Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : While Amazonian forests are extraordinarily diverse, the abundance of trees is skewed strongly towards relatively few 'hyperdominant' species. In addition to their diversity, Amazonian trees are a key component of the global carbon cycle, assimilating and storing more carbon than any other ecosystem on Earth. Here we ask, using a unique data set of 530 forest plots, if the functions of storing and producing woody carbon are concentrated in a small number of tree species, whether the most abundant species also dominate carbon cycling, and whether dominant species are characterized by specific functional traits. We find that dominance of forest function is even more concentrated in a few species than is dominance of tree abundance, with only ≈1% of Amazon tree species responsible for 50% of carbon storage and productivity. Although those species that contribute most to biomass and productivity are often abundant, species maximum size is also influential, while the identity and ranking of dominant species varies by function and by region.
ISSN: 2041-1723

hal-01204225
https://hal.archives-ouvertes.fr/hal-01204225
DOI : 10.1038/ncomms7857
PRODINRA : 305614
PUBMED : 25919449

Éditeur(s) : HAL CCSD American Association for the Advancement of Science
Résumé :  
Amazon forests are a key but poorly understood component of the global carbon cycle. If, as anticipated, they dry this century, they might accelerate climate change through carbon losses and changed surface energy balances. We used records from multiple long-term monitoring plots across Amazonia to assess forest responses to the intense 2005 drought, a possible analog of future events. Affected forest lost biomass, reversing a large long-term carbon sink, with the greatest impacts observed where the dry season was unusually intense. Relative to pre-2005 conditions, forest subjected to a 100-millimeter increase in water deficit lost 5.3 megagrams of aboveground biomass of carbon per hectare. The drought had a total biomass carbon impact of 1.2 to 1.6 petagrams (1.2 × 1015 to 1.6 × 1015 grams). Amazon forests therefore appear vulnerable to increasing moisture stress, with the potential for large carbon losses to exert feedback on climate change.
ISSN: 0036-8075

hal-01032111
https://hal.archives-ouvertes.fr/hal-01032111
DOI : 10.1126/science.1164033

Éditeur(s) : HAL CCSD Landes Bioscience
Résumé : International audience
In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
Autophagy

hal-00735751
https://hal.archives-ouvertes.fr/hal-00735751
PUBMED : 22966490

Éditeur(s) : HAL CCSD Oxford University Press
Résumé : International audience
The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations.
ISSN: 0305-1048

hal-01146849
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01146849
DOI : 10.1093/nar/gkv350
PUBMED : 25897122

Éditeur(s) : HAL CCSD Elsevier
Résumé : Eperua falcata (Aublet), a late-successional species in tropical rainforest and one of the most abundant tree in French Guiana, has developed an original strategy concerning N-acquisition by largely preferring nitrate, rather than ammonium (H. Schimann, S. Ponton, S. Hattenschwiler, B. Ferry, R. Lensi, A.M. Domenach, J.C. Roggy, Differing nitrogen use strategies of two tropical rainforest tree species in French Guiana: evidence from N-15 natural abundance and microbial activities, Soil Biol, Biochem. 40 (2008) 487-494). Given the preference of this species for nitrate, we hypothesized that root exudates would promote nitrate availability by (a) enhancing nitrate production by stimulating ammonium oxidation or (b) minimizing nitrate losses by inhibiting denitrification. Root exudates were collected in situ in monospecific planted plots. The phytochemical analysis of these exudates and of several of their corresponding root extracts was achieved using UHPLC/DAD/ESI-QTOF and allowed the identification of diverse secondary metabolites belonging to the flavonoid family. Our results show that (i) the distinct exudation patterns observed are related to distinct root morphologies, and this was associated with a shift in the root flavonoid content, (ii) a root extract representative of the diverse compounds detected in roots showed a significant and selective metabolic inhibition of isolated denitrifiers in vitro, and (iii) in soil plots the abundance of nirK-type denitrifiers was negatively affected in rhizosphere soil compared to bulk. Altogether this led us to formulate hypothesis concerning the ecological role of the identified compounds in relation to N-acquisition strategy of this species. (C) 2013 Elsevier Masson SAS. All rights reserved.
ISSN: 0981-9428

hal-01032437
https://hal.archives-ouvertes.fr/hal-01032437
DOI : 10.1016/j.plaphy.2013.05.003

