Éditeur(s) : HAL CCSD Cambridge University Press (CUP)
Résumé : International audience
In a recent paper, we gave a topological description of Colombeau type algebras introducing algebras of sequences with exponential weights. Embeddings of Schwartz spaces into the Colombeau algebra G are well known, but for ultradistribution and periodic hyperfunction type spaces we give new constructions. We show that the multiplication of regular enough functions (smooth, ultradifferentiable or quasianalytic), embedded into corresponding algebras, is the ordinary multiplication.
ISSN: 0305-0041

hal-00758568
https://hal.univ-antilles.fr/hal-00758568
https://hal.univ-antilles.fr/hal-00758568/document
https://hal.univ-antilles.fr/hal-00758568/file/DHPV2-9sep03-singlespaced.pdf
DOI : 10.1017/S0305004104007923

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
Despite the unique nature of endemic species, their origin and population history remain poorly studied. We investigated the population history of 28 coral reef fish species, close related, from the Gambier and Marquesas Islands, from five families, with range size varying from widespread to small-range endemic. We analyzed both mitochondrial and nuclear sequence data using neutrality test and Bayesian analysis (EBSP and ABC). We found evidence for demographic expansions for most species (24 of 28), irrespective of range size, reproduction strategy or archipelago. The timing of the expansions varied greatly among species, from 8,000 to 2,000,000 years ago. The typical hypothesis for reef fish that links population expansions to the Last Glacial Maximum fit for 14 of the 24 demographic expansions. We propose two evolutionary processes that could lead to expansions older than the LGM: (a) we are retrieving the signature of an old colonization process for widespread, large-range endemic and paleoendemic species or (b) speciation; the expansion reflects the birth of the species for neoendemic species. We show for the first time that the demographic histories of endemic and widespread reef fish are not distinctly different and suggest that a number of processes drive endemism.
ISSN: 2045-2322

hal-01469339
https://hal-univ-perp.archives-ouvertes.fr/hal-01469339
https://hal-univ-perp.archives-ouvertes.fr/hal-01469339/document
https://hal-univ-perp.archives-ouvertes.fr/hal-01469339/file/population%20expansions.pdf
DOI : 10.1038/srep40519

Éditeur(s) : HAL CCSD American Society of Tropical Medicine and Hygiene
Résumé : International audience
We investigated infection of rodents and shrews by Leptospira spp. in two localities of Cambodia (Veal Renh, Kaev Seima) and in four types of habitat (forests, non-flooded lands, lowland rain-fed paddy fields, houses) during the wet and the dry seasons. Habitat preference was common, and rodent and shrew species were found only in houses or in rain-fed paddy fields or in forests. Among 649 small mammals trapped belonging to 12 rodent species and 1 shrew species, 71 of 642 animals tested were carriers of Leptospira according to the 16S ribosomal RNA marker used. Rodent infection was higher in low-slope locations, corresponding to rain-fed paddy fields, especially in the rainy season and in Kaev Seima. Rodents (Rattus exulans) and shrews (Suncus murinus) inhabiting households showed significantly low levels of infections, whereas rodents living in and near to forests (shrubby wasteland, orchards) showed high levels of infection.
American Journal of Tropical Medicine and Hygiene

pasteur-00808144
https://hal-riip.archives-ouvertes.fr/pasteur-00808144
DOI : 10.4269/ajtmh.2012.11-0349
PUBMED : 22665613

Éditeur(s) : HAL CCSD Copernicus Publications
Résumé : International audience
During Ocean Drilling Program Leg 134, a mixed sequence of volcaniclastic and carbonate sediments was cored together with basaltic breccias and a single basalt sill in Hole 833B. In this study, data from Schlumberger's Geochemical Logging Tool, together with physical property logs, characterise part of the section and establish a complete log-derived lithostratigraphy. The major transition between the sedimentary rocks and a basaltic sill at 830 mbsf (metres below sea floor) is clearly seen as well as the distinction between the silicate-rich sediments and the carbonate-rich part of the section. The transition between the volcanic sandstone interbedded with basaltic and sed-lithic breccia of Unit III, and the volcanic sandstone of Unit IV is clearly marked by the physical property logs. The accuracy of the logging data was evaluated and discussed with an improved log versus core correlation. The cluster analysis of the complete data set shows a correlation with the data provided by the mechanical caliper device, which in turn indicates the quality of the borehole.
ISSN: 1816-8957

hal-00642165
http://hal.upmc.fr/hal-00642165
http://hal.upmc.fr/hal-00642165/document
http://hal.upmc.fr/hal-00642165/file/Rabaute_et_al-SciDrilling-1997.pdf

