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114 results on '"Region Occitanie"'

1. Towards a Large-Scale Assessment of the Relationship Between Biological and Chronological Aging: The Inspire Mouse Cohort

Author: Santin, Yohan, Lopez, Sébastien, Ader, Isabelle, Andrieu, Sandrine, Blanchard, Nicolas, Carrière, Audrey, Casteilla, Louis, Cousin, Béatrice, Davezac, Noelie, Barreto De Souto, Philipe, Dray, Cédric, Fazilleau, Nicolas, Gonzalez-Dunia, Daniel, Gourdy, Pierre, Guyonnet, Sophie, Jabrane-Ferrat, Nabila, Kunduzova, Oksana, Lezoualc'H, Frank, Liblau, Roland, Martinez, Laurent O., Moro, Cedric, Payoux, Pierre, Pénicaud, Luc, Planat-Benard, Valérie, Rampon, Claire, Rolland, Yves, Schanstra, Joost-Peter, Sierra, Felipe, Valet, Philippe, Varin, Audrey, Vergnolle, Nathalie, Vellas, Bruno, Viña, José, Guiard, Bruno P., Parini, Angelo, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Recherches sur la Cognition Animale (CRCA), Centre National de la Recherche Scientifique (CNRS)-Institut des sciences du cerveau de Toulouse. (ISCT), Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), STROMALab, Institut National de la Santé et de la Recherche Médicale (INSERM)-Etablissement Français du Sang-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Epidémiologie et analyses en santé publique : risques, maladies chroniques et handicaps (LEASP), Centre de Physiopathologie Toulouse Purpan ex IFR 30 et IFR 150 (CPTP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Toulouse Neuro Imaging Center (ToNIC), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôpital Purpan [Toulouse], CHU Toulouse [Toulouse]-CHU Toulouse [Toulouse], National Institute on Aging [Bethesda, USA] (NIA), National Institutes of Health [Bethesda] (NIH), Institut de Recherche en Santé Digestive (IRSD ), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universitat de València (UV), the Region Occitanie/Pyrenees-Mediterranee (Reference number: 1901175), the European Regional Development Fund (ERDF) (Project number: MP0022856), Inspire Chairs of Excellence - Alzheimer Prevention in Occitania and Catalonia (APOC), EDENIS, KORIAN, Pfizer, Pierre-Fabre, 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, Centre de Biologie Intégrative (CBI), 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-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut des sciences du cerveau de Toulouse. (ISCT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse - Jean Jaurès (UT2J)-CHU Toulouse [Toulouse]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Etablissement Français du Sang-Institut National de la Santé et de la Recherche Médicale (INSERM), Gérontopôle, 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)-CHU Toulouse [Toulouse], Centre de Physiopathologie Toulouse Purpan (CPTP), Institut de médecine moléculaire de Rangueil (I2MR), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-IFR150-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Santé et de la Recherche Médicale (INSERM), Universitat Politècnica de València (UPV), Region Occitanie/Pyrenees-Mediterranee (Reference number: 1901175), European Regional Development Fund (ERDF) (Project number: MP0022856), and Inspire Chairs of Excellence funded by: Alzheimer Prevention in Occitania and Catalonia (APOC)
Subjects: Cohort Studies, Male, mouse cohort, Aging, Mice, INSPIRE program, biological aging, [SDV.MHEP.GEG]Life Sciences [q-bio]/Human health and pathology/Geriatry and gerontology, Animals, biomarkers, Female, frailty
Abstract: International audience; Aging is the major risk factor for the development of chronic diseases. After decades of research focused on extending lifespan, current efforts seek primarily to promote healthy aging. Recent advances suggest that biological processes linked to aging are more reliable than chronological age to account for an individual's functional status, i.e. frail or robust. It is becoming increasingly apparent that biological aging may be detectable as a progressive loss of resilience much earlier than the appearance of clinical signs of frailty. In this context, the INSPIRE program was built to identify the mechanisms of accelerated aging and the early biological signs predicting frailty and pathological aging. To address this issue, we designed a cohort of outbred SWISS mice (1576 male and female mice) in which we will continuously monitor spontaneous and voluntary physical activity from 6 to 24 months of age under either normal or high fat/high sucrose diet. At different age points (6, 12, 18, 24 months), multiorgan functional phenotyping will be carried out to identify early signs of organ dysfunction and generate a large biological fluids/feces/organs biobank (100,000 samples). A comprehensive correlation between functional and biological phenotypes will be assessed to determine: 1) the early signs of biological aging and their relationship with chronological age; 2) the role of dietary and exercise interventions on accelerating or decelerating the rate of biological aging; and 3) novel targets for the promotion of healthy aging. All the functional and omics data, as well as the biobank generated in the framework of the INSPIRE cohort will be available to the aging scientific community. The present article describes the scientific background and the strategies employed for the design of the INSPIRE Mouse cohort.
Published: 2020
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2. Comparative transcriptomic studies identify specific expression patterns of virulence factors under the control of the master regulator PhcA in the Ralstonia solanacearum species complex

Author: Xavier Barlet, Rémi Peyraud, Anthony Perrier, David Rengel, Stéphane Genin, Alice Guidot, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), 'Institut National de la Recherche Agronomique' (INRA) : AAP SPE 2015, French Laboratory of Excellence project TULIP : ANR-10-LABX-41, ANR-11-IDEX-0002-02, EMBO (Long-Term Fellowship) : ALTF 1627-2011, Marie Curie Actions (EMBOCOFUND) : GA-2010-267146, INRA, Plant Health Division (SPE), 'Region Occitanie' : 15000183, 'Institut National de la Recherche Agronomique' (INRA) AAP SPE 2015French Laboratory of Excellence project TULIP ANR-10-LABX-41ANR-11-IDEX-0002-02European Molecular Biology Organization (EMBO)ALTF 1627-2011Marie Curie Actions (EMBOCOFUND) GA-2010-267146INRA, Plant Health Division (SPE) 'Region Occitanie' 15000183, and ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011)
Subjects: 0301 basic medicine, Virulence Factors, [SDV]Life Sciences [q-bio], 030106 microbiology, Virulence, Bacterial genome size, Microbiology, Genome, Regulon, Type three secretion system, 03 medical and health sciences, Bacterial Proteins, Plant pathogen, Gene, Genetics, Ralstonia solanacearum, biology, Sequence Analysis, RNA, Gene Expression Profiling, Bacterial wilt, food and beverages, Gene Expression Regulation, Bacterial, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, DNA-Binding Proteins, Quorum sensing, Infectious Diseases, Type 3 secretion system, RNA-seq, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Transcription Factors, Regulation
Abstract: International audience; The global regulator PhcA controls numerous traits associated to virulence and bacterial proliferation in strains of the plant pathogen Ralstonia solanacearum species complex. Here, we conducted a genome-wide RNA sequencing study of the GMI1000 wild-type strain and a derived phcA mutant grown in complete medium. The PhcA regulon we identified is the largest regulon described to date in the R. solanacearum species complex with 1581 regulated genes, representing about 30% of the bacterial genome. Among these genes, 166 transcription regulators were identified including known regulators controlling major cellular functions such as the Type 3 secretion system and 27 novel regulators that were not identified in previous transcriptomic studies. This study highlights that PhcA controls other functions beside pathogenicity stricto sensu which participate to the global cell homeostasis (metabolism, energy storage). We then compared the PhcA regulon identified in complete medium to the recently published PhcA regulon obtained in planta. This comparison of the set of GMI1000 genes subjected to PhcA regulation in both conditions revealed 383 common genes. Among them, 326 (85%) had a similar PhcA dependent regulation pattern in complete medium and in planta, and 57 (15%) displayed an opposite regulation pattern. A large majority of the genes repressed by PhcA in complete medium but activated in planta belong to the HrpG-HrpB regulon, which represents a set of key genes required for R. solanacearum pathogenesis. This latter class of genes appears to be specifically induced by PhcA in the plant environment whereas PhcA represses their expression in complete medium. The large set of direct and indirect targets identified in this study will contribute to enrich our knowledge of the intricate regulatory network coordinating the expression of virulence and metabolic functions in the model plant pathogen R. solanacearum.
Published: 2018
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3. Does short food supply chain participation improve farm economic performance? A meta‐analysis

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

Author: Nelia Luviano, Ludovic Halby, Corinne Jallet, Paola B. Arimondo, Celine Cosseau, Christoph Grunau, Interactions Hôtes-Pathogènes-Environnements (IHPE), Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Chimie biologique épigénétique - Epigenetic Chemical Biology (EpiCBio), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), This study is set within the framework of the « Laboratoire d’Excellence (LabEx) » TULIP (ANR-10-LABX-41) and CeMEB (ANR- 10-LABX-04-01). N.L. was supported by a PhD grant of the Region Occitanie, France and the UPVD, ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), and ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010)
Subjects: molluscicide, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, schistosomiases, epigenetics, DNA methylation inhibitor, [CHIM.THER]Chemical Sciences/Medicinal Chemistry, Biomphalaria glabrata
Abstract: Biomphalaria glabratais a fresh-water mollusk that serves as obligatory intermediate host toSchistosoma mansoni, agent of the neglected tropical disease schistosomiasis that affects roughly 250 Mio people. One of the ways to control the pathogenic agent is to interrupt the life cycle by eliminating the intermediate snail host though foal treatment of water bodies with molluscicides. Currently recommended molluscicides were developed in the 1950ths and lack sufficient specificity, e.g., they are toxic to fish. To provide new lead compounds for the development of a new type of molluscicides we used a rational approach based on the hypotheses that interfering with an important epigenetic mark, DNA methylation, would impede development of the snail host. We present here the compound 29, analogues-based compound that mimic substrates of DNA methyltransferases. We show that compound 29 has (i) low cytotoxicity for human cells, (ii) it inhibits DNA methylation, and (iii) it decreases fecundity inB.glabrata. It is therefore conceivable to produce compounds that act as specific epigenetic molluscicides.
Published: 2023

5. Modelling coarse-sediment propagation following gravel augmentation: The case of the Rhône River at Péage-de-Roussillon (France)

Author: Vázquez-Tarrío, Daniel, Peeters, Alexandre, Cassel, Mathieu, Piégay, Hervé, Environnement, Ville, Société (EVS), École normale supérieure de Lyon (ENS de Lyon)-École des Mines de Saint-Étienne (Mines Saint-Étienne MSE), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université Lumière - Lyon 2 (UL2)-Université Jean Moulin - Lyon 3 (UJML), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet - Saint-Étienne (UJM)-École Nationale des Travaux Publics de l'État (ENTPE)-École nationale supérieure d'architecture de Lyon (ENSAL)-Centre National de la Recherche Scientifique (CNRS), Agence de l'eau Rhône Méditerranée Corse, CNR, EDF, Region Auvergne-Rhône-Alpes, Region PACA, Region Occitanie, Spanish Ministry of Science and Innovation, ANR-17-EURE-0018,H2O'LYON,School of Integrated Watershed Sciences(2017), and ANR-11-LABX-0010,DRIIHM / IRDHEI,Dispositif de recherche interdisciplinaire sur les Interactions Hommes-Milieux(2011)
Subjects: History, Hidrología, Geodinámica, Polymers and Plastics, Sediment pulse, Bedload, Geografía física, Gravel augmentation, Sediment transport, Industrial and Manufacturing Engineering, Gravel-bed rivers, [SDE]Environmental Sciences, Geología, Business and International Management, Earth-Surface Processes
Abstract: International audience; Over the last two centuries, rivers worldwide have been affected by human interventions, including dams, river training, and gravel mining. Such actions have often involved river fragmentation and sediment starvation. In this regard, gravel augmentation is an increasingly common restoration practice for mitigating sediment starvation in gravel-bed rivers. However, uncertainties remain on how to better implement and design such operations. This is the case for the Rhône River at Péage-de-Roussillon, France, where 6885 m3 of gravels were augmented in 2017. This work raised some concerns from river managers about the potential threat posed to a downstream reservoir from the arrival of the sediment, and explains why they were interested in the timeframe of sediment propagation, and travel distances and velocities of the augmented sediment. To answer these questions, we propose a modelling framework for simulating the long-term downstream propagation of a pulse of augmented sediment, with this framework being based on a combination of particle tracking data collected in the field and bedload transport capacity estimates. This workflow allowed us to successfully model propagation of gravels along the study reach, and provided useful information on how the sediment wave would behave over the long term. We believe that the methodology proposed in this study has much potential for exploring and investigating the kinematics of sediment wave propagation in gravel-bed rivers.
Published: 2023
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6. How to think about interdisciplinarity in practice? A question of disposition, indisciplinarity and complexity

Author: Nourrit-Lucas, Déborah, EuroMov - Digital Health in Motion (Euromov DHM), IMT - MINES ALES (IMT - MINES ALES), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Montpellier (UM), Region Occitanie, and European Project: FEDER
Subjects: Indisciplinarité, Interdisciplinarité, Complexité, Récursivité, [SHS]Humanities and Social Sciences
Abstract: Ce texte constitue le prologue du numéro 11 du Journal on Interdisciplinary Methodologies and Issues in Science : Penser l'interdisciplinarité en pratique. L'ensemble des 10 contributions est brièvement présenté à partir des fondements qui font l'interdisciplinarité en pratique : les dispositions des chercheurs, leur posture indisciplinaire et le contexte complexe dans lequel s'opère l'interdisciplinarité.
Published: 2023

7. Human papilloma virus‐16‐specific <scp>CD8</scp> + T‐cell expansions characterize different clinical forms of lichen planus and not lichen sclerosus et atrophicus

Author: Manuelle Viguier, Corine Pérals, Béatrice Poirier, Maxime Battistella, François Aubin, Hervé Bachelez, Jean‐Luc Prétet, Tarik Gheit, Massimo Tommasino, Antoine Touzé, Marie‐Lise Gougeon, Nicolas Fazilleau, Immuno-Régulation dans les Maladies Auto-Immunes Inflammatoires et le Cancer - EA 7509 (IRMAIC), Université de Reims Champagne-Ardenne (URCA), Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), 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 National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP), Service d'anatomo-pathologie [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Groupe Hospitalier Saint Louis - Lariboisière - Fernand Widal [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Cité (UPCité), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Genetic skin diseases : from disease mechanism to therapies (Equipe Inserm U1163), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Service de Dermatologie [AP-HP Hôpital Saint-Louis], Hopital Saint-Louis [AP-HP] (AP-HP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre National de Référence des Papillomavirus (CNRP), Centre International de Recherche contre le Cancer - International Agency for Research on Cancer (CIRC - IARC), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), IRCCS Ist Tumori Giovanni Paolo II, Bari, Italy, Partenaires INRAE, Infectiologie et Santé Publique (UMR ISP), Université de Tours (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), European Regional Development Fund, Grant/Award Number: MP0022856, Institut National de la Sante et de la Recherche Medicale, Region Occitanie Pyrenees-Mediterranee, Grant/Award Number: #1901175, and Societe Francaise de Dermatologie et de Pathologie Sexuellement Transmissible
Subjects: T-cell, lichen planus, human papilloma virus, T-cell receptor, Dermatology, cytotoxic T lymphocytes, Molecular Biology, Biochemistry, [SDV.MHEP.DERM]Life Sciences [q-bio]/Human health and pathology/Dermatology
Abstract: International audience; Lichen planus (LP) is a cutaneomucosal chronic inflammatory disease characterized by a CD8 + cytotoxic T-lymphocytes (CTL) infiltrate. In erosive oral LP, we found HPV16specific activated CTL in lesions, supporting a pathogenic contribution of HPV16. Here, we investigated whether a similar scenario occurs in other clinical forms of LP and in lichen sclerosus et atrophicus (LSA), another chronic disease also affecting the mucosa and/or the skin. Blood CTL from LP and LSA patients expressed significant higher levels of granzyme B, perforin and CD107a proteins than healthy donors. Expansions of TCRVß3 + CTL, with presence of TCR clonotypes identical to those previously detected in erosive oral LP, were found both in blood and mucosal/skin lesions of LP, and not of LSA patients. These expansions were enriched with HPV16-specific CD8 + T-cells as shown by their recognition of the E7 11-20 immunodominant epitope. In LSA patients, the peripheral repertoire of CTL was oligoclonal for TCRVß6 + CTL. Finally, although patients with LP and LSA have developed antibodies against HPV16
Published: 2023
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8. The Activation of the RIG-I/MDA5 Signaling Pathway upon Influenza D Virus Infection Impairs the Pulmonary Proinflammatory Response Triggered by Mycoplasma bovis Superinfection