Éditeur(s) : HAL CCSD Mont-Saint-Aignan : Publications des Universités de Rouen et du Havre
Résumé : International audience
The literature on the history of the Paralympics movement tends to present the British games of Stoke Mandeville as the unique origin of the movement and neurosurgeon, Guttman, as a founder hero. Yet, in France initiatives were carried out outside the British dynamics of sports for physically handicapped. They resulted in a range of sports offers stemming out of a self-organized movement created by and for civilian disabled and war-disabled. This self-organization of physically handicapped people, quickly took on a sporting dimension, distinguishing itself from the organizations doctors working in functional rehabilitation services would propose to their patients in the United Kingdom. The French movement quickly took part into the national sports movement. It got structured with a view to include all disabled people into the sporting sphere, then went further into the process of extension and sportivation within international standards. This study builds on a set of data drawn from various revues from different associations of sports movement for French physically disabled from 1954 to 1972. Interviews with major French leaders have also been inserted. We privileged internal sources to focus on the analysis of self-organization dynamics.
La littérature sur l’histoire du mouvement paralympique tend à faire des Jeux britanniques de Stoke Mandeville l’origine unique du mouvement, et du neurochirurgien Guttmann un héros fondateur. Or en France, des initiatives se structurent en dehors de la dynamique britannique du sport pour handicapés physiques. Elles produisent une offre sportive à partir d’une auto-organisation créée par et pour des mutilés de guerre et invalides civils.Cette auto-organisation d’individus handicapés physiques se démarque rapidement de l’organisation proposée par les médecins dans les services de réadaptation fonctionnelle comme au Royaume-Uni, en s’orientant vers une dimension sportive. En s’appuyant sur des réseaux militaires, civils et politiques, le mouvement français participe rapidement au mouvement sportif national. Il se structure alors à partir d’un objectif d’intégration de tous les publics déficients à la sphère sportive, et porte cette volonté d’ouverture et de sportivisation dans les instances internationales. Cette étude s’appuie sur un corpus de données issues des revues des différentes associations du mouvement sportif pour handicapés physiques français de 1954 à 1972, enrichi d’entretiens avec les principaux dirigeants français. Le privilège accordé aux sources internes correspond au choix de centrer l’analyse sur la dynamique d’auto-organisation.
ISSN: 1999-8589

hal-01681465
https://hal.archives-ouvertes.fr/hal-01681465

Éditeur(s) : HAL CCSD
Résumé : International audience
Les enseignements basés sur les effets de contexte visent à mettre les contextes au cœur du design pédagogique. A partir de l’exemple d’un apprentissage sur la grenouille impliquant des élèves de Repentigny (Québec) et du Moule (Guadeloupe) les modalités et les motivations de ce type d’enseignement seront exposées. Il s’appuie sur la gestion de l’émergence des effets de contextes liée aux écarts de conceptions des élèves tout au long d’une séquence pédagogique incluant notamment un environnement numérique de travail et une démarche d’investigation.Dans une méthodologie de design based research, de nombreuses données directes et indirectes ont été collectées. Les résultats préliminaires montrent différents types d’expression des effets de contexte ainsi que les thèmes et moments où ils émergent. Une modélisation des lieux et des moments d’émergence des effets de contexte est menée à partir des différences entre les contextes écologiques sur lesquels les élèves travaillent. Elle vise à fournir des outils prédictifs pour le chercheur comme pour le concepteur d’enseignement. La discussion portera sur La place de l’ ’environnement numérique de travail dans ce les enseignements basés sur les effets de contexte, les possibles généralisations de ce type d’enseignement et l’élaboration d’un « Context-Aware Intelligent Tutoring System ».
Congrès de l’Association francophone pour le savoir (ACFAS) 2014
Montréal, Canada

