Éditeur(s) : HAL CCSD Geological Society of America
Résumé : International audience
Integrated Ocean Drilling Program Expedition 313 continuously cored uppermost Eocene to Miocene sequences on the New Jersey shallow shelf (Sites M27, M28, and M29). Previously, 15 Miocene (ca. 23-13 Ma) seismic sequence boundaries were recognized on several generations of multichannel seismic profi les using criteria of onlap, downlap, erosional truncation, and toplap. We independently recognize sequence boundaries in the cores and logs based on an integrated study of core surfaces, lithostratigraphy and process sedimentology (grain size, mineralogy, facies, and paleoenvironments), facies successions, stacking patterns, benthic foraminiferal water depths, downhole logs, core gamma logs, and chronostratigraphic ages. We use a velocitydepth function to predict the depths of seismic sequence boundaries that were tested by comparison with major core surfaces, downhole and core logs, and synthetic seismograms. Using sonic velocity (core and downhole), core density, and synthetic seismograms, we show that sequence boundaries correspond with acoustic impedance contrasts, although other stratal surfaces (e.g., maximum fl ooding and transgressive surfaces) also produce refl ections. Core data are suffi cient to link seismic sequence boundaries to impedance contrasts in 9 of 12 instances at Site M27, 6 of 11 instances at Site M28, and 8 of 14 instances at Site M29. Oligocene sequences have minimal lithologic and seismic expression due to deep-water locations on clinoform bottomsets. Miocene sequences (ca. 23-13 Ma) were sampled across several unconformity clinothems (prograding units) on topset, foreset, and bottomset locations. Excellent recovery allows core-seismic integration that confi rms the hypothesis that unconformities are a primary source of impedance contrasts. Our core-seismic-log correlations predict that key seismic surfaces observed in other sub surface investigations without core and/or well logs are stratal surfaces with sequence stratigraphic signifi cance.
EISSN: 1553-040X

insu-00946235
https://hal-insu.archives-ouvertes.fr/insu-00946235
DOI : 10.1130/GES00858.1

Éditeur(s) : Elsevier
Résumé : Antimicrobial peptides play a major role in innate immunity. The penaeidins, initially characterized from the shrimp Litopenaeus vannamei, are a family of antimicrobial peptides that appear to be expressed in all penaeid shrimps. As of recent, a large number of penaeid nucleotide sequences have been identified from a variety of penaeid shrimp species and these sequences currently reside in several databases under unique identifiers with no nomenclatural continuity. To facilitate research in this field and avoid potential confusion due to a diverse number of nomenclatural designations, we have made a systematic effort to collect, analyse, and classify all the penaeidin sequences available in every database. We have identified a common penaeidin signature and subsequently established a classification based on amino acid sequences. In order to clarify the naming process, we have introduced a 'penaeidin nomenclature' that can be applied to all extant and future penaeidins. A specialized database, PenBase, which is freely available at http://www.penbase.immunaqua.com, has been developed for the penaeidin family of antimicrobial peptides, to provide comprehensive information about their properties, diversity and nomenclature. (c) 2005 Elsevier Ltd. All rights reserved.
Developmental & Comparative Immunology (0145-305X) (Elsevier), 2006 , Vol. 30 , N. 3 , P. 283-288

Droits : 2005 Elsevier Ltd All rights reserved
http://archimer.ifremer.fr/doc/2006/publication-2332.pdf
DOI:10.1016/j.dci.2005.04.003
http://archimer.ifremer.fr/doc/00000/2332/

Éditeur(s) : Wiley-blackwell
Résumé : The reef fauna connectivity of the West Indian Ocean (WIO) is one of the least studied globally. Here we use genetic analyses of the grouper Epinephelus merra (Bloch 1793) to determine patterns of connectivity and to identify barriers to dispersal in this WIO marine area. Phylogeographic and population-level analyses were conducted on cytochrome b sequences and microsatellites (13 loci) from 557 individuals sampled in 15 localities distributed across the West Indian Ocean. Additional samples from the Pacific Ocean were used to benchmark the WIO population structure. The high level of divergence revealed between Indian and Pacific localities (of about 4.5% in sequences) might be the signature of the major tectonic and climatic changes operating at the Plio-Pleistocene transition, congruently with numerous examples of Indo-Pacific speciation. In comparison, the E. merra sequences from the Indian Ocean constitute a monophyletic clade with a low average genetic distance (d < 0.5%). However both genetic markers indicated some structure within this ocean. The main structure revealed was the isolation of the Maldives from the WIO localities (a different group signature identified by clustering analysis, great values of differentiation). Both marker types reveal further significant structure within the WIO, mainly the isolation of the Mascarene Islands (significant AMOVA and isolation-by-distance patterns) and some patchy structure between the northernmost localities and within the Mozambique Channel. The WIO genetic structure of E. merra appeared congruent with main biogeographic boundaries and oceanographic currents.
Marine Ecology-an Evolutionary Perspective (0173-9565) (Wiley-blackwell), 2015-09 , Vol. 36 , N. 3 , P. 447-461

Droits : 2014 Blackwell Verlag GmbH
http://archimer.ifremer.fr/doc/00189/30046/28566.pdf
DOI:10.1111/maec.12153
http://archimer.ifremer.fr/doc/00189/30046/

