Éditeur(s) : HAL CCSD Ferrata Storti Foundation
Résumé : International audience
BackgroundRecent evidence suggests that autonomic nervous system activity could be involved in thepathophysiology of sickle cell disease, but it is unclear whether differences in autonomic nervoussystem activity are detectable during steady state in patients with mild and severe disease.The aim of the present study was to compare the autonomic nervous system activity, bloodrheology, and inflammation in patients with sickle cell anemia according to the frequency ofacute pain crisis.Design and MethodsTwenty-four healthy volunteers, 20 patients with sickle cell anemia with milder disease, and15 patients with sickle cell anemia with more severe disease were recruited. Milder disease wasdefined as having no pain crisis within the previous year. More severe disease was defined ashaving had within the previous year three or more pain crises which were documented by aphysician and required treatment with narcotics. The autonomic nervous system activity wasdetermined by spectral analysis of nocturnal heart rate variability. Blood viscosity determinationand measurements of several inflammatory markers (interleukin-6, soluble vascular celladhesion molecule-1, soluble CD40 ligand and sL-selectin) were made on blood samples collectedin steady-state conditions.ResultsResults showed that: 1) patients who had suffered more frequent pain crises had lowerparasympathetic activity and greater sympatho-vagal imbalance than both controls andpatients with milder disease. However, when adjusted for age, no significant difference wasdetected between the two sickle cell anemia patient groups; 2) patients who had suffered morefrequent pain crises had higher blood viscosity than patients with milder disease, and this wasnot dependent on age.ConclusionsResults from the present study indicate that both the autonomic nervous system activity andblood viscosity are impaired in patients with sickle cell anemia exhibiting high frequency ofpain crisis in comparison with those who did not experience a crisis within the previous year.
ISSN: 0390-6078

hal-01163973
https://hal.univ-antilles.fr/hal-01163973
DOI : 10.3324/haematol.2011.047365

Éditeur(s) : HAL CCSD National Academy of Sciences
Résumé : International audience
All evolutionary biologists are familiar with evolutionary units that evolve by vertical descent in a tree-like fashion in single lineages. However, many other kinds of processes contribute to evolutionary diversity. In vertical descent, the genetic material of a particular evolutionary unit is propagated by replication inside its own lineage. In what we call introgressive descent, the genetic material of a particular evolutionary unit propagates into different host structures and is replicated within these host structures. Thus, introgressive descent generates a variety of evolutionary units and leaves recognizable patterns in resemblance networks. We characterize six kinds of evolutionary units, of which five involve mosaic lineages generated by introgressive descent. To facilitate detection of these units in resemblance networks, we introduce terminology based on two notions, P3s (subgraphs of three nodes: A, B, and C) and mosaic P3s, and suggest an apparatus for systematic detection of introgressive descent. Mosaic P3s correspond to a distinct type of evolutionary bond that is orthogonal to the bonds of kinship and genealogy usually examined by evolutionary biologists. We argue that recognition of these evolutionary bonds stimulates radical rethinking of key questions in evolutionary biology (e.g., the relations among evolutionary players in very early phases of evolutionary history, the origin and emergence of novelties, and the production of new lineages). This line of research will expand the study of biological complexity beyond the usual genealogical bonds, revealing additional sources of biodiversity. It provides an important step to a more realistic pluralist treatment of evolutionary complexity.
ISSN: 0027-8424

hal-01544803
https://hal.archives-ouvertes.fr/hal-01544803
DOI : 10.1073/pnas.1206541109

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
BACKGROUND: Cancer/Testis (CT) genes are expressed in male gonads, repressed in most healthy somatic tissues and de-repressed in various somatic malignancies including prostate cancers (PCa). Because of their specific expression signature and their associations with tumor aggressiveness and poor outcomes, CT genes are considered to be useful biomarkers and they are also targets for the development of new anti-cancer immunotherapies. The aim of this study was to identify novel CT genes associated with hormone-sensitive prostate cancer (HSPC), and castration-resistant prostate cancer (CRPC). METHODS: To identify novel CT genes we screened genes for which transcripts were detected by RNA profiling specifically in normal testis and in either HSPC or CRPC as compared to normal prostate and 44 other healthy tissues using GeneChips. The expression and clinicopathological significance of a promising candidate-NR6A1-was examined in HSPC, CRPC, and metastatic site samples using tissue microarrays. RESULTS: We report the identification of 98 genes detected in CRPC, HSPC and testicular samples but not in the normal controls. Among them, cellular levels of NR6A1 were found to be higher in HSPC compared to normal prostate and further increased in metastatic lesions and CRPC. Furthermore, increased NR6A1 immunoreactivity was significantly associated with a high Gleason score, advanced pT stage and cancer cell proliferation. CONCLUSIONS: Our results show that cellular levels of NR6A1 are correlated with disease progression in PCa. We suggest that this essential orphan nuclear receptor is a potential therapeutic target as well as a biomarker of PCa aggressiveness. Prostate © 2013 Wiley Periodicals, Inc.
ISSN: 0270-4137

inserm-00821963
http://www.hal.inserm.fr/inserm-00821963
DOI : 10.1002/pros.22659
PUBMED : 23532770

