Éditeur(s) : Public Library Science
Résumé : Subsurface sediments of the Sonora Margin (Guaymas Basin), located in proximity of active cold seep sites were explored. The taxonomic and functional diversity of bacterial and archaeal communities were investigated from 1 to 10 meters below the seafloor. Microbial community structure and abundance and distribution of dominant populations were assessed using complementary molecular approaches (Ribosomal Intergenic Spacer Analysis, 16S rRNA libraries and quantitative PCR with an extensive primers set) and correlated to comprehensive geochemical data. Moreover the metabolic potentials and functional traits of the microbial community were also identified using the GeoChip functional gene microarray and metabolic rates. The active microbial community structure in the Sonora Margin sediments was related to deep subsurface ecosystems (Marine Benthic Groups B and D, Miscellaneous Crenarchaeotal Group, Chloroflexi and Candidate divisions) and remained relatively similar throughout the sediment section, despite defined biogeochemical gradients. However, relative abundances of bacterial and archaeal dominant lineages were significantly correlated with organic carbon quantity and origin. Consistently, metabolic pathways for the degradation and assimilation of this organic carbon as well as genetic potentials for the transformation of detrital organic matters, hydrocarbons and recalcitrant substrates were detected, suggesting that chemoorganotrophic microorganisms may dominate the microbial community of the Sonora Margin subsurface sediments.
Plos One (1932-6203) (Public Library Science), 2014-08 , Vol. 9 , N. 8 , P. e104427

Droits : This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
http://archimer.ifremer.fr/doc/00203/31408/29801.pdf
DOI:10.1371/journal.pone.0104427
http://archimer.ifremer.fr/doc/00203/31408/

Éditeur(s) : HAL CCSD Society for Range Management
Résumé : Grasslands and agroecosystems occupy one-third of the terrestrial area, but their contribution to the global carbon cycle remains uncertain. We used a set of 316 site-years of CO(2) exchange measurements to quantify gross primary productivity, respiration, and light-response parameters of grasslands, shrublands/savanna, wetlands, and cropland ecosystems worldwide. We analyzed data from 72 global flux-tower sites partitioned into gross photosynthesis and ecosystem respiration with the use of the light-response method (Gilmanov, T. G., D. A. Johnson, and N. Z. Saliendra. 2003. Growing season CO(2) fluxes in a sagebrushsteppe ecosystem in Idaho: Bowen ratio/energy balance measurements and modeling. Basic and Applied Ecology 4:167-183) from the RANGEFLUX and WORLDGRASSAGRIFLUX data sets supplemented by 46 sites from the FLUXNET La Thuile data set partitioned with the use of the temperature-response method (Reichstein, M., E. Falge, D. Baldocchi, D. Papale, R. Valentini, M. Aubinet, P. Berbigier, C. Bernhofer, N. Buchmann, M. Falk, T. Gilmanov, A. Granier, T. Grunwald, K. Havrankova, D. Janous, A. Knohl, T. Laurela, A. Lohila, D. Loustau, G. Matteucci, T. Meyers, F. Miglietta, J.M. Ourcival, D. Perrin, J. Pumpanen, S. Rambal, E. Rotenberg, M. Sanz, J. Tenhunen, G. Seufert, F. Vaccari, T. Vesala, and D. Yakir. 2005. On the separation of net ecosystem exchange into assimilation and ecosystem respiration: review and improved algorithm. Global Change Biology 11: 1.424-1439). Maximum values of the quantum yield (alpha = 75 mmol.mol(-1)), photosynthetic capacity (A(max) = 3.4 mg CO(2) . m(-2).s-1), gross photosynthesis (P(g,max) = 1.16 g CO(2) . m(-2).d(-1)), and ecological light-use efficiency (epsilon(ecol) = 59 mmol . mol(-1)) of managed grasslands and high-production croplands exceeded those of most forest ecosystems, indicating the potential of nonforest ecosystems for uptake of atmospheric CO(2). Maximum values of gross primary production (8 600 g CO(2) . m(-2).yr(-1)), total ecosystem respiration (7 900 g CO(2) . m(-2).yr(-1)), and net CO(2) exchange (2 400 g CO(2) . m(-2).yr(-1)) were observed for intensively managed grasslands and high-yield crops, and are comparable to or higher than those for forest ecosystems, excluding some tropical forests. On average, 80% of the nonforest sites were apparent sinks for atmospheric CO(2), with mean net uptake of 700 g CO(2) . m(-2).yr(-1) for intensive grasslands and 933 g CO(2) . m(-2).d(-1) for croplands. However, part of these apparent sinks is accumulated in crops and forage, which are carbon pools that are harvested, transported, and decomposed off site. Therefore, although agricultural fields may be predominantly sinks for atmospheric CO(2), this does not imply that they are necessarily increasing their carbon stock.
ISSN: 1550-7424

