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) : Copernicus Gesellschaft Mbh
Résumé : Deep-sea bivalves found at hydrothermal vents, cold seeps and organic falls are sustained by chemosynthetic bacteria which ensure part or all of their carbon nutrition. These symbioses are of prime importance for the functioning of the ecosystems. Similar symbioses occur in other bivalve species living in shallow and coastal reduced habitats worldwide. In recent years, several deep-sea species have been investigated from continental margins around Europe, West Africa, East America, the Gulf of Mexico, and from hydrothermal vents on the Mid-Atlantic Ridge. In parallel, numerous more easily accessible shallow marine species were studied. We here provide a summary of the current knowledge available on chemosymbiotic bivalves in the area ranging west-to-east from the Gulf of Mexico to Marmara Sea, and north-to-south from the Arctic to the Gulf of Guinea. Characteristics of symbioses in 51 species from the area are summarized for each of the five bivalve families documented to harbor chemosynthetic symbionts (Mytilidae, Vesicomyidae, Solemyidae, Thyasiridae and Lucinidae), and compared among families with special emphasis on ecology, life cycle, and connectivity. Chemosynthetic symbioses are a major adaptation to ecosystems and habitats exposed to reducing conditions, yet relatively little is known regarding their diversity and functioning apart from a few "model species" on which effort has focused over the last 30 yr. In the context of increasing concern about biodiversity and ecosystems, and increasing anthropogenic pressure on Oceans, we advocate for a better assessment of bivalve symbioses diversity in order to evaluate the capacities of these remarkable ecological and evolutionary units to withstand environmental change
Biogeosciences (1726-4170) (Copernicus Gesellschaft Mbh), 2013 , Vol. 10 , N. 5 , P. 3241-3267

Droits : Author(s) 2012. CC Attribution 3.0 License.
http://archimer.ifremer.fr/doc/00133/24417/22431.pdf
DOI:10.5194/bg-10-3241-2013
http://archimer.ifremer.fr/doc/00133/24417/

Éditeur(s) : HAL CCSD Wiley
Résumé : [b]1.[/b] Plant functional traits, in particular specific leaf area (SLA), wood density and seed mass, are often good predictors of individual tree growth rates within communities. Individuals and species with high SLA, low wood density and small seeds tend to have faster growth rates.[br/][br/][b]2.[/b] If community-level relationships between traits and growth have general predictive value, then similar relationships should also be observed in analyses that integrate across taxa, biogeographic regions and environments. Such global consistency would imply that traits could serve as valuable proxies for the complex suite of factors that determine growth rate, and, therefore, could underpin a new generation of robust dynamic vegetation models. Alternatively, growth rates may depend more strongly on the local environment or growth–trait relationships may vary along environmental gradients.[br/][br/][b]3.[/b] We tested these alternative hypotheses using data on 27 352 juvenile trees, representing 278 species from 27 sites on all forested continents, and extensive functional trait data, 38% of which were obtained at the same sites at which growth was assessed. Data on potential evapotranspiration (PET), which summarizes the joint ecological effects of temperature and precipitation, were obtained from a global data base.[br/][br/][b]4.[/b] We estimated size-standardized relative height growth rates (SGR) for all species, then related them to functional traits and PET using mixed-effect models for the fastest growing species and for all species together.[br/][br/][b]5.[/b] Both the mean and 95th percentile SGR were more strongly associated with functional traits than with PET. PET was unrelated to SGR at the global scale. SGR increased with increasing SLA and decreased with increasing wood density and seed mass, but these traits explained only 3.1% of the variation in SGR. SGR–trait relationships were consistently weak across families and biogeographic zones, and over a range of tree statures. Thus, the most widely studied functional traits in plant ecology were poor predictors of tree growth over large scales.[br/][br/][b]6.[/b] Synthesis. We conclude that these functional traits alone may be unsuitable for predicting growth of trees over broad scales. Determining the functional traits that predict vital rates under specific environmental conditions may generate more insight than a monolithic global relationship can offer.
ISSN: 0022-0477

hal-01204226
https://hal.archives-ouvertes.fr/hal-01204226
DOI : 10.1111/1365-2745.12401
PRODINRA : 307144

