Éditeur(s) : HAL CCSD European Centre for Disease Prevention and Control
Résumé : International audience
Leishmaniasis is endemic in southern Europe, and in other European countries cases are diagnosed in travellers who have visited affected areas both within the continent and beyond. Prompt and accurate diagnosis poses a challenge in clinical practice in Europe. Different methods exist for identification of the infecting Leishmania species. Sixteen clinical laboratories in 10 European countries, plus Israel and Turkey, conducted a study to assess their genotyping performance. DNA from 21 promastigote cultures of 13 species was analysed blindly by the routinely used typing method. Five different molecular targets were used, which were analysed with PCR-based methods. Different levels of identification were achieved, and either the Leishmania subgenus, species complex, or actual species were reported. The overall error rate of strains placed in the wrong complex or species was 8.5%. Various reasons for incorrect typing were identified. The study shows there is considerable room for improvement and standardisation of Leishmania typing. The use of well validated standard operating procedures is recommended, covering testing, interpretation, and reporting guidelines. Application of the internal transcribed spacer 1 of the rDNA array should be restricted to Old World samples, while the heat-shock protein 70 gene and the mini-exon can be applied globally.
ISSN: 1560-7917

hal-01460743
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01460743
DOI : 10.2807/1560-7917.ES.2016.21.49.30418
PUBMED : 27983510

Éditeur(s) : HAL CCSD Blackwell Publishing
Résumé : International audience
In the Causses platform (south-east France), Late Hettangian to Sinemurian deposits were interpreted previously as shallow-water carbonate ramp deposits. A new look at these deposits has shown a fault-controlled mosaic carbonate platform that is different from the carbonate ramp models. Within the platform mosaic, 15 lithofacies have been recognized, which are organized in four facies associations, including peritidal, restricted shallow sub-tidal, sand dunes and sub-tidal shelf facies associations. The rapid lateral and vertical facies changes, and the lack of consistent landward or seaward direction indicated by the pattern of facies changes, question the existence of a shoreline suggested by the traditional models for this region. Instead, the facies organization and cycle stacking pattern suggest deposition in a mosaic of intertidal islands between which sub-tidal restricted or open conditions could coexist in very close proximity. Such a platform mosaic would have been defined by tectonic activities along normal faults which segmented the shallow-water Causses platform. The facies and facies associations are arranged into metre-scale, peritidal and sub-tidal cycles that are also variable. Certain cycles show the same stacking pattern in all the sections and seem to be traceable over tens of kilometres. On the contrary, other cycles cannot be correlated; they are present only in specific sections and have a maximum lateral extension of 1 or 2 km. These metre-scale cycles stack to form four medium-scale cycles bounded by surfaces that display sub-aerial exposure features. Medium-scale cycles stack into two larger-scale cycles (tens of metres thick) and are bounded by well-defined karstic surfaces. Based on their lateral continuity and their stacking pattern, the metre-scale cycles are controlled probably by high frequency eustatic variations overprinting the topographic irregularities formed by differential subsidence of fault-bounded blocks. Episodic fault activities may reorganize the topography so that, even if eustatic changes may still be the major control of cycles, the expression and number of cycles could be different. Cycles of medium and large-scale are interpreted as being allogenic, controlled by changes in eustasy and/or subsidence rates as evidenced by their lateral continuity and the correlations of the large-scale cycles with third-order depositional sequences.
ISSN: 1469-3496

hal-00411940
https://hal.archives-ouvertes.fr/hal-00411940
DOI : 10.1111/j.1365-3091.2007.00896.x

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : The diversity and functional identity of organisms are known to be relevant to the maintenance of ecosystem processes but can be variable in different environments. Particularly, it is uncertain whether ecosystem processes are driven by complementary effects or by dominant groups of species. We investigated how community structure (i.e., the diversity and relative abundance of biological entities) explains the community-level contribution of Neotropical ant communities to different ecosystem processes in different environments. Ants were attracted with food resources representing six ant-mediated ecosystem processes in four environments: ground and vegetation strata in cropland and forest habitats. The exploitation frequencies of the baits were used to calculate the taxonomic and trophic structures of ant communities and their contribution to ecosystem processes considered individually or in combination (i.e., multifunctionality). We then investigated whether community structure variables could predict ecosystem processes and whether such relationships were affected by the environment. We found that forests presented a greater biodiversity and trophic complementarity and lower dominance than croplands, but this did not affect ecosystem processes. In contrast, trophic complementarity was greater on the ground than on vegetation and was followed by greater resource exploitation levels. Although ant participation in ecosystem processes can be predicted by means of trophic-based indices, we found that variations in community structure and performance in ecosystem processes were best explained by environment. We conclude that determining the extent to which the dominance and complementarity of communities affect ecosystem processes in different environments requires a better understanding of resource availability to different species.
ISSN: 0029-8549

hal-01606497
https://hal.archives-ouvertes.fr/hal-01606497
DOI : 10.1007/s00442-016-3741-z
PRODINRA : 407457

