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Auteur (down) Vandeputte, M.; Gagnaire, P.-A.; Allal, F. url  doi
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  Titre The European sea bass: a key marine fish model in the wild and in aquaculture Type Article scientifique
  Année 2019 Publication Revue Abrégée Animal Genetics  
  Volume Numéro Pages  
  Mots-Clés dicentrarchus labrax; genetics; heritability; population genetics  
  Résumé The European sea bass (Dicentrarchus labrax L.) is a marine fish of key economic and cultural importance in Europe. It is now more an aquaculture than a fisheries species (>96% of the production in 2016), although modern rearing techniques date back only from the late 1980s. It also has high interest for evolutionary studies, as it is composed of two semispecies (Atlantic and Mediterranean lineages) that have come into secondary contact following the last glaciation. Based on quantitative genetics studies of most traits of interest over the past 10–15 years, selective breeding programs are now applied to this species, which is at the beginning of its domestication process. The availability of a good quality reference genome has accelerated the development of new genomic resources, including SNP arrays that will enable genomic selection to improve genetic gain. There is a need to improve feed efficiency, both for economic and environmental reasons, but this will require novel phenotyping approaches. Further developments will likely focus on the understanding of genotype-by-environment interactions, which will be important both for efficient breeding of farmed stocks and for improving knowledge of the evolution of natural populations. At the interface between both, the domestication process must be better understood to improve production and also to fully evaluate the possible impact of aquaculture escapees on wild populations. The latter is an important question for all large-scale aquaculture productions.  
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  Langue en Langue du Résumé Titre Original  
  Éditeur de collection Titre de collection Titre de collection Abrégé  
  Volume de collection Numéro de collection Edition  
  ISSN 1365-2052 ISBN Médium  
  Région Expédition Conférence  
  Notes Approuvé pas de  
  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2541  
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Auteur (down) Vandeputte, M.; Bugeon, J.; Bestin, A.; Desgranges, A.; Allamellou, J.-M.; Tyran, A.-S.; Allal, F.; Dupont-Nivet, M.; Haffray, P. doi  openurl
  Titre First Evidence of Realized Selection Response on Fillet Yield in Rainbow Trout Oncorhynchus mykiss, Using Sib Selection or Based on Correlated Ultrasound Measurements Type Article scientifique
  Année 2019 Publication Revue Abrégée Front. Genet.  
  Volume 10 Numéro Pages 1225  
  Mots-Clés aquaculture; body shape; carcass; carp cyprinus-carpio; fillet yield; fish; genetic-parameters; heritability; production efficiency; production traits; quality traits; ratio; selection response; selective breeding; tilapia oreochromis-niloticus  
  Résumé Fillet yield, the proportion of edible fillet relative to body weight, is a major trait to improve in fish sold processed, as it has a direct impact on profitability and can simultaneously decrease the environmental impact of producing a given amount of fillet. However, it is difficult to improve by selective breeding, because it cannot be measured on live breeding candidates, its phenotypic variation is low, and, as a ratio, it is not normally distributed and a same change in fillet yield can be the result of different changes in fillet weight and body weight. Residual headless gutted carcass weight (rHGCW) is heritable and highly genetically correlated to Fillet% in rainbow trout, and can be predicted by the ratio of abdominal wall thickness to depth of the peritoneal cavity (E8/E23), measured on live fish by ultrasound tomography. We selected broodstock based on rHGCW, measured on sibs of the selection candidates, on ultrasound measurements (E8/E23) measured on the selection candidates, or a combination of both. Seven broodstock groups were selected: fish with 15% highest (rHGCW+) or lowest (rHGCW-) EBV for rHGCW, with 15% highest (E8/E23+) or lowest (E8/E23-) EBV for E8/E23, with both rHGCW+ and E8/E23+ (Both+) or rHGCW- and E8/E23- (Both-), or with close to zero EBVs for both traits (Mid). Seven corresponding groups of offspring were produced and reared communally. At harvest size (1.5 kg mean weight), 1,561 trout were slaughtered, measured for the traits of interest, and pedigreed with DNA fingerprinting. Offspring from groups Both+, rHGCW+ and E8/E23+ had a higher EBV for rHGCW than the control group, while down-selected groups had a lower EBV. Looking at the phenotypic mean for Fillet% (correlated response), up-selected fish had more fillet than down-selected fish. The highest difference was between Both+ (69.36%) and Both- (68.20%), a 1.16% units difference in fillet percentage. The change in Fillet% was explained by an opposite change in Viscera%, while Head% remained stable. Selection using sib information on rHGCW was on average more efficient than selection using the candidates' own E8/E23 phenotypes, and downward selection (decreasing Fillet%) was more efficient than upward selection.  