Author: Maria Gaudino, Adrien Lion, Eveline Sagné, Brandy Nagamine, Justine Oliva, Olivier Terrier, Elisabeth Errazuriz-Cerda, Anaëlle Scribe, Fatima-Zohra Sikht, Elisa Simon, Charlotte Foret-Lucas, Blandine Gausserès, Julie Lion, Ana Moreno, Emilie Dordet-Frisoni, Eric Baranowski, Romain Volmer, Mariette F. Ducatez, Gilles Meyer, Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Virology and human respiratory Pathologies - Virology and human respiratory Pathologies (VirPath), 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)-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), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna 'Bruno Ubertini' (IZSLER), Innovations Thérapeutiques et Résistances (InTheRes), This study was funded by the by the Ecole Nationale Veterinaire de Toulouse (ENVT), project BQR-2020-ANIMEX, and the ICRAD-ERA NET cofund ANR-21-ICRD-0007, 'Deciphering the role of influenza D virus in bovine and human respiratory diseases in Europe.' Maria Gaudino was supported by a Ph.D. scholarship funded by the Departement Sante Animale (INRAE Toulouse) and the Region Occitanie. Maria Gaudino, Adrien Lion, Justine Oliva, Olivier Terrier, Fatima-Zohra Sikht, Romain Volmer, Gilles Meyer, and Mariette F. Ducatez are members of the French research network on influenza viruses (ResaFlu, GDR2073) financed by the CNRS., and ANR-21-ICRD-0007,PREVENTER,Deciphering the role of influenza D virus in bovine and human respiratory diseases in Europe(2021)
Subjects: coinfections, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, PCLS, cattle, Virology, Insect Science, respiratory viruses, Immunology, ex vivo, precision-cut lung slices, mycoplasma, influenza, Microbiology
Abstract: International audience; Concurrent infections with multiple pathogens are often described in cattle with respiratory illness. However, how the host-pathogen interactions influence the clinical outcome has been only partially explored in this species. Influenza D virus (IDV) was discovered in 2011. Since then, IDV has been detected worldwide in different hosts. A significant association between IDV and bacterial pathogens in sick cattle was shown in epidemiological studies, especially with Mycoplasma bovis. In an experimental challenge, IDV aggravated M. bovis-induced pneumonia. However, the mechanisms through which IDV drives an increased susceptibility to bacterial superinfections remain unknown. Here, we used the organotypic lung model precision-cut lung slices to study the interplay between IDV and M. bovis coinfection. Our results show that a primary IDV infection promotes M. bovis superinfection by increasing the bacterial replication and the ultrastructural damages in lung pneumocytes. In our model, IDV impaired the innate immune response triggered by M. bovis by decreasing the expression of several proinflammatory cytokines and chemokines that are important for immune cell recruitment and the bacterial clearance. Stimulations with agonists of cytosolic helicases and Toll-like receptors (TLRs) revealed that a primary activation of RIG-I/MDA5 desensitizes the TLR2 activation, similar to what was observed with IDV infection. The cross talk between these two pattern recognition receptors leads to a nonadditive response, which alters the TLR2-mediated cascade that controls the bacterial infection. These results highlight innate immune mechanisms that were not described for cattle so far and improve our understanding of the bovine host-microbe interactions and IDV pathogenesis.IMPORTANCE: Since the spread of the respiratory influenza D virus (IDV) infection to the cattle population, the question about the impact of this virus on bovine respiratory disease (BRD) remains still unanswered. Animals affected by BRD are often coinfected with multiple pathogens, especially viruses and bacteria. In particular, viruses are suspected to enhance secondary bacterial superinfections. Here, we use an ex vivo model of lung tissue to study the effects of IDV infection on bacterial superinfections. Our results show that IDV increases the susceptibility to the respiratory pathogen Mycoplasma bovis. In particular, IDV seems to activate immune pathways that inhibit the innate immune response against the bacteria. This may allow M. bovis to increase its proliferation and to delay its clearance from lung tissue. These results suggest that IDV could have a negative impact on the respiratory pathology of cattle.
Published: 2023
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9. Urinary Metabolome Analysis Reveals Potential Microbiota Alteration and Electrophilic Burden Induced by High Red Meat Diet: Results from the French NutriNet‐Santé Cohort and an in vivo Intervention Study in Rats

Author: Loïc Mervant, Marie Tremblay‐Franco, Maïwenn Olier, Emilien Jamin, Jean‐Francois Martin, Lidwine Trouilh, Charline Buisson, Nathalie Naud, Claire Maslo, Cécile Héliès‐Toussaint, Edwin Fouché, Emmanuelle Kesse‐Guyot, Serge Hercberg, Pilar Galan, Mélanie Deschasaux‐Tanguy, Mathilde Touvier, Fabrice Pierre, Laurent Debrauwer, Francoise Guéraud, Metatoul AXIOM (E20 ), MetaboHUB-MetaToul, MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-ToxAlim (ToxAlim), Université de Toulouse (UT)-Ecole d'Ingénieurs de Purpan (INP - PURPAN), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole d'Ingénieurs de Purpan (INP - PURPAN), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ToxAlim (ToxAlim), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Réseau National Alimentation Cancer Recherche (réseau NACRe), Génome et Transcriptome (GeT) - Biopuces (TBI-GeT), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Toulouse Biotechnology Institute (TBI), 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)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Equipe 3: EREN- Equipe de Recherche en Epidémiologie Nutritionnelle (CRESS - U1153), Université Sorbonne Paris Nord-Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), In the context of NutriNet-Santé study, we especially thank Younes Esseddik andNathalie Arnault. We are also grateful to the Genotoul bioinformatics platform Toulouse Occitanieand Sigenae group for providing help and storage resources thanks to Galaxy instance (https://vmgalaxy-prod.toulouse.inra.fr). Sources of support for the work: PhD doctoral fellowship of LM wasco-funded by INRAE (Nutrition, Chemical Food Safety and Consumer Behaviour Scientific Division)and French region Occitanie. All MS experiments were performed on the instruments of theMetaToul-AXIOM platform, partner of the national infrastructure of metabolomics and fluxomics:MetaboHUB [MetaboHUB-ANR-11-INBS-0010, 2011]. This work has been funded by the 'InstitutNational du Cancer' (INCA_12705)-Project PLBIO18-130 and approved by the 'Réseau NACRe'.Graphical abstract was created with Biorender., and ANR-11-INBS-0010,METABOHUB,Développement d'une infrastructure française distribuée pour la métabolomique dédiée à l'innovation(2011)
Subjects: Red meat, Microbiota, [SDV]Life Sciences [q-bio], Lipid peroxidation, Metabolomics, Mercapturic acids, Food Science, Biotechnology
Abstract: International audience; Scope: High red and processed meat consumption is associated with several adverse outcomes such as colorectal cancer and overall global mortality. However, the underlying mechanisms remain debated and need to be elucidated.Methods and results: Urinary untargeted LC-MS metabolomics data from 240 subjects from the French cohort NutriNet-Santé were analysed. Individuals were matched and divided into 3 groups according to their consumption of red and processed meat: high red and processed meat consumers, non-red and processed meat consumers and an at random group. Results were supported by a preclinical experiment where rats were fed either a high red meat or a control diet. Microbiota derived metabolites, in particular indoxyl sulfate and cinnamoylglycine, were found impacted by the high red meat diet in both studies, suggesting a modification of microbiota by the high red/processed meat diet. Rat microbiota sequencing analysis strengthened this observation. Although not evidenced in the human study, rat mercapturic acid profile concomitantly revealed an increased lipid peroxidation induced by high red meat diet.Conclusion: Novel microbiota metabolites were identified as red meat consumption potential biomarkers, suggesting a deleterious effect, which could partly explain the adverse effects associated with high red and processed meat consumption.
Published: 2023
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10. From the Mediterranean to the Pacific: re-circumscription towards Notelaea s.l. and historical biogeography of a generic complex in Oleinae (Oleaceae)

Author: Julia Dupin, Cynthia Hong-Wa, Yohan Pillon, Guillaume Besnard, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Delaware State University (DSU), Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-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), This research was funded by the H2020 Marie Skłodowska-Curie Actions (grant 842234- FRUITFUL), and the Region Occitanie of France, through the BiodivOc programme (grant RepOl)., ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), and ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010)
Subjects: Canary Islands, Phillyrea, Plant Science, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, museomics, Picconia, Madeira, Azores, Canary Islands, Madeira, Morphology, Museomics, Nestegis, Osmanthus, Phillyrea, Picconia, Zealandia, Osmanthus, morphology, Zealandia, Nestegis, Ecology, Evolution, Behavior and Systematics, Azores
Abstract: Tackling the complicated infrafamilial classification of the economically important Oleaceae requires a piecemeal approach that addresses generic circumscriptions. Here, focusing on the distinct clade formed by the generic complexNestegis,Notelaea,Osmanthus,PhillyreaandPicconiain subtribe Oleinae, we aim to elucidate their boundaries and relationships and to evaluate their biogeographic history in light of their peculiar disjunct distribution in the Macaronesian, Mediterranean and Pacific regions. On the basis of phylogenomic data from plastid and nuclear DNA of an extensive sampling, the results show six subclades in this generic complex, which are also geographical segregates found in Australia (Notelaea), Hawaiian Islands (Nestegis sandwicensis), Macaronesia (PhillyreaandPicconia), Mediterranean Region (Phillyrea), New Caledonia (OsmanthussectionNotosmanthus) and New Zealand (Nestegis s.s.). Accounting for broad morphological overlaps in this clade, we recognize three genera (Phillyrea,PicconiaandNotelaea s.l.), subsuming all Pacific taxa underNotelaea.Molecular dating and biogeographic analyses indicate that this clade originated in Eurasia during the Early Miocene (mean 23.2 Mya, 95% HPD: 23.8–14.7). Finally, dispersal (rather than continental vicariance) is probably the main explanation for the global, disjunct distribution of this group, with island-hopping and local extinction as the hallmarks of its evolutionary history.
Published: 2022
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11. Potential of visible/near infrared spectroscopy coupled with chemometric methods for discriminating and estimating the thickness of clogging in drip-irrigation

Author: Julien Petit, Maxime Metz, Bruno Molle, Silvia Mas Mas Garcia, Ryad Bendoula, Nassim Ait-Mouheb, Gestion de l'Eau, Acteurs, Usages (UMR G-EAU), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Information – Technologies – Analyse Environnementale – Procédés Agricoles (UMR ITAP), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Region Occitanie, INRAE Montpellier, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-AgroParisTech-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Subjects: Materials science, Drippers, 0207 environmental engineering, Soil Science, Soil science, 02 engineering and technology, Drip irrigation, Clogging, [SDV.SA.STA]Life Sciences [q-bio]/Agricultural sciences/Sciences and technics of agriculture, Partial least squares regression, 020701 environmental engineering, Spectroscopy, Optical coherence tomography (OCT), Partial least squares with discriminant analysis (PLS-DA), Fouling, Visible near infrared, Near-infrared spectroscopy, Physical and chemical clogging, [CHIM.MATE]Chemical Sciences/Material chemistry, 04 agricultural and veterinary sciences, 6. Clean water, Control and Systems Engineering, Bentonite, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Absorbance spectroscopy, Partial least squares regression (PLSR), Agronomy and Crop Science, Food Science
Abstract: International audience; Drip irrigation is one of the most efficient irrigation techniques, but it is susceptible to dripper clogging. This study proposes a novel and non-destructive method based on visible and near infrared (Vis/NIR) spectroscopy coupled with chemometric methods for the discrimination and thickness estimation of physical and chemical fouling in drip-irrigation systems. Four representative materials linked to physical and chemical clogging (kaolin, bentonite, sand and calcium carbonate) at different thicknesses were selected to illustrate the potential of the approach. Partial least squares regression (PLSR) and its modification partial least squares with discriminant analysis (PLS-DA) were selected for the modelling of clogging materials. The PLS-DA model was able to predict with 96.97% accuracy all classes of materials. The PLSR models were able to estimate fouling thickness with relative prediction errors comprised between 134 μm and 164 μm. This difference appears mainly to be due to the physical properties of the selected materials. This prediction accuracy enabled the estimation of the clogging thickness between 10 and 21% of dripper channel coverage depending on the dripper channel section and the material under study. The proposed method offers an appropriate approach for clogging studies in drip irrigation systems that could be transferred to field applications.
Published: 2021
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12. Quantification and characterisation of commensal wild birds and their interactions with domestic ducks on a free-range farm in southwest France

Author: Chloé Le Gall-Ladevèze, Claire Guinat, Pierre Fievet, Benjamin Vollot, Jean-Luc Guérin, Julien Cappelle, Guillaume Le Loc’h, Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne = University of Lausanne (UNIL), Conservatoire d'Espaces Naturels de Provence-Alpes-Côte d'Azur (CEN PACA ), 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), This study was performed in the framework of the 'Chaire de Biosecurite Aviaire', hosted by the National Veterinary College of Toulouse (ENVT) and funded by the Direction Generale de l'Alimentation, Ministere de l'Agriculture et de l'Alimentation, France. This work was financially supported by the FEDER/Region Occitanie Recherche et Societes 2018-AI-TRACK. CG is funded by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 842621., and European Project: 777657,H2020-EU.1.3.3. - Stimulating innovation by means of cross-fertilisation of knowledge,777657,MSCA-RISE(2018)
Subjects: Farms, [SDV]Life Sciences [q-bio], animal diseases, Analyse de réseau, Animals, Wild, L73 - Maladies des animaux, Poultry, Birds, Passer domesticus, Animals, Canard, Élevage en liberté, Poultry Diseases, Moineau, Multidisciplinary, Passer montanus, Distribution spatiale, Oiseau, Ducks, Influenza in Birds, commensal, Élevage de volailles
Abstract: The role of commensal birds in the epidemiology of pathogens in poultry farms remains unclear. Our study aimed to identify potential key species for interactions with domestic ducks on one free-range duck farm in southwest France. Methods combined direct individual observations on duck outdoor foraging areas, network analysis, and general linear mixed models of abundances. Results showed a wide diversity of wild bird species visiting foraging areas, heavily dominated in frequency by White wagtails (Motacilla alba) and Sparrows (Passer domesticus and Passer montanus). These also were the only species seen entering duck premises or perching on drinkers in the presence of ducks. Moreover, White wagtails were the species most frequently observed on the ground and in close proximity to ducks. Network analysis suggested the role of White wagtails and Sparrows in linking ducks to other wild birds on the farm. The abundance of White wagtails was positively associated with open vegetation, with the presence of ducks and particularly in the afternoon, while the abundance of Sparrows was positively associated only with the fall-winter season. By precisely characterising interactions, the study was able to identify few wild bird species which should be prioritized in infectious investigations at the interface with poultry., Scientific Reports, 12, ISSN:2045-2322
Published: 2022
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13. Uncatalyzed Formation of Polyaminoboranes from Diisopropylaminoborane and Primary Amines: a Kinetically Controlled Polymerization Reaction

Author: Gilles Alcaraz, Elsa Caytan, Chiara Dinoi, Carlos Antonio De Albuquerque Pinheiro, Marc Devillard, Iker del Rosal, Claire Roiland, Institut des Sciences Chimiques de Rennes (ISCR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), 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)-Fédération de recherche « Matière et interactions » (FeRMI), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Brazilian Ministry of Education, CAPES, Region Bretagne Region Bretagne [17048], CALMIP Region Occitanie [2017-[p17010]], Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-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), Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-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), Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-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)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut de Chimie de Toulouse (ICT-FR 2599), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-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), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)
Subjects: Primary (chemistry), 010405 organic chemistry, aminoboranes, chemistry.chemical_element, [CHIM.CATA]Chemical Sciences/Catalysis, General Chemistry, 010402 general chemistry, Photochemistry, 01 natural sciences, 0104 chemical sciences, chemistry.chemical_compound, Monomer, BN compounds, Polymerization, chemistry, polymerization, Inorganic polymers, [CHIM]Chemical Sciences, boron, Boron, ComputingMilieux_MISCELLANEOUS
Abstract: International audience; Recently, we disclosed the uncatalyzed formation of polyaminoboranes (PABs) from monomeric diisopropylaminoborane ((Pr2N)-Pr-i-BH2) and primary amines (RNH2). Their structure is studied through a detailed multinuclear NMR study and their full spectroscopic characterization is presented revealing that N-alkyl substituted PABs exhibit magnetically non-equivalent methylenic protons in the close vicinity of the BN-backbone. We also performed an in-depth theoretical study of this global chemical process. The mechanism is fully apprehended and the strong influence of the temperature on the outcome of the reaction is unveiled. DFT-calculations clearly show that the formation of the polyaminoboranes (RNH-BH2)(n) results from a kinetically controlled step-growth polymerization reaction that can be globally viewed as a head-to-tail association process of the in situ generated transient monomeric monoalkylamino-borane [RNH-BH2].
Published: 2021
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14. Evolution of traditional agroforestry landscapes and development of invasive species: lessons from the Pyrenees (France)

Author: Claire Marais-Sicre, Sylvie Guillerme, Eric Maire, Hugues Barcet, Nicolas de Munnik, Géographie de l'environnement (GEODE), Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Centre d'études spatiales de la biosphère (CESBIO), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), CNRS through the project INVASCAPE (GEODE) CNRS through the project EI2P (Region Occitanie) CNRS through the project INVAVISION (PEPS TOHMIS CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse - Jean Jaurès (UT2J), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS), and Université Toulouse - Jean Jaurès (UT2J)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Landscape dynamics, Land abandonment, Health (social science), 010504 meteorology & atmospheric sciences, Sociology and Political Science, [SDE.MCG]Environmental Sciences/Global Changes, Geography, Planning and Development, Biodiversity, 010501 environmental sciences, Management, Monitoring, Policy and Law, 01 natural sciences, Invasive species, Place attachment, Agricultural land, Perceptions, Afforestation, Foothills, Agroforestry, 0105 earth and related environmental sciences, Nature and Landscape Conservation, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Sustainable development, Global and Planetary Change, geography.geographical_feature_category, Ecology, Invasive Alien Species (IAS), [SHS.GEO]Humanities and Social Sciences/Geography, 15. Life on land, [SDE.ES]Environmental Sciences/Environmental and Society, Geography, 13. Climate action, Sustainability, Landscape ecology, UAV Technology
Abstract: International audience; The term agroforestry covers practices that are promoted to maintain or even enhance biodiversity. However, the relationship between agroforestry and invasive species is rarely addressed, even though the spread of such species is an important issue, not only ecologically but also economically and socially. Over the past few decades, humans have greatly accelerated the process of biological invasions, to such an extent that they are now recognized as the second cause of rapid decline in biodiversity. In France (as in other parts in Europe), abandonment of agricultural land in remote areas is a major problem having socio-economic, landscape and environmental implications. The objective of the research presented here was to find a method for studying the relationship between traditional agroforestry systems and invasive species, despite a lack of available data. We investigated the evolution of a traditional agroforestry system in the Pyrenean foothills, where invasive species are abundant, by implementing two complementary methods: (1) interviews highlighting the local stakeholders' perception of landscape evolution, invasive species and the challenges they represent for the local traditional agroforestry landscapes, and (2) detailed mapping of an area occupied by invasive plants, by means of very high-resolution spatial technologies using UAV's and aerial photography. The results show that invasive species have spread in relation with the abandonment of agricultural land, which has also led to "landscape closure" by the encroachment of natural afforestation. They also underline the difficulty of assessing the spread of invasive species. This situation is of major importance in terms of land-use planning, as the various stakeholders have different perceptions of the problem, and it raises questions about the sustainability of practices and territories.
Published: 2020
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15. Optimal stopping for measure-valued piecewise deterministic Markov processes