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Geochronological studies of samples from continuous crustal sections of fossil intra-oceanic arcs are paramount for determining the precise timing of major processes that took place during the building of an oceanic island-arc crust. In this study, laser ablation ICP-MS U-Pb zircon (and conventional Rb-Sr) analyses pinpoint the timing of major events responsible for crustal growth of the Kohistan paleo-island arc (Northern Pakistan). Inheritance in magmatic rocks is evidence for recycling of intra-arc material and indicates that the Kohistan arc may have formed as early as 135 +/- 4 Ma. One older inherited grain indicates that the arc developed on a young oceanic lithosphere whose remnants include a c. 175 Ma old component. An interesting consequence is that intra-oceanic arc magmas can yield inherited zircons, which can be much older than the arc system itself without requiring recycling back into the mantle by subduction processes. In the case of the Kohistan arc, ante-arc Neotethys oceanic lithosphere was tapped by arc magmas during their way upward into the arc crust. The oldest magmatic ages measured in this study fall in the range 101-102 Ma (100.9 +/- 0.6 and 102.1 +/- 0.4 Ma). This period corresponds to arc build-up and thickening of the arc crust. Leucogranitic melts dated at 89.9 +/- 0.4 Ma and 90.9 +/- 1.0 Ma are considered as produced by dehydration/melting reaction accompanying granulitisation of the thickened lower arc crust. A maximum age for this event is 97.7 +/- 0.7 Ma, the age of emplacement of a garnet meta-tonalite affected by granulite facies metamorphism. Magmatic activity was still ongoing during and after the granulitisation as testified by emplacement of a diorite and a gabbro dated at 89.1 +/- 0.6 and 88.2 +/- 0.9 Ma respectively. The upper part of the metaplutonic sequence contains diorite samples dated at 84.6 +/- 0.5 Ma and 84.3 +/- 0.5 Ma and as young as 81.1 +/- 0.7 Ma. During this period, and based on the present day outcropping sequences, the mean crustal growth rate varied from 32 to 65 km(3)/km/Ma (volume per unit width along the strike of the arc) which is comparable to the range for present day arcs of the Western Pacific region. The correspondence of crustal growth rates observed for present-day island arcs and the good preservation of the crustal section in the Kohistan arc, make this area an exceptional natural laboratory to study arc related processes and to check models of continental crust formation by arc accretion.
ISSN: 0012-821X

hal-00644555
https://hal.archives-ouvertes.fr/hal-00644555
DOI : 10.1016/j.epsl.2011.07.016

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Analysis of microbial biodiversity is hampered by a lack of reference genomes from most bacteria, viruses, and algae. This necessitates either the cultivation of a restricted number of species for standard sequencing projects or the analysis of highly complex environmental DNA metagenome data. Single-cell genomics (SCG) offers a solution to this problem by constraining the studied DNA sample to an individual cell and its associated symbionts, prey, and pathogens. We used SCG to study marine heterotrophic amoebae related to Paulinella ovalis (A. Wulff) P.W. Johnson, P.E. Hargraves & J.M. Sieburth (Rhizaria). The genus Paulinella is best known for its photosynthetic members such as P.chromatophora Lauterborn that is the only case of plastid primary endosymbiosis known outside of algae and plants. Here, we studied the phagotrophic sister taxa of P.chromatophora that are related to P.ovalis and found one SCG assembly to contain -cyanobacterial DNA. These cyanobacterial contigs are presumably derived from prey. We also uncovered an associated cyanophage lineage (provisionally named phage PoL_MC2). Phylogenomic analysis of the fragmented genome assembly suggested a minimum genome size of 200Kbp for phage PoL_MC2 that encodes 179 proteins and is most closely related to Synechococcus phage S-SM2. For this phage, gene network analysis demonstrates a highly modular genome structure typical of other cyanophages. Our work demonstrates that SCG is a powerful approach for discovering algal and protist biodiversity and for elucidating biotic interactions in natural samples.
ISSN: 0022-3646

hal-01544797
https://hal.archives-ouvertes.fr/hal-01544797
DOI : 10.1111/jpy.12028