Éditeur(s) : Wiley-Blackwell
Résumé : The Climate Forecast System Reanalysis (CFSR) provides a wealth of information spanning 1979–2009 for investigation of ocean wind and wave climate. Preprocessing of the data is necessary to remove the dominant seasonal signals and to create time series of semimonthly averaged wind speed and significant wave height over a 0.5° global grid. We perform an empirical orthogonal function (EOF) analysis to extract the dominant space-time patterns. The results for the three major ocean basins show strong zonal structures in the winds and saturation of the swells corroborating prior works with various data sets. We reexamine the CFSR data in the frequency domain to identify periodic signals associated with published climate indices. The Fourier transform of the preprocessed time series generates spectra ranging from 1 month to 15 years period for an EOF analysis. The results demonstrate the spatial structures and periods of climate phenomena. The Arctic Oscillation dominates the Atlantic basin with a broad range of intra-annual signals off the European coasts. The Indian and Pacific Oceans are strongly influenced by inter-annual cycles of the El Niño Southern Oscillation (ENSO) and the Antarctica Oscillation. The Indian Ocean also has strong intra-annual components ranging from 50 to 80 days period. The ENSO proves to be a ubiquitous signal around the globe, and in particular, saturates the Pacific with strong influences in the equatorial region and the Southern Hemisphere Westerlies. A commonality of all basins is that the magnitude and the spatial structure of the intra-annual and inter-annual signals are similar suggesting a wide range of periods in each of the climate cycles examined.
Journal of Geophysical Research: Oceans (21699275) (Wiley-Blackwell), 2014-08 , Vol. 119 , N. 8 , P. 5563-5584

Droits : 2014. American Geophysical Union. All Rights Reserved.
http://archimer.ifremer.fr/doc/00210/32149/30606.pdf
http://archimer.ifremer.fr/doc/00210/32149/30607.pdf
DOI:10.1002/2013JC009729
http://archimer.ifremer.fr/doc/00210/32149/

Éditeur(s) : Elsevier
Résumé : Regardless of the degree of closure of a recirculation system, effluents are produced and replacement water is needed, which limits the possibility of locating a seawater production system away from the shoreline. At the Palavas Ifremer station, in the south of France, a High Rate Algal Pond (HRAP) was operated during several years to treat the effluent from a recirculating aquaculture system before reusing it. The effect of the HRAP-treated water on the recirculation system and on the fish was investigated and the optimal algae growing conditions were defined. The experiments were carried out in three rearing systems: one flow through, one recirculating and one recirculating with a HRAP. The water flow rate, temperature, pH and salinity conditions were similar in all systems. The effect of reusing the HRAP-treated water is very limited (1) on the functioning of the recirculation system and (2) on fish performance, but it allows a significant reduction of the dissolved inorganic nitrogen and phosphorus concentration in the rearing water. HRAP treatment reduced metal accumulation in muscle and liver of RAS fish, except for chromium and arsenic. All biomarkers presented no significant difference between systems, except for Superoxide Dismutase (SOD) and EROD, which showed a higher concentration in RAS and in both recirculating system respectively. (c) 2005 Elsevier B.V. All rights reserved.
Aquaculture (0044-8486) (Elsevier), 2006-03 , Vol. 252 , N. 1 , P. 92-101

Droits : 2005 Elsevier
http://archimer.ifremer.fr/doc/2006/publication-2306.pdf
DOI:10.1016/j.aquaculture.2005.11.053
http://archimer.ifremer.fr/doc/00000/2306/

Éditeur(s) : Inter-research
Résumé : Mixed beds of Ophiocomina nigra and Ophiothrix fragilis (Echinodermata, Ophiuroidea) are usually predominated by O. fragilis and are reported to be stable over time. The Bay of Brest (Brittany, France) is a highly productive ecosystem where both species co-occur in the main central part. Using a geostatistical approach, we tested for changes in O. nigra and O. fragilis density and total biomass patterns between 1987 and 2011. Our results highlighted an increase in O. nigra population size and the induction of a spatial shift of the co-occurring O. fragilis. O. nigra increased similar to 5 times in density and covered almost all the study area, while its density-dependent biomass increased similar to 3 times (22 t km(-2), ash-free dry mass) between 1987 and 2011. Overall, the O. fragilis population decreased in density by similar to 30%, but its total biomass did not change over time. The current distribution pattern revealed a clear spatial exclusion of O. fragilis from the central part of the study area toward the southern part, overlapping beds of dead slipper limpet Crepidula fornicata, which were formerly considered to be the dominant suspension-feeder species in the bay. The success of O. nigra colonization is linked to its biological and functional traits, as well as deep changes in food supply over the studied period. Ecological consequences of such a large change in the benthic compartment of the bay are explored in the light of associated changes in environmental patterns.
Marine Ecology-progress Series (0171-8630) (Inter-research), 2012 , Vol. 460 , P. 79-90