Éditeur(s) : HAL CCSD
Résumé : International audience
The aim of this study was to optimize the extraction and characterization of lycopene, a carotenoid, from a tropical fruit, Psidium guajava L. and to demonstrate its health benefits. Deionised water, mixed with organic solvents, was used for extraction, and the depletion stage was reached in order to define the number of extractions needed to extract most of the lycopene. Optimum extraction was achieved with petroleum ether combined with guava puree:deionised water ratio of 40% using 15 ml of water. Four extractions were a satisfactory compromise to maximize the amount of lycopene recovered and to minimize the use of organic solvent. Excellent purification of lycopene was obtained by HPLC-VIS detection (470 nm) with acetonitrile/methanol/tetrahydrofuran mobile phase. Characterization was confirmed by FTIR analysis. A modification of the DPPH test made it possible to assess the EC50, thereby ranking lycopene among good antioxidants. As Psidium guajava is already widely used in the food industry, these results support claims for health benefits for products derived from guava.
ISSN: 23192399

hal-01672063
https://hal.univ-antilles.fr/hal-01672063
DOI : 10.9790/2402-1104016773

Éditeur(s) : Université de la Nouvelle-Calédonie
Résumé : Estimating diversity and abundance of fish is fundamental for the understanding of community structure and dynamics of coral reefs. Observations are generally gathered using Underwater Visual Census (UVC). These informations can also be collected by underwater video techniques involving no diver and allowing a high spatial and temporal coverage. The first part of this PhD thesis is a review of publications using underwater video techniques between 1952 and 2012. The second part present two rotating video systems used to study the diversity of ichthyofauna and habitats in the lagoon of New Caledonia: the STAVIRO (for "STAtion VIdeo ROtative") and the MICADO (for "Module d’Imagerie Côtier, Autonome pour le Développement de l’Observation sous-marine"). The third part of this work is a comparison of these techniques with UVCs and an analysis of the “observer effect” for the rotating video techniques. The comparison between rotating video systems and UVC showed that: (i) fish community data collected by UVC and by STAVIRO differed significantly; (ii) species richness and density of large species were not significantly different between techniques; (iii) species richness and density of small species were higher for UVC; (iv) density of fished species was higher for STAVIRO; and (v) only UVC detected significant differences in fish assemblages structure across reef type. The comparison of fish counts obtained from the same videos by different observers showed that for a defined list of species, estimates of species richness and total abundance can be considered as similar between observers with sufficient experiences (> 6 months). The last part of this PhD is an application of rotating video techniques to the study of daily temporal variations of the ichthyofauna. Daily variations were observed depending on the time of day and the tidal state and typical patterns of variations have been described for some species groups. The outcomes of this work bring original insights of new techniques complementary to traditional techniques in order to enhance our understanding of the functioning and dynamic of coral reef.
L’estimation de la diversité et de l’abondance des espèces de poissons est fondamentale pour comprendre la structure des communautés et la dynamique des récifs coralliens. Les observations sont généralement obtenues par des recensements visuels en scaphandre autonome (UVC). Ces informations peuvent également être obtenues de manière originale grâce aux observations issues des techniques vidéo sous-marines modernes sans plongeur qui permettent des couvertures spatiales et temporelles accrues. La première phase de ce travail de thèse synthétise l’ensemble des travaux ayant été effectués avec des techniques vidéo entre 1952 et 2012. La seconde phase, présente deux systèmes vidéo rotatifs complémentaires, utilisés pour étudier la diversité de l’ichtyofaune et des habitats marins dans le lagon de Nouvelle-Calédonie : le STAVIRO (pour « STAtion VIdéo ROtative ») et le MICADO (pour « Module d’Imagerie Côtier, Autonome pour le Développement de l’Observation sous-marine »). La troisième phase de ce travail consiste à comparer ces systèmes vidéo aux UVC puis à examiner l’effet « observateur » inhérent aux techniques vidéo rotatives. Il résulte de cette étude que : (i) les observations des communautés de poissons par UVC et STAVIRO différaient significativement, (ii) la richesse spécifique et la densité des espèces de grande taille n'étaient pas significativement différentes entre les techniques, (iii) la diversité et la densité des espèces de petite taille étaient plus élevés avec les UVC; (iv) la densité des espèces pêchées était plus élevée avec les STAVIRO et (v) seuls les UVC ont détecté des différences de structure des assemblages en fonction du type de récif. L’étude de l’effet « observateur » a montré que sur une liste d’espèces définie, les dénombrements et les identifications des individus peuvent être considérées comme similaires entre observateurs ayant une expérience suffisante (> 6 mois). La dernière phase de ce travail a permis d’appliquer la technique MICADO à l’étude des variations temporelles de l’ichtyofaune d’un site corallien à l’échelle de la journée. Elle a permis de mettre en évidence des variations cycliques journalières en fonction de l’heure et de la marée et des « profils type » de variations ont pu être identifiés pour certains groupes d’espèces. Ce travail de thèse permet ainsi de participer au développement de nouvelles techniques d’observations complémentaires des techniques traditionnelles afin d’enrichir les connaissances du fonctionnement et de la dynamique des écosystèmes coralliens.

