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  • Open Access English
    Authors: 
    Uwe John; Yameng Lu; Sylke Wohlrab; Marco Groth; Jan Janouškovec; Gurjeet S. Kohli; Felix Christopher Mark; Ulf Bickmeyer; Sarah Farhat; Marius Felder; +7 more
    Publisher: HAL CCSD
    Countries: Germany, France, France, France
    Project: EC | MICRO B3 (287589)

    Dinoflagellates are microbial eukaryotes that have exceptionally large nuclear genomes; however, their organelle genomes are small and fragmented and contain fewer genes than those of other eukaryotes. The genus Amoebophrya (Syndiniales) comprises endoparasites with high genetic diversity that can infect other dinoflagellates, such as those forming harmful algal blooms (e.g., Alexandrium). We sequenced the genome (~100 Mb) of Amoebophrya ceratii to investigate the early evolution of genomic characters in dinoflagellates. The A. ceratii genome encodes almost all essential biosynthetic pathways for self-sustaining cellular metabolism, suggesting a limited dependency on its host. Although dinoflagellates are thought to have descended from a photosynthetic ancestor, A. ceratii appears to have completely lost its plastid and nearly all genes of plastid origin. Functional mitochondria persist in all life stages of A. ceratii, but we found no evidence for the presence of a mitochondrial genome. Instead, all mitochondrial proteins appear to be lost or encoded in the A. ceratii nucleus. The parasitic marine dinoflagellate Amoebophrya is the first known eukaryote with aerobic mitochondria without a genome.

  • Open Access English
    Authors: 
    Ferdinand Marlétaz; Panos N. Firbas; Ignacio Maeso; Juan J. Tena; Ozren Bogdanovic; Malcolm Perry; Christopher D. R. Wyatt; Elisa de la Calle-Mustienes; Stéphanie Bertrand; Demian Burguera; +51 more
    Publisher: HAL CCSD
    Countries: France, Spain, France, France, Portugal, Spain, United Kingdom, Spain, France, Spain ...
    Project: EC | NEURAL AS (637591), EC | BLUEandGREEN (692419), EC | DEVCOM (607142), EC | EVOREL (658521), EC | Evoland (740041), EC | GENEVA (268513), EC | NEURAL AS (637591), EC | BLUEandGREEN (692419), EC | DEVCOM (607142), EC | EVOREL (658521),...

    Vertebrates have greatly elaborated the basic chordate body plan and evolved highly distinctive genomes that have been sculpted by two whole-genome duplications. Here we sequence the genome of the Mediterranean amphioxus (Branchiostoma lanceolatum) and characterize DNA methylation, chromatin accessibility, histone modifications and transcriptomes across multiple developmental stages and adult tissues to investigate the evolution of the regulation of the chordate genome. Comparisons with vertebrates identify an intermediate stage in the evolution of differentially methylated enhancers, and a high conservation of gene expression and its cis-regulatory logic between amphioxus and vertebrates that occurs maximally at an earlier mid-embryonic phylotypic period. We analyse regulatory evolution after whole-genome duplications, and find that—in vertebrates—over 80% of broadly expressed gene families with multiple paralogues derived from whole-genome duplications have members that restricted their ancestral expression, and underwent specialization rather than subfunctionalization. Counter-intuitively, paralogues that restricted their expression increased the complexity of their regulatory landscapes. These data pave the way for a better understanding of the regulatory principles that underlie key vertebrate innovations. This research was funded primarily by the European Research Council (ERC) under the European Union’s Horizon 2020 and Seventh Framework Program FP7 research and innovation programs (ERC-AdG-LS8-740041 to J.L.G.-S., ERC-StG-LS2-637591 to M.I., a Marie Sklodowska-Curie Grant (658521) to I.M. and a FP7/2007-2013-ERC-268513 to P.W.H.H.), the Spanish Ministerio de Economía y Competitividad (BFU2016-74961-P to J.L.G.-S., RYC-2016-20089 to I.M., BFU2014-55076-P and BFU2017-89201-P to M.I. and BFU2014-55738-REDT to J.L.G.-S, M.I. and J.R.M.-M), the ‘Centro de Excelencia Severo Ochoa 2013-2017’(SEV-2012-0208), the ‘Unidad de Excelencia María de Maetzu 2017-2021’(MDM-2016-0687), the People Program (Marie Curie Actions) of the European Union’s Seventh Framework Program FP7 under REA grant agreement number 607142 (DevCom) to J.L.G.-S., and the CNRS and the ANR (ANR16-CE12-0008-01) to H.E. O.B. was supported by an Australian Research Council Discovery Early Career Researcher Award (DECRA; DE140101962).