Author: Maud Joubaud, Bertrand Cloez, Benoîte de Saporta, Institut Montpelliérain Alexander Grothendieck (IMAG), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Region Occitanie, Region Ile-de-France, French National Research Agency (ANR), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), and de Saporta, Benoîte
Subjects: Statistics and Probability, [MATH.MATH-PR] Mathematics [math]/Probability [math.PR], Mathematical optimization, General Mathematics, Population, Markov process, 01 natural sciences, Measure (mathematics), measure space, 010104 statistics & probability, 03 medical and health sciences, symbols.namesake, Bellman equation, FOS: Mathematics, population dynamics, Optimal stopping, 0101 mathematics, education, 030304 developmental biology, Mathematics, dynamic programming, 0303 health sciences, Sequence, education.field_of_study, Markov processes, Probability (math.PR), [MATH.MATH-PR]Mathematics [math]/Probability [math.PR], Dynamic programming, optimal stopping, symbols, Piecewise, Statistics, Probability and Uncertainty, Mathematics - Probability
Abstract: This paper investigates the random horizon optimal stopping problem for measure-valued piecewise deterministic Markov processes (PDMPs). This is motivated by population dynamics applications, when one wants to monitor some characteristics of the individuals in a small population. The population and its individual characteristics can be represented by a point measure. We first define a PDMP on a space of locally finite measures. Then we define a sequence of random horizon optimal stopping problems for such processes. We prove that the value function of the problems can be obtained by iterating some dynamic programming operator. Finally we prove via a simple counter-example that controlling the whole population is not equivalent to controlling a random lineage.
Published: 2020
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16. Pedo-geochemical background and sediment contamination of metal(loid)s in the old mining-district of Salsigne (Orbiel valley, France)

Author: Philippe Behra, Eva Schreck, Jérôme Viers, Priscia Oliva, Gauthier Delplace, Géosciences Environnement Toulouse (GET), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Chimie Agro-Industrielle (CAI), Ecole nationale supérieure des ingénieurs en arts chimiques et technologiques-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), This work was supported by the EC2CO program of the INSU/CNRS and by the Region Occitanie Pyrenees-Mediterranee (Diagnose project), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Ecole nationale supérieure des ingénieurs en arts chimiques et technologiques (ENSIACET), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Geologic Sediments, Environmental Engineering, Environmental contamination, Health, Toxicology and Mutagenesis, [SDV]Life Sciences [q-bio], chemistry.chemical_element, 010501 environmental sciences, 010502 geochemistry & geophysics, 01 natural sciences, Mining, Arsenic, Metal, Soil, Rivers, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, Metals, Heavy, Tributary, Sediment contamination, Environmental Chemistry, Humans, 0105 earth and related environmental sciences, geography, geography.geographical_feature_category, Flood myth, Orbiel valley, Public Health, Environmental and Occupational Health, General Medicine, General Chemistry, Contamination, Mines, Pollution, 6. Clean water, Current (stream), chemistry, 13. Climate action, visual_art, Environmental chemistry, Geochemical background, visual_art.visual_art_medium, Environmental science, metal(loid)s, Water Pollutants, Chemical, Environmental Monitoring
Abstract: International audience; The mining district of Salsigne in the Orbiel valley (Aude, France) was at one time the first gold mine in Europe and the first arsenic mine in the world. However, no scientific studies have evaluated the magnitude of its environmental impact. In this study, the pedo-geochemical background (PGB) was determined for 14 metal (loid) elements, including As. It appears that the PGB values for As and Sb are relatively high with 44±12 and 0.9±1.2 mg kg-1, respectively, because of the geological particularities of this area. In a second step, these PGB values (normalized with Ti concentrations) were used as local references to determine enrichment factors (EFs) of bed river sediments for the Orbiel River and two of its major tributaries (Gresillou and Russec rivers) collected between November 2018 and July 2020. Results showed that riverine sediments are contaminated by past mining activity and/or current storage areas. If we except the major elements (Fe, Ti and at a lesser extent Mn), we observed that As, Cu, Sb, Pb present the highest concentrations relative to the remaining elements (Cd, Co, V, Ni and Cr). In the case of As, EFs can reach 74 in the Orbiel River, 1000 in the Gresillou River and 27 in the Russec River. These calculations were also performed for sediments transported by the extreme flood of October 14, 2018, that killed 15 people and potentially remobilized contamination in the valley. We observed that the As concentrations of suspended samples from Grésillou and Russec rivers have reached 870 mg kg-1. Finally, the As concentrations measured in the river sediments of this valley are of the same order of magnitude than those published in the literature for environments strongly impacted by mining or mineral processing activities.
Published: 2022
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17. The Rice ILI2 Locus Is a Bidirectional Target of the African Xanthomonas oryzae pv. oryzae Major Transcription Activator-like Effector TalC but Does Not Contribute to Disease Susceptibility

Author: Doucouré, Hinda, Auguy, Florence, Blanvillain-Baufumé, Servane, Fabre, Sandrine, Gabriel, Marc, Thomas, Emilie, Dambreville, Fleur, Sciallano, Coline, Szurek, Boris, Koita, Ousmane, Verdier, Valérie, Cunnac, Sebastien, Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-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), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Monsanto’s Beachell-Borlaug International Scholars Program PhD fellowship, and Chercheur d’Avenir grant from the Region Occitanie
Subjects: disease, rice, TAL effector, Xanthomonas oryzae, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy
Abstract: International audience; Xanthomonas oryzae pv. oryzae (Xoo) strains that cause bacterial leaf blight (BLB) limit rice (Oryza sativa) production and require breeding more resistant varieties. Transcription activator-like effectors (TALEs) activate transcription to promote leaf colonization by binding to specific plant host DNA sequences termed effector binding elements (EBEs). Xoo major TALEs universally target susceptibility genes of the SWEET transporter family. TALE-unresponsive alleles of clade III OsSWEET susceptibility gene promoter created with genome editing confer broad resistance on Asian Xoo strains. African Xoo strains rely primarily on the major TALE TalC, which targets OsSWEET14. Although the virulence of a talC mutant strain is severely impaired, abrogating OsSWEET14 induction with genome editing does not confer equivalent resistance on African Xoo. To address this contradiction, we postulated the existence of a TalC target susceptibility gene redundant with OsSWEET14. Bioinformatics analysis identified a rice locus named ATAC composed of the INCREASED LEAF INCLINATION 2 (ILI2) gene and a putative lncRNA that are shown to be bidirectionally upregulated in a TalC-dependent fashion. Gain-of-function approaches with designer TALEs inducing ATAC sequences did not complement the virulence of a Xoo strain defective for SWEET gene activation. While editing the TalC EBE at the ATAC loci compromised TalC-mediated induction, multiplex edited lines with mutations at the OsSWEET14 and ATAC loci remained essentially susceptible to African Xoo strains. Overall, this work indicates that ATAC is a probable TalC off-target locus but nonetheless documents the first example of divergent transcription activation by a native TALE during infection.
Published: 2022
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18. New insights into the role of DNA methylation in Biomphalaria glabrata infection susceptibility

Author: Luviano, Nelia, Lopez, Marie, Gawehns, Fleur, Chaparro, Cristian, Arimondo, Paola, Halby, Ludovic, Verhoeven, Koen, Pujol, Benoit, Gourbal, Benjamin, Duval, David, Ittiprasert, Wannaporn, Allienne, Jean-François, Pouzol, Damien, Tavernier, Geneviève, Cosseau, Celine, Grunau, Christoph, Netherlands Institute of Ecology (NIOO), Terrestrial Ecology (TE), Interactions Hôtes-Pathogènes-Environnements (IHPE), Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut des Biomolécules Max Mousseron [Pôle Chimie Balard] (IBMM), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM), Université de Montpellier (UM), Centre National de la Recherche Scientifique (CNRS), Netherlands Institute of Ecology - NIOO-KNAW (NETHERLANDS), Chimie biologique épigénétique - Epigenetic Chemical Biology (EpiCBio), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Pharmacochimie de la Régulation Epigénétique du Cancer (ETaC), PIERRE FABRE-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Georgetown University [Washington] (GU), Institut de médecine moléculaire de Rangueil (I2MR), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)- Institut Fédératif de Recherche Bio-médicale Institution (IFR150)-Institut National de la Santé et de la Recherche Médicale (INSERM), This work was supported by Wellcome Trust strategic award (107475/Z/15/Z) and by a PhD grant to NL from the Region Occitanie (EPIPARA project) and the University of Perpignan Via Domitia graduate school ED305. With the support of LabEx CeMEB, an ANR'Investissements d’avenir' program (ANR-10-LABX-04-01) through the Environmental Epigenomics Platform and the 'projets de recherche exploratoires du CeMEB 2018' project 'Epigenetics of inbreeding depression (EPID)'. This study is set within the framework of the 'Laboratoires d'Excellences (LABEX)' TULIP (ANR-10-LABX-41). BQR UPVD provided funding for the Nanoject III Programmable Nanoliter Injector., FIOCRUZ, ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010), and ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010)
Subjects: [SDE]Environmental Sciences
Abstract: Introduction As for many transmissible diseases non-pharmacological interventions are one of the most effective ways to control schistosoma infections. One of theses, the control of the intermediate host, is also recognized by WHO as a key element to eradication of the disease in humans. Biomphalaria snails can show remarkable resistance to schistosomes and prevalence is low in snail populations even in regions where the parasite is highly present in the vertebrate host.Resistance is a heritable trait, but it shows also high plasticity e.g., snails can be become resistant to the same parasite strain after a primary infection. One of the components of heritable plasticity is epigenetic information that refers to the heritable but reversible changes in gene function, and one of the bearers of epigenetic information is DNA methylation. We reasoned that modifying DNA methylation in the snail would have potentially positive effects on resistance traits. Methods We developed chemical DNA methylation modulators to which the snails were exposed to modify their pan-genomic methylation and we established a method for targeted DNA methylation modifications based on dCas9/Crispr. For heritability of resistance measure we used epigenetic recombinant inbred lines (EpiRILs) and experimental infections. Results We applied a dCas9-SunTag-DNMT3A complex and synthetic sgRNA to transfect B. glabrata embryos and observed an increase of CpG methylation at the target site in 50% of the hatching snails. DNA methylations were also introduced in an inbred B.glabrata line by chemical treatment in F0. This led to phenotypic variation in F3 and methylation differences in F3. Both increase and decrease (up to 100% and down to 20% prevalence from 86% control) of infection success indicating variation in complex resistance/compatibility trait. Conclusions We show that DNA methylation can be modified in B.glabrata both chemically and dCas-based, and pan-genomic or targeted. These modifications produce heritable phenotypic variants and have an influence on infection susceptibility confirming the epigenetic component of this trait. A rational of DNA methylation-based vector control will be presented.
Published: 2022

19. A generalizable framework for spatially explicit exploration of soil organic carbon sequestration on global marginal land

Author: Ariane Albers, Angel Avadí, Lorie Hamelin, Toulouse Biotechnology Institute (TBI), 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)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Recyclage et risque (UPR Recyclage et risque), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Université de Montpellier (UM), Region Occitanie under the Cambioscop project18015981, ANR-17-MGPA-0006,MGPA,ANR-17-MGPA-0006, and European Project: 869192
Subjects: Carbon Sequestration, Soil, Multidisciplinary, [SDV]Life Sciences [q-bio], P34 - Biologie du sol, Agriculture, P01 - Conservation de la nature et ressources foncières, Carbon Dioxide, Carbon, Ecosystem
Abstract: Land-based CO2 removal demands changes in management or new suitable areas to sustainably grow additional biomass without reducing food supply or damaging natural ecosystems. The soil organic carbon (SOC) sequestration pathway is thought to transfer atmospheric CO2 into a land unit, through plants, plant residues and other organic solids stored as part of the soil organic matter. No previous study explored SOC sequestration potentials on global marginal land. Here we integrated, into a generalizable modelling framework, the mapping of a set of biophysical (climatic and edaphic) and land conservation constraints to (i) identify suitable matches (i.e. biophysically possible combinations) of target areas with plant species, and (ii) to quantify contributions of pairing to long-term SOC sequestration (2020–2100). The proposed framework represents a refinement to previous mapping exercises, which seldom consider biophysical constraints, soil erosion, plant species tolerances to pedoclimatic conditions, and world protected areas. The approach was tested on marginal lands featuring SOC-deficient stocks (≤ 50 Mg SOC ha−1 to 30 cm depth) at 30 arc-sec resolution, consolidated into world regions × global ecological zones based on geo-localised products. The framework was shown to enable better-informed decision-making on interventions at large geographical scales, revealing biophysically realistic options, while management should be determined locally.
Published: 2022
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20. Waste-to-nutrition: a review of current and emerging conversion pathways

Author: Michael J. O’Donohue, Lorie Hamelin, U. Javourez, Toulouse Biotechnology Institute (TBI), 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)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Region Occitanie (18015981), Metaprogram GLOFOODS (INRAE-CIRAD), ANR-17-MPGA-0006,CambioSCOP,Carbon management towards low fossil carbon use(2017), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National des Sciences Appliquées (INSA), Université Paris Descartes - Faculté de Pharmacie de Paris (UPD5 Pharmacie), Université Paris Descartes - Paris 5 (UPD5), Fractionnement des AgroRessources et Environnement (FARE), and Université de Reims Champagne-Ardenne (URCA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Crop residue, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Circular economy, Bioconversion, Alternative feed, Bioengineering, 010501 environmental sciences, Raw material, 01 natural sciences, Applied Microbiology and Biotechnology, Novel food, 12. Responsible consumption, 03 medical and health sciences, [CHIM.GENI]Chemical Sciences/Chemical engineering, Microbial protein, Biomass, 030304 developmental biology, 0105 earth and related environmental sciences, 2. Zero hunger, 0303 health sciences, Waste management, Sewage, Residual biomass, 15. Life on land, Biorefinery, Bioeconomy, Manure, Wood, 6. Clean water, Refuse Disposal, Food waste, 13. Climate action, Food, Biofuels, Food systems, Environmental science, Insect, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Biotechnology
Abstract: International audience; Residual biomass is acknowledged as a key sustainable feedstock for the transition towards circular and low fossil carbon economies to supply whether energy, chemical, material and food products or services. The latter is receiving increasing attention, in particular in the perspective of decoupling nutrition from arable land demand. In order to provide a comprehensive overview of the technical possibilities to convert residual biomasses into edible ingredients, we reviewed over 950 scientific and industrial records documenting existing and emerging waste-to-nutrition pathways, involving over 150 different feedstocks here grouped under 10 umbrella categories: (i) wood-related residual biomass, (ii) primary crop residues, (iii) manure, (iv) food waste, (v) sludge and wastewater, (vi) green residual biomass, (vii) slaughterhouse by-products, (viii) agrifood co-products, (ix) C 1 gases and (x) others. The review includes a detailed description of these pathways, as well as the processes they involve. As a result, we proposed four generic building blocks to systematize waste-to-nutrition conversion sequence patterns, namely enhancement, cracking, extraction and bioconversion. We further introduce a multidimensional representation of the biomasses suitability as potential as nutritional sources according to (i) their content in anti-nutritional compounds, (ii) their degree of structural complexity and (iii) their concentration of macro-and micronutrients. Finally, we suggest that the different pathways can be grouped into eight large families of approaches: (i) insect biorefinery, (ii) green biorefinery, (iii) lignocellulosic biorefinery, (iv) nonsoluble protein recovery, (v) gas-intermediate biorefinery, (vi) liquid substrate alternative, (vii) solid-substrate fermentation and (viii) more-out-of-slaughterhouse by-products. The proposed framework aims to support future research in waste recovery and valorization within food systems, along with stimulating reflections on the improvement of resources' cascading use.; Il est admis que la biomasse résiduaire sera une nouvelle matière première clef dans la future économie circulaire à bas carbone fossile, à la fois pour la production d'énergies, de molécules pour la chimie, des matériaux, des produits ou services alimentaires. La production d'aliments à partir de résidus est de plus en plus étudiée, notamment dans l'objectif de découpler la production alimentaire de l'utilisation des terres arables. Pour fournir une analyse exhaustive des possibilités techniques permettant de transformer la biomasse résiduaire en ingrédients alimentaires, nous avons examiné 950 documents (articles scientifiques et documents professionnels) décrivant des itinéraires de transformation "déchets aux produits nutritifs" actuels et émergents impliquant plus de 150 matières premières différentes qui sont groupées dans cet article sous 10 macro-catégories : (i) résidus issus de la production sylvicole, (ii) résidus des grandes cultures agricoles (iii) fumier (iv) déchets alimentaires (v) boues d’épuration et eaux résiduaires (vi) biomasse verte (vii) coproduits des abattoirs (viii) co-produits de la transformation alimentaire (ix) des gaz C1 et (x) autres résidus organiques. Cette revue fournit une description détaillée de ces itinéraires et les procédés utilisés. L'analyse a permis de proposer quatre briques génériques qui servent à générer des représentations des différents itinéraires. Ces briques sont le renforcement, le fractionnement, l'extraction et la bioconversion. De plus, nous proposons une représentation multidimensionnelle de l'aptitude des biomasses à servir comme sources de produits nutritifs. Cette représentation tient compte de (i) la teneur en composés anti-nutritifs (ii) la complexité structurale et (iii) la concentration en macro- et micro-nutriments. Enfin, nous postulons que les différents itinéraires puissent être regroupés en huit familles technologiques (i) bioraffinerie des insectes (ii) bioraffinerie verte (iii) bioraffinerie des lignocelluloses (iv) la production de protéines insoluble (v) la bioraffinerie des matières gazeuses (C1) (vi) le substrat liquide alternatif (vii) la fermentation en phase solide et (viii) la valorisation des coproduits des abattoirs. Il est escompté que ce cadre conceptuel servira comme support pour des futurs travaux de recherches visant la récupération et la valorisation dans le système alimentaire des matières résiduaires d'origines biologiques. De plus, nous espérons que nos propositions stimuleront de nouvelles recherche sur la valorisation en cascade des ressources résiduaires.
Published: 2021
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21. Phylodynamic Study of the Conserved RNA Structure Encompassing the Hemagglutinin Cleavage Site Encoding Region of H5 and H7 Low Pathogenic Avian Influenza Viruses

