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51 results on '"Regional Council of Brittany"'

1. A New In Vivo Zebrafish Bioassay Evaluating Liver Steatosis Identifies DDE as a Steatogenic Endocrine Disruptor, Partly through SCD1 Regulation

Author: Hélène Le Mentec, Emmanuelle Monniez, Antoine Legrand, Céline Monvoisin, Dominique Lagadic-Gossmann, Normand Podechard, Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), École des Hautes Études en Santé Publique [EHESP] (EHESP), Microenvironment and B-cells: Immunopathology,Cell Differentiation, and Cancer (MOBIDIC), Université de Rennes (UR)-Etablissement français du sang [Rennes] (EFS Bretagne)-Institut National de la Santé et de la Recherche Médicale (INSERM), 825712, European Union, and ARED, Regional Council of Brittany
Subjects: endocrine disruptor compounds, [SDV]Life Sciences [q-bio], Organic Chemistry, General Medicine, Catalysis, Computer Science Applications, Inorganic Chemistry, liver steatosis, bioassay, NAFLD, zebrafish larvae, DDE, Physical and Theoretical Chemistry, Molecular Biology, Spectroscopy
Abstract: International audience; Non-alcoholic fatty liver disease (NAFLD), which starts with liver steatosis, is a growing worldwide epidemic responsible for chronic liver diseases. Among its risk factors, exposure to environmental contaminants, such as endocrine disrupting compounds (EDC), has been recently emphasized. Given this important public health concern, regulation agencies need novel simple and fast biological tests to evaluate chemical risks. In this context, we developed a new in vivo bioassay called StAZ (Steatogenic Assay on Zebrafish) using an alternative model to animal experimentation, the zebrafish larva, to screen EDCs for their steatogenic properties. Taking advantage of the transparency of zebrafish larvae, we established a method based on fluorescent staining with Nile red to estimate liver lipid content. Following testing of known steatogenic molecules, 10 EDCs suspected to induce metabolic disorders were screened and DDE, the main metabolite of the insecticide DDT, was identified as a potent inducer of steatosis. To confirm this and optimize the assay, we used it in a transgenic zebrafish line expressing a blue fluorescent liver protein reporter. To obtain insight into DDE’s effect, the expression of several genes related to steatosis was analyzed; an up-regulation of scd1 expression, probably relying on PXR activation, was found, partly responsible for both membrane remodeling and steatosis.
Published: 2023
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2. Validity of Ultra-Short-Term HRV Analysis Using PPG-A Preliminary Study

Author: Taoum, Aline, Bisiaux, Alexis, Tilquin, Florian, Le Guillou, Yann, Carrault, Guy, Laboratoire Traitement du Signal et de l'Image (LTSI), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM), Biosency, and Regional Council of Brittany [18004519, 18004180]
Subjects: Biochemistry, Atomic and Molecular Physics, and Optics, Healthy Volunteers, Analytical Chemistry, Electrocardiography, Wearable Electronic Devices, wearable devices, Pregnancy, Heart Rate, ultra-short-term HRV analysis, Humans, [SDV.IB]Life Sciences [q-bio]/Bioengineering, Female, Electrical and Electronic Engineering, heart rate variability (HRV), Photoplethysmography, Instrumentation
Abstract: International audience; Continuous measurement of heart rate variability (HRV) in the short and ultra-short-term using wearable devices allows monitoring of physiological status and prevention of diseases. This study aims to evaluate the agreement of HRV features between a commercial device (Bora Band, Biosency) measuring photoplethysmography (PPG) and reference electrocardiography (ECG) and to assess the validity of ultra-short-term HRV as a surrogate for short-term HRV features. PPG and ECG recordings were acquired from 5 healthy subjects over 18 nights in total. HRV features include time-domain, frequency-domain, nonlinear, and visibility graph features and are extracted from 5 min 30 s and 1 min 30 s duration PPG recordings. The extracted features are compared with reference features of 5 min 30 s duration ECG recordings using repeated-measures correlation, Bland-Altman plots with 95% limits of agreements, Cliff's delta, and an equivalence test. Results showed agreement between PPG recordings and ECG reference recordings for 37 out of 48 HRV features in short-term durations. Sixteen of the forty-eight HRV features were valid and retained very strong correlations, negligible to small bias, with statistical equivalence in the ultra-short recordings (1 min 30 s). The current study concludes that the Bora Band provides valid and reliable measurement of HRV features in short and ultra-short duration recordings.
Published: 2022

3. A Multi-Skilled Mathematical Model of Bacterial Attachment in Initiation of Biofilms

Author: Chathoth, Kanchana, Fostier, Louis, Martin, Bénédicte, Baysse, Christine, Mahé, Fabrice, Nutrition, Métabolismes et Cancer (NuMeCan), Université de Rennes (UR)-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 de Recherche Mathématique de Rennes (IRMAR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), convention 13-2017, Fondation 'Sourire Quand Même', 8003593, Regional Council of Brittany, and HAL UR1, Admin
Subjects: Microbiology (medical), [MATH.MATH-NA] Mathematics [math]/Numerical Analysis [math.NA], Microbiology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, biofilm, iron, Virology, Streptococcus gordonii, bacterial attachment, mathematical model, Porphyromonas gingivalis, Treponema denticola, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [MATH.MATH-NA]Mathematics [math]/Numerical Analysis [math.NA]
Abstract: International audience; The initial step of biofilm formation is bacteria attachment to biotic or abiotic surfaces and other bacteria through intra or interspecies interactions. Adhesion can be influenced by physicochemical conditions of the environment, such as iron. There is no available mathematical model of bacterial attachment giving realistic initiation rather than random adhesion. We describe a simple stochastic attachment model, from the simplest case in two dimensions with one bacterial species attaching on a homogeneous flat surface to more complex situations, with either several bacterial species, inhomogeneous or non-flat surfaces, or in three dimensions. The model depends on attachment probabilities (on the surface, laterally, or vertically on bacteria). Effects of each of these parameters were analyzed. This mathematical model is then applied to experimental oral microcolonies of Porphyromonas gingivalis, Streptococcus gordonii, and Treponema denticola, either as mono-, two, or three species, under different iron concentrations. The model allows to characterize the adhesion of three bacterial species and explore the effect of iron on attachment. This model appears as a powerful tool for initial attachment analysis of bacterial species. It will enable further modeling of biofilm formation in later steps with biofilm initialization more relevant to real-life subgingival biofilms.
Published: 2022
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4. An integrated investigation of the effects of ocean acidification on adult abalone (Haliotis tuberculata)

Author: Arianna Servili, Manon Coheleach, Aïcha Badou, Stéphanie Auzoux-Bordenave, Sophie G. Martin, Sabine Roussel, Nicolas Richard, Philippe Dubois, Sarah Di Giglio, Fanny Gaillard, Sylvain Huchette, Loïc Malet, Solène Avignon, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie Marine (LBM), Université libre de Bruxelles (ULB), Station de Biologie Marine de Concarneau, Direction générale déléguée à la Recherche, à l’Expertise, à la Valorisation et à l’Enseignement-Formation (DGD.REVE), Muséum national d'Histoire naturelle (MNHN)-Muséum national d'Histoire naturelle (MNHN), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Scea France Haliotis, This work was supported in part by the ATM program 'Abalone shell mineralization' of the MNHN funded by theMinistère délégué à l’Enseignement Supérieur et à la Recherche (Paris, France), the program 'Acidification des Océans' (ICOBio project) funded by the Fondation pour la Recherche sur la Biodiversité (FRB) and the Ministère de la Transition Ecologique et Solidaire (MTES), and the French LabexMER program (OASYS project). SA was sup‐ported by a post-doctoral fellowship from the MNHN funded by the Ministère de la Transition Ecologique et Solidaire (MTES). SDG is holder of a FRIA PhD fellowship from the National Fund for Scientific Research (NFSR, Belgium) and PhD is a Research Director of the NFSR. The Regional Council of Brittany, the General Council of Finistère, the urban community of Concarneau Cornouaille Agglomération, and the European Regional Development Fund (ERDF) are acknowledged for the funding of the scanning electron microscope (Sigma 300 FE-SEM) at the Concarneau Marine Station., ANR-10-LABX-0019,LabexMER,LabexMER Marine Excellence Research: a changing ocean(2010), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER Centre de Bretagne), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, food.ingredient, Abalone, acl, growth, ocean acidification, shell microstructure, mechanical properties, Aquatic Science, Oceanography, 010603 evolutionary biology, 01 natural sciences, calcification, chemistry.chemical_compound, food, Aquaculture, Hemolymph, 14. Life underwater, Food science, Haliotis, Océanographie biologique, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, Ecology, Evolution, Behavior and Systematics, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, abalone, Ecology, business.industry, Chemistry, 010604 marine biology & hydrobiology, Ocean acidification, Metabolism, Calcium carbonate, [SDE]Environmental Sciences, physiology, gene expression, Seawater, [SDV.EE.BIO]Life Sciences [q-bio]/Ecology, environment/Bioclimatology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business
Abstract: Ocean acidification (OA) and its subsequent changes in seawater carbonate chemistry are threatening the survival of calcifying organisms. Due to their use of calcium carbonate to build their shells, marine molluscs being particularly vulnerable. This study investigated the effect of CO2-induced OA on adult European abalone (Haliotis tuberculata) using a multi- parameter approach. Biological (survival, growth), physiological (pHT of haemolymph, phagocytosis, metabolism, gene expression) and structural responses (shell strength, nanoindentation measurements, SEM imaging of microstructure) were evaluated throughout a 5-month exposure to ambient (8.0) and low (7.7) pH conditions. During the first two months, the haemolymph pH was reduced, indicating that abalone do not compensate for the pH decrease of their internal fluid. Overall metabolism and immune status were not affected, suggesting that abalone maintain their vital functions when facing OA. However, after four months of exposure, adverse effects on shell growth, calcification, microstructure and resistance were highlighted, whereas the haemolymph pH was compensated. Significant reduction in shell mechanical properties were revealed at pH 7.7, suggesting that OA altered the biomineral architecture leading to a more fragile shell. It is concluded that under lower pH, abalone metabolism is maintained at a cost to growth and shell integrity. This may impact both abalone ecology and aquaculture., info:eu-repo/semantics/inPress
Published: 2020

5. Virulence of Vibrio harveyi ORM4 towards the European abalone Haliotis tuberculata involves both quorum sensing and a type III secretion system

Author: Morot, Amandine, El Fekih, Sahar, Bidault, Adeline, Le Ferrand, Alizée, Jouault, Albane, Kavousi, Javid, Bazire, Alexis, Pichereau, Vianney, Dufour, Alain, Paillard, Christine, Delavat, François, Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biotechnologie et Chimie Marines (LBCM), Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), This work was supported by the ‘Laboratoire d'Excellence’ LabexMER (ANR-10-LABX-19), by the ‘Ecole Universitaire de Recherche’ ISblue (ANR-17-EURE-0015) and co-funded by a grant from the French government under the programme ‘Investissements d'Avenir’, and by a grant from the Regional Council of Brittany. This project received grants from the H2020 VIVALDI project (grant agreement n°678589), and the CNRS Prematuration (CoMAq project) and EC2CO (ViViMar project) programmes. The LBCM is supported by the Région Bretagne and European FEDER. A.M. and A.J. are the recipient of doctoral fellowships co-funded by the Région Bretagne, France, and the Université de Bretagne-Sud., ANR-17-EURE-0015,ISBlue,Interdisciplinary Graduate School for the Blue planet(2017), ANR-10-LABX-0019,LabexMER,LabexMER Marine Excellence Research: a changing ocean(2010), European Project: 678589,H2020,H2020-SFS-2015-2,VIVALDI(2016), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDE]Environmental Sciences, bacteria, ComputingMilieux_MISCELLANEOUS
Abstract: International audience; Environmental Vibrio strains represent a major threat in aquaculture, but the understanding of their virulence mechanisms heavily relies on the transposition of knowledge from human-pathogen vibrios. Here, the genetic bases of the virulence of Vibrio harveyi ORM4 towards the European abalone Haliotis tuberculata were characterized. We demonstrated that luxO, encoding a major regulator of the quorum sensing system, is crucial for the virulence of this strain, and that its deletion leads to a decrease in swimming motility, biofilm formation, and exopolysaccharide production. Furthermore, the biofilm formation by V. harveyi ORM4 was increased by abalone serum, which required LuxO. The absence of LuxO in V. harveyi ORM4 yielded opposite phenotypes compared with other Vibrio species including V. campbellii (still frequently named V. harveyi). In addition, we report a full type III secretion system (T3SS) gene cluster in the V. harveyi ORM4 genome. LuxO was shown to negatively regulate the promoter activity of exsA, encoding the major regulator of the T3SS genes, and the deletion of exsA abolished the virulence of V. harveyi ORM4. These results unveil virulence mechanisms set up by this environmentally important bacterial pathogen and pave the way for a better molecular understanding of the regulation of its pathogenicity.
Published: 2021

6. Experimental Study of a Heat Pump for Simultaneous Cooling and Desalination by Membrane Distillation

Author: Ahmadou Diaby, Thierry Maré, Ousmane Sow, Paul Byrne, Patrick Loulergue, Laboratoire du froid et des systèmes énergétiques et thermiques (Lafset), Conservatoire National des Arts et Métiers [CNAM] (CNAM), Laboratoire de Génie Civil et Génie Mécanique (LGCGM), 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), Institut des Sciences Chimiques de Rennes (ISCR), 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), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), This study was funded by BPO foundation, Université de Rennes 1 and the Regional Council of Brittany and Cheikh Anta Diop University., 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 de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA), and 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)
Subjects: cooling, 020209 energy, membrane distillation, Filtration and Separation, heating, TP1-1185, 02 engineering and technology, Membrane distillation, Desalination, Article, law.invention, simultaneous demand, desalination, Chemical engineering, 020401 chemical engineering, law, Physical phenomena, 0202 electrical engineering, electronic engineering, information engineering, [CHIM]Chemical Sciences, Chemical Engineering (miscellaneous), 0204 chemical engineering, Process engineering, business.industry, Chemical technology, Process Chemistry and Technology, 6. Clean water, Air conditioning, Environmental science, TP155-156, Cooling energy, business, Heat pump
Abstract: Heat pump systems can simultaneously produce cooling energy for space cooling in hotels, office and residential buildings and heat for desalination using membrane distillation (MD). The MD technique uses a heat input at a temperature compatible with the levels of heat pump condensers (&lt, 60 °C). A heat pump prototype coupled with an air-gap membrane distillation unit was constructed and tested. This paper presents the experimental study on a lab-scale prototype and details the two operating modes “continuous” and “controlled” simulating an air conditioning system and a food storage, respectively. The experimental results enable to analyze the performance of the prototype and the physical phenomena involved. Finally, the study shows that this system could be a promising solution to help supplying freshwater to people in hot regions of the world.
Published: 2021

7. Multiscale evaluations of global, national and regional digital soil mapping products in France

Author: Lemercier, Blandine, Lagacherie, Philippe, Amelin, Julien, Sauter, Joëlle, Pichelin, Pascal, Richer-De-Forges, Anne C, Arrouays, D., Sol Agro et hydrosystème Spatialisation (SAS), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, 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), Laboratoire d'étude des Interactions Sol - Agrosystème - Hydrosystème (UMR LISAH), Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Chambre Régionale d'Agriculture Grand Est, InfoSol (InfoSol), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and The authors thank the CNES (French National Centre for Space Studies) for funding the Centre of Scientific Expertise (CES) Théia 'Digital Soil Mapping', to which the authors belong. They also acknowledge the Regional Council of Brittany for financing the project 'Sols de Bretagne', which contributed financially and technically to the study. A.R.d.F., P.L. and D.A. are members of the research consortium GLADSOILMAP, supported by the STUDIUM Loire Valley Institute for advanced research studies.
Subjects: GlobalSoilMap, Digital soil mapping, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, Soil Science, Soil Grids, Pedological patterns, Evaluation, Soil survey
Abstract: International audience; As digital soil mapping (DSM) applications have been developed at multiple extents over the two last decades, large areas of the world are now covered by several DSM products with similar resolution and targeted soil properties. Thus, from these products, end-users must carefully select the one that will best meet their needs. The aim of this study was to evaluate three DSM products obtained at different scales (global, national and regional) over three local territories of increasing area selected in three contrasting regions of France (Alsace, Brittany and Languedoc-Roussillon). Three topsoil (5–15 cm) properties were evaluated: clay content, pH in water and soil organic carbon content. Evaluations were done at both point and soil mapping unit supports, the latter corresponding to quantitative assessment of visual accordance between DSM products and conventional local soil maps of acknowledged quality. The ability to predict soil properties well increased from global to national to regional DSM products. However, none of the DSM products tested was able to predict satisfactorily at the most local (1:25,000) scale. Evaluations of DSM products using local soil maps were generally in accordance with those using points. Evaluations using local soil maps also provided additional information about the utility of DSM products for small areas with too few soil measurements to perform punctual evaluation and for issues concerning areal-support uses of DSM products. These results suggest that when focusing on local areas, users of DSM products should evaluate their performance and, if unsatisfactory, invest in development of local DSM.
Published: 2022

8. Care consumption of people with multiple sclerosis: A multichannel sequence analysis in a population-based setting in British Columbia, Canada

