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1. Structural and molecular basis of cross-seeding barriers in amyloids

Author: Denis Martinez, Abdelmajid Noubhani, Loren B. Andreas, Guido Pintacuda, Benjamin Bardiaux, Brice Kauffmann, Asen Daskalov, Mélanie Berbon, Antoine Loquet, Joseph S. Wall, Virginie Coustou, Nadia El Mammeri, Jan Stanek, Sven J. Saupe, Birgit Habenstein, Chimie et Biologie des Membranes et des Nanoobjets (CBMN), Université de Bordeaux (UB)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de biochimie et génétique cellulaires (IBGC), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Centre de Résonance Magnetique Nucleaire (CRMN), Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Supérieure de Chimie Physique Électronique de Lyon (CPE)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Bioinformatique structurale - Structural Bioinformatics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Européen de Chimie et Biologie (IECB), Université de Bordeaux (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Brookhaven National Laboratory [Upton, NY] (BNL), UT-Battelle, LLC-Stony Brook University [SUNY] (SBU), State University of New York (SUNY)-State University of New York (SUNY)-U.S. Department of Energy [Washington] (DOE), We acknowledge financial support from the European Research Council (ERC) under the European Unions Horizon 2020 Research and Innovation Programme (ERC-2015-CoG GA 648974 to G.P. and ERC-2015-StG GA 639020 to A.L.), IdEx Bordeaux (Chaire d’Installation to B.H., ANR-10-IDEX-03-02), the Agence Nationale de la Recherche (ANR) (ANR-14-CE09-0020-01 to A.L., ANR-13-PDOC-0017-01 to B.H. and ANR-17-CE11-0035 to S.J.S), the INCEPTION project (Programme d'investissements d'avenir/ANR-16-CONV-0005) and the CNRS (IR-RMN FR3050). J.S. and L.B.A. were supported by individual Marie Sklodowska-Curie incoming fellowships (grant agreements 661799 'COMPLEX-FAST-MAS' and 624918 'MEM-MAS'). A.D. was supported by the Nouvelle Aquitaine Regional Council., We thank the Nouvelle Aquitaine Regional Council, University of Bordeaux, and the Contrat Plan Etat-Region (CPER) CampusB Bordeaux for the acquisition of the NMR equipment. This work has benefited from the Biophysical and Structural Chemistry Platform at IECB, CNRS UMS 3033, INSERM US001., ANR-10-IDEX-0003,IDEX BORDEAUX,Initiative d'excellence de l'Université de Bordeaux(2010), ANR-14-CE09-0020,NanoSSNMR,Nanostructures biologiques et synthétiques étudiées par Résonance Magnétique Nucléaire du Solide(2014), ANR-13-PDOC-0017,SUPRAMOL,Structures d'Assemblages Supramoléculaires par RMN du Solide : le Pseudopilus du Système de Sécrétion de Type II et le Tube de Queue du Bactériophage(2013), ANR-17-CE11-0035,SFAS,Structure et fonctions de motifs amyloïdes impliqués dans la transduction du signal(2017), ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), European Project: 648974,H2020,ERC-2014-CoG,P-MEM-NMR(2015), European Project: 639020,H2020,ERC-2014-STG,Weakinteract(2015), European Project: 661799,H2020,H2020-MSCA-IF-2014,COMPLEX-fastMAS-NMR(2016), European Project: 624918,EC:FP7:PEOPLE,FP7-PEOPLE-2013-IIF,MEM-MAS(2014), École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut de Chimie du CNRS (INC)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut de Chimie du CNRS (INC)-École Supérieure Chimie Physique Électronique de Lyon-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut de Chimie du CNRS (INC)-École Supérieure Chimie Physique Électronique de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM), U.S. Department of Energy [Washington] (DOE)-UT-Battelle, LLC-Stony Brook University [SUNY] (SBU), and State University of New York (SUNY)-State University of New York (SUNY)
Subjects: 0301 basic medicine, Protein Folding, Amyloid, Prions, Prion strain, Model system, Amyloidogenic Proteins, Computational biology, Biology, 010402 general chemistry, 01 natural sciences, Models, Biological, Podospora anserina, Fungal Proteins, prion, 03 medical and health sciences, Protein Aggregates, 0302 clinical medicine, Podospora, Amino Acid Sequence, Prion protein, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Conserved Sequence, 030304 developmental biology, cross-seeding, 0303 health sciences, Multidisciplinary, food and beverages, amyloid, Biological Sciences, biology.organism_classification, Sequence identity, 0104 chemical sciences, Protein Structure, Tertiary, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Strain specificity, nuclear magnetic resonance, 030104 developmental biology, sequence to fold, Sequence Alignment, 030217 neurology & neurosurgery
Abstract: Neurodegenerative disorders are frequently associated with β-sheet-rich amyloid deposits. Amyloid-forming proteins can aggregate under different structural conformations known as strains, which can exhibit a prion-like behaviour and distinct patho-phenotypes. Precise molecular determinants defining strain specificity and cross-strain interactions (cross-seeding) are currently unknown. The HET-s prion protein from the fungus Podospora anserina represents a model system to study the fundamental properties of prion amyloids. Here, we report the amyloid prion structure of HELLF, a distant homolog of the model prion HET-s. We find that these two amyloids, sharing only 17% sequence identity, have nearly identical β-solenoid folds but lack cross-seeding ability in vivo, indicating that prion specificity can differ in extremely similar amyloid folds. We engineer the HELLF sequence to explore the limits of the sequence-to-fold conservation and to pinpoint determinants of cross-seeding and prion specificity. We find that amyloid fold conservation occurs even at an exceedingly low level of identity to HET-s (5%). Next, we derive a HELLF-based sequence, termed HEC, able to breach the cross-seeding barrier in vivo between HELLF and HET-s, unveiling determinants controlling cross-seeding at residue level. These findings show that virtually identical amyloid backbone structures might not be sufficient for cross-seeding and that critical side-chain positions could determine the seeding specificity of an amyloid fold. Our work redefines the conceptual boundaries of prion strain and shed new light on key molecular features concerning an important class of pathogenic agents.
Published: 2021
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2. Effect of a low water concentration in chloride, sodium and potassium on oocyte maturation, oocyte hydration, ovulation and egg quality in rainbow trout

Author: Julien Bobe, Sandrine Skiba-Cassy, Emilien Segret, Emilie Cardona, Frédéric Cachelou, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Viviers de Sarrance, Nutrition, Métabolisme, Aquaculture (NuMéA), Université de Pau et des Pays de l'Adour (UPPA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), This work was supported by the National Association for Technologic Research (ANRT) grant number 2018/0457, and the Nouvelle-Aquitaine regional council grant number 3379120.
Subjects: Potassium, media_common.quotation_subject, Sodium, [SDV]Life Sciences [q-bio], chemistry.chemical_element, Broodstock, Aquatic Science, Biology, Ultrasound staging, Andrology, 03 medical and health sciences, medicine, 14. Life underwater, Ovulation, Gametogenesis, 030304 developmental biology, media_common, Egg viability, 0303 health sciences, Water transport, Ion and water transport, Chemistry, 04 agricultural and veterinary sciences, Oocyte, 6. Clean water, Salinity, medicine.anatomical_structure, 040102 fisheries, 0401 agriculture, forestry, and fisheries, Non-invasive phenotyping, VisEgg
Abstract: Water salinity is an important environmental factor known to have detrimental effects on salmonid reproduction, mostly when migrating female broodfish are held in sea water. In contrast, data obtained in freshwater are scarce and the impact of low water salinity, and more specifically of low water concentrations in sodium, chloride and potassium, during reproduction in freshwater is currently unknown. For this reason, and because ion and water fluxes are critical for the final steps of the female gamete formation, including oocyte hydration and ovulation, the aim of the present study was to investigate the impact of low salinity water on final oocyte maturation, ovulation and, ultimately, on egg quality, using rainbow trout as a physiological model and relevant aquaculture species.Fish from the same commercial strain were raised either in a site characterized by low concentrations of Na+, K+, and Cl- ions in the water or in a closely located control site exhibiting higher concentration in these elements. Egg quality and duration of final oocyte maturation were investigated using innovative phenotyping tools such as automatic assessment of egg viability using the VisEgg system and non-invasive echograph-based monitoring of final oocyte maturation duration, respectively. Oocyte hydration during final oocyte maturation and after ovulation was also investigated. Finally, molecular phenotyping was performed using real-time PCR-based monitoring of several key players of final oocyte maturation and ovulation associated with ion and water transport, inflammation, proteolytic activity, and coagulation. Oocyte hydration and gene expression data were analyzed in the light of the duration of final oocyte maturation.Here we show that low water salinity (i.e., low water concentration in chloride, sodium and potassium) negatively influences final oocyte maturation, ovulation and, ultimately, egg quality. Low water salinity triggered delayed ovulation and lower oocyte viability. When investigating the impact of low water salinity on final oocyte maturation duration, individuals presenting the most severe phenotypes exhibited impaired oocyte hydration and abnormally reduced gene expression levels of several key players of the ovulatory process. While the under expression of water (i.e., aquaporins) and ion (i.e., solute carriers) transporters is consistent with impaired oocyte hydration, our observations also indicate that the overall ovulatory gene expression program is disrupted. Our results raise the question of the mechanisms underlying the negative influence of low salinity water on the dynamics of the preovulatory phase, on the control of the oocyte homeostasis, including hydration, and on the overall success of the maturation-ovulation process.HighlightsLow water salinity impairs final oocyte maturation and egg quality in rainbow troutLow water salinity induces delayed ovulation and impaired oocyte hydrationLow water salinity induces a dysregulation of several key ovulatory genesMonitoring of final oocyte maturation can be performed using ultrasound staging
Published: 2022
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3. Critical assessment of metabolism and related growth and quality traits in trout fed spirulina-supplemented plant-based diets