Éditeur(s) : HAL CCSD
Résumé : Designing biodiversity conservation plans requires knowledge on the biogeographic distribution of taxabut also accurate estimates of species richness and diversification processes. However, measuring the phyleticrichness can be biased by the use of inappropriate taxonomical characters, leading to erroneous speciesdelimitation and diversity estimates.This work explores the phyletic richness at several taxonomic levels (generic, specific and intraspecific) ofthe hydrozoan family Aglaopheniidae (Marktanner-Turneretscher, 1890), with a particular focus on the South-Western Indian Ocean. Firstly, using several newly constructed phylogenies based on mitochondrial andnuclear markers, this study reveals that the phyletic diversity of this family is at underestimated by at least 50%:all studied genera are polyphyletic or with doubtful monophyletic status. Then, using several speciesdelimitation methods based on molecular markers, it sheds light on the richness of cryptic diversity of thisfamily, enlightening the potential of using an integrative taxonomic approach on these morphologically simpleorganisms. Finally, the population genetics of an Aglaopheniidae brooding species shows a high populationsstructuring with pervasive pattern of isolation by distance at several geographic scales (several to thousands ofkilometres), implying a potentially high cryptic diversity existing in this family.The results of this work provide new insights on Aglaopheniidae diversity, underlining the potentialinfluence of reproductive mode on the phyletic diversity and diversification processes of brooding hydrozoanbrooders. This thesis further highlights the relevance of using several complementary
La conservation et la gestion sur le long terme de la biodiversité nécessitent une connaissance de larépartition des taxons, mais également une estimation précise de leur diversité spécifique ainsi que desprocessus de spéciation ayant permis leur formation. Cependant, la mesure de la richesse phylétique peut êtrebiaisée par l’utilisation de caractères taxinomiques ne permettant pas de délimiter les espèces de manièreappropriée.Ce travail de thèse propose d’explorer la diversité phylétique à plusieurs niveaux taxinomiques(générique, spécifique et intra-spécifique) des Aglaopheniidae, une famille d’hydrozoaires, notamment présentedans le Sud-Ouest de l’océan Indien. Dans un premier temps, en utilisant des phylogénies basées sur plusieursmarqueurs (mitochondriaux et nucléaires), ce travail démontre que la diversité phylétique de cette famille est,au minimum, sous-estimée de moitié: tous les genres de la famille sont polyphyléthiques ou présentent un statutmonophylétique restant à confirmer. Dans un deuxième temps, l’utilisation de méthodes de délimitationd’espèces basées sur des données moléculaires met en évidence la diversité cryptique très élevée des morphoespècesétudiées, révélant l’intérêt potentiel des protocoles de taxinomie intégrative chez les organismesmorphologiquement simples. Enfin, l’étude de génétique des populations d’une espèce incubatriced’Aglaopheniidae révèle l’importance de la structuration des populations et de l’isolement par la distance chezcette espèce à plusieurs échelles géographiques (de quelques kilomètres à plusieurs milliers), impliquant unepotentielle diversité cryptique extrêmement élevée chez cette famille.L’ensemble des connaissances acquises lors de ce travail de thèse fournit un nouveau regard sur ladiversité de la famille des Aglaopheniidae, soulignant le potentiel impact du cycle de reproduction sur ladiversité phylétique et les processus de spéciation des hydrozoaires incubateurs. Cette thèse met en évidence lapertinence de l’utilisation de plusieurs procédures complémentaires de délimitation d’espèces pour étudier ladiversité des organismes morphologiquement simples.
https://hal.archives-ouvertes.fr/tel-01359424

tel-01359424
https://hal.archives-ouvertes.fr/tel-01359424
https://hal.archives-ouvertes.fr/tel-01359424/document
https://hal.archives-ouvertes.fr/tel-01359424/file/These%20manuscrit%20final.pdf

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
Interleukin-33 (IL-33), a cytokine belonging to the IL-1 family, is crucially involved in inflammatory pathologies including liver injury and linked to various modes of cell death. However, a link between IL-33 and necroptosis or programmed necrosis in liver pathology remains elusive. We aimed to investigate the regulation of IL-33 during necroptosis-associated liver injury. The possible regulation of IL-33 during liver injury by receptor-interacting protein kinase 1 (RIPK1) and poly(ADP-ribose) polymerase 1 (PARP-1) was investigated in mice in vivo and in hepatic stellate cells in vitro. The liver immunohistopathology, flow cytometry, serum transaminase measurement, ELISA, and qPCR-based cytokine measurement were carried out. By using a chemical approach, we showed that pretreatment of mice with Necrostatin-1 (Nec-1) (inhibitor of RIPK1) and/or PJ34 (inhibitor of PARP-1) significantly protected mice against concanavalin A (ConA) liver injury (aspartate amino-transferase (AST)/alanine amino-transferase (ALT)) associated with down-regulated hepatocyte-specific IL-33 expression. In contrast, the expression level of most systemic cytokines (except for IL-6) or activation of liver immune cells was not altered by chemical inhibitors rather an increased infiltration of neutrophils in the liver. During polyinosine-polycytidylic acid (Poly(I:C))-induced acute hepatitis, liver injury and hepatocyte-specific IL-33 expression was also inhibited by PJ34 without any protective effect of PJ34 in CCl4-induced liver injury. Moreover, PJ34 down-regulated the protein expression of IL-33 in activated hepatic stellate cells by cocktail of cytokines or staurosporine in vitro. In conclusion, we evidenced that the Nec-1/PJ34 is a potent inhibitor of liver injury and Nec-1/PJ34 down-regulated hepatocyte-specific IL-33 expression in the liver in vivo or in hepatic stellate cells in vitro, suggesting IL-33 as a possible readout of necroptosis-involved liver pathologies. Necroptosis inhibitors can protect mice against liver injury induced by ConA or Poly(I:C). IL-33 expression in liver injury in vivo is inhibited by PJ34. IL-33 expression in hepatic stellate cells in vitro is inhibited by PJ34. Hepatocyte-specific IL-33 expression is down-regulated by Nec-1/PJ34 during hepatitis. IL-33 is a new marker of necroptosis-associated liver injuries.
ISSN: 0946-2716

hal-01134319
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01134319
DOI : 10.1007/s00109-015-1270-6
PUBMED : 25747661