Author: Feng Zhu, Helen Tremlett, Jonathan Roux, Emmanuelle Leray, Elaine Kingwell, Centre d'Investigation Clinique [Rennes] (CIC), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Hôpital Pontchaillou-Institut National de la Santé et de la Recherche Médicale (INSERM), Recherche en Pharmaco-épidémiologie et Recours aux Soins (REPERES), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École des Hautes Études en Santé Publique [EHESP] (EHESP), École des Hautes Études en Santé Publique [EHESP] (EHESP), Département Méthodes quantitatives en santé publique (METIS), University of British Columbia (UBC), University College of London [London] (UCL), Collectif de recherche handicap, autonomie et société inclusive (CoRHASI), This study was supported by the Canadian Institutes of Health Research (CIHR) [MOP-93646] and the US National MS Society [#RG 4202-A-2], 2009-12, PI: Tremlett]. For his PhD, Jonathan Roux was supported by the French National Agency for Medicines and Health Product Safety (ANSM) through the PEPS platform (Pharmacoepidemiology of Health Products). For this internship which was part of his PhD, JR was supported by the French public health doctoral network, the ‘Ecole des Docteurs’ of Bretagne-Loire University and the Regional Council of Brittany., Jonchère, Laurent, Université de Rennes (UR)-Hôpital Pontchaillou-Institut National de la Santé et de la Recherche Médicale (INSERM), and Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)
Subjects: Gerontology, [SDV]Life Sciences [q-bio], Comorbidity, Population based, multiple sclerosis, 01 natural sciences, 010104 statistics & probability, 03 medical and health sciences, 0302 clinical medicine, multichannel sequence analysis, cohort studies, Multidisciplinary approach, Care pathway, Humans, Medicine, 0101 mathematics, Consumption (economics), British Columbia, business.industry, Multiple sclerosis, medicine.disease, 3. Good health, population-based, [SDV] Life Sciences [q-bio], Neurology, health administrative data, Neurology (clinical), business, Sequence Analysis, 030217 neurology & neurosurgery, Cohort study
Abstract: Background: Persons with multiple sclerosis (PwMS) typically require complex multidisciplinary care, which is rarely formally assessed. Objectives: We applied multichannel sequence analysis (MCSA) to identify care consumption patterns by PwMS in British Columbia, Canada. Methods: We created two cohorts, comprising incident and prevalent MS cases, using linked clinical and administrative data. We applied MCSA to quantify and compare the care pathways of PwMS, based on all-cause hospitalizations and physician visits (divided into five specialities). Care consumption clusters were characterized using demographic and clinical features. Results: From 1048 incident and 3180 prevalent PwMS, the MCSA identified 12 and 6 distinct care consumption clusters over a median follow-up of 9.6 and 13.0 years, respectively. Large disparities between clusters were observed; the median number of annual consultations ranged from 5.6 to 21.3 for general practitioners, 1.2 to 4.6 for neurologists and 0 to 5.3 for psychiatrists in the incident cohort. Characteristics at MS symptom onset associated with the highest care consumption included high comorbidity burden and older age. There were similar disparities and associations for prevalent PwMS. Conclusion: The distinct patterns of care consumption, which were reminiscent of the heterogeneity of MS itself, may facilitate health service planning and evaluation, and provide a novel outcome measure in health research.
Published: 2021

9. On the role of stochastic geometry in sixth generation wireless networks

Author: Samir Saoudi, Mustapha Benjillali, Yassine Hmamouche, Département Mathematical and Electrical Engineering (IMT Atlantique - MEE), IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Equipe Communication System Design (Lab-STICC_COSYDE), Laboratoire des sciences et techniques de l'information, de la communication et de la connaissance (Lab-STICC), École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-Université Bretagne Loire (UBL)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-Université Bretagne Loire (UBL)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT), Institut National des Postes et Télécommunications [Rabat] (INPT), and This work is funded by a research grant from PRACOM and the Regional Council of Brittany, France.
Subjects: Computer science, business.industry, Wireless network, Interface (computing), [SPI]Engineering Sciences [physics], Systems engineering, Milestone (project management), Key (cryptography), Robot, Mobile telephony, [MATH]Mathematics [math], business, Stochastic geometry, 5G
Abstract: International audience; Over the past four decades, the mobile communications industry has evolved from the first generation (1G) to the 5G premises, while the research community is currently discussing the broad outlines of the 6G system foreseen from 2030 onwards. In fact, even if 5G is extensively advocated as the expected ecosystem to fully meet the requirements of internet of things (IoT) applications, e.g., autonomous robots and vehicles, extended reality (XR) platforms, and brain-computer interface (BCI), it is only by the advent of 6G that such a bold achievement can be truly met. One key milestone towards the 6G vision is the development of a multi-objective analytical tool enabling the joint optimization of communication, control, localization, sensing, energy, and other parameters and resources. In this paper, we discuss how stochastic geometry (SG) can serve as a potential candidate for such aim. We also outline some fundamental limitations of SG, as well as some avenues to address them, and develop new seminal results ready-to-use in the analysis and modeling of future 6G networks.
Published: 2021

10. Optimal operation of a grid-connected battery energy storage system over its lifetime

Author: Alexandros C. Charalampidis, Pierre Haessig, Ioannis Kordonis, Institut d'Électronique et des Technologies du numéRique (IETR), Université de Nantes (UN)-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)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Technische Universität Berlin (TU), Regional Council of Brittany Region Bretagne [9693], European Union European Commission [PCOFUND-GA-2013-609102, 705982], Nantes Université (NU)-Université de Rennes 1 (UR1), Université de Nantes (UN)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), and Technical University of Berlin / Technische Universität Berlin (TU)
Subjects: dynamic programming, Control and Optimization, business.industry, Computer science, 020209 energy, Applied Mathematics, Electrical engineering, 02 engineering and technology, 021001 nanoscience & nanotechnology, Grid, 7. Clean energy, Battery energy storage system, [SPI]Engineering Sciences [physics], Control and Systems Engineering, 0202 electrical engineering, electronic engineering, information engineering, ratio cost problems, stochastic optimal control, battery energy storage systems, 0210 nano-technology, business, Software, battery degradation
Abstract: International audience; This paper deals with the optimal control of grid-connected Battery Energy Storage Systems (BESSs) operating for energy arbitrage. An important issue is that BESSs degrade over time, according to their use, and thus they are usable only for a limited number of cycles. Therefore, the time horizon of the optimization depends on the actual operation of the BESS. We focus on Li-ion batteries and use an empirical model to describe battery degradation. The BESS model includes an equivalent circuit for the battery and a simplified model for the power converter. In order to model the energy price variations, we use a linear stochastic model that includes the effect of the time-of-the-day. The problem of maximizing the revenues obtained over the BESS lifetime is formulated as a stochastic optimal control problem with a long, operation-dependent time horizon. First, we divide this problem into a finite set of subproblems, such that for each one of them, the State of Health (SoH) of the battery is approximately constant. Next, we reformulate approximately every subproblem into the minimization of the ratio of two long-time average-cost criteria and use a value-iteration-type algorithm to derive the optimal policy. Finally, we present some numerical results and investigate the effects of the energy loss parameters, degradation parameters, and price dynamics on the optimal policy.
Published: 2021

11. Linking Spatial and Temporal Dynamic of Bacterioplankton Communities With Ecological Strategies Across a Coastal Frontal Area

Author: Lemonnier, Clarisse, Perennou, Morgan, Eveillard, Damien, Fernandez-Guerra, Antonio, Leynaert, Aude, Marié, Louis, Morrison, Hilary, Mémery, Laurent, Paillard, Christine, Maignien, Lois, Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences du Numériques de Nantes (LS2N), Microbial genomics and bioinformatics research group, Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Lundbeck Foundation GeoGenetics Center, Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, Laboratoire d'Océanographie Physique et Spatiale (LOPS), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Marine Biological Laboratory (MBL), University of Chicago, This work was supported by the 'Laboratoire d’Excellence' LabexMER (ANR-10-LABX-19) and co-funded by a grant from the French government under the program 'Investissements d’Avenir,' and the Regional Council of Brittany. It was also supported by the University of Western Brittany (UBO)., ANR-10-LABX-0019,LabexMER,LabexMER Marine Excellence Research: a changing ocean(2010), Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences du Numérique de Nantes (LS2N), IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS), Combinatoire et Bioinformatique (COMBI), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), ISBlue - Interdisciplinary Graduate School for the Blue planet (2017), and ANR-17-EURE-0015,ISBlue,Interdisciplinary Graduate School for the Blue planet(2017)
Subjects: dynamic, USHANT TIDAL FRONT, SUCCESSION, [SDV]Life Sciences [q-bio], [INFO.INFO-OH]Computer Science [cs]/Other [cs.OH], fungi, GENOME SEQUENCE, BRITTANY, bacterial communities, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], ecological strategies, VARIABILITY, PHYTOPLANKTON, network, PATTERNS, ECOSYSTEM, MICROBES, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], marine front, ComputingMilieux_MISCELLANEOUS, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: Ocean frontal systems are widespread hydrological features defining the transition zone between distinct water masses. They are generally of high biological importance as they are often associated with locally enhanced primary production by phytoplankton. However, the composition of bacterial communities in the frontal zone remains poorly understood. In this study, we investigate how a coastal tidal front in Brittany (France) structures the free-living bacterioplankton communities in a spatio-temporal survey across four cruises, five stations and three depths. We used 16S rRNA gene surveys to compare bacterial community structures across 134 seawater samples and defined groups of co-varying taxa (modules) exhibiting coherent ecological patterns across space and time. We found that bacterial communities composition was strongly associated with the biogeochemical characteristics of the different water masses and that the front act as an ecological boundary for free-living bacteria. Seasonal variations in primary producers and their distribution in the water column appeared as the most salient parameters controlling heterotrophic bacteria which dominated the free-living community. Different dynamics of modules observed in this environment were strongly consistent with a partitioning of heterotrophic bacterioplankton in oligotroph and copiotroph ecological strategies. Oligotroph taxa, dominated by SAR11 Clade members, were relatively more abundant in low phytoplankton, high inorganic nutrients water masses, while copiotrophs and particularly opportunist taxa such as Tenacibaculum sp. or Pseudoalteromonas sp. reached their highest abundances during the more productive period. Overall, this study shows a remarkable coupling between bacterioplankton communities dynamics, trophic strategies, and seasonal cycles in a complex coastal environment.
Published: 2020

12. Involvement of caspase-1 in inflammasomes activation and bacterial clearance in S. aureus-infected osteoblast-like MG-63 cells

Author: Fillipe Luiz Rosa do Carmo, Vasco Azevedo, Elma Lima Leite, Nadia Berkova, David Gilot, Yves Le Loir, Michael Otto, Aurélie Nicolas, Jordane Ossemond, Martine Deplanche, Arthur Gautron, Friedrich Götz, Minh-Thu Nguyen, Science et Technologie du Lait et de l'Oeuf (STLO), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Federal University of Minas Gerais (UFMG), Institut de Génétique et Développement de Rennes (IGDR), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Paul-Ehrlich-Institute - Federal Institute for Vaccines and Biomedicines (EPI), Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES Brazil), Deutsche Forschungsgemeinschaft (DFG)German Research Foundation (DFG) [SFB766], European Union (FEDER), French Ministry of Education, Research and Innovation, Regional Council of Brittany / Region Bretagne, INRAE, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, MP GISA LONGhealth [MPP10573], United States Department of Health and Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of Allergy and Infectious Diseases (NIAID) [1 ZIA AI000904], Program Germaine de Stael, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Universidade Federal de Minas Gerais = Federal University of Minas Gerais [Belo Horizonte, Brazil] (UFMG), and Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )
Subjects: Proteases, Staphylococcus aureus, THP-1 Cells, [SDV]Life Sciences [q-bio], Interleukin-1beta, Immunology, Caspase 1, caspase-1, Biology, medicine.disease_cause, Microbiology, Cell Line, bacterial clearance, 03 medical and health sciences, Immune system, Virology, medicine, Humans, Secretion, inflammasomes, Pathogen, 030304 developmental biology, 0303 health sciences, Osteoblasts, CRISPR-Cas9 gene editing, 030306 microbiology, Osteoblast, Inflammasome, 3. Good health, medicine.anatomical_structure, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, CRISPR-Cas Systems, Gene Deletion, medicine.drug
Abstract: International audience; Staphylococcus aureus, a versatile Gram-positive bacterium, is the main cause of bone and joint infections (BJI), which are prone to recurrence. The inflammasome is an immune signaling platform that assembles after pathogen recognition. It activates proteases, most notably caspase-1 that proteolytically matures and promotes the secretion of mature IL-1 beta and IL-18. The role of inflammasomes and caspase-1 in the secretion of mature IL-1 beta and in the defence of S. aureus-infected osteoblasts has not yet been fully investigated. We show here that S. aureus-infected osteoblast-like MG-63 but not caspase-1 knock-out CASP1( -/-)MG-63 cells, which were generated using CRISPR-Cas9 technology, activate the inflammasome as monitored by the release of mature IL-1 beta. The effect was strain-dependent. The use of S. aureus deletion and complemented phenole soluble modulins (PSMs) mutants demonstrated a key role of PSMs in inflammasomes-related IL-1 beta production. Furthermore, we found that the lack of caspase-1 in CASP1( -/-)MG-63 cells impairs their defense functions, as bacterial clearance was drastically decreased in CASP1( -/-) MG-63 compared to wild-type cells. Our results demonstrate that osteoblast-like MG-63 cells play an important role in the immune response against S. aureus infection through inflammasomes activation and establish a crucial role of caspase-1 in bacterial clearance.
Published: 2020

13. Ocean acidification impacts growth and shell mineralization in juvenile abalone (Haliotis tuberculata)

Author: Philippe Dubois, Stéphanie Auzoux-Bordenave, Aïcha Badou, Sylvain Huchette, Nathalie Wessel, Sabine Roussel, Solène Avignon, Sophie G. Martin, Saloua M'Zoudi, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Sorbonne Université (SU), Biogéochimie et Ecotoxicologie (IFREMER BE), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Station de Biologie Marine de Concarneau, Direction générale déléguée à la Recherche, à l’Expertise, à la Valorisation et à l’Enseignement-Formation (DGD.REVE), Muséum national d'Histoire naturelle (MNHN)-Muséum national d'Histoire naturelle (MNHN), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université libre de Bruxelles (ULB), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), Scea France Haliotis, This work was supported in part by the ATM program 'Biomineralization' of the MNHN funded by the Ministère délégué à l’Enseignement Supérieur et à la Recherche (Paris, France) and by the ICOBio project under the program 'Acidification des Océans' funded by the Fondation pour la Recherche sur la Biodiversité (FRB) and the Ministère de la Transition Ecologique et Solidaire (MTES). We thank Dr. Chakib Djejat and Stéphane Formosa for their assistance in scanning electron microscopy (SEM, Plateau technique de Microscopie Electronique, MNHN, Paris and Concarneau, France). The Regional Council of Brittany, the General Council of Finistère, the urban community of Concarneau Cornouaille Agglomération and the European Regional Development Fund (ERDF) are acknowledged for the funding of the Sigma 300 FE-SEM of the Concarneau Marine Station, Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Service Valorisation de l'Information pour la gestion Intégrée Et la Surveillance (VIGIES), Dynamiques des Écosystèmes Côtiers (DYNECO), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, food.ingredient, Abalone, Periostracum, growth, ocean acidification, Aquatic Science, engineering.material, Biology, 010603 evolutionary biology, 01 natural sciences, Mineralization (biology), shell mineralization, chemistry.chemical_compound, food, Aquaculture, 14. Life underwater, Haliotis, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, abalone, Ecology, business.industry, 010604 marine biology & hydrobiology, Aragonite, ACL, Ocean acidification, Calcium carbonate, juvenile, chemistry, 13. Climate action, Environmental chemistry, [SDE]Environmental Sciences, engineering, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, Sciences exactes et naturelles
Abstract: International audience; Ocean acidification (OA) is a major global driver that leads to substantial changes in seawater carbonate chemistry, with potentially serious consequences for calcifying organisms. Marine shelled molluscs are ecologically and economically important species, providing essential ecosystem services and food sources for other species. Due to their physiological characteristics and their use of calcium carbonate (CaCO 3) to build their shells, molluscs are among the most vulnerable invertebrates with regard to OA, with early developmental stages being particularly sensitive to pH changes. This study investigated the effects of CO 2-induced OA on juveniles of the European abalone Haliotis tuberculata, a commercially important gastropod species. Six-month-old juvenile abalones were cultured for 3 months at four pH levels (8.1, 7.8, 7.7, 7.6) representing current and predicted near-future conditions. Survival, growth, shell microstructure, thickness, and strength were compared across the four pH treatments. After 3 months of exposure, significant reductions in juvenile shell length, weight, and strength were revealed in the pH 7.6 treatment. Scanning electron microscopy observations also revealed modified texture and porosity of the shell mineral layers as well as alterations of the periostracum at pH 7.6 which was the only treatment with an aragonite saturation state below 1. It is concluded that low pH induces both general effects on growth mechanisms and corrosion of deposited shell in H. tuberculata. This will impact both the ecological role of this species and the costs of its aquaculture.
Published: 2020

14. From platform top to adjacent deep sea: New source-to-sink insights into carbonate sediment production and transfer in the SW Indian Ocean (Glorieuses archipelago)

