Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The ∼55 km-long Firouzkuh fault is located in the Central Alborz Mountains of Iran. It is a left-lateral fault, which dips to the south, and possesses a small dip-slip component of motion that we interpret to result from extension. The ratio of horizontal to vertical displacement across the fault, calculated from the cumulative displacement of landscape features, is 7.6. We provide constraints on the timing of the last earthquake on the Firouzkuh fault from two trenches (T1 and T2) across the fault zone, excavated in 2004, and located east of Firouzkuh city. The trenches expose faulted sedimentary deposits. Two optically-stimulated luminescence (OSL) ages from sediments in the lower part of trench T1 date from the late Pleistocene (15.9 ± 0.9 ka and 27.1 ± 1.7 ka). The younger of the two dated units in T1 is displaced vertically across the fault by 2.2–4.4 m, from which we estimate a strike-slip displacement of 18.2–33.4 m, and hence a average horizontal slip-rate of 1.1–2.2 mm/yr. The sediments exposed in T1 do not yield constraints on the most recent earthquake history. In trench T2, however, human skeletal remains of a middle aged male, which yield a radiocarbon age of 1159 ± 28 BP (corresponding to a mean calendar age of 791 AD), were found within a faulted alluvial layer at a depth of 60–70 cm from the surface. The existence of these medieval human places shows that a surface-rupturing earthquake occurred at some time after 1159 ± 28 BP. The amount of slip in each earthquake on the Firouzkuh fault is difficult to estimate, but assuming the entire ∼55 km fault length ruptures in each event, they will have had a maximum magnitude of 7.1. At our estimated late Quaternary slip-rate of ∼1.1–2.2 mm/yr magnitude 7.1 earthquakes, involving ∼1.2 m average displacement, would be expected to occur every ∼1100–540 years. As the last earthquake on the Firouzkuh fault may be up to ∼700 years in age we suggest that the Firouzkuh fault is a major hazard for earthquakes in the near future.
ISSN: 0743-9547

hal-01122835
https://hal.archives-ouvertes.fr/hal-01122835
DOI : 10.1016/j.jseaes.2013.12.018

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
A high-resolution record of paleostorm events along the French Mediterranean coast over the past 7000 years was established from a lagoonal sediment core in the Gulf of Lions. Integrating grain size, faunal analysis, clay mineralogy and geochemistry data with a chronology derived from radiocarbon dating, we recorded seven periods of increased storm activity at 6300-6100, 5650-5400, 4400-4050, 3650-3200, 2800-2600, 1950-1400 and 400-50 cal yr BP (in the Little Ice Age). In contrast, our results show that the Medieval Climate Anomaly (1150-650 cal yr BP) was characterised by low storm activity.;The evidence for high storm activity in the NW Mediterranean Sea is in agreement with the changes in coastal hydrodynamics observed over the Eastern North Atlantic and seems to correspond to Holocene cooling-in the North Atlantic. Periods of low SSTs there may have led to a stronger meridional temperature gradient and a southward migration of the westerlies. We hypothesise that the increase in storm activity during Holocene cold events over the North Atlantic and Mediterranean regions was probably due to an increase in the thermal gradient that led to an enhanced lower tropospheric baroclinicity over a large Central Atlantic-European domain. (C) 2011 University of Washington. Published by Elsevier Inc. All rights reserved.
ISSN: 0033-5894

hal-00760909
https://hal.archives-ouvertes.fr/hal-00760909
DOI : 10.1016/j.yqres.2011.09.002

Éditeur(s) : Gauthier-Villars
Résumé : Marine muds deposited on the French Guiana coast mostly originate in the Amazon. Recent sediments are composed of (a) illite (33 %) and chlorite (13 %) of Andean mountain origin; and (b) kaolinite (28 %) and smectite (26 %), principally from the Amazonian lowlands but also from the Guiana Shield. In the coastal mud prism, high-resolution seismic profiles, together with sedimentological, micropaleontological and soil engineering studies, supplemented by C-14 dates, permitted a stratigraphic interpretation of eight cores. Three episodes have been determined on the basis of clay-mineral variations related to Amazonian lowland, Andean and Guiana shield sources. The older episodes 3 (3000-1700 y BP) and 2 (1700-1000 y BP) are predominantly characterized by lowland-derived clays (smectite = 43 %, kaolinite = 26 %) from Amazonian and local sources. The most important event is a reduction of the Andean source, due to successive dry phases which occurred in western Amazonia about 2200 and 1200 y BP, confirming that regional decreases in rainfall, water discharge and erosion were associated with climatic fluctuations. It is suggested that these dry phases (within the last 3000 years) are the consequence of several protracted (10-100 years) periods, during which atmospheric conditions mimicked the present-day ''El Nino Southern Oscillation'' (ENSO) phenomenon. As a result, particulate flux from the ocean decreased, leading to reduced silting of the Guiana coast, In the past 1000 years (episode 1), illite and chlorite have increased, indicating a stronger Andean contribution to the Amazonian continental flux that reaches the ocean. This is the first demonstration that the nature of the coastal marine muds of northern South America reflects climatic changes in the Amazon basin.
Oceanologica Acta (0399-1784) (Gauthier-Villars), 1996 , Vol. 19 , N. 5 , P. 477-487