Résumé : L'agriculture actuelle est impliquée dans de multiples problématiques environnementales, sociales et économiques, aux échelles locales et globales. En agronomie, de nombreux travaux à l'échelle du champ et de l'exploitation visent aujourd'hui à concevoir des systèmes de culture et des systèmes de production en lien avec ces problématiques. En revanche, peu de travaux portent sur la conception et l'évaluation de systèmes agricoles à l'échelle du territoire, alors que cette échelle apparaît pourtant incontournable pour faire face à des enjeux de développement durable. Pour combler ce manque, nous proposons un ensemble méthodologique permettant i) de simuler les conséquences de scénarios de politiques agricoles sur les choix d'assolement des agriculteurs, décrits individuellement, en modélisant l'évolution de leurs système de production et ii) d'évaluer l'impact de ces changements d'assolements à l'échelle du territoire, à l'aide d'indicateurs qui apportent de l'information spatiale sur la contribution de l'agriculture au développement durable. L'ensemble méthodologique proposé débute par la construction d'une typologie des exploitations agricoles du territoire sur la base de la similarité de leur assolement. Parallèlement, l'adaptation d'indicateurs à l'échelle du territoire permet d'évaluer les impacts des externalités des systèmes de culture en mobilisant des procédures de changements d'échelles. Un modèle bioéconomique générique, multi-échelle, spatialement explicite, appelé MOSAICA, qui utilise la typologie et les indicateurs d'impact de l'agriculture à l'échelle régionale, est créé pour produire des mosaïques de systèmes de culture et évalue leur contribution au développement durable du territoire. Ce modèle, couplé à un itinéraire de définition de scénarios exploratoires et normatifs permet de tester l'impact de différents types de leviers agronomiques, socio-économiques, environnementaux, organisationnels et techniques sur les choix des exploitants et in fine sur la contribution de la mosaïque de systèmes de culture au développement durable du territoire. Nous avons appliqué cet ensemble méthodologique à la conception de scénarios de développement agricoles durables en Guadeloupe. Nous avons dans un premier temps développé une typologie des systèmes de production comprenant huit types distincts et relevant de processus décisionnel différents. Puis nous avons adapté à l'échelle du territoire 19 indicateurs pour l'évaluation des mosaïques de systèmes de culture. L’évaluation de la mosaïque actuelle nous a permis de repérer de faibles niveaux de contribution aux enjeux d’autonomie alimentaire et énergétique. Différents scénarios normatifs et exploratoires intégrant des leviers de changement de la mosaïque ont été testés avec MOSAICA. Les évaluations réalisées nous ont permis d'identifier que des leviers agronomiques comme le développement du maraîchage sans intrants chimiques et des leviers sociaux comme la formation de main-d'oeuvre supplémentaire permettraient d'améliorer la contribution de l’agriculture au développement durable du territoire Guadeloupéen. La modélisation mécaniste de l’évolution du territoire agricole permet d'intégrer des connaissances sur la localisation, les performances, les impacts des systèmes de culture et sur les processus décisionnels des exploitants régissant l’orientation productive et le fonctionnement des exploitations. Cette démarche permet de visualiser les changements de système de culture et leurs impacts de manière spatialement explicite, ce qui permet de générer des connaissances sur les leviers susceptibles de faire évoluer positivement l'agriculture du territoire. La démarche et les outils mis en oeuvre sont donc particulièrement utiles pour l'aide à la décision publique pour améliorer la durabilité de l'agriculture dans son ensemble.
Current agricultural systems are responsible for many different environmental, social and economic issues at both local and global scales. Agricultural sciences have contributed to the design of several methods at the farm and field scale in order to prototype cropping systems and farming systems to address these issues. However, few methods have been designed at the regional scale, while this scale seems to be essential in order to address these issues. In order to fill this gap, we here propose a new methodological framework for i) simulating the consequences of policy changes on farmer's cropping plan, described individually, by modeling the evolution of farming systems and to ii) assess the impacts of cropping system changes at the regional scale, with a set of indicators that generate spatially explicit information on the contribution of agriculture to sustainable development. The methodological framework starts with the design of a farm typology over the territory based on the similarity of farmer's crop acreages. In parallel, a set of indicators is adapted to the landscape scale in order to assess the impacts of cropping system externalities by integrating a set of scale change procedures. A generic, multi-scale, spatially explicit bioeconomic model called MOSAICA, which uses the farm typology and the indicators, is created for generating cropping system mosaics and assessing their contribution to sustainable development. This model coupled to a scenario approach composed of exploratory and normative scenarios can simulate the impact of several types of agronomic, socio-economic, environmental, organizational and technical levers of change on the farmer's choices in terms of cropping systems and in fine the impacts of new cropping system mosaics on the contribution to sustainable development of territories. We applied this methodological framework for building scenarios of sustainable agricultural development in Guadeloupe. We first developed a typology of farming systems encompassing eight types of farming systems that revealed several different farmer's decision processes. Then, we developed 19 indicators to assess cropping system mosaics. The assessment of the current cropping system mosaic showed low levels of response of the current mosaic to economic and social issues especially the food and energy self-sufficiency. Different normative and exploratory scenarios integrating levers of change have been simulated with MOSAICA. The assessment of cropping system mosaics from these scenarios highlighted the positive effect of agronomic levers of change such as organic crop-gardening and social levers such as the vocational training of supplementary workforce for improving the contribution of agriculture to sustainable development of the guadeloupean territory. The mechanistic modeling of the agricultural territory allows us to integrate a wide range of knowledge on the location of cropping systems, their levels of performance , their impacts and the decision process of farmer's that drive the farming system characteristics and the farm functioning. This methodological framework helps visualize the cropping system changes at the regional scale and their associated impacts at the landscape scale which is helpful in order to produce knowledge on the levers of change that can improve the response of local agriculture to local and global issues. The framework and tools designed are particularly useful for decision-aid on the future levels of contribution of agriculture to sustainable development.