Author: Elda Miramontes, Samuel Toucanne, Simon Courgeon, Gwenael Jouet, Evan N. Edinger, John W. Counts, Pascal Roy, Gilbert Camoin, Stephan J. Jorry, Natalia Vázquez Riveiros, Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Unité de recherche Géosciences Marines (Ifremer) (GM), Mem Univ Newfoundland, Dept Biol, St John, NF, Canada, Partenaires INRAE, University College Dublin [Dublin] (UCD), Universität Bremen, Domaines Océaniques (LDO), Centre National de la Recherche Scientifique (CNRS)-Institut d'écologie et environnement-Observatoire des Sciences de l'Univers-Université de Brest (UBO)-Institut national des sciences de l'Univers (INSU - CNRS), Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), TOTAL [FR00006152], IFREMER, CNRSCentre National de la Recherche Scientifique (CNRS), France's 'Iles Eparses' program, CEREGE, 'Laboratoire d'Excellence' LabexMER [ANR-10-LABX-19], French Government, Regional Council of Brittany (SAD program)Region Bretagne, Memorial University of Newfoundland sabbatical research grant, NSERCNatural Sciences and Engineering Research Council of Canada, IFPEN, Universite de Rennes, Universite de Brest, UPMC, ANR-10-LABX-0019,LabexMER,LabexMER Marine Excellence Research: a changing ocean(2010), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Observatoire des Sciences de l'Univers-Institut d'écologie et environnement-Centre National de la Recherche Scientifique (CNRS), and Laboratoire Environnements Sédimentaires - Géosciences Marines (GM/LES)
Subjects: 010504 meteorology & atmospheric sciences, Carbonate platform, Carbonate budget, Structural basin, engineering.material, 010502 geochemistry & geophysics, Oceanography, 01 natural sciences, Deep sea, Paleontology, chemistry.chemical_compound, Geochemistry and Petrology, 14. Life underwater, Indian Ocean, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, geography, geography.geographical_feature_category, Continental shelf, Aragonite, Geology, Coral reef, Calciturbidite, Sedimentary basin, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, chemistry, 13. Climate action, [SDE]Environmental Sciences, engineering, Carbonate, Siliciclastic
Abstract: International audience; Over the past ten years, a huge amount of source-to-sink studies have aimed to unravel the tectonic, climatic and other processes that shape the landscape from mountains to the deep ocean. Interestingly, these studies have been mainly dedicated to siliciclastic or mixed systems, for which the connection between drainage basins, continental shelves, slope and basin environments are often well constrained. Here we present a study focusing on a source-to-sink study dedicated to a pure carbonate system, located in the SW Indian Ocean (Glorieuses archipelago). Extensive field sampling and geophysical acquisition across the carbonate platform have allowed us to estimate the composition, the lateral variability, and volumes of neritic sands deposited on the platform top. Additional seismic and bathymetric surveys across the platform interior illustrate the presence of plurimetric sandy bodies deposited along the leeward platform edge, corresponding to the export of carbonate sediments from the platform top toward the platform edge, under the influence of dominant currents and winddriven processes. High-resolution seismic, bathymetric data and sediment cores acquired along the leeward slope and basin adjacent to the carbonate platform highlight the presence of channel-levee complexes and turbiditic lobes, which have accumulated on the seafloor on top of a 250 m-thick sedimentary basin at 2000-3400 m water depth. Our study points out that carbonate sands and aragonitic mud produced on the platform top during the Holocene have been shed to the adjacent basin. We also demonstrate that this routing system was active at least throughout the last three glacial/interglacial cycles. This study has important consequences for our understanding of carbonate sedimentation processes occurring in the vicinity of isolated carbonate platforms: 1 - it highlights the role of oceanographic conditions in the distribution of sediment on a platform top and its export along the platform edge and the adjacent basin; 2 - it contributes to quantify the productivity of a carbonate platform as well as its sediment storage capacity; 3 - a first estimate of a carbonate source-to-sink system is proposed, demonstrating that 0,57 km(3) of sediments have been produced during the Holocene, 0,3 km(3) being presently stored on the platform, and the remaining having been exported to the deep basin.
Published: 2020

15. The Messinian Ebro River incision

Author: Speranta-Maria Popescu, Jean-Loup Rubino, Romain Pellen, Jean-Pierre Suc, Marina Rabineau, Christian Blanpied, Christian Gorini, Carmine Silenziario, Daniel Aslanian, Estelle Leroux, Laboratoire Géosciences Océan (LGO), Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER Centre de Bretagne), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Unité de recherche Géosciences Marines (Ifremer) (GM), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), PaleoEnvironnements et PaleobioSphere (PEPS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences de la Terre de Paris (iSTeP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Centre scientifique et Technique Jean Feger (CSTJF), TOTAL FINA ELF, This work was co-funded by a grant from the French government under the program 'Investissements d'Avenir' the 'Laboratoire d'Excellence' LabexMER (ANR-10-LABX-19), and ISBLUE (ANR-17-EURE-0015) and by a grant from the Regional Council of Brittany. It was further supported by CNRS and IFREMER, with additional support from the French Actions-Marges Program (JL Rubino & P. Unternehr) and the GRI Méditerranée (Groupement Recherche et Industrie TOTAL-UPMC)., The Data base was built thanks to the SIGEOF spanish site, to academic cruises from France including PROGRES, AM-MED-1 (Leg 1 and Leg2), SARDINIA, WESTMEDFLUX, SEEPGOL, VALSIS) and Spain. We wish to thank TOTAL and Schlumberger for giving access to the seismic data and well data used in this study. The biostratigraphic studies and re-evaluations were performed by biostratigraphers from TOTAL. The authors acknowledge the fruitful and constructive reviews by Antonio Pedrera, Agnes Maillard, Lluís Cabrera and Dennis Brown, as well as those from the editor Liviu Matenco that greatly improved the manuscript., ANR-10-LABX-0019,LabexMER,LabexMER Marine Excellence Research: a changing ocean(2010), ANR-17-EURE-0015,ISBlue,Interdisciplinary Graduate School for the Blue planet(2017), Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 010504 meteorology & atmospheric sciences, Drainage basin, 02 engineering and technology, Structural basin, Messinian Salinity Crisis, Oceanography, 01 natural sciences, Sedimentary depositional environment, Paleontology, NW Mediterranean Sea, Segmentation, Continental margin, 0202 electrical engineering, electronic engineering, information engineering, [SDU.STU.VO]Sciences of the Universe [physics]/Earth Sciences/Volcanology, Sea level, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 0105 earth and related environmental sciences, [SDU.STU.TE]Sciences of the Universe [physics]/Earth Sciences/Tectonics, Global and Planetary Change, geography, geography.geographical_feature_category, Knickpoint, Continental shelf, 020206 networking & telecommunications, NW Mediterranean, Incised-valley system, [SDU.STU.ST]Sciences of the Universe [physics]/Earth Sciences/Stratigraphy, Sedimentary rock, Ebro fluvial system, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, Geology, Sea Segmentation
Abstract: International audience; Morphological sills condition sedimentary, water and fauna exchanges between different domains. In particular, sills are crucial factors to consider during the Messinian Salinity Crisis (MSC) palaeogeographic evolution (5.97–5.33 Ma) of the NW Mediterranean area. Here we focus on the Ebro River and its up to now unexplained short Messinian onshore length (~100 km) compared to that of the Messinian Rhone River (~480 km) despite similar present-day drainage basins. Thanks to an extensive seismic and borehole dataset, we present a new interpretation of a complete 270 km long Messinian Ebro incised-valley system course underneath the present-day continental margin and bathyal basin and its related distal detrital deposits. These results favour a syn-MSC or pre-MSC opening of the (endorheic) Ebro Basin to the Mediterranean. We propose a mechanism of retrogressive erosional process, localized at structural knickpoints that shift seaward through time. This mechanism resulted in the development of the complete incised-valley system and the falling stage system tract (FSST) during the MSC sea level fall with negligible or even null retrogressive inland erosion beyond the Catalan Coastal Range. The shifting of erosion-deposition is controlled by the pre-Messinian stepwise morphology and segmentation in the Valencia, Menorca and Liguro-Provence Basins. By comparison, the Rhone system is simpler, characterized by the key role of a single knickpoint (at the shelf-break) and a steeper continental slope. Both cases highlight the relationship between kinematic, segmentation and their relative morphologies, base-level fall and erosional/depositional response particularly well expressed during the outstanding MSC associated with a huge relative sea-level drop that we measured down to -1100 m below present day sea-level.
Published: 2019

16. Stochastic Analysis of UDNs With Resource Capacity and User Scheduling

Author: Samir Saoudi, Yassine Hmamouche, Mustapha Benjillali, Lab-STICC_IMTA_CACS_COM, Laboratoire des sciences et techniques de l'information, de la communication et de la connaissance (Lab-STICC), École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-Université Bretagne Loire (UBL)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-Université Bretagne Loire (UBL)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT), Département Signal et Communications (IMT Atlantique - SC), IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Institut National des Postes et Télécommunications [Rabat] (INPT), and This work is funded by a research grant from PRACOM and the Regional Council of Brittany, France.
Subjects: [SPI]Engineering Sciences [physics], Mathematical optimization, Computational complexity theory, Computer science, Stochastic process, 0202 electrical engineering, electronic engineering, information engineering, 020206 networking & telecommunications, 02 engineering and technology, [MATH]Mathematics [math], Transmitter power output, Stochastic geometry, ComputingMilieux_MISCELLANEOUS, Scheduling (computing)
Abstract: In this paper, we investigate the impact of antenna elevation, resource capacity and user scheduling on the performance of ultra-dense networks (UDNs). Using tools from stochastic geometry (SG), we extend a recently introduced definition of coverage probability by inducing a generic thinning that can capture BSs with available resource capacity to transmit users data. Analytical results are then derived for the coverage probability and the average achievable rate, where we obtain closed-form expressions allowing to assess UDNs performance in a more tractable and meaningful fashion compared to the conventional definition of coverage probability. Moreover, we show that the average rate under the new definition requires only the computation of a two-fold numerical integral rather than a four-fold integral in the previous works, which is expected to significantly reduce computational complexity. Comparing the obtained results, we find that the impact of parameters, such as resource capacity, BS transmit power as well as the implementation complexity of scheduling schemes are irrelevant as network density increases, which suggests new insights into the role of these parameters in UDNs.
Published: 2019

17. On the physical mechanisms of the two-way coupling between a surface wave field and a circulation consisting of a roll and streak

Author: Suzuki, Nobuhiro, Helmholtz-Zentrum Geesthacht (GKSS), Laboratoire d'Océanographie Physique et Spatiale (LOPS), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), 'Laboratoire d'Excellence' LabexMER [ANR-10-LABX-19], ISblue project, 'Interdisciplinary graduate school for the blue planet' [ANR-17-EURE-0015], French government under the program 'Investissements d'Avenir'French National Research Agency (ANR), Regional Council of Brittany (SAD programme)Region Bretagne, European UnionEuropean Union (EU) [609102], Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), and ANR-17-EURE-0015,ISBlue,Interdisciplinary Graduate School for the Blue planet(2017)
Subjects: wave-turbulence interactions, surface gravity waves, general fluid mechanics, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography
Abstract: International audience; The governing equations of a surface wave field and a coexisting roll-streak circulation typical of Langmuir circulations or submesoscale frontal circulations are derived to better describe their two-way interactions. The gradients and vertical velocities of the roll-streak circulation induce wave refraction, amplitude modulation and higher-order waves. These changes then produce wave-wave nonlinear forces and divergence of the wave-induced mass transport, both of which in turn affect the circulation. To accurately represent these processes, both a wave theory and a wave-averaged theory are developed without relying on any extrapolation, any spatiotemporal mapping or an approximation that treats the wave-induced mass divergence as being concentrated at the surface. This wave theory finds seven types of current-induced higher-order wave motions. It also determines the wave dynamics such as the governing equation of the wave action density valid in the presence of the complex circulation. The evolution of the wave action density is clearly affected by the upwelling or downwelling. The new wave-averaged theory presents the governing equations of the wave-averaged circulation which satisfies the wave-averaged mass conservation. This circulation is different from the circulation considered to satisfy the mass conservation in the Craik-Leibovich theory, and the difference becomes critical when the wave field evolves due to refraction. In this case, compared to the Craik-Leibovich theory, long waves are more important and also the rolls are more weakly forced.
Published: 2019

18. Lithospheric and sublithospheric deformation under the Borborema Province of northeastern Brazil from receiver function harmonic stripping

Author: Lamarque, Gaelle, Julià, Jordi, Federal University of Rio Grande do Norte, Unité de recherche Géosciences Marines (Ifremer) (GM), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), national oil company Petrobras, Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq)National Council for Scientific and Technological Development (CNPq), Programa Nacional de Posdoutorado da Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (PNPD/CAPES), 'Laboratoire d'Excellence' LabexMer [ANR-10-LABX-19], French government under the 'Investissements d'Avenir' programFrench National Research Agency (ANR), and Regional Council of Brittany (SAD programme)Region Bretagne
Subjects: [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography
Abstract: The depth-dependent anisotropic structure of the lithosphere under the Borborema Province in northeast Brazil has been investigated via harmonic stripping of receiver functions developed at 39 stations in the region. This method retrieves the first (k=1) and second (k=2) degree harmonics of a receiver function dataset, which characterize seismic anisotropy beneath a seismic station. Anisotropic fabrics are in turn directly related to the deformation of the lithosphere from past and current tectonic processes. Our results reveal the presence of anisotropy within the crust and the lithospheric mantle throughout the entire province. Most stations in the continental interior report consistent anisotropic orientations in the crust and lithospheric mantle, suggesting a dominant northeast–southwest pervasive deformation along lithospheric-scale shear zones developed during the Brasiliano–Pan-African orogeny. Several stations aligned along a northeast–southwest trend located above the (now aborted) Mesozoic Cariri–Potiguar rift display large uncertainties for the fast-axis direction. This non-azimuthal anisotropy may be related to a complex anisotropic fabric resulting from a combination of deformation along the ancient collision between Precambrian blocks, Mesozoic extension and thermomechanical erosion dragging by sublithospheric flow. Finally, several stations along the Atlantic coast reveal depth-dependent anisotropic orientations roughly (sub)perpendicular to the margin. These results suggest a more recent overprint, probably related to the presence of frozen anisotropy in the lithosphere due to stretching and rifting during the opening of the South Atlantic.
Published: 2019

19. Influence of lactose on the formation of whey protein microparticles obtained by dry heating at alkaline pH

Author: Marie-Hélène Famelart, Elise Schong, Science et Technologie du Lait et de l'Oeuf (STLO), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Regional council of Brittany (grant N°13008651) and Regional Council of Pays de la Loire (grant n°2014- 07081) for financial support and INRA for scientific coordination (J. Leonil) through the interregional project PROFIL, managed by the BBA industrial association.
Subjects: séchage, Whey protein, Water activity, General Chemical Engineering, medicine.medical_treatment, technologie laitière, lactase, agrégat protéique, whey paste, procédé de séchage, 01 natural sciences, produit laitier, Whey protein isolate, lactose, chemistry.chemical_compound, symbols.namesake, 0404 agricultural biotechnology, protéine de lait, microparticule, 0103 physical sciences, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Browning, medicine, Food science, Lactose, Microparticle, lactosérum, 010304 chemical physics, biology, nonenzymic browning, Chemistry, Lactase, 04 agricultural and veterinary sciences, General Chemistry, protéine de lactoserum, 040401 food science, agrégation, Maillard reaction, microparticle, dairy product, réaction de maillard, biology.protein, symbols, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Food Science
Abstract: Dry heating (DH) at 100 °C of a whey protein isolate powder conditioned at pH 9.5 leads to the formation of stable, large and porous whey protein microparticles (WPM), resulting from crosslinking of proteins in the powder. The Maillard reaction (MR) is probably involved in the formation of these WPM. To confirm the role played by the MR and understand the protein changes occurring during particle formation, we analyzed the properties of the powders (such as their water activity (aw) and color) and characterized the WPM formed after 3 and 36 h of DH in powders with increasing amounts of added lactose. Adding lactose and prolonging the time of DH increased the extent of protein denaturation and the rate of formation of WPM and the yield of conversion of powder into WPM, but led to decreases in their water content. Addition of lactose also altered the kinetics of the MR, the increase in aw and the formation of WPM. The MR, as followed by powder browning, was complete within 3 h of DH irrespective of the amount of added lactose. In contrast, the increase in aw, thought to be due to progress of the MR, continued to increase from 3 to 36 h of DH. Formation of WPM went on increasing from 3 to 36 h of DH at low to medium levels of lactose, but was complete by 3 h of DH at high levels of lactose. In conclusion, the formation of WPM was not simply related to the MR and needs further investigation.
Published: 2019

20. Ecology and trophic role of Oncholaimus dyvae sp. nov. (Nematoda: Oncholaimidae) from the lucky strike hydrothermal vent field (Mid-Atlantic Ridge)

