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704 results on '"University College Cork ( UCC )"'

1. Italia e Francia: il caso di Ugo Foscolo

Author: Graduate Conference in Italian Studies (04.02.2012: University College Cork (UCC)), Bearelle, Sarah, Graduate Conference in Italian Studies (04.02.2012: University College Cork (UCC)), and Bearelle, Sarah
Abstract: info:eu-repo/semantics/nonPublished
Published: 2012

2. Archaea, specific genetic traits, and development of improved bacterial live biotherapeutic products: another face of next-generation probiotics

Author: Matthieu Martineau, Paul W. O'Toole, Marie-Edith Arnal, Khaled Fadhlaoui, Paméla Camponova, Jean-François Brugère, Bernard Ollivier, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Chimie Interface Biologie pour l’Environnement, la Santé et la Toxicologie (CIBEST ), SYstèmes Moléculaires et nanoMatériaux pour l’Energie et la Santé (SYMMES), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Alimentary Pharmabiotic Centre (APC), Biosciences Institute (BSI), University College Cork (UCC)-University College Cork (UCC), and ANR-16-IDEX-0001,CAP 20-25,CAP 20-25(2016)
Subjects: [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Genetic traits, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Gut flora, urologic and male genital diseases, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Applied Microbiology and Biotechnology, law.invention, chemistry.chemical_compound, Probiotic, Mice, law, [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], ComputingMilieux_MISCELLANEOUS, chemistry.chemical_classification, 0303 health sciences, biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], General Medicine, 3. Good health, Amino acid, Biological Therapy, Biochemistry, Cardiovascular Diseases, Biotechnology, Methanogenesis, Pyrrolysine, digestive system, 03 medical and health sciences, Methylamines, Human gut, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Animals, Humans, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], 030304 developmental biology, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, 030306 microbiology, Probiotics, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV.MHEP.HEG]Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, biology.organism_classification, Archaea, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Diet, Gastrointestinal Microbiome, chemistry, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Metabolism, Inborn Errors, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: Trimethylamine (TMA) and its oxide TMAO are important biomolecules involved in disease-associated processes in humans (e.g., trimethylaminuria and cardiovascular diseases). TMAO in plasma (pTMAO) stems from intestinal TMA, which is formed from various components of the diet in a complex interplay between diet, gut microbiota, and the human host. Most approaches to prevent the occurrence of such deleterious molecules focus on actions to interfere with gut microbiota metabolism to limit the synthesis of TMA. Some human gut archaea however use TMA as terminal electron acceptor for producing methane, thus indicating that intestinal TMA does not accumulate in some human subjects. Therefore, a rational alternative approach is to eliminate neo-synthesized intestinal TMA. This can be achieved through bioremediation of TMA by these peculiar methanogenic archaea, either by stimulating or providing them, leading to a novel kind of next-generation probiotics referred to as archaebiotics. Finally, specific components which are involved in this archaeal metabolism could also be used as intestinal TMA sequesters, facilitating TMA excretion along with stool. Referring to a standard pharmacological approach, these TMA traps could be synthesized ex vivo and then delivered into the human gut. Another approach is the engineering of known probiotic strain in order to metabolize TMA, i.e., live engineered biotherapeutic products. These alternatives would require, however, to take into account the necessity of synthesizing the 22nd amino acid pyrrolysine, i.e., some specificities of the genetics of TMA-consuming archaea. Here, we present an overview of these different strategies and recent advances in the field that will sustain such biotechnological developments. KEY POINTS: • Some autochthonous human archaea can use TMA for their essential metabolism, a methyl-dependent hydrogenotrophic methanogenesis. • They could therefore be used as next-generation probiotics for preventing some human diseases, especially cardiovascular diseases and trimethylaminuria. • Their genetic capacities can also be used to design live recombinant biotherapeutic products. • Encoding of the 22nd amino acid pyrrolysine is necessary for such alternative developments.
Published: 2020

3. Development of a core outcome set for medication review in older patients with multimorbidity and polypharmacy: a study protocol

Author: Anne Spinewine, Jean-Baptiste Beuscart, Olivia Dalleur, Wilma Knol, Shane Cullinan, Stefanie Thevelin, Claudio Schneider, Benoît Boland, Nicolas Rodondi, Denis O'Mahony, Evaluation des technologies de santé et des pratiques médicales - ULR 2694 (METRICS), Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Université Catholique de Louvain = Catholic University of Louvain (UCL), Cliniques Universitaires Saint-Luc [Bruxelles], University Medical Center [Utrecht], Royal College of Surgeons in Ireland (RCSI), Bern University Hospital [Berne] (Inselspital), University College Cork (UCC), University of Bern, Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille, CHU Lille, Université de Lille, Université Catholique de Louvain = Catholic University of Louvain [UCL], METRICS : Evaluation des technologies de santé et des pratiques médicales - ULR 2694, Evaluation des technologies de santé et des pratiques médicales - ULR 2694 [METRICS], Royal College of Surgeons in Ireland [RCSI], Bern University Hospital [Berne] [Inselspital], University College Cork [UCC], UCL - SSS/LDRI - Louvain Drug Research Institute, UCL - SSS/IRSS - Institut de recherche santé et société, UCL - (MGD) Département de pharmacie, UCL - (SLuc) Département de pharmacie, and UCL - (SLuc) Service de gériatrie
Subjects: Research design, Delphi Technique, [SDV]Life Sciences [q-bio], Delphi method, 030204 cardiovascular system & hematology, 0302 clinical medicine, Surveys and Questionnaires, Health care, 030212 general & internal medicine, 610 Medicine & health, Mesh:Aged, Clinical Trials as Topic, General Medicine, Mesh:Delphi Technique, 3. Good health, Systematic review, Research Design, 360 Social problems & social services, Mesh:Surveys and Questionnaires, medicine.medical_specialty, multimorbidity, Medication Therapy Management, Mesh:Clinical Trials as Topic/standards, Mesh:Research Design, 03 medical and health sciences, Study protocol, Medication therapy management, Mesh:Polypharmacy, medicine, Humans, polypharmacy, Aged, Mesh:Multimorbidity, Protocol (science), Polypharmacy, business.industry, RC952-954.6, Multimorbidity, Core outcome set, core outcome set, study protocol, Mesh:Medication Therapy Management/standards, Clinical trial, Mesh:Humans, Geriatrics, Clinical Interventions in Aging, Family medicine, Geriatrics and Gerontology, business
Abstract: Jean-Baptiste Beuscart,1 Olivia Dalleur,1 Benoit Boland,2 Stefanie Thevelin,1 Wilma Knol,3 Shane Cullinan,4 Claudio Schneider,5 Denis O’Mahony,6 Nicolas Rodondi,4,7 Anne Spinewine1,8 1Université catholique de Louvain, Louvain Drug Research Institute, Clinical Pharmacy Research Group, Brussels, Belgium; 2Geriatric Medicine, Cliniques universitaires Saint-Luc, Brussels, Université catholique de Louvain, Belgium; 3Department of Geriatric Medicine and Expertise Centre Pharmacotherapy in Old Persons (EPHOR), University Medical Centre Utrecht, Netherlands; 4School of Pharmacy, Royal College of Surgeons in Ireland, Dublin, Ireland; 5Department of General Internal Medicine, Bern University Hospital, Bern, Switzerland; 6Department of Medicine (Geriatrics), University College Cork, Cork, Ireland; 7Institute of Primary Health Care (BIHAM), University of Bern, Bern, Switzerland; 8Université catholique de Louvain, CHU UCL Namur, Pharmacy Department, Yvoir, Belgium Background: Medication review has been advocated to address the challenge of polypharmacy in older patients, yet there is no consensus on how best to evaluate its efficacy. Heterogeneity of outcomes reported in clinical trials can hinder the comparison of clinical trial findings in systematic reviews. Moreover, the outcomes that matter most to older patients might be under-reported or disregarded altogether. A core outcome set can address this issue as it defines a minimum set of outcomes that should be reported in all clinical trials in any particular field of research. As part of the European Commission-funded project, called OPtimising thERapy to prevent Avoidable hospital admissions in the Multimorbid elderly, this paper describes the methods used to develop a core outcome set for clinical trials of medication review in older patients with multimorbidity. Methods/design: The study was designed in several steps. First, a systematic review established which outcomes were measured in published and ongoing clinical trials of medication review in older patients. Second, we undertook semistructured interviews with older patients and carers aimed at identifying additional relevant outcomes. Then, a multilanguage European Delphi survey adapted to older patients was designed. The international Delphi survey was conducted with older patients, health care professionals, researchers, and clinical experts in geriatric pharmacotherapy to validate outcomes to be included in the core outcome set. Consensus meetings were conducted to validate the results. Discussion: We present the method for developing a core outcome set for medication review in older patients with multimorbidity. This study protocol could be used as a basis to develop core outcome sets in other fields of geriatric research. Keywords: core outcome set, study protocol, polypharmacy, multimorbidity
Published: 2017

4. Viromes of one year old infants reveal the impact of birth mode on microbiome diversity

Author: Feargal J. Ryan, Angela McCann, Paul Ross, Colin Hill, Susan Mills, Catherine Stanton, Tony Blake, Stephen R. Stockdale, C. Anthony Ryan, Marion Dalmasso, University College Cork (UCC), Aliments Bioprocédés Toxicologie Environnements (ABTE), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Alimentary Pharmabiotic Centre (APC), Biosciences Institute (BSI), and University College Cork (UCC)-University College Cork (UCC)
Subjects: 0301 basic medicine, medicine.medical_treatment, Physiology, lcsh:Medicine, Gut flora, Microbiology, Pediatrics, General Biochemistry, Genetics and Molecular Biology, Birth mode, 03 medical and health sciences, Virology, medicine, Human virome, Caesarean section, Microbiome, Bacteriophage, biology, Transmission (medicine), Virome, General Neuroscience, lcsh:R, Infant, General Medicine, crAssphage, biology.organism_classification, 030104 developmental biology, Metagenomics, Cohort, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, General Agricultural and Biological Sciences
Abstract: International audience; Establishing a diverse gut microbiota after birth is being increasingly recognised as important for preventing illnesses later in life. It is well established that bacterial diversity rapidly increases post-partum; however, few studies have examined the infant gut virome/phageome during this developmental period. We performed a metagenomic analysis of 20 infant faecal viromes at one year of age to determine whether spontaneous vaginal delivery (SVD) or caesarean section (CS) influenced viral composition. We find that birth mode results in distinctly different viral communities, with SVD infants having greater viral and bacteriophage diversity. We demonstrate that CrAssphage is acquired early in life, both in this cohort and two others, although no difference in birth mode is detected. A previous study has shown that bacterial OTU's (operational taxonomic units) identified in the same infants could not discriminate between birth mode at 12 months of age. Therefore, our results indicate that vertical transmission of viral communities from mother to child may play a role in shaping the early life microbiome, and that birth mode should be considered when studying the early life gut virome.
Published: 2018

5. Impact of functional properties and release kinetics on antioxidant activity of biopolymer active films and coatings

Author: Cadhla Tanner, Thomas Karbowiak, Frédéric Debeaufort, Philippe Cayot, Nasreddine Benbettaïeb, Procédés Alimentaires et Microbiologiques [Dijon] ( PAM ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté ( UBFC ), Département Génie biologique [IUT de Dijon/Auxerre - université de Bourgogne], Institut Universitaire de Technologie - IUT Dijon/Auxerre, Université de Bourgogne ( UB ) -Université de Bourgogne ( UB ), Department of Microbiology and Environmental Research Institute (Cork, Ireland), University College Cork ( UCC ), Procédés Alimentaires et Microbiologiques [Dijon] (PAM), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut Universitaire de Technologie - Dijon/Auxerre (IUT Dijon), Université de Bourgogne (UB)-Université de Bourgogne (UB), and University College Cork (UCC)
Subjects: Antioxidant, food.ingredient, Coumaric Acids, DPPH, [SDV]Life Sciences [q-bio], medicine.medical_treatment, Kinetics, Chitosan-fish gelatin film, engineering.material, Gelatin, Antioxidants, Permeability, Analytical Chemistry, Ferulic acid, chemistry.chemical_compound, Functional and structural properties, Biopolymers, Caffeic Acids, 0404 agricultural biotechnology, food, Tensile Strength, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Fish Products, Caffeic acid, medicine, Organic chemistry, Chitosan, Free radical scavenging activity, [ SDV ] Life Sciences [q-bio], Release properties, [ SDV.IDA ] Life Sciences [q-bio]/Food engineering, 04 agricultural and veterinary sciences, General Medicine, Phenylethyl Alcohol, 040401 food science, Tyrosol, chemistry, engineering, Active packaging, Biopolymer, Food Science, Nuclear chemistry
Abstract: International audience; This work deals with the study of the release kinetics of some natural antioxidants (ferulic acid, caffeic acid and tyrosol) from chitosan-fish gelatin edible films immersed ethanol at 96%, as well as the kinetics of their antioxidant activity using the DPPH assay. The aim was to determine how film functional properties influence the release kinetic and antioxidant activity. The addition of antioxidants to chitosan-fish gelatin matrix decreased the water vapour permeability by more than 30%. The tensile strength (TS) increased up to 50% after the incorporation of antioxidants. Some molecular interactions between polymer chains and antioxidants were confirmed by FTIR where spectra displayed a shift of the amide-III peak. Films containing caffeic acid or a caffeic-ferulic acid mixture exhibited the highest radical scavenging activity, leading to a 90% antioxidant activity at equilibrium but the release rate controlled the efficacy of the system.
Published: 2018

6. The impact of human activities and lifestyles on the interlinked microbiota and health of humans and of ecosystems

Author: Tari Haahtela, Hubert Plovier, Lucette Flandroy, Eeva Furman, Graham A. W. Rook, Gerard Clarke, Gabriele Berg, Ellen Decaestecker, Yolanda Sanz, Maria Carlota Dao, Sébastien Massart, Theofilos Poutahidis, Science Foundation Ireland, European Commission, Technische Universität Graz ( TU Graz ), University College Cork ( UCC ), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Institute of cardiometabolism and nutrition ( ICAN ), CHU Pitié-Salpêtrière [APHP]-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Assistance publique - Hôpitaux de Paris (AP-HP)-Université Pierre et Marie Curie - Paris 6 ( UPMC ), Katholieke Universiteit Leuven ( KU Leuven ), Finnish Environment Institute ( SYKE ), University of Helsinki [Helsinki], Université de Liège, Instituto de Agroquímica y Tecnología de Alimentos - Institute of Agrochemistry and Food Technology [Valencia] ( IATA-CSIC ), University College of London [London] ( UCL ), Department of Dermatology, Allergology and Venereology, Clinicum, University of Helsinki, HUS Inflammation Center, UCL - SSS/LDRI - Louvain Drug Research Institute, SPF Santé publique, sécurité de la chaîne alimentaire et environnement [Saint-Gilles, Belgique], Laboratory of Pathology [Thessaloniki, Greece] (Faculty of Health Sciences), Aristotle University of Thessaloniki-School of Veterinary Medicine [Thessaloniki, Greece], Technische Universität Graz (TU Graz), University College Cork (UCC), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Institute of cardiometabolism and nutrition (ICAN), Université Pierre et Marie Curie - Paris 6 (UPMC)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Finnish Environment Institute (SYKE), Instituto de Agroquímica y Tecnología de Alimentos - Institute of Agrochemistry and Food Technology [Valencia] (IATA-CSIC), University College of London [London] (UCL), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Research Unit on Cardiovascular and Metabolic Diseases (ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, and HAL UPMC, Gestionnaire
Subjects: 0301 basic medicine, Biodiversity, EcoHealth, Soil, [ SDV.MP ] Life Sciences [q-bio]/Microbiology and Parasitology, Environmental Microbiology, Human Activities, Waste Management and Disposal, Natural environment, 1183 Plant biology, microbiology, virology, Ecology, Microbiota, [ SDV.SPEE ] Life Sciences [q-bio]/Santé publique et épidémiologie, ENVIRONMENTAL CHEMICALS, Plants, RUSSIAN KARELIA, AKKERMANSIA-MUCINIPHILA, Pollution, 3. Good health, Microbes, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, One Health, Health, BACTERIAL COMMUNITIES, Environmental Monitoring, Environmental Engineering, 030106 microbiology, HUMAN GUT MICROBIOME, CANCER-RISK, Context (language use), Biology, 03 medical and health sciences, Microbial ecology, INTESTINAL MICROBIOTA, COMMENSAL BACTERIA, Environmental Chemistry, Animals, Humans, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Life Style, Ecosystem, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, business.industry, fungi, Immunoregulation, ALLERGIC SENSITIZATION, Commensalism, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, 13. Climate action, Agriculture, SEA SPRAY AEROSOL, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Adaptation, business
Abstract: Plants, animals and humans, are colonized by microorganisms (microbiota) and transiently exposed to countless others. The microbiota affects the development and function of essentially all organ systems, and contributes to adaptation and evolution, while protecting against pathogenic microorganisms and toxins. Genetics and lifestyle factors, including diet, antibiotics and other drugs, and exposure to the natural environment, affect the composition of the microbiota, which influences host health through modulation of interrelated physiological systems. These include immune system development and regulation, metabolic and endocrine pathways, brain function and epigenetic modification of the genome. Importantly, parental microbiotas have transgenerational impacts on the health of progeny. Humans, animals and plants share similar relationships with microbes. Research paradigms from humans and other mammals, amphibians, insects, planktonic crustaceans and plants demonstrate the influence of environmental microbial ecosystems on the microbiota and health of organisms, and indicate links between environmental and internal microbial diversity and good health. Therefore, overlapping compositions, and interconnected roles of microbes in human, animal and plant health should be considered within the broader context of terrestrial and aquatic microbial ecosystems that are challenged by the human lifestyle and by agricultural and industrial activities. Here, we propose research priorities and organizational, educational and administrative measures that will help to identify safe microbe-associated health-promoting modalities and practices. In the spirit of an expanding version of “One health” that includes environmental health and its relation to human cultures and habits (EcoHealth), we urge that the lifestyle-microbiota-human health nexus be taken into account in societal decision making., GC's attendance at the workshop was supported by the APC Microbiome Institute via Science Foundation Ireland funding (Grant number SFI/12/RC/2273). ED was supported by FWO grant G.0643.13. GB was funded by the European Union (BIOCOMES; 612713) and by the Austrian and Styrian Science Fund (FWF; P29285-BBL). M-CD received funding from the Programme for Research, Technological Development and Demonstration under grant agreement HEALTH-F4-2012-305312 (METACARDIS) and Horizon 2020 Framework Programme (EPoS, grant #634413) as well as Assistance Publique Hôpitaux de Paris. HP is a research fellow at FRS-FNRS, Belgium. The contribution of YS is supported by the European Union's Seventh Framework Program under the grant agreement no 613979 (MyNewGut).
Published: 2018