  • Open Access
    Authors: 
    K. Mathias Wegner; Damien Piel; Damien Piel; Maxime Bruto; Uwe John; Uwe John; Zhijuan Mao; Marianne Alunno-Bruscia; Marianne Alunno-Bruscia; Bruno Petton; +3 more
    Countries: France, Germany, Germany
    Project: ANR | REVENGE (ANR-16-CE32-0008), ANR | REVENGE (ANR-16-CE32-0008)

    International audience; Bacteria of the Vibrio genus are the most predominant infectious agents threatening marine wildlife and aquaculture. Due to the large genetic diversity of these pathogens, the molecular determinants of Vibrio virulence are only poorly understood. Furthermore, studies tend to ignore co-evolutionary interactions between different host populations and their locally encountered Vibrio communities. Here, we explore the molecular targets of such co-evolutionary interactions by analyzing the genomes of nine Vibrio strains from the Splendidus-clade showing opposite virulence patterns towards two populations of Pacific oysters introduced into European Wadden Sea. By contrasting Vibrio phylogeny to their host specific virulence patterns, we could identify two core genome genes (OG1907 and OG 3159) that determine the genotype by genotype (G × G) interactions between oyster larvae and their sympatric Vibrio communities. Both genes show positive selection between locations targeting only few amino acid positions. Deletion of each gene led to a loss of the host specific virulence patterns while complementation with OG3159 alleles from both locations could recreate the wild type phenotypes matching the origin of the allele. This indicates that both genes can act as a genetic switch for Vibrio-oyster coevolution demonstrating that local adaptation in distinct Vibrio lineages can rely on only few genes independent of larger pathogenicity islands or plasmids.

  • Publication . Article . Other literature type . 1975
    Open Access French
    Authors: 
    Charlon, Nicole;
    Publisher: HAL CCSD
    Country: France

    The problem of the clogging up of sea water pipes by Mytilus edulis larvae is a very real problem. A study has been made of the ways to destroy these larvae, (1) by electricity (publication in preparation), (2) by ultrasound. This last technique has given interesting data, but exploitation of results on a large scale presents many difficulties. An interesting general phenomenon is to be underlined. For ultrasound treatments of short duration (10s), many larvae are simply stressed and recover later on. For longer treatments, there is actual dislocation of the larvae and instant mortality, this mortality increases with time.

  • Open Access
    Authors: 
    Marina Rabineau; Serge Berné; Daniel Aslanian; Jean-Louis Olivet; Philippe Joseph; François Guillocheau; Jean-François Bourillet; Eliane Ledrezen; Didier Granjeon;
    Publisher: Elsevier BV
    Country: France

    The wide continental shelf of the Gulf of Lion (up to 70 km) has been the object of numerous investigations since the early days of oceanography. Yet, the question of sequences duration, the mechanisms of deposition and factors implied remained unanswered. A study of a very dense grid of Very High Resolution (VHR) seismic reflection (Sparker) data associated with surficial cores both, collected by IFREMER between 1992 and 2001 on the outer shelf and upper slope offshore of Sète in the Languedoc region gives a new insight into these issues. Analysis of the 3D geometry of the sedimentary record reveals a basic depositional pattern consisting of a pair of horizontally juxtaposed and downlapping prisms. Prism PI with low angle clinoforms (<1°) lies on the upper part of the shelf and is interpreted to be prodeltaic-offshore deposits. Prism PII with steeply dipping clinoforms (approximately 4°) lies on the outer shelf between 40 and 70 km from the present day coastline and is interpreted to be littoral deposits. Results obtained from integrating lithology, palynology, micropaleontology, seismic stratigraphy, stratigraphic simulation, support the hypothesis that the basic depositional pattern records a 100 000-years glacioeustatic (interglacial/glacial) cycle. As previously suggested by Aloïsi [Aloïsi, J.C., 1986. Sur un modèle de sédimentation deltaïque: contribution à la connaissance des marges passive, Thèse de Doctorat d'Etat. Université de Perpignan, 162 pp], prisms PI corresponds to deposition at high sea level and prisms PII to deposition during low sea level at glacial maxima. Five sequences of paired prisms capped by five major erosion surfaces have been identified and modelled showing that the corresponding glacioeustatic cycles (the last five cycles at least) are recorded on the shelf of the western part of the Gulf of Lion.