Author: Zeppilli, Daniela, Bellec, Laure, Cambon-Bonavita, Marie-Anne, Decraemer, Wilfrida, Fontaneto, Diego, Fuchs, Sandra, Gayet, Nicolas, Mandon, Perrine, Michel, Loic N., Portail, Marie, Smol, Nic, Sorensen, Martin, Vanreusel, Ann, Sarrazin, Jozée, Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER Centre de Bretagne), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Universiteit Gent = Ghent University [Belgium] (UGENT), CNR Institute of Ecosystem Study (ISE), Consiglio Nazionale delle Ricerche (CNR), IFREMER- Département Etude des Ecosystèmes Profonds (DEEP/LEP), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), University of Southern Denmark (SDU), project 'Deep-sea hYdrothermal Vent nematodes as potential source of new Antibiotics' (DYVA), project 'Prokaryote-nematode Interaction in marine extreme envirOnments: a uNiquE source for ExploRation of innovative biomedical applications' (PIONEER) - Total Fondation, Ifremer, French Government (ANR LuckyScales)French National Research Agency (ANR) [ANR-14-CE02-0008-02], 'Laboratoire d'Excellence' LabexMER [ANR-10-LABX-19], French government under the program 'Investissements d'Avenir' by a grant from the Regional Council of Brittany (SAD programme)French National Research Agency (ANR), SYNTHESYS ECEuropean Commission Joint Research Centre, and EGIDE-CAMPUS France
Subjects: Hydrothermal vents, Oncholaimus dyvae sp. nov, lcsh:Zoology, lcsh:QL1-991, Carbon and nitrogen isotopic ratios, Deep sea, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography
Abstract: International audience; Background: Nematodes are an important component of deep-sea hydrothermal vent communities, but only few nematode species are able to cope to the harsh conditions of the most active vent sites. The genus Oncholaimus is known to tolerate extreme geothermal conditions and high sulphide concentrations in shallow water hydrothermal vents, but it was only occasionally reported in deep-sea vents. In this study, we performed morphological, genetic and ecological investigations (including feeding strategies) on an abundant species of Oncholaimus recently discovered at Lucky strike vent field on the Mid-Atlantic Ridge at 1700 m water depth. Results: We described this species as Oncholaimus dyvae sp. nov.. This new species differs from all other members of the genus by the combination of the following characters: body length (up to 9 mm), the presence of a long spicule (79 mu m) with a distally pointed end, a complex pericloacal setal ornamentation with one precloacal papilla surrounded by short spines, and a body cuticule with very fine striation shortly posterior to the amphid opening. Overall, O. dyvae sp. nov. abundance increased with increasing temperature and vent emissions. Carbon isotopic ratios suggest that this species could consume both thiotroph and methanotrophic producers. Furthermore sulfur-oxidizing bacteria related to Epsilonproteobacteria and Gammaproteobacteria were detected in the cuticle, in the digestive cavity and in the intestine of O. dyvae sp. nov. suggesting a potential symbiotic association. Conclusions: This study improves our understanding of vent biology and ecology, revealing a new nematode species able to adapt and be very abundant in active vent areas due to their association with chemosynthetic micro-organisms. Faced by the rapid increase of anthropogenic pressure to access mineral resources in the deep sea, hydrothermal vents are particularly susceptible to be impacted by exploitation of seafloor massive sulfide deposits. It is necessary to document and understand vent species able to flourish in these peculiar ecosystems.
Published: 2019

21. Herbicide-related signaling in plants reveals novel insights for herbicide use strategies, environmental risk assessment and global change assessment challenges

Author: Anne-Antonella Serra, Gwenola Gouesbet, Diana Alberto, Cécile Sulmon, Ivan Couée, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Ecosphere continentale et cotiere interdisciplinary program from the Centre National de la Recherche Scientifique (CNRS, France), 'Ingenierie ecologique' interdisciplinary program from the Centre National de la Recherche Scientifique (CNRS, France), Fondation pour la recherche sur la biodiversite (FRB, France), Ministere de l'Education nationale, de l'Enseignement superieur et de la Recherche (France), regional council of Brittany (France), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), and Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Environmental Engineering, Circadian clock, activated protein-kinase, sugar-induced tolerance, planetary boundary threats, arabidopsis-thaliana, Biology, Risk Assessment, 01 natural sciences, stress responses, 03 medical and health sciences, Stress, Physiological, circadian clock, site-based resistance, Environmental Chemistry, Environmental impact assessment, Mode of action, Hormone signaling, lolium-rigidum, Waste Management and Disposal, Plant Physiological Phenomena, Environmental risk assessment, 2. Zero hunger, Herbicides, business.industry, Abiotic stress, gene-expression, Pollution, Biotechnology, amino-acid-metabolism, Crosstalk (biology), 030104 developmental biology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, Risk assessment, Signal Transduction, 010606 plant biology & botany
Abstract: International audience; Herbicide impact is usually assessed as the result of a unilinear mode of action on a specific biochemical target with a typical dose-response dynamics. Recent developments in plant molecular signaling and crosstalk between nutritional, hormonal and environmental stress cues are however revealing a more complex picture of inclusive toxicity. Herbicides induce large-scale metabolic and gene-expression effects that go far beyond the expected consequences of unilinear herbicide-target-damage mechanisms. Moreover, groundbreaking studies have revealed that herbicide action and responses strongly interact with hormone signaling pathways, with numerous regulatory protein-kinases and -phosphatases, with metabolic and circadian clock regulators and with oxidative stress signaling pathways. These interactions are likely to result in mechanisms of adjustment that can determine the level of sensitivity or tolerance to a given herbicide or to a mixture of herbicides depending on the environmental and developmental status of the plant. Such regulations can be described as rheostatic and their importance is discussed in relation with herbicide use strategies, environmental risk assessment and global change assessment challenges. (C) 2016 Elsevier B.V. All rights reserved.
Published: 2016

22. Differentiation of vegetative cells into spores: a kinetic model applied to Bacillus subtilis

Author: Anne-Gabrielle Mathot, Louis Coroller, Olivier Couvert, Matthieu Jules, Ivan Leguérinel, Emilie Gauvry, Université de Brest (UBO), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Quimper Bretagne Occidentale, and regional council of Brittany (Region Bretagne, France)
Subjects: sporulation, Gram-positive bacteria, [SDV]Life Sciences [q-bio], Bacillus cereus, Bacillus subtilis, Endospore, Applied Microbiology and Biotechnology, Models, Biological, Green fluorescent protein, 03 medical and health sciences, Sporogenesis, cellular heterogeneity, growth modeling, Bacillus licheniformis, 030304 developmental biology, Spores, Bacterial, 0303 health sciences, Ecology, Strain (chemistry), biology, Kinetic model, 030306 microbiology, Chemistry, fungi, biology.organism_classification, spore-forming bacteria, Spore, Kinetics, Biochemistry, Food Microbiology, Bacteria, Food Science, Biotechnology
Abstract: Bacterial spores are formed within vegetative cells as thick-walled bodies resistant to physical and chemical treatments which allow the persistence and dissemination of the bacterial species. Spore-forming bacteria are natural contaminants of food raw materials and sporulation can occur in many environments from farm to fork. In order to predict spore formation over time, we developed a model that describes both the kinetics of growth and the differentiation of vegetative cells into spores. The model includes a classical growth model with the addition of only two sporulation-specific parameters: the probability of each vegetative cell to sporulate, and the time needed to form a spore once the cell is committed to sporulation. The growth-sporulation model was evaluated using the spore-forming, Gram positive bacterium,Bacillus subtilisand the biological meaning of the sporulation-specific parameters was validated using a derivative strain that produces the green fluorescent protein as a marker of sporulation initiation. The model accurately describes the growth and the sporulation kinetics in different environmental conditions and further provides valuable, physiological information on the temporal abilities of vegetative cells to differentiate into spores.ImportanceThe growth-sporulation model we developed accurately describes growth and sporulation kinetics. It describes the progressive transition from vegetative cells to spores with sporulation parameters which are meaningful and relevant to the sporulation process. The first parameter is the mean time required for a vegetative cell to differentiate into a spore (i.e. the duration of the sporulation process). The second sporulation parameter is the probability of each vegetative cell forming a spore over time. This parameter assesses how efficient the sporulation process is, how fast vegetative cells sporulate and how synchronous the bacterial population is for sporulation. The model constitutes a very interesting tool to describe the growth and the sporulation kinetics in different environmental conditions and it provides qualitative information on the sporulation of a bacterial population over time.
Published: 2018
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23. Differences for traits associated with early N acquisition in a grain legume and early complementarity in grain legume–triticale mixtures

Author: Nicolas Carton, Guénaëlle Corre-Hellou, Rim Baccar, Christophe Naudin, Guillaume Piva, Corre Hellou, Guénaëlle, Institut National de la Recherche Agronomique (INRA), Université Bretagne Loire (COMUE) (UBL), Légumineuses, Ecophysiologie Végétale, Agroécologie (LEVA), Institut National de la Recherche Agronomique (INRA)-Ecole supérieure d'Agricultures d'Angers (ESA), and Europe and Regional Council of Brittany (France) within the project PROGRAILIVE carried out by the association Pole Agronomique de l'Ouest
Subjects: 0106 biological sciences, Plant Science, 01 natural sciences, Intraspecific competition, Lupinus, Root length, mineral soil N uptake, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Legume, Vegetal Biology, biology, digestive, oral, and skin physiology, Rhizotron, food and beverages, Intercropping, 04 agricultural and veterinary sciences, Triticale, biology.organism_classification, Cereal-legume intercropping, crop competitive ability, early growth, root traits, Agronomy, Shoot, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Biologie végétale, Research Article, Cereal–legume intercropping, 010606 plant biology & botany
Abstract: We grew a grain legume in rhizotrons, alone and mixed with a cereal. There were differences between some of the genotypes of the grain legume but they all demonstrated slow early growth and low ability to absorb mineral soil nitrogen compared to the cereal. The two species were complementary for nitrogen acquisition in the first 2 months of growth. Mixtures showed a higher total soil mineral nitrogen uptake than pure grain legume. Complementarity allowed higher cereal biomass production than in pure cereal, without compromising grain legume growth., Early strategies of crop growth and N acquisition can be critical for determining competitive interactions between weeds and crops. Grain legumes and especially lupins are known to be poor competitors against weeds. Grain legumes are known to have low mineral soil N uptake abilities. However, inter- and intraspecific differences in N uptake ability in relation to below-ground traits have received little attention. Our objectives were (i) to measure differences among lupins for a set of traits associated with early growth and N acquisition; (ii) to examine how this variation compares to differences between lupin and a cereal, triticale, and (iii) to assess if mixing lupin with triticale provides a higher potential than does pure lupin regarding plant biomass and mineral soil N acquisition early in the crop cycle. Lupin (12 genotypes) and triticale plants were grown separately and in mixed species pairs in a replacement design for 1 and 2 months in three rhizotron experiments. Shoot and root biomass, root length, root expansion dynamics, N2 fixation and mineral soil N uptake were measured. Differences among lupin species and genotypes regarding traits related to early growth and to mineral soil N uptake were observed, but all lupins demonstrated slow early growth and low ability to absorb mineral soil N compared to triticale. In lupin–triticale mixture, a contrast in early growth strategies between species induced a higher total soil mineral N uptake compared with pure lupin. Complementarity between lupin and triticale persisted during the second month, when interactions began. This complementarity may allow for reduced competition between species, favouring higher triticale biomass production than in pure triticale, without compromising lupin growth.
Published: 2018

24. Effect of thermal pretreatment at 70 degrees C for one hour (EU hygienization conditions) of various organic wastes on methane production under mesophilic anaerobic digestion

Author: Jean-Louis Lanoisellé, Xiaojun Liu, Claire Sabourin, Yves Lemée, Ikbel Souli, Thomas Lendormi, Ali Ferchichi, Mohamad-Amr Chamaa, Nizar Chaira, Pascal Morançais, Virginie Boy, Institut de Recherche Dupuy de Lôme (IRDL), Université de Bretagne Sud (UBS)-Université de Brest (UBO)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Centre National de la Recherche Scientifique (CNRS), University of medicine, Tunis El Manar, Laboratoire de Biotechnologie et Chimie Marines (LBCM), Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), French Ministry of National Education, Higher Education and Research, French Regional Council of Brittany, French Departmental Council of Morbihan, University of Tunis (Faculty of Sciences of Tunis), and mixed economy company LIGER (Locmine, France)
Subjects: 020209 energy, 02 engineering and technology, 010501 environmental sciences, 01 natural sciences, 7. Clean energy, Methane, experimental study, 12. Responsible consumption, chemistry.chemical_compound, Hydrolysis, 0202 electrical engineering, electronic engineering, information engineering, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, lcsh:Environmental sciences, 0105 earth and related environmental sciences, General Environmental Science, lcsh:GE1-350, hygienization, Chemistry, mesophilic anaerobic digestion, food and beverages, Pulp and paper industry, 6. Clean water, Anaerobic digestion, Wastewater, mild thermal pretreatment, Digestate, Slurry, Sewage treatment, modified Gompertz model, Mesophile
Abstract: The impact of hygienization as mild thermal pretreatment on the methane production of various organic wastes was investigated, including digestate issued from hydrolysis tank, thickened sludge from a municipal wastewater treatment plant (MWWTP sludge) and from a mixed domestic-industrial wastewater treatment plant (D-I WWTP sludge), sludge from a meat-processing plant (MP sludge), sieving rejection from a pork slaughterhouse, pork liver, cattle slurry, cattle scraping slurry and date seeds. They were thermally pretreated at 70 °C for one hour and subsequently put into AD digesters incubated at 37 °C for individual methane potential test. The modified Gompertz model was employed to evaluate the kinetic parameters of methane production curves (R2 = 0.944–0.999). The results were compared with the untreated samples. Significant enhancement of methane potentials induced by thermal treatment (p < 0.05) was observed when it comes to the pork liver (+8.6%), the slaughterhouse sieving rejection (+11.1%), the thickened MWWTP sludge (+12.5%) and the digestate issued from hydrolysis tank (+18.0%). The maximum methane production rates of the 4 substrates mentioned above were increased by thermal pretreatment as well (from 13.5% to 64%, p < 0.05). The lag time of the methane production was shortened for the digestate from hydrolysis tank and the MWWTP sludge (by 48.6% and 62.2% respectively, p < 0.05). No significant enhancement was obtained for the cattle slurry, the cattle scraping slurry and the D-I WWTP sludge. Additionally, the maximum methane production rate and the methane potential were reduced by thermal pretreatment for the MP sludge and the date seeds respectively (p < 0.05). In this paper, possible mechanisms were discussed to explain the different methane production behaviors of substrates after the mild thermal pretreatment.
Published: 2018

25. Spatial disaggregation of complex Soil Map Units at the regional scale based on soil-landscape relationships

Author: Sébastien Vincent, Christian Walter, Blandine Lemercier, Lionel Berthier, Aix-Marseille Université - Institut d'Urbanisme et d'Aménagement Régional (AMU IUAR), Aix Marseille Université (AMU), Sol Agro et hydrosystème Spatialisation (SAS), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Université européenne de Bretagne - European University of Brittany (UEB), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), French Ministry of Agriculture, Regional Council of Brittany, AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)
Subjects: Classification trees, [SDV]Life Sciences [q-bio], Soil Science, Terrain, Soil science, 010501 environmental sciences, [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, Soil-landscape ruleset, Soil map units, 01 natural sciences, Digital soil mapping, Regional scale, [INFO]Computer Science [cs], [SDU.STU.HY]Sciences of the Universe [physics]/Earth Sciences/Hydrology, Soil-landscape rule set, 0105 earth and related environmental sciences, Soil map, Soil classification, 04 agricultural and veterinary sciences, 15. Life on land, Soil type, Ancillary data, [SDE]Environmental Sciences, 040103 agronomy & agriculture, Spatial ecology, 0401 agriculture, forestry, and fisheries, Environmental science, Spatial disaggregation, Scale (map), Cartography, Soil type units
Abstract: International audience; Digital soil mapping is becoming a powerful tool to increase the spatial detail of soil information over large areas, which is essential to address agronomic and environmental issues. When it exists, information about soil is often sparse or available at a coarser resolution than required. The spatial distribution of soil at the regional scale is usually represented as a set of polygons defining Soil Map Units (SMUs), each including several Soil Type Units (STUs), which are not spatially delineated but semantically described in a database. Delineation of STUs within SMUs, i.e. spatial disaggregation of SMU, should improve the precision of soil information derived from legacy and ancillary data. The aim of this study was to predict STUs by spatially disaggregating SMUs through a decision-tree approach that considered expert knowledge about soil-landscape relationships embedded in soil databases. In a 27,376 km(2) study area in north-western France (Brittany), 434 SMUs were delineated at 1:250,000 scale, and 320 STUs, their relative area in the SMUs, and their geomorphological and geological contexts were described. A calibration dataset of points was established using stratified random sampling,(n = 352,188). To retrieve soil-landscape relationships, expert rules for soil distribution defined by soil surveyors and based on topography, parent material and waterlogging index were considered in order to allocate an STU to 83% of the calibration dataset. The calibration dataset and covariates (i.e. pedological, geological and terrain attributes; land use; airborne gamma-ray spectrometry) were then used to: build and extrapolate the decision tree using the C.5 algorithm in DSMART software. Several iterations were performed, providing a probability of occurrence of each possible STU within the study area. External validation was perforined by comparing predictions of the disaggregation procedure to available soil maps at scales of 1:25,000 or 1:50,000 and observed profiles. Overall accuracies ranged from 41 to 72%, depending on the validation method.(per pixel vs. 3 x 3 windows of pixels, per STU vs. STU grouped by semantic proximity (n = 204)). Introducing expert rules based on soil-landscape relationships to allocate STUs to calibration samples enabled production of a soil"map with clear spatial structures, yielding expected spatial patterns of soil organisation. Future work notably concerns estimating soil properties at multiple depths deriving from STU predictions, according to the GlobalSoilMap project.
Published: 2018