7. Minimum Information about a Biosynthetic Gene cluster

Author: Patrick Caffrey, Renzo Kottmann, Eriko Takano, Sean Doyle, Axel A. Brakhage, Matthew Cummings, Juan Pablo Gomez-Escribano, Yvonne Mast, Ryan F. Seipke, Rob Lavigne, Markus Nett, Hans-Wilhelm Nützmann, Jan Claesen, David H. Sherman, Daniel Petras, Pablo Cruz-Morales, Carl J. Balibar, Anne Osbourn, Oscar P. Kuipers, Leonilde M. Moreira, Xinyu Liu, Marcia S. Osburne, Bohdan Ostash, David P. Fewer, Changsheng Zhang, Pelin Yilmaz, Mohamed S. Donia, Anja Greule, Hyun Uk Kim, Nicholas J. Tobias, Frank Oliver Glöckner, Christoph Geiger, Chia Y. Lee, William H. Gerwick, Philipp Wiemann, Bertolt Gust, Susan E. Jensen, Wilfred A. van der Donk, Jan Kormanec, Ben Shen, Christopher M. Thomas, Jason Micklefield, Srikanth Duddela, R. Cameron Coates, René De Mot, Anthony S. Haines, Neha Garg, Guohui Pan, Roderich D. Süssmuth, Hyung Jin Kwon, Jonathan D. Walton, Lena Gerwick, Jörn Piel, Monika Ehling-Schulz, Zhenhua Tian, Jonathan L. Klassen, Xiaohui Yan, Emily A. Monroe, Yunchang Xie, Russell J. Cox, Keishi Ishida, Grace Yim, Stefano Donadio, Nadine Ziemert, Yuta Tsunematsu, Matthew L. Hillwig, Miroslav Petricek, Sylvie Lautru, Tilmann Weber, Andrew W. Truman, Rainer Breitling, Peter Kötter, Nikos C. Kyrpides, Stephanie Düsterhus, Christian Hertweck, Hideaki Oikawa, Sean F. Brady, Christopher T. Walsh, Adam C. Jones, Marcus A. Moore, Bradley S. Moore, Barrie Wilkinson, Simone M. Mantovani, Nathan A. Moss, Elizabeth E. Wyckoff, Emily P. Balskus, Kapil Tahlan, Fengan Yu, Monica Höfte, Jos M. Raaijmakers, Taifo Mahmud, Yit-Heng Chooi, Yi Tang, Andreas Bechthold, Douglas A. Mitchell, Joanne M. Willey, Helge B. Bode, John B. Biggins, Margherita Sosio, Yi-Qiang Cheng, Carmen Méndez, Leonard Kaysser, Joleen Masschelein, Daniel Krug, Federico Rosconi, Marnix H. Medema, Kaarina Sivonen, Tomohisa Kuzuyama, Mikko Metsä-Ketelä, Esther K. Schmitt, Carsten Kegler, Andriy Luzhetskyy, Gilles P. van Wezel, Bai Linquan, Kai Blin, Jens Nielsen, Bertrand Aigle, Amrita Pati, Harald Gross, Muriel Viaud, Pieter C. Dorrestein, Carla S. Jones, Michael A. Fischbach, Shelley M. Payne, Zhe Rui, Gerard D. Wright, Wen Liu, Alexey V. Melnik, Barry Scott, Brett A. Neilan, Nancy P. Keller, Rainer Borriss, Katrin Jungmann, Michalis Hadjithomas, Evi Stegmann, Daniel J. Edwards, F. Jerry Reen, Alexander Kristian Apel, Wolfgang Wohlleben, Michael J. Smanski, Leonard Katz, Fergal O'Gara, Eric J. N. Helfrich, Sergey B. Zotchev, Olivier Ploux, Arnold J. M. Driessen, Rolf Müller, Jean-Luc Pernodet, K. D. Entian, José A. Salas, Irene de Bruijn, Francisco Barona-Gómez, Jianhua Ju, Jon Clardy, Molecular Microbiology, Molecular Genetics, Jacobs University [Bremen], Microbial genomics and bioinformatics research group, Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Max-Planck-Gesellschaft, Atmospheric Chemistry Observations and Modeling Laboratory (ACOML), National Center for Atmospheric Research [Boulder] (NCAR), Department of Food and Environmental Sciences, Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Collaborative Mass Spectrometry Innovation Center, University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC), Heilongjiang Institute of Science and Technology, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Merck Stiftungsprofessur fûr Molekulare Biotechnologie Fachbereich Biowissenscharten, Goethe-University Frankfurt am Main, Department of Opto-Mechatronics Engineering and Cogno-Mechatronics Engineering, Pusan National University, University of Liverpool, College of Computer Science and Technology [Zhejiang] (Zhejiang University), University of Florida [Gainesville] (UF), School of Management, University of Science and Technology of China [Hefei] (USTC), State Key Laboratory of Nuclear Physics and Technology (SKL-NPT), Peking University [Beijing], Massachusetts Institute of Technology (MIT), Memorial Sloane Kettering Cancer Center [New York], South China Sea Institute of Oceanology, Chinese Academy of Sciences [Beijing] (CAS), Dynamique des Génomes et Adaptation Microbienne (DynAMic), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Institut für Biologie [Berlin] (IFB), Humboldt University Of Berlin, School of Biomolecular and Biomedical Science and Centre for Synthesis and Chemical Biology, University College Dublin [Dublin] (UCD), Parallélisme, Réseaux, Systèmes, Modélisation (PRISM), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Centre National de la Recherche Scientifique (CNRS), Skaggs School of Pharmacy and Pharmaceutical Sciences [San Diego], Grenoble Institut des Neurosciences (GIN), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Santé et de la Recherche Médicale (INSERM), Pixyl Medical [Grenoble], Integrated Optical MicroSystems (IOMS), University of Twente-MESA+ Institute for Nanotechnology, 7Lehrstuhl für Mikrobielle Ökologie, Department für Grundlagen der Biowissenschaften, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Service Néphrologie Pédiatrique, CHU Strasbourg-Hôpital de Hautepierre [Strasbourg], Advanced Resources and Risk Technology, Laboratory of Phytopathology (K.C., H.S., B.A., M.H.), Universiteit Gent = Ghent University (UGENT), Trifork Aarhus C, Aalborg University [Denmark] (AAU), Centers for Disease Control and Prevention [Atlanta] (CDC), Centers for Disease Control and Prevention, Groupe d'Etude de la Matière Condensée (GEMAC), Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen [Groningen], DOE Joint Genome Institute [Walnut Creek], Microbiologie Moléculaire des Actinomycètes (ACTINO), Département Microbiologie (Dpt Microbio), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Laboratory of Gene Technology, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Joint Center for Structural Genomics (JCSG), Stanford University, Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherches et d'Applications Pédagogiques en Langues (CRAPEL), Université Nancy 2, Space Sciences Laboratory [Berkeley] (SSL), University of California [Berkeley] (UC Berkeley), Polytechnic Institute of Leiria, NMR Laboratory, Université de Mons, Université de Mons (UMons), School of Biomedical Science, Curtin University [Perth], Planning and Transport Research Centre (PATREC)-Planning and Transport Research Centre (PATREC), BIOMERIT Research Centre, School of Microbiology, University College Cork (UCC), Department of Engineering Science, University of Oxford, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Laboratoire Charles Friedel, Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratory of Phytopathology, Wageningen University and Research [Wageningen] (WUR), Department of Microbial Ecology, Netherlands Institute of Ecology, Department of Animal Production, Universidad de Córdoba = University of Córdoba [Córdoba], IMV Technologies, Gulliver (UMR 7083), Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Institut für Chemie, Technical University of Berlin / Technische Universität Berlin (TU), Lipides - Nutrition - Cancer (U866) (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Ecole Nationale Supérieure de Biologie Appliquée à la Nutrition et à l'Alimentation de Dijon (ENSBANA), Centre de Recherche Paul Pascal (CRPP), Université de Bordeaux (UB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), DEPARTMENT OF CHEMISTRY, Durham University, Molekulare Ökologie, Joint Attosecond Science Laboratory, University of Ottawa and National Research Council, Department of Mechanical and Aerospace Engineering [Univ California Davis] (MAE - UC Davis), University of California [Davis] (UC Davis), University of Helsinki, University of California-University of California, Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Humboldt-Universität zu Berlin, University of Twente [Netherlands]-MESA+ Institute for Nanotechnology, Technische Universität München [München] (TUM), Universiteit Gent = Ghent University [Belgium] (UGENT), Department of Biosystems, KU Leuven, Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Collège de France (CdF (institution))-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), University of California [Berkeley], NMR and Molecular Imaging Laboratory [Mons], University of Mons [Belgium] (UMONS), University of Oxford [Oxford], Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC), Universidad de Córdoba [Cordoba], Technische Universität Berlin (TU), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Bourgogne (UB)-Ecole Nationale Supérieure de Biologie Appliquée à la Nutrition et à l'Alimentation de Dijon (ENSBANA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Department of Mechanical and Aerospace Engineering [Davis], Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), University of Florida [Gainesville], Institut für Biologie, Humboldt Universität zu Berlin, Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Grenoble-Université Joseph Fourier - Grenoble 1 (UJF), Ghent University [Belgium] (UGENT), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Stanford University [Stanford], Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Collège de France (CdF)-Institut national des sciences de l'Univers (INSU - CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), NMR and Molecular Imaging Laboratory, Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Ecole Nationale Supérieure de Chimie de Paris- Chimie ParisTech-PSL (ENSCP)-Centre National de la Recherche Scientifique (CNRS), Wageningen University and Research Centre [Wageningen] (WUR), Gulliver, ESPCI ParisTech-Centre National de la Recherche Scientifique (CNRS), Technische Universität Berlin (TUB), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Max Planck Society (GERMANY), Max Planck Society (GERMANY)-Max Planck Society (GERMANY), Laboratoire Leprince-Ringuet ( LLR ), Institut National de Physique Nucléaire et de Physique des Particules du CNRS ( IN2P3 ) -École polytechnique ( X ) -Centre National de la Recherche Scientifique ( CNRS ), Atmospheric Chemistry Observations and Modeling Laboratory ( ACOML ), National Center for Atmospheric Research [Boulder] ( NCAR ), University of California [San Diego] ( UC San Diego ), Eidgenössische Technische Hochschule [Zürich] ( ETH Zürich ), University of Science and Technology of China [Hefei] ( USTC ), State Key Laboratory of Nuclear Physics and Technology ( SKL-NPT ), Massachusetts Institute of Technology ( MIT ), Memorial Sloan Kettering Cancer Center ( MSKCC ), Shanghai Ocean University, Dynamique des Génomes et Adaptation Microbienne ( DynAMic ), Institut National de la Recherche Agronomique ( INRA ) -Université de Lorraine ( UL ), University College Dublin [Dublin] ( UCD ), Parallélisme, Réseaux, Systèmes, Modélisation ( PRISM ), Université de Versailles Saint-Quentin-en-Yvelines ( UVSQ ) -Centre National de la Recherche Scientifique ( CNRS ), Grenoble Institut des Neurosciences ( GIN ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -CHU Grenoble-Université Joseph Fourier - Grenoble 1 ( UJF ), Integrated Optical MicroSystems ( IOMS ), Technische Universität München [München] ( TUM ), Ghent University [Belgium] ( UGENT ), Aalborg University [Denmark] ( AAU ), Centers for Disease Control and Prevention [Atlanta] ( CDC ), Groupe d'Etude de la Matière Condensée ( GEMAC ), Groningen Biomolecular Sciences and Biotechnology Institute ( GBB ), Microbiologie Moléculaire des Actinomycètes ( ACTINO ), Département Microbiologie ( Dpt Microbio ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Institut de génétique et microbiologie [Orsay] ( IGM ), Université Paris-Sud - Paris 11 ( UP11 ) -Centre National de la Recherche Scientifique ( CNRS ), Joint Center for Structural Genomics ( JCSG ), Centre européen de recherche et d'enseignement de géosciences de l'environnement ( CEREGE ), Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Collège de France ( CdF ) -Institut National de la Recherche Agronomique ( INRA ) -Institut national des sciences de l'Univers ( INSU - CNRS ), Centre de Recherches et d'Applications Pédagogiques en Langues ( CRAPEL ), Space Sciences Laboratory [Berkeley] ( SSL ), Université de Mons ( UMons ), Planning and Transport Research Centre ( PATREC ) -Planning and Transport Research Centre ( PATREC ), University College Cork ( UCC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Ecole Nationale Supérieure de Chimie de Paris- Chimie ParisTech-PSL ( ENSCP ) -Centre National de la Recherche Scientifique ( CNRS ), Wageningen University and Research Centre [Wageningen] ( WUR ), ESPCI ParisTech, Technische Universität Berlin ( TUB ), Lipides - Nutrition - Cancer (U866) ( LNC ), Université de Bourgogne ( UB ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Ecole Nationale Supérieure de Biologie Appliquée à la Nutrition et à l'Alimentation de Dijon ( ENSBANA ), Centre de recherche Paul Pascal, CNRS, Université de Bordeaux ( UPR8641 ), Centre de Recherche Paul Pascal, CNRS, Université de Bordeaux, University Durham, University of California [Davis] ( UC Davis ), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), [GIN] Grenoble Institut des Neurosciences (GIN), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), and Saarland University, Building A4.1, 66123 Saarbruecken, Germany.
Subjects: MESH : Protein Biosynthesis, protein synthesis, Operon, MESH : Polysaccharides, International Cooperation, MESH: Plants, plant, Review, MESH: Terpenes, gene cluster, polyketide, data base, genetic database, Gene cluster, acyltransferase, Databases, Genetic, MESH : Metagenome, MESH : Genetic Markers, genetics, terpene, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), ComputingMilieux_MISCELLANEOUS, MESH : Peptides, MESH: Peptides, biology, fungus, nonribosomal peptide synthesis, Plants, bacterium, peptide, priority journal, MESH: Protein Biosynthesis, Multigene Family, MESH : Terpenes, MESH: Computational Biology, Genetic Markers, MESH: Terminology as Topic, Bioinformatics, MESH : Multigene Family, biological activity, Article, metagenome, Alkaloids, Manchester Institute of Biotechnology, Terminology as Topic, Bioinformatica, MESH : Bacteria, Peptide Biosynthesis, MESH : Databases, Genetic, Molecular Biology, MESH : Fungi, MESH: Polyketides, standardization, secondary metabolism, [ SDV ] Life Sciences [q-bio], Bacteria, ta1182, Computational Biology, MESH : Terminology as Topic, operon, Laboratorium voor Phytopathologie, MESH: International Cooperation, gene function, Metagenomics, polysaccharide, Laboratory of Phytopathology, chemical structure, Metagenome, MESH: Multigene Family, EPS, biosynthesis, Peptides, MESH : Computational Biology, MESH : International Cooperation, [SDV]Life Sciences [q-bio], MESH: Genetic Markers, information, MESH : Alkaloids, Synthetic biology, MESH: Peptide Biosynthesis, Nucleic Acid-Independent, database, MESH: Databases, Genetic, Genetics, MESH : Polyketides, MESH : Peptide Biosynthesis, Nucleic Acid-Independent, ddc:540, standards, Peptide Biosynthesis, Nucleic Acid-Independent, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, nomenclature, genetic marker, alkaloid derivative, MESH: Fungi, Biology, MESH : Plants, peptide derivative, Polyketide, MESH: Alkaloids, Polysaccharides, ddc:570, Life Science, 14. Life underwater, Secondary metabolism, enzyme specificity, Gene, nonhuman, Terpenes, Fungi, nucleotide sequence, Cell Biology, MESH: Metagenome, ResearchInstitutes_Networks_Beacons/manchester_institute_of_biotechnology, alkaloid, MESH: Bacteria, MESH: Polysaccharides, 13. Climate action, Polyketides, Protein Biosynthesis, synthetic biology, metabolism
Abstract: M.H.M. was supported by a Rubicon fellowship of the Netherlands Organization for Scientific Research (NWO;Rubicon 825.13.001). The work of R.K. was supported by the European Union’s Seventh Framework Programme(Joint Call OCEAN.2011–2: Marine microbial diversity—new insights into marine ecosystems functioning and its biotechnological potential) under the grant agreement no.287589 (Micro B3). M.C. was supported by a Biotechnology and Biological Sciences Research Council (BBSRC)studentship (BB/J014478/1). The GSC is supported by funding from the Natural Environment Research Council(UK), the National Institute for Energy Ethics and Society(NIEeS; UK), the Gordon and Betty Moore Foundation,the National Science Foundation (NSF; US) and the US Department of Energy. The Manchester Synthetic Biology Research Centre, SYNBIOCHEM, is supported by BBSRC/Engineering and Physical Sciences Research Council(EPSRC) grant BB/M017702/1, Medema, M.H., Kottmann, R., Yilmaz, P., Cummings, M., Biggins, J.B., Blin, K., De Bruijn, I., Chooi, Y.H., Claesen, J., Coates, R.C., Cruz-Morales, P., Duddela, S., Düsterhus, S., Edwards, D.J., Fewer, D.P., Garg, N., Geiger, C., Gomez-Escribano, J.P., Greule, A., Hadjithomas, M., Haines, A.S., Helfrich, E.J.N., Hillwig, M.L., Ishida, K., Jones, A.C., Jones, C.S., Jungmann, K., Kegler, C., Kim, H.U., Kötter, P., Krug, D., Masschelein, J., Melnik, A.V., Mantovani, S.M., Monroe, E.A., Moore, M., Moss, N., Nützmann, H.-W., Pan, G., Pati, A., Petras, D., Reen, F.J., Rosconi, F., Rui, Z., Tian, Z., Tobias, N.J., Tsunematsu, Y., Wiemann, P., Wyckoff, E., Yan, X., Yim, G., Yu, F., Xie, Y., Aigle, B., Apel, A.K., Balibar, C.J., Balskus, E.P., Barona-Gómez, F., Bechthold, A., Bode, H.B., Borriss, R., Brady, S.F., Brakhage, A.A., Caffrey, P., Cheng, Y.Q., Clardy, J., Cox, R.J., De Mot, R., Donadio, S., Donia, M.S., Van Der Donk, W.A., Dorrestein, P.C., Doyle, S., Driessen, A.J.M., Ehling-Schulz, M., Entian, K.-D., Fischbach, M.A., Gerwick, L., Gerwick, W.H., Gross, H., Gust, B., Hertweck, C., Höfte, M., Jensen, S.E., Ju, J., Katz, L., Kaysser, L., Klassen, J.L., Keller, N.P., Kormanec, J., Kuipers, O.P., Kuzuyama, T., Kyrpides, N.C., Kwon, H.-J., Lautru, S., Lavigne, R., Lee, C.Y., Linquan, B., Liu, X., Liu, W., Luzhetskyy, A., Mahmud, T., Mast, Y., Méndez, C., Metsä-Ketelä, M., Micklefield, J., Mitchell, D.A., Moore, B.S., Moreira, L.M., Müller, R., Neilan, B.A., Nett, M., Nielsen, J., O'Gara, F., Oikawa, H., Osbourn, A., Osburne, M.S., Ostash, B., Payne, S.M., Pernodet, J.-L., Petricek, M., Piel, J., Ploux, O., Raaijmakers, J.M., Salas, J.A., Schmitt, E.K., Scott, B., Seipke, R.F., Shen, B., Sherman, D.H., Sivonen, K., Smanski, M.J., Sosio, M., Stegmann, E., Süssmuth, R.D., Tahlan, K., Thomas, C.M., Tang, Y., Truman, A.W., Viaud, M., Walton, J.D., Walsh, C.T., Weber, T., Van Wezel, G.P., Wilkinson, B., Willey, J.M., Wohlleben, W., Wright, G.D., Ziemert, N., Zhang, C., Zotchev, S.B., Breitling, R., Takano, E., Glöckner, F.O.
Published: 2015

8. Structural studies of the deacylated glycolipids and lipoteichoic acid of Lactococcus cremoris 3107

Author: Ruiz-Cruz, Sofía, Sadovskaya, Irina, Mahony, Jennifer, Grard, Thierry, Chapot-Chartier, Marie-Pierre, van Sinderen, Douwe, Vinogradov, Evguenii, Transfrontalière BioEcoAgro - UMR 1158 (BioEcoAgro), Université d'Artois (UA)-Université de Liège-Université de Picardie Jules Verne (UPJV)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-JUNIA (JUNIA), Université catholique de Lille (UCL)-Université catholique de Lille (UCL), Biochimie des Produits Aquatiques (BPA), Université du Littoral Côte d'Opale (ULCO)-Transfrontalière BioEcoAgro - UMR 1158 (BioEcoAgro), Université catholique de Lille (UCL)-Université catholique de Lille (UCL)-Université d'Artois (UA)-Université de Liège-Université de Picardie Jules Verne (UPJV)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-JUNIA (JUNIA), University College Cork (UCC), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institute for Biological Science, and National Research Council of Canada (NRC)
Subjects: Lactococcus cremoris 3107, [SDV]Life Sciences [q-bio], Lactic acid bacteria, Glycolipids, Lipoteichoic acid, Cell walls, NMR
Abstract: International audience; Lactococcus cremoris and Lactococcus lactis are among the most extensively exploited species of lactic acid bacteria in dairy fermentations. The cell wall of lactococci, like other Gram-positive bacteria, possesses a thick peptidoglycan layer, which may incorporate cell wall polysaccharides (CWPS), wall teichoic acids (WTA), and/or lipoteichoic acids (LTA).In this study, we report the isolation, purification and structural analysis of the carbohydrate moieties of glycolipids (GL) and LTA of the L. cremoris model strain 3107. Chemical structures of these compounds were studied by chemical methods, NMR spectroscopy and positive and negative mode ESI MS. We found that the LTA of strain 3107 is composed of short chains of 1,3-polyglycerol phosphate (PGP), attached to O-6 of the non-reducing glucose of the kojibiose-Gro backbone of the glycolipid anchor. Extraction of cells with cold TCA afforded the detection of 1,3-glycerol phosphate chains randomly substituted at O-2 of glycerol by D-Ala. Unlike the LTA of L. lactis strains studied to date, the PGP backbone of the LTA of L. cremoris 3107 did not carry any glycosyl substitution. The deacylated glycolipid fraction contained the free kojibiose-Gro oligosaccharide, identical to the backbone of the GL anchor of LTA, and its shorter fragment α-Glc-1-Gro. These OS may have originated from the GL precursors of LTA biosynthesis.
Published: 2023

9. Archaea microbial candidates in next-generation probiotics development

Author: Paul W. O'Toole, Nathalie Ballet, Céline Ribière, Pascal Vandeckerkove, Wajdi Ben Hania, Jean-François Brugère, Marie-Edith Arnal, Bernard Ollivier, Microbiologie Environnement Digestif Santé (MEDIS), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Aix Marseille Université (AMU), University College Cork (UCC), Lesaffre International, Science Foundation Ireland through a Centre award SFI/12/RC/2273, Lesaffre International for research development on some aspects of Methanomassiliicoccales biology, Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Alimentary Pharmabiotic Centre (APC), Biosciences Institute (BSI), University College Cork (UCC)-University College Cork (UCC), Société Industrielle Lesaffre, INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)
Subjects: 0301 basic medicine, trimethylamine oxide, archaea, [SDV]Life Sciences [q-bio], 030106 microbiology, TMAO, [SDV.BID]Life Sciences [q-bio]/Biodiversity, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 03 medical and health sciences, Human gut, cardiovascular disease, Three-domain system, Medicine, Microbiome, développement, Genetics, biology, business.industry, Gastrointestinal Microbiome, Gastroenterology, probiotique, biology.organism_classification, 030104 developmental biology, Metabolic phenotype, atherosclerosis, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, methanomassiliicoccales, Bacteria, Archaea
Abstract: International audience; Pharmabiotics and probiotics in current use or under development belong to 2 of 3 domains of life, Eukarya (eg, yeasts) and Bacteria (eg, lactobacilli). Archaea constitute a third domain of life, and are currently not used as probiotics, despite several interesting features. This includes the absence of known pathogens in humans, animals, or plants and the existence of some archaea closely associated to humans in various microbiomes. We promote the concept that some specific archaea that naturally thrive in the human gut are potential next-generation probiotics that can be rationally selected on the basis of their metabolic phenotype not being encountered in other human gut microbes, neither Bacteria nor Eukarya. The example of the possible bioremediation of the proatherogenic compound trimethylamine into methane by archaeal microbes is described.
Published: 2017