Éditeur(s) : HAL CCSD Linnean Society of London
Résumé : Disentangling the impact of landscape features such as rivers and historical events on dispersal is a challenging but necessary task to gain a comprehensive picture of the evolution of diverse biota such as that found in Amazonia. Adenomera andreae, a small, territorial, terrestrial frog species of the Amazonian forest represents a good model for such studies. We combined cytochrome b sequences with 12 microsatellites to investigate the genetic structure at two contrasted spatial scales in French Guiana: along a similar to 6-km transect, to evaluate dispersal ability, and between paired bank populations along a similar to 65-km stretch of the Approuague river, to test the effect of rivers as barriers to dispersal. We observed significant spatial genetic structure between individuals at a remarkably small geographical scale, and conclude that the species has a restricted dispersal ability that is probably tied to its life-history traits. Mitochondrial and microsatellite data also indicate a high level of differentiation among populations on opposite banks of the river, and, in some cases, among populations on the same riverbank. These results suggest that the observed population structure in A. andreae is the result of restricted dispersal abilities combined with the action of rivers and Quaternary population isolation. Given that Amazonia hosts a great portion of anurans, as well as other small vertebrates, that display life-history traits comparable with A. andreae, we argue that our analyses provide new insights into the complex interactions among evolutionary processes shaping Amazonian biodiversity. (c) 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106, 356373.
ISSN: 0024-4066

hal-01032422
https://hal.archives-ouvertes.fr/hal-01032422
DOI : 10.1111/j.1095-8312.2012.01871.x

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
Here, the first description of an epsilon sulfur-oxidizing bacterium from sulfide-rich sediments of marine mangrove in Caribbean is reported. According to TEM, this new strain contains intracytoplasmic large internal sulfur granules as confirmed by EDXS analyses performed using ESEM. The sulfur distribution obtained for this sulfur-oxidizing bacterial strain allows to conclude that elemental sulfur is formed as an intermediate oxidation product and stored intracellularly. According to conventional SEM observations, bacterial cells are ovoid, extremely motile by lophotrichous flagella. Phylogenetic analyses based on the analysis of partial sequence of 16S rDNA confirm that such bacterial strain belongs to the Thiovulum cluster and could be a representative of a new species in this poorly studied genus of sulfur-oxidizing free-living bacteria. Thus, reduced sediment of marine mangrove represents sulfide-rich environment sustaining development of both gamma and epsilon sulfur-oxidizing Proteobacteria
ISSN: 0378-1097

hal-01682113
https://hal.univ-antilles.fr/hal-01682113
DOI : 10.1093/femsle/fnx172

Éditeur(s) : Wiley-blackwell
Résumé : Aims Exopolysaccharides (EPS) are industrially valuable molecules with numerous useful properties. This study describes the techniques used for the identification of a novel Vibrio bacterium and preliminary characterization of its EPS. Methods and Results Bioprospection in marine intertidal areas of New Caledonia followed by screening for EPS producing brought to selection of the isolate NC470. Phylogenetic analysis (biochemical tests, gene sequencing and DNADNA relatedness) permitted to identify NC470 as a new member of the Vibrio genus. The EPS was produced in batch fermentation, purified using the ultrafiltration process and analysed by colorimetry, Fourier Transform Infrared spectroscopy, gas chromatography, Nuclear Magnetic Resonance and HPLC-size exclusion chromatography. This EPS exhibits a high N-acetyl-hexosamines and uronic acid content with a low amount of neutral sugar. The molecular mass was 672x103Da. These data are relevant for possible technological exploitation. Conclusions We propose the name Vibrio neocaledonicus sp. nov for this isolate NC470, producing an EPS with an unusual sugar composition. Comparison with other known polymers permitted to select applications for this polymer. Significance and Impact of the Study This study contributes to evaluate the marine biodiversity of New Caledonia. It also highlights the biotechnological potential of New Caledonia marine bacteria.
Journal Of Applied Microbiology (1364-5072) (Wiley-blackwell), 2013-06 , Vol. 114 , N. 6 , P. 1702-1712

Droits : 2013 The Society for Applied Microbiology
http://archimer.ifremer.fr/doc/00144/25501/24036.pdf
DOI:10.1111/jam.12184
http://archimer.ifremer.fr/doc/00144/25501/