26. A Review of the Stable Isotope Bio-geochemistry of the Global Silicon Cycle and Its Associated Trace Elements

Author: Jill N. Sutton, Luc André, Damien Cardinal, Daniel J. Conley, Gregory F. de Souza, Jonathan Dean, Justin Dodd, Claudia Ehlert, Michael J. Ellwood, Patrick J. Frings, Patricia Grasse, Katharine Hendry, Melanie J. Leng, Panagiotis Michalopoulos, Virginia N. Panizzo, George E. A. Swann, Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Royal Museum for Central Africa [Tervuren] (RMCA), Cycles biogéochimiques marins : processus et perturbations (CYBIOM), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), Department of Geology [Lund], Lund University [Lund], Institute of Geochemistry and Petrology [ETH Zürich], Department of Earth Sciences [Swiss Federal Institute of Technology - ETH Zürich] (D-ERDW), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)- Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), University of Hull [United Kingdom], British Geological Survey [Keyworth], British Geological Survey (BGS), Northern Illinois University, Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Marine Isotope Geochemistry Group, University of Oldenburg-University of Oldenburg-Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Australian National University (ANU), GeoForschungsZentrum - Helmholtz-Zentrum Potsdam (GFZ), Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), School of Earth Sciences [Bristol], University of Bristol [Bristol], University of Nottingham, UK (UON), Hellenic Center for Marine Research (HCMR), French government under the program 'Investissements d'Avenir' Regional Council of Brittany (SAD programme) Knut and Alice Wallenberg Foundation Swedish Research Council Marie Sklodowska-Curie Research Fellowship under EU Horizon 708407 American Chemical Society Petroleum Research Fund 53798-DNI2 Institute for Chemistry and Biology of the Marine Environment (Oldenburg, Germany) Max Planck Institute for Marine Microbiology (Bremen, Germany) Royal Society UF120084 European Research Council ERC-2015-StG - 678371_ICY-LAB Collaborative Research Centre 'Climate-Biogeochemistry interactions in the Tropical Ocean' - Deutsche Forschungsgemeinschaft (DFG) 754, ANR-10-LABX-0019,LabexMER,LabexMER Marine Excellence Research: a changing ocean(2010), European Project: 294146,EC:FP7:PEOPLE,FP7-PEOPLE-2011-CIG,MUSICC(2011), European Project: 708407,H2020,H2020-MSCA-IF-2015,SOSiC(2016), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), and Hellenic Centre for Marine Research (HCMR)
Subjects: Biogeochemical cycle, 010504 meteorology & atmospheric sciences, Silicon, Geochemistry, C – N – O - Si isotopes, biogenic silica, element/Si ratios, biogeochemical cycles, silicon, chemistry.chemical_element, [PHYS.PHYS.PHYS-GEO-PH]Physics [physics]/Physics [physics]/Geophysics [physics.geo-ph], Oceanografi, hydrologi och vattenresurser, Biogenic silica, 010502 geochemistry & geophysics, 01 natural sciences, Carbon cycle, Oceanography, Hydrology and Water Resources, chemistry.chemical_compound, Silicic acid, Geosciences, Multidisciplinary, lcsh:Science, 0105 earth and related environmental sciences, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Stable isotope ratio, ACL, Trace element, Geokemi, Multidisciplinär geovetenskap, chemistry, 13. Climate action, General Earth and Planetary Sciences, Environmental science, lcsh:Q, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, C - N - O - Si isotopes, Earth (classical element)
Abstract: International audience; Silicon (Si) is the second most abundant element in the Earth's crust and is an important nutrient in the ocean. The global Si cycle plays a critical role in regulating primary productivity and carbon cycling on the continents and in the oceans. Development of the analytical tools used to study the sources, sinks, and fluxes of the global Si cycle (e.g., elemental and stable isotope ratio data for Ge, Si, Zn, etc.) have recently led to major advances in our understanding of the mechanisms and processes that constrain the cycling of Si in the modern environment and in the past. Here, we provide background on the geochemical tools that are available for studying the Si cycle and highlight our current understanding of the marine, freshwater and terrestrial systems. We place emphasis on the geochemistry (e.g., Al/Si, Ge/Si, Zn/Si, delta C-13, delta N-15, delta O-18, delta Si-30) of dissolved and biogenic Si, present case studies, such as the Silicic Acid Leakage Hypothesis, and discuss challenges associated with the development of these environmental proxies for the global Si cycle. We also discuss how each system within the global Si cycle might change over time (i.e., sources, sinks, and processes) and the potential technical and conceptual limitations that need to be considered for future studies.
Published: 2018

27. Water loss and crust formation during bread baking, part I: interpretation aided by mathematical models with highlights on the role of local porosity

Author: C. Doursat, L. Zhang, Denis Flick, Tiphaine Lucas, Fernanda Maria Vanin, Optimisation des procédés en Agriculture, Agroalimentaire et Environnement (UR OPAALE), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Université Bretagne Loire (COMUE) (UBL), Ingénierie, Procédés, Aliments (GENIAL), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), French Ministry of Research (RARE-Canal-salve) [01 P0838-01 P 0839-01 P 0840], Regional Council of Brittany, Ingénierie Procédés Aliments (GENIAL), and Institut National de la Recherche Agronomique (INRA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-AgroParisTech-Conservatoire National des Arts et Métiers [CNAM] (CNAM)
Subjects: 0106 biological sciences, porosity, water transport, baking, General Chemical Engineering, bread, Mineralogy, crust, crust thickness, 01 natural sciences, 0404 agricultural biotechnology, 010608 biotechnology, Phase (matter), Vaporization, Gaseous diffusion, drying, Physical and Theoretical Chemistry, crust density, Porosity, evaporation-condensation-diffusion, density, dough, Darcy's law, Water transport, Chemistry, Front (oceanography), 04 agricultural and veterinary sciences, Mechanics, Permeation, 040401 food science, [SDE]Environmental Sciences, water loss, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract: International audience; This study aimed to achieve greater understanding of the contributions of different mechanisms of water transport to the overall amount of water lost by bread loaves during baking. The analysis was based on simulations from a previously published baking model which takes into account heat and mass transport as well as the expansion of the gaseous phase leading to oven rise. Liquid and gaseous diffusion, convective transport through the gaseous phase (Darcy's law), and the diffusive transport of vapor (evaporation-condensation-diffusion) were considered. When only permeation (Darcy's law) prevailed, the greater the porosity of the top dough surface, the lower and slower the water loss (WL): in fact, the greater the porosity, the thicker the top area. This in turn limited the rate at which heat penetrated the top layers down to the vaporization front and slowed WL. At earlier baking times, when the ebullition temperature was not reached uniformly through the crumb, the evaporation-condensation-diffusion was involved at the same time as permeation. The water flux by evaporation-condensation-diffusion was orientated toward the dough core; it accelerated the crust thickening and slowed WL. It appeared that the higher the porosity in the crumb beneath the crust, the higher the flux by evaporation-condensation-diffusion, and the lower the WL. Local porosity variations in the crust (top surface) and the crumb beneath the crust could be reproduced experimentally by constraining the total expansion of the loaf with a permeable fabric cover. Experimental and simulated trends in WL were consistent, supporting the understanding of WL proposed.
Published: 2017

28. Gene expression variation in natural populations of hexaploid and allododecaploid Spartina species (Poaceae)

Author: Houda Chelaifa, Armel Salmon, Malika L. Aïnouche, Julie Ferreira de Carvalho, Julien Boutte, Pierre Bourdaud, Kader Ainouche, Department of Terrestrial Ecology, Netherlands Institute of Ecology, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), International Associated Laboratory 'Ecological Genomics of Polyploidy' - CNRS (INEE) [UMR CNRS 6553 Ecobio], University of Rennes 1, Iowa State University (Ames, USA), Partner University, Regional Council of Brittany, Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), and Terrestrial Ecology (TE)
Subjects: 0301 basic medicine, Candidate gene, Plant Science, Genome, 03 medical and health sciences, Quantitative PCR, Polyploid, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Gene, Hybridization, Ecology, Evolution, Behavior and Systematics, Illumina dye sequencing, 2. Zero hunger, Genetics, Spartina, Phylogenetic tree, biology, food and beverages, Allopolyploidy, Polyploid complex, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, 030104 developmental biology, international, Haplotype detection, Gene expression
Abstract: International audience; Allopolyploidy is a peculiar process entailing the cohabitation of two (or more) divergent genomes. Consequences on plant genomes are varied and can utlimately alter gene expression and regulatory interactions. Most studies have explored polyploid expression evolution in experimental controlled conditions. Here, we analyzed global gene expression variation in natural populations of the Spartina polyploid complex including hexaploid parental species (S. maritima and S. alterniflora), two F1 hybrids (S. x townsendii and S. x neyrautii) and the allododecaploid S. anglica. In situ sampling and quantitative PCR were performed for comparing global expression of candidate genes involved in responses to abiotic stresses, lignin and cellulose metabolisms between five Spartina taxa. Illumina sequencing datasets and dedicated bioinformatic pipelines were employed to explore sequence heterogeneity in these highly duplicated genomes. Levels of gene expression were significantly higher in S. alterniflora (compared to the other hexaploid parent S. maritima) for seven of the analyzed genes. Effects of both hybridization and polyploidization are detected and consistent with previous global transcriptome analyses performed on Spartina plants grown in controlled conditions. Duplicated copies present in the hybrids and the allododecaploid were successfully assigned to either one of the parental genomes. Phylogenetic analyses identified for each of the parental hexaploid species, the presence of two distinct clades including two or more expressed copies. We provide here a comprehensive gene expression study based on individuals sampled in their natural habitat and detected the superimposed effect of environmental heterogeneity, hybridization and allopolyploidy.
Published: 2017

29. μ-ViP: Customized virtual phantom for quantitative magnetic resonance micro-imaging at high magnetic field

Author: R Kovrlija, Giulio Gambarota, Hervé Saint-Jalmes, Corinne Rondeau-Mouro, Senhadji, Lotfi, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), Institut National de la Recherche Agronomique (INRA), Laboratoire Traitement du Signal et de l'Image (LTSI), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM), CRLCC Eugène Marquis (CRLCC), Regional Council of Brittany (Rennes, France) and the GIS IBISA (Infrastructures en Biologie, Santé et Agronomie, France), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: Nuclear and High Energy Physics, Micro imaging, Materials science, [SDV.IB.IMA]Life Sciences [q-bio]/Bioengineering/Imaging, Biophysics, Biochemistry, Signal, MRμI, Imaging phantom, 030218 nuclear medicine & medical imaging, 03 medical and health sciences, 0302 clinical medicine, Nuclear magnetic resonance, Optics, Quality (physics), medicine, Reference signal, [SPI.SIGNAL] Engineering Sciences [physics]/Signal and Image processing, Spectrometer, medicine.diagnostic_test, business.industry, Magnetic resonance imaging, Condensed Matter Physics, Sample (graphics), [SDV.IB.IMA] Life Sciences [q-bio]/Bioengineering/Imaging, business, [SPI.SIGNAL]Engineering Sciences [physics]/Signal and Image processing, 030217 neurology & neurosurgery, High magnetic field, Virtual phantom, MRI
Abstract: [Departement_IRSTEA]Ecotechnologies [TR1_IRSTEA]SPEE; International audience; The applications of Magnetic Resonance micro-Imaging (MRμI) cover nowadays a wide range of fields. However few of them present quantitative measurements when the sample of interest changes over time or in case of a long acquisition time. In this domain, two challenges have to be overcome: the introduction of a phantom as a reference signal and the guarantee that this signal is stable over the experiment duration while some conditions such as temperature and/or the moisture are varied. The aim of the present study was to implement a dedicated experimental set-up to generate a virtual phantom (ViP) signal in a vertical-bore 11.7 T NMR spectrometer, equipped with a micro-imaging probe. This study shows that the generation of a micro-imaging-dedicated ViP (μ-ViP) signal is of great benefit for on-line quality control of the spectrometer performance during acquisition in the case of real-time experiments. Thus, μViP represents a step towards improvement of the magnetic resonance signal quantification in small samples.
Published: 2017

30. Diversity of spoilage fungi associated with various French dairy products

Author: Florence Valence, Nicolas Frotté, Emmanuel Coton, Riccardo Baroncelli, Franck Déniel, Jérôme Mounier, Lucille Garnier, Lizaveta Auhustsinava-Galerne, Audrey Pawtowski, Science et Technologie du Lait et de l'Oeuf (STLO), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, ESIAB, Université de Brest (UBO), Regional Council of Brittany (grant no. 13008651) and Pays de la Loire (grant no. 2014-07081) for the financial support and INRA for scientific coordination (J. Leonil) through the interregional project PROFIL, managed by BBA industrial association., 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), Garnier L., Valence F., Pawtowski A., Auhustsinava-Galerne L., Frotte N., Baroncelli R., Deniel F., Coton E., and Mounier J.
Subjects: 0301 basic medicine, Preservative, sequence analysis, Food spoilage, champignon, Colony Count, Microbial, brassage génétique, conservateur naturel, chemistry.chemical_compound, contamination, Sodium Benzoate, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Food science, Penicillium antarcticum, 2. Zero hunger, Diversity, biology, food preservation, Biodiversity, General Medicine, Sorbic Acid, conservation des aliments, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, dairy product, dépôt, contamination des aliments, analyse de séquences, Cladosporium, medicine.drug, levure aliment, Food Contamination, Microbiology, produit laitier, 03 medical and health sciences, Penicillium salamii, Natamycin, food yeast, conservateur chimique, medicine, levure, Penicillium commune, diversité, food additive, additif alimentaire, Spoilage, Potassium sorbate, Fungi, biology.organism_classification, Preservative resistance, 030104 developmental biology, chemistry, Food Preservatives, Dairy Products, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Food Science
Abstract: Yeasts and molds are responsible for dairy product spoilage, resulting in significant food waste and economic losses. Yet, few studies have investigated the diversity of spoilage fungi encountered in dairy products. In the present study, 175 isolates corresponding to 105 from various spoiled dairy products and 70 originating from dairy production environments, were identified using sequencing of the ITS region, the partial β-tubulin, calmodulin and/or EFα genes, and the D1–D2 domain of the 26S rRNA gene for filamentous fungi and yeasts, respectively. Among the 41 species found in spoiled products, Penicillium commune and Penicillium bialowiezense were the most common filamentous fungi, representing around 10% each of total isolates while Meyerozyma guilliermondii and Trichosporon asahii were the most common yeasts (4.8% each of total isolates). Several species (e.g. Penicillium antarcticum, Penicillium salamii and Cladosporium phyllophilum) were identified for the first time in dairy products or their environment. In addition, numerous species were identified in both spoiled products and their corresponding dairy production environment suggesting that the latter acts as a primary source of contamination. Secondly, the resistance to chemical preservatives (sodium benzoate, calcium propionate, potassium sorbate and natamycin) of 10 fungal isolates representative of the observed biodiversity was also evaluated. Independently of the fungal species, natamycin had the lowest minimum inhibitory concentration (expressed in gram of preservative/l), followed by potassium sorbate, sodium benzoate and calcium propionate. In the tested conditions, Cladosporium halotolerans and Didymella pinodella were the most sensitive fungi while Yarrowia lipolytica and Candida parapsilosis were the most resistant towards the tested preservatives. This study provides interesting information on the occurrence of fungal contaminants in dairy products and environments that may help developing adequate strategies for fungal spoilage control.
Published: 2017

31. Lipid remodelling in the reef-building honeycomb worm, Sabellaria alveolata, reflects acclimation and local adaptation to temperature

Author: Flavia L. D. Nunes, Stanislas F. Dubois, Anna P. Muir, Fabrice Pernet, Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Biological Sciences, University of Chester, Laboratoire d'Ecologie Benthique Côtière (LEBCO), Dynamiques des Écosystèmes Côtiers (DYNECO), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratoire de Physiologie des Invertébrés (LPI), Physiologie Fonctionnelle des Organismes Marins (PFOM), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), This work was supported by a grant from the Regional Council of Brittany, from the European Funds (ERDF) and supported by the 'Laboratoire d’Excellence' LabexMER (ANR-10-LABX-19) and co-funded by a grant from the French government under the program 'Investissements d’Avenir', ANR-10-LABX-0019,LabexMER,LabexMER Marine Excellence Research: a changing ocean(2010), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Dynamiques de l'Environnement Côtier (DYNECO), and Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER Centre de Bretagne)
Subjects: 0106 biological sciences, ethanolamine, Membrane lipids, Acclimatization, 010603 evolutionary biology, 01 natural sciences, Article, Sabellaria alveolata, Membrane Lipids, thermal adaptation, Animals, phospholipids, Local adaptation, Polychaete, Multidisciplinary, biology, Ecology, 010604 marine biology & hydrobiology, ACL, membrane fluidity, homeoviscous adaptation, Temperature, Homeoviscous adaptation, Lipid metabolism, Polychaeta, fatty-acids, biology.organism_classification, Lipid Metabolism, rainbow-trout, Poikilotherm, 13. Climate action, climate-change, escherichia-coli, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, plasmalogens
Abstract: Acclimation and adaptation, which are key to species survival in a changing climate, can be observed in terms of membrane lipid composition. Remodelling membrane lipids, via homeoviscous adaptation (HVA), counteracts membrane dysfunction due to temperature in poikilotherms. In order to assess the potential for acclimation and adaptation in the honeycomb worm, Sabellaria alveolata, a reef-building polychaete that supports high biodiversity, we carried out common-garden experiments using individuals from along its latitudinal range. Individuals were exposed to a stepwise temperature increase from 15 °C to 25 °C and membrane lipid composition assessed. Our results suggest that S. alveolata was able to acclimate to higher temperatures, as observed by a decrease in unsaturation index and 20:5n-3. However, over the long-term at 25 °C, lipid composition patterns are not consistent with HVA expectations and suggest a stress response. Furthermore, unsaturation index of individuals from the two coldest sites were higher than those from the two warmest sites, with individuals from the thermally intermediate site being in-between, likely reflecting local adaptation to temperature. Therefore, lipid remodelling appears limited at the highest temperatures in S. alveolata, suggesting that individuals inhabiting warm environments may be close to their upper thermal tolerance limits and at risk in a changing climate.
Published: 2016