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
IntroductionLeishmania RNA virus type 1 (LRV1) is an endosymbiont of some Leishmania (Vianna) species in South America. Presence of LRV1 in parasites exacerbates disease severity in animal models and humans, related to a disproportioned innate immune response, and is correlated with drug treatment failures in humans. Although the virus was identified decades ago, its genomic diversity has been overlooked until now.Methodology/Principles findingsWe subjected LRV1 strains from 19 L. (V.) guyanensis and one L. (V.) braziliensis isolates obtained from cutaneous leishmaniasis samples identified throughout French Guiana with next-generation sequencing and de novo sequence assembly. We generated and analyzed 24 unique LRV1 sequences over their full-length coding regions. Multiple alignment of these new sequences revealed variability (0.5%±23.5%) across the entire sequence except for highly conserved motifs within the 5' untranslated region. Phylogenetic analyses showed that viral genomes of L. (V.) guyanensis grouped into five distinct clusters. They further showed a species-dependent clustering between viral genomes of L. (V.) guyanensis and L. (V.) braziliensis, confirming a long-term co-evolutionary history. Noteworthy, we identified cases of multiple LRV1 infections in three of the 20 Leishmania isolates.Conclusions/SignificanceHere, we present the first-ever estimate of LRV1 genomic diversity that exists in Leishmania (V.) guyanensis parasites. Genetic characterization and phylogenetic analyses of these viruses has shed light on their evolutionary relationships. To our knowledge, this study is also the first to report cases of multiple LRV1 infections in some parasites. Finally, this work has made it possible to develop molecular tools for adequate identification and genotyping of LRV1 strains for diagnostic purposes. Given the suspected worsening role of LRV1 infection in the pathogenesis of human leishmaniasis, these data have a major impact from a clinical viewpoint and for the management of Leishmania-infected patients.
ISSN: 1935-2727

pasteur-01583523
https://hal-riip.archives-ouvertes.fr/pasteur-01583523
DOI : 10.1371/journal.pntd.0005764
PUBMED : 28715422

Éditeur(s) : HAL CCSD
Résumé : International audience
Symbiosis is a widespread phenomenon in the biosphere. In marine benthic environments breakdown of symbiosis is responsible for coral bleaching and dramatically affects coral reef ecosystems functioning [1]. In the water column, planktonic organisms are key component of pelagic ecosystems and a number of species form mutualistic association with microalgae forming a photosymbiosis [2]. Here we intended to investigate the genetic basis of photosymbiosis, through a transcriptomic approach on marine plankton organisms. We focused more specifically on associations occurring between radiolarian host (protist, zooplankton) and dinoflagellates symbiont (protist, phytoplankton) living inside the host cell. It has recently been highlighted that these holobionts are widespread in oligotrophic open oceans and there are also evidences of their fundamental implication in biogeochemical carbon, silica and strontium cycles [3, 4, 5, 6]. RNA-seq technologies allow obtaining an unprecedented amount of data for unicellular organisms isolated from the environment [7]. The study of such non-model holobionts datasets requires de novo assembly, which implies considerable computational resources and the potential production of chimeric sequences [8, 9].We therefore developed an original strategy aiming at accelerating and improving de novo assembly for holobiont datasets. We chose SIMKA [10] a fast kmer-based method initially developed to estimate the similarity between numerous metagenomic datasets, and which has been recently adapted to extract their common sequences. As our symbionts are identified, we used SIMKA to compare our holobionts transcriptomes to publicly available dinoflagellates transcriptomes [11] generating two datasets, one composed of reads from the symbionts and another with reads from the host (for which no reference data are currently available). Independent assemblies were then performed in parallel, accelerating the study process, and minimizing the proportion of resulting chimeric sequences. Our strategy produced a unique and comprehensive genomic dataset for Radiolaria [12, 13], and offers a pragmatic, large scale, comparison strategy to assemble and study holobionts [9]. Our new sequences obtained from holobionts study will be used for phylogenomics investigation, as reference for environmental metagenomic studies and ultimately to understand and characterize the molecular basis of symbiotic relationships in the plankton.Bibliografic references :[1] Simon K. Davy, Denis Allemand, and Virginia M. Weis. “Cell Biology of Cnidarian-Dinoflagellate Symbiosis”. In: Microbiology and Molecular Biology Reviews 76.2 (June 1, 2012), pp. 229–261. issn: 1092-2172, 1098- 5557. doi: 10.1128/MMBR.05014-11.[2] Janouškovec, J. et al. “Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics”. in: PNAS 201614842 (2016). doi:10.1073/pnas.1614842114[3] Tristan Biard et al. “In situ imaging reveals the biomass of giant protists in the global ocean”. In: Nature advance online publication (Apr. 20, 2016). issn: 0028-0836. doi: 10.1038/nature17652.[4] Lionel Guidi et al. “Plankton networks driving carbon export in the olig- otrophic ocean”. In: Nature 532.7600 (Apr. 28, 2016), pp. 465–470. issn: 0028-0836. doi: 10.1038/nature16942.[5] Diane K. Stoecker et al. “Acquired phototrophy in aquatic protists”. In: Aquatic Microbial Ecology 57.3 (Nov. 24, 2009), pp. 279–310. doi: 10.3354/ame01340.[6] Johan Decelle et al. “An original mode of symbiosis in open ocean plankton”. In: Proceedings of the National Academy of Sciences 109.44 (Oct. 30, 2012), pp. 18000–18005. issn: 0027-8424, 1091-6490. doi: 10. 1073/pnas.1212303109.[7] Sergio Balzano et al. “Transcriptome analyses to investigate symbiotic relationships between marine protists”. In: Frontiers in Microbiology 6 (Mar. 17, 2015). issn: 1664-302X. doi: 10.3389/fmicb.2015.00098.[8] Li, B. et al. “Evaluation of de novo transcriptome assemblies from RNA-Seq data”. In: Genome Biology 15, 553 (2014).[9] Sangwan, N., Xia, F. & Gilbert, J. A. “Recovering complete and draft population genomes from metagenome datasets”. In: Microbiome 4, 8 (2016).[10] Gaëtan Benoit et al. “Multiple comparative metagenomics using mul- tiset k -mer counting”. In: PeerJ Computer Science 2 (Nov. 14, 2016). doi: 10.7717/peerj-cs.94.[11] Patrick J. Keeling et al. “The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing”. In: PLOS Biol 12.6 (June 2014), e1001889. issn: 1545-7885. doi: 10.1371/journal.pbio.1001889.[12] Burki, F. et al. “Evolution of Rhizaria: new insights from phylogenomic analysis of uncultured protists”. In BMC Evolutionary Biology 10, 377 (2010).
International Conference on Holobionts
Paris, France