Éditeur(s) : HAL CCSD Wiley
Résumé : The evolutionary potential of long-lived species, such as forest trees, is fundamental for their local persistence under climate change (CC). Genome–environment association (GEA) analyses reveal if species in heterogeneous environments at the regional scale are under differential selection resulting in populations with potential preadaptation to CC within this area. In 79 natural [i]Fagus sylvatica[/i] populations, neutral genetic patterns were characterized using 12 simple sequence repeat (SSR) markers, and genomic variation (144 single nucleotide polymorphisms (SNPs) out of 52 candidate genes) was related to 87 environmental predictors in the latent factor mixed model, logistic regressions and isolation by distance/environmental (IBD/IBE) tests. SSR diversity revealed relatedness at up to 150m intertree distance but an absence of large-scale spatial genetic structure and IBE. In the GEA analyses, 16 SNPs in 10 genes responded to one or several environmental predictors and IBE, corrected for IBD, was confirmed. The GEA often reflected the proposed gene functions, including indications for adaptation to water availability and temperature. Genomic divergence and the lack of large-scale neutral genetic patterns suggest that gene flow allows the spread of advantageous alleles in adaptive genes. Thereby, adaptation processes are likely to take place in species occurring in heterogeneous environments, which might reduce their regional extinction risk under CC
ISSN: 0028-646X

hal-01309135
https://hal.archives-ouvertes.fr/hal-01309135
PRODINRA : 343710
DOI : 10.1111/nph.13809

Résumé : Face aux difficultés d’identification des arbres de la famille des Lauracées et dans un but d’établissement d’une production durable et certifiée d’huiles essentielles, l’entreprise KLR a voulu mettre en place un nouvel outil d’identification multi-critères qui consiste à croiser plusieurs types de caractères afin d’obtenir une détermination taxonomique fiable.Trois méthodes d’identification ont été utilisées : la chimie (analyse de l’odeur de l’écorce), le code barre génétique et l’anatomie du bois. Une analyse par positionnement multidimensionnel non-métrique a permis de faire un tri des critères anatomiques du bois pertinents dans l’identification des Lauracées étudiées, au final 14 critères ont été retenus. D’après les données anatomiques dont nous disposons, nous proposons une clé de détermination au genre. En génétique, la technique de code barres de la région chloroplastique intergénique trnH-psbA a été appliquée aux individus récoltés. En comparant les séquences de tous les individus, 40% des individus peuvent être identifiés au genre car ils présentent des haplotypes uniques. Des haplotypes au sein des genres ont été déterminés et permettent d’identifier l’espèce pour 40 à 100 % des individus selon le genre. L’analyse SPME de l’odeur des écorces a permis de définir pour chaque espèce une carte d’identité chimique à partir des molécules majoritaires. Des chémotypes ont été définis au sein des espèces Licaria cannella, Ocotea indirectinervia et Sextonia rubra. Ces trois domaines d’observation ont permis de constituer une base de type Xper2 pour l’identification.Un criblage des essences intéressantes de par leur rendement en huile essentielle a été effectué. En ce qui concerne la partie extraction de l’huile essentielle, trois espèces montrent un rendement en huile essentielle de l’écorce supérieur à 0,3% et 5 espèces montrent un rendement en huile essentielle du bois supérieur à 0,3%. Les évaluations olfactives menées par un expert ont permis de séparer les huiles distillées en 5 différentes notes. Nous avons jugé intéressant de savoir si l’outil d’identification multicritère pouvait prédire les compositions et rendements en huile essentielle de l’espèce identifiée avant l’abattage de l’arbre. Des études complémentaires ont donc été menées. Pour plus de la moitié des arbres, la signature de l’écorce, la composition de l’huile essentielle de l’écorce et la composition de l’huile essentielle du bois sont similaires. La tentative d’établir un lien entre les caractéristiques des cellules à huile et le rendement s’est avérée infructueuse.
In order to develop a sustainable production of certified essential oils extracts, the compangy KLR has struggled with the identification of the trees from the family of Lauraceae. This is the main reason that led to the project of creating an identification tool for this family.This tool would be based on three approaches: chemistry (chemical signature of the dark), wood anatomy and genetic barcoding. By means of a non-metric multidimensional scaling analysis, we selected a list of 14 relevant wood anatomical features that can identify the trees to the genera. For the genetics, the barcoding of trnH-psbA an intergenic region of the DNA has been used. When comparing all the sequences from all the individuals, 40% of the individuals can be identified to the genera because of their specific haplotype. Haplotypes within the genera have also been established. Chemical identity cards have been set with the SPME analysis technique and chemotypes have been defined inside the species Licaria cannella, Ocotea indirectinervia and Sextonia rubra. These three identification approaches allowed us to construct an identification tool on Xper².During the study, we aimed to screen what species would be interesting for its essential oil yield. Three species showed an essential oil bark yield above 0.3%. five species showed an essential oil wood yield above 0.3%. An expert held an olfactory evaluation on the oils and divided the essential oils in five olfactory groups. We found it relevant to improve the identification tool by trying to predict the compositions of the oils before the three was cut down. In the case of the half of trees studied by SPME analyses, the composition of the wood and the bark essential oils were similar. On the other hand, no link was found between the oil cells dimensions and the essential oil yield.