Droits : 2012 Inter-Research
http://archimer.ifremer.fr/doc/00090/20136/17782.pdf
DOI:10.3354/meps09784
http://archimer.ifremer.fr/doc/00090/20136/

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Motivation: Gene fusion is an important evolutionary process. It can yield valuable information to infer the interactions and functions of proteins. Fused genes have been identified as non-transitive patterns of similarity in triplets of genes. To be computationally tractable, this approach usually imposes an a priori distinction between a dataset in which fused genes are searched for, and a dataset that may have provided genetic material for fusion. This reduces the `genetic space' in which fusion can be discovered, as only a subset of triplets of genes is investigated. Moreover, this approach may have a high-false-positive rate, and it does not identify gene families descending from a common fusion event. Results: We represent similarities between sequences as a network. This leads to an efficient formulation of previous methods of fused gene identification, which we implemented in the Python program FusedTriplets. Furthermore, we propose a new characterization of families of fused genes, as clique minimal separators of the sequence similarity network. This well-studied graph topology provides a robust and fast method of detection, well suited for automatic analyses of big datasets. We implemented this method in the C++ program MosaicFinder, which additionally uses local alignments to discard false-positive candidates and indicates potential fusion points. The grouping into families will help distinguish sequencing or prediction errors from real biological fusions, and it will yield additional insight into the function and history of fused genes.
ISSN: 1367-4803

hal-01544795
https://hal.archives-ouvertes.fr/hal-01544795
DOI : 10.1093/bioinformatics/btt049

Éditeur(s) : HAL CCSD Nordic Ecological Society
Résumé : Niche differentiation and ecological filtering are primary ecological processes that shape community assembly, but their relative importance remains poorly understood. Analyses of the distributions of functional traits can provide insight into the community structure generated by these processes. We predicted the trait distributions expected under the ecological processes of niche differentiation and environmental filtering, then tested these predictions with a dataset of 4672 trees located in nine 1-ha plots of tropical rain forest in French Guiana. Five traits related to leaf function (foliar N concentration, chlorophyll content, toughness, tissue density and specific leaf area), and three traits related to stem function (trunk sapwood density, branch sapwood density, and trunk bark thickness), as well as laminar surface area, were measured on every individual tree. There was far more evidence for environmental filtering than for niche differentiation in these forests. Furthermore, we contrasted results from species-mean and individual-level trait values. Analyses that took within-species trait variation into account were far more sensitive indicators of niche differentiation and ecological filtering. Species-mean analyses, by contrast, may underestimate the effects of ecological processes on community assembly. Environmental filtering appeared somewhat more intense on leaf traits than on stem traits, whereas niche differentiation affected neither strongly. By accounting for within-species trait variation, we were able to more properly consider the ecological interactions among individual trees and between individual trees and their environment. In so doing, our results suggest that the ecological processes of niche differentiation and environmental filtering may be more pervasive than previously believed.
ISSN: 0030-1299

hal-01032397
https://hal.archives-ouvertes.fr/hal-01032397
DOI : 10.1111/j.1600-0706.2010.19110.x

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
The equilibrium phase relations of a mafic durbachite (53 wt.% SiO2) from the TA (TM) ebi pluton, representative of the Variscan ultrapotassic magmatism of the Bohemian Massif (338-335 Ma), have been determined as a function of temperature (900-1,100A degrees C), pressure (100-200 MPa), and H2O activity (1.1-6.1 wt.% H2O in the melt). Two oxygen fugacity ranges were investigated: close to the Ni-NiO (NNO) buffer and 2.6 log unit above NNO buffer (a dagger NNO + 2.6). At 1,100A degrees C, olivine is the liquidus phase and co-crystallized with phlogopite and augite at 1,000A degrees C for the whole range of investigated pressure and water content in the melt. At 900A degrees C, the mineral assemblage consists of augite and phlogopite, whereas olivine is not stable. The stability field of both alkali feldspar and plagioclase is restricted to low pressure (100 MPa) at nearly water-saturated conditions (< 3-4 wt.% H2O) and T < 900A degrees C. A comparison between experimental products and natural minerals indicates that mafic durbachites have a near-liquidus assemblage of olivine, augite, Ti-rich phlogopite, apatite and zircon, followed by alkali feldspar and plagioclase, similar to the mineral assemblage of minette magma. Natural amphibole, diopside and orthopyroxene were not reproduced experimentally and probably result from sub-solidus reactions, whereas biotite re-equilibrated at low temperature. The crystallization sequence olivine followed by phlogopite and augite reproduces the sequence inferred in many mica-lamprophyre rocks. The similar fractionation trends observed for durbachites and minettes indicate that mafic durbachites are probably the plutonic equivalents of minettes and that K- and Mg-rich magmas in the Bohemian Massif may have been generated from partial melting of a phlogopite-clinopyroxene-bearing metasomatized peridotite. Experimental melt compositions also suggest that felsic durbachites can be generated by simple fractionation of a more mafic parent and mixing with mantle-derived components at mid crustal pressures.
ISSN: 0010-7999