Author: Simon Roques, Catherine Deborde, Sandrine Skiba, Olivier Cala, Yann Marchand, Annick Moing, Benoit Fauconneau, Nutrition, Métabolisme, Aquaculture (NuMéA), Université de Pau et des Pays de l'Adour (UPPA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Phileo Lesaffre Animal Care, Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plateforme Bordeaux Metabolome, Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-MetaboHUB-Bordeaux, MetaboHUB-MetaboHUB, Centre de RMN à très hauts champs de Lyon (CRMN), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Coopérative Le Gouessant [Lamballe], This work was supported by FUI 2014 NINAqua [grant number 15008485-056 Nouvelle-Aquitaine Regional Council] and MetaboHUB [grant number ANR-11-INBS-0010]. Simon Roques was funded by 'Phileo by Lesaffre' and the French ANRT (Association Nationale Recherche Technologie). Financial support from the IR-RMN-THC Fr3050 CNRS for conducting the research is gratefully acknowledged., and ANR-11-INBS-0010,METABOHUB,Développement d'une infrastructure française distribuée pour la métabolomique dédiée à l'innovation(2011)
Subjects: [SDV]Life Sciences [q-bio], [SDV.BA]Life Sciences [q-bio]/Animal biology, Single-cell ingredient, Proton NMR, Metabolomics, spirulina, Fish nutrition, Aquatic Science, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, ComputingMilieux_MISCELLANEOUS, Plant-based diet
Abstract: International audience
Published: 2022
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4. Theoretical study of spatiotemporal focusing for in-bulk laser structuring of dielectrics

Author: B. Chimier, Paul Quinoman, Guillaume Duchateau, Centre d'Etudes Lasers Intenses et Applications (CELIA), Université de Bordeaux (UB)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), and the Aquitaine Regional Council for support and funding via the SIMULER project. This work was granted access to the HPC resources of TGCC under allocation A0030506129 made by GENCI and allocation 2017174175 made by PRACE.
Subjects: Materials science, business.industry, Laser structuring, [SPI.OPTI]Engineering Sciences [physics]/Optics / Photonic, Optoelectronics, Statistical and Nonlinear Physics, Dielectric, business, Atomic and Molecular Physics, and Optics
Abstract: International audience; For laser processing applications and creation of microstructures inside dielectric materials, focusing of a femtosecond Gaussian pulse within the bulk of these materials is commonly used. The laser energy is mainly absorbed in the focal spot due to the nonlinear feature of laser-dielectric interaction. Recently, to get further control of laser energy absorption, the spatiotemporal focusing technique, for which the pulse duration evolves in the course of propagation, has been introduced. However, spatiotemporal focusing also leads to an inclination of the wavefront, the pulse-front tilt. In this work, the influence of the pulse-front tilt on pulse propagation and interaction is studied by solving numerically the Maxwell's equations coupled to laser induced electron dynamics in dielectrics. The qualitative behavior of energy absorption, and geometric features of the resulting absorption volume are presented. By varying the laser intensity and pulse-front tilt, both the aspect ratio and symmetry of the absorption volume are changed. A simple model predicting the evolution of this aspect ratio is provided.
Published: 2022
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5. Full waveform inversion for bore reconstruction of woodwind-like instruments

Author: Samuel Rodriguez, Juliette Chabassier, Augustin Humeau, Augustin Ernoult, Modélisation et simulation de la propagation des ondes fondées sur des mesures expérimentales pour caractériser des milieux géophysiques et héliophysiques et concevoir des objets complexes (MAKUTU), Laboratoire de Mathématiques et de leurs Applications [Pau] (LMAP), Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS)-Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut Polytechnique de Bordeaux (Bordeaux INP), Institut de Mécanique et d'Ingénierie (I2M), Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Arts et Métiers Sciences et Technologies, 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), Humeau Factory, This research has been supported by the Nouvelle-Aquitaine regional council (Cofimus project)., openwind, and HESAM Université (HESAM)-HESAM Université (HESAM)
Subjects: Physics, [SPI.ACOU]Engineering Sciences [physics]/Acoustics [physics.class-ph], Acoustics in engineering. Acoustical engineering, Acoustics and Ultrasonics, Discretization, Acoustics, Linear system, Acoustics. Sound, QC221-246, Observable, Function (mathematics), 010502 geochemistry & geophysics, 01 natural sciences, Finite element method, Computer Science Applications, Speech and Hearing, Resonator, TA365-367, 0103 physical sciences, Range (statistics), openwind, Electrical and Electronic Engineering, 010301 acoustics, Electrical impedance, 0105 earth and related environmental sciences
Abstract: International audience; The internal geometry of a wind instrument can be estimated from acoustic measurements. For woodwind instruments, this involves characterizing the inner shape (bore) but also the side holes (dimensions and location). In this study, the geometric parameters are recovered by a gradient-based optimization process, which minimizes the deviation between simulated and measured linear acoustic responses of the resonator for several fingerings through an observable function. The acoustic fields are computed by solving a linear system resulting from the 1D spectral finite elements spatial discretization of the wave propagation equations (including thermo-viscous effects, radiation and side holes). The “full waveform inversion” (FWI) technique exploits the fact that the gradient of the cost function can be computed by solving the same linear system as that of the direct problem but with a different source term. The gradient is computed with better accuracy and less additional cost than with finite-difference. The dependence of the cost function on the choice of the observed quantity, the frequency range and the fingerings used, is first analyzed. Then, the FWI is used to reconstruct, from measured impedances, an elementary instrument with 14 design variables. The results, obtained in about 1 minute on a laptop, are in excellent agreement with the direct geometric measurements.
Published: 2021
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6. Health Care Students’ Knowledge of and Attitudes, Beliefs, and Practices Toward the French COVID-19 App: Cross-sectional Questionnaire Study

Author: Montagni, Ilaria, Roussel, Nicolas, Thiébaut, Rodolphe, Tzourio, Christophe, Bordeaux population health (BPH), Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM), Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria), Statistics In System biology and Translational Medicine (SISTM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)- Bordeaux population health (BPH), Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Bordeaux [Bordeaux], Conseil Régional Aquitaine, Université de Bordeaux, The i-Share team is currently supported by an unrestricted grant of the Nouvelle-Aquitaine Regional Council (Conseil Régional Nouvelle-Aquitaine, grant no. 4370420) and by the Bordeaux Initiatives d’excellence program of the University of Bordeaux(ANR-10-IDEX-03-02). The team has also received grants from Public Health France (Santé Publique France, contract no.19DPPP023-0) and the Nouvelle-Aquitaine Regional Health Agency (Agence Régionale de Santé Nouvelle-Aquitaine)., and Admin, Oskar
Subjects: Practice, Monitoring, lcsh:Public aspects of medicine, Field survey, Communication, Mobile app, COVID-19, lcsh:RA1-1270, lcsh:Computer applications to medicine. Medical informatics, Knowledge, Contact tracing, Attitude, Belief, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, lcsh:R858-859.7, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Use, Students, App, Survey
Abstract: BackgroundMany countries worldwide have developed mobile phone apps capable of supporting instantaneous contact tracing to control the COVID-19 pandemic. In France, a few people have downloaded and are using the StopCovid contact tracing app. Students in the health domain are of particular concern in terms of app uptake. Exploring their use and opinions about the app can inform improvements and diffusion of StopCovid among young people. ObjectiveThe aim of this study is to investigate health care students’ knowledge of and attitudes, beliefs, and practices (KABP) toward the StopCovid app. MethodsA field survey was conducted among 318 students at the health sciences campus of the University of Bordeaux, France, between September 25 and October 16, 2020. A quota sampling method was used, and descriptive statistics and univariate analyses were performed. ResultsOf the 318 respondents, 77.3% (n=246) had heard about the app, but only 11.3% (n=36) had downloaded it, and 4.7% (n=15) were still using it at the time of the survey. Among the 210 participants who had heard about the app but did not download it, the main reasons for not using the app were a belief that it was not effective given its limited diffusion (n=37, 17.6%), a lack of interest (n=37, 17.6%), and distrust in the data security and fear of being geolocated (n=33, 15.7%). Among the 72 students who had not heard of the app and were given a brief description of its functioning and confidentiality policy, 52.7% (n=38) said they would use it. Participants reported that the main solution for increasing the use of the app would be better communication about it (227/318, 71.4%). ConclusionsEven among health students, the contact tracing app was poorly used. The findings suggest that improved communication about its advantages and simplicity of use as well as clarifying false beliefs about it could help improve uptake.
Published: 2021
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7. Structures of Pathological and Functional Amyloids and Prions, a Solid-State NMR Perspective