http://www.theses.fr/2012AGUY0516/document

Éditeur(s) : Gauthier-Villars
Résumé : Global changes in marine geochemistry, on scales between one thousand and one million years permit the detailed correlation of sedimentary sequences in different ocean basins. The condition is that the geochemical signals are at least approximately dated by biostratigraphy (and magnetostratigraphy, where applicable). Through mutual reenforcement of chemostratigraphy and biostratigraphy unusually high stratigraphic resolution can be obtained. The integration of chemostratigraphy and biostratigraphy opens new avenues for analyzing the record-producing system within the framework of systemic stratigraphy. This type of stratigraphy focuses on global change in sea level, climate, and general geologic setting. It attempts to identify the underlying causes of global stratigraphic signals by considering 1) changes in input of matter and energy ; 2) changes in spatial distribution of sediments ; and 3) temporary changes in the partitioning of materials between active geochemical reservoirs. Examples from Pleistocene and Neogene deep-sea records illustrate the concepts and tools of this type of analysis.
Oceanologica Acta, Special issue (0399-1784) (Gauthier-Villars), 1981

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00246/35689/34197.pdf
http://archimer.ifremer.fr/doc/00246/35689/

Éditeur(s) : HAL CCSD Geological Society of London
Résumé : Permo-Triassic rift basins offer important hydrocarbon targets along the Atlantic margins. Their fill is dominated by continental red beds, comprising braided fluvial, alluvial fan, aeolian, floodplain and lacustrine facies. These relatively lightly explored basins span both the Atlantic and Tethyan domains and developed above a complex basement with inherited structural fabrics. Sparse data in offshore regions constrain understanding of depositional geometries and sedimentary architecture, further impeded by their deep burial beneath younger strata, combined with the effects of later deformation during continental breakup. This paper provides results from a multidisciplinary analysis of basins along the Atlantic margin. Regional seismic and well data, combined with geochemical provenance analysis from the European North Atlantic margins, are integrated with detailed outcrop studies in Morocco and Nova Scotia. The research provides new insights into regional basin tectonostratigraphic evolution, sediment fill, and reservoir distribution, architecture and quality at a range of scales. Regional seismic profiles, supported by key well data, indicate the presence of post-orogenic collapse basins, focused narrow rifts and low-magnitude multiple extensional depocentres. Significantly, Permo-Triassic basin geometries are different and more varied than the overlying Jurassic and younger basins. Provenance analysis using Pb isotopic composition of detrital K-feldspar yields new and robust controls on the sediment dispersal patterns of Triassic sandstones in the NE Atlantic margin. The evolving sedimentary architecture is characterized by detailed sedimentological studies of key outcrops of age equivalent Permian-Triassic rifts in Morocco and Nova Scotia. The interplay of tectonics and climate is observed to influence sedimentation, which has significant implications for reservoir distribution in analogue basins. New digital outcrop techniques are providing improved reservoir models, and identification of key marker horizons and sequence boundaries offers a potential subsurface correlation tool. Future work will address source and seal distribution within the potentially petroliferous basins.
Petroleum Geology: From Mature Basins to New Frontiers Proceedings of the 7th Petroleum Geology Conf

