Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
Dentin matrix acidic phosphoprotein 1 (DMP1) is an acidic, highly phosphorylated, noncollagenous protein secreted during dentin and bone formation. Previous functional studies of DMP1 have revealed various motifs playing a role in either mineralization or cell differentiation. We performed an evolutionary analysis of DMP1 to identify residues and motifs that were conserved during 220 millions years (Ma) of mammalian evolution, and hence have an important function. In silico search provided us with 41 sequences that were aligned and analyzed using the Hyphy program. We showed that DMP1 contains 55 positions that were kept unchanged for 220 Ma. We also defined in a more precise manner some motifs that were already known (i.e., cleavage sites, RGD motif, ASARM peptide, glycosaminoglycan chain attachment site, nuclear localization signal sites, and dentin sialophosphoprotein-binding site), and we found five, highly conserved, new functional motifs. In the near future, functional studies could be performed to understand the role played by them.
ISSN: 0022-2844

hal-01545482
https://hal.archives-ouvertes.fr/hal-01545482
DOI : 10.1007/s00239-013-9539-2

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
We conducted a survey along three belt transects located at increasing distances from the coast to determine whether a non-random arboreal ant assemblage, such as an ant mosaic, exists in the rainforest on the Masoala Peninsula, Madagascar. In most tropical rainforests, very populous colonies of territorially dominant arboreal ant species defend absolute territories distributed in a mosaic pattern. Among the 29 ant species recorded, only nine had colonies large enough to be considered potentially territorially dominant; the remaining species had smaller colonies and were considered non-dominant. Nevertheless, the null-model analyses used to examine the spatial structure of their assemblages did not reveal the existence of an ant mosaic. Inland, up to 44% of the trees were devoid of dominant arboreal ants, something not reported in other studies. While two Crematogaster species were not associated with one another, Brachymyrmex cordemoyi was positively associated with Technomyrmex albipes, which is considered an invasive species-a non-indigenous species that has an adverse ecological effect on the habitats it invades. The latter two species and Crematogaster ranavalonae were mutually exclusive. On the other hand, all of the trees in the coastal transect and at least 4 km of coast were occupied by T. albipes, and were interconnected by columns of workers. Technomyrmex albipes workers collected from different trees did not attack each other during confrontation tests, indicating that this species has formed a supercolony along the coast. Yet interspecific aggressiveness did occur between T. albipes and Crematogaster ranavalonae, a native species which is likely territorially dominant based on our intraspecific confrontation tests. These results suggest that the Masoala rainforest is threatened by a potential invasion by T. albipes, and that the penetration of this species further inland might be facilitated by the low density of native, territorially dominant arboreal ants normally able to limit its progression.
ISSN: 1932-6203

hal-00817444
https://hal.archives-ouvertes.fr/hal-00817444
https://hal.archives-ouvertes.fr/hal-00817444/document
https://hal.archives-ouvertes.fr/hal-00817444/file/Dejean2010_Spatial.pdf
DOI : 10.1371/journal.pone.0009319