Author: Jayakrishna Shenoy, Yann Fichou, Denis Martinez, Nadia El Mammeri, Brice Kauffmann, Ahmad Saad, Mathias Ferber, Gaelle Lamon, Antoine Loquet, Estelle Morvan, Asen Daskalov, Alons Lends, Mélanie Berbon, Benjamin Bardiaux, Axelle Grélard, Birgit Habenstein, Sven J. Saupe, Bardiaux, Benjamin, Structure et fonctions de motifs amyloïdes impliqués dans la transduction du signal - - SFAS2017 - ANR-17-CE11-0035 - AAPG2017 - VALID, Amyloïdes fonctionnels formés par les hydrophobines du pathogène fongique Aspergillus fumigatus - - FUNHYDRO2016 - ANR-16-CE11-0020 - AAPG2016 - VALID, Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs - - INCEPTION2016 - ANR-16-CONV-0005 - CONV - VALID, Weak interactions in self-organizations studied by NMR spectroscopy in the supramolecular solid-state - Weakinteract - - H20202015-09-01 - 2020-09-01 - 639020 - VALID, Chimie et Biologie des Membranes et des Nanoobjets (CBMN), Université de Bordeaux (UB)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Soutien à la Recherche de l'Institut Européen de Chimie Biologique, Université Sciences et Technologies - Bordeaux 1 (UB)-Institut Européen de Chimie et de Biologie-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Bioinformatique structurale - Structural Bioinformatics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut de biochimie et génétique cellulaires (IBGC), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), We acknowledge financial support from the European Research Council (ERC) under the European Unions Horizon 2020 Research and Innovation Program (ERC-2015-StG GA no. 639020 to ALo), the ANR (ANR-17-CE11-0035 to SJS and ANR-16-CE11-0020-01 to MF, GL, BB and ALo), and INCEPTION project (PIA/ANR-16-CONV-0005) to BB. AD was supported by the Nouvelle Aquitaine Regional Council. ALe was supported by the Swiss National Science Foundation for early postdoc mobility project P2EZP2_184258. This work has benefited from the facilities and expertise of the Biophysical and Structural Chemistry platform (BPCS) at IECB, CNRS UMS3033, Inserm US001, Bordeaux University., ANR-17-CE11-0035,SFAS,Structure et fonctions de motifs amyloïdes impliqués dans la transduction du signal(2017), ANR-16-CE11-0020,FUNHYDRO,Amyloïdes fonctionnels formés par les hydrophobines du pathogène fongique Aspergillus fumigatus(2016), ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), European Project: 639020,H2020,ERC-2014-STG,Weakinteract(2015), École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut de Chimie du CNRS (INC)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Européen de Chimie et de Biologie-Université Sciences et Technologies - Bordeaux 1-Institut de Chimie du CNRS (INC), and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: Conformational change, Amyloid, [SDV.BBM.BP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Neurosciences. Biological psychiatry. Neuropsychiatry, Review, Computational biology, Fibril, 03 medical and health sciences, Cellular and Molecular Neuroscience, 0302 clinical medicine, amyloid fibril, structural biology, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], [SDV.BBM.BC] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Molecular Biology, 030304 developmental biology, 0303 health sciences, Chemistry, A protein, Pathogenicity, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Structural biology, Solid-state nuclear magnetic resonance, functional amyloids, prion structure, solid-state NMR, Protein folding, 030217 neurology & neurosurgery, RC321-571, Neuroscience
Abstract: International audience; Infectious proteins or prions are a remarkable class of pathogens, where pathogenicity and infectious state correspond to conformational transition of a protein fold. The conformational change translates into the formation by the protein of insoluble amyloid aggregates, associated in humans with various neurodegenerative disorders and systemic protein-deposition diseases. The prion principle, however, is not limited to pathogenicity. While pathological amyloids (and prions) emerge from protein misfolding, a class of functional amyloids has been defined, consisting of amyloid-forming domains under natural selection and with diverse biological roles. Although of great importance, prion amyloid structures remain challenging for conventional structural biology techniques. Solid-state nuclear magnetic resonance (SSNMR) has been preferentially used to investigate these insoluble, morphologically heterogeneous aggregates with poor crystallinity. SSNMR methods have yielded a wealth of knowledge regarding the fundamentals of prion biology and have helped to solve the structures of several prion and prion-like fibrils. Here, we will review pathological and functional amyloid structures and will discuss some of the obtained structural models. We will finish the review with a perspective on integrative approaches combining solid-state NMR, electron paramagnetic resonance and cryo-electron microscopy, which can complement and extend our toolkit to structurally explore various facets of prion biology.
Published: 2021
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8. Proton-NMR Metabolomics of Rainbow Trout Fed a Plant-Based Diet Supplemented with Graded Levels of a Protein-Rich Yeast Fraction Reveal Several Metabolic Processes Involved in Growth

Author: Benoit Fauconneau, Nadège Richard, Yann Marchand, Annick Moing, Sandrine Skiba-Cassy, Catherine Deborde, Sylvain Prigent, Simon Roques, Laurence Larroquet, Biologie du fruit et pathologie (BFP), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Bordeaux (UB), Nutrition, Métabolisme, Aquaculture (NuMéA), Université de Pau et des Pays de l'Adour (UPPA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Phileo Lesaffre Animal Care, Plateforme Metabolome Bordeaux, Institut National de la Recherche Agronomique (INRA), Coopérative Le Gouessant [Lamballe], Phileo by Lesaffre, Association Nationale de la Recherche et de la Technologie, Grant No. CIFRE 2016/0775, FUI 2014 NINAqua (Nouvelle-Aquitaine Regional Council funding 15008485-056), and ANR-11-INBS-0010,METABOHUB,Développement d'une infrastructure française distribuée pour la métabolomique dédiée à l'innovation(2011)
Subjects: Magnetic Resonance Spectroscopy, [SDV]Life Sciences [q-bio], Metabolite, Medicine (miscellaneous), Saccharomyces cerevisiae, yeast, Feed conversion ratio, Fungal Proteins, 03 medical and health sciences, chemistry.chemical_compound, Betaine, Metabolomics, Animals, 14. Life underwater, Food science, Muscle, Skeletal, 030304 developmental biology, 0303 health sciences, metabolic process, Nutrition and Dietetics, Dose-Response Relationship, Drug, biology, fish nutrition, [SDV.BA]Life Sciences [q-bio]/Animal biology, Body Weight, 04 agricultural and veterinary sciences, Metabolism, Plants, biology.organism_classification, Animal Feed, metabolomics, rainbow trout, NMR, Yeast, Diet, Trout, Liver, chemistry, Oncorhynchus mykiss, Dietary Supplements, 040102 fisheries, 0401 agriculture, forestry, and fisheries, Female, Rainbow trout, Dietary Proteins, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract: Background Plant raw materials are commonly used in aquafeeds, as marine resources are unsustainable. However, full plant-based diets lead to poorer fish growth performance. Objective We aimed to understand the metabolic effects of a yeast fraction as a protein supplement in a plant-based diet and to integrate such effects with phenotypic traits as a new approach to assess the interest of this raw material. Methods Juvenile (49 g) rainbow trout (Oncorhynchus mykiss) were fed graded levels of a yeast protein-rich fraction (5% YST05, 10% YST10, 15% YST15) in a plant-based diet (PB) for 84 d. Final body weight, feed conversion ratio, and hepatosomatic and viscerosomatic indexes were measured. Plasma, liver, and muscle 1H-NMR fingerprints were analyzed with principal component analyses, and their metabolite patterns were clustered according to the yeast level to identify concomitant metabolic effects. A regression modeling approach was used to predict tissue metabolite changes from plasma fingerprints. Results In tissues, the patterns of metabolite changes followed either linear trends with the gradual inclusion of a yeast fraction (2 patterns out of 6 in muscle, 1 in liver) or quadratic trends (4 patterns in muscle, 5 in liver). Muscle aspartate and glucose (395 and 138% maximum increase in relative content compared with PB, respectively) revealing modification in energy metabolism, as well as modification of liver betaine (163% maximum increase) and muscle histidine (57% maximum decrease) related functions, indicates that the yeast fraction could improve growth in several ways. The highest correlation between measured and predicted metabolite intensities in a tissue based on plasma fingerprints was observed for betaine in liver (r = 0.80). Conclusions These findings herald a new approach to assess the plurality of metabolic effects induced by diets and establish the optimal level of raw materials. They open the way for using plasma as a noninvasive matrix in trout nutrition studies.
Published: 2020
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9. 'Gueule cassée' (facial injuries): a 3D paleotraumatology study and facial approximation of a Napoleonic soldier who died in 1812 at Königsberg during the Russian Campaign

Author: Natalia Berezina, Alexandra P. Buzhilova, Alexandr Vasil'Iev, Florent Comte, Dany Coutinho Nogueira, Hélène Coqueugniot, Olivier Dutour, Tatiana Shvedchikova, Bruno Dutailly, A. A. Khokhlov, École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL), De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (PACEA), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Ausonius-Institut de recherche sur l'Antiquité et le Moyen âge, Université Bordeaux Montaigne-Centre National de la Recherche Scientifique (CNRS), Institute of Archaeology of Russian, Russian Academy of Sciences [Moscow] (RAS), LIA K1812, Anthropology and Archaeology of the Retreat of Russia, directed by Olivier Dutour and Alexandra BuzhilovaNouvelle‐Aquitaine Regional Council in the framework of the project VIRTOS (virtothèque ostéologique de Bordeaux, directed by Olivier Dutour), and ANR-10-LABX-0052,LaScArBx,Using the world in ancient societies : processes and forms of appropriation of space in Long Time(2010)
Subjects: Archeology, medicine.medical_specialty, 060101 anthropology, History, 060102 archaeology, paleopathology, General surgery, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Mandible, Forensic anthropology, 06 humanities and the arts, Bone transplant, Paleotraumatology, 16. Peace & justice, facial approximation, Gueule cassée, Facial appearance, Viscerocranium, Anthropology, medicine, 0601 history and archaeology, Russian federation, 3D reconstruction, Paleopathology, Young male
Abstract: International audience; The invasion of Russia by the Napoleonic Grande Armée was a complete disaster. The French army was decimated during the retreat from Russia. Thousands of victims were buried in mass graves located near several cities during the retreat. One of these mass graves was discovered in in the centre of Kaliningrad (formerly Königsberg), presently the most occidental oblast of the Russian Federation. Some skeletons revealed evidence of violence related traumatic injuries. Among them, the skeleton C2 belonged to a young male, who had suffered a serious injury to the lower face. The state of post‐traumatic remodelling indicated survival of about 2 months (between more than 6 weeks and less than 3 months).The 3D reconstruction of the mandible and the maxilla contributed additional information about the injury, its cause, and treatment. This permitted pretraumatic reconstruction of the viscerocranium and mandible through the application of two new techniques: virtual osteotomy and virtual bone transplant from another individual and perform an approximation of the face (to recreate the soft tissues) of this unidentified soldier using anthropological facial approximation in three dimensions software. These results highlight the use of 3D methods in paleopathology and forensic anthropology to reconstruct traumatic facial injuries and the pretraumatic facial appearance.
Published: 2019
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10. Development of a cell-free and growth factor-free hydrogel capable of inducing angiogenesis and innervation after subcutaneous implantation