hal-00590618
https://hal.archives-ouvertes.fr/hal-00590618

Éditeur(s) : HAL CCSD Elsevier
Résumé : Rh (Rhesus) is a major blood group system in man, which is clinically significant in transfusion medicine. Rh antigens are carried by an oligomer of two major erythroid specific polypeptides, the Rh (D and CcEe) proteins and the RhAG glycoprotein, that shared a common predicted structure with 12 transmembrane a-helices (M0 to M11). Non erythroid homologues of these proteins have been identified (RhBG and RhCG), notably in diverse organs specialized in ammonia production and excretion, such as kidney, liver and intestine. Phylogenetic studies and experimental evidence have shown that these proteins belong to the Amt/Mep/Rh protein superfamily of ammonium/methylammonium permease, but another view suggests that Rh proteins might function as CO2 gas channels. Until recently no information on the structure of these proteins were available. However, in the last two years, new insight has been gained into the structural features of Rh proteins (through the determination of the crystal structures of bacterial AmtB and archeaebacterial Amt-1. Here, models of the subunit and oligomeric architecture of human Rh proteins are proposed, based on a refined alignment with and crystal structure of the bacterial ammonia transporter AmtB, a member of the Amt/ Mep/Rh superfamily. This alignment was performed considering invariant structural features, which were revealed through Hydrophobic Cluster Analysis, and led to propose alternative predictions for the less conserved regions, particularly in the N-terminal sequences. The Rh models, on which an additional Rh-specific, N-terminal helix M0 was tentatively positioned, were further assessed through the consideration of biochemical and immunochemical data, as well as of stereochemical and topological constraints. These models highlighted some Rh specific features that have not yet been reported. Among these, are the prediction of some critical residues, which may play a role in the channel function, but also in the stability of the subunit structure and oligomeric assembly. These results provide a basis to further understand the structure/function relationships of Rh proteins, and the alterations occurring in variant phenotypes.
ISSN: 1246-7820

hal-00068842
https://hal.archives-ouvertes.fr/hal-00068842

Éditeur(s) : HAL CCSD PeerJ
Résumé : International audience
Understanding the role of predators in food webs can be challenging in highly diverse predator/prey systems composed of small cryptic species. DNA based dietary analysis can supplement predator removal experiments and provide high resolution for prey identification. Here we use a metabarcoding approach to provide initial insights into the diet and functional role of coral-dwelling predatory fish feeding on small invertebrates. Fish were collected in Moorea (French Polynesia) where the BIOCODE project has generated DNA barcodes for numerous coral associated invertebrate species. Pyrosequencing data revealed a total of 292 Operational Taxonomic Units (OTU) in the gut contents of the arc-eye hawkfish (Paracirrhites arcatus), the flame hawkfish (Neocirrhites armatus) and the coral croucher (Caracanthus maculatus). One hundred forty-nine (51%) of them had species-level matches in reference libraries (>98% similarity) while 76 additional OTUs (26%) could be identified to higher taxonomic levels. Decapods that have a mutualistic relationship with Pocillopora and are typically dominant among coral branches, represent a minor contribution of the predators' diets. Instead, predators mainly consumed transient species including pelagic taxa such as copepods, chaetognaths and siphonophores suggesting non random feeding behavior. We also identified prey species known to have direct negative interactions with stony corals, such as Hapalocarcinus sp, a gall crab considered a coral parasite, as well as species of vermetid snails known for their deleterious effects on coral growth. Pocillopora DNA accounted for 20.8% and 20.1% of total number of sequences in the guts of the flame hawkfish and coral croucher but it was not detected in the guts of the arc-eye hawkfish. Comparison of diets among the three fishes demonstrates remarkable partitioning with nearly 80% of prey items consumed by only one predator. Overall, the taxonomic resolution provided by the metabarcoding approach highlights a highly complex interaction web and demonstrates that levels of trophic partitioning among coral reef fishes have likely been underestimated. Therefore, we strongly encourage further empirical approaches to dietary studies prior to making assumptions of trophic equivalency in food web reconstruction. How to cite this article Leray et al. (2015), Metabarcoding dietary analysis of coral dwelling predatory fish demonstrates the minor contribution of coral mutualists to their highly partitioned, generalist diet. PeerJ 3:e1047
ISSN: 2167-8359

Droits : http://creativecommons.org/licenses/by/
hal-01174184
https://hal-univ-perp.archives-ouvertes.fr/hal-01174184
https://hal-univ-perp.archives-ouvertes.fr/hal-01174184/document
https://hal-univ-perp.archives-ouvertes.fr/hal-01174184/file/peerj-1047.pdf
DOI : 10.7717/peerj.1047