Résumé : La connaissance des facteurs qui influent sur les populations de tiques et en particulier sur leurs distributions est un préalable indispensable à l’étude des maladies qu’elles transmettent. Parmi eux, l’importance des facteurs biotiques et en particulier celle de la compétition interspécifique est peu connue et souvent négligée. L’objectif de ce travail était d’évaluer le rôle de la compétition interspécifique sur la distribution de deux espèces de tiques d’importance vétérinaire, Amblyomma variegatum et A. hebraeum. Alors que seule A. variegatum favorise la transmission de la dermatophilose, une maladie de peau débilitante pour les ruminants, les deux espèces sont vectrices de la cowdriose, maladie due à une bactérie Ehrlichia ruminantium qui représente une contrainte économique majeure pour l’élevage. L’impact de l’espèce vectrice dans l’épidémiologie de la cowdriose (différences de souches circulantes, sévérité des cas,…) est inconnu bien qu’ayant potentiellement des conséquences en termes de surveillance (risque épidémiologique à l’introduction d’animaux) et de contrôle (développement de vaccin régional adapté aux souches circulantes) de la maladie. Ces deux espèces ont une distribution contiguë en Afrique australe avec peu de chevauchement (distribution parapatrique) suggérant une préférence environnementale différentielle ou une compétition exclusive entre elles. Une revue des données de la littérature a permis de mettre en évidence un chevauchement de leur niche trophique, climatique, et temporelle, et une interférence comportementale via la production de leurs phéromones. Les deux espèces pourraient donc rentrer en compétition directement par interférence communicative ou reproductive (hybridation stérile), ou indirectement via le partage de ressources, prédateurs ou pathogènes communs. Le rôle des facteurs biotiques et abiotiques sur le maintien de la parapatrie de ces deux espèces a été analysée (i) d’une part par la comparaison de leur niche environnementale réalisée en Afrique australe, et aux deux zones de contact au Zimbabwe et Mozambique, par des méthodes d’ordination et de modèles de niche (Maxent) ; (ii) et d’autre part par l’étude de leurs distributions et de leurs interactions (distribution sur les hôtes, croisements hétérospécifiques) dans la zone de contact au Mozambique. Globalement les résultats montrent qu’en Afrique Sud-Est et au Zimbabwe les deux espèces occupent des niches environnementales distinctes, celle d’A. hebraeum incluant des zones plus chaudes et plus sèches que celle d’A. variegatum. Au contraire au Mozambique les deux niches se chevauchent considérablement. L’enquête de terrain dans cette zone montre que les deux espèces y sont moins souvent trouvées en sympatrie que les données prédites, suggérant une distribution en partie déterminée par des interactions biotiques. Dans les rares sites avec présence des deux espèces, A. variegatum et A. hebraeum partagent les mêmes sites de fixation sur les animaux et forment un pourcentage relativement élevé de couples hétérospécifiques. Ce pourcentage, bien que similaire entre les femelles A. variegatum et A. hebraeum, semble impliquer des processus de discrimination spécifique propres aux deux espèces intervenant au niveau de l’agrégation, de la fixation et du contact des individus. Nos résultats suggèrent l’existence d’une compétition exclusive entre les deux espèces, due à une compétition sexuelle probablement associée à une compétition indirecte. La frontière parapatrique semble occuper une position stable le long d’un gradient environnemental au Zimbabwe mais pas au Mozambique. Les conditions entrainant la coexistence ou l’exclusion des deux espèces avec formation d’une frontière parapatrique sont discutés à l’aide de modèles théoriques de compétition.
Studying the factors that influence tick populations and their distributions is an essential pre-requisite to understanding the dynamics of the diseases they transmit. The relative importance of biotic factors such as interspecific competition is not well known and often neglected. The objective of this study was to assess the influence of interspecific competition on the distribution of two tick species of veterinary importance, Amblyomma variegatum and A. hebraeum. Whereas only A. variegatum is known to favor dermatophilosis, a debilitating skin disease of ruminants, both species are good vectors of Ehrlichia ruminantium, the bacteria causing heartwater, a fatal disease of ruminants that presents a major constraint for livestock development in Africa. The impact of vector species in heartwater epidemiology (differences of circulating strains, severity of clinical cases…) is poorly known but may have important implications for surveillance (epidemiological risk of imported animals) and control (adapting regional vaccine programs to circulating strains) of the disease. These two ticks have abutting and marginally overlapping (i.e. parapatric) distributions in southern Africa, suggesting either differential environmental preferences or exclusive competition between the two species. A review of published data highlighted an important overlap of their trophic, climatic and seasonal niche, and existence of chemical behavior interference through pheromone production. Therefore, the two species might compete either directly by communicative or reproductive interference (sterile hybridization), or indirectly by sharing the same resources, predators or pathogens. The role of biotic and abiotic factors in determining parapatry of these species was assessed by (i) comparing their realized environmental niche in southern Africa, and at contact zones in Zimbabwe and Mozambique, using ordination techniques and environmental niche modeling (Maxent); (ii) studying their distributions and their interactions (distribution on co-infested host, heterospecific mating) at the contact zone in Mozambique. Globally, the results indicated the two species occupied distinctly different environmental niches in southern Africa and at the contact zone in Zimbabwe, with the niche of A. hebraeum including both hotter and drier areas than that of A. variegatum. However, in Mozambique their niches overlapped considerably. Field studies within this zone showed that sympatry was observed less frequently than predicted by niche models, suggesting an importance of biotic interactions. At the rare sites where both species were present, A. variegatum and A. hebraeum were observed to share the same preference sites on hosts and formed a high percentage of heterospecific pairs. Though this cross-mating rate was not significantly different between A. variegatum and A. hebraeum females, our observations suggest different mechanism of species discrimination involved for the two species acting at the aggregation, fixation and partner contact level. Our results strongly suggest exclusive competition between these species may arise from sexual competition probably interacting with other indirect forms of competition. The parapatric boundary apparently occupies a stable location along an environmental gradient at the contact zone in Zimbabwe but not in Mozambique. Conditions inducing coexistence or exclusion of both species with the formation of parapatric distributions are discussed in relation to theoretical models of competition. When sexual competition is introduced in these models, the relative frequency of two species is determined by their endogenous fitness (a function of environmental conditions), density dependent effects of competitive interactions, historical distributions and dispersal rates: survival of the first prevails when the immigration rate of a fitter invading species remains lower than an invasion threshold.

http://www.theses.fr/2014AGUY0705/document

Éditeur(s) : Springer
Résumé : Clonality and genetic structure of the coral Pocillopora damicornis sensu lato were assessed using five microsatellites in 12 populations from four islands of the Society Archipelago (French Polynesia) sampled in June 2008. The 427 analysed specimens fell into 132 multilocus genotypes (MLGs), suggesting that asexual reproduction plays an important role in the maintenance of these populations. A haploweb analysis of ITS2 sequences of each MLG was consistent with all of them being conspecific. Genetic differentiation was detected both between and within islands, but when a single sample per MLG was included in the analyses, the populations turned out to be nearly panmictic. These observations provide further evidence of the marked variability in reproductive strategies and genetic structure of P. damicornis throughout its geographic range; comparison with results previously obtained for the congeneric species Pocillopora meandrina underlines the importance of life history traits in shaping the genetic structure of coral populations
Marine Biology (0025-3162) (Springer), 2014-03 , Vol. 161 , N. 3 , P. 531-541

Droits : Springer-Verlag Berlin Heidelberg 2013
http://archimer.ifremer.fr/doc/00171/28209/26518.pdf
DOI:10.1007/s00227-013-2355-9
http://archimer.ifremer.fr/doc/00171/28209/