Author: Mathilde Fenelon, Marie Rosselin, Elisabeth Garanger, Joëlle Amédée, Bertrand Garbay, Hugo Oliveira, Sébastien Lecommandoux, Bruno Paiva dos Santos, Bioingénierie tissulaire (BIOTIS), Université de Bordeaux (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Chimie des Polymères Organiques (LCPO), Centre National de la Recherche Scientifique (CNRS)-Institut Polytechnique de Bordeaux-Ecole Nationale Supérieure de Chimie, de Biologie et de Physique (ENSCBP)-Université de Bordeaux (UB)-Institut de Chimie du CNRS (INC), Team 3 LCPO : Polymer Self-Assembly & Life Sciences, Centre National de la Recherche Scientifique (CNRS)-Institut Polytechnique de Bordeaux-Ecole Nationale Supérieure de Chimie, de Biologie et de Physique (ENSCBP)-Université de Bordeaux (UB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Polytechnique de Bordeaux-Ecole Nationale Supérieure de Chimie, de Biologie et de Physique (ENSCBP)-Université de Bordeaux (UB)-Institut de Chimie du CNRS (INC), BordeauxConsortium for Regenerative Medicine (BxCRM), Medical Research Foundation (FRM) Grant nb. FRM SPF20170938783, Aquitaine Regional Council (CRA) Grant nb. 2016-1R30403, Sandre, Olivier, Université de Bordeaux (UB)-Ecole Nationale Supérieure de Chimie, de Biologie et de Physique (ENSCBP)-Institut Polytechnique de Bordeaux-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and Université de Bordeaux (UB)-Ecole Nationale Supérieure de Chimie, de Biologie et de Physique (ENSCBP)-Institut Polytechnique de Bordeaux-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-Ecole Nationale Supérieure de Chimie, de Biologie et de Physique (ENSCBP)-Institut Polytechnique de Bordeaux-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Vascular Endothelial Growth Factor A, Angiogenesis, medicine.medical_treatment, Bone Morphogenetic Protein 2, Biocompatible Materials, Core Binding Factor Alpha 1 Subunit, 02 engineering and technology, Bone tissue, Biochemistry, Polyethylene Glycols, Mice, Tissue engineering, IKVAV, Neurons, Tissue Scaffolds, Chemistry, Hydrogels, elastin-like polypeptide, General Medicine, 021001 nanoscience & nanotechnology, Cell biology, Elastin-like polypeptides, Vascular endothelial growth factor A, medicine.anatomical_structure, Sp7 Transcription Factor, Self-healing hydrogels, Rheology, 0210 nano-technology, Porosity, Biotechnology, [CHIM.POLY] Chemical Sciences/Polymers, neurite outgrowth, Surface Properties, 0206 medical engineering, IKVAV peptide, Biomedical Engineering, Bone morphogenetic protein 2, osteogenesis, Prosthesis Implantation, Biomaterials, medicine, Animals, Humans, Rats, Wistar, [SDV.IB.BIO]Life Sciences [q-bio]/Bioengineering/Biomaterials, Molecular Biology, Cell Proliferation, Tissue Engineering, Growth factor, Mesenchymal stem cell, Endothelial Cells, Mesenchymal Stem Cells, 020601 biomedical engineering, Peptide Fragments, Elastin, [SDV.IB.BIO] Life Sciences [q-bio]/Bioengineering/Biomaterials, sensory neurons, [CHIM.POLY]Chemical Sciences/Polymers, Gene Expression Regulation, Angiogenesis Inducing Agents, Osteopontin, Laminin, Peptides
Abstract: International audience; Despite significant progress in the field of biomaterials for bone repair, the lack of attention to the vascular and nervous networks within bone implants could be one of the main reasons for the delayed or impaired recovery of bone defects. The design of innovative biomaterials should improve the host capacity of healing to restore a functional tissue, taking into account that the nerve systems closely interact with blood vessels in the bone tissue. The aim of this work is to develop a cell-free and growth factor-free hydrogel capable to promote angiogenesis and innervation. To this end, we have used elastin-like polypeptides (ELPs), poly(ethylene glycol) (PEG) and increasing concentrations of the adhesion peptide IKVAV (25% (w/w) representing 1.7 mM and 50% (w/w) representing 4.1 mM) to formulate and produce hydrogels. When characterized in vitro, hydrogels have fine-tunable rheological properties, microporous structure and are biocompatible. At the biological level, 50% IKVAV composition up-regulated Runx2, Osx, Spp1, Vegfa and Bmp2 in mesenchymal stromal cells and Tek in endothelial cells, and sustained the formation of long neurites in sensory neurons. When implanted subcutaneously in mice, hydrogels induced no signals of major inflammation and the 50% IKVAV composition induced higher vessel density and formation of nervous terminations in the peripheral tissue. This novel composite has important features for tissue engineering, showing higher osteogenic, angiogenic and innervation potential in vitro, being not inflammatory in vivo, and inducing angiogenesis and innervation subcutaneously. STATEMENT OF SIGNIFICANCE: One of the main limitations in the field of tissue engineering remains the sufficient vascularization and innervation during tissue repair. In this scope, the development of advanced biomaterials that can support these processes is of crucial importance. Here, we formulated different compositions of Elastin-like polypeptide-based hydrogels bearing the IKVAV adhesion sequence. These compositions showed controlled mechanical properties, and were degradable in vitro. Additionally, we could identify in vitro a composition capable to promote neurite formation and to modulate endothelial and mesenchymal stromal cells gene expression, in view of angiogenesis and osteogenesis, respectively. When tested in vivo, it showed no signs of major inflammation and induced the formation of a highly vascularized and innervated neotissue. In this sense, our approach represents a potential advance in the development of new strategies to promote tissue regeneration, taking into account both angiogenesis and innervation.
Published: 2019
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11. Dynamics of particulate organic matter in a coastal system characterized by the occurrence of marine mucilage – A stable isotope study

Author: Béatrice Lauga, Karine Charlier, Robert Duran, Joana Cavalheiro, Sabrina Bichon, Vanessa Rouaud, Thierry Pigot, Valérie David, Mathilde Monperrus, Camilla Liénart, Yolanda Del Amo, Nicolas Savoye, Nicolas Susperregui, Laboratoire de physique et chimie des nano-objets (LPCNO), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut de Chimie de Toulouse (ICT-FR 2599), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Environnements et Paléoenvironnements OCéaniques (EPOC), Observatoire aquitain des sciences de l'univers (OASU), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Pau et des Pays de l'Adour (UPPA), UMR 5805 Environnements et Paléoenvironnements Océaniques et Continentaux (EPOC), Analytical, Environmental and Geo- Chemistry, Vrije Universiteit Brussel (VUB), PERMALA-LIGA (Aquitaine Regional Council), EC2CO-DRIL MOSLIT (French national program), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut de Chimie de Toulouse (ICT), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École Pratique des Hautes Études (EPHE), and Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, Marine mucilage, Aquatic Science, Oceanography, 01 natural sciences, Water column, Particulate organic matter, Phytoplankton, [CHIM]Chemical Sciences, Coastal systems, Organic matter, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, Stable isotopes, 0105 earth and related environmental sciences, chemistry.chemical_classification, 010604 marine biology & hydrobiology, Sediment, 15. Life on land, Bay of Biscay, Annual cycle, Deposition (aerosol physics), chemistry, Mucilage, 13. Climate action, Environmental science, Bay
Abstract: International audience; In coastal systems, particulate organic matter (POM) originates from various autochthonous and allochthonous organic matter sources. Also, some coastal systems are characterized by the occurrence of large amounts of mucilaginous material of biologic origin (i.e. phytoplankton, bacteria), which aggregates and potentially traps other organisms and particles present in the water column. This study focuses on POM origin and spatio-temporal dynamics in the South-East coast of the Bay of Biscay, an area subject to mucilage occurrence. In order to investigate POM quantitative and qualitative (C and N elemental and isotopic ratios) characteristics, sampling was performed over an annual cycle at two sites experiencing different mucilage occurrence and river influence. Contribution of phytoplankton, terrestrial POM and anthropogenic POM to coastal-POM composition was calculated using a three-sources mixing model. Overall, phytoplankton dominated the coastal-POM composition at all seasons, sites and most of the depths (71.6 ± 24.2%). Terrestrial-POM contribution was moderate (22.7 ± 21.8%) and anthropogenic-POM contribution was usually negligible (5.7 ± 7.4%). Both sites mainly exhibited similar vertical and temporal variations in terms of POM origin and dynamics: terrestrial-POM contribution increased with depth and was higher in winter at all depths and in autumn in bottom waters, compared to other seasons. The main differences between both sites were related to the vertical dynamics of the terrestrial contribution to the coastal POM. Horizontal, vertical and temporal variation of POM composition was linked to processes driving the sedimentary hydrodynamics: the river flow, the direction of the river plume and events of sediment resuspension/deposition. During the study period, the mucilage occurred only as flocs (small aggregates). The mucilage was of autochthonous origin and did not trap detectable amount of allochthonous material. © 2016 Elsevier B.V.
Published: 2016
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12. Dynamics of particulate organic matter composition in coastal systems: Forcing of spatio-temporal variability at multi-systems scale