10. Potentially Modifiable Determinants of Malnutrition in Older Adults: A Systematic Review

Author: O’keeffe, M., Kelly, M., O’herlihy, E., O’toole, P., Kearney, P., Timmons, S., Stanton, C., Rolland, Y., Sulmont-Rossé, Claire, Maitre, I., Boeing, H., Stelmach, M., Nagel, G., Wolters, M., Hebestreit, A., De GROOT, L., Teh, R., Peyron, Marie-Agnès, Dardevet, Dominique, Papet, Isabelle, Streicher, M., Torbahn, G., Kiesswetter, E., Visser, M., Volkert, D., O’connor, E., Department of Biological Sciences, Dartmouth College, University College Cork (UCC), Gérontopôle, Epidémiologie et analyses en santé publique : risques, maladies chroniques et handicaps (LEASP), 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), Centre des Sciences du Goût et de l'Alimentation [Dijon] (CSGA), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Ecole supérieure d'Agricultures d'Angers (ESA), Deutsches Institut für Ernährungsforschung Potsdam-Rehbrücke (DifE), Leibniz Association, Universität Ulm - Ulm University [Ulm, Allemagne], Leibniz Institute for Prevention Research and Epidemiology - BIPS, Wageningen University and Research Center (WUR), University of Auckland [Auckland], Unité de Nutrition Humaine - Clermont Auvergne (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), VU University Amsterdam, University of Limerick, University College Cork ( UCC ), CHU Toulouse [Toulouse], Centre des Sciences du Goût et de l'Alimentation [Dijon] ( CSGA ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Ecole Supérieure d'Agricultures d'Angers ( ESA d'Angers ), Institute of Human Nutrition Potsdam-Rehbruecke, University of Ulm, Leibniz Institute for Prevention Research and Epidemiology - BIPS GmbH, Wageningen University and Research Center ( WUR ), University of Auckland, Unité de Nutrition Humaine - Clermont Auvergne ( UNH ), Université Clermont Auvergne ( UCA ) -Institut national de la recherche agronomique [Auvergne/Rhône-Alpes] ( INRA Auvergne/Rhône-Alpes ), Friedrich-Alexander-Universität Erlangen-Nürnberg, Dartmouth College [Hanover], 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-CHU Toulouse [Toulouse], Centre National de la Recherche Scientifique (CNRS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB), Wageningen University and Research [Wageningen] (WUR), Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), University of Limerick (UL), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Vrije Universiteit Amsterdam [Amsterdam] (VU), and Vrije universiteit = Free university of Amsterdam [Amsterdam] (VU)
Subjects: personne âgée, [ SDV.AEN ] Life Sciences [q-bio]/Food and Nutrition, méthode de prévention, nutritional deficiency, malnutrition, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, senior citizens
Abstract: Part of special issue: Abstracts of the 39th ESPEN CongressPart of special issue:Abstracts of the 39th ESPEN Congress; Potentially Modifiable Determinants of Malnutrition in Older Adults: A Systematic Review. 39. ESPEN Congress
Published: 2017

11. Another Brick in the Wall: a Rhamnan Polysaccharide Trapped inside Peptidoglycan of Lactococcus lactis

Author: Irina Sadovskaya, Evgeny Vinogradov, Pascal Courtin, Julija Armalyte, Mickael Meyrand, Efstathios Giaouris, Simon Palussière, Sylviane Furlan, Christine Pèéchoux, Stuart Ainsworth, Jennifer Mahony, Douwe van Sinderen, Saulius Kulakauskas, Yann Guèéérardel, Marie-Pierre Chapot-Chartier, Mark S. Turner, Indranil Biswas, Université du Littoral Côte d'Opale (ULCO), Institut Charles Viollette (ICV) - EA 7394 (ICV), Université d'Artois (UA)-Institut National de la Recherche Agronomique (INRA)-Université du Littoral Côte d'Opale (ULCO)-Institut Supérieur d'Agriculture-Université de Lille, Institute for Biological Sciences, National Research Council of Canada (NRC), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Génétique Animale et Biologie Intégrative (GABI), School of Microbiology, University College Cork (UCC), APC Microbiome Institute [Cork], Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Région Ile-de-France, French ANR project 'Lactophages' [ANR-11-BSV8-004-01], Science Foundation Ireland (SFI) [14/TIDA/2287, 15/SIRG/3430], SFI [13/IA/1953], Chapot-Chartier, Marie-Pierre, CNRS, INRA, ISA, Univ. Artois, Univ. Littoral Côte d’Opale, Université de Lille, Institut Charles Viollette (ICV) - EA 7394 [ICV], Unité de Glycobiologie Structurale et Fonctionnelle (UGSF) - UMR 8576, Université du Littoral Côte d'Opale [ULCO], National Research Council of Canada [NRC], MICrobiologie de l'ALImentation au Service de la Santé [MICALIS], Génétique Animale et Biologie Intégrative [GABI], University College Cork [UCC], Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 [UGSF], Turner, Mark S., Biswas, Indranil, and Institut National de la Recherche Agronomique (INRA)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Magnetic Resonance Spectroscopy, Lactococcus, 030106 microbiology, Mutant, polysaccharides, Peptidoglycan, rhamnan, Polysaccharide, Microbiology, Bacterial cell structure, Cell wall, Mannans, 03 medical and health sciences, chemistry.chemical_compound, Bacterial Proteins, Polysaccharides, Virology, Glycosyltransferase, Deoxy Sugars, chemistry.chemical_classification, Cell Wall, HR-MAS NMR, Rhamnan, biology, Lactococcus lactis, Cell Membrane, Microbiology and Parasitology, biology.organism_classification, Microbiologie et Parasitologie, eye diseases, QR1-502, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, chemistry, Biochemistry, cell wall, Mutation, biology.protein, ATP-Binding Cassette Transporters, Research Article
Abstract: Polysaccharides are ubiquitous components of the Gram-positive bacterial cell wall. In Lactococcus lactis, a polysaccharide pellicle (PSP) forms a layer at the cell surface. The PSP structure varies among lactococcal strains; in L. lactis MG1363, the PSP is composed of repeating hexasaccharide phosphate units. Here, we report the presence of an additional neutral polysaccharide in L. lactis MG1363 that is a rhamnan composed of α-l-Rha trisaccharide repeating units. This rhamnan is still present in mutants devoid of the PSP, indicating that its synthesis can occur independently of PSP synthesis. High-resolution magic-angle spinning nuclear magnetic resonance (HR-MAS NMR) analysis of whole bacterial cells identified a PSP at the surface of wild-type cells. In contrast, rhamnan was detected only at the surface of PSP-negative mutant cells, indicating that rhamnan is located underneath the surface-exposed PSP and is trapped inside peptidoglycan. The genetic determinants of rhamnan biosynthesis appear to be within the same genetic locus that encodes the PSP biosynthetic machinery, except the gene tagO encoding the initiating glycosyltransferase. We present a model of rhamnan biosynthesis based on an ABC transporter-dependent pathway. Conditional mutants producing reduced amounts of rhamnan exhibit strong morphological defects and impaired division, indicating that rhamnan is essential for normal growth and division. Finally, a mutation leading to reduced expression of lcpA, encoding a protein of the LytR-CpsA-Psr (LCP) family, was shown to severely affect cell wall structure. In lcpA mutant cells, in contrast to wild-type cells, rhamnan was detected by HR-MAS NMR, suggesting that LcpA participates in the attachment of rhamnan to peptidoglycan., IMPORTANCE In the cell wall of Gram-positive bacteria, the peptidoglycan sacculus is considered the major structural component, maintaining cell shape and integrity. It is decorated with other glycopolymers, including polysaccharides, the roles of which are not fully elucidated. In the ovococcus Lactococcus lactis, a polysaccharide with a different structure between strains forms a layer at the bacterial surface and acts as the receptor for various bacteriophages that typically exhibit a narrow host range. The present report describes the identification of a novel polysaccharide in the L. lactis cell wall, a rhamnan that is trapped inside the peptidoglycan and covalently bound to it. We propose a model of rhamnan synthesis based on an ABC transporter-dependent pathway. Rhamnan appears as a conserved component of the lactococcal cell wall playing an essential role in growth and division, thus highlighting the importance of polysaccharides in the cell wall integrity of Gram-positive ovococci.
Published: 2017

12. Randomised controlled trial demonstrates that fermented infant formula with short-chain galacto-oligosaccharides and long-chain fructo-oligosaccharides reduces the incidence of infantile colic

Author: Derek Forde, Frédéric Huet, Thomas Ludwig, Jonathan O'b Hourihane, Philippe Alliet, Hetty Bouritius, Yvan Vandenplas, Stefaan Peeters, Growth and Development, Clinical sciences, Units of Pediatric Gastroenterology, Universitair Ziekenhuis Brussel, Nutricia Research, Kinderartsenpraktijk, Slaney Medical Centre, Algemeen Stedelijk Ziekenhuis Aalst, Génétique des Anomalies du Développement (GAD), Université de Bourgogne (UB)-IFR100 - Structure fédérative de recherche Santé-STIC, Paediatric & Child Hlth, University College Cork (UCC), Nutricia Research, the Netherlands, Génétique des Anomalies du Développement ( GAD ), Université de Bourgogne ( UB ) -IFR100 - Structure fédérative de recherche Santé-STIC, University College Cork ( UCC ), and IFR100 - Structure fédérative de recherche Santé-STIC-Université de Bourgogne (UB)
Subjects: Colic, Cultured Milk Products, [ SDV.AEN ] Life Sciences [q-bio]/Food and Nutrition, Breastfeeding, Oligosaccharides, Prebiotic, Gastrointestinal tolerance, Gastroenterology, law.invention, 0302 clinical medicine, birth, Randomized controlled trial, law, Prospective Studies, functional gastrointestinal disorders, Prospective cohort study, Crying, Incidence (epidemiology), Regular Article, health, infant formula, General Medicine, Infantile colic, 3. Good health, mixture, prebiotic, Infant formula, 030211 gastroenterology & hepatology, medicine.symptom, Long chain, infantile colic, medicine.medical_specialty, life, 03 medical and health sciences, Double-Blind Method, children, 030225 pediatrics, Internal medicine, medicine, Humans, Pediatrics, Perinatology, and Child Health, childhood, business.industry, Infant, Newborn, Infant, constipation, medicine.disease, Surgery, Prebiotics, age, gastrointestinal tolerance, Pediatrics, Perinatology and Child Health, symptoms, Fermented formula, fermented formula, business, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Regular Articles
Abstract: Aim: We examined the effects on gastrointestinal (GI) tolerance of a novel infant formula that combined specific fermented formula (FERM) with short-chain galacto-oligosaccharides and long-chain fructo-oligosaccharides (scGOS/lcFOS), with a 9: 1 ratio and concentration of 0.8 g/100 mL. Methods: This prospective, double-blind, randomised, controlled trial comprised 432 healthy, term infants aged 0-28 days whose parents decided to not start, or discontinued, breastfeeding. Infant formula with scGOS/lcFOS+50%FERM, scGOS/lcFOS+15%FERM, 50%FERM and scGOS/lcFOS were tested. Parents completed standardised seven-day diaries on GI symptoms, crying, sleeping and stool characteristics each month until the infants were 17 weeks. Results: All the formulas were well tolerated. At four weeks, the overall incidence of infantile colic was significantly lower (8%) with scGOS/lcFOS+50%FERM than scGOS/lcFOS (20%, p = 0.034) or 50% FERM (20%, p = 0.036). Longitudinal modelling showed that scGOS/lcFOS+ 50%FERM-fed infants also displayed a persistently lower daily crying duration and showed a consistent stool-softening effect than infants who received formula without scGOS/lcFOS. Conclusion: The combination of fermented formula with scGOS/lcFOS was well tolerated and showed a lower overall crying time, a lower incidence of infantile colic and a stool-softening effect in healthy term infants. These findings suggest for the first time that a specific infant formula has a preventive effect on infantile colic in formula-fed infants. Nutricia Research, the Netherlands, provided the funding to conduct the study. The funder contributed to the design of the study, interpretation of the findings and writing of the manuscript.
Published: 2017

13. Stable isotope analysis reveals biases in the performance of a morphological method to distinguish the migratory behaviour of European robins Erithacus rubecula

Author: Iván de la Hera, José Luis Tellería, Antón Pérez-Rodríguez, Guillermo Fandos, Javier Pérez-Tris, Alejandro Onrubia, Javier Fernández-López, Departamento de Zoología y Antropología Física, Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), School of Biological, Earth and Environmental Sciences [Cork] (BEES), University College Cork (UCC), Real Jardín Botánico de Madrid, Spanish National Research Council (CSIC), Fundación Migres, Biogéosciences [UMR 6282] [Dijon] (BGS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Research funded by the Spanish Ministry of Economy and Competitiveness (Project CGL2011- 22953/BOS, CGL2007-62937/BOS and CGL2013-41642-P/BOS, and PhD grants)., Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Universidad Complutense de Madrid [Madrid] ( UCM ), School of Biological, Earth and Environmental Sciences, University College Cork ( UCC ), Spanish National Research Council ( CSIC ), Biogéosciences [Dijon] ( BGS ), and Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS )
Subjects: 0106 biological sciences, Species complex, funciones discriminantes, Erithacus, Plumas rectrices, deuterio, Biology, 010603 evolutionary biology, 01 natural sciences, 010605 ornithology, Rectrix feathers, Deuterio, sympatric interactions, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Ecology, Evolution, Behavior and Systematics, Overwintering, deuterium, plumas rectrices, Isotope analysis, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, Discriminant functions, Ecology, Hydrogen isotope, Campo de Gibraltar, Deuterium, biology.organism_classification, Sympatric interactions, Discriminant functions, Rectrix feathers, Sympatric interactions, Campo de Gibraltar, Interacciones simpátricas, Funciones discriminantes, Sympatric speciation, [ SDV.BA.ZV ] Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, rectrix feathers, Habitat distribution, Animal Science and Zoology, interacciones simpátricas, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, discriminant functions
Abstract: Morphological methods to distinguish between avian groups of research interest (e.g. different sexes, populations or cryptic species) need to be externally validated to ensure reliable performance across situations. In this study, we used stable hydrogen isotope ratios of feathers (δHf) to test the validity of morphological classification functions (MCFs) previously designed to assess the migratory behaviour of European Robins Erithacus rubecula wintering in southern Iberia. Our results show that a great number of migrants (mostly females and juveniles) were erroneously assigned as sedentary, which could compromise the reliability of previous ecological studies that made use of these MCFs. The development of improved MCFs or the use of alternative differentiation methods (δHf) could help us to gain a more realistic insight into the habitat distribution and ecological interactions of sympatric migratory and sedentary robins overwintering in southern Iberia., Los métodos morfológicos para distinguir grupos de aves con interés de investigación (e.g. distinción de sexos, poblaciones o especies crípticas) requieren de validación independiente para asegurar su funcionamiento adecuado de forma consistente. En este estudio, usamos la relación de isó- topos estables del hidrógeno en las plumas (δ2 Hf ) para comprobar la validez de las funciones de clasificación morfológicas (MCFs) diseñadas con anterioridad para identificar el comportamiento migratorio de los petirrojos Erithacus rubecula invernantes en el sur ibérico. Los resultados revelaron que un gran número de migrantes (sobre todo hembras y jóvenes) fueron clasificados erróneamente como sedentarios, lo que podría comprometer la fiabilidad de los estudios ecológicos previos que han hecho uso de estas MCFs. El desarrollo de MCFs mejoradas o el uso de métodos de diferenciación alternativos (δ2 Hf ) podrían ayudarnos a obtener una idea más realista acerca de la distribución entre hábitats e interacciones ecológicas de los petirrojos migratorios y sedentarios que invernan en simpatría en el sur ibérico
Published: 2017

14. Genetic and functional characterisation of the lactococcal P335 phage-host interactions

Author: Laurens Hanemaaijer, Jennifer Mahony, Joana Oliveira, Marco Ventura, Douwe van Sinderen, Horst Neve, Gabriele Andrea Lugli, Barry Collins, Christian Cambillau, Thijs R. H. M. Kouwen, School of Microbiology, University College Cork (UCC), Università degli studi di Parma [Parme, Italie], Dept Microbiol & Biotechnol, Max Rubner Inst, 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), Department of Microbiology, University College Cork, Università degli studi di Parma = University of Parma (UNIPR), University of Parma = Università degli studi di Parma [Parme, Italie], Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), University College Cork ( UCC ), Università degli studi di Parma, Architecture et fonction des macromolécules biologiques ( AFMB ), and Centre National de la Recherche Scientifique ( CNRS ) -Aix Marseille Université ( AMU ) -Institut National de la Recherche Agronomique ( INRA )
Subjects: 0301 basic medicine, viruses, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Proteomics, Siphoviridae, Bacteriophage, Phage group, Bacteriophages, MESH: Genetic Variation, MESH : Viral Proteins, 2. Zero hunger, Genetics, biology, Dairy Fermentation, MESH: Genomics, Genomics, MESH : Host Specificity, MESH : Bacteriophages, Lactococcus lactis, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MESH: Calcium, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, DNA microarray, Research Article, Biotechnology, MESH: Host Specificity, Context (language use), [ SDV.MP.VIR ] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Host Specificity, Microbiology, Dairy, Viral Proteins, 03 medical and health sciences, MESH : Genetic Variation, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MESH: Bacteriophages, MESH : Calcium, Host (biology), MESH : Genomics, Genetic Variation, biology.organism_classification, MESH: Viral Proteins, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 030104 developmental biology, MESH: Lactococcus lactis, Fermentation, Receptor-binding protein, Calcium, MESH : Lactococcus lactis
Abstract: Background Despite continuous research efforts, bacterio(phages) infecting Lactococcus lactis starter strains persist as a major threat to dairy fermentations. The lactococcal P335 phages, which are currently classified into four sub-groups (I-IV), are the second most frequently isolated phage group in an industrial dairy context. Results The current work describes the isolation and comparative genomic analysis of 17 novel P335 group phages. Detailed analysis of the genomic region of P335 phages encoding the so-called “baseplate”, which includes the receptor binding protein (RBP) was combined with a functional characterization of the RBP of sub-group III and IV phages. Additionally, calcium-dependence assays revealed a specific requirement for calcium by sub-group IV phages while host range analysis highlighted a higher number of strains with CWPS type A (11 of 39 strains) are infected by the P335 phages assessed in this study than those with a C (five strains), B (three of 39 strains) or unknown (one of 39 strains) CWPS type. Conclusions These analyses revealed significant divergence among RBP sequences, apparently reflecting their unique interactions with the host and particularly for strains with a type A CWPS. The implications of the genomic architecture of lactococcal P335 phages on serving as a general model for Siphoviridae phages are discussed. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3537-5) contains supplementary material, which is available to authorized users.
Published: 2017

15. A long and abundant non-coding RNA in Lactobacillus salivarius

Author: Marion Dalmasso, Hugh M. B. Harris, Angela McCann, Fabien J. Cousin, Paul W. O'Toole, Victoria Chuat, Denise B. Lynch, Pat G. Casey, Maxence J. B. Bourin, School of Microbiology, University College Cork (UCC), APC Microbiome Institute [Cork], Science et Technologie du Lait et de l'Oeuf (STLO), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Science Foundation Ireland through a Centre award (SFI/12/RC/2273)., Aliments Bioprocédés Toxicologie Environnements (ABTE), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), School of Microbiology and Alimentary Pharmabiotic Centre, Alimentary Pharmabiotic Centre (APC), Biosciences Institute (BSI), University College Cork (UCC)-University College Cork (UCC), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: Proteomics, 0301 basic medicine, megaplasmid, approche transcriptomique, non-coding RNA, L. salivarius, RNA-Seq, Transcriptome, Mice, expression de gène, RNA, Ribosomal, 16S, microbiological analysis, ComputingMilieux_MISCELLANEOUS, séquencage, Genetics, biology, Lactobacillus salivarius, General Medicine, Non-coding RNA, RNA, Bacterial, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, RNA, Long Noncoding, Research Article, lactobacillus salivarius, expression des gènes, 030106 microbiology, Systems Microbiology, arn non codant, 03 medical and health sciences, arn, Animals, Humans, Transcriptomics, Gene, analyse microbiologique, Sequence Analysis, RNA, Gene Expression Profiling, RNA, Ribosomal RNA, biology.organism_classification, Gastrointestinal Microbiome, Gene expression profiling, Lactobacillus, 030104 developmental biology, Ligilactobacillus salivarius, Megaplasmid, Networks, RNA-seq, transcriptome, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract: International audience; Lactobacillus salivarius, found in the intestinal microbiota of humans and animals, is studied as an example of the sub-dominant intestinal commensals that may impart benefits upon their host. Strains typically harbour at least one megaplasmid that encodes functions contributing to contingency metabolism and environmental adaptation. RNA sequencing (RNA-seq) transcriptomic analysis of L. salivarius strain UCC118 identified the presence of a novel unusually abundant long non-coding RNA (lncRNA) encoded by the megaplasmid, and which represented more than 75 % of the total RNA-seq reads after depletion of rRNA species. The expression level of this 520 nt lncRNA in L. salivarius UCC118 exceeded that of the 16S rRNA, it accumulated during growth, was very stable over time and was also expressed during intestinal transit in a mouse. This lncRNA sequence is specific to the L. salivarius species; however, among 45 L. salivarius genomes analysed, not all (only 34) harboured the sequence for the lncRNA. This lncRNA was produced in 27 tested L. salivarius strains, but at strain-specific expression levels. High-level lncRNA expression correlated with high megaplasmid copy number. Transcriptome analysis of a deletion mutant lacking this lncRNA identified altered expression levels of genes in a number of pathways, but a definitive function of this new lncRNA was not identified. This lncRNA presents distinctive and unique properties, and suggests potential basic and applied scientific developments of this phenomenon.
Published: 2017

16. The Role of Research Infrastructures in the Research Assessment Reform: A DARIAH Position Paper

Author: Tasovac, Toma, Romary, Laurent, Tóth-Czifra, Erzsébet, Ackermann, Rahel C., Alves, Daniel, Chambers, Sally, Cosgrave, Mike, Denoyelle, Martine, Garnett, Vicky, Gautschy, Rita, Gray, Edward, Malínek, Vojtěch, di Meo, Carmen, Perkis, Andrew, Reinsone, Sanita, Rißler-Pipka, Nanette, Scharnhorst, Andrea, Viola, Lorella, Digital Research Infrastructure for the Arts and Humanities (DARIAH), Belgrade Center for Digital Humanities (BCDH), Direction de la Culture et de l’Information Scientifiques (DCIS), Inria Siège, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Inventar der Fundmünzen der Schweiz (IFS), Schweizerische Akademie der Geistes- und Sozialwissenschaften (SAGW), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), University College Cork (UCC), Institut National d'Histoire de l'Art (INHA), INHA, University of Basel (Unibas), Institute of Czech Literature (ÚČL AVČR), Czech Academy of Sciences [Prague] (CAS), Istituto Opera del Vocabolario Italiano (OVI-CNR), Norwegian University of Science and Technology [Trondheim] (NTNU), Norwegian University of Science and Technology (NTNU), Institute of Literature, Folklore and Art of the University of Latvia (ILFA), Max Weber Stiftung - Deutsche Geisteswissenschaftliche Institute im Ausland, and Luxembourg Centre for Contemporary and Digital History (C2DH)
Subjects: arts and humanities, Research infrastructures, Research Assessment, [SHS]Humanities and Social Sciences
Abstract: Research assessment reform is crucial for the social sustainability of research infrastructures (RIs): RIs can only thrive in the long term if the researchers who contribute to their development and growth receive academic credit for the kind of work they do in and around research infrastructures. To put it bluntly, research infrastructures have a vested interest in supporting the reform of research assessment. But, conversely, ongoing attempts to reform research assessment can also benefit from the work of research infrastructures because RIs have a great deal of experience creating and maintaining public services for producing, curating and harvesting both traditional and non-traditional academic outputs. The goal of this paper is to outline DARIAH’s position on the importance of research assessment reform for thematic RIs and the importance of thematic RIs for research assessment reform at the European level.
Published: 2023