hal-00618418
https://hal.archives-ouvertes.fr/hal-00618418
DOI : 10.1007/s00410-009-0430-5

Éditeur(s) : Wiley / Blackwell
Résumé : P>The distribution of the archaeal communities in deep subseafloor sediments [0-36 m below the seafloor (mbsf)] from the New Caledonia and Fairway Basins was investigated using DNA- and RNA-derived 16S rRNA clone libraries, functional genes and denaturing gradient gel electrophoresis (DGGE). A new method, Co-Migration DGGE (CM-DGGE), was developed to access selectively the active archaeal diversity. Prokaryotic cell abundances at the open-ocean sites were on average similar to 3.5 times lower than at a site under terrestrial influence. The sediment surface archaeal community (0-1.5 mbsf) was characterized by active Marine Group 1 (MG-1) Archaea that co-occurred with ammonia monooxygenase gene (amoA) sequences affiliated to a group of uncultured sedimentary Crenarchaeota. However, the anoxic subsurface methane-poor sediments (below 1.5 mbsf) were dominated by less active archaeal communities, such as the Thermoplasmatales, Marine Benthic Group D and other lineages probably involved in the methane cycle (Methanosarcinales, ANME-2 and DSAG/MBG-B). Moreover, the archaeal diversity of some sediment layers was restricted to only one lineage (Uncultured Euryarchaeota, DHVE6, MBG-B, MG-1 and SAGMEG). Sequences forming two clusters within the Thermococcales order were also present in these cold subseafloor sediments, suggesting that these uncultured putative thermophilic archaeal communities might have originated from a different environment. This study shows a transition between surface and subsurface sediment archaeal communities.
Environmental Microbiology (1462-2912) (Wiley / Blackwell), 2009-09 , Vol. 11 , N. 9 , P. 2446-2462

Droits : 2009 Society for Applied Microbiology and Wiley - Blackwell Publishing Ltd.
http://archimer.ifremer.fr/doc/2009/publication-6801.pdf
DOI:10.1111/j.1462-2920.2009.01976.x
http://archimer.ifremer.fr/doc/00000/6801/

Éditeur(s) : HAL CCSD Wiley
Résumé : 1. Niche theory proposes that species differences underlie both coexistence within communities and the differentiation in species composition among communities via limiting similarity and environmental filtering. However, it has been difficult to extend niche theory to species-rich communities because of the empirical challenge of quantifying niches for many species. This has motivated the development of functional and phylogeny-based approaches in community ecology, which represent two different means of approximating niche attributes. 2. Here, we assess the utility of plant functional traits and phylogenetic relationships in predicting community assembly processes using the largest trait and phylogenetic data base to date for any set of species-rich communities. 3. We measured 17 functional traits for all 4672 individuals of 668 tree species co-occurring in nine tropical rain forest plots in French Guiana. Trait variation was summarized into two ordination axes that reflect species niche overlap. 4. We also generated a dated molecular phylogenetic tree based on DNA sequencing of two plastid loci (rbcL and matK) comprising 97% of the individuals and 91% of the species in the plots. 5. We found that, on average, co-occurring species had greater functional and, to a lesser extent, phylogenetic similarity than expected by chance. 6. We also found that functional traits and their ordination loadings showed significant, albeit weak, phylogenetic signal, suggesting that phylogenetic distance provides pertinent information on niche overlap in tropical tree communities. 7. Synthesis. We provide the most comprehensive examination to date of the relative importance of environmental filtering and limiting similarity in structuring tropical tree communities. Our results confirm that environmental filtering is the overriding influence on community assembly in these species-rich systems.
ISSN: 0141-6707

hal-01032423
https://hal.archives-ouvertes.fr/hal-01032423
DOI : 10.1111/j.1365-2745.2012.01966.x