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00094/20506/18175.pdf
http://archimer.ifremer.fr/doc/00094/20506/

Éditeur(s) : Scientific Technical Research Council Turkey-tubitak
Résumé : In 2002, the Bosphorus outlet was mapped using an EM 300 multibeam echo-sounder together with a Chirp sonar system. This survey, carried out on board the Ifremer RV 'Le Suroit' in the frame of the BlaSON project, completes the data previously acquired directly at the mouth of the Bosphorus by Di Iorio et al. (1999) in the frame of a NATO SACLANT Undersea Research project using jointly the NATO RV Alliance, and the Turkish Navy Survey ship 'Cubuklu'. This acoustic imaging has identified a canyon system at the slope and a shallow marine fan, which contains shelf incisions extending the Istanbul Strait incision. Multibeam bathymetry, ultra-high resolution seismic profiling and coring correlations on this subaqueous fan area allowed reconstruction of morphology and patterns of sediment distribution indicative of high energy sediment transport processes. The discovery of a shallow water/shelf type fan directly off shore from the Bosphorus and connected to its outlet is consistent with the theories of sudden discharges of large volumes of water. Age dating obtained at the bottom of this subaqueous shelf fan yielded an age of 6700 yr C-14 BP (uncorrected age) for the first marine mollusc encountered at the base. This is in accordance with a last and abrupt reconnection of the Marmara Sea to the Black Sea. A detailed morphological map of the shelf and slope along with seismic profile interpretation and core correlation is presented here. A synthesis is proposed to explain the formation of this subaqueous fan and its relationship with the last connection between Black and Marmara seas aft er the Last Glacial Maximum. This interpretation can be summarized as follows: stage A corresponds to the first erosion surface seen on the shelf related to the Last Glacial Maximum low stand; stage B is the ravine surface onlapping to ca. -30, -40 m; stage C is a second erosional surface related to a sea level fall and eroding most of underlying Unit 1B; and stage D corresponds to the onset of the fan deposit during a period of high water run-off from the Black Sea entering from the Bosphorus. Avulsion branches show that this fan has been active for a long time.
Turkish Journal Of Earth Sciences (1300-0985) (Scientific Technical Research Council Turkey-tubitak), 2011 , Vol. 20 , N. 3 , P. 287-305

Droits : 2011 TÜBİTAK
http://archimer.ifremer.fr/doc/00036/14676/13677.pdf
http://archimer.ifremer.fr/doc/00036/14676/

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
The scleractinian coral Pocillopora damicornis type β is known to present a mixed reproduction mode: through sexual reproduction, new genotypes are created, while asexual reproduction insures their propagation. In order to investigate the relative proportion of each reproduction mode in P. damicornis type β populations from Reunion Island, Indian Ocean, clonal propagation along the west coast was assessed through four sampling sites with increasing geographical distance between sites. Coral colonies were sampled either exhaustively, randomly or haphazardly within each site, and genotypic diversity was assessed using 13 microsatellite loci over a total of 510 P. damicornis type β determined a posteriori from their mtDNA haplotype (a 840 bp sequenced fragment of the Open Reading Frame). Overall, 47% of all the sampled colonies presented the same multi-locus genotype (MLG), a superclone, suggesting that asexual propagation is extremely important in Reunion Island. Within each site, numerous MLGs were shared by several colonies, suggesting local clonal propagation through fragmentation. Moreover, some of these MLGs were found to be shared among several sites located 40 km apart. While asexual reproduction by fragmentation seems unlikely over long distances, our results suggest a production of parthenogenetic larvae. Despite shared MLGs, two differentiated clusters were enclosed among populations of the west coast of Reunion Island, revealing the necessity to set up appropriate managing strategies at a local scale.
ISSN: 1932-6203

hal-01450078
http://hal.univ-reunion.fr/hal-01450078
DOI : 10.1371/journal.pone.0169692