17. Partly Fermented Infant Formulae With Specific Oligosaccharides Support Adequate Infant Growth and Are Well-Tolerated

Author: Umberto Simeoni, Christoph Savagner, Gérard Beley, Yvan Vandenplas, Marieke Abrahamse-Berkeveld, Jonathan O'b Hourihane, Frédéric Huet, Sebastian Tims, Génétique des Anomalies du Développement (GAD), Université de Bourgogne (UB)-IFR100 - Structure fédérative de recherche Santé-STIC, Laboratory of Microbiology, Wageningen University and Research [Wageningen] (WUR), Maison de l'enfant Essey, Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM), Units of Pediatric Gastroenterology, Universitair Ziekenhuis Brussel, Dept Paediat & Child Hlth, University College Cork (UCC), Génétique des Anomalies du Développement ( GAD ), Université de Bourgogne ( UB ) -IFR100 - Structure fédérative de recherche Santé-STIC, Wageningen University and Research Centre [Wageningen] ( WUR ), Centre Hospitalier Universitaire d'Angers ( CHU Angers ), PRES Université Nantes Angers Le Mans ( UNAM ), University College Cork ( UCC ), Growth and Development, and Clinical sciences
Subjects: 0301 basic medicine, safety, Male, Clostridium difficile/isolation & purification, Double-Blind Method, Feces/microbiology, Female, Follow-Up Studies, Humans, Infant, Infant Formula/adverse effects, Infant, Newborn, Oligosaccharides/adverse effects, Outcome Assessment (Health Care), Prospective Studies, Weight Gain, Population, [ SDV.MHEP.PED ] Life Sciences [q-bio]/Human health and pathology/Pediatrics, Oligosaccharides, 030209 endocrinology & metabolism, Secretory Immunoglobulin A, 03 medical and health sciences, Feces, 0302 clinical medicine, Animal science, Primary outcome, Outcome Assessment, Health Care, Original Article: Nutrition, microbiota, Medicine, Food science, education, fermented formula, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, education.field_of_study, [SDV.MHEP.PED]Life Sciences [q-bio]/Human health and pathology/Pediatrics, 030109 nutrition & dietetics, business.industry, Clostridioides difficile, Gastroenterology, Anthropometry, Infant Formula, 3. Good health, Pediatrics, Perinatology and Child Health, Normal growth, Fermentation, medicine.symptom, Gastrointestinal function, business, Weight gain, scGOS/lcFOS
Abstract: Objective: Fermented formulae (FERM) and a specific mixture of 90% short-chain galacto-oligosaccharides and 10% long-chain fructo-oligosaccharides (scGOS/lcFOS; 9:1) have a potential beneficial effect on gastrointestinal function and microbiota development in infants. The present study assessed the safety and tolerance of the combination of partly fermented infant milk formulae and scGOS/lcFOS compared with either 1 feature, in healthy term infants. Methods: Four hundred thirty-two infants were enrolled before 28 days of age and followed up to 17 weeks of age and assigned to 1 of the 4 groups: (i) formula with scGOS/lcFOS, (ii) scGOS/lcFOS + 15% FERM, (iii) scGOS/lcFOS + 50% FERM, or (iv) 50% fermented formula (50% FERM). Primary outcome was daily weight gain during intervention (equivalence criterion: difference in daily weight gain ≤3 g/day). Infants’ anthropometrics, formula intake, number, and type of (serious) AEs were monitored monthly. Stool samples were collected at baseline and after 17 weeks for analysis of physiological and microbiological parameters. Results: Equivalence of weight gain per day was demonstrated in both the intention-to-treat and per-protocol population, with a mean weight gain (SD) of 29.7 (6.1), 28.2 (4.8), 28.5 (5.0), and 28.7 (5.9) g/day for the groups i to iv respectively. No differences were observed in other growth parameters, formula intake, and the number or severity of AEs. In all scGOS/lcFOS-containing formulae, a beneficial effect of scGOS/lcFOS was observed, indicated by the lower pH, lower Clostridium difficile levels, and higher secretory immunoglobulin A levels. Conclusions: The partly fermented infant milk formulae containing the specific mixture scGOS/lcFOS were well-tolerated and resulted in normal growth in healthy infants.
Published: 2016

18. SlyA regulator is involved in bile salts stress response of Enterococcus faecalis

Author: Axel Hartke, Yanick Auffray, Cecilia Martini, Aurélie Hanin, Charlotte Michaux, Jean-Christophe Giard, Laboratoire de Microbiologie de l’Environnement (LME), Institut National de la Recherche Agronomique (INRA)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Alimentary Pharmabiotic Centre (APC), Biosciences Institute (BSI), University College Cork (UCC)-University College Cork (UCC), Université de Caen Normandie (UNICAEN), and Normandie Université (NU)-Normandie Université (NU)-Institut National de la Recherche Agronomique (INRA)
Subjects: Enterococci, [SDV]Life Sciences [q-bio], Regulator, Virulence, Models, Biological, Regulon, Microbiology, Enterococcus faecalis, Bile Acids and Salts, 03 medical and health sciences, Bacterial Proteins, Stress, Physiological, Genes, Regulator, Hydrolase, Genetics, Transcriptional regulation, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Choloylglycine hydrolase, Molecular Biology, Transcription factor, 030304 developmental biology, 0303 health sciences, biology, 030306 microbiology, Stress response, Gene Expression Regulation, Bacterial, biology.organism_classification, Gastrointestinal Tract, SlyA regulator, Transcription Factors
Abstract: International audience; SlyA is a newly transcriptional regulator identified in Enterococcus faecalis that is involved in the virulence, persistence in mouse kidneys and liver, and survival inside peritoneal macrophages. In this study we searched for environmental conditions that affect expression of the corresponding gene. Of the several stress conditions tested, only bile salts (0.08%) significantly induced transcription of slyA. In addition, the growth of ΔslyA mutant strain was significantly impaired in the presence of bile salts. To increase knowledge of SlyA regulon, real-time quantitative PCR was performed and revealed that expression of EF_3005, which encodes a choloylglycine hydrolase, is negatively regulated by SlyA.
Published: 2011

19. Gestational stress and perinatal <scp>SSRIs</scp> differentially impact the maternal and neonatal microbiome‐gut‐brain axis

Author: Jodi L. Pawluski, Pauline Murail, Florine Grudet, Lena Bys, Anna V. Golubeva, Thomaz Bastiaanssen, Tim F. Oberlander, John F. Cryan, Siobhain M. O'Mahony, Thierry D. Charlier, École des Hautes Études en Santé Publique [EHESP] (EHESP), Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), University College Cork (UCC), and University of British Columbia (UBC)
Subjects: Cellular and Molecular Neuroscience, Endocrinology, hippocampus, Endocrine and Autonomic Systems, [SDV]Life Sciences [q-bio], Endocrinology, Diabetes and Metabolism, motherhood, neuroplasticity, microbiome, development
Abstract: International audience; Selective serotonin reuptake inhibitors (SSRIs) are the most popular antidepressant medications used to manage perinatal mood disturbances, yet our understanding of how they affect the microbiome-gut-brain axis of the mother and offspring is limited. The purpose of this study was to determine how peripartum SSRI treatment may prevent the effects of gestational stress on plasticity in the maternal hippocampus, plasticity in the neonatal brain and related changes in gut microbiota. To do this Sprague-Dawley female rats were left untreated or subjected to unpredictable stress during pregnancy. Half of the females were supplemented daily with fluoxetine. On postpartum day 2 brains were collected for measurement of plasticity (neurogenesis and microglia content) in the maternal hippocampus and in the neonatal brain. Glucocorticoid receptor density was also investigated in the maternal hippocampus. Microbiota composition was analyzed in fecal samples of dams during and after pregnancy, and colon tissue samples from offspring on postnatal day 2. Main findings show there are significant changes to the maternal microbiome-gut-brain axis that may be fundamental to mediating plasticity in the maternal hippocampus. In addition, there is significant impact of gestational stress on neonatal gut microbiota and brain microglia density, while the effects of SSRIs are limited. This is the first study to explore the impact of gestational stress and SSRIs on the microbiome-gut-brain axis in the mother and neonate. Findings from this study will help inform pathways to intervention strategies including stress reduction techniques and/or microbiota targeted nutritional approaches directed towards improving maternal gut health and outcomes for mother and neonate.
Published: 2023

20. A keystone avian predator faces elevated energy expenditure in a warming Arctic

Author: Melissa L. Grunst, Andrea S. Grunst, David Grémillet, Akiko Kato, Paco Bustamante, Céline Albert, Émile Brisson‐Curadeau, Manon Clairbaux, Marta Cruz‐Flores, Sophie Gentès, Antoine Grissot, Samuel Perret, Eric Ste‐Marie, Dariusz Jakubas, Katarzyna Wojczulanis‐Jakubas, Jérôme Fort, LIttoral ENvironnement et Sociétés (LIENSs), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), McGill University = Université McGill [Montréal, Canada], University College Cork (UCC), University of Gdańsk (UG), and ANR-20-CE34-0006,ARCTIC-STRESSORS,Effets combinés des stresseurs environnementaux multiples sur les oiseaux marins Arctiques(2020)
Subjects: climate change, mercury, sea surface temperature, activity budgets, daily energy expenditure, plasticity, [SDV.TOX.ECO]Life Sciences [q-bio]/Toxicology/Ecotoxicology, [SDV.EE.BIO]Life Sciences [q-bio]/Ecology, environment/Bioclimatology, dovekie, Ecology, Evolution, Behavior and Systematics, ecotoxicology
Abstract: International audience; Climate change is transforming bioenergetic landscapes, challenging behavioral and physiological coping mechanisms. A critical question involves whether animals can adjust behavioral patterns and energy expenditure to stabilize fitness given reconfiguration of resource bases, or whether limits to plasticity ultimately compromise energy balance. In the Arctic, rapidly warming temperatures are transforming food webs, making Arctic organisms strong models for understanding biological implications of climate change-related environmental variability. We examined plasticity in the daily energy expenditure (DEE) of an Arctic seabird, the little auk (Alle alle) in response to variability in climate change-sensitive drivers of resource availability, sea surface temperature (SST) and sea ice coverage (SIC), and tested the hypothesis that energetic ceilings and exposure to mercury, an important neurotoxin and endocrine disrupter in marine ecosystems, may limit scope for plasticity. To estimate DEE, we used accelerometer data obtained across years from two colonies exposed to distinct environmental conditions (Ukaleqarteq [UK], East Greenland; Hornsund [HS], Svalbard). We proceeded to model future changes in SST to predict energetic impacts. At UK, high flight costs linked to low SIC and high SST drove DEE from below to above 4 × basal metabolic rate (BMR), a proposed energetic threshold for breeding birds. However, DEE remained below 7 × BMR, an alternative threshold, and did not plateau. Birds at HS experienced higher, relatively invariable SST, and operated above 4 × BMR. Mercury exposure was unrelated to DEE, and fitness remained stable. Thus, plasticity in DEE currently buffers fitness, providing resiliency against climate change. Nevertheless, modeling suggests that continued warming of SST may promote accelerating increases in DEE, which may become unsustainable.
Published: 2023

21. MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes

Author: Bertrand Néron, Eduardo Rocha, Rémi Denise, Marie Touchon, Sophie Abby, Charles Coluzzi, Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Génomique évolutive des Microbes / Microbial Evolutionary Genomics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), University College Cork (UCC), Translational Innovation in Medicine and Complexity / Recherche Translationnelle et Innovation en Médecine et Complexité - UMR 5525 (TIMC ), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), EPCR lab acknowledges funding from the INCEPTION project (ANR-16-CONV-0005), Equipe FRM(Fondation pour la Recherche Médicale): EQU201903007835, and Laboratoire d’Excellence IBEIDIntegrative Biology of Emerging Infectious Diseases (ANR-10-LABX-62-IBEID). SSA received financial supportfrom the CNRS and TIMC lab (INSIS 'starting grant') and the French National Research Agency,'Investissements d’avenir' program ANR-15-IDEX-02, ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), and ANR-15-IDEX-0002,UGA,IDEX UGA(2015)
Subjects: [SDV]Life Sciences [q-bio], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Abstract: Complex cellular functions are usually encoded by a set of genes in one or a few organized genetic loci in microbial genomes. Macromolecular System Finder (MacSyFinder) is a program that uses these properties to model and then annotate cellular functions in microbial genomes. This is done by integrating the identification of each individual gene at the level of the molecular system. We hereby present a major release of MacSyFinder (version 2) coded in Python 3. The code was improved and rationalized to facilitate future maintainability. Several new features were added to allow more flexible modelling of the systems. We introduce a more intuitive and comprehensive search engine to identify all the best candidate systems and sub-optimal ones that respect the models' constraints. We also introduce the novel macsydata companion tool that enables the easy installation and broad distribution of the models developed for MacSyFinder (macsy-models) from GitHub repositories. Finally, we have updated and improved MacSyFinder popular models: TXSScan to identify protein secretion systems, TFFscan to identify type IV filaments, CONJscan to identify conjugative systems, and CasFinder to identify CRISPR associated proteins. MacSyFinder and the updated models are available at: https://github.com/gem-pasteur/macsyfinder and https://github.com/macsy-models.
Published: 2023

22. Upconversion channels in Er3+:ZBLALiP fluoride glass microspheres

Author: Michel Mortier, Patrice Feron, Jonathan M. Ward, Danny O'Shea, B.J. Shortt, S. Nic Chormaic, Quantum Optics Group, University College Cork (UCC)-Science Foundation Ireland-Tyndall National Institute, Photonics Centre, University College Cork (UCC), Department of Applied Physics and Instrumentation, Cork Institute of Technology (CIT), Laboratoire de Chimie de la Matière Condensée de Paris (site Paris VI) (LCMCP (site Paris VI)), Université Pierre et Marie Curie - Paris 6 (UPMC)-Collège de France (CdF (institution))-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Fonctions Optiques pour les Technologies de l'informatiON (FOTON), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École Nationale Supérieure des Sciences Appliquées et de Technologie (ENSSAT)-Télécom Bretagne-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-École Nationale Supérieure des Sciences Appliquées et de Technologie (ENSSAT)-Télécom Bretagne
Subjects: Materials science, Infrared, Analytical chemistry, Physics::Optics, chemistry.chemical_element, 02 engineering and technology, medicine.disease_cause, 01 natural sciences, law.invention, 010309 optics, Erbium, law, PACS: 42.55.Sa, 42.70, 0103 physical sciences, Radiative transfer, medicine, Instrumentation, Astrophysics::Galaxy Astrophysics, Laser materials, [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], business.industry, Quartz, 021001 nanoscience & nanotechnology, Condensed Matter Physics, Laser, Photon upconversion, Electronic, Optical and Magnetic Materials, chemistry, Microcavity and microdisk lasers, Optoelectronics, Glass, Whispering-gallery wave, 0210 nano-technology, business, Lasing threshold, Ultraviolet
Abstract: Topic "Laser and Optics"; International audience; We present results on the realization of a multicolour microspherical glass light source fabricated from the erbium doped fluoride glass ZBLALiP.Whispering gallery mode lasing and upconversion processes give rise to laser and fluorescent emissions at multiple wavelengths from the ultraviolet to the infrared. Thirteen discrete emissions ranging from 320 to 849 nm have been observed in the upconversion spectrum. A Judd-Ofelt analysis was performed to calculate the radiative properties of Er3+ :ZBLALiP microspheres, including the radiative transition probabilities, the electric dipole strengths, the branching ratios and the radiative lifetimes of the transitions involved. We have also identified the primary processes responsible for the generation of the observed wavelengths and have shown that this material has an improved range of emissions over other erbium doped fluoride glasses.
Published: 2007

23. Induction of oxiapoptophagy on 158N murine oligodendrocytes treated by 7-ketocholesterol-, 7 beta-hydroxycholesterol-, or 24(S)-hydroxycholesterol: Protective effects of alpha-tocopherol and docosahexaenoic acid (DHA; C22:6 n-3)

Author: Mohammad Samadi, Anne Vejux, Michel Prost, Emeric Limagne, Régis Delage-Mourroux, Thibault Moreau, Amira Zarrouk, Nora M. O'Brien, Dominique Delmas, Jean-Marc Riedinger, Margaux Doria, Thomas Nury, Gérard Lizard, Mohamed Hammami, Philippe Durand, John J. Mackrill, Université de Bourgogne (UB), UR12ES05, Laboratory of Nutrition-Functional Food & Vascular Health, Faculté de Médecine de Monastir [Tunisie], University College Cork (UCC), Laboratoire de Chimie et Physique - Approche Multi-échelle des Milieux Complexes (LCP-A2MC), Université de Lorraine (UL), Modélisation mathématique et numérique (M2N), Conservatoire National des Arts et Métiers [CNAM] (CNAM), Laboratoire de Biologie Médicale [Centre Georges-François leclerc], Centre Régional de Lutte contre le cancer Georges-François Leclerc [Dijon] (UNICANCER/CRLCC-CGFL), UNICANCER-UNICANCER, Laboratoire Bio-PeroxIL. Biochimie du Peroxysome, Inflammation et Métabolisme Lipidique (Bio-PeroxIL), Lipides - Nutrition - Cancer (U866) (LNC), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Bourgogne (UB)-Ecole Nationale Supérieure de Biologie Appliquée à la Nutrition et à l'Alimentation de Dijon (ENSBANA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Laboratoire de Recherche Appliquée Spiral [Bourgogne] (LARA SPIRAL), Service de Neurologie générale, vasculaire et dégénérative (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Estrogènes, Expression génique et pathologies du Système Nerveux Central - UFC (E2SNC / ESTROGENES), Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Department of Food and Nutritional Sciences, Université de Bourgogne ( UB ), United College Cork (National University of Ireland) ( UCC ), Laboratoire de Chimie et Physique - Approche Multi-échelle des Milieux Complexes ( LCP-A2MC ), Université de Lorraine ( UL ), Modélisation mathématique et numérique ( M2N ), Conservatoire National des Arts et Métiers [CNAM] : EA7340, Centre Régional de Lutte contre le cancer - Centre Georges-François Leclerc ( CRLCC - CGFL ), Laboratoire Bio-PeroxIL. Biochimie du Peroxysome, Inflammation et Métabolisme Lipidique ( Bio-PeroxIL ), Lipides - Nutrition - Cancer (U866) ( LNC ), Université de Bourgogne ( UB ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Ecole Nationale Supérieure de Biologie Appliquée à la Nutrition et à l'Alimentation de Dijon ( ENSBANA ), Laboratoire de Recherche Appliquée Spiral [Bourgogne] ( LARA SPIRAL ), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand ( CHU Dijon ), Estrogènes, Expression génique et pathologies du Système Nerveux Central - UFC ( E2SNC / ESTROGENES ), Université de Franche-Comté ( UFC ), and University College Cork ( UCC )
Subjects: Anions, Programmed cell death, Docosahexaenoic Acids, 7 beta-Hydroxycholesterol, Clinical Biochemistry, alpha-Tocopherol, [ PHYS.COND.CM-MS ] Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], Apoptosis, Biology, Protective Agents, medicine.disease_cause, Biochemistry, Mice, Endocrinology, Superoxides, Autophagy, medicine, Animals, Microscopy, Phase-Contrast, Fragmentation (cell biology), Ketocholesterols, Molecular Biology, Cell Proliferation, Pharmacology, chemistry.chemical_classification, Reactive oxygen species, Oxiapoptophagy, Cell growth, Organic Chemistry, Hydrogen Peroxide, Molecular biology, 7-Ketocholesterol, Hydroxycholesterols, Mitochondria, 3. Good health, Oligodendroglia, Docosahexaenoic acid, chemistry, 24(S)-hydroxycholesterol, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], sense organs, Oxidation-Reduction, Biomarkers, Oxidative stress
Abstract: International audience; In demyelinating or non-demyelinating neurodegenerative diseases, increased levels of 7-ketocholesterol (7KC), 7 beta-hydroxycholesterol (7 beta-OHC) and 24(S)-hydroxycholesterol (24S-OHC) can be observed in brain lesions. In 158N murine oligodendrocytes, 7KC triggers a complex mode of cell death defined as oxiapoptophagy, involving simultaneous oxidative stress, apoptosis and autophagy. In these cells, 7KC as well as 7 beta-OHC and 24S-OHC induce a decrease of cell proliferation evaluated by phase contrast microscopy, an alteration of mitochondrial activity quantified with the MU test, an overproduction of reactive oxygen species revealed by staining with dihydroethidium and dihydrorhodamine 123, caspase-3 activation, PARP degradation, reduced expression of Bcl-2, and condensation and/or fragmentation of the nuclei which are typical criteria of oxidative stress and apoptosis. Moreover, 7KC, 7 beta-OHC and 24S-OHC promote conversion of microtubule-associated protein light chain 3 (LC3-I) to LC3-II which is a characteristic of autophagy. Consequently, 7 beta-OHC and 24S-OHC, similarly to 7KC, can be considered as potent inducers of oxiapoptophagy. Furthermore, the different cytotoxic effects associated with 7KC, 7 beta-OHC and 24S-OHC-induced oxiapoptophagy are attenuated by vitamin E (VitE, alpha-tocopherol) and DHA which enhances VitE protective effects. In 158N murine oligodendrocytes, our data support the concept that oxiapoptophagy, which can be inhibited by VitE and DHA, could be a particular mode of cell death elicited by cytotoxic oxysterols.
Published: 2015

24. Accelerating clinical trial implementation in the context of the COVID-19 pandemic: challenges, lessons learned and recommendations from DisCoVeRy and the EU-SolidAct EU response group