Éditeur(s) : Université de Bretagne Occidentale
Résumé : Several small pelagic fish species contribute remarkably to world catch. Their populations are, however, characterized by large biomass fluctuations strongly affecting fisheries. The fishing gears and methods used to capture small pelagics have evolved to exploit the highly developed shoaling behavior of these species. Hence, faced to modern fishing this gregarious behavior becomes a disadvantage for fish. Fish behavior may be affected by environmental conditions and by fishing, at the same time that behavior impacts fishing. In this study, we seek to characterize the aggregative systems of small pelagic fishes inhabiting the Bay of Biscay by analyzing "acoustic images", defined as the group of echoes (planktonic layers, shoals, isolated targets) detected on a transect section of a given length. We analyzed the species composition, the spatial distribution and the evolution over time of acoustic images. We also studied the hydrological conditions of the bay, as well as the small pelagics French fishery in order to look for correlations between hydrology, commercial catch and fish aggregation patterns observed by acoustics. We observed the same species or group of species forming different types of aggregation according to habitat. Conversely, the same type of aggregation, associated with a particular habitat, can be produced by different species. The most notorious change observed during the studied period relates to small clupeoids aggregations in the vicinity of the Gironde estuary, whose structure evolved toward a greater fragmentation of shoals (a large number of small size detections) since 2000. Concerning commercial catches, pelagic trawlers fishing in pairs mainly seek for anchovy in the coastal areas, single pelagic trawlers capture mackerel and horse mackerel in deeper waters while purse seiners target mostly sardine near their fishing ports. Because of the coarse spatial resolution of commercial fishing data and the effect of the application of an international fisheries agreement limiting the fishing activity of French pelagic trawlers during spring, only small correlations between captures and types of aggregation were observed.
La participation des petits poissons pélagiques dans les captures est remarquable. Leurs populations sont cependant caractérisées par des importantes fluctuations de biomasse, impactant fortement les pêcheries. Les méthodes et appareils de pêche utilisés pour capturer ces espèces ont évolué dans le sens d'exploiter le comportement grégaire très développé des petits pélagiques. Cette tendance à former de bancs devient alors désavantageuse pour le poisson face à la pêche moderne. Les conditions environnementales et la pêche peuvent affecter le comportement du poisson, en même temps que ce dernier est susceptible d'affecter l'activité halieutique. Le but de cette étude est de caractériser les systèmes agrégatifs des petits poissons pélagiques dans le golfe de Gascogne en étudiant des « images acoustiques », définies comme l'ensemble des échos (couches planctoniques, bancs, cibles isolées) détectés sur une section de radiale de longueur donnée. Nous analysons leur composition en espèces ainsi que leur distribution spatiale et leur évolution au cours du temps. Nous étudions aussi les conditions hydrologiques du golfe, ainsi que la pêcherie française de ces espèces afin de chercher des corrélations entre l'hydrologie, la capture commerciale et les types d'agrégations observés par acoustique. Nous avons observé qu'une espèce est capable de former des agrégations différentes en fonction de l'habitat, et inversement, le même type d'agrégation, associé à un habitat particulier, peut être produit par des espèces différentes. Le changement observé le plus évident concerne les agrégations de petits clupéiformes, dont la structure a évolué vers une plus grande fragmentation des détections (des petits bancs plus nombreux) depuis 2000. Par rapport à la pêche des professionnels, les chalutiers pélagiques en boeufs recherchent en priorité l'anchois dans la zone côtière, les pélagiques simples capturent le chinchard et le maquereau au large et les senneurs recherchent principalement la sardine à proximité des ports de pêche. À cause de la résolution spatiale trop sommaire des données de pêche et l'effet de l'application des accords internationaux limitant l'activité des chalutiers pélagiques au printemps, nous n'avons observé que peu des corrélations entre les captures et les types d'agrégation établis à partir de données issues des campagnes scientifiques.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2008/these-6083.pdf
http://archimer.ifremer.fr/doc/00000/6083/

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Various types of genome and gene similarity networks along with their characteristics have been increasingly used for retracing different kinds of evolutionary and ecological relationships. Here, we present a new polynomial time algorithm and the corresponding software (BRIDES) to provide characterization of different types of paths existing in evolving (or augmented) similarity networks under the constraint that such paths contain at least one node that was not present in the original network. These different paths are denoted as Breakthroughs , Roadblocks, Impasses, Detours, Equal paths, and Shortcuts. The analysis of their distribution can allow discriminating among different evolutionary hypotheses concerning genomes or genes at hand. Our approach is based on an original application of the popular shortest path Dijkstra's and Yen's algorithms.
ISSN: 1932-6203

Droits : http://creativecommons.org/licenses/by/
hal-01361753
http://hal.upmc.fr/hal-01361753
http://hal.upmc.fr/hal-01361753/document
http://hal.upmc.fr/hal-01361753/file/journal.pone.0161474.PDF
DOI : 10.1371/journal.pone.0161474

Éditeur(s) : HAL CCSD Cambridge University Press
Résumé : International audience
Genetic variation was examined in two complex cases of Indo-Pacific pygmy angelfishes (genus Centropyge; Pomacanthidae). The lemonpeel pygmy angelfish C. flavissima (Cuvier and Valenciennes) has a geographically disjunct Indian vs. Pacific distribution and the individuals from these two regions differ by their colour patterns. Previous research on C. flavissima has shown mitochondrial introgression from two related species, C. eibli in the eastern Indian Ocean and C. vrolikii in the Pacific Ocean. Using the 16S rDNA and the CO1 gene as phylogeographic markers, we found no mitochondrial haplotypes in common between Indian Ocean C. flavissima and C. eibli, confirming partial genetic isolation, albeit recent. Also, we found substantial genetic differences between Indian and Pacific C. flavissima populations at the nuclear ETS-2 intron locus. The Indian Ocean form of C. flavissima, thus geographically isolated by >2000 km distance from its Pacific Ocean counterpart, is described as a new species, Centropyge cocosensis sp. nov. Centropyge cocosensis sp. nov. differs in appearance from C. flavissima in having a conspicuous blue iris and a fainter, bluish eye ring. We also found that the yellow pygmy angelfish C. heraldi Woods and Schultz consists of two genetically distinct entities, one distributed widely in the northern tropical Indo-West Pacific, the other distributed in the southern Pacific Ocean. The name originally given to the blackfin pygmy angelfish, C. woodheadi Kuiter, is here resurrected to designate the latter.
EISSN: 1755-2672

hal-01340521
https://hal-univ-perp.archives-ouvertes.fr/hal-01340521
DOI : 10.1007/s12526-016-0509-y