Éditeur(s) : Elsevier
Résumé : Genetic variation was surveyed at 11 microsatellite loci and at 517 bp of the mitochondrial control region to investigate the presence of genetic stock structure in swordfish (Xiphias gladius) in four proximal localities of the southwest Indian Ocean. One aim of this study was to serve as a preliminary examination for congruency of structure detected by these two genetic markers, prior to conducting a more comprehensive basin-wide survey of the Indian Ocean and nearby surrounding areas. Analyses of multilocus microsatellite genotypes and mitochondrial control region sequences both revealed a great homogeneity between samples. Genetic diversity detected at the regional scale was not significantly higher than detected at the local scale. Results suggest that the southwest Indian Ocean globally functions as a unique panmictic population. However, some discrete genetic differences appeared that could possibly indicate influence from a second genetic pool in the northern part of the Indian Ocean. This structure appeared to be sex-dependent with genetic differences higher among female than among male samples. This result may indicate a higher level of spawning area fidelity for females with a subsequent sampling bias tending to homogenise male genotypic distributions. (c) 2009 Elsevier B.V. All rights reserved.
Fisheries Research (0165-7836) (Elsevier), 2009-05 , Vol. 97 , N. 3 , P. 263-269

Droits : 2009 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/2009/publication-6455.pdf
DOI:10.1016/j.fishres.2009.03.004
http://archimer.ifremer.fr/doc/00000/6455/

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : Vertical displacements on the SW-NE T (e) over capt fault (Eastern Pyrenees Axial Zone, France), which separates the Variscan Canigou-Caranca and Mont-Louis massifs, were constrained using a thermochronologic multi-method approach. Ar-40/Ar-39 data from the granitic Mont-Louis massif record its Variscan cooling history and reveal no ages younger than Early Cretaceous, while the Canigou-Caranca gneiss massif records systematically younger Ar-40/Ar-39 ages. These younger Ar-40/Ar-39 ages in the Canigou-Caranca gneiss massif are the result of partial to total rejuvenation of argon isotopic systems related to a thermal flow coeval with the Cretaceous HT-BP metamorphism in the North Pyrenean Zone. Only the deepest rocks from the Canigou-Caranca suffered this extensive Mid-Cretaceous thermal overprint probably due to differential burial around 4 km at that time. The post Mid-Cretaceous vertical displacements along the T (e) over capt fault are recorded by "low" temperature thermochronology using K-feldspar Ar-40/Ar-39, zircon and apatite fission track and (U-Th)/He datings. The Mont-Louis granite samples experienced a long period of protracted cooling reflecting a lack of thermo-tectonic activity in this area from Late Palaeozoic to Early Cenozoic, followed by cooling from 55-60 Ma to Late Eocene at a mean rate of 15-20 degrees C/Ma in the final stage. This cooling stage corresponds to T (e) over capt fault reactivation with a reversed component, promoting exhumation of the Mont-Louis roof zone contemporaneously with the south-vergent Pyrenean thrusting. In the Canigou-Caranca massif, the main cooling event occurred from 32 to 18 Ma at a maximum rate of 30 degrees C/Ma during Early Oligocene followed by a more moderate rate of 3 degrees C/Ma from Late Oligocene to Early Burdigalian, coeval with the normal reactivation of the T (e) over capt fault in brittle conditions that accommodated the final exhumation of the massif during the opening of the Gulf of Lion.
ISSN: 1437-3254

hal-00411442
https://hal.archives-ouvertes.fr/hal-00411442
DOI : 10.1007/s00531-007-0179-x