http://www.theses.fr/2015AGUY0823/document

Éditeur(s) : HAL CCSD
Résumé : In this work on a complete transect of the west‐central Pyrenees, we combine low temperature thermochronology (apatite fission tracks, AFT) with a detailed structural analysis to describe vertical movements related to the thrusting system evolution, and to determine the influence of the latter on the sedimentation/burial/exhumation cycle of thesynorogenic deposits of the southern foreland basin (Jaca and Ainsa basins). AFT analysis from a transect of the south‐Pyrenean basin show the southward decrease of the fission track reset level from the southern edge of the Axial Zone to the South‐Pyreneanfrontal thrust, implying the southwards decrease of the burial amount from more than 5kmin the north to less than 3km in the south assuming an average geothermal gradient of 25°C.km‐1. The structural setting of the Jaca basin attests that the burial of the synorogenicsediments was mainly due to the sedimentary accumulation. AFT data from the northernpart of the basin display a late Oligocene‐early (middle) Miocene cooling event. Newinterpretation of industrial seismic reflection profiles across the Jaca basin suggests that the Oturia thrust is rooted in the Bielsa basement thrust, responsible for the early (‐middle) Miocene out‐of‐sequence tectonic reactivation of the southern flank of the Axial Zone (Jolivet et al., 2007). These results reveal a lower Miocene (Burdigalian ‐?Langhian) out‐of sequence episode of tectonic activity of the interior of the south‐Pyrenean foreland basin. AFT data from the Axial Zone and the North‐Pyrenean Zone confirm the general southwardmigration of the thrusting system, and also bring evidence of the late Oligocene‐lowe rMiocene out‐of‐sequence tectonic reactivation of the northern flank of the Axial Zone. All these results attest of a late Oligocene‐lower Miocene (Burdigalian‐?Langhian) "pop‐up" reactivation of the inner part of the west‐central Pyrenees, younger than the sealing of thesouth‐Pyrenean front (Aquitanian‐?Burdigalian) which is classically considered to mark the end of the Pyrenean compression. These results lead us to propose a new crustal scale evolution model of the west‐central Pyrenees in 3 stages: (i) From the Late Cretaceous to themiddle Eocene, the orogenic prism is characterised by the absence of relief, related to theinversion of Cretaceous extensional structures leading to the accretion of thin crustal units; (ii) The late Eocene‐Oligocene stage corresponds to the continental collision, marked by the creation of important relief associated with the accretion of thick crustal units; (iii) During the early Miocene, the inner part of the Pyrenean wedge is tectonically reactivated.
Ce travail de thèse concerne une transversale complète des Pyrénées centro-occidentales, où on a combiné la thermochronologie basse température (traces de fission sur apatites, TFA) avec une analyse structurale détaillée pour décrire les mouvements verticaux associés à l'évolution du système chevauchant, et pour déterminer l'influence de ce dernier sur le cycle sédimentation/enfouissement/exhumation des dépôts synorogéniques du bassin d'avant‐chaine sud (bassins de Jaca et Ainsa). L'analyse TFA complète les données déjà publiées dans la Zone Axiale et la Zone Nord‐Pyrénéenne, e tconstitue la première étude de ce genre dans un bassin d'avant‐chaîne pyrénéen. Les données TFA sur la transversale du bassin sud‐pyrénéen montrent une diminution vers le sud du degré d'effacement des traces de fission, traduisant la diminution vers le sud de la quantité d'enfouissement, supérieure à 5 km au nord et inférieure à 3 km au sud dans l'hypothèse un géotherme de 25°.km‐1. Le contexte géologique montre que l'enfouissement est principalement lié à l'accumulation des dépôts synorogéniques. Les données TFA de lapartie nord du bassin montrent un refroidissement d'âge Oligocène supérieur‐Miocèneinferieur (moyen). Par ailleurs, une nouvelle interprétation de profils de sismiques réflexiondans le bassin de Jaca montre que le chevauchement d'Oturia s'enracine dans lechevauchement de socle de Bielsa, responsable de l'exhumation tectonique hors‐séquencedu bord sud de la Zone Axiale au Miocène inférieur (‐moyen) (Jolivet et al., 2007). Cesrésultats attestent donc de l'exhumation tectonique hors‐séquence au Miocène inférieur (Burdigalien‐ ?Langhien) de la partie nord du bassin d'avant‐chaine sud‐pyrénéen. Des données TFA obtenues dans la Zone Axiale et la Zone Nord‐Pyrénéenne confirment lamigration générale vers le sud du système chevauchant, et mettent également en évidencela réactivation tectonique hors‐séquence du bord nord de la Zone Axiale à l'Oligocèneterminal‐Miocène inférieur. L'ensemble de ces résultats atteste donc de la réactivation en " pop‐up " de la parties interne des Pyrénées centre‐ouest à l'Oligocène supérieur‐Miocèneinférieur (Burdigalien‐ ?Langhien), postérieurement au scellement du front sud‐pyrénéen (Aquitanien‐ ?Burdigalien) classiquement considéré comme marquant la fin de lacompression pyrénéenne. Ces données nous ont permis de proposer un nouveau modèle d'évolution crustale des Pyrénées centro‐occidentales en 3 grandes étapes : (i) du Crétacé supérieur à l'Eocène moyen, le prisme est caractérisé par une absence de relief, en lien avec l'inversion de structures extensives crétacées conduisant à l'accrétion de petites écailles crustales ; (ii) la période Eocène supérieur‐Oligocène correspond à la collision continentale proprement dite, et est marquée par la création d'importants reliefs associés à l'accrétion d'épaisses unités crustales ; (iii) au Miocène inférieur, la partie interne du prisme pyrénéen est réactivée.
https://tel.archives-ouvertes.fr/tel-00772154