Author: Philippe Pineau, Aurore Gueux, Martine Bréret, Sophie Ferreira, Muriel Crouvoisier, Cédric Leroux, Pascal Claquin, Francois Dindinaud, Peggy Rimmelin-Maury, Camilla Liénart, Elsa Breton, Gaël Guillou, Pascal Conan, Mireille Pujo-Pay, Patrick Raimbault, Franck Petit, Béatrice Lauga, Emilie Grossteffan, Nicolas Susperregui, Michel Lafont, Paco Rodriguez Tress, Véronique Lagadec, Emmanuelle Sultan, Eric Maria, Pierre-Guy Sauriau, Yann Bozec, Julien Guillaudeau, Jézabel Lamoureux, Sandrine Geslin, Fabien Aubert, Orianne Jolly, Anne-Marie Corre, Nicolas Savoye, Maïa Durozier, Laurence Costes, Eric Feunteun, Sabrina Bichon, Stéphane L'Helguen, Eric Macé, Benoit Lebreton, Nicolas Lachaussée, Christophe Boinet, Valérie David, Vincent Marieu, Laure Mousseau, Jocelyne Caparros, Hervé Derriennic, Yolanda Del Amo, Vanessa Rouaud, Jean-Paul Lehodey, Sébastien Aubin, Robert Duran, Thierry Cariou, Nicole Garcia, Line Bourasseau, Pierre Ramond, Vincent Hanquiez, Eric Lecuyer, Jérémy Devesa, Antoine Nowaczyk, UMR 5805 Environnements et Paléoenvironnements Océaniques et Continentaux (EPOC), Observatoire aquitain des sciences de l'univers (OASU), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Dynamiques de l'Environnement Côtier (DYNECO), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Environnements et Paléoenvironnements OCéaniques (EPOC), Centre De Recherche et d'Enseignement sur les Systèmes Côtiers (CRESCO), Station marine Dinard, Centre National de la Recherche Scientifique (CNRS), LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), CHImie Marine (CHIM), 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)-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), Laboratoire d’Océanologie et de Géosciences (LOG) - UMR 8187 (LOG), Centre National de la Recherche Scientifique (CNRS)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut national des sciences de l'Univers (INSU - CNRS), Laboratoire d'Océanographie Microbienne (LOMIC), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), 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), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Nutrition et Neurobiologie intégrée (NutriNeuro), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1-Institut Polytechnique de Bordeaux-Ecole nationale supérieure de chimie, biologie et physique, Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Observatoire océanologique de Villefranche-sur-mer (OOVM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-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 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), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'océanographie et de biogéochimie (LOB), Université de la Méditerranée - Aix-Marseille 2-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Centre de recherches en environnement côtier (CREC), Université de Caen Normandie (UNICAEN), Institut des Milieux Aquatiques, PERMALA-LIGA, funded by the Aquitaine Regional Council, EC2CO-DRIL MOSLIT, Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École Pratique des Hautes Études (EPHE), 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), LIttoral ENvironnement et Sociétés (LIENSs), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS), 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 national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Institut national des sciences de l'Univers (INSU - CNRS)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Nord]), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Fédération de recherche de Roscoff (FR2424), 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), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB)-Institut Polytechnique de Bordeaux-Ecole nationale supérieure de chimie, biologie et physique, 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), Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut de Recherche pour le Développement (IRD), Analytical, Environmental and Geo- Chemistry, Vrije Universiteit [Brussels] (VUB), LIttoral ENvironnement et Sociétés - UMR 7266 (LIENSs), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université de Lille-Université du Littoral Côte d'Opale-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Institut Universitaire Européen de la Mer (IUEM), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Nutrition et Neurobiologie intégrée (NutriNeur0), Ecole nationale supérieure de chimie, biologie et physique-Institut Polytechnique de Bordeaux-Université Sciences et Technologies - Bordeaux 1-Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Evolution des Systèmes Naturels et Modifiés (LESNM), Muséum national d'Histoire naturelle (MNHN)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Centre de recherche et d'enseignement des systèmes côtiers (CRESCO), Muséum national d'Histoire naturelle (MNHN), UMS 3113, Institut Universitaire Européen de la Mer (IUEM), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO), Qualité des eaux et prévention des pollutions (UR QELY), Centre national du machinisme agricole, du génie rural, des eaux et forêts (CEMAGREF), Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD), Station Marine, Université de Lille, Sciences et Technologies-PRES Université Lille Nord de France-Centre National de la Recherche Scientifique (CNRS), Sorbonne Universités, Centre d'Analyse et d'Intervention Sociologiques (CADIS), École des hautes études en sciences sociales (EHESS)-Centre National de la Recherche Scientifique (CNRS), EMBIO, Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD), Laboratoire Biens, Normes, Contrats (LBNC), Avignon Université (AU), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Pau et des Pays de l'Adour (UPPA), Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Pau et des Pays de l'Adour (UPPA), 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)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, Environmental forcing, Forcing (mathematics), Aquatic Science, 01 natural sciences, Water column, Particulate organic matter, Phytoplankton, medicine, Coastal systems, 14. Life underwater, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, ComputingMilieux_MISCELLANEOUS, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 0105 earth and related environmental sciences, Trophic level, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, geography, geography.geographical_feature_category, 010604 marine biology & hydrobiology, ACL, Geology, Estuary, Seasonality, medicine.disease, Meta-analysis, Oceanography, 13. Climate action, Benthic zone, [SDE]Environmental Sciences, Environmental science, Sedimentary rock, France, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; In costal systems, particulate organic matter (POM) results from a multiplicity of sources having their respective dynamics in terms of production, decomposition, transport and burial. The POM pool experiences thus considerable spatial and temporal variability. In order to better understand this variability, the present study employs statistical multivariate analyses to investigate links between POM composition and environmental forcings for a panel of twelve coastal systems distributed along the three maritime regions of France and monitored weekly to monthly for 1 to 8 years.At multi-system scale, two main gradients of POC composition have been identified: a 'Continent-Ocean' gradient associated with hydrodynamics, sedimentary dynamics and depth of the water column, and a gradient of trophic status related to nutrient availability. At local scale, seasonality of POC composition appears to be station-specific but still related to part of the above-mentioned forcings. A typology of systems was established by coupling spatial and temporal variability of POC composition. Four groups were highlighted: (1) the estuarine stations where POC composition is dominated by terrestrial POM and driven by hydrodynamics and sedimentary processes, (2) the oligotrophic systems, characterized by the contribution of diazotrophs due to low nutrient availability, and the marine meso/eutroph systems whose POC composition is (3) either deeply dominated by phytoplankton or (4) dominated by phytoplankton but where the contribution of continental and benthic POC is not negligible and is driven by hydrodynamics, sedimentary processes and the height of the water column.Finally, the present study provides several insights into the different forcings to POM composition and dynamics in temperate coastal systems at local and multi-system scales. This work also presents a methodological approach that establishes statistical links between forcings and POM composition, helping to gain more objectively insight of forcings.
Published: 2018
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13. Rabbits in the grave! Consequences of bioturbation on the Neandertal 'burial' at Regourdou (Montignac-sur-Vézère, Dordogne)

Author: Stéphane Madelaine, Bruno Maureille, Trenton W. Holliday, Maxime Pelletier, Aurélien Royer, Emmanuel Discamps, Laboratoire méditerranéen de préhistoire Europe-Afrique (LAMPEA), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture (MC), Laboratoire Paléobiodiversité et Evolution (PALEVO), École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Departement of Anthropology, Tulane University, Evolutionary Studies Institute, University of the Witwatersrand [Johannesburg] (WITS), Travaux et recherches archéologiques sur les cultures, les espaces et les sociétés (TRACES), École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université de Toulouse (UT)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Musée National de Préhistoire, Ministère de la Culture et de la Communication (MCC), De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (PACEA), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Support from the Nouvelle Aquitaine Regional Council 2016 research program NATCH (convention 2016-1R40240-00007349-00007350), and from the Louisiana Board of Regents LEQSF (2015-18)-RD-A-22., ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011), ANR-10-IDEX-0003,IDEX BORDEAUX,Initiative d'excellence de l'Université de Bordeaux(2010), Laboratoire méditerranéen de préhistoire Europe-Afrique ( LAMPEA ), Centre National de la Recherche Scientifique ( CNRS ) -Institut national de recherches archéologiques préventives ( Inrap ) -Ministère de la Culture et de la Communication ( MCC ) -Aix Marseille Université ( AMU ), Laboratoire Paléobiodiversité et Evolution ( PALEVO ), École pratique des hautes études ( EPHE ), Biogéosciences [Dijon] ( BGS ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Tulane University - New Orleans, LA, University of the Witwatersrand [Johannesburg] ( WITS ), Travaux et recherches archéologiques sur les cultures, les espaces et les sociétés ( TRACES ), École des hautes études en sciences sociales ( EHESS ) -Université Toulouse - Jean Jaurès ( UT2J ) -Ministère de la Culture et de la Communication ( MCC ) -Institut national de recherches archéologiques préventives ( Inrap ) -Centre National de la Recherche Scientifique ( CNRS ), Ministère de la Culture et de la Communication ( MCC ), De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie ( PACEA ), Université de Bordeaux ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), ANR-11-IDEX-0001-02/11-IDEX-0001,Amidex,Amidex ( 2011 ), ANR-10-IDEX-03-02/10-LABX-0052,LaScArBx,Using the world in ancient societies : processes and forms of appropriation of space in Long Time ( 2010 ), École pratique des hautes études (EPHE), Biogéosciences [UMR 6282] [Dijon] (BGS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), and École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 010506 paleontology, Time Factors, Neanderthal, Taphonomy, Burial, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Context (language use), 01 natural sciences, Oryctolagus cuniculus, Natural (archaeology), law.invention, law, biology.animal, biology.domesticated_animal, Animals, Middle Palaeolithic, 0601 history and archaeology, Radiocarbon dating, Attritional accumulation, Ecology, Evolution, Behavior and Systematics, Neanderthals, [ SDU.STU.PG ] Sciences of the Universe [physics]/Earth Sciences/Paleontology, 0105 earth and related environmental sciences, 060101 anthropology, biology, Fossils, Ecology, Radiometric Dating, Reproducibility of Results, Mousterian, 06 humanities and the arts, 15. Life on land, Europe, [ SHS.ARCHEO ] Humanities and Social Sciences/Archaeology and Prehistory, [ SHS.ANTHRO-BIO ] Humanities and Social Sciences/Biological anthropology, Anthropology, Period (geology), Burrow, Rabbits, European rabbit, Bioturbation, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, Geology
Abstract: 17 pages; International audience; The understanding of Neanderthal societies, both with regard to their funerary behaviors and their subsistence activities, is hotly debated. Old excavations and a lack of taphonomic context are often factors that limit our ability to address these questions. To better appreciate the exact nature of what is potentially the oldest burial in Western Europe, Regourdou (Montignac-sur-Vézère, Dordogne), and to better understand the taphonomy of this site excavated more than 50 years ago, we report in this contribution a study of the most abundant animals throughout its stratigraphy: the European rabbit (Oryctolagus cuniculus). In addition to questions surrounding the potential bioturbation of the site's stratigraphy, analysis of the Regourdou rabbits could provide new information on Neandertal subsistence behavior. The mortality profile, skeletal-part representation, breakage patterns, surface modification, and comparison with modern reference collections supports the hypothesis that the Regourdou rabbit remains were primarily accumulated due to natural (attritional) mortality. Radiocarbon dates performed directly on the rabbit remains give ages ranging within the second half of Marine Isotope Stage 3, notably younger than the regional Mousterian period. We posit that rabbits dug their burrows within Regourdou's sedimentological filling, likely inhabiting the site after it was filled. The impact of rabbit activity now brings into question both the reliability of the archaeostratigraphy of the site and the paleoenvironmental reconstructions previously proposed for it, and suggests rabbits may have played a role in the distribution of the Neandertal skeletal remains.
Published: 2017
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14. The role of hot electrons in the dynamics of a laser-driven strong converging shock