hal-01575069
https://hal.inria.fr/hal-01575069

Éditeur(s) : HAL CCSD Blackwell Publishing
Résumé : International audience
Pliocene and Pleistocene deposits from Grande-Terre (Guadeloupe archipelago, French Lesser Antilles) provide a remarkable example of an isolated carbonate system built in an active margin setting, with sedimentation both controlled by rapid sea-level changes and tectonic movements. Based on new field, sedimentological and palaeontological analyses, these deposits have been organized into four sedimentary sequences (S1 to S4) separated by three subaerial erosion surfaces (SB0, SB1 and SB2). Sequences S1 and S2 ('Calcaires inférieurs à rhodolithes') deposited during the late Zanclean to early Gelasian (planktonic foraminiferal Zones PL2 to PL5) in low subsidence conditions, on a distally steepened ramp dipping eastward. Red algal-rich deposits, which dominate the western part of Grande-Terre, change to planktonic foraminifer-rich deposits eastward. Vertical movements of tens of metres were responsible for the formation of SB0 and SB1. Sequence S3 ('Formation volcano-sédimentaire', 'Calcaires supérieurs à rhodolithes' and 'Calcaires à Agaricia') was deposited during the late Piacenzian to early Calabrian (Zones PL5 to PT1a) on a distally steepened, red algal-dominated ramp that changes upward into a homoclinal, coral-dominated ramp. Deposition of Sequence S3 occurred during a eustatic cycle in quiet tectonic conditions. Its uppermost boundary, the major erosion surface SB2, is related to the Cala1 eustatic sea-level fall. Finally, Sequence S4 ('Calcaires à Acropora') probably formed during the Calabrian, developing as a coral-dominated platform during a eustatic cycle in quiet tectonic conditions. The final emergence of the island could then have occurred in late Calabrian times.
ISSN: 1469-3496

hal-00760906
https://hal.archives-ouvertes.fr/hal-00760906
DOI : 10.1111/j.1365-3091.2011.01311.x

Éditeur(s) : Public Library Science
Résumé : Background: The Astrophorida (Porifera, Demospongiae(rho)) is geographically and bathymetrically widely distributed. Systema Porifera currently includes five families in this order: Ancorinidae, Calthropellidae, Geodiidae, Pachastrellidae and Thrombidae. To date, molecular phylogenetic studies including Astrophorida species are scarce and offer limited sampling. Phylogenetic relationships within this order are therefore for the most part unknown and hypotheses based on morphology largely untested. Astrophorida taxa have very diverse spicule sets that make them a model of choice to investigate spicule evolution. Methodology/Principal Findings: With a sampling of 153 specimens (9 families, 29 genera, 89 species) covering the deep- and shallow-waters worldwide, this work presents the first comprehensive molecular phylogeny of the Astrophorida, using a cytochrome c oxidase subunit I (COI) gene partial sequence and the 59 end terminal part of the 28S rDNA gene (C1-D2 domains). The resulting tree suggested that i) the Astrophorida included some lithistid families and some Alectonidae species, ii) the sub-orders Euastrophorida and Streptosclerophorida were both polyphyletic, iii) the Geodiidae, the Ancorinidae and the Pachastrellidae were not monophyletic, iv) the Calthropellidae was part of the Geodiidae clade (Calthropella at least), and finally that v) many genera were polyphyletic (Ecionemia, Erylus, Poecillastra, Penares, Rhabdastrella, Stelletta and Vulcanella). Conclusion: The Astrophorida is a larger order than previously considered, comprising ca. 820 species. Based on these results, we propose new classifications for the Astrophorida using both the classical rank-based nomenclature (i.e., Linnaean classification) and the phylogenetic nomenclature following the PhyloCode, independent of taxonomic rank. A key to the Astrophorida families, sub-families and genera incertae sedis is also included. Incongruences between our molecular tree and the current classification can be explained by the banality of convergent evolution and secondary loss in spicule evolution. These processes have taken place many times, in all the major clades, for megascleres and microscleres.
Plos One (1932-6203) (Public Library Science), 2011-04 , Vol. 6 , N. 4 , P. -

Droits : 2011 Ca´rdenas et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
http://archimer.ifremer.fr/doc/00137/24817/22903.pdf
DOI:10.1371/journal.pone.0018318
http://archimer.ifremer.fr/doc/00137/24817/