Éditeur(s) : Université des Antilles Études caribéennes
Résumé : Afin de mettre en perspective les différents articles du dossier, le texte souligne les différentes étapes qui définissent la situation de la façade caraïbe à la fois au sein des Etats-nations et de la région centraméricaine. Depuis une position de marge ou d’enclave liée à la fois à la géographie et aux logiques de l’empire espagnol, cet ensemble territorial s’est construit à partir de fragments plus ou moins connectés entre eux et aux espaces régionaux maritimes (caribéen ou atlantique). Au cours de leur construction, les différents Etats-nations n’envisagent d’abord la façade caraïbe que dans sa dimension de connexion transisthmique. Pourtant, on constate au vingtième siècle différents processus d’intégration territoriale qui visent à relier espace continental et façade caraïbe, processus qu’il faut associer à de nouvelles dynamiques démographiques. Les sociétés d’interface qui en résultent, voient leurs composantes « ladinas », indiennes, ou afro-descendantes se réorganiser. Enfin, ces fragments qui composent la façade prennent de nouvelles couleurs à la lumière des projections faites par d’autres acteurs (ONG) ou à d’autres échelles (région américaine).
In order to put into perspective the different papers of the issue, this text highlights the successive stages by which the Caribbean coastline of Central American has been constructed, under the several States-nations and as a part of the Central American region. As a margin or enclave due to geographical characters as to the logics of Spanish Empire, these territories have been made from fragments more or less connected between them or to other regional maritime spaces (Caribbean or Atlantic). When growing, the States-nations in the region first exclusively consider their Caribbean coastline as a transisthmic connection. Yet, during the twentieth century, various process of territorial integration aim to connect continental spaces and maritime coastline, associating demographical dynamics. Societies of interface result of these process, where their ladina, indian, afro components are reorganized. Finally, theses fragments as elements of the façade take a new color in the look of new actors (NGO) or from other scales and spaces (Atlantic region, Caribbean Sea).
Para poner en perspectiva los diferentes artículos del numero temático, este texto subraya las varias etapas en que definieron la situación de la costa caribeña, a la vez en cada Estado-Nacion y al nivel de la región. Con una posición de margen o enclave, que se explica tan por motivos geográficos que por las lógicas del imperio español, este conjunto territorial se ha construido a partir de fragmentos más o menos conectados entre sí e con los espacios regionales marítimos (caribeño o atlántico). Cuando se desarrollaron, los Estados-naciones consideraban las costas caribeñas solo por su potencial transístmico. Sin embargo, en el siglo veinte, llevaron a cabo varios procesos de integración territorial que les permiten vincular su espacio continental con la fachada atlántica, y eso asociándose a importantes dinámicas poblacionales. Resultan de estos procesos sociedades de interfaz, cuyos componentes ladinos, indígenas y afros se ven reorganizados. Por fin, los fragmentos que componen la costa caribeña toman otro color a la luz de proyectos llevados por actores ajenos (ONG) o desde espacios y escalas diferentes (Espacio atlántico, región americana).
Amérique centrale
Caraïbes
Livingston
Guatemala

Droits : info:eu-repo/semantics/openAccess
urn:doi:10.4000/etudescaribeennes.6032
http://journals.openedition.org/etudescaribeennes/6032

Éditeur(s) : HAL CCSD
Résumé :  
The spatial genetic differentiation among European beech stands in western Germany was analysed by a new method. The genetic structure at 8 enzyme gene loci of 100 sampled populations was used as data base. The data represent authors' own results and published data from 8 different studies. For 10 geographic distance classes [h] from 0 to 500 km, the average genetic distance between the populations for each single gene locus, a gene-pool distance and the semivariances of genetic diversity gam were computed. Significant deviation from random spatial genetic structure was tested by permutation analysis. In many cases (Lap-B, Mdh-B, Mdh-C and 6Pgdh-C) the mean genetic distance between stands with spatial distance up to 200 km was significantly smaller and the genetic distance between stands with geographic distances of 200 and 400 km was significantly greater than expected for random spatial genetic structure. Similar tendencies were found for the gene-pool distance and the semivariances of diversity. Kriging, as a method for spatial interpolation, was used to draw synthetic maps of the spatial patterns of allelic frequencies and genetic diversity. The influence of postglacial recolonisation and regeneration with foreign seed material on the spatial genetic patterns are discussed
Forest genetics

hal-01032093
https://hal.archives-ouvertes.fr/hal-01032093

Éditeur(s) : HAL CCSD John Libbey Eurotext
Résumé : International audience
In mainland France, as in most Western countries, prostate cancer is the most frequent cancer in men. However, the incidence of this cancer is highly variable, depending on the region of the world. This variability is largely accounted for by differences in access to care, but also by environmental conditions and the ethnogeographic origins of the populations. The French West Indies--the archipelago of Guadeloupe and the island of Martinique--are unique in terms of their geography, environment and the lifestyle and origins of their populations. We report the incidence and mortality rates for prostate cancer in the French West Indies and also provide the first description of the major clinical and anatomical characteristics of this disease in this region.
ISSN: 0007-4551

hal-00671140
https://hal.archives-ouvertes.fr/hal-00671140
DOI : 10.1684/bdc.2008.0811
PUBMED : 19258223