hal-01539478
https://hal.univ-antilles.fr/hal-01539478

Éditeur(s) : HAL CCSD
Résumé : International audience
In, Ruffié S. et Ferez S. (dir), Corps, Sport, Handicaps (T1). L’institutionalisation du mouvement handisport (1954-2008), Paris, Téraèdre, 31- 47

hal-01681860
https://hal.archives-ouvertes.fr/hal-01681860

Éditeur(s) : HAL CCSD Presses université de Laval
Résumé : International audience
This article aims to specify the challenges related to adapting the Disability Creation Process (DCP) model to the experience of chronic disease, specifically Human immunodeficiency virus (HIV). In this perspective, a conceptual clarification is proposed because the DCP is mainly used to study populations in situations of disability due to motor, sensory, mental or behavioral disabilities. However, this model seems to be able to adequately read the specific experience of HIV, and help to understand differently life trajec-tories of people living with HIV (PLHIV). Indeed, HIV infection, despite its status as a "chronic disease", continues to contribute to the risk of social isolation. Body modifications induced by the disease or its treatment has an impact on how others view PLHIV. They expose the visibility of HIV status and, ultimately, the fear of social exclusion. In this respect, the analysis of the DCP may allow us to understand the varia-tions in the quality of social participation and identify the phases of vulnerability by focusing on body image in particular induced by the infection or treatments. This approach provides the opportunity for new insight into the influence of social environments (particularly health management or community support) with re-gards to the lifestyle and the daily experiences of socially disadvantaged people.
Cet article tente de spécifier les enjeux d’une adaptation du modèle du Processus de production du handicap (PPH) au vécu de la maladie chronique, et plus spécifiquement du virus de l’immunodéfi-cience humaine (VIH). Dans cette perspective, un éclaircissement conceptuel est proposé, car le PPH a principalement été utilisé pour étudier les populations vivant des situations de handicap liées à des incapa-cités motrices, sensorielles, intellectuelles ou comportementales. Ce modèle semble toutefois en mesure de renouveler la lecture de l’expérience spécifique du VIH, et d’aider à saisir autrement les trajectoires de vie des personnes vivant avec le VIH (PVVIH). En effet, l’infection au VIH, malgré son statut de « maladie chronique », demeure associée à un risque d’isolement social. Les modifications corporelles induites par la maladie ou par son traitement confronte les PVVIH au regard de l’autre. Elles exposent à la visibilité du statut sérologique et, in fine, à la peur de l’exclusion sociale. Dans ce cadre, l’analyse du Processus de production du handicap peut permettre de comprendre les variations de la qualité de la participation sociale et d’identifier les phases de vulnérabilité en s’intéressant notamment au rapport au corps induit par l’infection et les traitements. Cette approche offre l’opportunité d’un nouvel éclairage sur le poids des envi-ronnements sociaux (notamment des dispositifs de prises en charge sanitaire ou d’accompagnement communautaire) sur les habitudes de vie et l’expérience quotidienne d’un public fragilisé socialement.
ISSN: 1499-5549

hal-01681423
https://hal.archives-ouvertes.fr/hal-01681423

Éditeur(s) : HAL CCSD International Union of Crystallography
Résumé : International audience
ISSN: 0021-8898

cea-01377306
https://hal-cea.archives-ouvertes.fr/cea-01377306
DOI : 10.1107/S0021889813027453

Éditeur(s) : HAL CCSD EDP Sciences
Résumé : Cette communication présente les principaux résultats du projet ExtraFlo sur l'estimation des pluies et crues extrêmes. A partir d'un jeu de données conséquent de plusieurs milliers de stations, une procédure d'inter-comparaison a permis d'évaluer les performances d'une trentaine d'implémentations différentes issues de différentes combinaisons (modèle probabiliste, méthode d'estimation, cadre local / régional / mixte local et régional). Le projet ExtraFlo a permis de mettre en évidence le manque de robustesse des approches basées sur le traitement statistique d'une série de quelques dizaines d'années d'observation. Des alternatives intéressantes existent, basées sur l'exploitation des records de pluie et de débit à l'échelle d'une région, de la collecte de données historiques quand cela est possible, de méthodes de simulation basées sur le couplage d'un générateur d'averses avec un modèle hydrologique pour la transformation des pluies en débit, ou des traces morphologiques laissées par les crues anciennes.
ISSN: 0018-6368

hal-01054313
https://hal.archives-ouvertes.fr/hal-01054313
DOI : 10.1051/1hb/2014010