Éditeur(s) : HAL CCSD
Résumé : International audience
The Imiter silver mine is a world-class deposit located in the Easternpart of the Anti-Atlas (Morocco). The deposit is hosted by Cryogenianblack shales and Ediacaran volcanics, and unconformablyoverlain byPaleozoic sedimentary rocks. The paragenetic sequence for the ganguemineral is composedby amacroscopically white quartz (Qz1) associatedwith the deposition of galena and scarce silver mineralsas matrixof hydraulic breccias, followed by a grey quartz (Qz2) associated withthe main silver deposition event and a first generation of scarcedolomite(Dol1). A third episode is characterized by massive pink dolomite precipitation(Dol2) with minor quartz (Qz3) and base metals. Finally, asurficial event affects the mineralisation and is responsible for a secondaryore enrichment.Microthermometry study coupled with Raman analyses reveals thatfluid inclusions are CaCl2-dominated. The general trend is a decreaseof temperature from Qz1 (250°C) to Dol1 (80°C) then Dol 2 (probablybelow 70°C) depositions. Fluid salinity increases from Qz1 (6.3 to 19.0wt % NaCleq) to Dol1 (27.2 % wt NaCleq), and decreases with the precipitationof Dol2 associated with quartz 3 (15 %wt NaCleq). The 18Oisotopic composition of fluids in equilibrium with quartz and dolomitesuggestsamagmatic,metamorphic and/or basinal origin for the fluid atthe origin of Qz1, and that meteoric / surficial basinal brinesmay be atthe origin of Dol2.The proposed model to explain the ore forming processes in Imiter is amixing of Ca-brines, probably providing chloride complexes, with a hotNaCl fluid of lower salinity, leading to the precipitation of silver.Theresults favour the important role of calcic brines, whose origin remainsmatter to debate in such a giant depositand for whom age of emplacementis strongly discussed.
24 ème Réunion des sciences de la Terre 2014
Pau, France

insu-01080858
https://hal-insu.archives-ouvertes.fr/insu-01080858

Éditeur(s) : HAL CCSD American Society for Biochemistry and Molecular Biology
Résumé : International audience
The budding yeast Saccharomyces cerevisiae is a major model organism for important biological processes such as mitotic growth and meiotic development, it can be a human pathogen, and it is widely used in the food-, and biotechnology industries. Consequently, the genomes of numerous strains have been sequenced and a very large amount of RNA profiling data is available. Moreover, it has recently become possible to quantitatively analyze the entire yeast proteome; however, efficient and cost-effective high-throughput protein profiling remains a challenge. We report here a new approach to direct and label-free large-scale yeast protein identification using a tandem buffer system for protein extraction, two-step protein prefractionation and enzymatic digestion, and detection of peptides by iterative mass spectrometry. Our profiling study of diploid cells undergoing rapid mitotic growth identified 86% of the known proteins and its output was found to be widely concordant with genome-wide mRNA concentrations and DNA variations between yeast strains. This paves the way for comprehensive and straightforward yeast proteome profiling across a wide variety of experimental conditions.
ISSN: 1535-9476

hal-00682837
https://hal.archives-ouvertes.fr/hal-00682837
DOI : 10.1074/mcp.M111.012682
PUBMED : 21997732

Éditeur(s) : HAL CCSD
Résumé : International audience
BACKGROUND: Dairy working increases the prevalence of lower airway respiratory diseases, especially COPD and asthma. Epidemiological studies have reported that chronic inhalation of organic dusts released during specific daily tasks could represent a major risk factor for development of these pathologies in dairy workers. Knowledge on size, nature and biological activity of such organic dusts remain however limited. OBJECTIVE: To compare size distribution, microbial composition and cellular effects of dusts liberated by the spreading of straw bedding in five French dairy farms located in Brittany. RESULTS: Mechanized distribution of straw bedding generated a cloud of inhalable dusts in the five dairy farms' barns. Thoracic particles having a 3-7.5µm size constituted 58.9-68.3% of these dusts. Analyses of thoracic dusts by next generation sequencing showed that the microbial dust composition differed between the five French farms, although Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria represent more than 97.5% of the bacterial phyla detected in each sample. Several bacteria genera comprising of human pathogenic species, such as Pseudomonas, Staphylococcus, Thermoactinomyces or Saccharopolyspora were identified. Cladosporium and Alternaria fungal genera, which are potent environmental determinants of respiratory symptoms, were detected in dusts collected in the five farms and their levels reached 15.5-51.1% and 9-24.7% of assignable fungal sequences in each sample, respectively. Finally, all dust samples significantly and strongly increased the expression of the pro-inflammatory TNF-α, IL-1β, IL-6 and IL-8 cytokines at both mRNA and protein levels in human monocyte-derived macrophages. Their effects were dose-dependent and detectable from 1µg/ml. The intensity of the macrophage responses however differed according to the samples. CONCLUSIONS: Our results strengthen the hypothesis that organic dusts released during the distribution of straw bedding are mainly constituted of thoracic particles which are small enough to deposit on lower bronchial epithelium of dairy farmers and induce inflammation.
Environmental Research

hal-01579610
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01579610
DOI : 10.1016/j.envres.2017.07.025
PUBMED : 28735230