Éditeur(s) : HAL CCSD Wiley-Blackwell Wiley
Résumé : A new record from the heart of the Moroccan Middle Atlas cedar forests spans the last 18 000 years and provides valuable insight into our understanding of the natural vegetation and environmental changes. The approach is based on the study of pollen content, geochemical elements and grain size analysis. The pollen data indicate that the vegetation was dominated by herbaceous plants until 9000 BP. Such open landscape allowed greater soil erosion and an input of chemical elements from the watershed. After 9000 BP, tree cover, mainly oak, increased slightly and was accompanied by a higher taxonomic diversity. However, several steppe elements remain well represented in the area until 5000 BP, which suggests that the climate was rather dry during the first part of the Holocene. After 6000 BP, the climate became more favourable to expansion of the forest ecosystems, including Cedrus atlantica, thereby reducing erosion. A strong reduction of the tree pollen percentages is recorded after 2000 BP, which may be related to increasing human activities during the Roman period. These forest changes are concomitant with an increase of lead and copper concentrations in the record, probably related to Roman metalworking activities.
ISSN: 0267-8179

hal-01122848
https://hal.archives-ouvertes.fr/hal-01122848
DOI : 10.1002/jqs.2708

Éditeur(s) : HAL CCSD Springer Verlag (Germany) Springer Verlag
Résumé : The present study aims to review palaeoecological evidence for environmental changes induced by human activities over the last few millennia in the montane landscapes of Morocco. The study is based on well-dated pollen and geochemical records from the Rif and the Middle Atlas mountains, to show spatial and temporal variation in the onset and intensity of exploitation of forest, soil and mineral resources. Before ca. 2000 BP, anthropogenic impact was minimal. At about that time, abrupt changes of the arboreal pollen proportions, with a decline in all tree taxa, indicate a reduction of the forest cover interpreted as being anthropogenic. In the Rif Mountains, increased influx of carbonates (Ca) in the sedimentary records indicates enhanced soil erosion coincident with the reduction in tree cover. In the Middle Atlas, reduced forest cover is linked to geochemical evidence for mining and metallurgy of lead (Pb), copper (Cu) and zinc (Zn). These industrial activities correspond to the expansion of the Roman Empire into Morocco at around AD 40 and show a decline when the Romans were displaced by the Vandals about five centuries later.
ISSN: 0263-0338

hal-01217206
https://hal.archives-ouvertes.fr/hal-01217206
DOI : 10.1007/s10437-015-9186-7

Éditeur(s) : HAL CCSD
Résumé : Integrating ecological connectivity into marine ecosystem management and planning is important, especially in a global context of severe fish stocks depletion and growing habitat degradation. Environmental tools such as Marine Protected Areas have been proposed to protect biodiversity, restore damaged ecosystems, sustain fisheries, and rebuild overexploited stocks. The effectiveness of marine protected areas depends in part on the maintenance of connectivity between marine populations, linked by ecological processes such as larval dispersal. In this thesis, we applied a biophysical model driven by ocean currents derived from satellite altimetry to evaluate connectivity between Western Indian Ocean reefs and across the current MPA system in the Mediterranean Sea. We applied different methods of analysis such as graph-theoretic and clustering. In the Western Indian Ocean, marine connectivity analyses show that the number of connections between reefs increases with fish pelagic larval duration. It also highlights a low connectivity across the region and a high interconnectivity within several regions (Mozambique Channel, Mascarene archipelago). In the Mediterranean Sea, connectance is globally low at the regional scale. This connectance is more important in Western than Eastern Mediterranean. Moreover, the marine connectivity analyses revealed high domestic connectivity rates. Depending on the study area, priority reefs or sites for MPA implementation are proposed. Finally, implications for transboundary marine policies and regional cooperation are discussed.
Intégrer les connaissances sur la connectivité écologique dans la gestion des écosystèmes marins est essentiel, surtout dans un contexte d'appauvrissement des ressources marines et de dégradation des habitats côtiers à l'échelle mondiale. Des outils environnementaux, tels que les Aires Marines Protégées ont été mises en œuvre pour protéger la biodiversité, restaurer les écosystèmes endommagés, soutenir les pêcheries et reconstituer les stocks surexploités. Leur efficacité dépend en partie du maintien de la connectivité entre les populations marines, assurée à travers divers processus écologiques dont la dispersion larvaire. Dans le cadre de ce travail de thèse, un modèle biophysique intégrant des données de courants, issues de mesures d'altimétrie par satellite, a été utilisé pour évaluer la connectivité entre les récifs de l'océan Indien d'une part, et à travers le réseau d'AMP de Méditerranée d'autre part. Différentes méthodes d'analyse ont été utilisées, telles que la théorie des graphes et le clustering. Dans l'océan Indien occidental, l'analyse des connectivités marines montre que le nombre de connexions entre les récifs augmente avec la durée de vie larvaire des poissons. Elle met également en évidence une faible connectivité à l'échelle de la région, mais une forte inter-connectivité au sein de plusieurs sous-régions (Canal du Mozambique, Mascareignes). En Méditerranée, la connectance est globalement faible à l'échelle régionale, bien que plus importante dans le bassin occidental que le bassin oriental. L'analyse des connectivités marines montre également un taux de connectivité élevé à l'échelle d'un même pays. Selon le cas d'étude, une liste de récifs ou de sites prioritaires dans la mise en œuvre des AMP a été proposée. Enfin, les implications de ces résultats en termes de politiques transfrontalières et de coopération régionale sont discutées.
https://tel.archives-ouvertes.fr/tel-01269631