Éditeur(s) : HAL CCSD Wiley/Blackwell
Résumé : International audience
Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongoing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morphological characters and have complex life cycles. To interpret environmental sequences, metabarcoding necessarily relies on taxonomically curated databases containing reference sequences of the targeted gene (or barcode) from identified organisms. To date, no such reference framework exists for photosynthetic eukaryotes. In this study, we built the PhytoREF database that contains 6490 plastidial 16S rDNA reference sequences that originate from a large diversity of eukaryotes representing all known major photosynthetic lineages. We compiled 3333 amplicon sequences available from public databases and 879 sequences extracted from plastidial genomes, and generated 411 novel sequences from cultured marine microalgal strains belonging to different eukaryotic lineages. A total of 1867 environmental Sanger 16S rDNA sequences were also included in the database. Stringent quality filtering and a phylogeny-based taxonomic classification were applied for each 16S rDNA sequence. The database mainly focuses on marine microalgae, but sequences from land plants (representing half of the PhytoREF sequences) and freshwater taxa were also included to broaden the applicability of PhytoREF to different aquatic and terrestrial habitats. PhytoREF, accessible via a web interface (http://phytoref.fr), is a new resource in molecular ecology to foster the discovery, assessment and monitoring of the diversity of photosynthetic eukaryotes using high-throughput sequencing.
ISSN: 1755-098X

hal-01149047
http://hal.upmc.fr/hal-01149047
http://hal.upmc.fr/hal-01149047/document
http://hal.upmc.fr/hal-01149047/file/Decelle_2015_PhytoREF.pdf
DOI : 10.1111/1755-0998.12401

Éditeur(s) : HAL CCSD Elsevier
Résumé : Remerciements :- Dr. Jacques Delabie- Andrea Yockey-Dejean- Geoff Brown- Jean-Pierre Andrieu
Background: Most ant venoms consist predominantly of small linear peptides, although some contain disulfide linked peptides as minor components. However, in striking contrast to other ant species, some Anochetus venoms are composed primarily of disulfide-rich peptides. In this study, we investigated the venom of the ant Anochetus emarginatus with the aim of exploring these novel disulfide-rich peptides.Methods: The venom peptidome was initially investigated using a combination of reversed-phase HPLC and mass spectrometry, then the amino acid sequences of the major peptides were determined using a combination of Edman degradation and de novo MS/MS sequencing. We focused on one of these peptides, U-1-PONTX-Ae1a (Ae1a), because of its novel sequence, which we predicted would form a novel 3D fold. Ae1a was chemically synthesized using Fmoc chemistry and its 3D structure was elucidated using NMR spectroscopy. The peptide was then tested for insecticidal activity and its effect on a range of human ion channels.Results: Seven peptides named poneritoxins (PONTXs) were isolated and sequenced. The three-dimensional structure of synthetic Ae1a revealed a novel, compact scaffold in which a C-terminal beta-hairpin is connected to the N-terminal region via two disulfide bonds. Synthetic Ae1a reversibly paralyzed blowflies and inhibited human L-type voltage-gated calcium channels (Ca(v)1).Conclusions: Poneritoxins from Anochetus emarginatus venom are a novel class of toxins that are structurally unique among animal venoms.General significance: This study demonstrates that Anochetus ant venoms are a rich source of novel ion channel modulating peptides, some of which might be useful leads for the development of biopesticides.
ISSN: 0304-4165

hal-01511987
https://hal.archives-ouvertes.fr/hal-01511987
https://hal.archives-ouvertes.fr/hal-01511987/document
https://hal.archives-ouvertes.fr/hal-01511987/file/2016_Touchard_Biochimica_Biophysica_%7B4B3BE6A3-AE83-4C6E-B678-BBFB5CC84AF7%7D.pdf
DOI : 10.1016/j.bbagen.2016.07.027

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
IODP Site U1309 was drilled at Atlantis Massif, an oceanic core complex, at 30 degrees N on the Mid-Atlantic Ridge (MAR). We present the results of a bulk rock geochemical study (major and trace elements) carried out on 228 samples representative of the different lithologies sampled at this location. Over 96% of Hole U1309D is made up of gabbroic rocks. Diabases and basalts cross-cut the upper part of the section; they have depleted MORB compositions similar to basalts sampled at MAR 30 degrees N. Relics of mantle were recovered at shallow depth. Mantle peridotites show petrographic and geochemical evidence of extensive melt-rock interactions. Gabbroic rocks comprise: olivine-rich troctolites (>70% modal olivine) and troctolites having high Mg# (82-89), high Ni (up to 2300 ppm) and depleted trace element compositions (Yb 0.06-0.8 ppm); olivine gabbros and gabbros (including gabbronorites) with Mg# of 60-86 and low trace element contents (Yb 0.125-2.5 ppm); and oxide gabbros and leucocratic dykes with low Mg# (<50), low Ni (similar to 65 ppm) and high trace element contents (Yb up to 26 ppm). Troctolites and gabbros are amongst the most primitive and depleted oceanic gabbroic rocks. The main geochemical characteristics of Site U1309 gabbroic rocks are consistent with a formation as a cumulate sequence after a common parental MORB melt, although (lack of systematic) downhole variations indicate that the gabbroic series were built by multiple magma injections. In detail, textural and geochemical variations in olivine-rich troctolites and gabbronorites suggest chemical interaction (assimilation?) between the parental melt and the intruded lithosphere. Site U1309 gabbroic rocks do not represent the complementary magmatic product of 30 degrees N volcanics, although they sample the same mantle source. The bulk trace element composition of Site U1309 gabbroic rocks is similar to primitive MORB melt compositions; this implies that there was no large scale removal of melts from this gabbro section. The occurrence of such a large magmatic sequence implies that a high magmatic activity is associated with the formation of Atlantis Massif. Our results suggest that almost all melts feeding this magmatic system stays trapped into the intruded lithosphere.
ISSN: 0012-821X

hal-00413562
https://hal.archives-ouvertes.fr/hal-00413562
DOI : 10.1016/j.epsl.2008.12.034