Éditeur(s) : HAL CCSD European Geosciences Union
Résumé : International audience
During the GWADASEIS cruise (Lesser Antilles volcanic arc, February-March 2009) a very high resolution (VHR) seismic-reflection survey was performed in order to constrain Late Quaternary to Present faulting. The profiles we obtained evidence frequent "ponding" of reworked sediments in the deepest areas, similar to the deposition of Mediterranean "homogenites". These bodies are acoustically transparent (few ms t.w.t. thick) and are often deposited on the hanging walls of dominantly normal faults, at the base of scarps. Their thickness appears sufficient to compensate (i.e. bury) co-seismic scarps between successive earthquakes, resulting in a flat and horizontal sea floor through time. In a selected area (offshore Montserrat and Nevis islands), piston coring (4 to 7 m long) was dedicated to a sedimentological analysis of the most recent of these particular layers. It corresponds to non-stratified homogenous calcareous silty sand (reworked calcareous plankton and minor volcanoclastics). This layer can be up to 2 m thick, and overlies finegrained hemipelagites. The upper centimeters of the latter represent the normal RedOx water/sediment interface. 210Pb and 137Cs activities lack in the massive sands, while a normal profile of unsupported 210Pb decrease is observed in the hemipelagite below, together with a 137Cs peak correspond- ing to the Atmospheric Nuclear Experiments (1962). The RedOx level was thus capped by a recent instantaneous major sedimentary event considered as post-1970 AD; candidate seismic events to explain this sedimentary deposits are either the 16 March 1985 earthquake or the 8 October 1974 one (Mw=6.3 and Mw=7.4, respectively). This leads to consider that the syntectonic sedimentation in this area is not continuous but results from accumulation of thick homogenites deposited after the earthquakes (as observed in the following weeks after Haiti January 2010 event, McHugh et al., 2011). The existence of such deposits suggests that, in the area of study, vertical throw likely results from cumulated effects of separated earthquakes rather than from aseismic creep. Examination of VHR profiles shows that all major co-seismic offsets are recorded in the fault growth sequence and that co-seismic offsets can be precisely estimated. By using a sedimentation rate deduced from 210Pb decrease curve (0.5 mm yr−1) and taking into account minor reworking events detected in cores, we show that the Redonda system may have been responsible for five >M6 events during the last 34 000 yr. The approach presented in this work differs from fault activity analyses using displaced sets of isochronous surfaces and postulating co-seismic offsets. Combining VHR seismic imagery and coring we can decipher co-seismic vs. slow continuous displacement, and thus actually estimate the amplitude and the time distribution of major co-seismic offsets.
ISSN: 1561-8633

insu-00844581
https://hal-insu.archives-ouvertes.fr/insu-00844581
https://hal-insu.archives-ouvertes.fr/insu-00844581/document
https://hal-insu.archives-ouvertes.fr/insu-00844581/file/nhess-12-1755-2012.pdf
DOI : 10.5194/nhess-12-1755-2012

Éditeur(s) : Springer
Résumé : Clonality and genetic structure of the coral Pocillopora damicornis sensu lato were assessed using five microsatellites in 12 populations from four islands of the Society Archipelago (French Polynesia) sampled in June 2008. The 427 analysed specimens fell into 132 multilocus genotypes (MLGs), suggesting that asexual reproduction plays an important role in the maintenance of these populations. A haploweb analysis of ITS2 sequences of each MLG was consistent with all of them being conspecific. Genetic differentiation was detected both between and within islands, but when a single sample per MLG was included in the analyses, the populations turned out to be nearly panmictic. These observations provide further evidence of the marked variability in reproductive strategies and genetic structure of P. damicornis throughout its geographic range; comparison with results previously obtained for the congeneric species Pocillopora meandrina underlines the importance of life history traits in shaping the genetic structure of coral populations
Marine Biology (0025-3162) (Springer), 2014-03 , Vol. 161 , N. 3 , P. 531-541

Droits : Springer-Verlag Berlin Heidelberg 2013
http://archimer.ifremer.fr/doc/00171/28209/26518.pdf
DOI:10.1007/s00227-013-2355-9
http://archimer.ifremer.fr/doc/00171/28209/