Résumé : Les deux principaux objectifs de ce travail sont de proposer des outils pour la selection d'animaux résistants aux strongles gastro-intestinaux, parasites du tube digestif, et de faire progresser la compréhension des mécanismes de résistance chez la chèvre créole. La variabilité génétique du caractère de résistance au parasitisme digestif a été étudiée afin de vérifier quels critères décrivant le mieux la résistance, peuvent être utilisés pour la sélection. L'ensemble des résultats obtenus suggèrent que le critère d'excrétion d'oeufs et le critère d'éosinophilie sont les plus adaptés pour un schéma de sélection puisqu'ils possèdent une héritabillté moyenne et représentent le mieux la résistance. De plus, ils ne semblent pas en opposition avec le poids, principal critère de production. Le déterminisme génétique de la résistance aux strongles gastro-intestinaux a été étudié et a permis de mettre en évidence l'existence d'un gène majeur pour la résistance chez la population de chèvre créole. De plus, la primo-détection de qtl a permis d'identifier 13 régions du génome ayant un effet sur les critères de résistance. Les mécanismes responsables de la résistance aux strongles gastro-intestinaux ont également été à l'étude. L'ensemble des résultats met en évidence le rôle des éosinophiles dans la mise en place de la résistance aux strongles gastro-intestinaux. L'activité des immunogobulines e semblent dirigés vers les larves l3 d'haemonchus contortus et suggère la mise en place d'une réaction protectrice. Chez la chèvre créole. Ces deux mécanismes semblent donc jouer un rôle important dans la mise en place de la résistance aux strongles gastro-intestinaux
The two main objectives of this work are to propose tools for the selection of resistant animals to gastrointestinal nematodes and advance knowledge on mechanisms of resistance of creole goats. this work has analysed the genetic variability of resistance to digestive parasitism in order to determine which criteria best describes the resistance and can be use for selection. the overall results suggest that the egg excretion and the eosinophilia are the criteria most suitable for a breeding scheme because they have moderate heritability estimates and best represent the resistance. moreover, they do not seem in conflict with the weight, the main criterion of production. the genetic determinism of resistance to gastrointestinal parasites has been studied and has highlighted the existence of a major gene for resistance in creole goats. in addition, the primodetection of qtl identified 13 genomic regions that affect the resistance. the mechanisms behind the resistance to gastrointestinal parasites were also studied and first hypothesis regarding the involvment of the immune response in resistance have been made in goats. the overall results highlighted the role of eosinophils in the development of resistance to gastrointestinal nematodes. the activity of immunoglobulin e seems directed toward l3 larvae of haemonchus contortus and may be imply in the establishment of a protective response agasint nematode parasites. in creole goats, these two mechanisms seem to play an important role in the development of resistance to gastrointestinal nematode infections

http://www.theses.fr/2011AGUY0407/document

Éditeur(s) : Elsevier
Résumé : Evidence has accumulated that climate variability influences the state and functioning of marine ecosystems. At the same time increasing pressure from exploitation and other human activities has been shown to impact exploited and non-exploited species and potentially modify ecosystem structure. There has been a tendency among marine scientists to pose the question as a dichotomy, i.e., whether (1) "natural" climate variability or (2) fishery exploitation bears the primary responsibility for population declines in fish populations and the associated ecosystem changes. However, effects of both climate and exploitation are probably substantially involved in most cases. More importantly, climate and exploitation interact in their effects, such that climate may cause failure in a fishery management scheme but that fishery exploitation may also disrupt the ability of a resource population to withstand, or adjust to, climate changes. Here, we review how exploitation, by altering the structure of populations and ecosystems, can modify their ability to respond to climate. The demographic effects of fishing (removal of large-old individuals) can have substantial consequences on the capacity of populations to buffer climate variability through various pathways (direct demographic effects, effects on migration, parental effects). In a similar way, selection of population sub-units within metapopulations may also lead to a reduction in the capacity of populations to withstand climate variability and change. At the ecosystem level, reduced complexity by elimination of species, such as might occur by fishing, may be destabilizing and could lead to reduced resilience to perturbations. Differential exploitation of marine resources could also promote increased turnover rates in marine ecosystems, which would exacerbate the effects of environmental changes. Overall (and despite the specificities of local situations) reduction in marine diversity at the individual, population and ecosystem levels will likely lead to a reduction in the resilience and an increase in the response of populations and ecosystems to future climate variability and change. Future management schemes will have to consider the structure and functioning of populations and ecosystems in a wider sense in order to maximise the ability of marine fauna to adapt to future climates. (C) 2009 Elsevier B.V. All rights reserved.
Journal of Marine Systems (0924-7963) (Elsevier), 2010-02 , Vol. 79 , N. 3-4 , P. 403-417