Droits : Université de la Nouvelle-Calédonie
http://archimer.ifremer.fr/doc/00189/30050/28536.pdf
http://archimer.ifremer.fr/doc/00189/30050/

Éditeur(s) : HAL CCSD Laboratoire Arago
Résumé : International audience
As it is unlikely that successful settlement is solely a matter of chance (i.e. tofind a suitable habitat), one of the greatest challenges facing the fish larvae is how to locate therelatively rare patches of coral reef habitat on which they settle and ultimately reside as adults.The answer must lie partly in the sensory modalities of fishes at settlement. Habitat selection isonly possible if fish larvae could detect some environmental cues to select a suitable reef habitatat settlement. The present review aims at providing the latest works dealing with informationperception in coral reef fish larvae at settlement. Two decades ago, it was generally assumedthat larval behaviors and sensory abilities at settlement were considered too feeble to significantlyaffect dispersal outcomes. Several recent studies showed that recognition of suitable reefhabitats by fish larvae at settlement is based on a combination of visual, chemical and acousticcues. The first part of our review shows the main advances in the knowledge of visual, chemicaland acoustic cues used by fish larvae to detect an island, a reef, a micro-habitat, a conspecific orsome predators. The second part of our review deals with the effect of imprinting and/or innatecapabilities. The third part focuses on the different cues used at different scales and underlinessome contradictory results about the distance of transmission and detection of chemical andacoustic cues in coral reefs. Finally, as global and regional environmental changes have stressedcoral reefs to such an extent that they are either destroyed or in decline, the fourth part presentsthe effects of both anthropogenic and environmental stressors on information perception andresponse capacities in coral reef fish larvae. If polluted seawater disrupts the larval abilities tofind a suitable reef habitat, fish larvae may spend more time in the planktonic environment,resulting in increased energetic costs and predation risk, and consequently a lower larval settlement.We hypothesise that as the stability of fish communities is dependent, in part, on the stabilityof social interactions, the disruption of “larvae-habitat relationships” can have major consequencesfor larval settlement into adult population with further repercussions for the ecosystemas a whole. Overall, larval settlement of coral reef fish is an excellent example of the complexityof interactions between an organism and its environment as without perceiving environmentalcues, fish larva would have very little chance of selecting a suitable reef habitat. Moreover,understanding the relationship between reef state and settlement potential will allow managementplanning for the maintenance of coral reefs that are increasingly degraded.
ISSN: 0240-8759

hal-01191776
https://hal-univ-perp.archives-ouvertes.fr/hal-01191776

Éditeur(s) : HAL CCSD Inter-Research
Résumé : Precise knowledge of lifetime migrations is vital in exploited fish species, since all essential habitats must be protected to maintain sustainable stock levels. The present study used multi-element otolith fingerprints of the gilthead sea bream Sparus aurata (L.) to discriminate its main juvenile and adult habitats in the Languedoc-Roussillon region (Gulf of Lions, northwest Mediterranean) and infer the lifetime migrations of 12 individuals from the area (11 from the present day and 1 from the Roman era). This allowed for the first time the identification of key habitats for the successful completion of the species' life cycle in the Gulf of Lions, and the connectivity between them. Our results revealed that lagoon use by S. aurata is probably ancient (>2500 yr) and confirmed its current commonness. Yet, although most observed migration patterns were in accordance with the migratory behavior previously described for the species, strong inter-individual variations and new patterns in habitat use were detected. At the juvenile stage, a preference for shallow lagoons with low salinities was evidenced. Nevertheless, the first year of life can also be successfully completed in marine conditions. At the adult stage, lagoon use was shown to occur until at least age 4 yr, with periods of lagoon residency of up to 11 mo in a year, often including winter months. Because overwintering in the lagoons was previously thought to be impossible for S. aurata due to low temperatures, this finding has important implications for future stock management, especially since the species breeds in winter.
Marine Ecology Progress Series

hal-00682003
https://hal.archives-ouvertes.fr/hal-00682003
DOI : 10.3354/meps09444