NNT : 2015LARE0003
tel-01269631
https://tel.archives-ouvertes.fr/tel-01269631
https://tel.archives-ouvertes.fr/tel-01269631/document
https://tel.archives-ouvertes.fr/tel-01269631/file/2015lare0003_ECrochelet.pdf

Éditeur(s) : HAL CCSD European Geosciences Union (EGU)
Résumé : International audience
Storms and tsunamis, which may seriously endanger human society, are amongst the most devastating marine catastrophes that can occur in coastal areas. Many such events are known and have been reported for the Mediterranean, a region where high-frequency occurrences of these extreme events coincides with some of the most densely populated coastal areas in the world. In a sediment core from the Mar Menor (SE Spain), we discovered eight coarse-grained layers which document marine incursions during periods of intense storm activity or tsunami events. Based on radiocarbon dating, these extreme events occurred around 5250, 4000, 3600, 3010, 2300, 1350, 650, and 80 years cal BP. No comparable events have been observed during the 20th and 21st centuries. The results indicate little likelihood of a tsunami origin for these coarse-grained layers, although historical tsunami events are recorded in this region. These periods of surge events seem to coincide with the coldest periods in Europe during the late Holocene, suggesting a control by a climatic mechanism for periods of increased storm activity. Spectral analyses performed on the sand percentage revealed four major periodicities of 1228 ± 327, 732 ± 80, 562 ± 58, and 319 ± 16 years. Amongst the well-known proxies that have revealed a millennial-scale climate variability during the Holocene, the ice-rafted debris (IRD) indices in the North Atlantic developed by Bond et al. (1997, 2001) present a cyclicity of 1470 ± 500 years, which matches the 1228 ± 327-year periodicity evidenced in the Mar Menor, considering the respective uncertainties in the periodicities. Thus, an in-phase storm activity in the western Mediterranean is found with the coldest periods in Europe and with the North Atlantic thermohaline circulation. However, further investigations, such as additional coring and high-resolution coastal imagery, are needed to better constrain the main cause of these multiple events.
ISSN: 1814-9324

hal-01357199
https://hal.archives-ouvertes.fr/hal-01357199
https://hal.archives-ouvertes.fr/hal-01357199v2/document
https://hal.archives-ouvertes.fr/hal-01357199/file/cp-12-1389-2016.pdf
DOI : 10.5194/cp-12-1389-2016

Éditeur(s) : Inter-Research
Résumé : Experimental infections of Penaeus (Litopenaeus) stylirostris were performed with a Vibrio penaeicida strain (AM101) isolated in New Caledonia from Syndrome 93 diseased shrimp. Cumulative mortalities resulting from intramuscular injection or immersion of shrimp in bacterial suspensions demonstrated high virulence for this bacterial strain and suggested that V. penaeicida could be the etiological agent of Syndrome 93. The median lethal dose (LD50) for AM101 was 1.3 x 104 CFU (colony forming units) ml-1 by immersion and less than 5 CFU shrimp-1 by intramuscular challenge, with mortality outbreaks at 48 and 22 h after challenge, respectively. A polymerase chain reaction (PCR) detection assay using a primer set designed from the 16S ribosomal RNA gene of V. penaeicida was developed. It gave an expected amplicon of approximately 310 bp in ethidium bromide-stained agarose gels. The specificity of these primers was assessed with different Vibrio species. Furthermore, DNA extracted by the ChelexTM method could be used to detect fewer than 20 cultured Vibrio cells in seawater or shrimp hemolymph by this assay. It appears to be a reliable screening method for detecting V. penaeicida in shrimp and from the aquatic environment.
Diseases of aquatic organisms (0177-5103) (Inter-Research), 2000-03 , Vol. 49 , N. 2 , P. 109-115

