopictus survival and its associated bacterial communities. The results showed no effects of disturbances on mosquito survival. However, short-term temperature impacts on bacterial diversity were observed, while both the community structure and bacterial diversity were affected by early antibiotic ingestion. The genera Elizabethkingia, Chryseobacterium and Wolbachia, as well as an unclassified member of the Bacteroidales order were particularly affected. Antibiotics negatively impacted Elizabethkingia abundance, while Chryseobacterium was completely eliminated following both disturbances, to the benefit of Wolbachia and the unclassified Bacteroidales species. These results generated fresh insight into the effects of climate and anthropogenic activities such as the use of antibiotics on mosquito microbiota.
Published: 2018
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50. Seasonal changes in eicosanoid metabolism in the brown bear

Author: Stéphane Blanc, Georg Tascher, Isabelle Chery, Sylvain Giroud, Guillemette Gauquelin-Koch, Jon E. Swenson, Jon M. Arnemo, Etienne Lefai, Chantal Simon, Justine Bertrand-Michel, Fabrice Bertile, Alina L. Evans, Department of Integrative Biology and Evolution, Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Department of Forestry and Wildlife Management, Hedmark University College, Département Ecologie, Physiologie et Ethologie (DEPE-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Plateau de lipidomique, Hôpital Purpan [Toulouse], CHU Toulouse [Toulouse]-CHU Toulouse [Toulouse]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Claude de Preval, Centre National d'Études Spatiales [Toulouse] (CNES), Norwegian Institute for Nature Research (NINA), Cardiovasculaire, métabolisme, diabétologie et nutrition (CarMeN), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hospices Civils de Lyon (HCL), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Plateau MetaToul-LIPIDOMIQUE = MetaToul-Lipidomics, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-MetaToul-MetaboHUB, Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National de la Recherche Agronomique (INRA), Norwegian Environmental Agency, Swedish Environmental Protection Agency, Polish-Norwegian Research Program POL-NOR/198352/85/2013, Austrian Science Fund (FWF) P27267-B25, Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole Nationale Vétérinaire de Toulouse (ENVT)
Subjects: 0301 basic medicine, Hibernation, medicine.medical_specialty, Thromboxane, Zoology and botany: 480 [VDP], VDP::Zoologiske og botaniske fag: 480, 03 medical and health sciences, 0302 clinical medicine, Internal medicine, medicine, Animals, Ursus, Fatty acids, Muscle, Skeletal, Zoologiske og botaniske fag: 480 [VDP], Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, chemistry.chemical_classification, Leukotriene, Original Paper, biology, Eicosanoid metabolism, Chemistry, Skeletal muscle, General Medicine, biology.organism_classification, 030104 developmental biology, Endocrinology, medicine.anatomical_structure, Metabolism, Eicosanoid, [SDE]Environmental Sciences, cardiovascular system, Prostaglandins, Eicosanoids, VDP::Zoology and botany: 480, lipids (amino acids, peptides, and proteins), Seasons, 030217 neurology & neurosurgery, Ursidae, Polyunsaturated fatty acid
Abstract: International audience; Polyunsaturated fatty acids (PUFAs) exert several important functions across organ systems. During winter, hibernators divert PUFAs from oxidation, retaining them in their tissues and membranes, to ensure proper body functions at low body temperature. PUFAs are also precursors of eicosanoids with pro- and anti-inflammatory properties. This study investigated seasonal changes in eicosanoid metabolism of free-ranging brown bears (Ursus arctos). By using a lipidomic approach, we assessed (1) levels of specific omega-3 and omega-6 fatty acids involved in the eicosanoid cascade and (2) concentrations of eicosanoids in skeletal muscle and blood plasma of winter hibernating and summer active bears. We observed significant seasonal changes in the specific omega-3 and omega-6 precursors. We also found significant seasonal alterations of eicosanoid levels in both tissues. Concentrations of pro-inflammatory eicosanoids, such as thromboxane B2, 5-hydroxyeicosatetraenoic acid (HETE), and 15-HETE and 18-HETE, were significantly lower in muscle and/or plasma of hibernating bears compared to summer-active animals. Further, plasma and muscle levels of 5,6-epoxyeicosatrienoic acid (EET), as well as muscle concentration of 8,9-EET, tended to be lower in bears during winter hibernation vs. summer. We also found lower plasma levels of anti-inflammatory eicosanoids, such as 15dPGJ(2) and PGE(3), in bears during winter hibernation. Despite of the limited changes in omega-3 and omega-6 precursors, plasma and muscle concentrations of the products of all pathways decreased significantly, or remained unchanged, independent of their pro- or anti-inflammatory properties. These findings suggest that hibernation in bears is associated with a depressed state of the eicosanoid cascade.
Published: 2018
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