Éditeur(s) : HAL CCSD Wiley
Résumé : [b]Aim[/b][br/] Many tropical tree species have poorly delimited taxonomic boundaries and contain undescribed or cryptic species. We examined the genetic structure of a species complex in the tree genus Carapa in the Neotropics in order to evaluate age, geographic patterns of diversity and evolutionary relationships, and to quantify levels of introgression among currently recognized species.[br/] [br/] [b]Location[/b][br/] Lowland moist forests in the Guiana Shield, the Central and Western Amazon Basin, Chocó and Central America.[br/] [br/] [b]Methods[/b][br/] Genetic structure was analysed using seven nuclear simple sequence repeats (nuSSR), five chloroplast SSRs (cpSSR), and two chloroplast DNA (cpDNA) intergenic sequences (trnH-psbA and trnC-ycf6). Bayesian clustering analysis of the SSR data was used to infer population genetic structure and to assign 324 samples to their most likely genetic cluster. Bayesian coalescence analyses were performed on the two cpDNA markers to estimate evolutionary relationships and divergence times.[br/] [br/] [b]Results[/b][br/] Two genetic clusters (nu_guianensis and nu_surinamensis) were detected, which correspond to the Neotropical species C. guianensis (sensu latu) and C. surinamensis. Fourteen cpDNA haplotypes clustered into six haplogroups distributed between the two nuclear genetic clusters. Divergence between the haplogroups was initiated in the Miocene, with some haplotype structure evolving as recently as the Pleistocene. The absence of complete lineage sorting between the nuclear and chloroplast genomes and the presence of hybrid individuals suggest that interspecific reproductive barriers are incomplete. NuSSR diversity was highest in C. guianensis and, within C. guianensis, cpDNA diversity was highest in the Central and Western Amazon Basin. Regional genetic differentiation was strong but did not conform to an isolation-by-distance process or exhibit a phylogeographical signal.[br/] [br/] [b]Main conclusions[/b][br/] The biogeographical history of Neotropical Carapa appears to have been influenced by events that took place during the Neogene. Our results point to an Amazonian centre of origin and diversification of Neotropical Carapa, with subsequent migration to the Pacific coast of South America and Central America. Gene flow apparently occurs among species, and introgression events are supported by inconsistencies between chloroplast and nuclear lineage sorting. The absence of phylogeographical structure may be a result of the ineffectiveness of geographical barriers among populations and of reproductive isolation mechanisms among incipient and cryptic species in this species complex.
ISSN: 0305-0270

hal-01032395
https://hal.archives-ouvertes.fr/hal-01032395
DOI : 10.1111/j.1365-2699.2011.02678.x

Éditeur(s) : HAL CCSD
Résumé : International audience
The SOX8 and SOX9 transcription factors are involved in, among others, sex differentiation, male gonad development and adult maintenance of spermatogenesis. Sox8(-/-) mice lacking Sox9 in Sertoli cells fail to form testis cords and cannot establish spermatogenesis. Although genetic and histological data show an important role for these transcription factors in regulating spermatogenesis, it is not clear which genes depend upon them at a genome-wide level. To identify transcripts that respond to the absence of Sox8 in all cells and Sox9 in Sertoli cells we measured mRNA concentrations in testicular samples from mice at 0, 6 and 18 days post-partum. In total, 621 and 629 transcripts were found at decreased or increased levels, respectively, at different time points in the mutant as compared to the control samples. These mRNAs were categorized as preferentially expressed in Sertoli cells or germ cells using data obtained with male and female gonad samples and enriched testicular cell populations. Five candidate genes were validated at the protein level. Furthermore, we identified putative direct SOX8 and SOX9 target genes by integrating predicted SOX-binding sites present in potential regulatory regions upstream of the transcription start site. Finally, we used protein network data to gain insight into the effects on regulatory interactions that occur when Sox8 and Sox9 are absent in developing Sertoli cells. The integration of testicular samples with enriched Sertoli cells, germ cells and female gonads enabled us to broadly distinguish transcripts directly affected in Sertoli cells from others that respond to secondary events in testicular cell types. Thus, combined RNA profiling signals, motif predictions and network data identified putative SOX8/SOX9 target genes in Sertoli cells and yielded insight into regulatory interactions that depend upon these transcription factors. In addition, our results will facilitate the interpretation of genome-wide in vivo SOX8 and SOX9 DNA binding data.
Andrology

hal-00877013
https://hal.archives-ouvertes.fr/hal-00877013
DOI : 10.1111/j.2047-2927.2012.00049.x
PUBMED : 23315995

Éditeur(s) : Wiley-blackwell
Résumé : In bird species that have a high movement capacity, dispersal may connect subpopulations over vast geographical regions, with important consequences for the design of conservation management strategies. Here we used a molecular approach to infer the patterns and rates of dispersal among eight Mediterranean subpopulations of the endangered Bonelli's Eagle, based on 245 individuals screened at 17 microsatellite loci. There was moderate genetic differentiation between subpopulations sampled in the western (Iberia and Morocco) and eastern (Cyprus) Mediterranean, whereas differentiation among subpopulations in the former region was weak to moderate and followed a pattern of isolation by distance. Within the western Mediterranean, the small, peripheral and ecologically unique population of southwest Portugal had the lowest genetic diversity and the highest differentiation. The remaining subpopulations formed two loose clusters, one including Morocco and southwest and eastern Spain, and the other northeast Portugal and western and central Spain. Few recent migrants were detected, and they originated primarily from adjacent subpopulations. Our findings suggest that western Mediterranean Bonelli's Eagles may have a large-scale metapopulation structure, with subpopulations connected to some extent by distance-dependent dispersal, probably influenced by natal philopatry and the geographical configuration of subpopulations. The combination of marked ecological and genetic divergence suggests that the peripheral subpopulation of southwest Portugal may be regarded as a distinct management unit.
Ibis (0019-1019) (Wiley-blackwell), 2013-07 , Vol. 155 , N. 3 , P. 485-498

Droits : 2013 British Ornithologists’ Union
http://archimer.ifremer.fr/doc/00148/25924/24018.pdf
DOI:10.1111/ibi.12065
http://archimer.ifremer.fr/doc/00148/25924/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Toxoplasma gondii is highly virulent in New World monkeys, but despite numerous outbreaks observed in captive populations there are few reports of molecular characterization of strains. In this article, we describe two outbreaks of toxoplasmosis that occurred in 2001 and 2006 in an outdoor captive breeding colony of squirrel monkeys (Saimiri sciureus) kept by the Institut Pasteur in French Guiana. A microsatellite DNA analysis of the biological samples collected in the 2001 and 2006 outbreaks showed that two different Toxoplasma strains were involved. The 2001 strain exhibited a type II genotype whereas the 2006 strain showed a combination of type I, type III and atypical alleles. Infection could be related to oocysts contaminating water or food, or to ingestion of rats by monkeys. In 2006, a second episode was observed 3 weeks after the first, and was believed to be related to direct contamination by tachyzoites of bronchopulmonary origin from dying monkeys of the first event. During both outbreaks, a total of 50 monkeys died and none recovered spontaneously, confirming the virulence of both type II and non-type II Toxoplasma strains in New World monkeys.
ISSN: 0304-4017

hal-00408048
https://hal.archives-ouvertes.fr/hal-00408048
DOI : 10.1016/j.vetpar.2009.04.004
PUBMED : 19423226