hal-01190754
https://hal.archives-ouvertes.fr/hal-01190754
DOI : 10.2111/rem-d-09-00072.1
PRODINRA : 214043

Éditeur(s) : HAL CCSD
Résumé : National audience
Congrès de la SPTC - Société de Pharmaco-Toxicologie Cellulaire
Paris, France

hal-01122677
https://hal.archives-ouvertes.fr/hal-01122677

Éditeur(s) : HAL CCSD
Résumé : International audience
BACKGROUND: The aryl hydrocarbon receptor (AhR) has gradually emerged as a regulator of inflammation in the lung and other tissues. AhR may interact with the p65-subunit of the nuclear factor (NF)-κB transcription factors, but reported outcomes of AhR/NF-κB-interactions are conflicting. Some studies suggest that AhR possess pro-inflammatory activities while others suggest that AhR may be anti-inflammatory. The present study explored the impact of AhR and its binding partner AhR nuclear translocator (Arnt) on p65-activation and two differentially regulated chemokines, CXCL8 (IL-8) and CCL5 (RANTES), in human bronchial epithelial cells (BEAS-2B). RESULTS: Cells were exposed to CXCL8- and CCL5-inducing chemicals, 1-nitropyrene (1-NP) and 1-aminopyrene (1-AP) respectively, or the synthetic double-stranded RNA analogue, polyinosinic-polycytidylic acid (Poly I:C) which induced both chemokines. Only CXCL8, and not CCL5, appeared to be p65-dependent. Yet, constitutively active unligated AhR suppressed both CXCL8 and CCL5, as shown by siRNA knock-down and the AhR antagonist α-naphthoflavone. Moreover, AhR suppressed activation of p65 by TNF-α and Poly I:C as assessed by luciferase-assay and p65-phosphorylation at serine 536, without affecting basal p65-activity. In contrast, Arnt suppressed only CXCL8, but did not prevent the p65-activation directly. However, Arnt suppressed expression of the NF-κB-subunit RelB which is under transcriptional regulation by p65. Furthermore, AhR-ligands alone at high concentrations induced a moderate CXCL8-response, without affecting CCL5, but suppressed both CXCL8 and CCL5-responses by Poly I:C. CONCLUSION: AhR and Arnt may differentially and independently regulate chemokine-responses induced by both inhaled pollutants and pulmonary infections. Constitutively active, unligated AhR suppressed the activation of p65, while Arnt may possibly interfere with the action of activated p65. Moreover, ligand-activated AhR suppressed CXCL8 and CCL5 responses by other agents, but AhR ligands alone induced CXCL8 responses when given at sufficiently high concentrations, thus underscoring the duality of AhR in regulation of inflammation. We propose that AhR-signaling may be a weak activator of p65-signaling that suppresses p65-activity induced by strong activators of NF-κB, but that its anti-inflammatory properties also are due to interference with additional pathways.
Cell communication and signaling: CCS

hal-01063555
https://hal.archives-ouvertes.fr/hal-01063555
DOI : 10.1186/s12964-014-0048-8