Droits : 2009 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/2010/publication-7384.pdf
DOI:10.1016/j.jmarsys.2008.12.018
http://archimer.ifremer.fr/doc/00000/7384/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
During the treatment process of drinking water, disinfectants (chlorine, ozone, chlorine dioxide) react on water containing organic matter and bromide to produce disinfection by-products at trace levels. Among them, five of the nine existing halo-acetic acids (HAAs) are commonly found in drinking water (monochloroacetic acid (MCAA), dichloroacetic acid (DCAA), monobromoacetic acid (MBAA), dibromoacetic acid (DBAA), and Trichloroacetic acid (TCAA)), including four classified in the 2B IARC group of potential carcinogens (BCAA, DBAA, DCAA, TCAA). With respect to drinking water quality, guidelines are proposed by WHO (2006) and water quality standards are imposed in many countries such as less than 100 μg/L for the sum of the five HAAs by US EPA (1998) and Canadian Health Department (2008). For this purpose, two analytical methods are commonly used, GC/MS with derivatization and LC/MS, UV or conductivity. A new method, based on two-dimensional ion chromatography (IC 2D) with suppressed conductivity is proposed. This method presents the main advantage of offering a quick implementation compared to GC or LC methods: direct injection, slight maintenance, lower cost of investment, by leading to good performances (specificity and sensitivity). The use of two different selectivity columns, and the fractionation on the first dimension canceling interferences, improves the specificity. The sensitivity is enabled by interfacing a preconcentration column between the two different internal diameter columns. The analytical conditions are optimized for the analysis of nine HAAs. The performances of the method are evaluated. The optimized method applied to natural water samples demonstrates its ability to quantify HAAs at trace levels in drinking water.
Microchemical Journal

hal-00877151
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00877151
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00877151/document
DOI : 10.1016/j.microc.2013.07.012

Éditeur(s) : Elsevier
Résumé : Understanding of antimicrobial defence mechanisms of penaeid shrimp should help in the design of efficient strategies for the management and disease control in aquaculture. In this study, we have specifically analysed the expression in circulating hemocytes of antimicrobial peptides (AMPs) encoding genes, such as PEN2 and PEN3, ALF, crustin, lysozyme and a putative cysteine-rich peptide. We evidenced a relationship between the level of expression of some AMPs and the successful response of the shrimp, Litopenaeus stylirostris, to circumvent a pathogenic Vibrio penaeicida infection. Additionally, significant differences in some AMP transcript amounts are evidenced between control, non-selected shrimp line and the third generation breeding of shrimp selected for their survival to natural V. penaeicida infections. On the basis of these results, it will now be of great interest to determine if these AMPs are directly involved in the resistance of shrimp to infection or if they only reflect other acquired defence mechanisms which can confer a resistance. (C) 2008 Elsevier Ltd. All rights reserved.
Molecular Immunology (0161-5890) (Elsevier), 2008-07 , Vol. 45 , N. 12 , P. 3438-3445

Droits : 2008 Elsevier Ltd All rights reserved.
http://archimer.ifremer.fr/doc/2008/publication-4524.pdf
DOI:10.1016/j.molimm.2008.04.002
http://archimer.ifremer.fr/doc/00000/4524/

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background: Microbial genetic diversity is often investigated via the comparison of relatively similar 16S molecules through multiple alignments between reference sequences and novel environmental samples using phylogenetic trees, direct BLAST matches, or phylotypes counts. However, are we missing novel lineages in the microbial dark universe by relying on standard phylogenetic and BLAST methods? If so, how can we probe that universe using alternative approaches? We performed a novel type of multi-marker analysis of genetic diversity exploiting the topology of inclusive sequence similarity networks. Results: Our protocol identified 86 ancient gene families, well distributed and rarely transferred across the 3 domains of life, and retrieved their environmental homologs among 10 million predicted ORFs from human gut samples and other metagenomic projects. Numerous highly divergent environmental homologs were observed in gut samples, although the most divergent genes were over-represented in non-gut environments. In our networks, most divergent environmental genes grouped exclusively with uncultured relatives, in maximal cliques. Sequences within these groups were under strong purifying selection and presented a range of genetic variation comparable to that of a prokaryotic domain. Conclusions: Many genes families included environmental homologs that were highly divergent from cultured homologs: in 79 gene families (including 18 ribosomal proteins), Bacteria and Archaea were less divergent than some groups of environmental sequences were to any cultured or viral homologs. Moreover, some groups of environmental homologs branched very deeply in phylogenetic trees of life, when they were not too divergent to be aligned. These results underline how limited our understanding of the most diverse elements of the microbial world remains, and encourage a deeper exploration of natural communities and their genetic resources, hinting at the possibility that still unknown yet major divisions of life have yet to be discovered.
ISSN: 1745-6150

Droits : http://creativecommons.org/licenses/by/
hal-01257771
http://hal.upmc.fr/hal-01257771
http://hal.upmc.fr/hal-01257771/document
http://hal.upmc.fr/hal-01257771/file/s13062-015-0092-3.pdf
DOI : 10.1186/s13062-015-0092-3

Éditeur(s) : Elsevier
Résumé : Correlation between DNA microsatellite heterozygosity and growth rate was investigated in two hatchery-propagated stocks of the shrimp Penaeus stylirostris, which had been genetically isolated from wild founders for 17 generations, and from each other for five more generations. presumed demographic history of these populations suggested that they were maintained at small effective population sizes. and this was confirmed by significant changes in allelic frequencies between the two stocks. Despite a small sample size (n = 60) and a small number of loci screened, a significant positive correlation was detected between microsatellite tri-locus heterozygosity and growth rate in one of the two stocks (r = 0.3, P = 0.02). In the other stock (n = 48), the positive correlation was not significant, but the combined test of single locus heterozygote advantage over the three loci was significant (P = 0.005).Use of DNA microsatellite markers, whose selectively neutral status is generally accepted, allowed us to reject the hypothesis of direct overdominance at marker loci as an explanation for an association of growth rate with heterozygosity. The average depression associated with one locus in our case is above or equivalent to the amount observed for a 10% increase of inbreeding in other species. These results suggest that heterozygosity at neutral marker loci is sufficiently well correlated with individual inbreeding coefficients to reveal a significant residual inbreeding load for growth rate in Tahitian P. stylirostris stocks. Inbreeding during hatchery propagation was, thus, insufficient to purge the ancestral load.
Aquaculture (0044-8486) (Elsevier), 2000-04 , Vol. 184 , N. 3-4 , P. 203-219