Éditeur(s) : Université de la Méditerranée
Résumé : This study was supported by the Atlantic working site of the « Programme National d’Océanographie Côtière » (PNOC, PNEC since 1999). The objectives were (1) to check the existence and to understand the mechanisms of winter phytoplankton blooms in the bay of Biscay influenced by the Gironde waters (2) to determine the limiting nutrient of the primary production associated to these blooms and to follow the seasonal evolution of the limiting nutrient, (3) to understand the consequences of this early limitation on the structuration of algal populations in spring. Since phosphorus was supposed to be the major limiting nutrient of algal growth in the Gironde plume, the different forms of the phosphorus cycle as well as the bacterial compartment, central in this cycle, were also studied in term of stocks and fluxes. The sampling strategy consisted in three cruises in 1998, BIOMET 2 (January), BIOMET 3 (beginning of March), PEGASE (June) and six cruises in 1999, PLAGIA 1 to 6 (late February, late April, late May, late June, the middle of July and the beginning of October). Winter algal blooms, essentially diatoms, were actually observed both in the typical waters of the plume (S < 34.5) and at the limit of the plume and adjacent atlantic oceanic waters (S > 34.5) in the successives years 1998 and 1999. These blooms were initiated by the occurrence of short anticyclonic windows in winter, acting on physical processes which dominate the evolution and characteristics of the Gironde plume (runoff, wind direction and speed) and, ultimately, on the evolution of the depth of the mixed layer (haline stratification) and available light (decrease of turbidity). The algal growth was actually phosphorus limited in the typical waters of the plume at the end of the winter bloom, in spring and became nitrogen and phosphorus limited in summer until the first autumn gales restored the nutritive balance. More oceanic waters (S > 34.5) were probably N+P limited from the end of the winter-the beginning of spring to autumn. Phosphorus limitation of winter blooms, associated with girondine unbalanced nutritive supplies (high NO3/PO4 ratios) favoured the development of small cells at the beginning of spring and the later presence of spring blooms (June 1998, late May 1999) composed of pico and nanophytoplankton (nanoflagellates), instead of typical diatom spring blooms for temperate waters. This size reduction of algal communities is strongthened by the competition between phytoplankton and bacteria for the phosphate uptake, bacteria being more competitives at low concentrations and being phosphorus limited sometimes in spring. The decreasing size of algal cells probably acted on the structuration of the whole food web. The study of the different forms of phosphorus displayed the importance of the Dissolved Organic Phosphorus (DOP) pool. The potential biological lability and the capacity of algae and bacteria to use the DOP in spring when phosphate are undetectable was shown by the very high specific activities of alkaline phosphatases and the very rapid cycling of phosphate monoesters. According to the few estimations of actual phosphatasic activity and phosphate assimilation fluxes, the hydrolysis of DOP associated with the coupled assimilation of liberated phosphate would represent 91 to 99 % of the phosphorus fluxes into algal and bacterial cells when phosphate were exhausted. In such conditions DOP could satisfy most of microorganisms phosphorus needs.
Cette thèse s’inscrit dans le cadre du Chantier Atlantique du Programme National d’Océanographie Côtière (PNOC, PNEC depuis 1999). Les objectifs de ce travail étaient (1) de vérifier l’existence et comprendre le déterminisme de blooms phytoplanctoniques hivernaux dans les eaux du Golfe de Gascogne influencées par la Gironde, (2) de préciser le facteur limitant de la production primaire associée à ces blooms et de suivre l’évolution saisonnière de ce facteur et (3) de comprendre les conséquences de cette limitation précoce sur la structuration des populations algales au printemps. Le phosphore étant supposé être le principal élément limitant de la croissance algale dans le panache de la Gironde, les différentes composantes du cycle du phosphore ainsi que le compartiment bactérien, central dans ce cycle, ont été étudiés en terme de stock et de flux. La stratégie d’échantillonnage a consisté en trois campagnes en 1998, BIOMET 2 (janvier), BIOMET 3 (début mars), PEGASE (juin) et six campagnes en 1999, PLAGIA 1 à 6 (fin février, fin avril, fin mai, fin juin, mi-juillet et début octobre). Des efflorescences algales hivernales, constituées essentiellement de diatomées, ont effectivement été observées de façon récurrente dans les eaux typiques du panache (S < 34,5) et à la limite du panache et des eaux océaniques atlantiques adjacentes (S > 34,5) au cours des deux années successives 1998 et 1999. Ces blooms ont été engendrés par l’apparition de courtes fenêtres anticycloniques en période hivernale, ces fenêtres interférant sur les processus physiques qui prévalent sur l’évolution et les caractéristiques du panache de la Gironde (régime des débits, orientation et force du vent) et, de façon ultime, sur l’évolution de la profondeur de la couche de mélange (halostratification) et la disponibilité en lumière (diminution de la turbidité). La croissance algale était limitée par le phosphore dans les eaux typiques du panache à la fin du bloom hivernal, au printemps et devint limitée en azote et en phosphore en période estivale et ceci jusqu’à ce que les premières tempêtes automnales rétablissent l’équilibre nutritif des eaux. Les eaux à caractère plus océanique (S > 34,5) étaient plus probablement limitées par N+P dès la fin de l’hiverdébut du printemps et ce jusqu’à l’automne. La limitation des blooms hivernaux par le phosphore, associée à des apports nutritifs girondins déséquilibrés en phosphate (rapports NO3/PO4 élevés) a favorisé le développement de cellules de petite taille au début du printemps et la présence ultérieure de blooms printaniers (juin 1998, fin mai 1999) composés de pico- et de nanophytoplancton (nanoflagellés), blooms « atypiques » pour des eaux tempérées à cette saison. Cette structuration des communautés algales est renforcée par la compétition entre le phytoplancton et les bactéries pour l’acquisition du phosphate, les bactéries étant plus compétitives aux faibles teneurs en phosphate et pouvant être elles-mêmes limitées par le phosphore à certains moments du printemps. La diminution de taille des cellules algales a probablement une incidence sur la structure de taille de l’ensemble du réseau trophique. L’étude des différentes composantes du phosphore montre l’importance du pool de Phosphore Organique Dissous (POD), sa labilité biologique potentielle et la capacité des communautés algales et bactériennes à utiliser ce pool au printemps quand les phosphates sont indétectables (activités spécifiques des phosphatases alcalines très élevées, recyclage très rapide des monoesters de phosphate). Au vu des quelques estimations de l’activité phosphatasique réelle et des flux d’assimilation de phosphate, l’hydrolyse du POD associée à l’assimilation couplée du phosphate libéré représenterait 91 à 99 % des flux de phosphore vers les cellules algales et bactériennes, quand les phosphates du milieu sont déficients. Dans de telles conditions, le POD pourrait satisfaire l’essentiel des besoins des microorganismes en phosphore.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00013/12463/9298.pdf
http://archimer.ifremer.fr/doc/00013/12463/