Droits : Inter-Research 2000
http://archimer.ifremer.fr/doc/2000/publication-4436.pdf
DOI:10.3354/dao040109
http://archimer.ifremer.fr/doc/00000/4436/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Implication of immune processes in bipolar disorder (BD) has recently gained increasing attention. Tolerogenic molecules, among which HLA-G plays a prominent role, mediate the modulation of such processes. The HLA-G locus is characterized by a high number of polymorphisms including a functionally relevant 14 base pair (bp) insertion/deletion (Ins/Del) allele affecting the HLA-G expression. Here, we analyzed the distribution of this polymorphism in 561 BD patients and 161 healthy and found that the HLA-G 14bp Ins/Ins genotype was significantly more prevalent in healthy controls than in patients (corrected p; pc=0.032) and that the prevalence of such protective genotype is lower among patients born during the winter season as compared to those born in other periods (pc=0.006). Possible mechanisms between low HLA G expression and resistance to infections as well as potential relationships between infections in early life and susceptibility to BD are discussed.
ISSN: 0198-8859

inserm-00864639
http://www.hal.inserm.fr/inserm-00864639
http://www.hal.inserm.fr/inserm-00864639/document
http://www.hal.inserm.fr/inserm-00864639/file/HLA-G_and_BD_manuscript_-1.pdf
DOI : 10.1016/j.humimm.2012.11.032

Éditeur(s) : Elsevier
Résumé : In situ microbialites occurring in reef rocks dredged between 80 and 130 in water depth on the modern fore-reef slopes of Tahiti and the Marquesas islands yield ages ranging from 17,100 2900 to 4410 2250 years BP, suggesting that they played a prominent role during the last deglacial sea level rise. Microbialites developed in both shallow and deep water depositional environments where they characterize various zones of the reef tracts (reef crests, upper reef slopes, deep fore-reef slopes), reflecting contrasting scenarios of microbialite development involving ''reefal microbialites'' in shallow-water settings and ''slope microbialites'' that formed in environments deeper than 1020 in and extending down to more than 100 m. Reefal microbialites correspond to a late stage of encrustation of the dead parts of coral colonies, or more commonly, of related encrusting organisms (red algae and foraminifers), thus forming surface crusts. Slope microbialites generally form the ultimate stage of a biological succession indicating a deepening sequence, whereby shallow water corals and associated encrusting organisms are replaced by deeper water assemblages of red algae and foraminifers before microbialite growth. The precipitation of phosphatic-iron-manganese crusts and the deposition of planktonic micritic limestones on the microbialites characterize a deepening-upward sequence. The widespread development of microbialites in reef sequences from the Last Deglaciation characterizes a period of environmental degradation consequential oil the rapid sea-level rise and abrupt climatic changes of that time. The reported biological succession reflects changes in water quality, and especially an increase in nutrients. In shallow-water settings, increased alkalinity and nutrient availability in interstitial waters were related to surface fluxes and terrestrial groundwater seepage while slope environments were exposed to continuous upwelling of nutrient-rich deeper waters during the last deglacial sea level rise. The age differences between corals and overlying slope microbialites range from 1600 to 8400 years, based on high-precision U-series age measurements of both corals and microbialites, and indicates that a significant time (several thousand years) elapsed between the development of the coralgal frameworks and the growth of slope microbialite crusts. Microbialites cannot be considered as part of the drowning event some 14,000 years ago that resulted in the demise of reef frameworks in the 90-110 m present depth range, but are Substantially younger. (c) 2006 Elsevier B.V. All rights reserved.
Sedimentary Geology (0037-0738) (Elsevier), 2006-03 , Vol. 185 , N. 3-4 , P. 277-295

Droits : 2006 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/2006/publication-4204.pdf
DOI:10.1016/j.sedgeo.2005.12.018
http://archimer.ifremer.fr/doc/00000/4204/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
In this study, we report the cloning of three transcripts for leptin receptor in the European sea bass, a marine teleost of economic interest. The two shortest variants, generated by different splice sites, encode all functional extracellular and intracellular domains but missed the transmembrane domain. The resulting proteins are therefore potential soluble binding proteins for leptin. The longest transcript (3605 bp), termed sblepr, includes all the essential domains for binding and transduction of the signal. Thus, it is proposed as the ortholog for the human LEPR gene, the main responsible for leptin signalling. Phylogenetic analysis shows the sblepr clustered within the teleost leptin receptor group in 100% of the bootstrap replicates. The neuroanatomical localization of sblepr expressing cells has been assessed by in situ hybridization in brains of sea bass of both sexes during their first sexual maturation. At histological level, the distribution pattern of sblepr expressing cells in the brain shows no clear differences regarding sex or reproductive season. Transcripts of the sblepr have a widespread distribution throughout the forebrain and midbrain until the caudal portion of the hypothalamus. A high hybridization signal is detected in the telencephalon, preoptic area, medial basal and caudal hypothalamus and in the pituitary gland. In a more caudal region, sblepr expressing cells are identified in the longitudinal torus. The expression pattern observed for sblepr suggests that in sea bass, leptin is very likely to be involved in the control of food intake, energy reserves and reproduction
ISSN: 0016-6480