Author: Riccardo Betti, Arnaud Colaïtis, T. Nguyen-Bui, Vladimir Tikhonchuk, E. Llor Aisa, Guillaume Duchateau, W. Theobald, Xavier Ribeyre, A. Bose, Centre d'Etudes Lasers Intenses et Applications (CELIA), Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Bordeaux (UB), Lawrence Livermore National Laboratory (LLNL), Laboratory for lasers energetics - LLE (New-York, USA), University of Rochester [USA], This work has been carried out within the framework of the EUROfusion Consortium and has received funding from the Euratom research and training programme 2014–2018 under Grant Agreement No. 633053., Aquitaine Regional Council, Part of this work was supported by the DOE NNSA under Award No. DE-NA0001944 and DE-FC02-04ER54789, the Laboratory Basic Science Program, the University of Rochester, and the New York State Energy Research and Development Authority., European Project: 633053,H2020,EURATOM-Adhoc-2014-20,EUROfusion(2014), and Université de Bordeaux (UB)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Physics, Astrophysics::High Energy Astrophysical Phenomena, Dynamics (mechanics), Mechanics, Condensed Matter Physics, Laser, 01 natural sciences, Omega, 010305 fluids & plasmas, Shock (mechanics), law.invention, Time history, law, [PHYS.PHYS.PHYS-PLASM-PH]Physics [physics]/Physics [physics]/Plasma Physics [physics.plasm-ph], 0103 physical sciences, 010306 general physics, Hot electron, Excitation, Parametric statistics
Abstract: International audience; Experiments on strong shock excitation in spherical plastic targets conducted at the Omega Laser Facility are interpreted with the radiation–hydrodynamics code CHIC to account for parametric instabilities excitation and hot-electron generation. The effects of hot electrons on the shock-pressure amplification and upstream preheat are analyzed. It is demonstrated that both effects contribute to an increase in the shock velocity. Comparison of the measured laser reflectivity and shock flash time with numerical simulations makes it possible to reconstitute the time history of the ablation and shock pressures. Consequences of this analysis for the shock-ignition target design are discussed.
Published: 2017
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15. Suitability of a new mixed-strain starter for manufacturing uncooked raw ewe's milk cheeses

Author: Susana Garcia, Francisco José Pérez Elortondo, Ines Arana, Françoise Berthier, Fabienne Feutry, Paloma Torre, Syndicat de défense de l ’AOC Ossau-Iraty, Partenaires INRAE, Universidad Pública de Navarra [Espagne] = Public University of Navarra (UPNA), Universidad del Pais Vasco / Euskal Herriko Unibertsitatea [Espagne] (UPV/EHU), Unité de recherches en Technologie et Analyses Laitières (URTAL), Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Aquitaine Regional Council, Pyrenees Atlantiques Council, ONILAIT (Paris, France), French State (FNADT), and European Commission
Subjects: 0301 basic medicine, Streptococcus thermophilus, Food Handling, Microbial diversity, 030106 microbiology, Manufacturing conditions, Microbiology, 03 medical and health sciences, Starter, Milk products, Cheese, Raw Foods, Manufacturing Industry, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Animals, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Food science, Mathematics, 2. Zero hunger, Sheep, biology, 0402 animal and dairy science, 04 agricultural and veterinary sciences, Raw milk, biology.organism_classification, 040201 dairy & animal science, Sensory characteristics, Coliform bacteria, Lactococcus lactis, Milk, Ewe's raw milk cheese, Fermentation, Food Microbiology, Female, Food Science
Abstract: International audience; Most raw milk Ossau-Iraty cheeses are currently manufactured on-farm using the same commercial streptococcal-lactococcal starter (S1). One way to enhance the microbial diversity that gives raw milk its advantages for cheese-making is to formulate new starters combining diverse, characterized strains. A new starter (OI) combining 6 raw milk strains of lactococci, recently isolated and characterized, was tested in parallel with the current starter by making 12 Ossau-Iraty raw milk cheeses at 3 farmhouses under the conditions prevailing at each farm. Compliance of the sensory characteristics with those expected by the Ossau-Iraty professionals, physicochemical parameters and coliforms were quantified at key manufacturing steps. The new starter OI gave cheeses having proper compliance but having lower compliance than the S1 cheeses under most manufacturing conditions, while managing coliform levels equally well as starter S1. This lower compliance relied more on the absence of Streptococcus thermophilus in starter OI, than on the nature of the lactoccocal strains present in starter OI. The study also shows that variations in 5 technological parameters during the first day of manufacture, within the range of values applied in the 3 farmhouses, are powerful tools for diversifying the scores for the sensory characteristics investigated. (C) 2015 Elsevier Ltd. All rights reserved.
Published: 2016
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16. Femtosecond laser pulse train interaction with dielectric materials

Author: John Lopez, C. Javaux Léger, Vladimir Tikhonchuk, Guillaume Duchateau, O. Dematteo Caulier, A. Bourgeade, Rainer Kling, B. Chimier, Konstantin Mishchik, Stefan Skupin, C. Hönninger, Centre d'Etudes Lasers Intenses et Applications (CELIA), Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Bordeaux (UB), alphanov, ALPhANOV, Amplitude Systèmes, We acknowledge the European Commission, the French Ministry of Industry and the Aquitaine Regional Council for support and funding via the Femtoweld project. Numerical simulations were performed using computing resources at Mesocentre de Calcul Intensif Aquitain (MCIA) and Grand Equipement National pour le Calcul Intensif (GENCI, grant no. 2015-056129)., and Université de Bordeaux (UB)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Materials science, Physics and Astronomy (miscellaneous), FOS: Physical sciences, 02 engineering and technology, Dielectric, 01 natural sciences, 7. Clean energy, law.invention, 010309 optics, Thermal conductivity, law, [PHYS.PHYS.PHYS-PLASM-PH]Physics [physics]/Physics [physics]/Plasma Physics [physics.plasm-ph], 0103 physical sciences, Pulse wave, Absorption (electromagnetic radiation), [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], [PHYS.PHYS.PHYS-ATOM-PH]Physics [physics]/Physics [physics]/Atomic Physics [physics.atom-ph], 021001 nanoscience & nanotechnology, Laser, Pulse (physics), Femtosecond, Atomic physics, 0210 nano-technology, Glass transition, Physics - Optics, Optics (physics.optics)
Abstract: We investigate the interaction of trains of femtosecond microjoule laser pulses with dielectric materials by means of a multi-scale model. Our theoretical predictions are directly confronted with experimental observations in soda-lime glass. We show that due to the low heat conductivity, a significant fraction of the laser energy can be accumulated in the absorption region. Depending on the pulse repetition rate, the material can be heated to high temperatures even though the single pulse energy is too low to induce a significant material modification. Regions heated above the glass transition temperature in our simulations correspond very well to zones of permanent material modifications observed in the experiments., Comment: 4 pages, 4 figures
Published: 2015
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17. A Lagrangian VOF tensorial penalty method for the DNS of resolved particle-laden flows