Droits : 2000 Elsevier Science B.V. All rights reserved
http://archimer.ifremer.fr/doc/2000/publication-753.pdf
DOI:10.1016/S0044-8486(99)00331-2
http://archimer.ifremer.fr/doc/00000/753/

Résumé : Tahiti’s pearl farming industry plays a major socio-economic role in French Polynesia. In an increasingly competitive market where the production of high quality pearls becomes essential, research can help secure and ensure sustainable production. In that context, Ifremer, in close collaboration with the “direction des resources marines” (French Polynesian government agency) has developed research projects on the “sustainable development of pearl farming”. This program is organized along 3 axes: (1) understanding the animal physiology and initiating a genetically selective breeding program of donor oysters; (2) understanding pearl oyster larvae dispersal and recruitment; (3) understanding the molecular mechanisms underlying biomineralization processes during shell and pearl formation. It is in this frame that we have developed a highthroughput Expressed Sequence Tags pyrosequencing program on the calcifying mantle, combined with proteomic analyses of the shell and pearl. We analyzed 276738 EST sequences, leading to the constitution of a P. margaritifera mantle transcripts catalogue of 82 sequences potentially involved in biomineralization. Our results provided direct evidence that our ESTs data set covers a large number of the matrix proteins of P. margaritifera. In addition, our proteomic analysis enabled us to retrieve, in silico, all the sequences from P. margaritifera involved in the biomineralization process already published on databases. Integration of these two methods allowed, for the first time, the global composition of calcifying tissue and calcified structures to be examined in tandem.
Recent Advances in Pearl Research—Proceedings of the International Symposium on Pearl Research 2011.Edited by Shugo Watabe, Kaoru Maeyama and Hiromichi Nagasawa. 2013. ISBN : 978-4-88704-158-5. pp.184-194

Droits : 2013 TERRAPUB. All rights reserved.
http://archimer.ifremer.fr/doc/00167/27840/26049.pdf
http://archimer.ifremer.fr/doc/00167/27840/

Résumé : Les mutualismes, interactions interspécifiques où chaque partenaire retire un bénéfice net de leur association, sont centraux dans l’origine et l’organisation de la biodiversité. Bien que globalement bénéfiques pour chacun des partenaires, ces interactions n’enlèvent rien à l’égoïsme inhérent de chaque espèce pour sa survie et sa reproduction, générant des conflits d’intérêts entre les espèces. Ainsi, comprendre les processus écologiques et évolutifs qui maintiennent le caractère mutualiste d’interactions entre plusieurs espèces est primordial dans la compréhension du maintien de la biodiversité. Néanmoins, le corpus scientifique s’est jusqu'à présent surtout concentré sur des paires d’espèces en interaction. Or, ces avancées scientifiques restent partielles car la plupart de ces interactions s’englobent dans un contexte communautaire. C’est dans ce cadre conceptuel que se place mon travail de thèse. Alors que la diversité structurelle des mutualismes de protection entre plantes et fourmis en ont fait un modèle d’étude clé dans la compréhension des mutualismes, j’ai concentré mes recherches sur l’intégration d’un troisième partenaire fongique pour comprendre ses conséquences sur les résultantes écologiques et évolutives de ces mutualismes tripartites. Je me suis tout d’abord intéressé à définir la relation qui lie de façon mutualiste le champignon aux deux autres partenaires et à établir les conflits d’intérêts émanant de ces différentes interactions pour comprendre quels facteurs permettaient de les réguler. Ainsi, la relation qui lie le champignon aux fourmis peut être qualifiée d’agriculture. Les fourmis protègent, nourrissent et disséminent le champignon et celui-ci, via ses propriétés structurales, permet l’élaboration de galeries servant de piège pour capturer des proies. Ce phénomène crée cependant un conflit d’allocation de la force ouvrière des fourmis et nuit directement aux bénéfices de la plante par une diminution de l’intensité des patrouilles sur ses feuilles, diminuant consécutivement sa protection et sa fitness. Néanmoins, le rôle du champignon dans les transferts de nutriments entre les fourmis et la plante, ainsi que certaines réponses évolutives de la plante permettent de réguler ces conflits, stabilisant les bénéfices nets de chaque partenaire dans ce mutualisme tripartite. Puis, je me suis concentré à comprendre comment certains facteurs évolutifs pouvaient moduler cette résultante écologique. La prise en compte du caractère multipartite d’un mutualisme change radicalement la vision de l’évolution des mutualismes jusqu’alors étudiée entre paires d’espèces. Alors que le corpus scientifique s’accorde à dire que la spécialisation entre espèce par coévolution renforce la stabilité et les bénéfices perçus par chaque partenaire, le contexte multipartite semble altérer ces prédictions. Au contraire la spécialisation multipartite peut être dans certains cas un moteur d’instabilité et de baisse des bénéfices. Enfin cette thèse permet de faire le lien entre deux concepts qui s’opposent : la coévolution diffuse et la coévolution par paire. Je montre ainsi que la coévolution peut intervenir sur plus de deux espèces à la fois, mais qu’elle peut quand même entrainer une spécialisation multispécifique. Finalement, au contraire des prédictions de la coévolution diffuse, cette thèse montre que plusieurs pressions de sélection contrastées émanant de différentes espèces envers un seul trait d’une troisième espèce peuvent promouvoir la spécialisation multi-spécifique.
Mutualisms, defined as interspecific interactions where each partner receives net benefices from their interactions, are central to the organization of earth biodiversity. Although globally beneficial for each partner, such interactions do not modify the inherent selfishness of species for their survival and reproduction, generating conflicts of interests between species. Thus understanding the ecological and the evolutionary processes maintaining positive outcomes in mutualisms is fundamental to understand how mutualisms shape earth biodiversity. However, scientific research on mutualisms has most of the time focused on interaction between pairs of species. Such knowledge is thus partial as mutualisms are embraced in a community context. My doctoral thesis takes place in this conceptual framework. I focused my research on the integration of a third fungal partner in protective interactions between ants and plants to evaluate its consequences on the ecological and evolutionary outcomes of such mutualisms, taken as multispecies interactions. I first focused my researches in defining the mutualistic interaction linking the fungal partner with its two other associates and in revealing any conflict of interests and their regulation that may emerge from such tripartite interactions. The interactions between the ants and the fungi can be qualified as a case of non-food fungiculture. The ants protect, provide food and disseminate the fungus, and the latter, thanks to its structural properties, allows the elaboration of galleries used that are then used as trap to capture preys. This phenomenon creates a conflict of interest in the allocation of the worker force, altering host plant benefits through a decrease of worker patrolling activity and consequently leaves protection and thus fitness. However, the role of the fungus in the nutrient transfers between ants and plants added to evolutionary responses from the plant allows regulating this conflict, stabilizing the net benefits towards the plant. Then I have concentrated my researches in understanding how evolutionary factors would modulate the ecological outcomes of such interactions. Taking into account the multispecific character of mutualisms changes radically the vision on the evolution of mutualisms when pair of species are considered. While it is widely accepted that specialization of mutualist species through coevolution reinforce the stability of the interaction and the net benefit of each partner, the multispecific context seems to deviate these predictions. Conversely, I show that specialization between three mutualistic partners can drive instability and decrease of benefits. Finally, the results of this thesis join the gap between two previously opposed concepts: diffuse coevolution and pairwise coevolution. I show that coevolution can happen between more than two species simultaneously and that it can drive mutlispecific specialization. Opposed to the diffuse coevolution, I show that contrasting selective pressures on a same trait from different partner can promote specialization of species.