Author: Alpha Diallo, Marius Trøseid, Victoria Charlotte Simensen, Anaïs Boston, Jacques Demotes, Inge Christoffer Olsen, Florence Chung, José Artur Paiva, Maya Hites, Florence Ader, Jose Ramon Arribas, Andreas Baratt-Due, Øyvind Melien, Evelina Tacconelli, Thèrèse Staub, Richard Greil, Sotirios Tsiodras, Matthias Briel, Hélène Esperou, France Mentré, Joe Eustace, Juliette Saillard, Christelle Delmas, Soizic LeMestre, Marina Dumousseaux, Dominique Costagliola, John-Arne Røttingen, Yazdan Yazdanpanah, Agence Nationale de Recherches sur le Sida et les Hépatites Virales (ANRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Oslo University Hospital [Oslo], European Clinical Research Infrastructures Network [Dusseldorf] (ECRIN), Hospital de São João [Porto], Université libre de Bruxelles (ULB), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), La Paz University Hospital, Norwegian Institute of Public Health [Oslo] (NIPH), Università degli studi di Verona = University of Verona (UNIVR), Centre Hospitalier de Luxembourg [Luxembourg] (CHL), Paracelsus Medizinische Privatuniversität = Paracelsus Medical University (PMU), National and Kapodistrian University of Athens (NKUA), University Hospital Basel [Basel], Pôle de Recherche Clinique [Paris] (PRC), AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), University College Cork (UCC), Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), CIC - CHU Bichat, Infection, Anti-microbiens, Modélisation, Evolution (IAME (UMR_S_1137 / U1137)), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Université Sorbonne Paris Nord
Subjects: Microbiology (medical), Medical education, Coronavirus disease 2019 (COVID-19), Adaptive Clinical Trials as Topic, EU-RESPOSE, Financial hurdles, Legal hurdles, Platform trials, Regulatory hurdles, MEDLINE, COVID-19, Context (language use), General Medicine, Clinical trial, Infectious Diseases, Political science, Pandemic, Commentary, Government Regulation, Humans, European Union, Pandemics, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Published: 2022

25. Four principles to establish a universal virus taxonomy

Author: Peter Simmonds, Evelien M. Adriaenssens, F. Murilo Zerbini, Nicola G. A. Abrescia, Pakorn Aiewsakun, Poliane Alfenas-Zerbini, Yiming Bao, Jakub Barylski, Christian Drosten, Siobain Duffy, W. Paul Duprex, Bas E. Dutilh, Santiago F. Elena, Maria Laura García, Sandra Junglen, Aris Katzourakis, Eugene V. Koonin, Mart Krupovic, Jens H. Kuhn, Amy J. Lambert, Elliot J. Lefkowitz, Małgorzata Łobocka, Cédric Lood, Jennifer Mahony, Jan P. Meier-Kolthoff, Arcady R. Mushegian, Hanna M. Oksanen, Minna M. Poranen, Alejandro Reyes-Muñoz, David L. Robertson, Simon Roux, Luisa Rubino, Sead Sabanadzovic, Stuart Siddell, Tim Skern, Donald B. Smith, Matthew B. Sullivan, Nobuhiro Suzuki, Dann Turner, Koenraad Van Doorslaer, Anne-Mieke Vandamme, Arvind Varsani, Nikos Vasilakis, University of Oxford, Quadram Institute Bioscience [Norwich, U.K.] (QIB), Biotechnology and Biological Sciences Research Council (BBSRC), Universidade Federal de Viçosa = Federal University of Viçosa (UFV), Center for Cooperative Research in Biosciences [Derio, Spain], Mahidol University [Bangkok], University of Chinese Academy of Sciences [Beijing] (UCAS), Rutgers, The State University of New Jersey [New Brunswick] (RU), Rutgers University System (Rutgers), Utrecht University [Utrecht], Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], National Institutes of Health [Bethesda] (NIH), Virologie des archées - Archaeal Virology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University College Cork (UCC), MRC - University of Glasgow Centre for Virus Research, Lawrence Berkeley National Laboratory [Berkeley] (LBNL), CNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] (IPSP), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Mississippi State University [Mississippi], Okayama University, University of the West of England [Bristol] (UWE Bristol), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Arizona State University [Tempe] (ASU), The University of Texas Medical Branch (UTMB), European Project: 865694,H2020-EU.1.1. - EXCELLENT SCIENCE - European Research Council (ERC),DiversiPHI(2020), Instituto de Higiene e Medicina Tropical (IHMT), Global Health and Tropical Medicine (GHTM), TB, HIV and opportunistic diseases and pathogens (THOP), Faculty Common Matters (Faculty of Biology and Environmental Sciences), Molecular Principles of Viruses, Molecular and Integrative Biosciences Research Programme, and Molecular and Translational Virology
Subjects: Neuroscience(all), [SDV]Life Sciences [q-bio], principles, R Medicine, Medical and Health Sciences, General Biochemistry, Genetics and Molecular Biology, SDG 3 - Good Health and Well-being, Immunology and Microbiology(all), Humans, Bacteriophages, Phylogeny, Taxonomy, 11832 Microbiology and virology, Agricultural and Veterinary Sciences, General Immunology and Microbiology, Biochemistry, Genetics and Molecular Biology(all), General Neuroscience, universal virus taxonomy, Biodiversity, Biological Sciences, Medical Terminology, Infectious Diseases, 12D8623N#57012320, PDMT2/21/038#56345426, Viruses, 1181 Ecology, evolutionary biology, Metagenomics, Infection, General Agricultural and Biological Sciences, QR355 Virology, Developmental Biology
Abstract: 1759874.Y.B.wassupportedbythe ProfessionalAssociationoftheAllianceof Publisher Copyright: Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. A universal taxonomy of viruses is essential for a comprehensive view of the virus world and for communicating the complicated evolutionary relationships among viruses. However, there are major differences in the conceptualisation and approaches to virus classification and nomenclature among virologists, clinicians, agronomists, and other interested parties. Here, we provide recommendations to guide the construction of a coherent and comprehensive virus taxonomy, based on expert scientific consensus. Firstly, assignments of viruses should be congruent with the best attainable reconstruction of their evolutionary histories, i.e., taxa should be monophyletic. This fundamental principle for classification of viruses is currently included in the International Committee on Taxonomy of Viruses (ICTV) code only for the rank of species. Secondly, phenotypic and ecological properties of viruses may inform, but not override, evolutionary relatedness in the placement of ranks. Thirdly, alternative classifications that consider phenotypic attributes, such as being vector-borne (e.g., “arboviruses”), infecting a certain type of host (e.g., “mycoviruses,” “bacteriophages”) or displaying specific pathogenicity (e.g., “human immunodeficiency viruses”), may serve important clinical and regulatory purposes but often create polyphyletic categories that do not reflect evolutionary relationships. Nevertheless, such classifications ought to be maintained if they serve the needs of specific communities or play a practical clinical or regulatory role. However, they should not be considered or called taxonomies. Finally, while an evolution-based framework enables viruses discovered by metagenomics to be incorporated into the ICTV taxonomy, there are essential requirements for quality control of the sequence data used for these assignments. Combined, these four principles will enable future development and expansion of virus taxonomy as the true evolutionary diversity of viruses becomes apparent. publishersversion published
Published: 2023

26. Analysis of Small Non-coding RNAs as Signaling Intermediates of Environmentally Integrated Responses to Abiotic Stress

Author: Christophe Penno, Julien Tremblay, Mary O’Connell Motherway, Virginie Daburon, Abdelhak El Amrani, 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), National Research Council of Canada (NRC), Institut Armand Frappier (INRS-IAF), Institut National de la Recherche Scientifique [Québec] (INRS)-Réseau International des Instituts Pasteur (RIIP), University College Cork (UCC), and Couée I.
Subjects: Bacteria, microRNA, Bioinformatics, Rhizosphere, Fungi, Microorganisms, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Abiotic stress, NGS library, Interkingdom communication
Abstract: International audience; Research to date on abiotic stress responses in plants has been largely focused on the plant itself, but current knowledge indicates that microorganisms can interact with and help plants during periods of abiotic stress. In our research, we aim to investigate the interkingdom communication between the plant root and the rhizo-microbiota. Our investigation showed that miRNA plays a pivotal role in this interkingdom communication. Here, we describe a protocol for the analysis of miRNA secreted by the plant root, which includes all of the steps from the isolation of the miRNA to the bioinformatics analysis. Because of their short nucleotide length, Next Generation Sequencing (NGS) library preparation from miRNAs can be challenging due to the presence of dimer adapter contaminants. Therefore, we highlight some strategies we adopt to inhibit the generation of dimer adapters during library preparation. Current screens of miRNA targets mostly focus on the identification of targets present in the same organism expressing the miRNA. Our bioinformatics analysis challenges the barrier of evolutionary divergent organisms to identify candidate sequences of the microbiota targeted by the miRNA of plant roots. This protocol should be of interest to researchers investigating interkingdom RNA-based communication between plants and their associated microorganisms, particularly in the context of holobiont responses to abiotic stresses.
Published: 2023

27. Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee

Author: Dann Turner, Andrey N. Shkoporov, Cédric Lood, Andrew D. Millard, Bas E. Dutilh, Poliane Alfenas-Zerbini, Leonardo J. van Zyl, Ramy K. Aziz, Hanna M. Oksanen, Minna M. Poranen, Andrew M. Kropinski, Jakub Barylski, J Rodney Brister, Nina Chanisvili, Rob A. Edwards, François Enault, Annika Gillis, Petar Knezevic, Mart Krupovic, Ipek Kurtböke, Alla Kushkina, Rob Lavigne, Susan Lehman, Malgorzata Lobocka, Cristina Moraru, Andrea Moreno Switt, Vera Morozova, Jesca Nakavuma, Alejandro Reyes Muñoz, Jānis Rūmnieks, BL Sarkar, Matthew B. Sullivan, Jumpei Uchiyama, Johannes Wittmann, Tong Yigang, Evelien M. Adriaenssens, UCL - SST/ELI/ELIM - Applied Microbiology, University of the West of England [Bristol] (UWE Bristol), University College Cork (UCC), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), University of Leicester, Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], Utrecht University [Utrecht], Universidade Federal de Viçosa = Federal University of Viçosa (UFV), University of the Western Cape (UWC), Cairo University, Helsingin yliopisto = Helsingfors universitet = University of Helsinki, University of Guelph, Adam Mickiewicz University in Poznań (UAM), National Center for Biotechnology Information (NCBI), George Eliava Institute of Bacteriophages, Microbiology and Virology [Tbilisi, Georgia], Flinders Accelerator for Microbiome Exploration [Adelaide, Australia], Laboratoire Microorganismes : Génome et Environnement (LMGE), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), Université Catholique de Louvain = Catholic University of Louvain (UCL), University of Novi Sad, Virologie des archées - Archaeal Virology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of the Sunshine Coast (USC), D.K. Zabolotny Institute of Microbiology and Virology [Kyiv, Ukraine], National Academy of Sciences of Ukraine (NASU), University of Gdańsk (UG), Center for Biologics Evaluation and Research, U.S. Food and Drug Administration (FDA), Institute of Biochemistry and Biophysics [Warsaw] (IBB), University of Oldenburg, Pontificia Universidad Católica de Chile (UC), Institute of Chemical Biology and Fundamental Medicine [Novosibirsk, Russia] (ICBFM SB RAS), Siberian Branch of the Russian Academy of Sciences (SB RAS), Makerere University [Kampala, Ouganda] (MAK), Universidad de los Andes [Bogota] (UNIANDES), Latvian Biomedical Research and Study Center (BMC), National Institute of Cholera and Enteric Diseases, Ohio State University [Columbus] (OSU), Okayama University, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (DSMZ), Beijing University of Chemical Technology, Quadram Institute Bioscience [Norwich, U.K.] (QIB), Biotechnology and Biological Sciences Research Council (BBSRC), B.E.D. was supported by the European Research Council (ERC) Consolidator Grant 865694: DiversiPHI, the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy – EXC 2051 – Project-ID 390713860, the Alexander von Humboldt Foundation in the context of an Alexander von Humboldt Professorship funded by the German Federal Ministry of Education and Research, and the European Union’s Horizon 2020 Research and Innovation Program, under the Marie Skłodowska-Curie Actions Innovative Training Networks grant agreement no. 955974 (VIROINF). Work by J.R.B. was supported by the National Center for Biotechnology Information of the National Library of Medicine (NLM), National Institutes of Health. R.A.E was supported by an award from the National Institute of Diabetes and Digestive and Kidney Diseases of the National Institute of Health RC2DK116713 and an award from the Australian Research Council, DP220102915. R.L. is supported by the research grant PHAGEFORCE from the KU Leuven. C.L. is supported by the Research Foundation - Flanders (FWO Grant 12D8623N) and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy – EXC 2051 – Project-ID 390713860. V.M. is supported by the Russian state-funded project For ICBFM SB RAS, Grant 121031300043-8. H.M.O. was supported by the University of Helsinki and Academy of Finland by funding for FINStruct and Instruct Centre Finland, Instruct-ERIC. M.M.P. acknowledges funding from the Sigrid Jusélius Foundation and the Academy of Finland (grant 331627). A.N.S is supported by a Wellcome Trust Research Career Development Fellowship [220646/Z/20/Z] and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No 101001684). E.M.A. gratefully acknowledges funding by the Biotechnology and Biological Sciences Research Council (BBSRC), this research was funded by the BBSRC Institute Strategic Programme Gut Microbes and Health BB/R012490/1 and its constituent projects BBS/E/F/000PR10353 and BBS/E/F/000PR10356., European Project: 865694,H2020-EU.1.1. - EXCELLENT SCIENCE - European Research Council (ERC),DiversiPHI(2020), and European Project: 101001684,ERC-2020-COG,PHAGENET(2021)
Subjects: Science & Technology, [SDV]Life Sciences [q-bio], Virology, General Medicine, Life Sciences & Biomedicine
Abstract: This article summarises the activities of the Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses for the period of March 2021−March 2022. We provide an overview of the new taxa proposed in 2021, approved by the Executive Committee, and ratified by vote in 2022. Significant changes to the taxonomy of bacterial viruses were introduced: the paraphyletic morphological families Podoviridae, Siphoviridae, and Myoviridae as well as the order Caudovirales were abolished, and a binomial system of nomenclature for species was established. In addition, one order, 22 families, 30 subfamilies, 321 genera, and 862 species were newly created, promoted, or moved.
Published: 2023

28. Mercury contamination challenges the behavioral response of a keystone species to Arctic climate change

Author: Grunst, Andrea S., Grunst, Melissa L., Grémillet, David, Kato, Akiko, Bustamante, Paco, Albert, Céline, Brisson-Curadeau, Émile, Clairbaux, Manon, Cruz-Flores, Marta, Gentès, Sophie, Perret, Samuel, Ste-Marie, Eric, Wojczulanis-Jakubas, Katarzyna, Fort, Jérôme, LIttoral ENvironnement et Sociétés (LIENSs), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Percy FitzPatrick Institute of African Ornithology, University of Cape Town, Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), McGill University = Université McGill [Montréal, Canada], School of Biological, Earth and Environmental Sciences [Cork] (BEES), University College Cork (UCC), Department of Vertebrate Ecology and Zoology, University of Gdańsk (UG), and ANR-16-CE34-0005,ILETOP,Impact des polluants historiques et émergents sur les prédateurs supérieurs marins de l'Arctique(2016)
Subjects: multiple stressors, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, climate change, mercury (Hg), diving behavior, behavioral ecotoxicology, Environmental Chemistry, [SDV.TOX.ECO]Life Sciences [q-bio]/Toxicology/Ecotoxicology, General Chemistry, toxicant-induced climate change sensitivity, behavioral plasticity
Abstract: International audience; Combined effects of multiple, climate change-associated stressors are of mounting concern, especially in Arctic ecosystems. Elevated mercury (Hg) exposure in Arctic animals could affect behavioral responses to changes in foraging landscapes caused by climate change, generating interactive effects on behavior and population resilience. We investigated this hypothesis in little auks (Alle alle), a keystone Arctic seabird. We compiled behavioral data for 44 birds across 5 years using accelerometers while also quantifying blood Hg and environmental conditions. Warm sea surface temperature (SST) and low sea ice coverage reshaped time activity budgets (TABs) and diving patterns, causing decreased resting, increased flight, and longer dives. Mercury contamination was not associated with TABs. However, highly contaminated birds lengthened interdive breaks when making long dives, suggesting Hg-induced physiological limitations. As dive durations increased with warm SST, subtle toxicological effects threaten to increasingly constrain diving and foraging efficiency as climate change progresses, with ecosystem-wide repercussions.
Published: 2023
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29. Guidance for creating individual and batch latinized binomial virus species names

Author: Postler, Thomas S., Rubino, Luisa, Adriaenssens, Evelien M., Dutilh, Bas E., Harrach, Balázs, Junglen, Sandra, Kropinski, Andrew M., Krupovic, Mart, Wada, Jiro, Crane, Anya, Kuhn, Jens H., Mushegian, Arcady, Rūmnieks, Jānis, Sabanadzovic, Sead, Simmonds, Peter, Varsani, Arvind, Zerbini, F. Murilo, Callanan, Julie, Draper, Lorraine A., Hill, Colin, Stockdale, Stephen R., Theoretical Biology and Bioinformatics, Sub Bioinformatics, Columbia University Irving Medical Center (CUIMC), CNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] (IPSP), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Quadram Institute Bioscience [Norwich, U.K.] (QIB), Biotechnology and Biological Sciences Research Council (BBSRC), Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], Utrecht University [Utrecht], Institute for Veterinary Medical Research [Budapest] (AOTI), Centre for Agricultural Research [Budapest] (ATK), Hungarian Academy of Sciences (MTA)-Hungarian Academy of Sciences (MTA), Humboldt University Of Berlin, University of Guelph, Virologie des archées - Archaeal Virology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), National Institutes of Health [Bethesda] (NIH), National Science Foundation [Arlington] (NSF), Latvian Biomedical Research and Study Centre [Rīga], Mississippi State University [Mississippi], University of Oxford, Arizona State University [Tempe] (ASU), University of Cape Town, Universidade Federal de Viçosa = Federal University of Viçosa (UFV), University College Cork (UCC), This work was supported in part through Laulima Government Solutions, LLC prime contract with the U.S. National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272201800013C. A.C. and J.W. performed this work as employees or affiliates of Laulima Government Solutions, LLC. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC under Contract No. HHSN272201800013C. This publication has emanated from research conducted with the financial support of Science Foundation Ireland under grant numbers SFI/12/RC/2273_P2 and SFI/14/SP APC/B3032 (J.C., L.A.D, C.H. and S.R.S). E.M.A. gratefully acknowledges the support of the Biotechnology and Biological Sciences Research Council (BBSRC), this research was funded by the BBSRC Institute Strategic Program Gut Microbes and Health BB/R012490/1 and its constituent project(s) BBS/E/F/000PR10353 and BBS/E/F/000PR10356. B.E.D. was supported by the European Research Council (ERC) Consolidator grant 865694: DiversiPHI and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy EXC 2051 Project-ID 390713860. B.H. is supported by the National Research, Development and Innovation Office—NKFIH (NN140356). A.R.M. is a Program Director at the U.S. National Science Foundation (NSF), but the statements and opinions expressed herein are made in the personal capacity and do not constitute the endorsement by NSF or the government of the United States. S.S. acknowledges partial support from the Special Research Initiative (MAFES) USDA-ARS project 58-6066-9-033 and the National Institute of Food and Agriculture, U.S. Department of Agriculture, Hatch Project 1021494., European Project: 865694,H2020-EU.1.1. - EXCELLENT SCIENCE - European Research Council (ERC),DiversiPHI(2020), Theoretical Biology and Bioinformatics, and Sub Bioinformatics
Subjects: Virus taxonomy, Binomial, virus nomenclature, virus taxonomy, Virus nomenclature, International Committee on Taxonomy of Viruses, binomial, Ictv, ICTV, Virology, Latinization, Species name, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, species name
Abstract: The International Committee on Taxonomy of Viruses recently adopted, and is gradually implementing, a binomial naming format for virus species. Although full Latinization of these names remains optional, a standardized nomenclature based on Latinized binomials has the advantage of comparability with all other biological taxonomies. As a language without living native speakers, Latin is more culturally neutral than many contemporary languages, and words built from Latin roots are already widely used in the language of science across the world. Conversion of established species names to Latinized binomials or creation of Latinized binomials de novo may seem daunting, but the rules for name creation are straightforward and can be implemented in a formulaic manner. Here, we describe approaches, strategies and steps for creating Latinized binomials for virus species without prior knowledge of Latin. We also discuss a novel approach to the automated generation of large batches of novel genus and species names. Importantly, conversion to a binomial format does not affect virus names, many of which are created from local languages.
Published: 2022

30. Anisotropic electron g factor as a probe of the electronic structure of GaBi x As 1 − x / GaAs epilayers

Author: Broderick, Christopher, Mazzucato, Simone, Carrère, Hélène, Amand, Thierry, Makhloufi, Hajer, Arnoult, Alexandre, Fontaine, Chantal, Donmez, Omer, Erol, Ayşe, Usman, Muhammad, O'Reilly, Eoin, Marie, Xavier, Tyndall National Institute [Cork], Department of Physics [Cork], University College Cork (UCC), Laboratoire de physique et chimie des nano-objets (LPCNO), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut de Chimie de Toulouse (ICT), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Équipe Photonique (LAAS-PHOTO), Laboratoire d'analyse et d'architecture des systèmes (LAAS), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT), Service Techniques et Équipements Appliqués à la Microélectronique (LAAS-TEAM), Istanbul University, Centre for Quantum Computation and Communication Technology, Australian National University (ANU), University College Cork ( UCC ), Laboratoire de physique et chimie des nano-objets ( LPCNO ), 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 ( UPS ), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique ( CNRS ), Équipe Photonique ( LAAS-PHOTO ), Laboratoire d'analyse et d'architecture des systèmes [Toulouse] ( LAAS ), Centre National de la Recherche Scientifique ( CNRS ) -Université Toulouse III - Paul Sabatier ( UPS ), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse ( INSA Toulouse ), Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -Institut National Polytechnique [Toulouse] ( INP ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Toulouse III - Paul Sabatier ( UPS ), Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -Institut National Polytechnique [Toulouse] ( INP ), Service Techniques et Équipements Appliqués à la Microélectronique ( LAAS-TEAM ), Division of Imaging Sciences, King‘s College London, Institut National des Sciences Appliquées ( INSA ), Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie de Toulouse (ICT-FR 2599), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut de Chimie du CNRS (INC), Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), and Université Fédérale Toulouse Midi-Pyrénées
Subjects: Condensed Matter::Materials Science, [ SPI.MAT ] Engineering Sciences [physics]/Materials, [ PHYS.COND.CM-MS ] Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], [SPI.OPTI]Engineering Sciences [physics]/Optics / Photonic, [ SPI.OPTI ] Engineering Sciences [physics]/Optics / Photonic, [SPI.MAT]Engineering Sciences [physics]/Materials
Abstract: International audience; The electron Landé g factor (g∗) is investigated both experimentally and theoretically in a series of GaBixAs1−x/GaAs strained epitaxial layers, for bismuth compositions up to x=3.8%. We measure g∗ via time-resolved photoluminescence spectroscopy, which we use to analyze the spin quantum beats in the polarization of the photoluminescence in the presence of an externally applied magnetic field. The experimental measurements are compared directly to atomistic tight-binding calculations on large supercells, which allows us to explicitly account for alloy disorder effects. We demonstrate that the magnitude of g∗ increases strongly with increasing Bi composition x and, based on the agreement between the theoretical calculations and experimental measurements, elucidate the underlying causes of the observed variation of g∗. By performing measurements in which the orientation of the applied magnetic field is changed, we further demonstrate that g∗ is strongly anisotropic. We quantify the observed variation of g∗ with x, and its anisotropy, in terms of a combination of epitaxial strain and Bi-induced hybridization of valence states due to alloy disorder, which strongly perturbs the electronic structure.
Published: 2014