Author: Romain Volmer, Claire Hoede, Gabriel Dupré, Pierre Bessière, Thomas Figueroa, Stéphane Bertagnoli, Christine Gaspin, Mariette F. Ducatez, Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), This work was funded by a grant from the Agence Nationale de la Recherche (ANR-16-CE35-0005) to Romain Volmer. Pierre Bessière was supported by a Ph.D. scholarship funded by the Region Occitanie (France) and by the 'Chaire de Biosécurité' at the 'École Nationale Vétérinaire de Toulouse' (French Ministry of Agriculture). Gabriel Dupré is supported by Ph.D. scholarship fundedby the French Ministry of Research and Education., ANR-16-CE35-0005,RuleOfThree,Emergence de virus Influenza aviaires hautement pathogènes dans le contexte de la triade hôte-microbiote-virus(2016), Hoede, Claire, Emergence de virus Influenza aviaires hautement pathogènes dans le contexte de la triade hôte-microbiote-virus - - RuleOfThree2016 - ANR-16-CE35-0005 - AAPG2016 - VALID, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), and Université Toulouse III - Paul Sabatier (UT3)
Subjects: Hemagglutinin (influenza), Cleavage (embryo), medicine.disease_cause, Microbiology, 03 medical and health sciences, Virology, evolution, medicine, [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Nucleic acid structure, RNA structure, 030304 developmental biology, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, 0303 health sciences, biology, 030306 microbiology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], highly pathogenic avian influenza virus, virus diseases, Low pathogenic, Influenza A virus subtype H5N1, 3. Good health, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, biology.protein, influenza
Abstract: Highly pathogenic avian influenza viruses (HPAIVs) evolve from low pathogenic avian influenza viruses (LPAIVs) of the H5 and H7 subtypes. This evolution is characterized by the acquisition of a multi-basic cleavage site (MBCS) motif in the hemagglutinin (HA) that leads to an extended viral tropism and severe disease in poultry. One key unanswered question is whether the risk of transition to HPAIVs is similar for all LPAIVs H5 or H7 strains, or whether specific determinants in the HA sequence of some H5 or H7 LPAIV strains correlate with a higher risk of transition to HPAIVs. Here, we determined if specific features of the conserved RNA stem-loop located at the HA cleavage site-encoding region could be detected along the LPAIV to HPAIV evolutionary pathway. Analysis of the thermodynamic stability of the predicted RNA structures showed no specific patterns common to HA sequences leading to HPAIVs and distinct from those remaining LPAIVs. However, RNA structure clustering analysis revealed that most of the American lineage ancestors leading to H7 emergences via recombination shared the same viral RNA (vRNA) structure topology at the HA1/HA2 boundary region. Our study thus identified predicted secondary RNA structures present in the HA of H7 viruses, which could promote genetic recombination and acquisition of a multibasic cleavage site motif (MBCS).
Published: 2021
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22. FLO11, a Developmental Gene Conferring Impressive Adaptive Plasticity to the Yeast Saccharomyces cerevisiae

Author: Clara Bouyx, Jean Marie François, Marion Schiavone, Toulouse Biotechnology Institute (TBI), 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)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Lallemand SAS, Lallemand Inc. rue de Briquetiers, Blagnac, FranceSAIC2016/048SAIC/2018/010, Region Occitanie, Bd Marecal Juin, Toulouse, and France09003813
Subjects: Microbiology (medical), Saccharomyces cerevisiae, Biology, flocculins, Immunology and Allergy, Epigenetics, FLO11, Cell adhesion, Molecular Biology, Gene, Genetics, General Immunology and Microbiology, Biofilm, phenotypic variation, adhesins, biology.organism_classification, Yeast, Cell aggregation, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Medicine, cell wall, adaptive plasticity, Adaptation
Abstract: The yeast Saccharomyces cerevisiae has a remarkable ability to adapt its lifestyle to fluctuating or hostile environmental conditions. This adaptation most often involves morphological changes such as pseudofilaments, biofilm formation, or cell aggregation in the form of flocs. A prerequisite for these phenotypic changes is the ability to self-adhere and to adhere to abiotic surfaces. This ability is conferred by specialized surface proteins called flocculins, which are encoded by the FLO genes family in this yeast species. This mini-review focuses on the flocculin encoded by FLO11, which differs significantly from other flocculins in domain sequence and mode of genetic and epigenetic regulation, giving it an impressive plasticity that enables yeast cells to swiftly adapt to hostile environments or into new ecological niches. Furthermore, the common features of Flo11p with those of adhesins from pathogenic yeasts make FLO11 a good model to study the molecular mechanism underlying cell adhesion and biofilm formation, which are part of the initial step leading to fungal infections.
Published: 2021
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23. Quality-Based Reinforcement Learning in Intelligent Opportunistic Software Composition

Author: Hacid, Kahina, Trouilhet, Sylvie, Adreit, Françoise, Arcangeli, Jean-Paul, Systèmes Multi-Agents Coopératifs (IRIT-SMAC), Institut de recherche en informatique de Toulouse (IRIT), Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées, and French region Occitanie and the operational program FEDER-FSE 'Midi-Pyrénées et Garonne' : AILP (Assistance InteLligente et proactive enenvironnement Professionnel) project
Subjects: [INFO.INFO-IU]Computer Science [cs]/Ubiquitous Computing, Ambient Intelligence, Smart Assistance, [INFO.INFO-LG]Computer Science [cs]/Machine Learning [cs.LG], [INFO.INFO-MA]Computer Science [cs]/Multiagent Systems [cs.MA], Internet of Things, Agents, Emergence, Knowledge Sharing, Software Composition, Reinforcement Learning, Quality, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI]
Abstract: International audience; Internet of Things and cyber-physical systems are characterised by openness and an increasing number of devices and their associated services. In a previous work, we have proposed to exploit opportunistically these services in order to automatically make emerge customised applications that suit user preferences.For that, we have developed a generic solution for bottom-up opportunistic service composition, based on reinforcement learning.In this work, it is extended to handle more efficiently the appearance of new components using \textit{service annotation} and \textit{quality attributes} in order to generalise and share knowledge with new discovered services. A didactic use case is used for illustration and demonstration purposes.
Published: 2021

24. The methylome of Biomphalaria glabrata and other mollusks: enduring modification of epigenetic landscape and phenotypic traits by a new DNA methylation inhibitor

Author: Koen J. F. Verhoeven, Slavica Ivanovic, Fleur Gawehns, Christoph Grunau, Patrice David, Nelia Luviano, Cristian Chaparro, Céline Cosseau, Paola B. Arimondo, Marie Lopez, Interactions Hôtes-Pathogènes-Environnements (IHPE), Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut des Biomolécules Max Mousseron [Pôle Chimie Balard] (IBMM), Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche Pierre Fabre (Centre de R&D Pierre Fabre), PIERRE FABRE, Netherlands Institute of Ecology (NIOO-KNAW), Chimie biologique épigénétique - Epigenetic Chemical Biology (EpiCBio), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), This work was supported by Wellcome Trust strategic award [107475/Z/15/Z] and by a PhD grant to NL from the Region Occitanie (EPIPARA project) and the University of Perpignan Via Domitia graduate school ED305. With the support of LabEx CeMEB, an ANR 'Investissements d’avenir' program (ANR-10-LABX-04-01) through the Environmental Epigenomics Platform and the 'projets de recherche exploratoires du CeMEB 2018' project 'Epigenetics of inbreeding depression (EPID)'. This study is set within the framework of the 'Laboratoires d'Excellences (LABEX)' TULIP (ANR‐10‐LABX‐41)., ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Perpignan Via Domitia (UPVD), Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Pharmacochimie de la Régulation Epigénétique du Cancer (ETaC), PIERRE FABRE-Centre National de la Recherche Scientifique (CNRS), Netherlands Institute of Ecology - NIOO-KNAW (NETHERLANDS), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Royal Netherlands Academy of Arts and Sciences (KNAW), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM), and Terrestrial Ecology (TE)
Subjects: [SDV]Life Sciences [q-bio], Bisulfite sequencing, DNA Methyltransferase Inhibitor, Locus (genetics), [CHIM.THER]Chemical Sciences/Medicinal Chemistry, QH426-470, Biology, Plan_S-Compliant-OA, Epigenesis, Genetic, Epigenome, chemistry.chemical_compound, 03 medical and health sciences, 0302 clinical medicine, Epigenetic inheritance, Genetics, Animals, Biomphalaria glabrata, Epimutation, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, 14. Life underwater, Epigenetics, Molecular Biology, [SDV.BDD]Life Sciences [q-bio]/Development Biology, 030304 developmental biology, 0303 health sciences, Mollusks, Biomphalaria, Research, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Phenotypic trait, Methylation, DNA Methylation, biology.organism_classification, Invertebrates, 5-Methylcytosine, DNMT inhibitors, chemistry, Mollusca, international, 030220 oncology & carcinogenesis, DNA methylation, 030217 neurology & neurosurgery
Abstract: Background 5-Methylcytosine (5mC) is an important epigenetic mark in eukaryotes. Little information about its role exists for invertebrates. To investigate the contribution of 5mC to phenotypic variation in invertebrates, alteration of methylation patterns needs to be produced. Here, we apply new non-nucleoside DNA methyltransferase inhibitors (DNMTi) to introduce aleatory changes into the methylome of mollusk species. Results Flavanone inhibitor Flv1 was efficient in reducing 5mC in the freshwater snails Biomphalaria glabrata and Physa acuta, and to a lesser degree, probably due to lower stability in sea water, in the oyster Crassostrea gigas. Flv1 has no toxic effects and significantly decreased the 5mC level in the treated B. glabrata and in its offspring. Drug treatment triggers significant variation in the shell height in both generations. A reduced representation bisulfite-sequencing method called epiGBS corroborates hypomethylation effect of Flv1 in both B. glabrata generations and identifies seven Differential Methylated Regions (DMR) out of 32 found both in Flv1-exposed snails and its progeny, from which 5 were hypomethylated, demonstrating a multigenerational effect. By targeted bisulfite sequencing, we confirmed hypomethylation in a locus and show that it is associated with reduced gene expression. Conclusions Flv1 is a new and efficient DNMTi that can be used to induce transient and heritable modifications of the epigenetic landscape and phenotypic traits in mollusks, a phylum of the invertebrates in which epigenetics is understudied.
Published: 2021
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25. What drives the acceptability of restrictive health policies: An experimental assessment of individual preferences for anti-COVID 19 strategies

Author: Thierry Blayac, Dimitri Dubois, Sébastien Duchêne, Phu Nguyen-Van, Bruno Ventelou, Marc Willinger, Centre d'Economie de l'Environnement - Montpellier (CEE-M), Centre National de la Recherche Scientifique (CNRS)-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), Groupe Sup de Co Montpellier (GSCM) - Montpellier Business School, EconomiX, Université Paris Nanterre (UPN)-Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Sciences Economiques (AMSE), École des hautes études en sciences sociales (EHESS)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), Observatoire régional de la santé Provence-Alpes-Côte d'Azur [Marseille] (ORS PACA), Regional program 'Defiscles Urgence COVID-19' from the Region Occitanie, ANR-21-COVR-0041,RESPIRE,Résilience post-covid et préférences économiques et sociales: une étude d'économie comportementale avec un approfondissement sur la propension à coopérer(2021), and ANR-20-COVI-0003,GENCOVID,Identification des défauts monogéniques de l'immunité responsables des formes sévères de COVID-19 chez les patients précédemment en bonne santé(2020)
Subjects: Economics and Econometrics, Acceptability, Discrete choice experiment, JEL: C - Mathematical and Quantitative Methods/C.C9 - Design of Experiments/C.C9.C90 - General, JEL: D - Microeconomics/D.D9 - Intertemporal Choice/D.D9.D90 - General, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Policy design, [SHS.ECO]Humanities and Social Sciences/Economics and Finance, Individual preferences, JEL: I - Health, Education, and Welfare/I.I1 - Health/I.I1.I18 - Government Policy • Regulation • Public Health
Abstract: International audience; The public acceptability of a policy is an important issue in democracies, in particular for anti-COVID-19 policies, which require the adherence of the population to be applicable and efficient. Discrete choice experiment (DCE) can help elicit preference ranking among various policies for the whole population and subgroups. Using a representative sample of the French population, we apply DCE methods to assess the acceptability of various anti-COVID-19 measures, separately and as a package. Owing to the methods, we determine the extent to which acceptability depends on personal characteristics: political orientation, health vulnerability, or age. The young population differs in terms of policy preferences and their claim for monetary compensation, suggesting a tailored policy for them. The paper provides key methodological tools based on microeconomic evaluation of individuals’ preferences for improving the design of public health policies.
Published: 2021
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26. Oviposition Preference and Larval Performance of Drosophila suzukii (Diptera: Drosophilidae), Spotted-Wing Drosophila: Effects of Fruit Identity and Composition

Author: Anne Loiseau, Ruth A. Hufbauer, Nicolas O. Rode, Arnaud Estoup, Julien Foucaud, Virginie Ravigné, Aurélien Ausset, Mathieu Gautier, Nicolas Leménager, Laure Olazcuaga, Benoit Facon, 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), 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), Colorado State University [Fort Collins] (CSU), Region Occitanie, INRA Scientific Department SPE (AAP-SPE), French National Research Agency (ANR) : ANR-16-CE02-0015-01, National Science Foundation (NSF) : DEB-0949619, USDA Agriculture and Food Research Initiative award : 2014-67013-21594, United States Department of Agriculture (USDA) : 1012868, French Agropolis Fondation (LabEx Agro-Montpellier) : CfP 2015-02, French National Research Agency (ANR), LabEx CEMEB, CeMEB LabEx/University of Montpellier : ANR-10-LABX-04-01, European Union (EU), and Conseil Regional de la Reunion
Subjects: 0106 biological sciences, Integrated pest management, compound, Oviposition, Biology, Fragaria, 01 natural sciences, 03 medical and health sciences, Drosophilidae, Animals, chemical composition, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Drosophila suzukii, Drosophila, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Larva, Ecology, [SDV.BA]Life Sciences [q-bio]/Animal biology, fungi, food and beverages, biology.organism_classification, Preference, Blowing a raspberry, 010602 entomology, Horticulture, mother knows best hypothesis, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Fruit, Insect Science, host use, Female, PEST analysis
Abstract: A better understanding of the factors affecting host plant use by spotted-wing drosophila (Drosophila suzukii) could aid in the development of efficient management tools and practices to control this pest. Here, proxies of both preference (maternal oviposition behavior) and performance (adult emergence) were evaluated for 12 different fruits in the form of purees. The effect of the chemical composition of the fruits on preference and performance traits was then estimated. We synthesized the literature to interpret our findings in the light of previous studies that measured oviposition preference and larval performance of D. suzukii. We show that fruit identity influences different parts of the life cycle, including oviposition preference under both choice and no-choice conditions, emergence rate, development time, and number of emerging adults. Blackcurrant was always among the most preferred fruit we used, while grape and tomato were the least preferred fruits. Larvae performed better in cranberry, raspberry, strawberry, and cherry than in the other fruits tested. We found that fruit chemical compounds can explain part of the effect of fruit on D. suzukii traits. In particular, oviposition preference under choice conditions was strongly influenced by fruit phosphorus content. In general, the consensus across studies is that raspberry, blackberry, and strawberry are among the best hosts while blackcurrant, grape and rose hips are poor hosts. Our results generally confirm this view but also suggest that oviposition preferences do not necessarily match larval performances. We discuss opportunities to use our results to develop new approaches for pest management.
Published: 2019
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27. Inferring number of populations and changes in connectivity under the n-island model