Author: Jorge César Brändle de Motta, Olivier Simonin, Eric Climent, Stéphane Vincent, Arthur Sarthou, Jean-Luc Estivalezes, Institut de Mécanique et d'Ingénierie de Bordeaux (I2M), École Nationale Supérieure d'Arts et Métiers (ENSAM), Arts et Métiers Sciences et Technologies, HESAM Université (HESAM)-HESAM Université (HESAM)-Arts et Métiers Sciences et Technologies, HESAM Université (HESAM)-HESAM Université (HESAM)-Institut Polytechnique de Bordeaux-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB), Institut de mécanique des fluides de Toulouse (IMFT), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, ONERA - The French Aerospace Lab [Toulouse], ONERA, Institut National Polytechnique (Toulouse) (Toulouse INP), Transferts, écoulements, fluides, énergétique (TREFLE), Université Sciences et Technologies - Bordeaux 1-École Nationale Supérieure de Chimie et de Physique de Bordeaux (ENSCPB)-Centre National de la Recherche Scientifique (CNRS), ONERA - The French Aerospace Lab [Palaiseau], ONERA-Université Paris Saclay (COmUE), HESAM Université (HESAM)-HESAM Université (HESAM)-Institut Polytechnique de Bordeaux-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-Institut National de la Recherche Agronomique (INRA), Midi-Pyrennées Regional Council, Aquitaine Regional Council, French CINES (National Computing Center for Higher Education) and CCRT (National Computing Center of CEA) [x2012026115], CALMIP [2012-P0633], Agence Nationale de la Recherche ANR through the Player project, Arts et Métiers ParisTech (FRANCE), Centre National de la Recherche Scientifique - CNRS (FRANCE), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Institut National de la Recherche Agronomique - INRA (FRANCE), Institut Polytechnique de Bordeaux - IPB (FRANCE), Office National d'Etudes et Recherches Aérospatiales - ONERA (FRANCE), Université de Bordeaux 1 (FRANCE), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), Institut National Polytechnique de Toulouse - INPT (FRANCE), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)-École Nationale Supérieure d'Arts et Métiers (ENSAM), and HESAM Université (HESAM)-HESAM Université (HESAM)-Institut Polytechnique de Bordeaux-Centre National de la Recherche Scientifique (CNRS)
Subjects: Physics and Astronomy (miscellaneous), Mécanique des fluides, Direct numerical simulation, 02 engineering and technology, 01 natural sciences, 010305 fluids & plasmas, [SPI.MECA.MEFL]Engineering Sciences [physics]/Mechanics [physics.med-ph]/Fluids mechanics [physics.class-ph], Physics::Fluid Dynamics, 0203 mechanical engineering, Lagrangian VOF, 0103 physical sciences, Volume of fluid method, DNS of particle flows, Penalty method, [PHYS.MECA.MEFL]Physics [physics]/Mechanics [physics]/Fluid mechanics [physics.class-ph], ComputingMilieux_MISCELLANEOUS, Physics, Numerical Analysis, [PHYS.MECA.MEFL]Physics [physics]/Mechanics [physics]/Mechanics of the fluids [physics.class-ph], Augmented Lagrangian method, Applied Mathematics, Numerical analysis, Particle-laden flows, Equations of motion, Mechanics, Viscous penalty method, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Resolved scale particles, Computer Science Applications, Collision and lubrication models, Computational Mathematics, 020303 mechanical engineering & transports, Classical mechanics, Flow (mathematics), Modeling and Simulation, Fluidized beds, [MATH.MATH-NA]Mathematics [math]/Numerical Analysis [math.NA]
Abstract: International audience; The direct numerical simulation of particle flows is investigated by a Lagrangian VOF approach and penalty methods of second order convergence in space for incompressible flows interacting with resolved particles on a fixed structured grid. A specific Eulerian volume of fluid method is developed with a Lagrangian tracking of the phase function while the solid and divergence free constraints are ensured implicitly in the motion equations thanks to fictitious domains formulations, adaptive augmented Lagrangian approaches and viscous penalty methods. A specific strategy for handling particle collisions and lubrication effects is also presented. Various dilute particle laden flows are considered for validating the models and numerical methods. Convergence studies are proposed for estimating the time and space convergence orders of the global DNS approach. Finally, two dense particle laden flows are simulated, namely the flow across a fixed array of cylinders and the fluidization of 2133 particles in a vertical pipe. The numerical solutions are compared to existing theoretical and experimental results with success.
Published: 2014
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18. Investigation of longitudinal proton acceleration in exploded targets irradiated by intense short-pulse laser

Author: Julien Fuchs, M. Glesser, Sophia Chen, Bruno Albertazzi, Philippe Nicolai, H. Pépin, V. T. Tikhonchuk, Patrizio Antici, C. Beaucourt, Maxence Gauthier, Jérôme Breil, Jean-Luc Feugeas, V. Dervieux, Anna Lévy, Emmanuel d'Humières, Laboratoire pour l'utilisation des lasers intenses (LULI), Université Pierre et Marie Curie - Paris 6 (UPMC)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Institut des Nanosciences de Paris (INSP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), European Commission (CRISP) [283745], FRQNT/FRQSC [174726], CRSNG decouverte [435416], FP-7 Laserlab-Europe [602 284464, 001528], National Science Foundation [600 1064468], Aquitaine Regional Council, and LULI
Subjects: Physics, Proton, Plasma, Condensed Matter Physics, Laser, 7. Clean energy, 01 natural sciences, 010305 fluids & plasmas, Intensity (physics), law.invention, Shock (mechanics), Acceleration, law, Physics::Plasma Physics, 0103 physical sciences, Physics::Accelerator Physics, Plasma diagnostics, Irradiation, Atomic physics, [PHYS.COND]Physics [physics]/Condensed Matter [cond-mat], 010306 general physics
Abstract: International audience; It was recently shown that a promising way to accelerate protons in the forward direction to high energies is to use under-dense or near-critical density targets instead of solids. Simulations have revealed that the acceleration process depends on the density gradients of the plasma target. Indeed, under certain conditions, the most energetic protons are predicted to be accelerated by a collisionless shock mechanism that significantly increases their energy. We report here the results of a recent experiment dedicated to the study of longitudinal ion acceleration in partially exploded foils using a high intensity (similar to 5 x 10(18) W/cm(2)) picosecond laser pulse. We show that protons accelerated using targets having moderate front and rear plasma gradients (up to similar to 8 mu m gradient length) exhibit similar maximum proton energy and number compared to proton beams that are produced, in similar laser conditions, from solid targets, in the well-known target normal sheath acceleration regime. Particle-In-Cell simulations, performed in the same conditions as the experiment and consistent with the measurements, allow laying a path for further improvement of this acceleration scheme. (C) 2014 AIP Publishing LLC.
Published: 2014
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19. Co-inoculation with yeast and LAB under winery conditions: modification of the aromatic profile of merlot wines

Author: Guillaume Antalick, G. de Revel, Marie-Claire Perello, ProdInra, Migration, Institut des Sciences de la Vigne et du Vin (ISVV), Œnologie, Institut National de la Recherche Agronomique (INRA)-Université Victor Segalen - Bordeaux 2, Aquitaine Regional Council, and Bordeaux Wine Council (Conseil Interprofessionnel des Vins de Bordeaux, CIVB)
Subjects: 0106 biological sciences, biology, Chemistry, [SPI.GPROC] Engineering Sciences [physics]/Chemical and Process Engineering, food and beverages, 04 agricultural and veterinary sciences, [SDV.IDA] Life Sciences [q-bio]/Food engineering, biology.organism_classification, 040401 food science, 01 natural sciences, Diacetyl, Winery, Yeast, Lactic acid, chemistry.chemical_compound, 0404 agricultural biotechnology, Starter, Malolactic fermentation, co-inoculation, Oenococcus oeni, aromatic profile, metabolites, 010608 biotechnology, [SDV.IDA]Life Sciences [q-bio]/Food engineering, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Food science, Co inoculation, Aroma, Oenococcus oeni
Abstract: International audience; The present work reports the impact of yeast/LAB co-inoculation on the aromatic profile of Merlot wines made in wineries. This study was carried out over two consecutive years on five Merlot wines in Bordeaux and Swiss wineries, using Saccharomyces cerevisiae and Oenococcus oeni starter cultures. Seventy aromatic compounds were quantified and, in addition, the sensory profiles of two wines were determined in order to compare the aromatic notes of the sequential and co-inoculated wines. The influence of the timing of inoculation with lactic acid bacteria (LAB) on the metabolic profile of wines was observed. It confirmed previous work carried out on a micro-scale but, for the first time, the impact of yeast/LAB co-inoculation was significantly demonstrated from a sensory point of view under winery conditions. In particular, the fruity and lactic notes, as well as the markers associated with these descriptors, such as esters and diacetyl, were altered. Co-inoculation does not always favour fruity expression, nor does it reduce the diacetyl content and lactic aroma intensity. All of the trends were observed either in the production and degradation of metabolites, or by the development of an aromatic mask over the short and long term.
Published: 2013

20. Detection of QTL controlling metabolism, meat quality, and liver quality traits of the overfed interspecific hybrid mule duck

Author: Kileh-Wais, M., Elsen, J M, VIGNAL, A, Feves, K, Vignoles, F, Fernandez, X, Manse, H, Davail, Stéphane, André, Jean-Marc, Bastianelli, D, Bonnal, L, Filangi, O, Baéza, E, Guéméné, D, Genêt, C, Bernadet, M., Dubos, F., Marie-Etancelin, C., Station d'Amélioration Génétique des Animaux (SAGA), Institut National de la Recherche Agronomique (INRA), Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Tissus animaux, nutrition, digestion, écosystème et métabolisme (TANDEM), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT], Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Systèmes d'élevage méditerranéens et tropicaux (UMR SELMET), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-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), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Unité de Recherches Avicoles (URA), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Palmipèdes à Foie Gras (UEPFG), French National Research Agency (GENANIMAL program), Scientific Group for avian genome analysis (AGENAVI), Midi-Pyrenees council, INRA Animal Genetics Division, University of Djibouti, Aquitaine regional council, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-INP. Ecole Nationale Supérieure Agronomique de Toulouse, Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS), Unité de Recherches Avicoles, and Institut National de la Recherche Agronomique (INRA)-AgroParisTech
Subjects: Locus des caractères quantitatifs, Hybride, liver quality, [SDV.SA.ZOO]Life Sciences [q-bio]/Agricultural sciences/Zootechny, meat quality, pleiotropy, L52 - Physiologie animale - Croissance et développement, hybrid mule duck, Canard, Q04 - Composition des produits alimentaires, metabolic trait, Métabolisme des lipides, Viande de canard, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, U10 - Informatique, mathématiques et statistiques, Abats, Canard de Barbarie, food and beverages, quantitative trait loci, L10 - Génétique et amélioration des animaux, Physiologie animale, Carte génétique, Muscle, Anas, U30 - Méthodes de recherche, Amélioration des animaux, Foie, Qualité, Génotype, Modèle mathématique
Abstract: Chantier qualité GA; International audience; The mule duck, an interspecific hybrid obtained by crossing common duck (Anas platyrhynchos) females with Muscovy (Cairina moschata) drakes, is widely used for fatty liver production. The purpose of the present study was to detect and map single and pleiotropic QTL that segregate in the common duck species, and influence the expression of traits in their overfed mule duck offspring. To this end, we generated a common duck backcross (BC) population by crossing Kaiya and heavy Pekin experimental lines, which differ notably in regard to the BW and overfeeding ability of their mule progeny. The BC females were mated to Muscovy drakes and, on average, 4 male mule ducks hatched per BC female (1600 in total) and were measured for growth, metabolism during growth and the overfeeding period, overfeeding ability, and the quality of their breast meat and fatty liver. The phenotypic value of BC females was estimated for each trait by assigning to each female the mean value of the phenotypes of her offspring. Estimations allowed for variance, which depended on the number of male offspring per BC and the heritability of the trait considered. The genetic map used for QTL detection consisted of 91 microsatellite markers aggregated into 16 linkage groups (LG) covering a total of 778 cM. Twenty-two QTL were found to be significant at the 1% chromosome-wide threshold level using the single-trait detection option of the QTLMap software. Most of the QTL detected were related to the quality of breast meat and fatty liver: QTL for meat pH 20 min post mortem were mapped to LG4 (at the 1% genome-wide significance level), and QTL for meat lipid content and cooking losses were mapped to LG2a. The QTL related to fatty liver weight and liver protein and lipid content were for the most part detected on LG2c and LG9. Multitrait analysis highlighted the pleiotropic effects of QTL in these chromosome regions. Apart from the strong QTL for plasma triglyceride content at the end of the overfeeding period mapped to chromosome Z using single-trait analysis, all metabolic trait QTL were detected with the multitrait approach: the QTL mapped to LG14 and LG21 affected the plasma cholesterol and triglyceride contents, whereas the QTL mapped to LG2a seemed to impact glycemia and the basal plasma corticosterone content. A greater density genetic map will be needed to further fine map the QTL.
Published: 2013
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21. Lactococcus lactis strains from raw ewe’s milk samples from the PDO Ossau-Iraty cheese area: levels, genotypic and technological diversity