Éditeur(s) : HAL CCSD
Résumé : This work focus on the characterization of the source and dynamic of compactional fluids during sedimentary burial, through two complementary examples of late orogenic oil‐field half‐grabens: The exhumed Lodève Permian Basin and a deep buried Jurassic basin in the North Viking Graben (North Sea).Constituting the main part of the thesis, a multi‐disciplinary approach was conducted in the Lodève Basin where Ba‐F‐Cu‐Pb polymetallic mineralized systems are trapped into synrift faults and paleokarsts in the carbonate basement at the hinge point of the rollover. The source, timing and P/T conditions of fluid migration were deduced from the analysis of the microfabric, the fluid inclusions microthermometry, and the isotopic (Sr, S, O, H) and Rare Earth Element (REE) signature. Results are then crossed with a structural and thermal modeling that consolidates the sequence and dynamics of fluid during burial.A similar approach was conducted in the North Viking Graben where fluid markers are restricted to 3D seismic and well core data. Comparable Ba‐Pb‐Zn veins are reported in basin margin, plugging one of the most important siliciclastic hydrocarbon reservoir in the substratum. This analysis provides additional constraints on basinal fluid behavior and allows us to propose a global dynamic model for various compositions of fluids and reservoirs.We conclude to a polyphase fluid sequence history including:(a) In the carbonate basement of the Lodève Basin, karstic paleocanyon incisions and associated cavities coupled to synrift fault, act as major drain for fluids. These structures are early affected by hypogen‐sulfuric karstification in response to the interaction between bacterial oxidation of sulfides entrapped within Lower Permian blackshales and the basement oxidizing aquifer.(b) Disequilibrium compaction initiates overpressure‐driven basinal fluid migration towards basin margins, characterized by temperatures around 150‐180°C and salinities between 9 et 18wt%eq.NaCl. Isotopic (Sr, S, O) and REE analyses reveal that Ba‐M+‐rich mineralizing fluids derived mainly from buried blackshales diagenesis. External fluids coming from the lower crust are also identified that play a key role in fluorite precipitation by the leaching of late hercynian granites (mean temperature of 250°C and salinity > 20wt%eq.NaCl).(c) During the synrift period, fluid overpressure is responsible for the periodic reactivation of fault plane according to seismic‐valve process, bedded‐control shearing and hydraulic brecciation at the basement‐seal interface. These mechanisms induce cyclic polymetallic mineralization by the mixing between in‐situ formation water and deep ascending basinal fluids.(d) Thermogenic fluids expulsion starts with last basinal fluids during late burial stage. Hydrocarbons thus migrate along the same regional pathways up to the rollover crest, where they are partly rerouted by the previous mineralized baffle.(e) In the Lodève basin, post‐rift exhumation of the margins led to the remobilization of synrift deposits by subaerial biochemical processes at the sulfate‐methane transition. The latter results from the interaction between the still active hydrocarbon dysmigration with a playa lake sulfate‐rich aquifer. Secondary low‐temperature barite fronts precipitate then within basement meteoric karsts.In addition to the « source to sink » model of basinal fluids, this work provides new insights on the early plugging of hydrocarbon reservoirs and for the metallogenesis of Mississippi Valley‐Type deposits.
Ce travail porte sur la caractérisation de la source et de la dynamique des fluides de bassin au cours de leur chargement à travers deux exemples complémentaires de demi‐grabens tardi‐orogéniques pétroliers : Le Bassin Permien de Lodève, aujourd’hui à l’affleurement et un bassin jurassique enfouis dans le North Viking Graben (Mer du Nord).Le coeur de la thèse concerne le Bassin de Lodève où, à partir d’une approche pluridisciplinaire intégrée, nous avons caractérisé l’architecture des minéralisations (Ba, F, Cu, Pb) piégées dans un réseau paléokarstique alimenté par les failles syn‐rift, dans le substratum carbonaté à l’apex du roll‐over. La source, le calendrier et les conditions de migration des fluides ont été approchés à partir de l’analyse de la micro‐fabrique, la microthermométrie sur inclusions fluides, les analyses isotopiques (Sr, S, O, H) et de Terres Rares. Les résultats analytiques ont été enfin croisés avec un modèle thermique et structural du bassin qui conforte la séquence et la dynamique du système fluide en cours d’enfouissement.Une démarche similaire, mais plus limitée, a été conduite dans le bassin du North Viking Graben où l’accès aux marqueurs fluides est restreint aux données de sismique 3D et de carottes. Comme à Lodève, les minéralisations Ba‐Pb‐Zn colmatent un réservoir dans le substratum à l’apex du roll‐over. Elles se présentent sous forme de ciments dans des grès ou des fractures. Cette analyse apporte des contraintes complémentaires et permet de proposer un modèle dynamique général avec des variantes en fonction de la nature des fluides et des réservoirs.On retiendra donc la séquence fluide suivante :(a) Dans le cas du bassin de Lodève sur substratum carbonaté, les chemins préférentiels de drainage se développent dans des paléocanyons N‐S couplés à un réseau de fractures et d’endokarsts météoriques. Ces derniers sont élargis en début de rifting par la dissolution hypogène sulfurique produite par l’oxydation bactérienne des sulfates et des pyrites des blackshales, au contact de l’aquifère oxydant du Cambrien.(b) Le déséquilibre de compaction initie la migration des fluides interstitiels en surpression vers les marges avec des températures autour de 150‐180°C et des salinités entre 9 et 18wt%eq.NaCl. Les analyses isotopiques (Sr, S, O) révèlent que la majorité des fluides provient de l’altération diagénétique des blackshales riches en métaux. Des interactions sont également mises en évidence avec des fluides profonds (entre 240°C et 260°C ; salinités > à 20wt%eq.NaCl), qui lessivent les granites tardi‐hercyniens.(c) Pendant le syn‐rift, les conditions de surpression de fluide permettent la réactivation cyclique des failles, les décollements stratigraphiques et la formation de brèches hydrauliques, favorisant la mise en connexion avec les réservoirs superficiels à l’apex du rollover. Le modèle de Sibson ajusté aux fluides de bassins est alors le moteur de la migration verticale.(d) Les fluides thermogéniques commencent à être expulsés avec les derniers fluides de compaction au cours d’un stade plus évolué de l’enfouissement en empruntant les mêmes chemins jusqu’à l’apex du roll over. Ils sont alors partiellement freinés et déviés par les colmatages minéralisés antérieurs.(e) A Lodève, la continentalisation des minéralisations antérieures au cours de l’exhumation post‐rift conduit à leur remaniement partiel au niveau de la transition sulfate‐méthane induite par l’interaction entre une playa évaporitique et la dysmigration des hydrocarbures. Des barytines secondaires de basse température, déprimées en Sr sont alors précipitées de manière synsédimentaire dans des karsts météoriques du socle.Outre l’illustration d’un modèle complet (source to sink) de dynamique des fluides dans un bassin, ce travail apporte de nouvelles contraintes dans l’approche du colmatage des réservoirs à hydrocarbures sur les têtes de blocs basculés et sur la genèse des gîtes miniers de type Mississippi Valley‐Type.
https://hal.archives-ouvertes.fr/tel-01457583