Éditeur(s) : Université de la Réunion
Résumé : The green turtle (Chelonia mydas) is an emblematic species of marine life. However, nowadays it is subject to many threats (poaching, by-catch). Even if there is deep growing measures for its protection, the green turtle still is an endangered species and it is listed in Appendix I of Washington Convention (CITES). In order to elaborate efficient conservation and management plans, perfect knowledge of green turtle biology, but also of its population structure and their characteristics, are needed. In this thesis, we have assessed genetic structure of green turtle populations in the South-Western Indian Ocean by using genetic tools. In all, 1551 tissue samples have been collected from our study zone and from our control site French Polynesia (37 samples). All kinds if individuals were sampled (except males in reproductive phase) from 15 sampling sites including nesting, foraging, and immature development site. We used both control region of mitochondrial DNA and 6 microsatellite loci to better infer maternal and paternal lineages. We identified 29 haplotypes in the South-Western Indian Ocean. They are distributed in 3 independent and highly divergent clades, including one composed with haplotypes from Atlantic Ocean. For 7 of these haplotypes, it was the first time they were detected in the study zone. Fifteen haplotypes were previously undescribed, distributed in all the 3 clades. These new haplotypes seem to be specific to the South-Western Indian Ocean, which is then an original zone. Besides, we found a high allelic richness. These results show the South-western Indian Ocean is rich and very diversified. This region plays an important role in the global diversity of the species. The South-Western Indian Ocean is one of the two contact zones presently known between the two metapopulations of green turtles (Atlantic-Mediterranean and Indo-Pacific). This contact induces a genetic cline based on CM8 (Atlantic) and C3 (Indo-Pacific) haplotype frequencies. Analysis of the microsatellite differentiation between individuals provides evidence of genetic exchanges between the two metapopulations in the region. The South-Western Indian Ocean participates to green turtle global genetic mixing. Studying the influence of several intrinsic and extrinsic factors on population structuring provides useful information for management plan elaboration. We found no significant difference between genetic structures of foraging females and males, contrary to immature turtles which seem to be organised in 'regional pools'. This organisation could be due to both immature natal homing and influence of oceanic currents. High mitochondrial differentiation of nesting females and low global microsatellite differentiation of our samples indicate male-mediated gene flow among populations of the study zone. The genetic composition of a sampling site presents no significant variation along the year, even if we could notice some trends. Nevertheless, it can be significantly different from a year to an other one. This may result from alternation of distinct populations on the same site. We noticed different evolution in 10 or 20 years of the genetic composition depending on the sampling site. Geographic distance seems not to have significant influence on population structuring concerning microsatellite markers. Nesting females of Saziley Beach (Mayotte Island, Comoros Archipelago) present genetic divergence from females nesting in the two other sampled beaches of this island. The observed population structure shows no contradiction with the organisation of oceanic currents in the South-Western Indian Ocean. Comparing the results from the two genetic markers used, we identified 8 genetic differentiated clusters of turtles in the study zone and at least 6 distinct populations. These clusters constitute 8 potential management units (MUs) which could serve as basis in the elaboration of conservation and management plans.
La tortue verte (Chelonia mydas) constitue l'un des espèces emblématiques de la vie marine, pourtant de nombreuses menaces pèsent de nos jours encore sur sa survie (braconnage, captures accidentelles). Ainsi, malgré l'essor de mesures de protection menées à travers pour sa sauvegarde, la tortue verte constitue une espèce 'en danger d'extinction' et figure dans l'Annexe I de la Convention de Washington (CITES). Afin d'élaborer des plans de gestion et de conservation qui soient efficaces, il est important d'avoir une parfaite connaissance de la biologie de la tortue verte, mais aussi de la structure de ses populations et de leurs caractéristiques. C'est dans ce cadre que s'inscrit la présente étude. L'objectif de cette étude était d'acquérir des connaissances sur la structure des populations de tortues vertes dans le sud-ouest de l'océan Indien grâce à l'utilisation de l'outil génétique. Au total, 1551 échantillons de tissu ont été collectés dans la zone d'étude et dans notre site témoin la Polynésie française (37 échantillons). Toutes les catégories d'individus ont été échantillonnées (excepté les mâles en phase de reproduction) et les 15 sites d'échantillonnage comprennent à la fois des sites de ponte, d'alimentation et de développement pour les immatures. Deux types de marqueurs ont été utilisés : la région contrôle de l'ADN mitochondrial et 6 loci microsatellites, afin d'appréhender au mieux l'apport des lignées maternelles et paternelles. Nous avons pu mettre en évidence la présence dans le sud-ouest de l'océan Indien de 29 haplotypes distincts, appartenant à trois clades fortement divergents dont l'un constitué d'haplotypes originaires de l'océan Atlantique. Parmi ces haplotypes, 7 ont été détectés pour la première fois dans la zone d'étude, et 15 autres n'ont jamais été précédemment décrits chez cette espèce. Ils sont présents dans chacun des 3 clades d'haplotypes. Ces nouveaux haplotypes semblent spécifiques à la région, et en font une zone originale. On observe par ailleurs une grande richesse allélique dans les effectifs analysés. Ces résultats montrent que le sud-ouest de l'océan Indien est une zone riche et très diversifiée. Cette région joue un rôle important dans la diversité génétique globale de l'espèce. Le sud-ouest de l'océan Indien constitue l'une des deux seules zones connues à l'heure actuelle de contact entre les deux métapopulations de tortues vertes (Atlantique-Méditerranée et Indo-Pacifique). Ce contact a entraîné la formation d'un cline génétique portant principalement sur les fréquences relatives des haplotypes CM8 (Atlantique) et C3 (Indo-Pacifique). Les résultats obtenus lors de l'analyse microsatellite de la différenciation entre les individus originaires des deux métapopulations montrent que le sud-ouest de l'océan Indien constitue une zone d'échanges génétiques entre les deux métapopulations, participant au brasage génétique de l'espèce. L'étude de facteurs, intrinsèques et extrinsèques, pouvant influencer la structuration des populations apportent de nombreuses informations qui pourraient s'avérer utiles lors de l'élaboration de plans de gestion. La structure des femelles et des mâles en alimentation ne diffère pas, contrairement à celle des immatures qui semble s'organiser en 'pools régionaux' qui seraient le fruit de l'interaction d'un comportement de philopatrie et d'une influence des courants océaniques. La forte différenciation mitochondriale des femelles en ponte et la très faible différenciation microsatellite observée à l'échelle de la région, indiquent l'existence de flux de gènes via les mâles. La composition génétique d'un site ne varie pas de manière significative au cours de l'année. Par contre, elle peut varier d'une année à l'autre, signifiant l'alternance dans certains sites de ponte de plusieurs populations distinctes. L'évolution de la composition génétique d'un groupe, au cours de 10 ou 20 ans, diffère selon le site considéré. La distance ne semble pas influencer de manière significative la structuration des populations au niveau microsatellite. Les femelles en ponte sur la plage de Saziley (Mayotte) diffèrent génétiquement de celles pondant sur les deux autres plages de l'île. La structure observée des populations est en accord avec l'organisation des courants océanique dans la région. La confrontation des résultats obtenus à partir des deux marqueurs génétiques utilisés, permet la détermination de 8 ensembles génétiquement différenciés dans la zone d'étude et l'identification d'au moins 6 populations distinctes. Ces ensembles constituent autant d'unités de gestion (MUs) potentielles qui pourront servir de base à l'élaboration de plans de gestion et de conservation.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2007/these-3532.pdf
http://archimer.ifremer.fr/doc/00000/3532/