Éditeur(s) : Pergamon-elsevier Science Ltd
Résumé : Society's needs for a network of in situ ocean observing systems cross many areas of earth and marine science. Here we review the science themes that benefit from data supplied from ocean observatories. Understanding from existing studies is fragmented to the extent that it lacks the coherent long-term monitoring needed to address questions at the scales essential to understand climate change and improve geo-hazard early warning. Data sets from the deep sea are particularly rare with long-term data available from only a few locations worldwide. These science areas have impacts on societal health and well-being and our awareness of ocean function in a shifting climate. Substantial efforts are underway to realise a network of open-ocean observatories around European Seas that will operate over multiple decades. Some systems are already collecting high-resolution data from surface, water column, seafloor, and sub-seafloor sensors linked to shore by satellite or cable connection in real or near-real time, along with samples and other data collected in a delayed mode. We expect that such observatories will contribute to answering major ocean science questions including: How can monitoring of factors such as seismic activity, pore fluid chemistry and pressure, and gas hydrate stability improve seismic, slope failure, and tsunami warning? What aspects of physical oceanography, biogeochemical cycling, and ecosystems will be most sensitive to climatic and anthropogenic change? What are natural versus anthropogenic changes? Most fundamentally, how are marine processes that occur at differing scales related? The development of ocean observatories provides a substantial opportunity for ocean science to evolve in Europe. Here we also describe some basic attributes of network design. Observatory networks provide the means to coordinate and integrate the collection of standardised data capable of bridging measurement scales across a dispersed area in European Seas adding needed certainty to estimates of future oceanic conditions. Observatory data can be analysed along with other data such as those from satellites, drifting floats, autonomous underwater vehicles, model analysis, and the known distribution and abundances of marine fauna in order to address some of the questions posed above. Standardised methods for information management are also becoming established to ensure better accessibility and traceability of these data sets and ultimately to increase their use for societal benefit. The connection of ocean observatory effort into larger frameworks including the Global Earth Observation System of Systems (GEOSS) and the Global Monitoring of Environment and Security (GMES) is integral to its success. It is in a greater integrated framework that the full potential of the component systems will be realised. Crown Copyright (C) 2011 Published by Elsevier Ltd. All rights reserved.
Progress In Oceanography (0079-6611) (Pergamon-elsevier Science Ltd), 2011-10 , Vol. 91 , N. 1 , P. 1-33

Droits : 2011 Published by Elsevier Ltd. All rights reserved.
http://archimer.ifremer.fr/doc/00044/15557/15923.pdf
DOI:10.1016/j.pocean.2011.05.001
http://archimer.ifremer.fr/doc/00044/15557/

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 Springer Verlag
Résumé : The area of forest plantations is increasing worldwide helping to meet timber demand and protect natural forests. However, with global change, monospecific plantations are increasingly vulnerable to abiotic and biotic disturbances. As an adaption measure we need to move to plantations that are more diverse in genotypes, species, and structure, with a design underpinned by science. TreeDivNet, a global network of tree diversity experiments, responds to this need by assessing the advantages and disadvantages of mixed species plantations. The network currently consists of 18 experiments, distributed over 36 sites and five ecoregions. With plantations 1-15 years old, TreeDivNet can already provide relevant data for forest policy and management. In this paper, we highlight some early results on the carbon sequestration and pest resistance potential of more diverse plantations. Finally, suggestions are made for new, innovative experiments in understudied regions to complement the existing network.
ISSN: 0044-7447

hal-01204232
https://hal.archives-ouvertes.fr/hal-01204232
DOI : 10.1007/s13280-015-0685-1
PRODINRA : 324368
PUBMED : 26264716

Éditeur(s) : HAL CCSD
Résumé : International audience
The development of diabetic vascular complications is initiated, at least in part, by mitochondrial reactive oxygen species (ROS) production in endothelial cells. Hyperglycemia induces superoxide production in the mitochondria and initiates changes in the mitochondrial membrane potential that leads to mitochondrial dysfunction. Hydrogen sulfide (H2S) supplementation has been shown to reduce the mitochondrial oxidant production and shows efficacy against diabetic vascular damage in vivo. However, the half-life of H2S is very short and it is not specific for the mitochondria. We have therefore evaluated two novel mitochondria-targeted anethole dithiolethione and hydroxythiobenzamide H2S donors (AP39 and AP123 respectively) at preventing hyperglycemia-induced oxidative stress and metabolic changes in microvascular endothelial cells in vitro. Hyperglycemia (HG) induced significant increase in the activity of the citric acid cycle and led to elevated mitochondrial membrane potential. Mitochondrial oxidant production was increased and the mitochondrial electron transport decreased in hyperglycemic cells. AP39 and AP123 (30–300 nM) decreased HG-induced hyperpolarisation of the mitochondrial membrane and inhibited the mitochondrial oxidant production. Both H2S donors (30–300 nM) increased the electron transport at respiratory complex III and improved the cellular metabolism. Targeting H2S to mitochondria retained the cytoprotective effect of H2S against glucose-induced damage in endothelial cells suggesting that the molecular target of H2S action is within the mitochondria. Mitochondrial targeting of H2S also induced >1000-fold increase in the potency of H2S against hyperglycemia-induced injury. The high potency and long-lasting effect elicited by these H2S donors strongly suggests that these compounds could be useful against diabetic vascular complications. © 2016
Pharmacological Research