http://www.theses.fr/2013AGUY0622/document

Éditeur(s) : HAL CCSD American Society for Microbiology
Résumé : International audience
: We investigated the in vitro effects of four alkyl-galactofuranoside derivatives, i.e. octyl-β-D-galactofuranoside (1), 6-amino-β-D-galactofuranoside (2), 6-N-acetamido-β-D-galactofuranoside (3), and 6-azido-β-D-galactofuranoside (4) on Leishmania donovani. Their mechanism of action was explored using electron paramagnetic resonance spectroscopy (EPR) and nuclear magnetic resonance (NMR), and ultrastructural alterations by transmission electron microscopy (TEM). Compound 1 showed the most promising effects by inhibiting promastigote growth at IC50 8.96 ± 2.5 μM. All compounds exhibit low toxicity towards human macrophages. Compound 1 had a higher selectivity index than the comparative molecule used, i.e. miltefosine (159.7 versus 37.9, respectively). EPR showed that compound 1 significantly reduced membrane fluidity, compared to control promastigotes and to compound 3. The furanose ring was shown to support this effect since the isomer galactopyranose had no effect on parasite membrane fluidity or growth. NMR showed a direct interaction of all compounds (1>2>3>4) with the promastigote membrane, as well as with octyl-galactopyranose and octanol, providing evidence that the n-octyl chain was primarily involved in the anchoring with the parasite membrane, followed by the putative crucial role of furanose ring in the anti-leishmanial activity. A morphologic analysis of compound 1-treated promastigotes by TEM revealed profound alterations on parasite membrane and organelles, but not with compound 3. Quantification of annexinV binding by flow cytometry confirmed that compound 1 induced apoptosis in >90% promastigotes. The effect of compound 1 was also assessed on intra-macrophagic amastigotes, and showed a reduction in amastigote growth associated with an increase of ROS production, thus validating its promising effect.
ISSN: 0066-4804

hal-00941772
https://hal.archives-ouvertes.fr/hal-00941772
PUBMED : 24468785
DOI : 10.1128/AAC.01350-13

Éditeur(s) : Elsevier Science Bv
Résumé : The timing, routing and processes of sediment transfer from the continents to the oceans at millennial time-scale are still largely unknown. The potential of turbidite systems (dominantly deposited during sea-level lowstands) to record global or regional environmental fluctuations is usually under-exploited because of the difficulty to obtain robust chronostratigraphic constraints in turbiditic deposits, and therefore to tie changes in sedimentary processes to environmental fluctuations. We were able to obtain a millennial-scale chronostratigraphy based on oxygen isotopes of the scarce foraminifera preserved in turbiditic deposits of the Rhone Turbidite System within the Western Mediterranean. Our results show that 1) objective criteria can be defined for the selection of foraminifera preserved within the pelagic intervals between the turbiditic sequences, in order to obtain a reliable isotope stratigraphy; 2) Turbidites triggered by hyperpycnal currents are described for the first time within the Rhone Turbidite System. They are related to the periods of direct fluvial connection with the canyon head (during the sea-level lowstand and early rise), and to a period of high sediment flux in relation with the massive recession of the Rhone glaciers in the Alps; 3) The lithofacies change passing from hyperpycnal to “Bouma-type” is dated at ca 19 cal. ka BP, which might correspond to an acceleration of sea-level rise (19-ka Meltwater Pulse,).
Sedimentary Geology (0037-0738) (Elsevier Science Bv), 2015-06 , Vol. 323 , P. 148-166