Éditeur(s) : Elsevier
Résumé : Vibrio tapetis is the marine bacterium responsible for the brown ring disease (BRD) affecting die manila clam, Ruditapes philippinarum. Identification of V tapelis has been previously performed using biochemical criteria and serological procedures. All of these methods are time consuming and ill-adapted to individual screening. This study describes an oligonucleotidic probe (Vt446) and two PCR primers, deduced from the 16S rDNA sequence, allowing a fast and specific V tapetis identification using dot blot hybridisation and species-specific primed PCR (SSP-PCR). The probe and primers have been tested on 60 strains, including referenced Vibrio sp., Gram negative and positive bacteria, marine bacteria samples and isolated clam bacteria. For all the 19 V tapetis strains, the results of PCR assays consistently corroborated those of the agglutination tests. The detection limit was estimated to be 10(2) CFU ml(-1). The SSP-PCR method has resulted in V tapetis detection in larvae, m diseased clams, and in asymptomatic broodstock clams that later developed BRD. In conclusion, the two SSP-PCR primers were useful for direct and fast identification of V tapetis strains isolated in clams, and are well suited for the screening of individual R. philippilnarum broodstock clams and larvae from the hatchery. (C) 2005 Elsevier B.V. All rights reserved.
Aquaculture (0044-8486) (Elsevier), 2006-03 , Vol. 253 , N. 1-4 , P. 25-38

Droits : 2005 Elsevier B.V. All rights reserved
http://archimer.ifremer.fr/doc/2006/publication-1692.pdf
DOI:10.1016/j.aquaculture.2005.03.047
http://archimer.ifremer.fr/doc/00000/1692/

Éditeur(s) : HAL CCSD
Résumé : International audience
We used K562 cells sensitive or generated resistant to imatinib or nilotinib to investigate their response to mycophenolic acid (MPA). MPA induced DNA damage leading to cell death with a minor contribution of apoptosis, as revealed by annexin V labeling (up to 25%). In contrast, cell cycle arrest and positive staining for senescence-associated β-galactosidase activity were detected for a large cell population (80%). MPA-induced cell death was potentialized by the inhibition of autophagy and this is associated to the upregulation of apoptosis. In contrast, senescence was neither decreased nor abrogated in autophagy deficient K562 cells. Primary CD34 cells from CML patients sensitive or resistant to imatinib or nilotinib respond to MPA although apoptosis is mainly detected. These results show that MPA is an interesting tool to overcome resistance in vitro and in vivo mainly in the evolved phase of the disease.
Leukemia Research and Treatment

hal-00846103
https://hal.archives-ouvertes.fr/hal-00846103
https://hal.archives-ouvertes.fr/hal-00846103/document
https://hal.archives-ouvertes.fr/hal-00846103/file/Mycophenolic_Acid_Overcomes-accepted.pdf
PUBMED : 23213550

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Motivation: Gene fusion is an important evolutionary process. It can yield valuable information to infer the interactions and functions of proteins. Fused genes have been identified as non-transitive patterns of similarity in triplets of genes. To be computationally tractable, this approach usually imposes an a priori distinction between a dataset in which fused genes are searched for, and a dataset that may have provided genetic material for fusion. This reduces the `genetic space' in which fusion can be discovered, as only a subset of triplets of genes is investigated. Moreover, this approach may have a high-false-positive rate, and it does not identify gene families descending from a common fusion event. Results: We represent similarities between sequences as a network. This leads to an efficient formulation of previous methods of fused gene identification, which we implemented in the Python program FusedTriplets. Furthermore, we propose a new characterization of families of fused genes, as clique minimal separators of the sequence similarity network. This well-studied graph topology provides a robust and fast method of detection, well suited for automatic analyses of big datasets. We implemented this method in the C++ program MosaicFinder, which additionally uses local alignments to discard false-positive candidates and indicates potential fusion points. The grouping into families will help distinguish sequencing or prediction errors from real biological fusions, and it will yield additional insight into the function and history of fused genes.
ISSN: 1367-4803

hal-01544795
https://hal.archives-ouvertes.fr/hal-01544795
DOI : 10.1093/bioinformatics/btt049