Author: Lounès Chikhi, Beatriz Mourato, Camille Noûs, Khoa Nguyen, Simon Boitard, Olivier Mazet, Armando Arredondo, Willy Rodríguez, Institut de Mathématiques de Toulouse UMR5219 (IMT), 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), Instituto Gulbenkian de Ciência [Oeiras] (IGC), Fundação Calouste Gulbenkian, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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), Ecole Nationale de l'Aviation Civile (ENAC), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT), Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Armando Arredondo was funded by the Universite Federale Toulouse Midi Pyrenees (UFTMiP) and the Region Occitanie (formerly Midi-Pyrenees) with PhD grant No. 31I2017M248. Lounes Chikhi was funded by FundacAo para a Ciencia e Tecnologia (ref. PTDC-BIA-EVL/30815/2017). Olivier Mazet and Lounes Chikhi were funded by the 2015-2016 BiodivERsA COFUND call for research proposals, with the national funders ANR (ANR-16-EBI3-0014) and the FundacAo para a Ciencia e Tecnologia ref. Biodiversa/0003/2015 and PT-DLR (01LC1617A). This work was also supported by the LABEX entitled TULIP (ANR-10-LABX-41 and ANR-11-IDEX-0002) as well as the LIA BEEG-B (Laboratoire International Associe-Bioinformatics, Ecology, Evolution, Genomics and Behaviour). We acknowledge an Investissement d'Avenir grant of the Agence Nationale de la Recherche (CEBA: ANR-10-LABX-0025)., ANR-16-EBI3-0014,INFRAGECO,Inference, fragmentation, genomics and conservation(2016), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire Cogitamus, Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: 0301 basic medicine, 0106 biological sciences, Gene Flow, Island model, Population genetics, Demographic history, Population structure, Population, Biology, 010603 evolutionary biology, 01 natural sciences, Article, Gene flow, 03 medical and health sciences, Statistics, Genetics, Humans, education, Genetics (clinical), Biological models, 030304 developmental biology, Population Density, 0303 health sciences, Panmixia, education.field_of_study, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Population size, Contrast (statistics), Function (mathematics), Diploidy, Tree (data structure), 030104 developmental biology, Genetics, Population, Piecewise
Abstract: Correction to: Heredity https://doi.org/10.1038/s41437-021-00426-9, published online 12 April 2021.The author originally listed as Camille Noûs on this article [1] is fictitious (http://www.cogitamus.fr/indexen.html) and as such does not fulfil the requirements for authorship. The correct authorship list is: Armando Arredondo, Beatriz Mourato, Khoa Nguyen, Simon Boitard, Willy Rodríguez, Olivier Mazet & Lounès Chikhi. This has been corrected.; International audience; Inferring the demographic history of species is one of the greatest challenges in populations genetics. This history is often represented as a history of size changes, thus ignoring population structure. Alternatively, structure is defined a priori as a population tree and not inferred. Here we propose a framework based on the IICR (Inverse Instantaneous Coalescence Rate), which can be estimated using the PSMC method of Li and Durbin (2011) for a single diploid individual. For an isolated population, the IICR matches the population size history, which is how the PSMC outputs are generally interpreted. However, it is increasingly acknowledged that the IICR is a function of the demographic model and sampling scheme. Our automated method fits observed IICR curves of diploid individuals with IICR curves obtained under piecewise-stationary symmetrical island models, in which we assume a fixed number of time periods during which gene flow is constant. We infer the number of islands, their sizes, the periods at which connectivity changes and the corresponding rates of connectivity. Validation with simulated data showed that the method can accurately recover most of the scenario parameters. Our application to a set of five human PSMCs yielded demographic histories that are in agreement with previous studies using similar methods and with recent research suggesting ancient human structure. They are in contrast with the widely accepted view of human evolution consisting of one ancestral population branching into three large continental and panmictic populations with varying degrees of connectivity and no population structure within each continent.
Published: 2021
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28. Une approche opérationnelle pour la prédiction de la dynamique des ceintures de radiations terrestres

Author: Bernoux, Guillerme, Brunet, Antoine, Buchlin, Éric, Janvier, Miho, Sicard, Angélica, ONERA / DPHY, Université de Toulouse [Toulouse], ONERA-PRES Université de Toulouse, Institut d'astrophysique spatiale (IAS), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), and Funding from Region Occitanie and ONERA, under Grant Agreements 587 19008721/ALDOCT and 30196
Subjects: [PHYS]Physics [physics], [SPI]Engineering Sciences [physics], Space weather, Apprentissage statistique, Météorologie de l'espace, Solar wind, Machine learning, Prévision, Ceinture de radiations, Radiation belts, Vent solaire, Forecasting
Abstract: International audience; The Ca index is a time-integrated geomagnetic index that correlates well with the dynamics of high-energy electron fluxes in the outer radiation belts. Therefore it can be used as an indicator for the state of filling of the radiation belts for those electrons, with the advantage of being a groundbased measurement with extensive historical records. In this work we propose a data-driven model to forecast Ca up to 24 hours in advance from near-Earth solar wind parameters. Our model relies mainly on a recurrent neural network called Long Short Term Memory network that has shown good performances in forecasting other geomagnetic indices in previous papers. Most implementation choices in this study have been arbitrated from the point of view of a space system operator, including the data selection and split, the definition of a binary classification threshold and the evaluation methodology. We evaluate our model (against a linear baseline) using both classic and novel (in the space weather field) measures. In particular, we use the Temporal Distortion Mix (TDM) to assess the propensity of two time series to exhibit time lags. We also evaluate the ability of our model to detect storm onsets during calm periods. It is shown that our model has a high overall accuracy, with evaluation measures deteriorating in an almost linear trend over time. However, using the TDM and the metrics for evaluating the binary classification forecast, it is shown that after a time horizon of approximately 6 hours the forecasts lose some of their usefulness in an operational context. This behaviour was not observable when evaluating the model only with metrics such as the root-mean-square error or the Pearson linear correlation. Considering the physics of the problem, this result is not surprising and suggests that the use of more spatially remote data (such as solar imaging) could improve space weather forecasts.; L'indice Ca est un indice géomagnétique intégré dans le temps qui présente une bonne corrélation avec la dynamique des flux d'électrons de haute énergie dans les ceintures de radiation extérieures. Il peut donc être utilisé comme un indicateur de l'état de remplissage des ceintures de radiation pour ces électrons, avec les avantages d'être une mesure faite au sol et qui possède un historique important. Dans ce travail, nous proposons un modèle basé sur les données pour prévoir Ca jusqu'à 24 heures à l'avance à partir des paramètres du vent solaire proches de la Terre. Notre modèle s'appuie principalement sur un réseau de neurones récurrent appelé réseau de mémoire à long et à court terme (LSTM) qui a montré de bonnes performances dans la prévision d'autres indices géomagnétiques dans des articles précédents. La plupart des choix d'implémentation dans cette étude ont été arbitrés du point de vue d'un opérateur de système spatial, y compris la sélection et la division des données, la définition d'un seuil de classification binaire et la méthodologie d'évaluation. Nous évaluons notre modèle (par rapport à un modèle de base linéaire) en utilisant des métriques classiques et des métriques nouvelles (dans le domaine de la météorologie spatiale). En particulier, nous utilisons le Temporal Distortion Mix (TDM) pour évaluer la propension de deux séries temporelles à présenter des décalages temporels. Nous évaluons également la capacité de notre modèle à détecter les débuts de tempêtes pendant les périodes calmes. Nous montrons que notre modèle a une précision globale élevée, les mesures d'évaluation se détériorant selon une tendance presque linéaire dans le temps. Cependant, en utilisant le TDM et les mesures d'évaluation de la prévision par classification binaire, il est montré qu'après un horizon temporel d'environ 6 heures, les prévisions perdent une partie de leur utilité dans un contexte opérationnel. Ce comportement n'était pas observable lorsque le modèle était évalué uniquement avec des mesures telles que l'erreur quadratique moyenne ou la corrélation linéaire. Compte tenu de la physique du problème, ce résultat n'est pas surprenant et suggère que l'utilisation de données plus éloignées dans l'espace (comme l'imagerie solaire) pourrait améliorer les prévisions relevant de la météorologie de l'espace.
Published: 2021

29. Kmerator Suite: design of specific k-mer signatures and automatic metadata discovery in large RNA-Seq datasets

Author: Nicolas Gilbert, Thérèse Commes, Chloé Bessière, Anthony Boureux, Jérôme Audoux, Haoliang Xue, Benoit Guibert, Florence Ruffle, Sébastien Riquier, Anne-Laure Bougé, Daniel Gautheret, Cellules Souches, Plasticité Cellulaire, Médecine Régénératrice et Immunothérapies (IRMB), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), SeqOne [CHRU Montpellier], Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Hôpital Saint Eloi (CHRU Montpellier), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), 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), Agence Nationale de la recherche [ANR-10-INBS-09], Canceropole Grand Ouest [2017-EM24], Region Occitanie[R19073FF], and ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010)
Subjects: 0303 health sciences, Computer science, Interface (computing), Suite, Computational biology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Metadata discovery, Set (abstract data type), Metadata, 03 medical and health sciences, Identification (information), 0302 clinical medicine, k-mer, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Human genome, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract: The huge body of publicly available RNA-sequencing (RNA-seq) libraries is a treasure of functional information allowing to quantify the expression of known or novel transcripts in tissues. However, transcript quantification commonly relies on alignment methods requiring a lot of computational resources and processing time, which does not scale easily to large datasets. K-mer decomposition constitutes a new way to process RNA-seq data for the identification of transcriptional signatures, as k-mers can be used to quantify accurately gene expression in a less resource-consuming way. We present the Kmerator Suite, a set of three tools designed to extract specific k-mer signatures, quantify these k-mers into RNA-seq datasets and quickly visualize large dataset characteristics. The core tool, Kmerator, produces specific k-mers for 97% of human genes, enabling the measure of gene expression with high accuracy in simulated datasets. KmerExploR, a direct application of Kmerator, uses a set of predictor gene-specific k-mers to infer metadata including library protocol, sample features or contaminations from RNA-seq datasets. KmerExploR results are visualized through a user-friendly interface. Moreover, we demonstrate that the Kmerator Suite can be used for advanced queries targeting known or new biomarkers such as mutations, gene fusions or long non-coding RNAs for human health applications.
Published: 2021
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30. Transmission Line Approach for the PCB Gate Interconnection Design in GaN-Based High-Frequency Power Converters

Author: Galeano, A. G., Marcault, E., Alonso, C., David Trémouilles, CEA Tech en régions (CEA-TECH-Reg), Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Équipe Intégration de Systèmes de Gestion de l'Énergie (LAAS-ISGE), Laboratoire d'analyse et d'architecture des systèmes (LAAS), 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), Université Fédérale Toulouse Midi-Pyrénées, This work has been partially funded by the Region Occitanie Pyrénées-Méditerranée, 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), and Trémouilles, David
Subjects: [SPI]Engineering Sciences [physics], [SPI.ELEC]Engineering Sciences [physics]/Electromagnetism, [SPI] Engineering Sciences [physics], [SPI.NANO] Engineering Sciences [physics]/Micro and nanotechnologies/Microelectronics, [SPI.ELEC] Engineering Sciences [physics]/Electromagnetism, [SPI.NRJ]Engineering Sciences [physics]/Electric power, [SPI.NANO]Engineering Sciences [physics]/Micro and nanotechnologies/Microelectronics, [SPI.NRJ] Engineering Sciences [physics]/Electric power
Abstract: International audience; GaN-HEMTs allow power converters to achieve high switching frequencies. Therefore, novel design challenges arise in both power and frequency. In this context, this work aims to contribute with the integration of design concepts inspired both from power electronics and radio-frequency methods by using transmission-line approach. The developed study presented here focuses on the gate signal. Nevertheless, this methodology can be extended to any other power converter signals. The explored methodology associates coplanar transmission lines with the IPC9592B PCB design standard for the design of the gate PCB-trace layout. Experimentally, a Vector Network Analyzer verifies the transmission line parameters of the designed gate layout. Additionally, the gate signals are compared for different power levels in a high-frequency boost converter. Study results provide insights about the transmission line methodology for the development of high-frequency power converters based on GaN-HEMT.
Published: 2021

31. A Comparative Study to Decipher the Structural and Dynamics Determinants Underlying the Activity and Thermal Stability of GH-11 Xylanases

Author: Thomas Schiex, Jelena Vucinic, Claire Dumon, Cedric Montanier, Sophie Barbe, Gleb Novikov, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Toulouse Biotechnology Institute (TBI), 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)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), INRAE, Region Occitanie, Toulouse White Biotechnology, ANR-19-P3IA-0004,ANITI,Artificial and Natural Intelligence Toulouse Institute(2019), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0301 basic medicine, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Mutant, 01 natural sciences, Molecular dynamics, Catalytic Domain, Enzyme Stability, GH-11 xylanase, Biology (General), Spectroscopy, chemistry.chemical_classification, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], 010304 chemical physics, biology, Chemistry, Temperature, General Medicine, Computer Science Applications, enzyme activity, enzyme thermostability, Xylanase, QH301-705.5, free-energy landscape, Neocallimastix patriciarum, Molecular Dynamics Simulation, Catalysis, Article, Inorganic Chemistry, 03 medical and health sciences, 0103 physical sciences, Amino Acid Sequence, Physical and Theoretical Chemistry, QD1-999, Molecular Biology, Endo-1,4-beta Xylanases, Organic Chemistry, enzyme–substrate interaction, Active site, Substrate (chemistry), [CHIM.CATA]Chemical Sciences/Catalysis, molecular dynamics simulations, Kinetics, 030104 developmental biology, Enzyme, dynamic cross correlation, Helix, biology.protein, Biophysics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Neocallimastix
Abstract: With the growing need for renewable sources of energy, the interest for enzymes capable of biomass degradation has been increasing. In this paper, we consider two different xylanases from the GH-11 family: the particularly active GH-11 xylanase from Neocallimastix patriciarum, NpXyn11A, and the hyper-thermostable mutant of the environmentally isolated GH-11 xylanase, EvXyn11TS. Our aim is to identify the molecular determinants underlying the enhanced capacities of these two enzymes to ultimately graft the abilities of one on the other. Molecular dynamics simulations of the respective free-enzymes and enzyme–xylohexaose complexes were carried out at temperatures of 300, 340, and 500 K. An in-depth analysis of these MD simulations showed how differences in dynamics influence the activity and stability of these two enzymes and allowed us to study and understand in greater depth the molecular and structural basis of these two systems. In light of the results presented in this paper, the thumb region and the larger substrate binding cleft of NpXyn11A seem to play a major role on the activity of this enzyme. Its lower thermal stability may instead be caused by the higher flexibility of certain regions located further from the active site. Regions such as the N-ter, the loops located in the fingers region, the palm loop, and the helix loop seem to be less stable than in the hyper-thermostable EvXyn11TS. By identifying molecular regions that are critical for the stability of these enzymes, this study allowed us to identify promising targets for engineering GH-11 xylanases. Eventually, we identify NpXyn11A as the ideal host for grafting the thermostabilizing traits of EvXyn11TS.
Published: 2021
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32. Healthy Aging Biomarkers: The INSPIRE's Contribution

Author: Vergnolle, Nathalie, Ader, Isabelle, Penicaud, Luc, Raymond Letron, Isabelle, Andrieu, Sandrine, Rolland, Julien Yves, Barreto De Souto, Philippe, Vellas, Bruno, Guyonnet, Sophie, Beard, J.R., Parini, Angelo, Davezac, Noélie, Dray, Cédric, Gourdy, P., Rampon, Claire, Valet, Phillippe, Fazilleau, Nicolas, Payoux, Pierre, Sierra, Felipe, Institut de Recherche en Santé Digestive (IRSD ), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Geroscience and rejuvenation research center (RESTORE), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-EFS-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Epidémiologie et analyses en santé publique : risques, maladies chroniques et handicaps (LEASP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Gérontopôle, 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)-CHU Toulouse [Toulouse], University of New South Wales [Sydney] (UNSW), Centre de Recherches sur la Cognition Animale (CRCA), Centre de Biologie Intégrative (CBI), 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-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut des sciences du cerveau de Toulouse. (ISCT), Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse - Jean Jaurès (UT2J)-CHU Toulouse [Toulouse]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Toulouse Neuro Imaging Center (ToNIC), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôpital Purpan [Toulouse], CHU Toulouse [Toulouse]-CHU Toulouse [Toulouse], Institut du Vieillissement, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Region Occitanie/Pyrenees-Mediterranee (Reference number: 1901175), European Regional Development Fund (ERDF) (Project number: MP0022856), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Centre de Recherches sur la Cognition Animale - UMR5169 (CRCA), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Toulouse Mind & Brain Institut (TMBI), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Toulouse Mind & Brain Institut (TMBI), and SEGUIN, Nathalie
Subjects: [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, healthy aging, frailty, dependence, Biomarkers, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, [SDV.BIO] Life Sciences [q-bio]/Biotechnology
Abstract: International audience; The find solutions for optimizing healthy aging and increase health span is one of the main challenges for our society. A novel healthcare model based on integration and a shift on research and care towards the maintenance of optimal functional levels are now seen as priorities by the WHO. To address this issue, an integrative global strategy mixing longitudinal and experimental cohorts with an innovative transverse understanding of physiological functioning is missing. While the current approach to the biology of aging is mainly focused on parenchymal cells, we propose that age-related loss of function is largely determined by three elements which constitute the general ground supporting the different specific parenchyma: i.e. the stroma, the immune system and metabolism. Such strategy that is implemented in INSPIRE projects can strongly help to find a composite biomarker capable of predicting changes in capacity across the life course with thresholds signalling frailty and care dependence.
Published: 2021
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33. Comment on 'Tumor-initiating cells establish an IL-33–TGF-β niche signaling loop to promote cancer progression'