31. An experimental evaluation of CP/AI/OR solvers for optimization in graphical models

Author: De Givry, Simon, Hurley, Barry, Allouche, David, Katsirelos, George, Schiex, Thomas, O'Sullivan, Barry, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Insight Centre for Data Analytics, University College Cork (UCC), ANR-10-BLA-0214, Insight Centre for Data Analytics (INSIGHT), MIAT INRA, Institut National de la Recherche Agronomique (INRA)-Institut National de la Recherche Agronomique (INRA), MIAT INRA Toulouse, University College Cork (UCC)-University College Cork (UCC), and Société française de recherche opérationnelle et d'aide à la décision
Subjects: Markov random field, Integer linear programming, optimisation combinatoire, SAT, [INFO]Computer Science [cs], [INFO.INFO-RO]Computer Science [cs]/Operations Research [cs.RO], Weighted constraint satisfaction problem, [MATH]Mathematics [math], Max-SAT, Graphical model, Max
Abstract: International audience; Graphical models on discrete variables allows to model NP-hard optimization problems where the objective function is factorized into a set of local functions. In the graphical interpretation, each function's scope is represented by a clique. Deterministic graphical models such as Cost Function Network (CFN) aim at minimizing the sum of all functions (or constraints if zero/infinite costs are used). Probabilistic graphical models such as Markov Random Field (MRF) aim at maximizing the product of all functions (or constraints if using zero/one probabilities). A direct (-log) transformation exists between the two frameworks that can also be modeled as weighted MaxSAT or ILP. Strong connections exist between LP itself and bounds used in graphical models. We report a large comparison of state-of-the-art CP/AI/OR exact solvers on several deterministic and probabilistic graphical models coming from the Probabilistic Inference Challenge 2011, the Weighted Partial Max-SAT Evaluation 2013, the MiniZinc Challenge 2012 and 2013, and a library of Cost Function Networks. These competitions are usually restricted to a family of dedicated solvers. We instead compare the efficiency of eight state-of-the-art exact solvers of each optimization language on these encodings. It includes MRF solvers daoopt (https://github.com/lotten/daoopt version 1.1.2), mplp2 (http://cs.nyu.edu/~dsontag/ version 2), toulbar2 (http://mulcyber.toulouse.inra.fr/projects/toulbar2/ version 0.9.6), MaxSAT solver maxhs (http://www.cs.toronto.edu/~jdavies/), ILP solver cplex (version 12.2), and CP solvers numberjack-mistral (http://numberjack.ucc.ie/ version 1.3.40), gecode (http://www.gecode.org/ version 4.2.0), opturion-cpx (http://www.opturion.com version 1.0.2). All the 1062 instances are made publicly available in five different formats (uai, wcsp, wcnf, lp, mzn) and seven formulations at http://genoweb.toulouse.inra.fr/~degivry/evalgm. The results suggest the opportunity for a simple portfolio approach and we give preliminary results based on the numberjack platform.
Published: 2014

32. Exploring Structural Diversity among Adhesion Devices Encoded by Lactococcal P335 Phages with AlphaFold2

Author: Adeline Goulet, Jennifer Mahony, Christian Cambillau, Douwe van Sinderen, Laboratoire d'ingénierie des systèmes macromoléculaires (LISM), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and University College Cork (UCC)
Subjects: Microbiology (medical), phages adhesion device, phages structure, Bacteriophages, lactococcal P335 phages, alphafold2, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Virology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Microbiology
Abstract: International audience; Bacteriophages, or phages, are the most abundant biological entities on Earth. They possess molecular nanodevices to package and store their genome, as well as to introduce it into the cytoplasm of their bacterial prey. Successful phage infection commences with specific recognition of, and adhesion to, a suitable host cell surface. Adhesion devices of siphophages infecting Grampositive bacteria are very diverse and remain, for the majority, poorly understood. These assemblies often comprise long, flexible, and multi-domain proteins, which limit their structural analyses by experimental approaches. The protein structure prediction program AlphaFold2 is exquisitely adapted to unveil structural and functional details of such molecular machineries. Here, we present structure predictions of adhesion devices from siphophages belonging to the P335 group infecting Lactococcus spp., one of the most extensively applied lactic acid bacteria in dairy fermentations. The predictions of representative adhesion devices from types I-IV P335 phages illustrate their very diverse topology. Adhesion devices from types III and IV phages share a common topology with that of Skunavirus p2, with a receptor binding protein anchored to the virion by a distal tail protein loop. This suggests that they exhibit an activation mechanism similar to that of phage p2 prior to host binding.
Published: 2022

33. A Mass Spectrometry Study of the Peptides Produced During the [i]in vivo[/i] digestion of α-lactalbumin

Author: Kehoe, J.J., Boutrou, Rachel, Jardin, Julien, Sullivan, L., Barry, L., Buckley, M.J.M., Shanahan, F., Mok, K.H., Dupont, Didier, Brodkorb, A., Irish Agriculture and Food Development Authority, Science et Technologie du Lait et de l'Oeuf (STLO), Institut National de la Recherche Agronomique (INRA)-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), Trinity Biomedical Sciences Institute, School of Biochemistry & Immunology, Gastrointestinal clinical measurement laboratory, Department of gastroenterology, Mercy University Hospital, Alimentary Pharmabiotic Centre (APC), Biosciences Institute (BSI), University College Cork (UCC)-University College Cork (UCC), and Institut National de Recherche Agronomique (INRA). UMR Science et Technologie du Lait et de l'Oeuf (1253).
Subjects: in vivo, spectrométrie de masse, [SDV.IDA]Life Sciences [q-bio]/Food engineering, alpha-lactalbumine, digestion, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, peptide
Abstract: An α-lactalbumin beverage was consumed by ten healthy subject and samples removed from their stomach via a naso-gastric tube at three minute intervals. The stomach pH initially increased, but after 3 minutes it began to decrease dropping to ~pH 2.0. Gastric emptying occurred after approximately 30 minutes. The digestion ofα-lactalbumin was followed gel permeation chromatography. The peak for intact α-lactalbumin was predominant during the first 6 minutes of digestion and ~90% of the protein present is greater than 10 kDa. After 9 minutes, corresponding with a significant decrease in pH, only ~5% of the protein was greater than 10 kDa and nointact α-lactalbumin remained. During an STSM stay in INRA, Rennes some of the digests were analysed by massspectrometry, 113 different peptides were identified. The greatest diversity of peptides is present after 12 minutes of digestion, however the portion of the protein sequence covered by the peptides identified remains constant, even though the number of peptides identified in the digests decreases over time. The peptidesidentified are not distributed evenly through the α-lactalbumin sequence. The terminals give rise to a greater number of peptides than the centre of the protein. The intensity of the signal obtained by the mass spectrometer for each peptide was measured. The majority peptides coming from the c-terminal portion of the protein (residues 81-123) were their maximum concentrations between 0 and 9 minutes of digestion. By this time the protein has just unfolded and the pH of the stomach is not low enough for optimum pepsin activity, this indicates that (1-40) do not reach their maximum concentration until later in the digestion when α-lactalbumin has unfolded and pH has dropped to 2.0.
Published: 2013

34. Subtilomycin: A New Lantibiotic from Bacillus subtilis Strain MMA7 Isolated from the Marine Sponge Haliclona simulans

Author: Matthieu Barret, Rui Chen, John P. Morrissey, Robert W. Phelan, Teresa M. Barbosa, Alan D. W. Dobson, Paul D. Cotter, Fergal O'Gara, Paula M. O'Connor, University College Cork (UCC), Teagasc Agriculture and Food Development Authority (Teagasc), Alimentary Pharmabiotic Centre (APC), Biosciences Institute (BSI), University College Cork (UCC)-University College Cork (UCC), Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Baylor University-Baylor University, Department of Microbiology, and European Project: 287589,EC:FP7:KBBE,FP7-OCEAN-2011,MICRO B3(2012)
Subjects: Gram-negative bacteria, Operon, [SDV]Life Sciences [q-bio], Pharmaceutical Science, Bacillus subtilis, Gram-Positive Bacteria, Article, subtilomycin, Microbiology, 03 medical and health sciences, Bacteriocins, Haliclona, Bacteriocin, Gram-Negative Bacteria, Drug Discovery, Animals, 14. Life underwater, antimicrobial, lantibiotic, marine sponge, Pharmacology, Toxicology and Pharmaceutics (miscellaneous), lcsh:QH301-705.5, 030304 developmental biology, 0303 health sciences, biology, 030306 microbiology, Hydrogen-Ion Concentration, Lantibiotics, biology.organism_classification, Antimicrobial, Solubility, lcsh:Biology (General), Dehydratase
Abstract: This research was supported in parts by grants awarded to FOG by the Science Foundation of Ireland (08/RFP/GEN1295, 08/RFP/GEN1319, SFI09/RFP/BMT2350); the Department of Agriculture, Fisheries and Food (RSF grants 06-321 and 06-377; FIRM grants 06RDC459 06RDC506 and 08RDC629); the European Commission (MicroB3-287589-OCEAN2012, MACUMBA-CP-TP 311975; PharmaSea-CP-TP 312184), the Marine Institute Beaufort award (C & CRA 2007/082) and the HRB (RP/2006/271, RP/2007/290, HRA/2009/146). We thank Lorraine Draper for assistance with the RP-HPLC.; International audience; Bacteriocins are attracting increased attention as an alternative to classic antibiotics in the fight against infectious disease and multidrug resistant pathogens. Bacillus subtilis strain MMA7 isolated from the marine sponge Haliclona simulans displays a broad spectrum antimicrobial activity, which includes Gram-positive and Gram-negative pathogens, as well as several pathogenic Candida species. This activity is in part associated with a newly identified lantibiotic, herein named as subtilomycin. The proposed biosynthetic cluster is composed of six genes, including protein-coding genes for LanB-like dehydratase and LanC-like cyclase modification enzymes, characteristic of the class I lantibiotics. The subtilomycin biosynthetic cluster in B. subtilis strain MMA7 is found in place of the sporulation killing factor (skf) operon, reported in many B. subtilis isolates and involved in a bacterial cannibalistic behaviour intended to delay sporulation. The presence of the subtilomycin biosynthetic cluster appears to be widespread amongst B. subtilis strains isolated from different shallow and deep water marine sponges. Subtilomycin possesses several desirable industrial and pharmaceutical physicochemical properties, including activity over a wide pH range, thermal resistance and water solubility. Additionally, the production of the lantibiotic subtilomycin could be a desirable property should B. subtilis strain MMA7 be employed as a probiotic in aquaculture applications.
Published: 2013

35. GAC for a Linear Inequality and an Atleast Constraint with an Application to Learning Simple Polynomials

Author: Razakarison, Naina, Beldiceanu, Nicolas, Carlsson, Mats, Simonis, Helmut, École normale supérieure - Cachan (ENS Cachan), Theory, Algorithms and Systems for Constraints (TASC), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Département informatique - EMN, Mines Nantes (Mines Nantes)-Mines Nantes (Mines Nantes)-Laboratoire d'Informatique de Nantes Atlantique (LINA), Mines Nantes (Mines Nantes)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), SICS, Swedish Institute of Computer Science [Stockholm] (SICS), Cork Constraint Computation Centre (4C UCC), University College Cork (UCC), Helmert, Malte and Röger, Gabriele, Laboratoire d'Informatique de Nantes Atlantique (LINA), Mines Nantes (Mines Nantes)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Mines Nantes (Mines Nantes)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Département informatique - EMN, Mines Nantes (Mines Nantes)-Inria Rennes – Bretagne Atlantique, and Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)
Subjects: [INFO.INFO-RO]Computer Science [cs]/Operations Research [cs.RO], ComputingMilieux_MISCELLANEOUS, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI]
Abstract: We provide a filtering algorithm achieving GAC for the conjunction of constraints atleast (b, [x(0),x(1),...,x(n-1)], V) and (a(0)*x(0) +...+ a(n-1)*x(n-1))
Published: 2021

36. A structural discovery journey of streptococcal phages adhesion devices by AlphaFold2

Author: Adeline Goulet, Raphaela Joos, Katherine Lavelle, Douwe Van Sinderen, Jennifer Mahony, Christian Cambillau, Laboratoire d'ingénierie des systèmes macromoléculaires (LISM), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University College Cork (UCC), School of Microbiology, and APC Microbiome Institute [Cork]
Subjects: Phage-host interactions, [SDV]Life Sciences [q-bio], Streptococcus, receptor-binding protein, Biochemistry, Genetics and Molecular Biology (miscellaneous), Biochemistry, bacteriophage, carbohydratebinding module, phage-host interactions, Receptor-binding protein, Bacteriophage, AlphaFold2, Carbohydrate-binding module, Molecular Biology
Abstract: Successful bacteriophage infection starts with specific recognition and adhesion to the host cell surface. Adhesion devices of siphophages infecting Gram-positive bacteria are very diverse and remain, for the majority, poorly understood. These assemblies often comprise long, flexible, and multi-domain proteins, which limits their structural analyses by experimental approaches such as X-ray crystallography and electron microscopy. However, the protein structure prediction program AlphaFold2 is exquisitely adapted to unveil structural and functional details of such molecular machineries. Here, we present structure predictions of whole adhesion devices of five representative siphophages infecting Streptococcus thermophilus, one of the main lactic acid bacteria used in dairy fermentations. The predictions highlight the mosaic nature of these devices that share functional domains for which active sites and residues could be unambiguously identified. Such AlphaFold2 analyses of phage-encoded host adhesion devices should become a standard method to characterize phage-host interaction machineries and to reliably annotate phage genomes.
Published: 2022

37. Uplink Transmission Policies for LoRa-Based Direct-to-Satellite IoT

Author: Guido Alvarez, Juan A. Fraire, Khaled Abdelfadeel Hassan, Sandra Cespedes, Dirk Pesch, Comisión Nacional de Actividades Espaciales - Argentinian Space Agency (CONAE), AlGorithmes et Optimisation pour Réseaux Autonomes (AGORA), CITI Centre of Innovation in Telecommunications and Integration of services (CITI), 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)-Institut National de Recherche en Informatique et en Automatique (Inria)-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)-Institut National de Recherche en Informatique et en Automatique (Inria)-Inria Lyon, Institut National de Recherche en Informatique et en Automatique (Inria), Danalto (Danalto), Universidad de Chile = University of Chile [Santiago] (UCHILE), NIC Research Labs [Chile], and University College Cork (UCC)
Subjects: [INFO.INFO-NI]Computer Science [cs]/Networking and Internet Architecture [cs.NI], General Computer Science, LR-FHSS, INDEX TERMS Medium Access Control, Direct-to-Satellite IoT, General Engineering, General Materials Science, Electrical and Electronic Engineering, LoRa, LoRaWAN
Abstract: International audience; Direct-to-Satellite IoT (DtS-IoT) is a promising approach to deliver data transfer services to IoT devices in remote areas where deploying terrestrial infrastructure is not appealing or feasible. In this context, low-Earth orbit (LEO) satellites can serve as passing-by IoT gateways to which devices can offload buffered data to. However, transmission distances and channel dynamics, combined with highly constrained devices on the ground makes of DtS-IoT a very challenging problem. Here, we present LoRa-based approaches to realize scalable and energy-efficient DtS-IoT. Our study includes the Long Range-Frequency Hopping Spread Spectrum (LR-FHSS) physical layer, currently on the roadmap of future space IoT projects. Specifically, we propose uplink transmission policies that exploit satellite trajectory information. These schemes are framed with a theoretical Mixed Integer Linear Programming (MILP) model providing an upper bound on performance as well as inspiration for scheduled DtS-IoT solutions. Simulation results provide compelling evidence that trajectory based policies can duplicate the amount of IoT nodes, while specific variants can further boost the scalability by 30% without incurring energy penalties. We also quantify that LR-FHSS can improve the deployment scalability by a factor of 75x at the expenses of 30% higher device's power consumption compared to the legacy LoRa modulation.
Published: 2022

38. Using hematophagous fly blood meals to study the diversity of blood-borne pathogens infecting wild mammals

Author: Solomon Mwakasungula, Virginie Rougeron, Céline Arnathau, Larson Boundenga, Eve Miguel, Anne Boissière, Davy Jiolle, Patrick Durand, Alphonce Msigwa, Sarah Mswata, Ally Olotu, Yvon Sterkers, Benjamin Roche, Gerard Killeen, Frédérique Cerqueira, Paul Yannick Bitome‐Essono, François Bretagnolle, Honorati Masanja, Christophe Paupy, Robert Sumaye, Franck Prugnolle, Ifakara Health Institute [Dar-es-Salaam, Tanzania], Nelson Mandela University [Port Elizabeth], Health, Emergence, Adaptation and Transmission (MIVEGEC-HEAT), Processus Écologiques et Évolutifs au sein des Communautés (PEEC), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM), Centre International de Recherches Médicales de Franceville (CIRMF), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM), Tanzania National Parks, CHU Montpellier, Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM), University College Cork (UCC), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Centre national de la recherche scientifique et technologique (CENAREST), Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Agence Nationale de la Recherche, Grant/Award Number: ANR--10--LABX--04--01, Agence Nationale de la Recherche, Grant/Award Number: ANR--11-LABX--0024, Horizon 2020 Framework Programme, Grant/Award Number: ZIKAlliance(no734548), and ANR-11-LABX-0024,ParaFrap,Alliance française contre les maladies parasitaires(2011)
Subjects: Mammals, Swine, Diptera, invertebrate-derived DNA (iDNA), [SDV]Life Sciences [q-bio], Tsetse flies, blood meals, Animals, Wild, tsetse flies, Invertebrate-derived DNA (iDNA), African Swine Fever Virus, Blood meals, Viruses, wildlife infectious diseases, xenosurveillance, Blood-Borne Pathogens, Genetics, Wildlife infectious diseases, Animals, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Xenosurveillance, Meals, Ecology, Evolution, Behavior and Systematics, Biotechnology
Abstract: International audience; Many emerging infectious diseases originate from wild animals, so there is a profound need for surveillance and monitoring of their pathogens. However, the practical difficulty of sample acquisition from wild animals tends to limit the feasibility and effectiveness of such surveys. Xenosurveillance, using blood-feeding invertebrates to obtain tissue samples from wild animals and then detect their pathogens, is a promising method to do so. Here, we describe the use of tsetse fly blood meals to determine (directly through molecular diagnostic and indirectly through serology), the diversity of circulating blood-borne pathogens (including bacteria, viruses and protozoa) in a natural mammalian community of Tanzania. Molecular analyses of captured tsetse flies (182 pools of flies totalizing 1728 flies) revealed that the blood meals obtained came from 18 different vertebrate species including 16 non-human mammals, representing approximately 25% of the large mammal species present in the study area. Molecular diagnostic demonstrated the presence of different protozoa parasites and bacteria of medical and/or veterinary interest. None of the six virus species searched for by molecular methods were detected but an ELISA test detected antibodies against African swine fever virus among warthogs, indicating that the virus had been circulating in the area. Sampling of blood-feeding insects represents an efficient and practical approach to tracking a diversity of pathogens from multiple mammalian species, directly through molecular diagnostic or indirectly through serology, which could readily expand and enhance our understanding of the ecology and evolution of infectious agents and their interactions with their hosts in wild animal communities.
Published: 2022

39. Structure Prediction and Analysis of Hepatitis E Virus Non-Structural Proteins from the Replication and Transcription Machinery by AlphaFold2

Author: Adeline Goulet, Christian Cambillau, Alain Roussel, Isabelle Imbert, Laboratoire d'ingénierie des systèmes macromoléculaires (LISM), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and University College Cork (UCC)
Subjects: nonstructural proteins, [SDV]Life Sciences [q-bio], [SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], Al-phaFold2, RNA-dependent RNA polymerase, Virus Replication, Hepatitis E, helicase, Viral Proteins, Infectious Diseases, Virology, viral replication/transcription enzymes, Hepatitis E virus, Humans, RNA, Viral, macro domain, Furylfuramide, AlphaFold2, Polyproteins
Abstract: International audience; Hepatitis E virus (HEV) is a major cause of acute viral hepatitis in humans globally. Considered for a long while a public health issue only in developing countries, the HEV infection is now a global public health concern. Most human infections are caused by the HEV genotypes 1, 2, 3 and 4 (HEV-1 to HEV-4). Although HEV-3 and HEV-4 can evolve to chronicity in immunocompromised patients, HEV-1 and HEV-2 lead to self-limited infections. HEV has a positive-sense single-stranded RNA genome of ~7.2 kb that is translated into a large pORF1 replicative polyprotein, essential for the viral RNA genome replication and transcription. Unfortunately, the composition and structure of these replicases are still unknown. The recent release of the powerful machine-learning protein structure prediction software AlphaFold2 (AF2) allows us to accurately predict the structure of proteins and their complexes. Here, we used AF2 with the replicase encoded by the polyprotein pORF1 of the human-infecting HEV-3. The boundaries and structures reveal five domains or nonstructural proteins (nsPs): the methyltransferase, Zn-binding domain, macro, helicase, and RNA-dependent RNA polymerase, reliably predicted. Their substrate-binding sites are similar to those observed experimentally for other related viral proteins. Precisely knowing enzyme boundaries and structures is highly valuable to recombinantly produce stable and active proteins and perform structural, functional and inhibition studies.
Published: 2022