Droits : 2015 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/00266/37712/35730.pdf
DOI:10.1016/j.sedgeo.2015.04.009
http://archimer.ifremer.fr/doc/00266/37712/

Résumé : Les biofilms électroactifs (EA) sont des consortia bactériens mono ou pluri-espèces, qui ont la faculté d’échanger des électrons provenant de leur métabolisme avec les surfaces solides conductrices des électrodes. Cette découverte est à l’origine d’un nouveau dispositif énergétique : la pile à combustible microbienne (PACM). Depuis les années 2000, la littérature scientifique sur les biofilms EA et sur les PACM explose, notamment grâce à la découverte de bactéries capables de transférer par voie directe – par des pili ou protéines transmembranaires – des électrons vers les électrodes. Plusieurs sources de bactéries EA ont été à ce jour découvertes, allant de cultures pures à des communautés bactériennes plus complexes. Ces dernières sont issues de milieux aqueux naturels (milieux marins ou d’eau douce), industriels ou urbains (effluents d’industrie, eaux usées domestiques). La plupart de ces sources bactériennes proviennent d’environnements de climat tempéré. Dans ce travail de thèse, plusieurs sols de milieux humides de la Guyane ont été identifiés comme étant de sources de bactéries EA. Les expériences menées sous potentiel d’électrode imposé et constant ont permis d’étudier l’adhésion à la surface d’électrode des biofilms EA issus de la flore endogène des milieux sélectionnés. La formation de bioanodes et de biocathodes a été possible en présence respectivement d’acétate et d’oxygène dans les milieux. Une étude par voltammétrie cyclique a mis en évidence les pics d’oxydo-réduction en lien avec les échanges électroniques du biofilm EA et de l’électrode. En optimisant la procédure de formation des biofilms EA par chronoampérométrie (surface d’électrode plus importante, apport en continu et progressif du substrat), une densité de courant maximale de 12 A/m2 et un rendement faradique de 24 % ont été obtenus. Une autre méthode pour former des biofilms EA à partir d’un milieu choisi, la mangrove, a consisté à utiliser deux prototypes de PACM : une pile à compartiment unique et à cathode à air, et une pile benthique. Dans les deux cas, les biofilms EA ont pu être formés et étudiés, complétant certaines observations faites sous potentiel imposé. La PACM benthique s’est avérée être la plus proche d’une application à grande échelle puisqu’elle a été complètement autonome : anode et cathode utilisant uniquement le milieu pour fonctionner. Elle a pu être étudiée en laboratoire comme sur le terrain.
Electroactive biofilms (EA) are mono or multi-species bacterial consortia, which have the ability to exchange electrons from their metabolism with solid surfaces of conductive electrodes. This discovery is the basis for a device of energy production: microbial fuel cell (MFC). Since the 2000s, the scientific literature on EA biofilms and MFC explodes, thanks to the discovery of bacteria that are able to transfer directly – by pili or trans-membrane proteins – electrons to electrodes. Several sources of EA bacteria were discovered to date, ranging from pure cultures to more complex bacterial communities. Those last are from natural (marine and freshwater), industrial or urban (industrial effluents, domestic wastewater) aqueous environments. However, the vast majority of these are from temperate environments.In this thesis, several wetland soils of French Guiana have been identified as sources of EA bacteria. Experiments under poised and constant electrode potential were used to examine adherence to the electrode surface of EA biofilms from the endogenous flora of selected environments. Formation of bioanodes and biocathodes was possible in the presence respectively of acetate and oxygen in the media. A study by cyclic voltammetry showed the redox peaks related to electronic exchanges between EA biofilm and electrode. By optimizing the process of EA biofilm formation by chronoamperometry (larger electrode surface, providing continuous and progressive substrate), a maximum current density of 12 A/m2 and a coulombic efficiency of 24% were obtained.Another method to form EA biofilms from a chosen medium (mangrove) was to use two MFC prototypes: a single compartment and air cathode one, and a benthic one. In both cases, the EA biofilms have been trained and studied supplementing certain observations made under poised polarization. MFC benthic proved to be the closest to a wide application since it was completely autonomous, anode and cathode only using the medium to function. It has been studied in the laboratory and in the field.

http://www.theses.fr/2012AGUY0560/document

Éditeur(s) : Gauthier-Villars
Résumé : In developing countries, recourse to extensive aquaculture systems based on the exploitation of natural aquatic food webs is currently the subject of considerable interest. In this connection, the construction of artificial reefs (known as Acadja) for the development on substrates of living communities, and the utilization of this new production to enhance fish growth have been evaluated in Cote d'Ivoire. This paper describes the granulometric, chemical and biological transformation of the sedimentary ecosystem as a consequence of this practice. In the artificial habitat, an increase in the sedimentation rate of the mineral fraction (definitive trapping of particle resuspension generated by the waves and induced by the wind) and of the organic fraction (direct and indirect sedimentation of the epiphytic biomass) constitutes the starting point of significant modifications in epibenthic communities. In the Acadja, the meiofauna, dominated by nematodes and copepods, is somewhat less diversified, some groups being absent or poorly represented (turbellarians, gastrotrichs, ostracods). These characteristics were confirmed by a specific study of the nematode assemblages. In fact, the relatively high diversity of the nematode community in the natural lagoon sediment (dominated seasonally by Paraphanolaimus, Anonchus et Daptonema) contrasts with low diversity in the Acadja sediment, where the community is always dominated by Theristus sp. This lower specific diversity generates a reduction of the trophic types. In the Acadja, only the non-selective detritus feeders colonize the fine and organic sediment. These sedimentological and ecological transformations, which affect the entire ''brush park'' (Acadja), induce a strong eutrophication of the benthic ecosystem. Sustainable fish production in such tropical lagoons, in an environment where anaerobic processes dominate (especially sulfate-reduction), calls for strategic spatio-temporal planning to take of account of this progressive eutrophication.
Oceanologica Acta (0399-1784) (Gauthier-Villars), 1995 , Vol. 18 , N. 5 , P. 543-555