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  Volume de collection Numéro de collection Edition  
  ISSN ISBN Médium  
  Région Expédition Conférence  
  Notes WOS:000505700800001 Approuvé pas de  
  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2715  
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Auteur (down) van Lis, R.; Brugiere, S.; Baffert, C.; Coute, Y.; Nitschke, W.; Atteia, A. doi  openurl
  Titre Hybrid cluster proteins in a photosynthetic microalga Type Article scientifique
  Année 2019 Publication Revue Abrégée Febs J.  
  Volume Numéro Pages  
  Mots-Clés angstrom; Chlamydomonas; chlamydomonas-reinhardtii; desulfovibrio-vulgaris hildenborough; desulfuricans atcc-27774; escherichia-coli; hcp; metalloprotein; nitrate; nitric-oxide; prismane protein; proteomics; redox; spectroscopy; x-ray structures  
  Résumé Hybrid cluster proteins (HCPs) are metalloproteins characterized by the presence of an iron-sulfur-oxygen cluster. These proteins occur in all three domains of life. In eukaryotes, HCPs have so far been found only in a few anaerobic parasites and photosynthetic microalgae. With respect to all species harboring an HCP, the green microalga Chlamydomonas reinhardtii stands out by the presence of four HCP genes. The study of the gene and protein structures as well as the phylogenetic analyses strongly support a model in which the HCP family in the alga has emerged from a single gene of alpha proteobacterial origin and then expanded by several rounds of duplications. The spectra and redox properties of HCP1 and HCP3, produced heterologously in Escherichia coli, were analyzed by electron paramagnetic resonance spectroscopy on redox-titrated samples. Both proteins contain a [4Fe-4S]-cluster as well as a [4Fe-2O-2S]-hybrid cluster with paramagnetic properties related to those of HCPs from Desulfovibrio species. Immunoblotting experiments combined with mass spectrometry-based proteomics showed that both nitrate and darkness contribute to the strong upregulation of the HCP levels in C. reinhardtii growing under oxic conditions. The link to the nitrate metabolism is discussed in the light of recent data on the potential role of HCP in S-nitrosylation in bacteria.  
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  Langue English Langue du Résumé Titre Original  
  Éditeur de collection Titre de collection Titre de collection Abrégé  
  Volume de collection Numéro de collection Edition  
  ISSN 1742-464x ISBN Médium  
  Région Expédition Conférence  
  Notes WOS:000484247300001 Approuvé pas de  
  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2644  
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Auteur (down) van der Geest, M.; van der Lely, J.A.C.; van Gils, J.A.; Piersma, T.; Lok, T. doi  openurl
  Titre Density-dependent growth of bivalves dominating the intertidal zone of Banc d'Arguin, Mauritania: importance of feeding mode, habitat and season Type Article scientifique
  Année 2019 Publication Revue Abrégée Mar. Ecol.-Prog. Ser.  