tel-01457583
https://hal.archives-ouvertes.fr/tel-01457583
https://hal.archives-ouvertes.fr/tel-01457583/document
https://hal.archives-ouvertes.fr/tel-01457583/file/th%C3%A8seLaurent2015V2.pdf

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
New outcrops in the Sinis peninsula (Sardinia, Italy) allow a detailed description of the Messinian erosion surface. The correlation between outcrops, industrial seismic data and data collected offshore Oristano from a recent cruise permits reconstruction of the geometry of this surface from presently emerged interfluves to the deep canyons offshore, with: - onshore: an eroded karstic plateau presently cropping out over a 20 km × 5 km area. Well-preserved karst structures occur locally and can form several metres high reliefs. The southernmost edge of the plateau is limited by a cliff. The karstic plateau and the cliff are sealed by transgressive deposits of Pliocene age; - offshore, an interfluve zone with a mostly flat and low-angle dipping plateau, westward dissected by paleovalleys which were identified down to a depth of 2000 m. In the Oristano Gulf, Messinian paleovalleys were also identified. The Capo San Marco paleocliff was probably located on the edge of a canyon. Onshore, only one major erosion surface was identified, located at the top the Messinian sequence. Offshore, this surface extends down to the abyssal plain. The surface was emplaced above deposits related to the Terminal Carbonate Complex. This indicates that the marginal evaporites are older than the major drawdown of the Mediterranean sea-level. The major drawdown is related to the deposition of the deep evaporites.
ISSN: 0037-0738

hal-00407864
https://hal.archives-ouvertes.fr/hal-00407864
DOI : 10.1016/j.sedgeo.2008.06.005

Éditeur(s) : Wiley-blackwell
Résumé : Aims To describe the diversity of the culturable mesophilic and potentially pathogenic vibrios isolated at 22 and 37 degrees C on TCBS medium, in September 2009 from seawater and surface sediments. Methods and Results q-PCR assays previously selected for the identification of bacterial strains isolated at 37 degrees C were used in combination with the partial sequencing of two housekeeping genes, pyrH and toxR, to identify 315 strains isolated at 22 degrees C. The great majority of the 37 degrees C strains was identified by q-PCR assays, (five of the six species) with the predominance of Vibrio alginolyticus (85 center dot 9%) and V.harveyi (10 center dot 7%). The human pathogens V.parahaemolyticus and V.cholerae were rarely detected (two strains each). The 22 degrees C strains were successfully identified by the phylogeny analysis of pyrH and toxR genes, revealing 20 Vibrio species, with the predominance of the clam pathogen V.celticus (36 center dot 8%). The Splendidus and the Harveyi groups represented the main Vibrio group at 22 degrees C (80%) and 37 degrees C (99 center dot 5%), respectively. Conclusions The combination of q-PCR assays and the sequencing of pyrH and toxR genes highlighted two different Vibrio communities at 22 and 37 degrees C both dominated by pathogenic species for marine organisms. Significance and Impact of the Study The sequencing of the pyrH gene revealed to be a valuable tool to identify environmental Vibrio spp. strains isolated at 22 degrees C, as 92 center dot 3% of them were identified in this study.
Journal Of Applied Microbiology (1364-5072) (Wiley-blackwell), 2013-06 , Vol. 114 , N. 6 , P. 1713-1724