Éditeur(s) : HAL CCSD Wiley
Résumé : Over the past three decades, many small-scale floristic studies of white-sand forests across the Amazon basin have been published. Nonetheless, a basin-wide description of both taxonomic and phylogenetic alpha and beta diversity at regional scales has never been achieved. We present a complete floristic analysis of white-sand forests across the Amazon basin including both taxonomic and phylogenetic diversity. We found strong regional differences in the signal of phylogenetic community structure with both overall and regional Net Relatedness Index and Nearest Taxon Index values found to be significantly positive leading to a pattern of phylogenetic clustering. Additionally, we found high taxonomic dissimilarity but low phylogenetic dissimilarity in pairwise community comparisons. These results suggest that recent diversification has played an important role in the assembly of white-sand forests causing geographic neo-endemism patterns at the regional scale.
ISSN: 0006-3606

hal-01532549
https://hal.archives-ouvertes.fr/hal-01532549
DOI : 10.1111/btp.12298
PRODINRA : 353398

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
Studies on the periodicity of wood formation provide essential data on tree age and factors related to the control of tree growth. The aim of this work was to investigate the cambial phenology and its relation with leaf phenology and climatic seasonality in two tropical rainforest species belonging to the genus Parkia known for having a contrasted leaf phenology. From wood samples collected at 15 day intervals from April 2009 to February 2012 in five trees of both species, we quantified cambial activity by counting layers of cells in cambial zone, enlarging cells zone and wall thickening cells zone from wood prepared anatomical micro sections. In the same time, we observed leaf shedding behaviors in the crown of the studied trees. In both species, cambial activity was significantly reduced during leafless period. However, the cambial activity of P. velutina was not affected by seasonality while in P. nitida, we found a significant positive effect of the dry season on cambial activity. This diminution of activity associated to leaf shedding occurred annually during the dry season in P. nitida whereas the trees were not synchronous in time for P. velutina. On the contrary that is often admitted, the rest cambial period can be independent of environmental restriction such as dry season. Leaf phenology remains the best proxy to estimate cambial activity.
ISSN: 0931-1890

hal-01135166
https://hal.archives-ouvertes.fr/hal-01135166
https://hal.archives-ouvertes.fr/hal-01135166/document
https://hal.archives-ouvertes.fr/hal-01135166/file/Art_Morel_al_Seasonal_variations_phenological_traits_2015.pdf
DOI : 10.1007/s00468-015-1177-4

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
CD95 ligand (CD95L) is expressed by immune cells and triggers apoptotic death. Metalloprotease-cleaved CD95L (cl-CD95L) is released into the bloodstream but does not trigger apoptotic signaling. Hence, the pathophysiological role of cl-CD95L remains unclear. We observed that skin-derived endothelial cells from systemic lupus erythematosus (SLE) patients expressed CD95L and that after cleavage, cl-CD95L promoted T helper 17 (Th17) lymphocyte transmigration across the endothelial barrier at the expense of T regulatory cells. T cell migration relied on a direct interaction between the CD95 domain called calcium-inducing domain (CID) and the Src homology 3 domain of phospholipase C gamma 1. Th17 cells stimulated with cl-CD95L produced sphingosine-1-phosphate (S1P), which promoted endothelial transmigration by activating the S1P receptor 3. We generated a cell-penetrating CID peptide that prevented Th17 cell transmigration and alleviated clinical symptoms in lupus mice. Therefore, neutralizing the CD95 non-apoptotic signaling pathway could be an attractive therapeutic approach for SLE treatment.
ISSN: 1074-7613

hal-01359568
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01359568
DOI : 10.1016/j.immuni.2016.06.028
PUBMED : 27438772