  • Publication . Article . Other literature type . 2020
    Open Access English
    Authors: 
    Delphine Destoumieux-Garzón; Laura Canesi; Daniel Oyanedel; Marie-Agnes Travers; Guillaume M. Charrière; Carla Pruzzo; Luigi Vezzulli;
    Publisher: HAL CCSD
    Country: France
    Project: EC | VIVALDI (678589)

    International audience; In the marine environment, bivalve mollusks constitute habitats for bacteria of the Vibrionaceae family. Vibrios belong to the microbiota of healthy oysters and mussels, which have the ability to concentrate bacteria in their tissues and body fluids, including the hemolymph. Remarkably, these important aquaculture species respond differently to infectious diseases. While oysters are the subject of recurrent mass mortalities at different life stages, mussels appear rather resistant to infections. Thus, Vibrio species are associated with the main diseases affecting the worldwide oyster production. Here, we review the current knowledge on Vibrio-bivalve interaction in oysters (Crassostrea sp.) and mussels (Mytilus sp.). We discuss the transient versus stable associations of vibrios with their bivalve hosts as well as technical issues limiting the monitoring of these bacteria in bivalve health and disease. Based on the current knowledge of oyster/mussel immunity and their interactions with Vibrio species pathogenic for oyster , we discuss how differences in immune effectors could contribute to the higher resistance of mussels to infections. Finally, we review the multiple strategies evolved by pathogenic vibrios to circumvent the potent immune defences of bivalves and how key vir-ulence mechanisms could have been positively or negatively selected in the marine environment through interactions with predators.

  • Open Access English
    Authors: 
    Darius Ceburnis; Agne Masalaite; Jurgita Ovadnevaite; Andrius Garbaras; Vidmantas Remeikis; Willy Maenhaut; Magda Claeys; Jean Sciare; Dominique Baisnée; Colin D. O'Dowd;
    Publisher: Nature Publishing Group
    Countries: France, France, Belgium, France, Ireland
    Project: EC | ACTRIS-2 (654109), EC | BACCHUS (603445), EC | ACTRIS (262254)

    Abstract: Stable carbon isotope ratios in marine aerosol collected over the Southern Indian Ocean revealed delta C-13 values ranging from -20.0% to -28.2%. The isotope ratios exhibited a strong correlation with the fractional organic matter (OM) enrichment in sea spray aerosol. The base-level isotope ratio of -20.0% is characteristic of an aged Dissolved Organic Matter (DOM) pool contributing a relatively homogeneous background level of DOM to oceanic waters. The range of isotope ratios, extending down to -28.2%, is characteristic of more variable, stronger, and fresher Particulate Organic Matter (POM) pool driven by trophic level interactions. We present a conceptual dual-pool POM-DOM model which comprises a 'young' and variable POM pool which dominates enrichment in sea-spray and an 'aged' but invariant DOM pool which is, ultimately, an aged end-product of processed 'fresh' POM. This model is harmonious with the preferential enrichment of fresh colloidal and nano-gel lipid-like particulate matter in sea spray particles and the observed depleted delta C-13 ratio resulting from isotope equilibrium fractionation coupled with enhanced plankton photosynthesis in cold water (-2 degrees C to + 8 degrees C). These results re-assert the hypothesis that OM enrichment in sea-spray is directly linked to primary production and, consequently, can have implications for climate-aerosol-cloud feedback systems.