Droits : info:eu-repo/semantics/OpenAccess
tel-00772154
https://tel.archives-ouvertes.fr/tel-00772154
https://tel.archives-ouvertes.fr/tel-00772154/document
https://tel.archives-ouvertes.fr/tel-00772154/file/thesemeresse.pdf

Éditeur(s) : Elsevier Sci Ltd
Résumé : A detailed morphological analysis of the outer shelf and continental slope of the Western Gulf of Lion is presented, based on swath bathymetry data together with sub-bottom profiles and high resolution seismic reflection profiles. These data reveal two main erosive features, of very different dimensions: the axial incision and the canyon's major valley. The height of axial incisions' flanks with respect to the canyon deepest point (the thalweg) ranges from 40 to 150 m. It creates a small axial erosive path within the canyon's major valley, which is typically bounded by flanks of more than 700 m in height. We interpret the axial incision observed in the sea floor as the imprint of turbidity currents that eroded the floor of canyons during phases of connection to rivers (hyperpycnal turbidity current). Such currents are most likely to have formed during the Last Glacial Maximum (LGM) as both proximity of the shoreline (due to the lowstand of sea level) and high detrital sediment supply (due to glacial abrasion upstream) increased the flow of sediments delivered to the canyon heads. Fossil axial incisions, observed in seismic lines, are related to equivalent conditions. The axial incision, however, has a key influence on canyon evolution as it triggers mass wasting of different sizes that affect the canyon's major valley (head and flanks). We interpret the geometry of the canyon's major valley as the result of recurrent activity of axial incisions. These periods of activity occurred during low sea levels at glacial maxima and show a cyclicity of 100,000 years for the last 400,000 years.
Marine And Petroleum Geology (0264-8172) (Elsevier Sci Ltd), 2005-06 , Vol. 22 , N. 6-7 , P. 805-826

Droits : 2005 Elsevier Ltd All rights reserved
http://archimer.ifremer.fr/doc/2005/publication-353.pdf
DOI:10.1016/j.marpetgeo.2005.03.011
http://archimer.ifremer.fr/doc/00000/353/

Éditeur(s) : HAL CCSD
Résumé : Gravitropism is a major process in vertical growth as it allows the positioning of plant in the gravity field and thus, for trees, it takes part in the light foraging strategies. Without any gravitropism, trees would adopt a weeping habit or fall on the ground due to the increasing with growth supported weight, especially at the advance regeneration stage (sapling stage) in the understorey, where tree are very slender and poorly stiff. Most of the gravitropic studies are made by physiologists in order to understand the process and thus are associated to complex laboratory methods (genetic engineering, anatomical studies, accurate 2D ou 3D measurements of form changes with time). In order to study the ecological relevance and the specific diversity of gravitropic performances in natural forests, we developed a framework that uses different kinds of datas. Synchronical analysis has been done i) at the population level in large sample of trees and ii) at the tree level from destructive measurement of the dissymmetry maturation strains known to be the main motor of the posture control reaction of trees. In both cases, biomechanical models allows to estimate some aspects of the dynamic gravitropic process. Diachronical analysis has been done in natural conditions on permanent plots, or in a more traditional way, by observing in greenhouse experiments the righting movements of plants artificially tilted. In the first case, the problem is the high variability of natural disturbances and the slowness of growth and movements in the dark understorey. The second choice allows a measurement of a capacity (i.e. the ability of the species to react in quite extreme conditions of verticality disturbance but good for growth light and nutrient conditions) that is more easy to analyse, but is maybe not so relevant for estimating the ecological strategy (some species could have developed a high efficience of gravitropic reaction in natural conditions by avoiding the mechanical disturbance or adapting the reaction to slow growth and changing environments in natural conditions). All approaches use the same basic biomechanical modelling, i) to analyse simultaneously the reaction and the disturbance (due to the weight increase) during growth, or ii) to combine different parameters (geometry, growth, weight, maturation strains) involved in shape changes and posture control. They give a classification of the species according to their gravitropic performances. Results on 15 species are discussed, with relation to shade-tolerance or avoidance.
6th Plant Biomechanics Conference
Cayenne, France