Author: Julien Stackowicz, Aurélie Mougel, Pierre Bruhns, Jinmiao Chen, Eva Conde, William P. M. Worrall, Rebecca Gentek, Jasper B. J. Kamphuis, Nicolas Gaudenzio, Laurent L. Reber, Laurent Guilleminault, Emilie Mauré, Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU), Anticorps en thérapie et pathologie - Antibodies in Therapy and Pathology, Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris], CHU Toulouse [Toulouse], Unité différenciation épidermique et auto-immunité rhumatoïde (UDEAR), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Singapore Immunology Network (SIgN), Biomedical Sciences Institute (BMSI), University of Edinburgh, Supported by a fellowship from the Institut National de la Santé et de la Recherche Médicale (INSERM) ATIP-Avenir program (J.B.J.K.), a fellowship from INSERM-Region Occitanie (W.P.M.W.), the European Research Council (ERC)–Seventh Framework Program (ERC-2013-CoG 616050), the Institut Pasteur, and INSERM (P.B.), the Société Française de Dermatologie (SFD), the Société Française d’Allergologie (SFA), the Marie Skłodowska-Curie Individual Fellowship (H2020-MSCA-IF-2016 #749629), the European Research Council (ERC-2018-STG #802041), and the INSERM ATIP-Avenir program (N.G.), a Chancellor’s Fellowship of the University of Edinburgh and a Senior Research Fellowship from the Kennedy Trust for Rheumatology Research (R.G.), and the INSERM ATIP-Avenir program (L.L.R.), European Project: 616050,EC:FP7:ERC,ERC-2013-CoG,MYELOSHOCK(2014), European Project: 802041, European Project: 749629,H2020-EU.1.3.2. - Nurturing excellence by means of cross-border and cross-sector mobility ,H2020-MSCA-IF-2016,NEMESIS(2017), Université de Toulouse (UT)-Université de Toulouse (UT)-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 Hospitalier Universitaire de Toulouse (CHU Toulouse), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Bruhns, Pierre, Role of myeloid cells, their mediators and their antibody receptors in allergic shock (anaphylaxis) using humanized mouse models and clinical samples - MYELOSHOCK - - EC:FP7:ERC2014-09-01 - 2019-08-31 - 616050 - VALID, ERC-2018-STG - 802041 - INCOMING, and Neuron/mast cell interactions in skin diseases - NEMESIS - - H2020-EU.1.3.2. - Nurturing excellence by means of cross-border and cross-sector mobility 2017-07-01 - 2019-06-30 - 749629 - VALID
Subjects: 0301 basic medicine, [SDV.IMM] Life Sciences [q-bio]/Immunology, [SDV]Life Sciences [q-bio], medicine.medical_treatment, MESH: Receptors, IgE, Immunoglobulin E, 03 medical and health sciences, 0302 clinical medicine, Transforming Growth Factor beta, Neoplasms, medicine, Humans, Receptor, MESH: Transforming Growth Factor beta, MESH: Humans, Multidisciplinary, biology, Receptors, IgE, Cancer, Transforming growth factor beta, Interleukin-33, medicine.disease, MESH: Interleukin-33* / genetics, MESH: Neoplastic Stem Cells, 3. Good health, [SDV] Life Sciences [q-bio], Interleukin 33, MESH: Neoplasms* / genetics, 030104 developmental biology, Cytokine, 030220 oncology & carcinogenesis, Neoplastic Stem Cells, biology.protein, Cancer research, [SDV.IMM]Life Sciences [q-bio]/Immunology, Antibody, Transforming growth factor
Abstract: Taniguchi et al . (Research Articles, 17 July 2020, p. 269) claim that the cytokine interleukin-33 induces accumulation of tumor-associated macrophages expressing the immunoglobulin E receptor FcεRI. Although these findings hold great therapeutic promise, we provide evidence that the anti-FcεRI antibody used in this study is not specific for FcεRI on macrophages, which raises concerns about the validity of some of the conclusions.
Published: 2021
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34. Influenza D virus in respiratory disease in Canadian, province of Québec, cattle: Relative importance and evidence of new reassortment between different clades

Author: Olivier Ariel, André Broes, Gilles Meyer, Claude Saegerman, Maria Gaudino, Christian Savard, Mariette F. Ducatez, Fundamental and Applied Research for Animals & Health (FARAH), Faculté de Médecine Vétérinaire [Liège], Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biovet Inc., This work was partly funded by the French National Agency for Research, project ANR- 15- CE35- 0005 'FLUD'. M. Gaudino is supported by a PhD scholarship of the Animal Health Department of INRAE and of the Region Occitanie., and ANR-15-CE35-0005,FLUD,Eco-épidémiologie de virus influenza D : évaluation du risque d'émergence(2015)
Subjects: 040301 veterinary sciences, [SDV]Life Sciences [q-bio], Respiratory Tract Diseases, Orthomyxoviridae, Reassortment, Cattle Diseases, Bovine respiratory disease, Biology, Virus, 0403 veterinary science, 03 medical and health sciences, Orthomyxoviridae Infections, Nasopharynx, medicine, Animals, Natural reservoir, Pasteurella multocida, Disease Reservoirs, 030304 developmental biology, Bovine coronavirus, 2. Zero hunger, 0303 health sciences, General Veterinary, General Immunology and Microbiology, Quebec, 04 agricultural and veterinary sciences, General Medicine, medicine.disease, biology.organism_classification, Virology, Bovine herpesvirus 1, Nasal Mucosa, Dyspnea, Cough, Cattle, Thogotovirus, Reassortant Viruses
Abstract: International audience; BACKGROUND: Influenza D virus (IDV), a segmented single-stranded negative-sense ribonucleic acid (RNA) virus, belongs to the new Delta influenza virus genus of the Orthomyxoviridae family. Cattle were proposed as the natural reservoir of IDV in which infection was associated with mild-to-moderate respiratory clinical signs (i.e. cough, nasal discharge and dyspnoea).METHODS AND PRINCIPAL FINDINGS: In order to investigate the role of IDV in bovine respiratory disease, during the period 2017-2020, 883 nasal or naso-pharyngeal swabs from Canadian cattle with respiratory signs (cough and/or dyspnoea) were tested by (RT-)qPCR for IDV and other major bovine viral (bovine herpesvirus 1, bovine viral diarrhoea virus, bovine respiratory syncytial virus, bovine parainfluenza virus 3 and bovine coronavirus) and bacterial (Mannheimia haemolytica, Pasteurella multocida, Histophilus somni and Mycoplasma bovis) respiratory pathogens. In addition, whole-genome sequencing and phylogenetic analyses were carried out on five IDV-positive samples. The prevalence of IDV RT-qPCR (with cut-off: Cq
Published: 2021
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35. Biosecurity measures in French poultry farms are associated with farm type and location

Author: Claire Guinat, Jean-Pierre Vaillancourt, Jean-Luc Guérin, Mattias Delpont, Mathilde Paul, Eric Le leu, Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Direction Régionale de l'Alimentation, de l'Agriculture et de la Forêt de Bretagne (DRAAF Bretagne ), Université de Montréal (UdeM), and This work was carried out within the framework of the Chaire de Biosecurite at the Ecole Nationale Veterinaire de Toulouse (ENVT), which is funded by the French Ministry of Agriculture and was supported by the UMR IHAP 1225 ENVT-INRAE. This work was financially supported by the FEDER/Region Occitanie Recherche et Societes 2018 - AI-TRACK.
Subjects: Highly pathogenic avian influenza, Disease prevention, Farms, 040301 veterinary sciences, Highly pathogenic, animal diseases, [SDV]Life Sciences [q-bio], 030231 tropical medicine, Biosecurity, medicine.disease_cause, French poultry farms, Poultry, Disease Outbreaks, 0403 veterinary science, 03 medical and health sciences, Agricultural science, 0302 clinical medicine, Cluster analysis, Food Animals, medicine, Animals, Poultry Diseases, 2. Zero hunger, business.industry, Outbreak, 04 agricultural and veterinary sciences, Poultry farming, Multiple species, Influenza A virus subtype H5N1, Geography, Cross-Sectional Studies, Ducks, Influenza in Birds, Animal Science and Zoology, France, business, Chickens
Abstract: International audience; The severe impact of recently reported Highly Pathogenic Avian Influenza (HPAI) outbreaks have emphasized the need to better monitor biosecurity practices among the different French poultry production systems. Between October 2016 and September 2018, a large national cross-sectional study was carried out in France to assess biosecurity levels in high-risk poultry farms and identify farm biosecurity profiles, using Multiple Correspondence and Hierarchical Cluster Analyses. Results indicate that there is substantial room for improvement in cleaning and disinfection, anteroom management and delimitation of farm and production units for more than 50 % of the 1,004 analyzed farms. The farm biosecurity profile showing the highest level of biosecurity included commercial intensive poultry farms (gallinaceous poultry farms, in North-Western France), and those with a recent history of HPAI outbreak (duck farms, in South-Western France). The farms biosecurity profiles showing the lowest level of biosecurity included farms with multiple species (duck and gallinaceous poultry) or multiple production types (broilers and egg-layers), located in regions with a lower poultry density and without a recent history of HPAI outbreak. Outcomes provide support to adapt biosecurity improvement and inspection plans.
Published: 2021
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36. Termite Gut Microbiota Contribution to Wheat Straw Delignification in Anaerobic Bioreactors

Author: Gijs van Erven, Pui Ying Lam, Guillermina Hernandez-Raquet, Fabien Mounet, Jacqueline Grima-Pettenati, Mirjam A. Kabel, Yuki Tobimatsu, Louison Dumond, Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Kyoto University [Kyoto], Wageningen University and Research [Wageningen] (WUR), Régulation et Dynamique de la Formation du Bois, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), 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-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), French National Institute of Research for Agriculture, Food and Environment (INRAE), Region Occitanie (31000553), Carnot Institute 3BCAR-Insyme project, PHC Sakura program from Campus France (45094PM), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Kyoto University, Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV.BIO]Life Sciences [q-bio]/Biotechnology, General Chemical Engineering, 02 engineering and technology, Gut flora, Termite gut microbiome, 010402 general chemistry, 01 natural sciences, complex mixtures, Lignin, chemistry.chemical_compound, NMR spectroscopy, Anaerobic digestion, Levensmiddelenchemie, Bioreactor, Environmental Chemistry, biology, Food Chemistry, Renewable Energy, Sustainability and the Environment, Chemistry, py-GC-MS, technology, industry, and agriculture, food and beverages, General Chemistry, Straw, 021001 nanoscience & nanotechnology, biology.organism_classification, Pulp and paper industry, 0104 chemical sciences, Delignification, BBP Biorefinery & Sustainable Value Chains, 0210 nano-technology, Anaerobic exercise, Lignocellulose
Abstract: Lignin is a major lock for lignocellulose valorizationin biorefineries, prompting a need tofind newligninolytic systems. Termites are efficient lignocellulose degraders, and a large part ofthis ability comes from its anaerobic gut microbiome. However, thepotential of termite gut microbiomes to degrade lignin underanaerobicconditions has yet to be elucidated. By applying wetchemistry, multidimensional NMR spectroscopy, and quantitative13C-IS py-GC-MS, we determined the chemical and structuralcharacteristics of wheat straw digested by the gut microbiomes ofhigher termitesNasutitermes ephratae,Nasutitermes lujae,Micro- cerotermes parvus, andTermes hospesimplemented in anaerobicbioreactors. Interestingly, all gut microbiomes managed to removelignin (up to 37%), although hemicellulose (mean 51%) andcellulose(mean 41%) were degraded more efficiently. Important structural differences, indicative of ligninolytic action, were discerned in the residual lignin. For the studied termite gut microbiomes, a slight decrease of S/G ratio was observed upon digestion, whereas lignin’s interunit linkages and Cα-oxidized moieties, including benzaldehyde and hydroxypropiovanillone/syringone substructures, accumulated. Additionally, tricin terminal units were clearly depleted, along with decreases inp-coumarate and ferulate pendant units. At least 80% of the observed delignification is estimated to be due to the removal of“true”lignin, with the remainder being explained by the removal of hydroxycinnamic acids and tricin. Collectively, ourfindings suggest a partial deconstruction of lignin, with“peripheral”lignin subunits being preferentially targeted. The present work thus provides new insights into the anaerobic deconstruction of lignin by termite gut microbiomes.
Published: 2021
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37. 'All in One' Epoxy-Based Microfluidic Chips at Your Fingertips

Author: Guillaume Lefebvre, Nicolas Rolley, Etienne Palleau, Guillaume Brotons, Simon Raffy, Laurence Ressier, Gilles Truan, Sara Castaño Cerezo, Brice Calvignac, Sébastien Teychené, Bernard Viguier, Laboratoire de physique et chimie des nano-objets (LPCNO), Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-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 d'Angers (UA), Micro et Nanomédecines Translationnelles (MINT), Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Le Mans Université (UM), Institut des Molécules et Matériaux du Mans (IMMM), Le Mans Université (UM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Génie Chimique (LGC), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Centre interuniversitaire de recherche et d'ingenierie des matériaux (CIRIMAT), 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 Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC), Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ALDEV, Region Occitanie via PUCE-AN-ORE project, ANR-17-CE24-0033,Resolve,Fabrication Supramoléculaire de Dispositifs OLED Haute Résolution par voie Imprimable(2017), 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)-Fédération de recherche « Matière et interactions » (FeRMI), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), and Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Materials science, Polymers and Plastics, Microfluidics, microfluidic chips, microfluidics, Nanotechnology, Hardware_PERFORMANCEANDRELIABILITY, 02 engineering and technology, 01 natural sciences, epoxy, [SPI.MAT]Engineering Sciences [physics]/Materials, Hardware_INTEGRATEDCIRCUITS, microfabrication, reversible sealing, Chip fabrication, Process Chemistry and Technology, 010401 analytical chemistry, Organic Chemistry, prototyping, Epoxy, 021001 nanoscience & nanotechnology, 0104 chemical sciences, visual_art, visual_art.visual_art_medium, 0210 nano-technology, Microfabrication
Abstract: International audience; The choice of materials used in the chip fabrication is crucial in microfluidics. They are selected and adapted depending on the available production techniques and associated processes, the involved characterization and measurement methods, the physical and chemical experimental conditions, and the cost. Here, we propose a versatile approach using a combination of epoxy materials to fabricate manually resealable and reusable (>40 times) microfluidic chips which demonstrate numerous potentialities: good chemical resistance, optical (visible and X-ray) transparency, biocompatibility, capability to undergo in average 2.9 bar of liquid pressure, or integration of high aspect ratio (>1500) channels. It thus represents a promising alternative for prototyping in a large panel of applications and fundamental studies.
Published: 2021
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38. Hybrid Numerical Methodology for Efficient Design and Optimization of Transmit-Array Antennas, X-Band Application

Author: Jeanne Pages-Mounic, Alessandro De Oliveira Cabral Junior, Andre Barka, Hamza Kaouach, ONERA / DEMR, Université de Toulouse [Toulouse], ONERA-PRES Université de Toulouse, LAboratoire PLasma et Conversion d'Energie (LAPLACE), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, and This work was supported in part by the Region Occitanie under Research Project N◦ 2018 001223/ALDOCT-00384, and in part bythe GENCI from which the full wave simulation results have been obtained using HPC resources under Grant c2014109083.
Subjects: Linear polarization, Finite element methods, [PHYS]Physics [physics], Phase compensation, Phase rotation, CST Microwave Studio, Transmit-array, Domain decomposition methods, TK1-9971, FETI, FACTOPO, [SPI]Engineering Sciences [physics], Finite element tearing and interconnecting, Electrical engineering. Electronics. Nuclear engineering, X-band
Abstract: International audience; This paper presents a complete hybrid numerical methodology for the efficient design and optimization of large-scale Transmit-Array (TA) antennas for modern telecommunication applications. There are four main components to the proposed work and methodology: 1) the implementation through Python scripts of a hybrid scheme based on the Friis analytical formula for linking gain and phase of the primary source and elementary cells of the studied transmit-array; 2) the implementation of a Particle Swarm Optimizer (PSO) for efficient characterization of the optimal phase distribution on the in-plane lens maximizing the gain of the antenna and minimizing the side-lobe levels for multiple fed TA antennas; 3) the implementation of a full-wave Finite element and Interconnecting domain decomposition (FETI) for the final analysis of the TA radiating performance; 4) the design, optimization, fabrication and proof of concept of an X band transmit-array including the focal source. This work presents the main functionalities of the hybrid Python/CST tool associated with phase compensation PSO, FETI implementation for transmit-arrays and as an application of this numerical strategy, a new compact unit-cell operating in the X-band (thickness of 3.2 mm) able to easily generate Phase Rotations (PR) necessary for TAs with phase compensation on the aperture. The proposed unit-cell is a completely symmetric design including a metallic via interconnecting two identical square patches (including a circular hole in the center and a microstrip line) by crossing through a ground plane. A particle swarm optimization (PSO) routine is proposed as a way to quickly optimize the phase distribution of the transmit-array unit-cells. The optimization routine is tested through multiple sources and focal ratios, demonstrating a reduction of over 50% of the volume occupied by the antenna, while keeping a high gain (19.5 dBi) and overall good performance.
Published: 2021
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39. Large scale dog population demography, dog management and bite risk factors analysis: A crucial step towards rabies control in Cambodia