32. Radical-scavenging capacity of phenol fractions in the brown seaweed Ascophyllum nodosum: An electrochemical approach

Author: Nathalie Blanc, Erwan Ar Gall, Didier Hauchard, Laetitia Audibert, Institut des Sciences Chimiques de Rennes (ISCR), 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)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Écophysiologie et de Biotechnologie des Halophytes et des Algues Marines (LEBHAM), Université de Brest (UBO), This study received a financial support from the Regional Council of Brittany (PRIR n◦1125). The authors acknowledge the CEVA ('Centre d'Etudes et de Valorisation des Algues', Pleubian, Brittany, France) for its participation to PRIR n◦1125., Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and 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)
Subjects: 0106 biological sciences, DPPH, Phlorotannins, Phenol content, 01 natural sciences, Antioxidants, Analytical Chemistry, chemistry.chemical_compound, [CHIM.GENI]Chemical Sciences/Chemical engineering, Phenols, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Electrochemistry, Organic chemistry, Phenol, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Radical-scavenging, Colorimetry, Ascophyllum, Chromatography, ABTS, biology, Molecular mass, [SDE.IE]Environmental Sciences/Environmental Engineering, 010604 marine biology & hydrobiology, 010401 analytical chemistry, Free Radical Scavengers, Seaweed, biology.organism_classification, 0104 chemical sciences, chemistry, Cyclic voltammetry
Abstract: International audience; In this article, the radical-scavenging capacity of phenol fractions extracted from the brown seaweed Ascophyllum nodosum was assessed using in parallel colorimetric methods (ABTS and DPPH) and electrochemistry (cyclic voltammetry). Results obtained by the three methods correlated in the case of global fractions, whereas only ABTS and DPPH correlated when activities were expressed on a phenol basis. The successive fractions separated by both their average molecular size and their polarity exhibited activities largely dependent on their phenol content, suggesting that phlorotannins are the main anti-oxidant molecules in hydro-alcoholic extracts of A. nodosum. In addition, phenol fractions of relative low molecular weight were clearly more active than others. This work opens new opportunities to better evaluate the radical-scavenging potential of phenol pools in algae using both bi-parametric fractionating and electrochemistry.
Published: 2011

33. Immunomodulation properties of multi-species fermented milks

Author: Gwénaël Jan, Redouane Cheddani, Marie-Noelle Madec, Benoît Foligné, Stéphanie-Marie Deutsch, Jérôme Breton, Marie-Hélène Famelart, Sandrine Parayre, Joëlle Dewulf, Coline Plé, Lactic Acid Bacteria & Mucosal Immunity - CIIL, Centre d’Infection et d’Immunité de Lille (CIIL) - U1019 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Science et Technologie du Lait et de l'Oeuf (STLO), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, This work received funding from the Regional Council for Brittany via the CBB D eveloppement call for projects. The authors would like to thank 'Actalia Dairy Products' for supplying the ITG P20 strain of P. freudenreichii and Laboratoires Standa for providing the industrial starters., Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: 0301 basic medicine, Cultured Milk Products, bactérie lactique, Context (language use), immunomodulation, Microbiology, produit laitier, law.invention, 03 medical and health sciences, Probiotic, chemistry.chemical_compound, Mice, Starter, lait fermenté, law, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Animals, Humans, Food science, 2. Zero hunger, biology, Propionibacterium freudenreichii, Probiotics, Propionibacterium, food and beverages, Lactobacillaceae, biology.organism_classification, Inflammatory Bowel Diseases, Interleukin-12, anti inflammatoire, Lactic acid, Interleukin-10, 030104 developmental biology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, chemistry, propionibacteria, propionibacterium freudenreichii, Leukocytes, Mononuclear, Fermentation, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Food Science
Abstract: Dairy propionibacteria (PAB) are used as a ripening starter in combination with Lactic acid bacteria (LAB) for dairy products such as Swiss-type cheese. LAB and PAB have also been studied for their probiotic properties but little is still known about their individual and/or synergistic beneficial effects within dairy matrices. In the context of a rising incidence of Inflammatory Bowel Diseases, it has become crucial to evaluate the immunomodulatory potential of bacteria ingested in large numbers via dairy products. We therefore selected different strains and combinations of technological LAB and PAB. We determined their immunomodulatory potential by IL-10 and IL-12 induction, in human peripheral blood mononuclear cells, on either single or mixed cultures, grown on laboratory medium or directly in milk. Milk was fermented with selected anti-inflammatory strains of LAB or PAB/LAB mixed cultures and the resulting bacterial fractions were also evaluated for these properties, together with starter viability and optimum technological aspects. The most promising fermented milks were evaluated in the context of TNBS- or DSS-induced colitis in mice. The improvement in inflammatory parameters evidenced an alleviation of colitis symptoms as a result of fermented milk consumption. This effect was clearly strain-dependent and modulated by growth within a fermented dairy product. These findings offer new tools and perspectives for the development of immunomodulatory fermented dairy products for targeted populations.
Published: 2015

34. Control of nitrogen behaviour by phosphate concentration during microalgal-bacterial cultivation using digestate

Author: Nicolas Bernet, Cyril Marcilhac, Anne-Marie Pourcher, Christine Ziebal, Fabrice Béline, Bruno Sialve, Gestion environnementale et traitement biologique des déchets (UR GERE), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Université européenne de Bretagne - European University of Brittany (UEB), Laboratoire de Biotechnologie de l'Environnement [Narbonne] (LBE), 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), Regional Council of Brittany, ADEME, and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)
Subjects: community evolution, Environmental Engineering, Nitrogen, 020209 energy, Nitrogen assimilation, [SDV]Life Sciences [q-bio], chemistry.chemical_element, Bioengineering, Aquaculture, Chlorella, 02 engineering and technology, 010501 environmental sciences, 01 natural sciences, Phosphates, chemistry.chemical_compound, Species Specificity, Botany, 0202 electrical engineering, electronic engineering, information engineering, Biomass, phosphorus, Waste Management and Disposal, Scenedesmus, 0105 earth and related environmental sciences, biology, Renewable Energy, Sustainability and the Environment, Phosphorus, microalgae, General Medicine, Phosphate, biology.organism_classification, nitrification, Anaerobic digestion, chemistry, Environmental chemistry, digestate, Digestate, Nitrification
Abstract: The cultivation of microalgae with digestate supernatant is a promising process for the recovery of mineralized nutrients (P, N) from anaerobic digestion. Nevertheless, the variability of phosphorus concentration in the influent could limit this process. The impact of initial N:P ratios between 3 and 76gNgP(-1) was studied and proved no growth limitation over 14-day batch experiments even when P was depleted. Nitrogen assimilation was not affected by phosphorus concentrations and reached 10.1mgNL(-1)d(-1) whereas phosphorus removal ranged from 0.6 to 2.0mgPL(-1)d(-1). The biomass N:P ratio was found to be a function of the influent N:P ratio. Phosphorus storage by microalgae was thus confirmed. Nitrification was found to be highly dependent on the initial phosphorus concentration. The evolution of microalgae communities was also monitored and revealed the advantage of Scenedesmus over Chlorella when the media was phosphorus-depleted.
Published: 2015

35. Diffusion behavior of dextrans in dairy systems of different microstructures

Author: Juliana Valle Costa Silva, Juliane Floury, Sylvie Lortal, Science et Technologie du Lait et de l'Oeuf (STLO), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Regional Council of Brittany and from INRA Rennes, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: chemistry.chemical_classification, soluté, Work (thermodynamics), GEL, Water activity, Chemistry, Diffusion, diffusion, microstructure, Analytical chemistry, Fluorescence recovery after photobleaching, Polymer, Microstructure, produit laitier, Suspension (chemistry), Chemical engineering, Transmission electron microscopy, [SDV.IDA]Life Sciences [q-bio]/Food engineering, FRAP, suspension, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Food Science
Abstract: The diffusion of solutes through milk and milk-derived media (i.e. dairy systems) is an important factor in the transformation and stabilization of dairy products. In several polymer systems, the diffusion of solutes largely depends on the microstructure within the material. The aim of this work was to establish how the diffusion of solutes is affected by the microstructure of dairy systems. Diffusion measurements were carried out using the technique of fluorescence recovery after photobleaching (FRAP). Diffusion coefficients of a range of 8 fluorescein isothiocyanate (FITC)–dextrans (molecular weights from 4 to 2000 kDa) were measured in dairy systems. These systems had the same casein concentration (130 g kg − 1 ) and water activity but their microstructure had been altered by different treatments: heat-treatment and rennet-induced coagulation. Microstructural parameters of these systems were estimated by the image analysis of transmission electron microscopy (TEM) micrographs. The results showed that the diffusion of solutes was affected by the microstructure of dairy systems. The application of heat-treatment hindered the diffusion of all solutes (irrespective of molecular weight), whereas rennet coagulation only increased the diffusion of the larger solute molecules (> 20 kDa). At the microscopic scale, the diffusion of solutes in dairy systems was mainly explained by both the pore size within the structure and by the interface area between the solute molecules and the surrounding matrix. Larger solutes diffused faster in dairy systems with larger pore sizes and less interface area.
Published: 2015

36. Digestate color and light intensity affect nutrient removal and competition phenomena in a microalgal-bacterial ecosystem

Author: Christine Ziebal, Nicolas Bernet, Fabrice Béline, Anne-Marie Pourcher, Cyril Marcilhac, Bruno Sialve, Gestion environnementale et traitement biologique des déchets (UR GERE), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), UNIVERSITE EUROPEENNE DE BRETAGNE FRA, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Institut National de la Recherche Agronomique (INRA), Université européenne de Bretagne - European University of Brittany (UEB), Laboratoire de Biotechnologie de l'Environnement [Narbonne] (LBE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), Regional Council of Brittany, French Agency for the Environment and Energy Management (ADEME), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: 0106 biological sciences, Environmental Engineering, Light, Nitrogen, [SDV]Life Sciences [q-bio], Color, Chlorella, 010501 environmental sciences, Biology, Wastewater, 7. Clean energy, 01 natural sciences, Waste Disposal, Fluid, MICROALGAE, 010608 biotechnology, Botany, Waste Management and Disposal, Scenedesmus, 0105 earth and related environmental sciences, Water Science and Technology, Civil and Structural Engineering, AOB COMMUNITY EVOLUTION, Bacteria, Ecological Modeling, Phosphorus, Pulp and paper industry, biology.organism_classification, Pollution, DIGESTATE, Dilution, Anaerobic digestion, Light intensity, Nitrifying bacteria, Digestate, [SDE]Environmental Sciences, Nitrification, MICROALGUE
Abstract: During anaerobic digestion, nutrients are mineralized and may require post-treatment for optimum valorization. The cultivation of autotrophic microalgae using the digestate supernatant is a promising solution; however the dark color of the influent poses a serious problem. First, the color of the digestates was studied and the results obtained using three different digestates demonstrated a strong heterogeneity although their color remained rather constant over time. The digestates absorbed light over the whole visible spectrum and remained colored even after a ten-fold dilution. Secondly, the impact of light and of substrate color on the growth of Scenedesmus sp. and on nitrogen removal were assessed. These experiments led to the construction of a model for predicting the impact of influent color and light intensity on N removal. Maximum N removal (8.5 mgN- [Formula: see text] L(-1) d(-1)) was observed with an initial optical density of 0.221 and 244 μmolE m(-)² s(-1) light and the model allows to determine N removal between 15.9 and 22.7 mgN- [Formula: see text] L(-1) d(-1) in real conditions according to the dilution level of the influent and related color. Changes in the microalgae community were monitored and revealed the advantage of Chlorella over Scenedesmus under light-limitation. Additionally microalgae outcompeted nitrifying bacteria and experiments showed how microalgae become better competitors for nutrients when phosphorus is limiting. Furthermore, nitrification was limited by microalgae growth, even when P was not limiting.
Published: 2014

37. Sand dunes as migrating string

Author: Dimitri Lague, Hirofumi Niiya, Lucie Guignier, Alexandre Valance, Hiraku Nishimori, Institut de Physique de Rennes (IPR), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), Géosciences Rennes (GR), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), French Ministry of Defense (DGA), regional council of Brittany, Japan Ministry of Education, Science and Culture (Grant No. 22540391), Global COE Program 'Formation and Development of Mathematical Sciences Based on Modeling and Analysis', Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), and Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Models, Molecular, 010504 meteorology & atmospheric sciences, Pattern formation, Slip (materials science), Silicon Dioxide, 01 natural sciences, Pattern selection, Sand dune stabilization, Transverse plane, Motion, Barchan, Models, Chemical, 0103 physical sciences, Computer Simulation, Colloids, 010306 general physics, Rheology, Geomorphology, 45.70.Mg, 45.70.Qj, 47.54.−r, [PHYS.COND.CM-SCM]Physics [physics]/Condensed Matter [cond-mat]/Soft Condensed Matter [cond-mat.soft], Geology, Crest line, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences
Abstract: We develop a reduced complexity model for three-dimensional sand dunes, based on a simplified description of the longitudinal and lateral sand transport. The spatiotemporal evolution of a dune migrating over a nonerodible bed under unidirectional wind is reduced to the dynamics of its crest line, providing a simple framework for the investigation of three-dimensional dunes, such as barchan and transverse dunes. Within this model, we derive analytical solutions for barchan dunes and investigate the stability of a rectilinear transverse dune against lateral fluctuations. We show, in particular, that the latter is unstable only if the lateral transport on the dune slip face prevails over that on the upwind face. We also predict the wavelength and the characteristic time that control the subsequent evolution of an unstable transverse dune into a wavy ridge and the ultimate fragmentation into barchan dunes.
Published: 2013

38. Digital assessment of soil-salinity dynamics after a major flood in the Niger River valley

Author: Didier Michot, Issifou Adam, Christian Walter, Yadji Guero, Sol Agro et hydrosystème Spatialisation (SAS), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Université européenne de Bretagne - European University of Brittany (UEB), Fac Agron, Lab Sci Sol, Université Abdou Moumouni [Niamey], Regional Council of Brittany, Egide organization, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: Irrigation, Soil salinity, Soil test, Monitoring, [SDV]Life Sciences [q-bio], Soil Science, Soil science, Vertisol, 010501 environmental sciences, 01 natural sciences, Vertisols, 100-year flood, Soil digital mapping, Dryland salinity, Niger, 0105 earth and related environmental sciences, 2. Zero hunger, Hydrology, geography, geography.geographical_feature_category, Electrical resistivity, 04 agricultural and veterinary sciences, 15. Life on land, 6. Clean water, Leaching model, Salinity, 13. Climate action, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Environmental science, Levee
Abstract: Salinisation threatens the sustainability of irrigated paddy fields in western Africa. To reclaim saline soils and improve the management of irrigated paddy fields, it is necessary to evaluate and monitor soil salinity in space and time. Proximal soil sensing by apparent electrical resistivity (ER) measurements can help to survey soil salinity. This study aimed to assess changes in the spatial pattern of salinity in vertisols using high resolution 3D mapping at 2 dates on an 8-ha experimental site located at Kollo, Niger, along the Niger River. For each measurement campaign, the survey combined ER and electrical conductivity (EC) measurements of a 1:5 soil:water extract. This procedure was performed in May 2008 and again in March 2011 after a 100-year flood of the study area by the Niger River. EC measurements were performed on soil samples collected at 3 depths at 140 points. ER measurements were performed at 420 points at 2 and 4 depths for the first and second campaigns, respectively. We built an inference model of EC using a regression-tree method for 3 prediction depths. The predictive data were the two ER measurements, their ratio and a qualitative description of land use. The maps generated by ordinary kriging of predicted EC revealed strong lateral salinity gradients ranging from 03 to 5.0 dS/m (RMSE = 0.79-0.83 dS/m). Vertical variability in salinity was also significant and its pattern could be explained by land use, mainly irrigation intensity. In 2011, salt stocks in the upper 60 cm of the soil ranged from low stocks (
Published: 2013

39. Analysis of Allele-Specific Expression in Mouse Liver by RNA-Seq: A Comparison With Cis-eQTL Identified Using Genetic Linkage