hal-01290500
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01290500
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01290500/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01290500/file/Leptin%20receptor%20gene%20in%20the%20European%20sea%20bass%20postprint.pdf
DOI : 10.1016/j.ygcen.2016.03.017

Éditeur(s) : Elsevier Science Bv
Résumé : The modern Rhone delta in the Gulf of Lions (NW Mediterranean) is a typical wave-dominated delta that developed after the stabilization of relative sea level following the last deglacial sea-level rise. Similar to most other deltas worldwide, it displays several stacked parasequences and lobes that reflect the complex interaction between accommodation, sediment supply and autogenic processes on the architecture of a wave-dominated delta. The interpretation of a large set of newly acquired very high-resolution seismic and sedimentological data, well constrained by 14C dates, provides a refined three-dimensional image of the detailed architecture (seismic bounding surfaces, sedimentary facies) of the Rhone subaqueous delta, and allows us to propose a scenario for delta evolution during the last deglaciation and Holocene. The subaqueous delta consists of “parasequence-like” depositional wedges, a few meters to 20–30 m in thickness. These wedges first back-stepped inland toward the NW in response to combined global sea-level rise and overall westward oceanic circulation, at a time when sediment supply could not keep pace with rapid absolute (eustatic) sea-level rise. At the the Younger Dryas-Preboreal transition, more rapid sea-level rise led to the formation of a major flooding surface (equivalent to a wave ravinement surface). After stabilization of global sea level in the mid-Holocene, accommodation became the leading factor controlling delta architecture. An eastward shift of depocenters occurred, probably favoured by higher subsidence rate within the thick Messinian Rhone valley fill. The transition between transgressive (backstepping geometry) and regressive (prograding geometry) (para)sequences resulted in creation of a Maximum Flooding Surface (MFS) that differs from a “classical” MFS described in the literature. It consists of a coarse-grained interval incorporating reworked shoreface material within a silty clay matrix. This distinct lithofacies results from condensation/erosion, which appears as an important process even within supply-dominated deltaic systems, due to avulsion of distributaries. The age of the MFS varies along-strike between ca. 7.8-5.6 kyr cal. BP in relation to the position of depocenters and climatically-controlled sediment supply. The last rapid climate change of the Holocene, the Little Ice Age (1250–1850 AD), had a distinct stratigraphic influence on the architecture and lithofacies of the Rhone subaqueous delta through the progradation of two deltaic lobes. In response to changes in sediment supply linked to rapid climate changes (and to anthropic factors), the Rhone delta evolved from wave-dominated to fluvial dominated, and then wave dominated again.
Sedimentary Geology (0037-0738) (Elsevier Science Bv), 2014-05 , Vol. 305 , P. 35-53

Droits : 2014 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/00179/29017/27445.pdf
DOI:10.1016/j.sedgeo.2014.02.004
http://archimer.ifremer.fr/doc/00179/29017/

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 Lippincott, Williams & Wilkins
Résumé : International audience
Purpose of review Toxoplasmosis in immunocompromised patients is associated with a high mortality rate. Molecular techniques are important tools to diagnose acute disease in immunocompromised patients, but there are various methods with variable efficiency. Some of them have been validated for the diagnosis of congenital toxoplasmosis, but the impact of their use has not been evaluated in immunocompromised patients. Recent findings Toxoplasmosis is of increasing importance in non-HIV immunocompromised patients. In addition, the picture of disease shows greater severity in South America, both in immunocompetent study participants and in congenitally infected infants. These epidemiological differences could influence the sensitivity of diagnostic methods. This review analyzes recent data on molecular diagnosis and compares them with older ones, in light of progress gained in molecular techniques and of recent epidemiological findings. Most recent studies were conducted in South America and used PCR targeting the B1 gene. PCR on blood could allow diagnosing a significant proportion of patients with ocular toxoplasmosis in Brazil. Summary Quantitative PCR methods with specific probes should be used to improve sensitivity and warrant specificity. Performance of quantitative PCR targeting the repeated 529 bp sequence for the diagnosis of toxoplasmosis in immunocompromised patients needs evaluation in field studies in South America and in western countries.
ISSN: 0951-7375

hal-01390970
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01390970
DOI : 10.1097/QCO.0000000000000275
PUBMED : 27191201

