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Auteur Joux, F.; Bertrand, J.-C.; De Wit, R.; Grossi, V.; Intertaglia, L.; Lebaron, P.; Michotey, V.; Normand, P.; Peyret, P.; Raimbault, P.; Tamburini, C.; Urios, L.
Titre Methods for Studying Microorganisms in the Environment Type Chapitre de livre
Année 2015 Publication (down) Revue Abrégée
Volume Numéro Pages 757-829
Mots-Clés Bacterial isolation; Biomarkers; Cultural techniques; Cytometry; DNA microarray; Microbial activities; Microbial Ecology; Microelectrodes; Molecular fingerprints; Pcr; Phospholipid fatty acid analyses; Pigment analyses; Sampling techniques
Résumé The main methods for the study of microorganisms in the environment (water, soil, sediment, biofilms), the different techniques of sampling for measuring biomass, the activities, and the diversity of the microorganisms are presented. To respond to these various issues, techniques as varied as those of flow cytometry, molecular biology, biochemistry, molecular isotopic tools, or electrochemistry are implemented. These different techniques are described with their advantages and disadvantages for different types of biotopes. The question of the isolation, culture, and conservation of microorganisms from the environment are also addressed. Without being exhaustive, this chapter emphasizes the importance of using appropriate and efficient methodological tools to properly explore the still mysterious compartment of microorganisms in the environment.
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Editeur Springer Netherlands Lieu de Publication Éditeur Bertrand, J.-C.; Caumette, P.; Lebaron, P.; Matheron, R.; Normand, P.; Sime-Ngando, T.
Langue en Langue du Résumé Titre Original
Éditeur de collection Titre de collection Titre de collection Abrégé Environmental Microbiology: Fundamentals and Applications
Volume de collection Numéro de collection Edition
ISSN ISBN 978-94-017-9117-5 978-94-017-9118-2 Médium
Région Expédition Conférence
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Numéro d'Appel MARBEC @ alain.herve @ collection 1393
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Auteur Mahé, K.; Evano, H.; Mille, T.; Muths, D.; Bourjea, J.
Titre Otolith shape as a valuable tool to evaluate the stock structure of swordfish Xiphias gladius in the Indian Ocean Type Article scientifique
Année 2016 Publication (down) Revue Abrégée African Journal of Marine Science
Volume 38 Numéro 4 Pages 457-464
Mots-Clés Connectivity; Fourier descriptors; morphometric markers; sagittal otoliths; stock discrimination
Résumé Swordfish Xiphias gladius is an oceanic-pelagic species. Its population structure in the Western Indian Ocean was studied from the shape of the sagittal otoliths of 391 individuals collected from 2009 to 2014. Normalised elliptical Fourier descriptors (EFDs) were extracted automatically using TNPC software. Principal components analysis (PCA) conducted on EFDs showed no significant effect of side (i.e. left or right otolith). Consequently, all 391 sagittal otoliths were used to identify stocks among six geographical areas: Reunion Island, Mozambique Channel, Rodrigues, South Africa, Madagascar South and Sri Lanka. To investigate the effects of sex, sampling year, sampling season, lower jaw fork length or geographical area on variations in otolith shape, redundancy analyses (RDAs) with permutation tests were conducted. The first four were non-significant (respectively, p = 0.124, p = 0.721, p = 0.197, p = 0.463), but geographical area appeared to discriminate groups significantly (p < 0.05). Furthermore, linear discriminant analysis (LDA) was performed and overall jackknife classification success reached 30%. Finally, a cluster analysis was conducted using Ward’s hierarchical algorithm, which discriminated three different groups. However, each group consisted of individual samples from all geographical areas. In conclusion, our results were unable to identify a clear geographical separation of swordfish at the Indian Ocean scale, corroborating recent genetic studies in this region.
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Editeur Lieu de Publication Éditeur
Langue Langue du Résumé Titre Original
Éditeur de collection Titre de collection Titre de collection Abrégé
Volume de collection Numéro de collection Edition
ISSN 1814-232x ISBN Médium
Région Expédition Conférence
Notes Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1708
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Auteur van der Oost, R.; McKenzie, D.J.; Verweij, F.; Satumalay, C.; van der Molen, N.; Winter, M.J.; Chipman, J.K.
Titre Identifying adverse outcome pathways (AOP) for Amsterdam city fish by integrated field monitoring Type Article scientifique
Année 2020 Publication (down) Revue Abrégée Environ. Toxicol. Pharmacol.