hal-01373947
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01373947
DOI : 10.1016/j.phrs.2016.08.019
PUBMED : 27565382

Éditeur(s) : HAL CCSD Taylor & Francis (Routledge)
Résumé : International audience
The Maroni basin, an isolated region delineating the border between Suriname and French Guiana has been affected by the human immunodeficiency virus (HIV) epidemic 10 years after coastal French Guiana. However, the rise in HIV prevalence was sharp, exceeding 1% within 10 years. The aim of the present study is to compare, using the first quantitative data from the general population in remote villages, the knowledge, attitudes, and behaviors regarding HIV between Maroon and Amerindian populations, the two most frequent populations living along the Maroni. Data were collected in 2012 using a structured questionnaire among a random sample of 896 individuals residing in the remote villages on the Maroni river. Proportions were compared between the Maroni and the coastal general population, and between Maroon and Amerindian populations. The present study shows significant differences between territories and between communities living on the Maroni river: the multiple sexual partnerships, more common among population living on the Maroni river, were more frequently reported in Maroons than in Amerindians. Condom use was more frequently reported among men on the Maroni river than on the coast, but these findings were reversed for women. Moreover, among people living on the Maroni river, condom use was more frequently reported among Maroons than among Amerindians. Regarding genital factors that may affect transmission, penile implant seemed to have no ethnic boundaries, steam baths seemed specific to Maroon women. The present results should help to improve community-based specific interventions.
ISSN: 0954-0121

hal-01260915
https://hal.archives-ouvertes.fr/hal-01260915
https://hal.archives-ouvertes.fr/hal-01260915/document
https://hal.archives-ouvertes.fr/hal-01260915/file/2015%2C%20Van%20Melle%20-%20Knowledge%2C%20attitudes%2C%20behaviors%2C%20and%20practices%20differences%20regarding%20HIV.pdf
DOI : 10.1080/09540121.2015.1032203

Éditeur(s) : HAL CCSD John Libbey Eurotext
Résumé : International audience
Environmental health risk assessment is commonly used in France for risk management purposes. The Methodology section of the "Société française de santé environnement" (French Society for Environmental Health) seeks to improve the utility and implementation of risk assessment in France. An initial operational objective is to make a list of short-, intermediate- and long-term improvements. This inventory is based in part on the experience and expertise of society members in this area and in part on their analysis of "Science and Decisions: Advancing Risk Assessment" (National Research Council 2009). In this paper, the Society recommends modifications in the indications for and use of risk assessments, during each of the four stages of the process: hazard identification and dose-response assessment, exposure assessment, risk characterization, and results interpretation. Some may be implemented now, while others need consensus building or research because of gaps in knowledge. Environmental health risk assessment must be understood as a decision tool for risk management in situations of uncertainly. Thus, appropriate linkage is required between decision making and assessment, and between the methods and the expected results.
L'évaluation des risques sanitaires est fréquemment utilisée en France dans les processus de décision en santé environnementale. La section " Méthodologie d'évaluation des risques sanitaires " de la Société française de santé environnement (SFSE) s'est donnée pour objectif de proposer des éléments de réflexion et des outils méthodologiques en vue d'améliorer l'utilité et les pratiques de l'évaluation des risques sanitaires. Un premier objectif opérationnel est l'inventaire des améliorations possibles à court, moyen et long termes à apporter à la démarche et à son utilisation. Ce travail s'est fondé, d'une part, sur la pratique et l'expertise des membres de la section, et, d'autre part, sur une lecture critique du rapport " Science and Decisions : Advancing Risk Assessment " publié en 2009 par le National Research Council et portant également sur les évolutions de la démarche. Dans cet article, la section restitue les conclusions de cet inventaire critique et propose un certain nombre d'améliorations en termes d'indications et d'utilisations de l'évaluation des risques sanitaires pour chacune des quatre étapes : identification des dangers et relation dose-réponse ; évaluation de l'exposition ; caractérisation des risques ; et interprétation des résultats. Certaines recommandations peuvent être mises en oeuvre immédiatement ; d'autres, en préalable à leur mise en oeuvre, nécessitent un consensus ou encore de la recherche car les connaissances manquent. En conclusion, la section insiste sur le fait que l'évaluation des risques sanitaires doit être comprise comme une aide à la décision en situation d'incertitude ; l'articulation entre le contexte décisionnel et l'évaluation, sa méthodologie et les résultats attendus est donc primordiale.
ISSN: 1635-0421