Éditeur(s) : HAL CCSD
Résumé : This thesis compiles two distinct studies that both document the control of microstructures on rock seismic properties. The first part deals with the development of crystallographic preferred orientations (CPO) in the uppermost mantle associated with melt/fluid-rock interactions, recorded in peridotites xenoliths from the Japan sea back-arc basin. The microstructural and geochemical characteristics of the studied samples reveal that active spreading is associated to uppermost mantle deformation similar to that observed in the Oman ophiolite. At the onset of back-arc spreading, there are no strong interactions between melt percolation and deformation in comparison to continental rift zones, probably due to the relatively small size and short duration of the spreading event. The second part presents a unique database of plagioclase CPO from variously deformed mafic rocks. CPO are grouped in three main types; their characteristics as a function of deformation regime (magmatic or crystal-plastic) are outlined and discussed. Calculated seismic properties of gabbroic rocks show that anisotropy tends to increase as a function of fabric strength, although it is generally weak, due to the competing effect of olivine/clinopyroxene and plagioclase.
Cette thèse regroupe deux études distinctes, qui documentent le contrôle des microstructures sur les propriétés sismiques des roches. La première partie traite du développement des orientations préférentielles cristallographiques (OPC) dans le manteau supérieur, associé aux interactions liquide/magma-roche, enregistré dans des xénolites de péridotites du bassin d'arrière-arc de la mer du Japon. Les caractéristiques microstucturales et géochimiques des échantillons étudiés montrent que l'ouverture arrière-arc active est associée à une déformation du manteau supérieure similaire à celle observée dans l'ophiolite d'Oman. L'initiation de l'extension d'arrière-arc n'est pas associée à de fortes interactions entre percolation magmatique et déformation, en comparaison avec les zones de rifting continentales, probablement en raison des taille et durée relativement petites de l'épisode d'ouverture. La seconde partie présente une base de données unique d'OPC de plagioclase de roches mafiques plus ou moins déformées. Les OPC sont classées en 3 types principaux; leurs caractéristiques en fonction du régime de déformation (magmatique ou plastique) sont présentées et discutées. Les propriétés sismiques calculées des roches gabbroiques montrent que l'anisotropie tend à croitre avec l'intensité des fabriques, bien qu'elle soit généralement faible, en raison des effets opposés des olivines/clinopyroxènes et du plagioclase.
https://tel.archives-ouvertes.fr/tel-00795505

tel-00795505
https://tel.archives-ouvertes.fr/tel-00795505
https://tel.archives-ouvertes.fr/tel-00795505/document
https://tel.archives-ouvertes.fr/tel-00795505/file/Satsukawa_thesis_UM2.pdf

Éditeur(s) : HAL CCSD BioMed Central
Résumé : [b]Background[/b][br/] [br/] The Amazonian rainforest is predicted to suffer from ongoing environmental changes. Despite the need to evaluate the impact of such changes on tree genetic diversity, we almost entirely lack genomic resources.[br/] [br/] [b]Results[/b][br/] [br/] In this study, we analysed the transcriptome of four tropical tree species (Carapa guianensis, Eperua falcata, Symphonia globulifera and Virola michelii) with contrasting ecological features, belonging to four widespread botanical families (respectively Meliaceae, Fabaceae, Clusiaceae and Myristicaceae). We sequenced cDNA libraries from three organs (leaves, stems, and roots) using 454 pyrosequencing. We have developed an R and bioperl-based bioinformatic procedure for de novo assembly, gene functional annotation and marker discovery. Mismatch identification takes into account single-base quality values as well as the likelihood of false variants as a function of contig depth and number of sequenced chromosomes. Between 17103 (for Symphonia globulifera) and 23390 (for Eperua falcata) contigs were assembled. Organs varied in the numbers of unigenes they apparently express, with higher number in roots. Patterns of gene expression were similar across species, with metabolism of aromatic compounds standing out as an overrepresented gene function. Transcripts corresponding to several gene functions were found to be over- or underrepresented in each organ. We identified between 4434 (for Symphonia globulifera) and 9076 (for Virola surinamensis) well-supported mismatches. The resulting overall mismatch density was comprised between 0.89 (S. globulifera) and 1.05 (V. surinamensis) mismatches/100 bp in variation-containing contigs.[br/] [br/] [b]Conclusion[/b][br/] [br/] The relative representation of gene functions in the four transcriptomes suggests that secondary metabolism may be particularly important in tropical trees. The differential representation of transcripts among tissues suggests differential gene expression, which opens the way to functional studies in these non-model, ecologically important species. We found substantial amounts of mismatches in the four species. These newly identified putative variants are a first step towards acquiring much needed genomic resources for tropical tree species.
ISSN: 1471-2164

hal-01032439
https://hal.archives-ouvertes.fr/hal-01032439
https://hal.archives-ouvertes.fr/hal-01032439/document
https://hal.archives-ouvertes.fr/hal-01032439/file/art_10-1186_1471-2164-15-238.pdf
DOI : 10.1186/1471-2164-15-238