hal-00565956
https://hal.archives-ouvertes.fr/hal-00565956

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé :  
Cross-species analyses of plant functional traits have shed light on factors contributing to differences in performance and distribution, but to date most studies have focused on either leaves or stems. We extend these tissue-specific analyses of functional strategy towards a whole-plant approach by integrating data on functional traits for 13 448 leaves and wood tissues from 4672 trees representing 668 species of Neotropical trees. Strong correlations amongst traits previously defined as the leaf economics spectrum reflect a tradeoff between investments in productive leaves with rapid turnover vs. costly physical leaf structure with a long revenue stream. A second axis of variation, the 'stem economics spectrum', defines a similar tradeoff at the stem level: dense wood vs. high wood water content and thick bark. Most importantly, these two axes are orthogonal, suggesting that tradeoffs operate independently at the leaf and at the stem levels. By simplifying the multivariate ecological strategies of tropical trees into positions along these two spectra, our results provide a basis to improve global vegetation models predicting responses of tropical forests to global change.
Ecology Letters

hal-01032142
https://hal.archives-ouvertes.fr/hal-01032142
DOI : 10.1111/j.1461-0248.2010.01517.x

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
Although protists are critical components of marine ecosystems, they are still poorly characterized. Here we analysed the taxonomic diversity of planktonic and benthic protist communities collected in six distant European coastal sites. Environmental deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) from three size fractions (pico-, nano- and micro/mesoplankton), as well as from dissolved DNA and surface sediments were used as templates for tag pyrosequencing of the V4 region of the 18S ribosomal DNA. Beta-diversity analyses split the protist community structure into three main clusters: picoplankton-nanoplankton-dissolved DNA, micro/mesoplankton and sediments. Within each cluster, protist communities from the same site and time clustered together, while communities from the same site but different seasons were unrelated. Both DNA and RNA-based surveys provided similar relative abundances for most class-level taxonomic groups. Yet, particular groups were overrepresented in one of the two templates, such as marine alveolates (MALV)-I and MALV-II that were much more abundant in DNA surveys. Overall, the groups displaying the highest relative contribution were Dinophyceae, Diatomea, Ciliophora and Acantharia. Also, well represented were Mamiellophyceae, Cryptomonadales, marine alveolates and marine stramenopiles in the picoplankton, and Monadofilosa and basal Fungi in sediments. Our extensive and systematic sequencing of geographically separated sites provides the most comprehensive molecular description of coastal marine protist diversity to date.
ISSN: 1462-2912

hal-01191731
http://hal.upmc.fr/hal-01191731
http://hal.upmc.fr/hal-01191731/document
http://hal.upmc.fr/hal-01191731/file/Massana_2015_Marine_protist.pdf
DOI : 10.1111/1462-2920.12955

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
We present evidence that GPS velocity estimates of plate motions and fault slip rates agree to within uncertainties with geologic estimates during the most recent phase of the geologic evolution of the E Mediterranean region (post-Late Miocene). On this basis, we use the GPS differential velocities to estimate the timing of initiation of the principal structures in NW Turkey, the N Aegean Sea, and central Greece, including, the Marmara Sea, the Gulfs of Evia (GoE) and Corinth (GoC). and the Kephalonia Transform fault (KTF). We interpret these ages to indicate that the North Anatolian fault propagated across the N Aegean, opening the GoE and GoC and initiating the KTF, during the past 1-4 Ma. We further suggest that Aegean extension that was earlier more distributed across the Aegean Basin became focused on this new fault system allowing the southern Aegean and Peloponnisos to translate SW with little internal deformation, as observed today with GPS. This change in tectonic configuration may account for the clear geologic evidence for crustal thinning throughout the S Aegean in apparent contradiction with low present-day strain rates. We further show that the low present-day strain rate along the southern edge of the Aegean micro-plate requires substantial aseismic slip along the plate interface below Crete, consistent with the low level of historic, subduction-type earthquakes along this segment of the subduction zone.
ISSN: 0040-1951

hal-00512634
https://hal.archives-ouvertes.fr/hal-00512634
DOI : 10.1016/j.tecto.2009.05.027

Éditeur(s) : HAL CCSD
Résumé : International audience
Based on US national cancer registry data, age differences at breast cancer diagnosis have been reported between African-American women and European-American women. Such differences between populations of African and European ancestry have not been studied in other countries at a nationwide level. Here, we report and compare descriptive nationwide epidemiological indicators of invasive breast cancer for the populations of European ancestry living in the US and in mainland France and for women of African ancestry living in the US and in the French West Indies (Martinique and Guadeloupe). Based on the available data, we determined age frequency distributions, world age-standardized incidence, and the distribution of expected cases of breast cancer in a standard population of women by age. The age frequency distributions revealed that women of African ancestry were younger at diagnosis than women of European ancestry. By contrast, compared with the US regardless of ancestry and mainland France, the standardized incidences appeared lower, and the largest numbers of expected cases younger, in the French West Indies. The populations with African ancestry were not homogeneous in terms of epidemiologic indicators of age-related breast cancer. These descriptive findings suggest that populations of African ancestry cannot be considered uniform when determining whether it would be appropriate to decrease the age of entry into screening programs for breast cancer.
The Breast Journal

hal-01063922
https://hal.archives-ouvertes.fr/hal-01063922
DOI : 10.1111/tbj.12228
PUBMED : 24617611