Éditeur(s) : HAL CCSD American Society for Microbiology
Résumé : International audience
We investigated the characteristics of the sulfur-oxidizing symbiont hosted in the gills of Codakia orbicularis, a bivalve living in shallow marine tropical environments. Special attention was paid to describing the heterogeneity of the population by using single-cell approaches including flow cytometry (FCM) and different microscopic techniques and by analyzing a cell size fractionation experiment. Up to seven different subpopulations were distinguished by FCM based on nucleic acid content and light side scattering of the cells. The cell size analysis of symbionts showed that the symbiotic population was very heterogeneous in size, i.e., ranging from 0.5 to 5 _m in length, with variable amounts of intracellular sulfur. The side-scatter signal analyzed by FCM, which is often taken as a proxy of cell size, was greatly influenced by the sulfur content of the symbionts. FCM revealed an important heterogeneity in the relative nucleic acid content among the subclasses. The larger cells contained exceptionally high levels of nucleic acids, suggesting that these cells contained multiple copies of their genome, i.e., ranging from one copy for the smaller cells to more than four copies for the larger cells. The proportion of respiring symbionts (5-cyano-2,3-ditolyl-terazolium chloride positive) in the bacteriocytes of Codakia revealed that around 80% of the symbionts hosted by Codakia maintain respiratory activity throughout the year. These data allowed us to gain insight into the functioning of the symbionts within the host and to propose some hypotheses on how the growth of the symbionts is controlled by the host.
ISSN: 0099-2240

hal-00716079
https://hal.univ-antilles.fr/hal-00716079
DOI : 10.1128/AEM.01683-06

Résumé : Aux Antilles, la faible fréquence des coronaropathies pourrait être liée à des facteurs génétiques, ethniques et/ou une distribution spécifique des facteurs de risque cardio-vasculaire (FDRCV). Les propriétés l'ANP (Atrial Natriuretic Peptide) et l'influence de certains polymorphismes de son gène, fréquents dans les populations d'ascendance Africaine pourraient également être en cause. L'analyse des dossiers de 638 patients coronariens consécutifs a mis en évidence une forte prévalence de l'hypertension artérielle et du diabète dans cette population et révélé des différences significatives dans la prévalence des FDRCV entre Afro-Caribéens (AC), Caucasiens et descendants de migrants Indiens. L'analyse angiographique de 420 patients AC a révélé que le diabète était le FDRCV le plus fortement lié à la sévérité des lésions coronaires alors l'obésité apparaissait comme un facteur protecteur. La transfection in vitro, de cellules musculaires lisses artérielles par une construction adénovirale porteuse du gène de l'ANP a entrainé une inhibition de la prolifération et de la migration cellulaire de 31 % et 25% respectivement. In vivo, cet effet s'est traduit par une réduction de 25% de la formation néotimale et de 28% du rapport intima/média dans un modèle d'hyperplasie de carotide de rat. Dans étude transversale incluant 210 sujets diabétiques AC nous avons mis en évidence une association entre le polymorphisme rs5065 (22381>C) du gène de l'ANP et l'existence d'une coronaropatbie. Dans cette étude, l'odds ratio de la présence d'une coronaropathie chez les porteurs de l'allèle mineur de cette mutation (TC/CC) était de 0,50 (0,26- 0,96; P = 0,038).
In Guadeloupe and Martinique, the low frequency ofcoronary artery disease (CAD) could be related to genetic or ethniefactors and/or specifie distribution ofcardiovascular risk factors (CRFs). Atrial Natriuretic Peptide (ANP) properties and influence of sorne of ANP gene polymorphism that are frequent in populations of African descent could also be involved in CAD occurrence. We retrospectively studied 638 consecutive patients with documented CAO and found a high prevalence of hypertension and diabetes in this population. This study also demonstrated significant differences in the prevalence of CRFs between Afro-Caribbean (AC), Caucasians and Indians migrants. The angiographie analysis of420 patients revealed that in AC, diabetes emerged as the strongest CFR related to the severity ofcoronary lesions while obesity appeared as a protective factor. After transfection by an adenoviral construct carrying the ANP gene, vascular smooth muscle cell proliferation stimulated by 10% fetal calf serum was reduced by 31% and migration by 25%. In vivo, in rat carotid artery model ofvascular injury, neointima formation and intima/media ratio was reduced by 25% and 28% respectively. In a cross-sectional study inc1uding 210 AC diabetics we found an association between rs5065 (22381> C) polymorpbism and the presence of coronary artery disease suggesting that the minor allele could have a protective effect against CAD. The odds ratio for the presence ofCAD in carriers ofthe minor allele ofthis mutation (TC / CC) was 0.50 (0.26-0.96, P = 0.038).