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
The objective of this study is to assess the association of clinical manifestations of systemic sclerosis (SSc) with the absolute count of circulating blood monocyte subpopulations according to their membrane expression of CD16. Forty-eight consecutive patients fulfilling the 2013 ACR/EULAR classification criteria for SSc were included in this cross-sectional study. CD16+ monocyte absolute count was defined by flow cytometry and confronted to the clinical characteristics of SSc patients. Twenty-three healthy donors (HD) were randomly selected for comparison. SSc patients had an increased number of total circulating blood monocytes compared to HD (p < 0.001). The CD16- subpopulation absolute count was increased in SSc patients compared to HD (p < 0.001) but was similar in limited SSc (lSSc) and diffuse SSc (dSSc). On the contrary, the CD16+ population absolute count was increased in dSSc compared to both HD and lSSc patients (dSSc 0.071 Giga/L (+/- 0.034) vs HD 0.039 Giga/L (+/- 0.030), p < 0.01, and dSSc 0.071 Giga/L (+/- 0.034) vs lSSc 0.048 Giga/L (+/- 0.024), p < 0.05). The CD16+ monocyte subpopulation absolute count was significantly correlated with the severity of skin fibrosis evaluated by the modified Rodnan skin score (p < 0.001). The CD16+ monocyte subpopulation was also associated with pulmonary fibrosis (p < 0.05), with the severity of the restrictive ventilatory defect evaluated by total lung capacity (p < 0.05) and with the pulmonary function impairment reflected by diffusing capacity of the lungs for carbon monoxyde measures (p < 0.01). These results suggest that CD16+ monocytes are associated with the main fibrotic manifestations of SSc and their role in the pathogenesis of fibrosis in this autoimmune disorder should therefore be further considered.
ISSN: 0770-3198

hal-01560150
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01560150
DOI : 10.1007/s10067-017-3597-6
PUBMED : 28293753

Éditeur(s) : HAL CCSD
Résumé : International audience
The Corinth Rift is the most seismically active zone in Europe. Since the year 2000, the Corinth Rift Laboratory (CRL, http://crlab.eu) consisting in a multidisciplinary natural observatory, aims at understanding the mechanics of faulting and earthquake nucleation in the Rift. Recent studies have improved our view about fault geometry and mechanics within CRL but there is still a critical need for a better knowledge of the structure at depth.In this project, we aim to analyze the complete seismological database (13 years of recordings) of CRL by using recently developed methodologies of structural imaging in order to determine, with high resolution, the local 3D structure and the earthquake locations. We perform an iterative joint determination of 3D velocity model and earthquake coordinates. P and S velocity models are estimated through a first arrival traveltime tomography by using the adjoint state method proposed by Taillandier et al. (2009). It consists in the minimization of the cost function between observed and theoretical arrival times,which is achieved by estimating the gradient of the cost function. Earthquake locations are also estimated with a linearized inversion approach by computing the gradient of the misfit function. Iterations are repeated until the cost function no longer decreases. We present preliminary results consisting in: (1) the adjustment of a 1D velocity model that is used as initial model of the 3D tomography and (2) a first attempt of the joint determination of 3D velocity model and earthquake locations.We also perform a preliminary receiver function analysis of teleseismic data recorded by the broadband stations of the CRL network. The multiscale approach (Gesret et. al., 2010) analysis of teleseismic P to S converted waves allows to analyze the signal toward the higher frequencies and thus to characterize the structure at depth with a high resolution. Our multiscale approach should give us reliable depth of interfaces beneath seismometers in the CRL area. In this first attempt, we adjust the 1D velocity model that produces a synthetic RF as similar as possible to the stack of observed RF for a subset of data. The identified interfaces could then be compared with heterogeneities imaged by the tomography.
AGU Fall Meeting
San Fransico, United States