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00097/20796/18421.pdf
http://archimer.ifremer.fr/doc/00097/20796/

Éditeur(s) : HAL CCSD Royal Society of Chemistry
Résumé : Fluorescence is a remarkable property of many natural products in addition to their medicinal and biological values. Herein, we provide a review on these peculiar secondarymetabolites to stimulate prospecting of them as original fluorescent tracers, endowed with unique photophysical properties and with applications in most fields of biology. The compounds are spectrally categorized (i.e. fluorescing from violet to the near infra-red) and further structurally classified within each category. Natural products selected for their high impact in modern fluorescence-based biological studies are highlighted throughout the article. Finally, we discuss aspects of chemical ecology where fluorescent natural products might have key evolutionary roles and thus open new research directions in the field.
ISSN: 0265-0568

hal-01604139
https://hal.archives-ouvertes.fr/hal-01604139
DOI : 10.1039/c6np00111d
PRODINRA : 391732
PUBMED : 28125109

Éditeur(s) : Wiley-blackwell
Résumé : Managing fisheries resources to maintain healthy ecosystems is one of the main goals of the ecosystem approach to fisheries (EAF). While a number of international treaties call for the implementation of EAF, there are still gaps in the underlying methodology. One aspect that has received substantial scientific attention recently is fisheries-induced evolution (FIE). Increasing evidence indicates that intensive fishing has the potential to exert strong directional selection on life-history traits, behaviour, physiology, and morphology of exploited fish. Of particular concern is that reversing evolutionary responses to fishing can be much more difficult than reversing demographic or phenotypically plastic responses. Furthermore, like climate change, multiple agents cause FIE, with effects accumulating over time. Consequently, FIE may alter the utility derived from fish stocks, which in turn can modify the monetary value living aquatic resources provide to society. Quantifying and predicting the evolutionary effects of fishing is therefore important for both ecological and economic reasons. An important reason this is not happening is the lack of an appropriate assessment framework. We therefore describe the evolutionary impact assessment (EvoIA) as a structured approach for assessing the evolutionary consequences of fishing and evaluating the predicted evolutionary outcomes of alternative management options. EvoIA can contribute to EAF by clarifying how evolution may alter stock properties and ecological relations, support the precautionary approach to fisheries management by addressing a previously overlooked source of uncertainty and risk, and thus contribute to sustainable fisheries.
Fish And Fisheries (1467-2960) (Wiley-blackwell), 2014-03 , Vol. 15 , N. 1 , P. 65-96

Droits : 2012 John Wiley & Sons Ltd
http://archimer.ifremer.fr/doc/00124/23522/21409.pdf
DOI:10.1111/faf.12007
http://archimer.ifremer.fr/doc/00124/23522/

Éditeur(s) : HAL CCSD Montpellier : CIRAD
Résumé : This article presents the effects of logging on the dynamics of above-ground biomass from the results of the post-logging study within two forests: Cikel in Eastern Para, Brazil and Paracou in French Guiana. The main objective is to compare the impact of commercial logging on the regeneration of the above-ground biomass in these forests whose characteristics differ in terms of structure and growth. In both sites, the intensity of exploitation is a key factor in determining the loss of biomass and the time required for its regeneration. In Paracou, the regeneration of biomass lost during conventional logging of 10 trees per hectare takes 45 years and more than 100 years when operating with higher intensity (21 trees/ha). In Cikei the forest biomass regenerates after 49 years harvesting 6 trees/ha and that takes 87 years after removal of 8 trees/ha. This regeneration needs similar time on both sites but with lower logging intensity at Cikel, in which felled trees are larger with a greater biomass than those of Paracou. This post-logging study has established a direct correlation of the dynamics of the biomass with the initial structure of the forest, as well as with the parameters of forest dynamics: mortality, growth and recruitment. The accumulation of biomass by the tree growth of the two remaining stands is a key parameter for the net carbon storage, while the contribution of recruitment in Paracou becomes significant only after 10 years after felling. Therefore in view to improve the growth of residual trees, it is compulsory to apply adequate silvicultural treatments such as selective thinning or removal of vines. While the two forests are geographically close enough, their regenerative abilities differ and because of the significant difference in size of the trees, the forest could tolerate more intensive harvesting in French Guiana
ISSN: 0006-579X

