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  • 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
    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 . 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.

  • Open Access English
    Authors: 
    D. Van Rooij; Dominique Blamart; Thomas G. Richter; Andrew J. Wheeler; M. Kozachenko; Jean-Pierre Henriet;
    Publisher: HAL CCSD
    Countries: Belgium, France, France, France

    The Belgica cold-water coral banks on the eastern slope of the Porcupine Seabight are closely associated with bottom currents. In order to better understand the local temporal and spatial characteristics, as well as the palaeoclimatologic influences, a 26 m long core, taken on a small contourite drift, was studied. This sediment record of approximately 100 ka BP reveals new insights into the regional glacial and sedimentary processes, which are intrinsically linked to several geological, climatological, biological and hydrodynamic variables. The glacial sequences in the core contain six ice-rafting events (IRE). They are comparable with the North Atlantic Heinrich Events, although their characteristics show dominant influences from the proximal British-Irish Ice Sheet (BIIS). These IRE have a low magnetic susceptibility and are deposited during two or three ice-rafting pulses. The record of ice-rafting suggests a millennial-scaled BIIS destabilisation and confirms the start of a final retreat about 25 ka ago. Additionally, the glacial sequence corresponds to a muddy contourite, influenced by bottom-current strength variations during interstadials, possibly triggered by sporadic reintroductions of Mediterranean Outflow Water in a glacial North Atlantic Ocean. The interglacial sequence features an 11-m thick deep-water massive sand unit, probably deposited under a high-energy bottom-current regime.

  • Open Access English
    Authors: 
    Marine Remize; Frédéric Planchon; Ai Ning Loh; Fabienne Le Grand; Antoine Bideau; Nelly Le Goïc; Elodie Fleury; Philippe Miner; Rudolph Corvaisier; Aswani K. Volety; +1 more
    Publisher: Multidisciplinary Digital Publishing Institute
    Country: France

    : The present study sought to characterize the synthesis pathways producing the essential polyunsaturated fatty acid (PUFA) 20:5n-3 (EPA). For this, the incorporation of 13C was experimentally monitored into 10 fatty acids (FA) during the growth of the diatom Chaetoceros muelleri for 24 h. Chaetoceros muelleri preferentially and quickly incorporated 13C into C18 PUFAs such as 18:2n-6 and 18:3n-6 as well as 16:0 and 16:1n-7, which were thus highly 13C-enriched. During the experiment, 20:5n-3 and 16:3n-4 were among the least-enriched fatty acids. The calculation of the enrichment percentage ratio of a fatty acid B over its suspected precursor A allowed us to suggest that the diatom produced 20:5n-3 (EPA) by a combination between the n-3 (via 18:4n-3) and n-6 (via 18:3n-6 and 20:4n-6) synthesis pathways as well as the alternative &omega -3 desaturase pathway (via 20:4n-6). In addition, as FA from polar lipids were generally more enriched in 13C than FA from neutral lipids, particularly for 18:1n-9, 18:2n-6 and 18:3n-6, the existence of acyl-editing mechanisms and connectivity between polar and neutral lipid fatty acid pools were also hypothesized. Because 16:3n-4 and 20:5n-3 presented the same concentration and enrichment dynamics, a structural and metabolic link was proposed between these two PUFAs in C. muelleri.

  • Open Access English
    Authors: 
    Mathieu Woillez; Jacques Rivoirard; Pierre Petitgas;
    Publisher: HAL CCSD
    Country: France

    Fisheries research monitoring surveys provide an ensemble of measurements on fish stocks and their environment. Because the interannual variability in such survey-based indicators is high and because diagnostics on fish stocks cannot be based on noise, our concern is to make use of what is continuous in time to obtain a reliable diagnostic. In this paper, we show how min/max autocorrelation factors (MAFs) can be useful for assessing the status of a fish stock. Indeed, MAFs will allow us to (i) summarize the multivariate indicator signals into orthogonal factors that are continuous in time, (ii) select those indicators that carry the major signal in time, and (iii) forecast stock status by modelling the time continuity of the MAFs. These different potential uses of MAFs in an indicator-based approach to assessment were illustrated with North Sea cod, for which a suite of biological and spatial indicators are available over a 21-year survey series.

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