http://www.theses.fr/2012AGUY0553/document

Éditeur(s) : HAL CCSD Springer
Résumé : International audience
We isolated and characterized 16 polymorphic microsatellite loci for Lytocarpia brevirostris (Aglaophe- niidae), a hydrozoan common in the tropical Indo-Pacific region. Four to 34 alleles per locus were detected at the Indo-Pacific scale. At the population level, observed (Ho) and expected (He) heterozygosities ranged across 0.100–0.625 and 0.097–0.597, respectively. Three markers showed significant deviation from Hardy–Weinberg equi- librium, all of them presenting null alleles. Linkage dis- equilibrium was detected in three pairs of loci among 120. These primers provide powerful tools for studying popu- lation genetic diversity and the implication of life cycle strategies on population differentiation in tropical hydro- zoans. This will be valuable for the conservation of coral reefs biodiversity and the design of marine protected areas.
ISSN: 1877-7252

hal-01185722
https://hal.archives-ouvertes.fr/hal-01185722
https://hal.archives-ouvertes.fr/hal-01185722/document
https://hal.archives-ouvertes.fr/hal-01185722/file/Postaire%20et%20al.%20-%202015%20-%20Isolation%20and%20characterisation%20of%2016%20microsatellit_hal.pdf
DOI : 10.1007/s12686-014-0407-1

Éditeur(s) : HAL CCSD Presses université de Laval
Résumé : International audience
This article aims to specify the challenges related to adapting the Disability Creation Process (DCP) model to the experience of chronic disease, specifically Human immunodeficiency virus (HIV). In this perspective, a conceptual clarification is proposed because the DCP is mainly used to study populations in situations of disability due to motor, sensory, mental or behavioral disabilities. However, this model seems to be able to adequately read the specific experience of HIV, and help to understand differently life trajec-tories of people living with HIV (PLHIV). Indeed, HIV infection, despite its status as a "chronic disease", continues to contribute to the risk of social isolation. Body modifications induced by the disease or its treatment has an impact on how others view PLHIV. They expose the visibility of HIV status and, ultimately, the fear of social exclusion. In this respect, the analysis of the DCP may allow us to understand the varia-tions in the quality of social participation and identify the phases of vulnerability by focusing on body image in particular induced by the infection or treatments. This approach provides the opportunity for new insight into the influence of social environments (particularly health management or community support) with re-gards to the lifestyle and the daily experiences of socially disadvantaged people.
Cet article tente de spécifier les enjeux d’une adaptation du modèle du Processus de production du handicap (PPH) au vécu de la maladie chronique, et plus spécifiquement du virus de l’immunodéfi-cience humaine (VIH). Dans cette perspective, un éclaircissement conceptuel est proposé, car le PPH a principalement été utilisé pour étudier les populations vivant des situations de handicap liées à des incapa-cités motrices, sensorielles, intellectuelles ou comportementales. Ce modèle semble toutefois en mesure de renouveler la lecture de l’expérience spécifique du VIH, et d’aider à saisir autrement les trajectoires de vie des personnes vivant avec le VIH (PVVIH). En effet, l’infection au VIH, malgré son statut de « maladie chronique », demeure associée à un risque d’isolement social. Les modifications corporelles induites par la maladie ou par son traitement confronte les PVVIH au regard de l’autre. Elles exposent à la visibilité du statut sérologique et, in fine, à la peur de l’exclusion sociale. Dans ce cadre, l’analyse du Processus de production du handicap peut permettre de comprendre les variations de la qualité de la participation sociale et d’identifier les phases de vulnérabilité en s’intéressant notamment au rapport au corps induit par l’infection et les traitements. Cette approche offre l’opportunité d’un nouvel éclairage sur le poids des envi-ronnements sociaux (notamment des dispositifs de prises en charge sanitaire ou d’accompagnement communautaire) sur les habitudes de vie et l’expérience quotidienne d’un public fragilisé socialement.
ISSN: 1499-5549

hal-01681423
https://hal.archives-ouvertes.fr/hal-01681423

Éditeur(s) : Wiley-blackwell
Résumé : The history of colonization and dispersal in fauna distributed among deep-sea chemosynthetic ecosystems remains enigmatic and poorly understood because of an inability to mark and track individuals. A combination of molecular, morphological and environmental data improves understanding of spatial and temporal scales at which panmixia, disruption of gene flow or even speciation may occur. Vestimentiferan tubeworms of the genus Escarpia are important components of deep -sea cold seep ecosystems, as they provide long-term habitat for many other taxa. Three species of Escarpia, Escarpia spicata [Gulf of California (GoC)], Escarpia laminata [Gulf of Mexico (GoM)] and Escarpia southwardae (West African Cold Seeps), have been described based on morphology, but are not discriminated through the use of mitochondrial markers (cytochrome oxidase subunit 1; large ribosomal subunit rDNA, 16S; cytochrome b). Here, we also sequenced the exon-primed intron-crossing Haemoglobin subunit B2 intron and genotyped 28 microsatellites to (i) determine the level of genetic differentiation, if any, among the three geographically separated entities and (ii) identify possible population structure at the regional scale within the GoM and West Africa. Results at the global scale support the occurrence of three genetically distinct groups. At the regional scale among eight sampling sites of E. laminata (n=129) and among three sampling sites of E. southwardae (n=80), no population structure was detected. These findings suggest that despite the patchiness and isolation of seep habitats, connectivity is high on regional scales.
Molecular Ecology (0962-1083) (Wiley-blackwell), 2013-08 , Vol. 22 , N. 16 , P. 4147-4162

Droits : 2013 John Wiley & Sons Ltd
http://archimer.ifremer.fr/doc/00152/26354/24515.pdf
DOI:10.1111/mec.12379
http://archimer.ifremer.fr/doc/00152/26354/