  • Open Access
    Authors: 
    Florane Le Bihanic; Vivien Sommard; de Lansalut Perrine; Anaïk Pichon; Julie Grasset; Saadia Berrada; Hélène Budzinski; Xavier Cousin; Bénédicte Morin; Jérôme Cachot;
    Publisher: Elsevier BV
    Country: France

    Benz[a]anthracene (BaA) is a ubiquitous polycyclic aromatic hydrocarbon found in numerous aquatic ecosystems. However, ecotoxicological data in aquatic organisms are scarce. To remedy this lack of data, Japanese medaka (Oryzias latipes) embryos were exposed to BaA and toxic effects were investigated at multiple toxicological endpoints. Japanese medaka embryos were incubated onto BaA-spiked artificial sediment for 9 days at low or moderate environmental concentrations ranging from 0.9 to 12µgg(-1) dw. BaA-exposed embryos exhibited significant tachycardia. BaA exposure was also shown to increase CYP1A activity in the hepato-biliary tissue as well as craniofacial deformities and DNA damage in pro-larvae. The photomotor response of BaA-exposed larvae was reduced in comparison to the control group. According to this set of tests, the lowest tested and observed effect concentration (LOEC) for Japanese medaka early life stages was equivalent to 0.92µgg(-1) dw of BaA. This concentration fall into the range of concentrations frequently encountered in sediments of polluted aquatic ecosystems. Taking into consideration these results, BaA represents a threat for fish early life stages in particular those developing onto or into contaminated sediments.

  • Publication . Part of book or chapter of book . 2014
    French
    Authors: 
    Bramoullé, David;
    Publisher: HAL CCSD
    Country: France

    International audience; Du début du Xe siècle au milieu du XIe siècle environ, la Sicile constitua un des territoires composant le monde fatimide au même titre que la Syrie ou l’Ifrīqiya. Si chacune de ces provinces avaient une utilité pour la dynastie, la Sicile occupa longtemps une place de choix pour ces hommes pourtant largement tournés vers l’Orient mais soucieux de trouver une légitimité dans un monde musulman largement sunnite. Dès la période maghrébine (909-973), les califes développèrent une marine de guerre capable de rivaliser avec la flotte byzantine considérée alors comme la plus puissante marine de la Méditerranée. Les califes comprirent peu à peu l’intérêt de la Sicile qui, bien que située à l’opposé géographique de ce qui semblait être au centre des préoccupations des souverains fatimides, devint un des territoires clés de la dynastie califale jusqu’à l’éclatement de l’unité de l’île dans les années 1040-1050, puis à sa conquête par les troupes normandes. Ainsi, la documentation met en évidence les diverses fonctions qu’occupa la Sicile entre 909 et les années 1050-1090 qui virent l’ordre normand s’imposer. Les textes permettent de voir la politique fatimide à l’œuvre dans le cadre insulaire. Au-delà de son rôle économique, les sources mettent en évidence, d’une part, l’importance stratégique de la Sicile dès lors que les imams choisirent de développer le jihād à l’aide de la marine ainsi que, d’autre part, son rôle idéologique pour une dynastie qui développa une activité de propagande au service de la cause ismaélienne en recherche de légitimité.

  • Publication . Article . Other literature type . 2010
    Open Access English
    Authors: 
    Laurent Brodeau; Bernard Barnier; Anne-Marie Tréguier; Thierry Penduff; Sergei K. Gulev;
    Publisher: HAL CCSD
    Country: France

    We develop, calibrate and test a dataset intended to drive global ocean hindcasts simulations of the last five decades. This dataset provides surface meteorological variables needed to estimate air-sea fluxes and is built from 6-hourly surface atmospheric state variables of ERA40. We first compare the raw fields of ERA40 to the CORE.v1 clataset of Large and Yeager (2004). used here as a reference, and discuss our choice to use daily radiative fluxes and monthly precipitation products extracted from satellite data rather than their ERA40 counterparts. Both datasets lead to excessively high global imbalances of heat and freshwater fluxes when tested with a prescribed climatological sea surface temperature. After identifying unrealistic time discontinuities (induced by changes in the nature of assimilated observations) and obvious global and regional biases in ERA40 fields (by comparison to high quality observations), we propose a set of corrections. Tropical surface air humidity is decreased from 1979 onward, representation of Arctic surface air temperature is improved using recent observations and the wind is globally increased. These corrections lead to a significant decrease of the excessive positive global imbalance of heat. Radiation and precipitation fields are then submitted to a small adjustment (in zonal mean) that yields a near-zero global imbalance of heat and freshwater. A set of 47-year-long simulations is carried out with the coarse-resolution (2 degrees x 2 degrees) version of the NEMO OGCM to assess the sensitivity of the model to the proposed corrections. Model results show that each of the proposed correction contributes to improve the representation of central features of the global ocean circulation. (c) 2009 Elsevier Ltd. All rights reserved.

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