Author: Véronique Chevalier, Holl Davun, Sopheak Sorn, Pitou Ly, Vutha Pov, Sowath Ly, 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), Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur (RIIP), Ministry of Agriculture, Forestry and Fisheries [Cambodia], Royal University of Agriculture (RUA), and This survey has been jointly granted by the Swedish Research Council, Region Occitanie, the French Embassy in Cambodia, and the World Health Organization.
Subjects: Male, Viral Diseases, Epidemiology, [SDV]Life Sciences [q-bio], Social Sciences, Cat Diseases, Geographical Locations, Medical Conditions, Sociology, Animal Products, Risk Factors, Zoonoses, Surveys and Questionnaires, Medicine and Health Sciences, Public and Occupational Health, Bites and Stings, Dog Diseases, Human Families, Mammals, Eukaryota, Agriculture, Vaccination and Immunization, Infectious Diseases, Vertebrates, Medicine, Female, Cambodia, Research Article, Neglected Tropical Diseases, Asia, Meat, Rabies, Science, Immunology, Dogs, Animals, Humans, Nutrition, Ownership, Organisms, Biology and Life Sciences, Tropical Diseases, Diet, Food, Medical Risk Factors, Amniotes, People and Places, Cats, Preventive Medicine, Zoology
Abstract: International audience; Cambodia is a rabid-endemic country. However, data on dog population characteristics are lacking, and there is no national dog vaccination program. We implemented the first extensive door-to-door longitudinal survey in 2 Cambodian provinces, namely Kandal and Battambang, to estimate dog population demographic parameters, identify dog ownership determinants, analyze dog management practices and estimate the yearly cumulative bite incidence and associated factors. During the first session, more than 5000 dogs were recorded and identified. Data on families, dogs and cats characteristics, as well as the number of bites experienced the year before in the family, were recorded. One year later, a second session was performed in both provinces to record missing dogs and the reasons for missing. Age-specific survival rates of the dog populations were computed using Kaplan-Meier estimates. Ownership determinants and bite risk factors were identified using a negative binomial regression model. Dog trade and dog meat consumption were often reported. We estimated high dog-to-human ratios (1:3.8 in Kandal, and 1:3.3 in Battambang). The mean age of dog populations was 26.4 months in Kandal against 24.3 in Battambang, with a survival rate of 52% at 24 months in Kandal (34% only in Battambang). They were no feral dogs, but the large majority of recorded dogs were free roaming. In both provinces, the number of dogs significantly increased in families with children younger than 15, and when the head of the family was a male. The estimated yearly cumulative bite incidences were 2.3 and 3.1% in Kandal and Battambang provinces respectively, and are among the highest in the world. Our survey provides valuable data to focus information programs, parametrize transmission models and identify efficient vaccination strategies to control rabies in Cambodia in the future.
Published: 2021
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40. Anxiety is a potential effect modifier of the association between red and processed meat consumption and cancer risk: findings from the NutriNet-Santé cohort

Author: Vassilia Theodorou, Mélanie Deschasaux, Paule Latino-Martel, Bernard Srour, Valentina A. Andreeva, Eloi Chazelas, Marie Beslay, Françoise Guéraud, Serge Hercberg, Fabrice Pierre, Edwin Fouché, Nathalie Naud, Sandrine Péneau, Mathilde Touvier, Charlotte Debras, Valerie Bacquie, ToxAlim (ToxAlim), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Equipe 3: EREN- Equipe de Recherche en Epidémiologie Nutritionnelle (CRESS - U1153), Université Sorbonne Paris Nord-Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Prévention et promotion de la cancérogénèse par les aliments (ToxAlim-PPCA), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Toxicologie Intégrative & Métabolisme (ToxAlim-TIM), Hôpital Avicenne [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Neuro-Gastroentérologie & Nutrition (ToxAlim-NGN), and This research was supported by the regular financial support of INRAE. The NutriNet-Sante study was supported by the following public institutions: Ministere de la Sante, Sante Publique France, Institut National de la Sante et de la Recherche Medicale (INSERM), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Conservatoire National des Arts et Metiers (CNAM) and Sorbonne Paris Nord University. MB was supported by a doctoral grant from the Ecole d'ingenieurs de Purpan and the region Occitanie. CD was supported by a grant from the French National Cancer Institute (INCa). EC was supported by a Doctoral Funding from Universite Paris 13-Galilee Doctoral School. MD was supported by a Post-doctoral grant from the Fondation pour la Recherche Medicale.
Subjects: 0301 basic medicine, Oncology, Male, medicine.medical_specialty, Meat, Red and processed meat, Colorectal cancer, [SDV]Life Sciences [q-bio], Medicine (miscellaneous), 030209 endocrinology & metabolism, Breast Neoplasms, Anxiety, Cohort Studies, 03 medical and health sciences, 0302 clinical medicine, Breast cancer, Risk Factors, Internal medicine, Medicine, Humans, Prospective Studies, Prospective cohort study, Intestinal barrier, Carcinogen, 030109 nutrition & dietetics, Nutrition and Dietetics, Proportional hazards model, business.industry, Cancer, medicine.disease, 3. Good health, Diet, Meat Products, Red Meat, Heme iron, Cohort, Female, medicine.symptom, business, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract: International audience; Purpose Red and processed meats are recognized by the International Agency for Research on Cancer as probably carcinogenic and carcinogenic to humans, respectively. Heme iron has been proposed as a central factor responsible for this effect. Furthermore, anxiety affects the intestinal barrier function by increasing intestinal permeability. The objective of this work was to assess how anxiety modifies the association between red and processed meat consumption and cancer risk in the NutriNet-Santé prospective cohort (2009–2019).Methods Using multi-adjusted Cox models in a sample of 101,269 subjects, we studied the associations between the consumption of red and processed meat, the amount of heme iron coming from these meats and overall, colorectal, prostate, and breast cancer risks, overall and separately among participants with and without anxiety.Results An increase in red and processed meat consumption was associated with an increased risk of developing colorectal cancer in the total population (HR for an increase of 50 g/day = 1.18 (1.01–1.37), p = 0.03). After stratification on anxiety, the HR 50 g/day was 1.42 (1.03–1.94, p = 0.03) in anxious participants and 1.12 (0.94–1.33, p = 0.20) in other participants. Similar trends were observed for overall cancer risk. Analyses conducted with heme iron also provided similar results. Conclusions Our results strengthen the existing body of evidence supporting that red and processed meat consumption and heme iron intake are associated with an increased risk of overall and more specifically colorectal cancer, and suggest that anxiety modifies these associations, with an increased risk in anxious participants.
Published: 2021
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41. Oxidative Stress in NAFLD: Role of Nutrients and Food Contaminants

Author: Sandrine Ellero-Simatos, Anne Fougerat, Walter Wahli, Laurence Gamet-Payrastre, Nicolas Loiseau, Clémence Rives, Hervé Guillou, Toxicologie Intégrative & Métabolisme (ToxAlim-TIM), ToxAlim (ToxAlim), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Nanayang Technological University (NTU), Nanayang Technological University, Center for Integrative Genomics - Institute of Bioinformatics, Génopode (CIG), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne (UNIL)-Université de Lausanne (UNIL), A.F. is supported by the AgreenSkills and fellowship program. W.W. was supported by the Start-Up Grant from the Lee Kong Chian School of Medicine, NanyangTechnological University Singapore. This work was also funded by ANR Syneract and by grants from Region Occitanie (L.G.P., N.L., H.G., W.W.)., ANR-18-CE34-0009,SYNERACT,Activation synergique de recepteurs nucléaires(2018), and Lee Kong Chian School of Medicine (LKCMedicine)
Subjects: 0301 basic medicine, Liver Cirrhosis, Steatosis, Cirrhosis, [SDV]Life Sciences [q-bio], lcsh:QR1-502, Disease, Review, Bioinformatics, medicine.disease_cause, Biochemistry, lcsh:Microbiology, Antioxidants, Liver disorder, 0302 clinical medicine, Non-alcoholic Fatty Liver Disease, Risk Factors, steatosis, oxidative stress, Homeostasis, Fatty liver, Liver Neoplasms, 3. Good health, Mitochondria, Liver, [SDV.TOX]Life Sciences [q-bio]/Toxicology, Disease Progression, 030211 gastroenterology & hepatology, non-alcoholic fatty liver disease (NAFLD), Carcinoma, Hepatocellular, non-alcoholic steatohepatitis (NASH), macronutrients, Food Contamination, reactive oxygen species (ROS), digestive system, 03 medical and health sciences, medicine, Humans, Medicine [Science], Molecular Biology, food contaminant, Inflammation, business.industry, nutritional and metabolic diseases, Nutrients, medicine.disease, digestive system diseases, 030104 developmental biology, micronutrients, Hepatocytes, Metabolic syndrome, Steatohepatitis, Insulin Resistance, business, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Oxidative stress
Abstract: Non-alcoholic fatty liver disease (NAFLD) is often the hepatic expression of metabolic syndrome and its comorbidities that comprise, among others, obesity and insulin-resistance. NAFLD involves a large spectrum of clinical conditions. These range from steatosis, a benign liver disorder characterized by the accumulation of fat in hepatocytes, to non-alcoholic steatohepatitis (NASH), which is characterized by inflammation, hepatocyte damage, and liver fibrosis. NASH can further progress to cirrhosis and hepatocellular carcinoma. The etiology of NAFLD involves both genetic and environmental factors, including an unhealthy lifestyle. Of note, unhealthy eating is clearly associated with NAFLD development and progression to NASH. Both macronutrients (sugars, lipids, proteins) and micronutrients (vitamins, phytoingredients, antioxidants) affect NAFLD pathogenesis. Furthermore, some evidence indicates disruption of metabolic homeostasis by food contaminants, some of which are risk factor candidates in NAFLD. At the molecular level, several models have been proposed for the pathogenesis of NAFLD. Most importantly, oxidative stress and mitochondrial damage have been reported to be causative in NAFLD initiation and progression. The aim of this review is to provide an overview of the contribution of nutrients and food contaminants, especially pesticides, to oxidative stress and how they may influence NAFLD pathogenesis. Nanyang Technological University Published version A.F. is supported by the AgreenSkills and fellowship program. W.W. was supported by the Start-Up Grant from the Lee Kong Chian School of Medicine, Nanyang Technological University Singapore. This work was also funded by ANR Syneract and by grants from Région Occitanie (L.G.P., N.L., H.G., W.W.).
Published: 2020
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42. Assessing macro- (P, K, Ca, Mg) and micronutrient (Mn, Fe, Cu, Zn, B) concentration in vine leaves and grape berries of vitis vinifera by using near-infrared spectroscopy and chemometrics

Author: Didier Kleiber, Cecile Levasseur-Garcia, Valerie Lemetter, Sebastien Cuq, Physiologie, Pathologie et Génétique Végétales (PPGV), INP-PURPAN, Université Fédérale Toulouse Midi-Pyrénées, Chimie Agro-Industrielle (CAI), Ecole nationale supérieure des ingénieurs en arts chimiques et technologiques-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and This work was supported by Qualisol, Bpifrance, and Region Occitanie/Pyrenees-Mediterranee [3745063/1]
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Potassium, [SDV]Life Sciences [q-bio], chemistry.chemical_element, Manganese, Zinc, Horticulture, 01 natural sciences, Nutrient, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Boron, 2. Zero hunger, Magnesium, Phosphorus, food and beverages, Forestry, 04 agricultural and veterinary sciences, Copper, Computer Science Applications, chemistry, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; Macronutrients (phosphorus, potassium, calcium, and magnesium) and micronutrients (manganese, iron, copper, zinc, and boron) play an essential role not only in the general physiology of vines but also in the quality of wine produced. The quantity of each nutrient in the vine is generally determined by analyzing the leaf blades or petioles, but this approach imposes a typical delay of two weeks between sampling and receiving the results, which precludes real-time detection of nutritional deficiencies (e.g., boron deficiency at flowering). Therefore, a method to rapidly analyze vine organs is highly desirable. One candidate for such a method is near-infrared (NIR) reflectance spectroscopy coupled with chemometric methods, based on which winegrowers have already developed prediction models. This approach is widely used today in agriculture. The aim of the present study is to determine whether NIR spectroscopy can be used to obtain accurate information about the nutritional status of vines. In this study, we focus on the mass of phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), manganese (Mn), iron (Fe), copper (Cu), zinc (Zn), and boron (B) contained in different vine organs (leaf blades, petioles and berries) over the course of a year. The concentration of these elements was determined based on NIR absorbance spectra from 677 samples of various dried vine organs. Partial least square models for classification and prediction were then developed based on raw and pretreated spectra for each organ, following which the models were tested on an external prediction set. The results show that, for Ca and Mg, all organ models can be used routinely for classification or prediction. For prediction, the Ca (Mg), model produces r2 = 0.88, 0.70, and 0.72 (0.60, 0.72, and 0.80) for leaf blades, petioles, and berries, respectively. Only for leaf blades (berries) is the Ca (Mg) model sufficiently accurate to be used for prediction. For berries, the P, K, and Zn models produce r2 in prediction of 0.77, 0.79, and 0.82, respectively. For petioles, the K model proves reliable for prediction, with r2 = 0.76. The Fe, Cu, and B models produce r2 = 0.72, 0.71, and 0.52, which are suitable for classification but not for prediction. Finally, for leaf blades, the Fe and Cu models produce r2 0.58 and 0.61, respectively, in prediction and thus can be used routinely for classification.
Published: 2020
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43. Extracellular Matrix Mechanical Properties and Regulation of the Intestinal Stem Cells: When Mechanics Control Fate

Author: Audrey Ferrand, Laurent Malaquin, Dimitri Hamel, Julie Foncy, Lauriane Onfroy-Roy, Institut de Recherche en Santé Digestive (IRSD ), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Équipe Ingénierie pour les sciences du vivant (LAAS-ELIA), 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 Instrumentation Conception Caractérisation (LAAS-I2C), Region Occitanie, Universite de Toulouse III : APR2017-405, Universite de Toulouse III : 2018-046-CIF-D-DRDV, Plan Cancer 'System biology'2017 : C18006BS, European Project: 760927,H2020-HoliFAB project, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse Capitole (UT Capitole), Université Fédérale Toulouse Midi-Pyrénées, SEGUIN, Nathalie, HoliFAB - H2020-HoliFAB project - 760927 - INCOMING, 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), and Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1)
Subjects: 0301 basic medicine, [SDV.MHEP.PHY] Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], microfluidic, Review, [SDV.GEN] Life Sciences [q-bio]/Genetics, mechanical properties, scaffold, Epithelium, Extracellular matrix, Mice, stiffness, 0302 clinical medicine, Homeostasis, deformability, Intestinal Mucosa, Stem Cell Niche, lcsh:QH301-705.5, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, Tissue Scaffolds, Stem Cells, Cell Differentiation, General Medicine, Phenotype, Cell biology, Intestines, Organoids, 030220 oncology & carcinogenesis, Stem cell, inorganic chemicals, extracellular matrix, organoid, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, digestive system, 03 medical and health sciences, topography, Organoid, [SDV.MHEP.PHY]Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], Animals, Humans, Cell Lineage, Secretion, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, Cell Proliferation, Inflammation, [SDV.GEN]Life Sciences [q-bio]/Genetics, colon, Regeneration (biology), Mesenchymal stem cell, fungi, Epithelial Cells, Inflammatory Bowel Diseases, 030104 developmental biology, lcsh:Biology (General), hydrogel, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: International audience; Intestinal stem cells (ISC) are crucial players in colon epithelium physiology. The accurate control of their auto-renewal, proliferation and differentiation capacities provides a constant flow of regeneration, maintaining the epithelial intestinal barrier integrity. Under stress conditions, colon epithelium homeostasis in disrupted, evolving towards pathologies such as inflammatory bowel diseases or colorectal cancer. A specific environment, namely the ISC niche constituted by the surrounding mesenchymal stem cells, the factors they secrete and the extracellular matrix (ECM), tightly controls ISC homeostasis. Colon ECM exerts physical constraint on the enclosed stem cells through peculiar topography, stiffness and deformability. However, little is known on the molecular and cellular events involved in ECM regulation of the ISC phenotype and fate. To address this question, combining accurately reproduced colon ECM mechanical parameters to primary ISC cultures such as organoids is an appropriated approach. Here, we review colon ECM physical properties at physiological and pathological states and their bioengineered in vitro reproduction applications to ISC studies.
Published: 2020
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44. Perinatal exposure to a dietary pesticide cocktail does not increase susceptibility to high-fat diet-induced metabolic perturbations at adulthood but modifies urinary and fecal metabolic fingerprints in C57Bl6/J mice