  Volume 610 Numéro Pages 51-63  
  Mots-Clés biomass; Carrying capacity; Chemosymbiosis; competition; Density dependence; dynamics; ecosystem; Environmental heterogeneity; Feeding guild; flats; populations; seagrass; Seagrass; sediment; site; Soft-sediment habitat; variability  
  Résumé Accurate predictions of population dynamics require an understanding of the ways by which environmental conditions and species-specific traits affect the magnitude of density dependence. Here, we evaluated the potential impact of season and habitat (characterized by sediment grain size and seagrass biomass) on the magnitude of density dependence in shell growth of 3 infaunal bivalve species dominating the tropical intertidal benthic communities of Banc d'Arguin, Mauritania. Two of our focal species were filter feeders (Senilia senilis and Pelecyora isocardia) and one was a facultative mixotroph (Loripes orbiculatus), mainly relying on organic carbon provided by sulphide-oxidizing endosymbiotic gill-bacteria (i.e. chemosymbiotic). Distinguishing 2 seasons, winter and summer, we manipulated local bivalve densities across habitats (from bare sandy sediments to seagrass-covered mud). In situ growth of individually tagged and relocated clams was measured and compared with those of tagged clams that were allocated to adjacent sites where local bivalve densities were doubled. Growth was negatively density-dependent in both winter and summer in P. isocardia and L. orbiculatus, the 2 species that mainly inhabit seagrass sediments, but not in S. senilis, usually found in bare sediments. As reproduction and survival rates are generally size-dependent in bivalves, our results suggest that in our tropical study system, the bivalve community of seagrass-covered sediments is more strongly regulated than that of adjacent bare sediments, regardless of species-specific feeding mode or season. We suggest that ecosystem engineering by seagrasses enhances environmental stability, which allows bivalve populations within tropical seagrass beds to stay close to carrying capacity.  
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  Editeur Lieu de Publication Éditeur  
  Langue English Langue du Résumé Titre Original  
  Éditeur de collection Titre de collection Titre de collection Abrégé  
  Volume de collection Numéro de collection Edition  
  ISSN 0171-8630 ISBN Médium  
  Région Expédition Conférence  
  Notes Approuvé pas de  
  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2593  
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Auteur (down) van der Geest, M.; van der Lely, J.A.C.; van Gils, J.A.; Piersma, T.; Lok, T. url  doi
openurl 
  Titre Density-dependent growth of bivalves dominating the intertidal zone of Banc d’Arguin, Mauritania: importance of feeding mode, habitat and season Type Article scientifique
  Année 2019 Publication Revue Abrégée Marine Ecology Progress Series  
  Volume 610 Numéro Pages 51-63  
  Mots-Clés Carrying capacity; Chemosymbiosis; Density dependence; Environmental heterogeneity; Feeding guild; Seagrass; Soft-sediment habitat  
  Résumé Accurate predictions of population dynamics require an understanding of the ways by which environmental conditions and species-specific traits affect the magnitude of density dependence. Here, we evaluated the potential impact of season and habitat (characterized by sediment grain size and seagrass biomass) on the magnitude of density dependence in shell growth of 3 infaunal bivalve species dominating the tropical intertidal benthic communities of Banc d’Arguin, Mauritania. Two of our focal species were filter feeders (Senilia senilis and Pelecyora isocardia) and one was a facultative mixotroph (Loripes orbiculatus), mainly relying on organic carbon provided by sulphide-oxidizing endosymbiotic gill-bacteria (i.e. chemosymbiotic). Distinguishing 2 seasons, winter and summer, we manipulated local bivalve densities across habitats (from bare sandy sediments to seagrass-covered mud). In situ growth of individually tagged and relocated clams was measured and compared with those of tagged clams that were allocated to adjacent sites where local bivalve densities were doubled. Growth was negatively density-dependent in both winter and summer in P. isocardia and L. orbiculatus, the 2 species that mainly inhabit seagrass sediments, but not in S. senilis, usually found in bare sediments. As reproduction and survival rates are generally size-dependent in bivalves, our results suggest that in our tropical study system, the bivalve community of seagrass-covered sediments is more strongly regulated than that of adjacent bare sediments, regardless of species-specific feeding mode or season. We suggest that ecosystem engineering by seagrasses enhances environmental stability, which allows bivalve populations within tropical seagrass beds to stay close to carrying capacity.  
  Adresse  
  Auteur institutionnel Thèse  
  Editeur Lieu de Publication Éditeur  
  Langue en Langue du Résumé Titre Original  
  Éditeur de collection Titre de collection Titre de collection Abrégé  
  Volume de collection Numéro de collection Edition  
  ISSN 0171-8630, 1616-1599 ISBN Médium  
  Région Expédition Conférence  
  Notes Approuvé pas de  
  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2488  
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