ineris-00963325
https://hal-ineris.archives-ouvertes.fr/ineris-00963325
DOI : 10.1684/ers.2011.0435
INERIS : EN-2012-016

Éditeur(s) : HAL CCSD American Association for the Advancement of Science
Résumé : The biodiversity-productivity relationship (BPR) is foundational to our understanding of the global extinction crisis and its impacts on ecosystem functioning. Understanding BPR is critical for the accurate valuation and effective conservation of biodiversity. Using ground-sourced data from 777,126 permanent plots, spanning 44 countries and most terrestrial biomes, we reveal a globally consistent positive concave-down BPR, showing that continued biodiversity loss would result in an accelerating decline in forest productivity worldwide. The value of biodiversity in maintaining commercial forest productivity alone-US$166 billion to 490 billion per year according to our estimation-is more than twice what it would cost to implement effective global conservation. This highlights the need for a worldwide reassessment of biodiversity values, forest management strategies, and conservation priorities.
ISSN: 0036-8075

hal-01607784
https://hal.archives-ouvertes.fr/hal-01607784
DOI : 10.1126/science.aaf8957
PRODINRA : 389856

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
ISSN: 1354-1013

hal-01080954
https://hal-agroparistech.archives-ouvertes.fr/hal-01080954
DOI : 10.1111/j.1365-2486.2007.01439.x

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 : International audience
The detailed morphology and internal structure of the Calabrian accretionary wedge and adjacent Eastern Sicily margin are imaged in unprecedented detail by a combined dataset of multi-beam bathymetry and high-resolution seismic profiles. The bathymetric data represent the results of 6 recent marine geophysical surveys since 2010 as well as a compilation of earlier surveys presented as a 2 arc-sec (60 m) grid. Several distinct morpho-tectonic provinces are identified including: the deeply incised Malta–Hyblean Escarpment, numerous submarine canyons, broad regions of relatively flat seafloor dominated by fields of sediment waves, the gently undulating anticlinal fold-and-thrust belts of the external Calabrian accretionary wedge and the adjacent portion of the Western Mediterranean Ridge. The Calabrian arc can be divided into 4 domains (from SE to NW): 1) the undeformed Ionian abyssal plain, 2) the external evaporitic wedge, 3) the internal clastic wedge, 4) the Calabrian backstop (Variscan crystalline basement). The Calabrian accretionary wedge can also be divided laterally into two major lobes, the NE- and the SW lobes, and two minor lobes. The kinematics of the limit between the two major lobes is investigated and shown to be sinistral in the external (evaporitic) wedge. A network of radial slip lines within the southernmost external wedge unequivocally demonstrate ongoing dextral displacement of a rigid indenter (representing the corner of the clastic wedge) into the evaporitic wedge thereby confirming the geodynamic model of an active lateral slab tear fault here off eastern Sicily. The slab tear produces a series of major sub-parallel dextral strike-slip faults offshore Mt. Etna and south of the Straits of Messina consistent with the relative motions between Calabria and the Peloritan domain (NE Sicily). Abundant strike-slip faulting, and wide-spread folding and thrusting observed throughout the entire accretionary wedge, indicate regional shortening between the Ionian abyssal plain (foreland) and the Calabrian–Peloritan backstop caused by active subduction.
ISSN: 0012-821X

hal-01523990
https://hal.archives-ouvertes.fr/hal-01523990
DOI : 10.1016/j.epsl.2016.12.020