hal-01032427
https://hal.archives-ouvertes.fr/hal-01032427

Résumé : La problématique migratoire dans l’ultrapériphérie de l’Union européenne constitue un angle d’approche peu commun dans les études européennes. Espace de réflexion et de concertation qui cherche constamment à s’affirmer, l’ultrapériphérie européenne s’est, pour la première fois de son existence, penchée sur la thématique des flux migratoires. L’intérêt de cette situation sans précédent s’est confirmé lorsque la Commission européenne a officiellement décidé à travers sa communication du 12 septembre 2007 [COM(2007)507] intitulée « Stratégie pour les régions ultrapériphériques : bilan et perspectives », de prêter attention à la situation des régions ultrapériphériques (RUP) face au phénomène d’immigration. Si la plupart des travaux en la matière concernent les espaces nationaux ou transnationaux, rares sont ceux qui traitent d’un espace transrégional aussi éclaté géographiquement et dans sa composition juridico-institutionnelle.L’objet de la thèse porte ainsi sur la problématisation migratoire dans l’ultrapériphérie et l’étude de la fenêtre d’opportunité déclenchée par la communication de 2007. Ce qu’il s’agit d’observer, ce sont les conséquences de cette inscription à l’agenda européen pour l’espace ultrapériphérique sur cette thématique, à savoir la forme d’un processus d’élaboration d’un référentiel européen ultrapériphérique. Pour cela, il est nécessaire de comprendre les paramètres nationaux, régionaux, européens et ultrapériphériques qui englobent cet évènement.Cette étude de politiques publiques prend pour point de départ la notion d’européanisation définie de façon interactionnelle, et débouche sur un cadre théorique basé sur la Théorie du choix rationnel et l’Approche cognitive et normative. A l’aide de la méthode comparative, elle tente de confronter deux régions ultrapériphériques sélectionnées à cet effet : une région française, la Guadeloupe, et une région espagnole, les Iles Canaries. Deux archipels aux réalités juridiques, politiques et sociales différentes, ayant manifesté une inquiétude au sujet du phénomène d’immigration sur leur territoire dans la période précédant la prise en charge de 2007.L’analyse a mis en avant l’enchevêtrement de niveaux d’action publique assez complexe auquel sont confrontées ces régions. La diversité au sein de l’ultrapériphérie complique l’élaboration de bases communes au sujet de la question migratoire. Un processus d’européanisation directe dans l’ultrapériphérie a bien été lancé en 2007, mais reste à développer.L’objectif de la thèse est donc d’apporter des réponses aux difficultés observées, en menant une analyse assez précise de l’évènement de 2007. La démarche s’effectue en deux temps. D’une part, une analyse des paramètres internes (nationaux et régionaux) pouvant conditionner le processus étudié. D’autre part, un décryptage des racines conceptuelles et des premières observations de terrain pour comprendre la teneur du processus.
TraductionDésactiver la traduction instantanéeMigration into the outermost regions of the European Union is an angle unusual approach in European studies. Space for reflection and dialogue that constantly seeks to assert, Outermost Europe has for the first time in its existence, addressed the theme of migration. The advantage of this unprecedented situation is confirmed when the European Commission formally decided through its communication of 12 September 2007 [COM (2007) 507] entitled "Strategy for the outermost regions: achievements and perspectives", pay attention the situation of the outermost regions (OR) face to the immigration phenomenon. If most of the work on the subject relate to national or transnational, few areas are those that deal with cross-regional space also broke geographically and in its legal and institutionnelle.L'objet composition of the thesis and deals with migration in problematisation outermost regions and the study of the window of opportunity triggered by the communication of 2007. what is observed, it is the consequences of this inscription on the European agenda for the outermost space on this theme , namely as a process of developing a European outermost repository. For this it is necessary to understand the national parameters, regional, European and outermost encompassing évènement.Cette this policy study takes as its starting point the notion of Europeanization set of interactional way, and results in a theoretical framework based on Theory of rational choice and cognitive and normative approach. Using the comparative method, she tries to confront two outermost regions selected for this purpose: a French region, Guadeloupe, and one in Spain, the Canary Islands. Two archipelagos legal realities, different political and social, have expressed a concern about the phenomenon of immigration on their territory in the period preceding the care 2007.L'analyse highlighted the tangle of levels rather complex prosecution faced by these regions. The diversity of the outermost regions complicates the common foundations for development on the migration issue. A direct Europeanization process in the outermost regions has been launched in 2007, but remains développer.L'objectif of the thesis is to provide answers to the difficulties observed, leading a fairly accurate analysis of the event 2007. The process is carried out in two stages. On the one hand, an analysis of internal parameters (national and regional) that can condition the studied process. On the other hand, a decryption conceptual roots and the first field observations to understand the content of the process

http://www.theses.fr/2015AGUY0826/document

Éditeur(s) : HAL CCSD Portland Press
Résumé : International audience
CP12 is a small chloroplastic protein involved in the Calvin cycle that was shown to bind copper, a metal ion involved in modulation of its transition from reduced to oxidized state. In order to describe CP12 copper binding properties, copper-IMAC experiments and site-directed mutagenesis based on computational modeling, were coupled to top-down mass spectrometry (ESI-MS and MSMS). Copper-IMAC experiments allowed the primary characterization of mutation effects upon copper binding. Top-down MSMS experiments carried out under non-denaturing conditions on wild-type and mutant CP12/Cu2+ complexes then allowed fragment ions specifically liganding the copper ion to be determined. Comparison of MSMS datasets defined three regions involved in metal ion binding: residues D16 to D23, D38 to K50 and D70 to E76, with the two first regions containing selected residues for mutation. These data confirmed that copper ligands involved glutamic and aspartic residues in contrast to typical protein copper chelators. We propose that copper might play a role in regulation of CP12 biological activity.
ISSN: 0264-6021

hal-00479106
https://hal.archives-ouvertes.fr/hal-00479106
https://hal.archives-ouvertes.fr/hal-00479106/document
https://hal.archives-ouvertes.fr/hal-00479106/file/PEER_stage2_10.1042%252FBJ20082004.pdf
DOI : 10.1042/BJ20082004