hal-01417184
https://hal-mines-paristech.archives-ouvertes.fr/hal-01417184

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
: Until recently, synonymous mutations (which do not change amino acids) have been much neglected. Some evidence suggests that this kind of mutations could affect mRNA secondary structure or stability, translation kinetics and protein structure. To explore deeper the role of synonymous mutations, we studied their consequence on the functional activity of the estrogen receptor alpha (ERα). The ERα is a ligand-inducible transcription factor that orchestrates pleiotropic cellular effects, at both genomic and non-genomic levels in response to estrogens. In this work we analyzed in transient transfection experiments, the activity of ERα carrying the synonymous mutation Ala87, a polymorphism involving about 5-10% of the population. In comparison to the wild type receptor, our results show that ERαA87 mutation reduces the transactivation efficiency of ERα on an ERE reporter gene while its expression level remains similar. This mutation enhances 4-OHT-induced transactivation of ERα on an AP1 reporter gene. Finally, the mutation affects the subcellular localization of ERα in a cell type specific manner. It enhances the cytoplasmic location of ERα without significant changes in non-genomic effects of E2. The functional alteration of the ERαA87 determined in this work highlights the relevance of synonymous mutations for biomedical and pharmacological points of view.
Journal of steroid biochemistry and molecular biology

inserm-01015532
http://www.hal.inserm.fr/inserm-01015532
DOI : 10.1016/j.jsbmb.2014.02.016
PUBMED : 24607813

Éditeur(s) : HAL CCSD Ecological Society of America
Résumé : Line transect surveys are widely used in neotropical rainforests to estimate the population abundance of medium- and large-sized vertebrates. The use of indices such as Encounter Rate has been criticized because the probability of animal detection may fluctuate due to the heterogeneity of environmental conditions among sites. In addition, the morphological and behavioral characteristics (biological traits) of species affect their detectability. In this study, we compared the extent to which environmental conditions and species' biological traits bias abundance estimates in terra firme rainforests in French Guiana. The selected environmental conditions included both physical conditions and forest structure covariates, while the selected biological traits included the morphological and behavioral characteristics of species. We used the distance sampling method to model the detection probability as an explicit function of environmental conditions and biological traits and implemented a model selection process to determine the relative importance of each group of covariates. Biological traits contributed to the variability of animal detectability more than environmental conditions, which had only a marginal effect. Detectability was best for large animals with uniform or disruptive markings that live in groups in the canopy top. Detectability was worst for small, solitary, terrestrial animals with mottled markings. In the terra firme rainforests which represent ~80% of the Amazonia and Guianas regions, our findings support the use of relative indices such as the encounter rate to compare population abundance between sites in species-specific studies. Even though terra firme rainforests may appear similar between regions of Amazonia and the Guianas, comparability must be ensured, especially in forests disturbed by human activity. The detection probability can be used as an indicator of species' vulnerability to hunting and, thus, to the risk of local extinction. Only a few biological trait covariates are required to correctly estimate the detectability of the majority of medium- and large-sized vertebrates. Thus, a biological trait model could be useful in predicting the detection probabilities of rare, uncommon or localized species for which few data are available to fit the detection function.
ISSN: 1051-0761

hal-01555267
https://hal.archives-ouvertes.fr/hal-01555267
DOI : 10.1002/eap.1549
PRODINRA : 396614
PUBMED : 28419598

Éditeur(s) : Elsevier
Résumé : Evidence has accumulated that climate variability influences the state and functioning of marine ecosystems. At the same time increasing pressure from exploitation and other human activities has been shown to impact exploited and non-exploited species and potentially modify ecosystem structure. There has been a tendency among marine scientists to pose the question as a dichotomy, i.e., whether (1) "natural" climate variability or (2) fishery exploitation bears the primary responsibility for population declines in fish populations and the associated ecosystem changes. However, effects of both climate and exploitation are probably substantially involved in most cases. More importantly, climate and exploitation interact in their effects, such that climate may cause failure in a fishery management scheme but that fishery exploitation may also disrupt the ability of a resource population to withstand, or adjust to, climate changes. Here, we review how exploitation, by altering the structure of populations and ecosystems, can modify their ability to respond to climate. The demographic effects of fishing (removal of large-old individuals) can have substantial consequences on the capacity of populations to buffer climate variability through various pathways (direct demographic effects, effects on migration, parental effects). In a similar way, selection of population sub-units within metapopulations may also lead to a reduction in the capacity of populations to withstand climate variability and change. At the ecosystem level, reduced complexity by elimination of species, such as might occur by fishing, may be destabilizing and could lead to reduced resilience to perturbations. Differential exploitation of marine resources could also promote increased turnover rates in marine ecosystems, which would exacerbate the effects of environmental changes. Overall (and despite the specificities of local situations) reduction in marine diversity at the individual, population and ecosystem levels will likely lead to a reduction in the resilience and an increase in the response of populations and ecosystems to future climate variability and change. Future management schemes will have to consider the structure and functioning of populations and ecosystems in a wider sense in order to maximise the ability of marine fauna to adapt to future climates. (C) 2009 Elsevier B.V. All rights reserved.
Journal of Marine Systems (0924-7963) (Elsevier), 2010-02 , Vol. 79 , N. 3-4 , P. 403-417