40. Service software engineering for innovative infrastructure for global financial services

Author: MAAD, Soha, MCCARTHY, James B., GARBAYA, Samir, BEYNON, Meurig, NAGARAJAN, Rajagopal, University College Cork ( UCC ), Laboratoire Electronique, Informatique et Image ( Le2i ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Department of Computer Science [Warwick], University of Warwick [Coventry], University College Cork (UCC), Laboratoire Electronique, Informatique et Image [UMR6306] (Le2i), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Arts et Métiers (ENSAM), Arts et Métiers Sciences et Technologies, HESAM Université (HESAM)-HESAM Université (HESAM)-Arts et Métiers Sciences et Technologies, and HESAM Université (HESAM)-HESAM Université (HESAM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement
Subjects: Infrastructure, Integrative Framework, [ INFO.INFO-MO ] Computer Science [cs]/Modeling and Simulation, Service Software Engineering, [ SHS.ECO ] Humanities and Social Sciences/Economies and finances, Modélisation et simulation [Informatique], [SHS.ECO]Humanities and Social Sciences/Economics and Finance, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Economies et finances [Sciences de l'Homme et Société], Financial Services
Abstract: International audience; The recent financial crisis motivates our re-thinking of the engineering principles for service software and infrastructures intended to create business value in vital sectors. Existing monolithic, inwarddirected, cost insensitive and highly regulated technical and organizational infrastructures for financial services make it difficult for the domain to benefit from opportunities offered by new computing models such as cloud computing, software as a service, hardware as a service, and utility computing. The scale and global impact of the recent financial and economic crisis justify our domain focus to explore, from a service software engineering perspective, potential for increased uptake of “software as a service” in financial services as well as extrapolating our results to services in other vital domains. We describe in this paper an on going research agenda to develop service software engineering (SSE) for Innovative Global Infrastructure for Financial Services. We propose novel service software engineering involving a coherent blend of domain knowledge, policy modelling, social, cultural, and global factors with converged IT, telecom and media. Parts of this paper are based on an European Union Framework Program FP7 ICT call 5 proposal addressing challenge 1- Objective 1.2 - Service/Software Engineering methods and tools.
Published: 2010

41. Biochemical and genomic comparison of inorganic phosphate solubilization in Pseudomonas species

Author: H. Miller, Simon, Browne, Patrick, Prigent-Combaret, Claire, Combes-Meynet, Emeline, P. Morrissey, John, O'Gara, Fergal, BIOMERIT Research Centre, University College Cork (UCC), 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), 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), University College Cork ( UCC ), Ecologie microbienne ( EM ), 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 ( VAS )
Subjects: [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [ SDV.BBM.BM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Mobilization of insoluble soil inorganic phosphate by plant beneficial rhizobacteria is a trait of key importance to the development of microbial biofertilizers. In this study, the ability of several Pseudomonas spp. to solubilize Ca3(PO4)2 was compared. While all Pseudomonas spp. were found to facilitate a decrease in pH and solubilize inorganic phosphate by the production of extracellular organic acids, strains varied by producing either gluconic or 2-ketogluconic acid. Furthermore, comparison between the Pseudomonas spp. of the genes involved in oxidative glucose metabolism revealed variations in genomic organization. To further investigate the genetic mechanisms involved in inorganic phosphate solubilization by Pseudomonas spp., a transposon mutant library of P. fluorescens F113 was screened for mutants with reduced Ca3(PO4)2 solubilization ability. Mutations in the gcd and pqqE genes greatly reduced the solubilization ability, whereas mutations in the pqqB gene only moderately reduced this ability. The combination of biochemical analysis and genomic comparisons revealed that alterations in the pqq biosynthetic genes, and the presence/absence of the gluconate dehydrogenase (gad) gene, fundamentally affect phosphate solublization in strains of P. fluorescens.
Published: 2010

42. Virtual and Augmented Reality in Finance: State Visibility of Events and Risk'

Author: Samir Garbaya, Meurig Beynon, Saida Bouakaz, Rajagopal Nagarajan, Soha Maad, James B. McCarthy, Institut Image ENSAM, Laboratoire Electronique, Informatique et Image ( Le2i ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Simulation, Analyse et Animation pour la Réalité Augmentée ( SAARA ), Laboratoire d'InfoRmatique en Image et Systèmes d'information ( LIRIS ), Université Lumière - Lyon 2 ( UL2 ) -École Centrale de Lyon ( ECL ), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Centre National de la Recherche Scientifique ( CNRS ) -Institut National des Sciences Appliquées de Lyon ( INSA Lyon ), Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -Université Lumière - Lyon 2 ( UL2 ) -École Centrale de Lyon ( ECL ), Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ), IN-TECH Education and Publishing, University College Cork (UCC), Laboratoire Electronique, Informatique et Image [UMR6306] (Le2i), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Arts et Métiers (ENSAM), Arts et Métiers Sciences et Technologies, HESAM Université (HESAM)-HESAM Université (HESAM)-Arts et Métiers Sciences et Technologies, HESAM Université (HESAM)-HESAM Université (HESAM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Department of Computer Science [Warwick], University of Warwick [Coventry], Simulation, Analyse et Animation pour la Réalité Augmentée (SAARA), Laboratoire d'InfoRmatique en Image et Systèmes d'information (LIRIS), 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)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-École Centrale de Lyon (ECL), Université de Lyon-Université Lumière - Lyon 2 (UL2)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Université Lumière - Lyon 2 (UL2), University College Cork ( UCC ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Department of Computer Science, University of Warwick, UK, Université de Lille, Sciences Humaines et Sociales, HESAM Université (HESAM)-HESAM Université (HESAM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Arts et Métiers (ENSAM), and Garbaya, Samir
Subjects: Augmented Reality,Finance,Virtual reality, Engineering, media_common.quotation_subject, [INFO.INFO-SE] Computer Science [cs]/Software Engineering [cs.SE], 0211 other engineering and technologies, 02 engineering and technology, [INFO.INFO-SE]Computer Science [cs]/Software Engineering [cs.SE], [ INFO.INFO-SE ] Computer Science [cs]/Software Engineering [cs.SE], Recession, Virtual reality, [ INFO.INFO-HC ] Computer Science [cs]/Human-Computer Interaction [cs.HC], 021105 building & construction, 0502 economics and business, [ SHS.ECO ] Humanities and Social Sciences/Economies and finances, [INFO.INFO-HC]Computer Science [cs]/Human-Computer Interaction [cs.HC], media_common, Grand Challenges, Finance, Augmented Reality, business.industry, Financial risk, 05 social sciences, [ INFO.INFO-GR ] Computer Science [cs]/Graphics [cs.GR], Business value, [SHS.ECO]Humanities and Social Sciences/Economics and Finance, [INFO.INFO-GR]Computer Science [cs]/Graphics [cs.GR], Unexpected events, Business intelligence, Financial crisis, Augmented reality, [INFO.INFO-HC] Computer Science [cs]/Human-Computer Interaction [cs.HC], business, 050203 business & management
Abstract: This chapter reflected on the potential of Virtual Reality and Augmented Reality (VR / AR) technologies in supporting the dynamics of global financial systems and in addressing the grand challenges posed by unexpected events and crisis. The chapter briefly overviewed traditional VR/AR uses and described three early attempts to use 3D/ VR / AR technologies in Finance. In light of the recent financial crisis, there is a potential added valued in harnessing the use of VR/AR technologies to convey a greater visibility of the financial state (including visibility of financial risk). Various dimensions of the problem are considered. The chapter suggested a blend of service oriented computing SOC and empirical modelling technologies to support the use of VR / AR technologies in raising the perception of financial state and risk. There is a very significant distinction between VR modelling for areas such as assembly planning as represented in papers such as (Garbaya et al, 2000), and its application for greater visibility of the financial state and risk. Whilst we can reasonably speak of "using VR to model the reality of the process of assembly planning", the reality of the financial state is an altogether more elusive concept. Where manufacturing assembly deals with objects and actions whose objectivity and real-world authenticity is uncontroversial, financial state visibility is a prime example of an activity in which the impact of technology upon human cognition is prominent, and character of its agencies and observables is accordingly hard to capture in objective terms. Empirical Modelling supplies an appropriate framework within which to address the ontological issues raised by such applications of VR / AR (Beynon, 1999). This chapter points to the following conclusions: · 3D/ VR/ AR technologies can help in exploring a particular state in a social context. · The pre-construction phase of the virtual world can benefit greatly from concepts drawn from the Empirical Modelling literature such as modelling state, state change, and the initiators of state change. · 3D/ VR / AR technologies needs to be better adapted for the representation of multiple agents acting to change the state and corresponding visualisation. · The successful application of 3D / VR /AR technologies in modelling social and data intensive environment relies upon integrating these technologies with other programming paradigms and architectures such as service oriented computing and architecture (SOC and SOA). Future research agenda involves the development of quantitative and qualitative metrics to assess the potential benefits of 3D / VR / AR in modelling a state in a social context. Two dimensions are appropriate: the visibility and the viscosity.
Published: 2010

43. Permanent Genetic Resources added to Molecular Ecology Resources Database 1 December 2009-31 January 2010

Author: Anderson, Cynthia M., Aparicio, Gallego J., Atangana, Alain R., Beaulieu, Jean, Bruford, Michael W., Cain, Forest, Campos, T., Cariani, A., Carvalho, M.A., Chen, Nan, Chen, P.P., Clamens, Anne-Laure, Clark, Ann M., Coeur D'Acier, A., Connolly, Paul, Cordero-Rivera, Adolfo, Coughlan, James P., Cross, Thomas S., DAVID, Bruno, De Bruyn, Colin, De Meyer, M., De Ridder, Chantal, Delatte, Hélène, Dettori, M.T., Downer, S.J., Dubreuil, Christine, Evans, K.J., Fan, Bin, Ferrara, G., Gagné, André, Gaillard, Maria, Gigliarelli, L., Giovinazzi, J., Gomez, D.R., Grünwald, N.J., Hansson, Bengt, Huotari, T., Jank, L., Jousselin, Emmanuelle, Jungmann, L., Kaczmarek, M.E., Khasa, Damase P., Kneebone, Jeff, Korpelainen, H., Kostamo, K., Lanfaloni, L., Lin, Haoran, Liu, Xiaochun, Lucentini, L., Maes, G.E., Mahaffee, W.F., Meng, Zining, Micali, S., Milano, I., Mok, H.F., Morin, L., Neill, T.M., Newton, Craig H., Ostrow, D. Gigi, Palomba, A., Panara, F., Puletti, M.E., Quarta, R., Quilici, Serge, Ramos, A.K.B., Rigaud, Thierry, Risterucci, Ange Marie, Salomon, Matthew P., Sánchez-Guillén, Rosa A., Sarver, Shane K., Sequeira, A.S., Sforça, D.A., Simiand, Christophe, Smith, Brian, Sousa, A.C.B., Souza, A.P., Stepien, C.C., Stuckert, A.J., Sulikowski, James, Tayeh, A., Tinti, F., Tsang, Paul C.W., Van Houdt, J.K.J., Vendramin, E., Verde, I., Virgilio, M., Wang, Huan L., Wang, Le, Wattier, Rémi A., Wellenreuther, Maren, Xie, Cong X., Zane, L., Zhang, Xiu J., Zhang, Yong, Zhuang, Zhimeng, Zucchi, M.I., Center for the Conservation of Biological Resources, Black Hills State University, Universitat Politècnica de València (UPV), Centre d'étude de la forêt (CEF), Université de Sherbrooke (UdeS)-Université Laval [Québec] (ULaval)-McGill University = Université McGill [Montréal, Canada]-Université du Québec à Chicoutimi (UQAC)-Université de Montréal (UdeM)-Université Téluq (TELUQ)-Université du Québec en Abitibi-Témiscamingue (UQAT)-Université du Québec à Rimouski (UQAR)-Concordia University [Montreal]-Université du Québec à Montréal = University of Québec in Montréal (UQAM)-Université du Québec en Outaouais (UQO), Natural Resources Canada (NRCan), School of Biosciences [Cardiff], Cardiff University, Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Department of Experimental Evolutionary Biology, Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), Empresa Brasileira de Pesquisa Agropecuária (Embrapa), Ministério da Agricultura, Pecuária e Abastecimento [Brasil] (MAPA), Governo do Brasil-Governo do Brasil, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, ministry of education-Huazhong Agricultural University, Department of Biological Sciences [Wellesley], Wellesley College, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Interdisciplinary Center for Biotechnology Research, University of Florida [Gainesville] (UF), Marine Institute, Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, Department of Zoology, Ecology and Plant Science, University College Cork (UCC), Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Laboratoire de Biologie marine, Université libre de Bruxelles (ULB), Royal Museum for Central Africa [Tervuren] (RMCA), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), Centro di Ricerca per la Frutticoltura, CRA, Tasmanian Institute of Agricultural Research, University of Tasmania [Hobart, Australia] (UTAS), State Key Laboratory of Biocontrol, Sun Yat-Sen University [Guangzhou] (SYSU), Dipartimento di Biologia Cellulare e Ambientale, Università degli Studi di Perugia (UNIPG), CSIRO Entomology [Canberra], CSIRO Entomology, Horticultural Crops Research Laboratory, USDA-ARS : Agricultural Research Service, Department of Animal Ecology, Lund University [Lund], Department of Applied Biology, Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire (UNH), Finnish Environment Institute (SYKE), Laboratory of Animal Diversity and Systematics, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Vizon SciTecInc., Department of Biology [Gainesville] (UF|Biology), Polymorphismes d'intérêt agronomique (UMR PIA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Departamento de Biologia Vegetal (DBV), Marine Science Center, University of New England (UNE), Laboratory for Cytogenetics and Genome Research, Royal Belgian Institute of Natural Sciences (RBINS), Department of Biology, Universita degli Studi di Padova, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Pólo Apta Centro Sul, CYNTHIA M. ANDERSON, GALLEGO J. APARICIO, ALAIN R. ATANGANA, JEAN BEAULIEU, M.W. BRUFORD, FORREST CAIN, T. CAMPOS, A. CARIANI, M.A. CARVALHO, NAN CHEN, P.P. CHEN, A.-L. CLAMENS, ANN M. CLARK, A. COEUR D’ACIER, PAUL CONNOLLY, ADOLFO CORDERO-RIVERA, JAMES P. COUGHLAN, THOMAS S. CROSS, BRUNO DAVID, COLIN DE BRUYN, M. DE MEYER, CHANTAL DE RIDDER, H. DELATTE, M.T. DETTORI, S.J. DOWNER, CHRISTINE DUBREUIL, K.J. EVANS, BIN FAN, G. FERRARA, ANDRÉ GAGNÉ, MARIA GAILLARD, L. GIGLIARELLI, J. GIOVINAZZI, D.R. GOMEZ, N.J. GRÜNWALD, BENGT HANSSON, T. HUOTARI, L. JANK, E. JOUSSELIN, L. JUNGMANN, M.E. KACZMAREK, DAMASE P. KHASA, JEFF KNEEBONE, H. KORPELAINEN, K. KOSTAMO, L. LANFALONI, HAORAN LIN, XIAOCHUN LIU, L. LUCENTINI, G.E. MAES, W.F. MAHAFFEE, ZINING MENG, S. MICALI, I. MILANO, H.F. MOK, L. MORIN, T.M. NEILL, CRAIG H. NEWTON, D. GIGI OSTROW, A. PALOMBA, F. PANARA, M.E. PULETTI, R. QUARTA, S. QUILICI, A.K.B. RAMOS, THIERRY RIGAUD, A.M. RISTERUCCI, MATTHEW P. SALOMON, ROSA A. SÁNCHEZ-GUILLÉN, SHANE K. SARVER, A.S. SEQUEIRA, D.A. SFORÇA, C. SIMIAND, BRIAN SMITH, A.C.B. SOUSA, A.P. SOUZA, C.C. STEPIEN, A.J. STUCKERT, JAMES SULIKOWSKI, A. TAYEH, F. TINTI, PAUL C.W. TSANG, J.K.J. VAN HOUDT, E. VENDRAMIN, I. VERDE, M. VIRGILIO, HUAN L. WANG, LE WANG, RÉMI A. WATTIER, MAREN WELLENREUTHER, CONG X. XIE, L. ZANE, XIU J. ZHANG, YONG ZHANG, ZHIMENG ZHUANG, M.I. ZUCCHI, Universidad Politecnica de Valencia, Universidad Politécnica de Valencia, Université de Sherbrooke [Sherbrooke]-Université du Québec à Montréal (UQAM)-Université du Québec à Chicoutimi (UQAC)-Université Laval-Université Téluq (TELUQ)-Université de Montréal (UdeM)-Université du Québec en Outaouais (UQO)-Concordia University [Montreal]-Université McGill -Université du Québec en Abitibi-Témiscamingue (UQAT)-Université du Québec à Rimouski (UQAR), Università di Bologna [Bologna] (UNIBO), Empresa Brasileira de Pesquisa Agropecuária, University of Florida [Gainesville], Universidate de Vigo, Université Libre de Bruxelles [Bruxelles] (ULB), University of Tasmania (UTAS), Sun Yat-Sen University (SYSU), Centre d'étude de la forêt ( CEF ), Université Laval, Natural Resources Canada, Canadian Forest Service - CFS (CANADA)-Laurentian Forestry Centre, Centro de Biologia Molecular e Engenharia Genética ( CBMEG ), Universidade Estadual de Campinas ( UNICAMP ), Università di Bologna [Bologna] ( UNIBO ), Empresa Brasileira de Pesquisa Agropecuária ( Embrapa ), Centre de Biologie pour la Gestion des Populations ( CBGP ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Institut de Recherche pour le Développement ( IRD [France-Sud] ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), University College Cork ( UCC ), Biogéosciences [Dijon] ( BGS ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Université Libre de Bruxelles [Bruxelles] ( ULB ), Royal Museum for Central Africa, UMR Peuplements végétaux et bioagresseurs en milieu tropical ( UMR PVBMT - Université de La Réunion ), Université de la Réunion ( UR ), University of Tasmania, Sun Yat-Sen University, Università degli Studi di Perugia ( UNIPG ), USDA-ARS, Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire ( UNH ), The Finnish Environment Institute, Katholieke Universiteit Leuven ( KU Leuven ), Polymorphismes d'intérêt agronomique ( PIA ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Institut National de la Recherche Agronomique ( INRA ), Departamento de Biologia Vegetal ( DBV ), University of New England ( UNE ), Royal Belgian Institute of Natural Sciences ( RBINS ), and Universita degli Studi di Padova = University of Padua = Université de Padoue
Subjects: 0106 biological sciences, microsatellite, Population genetics, Conservation Genetic, Allanblackia, Atlantic bluefin tuna, computer.software_genre, 010603 evolutionary biology, 01 natural sciences, Pistacia terebinthus, microsatellites, F30 - Génétique et amélioration des plantes, 03 medical and health sciences, Botany, Genetics, Bactrocera, EST, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, Database, biology, Pistacia, Thunnu, Animal, Ceratitis rosa, Ceratitis capitata, L10 - Génétique et amélioration des animaux, biology.organism_classification, Ischnura, Allanblackia floribunda, Fish, Genetic markers, Plante, GENETIQUE DES POPULATIONS, [ SDV.GEN ] Life Sciences [q-bio]/Genetics, computer, ECOLOGIE, Biotechnology
Abstract: 4 pages; International audience; This article documents the addition of 220 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Allanblackia floribunda, Amblyraja radiata, Bactrocera cucurbitae, Brachycaudus helichrysi, Calopogonium mucunoides, Dissodactylus primitivus, Elodea canadensis, Ephydatia fluviatilis, Galapaganus howdenae howdenae, Hoplostethus atlanticus, Ischnura elegans, Larimichthys polyactis, Opheodrys vernalis, Pelteobagrus fulvidraco, Phragmidium violaceum, Pistacia vera, and Thunnus thynnus. These loci were cross-tested on the following species: Allanblackia gabonensis, Allanblackia stanerana, Neoceratitis cyanescens, Dacus ciliatus, Dacus demmerezi, Bactrocera zonata, Ceratitis capitata, Ceratitis rosa, Ceratits catoirii, Dacus punctatifrons, Ephydatia mülleri, Spongilla lacustris, Geodia cydonium, Axinella sp., Ischnura graellsii, Ischnura ramburii, Ischnura pumilio, Pistacia integerrima and Pistacia terebinthus.
Published: 2010

44. Supporting strategies for enhancing vegetable liking in the early years of life: an umbrella review of systematic reviews