Éditeur(s) : HAL CCSD Elsevier Science
Résumé : International audience
Some anthropogenic noise is now considered pollution, with evidence building that noise from human activities such as transportation, construction and exploration can impact behaviour and physiology in a broad range of taxa. However, relatively little research has considered the effects of repeated or chronic noise; extended exposures may result in habituation or sensitisation, and thus changes in response. We conducted a field-based experiment at Moorea Island to investigate how repeated exposure to playback of motorboat noise affected a coral reef fish (Dascyllus trimaculatus). We found that juvenile D. trimaculatus increased hiding behaviour during motorboat noise after two days of repeated exposure, but no longer did so after one and two weeks of exposure. We also found that naïve individuals responded to playback of motorboat noise with elevated ventilation rates, but that this response was diminished after one and two weeks of repeated exposure. We found no strong evidence that baseline blood cortisol levels, growth or body condition were affected by three weeks of repeated motorboat-noise playback. Our study reveals the importance of considering how tolerance levels may change over time, rather than simply extrapolating from results of short-term studies, if we are to make decisions about regulation and mitigation.
ISSN: 0013-9327

Droits : http://creativecommons.org/licenses/by/
hal-01357915
https://hal-univ-perp.archives-ouvertes.fr/hal-01357915
https://hal-univ-perp.archives-ouvertes.fr/hal-01357915/document
https://hal-univ-perp.archives-ouvertes.fr/hal-01357915/file/1-s2.0-S0269749116304468-main.pdf
DOI : 10.1016/j.envpol.2016.05.058

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
During their immature life stages, malaria mosquitoes are exposed to a wide array of microbes and contaminants from the aquatic habitats. Although prior studies have suggested that environmental exposure shapes the microbial community structure in the adult mosquito, most reports have focused on laboratory-based experiments and on a single mosquito epithelium, the gut. In this study, we investigated the influence of the breeding site on the development of the Anopheles coluzzii and Anopheles gambiae microbiota in natural conditions. We characterized bacterial communities from aquatic habitats, at surface microlayer and subsurface water levels, to freshly emerge adult mosquitoes using multiplexed 16S rRNA gene pyrosequencing and we separately analyzed the microbiota associated with the different epithelia of adult individual, midguts, ovaries and salivary glands. We found that the distribution of bacterial communities in the aquatic habitats differed according to the depth of water collections. Inter-individual variation of bacterial composition was large in larvae guts but adult mosquitoes from a same breeding site shared quite similar microbiota. Although some differences in bacterial abundances were highlighted between the different epithelia of freshly emerged An. coluzzii and An. gambiae, an intriguing feature from our study is the particular similarity of the overall bacterial communities. Our results call for further investigations on the bacterial population dynamics in the different tissues to determine the distinctive characteristics of each microbiota during the mosquito lifespan and to identify specific interactions between certain key phyla or species and the insect life history traits.
ISSN: 1567-1348

hal-01546167
https://hal.archives-ouvertes.fr/hal-01546167
DOI : 10.1016/j.meegid.2014.09.029

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
The mechanism for tree orientation in angiosperms is based on the production of high tensile stress on the upper side of the inclined axis. In many species, the stress level is strongly related to the presence of a peculiar layer, called G-layer, in the fibre wall. The structure of G-layer has been recently described as a hydrogel thanks to N2 adsorption-desorption isotherms of supercritically dried samples showing a high mesoporosity (pores size from 2 to 50 nm). This led us to revisit the concept of G-layer that was until now only described from anatomical observation. Adsorption isotherms of both normal wood and tension wood have been measured on six tropical species. Measurements show that mesoporosity is high in tension wood with typical thick G-layer while it is much less with thinner G-layer, sometimes no more than normal wood. The mesoporosity of tension wood species without G-layer is as low as in normal wood. Not depending on the amount of pores, the pore sizes distribution are always centred around 6-12 nm. These results suggest that, among species producing fibres with G-layer, large structural differences of G-layer exist between species
ISSN: 0022-0957

hal-00387861
https://hal.archives-ouvertes.fr/hal-00387861
DOI : 10.1093/jxp/erp133