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Xenoestrogens may persist in the environment by binding to sediments or suspended particulate matter serving as long-term reservoir and source of exposure, particularly for organisms living in or in contact with sediments. In this study, we present for the first time an effect-directed analysis (EDA) for identifying estrogenic compounds in a sediment sample using embryos of a transgenic reporter fish strain. In the tg(cyp19a1b-GFP) transgenic zebrafish strain, the expression of GFP (green fluorescent protein) in the brain is driven by an oestrogen responsive element in the promoter of the cyp19a1b (aromatase) gene. The selected sediment sample of the Czech river Bilina had already been analysed in a previous EDA using the yeast oestrogen screening assay and had revealed fractions containing estrogenic compounds. When normal phase HPLC (high performance liquid chromatography) fractionation was used for the separation of the sediment sample, the biotest with transgenic fish embryos revealed two estrogenic fractions. Chemical analysis of candidate compounds in these sediment fractions suggested alkylphenols and estrone as candidate compounds responsible for the observed estrogenic effect. Alkylphenol concentrations could partially explain the estrogenicity of the fractions. However, xenoestrogens below the analytical detection limit or non-targeted estrogenic compounds have probably also contributed to the sample's estrogenic potency. The results indicated the suitability of the tg(cyp19a1b-GFP) fish embryo for an integrated chemical-biological analysis of estrogenic effects.
ISSN: 0166-445X

hal-01072210
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01072210
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01072210/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01072210/file/Effect-directed_analysis_for_estrogenic_compounds-final.pdf
DOI : 10.1016/j.aquatox.2014.05.016

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
BACKGROUND AND AIMS: Determining the sources of variation in floral morphology is crucial to understanding the mechanisms underlying Angiosperm evolution. The selection of floral and reproductive traits is influenced by the plant's abiotic environment, florivores and pollinators. However, evidence that variations in floral traits result from mutualistic interactions with insects other than pollinators is lacking in the published literature and has rarely been investigated. We aimed to determine whether the association with either Camponotus femoratus or Pachycondyla goeldii (both involved in seed dispersal and plant protection) mediates the reproductive traits and allocation of Aechmea mertensii, an obligatory ant-garden tank-bromeliad, differently. METHODS: Floral and reproductive traits were compared between the two A. mertensii ant-gardens. The nitrogen flux from the ants to the bromeliads was investigated through experimental enrichments with stable isotopes ((15)N). KEY RESULTS: Camponotus femoratus-associated bromeliads produced inflorescences up to four times longer than did P. goeldii-associated bromeliads. Also, the numbers of flowers and fruits were close to four times higher, and the number of seeds and their mass per fruit were close to 1*5 times higher in C. femoratus than in P. goeldii-associated bromeliads. Furthermore, the (15)N-enrichment experiment showed that C. femoratus-associated bromeliads received more nitrogen from ants than did P. goeldii-associated bromeliads, with subsequent positive repercussions on floral development. Greater benefits were conferred to A. mertensii by the association with C. femoratus compared with P. goeldii ants. CONCLUSIONS: We show for the first time that mutualistic associations with ants can result in an enhanced reproductive allocation for the bromeliad A. mertensii. Nevertheless, the strength and direction of the selection of floral and fruit traits change based on the ant species and were not related to light exposure. The different activities and ecological preferences of the ants may play a contrasting role in shaping plant evolution and speciation.
ISSN: 0305-7364

hal-00819112
https://hal.archives-ouvertes.fr/hal-00819112
DOI : 10.1093/aob/mcr253
PUBMED : 21984729

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
In 2008 a fatal case of primary amoebic meningoencephalitis, due to the amoeboflagellate Naegleria fowleri, occurred in Guadeloupe, French West Indies, after a child swam in a bath fed with geothermal water. In order to improve the knowledge on free-living amoebae in this tropical part of France, we investigated on a monthly basis, the presence of Naegleria spp. in the recreational baths, and stream waters which feed them. A total of 73 water samples, 48 sediments and 54 swabs samples were collected from 6 sampling points between June 2011 and July 2012. The water samples were filtered and the filters transferred to non-nutrient agar plates seeded with a heat-killed suspension of Escherichia coli while sediment and swab samples were placed directly on these plates. The plates were incubated at 44°C for the selective isolation of thermophilic Naegleria. To identify the Naegleria isolates the internal transcribed spacers, including the 5.8S rDNA, were amplified by polymerase chain reaction and the sequence of the PCR products was determined. Thermophilic amoebae were present at nearly all collection sites. The pathogenic N. fowleri was the most frequently encountered thermophilic species followed by N. lovaniensis. The concentration of N. fowleri was rather low in most water samples, ranging from 0 to 22 per liter. Sequencing revealed that all N. fowleri isolates belonged to a common Euro-American genotype, the same as detected in the human case in Guadeloupe. These investigations need to be continued in order to counsel the health authorities about prevention measures, because these recreational thermal baths are used daily by local people and tourists.
ISSN: 1932-6203

pasteur-00782031
https://hal-riip.archives-ouvertes.fr/pasteur-00782031
https://hal-riip.archives-ouvertes.fr/pasteur-00782031/document
https://hal-riip.archives-ouvertes.fr/pasteur-00782031/file/article_naegleria_plos_one.pdf
DOI : 10.1371/journal.pone.0054414