Droits : 2013 The Society for Applied Microbiology
http://archimer.ifremer.fr/doc/00144/25502/24832.pdf
DOI:10.1111/jam.12181
http://archimer.ifremer.fr/doc/00144/25502/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
A novel antimicrobial peptide, named Bicarinalin, has been isolated from the venom of the ant Tetramorium bicarinatum. Its amino acid sequence has been determined by de novo sequencing using mass spectrometry and by Edman degradation. Bicarinalin contained 20 amino acid residues and was C-terminally amidated as the majority of antimicrobial peptides isolated to date from insect venoms. Interestingly, this peptide had a linear structure and exhibited no meaningful similarity with any known peptides. Antibacterial activities against Staphylococcus aureus and S. xylosus strains were evaluated using a synthetic replicate. Bicarinalin had a potent and broad antibacterial activity of the same magnitude as Melittin and other hymenopteran antimicrobial peptides such as Pilosulin or Defensin. Moreover, this antimicrobial peptide has a weak hemolytic activity compared to Melittin on erythrocytes, suggesting potential for development into an anti-infective agent for use against emerging antibiotic-resistant pathogens.
ISSN: 0196-9781

hal-00996401
https://hal.archives-ouvertes.fr/hal-00996401
DOI : 10.1016/j.peptides.2012.08.018
PUBMED : 22960382

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Well studied in mammals, amelogenesis is less known at the molecular level in reptiles and amphibians. In the course of extensive studies of enamel matrix protein (EMP) evolution in tetrapods, we look for correlation between changes in protein sequences and temporospatial protein gene expression during amelogenesis, using an evo-devo approach. Our target is the major EMP, amelogenin (AMEL) that plays a crucial role in enamel structure. We focused here our attention to an amphibian, the salamander Pleurodeles waltl. RNAs were extracted from the lower jaws of a juvenile P. waltl and the complete AMEL sequence was obtained using PCR and RACE PCR. The alignment of P. waltl AMEL with other tetrapodan (frogs, reptiles and mammals) sequences revealed residue conservation in the N- and C-terminal regions, and a highly variable central region. Using sense and anti-sense probes synthetized from the P. waltl AMEL sequence, we performed in situ hybridization on sections during amelogenesis in larvae, juveniles, and adults. We demonstrated that (i) AMEL expression was always found to be restricted to ameloblasts, (ii) the expression pattern was conserved through ontogeny, even in larvae where enameloid is present in addition to enamel, and (iii) the processes are similar to those described in lizards and mammals. These findings indicate that high variations in the central region of AMEL have not modified its temporospatial expression during amelogenesis for 360 million years of tetrapod evolution. J. Exp. Zool. (Mol. Dev. Evol.) 320B:200209, 2013.
ISSN: 1552-5007

hal-01545483
https://hal.archives-ouvertes.fr/hal-01545483
DOI : 10.1002/jez.b.22494

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Big storm events represent a major risk for populations and infrastructures settled on coastal lowlands. In the Western Mediterranean, where human societies colonized and occupied the coastal areas since the Ancient times, the variability of storm activity for the past three millennia was investigated with a multi-proxy sedimentological and geochemical study from a lagoonal sequence. Mappings of the geochemistry and magnetic susceptibility of detrital sources in the watershed of the lagoon and from the coastal barriers were undertaken in order to track the terrestrial or coastal/marine origin of sediments deposited into the lagoon. The multi-proxy analysis shows that coarser material, low magnetic susceptibility, and high strontium content characterize the sedimentological signature of the paleostorm levels identified in the lagoonal sequence. A comparison with North Atlantic and Western Mediterranean paleoclimate proxies shows that the phases of high storm activity occurred during cold periods, suggesting a climatically-controlled mechanism for the occurrence of these storm periods. Besides, an in-phase storm activity pattern is found between the Western Mediterranean and Northern Europe. Spectral analyses performed on the Sr content revealed a new 270-year solar-driven pattern of storm cyclicity. For the last 3000 years, this 270-year cycle defines a succession of ten major storm periods (SP) with a mean duration of 96 ± 54 yr. Periods of higher storm activity are recorded from >680 to 560 cal yr BC (SP10, end of the Iron Age Cold Period), from 140 to 820 cal yr AD (SP7 to SP5) with a climax of storminess between 400 and 800 cal yr AD (Dark Ages Cold Period), and from 1230 to >1800 cal yr AD (SP3 to SP1, Little Ice Age). Periods of low storm activity occurred from 560 cal yr BC to 140 cal yr AD (SP9 and SP8, Roman Warm Period) and from 820 to 1230 cal yr AD (SP4, Medieval Warm Period).
ISSN: 0277-3791

hal-01277796
https://hal.archives-ouvertes.fr/hal-01277796
DOI : 10.1016/j.quascirev.2015.10.009

Éditeur(s) : Copernicus Gesellschaft Mbh
Résumé : 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 7m 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 fine-grained hemipelagites. The upper centimeters of the latter represent the normal RedOx water/sediment interface. Pb-210 and Cs-137 activities lack in the massive sands, while a normal profile of unsupported Pb-210 decrease is observed in the hemipelagite below, together with a Cs-137 peak corresponding 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 (M-w = 6.3 and M-w = 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 Pb-210 decrease curve (0.5 mmyr(-1)) and taking into account minor reworking events detected in cores, we show that the Redonda system may have been responsible for five > M-6 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.
Natural Hazards And Earth System Sciences (1561-8633) (Copernicus Gesellschaft Mbh), 2012 , Vol. 12 , N. 5 , P. 1755-1767

Droits : Author(s) 2012. CC Attribution 3.0 License.
http://archimer.ifremer.fr/doc/00089/20040/21990.pdf
DOI:10.5194/nhess-12-1755-2012
http://archimer.ifremer.fr/doc/00089/20040/