Author: Olivier Demeure, Pierre-François Roux, Aldons J. Lusis, Anatole Ghazalpour, Atila van Nas, Sandrine Lagarrigue, Calvin Pan, Rita M. Cantor, Lisa J. Martin, Eleazar Eskin, Farhad Hormozdiari, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université européenne de Bretagne - European University of Brittany (UEB), Department of Medicine/Division of Cardiology, University of California, Department of Computer Sciences, Department of Human Genetics, Department of Microbiology, Immunology and Molecular Genetics, Funding was provided by the National Institutes of Health (NIH) grants HL28481 and HL30568 to A.J.L. F.H. and E.E. are supported by National Science Foundation grants 0513612, 0731455, 0729049, 0916676, and 1065276 and NIH grants HL080079 and DA024417. S.L. was supported by Agrocampus Ouest for her mobility at UCLA for 6 months. P.F.R was a Ph.D fellow supported by INRA and the regional council of Brittany. HD07228 provided funding for L.J.M., and AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)
Subjects: Male, Genetic Linkage, [SDV]Life Sciences [q-bio], Gene Expression, RNA-Seq, Inbred C57BL, Mice, 0302 clinical medicine, Antineoplastic Combined Chemotherapy Protocols, Allele specific, Etoposide, Genetics, 0303 health sciences, Single Nucleotide, genomic imprinting, Liver, rna-seq, Multigene Family, Female, Sequence Analysis, Biotechnology, Quantitative Trait Loci, allele-specific expression, Biology, Crosses, Investigations, Polymorphism, Single Nucleotide, DNA sequencing, 03 medical and health sciences, Genomic Imprinting, Genetic, Genetic linkage, Animals, linkage analysis, Polymorphism, Gene, Cyclophosphamide, Alleles, Crosses, Genetic, 030304 developmental biology, Sequence Analysis, RNA, Human Genome, Mice, Inbred C57BL, Expression quantitative trait loci, RNA, Prednisone, Mitoxantrone, Genomic imprinting, Parental Imprinting, 030217 neurology & neurosurgery, Developmental Biology
Abstract: We report an analysis of allele-specific expression (ASE) and parent-of-origin expression in adult mouse liver using next generation sequencing (RNA-Seq) of reciprocal crosses of heterozygous F1 mice from the parental strains C57BL/6J and DBA/2J. We found a 60% overlap between genes exhibiting ASE and putative cis-acting expression quantitative trait loci (cis-eQTL) identified in an intercross between the same strains. We discuss the various biological and technical factors that contribute to the differences. We also identify genes exhibiting parental imprinting and complex expression patterns. Our study demonstrates the importance of biological replicates to limit the number of false positives with RNA-Seq data.
Published: 2013

40. Folate-equipped nanolipoplexes mediated efficient gene transfer into human epithelial cells

Author: Tony Le Gall, Emmanuel Mornet, Céline Lainé, Pierre Lehn, Nathalie Carmoy, Tristan Montier, Remi Marianowski, Isabelle Laurent, Claude Férec, Thierry Benvegnu, Loïc Lemiègre, Génétique moléculaire et génétique épidémiologique, Université de Brest (UBO)-Institut National de la Santé et de la Recherche Médicale (INSERM), Génétique, génomique fonctionnelle et biotechnologies (UMR 1078) (GGB), Institut Brestois Santé Agro Matière (IBSAM), Université de Brest (UBO)-Université de Brest (UBO)-EFS-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut des Sciences Chimiques de Rennes (ISCR), 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), Ecologie et Evolution des Microorganismes (EEM), Université Paris Diderot - Paris 7 (UPD7)-Université Paris 13 (UP13)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Vaincre la mucoviscidose (The French Cystic Fibrosis Association), Association Francaise contre les Myopathies (The French Myopathies Association), Association de Transfusion Sanguine et de Biogenetique Gaetan Saleun (The Blood Transfusion and Biogenetics Gaetan Saleun Association), Conseil Regional de Bretagne (The Regional Council of Brittany), college francais d'ORL (The French college of Auto rhino laryngologist), EFS-Université de Brest (UBO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Brestois Santé Agro Matière (IBSAM), Université de Brest (UBO), 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), and Université Paris 13 (UP13)-Université Paris Diderot - Paris 7 (UPD7)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: folate receptors, 02 engineering and technology, cationic lipids, lcsh:Chemistry, cystic fibrosis, Mice, Cytotoxicity, Luciferases, lcsh:QH301-705.5, Spectroscopy, 0303 health sciences, General Medicine, 021001 nanoscience & nanotechnology, 3. Good health, Computer Science Applications, Trachea, Biochemistry, Folate receptor, Nasal Cavity, 0210 nano-technology, Plasmids, Cell Survival, Transgene, Blotting, Western, Gene delivery, Biology, Endocytosis, Transfection, Catalysis, Article, Viral vector, Cell Line, Inorganic Chemistry, 03 medical and health sciences, folic acid, neutral lipid nanocomplexes, Cell Line, Tumor, Animals, Humans, Luciferase, Folate Receptor 1, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Physical and Theoretical Chemistry, Molecular Biology, 030304 developmental biology, Organic Chemistry, Reproducibility of Results, epithelial cells, lcsh:Biology (General), lcsh:QD1-999, Microscopy, Fluorescence, Liposomes, Nanoparticles, Nanocarriers, HeLa Cells
Abstract: International audience; Since recombinant viral vectors have been associated with serious side effects, such as immunogenicity and oncogenicity, synthetic delivery systems represent a realistic alternative for achieving efficacy in gene therapy. A major challenge for non-viral nanocarriers is the optimization of transgene expression in the targeted cells. This goal can be achieved by fine-tuning the chemical carriers and the adding specific motifs to promote cellular penetration. Our study focuses on the development of novel folate-based complexes that contain varying quantities of folate motifs. After controlling for their physical properties, neutral folate-modified lipid formulations were compared in vitro to lipoplexes leading to comparable expression levels. In addition, no cytotoxicity was detected, unlike what was observed in the cationic controls. Mechanistically, the delivery of the transgene appeared to be, in part, due to endocytosis mediated by folate receptor targeting. This mechanism was further validated by the observation that adding free folate into the medium decreased luciferase expression by 50%. In vivo transfection with the folate-modified MM18 lipid, containing the highest amount of FA-PEG(570)-diether co-lipid (w:w; 90:10), at a neutral charge ratio, gave luciferase transgene expression. These studies indicate that modification of lipids with folate residues could enhance non-toxic, cell-specific gene delivery.
Published: 2013

41. Exposure to Phthalates and Phenols during Pregnancy and Offspring Size at Birth

Author: Manori J. Silva, Antonia M. Calafat, Christian Brambilla, Isabelle Pin, Sylvaine Cordier, Claire Philippat, Claire Petit, Marie-Aline Charles, Xiaoyun Ye, Rémy Slama, Cécile Chevrier, Marion Mortamais, Epidémiologie pronostique des cancers et affections graves, Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut d'oncologie/développement Albert Bonniot de Grenoble (INSERM U823), Université Joseph Fourier - Grenoble 1 (UJF)-CHU Grenoble-EFS-Institut National de la Santé et de la Recherche Médicale (INSERM), Neuropsychiatrie : recherche épidémiologique et clinique (PSNREC), Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Groupe d'Etude de la Reproduction Chez l'Homme et les Mammiferes (GERHM), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centers for Disease Control and Prevention [Atlanta] (CDC), Centers for Disease Control and Prevention, Bases Moléculaires de la Progression des Cancers du Poumon, Groupe de Recherche Sur Le Cancer du Poumon : Bases Moléculaires de la Progression Tumorale, Dépistage et Thérapie Génique, Institut Albert Bonniot-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Albert Bonniot-Institut National de la Santé et de la Recherche Médicale (INSERM)-Epidémiologie pronostique des cancers et affections graves, Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Santé et de la Recherche Médicale (INSERM), Département de pédiatrie, CHU Grenoble-Hôpital Michallon, Recherche en épidémiologie et biostatistique, Université Paris-Sud - Paris 11 (UP11)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de recherche en épidémiologie et santé des populations (CESP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Sud - Paris 11 (UP11)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM), Epidémiologie environnementale appliquée à la reproduction et la santé respiratoire, Université Joseph Fourier - Grenoble 1 (UJF)-CHU Grenoble-EFS-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Joseph Fourier - Grenoble 1 (UJF)-CHU Grenoble-EFS-Institut National de la Santé et de la Recherche Médicale (INSERM)-Epidémiologie pronostique des cancers et affections graves, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), la Fondation pour la Recherche Médicale, INSERM, Institut de Recherche en Santé Publique, Nestlé, French Ministry of Health, Agence Nationale de la Recherche (ANR), Université Paris-Sud, Institut de veille sanitaire (InVS), ANSES, Mutuelle Générale de l'Education Nationale, Regional Council of Brittany, Brébion, Alice, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris-Sud - Paris 11 (UP11)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut National de la Santé et de la Recherche Médicale (INSERM)-EFS-CHU Grenoble-Université Joseph Fourier - Grenoble 1 (UJF), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), and Institut National de la Santé et de la Recherche Médicale (INSERM)-EFS-CHU Grenoble-Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Santé et de la Recherche Médicale (INSERM)-EFS-CHU Grenoble-Université Joseph Fourier - Grenoble 1 (UJF)-Epidémiologie pronostique des cancers et affections graves
Subjects: Male, Health, Toxicology and Mutagenesis, Male genitalia, Physiology, phenols, 010501 environmental sciences, 01 natural sciences, Cohort Studies, chemistry.chemical_compound, Pregnancy, pregnancy exposure, Fetal growth, Birth Weight, 0303 health sciences, phthalates, Phenols toxicity, Pregnancy Outcome, Middle Aged, 3. Good health, Prenatal Exposure Delayed Effects, Maternal Exposure, Environmental Pollutants, Female, France, Adult, medicine.medical_specialty, Offspring, Birth weight, Phthalic Acids, Genitalia, Male, Biology, Young Adult, 03 medical and health sciences, Internal medicine, medicine, Humans, [SDV.EE.SANT] Life Sciences [q-bio]/Ecology, environment/Health, Phenols, urinary biomarkers, 030304 developmental biology, 0105 earth and related environmental sciences, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, Research, Infant, Newborn, Public Health, Environmental and Occupational Health, birth outcomes, medicine.disease, Endocrinology, chemistry, Case-Control Studies, fetal growth
Abstract: International audience; Background: Data concerning the effects of prenatal exposures to phthalates and phenols on fetal growth are limited in humans. Previous findings suggest possible effects of some phenols on male birth weight.Objective: Our aim was to assess the relationships between prenatal exposures to phthalates and phenols and fetal growth among male newborns.Methods: We conducted a case-control study on male malformations of the genitalia nested in two French mother-child cohorts with recruitment between 2002 and 2006. We measured, in maternal urinary samples collected between 6 and 30 gestational weeks, the concentrations (micrograms per liter) of 9 phenol (n = 191 pregnant women) and 11 phthalate metabolites (n = 287). Weight, length, and head circumference at birth were collected from maternity records. Statistical analyses were corrected for the oversampling of malformation cases.Results: Adjusted birth weight decreased by 77 g [95% confidence interval (CI): -129, -25] and by 49 g (95% CI: -86, -13) in association with a 1-unit increase in ln-transformed 2,4-dichlorophenol (DCP) and 2,5-DCP urinary concentrations, respectively. Benzophenone-3 (BP3) ln-transformed concentrations were positively associated with weight (26 g; 95% CI: -2, 54) and head circumference at birth (0.1 cm; 95% CI: 0.0, 0.2). Head circumference increased by 0.3 cm (95% CI: 0.0, 0.7) in association with a 1-unit increase in ln-transformed BPA concentration. For phthalate metabolites there was no evidence of monotonic associations with birth weight.Conclusions: Consistent with findings of a previous study, we observed evidence of an inverse association of 2,5-DCP and a positive association of BP3 with male birth weight.
Published: 2012

42. Extrapolation at regional scale of local soil knowledge using boosted classification trees: a two-step approach

Author: Blandine Lemercier, Christian Walter, Macoumba Loum, Marine Lacoste, Sol Agro et hydrosystème Spatialisation (SAS), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Sols de Bretagne, French Ministry of Agriculture, Regional Council of Brittany, Departmental Council of Cotes-d'Armor, Departmental Council of Finistere, Departmental Council of Ille-et-Vilaine, and Departmental Council of Morbihan
Subjects: [SDE.SDS]Environmental Sciences/domain_sde.sds, 010504 meteorology & atmospheric sciences, Extrapolation, Soil Science, Terrain, Soil science, 01 natural sciences, GeneralLiterature_MISCELLANEOUS, Soil drainage class, Regional scale, 0105 earth and related environmental sciences, Boosted classification tree, 2. Zero hunger, Soil map, geography, geography.geographical_feature_category, Predictive soil mapping, Bedrock, Decision tree learning, Elevation, 04 agricultural and veterinary sciences, 15. Life on land, ComputingMethodologies_PATTERNRECOGNITION, Parent material, Physical Geography, Digital soil mapping, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Environmental science, Scale (map)
Abstract: Digital soil mapping can be helpful in providing pedological information over wide areas where existing soil information is limited. The aim of this study was to predict soil properties at a regional scale by parametrizing soil-landscape models using a machine-learning method recently applied to soil science concerns: boosted classification and regression trees. To examine soil properties interdependence, a two-step approach was tested: first soil parent material (PM), including bedrock formations and superficial deposits, was predicted; then, predicted PM was included as a predictive variable to estimate natural soil drainage (SD). Others predictive variables included environmental data representing known soil-forming factors: terrain attributes (elevation, slope, profile and plan curvatures, sub-watershed hillslope length, hydrological distance from the nearest stream, aspect, relative elevation above the nearest stream and a Compound Index initially proposed by Beven and Kirkby (1979) and modified by Merot et al. (1995)), geological data, airborne gamma-ray spectrometry (K:Th ratio, deviation from mean K emissions of the related lithological unit) and landscape data (derived from remotely sensed data). The study area is located in Brittany (northwestern France) and covers 4645 km². The training dataset was constructed from existing detailed soil maps (scale 1:25,000) available for 11% of the study area. An additional set of 1148 punctual soil observations spread over the study area represented an independent validation dataset. Based on 20,000 randomly selected pixels from the training area, PM and SD were predicted with overall accuracies of 73 and 70% respectively. While calculated on punctual observations, correct agreement between prediction and observation decreased to 49% for PM and 52% for SD. Predicted PM was the most influential variable for SD prediction, illustrating the relevance of the two-step approach tested. Boosted classification tree appeared to be a particularly adequate and robust procedure for predicting soil properties. Probability of occurrence of the predicted PM was demonstrated to be a relevant indication of prediction quality, allowing distinction between well-predicted and poorly-predicted situations.
Published: 2012

43. AnnotQTL: a new tool to gather functional and comparative information on a genomic region

Author: Olivier Sallou, Colette Désert, Olivier Demeure, Sandrine Lagarrigue, Anthony Bretaudeau, Yuna Blum, Frédéric Lecerf, Génétique Animale (GARen), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Ecole Nationale Supérieure Agronomique de Rennes, AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Biological systems and models, bioinformatics and sequences (SYMBIOSE), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), 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)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria), Plateforme bioinformatique GenOuest [Rennes], Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Télécom Bretagne-CentraleSupélec, Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST-Ecole Nationale Supérieure Agronomique de Rennes, Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Applied Mathematics Department, 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 Agronomique (INRA). UMR Génétique Animale (0598)., GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, IFR140-Ecole Nationale Supérieure Agronomique de Rennes-AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Plateforme Génomique Santé Biogenouest®-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), INRA, Agrocampus Ouest, the Regional Council of Brittany, French Ministry in charge of Agriculture (DGER). Funding for open access charge: INRA., and Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST-Ecole Nationale Supérieure Agronomique de Rennes-IFR140
Subjects: genomic region, information, Candidate gene, Livestock, information scientifique, QTL, [SDV]Life Sciences [q-bio], Quantitative Trait Loci, HUGO Gene Nomenclature Committee, Genome Scan, Genomics, Computational biology, Biology, Quantitative trait locus, Genome, 03 medical and health sciences, Mice, Genetics, Ensembl, Animals, Humans, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Synteny, 0303 health sciences, Internet, 0402 animal and dairy science, Molecular Sequence Annotation, Genomic regions, 04 agricultural and veterinary sciences, Articles, 040201 dairy & animal science, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], outil informatique, annotation, gene ontology, Cattle, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Software
Abstract: Session 1 . Methods for QTL detection and Genetic Architecture Analysis; International audience; AnnotQTL is a web tool designed to aggregate functional annotations from different prominent websites by minimizing the redundancy of information. Although thousands of QTL regions have been identified in livestock species, most of them are large and contain many genes. This tool was therefore designed to assist the characterization of genes in a QTL interval region as a step towards selecting the best candidate genes. It localizes the gene to a specific region (using NCBI and Ensembl data) and adds the functional annotations available from other databases (Gene Ontology, Mammalian Phenotype, HGNC and Pubmed). Both human genome and mouse genome can be aligned with the studied region to detect synteny and segment conservation, which is useful for running inter-species comparisons of QTL locations. Finally, custom marker lists can be included in the results display to select the genes that are closest to your most significant markers. We use examples to demonstrate that in just a couple of hours, AnnotQTL is able to identify all the genes located in regions identified by a full genome scan, with some highlighted based on both location and function, thus considerably increasing the chances of finding good candidate genes. AnnotQTL is available at http://annotqtl.genouest.org.
Published: 2011