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Human exposure to dechloranes has been evaluated in Western Europe (France) with the analysis of Dechlorane Plus (DP), Dechloranes (Dec) 602, 603 and 604, Chlordene Plus (CP) and Mirex in 48 serum samples collected between 2003 and 2005. While no production source has been identified in Europe until now, detection frequencies for all investigated dechloranes were high, except for Dec 604 which was below detection limit for all samples. The mean DP concentration was 1.40±1.40ng/g lipid weight (lw), lower than levels reported in serum from Chinese population, but higher than levels reported in Canadian human milk. To the best of our knowledge, this is the first time that ∑5dechlorane levels are reported for human serum. A specific pattern of contamination was found (Dec 603>DP>Mirex>Dec 602>CP) compared to other biota samples that have been analyzed from Europe, with Dec 603 as the most abundant dechlorane (mean level: 2.61±2.63ng/g lw). Dec 603 and CP levels were correlated with age and with levels of some bioaccumulative organochlorine pesticides (OCPs). These results indicate that bioaccumulation properties should be further investigated and taken in consideration when assessing human exposure to dechloranes. For comparison purposes, polybrominated diphenyl ether (PBDE) levels were also measured for BDE-47, -99, -100, -153 and -154 in the serum samples. As expected, BDE-47 and BDE-153 were the major congeners with mean levels of 2.06±1.80ng/g lw and 1.39±0.97ng/g lw, respectively. The mean ∑5PBDE levels (4.32±2.99ng/g lw) were in the range typical of Western Europe levels, but lower than the mean ∑5dechlorane levels (6.24±4.16ng/g lw). These results indicate that the attention to dechloranes should be continued if research indicates toxicological concerns.
ISSN: 0160-4120

hal-01004642
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01004642
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01004642/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01004642/file/Levelssur dechloranes_and_polybrominated_diphenyl_ethers_accepted.pdf
DOI : 10.1016/j.envint.2013.12.014

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Dietary exposure to pesticide residues may present a risk to public health, especially for sensitive populations such as pregnant women. To characterize this risk, this study assessed chronic dietary exposure to pesticide residues based on the French ELFE cohort. A self-administered food frequency questionnaire (FFQ) about the last three months of pregnancy filled in by pregnant women in 2011 was used in combination with occurrence data from French Total Diet Studies completed by the results of national monitoring programs on pesticide residues in food. The dietary intake of pesticides (μg/kg of body weight/day) was estimated for 14,099 pregnant women with a complete FFQ, for 317 substances under two occurrence scenarios to handle left-censored data: a lower-bound scenario (LB), where undetected results were set to zero, and an upper-bound scenario (UB), where undetected results were set to the detection limit if the substance was expected to be found in food and zero if it was not. The risk was assessed for 284 substances with a toxicological reference value (TRV) and a good coverage level of the diet potentially contributing to pesticide intake. The cumulative risk was also assessed for seven effects on nervous and thyroid systems using the hazard index and the Cumulative Assessment Groups defined by EFSA. Substances with the highest exposure levels under the LB scenario were, in decreasing order, imazalil, piperonyl butoxide, chlorpropham, thiabendazole, iprodione and propargite. Under the LB scenario, only for lindane did women have a statistically significant probability of exceeding the TRV (2.4%). Under the UB scenario, risk could not be excluded for nine other substances. A better management of left-censored data and more sensitive analyses of the main food contributors might help to refine the UB exposure and risk assessments. A statistically significant cumulative risk was found for neurochemical effects related to high intake levels of three organophosphate insecticides (chlorpyrifos, pirimiphos-methyl and dimethoate) mainly detected in fruits and cereals
ISSN: 0160-4120

hal-01319892
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01319892
DOI : 10.1016/j.envint.2016.04.007
PUBMED : 27187793

Éditeur(s) : HAL CCSD John Wiley & Sons
Résumé : International audience
Kisspeptins are now considered key players in the neuroendocrine control of puberty and reproduction, at least in mammals. Most teleosts have two kiss genes, kiss1 and kiss2, but their sites of expression are still poorly documented. As a first step in investigating the role of kisspeptins in the European sea bass, a perciform fish, we studied the distribution of kiss1 and kiss2-expressing cells in the brain of males and females undergoing their first sexual maturation. Animals were examined at early and late in the reproductive season. We also examined the putative expression of estrogen receptors in kiss-expressing cells and, finally, we investigated whether kisspeptins are expressed in the pituitary gland. We show that kiss1-expressing cells were consistently detected in the habenula and, in mature males and females, in the rostral mediobasal hypothalamus. In both sexes, kiss2-expressing cells were consistently detected at the level of the preoptic area, but the main kiss2 mRNA-positive population was observed in the dorsal hypothalamus, above and under the lateral recess. No obvious sexual differences in kiss1 and kiss2 mRNA expression were detected. Additional studies based on confocal imaging clearly showed that most kiss1 mRNA-containing cells of the mediobasal hypothalamus strongly express ERα and slightly express ERβ2. At the pituitary level, both sexes exhibited kiss1 mRNA expression in most FSHβ-positive cells and never in LHβ-positive cells.
ISSN: 0092-7317

hal-00877326
https://hal.archives-ouvertes.fr/hal-00877326
PUBMED : 22886357
DOI : 10.1002/cne.23211