Author: Karen Matvienko-Sikar, Sophie Nicklaus, Maeva Cochet-Broch, Lucinda K Bell, Claire Gardner, Saravana Kumar, Rebecca K. Golley, Esther Jie Tian, Astrid A.M. Poelman, Lynne Daniels, David N. Cox, Flinders University [Adelaide, Australia], University of South Australia [Adelaide], CSIRO Agriculture and Food (CSIRO), CSIRO Health & Biosecurity, Centre des Sciences du Goût et de l'Alimentation [Dijon] (CSGA), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Bourgogne Franche-Comté [COMUE] (UBFC), University College Cork (UCC), Hort Innovation and contributions from the Australian Government., Bell, Lucinda K, Gardner, Claire, Tian, Esther J, Cochet-Broch, Maeva O, Poelman, Astrid AM, Cox, David N, Nicklaus, Sophie, Matvienko-Sikar, Karen, Daniels, Lynne A, Kumar, Saravana, and Golley, Rebecca K
Subjects: vegetables, 030309 nutrition & dietetics, media_common.quotation_subject, Medicine (miscellaneous), hedonics, lactation, associative learning, taste, Food Preferences, 03 medical and health sciences, 0302 clinical medicine, Consistency (negotiation), Primary outcome, conditioning, Environmental health, Humans, Observational learning, Quality (business), 030212 general & internal medicine, perinatal, media_common, 2. Zero hunger, [SDV.MHEP.PED]Life Sciences [q-bio]/Human health and pathology/Pediatrics, 0303 health sciences, Nutrition and Dietetics, Feeding Behavior, preschooler, Guideline, infant, Associative learning, observational learning, Systematic review, Data extraction, exposure, Psychology, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract: Background: Many children worldwide do not eat recommended amounts of vegetables. Disliking vegetables is a key factor associated with low intake. Objective: This umbrella review synthesized systematic reviews to determine the effectiveness of sensory and behavioral strategies to facilitate liking of vegetables (primary outcome) in young children up to 5 y of age, as key predictors of vegetable intake (secondary outcome). Methods: Nine databases were searched up to May 2019 (updated in September 2020). Two reviewers independently conducted study screening and selection, data extraction, and assessment of methodological quality using AMSTAR 2 (A MeaSurement Tool to Assess systematic Reviews). Eleven reviews (n = 1 rated strong quality, n = 4 moderate quality, n = 6 low/critically low quality)examining 85 primary studies met the review criteria: systematic reviews and meta-analyses of primary studies (any quantitative design) that examined sensory or behavioral strategies on vegetable liking or intake (outcomes reported separately for children ≤5y). Strategy effectiveness was synthesized into 3 categories based on evidence strength: 1) promising (large and consistent body of moderate quality evidence), 2) emerging (small to moderate body of mixed consistency and quality evidence), and 3) limited (small body of limited consistency and quality evidence). Results: Promising evidence was identified for repeated exposure to a single or a variety of vegetables. Emerging evidence was identified for several strategies that increase familiarity with vegetable flavors(e.g., via exposure in utero and through breast milk, and a “vegetable first” approach to complementary feeding) and/or willingness to try vegetables (e.g., via parental role modeling, nonfood rewards, and vegetable-based story books). Conclusions: Current evidence supports incorporation of tailored advice into guideline documents for parents and carers to repeatedly expose their children to a variety of vegetables to increase vegetable intake. Ongoing robust research on strategies to facilitate children’s liking of vegetables is warranted to strengthen the evidence base underpinning advice for parents and health professionals Refereed/Peer-reviewed
Published: 2021

45. COVID-19 pandemic

Author: W. J. Fokkens, Jürgen Schwarze, Cezmi A. Akdis, J Mullol, W. Czarlewski, Claudia Traidl-Hoffmann, Claus Bachert, D. Larenas-Linnemann, Tomas Chivato, M. Gotua, Mateo Bonini, Ludger Klimek, Vincenzo Patella, A. A. Cruz, Stephanie Dramburg, Kari C. Nadeau, H W Fritsch, K. Ohta, Thomas Eiwegger, Robert M. Naclerio, Antti Lauerma, A. Yorgancioglu, Aslı Gelincik, Piotr Kuna, Oliver Pfaar, Carmen Riggioni, Violeta Kvedariene, Markus Ollert, Sinthia Bosnic-Anticevich, V. Cardona, S. Del Giacco, Sanna Toppila-Salmi, Helen A. Brough, Heimo Breiteneder, Valérie Hox, B. Samolinski, Zuzana Diamant, G.W. Canonica, Lihong Zhang, María José Torres, Y. Okamoto, Liam O'Mahony, Radosław Gawlik, Jolanta Walusiak-Skorupa, Sharon Chinthrajah, Winfried Rief, T. Haatela, M. Morais-Almeida, Ioana Agache, Manfred Schedlowski, I Skypala, R. Brehler, D. Y. Wang, João Fonseca, I. J. Ansotegui, Robyn E O'Hehir, Oscar Palomares, Charlotte G. Mortz, J. C. Ivancevich, C. Suppli Ulrik, M. T. Ventura, P M Matricardi, S Untersmayr, Gabrielle L. Onorato, Amir Hamzah Abdul Latiff, Frederico S. Regateiro, Vanitha Sampath, Arũnas Valiulis, Marek Jutel, Luisa Brussino, Pedro Carreiro-Martins, Jean Bousquet, Nikolaos G. Papadopoulos, A. Bedbrook, Torsten Zuberbier, Karin Hoffmann-Sommergruber, Edward F. Knol, Ear, Nose and Throat, AII - Inflammatory diseases, UCL - SSS/IREC/PNEU - Pôle de Pneumologie, ORL et Dermatologie, UCL - (SLuc) Service d'oto-rhino-laryngologie, Philipps Universität Marburg = Philipps University of Marburg, Allergologie, Stimm und Sprachstörungen [Wiesbaden, Germany], Zentrum für Rhinologie und Allergologie [Wiesbaden, Germany], University of Wrocław [Poland] (UWr), ALL-MED, Swiss Institute of Allergy and Asthma Research (SIAF), Universität Zürich [Zürich] = University of Zurich (UZH), Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), 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), Commission Européenne-Commission Européenne-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Medizinische Universität Wien = Medical University of Vienna, Stanford University, Skane University Hospital [Malmo], Lund University [Lund], Charles University [Prague] (CU), University Medical Center Groningen [Groningen] (UMCG), Univ Toronto, Hosp Sick Children, Peter Gilgan Ctr Res & Learning, Mol Med, Toronto, ON M5G 0A4, Canada, The Hospital for sick children [Toronto] (SickKids), University of Toronto, Amsterdam UMC - Amsterdam University Medical Center, Alfred Health, Victoria University [Melbourne], University College Cork (UCC), Sean N. Parker Center for Allergy and Asthma Research [Stanford], Stanford Medicine, Stanford University-Stanford University, University Clinics of Essen, University of Essen, Allergy Unit [Malaga, Spain] (National Network ARADyAL), Hospital Regional Universitario de Málaga = Regional University Hospital of Malaga [Spain], Helmholtz Zentrum München = German Research Center for Environmental Health, University Hospital Augsburg, National University of Singapore (NUS), Beijing Tongren Hospital, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, National Heart and Lung Institute [London] (NHLI), Imperial College London-Royal Brompton and Harefield NHS Foundation Trust, University Hospital Münster - Universitaetsklinikum Muenster [Germany] (UKM), Evelina London Children's Hospital, King‘s College London, CEU-San Pablo University and HM-Hospitals School of Medicine, University of Cagliari, Medical University of Silesia (SUM), Istanbul University, Cliniques Universitaires Saint-Luc [Bruxelles], University Medical Center [Utrecht], Helsinki University Central Hospital, University of Helsinki, Odense University Hospital (OUH), Luxembourg Institute of Health (LIH), Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Hospital Sant Joan de Déu [Barcelona], Institut de Recerca Pediàtrica Hospital Sant Joan de Déu [Barcelona, Spain], University of Edinburgh, NHS Foundation Trust [London], The Royal Marsden, Nofer Institute of Occupational Medicine (NIOM), Hospital Quirónsalud Bizkaia [Bilbao], Ghent University Hospital, Sun Yat-Sen University [Guangzhou] (SYSU), Karolinska Institutet [Stockholm], Woolcock Institute of Medical Research [Sydney], The University of Sydney, University of Turin, Mauriziano Umberto I Hospital, Humanitas University [Milan] (Hunimed), Vall d'Hebron University Hospital [Barcelona], Hospital de Dona Estefania, NOVA Medical School - Faculdade de Ciências Médicas (NMS), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Federal University of Bahia School of Medicine, Global Alliance Against Chronic Respiratory Diseases (GARD-WHO), Medical Consulting Czarlewski, Faculdade de Medicina da Universidade do Porto (FMUP), Universidade do Porto = University of Porto, MEDIDA, Lda, David Tvildiani Medical University (DTMU), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Servicio de Alergia e ImmunologiaBuenos Aires (Clinica Santa Isabel), Barlicki University Hospital, Vilnius University [Vilnius], Hospital Medica Sur [Mexico City, Mexico], Pantai Hospital [Kuala Lumpur], Hospital CUF Descobertas, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona (UB), CIBER de Epidemiología y Salud Pública (CIBERESP), Johns Hopkins University School of Medicine [Baltimore], Fukujuji Hospital, Tokyo National Hospital, Chiba Rosai Hospital, Chiba University Hospital, Royal Manchester Children's Hospital, University of Manchester [Manchester], General Children's Hospital of Athens P & A Kyriakou, 'Santa Maria della Speranza' Hospital, Centro Hospitalar e Universitário [Coimbra], Coimbra Institute for Clinical and Biomedical Research [Coimbra, Portugal] (iCBR - Faculty of Medicine), University of Coimbra [Portugal] (UC), Medical University of Warsaw - Poland, Hvidovre Hospital, University of Copenhagen = Københavns Universitet (UCPH), Università degli studi di Bari Aldo Moro = University of Bari Aldo Moro (UNIBA), Manisa Celal Bayar University, Transilvania University of Brasov, Salvy-Córdoba, Nathalie, Department of Dermatology, Allergology and Venereology, and HUS Inflammation Center
Subjects: 0301 basic medicine, viruses, Eaaci Position Paper, Medizin, Cochrane Library, GUIDELINES, FOOD ALLERGY, allergen immunotherapy, allergy clinic, anaphylaxis, asthma, clinical trials, COVID-19, Position Paper, psychological impact, SARS-CoV-2, Allergists, Health Personnel, Humans, Hypersensitivity, Information Technology, Patient Care Team, Triage, SARS‐CoV‐2, DESENSITIZATION, 0302 clinical medicine, MESH: Patient Care Team, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, HDE ALER, Pandemic, Health care, Immunology and Allergy, ATOPIC-DERMATITIS, MESH: COVID-19, [SDV.IMM.ALL]Life Sciences [q-bio]/Immunology/Allergology, [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, allergen immunotherapy (AIT), virus diseases, DRUG HYPERSENSITIVITY REACTIONS, 3. Good health, INFECTIONS, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Triage, [SDV.IMM.ALL] Life Sciences [q-bio]/Immunology/Allergology, Allergen immunotherapy, medicine.medical_specialty, MESH: Information Technology, MESH: Hypersensitivity, Immunology, education, MEDLINE, DIAGNOSIS, psychological COVID, 03 medical and health sciences, MESH: Allergists, COVID‐19, medicine, MESH: SARS-CoV-2, ddc:610, RHINOSINUSITIS, MESH: Humans, business.industry, Clinical trial, Coronavirus, EXACERBATIONS, 030104 developmental biology, 030228 respiratory system, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Family medicine, 3121 General medicine, internal medicine and other clinical medicine, Position paper, MESH: Health Personnel, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business
Abstract: BackgroundThe Coronavirus disease 2019 (COVID‐19) has evolved as a pandemic infectious disease transmitted by the severe acute respiratory syndrome coronavirus (SARS‐CoV‐)2. Allergists and other health care providers (HCPs) in the field of allergies and associated airway diseases are in the front line, taking care of patients potentially infected with SARS‐CoV‐2. Hence, strategies and practices to minimize risks of infection for both HCPs and treated patients have to be developed and followed by allergy clinics.MethodThe scientific information on COVID‐19 was analyzed by a literature search in Medline, Pubmed, national and international guidelines from the European Academy of Allergy and Clinical Immunology (EAACI), the Cochrane Library and the Internet.ResultsBased on diagnostic and treatment standards developed by EAACI, on international information regarding COVID‐19, on guidelines of the World Health Organization (WHO) and other international organizations as well as on previous experience, a panel of experts including clinicians, psychologists, IT experts and basic scientists along with EAACI and the “Allergic Rhinitis and its Impact on Asthma (ARIA)” inititiative have developed recommendations for the optimal management of allergy clinics during the current COVID‐19 pandemic. These recommendations are grouped into nine sections on different relevant aspects for the care of patients with allergies.ConclusionsThis international Position Paper provides recommendations on operational plans and procedures to maintain high standards in the daily clinical care of allergic patients whilst ensuring necessary safety in the current COVID‐19 pandemic.
Published: 2021

46. Regularized reconstruction of wave fields from refracted images of water

Author: Roy Choudhury, Kingshuk, O'Sullivan, Finbarr, Samanta, Mayukh, Shrira, Victor, Caulliez, Guillemette, Caulliez, Guillemette, Department of Statistics University College Cork (UCC), University College Cork (UCC), Department of Mathematics, Keele University, Institut de Recherche sur les Phénomènes Hors Equilibre (IRPHE), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM), INTAS 05-1000008-8014, and Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, [SDU.OCEAN] Sciences of the Universe [physics]/Ocean, Atmosphere
Published: 2009

47. Regularized reconstruction of water surfaces from noisy gradient information via plane-wave superposition

Author: Kingshuk Roy Choudhury, Guillemette Caulliez, Victor I. Shrira, Jian Huang, Finbarr O'Sullivan, Department of Statistics University College Cork (UCC), University College Cork (UCC), Institut de Recherche sur les Phénomènes Hors Equilibre (IRPHE), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM), Department of Mathematics, Keele University, INTAS 05-1000008-8014, IRCSET, and Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Plane wave, Geometry, 01 natural sciences, 010305 fluids & plasmas, Theoretical Computer Science, 010104 statistics & probability, Superposition principle, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], 0103 physical sciences, Wave height, water surface height reconstruction, Wave tank, 0101 mathematics, Mathematical Physics, Mathematics, Wavefront, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Applied Mathematics, Mathematical analysis, [STAT.TH]Statistics [stat]/Statistics Theory [stat.TH], Inverse problem, surface waves, wave patterns, Computer Science Applications, plane-wave approximation, Surface wave, Signal Processing, Smoothing
Abstract: International audience; Refraction-based imaging systems, used in wave tank facilities, provide measurements of local water surface gradients. The reconstruction of wave height fields from this information is considered. Utilizing the convenient approximation of target wave height fields by superposition of simple plane waves, we explore the possibility of adaptive plane-wave approximation for computation of the regularized solutions to the wave height reconstruction problem. A greedy algorithm is employed. The method developed allows for non-parametric estimation of wave-front shapes and their periodicities. Regularization forces a natural inverse relation between the smoothness of wave-front shapes and their periodicities. A generalized cross-validation statistic based on a novel tomographic approximation to the model degrees of freedom is developed to assess the regularization parameter. The approximation technique would appear to have wider utility in multi-dimensional smoothing via regularization. The methodology is illustrated by application to real and synthetic data associated with an operational imaging system. Generalization of the approach to the nonlinear problem of reconstructing water surfaces from reflectance data is also considered and some preliminary results for Lambertian reflection are provided. The approach is found to offer substantial potential for this class of reconstruction problems.
Published: 2008

48. The evolution and role of the periplasmic asparaginase Asp3 in yeast

Author: Angela Coral-Medina, Darren A Fenton, Javier Varela, Pavel V Baranov, Carole Camarasa, John P Morrissey, University College Cork (UCC), Sciences Pour l'Oenologie (SPO), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), CarboCode GmbH, and European Project: 764927
Subjects: [SDV.BIO]Life Sciences [q-bio]/Biotechnology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Nitrogen, Fermentation, Asparaginase, General Medicine, Saccharomyces cerevisiae, Asparagine, Applied Microbiology and Biotechnology, Microbiology
Abstract: The study of nitrogen assimilation in yeast is of interest from genetic, evolutionary, and biotechnological perspectives. Over the course of evolution, yeasts have developed sophisticated control mechanisms to regulate nitrogen metabolism, with domesticated lineages sometimes displaying particular specialisation. The focus of this study was on assimilation of asparagine, which is a significant nutritional source for some alcoholic fermentations. We were particularly interested in ASP3, which encodes a periplasmic asparaginase and that was proposed to have been acquired relatively recently in S. cerevisiae by horizontal gene transfer. We examined 1680 S. cerevisiae genome assemblies to evaluate the distribution and evolutionary trajectory of ASP3. Our findings suggest an alternative hypothesis that ASP3 is an ancient Saccharomyces gene that has generally been lost over the course of evolution but has been retained in certain fermentative environments. As asparagine is the major nitrogen source in apple juice, we explored whether the presence of ASP3 would confer a growth advantage. Interestingly, we found that although ASP3 enhances growth when asparagine is the sole nitrogen source, the same effect is not seen in apple juice. These data indicate that growth in pure culture may not reflect the original selective environment for ASP3+ strains and highlight the role that complex regulation may play in optimising nitrogen assimilation in yeasts.
Published: 2022

49. Elucidating the role of the gut microbiota in the physiological effects of dietary fiber

Author: Edward C. Deehan, Zhengxiao Zhang, Alessandra Riva, Anissa M. Armet, Maria Elisa Perez-Muñoz, Nguyen K. Nguyen, Jacqueline A. Krysa, Benjamin Seethaler, Yuan-Yuan Zhao, Janis Cole, Fuyong Li, Bela Hausmann, Andreas Spittler, Julie-Anne Nazare, Nathalie M. Delzenne, Jonathan M. Curtis, Wendy V. Wismer, Spencer D. Proctor, Jeffrey A. Bakal, Stephan C. Bischoff, Dan Knights, Catherine J. Field, David Berry, Carla M. Prado, Jens Walter, University of Alberta, Jimei University [Fujian, China] (JMU), University of Vienna [Vienna], University of Hohenheim, Medizinische Universität Wien = Medical University of Vienna, Cardiovasculaire, métabolisme, diabétologie et nutrition (CarMeN), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), French-Clinical Research Infrastructure Network / F-CRIN [Lyon] (Cardiovascular & Renal Clinical Trialists - INI-CRCT ), Centre Hospitalier Lyon Sud [CHU - HCL] (CHLS), Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL)-Centre de Recherche en Nutrition Humaine Rhône-Alpes (CRNH-RA), Université de Lyon-Université de Lyon-CHU Grenoble-Hospices Civils de Lyon (HCL)-CHU Saint-Etienne-Université Jean Monnet - Saint-Étienne (UJM)-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 Grenoble Alpes (UGA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-CHU Grenoble-CHU Saint-Etienne-Université Jean Monnet - Saint-Étienne (UJM)-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 Grenoble Alpes (UGA), Université Catholique de Louvain = Catholic University of Louvain (UCL), University of Minnesota [Twin Cities] (UMN), University of Minnesota System, University College Cork (UCC), National University of Ireland [Galway] (NUI Galway), CarMeN, laboratoire, and UCL - SSS/LDRI - Louvain Drug Research Institute
Subjects: Inflammation, Adult, Dietary Fiber, Male, Microbiology (medical), Bacteria, [SDV]Life Sciences [q-bio], Insulin resistance, Gut microbiota, Microbiology, Satiety, Gastrointestinal Microbiome, [SDV] Life Sciences [q-bio], Bile Acids and Salts, Feces, Adults, Humans, Female, Obesity, Leukocyte L1 Antigen Complex, Biomarkers
Abstract: BackgroundDietary fiber is an integral part of a healthy diet, but questions remain about the mechanisms that underlie effects and the causal contributions of the gut microbiota. Here, we performed a 6-week exploratory trial in adults with excess weight (BMI: 25–35 kg/m2) to compare the effects of a high-dose (females: 25 g/day; males: 35 g/day) supplement of fermentable corn bran arabinoxylan (AX;n= 15) with that of microbiota-non-accessible microcrystalline cellulose (MCC;n= 16). Obesity-related surrogate endpoints and biomarkers of host-microbiome interactions implicated in the pathophysiology of obesity (trimethylamineN-oxide, gut hormones, cytokines, and measures of intestinal barrier integrity) were assessed. We then determined whether clinical outcomes could be predicted by fecal microbiota features or mechanistic biomarkers.ResultsAX enhanced satiety after a meal and decreased homeostatic model assessment of insulin resistance (HOMA-IR), while MCC reduced tumor necrosis factor-α and fecal calprotectin. Machine learning models determined that effects on satiety could be predicted by fecal bacterial taxa that utilized AX, as identified by bioorthogonal non-canonical amino acid tagging. Reductions in HOMA-IR and calprotectin were associated with shifts in fecal bile acids, but correlations were negative, suggesting that the benefits of fiber may not be mediated by their effects on bile acid pools. Biomarkers of host-microbiome interactions often linked to bacterial metabolites derived from fiber fermentation (short-chain fatty acids) were not affected by AX supplementation when compared to non-accessible MCC.ConclusionThis study demonstrates the efficacy of purified dietary fibers when used as supplements and suggests that satietogenic effects of AX may be linked to bacterial taxa that ferment the fiber or utilize breakdown products. Other effects are likely microbiome independent. The findings provide a basis for fiber-type specific therapeutic applications and their personalization.Trial registrationClinicaltrials.gov,NCT02322112, registered on July 3, 2015.
Published: 2022

50. A responsible AI framework: pipeline contextualisation

Author: Eduardo Vyhmeister, Gabriel Castane, P.-O. Östberg, Simon Thevenin, University College Cork (UCC), Umeå University, Modélisation, Optimisation et DEcision pour la Logistique, l'Industrie et les Services (LS2N - équipe MODELIS), Laboratoire des Sciences du Numérique de Nantes (LS2N), Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-École Centrale de Nantes (Nantes Univ - ECN), Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes université - UFR des Sciences et des Techniques (Nantes univ - UFR ST), Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Nantes Université (Nantes Univ), Département Automatique, Productique et Informatique (IMT Atlantique - DAPI), IMT Atlantique (IMT Atlantique), and Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)
Subjects: Mechanical Engineering, Energy Engineering and Power Technology, Management Science and Operations Research, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI]
Abstract: Incorporating ethics and values within the life cycle of an AI asset means securing its development, deployment, use, and decommission under these perspectives. These approaches depend on the market domain where AI is operational – considering the interaction and the impact on humans if any process does not perform as expected – and the legal compliance, both required to ensure adequate fulfilment of ethics and values. Specifically, in the manufacturing sector, standards were developed since the 1990’s to guarantee, among others, the correct use of mechanical machinery, systems robustness, low product variability, workers safety, system security, and adequate implementation of system constraints. However, it is challenging to blend the existing practices with the needs associated with deployments of AI in a trustworthy manner. This document provides an extended framework for AI Management within the Manufacturing sector. The framework is based on different perspectives related to responsible AI that handle trustworthy issues as risk. The approach is based on the idea that ethical considerations can and should be handled as hazards. If these requirements or constraints are not adequately fulfilled and managed, it is expected severe negative impact on different sustainable pillars. We are proposing a well-structured approach based on risk management that would allow implementing ethical concerns in any life cycle stages of AI components in the manufacturing sector. The framework follows a pipeline structure, with the possibility of being extended and connected with other industrial Risk Management Processes, facilitating its implementation in the manufacturing domain. Furthermore, given the dynamic condition of the regulatory state of AI, the framework allows extension and considerations that could be developed in the future.
Published: 2022

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