44. Regional mapping of soil parent material by machine learning based on point data

Author: Christian Walter, Marine Lacoste, Blandine Lemercier, Sol Agro et hydrosystème Spatialisation (SAS), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), French Ministry of Agriculture, regional council of Brittany, departmental council of Cotes-d'Armor, departmental council of Finistere, departmental council of Ille-et-Vilaine, departmental council of Morbihan, and ANR (Agence Nationale de la Recherche) VMCS [(ANR-08-VULN-006-01)]
Subjects: [SDE.SDS]Environmental Sciences/domain_sde.sds, 010504 meteorology & atmospheric sciences, classification tree analysis, Parent material, scales, boosted regression trees, Terrain, Machine learning, computer.software_genre, 01 natural sciences, susceptibility, Boosted, Superficial deposits, models, environmentaLandcorrelation, spatial prediction, map, Regional scale, classification tree, 0105 earth and related environmental sciences, Earth-Surface Processes, Remote sensing, Soil map, business.industry, 04 agricultural and veterinary sciences, 15. Life on land, landscape, Geologic map, gradient, Pedogenesis factor, Digital soil mapping, Loam, 040103 agronomy & agriculture, Soil parent materiaLandDigital soil mapping, 0401 agriculture, forestry, and fisheries, Artificial intelligence, Scale (map), business, computer, Geology
Abstract: A machine learning system (MART) has been used to predict soil parent material (SPM) at the regional scale with a 50-m resolution. The use of point-specific soil observations as training data was tested as a replacement for the soil maps introduced in previous studies, with the aim of generating a more even distribution of training data over the study area and reducing information uncertainty. The 27,020-km2 study area (Brittany, northwestern France) contains mainly metamorphic, igneous and sedimentary substrates. However, superficial deposits (aeolian loam, colluvial and alluvial deposits) very often represent the actual SPM and are typically under-represented in existing geological maps. In order to calibrate the predictive model, a total of 4920 point soil descriptions were used as training data along with 17 environmental predictors (terrain attributes derived from a 50-m DEM, as well as emissions of K, Th and U obtained by means of airborne gamma-ray spectrometry, geological variables at the 1:250,000 scale and land use maps obtained by remote sensing). Model predictions were then compared: i) during SPM model creation to point data not used in model calibration (internal validation), ii) to the entire point dataset (point validation), and iii) to existing detailed soil maps (external validation). The internal, point and external validation accuracy rates were 56%, 81% and 54%, respectively. Aeolian loam was one of the three most closely predicted substrates. Poor prediction results were associated with uncommon materials and areas with high geological complexity, i.e. areas where existing maps used for external validation were also imprecise. The resultant predictive map turned out to be more accurate than existing geological maps and moreover indicated surface deposits whose spatial coverage is consistent with actual knowledge of the area. This method proves quite useful in predicting SPM within areas where conventional mapping techniques might be too costly or lengthy or where soil maps are insufficient for use as training data. In addition, this method allows producing repeatable and interpretable results, whose accuracy can be assessed objectively.
Published: 2011

45. Experimental infection of SPF pigs with Actinobacillus pleuropneumoniae serotype 9 alone or in association with Mycoplasma hyopneumoniae

Author: Marcelo Gottschalk, Christelle Fablet, Corinne Marois, Hervé Morvan, François Madec, Marylène Kobisch, Laboratoire d'études et de recherches avicoles, porcines et piscicoles, Agence Française de Sécurité Sanitaire des Aliments (AFSSA), Groupe de Recherche sur les Maladies Infectieuses du Porc, Faculté de Médecine Vétérinaire, Université de Montréal (UdeM), Laboratoire de Développement et d'Analyses des Côtes d'Armor (LDA22), Ministère de l'agriculture, and The authors would like to thank the Regional Council of Brittany, the 'Comité Régional Porcin' and Boehringer Ingelheim Animal Health France, Fort Dodge Animal Health, Intervet S.A., Pfizer Animal Health and Schering-Plough Animal Health for their financial support.
Subjects: Serotype, 040301 veterinary sciences, Swine, animal diseases, Actinobacillus pleuropneumoniae serotype 9, Mycoplasmataceae, Microbiology, 0403 veterinary science, 03 medical and health sciences, Actinobacillus Infections, Mycoplasma hyopneumoniae, medicine, Animals, dual infection, Seroconversion, Actinobacillus pleuropneumoniae, Lung, ComputingMilieux_MISCELLANEOUS, Swine Diseases, 0303 health sciences, General Veterinary, biology, 030306 microbiology, Pasteurellaceae, 04 agricultural and veterinary sciences, General Medicine, SPF pigs, respiratory system, Pneumonia of Swine, Mycoplasmal, biology.organism_classification, medicine.disease, bacterial infections and mycoses, Virology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Survival Analysis, 3. Good health, respiratory tract diseases, Specific Pathogen-Free Organisms, experimental infection, Pleuropneumonia, Mollicutes, Medicine
Abstract: 23 pages; The purpose of this study was to compare in SPF pigs, the pathogenicity of an Actinobacillus pleuropneumoniae serotype 9 strain 21 (isolated from the palatine tonsils of a healthy gilt on a French nucleus pig farm, with no clinical signs or lung lesions but a highly positive reaction to A. pleuropneumoniae serotype 9 antibodies) with a pathogenic A. pleuropneumoniae strain 4915 serotype 9 (isolated in France from an outbreak of porcine pleuropneumonia). The pathogenicity of one Mycoplasma hyopneumoniae strain alone or associated with A. pleuropneumoniae strain 21 was also compared. Eight groups of 7 pigs were infected (at 6 or 10 weeks of age) and a control group was kept non-infected. Results showed that sensitivity to A. pleuropneumoniae was related to the age of the pig (6 weeks vs 10 weeks) whatever the strain. Surviving pigs infected at 6 weeks of age developed severe clinical signs, lung lesions typical of A. pleuropneumoniae and they seroconverted. In contrast, symptoms and lung lesions were almost non-existent in pigs infected with strain 21 at 10 weeks of age, but a seroconversion was observed with very high ELISA titres. These results were in accordance with those observed in the nucleus pig farm. Infection with M. hyopneumoniae alone induced typical mycoplasmal symptoms, pneumonia and seroconversion. Symptoms and lung lesions were the most noticeable in pigs infected with M. hyopneumoniae at 6 weeks of age and with A. pleuropneumoniae 4 weeks later. Our results show that the presence of A. pleuropneumoniae serotype 9 in a pig herd may be clinically unnoticed and that M. hyopneumoniae may potentiate A. pleuropneumoniae infection.
Published: 2008

46. Brain Source Localization Using a Fourth-Order Deflation Scheme

Author: Laurent Albera, D. Cosandier-Rimele, Anne Ferreol, Fabrice Wendling, Isabelle Merlet, Senhadji, Lotfi, Laboratoire Traitement du Signal et de l'Image (LTSI), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM), Thales Research and Technology [Palaiseau], THALES [France], This work was supported in part by the Regional Council of Brittany (http://www.region-bretagne.fr) and it is protected by a patent whose reference is WO 2007/057453., Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM), and THALES
Subjects: magnetoencephalography, Covariance function, [INFO.INFO-TS] Computer Science [cs]/Signal and Image Processing, Speech recognition, 0206 medical engineering, Biomedical Engineering, Higher-order statistics, 02 engineering and technology, Article, Pattern Recognition, Automated, MUSIC, symbols.namesake, Matrix (mathematics), [INFO.INFO-TS]Computer Science [cs]/Signal and Image Processing, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], 0202 electrical engineering, electronic engineering, information engineering, Humans, Diagnosis, Computer-Assisted, EEG, fourth-order (FO) statistics, sequential source localization, [MATH.MATH-ST] Mathematics [math]/Statistics [math.ST], Mathematics, [SPI.SIGNAL] Engineering Sciences [physics]/Signal and Image processing, [SDV.IB] Life Sciences [q-bio]/Bioengineering, Brain Mapping, MEG, Orientation (computer vision), [STAT.TH] Statistics [stat]/Statistics Theory [stat.TH], [SCCO.NEUR]Cognitive science/Neuroscience, [SCCO.NEUR] Cognitive science/Neuroscience, Brain, 020206 networking & telecommunications, multiple signal classification, [STAT.TH]Statistics [stat]/Statistics Theory [stat.TH], Inverse problem, 020601 biomedical engineering, Backward problem, Dependent source, Gaussian noise, symbols, [SDV.IB]Life Sciences [q-bio]/Bioengineering, Multidimensional systems, Algorithm, [SPI.SIGNAL]Engineering Sciences [physics]/Signal and Image processing, Algorithms, Fourth Order Statistics, electroencephalography
Abstract: International audience; In this paper, a high-resolution method for solving potentially ill-posed inverse problems is proposed. This method named FO-D-MUSIC allows for localization of brain current sources with unconstrained orientations from surface electroencephalographic (EEG) or magnetoencephalographic (MEG) data using spherical or realistic head geometries. The FO-D-MUSIC method is based on the following: 1) the separability of the data transfer matrix as a function of location and orientation parameters, 2) the fourth-order (FO) virtual array theory, and 3) the deflation concept extended to FO statistics accounting for the presence of potentially but not completely statistically dependent sources. Computer results display the superiority of the FO-D-MUSIC approach in different situations (very closed sources, small number of electrodes, additive Gaussian noise with unknown spatial covariance, etc.) compared to classical algorithms.
Published: 2008

47. Angioplasty simulation using ChainMail method

Author: Oscar Acosta-Tamayo, Tanguy Le Fol, Antoine Lucas, Pascal Haigron, Senhadji, Lotfi, SPIE, Laboratoire Traitement du Signal et de l'Image (LTSI), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM), Autonomous Systems Laboratory (BIOMEDIA), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), The project was supported by Regional Council of Brittany and INSERM (Institut national de la santé et de la recherche médicale)., Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: Engineering, Surgical Simulation, 020205 medical informatics, [INFO.INFO-TS] Computer Science [cs]/Signal and Image Processing, [SDV.IB.IMA]Life Sciences [q-bio]/Bioengineering/Imaging, [INFO.INFO-IM] Computer Science [cs]/Medical Imaging, Context (language use), 02 engineering and technology, minimally invasive intervention, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [INFO.INFO-TS]Computer Science [cs]/Signal and Image Processing, 0202 electrical engineering, electronic engineering, information engineering, [INFO.INFO-IM]Computer Science [cs]/Medical Imaging, Simulation, Visualization, [SPI.SIGNAL] Engineering Sciences [physics]/Signal and Image processing, [SDV.IB] Life Sciences [q-bio]/Bioengineering, Pixel, business.industry, Work (physics), Modeling, Relaxation (iterative method), 020207 software engineering, Computer assisted intervention, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, [SDV.MHEP.CSC] Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.IB.IMA] Life Sciences [q-bio]/Bioengineering/Imaging, [SDV.IB]Life Sciences [q-bio]/Bioengineering, [INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation, business, Realization (systems), Algorithm, ChainMail, [SPI.SIGNAL]Engineering Sciences [physics]/Signal and Image processing, Energy (signal processing), Pixel density, Image guided intervention
Abstract: International audience; Tackling transluminal angioplasty planning, the aim of our work is to bring, in a patient specific way, solutions to clinical problems. This work focuses on realization of simple simulation scenarios taking into account macroscopic behaviors of stenosis. It means simulating geometrical and physical data from the inflation of a balloon while integrating data from tissues analysis and parameters from virtual tool-tissues interactions. In this context, three main behaviors has been identified: soft tissues crush completely under the effect of the balloon, calcified plaques, do not admit any deformation but could move in deformable structures, the blood vessel wall undergoes consequences from compression phenomenon and tries to find its original form. We investigated the use of Chain-Mail which is based on elements linked with the others thanks to geometric constraints. Compared with time consuming methods or low realism ones, Chain-Mail methods provide a good compromise between physical and geometrical approaches. In this study, constraints are defined from pixel density from angio-CT images. The 2D method, proposed in this paper, first initializes the balloon in the blood vessel lumen. Then the balloon inflates and the moving propagation, gives an approximate reaction of tissues. Finally, a minimal energy level is calculated to locally adjust element positions, throughout elastic relaxation stage. Preliminary experimental results obtained on 2D computed tomography (CT) images (100x100 pixels) show that the method is fast enough to handle a great number of linked-element. The simulation is able to verify real-time and realistic interactions, particularly for hard and soft plaques.
Published: 2007

48. Goal-oriented Dialog as a Collaborative Subordinated Activity involving Collective Acceptance

Author: Saget, Sylvie, Guyomard, Marc, Human-machine spoken dialogue (CORDIAL), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-INRIA Rennes, Institut National de Recherche en Informatique et en Automatique (Inria)-École Nationale Supérieure des Sciences Appliquées et de Technologie (ENSSAT), This work is partially financed by the grant A3CB22 / 2004 96 70 of the regional council of Brittany., 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)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), and Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-INRIA Rennes
Subjects: FOS: Computer and information sciences, Computer Science - Computation and Language, Computer Science - Artificial Intelligence, [SHS.INFO]Humanities and Social Sciences/Library and information sciences, [SCCO.COMP]Cognitive science/Computer science, grounding, [SCCO.LING]Cognitive science/Linguistics, [INFO.INFO-CL]Computer Science [cs]/Computation and Language [cs.CL], Extern, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], Artificial Intelligence (cs.AI), social epistemic attitude, dialog modeling, [INFO.INFO-HC]Computer Science [cs]/Human-Computer Interaction [cs.HC], ddc:400, common ground, [SHS.LANGUE]Humanities and Social Sciences/Linguistics, Computation and Language (cs.CL), belief, acceptance
Abstract: International audience; Modeling dialog as a collaborative activity consists notably in specifying the content of the Conversational Common Ground and the kind of social mental state involved. In previous work (Saget, 2006), we claim that Collective Acceptance is the proper social attitude for modeling Conversational Common Ground in the particular case of goal-oriented dialog. In this paper, a formalization of Collective Acceptance is shown, besides elements in order to integrate this attitude in a rational model of dialog are provided; and finally, a model of referential acts as being part of a collaborative activity is presented. The particular case of reference has been chosen in order to exemplify our claims.
Published: 2006

49. Performance scalability of the JXTA P2P framework

Author: Mathieu Jan, Loïc Cudennec, Gabriel Antoniu, M. Duigou, Programming distributed parallel systems for large scale numerical simulation (PARIS), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Cachan (ENS Cachan)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria), Project JXTA - Sun Microsystems (JXTA), Sun Microsystems, This work has been supported by a Sun Microsystems - INRIA scientific collaboration contract (2005-2008) and by the Regional Council of Brittany, France., INRIA, Grid'5000, 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)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), and Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Cachan (ENS Cachan)-Inria Rennes – Bretagne Atlantique
Subjects: Computer science, Distributed computing, Testbed, ComputerSystemsOrganization_COMPUTER-COMMUNICATIONNETWORKS, 020206 networking & telecommunications, 02 engineering and technology, Overlay, peer-to-peer, Peer-to-peer, computer.software_genre, experimentation, peerview, Grid computing, Scalability, 0202 electrical engineering, electronic engineering, information engineering, large scale, 020201 artificial intelligence & image processing, Use case, [INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC], computer, discovery
Abstract: International audience; Features of the P2P model, such as scalability and volatility tolerance, have motivated its use in distributed systems. Several generic P2P libraries have been proposed for building distributed applications. However, very few experimental evaluations of these frameworks have been conducted, especially at large scales. Such experimental analyses are important, since they can help system designers to optimize P2P protocols and better understand the benefits of the P2P model. This is particularly important when the P2P model is applied to special use cases, such as grid computing. This paper focuses on the scalability of two main protocols proposed by the JXTA P2P platform. First, we provide a detailed description of the underlying mechanisms used by JXTA to manage its overlay and propagate messages over it: the rendezvous protocol. Second, we describe the discovery protocol used to find resources inside a JXTA network. We then report a detailed, large-scale, multi-site experimental evaluation of these protocols, using the nine clusters of the French Grid'5000 testbed.
Published: 2006

50. A practical evaluation of a data consistency protocol for efficient visualization in grid applications

Author: Sébastien Monnet, Gabriel Antoniu, Loïc Cudennec, Programming distributed parallel systems for large scale numerical simulation (PARIS), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), 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)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Cachan (ENS Cachan)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria), This work was supported by the GDS project (ACI MD - French Ministry of Research, INRIA, CNRS), by the RESPIRE project of the French National Research Agency (ARA MDMSA), by the Regional Council of Brittany and by Sun Microsystems} \thanks{Candidate to th, Grid'5000, Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Cachan (ENS Cachan)-Inria Rennes – Bretagne Atlantique
Subjects: Data consistency, business.industry, Computer science, JUXMEM, Distributed computing, Consistency model, 020206 networking & telecommunications, 02 engineering and technology, Grid, Visualization, CONSISTENCY, Consistency (database systems), Data visualization, 0202 electrical engineering, electronic engineering, information engineering, VISUALIZATION, 020201 artificial intelligence & image processing, [INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC], business, Protocol (object-oriented programming), Abstraction (linguistics)
Abstract: Selected for publication in the post-conference book; Data visualization is important in the context of grid applications, especially when successive refinements are iteratively realized based on intermediate results. We mainly focus on code coupling grid applications, structured as a set of distributed, autonomous, weakly-coupled codes. We consider the case where the codes are able to interact using the abstraction of a shared data space. In previous work, we have proposed an efficient visualization scheme by introducing a new operation called relaxed read, as an extension to the entry consistency model. This operation can efficiently take place without locking, in parallel with write operations. On the other hand, the user has to relax the consistency constraints, and accept slightly older versions of the data, whose ''freshness'' can however still be controlled. In this paper, we discuss and extensively evaluate the proposed consistency protocol, whose efficiency is clearly demonstrated by our experimental results.

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