Éditeur(s) : HAL CCSD Society of Environmental Toxicology and Chemistry Press (SETAC)
Résumé : International audience
Tributyltin (TBT) and triphenyltin (TPT) are emblematic endocrine disruptors, which have been mostly studied in gonochoric prosobranchs. Although both compounds can simultaneously occur in the environment, they have mainly been tested separately for their effects on snail reproduction. Because large discrepancies in experimental conditions occurred in these tests, the present study aimed to compare the relative toxicity of TBT and TPT under similar laboratory conditions in the range of 0 ng Sn/L to 600 ng Sn/L. Tests were performed on the simultaneous hermaphrodite Lymnaea stagnalis, a freshwater snail in which effects of TPT were unknown. Survival, shell length, and reproduction were monitored in a 21-d semistatic test. Frequency of abnormal eggs was assessed as an additional endpoint. Triphenyltin hampered survival while TBT did not. Major effects on shell solidity and reproduction were observed for both compounds, reproductive outputs being more severely hampered by TBT than by TPT. Considering the frequency of abnormal eggs allowed increasing test sensitivity, because snail responses to TBT could be detected at concentrations as low as 19 ng Sn/L. However, the putative mode of action of the 2 compounds could not be deduced from the structure of the molecules or from the response of apical endpoints. Sensitivity of L. stagnalis to TBT and TPT was compared with the sensitivity of prosobranch mollusks with different habitats and different reproductive strategies.
Environmental Toxicology and Chemistry

hal-00877955
https://hal.archives-ouvertes.fr/hal-00877955
DOI : 10.1002/etc.2200
PUBMED : 23450754

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Whilst it used to affect mostly intravenous drug users and patients who underwent valvular surgery with suboptimal infection control procedures, fungal endocarditis is now mostly observed in patients with severe immunodeficiency (onco-haematology), in association with chronic central venous access and broad-spectrum antibiotic use. The incidence of fungal endocarditis has probably decreased in most developed countries with access to harm-reduction policies (i.e. needle exchange programmes) and with improved infection control procedures during cardiac surgery. Use of specific blood culture bottles for diagnosis of fungal endocarditis has decreased due to optimisation of media and automated culture systems. Meanwhile, the advent of rapid techniques, including fungal antigen detection (galactomannan, mannan/anti-mannan antibodies and β-1,3-d-glucans) and PCR (e.g. universal fungal PCR targeting 18S rRNA genes), shall improve sensitivity and reduce diagnostics delays, although limited data are available on their use for the diagnosis of fungal endocarditis. New antifungal agents available since the early 2000s may represent dramatic improvement for fungal endocarditis: (i) a new class, the echinocandins, has the potential to improve the management of Candida endocarditis owing to its fungicidal effect on yeasts as well as tolerability of increased dosages; and (ii) improved survival in patients with invasive aspergillosis with voriconazole compared with amphotericin B, and this may apply to Aspergillus sp. endocarditis as well, although its prognosis remains dismal. These achievements may allow selected patients to be cured with prolonged medical treatment alone when surgery is considered too risky.
ISSN: 0924-8579

hal-01118441
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01118441
DOI : 10.1016/j.ijantimicag.2014.07.003
PUBMED : 25178919

Éditeur(s) : HAL CCSD Masson
Résumé : International audience
In French Guiana, the age-standardized incidence rate of cervical cancer is four times higher than in France and the mortality rate 5.5 times higher. A survival study revealed that stage at diagnosis was the main factor influencing the prognosis, showing that early detection is crucial to increase cervical cancer survival. The present study aimed at evaluating the cervical cancer screening rate between 2006 and 2011 by age and for 3-years period in French Guiana. All pap smears realised in French Guiana were analysed in two laboratories allowing exhaustive review of screening data. The screening rate was estimated at about 54% from 2006 to 2011, with a statistical difference between coastal and rural area (56.3% versus 18.7%).Although the methodological difference did not allow comparisons with mainland France, these results could be used to evaluate the impact of organised cervical cancer screening by the French Guiana Association for Organized Screening of Cancers implemented in French Guiana since 2012.
ISSN: 0037-9085

hal-01260391
https://hal.archives-ouvertes.fr/hal-01260391
https://hal.archives-ouvertes.fr/hal-01260391/document
https://hal.archives-ouvertes.fr/hal-01260391/file/2015%2C%20Douine%20-%20Servical%20cancer.pdf