Droits : 2009 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/2010/publication-7384.pdf
DOI:10.1016/j.jmarsys.2008.12.018
http://archimer.ifremer.fr/doc/00000/7384/

Éditeur(s) : HAL CCSD American College of Sports Medicine (ACSM)
Résumé : International audience
PURPOSE AND METHODS: To determine the effects of cycling on a subsequent triathlon run, nine male triathletes underwent four successive laboratory trials: 1) an incremental treadmill test, 2) an incremental cycle test, 3) 30 min of cycling followed by 5 km of running (C-R), and 4) 30 min of running followed by 5 km of running (R-R). Before and 10 min after the third and fourth trials, the triathletes underwent pulmonary function testing including spirometry and diffusing capacity testing for carbon monoxide (DL(CO)). During the C-R and R-R trials, arterialized blood samples were obtained to measure arterial oxygen pressure (PaO2). During all trials, ventilatory data were collected every minute using an automated breath-by-breath system. RESULTS: The results showed that 1) the oxygen uptake (VO2) observed during subsequent running was similar for the C-R and R-R trials; 2) the ventilatory response (VE) during the first 8 min of subsequent running was significantly greater in the C-R than in R-R trial (P < 0.05); 3) only the C-R trial induced a significant increase (P < 0.05) in residual volume (RV), functional residual capacity (FRC), and the ratio of residual volume to total lung capacity (RV/TLC); and 4) although a significant decrease (P < 0.05) in DL(CO) was noted after C-R, no difference between the two exercise trials was found for the maximal drop in PaO2. CONCLUSIONS: We concluded that 1) the C-R trial induced specific alterations in pulmonary function that may be associated with respiratory muscle fatigue and/or exercise-induced hypoxemia, and 2) the greater VE observed during the first minute of running after cycling was due to the specificity of cycling. This reinforces the necessity for triathletes to practice multi-trial training to stimulate the physiological responses experienced during the swim-cycle and the cycle-run transitions.
ISSN: 0195-9131

hal-00720412
https://hal.univ-antilles.fr/hal-00720412
https://hal.univ-antilles.fr/hal-00720412/document
https://hal.univ-antilles.fr/hal-00720412/file/Article.pdf

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
It is unclear whether vascular function is affected similarly in children with sickle cell anaemia (SS) and children with sickle haemoglobin C (SC) disease. Therefore, we compared micro and macrovascular functions in healthy (AA) children, children with SS and SC disease, and assessed their association with physical activity. Participants (24 SS, 22 SC and 16 AA), were compared in terms of 1) thermal hyperaemic response (finger pad warming to 42 °C) measured by Laser Doppler techniques, 2) arterial stiffness determined by pulse wave velocity, 3) daily energy expenditure related to moderate and intense physical activities estimated by questionnaire and 4) fitness level, evaluated by the six-minute walk test. Response to heating differed between SS, SC and controls. Peripheral microvascular reactivity was lower and pulse wave velocity higher in SS compared to AA. SC had blunted microvascular reactivity in response to heating compared to AA but pulse wave velocity was not different within the two groups. Physical activity and fitness levels were markedly lower in sickle cell patients compared to healthy controls but no association was observed with vascular function. Microvasodilatory reserve is decreased in both SS and SC patients but only SS patients were also characterised by impaired macrovascular function.
ISSN: 1079-9796

hal-01496857
https://hal.archives-ouvertes.fr/hal-01496857
https://hal.archives-ouvertes.fr/hal-01496857/document
https://hal.archives-ouvertes.fr/hal-01496857/file/Mo%CC%88ckesch%20et%20al%20BCMD%20non%20apparent%20corrections%20final.pdf
DOI : 10.1016/j.bcmd.2017.02.001