Résumé : Tahiti’s pearl farming industry plays a major socio-economic role in French Polynesia. In an increasingly competitive market where the production of high quality pearls becomes essential, research can help secure and ensure sustainable production. In that context, Ifremer, in close collaboration with the “direction des resources marines” (French Polynesian government agency) has developed research projects on the “sustainable development of pearl farming”. This program is organized along 3 axes: (1) understanding the animal physiology and initiating a genetically selective breeding program of donor oysters; (2) understanding pearl oyster larvae dispersal and recruitment; (3) understanding the molecular mechanisms underlying biomineralization processes during shell and pearl formation. It is in this frame that we have developed a highthroughput Expressed Sequence Tags pyrosequencing program on the calcifying mantle, combined with proteomic analyses of the shell and pearl. We analyzed 276738 EST sequences, leading to the constitution of a P. margaritifera mantle transcripts catalogue of 82 sequences potentially involved in biomineralization. Our results provided direct evidence that our ESTs data set covers a large number of the matrix proteins of P. margaritifera. In addition, our proteomic analysis enabled us to retrieve, in silico, all the sequences from P. margaritifera involved in the biomineralization process already published on databases. Integration of these two methods allowed, for the first time, the global composition of calcifying tissue and calcified structures to be examined in tandem.
Recent Advances in Pearl Research—Proceedings of the International Symposium on Pearl Research 2011.Edited by Shugo Watabe, Kaoru Maeyama and Hiromichi Nagasawa. 2013. ISBN : 978-4-88704-158-5. pp.184-194

Droits : 2013 TERRAPUB. All rights reserved.
http://archimer.ifremer.fr/doc/00167/27840/26049.pdf
http://archimer.ifremer.fr/doc/00167/27840/

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background: Microbial genetic diversity is often investigated via the comparison of relatively similar 16S molecules through multiple alignments between reference sequences and novel environmental samples using phylogenetic trees, direct BLAST matches, or phylotypes counts. However, are we missing novel lineages in the microbial dark universe by relying on standard phylogenetic and BLAST methods? If so, how can we probe that universe using alternative approaches? We performed a novel type of multi-marker analysis of genetic diversity exploiting the topology of inclusive sequence similarity networks. Results: Our protocol identified 86 ancient gene families, well distributed and rarely transferred across the 3 domains of life, and retrieved their environmental homologs among 10 million predicted ORFs from human gut samples and other metagenomic projects. Numerous highly divergent environmental homologs were observed in gut samples, although the most divergent genes were over-represented in non-gut environments. In our networks, most divergent environmental genes grouped exclusively with uncultured relatives, in maximal cliques. Sequences within these groups were under strong purifying selection and presented a range of genetic variation comparable to that of a prokaryotic domain. Conclusions: Many genes families included environmental homologs that were highly divergent from cultured homologs: in 79 gene families (including 18 ribosomal proteins), Bacteria and Archaea were less divergent than some groups of environmental sequences were to any cultured or viral homologs. Moreover, some groups of environmental homologs branched very deeply in phylogenetic trees of life, when they were not too divergent to be aligned. These results underline how limited our understanding of the most diverse elements of the microbial world remains, and encourage a deeper exploration of natural communities and their genetic resources, hinting at the possibility that still unknown yet major divisions of life have yet to be discovered.
ISSN: 1745-6150

Droits : http://creativecommons.org/licenses/by/
hal-01257771
http://hal.upmc.fr/hal-01257771
http://hal.upmc.fr/hal-01257771/document
http://hal.upmc.fr/hal-01257771/file/s13062-015-0092-3.pdf
DOI : 10.1186/s13062-015-0092-3

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The Karukéra spur is an easternmost submerged rise of the Lesser Antilles fore-arc in the Guadeloupe archipelago, culminating about 4000 m above the fore-arc basin 150 km west of the deformation front. The analysis of 3500 km 2D high-resolution multichannel seismic reflection and multibeam bathymetric data, and the study of 14 core samples, allow for the first time to reconstruct its sedimentary anatomy and tectonic evolution. Seven seismic units (US1 to US7) are evidenced, organised into four major depositional sequences separated by erosional surfaces. Units US1 to US4 thicken to the south-southeast on the spur. The sedimentary deposits rest upon a deeply eroded metamorphic basement of the Caribbean Plate as in La Désirade Island. Sequence 1 (units US1 and US2) remains unknown in its lower part because it does not outcrop. Its upper part comprises early Miocene shallow water carbonates. Sequence S2 (Unit US3) only comprises an upper Miocene transgressive systems tract deposited into basinal environment. It is bounded by major erosional surfaces SB2 and SB3. Sequence 3 (US4 to US6) is Zanclean to Pleistocene. It is dominantly composed of shallow water, reefal deposits. Sequence 4 corresponds to recent deposits. The Karukéra spur experienced three main extensional episodes with alternations between uplift and subsidence periods. Uplifts are responsible for emersions and erosions. Subsidence severely drowned shallow water deposits. The first extensional episode led to the formation of horsts and grabens in the basement, prior to early Miocene deposits. The second extensional episode occurred during upper Miocene, in accordance with data in surrounding islands. The third tectonic episode developed since Calabrian. Noticeable is the constant reactivation of N130°–N150°, N150°–N180° and N40° trending faults since early Miocene and the neoformation of E–W trending faults since Calabrian. Our results suggest that at the latitude of Guadeloupean archipelago the Lesser Antilles subduction zone is an erosional margin because of the successive sweepings of the Santa Lucia then Tiburon Ridges.
ISSN: 0025-3227

hal-01172231
https://hal.archives-ouvertes.fr/hal-01172231
DOI : 10.1016/j.margeo.2015.02.007