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Haplognathia ruberrima is a cosmopolitan gnathostomulid species found in sulfur bacterial mats in mangroves in Guadeloupe (French West Indies). Haplognathia ruberrima presents a d13C value lower than all measured meiofaunal grazers and lower than the available measured food sources of this environment. This low d13C value can not be due to specific ingestion of 13C-depleted methanogenic bacteria because abundances of those bacteria are reduced in surficial and deep sediments as revealed by d13C of bacterial fatty acid. According to scanning electron microscope observations, no bacterial ectosymbionts were observed at the surface of the gnathostomulids, and transmission electronmicroscope views revealed the absence of bacterial endosymbionts. Energy-dispersive X-ray spectroscopy analysis detected low levels of sulfur (0.32%+-0.8) in biological tissues of H. ruberrima, confirming the absence of thioautotrophic bacterial symbionts in these animals. Consequently, the low d13C value of H. ruberrima can not be due to the presence of sulfur-oxidizing symbionts but more probably to the selective and exclusive consumption of free-living, sulfuroxidizing bacteria
ISSN: 0173-9565

hal-01253239
https://hal.archives-ouvertes.fr/hal-01253239
DOI : 10.1111/maec.12296

Éditeur(s) : Station Biologique de Roscoff
Résumé : The hydrothermal vent shrimp genus Mirocaris is reviewed. Morphological comparison between the two nominal species in the genus, M. fortunata and M. keldyshi, was made based on the re-examination of the holotype and paratypes of Mirocarisfortunata and the paratypes of M. keldyshi. Samples newly collected from various sites on the Mid-Atlantic Ridge were also examined. The validity of the genus Mirocaris has been confirmed. However, our study has revealed that the supposed morphological characters distinguishing M. fortunata and M. keldyshi do not provide significant taxonomic differences and further comparison failed to detect morphological differences between the two taxa. Thus M. keldyshi is synonymized with M. fortunata, and so there is only one single species in the genus Mirocaris. This supports the suggestion by Shank et al. (1999), based on a molecular study, that the two taxa might be conspecific. A redescription of M. fortunata is provided to better establish the morphology of the species. The clarification led us to improve the morphological descriptions of the caridean species associated with vent or seep environments and to reassess the relationships among Mirocaris and the other shrimp taxa in the superfamily Bresilioidea. The generic diagnosis of Mirocaris is emended. Because a number of presumably apomorphic characters are shared by Mirocaris and other alvinocaridid genera, the genus Mirocaris is now assigned to the family Alvinocarididae. The family Mirocarididae is synonymized with the Alvinocarididae and the diagnosis of this family is emended.
Révision du genre Mirocaris, crevette des sources hydrothermales océaniques, redescription de M. fortunata et réexamen du statut de la famille des Alvinocarididae. Le genre Mirocaris, créé pour des crevettes hydrothermales, est révisé. Une étude morphologique comparative des deux espèces Mirocaris fortunata et M. keldyshi, basée sur le réexamen des holo-types et paratypes et sur l'étude de nombreux échantillons provenant de divers sites hydrothermaux de la dorsale médio-atlantique, a été effectuée. La validité du genre Mirocaris est confirmée. Il apparaît que les caractères qui distinguent M. keldyshi et M.fortunata ne sont pas des critères taxonomiques suffisants et une étude morphologique plus poussée n'a pas révélé de différences morphologiques entre les deux taxa. Ceci est en accord avec l'interprétation de Shank et al. (1999) qui, à la suite d'une étude moléculaire, suggèrent la synonymie des deux espèces. Une redescription détaillée de M. fortunata est donnée et les relations entre Mirocaris et les autres genres de la superfamille des Bresilioidea sont discutées. La diagnose générique de Mirocaris est modifiée. Comme plusieurs caractères apomorphes sont partagés par Mirocaris et les autres genres de la famille des Alvinocarididae, le genre Mirocaris est maintenant affecté à cette famille. La famille des Mirocarididae est mise en synonymie avec celle des Alvinocarididae dont la diagnose est modifiée.
CBM - Cahiers de Biologie Marine (0007-9723) (Station Biologique de Roscoff), 2003-03 , Vol. 44 , N. 2 , P. 199-215

Droits : 2003 Station Biologique de Roscoff
http://archimer.ifremer.fr/doc/2003/publication-883.pdf
http://archimer.ifremer.fr/doc/00000/883/

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
The tg(cyp19a1b-GFP) transgenic zebrafish expresses GFP (green fluorescent protein) under the control of the cyp19a1b gene, encoding brain aromatase. This gene has two major characteristics: (i) it is only expressed in radial glial progenitors in the brain of fish and (ii) it is exquisitely sensitive to estrogens. Based on these properties, we demonstrate that natural or synthetic hormones (alone or in binary mixture), including androgens or progestagens, and industrial chemicals induce a concentration-dependent GFP expression in radial glial progenitors. As GFP expression can be quantified by in vivo imaging, this model presents a very powerful tool to screen and characterize compounds potentially acting as estrogen mimics either directly or after metabolization by the zebrafish embryo. This study also shows that radial glial cells that act as stem cells are direct targets for a large panel of endocrine disruptors, calling for more attention regarding the impact of environmental estrogens and/or certain pharmaceuticals on brain development. Altogether these data identify this in vivo bioassay as an interesting alternative to detect estrogen mimics in hazard and risk assessment perspective.
ISSN: 1932-6203

hal-00877371
https://hal.archives-ouvertes.fr/hal-00877371
https://hal.archives-ouvertes.fr/hal-00877371/document
https://hal.archives-ouvertes.fr/hal-00877371/file/Screening_Estrogenic_Activities-accepted.pdf
DOI : 10.1371/journal.pone.0036069