Volume 74 Numéro Pages 103301
Mots-Clés Adverse outcome pathways; bioanalytical strategy; Biochemical & physiological biomarkers; biomarker responses; Ecological studies; eel anguilla-anguilla; environmental risk-assessment; Micropollutants risk assessment; oxygen-consumption; rainbow-trout; sole parophrys-vetulus; swimming performance; trout oncorhynchus-mykiss; xenobiotic-metabolizing enzymes
Résumé The European City Fish project aimed to develop a generic methodology for ecological risk assessment for urban rivers. Since traditional methods only consider a small fraction of substances present in the water cycle, biological effect monitoring is required for a more reliable assessment of the pollution status. A major challenge for environmental risk assessment (ERA) is the application of adverse outcome pathways (AOP), i.e. the linking of pollutant exposure via early molecular and biochemical changes to physiological effects and, ultimately, effects on populations and ecosystems. We investigated the linkage between responses at these different levels. Many AOP aspects were investigated, from external and internal exposure to different classes of micropollutants, via molecular key events (MICE) the impacts on organs and organisms (fish physiology), to changes in the population dynamics of fish. Risk assessment procedures were evaluated by comparing environmental quality standards, bioassay responses, biomarkers in caged and feral fish, and the impact on fish populations. Although no complete AOP was observed, indirect relationships linking pollutant exposure via MICE to impaired locomotion were demonstrated at the most polluted site near a landfill for chemical waste. The pathway indicated that several upstream key events requiring energy for stress responses and toxic defence are likely to converge at a single common MKE: increased metabolic demands. Both fish biomarkers and the bioanalytical SIMONI strategy are valuable indicators for micropollutant risks to fish communities.
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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 1382-6689 ISBN Médium
Région Expédition Conférence
Notes WOS:000514007200016 Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2753
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Auteur Griot, R.; Allal, F.; Brard-Fudulea, S.; Morvezen, R.; Haffray, P.; Phocas, F.; Vandeputte, M.
Titre APIS: An auto-adaptive parentage inference software that tolerates missing parents Type Article scientifique
Année 2020 Publication (down) Revue Abrégée Mol. Ecol. Resour.
Volume 20 Numéro 2 Pages 579-590
Mots-Clés errors; fitness; genetic-parameters; guide; identification; impact; markers; microsatellites; missing parents; natural-populations; parentage assignment; pedigree; snp
Résumé In the context of parentage assignment using genomic markers, key issues are genotyping errors and an absence of parent genotypes because of sampling, traceability or genotyping problems. Most likelihood-based parentage assignment software programs require a priori estimates of genotyping errors and the proportion of missing parents to set up meaningful assignment decision rules. We present here the R package APIS, which can assign offspring to their parents without any prior information other than the offspring and parental genotypes, and a user-defined, acceptable error rate among assigned offspring. Assignment decision rules use the distributions of average Mendelian transmission probabilities, which enable estimates of the proportion of offspring with missing parental genotypes. APIS has been compared to other software (CERVUS, VITASSIGN), on a real European seabass (Dicentrarchus labrax) single nucleotide polymorphism data set. The type I error rate (false positives) was lower with APIS than with other software, especially when parental genotypes were missing, but the true positive rate was also lower, except when the theoretical exclusion power reached 0.99999. In general, APIS provided assignments that satisfied the user-set acceptable error rate of 1% or 5%, even when tested on simulated data with high genotyping error rates (1% or 3%) and up to 50% missing sires. Because it uses the observed distribution of Mendelian transmission probabilities, APIS is best suited to assigning parentage when numerous offspring (>200) are genotyped. We have demonstrated that APIS is an easy-to-use and reliable software for parentage assignment, even when up to 50% of sires are missing.
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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 1755-098x ISBN Médium
Région Expédition Conférence
Notes WOS:000496576600001 Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2760
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Auteur Zarski, D.; Nguyen, T.; Le Cam, A.; Montfort, J.; Dutto, G.; Vidal, M.O.; Fauvel, C.; Bobe, J.
Titre Transcriptomic Profiling of Egg Quality in Sea Bass (Dicentrarchus labrax) Sheds Light on Genes Involved in Ubiquitination and Translation Type Article scientifique
Année 2017 Publication (down) Revue Abrégée Mar. Biotechnol.
Volume 19 Numéro 1 Pages 102-115
Mots-Clés aquaculture; broodstock management; Controlled reproduction; expression; fish; gadus-morhua l.; genomics; indicator; lipid droplets; markers; Microarray; oncorhynchus-mykiss; rainbow-trout; reproduction; Transcriptomics
Résumé Variable and low egg quality is a major limiting factor for the development of efficient aquaculture production. This stems from limited knowledge on the mechanisms underlying egg quality in cultured fish. Molecular analyses, such as transcriptomic studies, are valuable tools to identify the most important processes modulating egg quality. However, very few studies have been devoted to this aspect so far. Within this study, the microarray-based transcriptomic analysis of eggs (of different quality) of sea bass (Dicentrarchus labrax) was performed. An Agilent oligo microarray experiment was performed on labelled mRNA extracted from 16 batches of eggs (each batch obtained from a different female) of sea bass, in which over 24,000 published probe arrays were used. We identified 39 differentially expressed genes exhibiting a differential expression between the groups of low (fertilization rate < 60 %) and high (fertilization rate > 60 %) quality. The mRNA levels of eight genes were further analyzed by quantitative PCR. Seven genes were confirmed by qPCR to be differentially expressed in eggs of low and high quality. This study confirmed the importance of some of the genes already reported to be potential molecular quality indicators (mainly rnf213 and irf7), but we also found new genes (mainly usp5, mem-prot, plec, cenpf), which had not yet been reported to be quality-dependent in fish. These results suggest the importance of genes involved in several important processes, such as protein ubiquitination, translation, DNA repair, and cell structure and architecture; these probably being the mechanisms that contribute to egg developmental competence in sea bass.
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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 1436-2228 ISBN Médium
Région Expédition Conférence
Notes Approuvé pas de
Numéro d'Appel MARBEC @ alain.herve @ collection 2112
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