Éditeur(s) : HAL CCSD Royal Society
Résumé : International audience
The 2 465 177 bp genome of Sulfolobus islandicus LAL14/1, host of the model rudivirus SIRV2, was sequenced. Exhaustive comparative genomic analysis of S. islandicus LAL14/1 and the nine other completely sequenced S. islandicus strains isolated from Iceland, Russia and USA revealed a highly syntenic common core genome of approximately 2 Mb and a long hyperplastic region containing most of the strain-specific genes. In LAL14/1, the latter region is enriched in insertion sequences, CRISPR (clustered regularly interspaced short palindromic repeats), glycosyl transferase genes, toxin-antitoxin genes and MITE (miniature inverted-repeat transposable elements). The tRNA genes of LAL14/1 are preferential targets for the integration of mobile elements but clusters of atypical genes (CAG) are also integrated elsewhere in the genome. LAL14/1 carries five CRISPR loci with 10 per cent of spacers matching perfectly or imperfectly the genomes of archaeal viruses and plasmids found in the Icelandic hot springs. Strikingly, the CRISPR_2 region of LAL14/1 carries an unusually long 1.9 kb spacer interspersed between two repeat regions and displays a high similarity to pING1-like conjugative plasmids. Finally, we have developed a genetic system for S. islandicus LAL14/1 and created ΔpyrEF and ΔCRISPR_1 mutants using double cross-over and pop-in/pop-out approaches, respectively. Thus, LAL14/1 is a promising model to study virus-host interactions and the CRISPR/Cas defence mechanism in Archaea.
ISSN: 2046-6390

hal-00818894
https://hal.archives-ouvertes.fr/hal-00818894
DOI : 10.1098/rsob.130010
PUBMED : 23594878

Éditeur(s) : Academic Press Ltd- Elsevier Science Ltd
Résumé : The understanding of reciprocal interactions between Crassostrea gigas and Vibrio sp., whether these be virulent or avirulent, is vital for the development of methods to improve the health status of cultured oysters. We describe an original non-invasive experimental infection technique using cohabitation, designed to explore these interactions. Using real-time PCR techniques we examined the dynamics of virulent and avirulent Vibrio sp. in oyster hemolymph and tank seawater, and made a parallel study of the expression of four genes involved in oyster immune defense: Cg-BPI, Cg-EcSOD, Cg-IκB, Cg-TIMP. No mortality occurred in control animals, but oysters put in cohabitation for 2–48 h with animals previously infected by two Vibrio pathogens suffered mortalities from 2 to 16 days post-cohabitation. Our results show that virulent Vibrio infect healthy individuals after only 2 h of cohabitation, with values ranging from 4.5×102 to 2×104 cells ml−1 hemolymph. Simultaneously, an approximate ten-fold increase of the total Vibrio population was observed in control animals, with a 6.6–78.5-fold up-expression of targeted genes. In contrast, oysters exposed to harmful bacteria had mean expression levels strongly down-regulated by a factor of 9.2–29 (depending on the gene) compared with control animals. Although oysters were still found to be infected by virulent Vibrio after 6–48 h of cohabitation, no significant differences were noted when comparing levels of each transcript in control and infected oysters at the same sampling times during this period: the important differences were noted before 6 h cohabitation. Taken together, our data support (1) the hypothesis that virulent Vibrio disturbs the immune response of this invertebrate host both rapidly and significantly, although this occurs specifically during an early and transient period during the first 6 h of cohabitation challenge, and that (2) expression of targeted genes is not correlated with vibriosis resistance.
Fish & Shellfish Immunology (1050-4648) (Academic Press Ltd- Elsevier Science Ltd), 2011-02 , Vol. 30 , N. 2 , P. 691-699

Droits : 2011 Elsevier Ltd All rights reserved.
http://archimer.ifremer.fr/doc/00025/13604/10681.pdf
DOI:10.1016/j.fsi.2010.12.017
http://archimer.ifremer.fr/doc/00025/13604/