Éditeur(s) : HAL CCSD
Résumé : International audience
This paper describes a blood alcohol content estimation method for car driver, based on a comportment analysis performed within a realistic simulation. An artificial neural network learns how to estimate subject's blood alcohol content. Low-level recording of user actions on the steering wheel and pedals are used to feed a multilayer perceptron, and a breathalyzer is used to build the learning examples set (desired output). Results are compared with a successful previous work based on a simple video game and demonstrate the ''complexity scalability'' of the approach.
The 20 th European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning - Proceedings - Bruges, Belgium from 25 to 27 April 2012 .
Bruges, Belgium

hal-00850136
https://hal.archives-ouvertes.fr/hal-00850136

Éditeur(s) : HAL CCSD Springer Verlag (Germany)
Résumé : International audience
*Context Increased knowledge on diversity in wood properties would have implications both for fundamental research and for promoting a diversification of uses as material. *Aims The objective is to contribute to overcoming the critical lack of data on the diversity of wood dynamic mechanical/viscoelastic vibrational properties, by testing lesser-known species and categorizing sources of variability. *Methods Air-dry axial specific dynamic modulus of elasticity (E'/γ) and damping coefficient (tanδ) were measured on a wide sampling (1792 specimens) of 98 wood types from 79 species. An experimental device and protocol was designed for conducting systematic (i.e. rapid and reproducible) characterizations. *Results Diversity at the specimens' level corroborates the "standard" relationship between tanδ and E'/γ, which is discussed in terms of orientation of wood elements and of chemical composition. Diversity at the species level is expressed on the basis of results for normal heartwood, with specific gravity (γ) ranging from 0.2 to 1.3. Axial E'/γ ranges from 9 to 32 GPa and tanδ from 4×10-3 to 19×10-3. Properties distribution follows a continuum, but with group characteristics. The lowest values of tanδ are only found in certain tropical hardwoods. Results can also suggest alternative species for musical instruments making.
Annals of Forest Science

hal-00808242
https://hal.archives-ouvertes.fr/hal-00808242
https://hal.archives-ouvertes.fr/hal-00808242/document
DOI : 10.1007/s13595-011-0166-z

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
New investigations in the Neogene Boudinar basin (Morocco) provide new information about the Messinian Salinity Crisis (MSC) and Zanclean reflooding in the southern part of the Alboran realm (westernmost Mediterranean). Based on a new field, sedimentological and palaeontological analyses, the age and the geometry of both the Messinian erosional surface (MES) and the overlying deposits have been determined. The MES is of late Messinian age and was emplaced in subaerial settings. In the Boudinar basin, a maximum of 200 m of Miocene sediments was eroded, including late Messinian gypsum blocks. The original geometry of the MES is preserved only when it is overlain by late Messinian continental deposits, conglomeratic alluvial fans or lacustrine marly sediments. These sediments are interpreted as indicators of the sea-level fall during the MSC. Elsewhere in the basin, the contact between late Messinian and early Pliocene deposits is a low-angle dipping, smooth surface that corresponds to the early Pliocene transgression surface that subsequently re-shaped the regressive MES. The early Pliocene deposits are characterized by: (i) their onlap onto either the basement of the Rif chain or the late Miocene deposits; (ii) lagoonal deposits at the base to offshore marls and sands at the top (earliest Pliocene; 5.33–5.04 Ma interval; foraminifer zone PL1); (iii) marine recovery occurring in the 5.32–5.26 Ma interval; and (iv) the change from lagoonal to offshore environments occurring within deposits tens of metres thick. This information indicates that at least the end of the reflooding period was progressive, not catastrophic as previously thought.
ISSN: 0037-0738

hal-01306672
https://hal.archives-ouvertes.fr/hal-01306672
DOI : 10.1016/j.sedgeo.2015.12.014

Éditeur(s) : HAL CCSD Endocrine Society
Résumé : International audience
: Context:Masculinization depends on the fetal testis. Exposure of the human fetus during pregnancy to paracetamol or/and to other mild-analgesics is associated with an increased risk of cryptorchidism.Objective:We aimed at determining whether mild analgesics disrupted the morphology and endocrine function of the human testis.Design:We used an in vitro system based on the culture of human fetal testes exposed or not to paracetamol, its metabolite AM404, aspirin, indomethacin, ketoconazole at 10(-4) M to 10(-7) M.Setting:The study was conducted at the University of Rennes I.Patients/Participants:Human fetal testes were from pregnant women following induced abortion, between 7 and 12 weeks of gestation (GW).Main Outcome Measures:Testosterone (radioimmunoassay: RIA), Anti-Müllerian Hormone (AMH; ELISA), insulin-like factor 3 (INSL3; RIA), prostaglandin D2 and E2 (PGD2 and PGE2, respectively; ELISA), were assayed in the media. Testicular cells were counted using histology and image analysis. The possible nuclear receptor-mediated activities of the analgesics were investigated using reporter cell lines expressing estrogen (ERs), androgen (AR) and peroxysome proliferator-activated γ ( PPARγ) receptors.Results:Indomethacin and aspirin stimulated testosterone production, particularly by the younger testes (8-9 GW vs 10-12 GW). Paracetamol, AM404 and ketoconazole decreased INSL3 levels. Aspirin stimulated, whereas ketoconazole inhibited AMH production. PGE2 levels were inhibited by paracetamol, and aspirin in the 7-12 GW testes, and by indomethacin but only in 7-9.86 GW old testes. The inhibitory trends seen for PGD2 were not statistically significant.Conclusions:Analgesics at concentrations relevant to human exposure cause endocrine disturbances in the fetal testis. We suggest that the fetal human testis displays slight critical age windows for sensitivity to direct exposure to aspirin, indomethacin and paracetamol. The analgesic-induced inhibition of INSL3 may be the mechanism by which analgesics increase the risk of cryptorchidism. Greater caution is required concerning consumption of analgesics during pregnancy.
ISSN: 0021-972X

inserm-00876125
http://www.hal.inserm.fr/inserm-00876125
DOI : 10.1210/jc.2013-2531
PUBMED : 24030937