Author: Erick Casalta, Susana Garcia, Ines Arana, Fabienne Feutry, Paloma Torre, Nathalie Desmasures, Centre de Formation des Apprentis Agricoles des Pyrénées Atlantiques (CFAA64), Aliments Bioprocédés Toxicologie Environnements (ABTE), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Sciences Pour l'Oenologie (SPO), Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Syndicat de défense de l ’AOC Ossau-Iraty, Partenaires INRAE, Universidad de Navarra [Pamplona] (UNAV), Universidad Pública de Navarra [Espagne] (UPNA), Interactions Cellules Organismes Environnement (ICORE), CHU Caen, Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN)-Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN)-Université de Caen Normandie (UNICAEN), 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), Aquitaine Regional Council, Pyrenees Atlantiques Council, ONILAIT (Paris, France), French State (FNADT), European Commission, Universidad Pública de Navarra [Espagne] = Public University of Navarra (UPNA), Normandie Université (NU)-Normandie Université (NU)-CHU Caen, Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN)-Tumorothèque de Caen Basse-Normandie (TCBN), and Université Montpellier 1 (UM1)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Subjects: Technological, Lactococcus lactis, Wild strain, Diversity, Genotypic, Ewe's milk, Biochemistry, law.invention, 03 medical and health sciences, Starter, law, Genotype, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Technological diversity, Food science, Polymerase chain reaction, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, biology, 030306 microbiology, Strain (biology), food and beverages, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Food Science, Bacterial dna
Abstract: International audience; The aims of this work were to assess the levels of Lactococcus lactis (L. lactis) in ewe's milk produced in three Ossau-Iraty cheese sub-areas and to investigate the genotypic and technological diversity of isolated wild strains of L. lactis in order to assess their suitability for use as components of starter formulations. Thirty-two milk samples from 32 farms were collected. Strains of L. lactis were identified and quantified using a combination of species and subspecies-specific polymerase chain reaction (PCR) and PCR amplification of repetitive bacterial DNA elements (Rep-PCR). The genotypic and technological diversity of the indigenous strains was compared to that of 12 commercial strains. L. lactis was detected in milk samples from only 20 farms. The levels detected were below 4 log(10) cfu.mL(-1) in 75% of the milks. L. lactis subsp. lactis dominated in 66% of the samples. Forty-three genotypic profiles of wild L. lactis strains were detected and showed greater diversity than those of the commercial strains. Milks containing L. lactis contained one to four distinct strains. With the exception of two strains, each strain was found in milk from only one farm. The Prt(+) strains were the most acidifying. Sensitivity to phages collected from wheys differed widely between the commercial (60%) and indigenous strains (5%). Wild strains of L. lactis displayed a wide genotypic and technological diversity. Genotypic diversity seemed to be linked to the farm of origin. This study addresses questions regarding the environmental factors which influence such natural diversity. A deeper knowledge of the strain-dependent technological properties would be useful in selecting strains for use in starter blends.
Published: 2012
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22. The RTM resistance to potyviruses in Arabidopsis thaliana: natural variation of the RTM genes and evidence for the implication of additional genes

Author: Frédéric Revers, Patrick Cosson, Valérie Schurdi-Levraud, Thierry Candresse, Ophélie Sicard, Quang Hien Le, Mélodie Caballero, Olivier Le Gall, Fabrice Roux, Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Génétique et évolution des populations végétales (GEPV), Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Sciences et Technologies, INRA's 'Jeune Equipe' program, Etablissement Public Regional Aquitaine [20000307004], French Research Ministry, INRA (Plant Health and Plant Genetics divisions), Aquitaine regional council, Université de Lille, Sciences et Technologies-Centre National de la Recherche Scientifique (CNRS), and Revers, Frédéric
Subjects: 0106 biological sciences, virus de la gravure du tabac, Arabidopsis, affection virale, Plant Science, Plant Genetics, 01 natural sciences, tobacco etch virus, Plant Microbiology, Gene Expression Regulation, Plant, potyvirus, santé des plantes, virus de la mosaïque de la laitue, Arabidopsis thaliana, pathologie végétale, Heat-Shock Proteins, Genetics, 0303 health sciences, Multidisciplinary, biology, Tobacco etch virus, Potyvirus, Chromosome Mapping, gène de résistance, Lettuce mosaic virus, lettuce mosaic virus, Host-Pathogen Interaction, Medicine, Plant Lectins, virologie végétale, Research Article, Sequence analysis, Phytopathology and phytopharmacy, Science, Mechanisms of Resistance and Susceptibility, Plant Cell Biology, Plant Pathogens, Phloem, Genes, Plant, Microbiology, 03 medical and health sciences, resistance gene, Virology, Genetic variation, Genetic Predisposition to Disease, Biology, Gene, Alleles, Plant Diseases, 030304 developmental biology, Arabidopsis Proteins, arabidopsis thaliana, Genetic Variation, Plant Pathology, biology.organism_classification, Phytopathologie et phytopharmacie, viral disease, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Amino Acid Substitution, plant health, mouvement à longue distance, résistance antivirale, 010606 plant biology & botany
Abstract: International audience; Background: The non conventional RTM (Restricted Tobacco etch virus Movement) resistance which restricts long distance movement of some plant viruses in Arabidopsis thaliana is still poorly understood. Though at least three RTM genes have been identified, their precise role(s) in the process as well as whether other genes are involved needs to be elucidated.Methodology/Principal Findings: In this study, the natural variation of the RTM genes was analysed at the amino acid level in relation with their functionality to restrict the long distance movement of Lettuce mosaic potyvirus (LMV). We identified non-functional RTM alleles in LMV-susceptible Arabidopsis accessions as well as some of the mutations leading to the nonfunctionality of the RTM proteins. Our data also indicate that more than 40% of the resistant accessions to LMV are controlled by the RTM genes. In addition, two new RTM loci were genetically identified. Conclusions/Significance: Our results show that the RTM resistance seems to be a complex biological process which would involves at least five different proteins. The next challenges will be to understand how the different RTM protein domains are involved in the resistance mechanism and to characterise the new RTM genes for a better understanding of the blocking of the long distance transport of plant viruses.
Published: 2012
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22 results on '"Aquitaine regional council"'

1. Structural and molecular basis of cross-seeding barriers in amyloids

2. Effect of a low water concentration in chloride, sodium and potassium on oocyte maturation, oocyte hydration, ovulation and egg quality in rainbow trout

3. Critical assessment of metabolism and related growth and quality traits in trout fed spirulina-supplemented plant-based diets

4. Theoretical study of spatiotemporal focusing for in-bulk laser structuring of dielectrics

5. Full waveform inversion for bore reconstruction of woodwind-like instruments

6. Health Care Students’ Knowledge of and Attitudes, Beliefs, and Practices Toward the French COVID-19 App: Cross-sectional Questionnaire Study

7. Structures of Pathological and Functional Amyloids and Prions, a Solid-State NMR Perspective

8. Proton-NMR Metabolomics of Rainbow Trout Fed a Plant-Based Diet Supplemented with Graded Levels of a Protein-Rich Yeast Fraction Reveal Several Metabolic Processes Involved in Growth

9. 'Gueule cassée' (facial injuries): a 3D paleotraumatology study and facial approximation of a Napoleonic soldier who died in 1812 at Königsberg during the Russian Campaign

10. Development of a cell-free and growth factor-free hydrogel capable of inducing angiogenesis and innervation after subcutaneous implantation

11. Dynamics of particulate organic matter in a coastal system characterized by the occurrence of marine mucilage – A stable isotope study

12. Dynamics of particulate organic matter composition in coastal systems: Forcing of spatio-temporal variability at multi-systems scale

13. Rabbits in the grave! Consequences of bioturbation on the Neandertal 'burial' at Regourdou (Montignac-sur-Vézère, Dordogne)

14. The role of hot electrons in the dynamics of a laser-driven strong converging shock

15. Suitability of a new mixed-strain starter for manufacturing uncooked raw ewe's milk cheeses

16. Femtosecond laser pulse train interaction with dielectric materials

17. A Lagrangian VOF tensorial penalty method for the DNS of resolved particle-laden flows

18. Investigation of longitudinal proton acceleration in exploded targets irradiated by intense short-pulse laser

19. Co-inoculation with yeast and LAB under winery conditions: modification of the aromatic profile of merlot wines

20. Detection of QTL controlling metabolism, meat quality, and liver quality traits of the overfed interspecific hybrid mule duck

21. Lactococcus lactis strains from raw ewe’s milk samples from the PDO Ossau-Iraty cheese area: levels, genotypic and technological diversity

22. The RTM resistance to potyviruses in Arabidopsis thaliana: natural variation of the RTM genes and evidence for the implication of additional genes

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22 results on '"Aquitaine regional council"'

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