Author: Wendy Klement, Hervé Guillou, Léonie Dopavogui, Lorraine Smith, Laurence Gamet-Payrastre, Guylène Feuillet, Nicola Marchi, Arnaud Polizzi, Frédéric de Bock, Emilien L. Jamin, Laurent Debrauwer, Sandrine Ellero-Simatos, Céline Lukowicz, Benoist Schaal, Sharon Barretto, Nicolas Loiseau, Bruno Patris, Cécile Canlet, Laila Mselli-Lakhal, Frédéric Lasserre, Anne Fougerat, Colette Denis, Toxicologie Intégrative & Métabolisme (ToxAlim-TIM), ToxAlim (ToxAlim), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génomique Fonctionnelle (IGF), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), 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), Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Analyse de Xénobiotiques, Identification, Métabolisme (E20 Metatoul-AXIOM), MetaToul-MetaboHUB, Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-ToxAlim (ToxAlim), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Exposition, Perturbation Endocrino-métabolique et Reproduction (ToxAlim-EXPER), L.S. PhD is supported by grants from the Ministry for Agriculture and Food and the Ministry for an Ecological and Solidary Transition, with the financial support of the French Biodiversity Agency and from the department AlimH of INRAE. This work was supported by a grant from the Ministry for Agriculture and Food and the Ministry for an Ecological and Solidary Transition, with the financial support of the French Biodiversity Agency (Epidemicmac and GepeTho), by ANR, France (Syneract and Hepatobrain) and Region Occitanie. We thank Anexplo Genotoul MetaToul for their excellent work on plasma biochemistry. All MS and NMR experiments were performed using instruments of the Metatoul-AXIOM platform, partner of the national infrastructure of metabolomics and fluxomics: MetaboHUB [MetaboHUB-ANR-11-INBS-0010, 2011], ANR-11-INBS-0010,METABOHUB,Développement d'une infrastructure française distribuée pour la métabolomique dédiée à l'innovation(2011), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Metatoul AXIOM (E20 ), MetaboHUB-MetaToul, Guerineau, Nathalie C., and Développement d'une infrastructure française distribuée pour la métabolomique dédiée à l'innovation - - METABOHUB2011 - ANR-11-INBS-0010 - INBS - VALID
Subjects: Tolerable daily intake, 010504 meteorology & atmospheric sciences, [SDV]Life Sciences [q-bio], Physiology, Urine, 010501 environmental sciences, Perinatal, Diet, High-Fat, 01 natural sciences, Energy homeostasis, Dietary exposure, chemistry.chemical_compound, Feces, Mice, Lactation, Medicine, Animals, Metabolomics, Pesticides, lcsh:Environmental sciences, Captan, 0105 earth and related environmental sciences, General Environmental Science, lcsh:GE1-350, 2. Zero hunger, Perinatal Exposure, business.industry, Pesticide, Pesticide cocktail, Gastrointestinal Microbiome, [SDV] Life Sciences [q-bio], Mice, Inbred C57BL, medicine.anatomical_structure, Metabolism, chemistry, 13. Climate action, Female, business
Abstract: International audience; Background: We recently demonstrated that chronic dietary exposure to a mixture of pesticides at low-doses induced sexually dimorphic obesogenic and diabetogenic effects in adult mice. Perinatal pesticide exposure may also be a factor in metabolic disease etiology. However, the long-term consequences of perinatal pesticide exposure remain controversial and largely unexplored.Objectives: Here we assessed how perinatal exposure to the same low-dose pesticide cocktail impacted metabolic homeostasis in adult mice.Methods: Six pesticides (boscalid, captan, chlopyrifos, thiachloprid, thiophanate, and ziram) were incorporated in food pellets. During the gestation and lactation periods, female (F0) mice were fed either a pesticide-free or a pesticide-enriched diet at doses exposing them to the tolerable daily intake (TDI) level for each compound, using a 1:1 body weight scaling from humans to mice. All male and female offsprings (F1) were then fed the pesticide-free diet until 18 weeks of age, followed by challenge with a pesticide-free high-fat diet (HFD) for 6 weeks. Metabolic parameters, including body weight, food and water consumption, glucose tolerance, and urinary and fecal metabolomes, were assessed over time. At the end of the experiment, we evaluated energetic metabolism and microbiota activity using biochemical assays, gene expression profiling, and 1H NMR-based metabolomics in the liver, urine, and feces.Results: Perinatal pesticide exposure did not affect body weight or energy homeostasis in 6- and 14-week-old mice. As expected, HFD increased body weight and induced metabolic disorders as compared to a low-fat diet. However, HFD-induced metabolic perturbations were similar between mice with and without perinatal pesticide exposure. Interestingly, perinatal pesticide exposure induced time-specific and sex-specific alterations in the urinary and fecal metabolomes of adult mice, suggesting long-lasting changes in gut microbiota.Conclusions: Perinatal pesticide exposure induced sustained sexually dimorphic perturbations of the urinary and fecal metabolic fingerprints, but did not significantly influence the development of HFD-induced metabolic diseases.
Published: 2020
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45. Agricultural residues bioenergy potential that sustain soil carbon depends on energy conversion pathways

Author: Julie Houge Hansen, Arezoo Taghizadeh-Toosi, Jørgen E. Olesen, Lorie Hamelin, Henrik Wenzel, Institute of Chemical Engineering, Biotechnology and Environmental Technology, SDU Life Cycle Engineering, University of Southern Denmark (SDU), Energinet, Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Aarhus University [Aarhus], iCLIMATE Aarhus University Interdisciplinary Centre for Climate Change, ANR-17-MGPA-0006, Region Occitanie 18015981, and Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: [SDV.BIO]Life Sciences [q-bio]/Biotechnology, 020209 energy, lcsh:TJ807-830, lcsh:Renewable energy sources, 02 engineering and technology, lcsh:HD9502-9502.5, 7. Clean energy, ORGANIC-CARBON, Environmental protection, Bioenergy, CROP RESIDUES, 0202 electrical engineering, electronic engineering, information engineering, Energy transformation, STOCKS, CATCH CROPS, soil carbon, Waste Management and Disposal, 2. Zero hunger, energy system analyses, Renewable Energy, Sustainability and the Environment, business.industry, AVAILABILITY, C-TOOL, Forestry, 04 agricultural and veterinary sciences, Soil carbon, C‐TOOL, 15. Life on land, WINTER-WHEAT, biomass potential, lcsh:Energy industries. Energy policy. Fuel trade, energy conversion pathway, Agriculture, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Environmental science, STRAW, business, Agronomy and Crop Science
Abstract: International audience; Agricultural crop residues represent a significant part of the biomass potentially available for renewable energy systems. Sustaining soil organic carbon (C) is a common limiting factor applied to the biophysically available resource to determine crop residues potential for bioenergy. Studies quantifying this potential have so far largely considered crop biomass to produce renewable energy as being independent from the energy conversion pathway. However, the conversion method has great influence on how much C in crop residues can be returned back and retained in soils. Here, we applied the C-TOOL soil C model for two extreme conversion pathways of agricultural straw management in terms of C returned back to soils, using Denmark as a case study. Those were anaerobic digestion, involving the return of recalcitrant C to fields, and combustion, involving no C returns to agricultural fields. Danish agriculture was represented by six different soil-cropping schemes units on which our two extreme bioenergy pathways were modelled. We applied a premise that for a given geographical unit, the same long-term soil C level needs to be achieved under these extreme bioenergy scenarios; therefore, we identified how much straw could be removed from agricultural fields in each case while maintaining equal soil organic carbon (SOC) levels. We found that at the scale of the whole country, only 26% of the straw potential can be harvested for use in combustion to maintain in average long-term SOC at the same level as it would have been with the anaerobic digestion scenario. Thus, consideration for the biomass conversion pathway is important when identifying agricultural residue potentials for energy conversion while ensuring that SOC level is not compromised.
Published: 2020
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46. Culture of rabbit caecum organoids by reconstituting the intestinal stem cell niche in vitro with pharmacological inhibitors or L-WRN conditioned medium

Author: Nathalie Vergnolle, Claire Cherbuy, Eloïse Mussard, Géraldine Pascal, Virginie Helies, Martin Beaumont, Aude Rubio, Sylvie Combes, Cécile Pouzet, Sandra Fourre, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), FRAIB-TRI Imaging Platform Facilities, Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Recherche en Santé Digestive (IRSD ), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), INRAE PHASE division ('MiniGut' project), 'Fond Unique Interministeriel' (FUI) program, Banque Publique d’Investissement (BPI) de France, Fonds Européens de Développement Régional (FEDER), the region Occitanie funds, Plateforme TRI FR-AIB, Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), 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-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Toulouse Réseau Imagerie-Genotoul ( TRI-Genotoul), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), and SEGUIN, Nathalie
Subjects: 0301 basic medicine, Cell, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Epithelium, Caecum, 03 medical and health sciences, 0302 clinical medicine, medicine, Organoid, Animals, Intestinal Mucosa, Stem Cell Niche, lcsh:QH301-705.5, Cecum, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, Enteroid, Barrier function, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, [SDV.BA.MVSA] Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, Monolayer, Culture medium, Cell Biology, General Medicine, biology.organism_classification, Intestinal epithelium, In vitro, Cell biology, Intestines, Organoids, 030104 developmental biology, medicine.anatomical_structure, Spheroid, lcsh:Biology (General), Culture Media, Conditioned, Rabbits, Stem cell, 030217 neurology & neurosurgery, Developmental Biology
Abstract: Intestinal organoids are self-organized 3-dimensional (3D) structures formed by a single layer of polarized epithelial cells. This innovative in vitro model is highly relevant to study physiology of the intestinal epithelium and its role in nutrition and barrier function. However, this model has never been developed in rabbits, while it would have potential applications for biomedical and veterinary research. Here, we cultured rabbit caecum organoids with either pharmacological inhibitors (2Ki medium) or L-WRN cells conditioned medium (L-WRN CM) to reconstitute the intestinal stem cell niche in vitro. Large spherical organoids were obtained with the 2Ki medium and this morphology was associated with a high level of proliferation and stem cells markers gene expression. In contrast, organoids cultured with L-WRN CM had a smaller diameter; a greater cell height and part of them were not spherical. When the L-WRN CM was used at low concentration (5%) for two days, the gene expression of stem cells and proliferation markers were very low, while absorptive and secretory cells markers and antimicrobial peptides were elevated. Epithelial cells within organoids were polarized in 3D cultures with 2Ki medium or L-WRN CM (apical side towards the lumen). We cultured dissociated organoid cells in 2D monolayers, which allowed accessibility to the apical compartment. Under these conditions, actin stress fibers were observed with the 2Ki medium, while perijonctionnal localization of actin was observed with the L-WRN CM suggesting, in 2D cultures as well, a higher differentiation level in the presence of L-WRN CM. In conclusion, rabbit caecum organoids cultured with the 2Ki medium were more proliferative and less differentiated than organoids cultured with L-WRN CM. We propose that organoids cultured with the 2Ki medium could be used to rapidly generate in vitro a large number of rabbit intestinal epithelial stem cells while organoids cultured with the L-WRN CM used at low concentration represent a suitable model to study differentiated rabbit epithelium.
Published: 2020
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47. Predicting Transverse Mixing Efficiency Downstream of a River Confluence

Author: Emmanuel Mignot, S. Pouchoulin, L. Gond, Nicolas Riviere, J. Le Coz, Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA), Laboratoire de Mecanique des Fluides et d'Acoustique (LMFA), École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), RiverLy - Fonctionnement des hydrosystèmes (RiverLy), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Region Auvergne-Rhone-Alpes-European Commission :CNRS-144140-Agence de l'eau Rhone-Mediterranee-Corse (France) : 2018 1063-Consiglio Nazionale delle Ricerche (CNR)-EDF -Region Provence-Alpes-Cote d'Azur-Region Occitanie, ANR-17-EURE-0018,H2O'LYON,School of Integrated Watershed Sciences(2017), ANR-11-LABX-0010,DRIIHM / IRDHEI,Dispositif de recherche interdisciplinaire sur les Interactions Hommes-Milieux(2011), Institut National des Sciences Appliquées (INSA)-Université de Lyon, and Riverly (Riverly)
Subjects: 010504 meteorology & atmospheric sciences, [SDE.IE]Environmental Sciences/Environmental Engineering, transverse mixing, 0207 environmental engineering, River confluence, ADCP, 02 engineering and technology, Mechanics, tracer, 01 natural sciences, Transverse plane, Downstream (manufacturing), 13. Climate action, TRACER, Dispersion (optics), river confluence, dispersion, 020701 environmental engineering, Mixing (physics), Geology, 0105 earth and related environmental sciences, Water Science and Technology
Abstract: International audience; Predicting mixing processes, especially transverse mixing, downstream of river confluences, is necessary for assessing and modeling the fate of pollutants transported in river networks, but it is still challenging. Typically, there is a lack of transverse mixing solutions implemented in 1-D hydrodynamical models widely used in river engineering applications. To investigate the mixing processes developing downstream of a medium-sized river confluence, three high-resolution in situ surveys are conducted at the Rhône-Saône confluence in France, based on geolocated specific conductivity and hydroacoustic measurements. Contrasting mixing situations are observed depending on hydrological conditions. In some cases, the two flows mix slowly due to turbulent shear at their vertical interface. This can be modeled by an analytical solution of the advection-diffusion equation. In other cases, the waters from one of the two tributaries move under the waters of the other tributary. The induced local circulation enhances transverse mixing but not vertical mixing and the flow remains stratified vertically, which may be missed when surface or satellite images are analyzed qualitatively. Stratification may be predicted by comparing the time scales for shear and density-driven adjustment. Shear-dominated transverse mixing of depth-averaged concentrations can be predicted analytically and implemented in 1-D hydrodynamical models. However, the initiation of apparently rapid transverse mixing due to density-driven circulation remains to be better understood and quantified. Plain Language Summary Predicting how waters mix downstream of river confluences is necessary for assessing and modeling the fate of pollutants transported in river networks, but it is still challenging. Typically, there is a lack of transverse mixing solutions implemented in models widely used in river engineering applications. To investigate the mixing processes developing downstream of a medium-sized river confluence, three high-resolution in situ surveys are conducted at the Rhône-Saône confluence in France. Contrasting slow or rapid mixing situations are observed depending on hydrological conditions. The transverse mixing of depth-averaged concentrations can be predicted analytically and implemented in 1-D hydrodynamical models. However, the initiation of rapid transverse mixing due to difference in fluid density remains to be better understood and quantified.
Published: 2020
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48. Proteomic analysis of two weight classes of mule duck 'foie gras' at the end of an overfeeding period

Author: Lo, Bara, Marty-Gasset, Nathalie, Pichereaux, Carole, Bravo, Céline, Manse, Hélène, Domitile, Renaud, Rémignon, Hervé, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Institut de pharmacologie et de biologie structurale (IPBS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, IDENA, Region Provence-Alpes-Cote d'Azur, Region Occitanie, Fonds Europeens de Developpement Regional (FEDER), Toulouse Metropole, Ministry of Research, France, and ANR-10-INBS-0008,ProFI,Infrastructure Française de Protéomique(2010)
Subjects: liver weight, cell death, mule duck, Physiology, Physiology (medical), “foie gras”, oxidative stress, Foie gras, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, proteomic, Original Research, cell structure
Abstract: International audience; The weight of the liver is one of the important selection criteria in the quality of "foie gras". This factor is highly variable despite the fact that individuals are reared, overfed and slaughtered in the same way. In this study, we performed an analysis of the proteome profile of two weight classes of light (between 550 and 599 g) and heavy (more than 700 g) livers. For the analysis of the proteic extracts, a liquid chromatographic analysis coupled with mass spectrometry was carried out. In low-weight livers, aerobic energy metabolism, protein metabolism and lipid metabolism oriented toward export and beta-oxidation were overexpressed. On the contrary, high weight livers were characterized by anaerobic energy metabolism and a more active protein catabolism associated with cell apoptosis and reorganization of the cell structure.
Published: 2020
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49. Automatic and Intelligent Composition of Services in Ambient Environments: A Demonstration

Author: Delcourt, Kevin, Adreit, Françoise, Arcangeli, Jean-Paul, Hacid, Kahina, Trouilhet, Sylvie, Younes, Walid, Systèmes Multi-Agents Coopératifs (IRIT-SMAC), Institut de recherche en informatique de Toulouse (IRIT), Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées, Université Toulouse - Jean Jaurès (UT2J), Université Toulouse III - Paul Sabatier (UT3), French region Occitanie and operational program FEDER-FSE Midi-Pyrénées et Garonne., and Institut de Recherche en Informatique deToulouse
Subjects: [INFO.INFO-IU]Computer Science [cs]/Ubiquitous Computing, Software Component, Service, Ambient Intelligence, Demonstration, Emergence, User-Centered Composition, Use Case, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI]
Abstract: This report demonstrates our prototype solution of opportunistic software composition through a realistic use case: a user in his car benets from an emerging service that guides him to the battery recharging station closest to its current position. The demonstration video is available online.
Published: 2020

50. LJ000328, a novel ALK2/3 kinase inhibitor, represses hepcidin and significantly improves the phenotype of IRIDA

Author: Belot, Audrey, Gourbeyre, Ophélie, Fay, Alexis, Palin, Anais, Besson-Fournier, Céline, Latour, Chloé, Hopkins, Corey R., Tidmarsh, George F., Coppin, Hélène, Roth, Marie-Paule, Ritter, Matthew R., Hong, Charles C., Meynard, Delphine, Institut de Recherche en Santé Digestive (IRSD ), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Nebraska Medical Center, University of Nebraska System, La Jolla Pharmaceut Co, University of Maryland School of Medicine, University of Maryland System, Cooley's Anemia Foundation, French Foundation for Rare Diseases, Region Provence-Alpes-Cote d'Azur, Region Occitanie, Fondation pour la Recherche Medicale (DEQ2000326528), ANR-17-CE14-0036,IRONASH,Rôle du fer dans la pathologie du NASH(2017), ANR-17-CE14-0031,MTREAT-2,Manipuler la Matriptase-2 pour traiter les pathologies associées à une dérégulation du métabolisme du fer(2017), ANR-13-BSV3-0015,RESTRICTIRON,Limitation du fer disponible pour les pathogènes : mécanismes et contribution à la défense antimicrobienne de l'hôte(2013), ANR-11-EQPX-0003,ANINFIMIP,Equipements plateforme animalerie infectieuse de haute-sécurité de Midi Pyrénées(2011), SEGUIN, Nathalie, Rôle du fer dans la pathologie du NASH - - IRONASH2017 - ANR-17-CE14-0036 - AAPG2017 - VALID, Manipuler la Matriptase-2 pour traiter les pathologies associées à une dérégulation du métabolisme du fer - - MTREAT-22017 - ANR-17-CE14-0031 - AAPG2017 - VALID, Blanc 2013 - Limitation du fer disponible pour les pathogènes : mécanismes et contribution à la défense antimicrobienne de l'hôte - - RESTRICTIRON2013 - ANR-13-BSV3-0015 - Blanc 2013 - VALID, and Equipements plateforme animalerie infectieuse de haute-sécurité de Midi Pyrénées - - ANINFIMIP2011 - ANR-11-EQPX-0003 - EQPX - VALID
Subjects: [SDV.MHEP.HEM] Life Sciences [q-bio]/Human health and pathology/Hematology, Phenotype, Anemia, Iron-Deficiency, Hepcidins, Humans, [SDV.MHEP.HEM]Life Sciences [q-bio]/Human health and pathology/Hematology, Online Only Articles
Published: 2020
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