Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Beggiatoaceae, giant sulphur-oxidizing bacteria, are well known to occur in cold and temperatewaters, as well as hydrothermal vents, where they form dense mats on the floor.However, they have never been described in tropical marine mangroves. Here, we describetwo new species of benthic Beggiatoaceae colonizing a marine mangrove adjacent to mangroveroots. We combined phylogenetic and lipid analysis with electron microscopy in orderto describe these organisms. Furthermore, oxygen and sulphide measurements in and exsitu were performed in a mesocosm to characterize their environment. Based on this, two new species, Candidatus Maribeggiatoa sp. and Candidatus Isobeggiatoa sp. inhabiting tropical marine mangroves in Guadeloupe were identified. The species identified as CandidatusMaribeggiatoa group suggests that this genus could harbour a third cluster with organisms ranging from 60 to 120 μm in diameter. This is also the first description of an Isobeggiatoa species outside of Arctic and temperate waters. The multiphasic approach also gives information about the environment and indications for the metabolism of these bacteria. Our study shows the widespread occurrence of members of Beggiatoaceae family and provides new insight in their potential role in shallow-water marine sulphide-rich environments such as mangroves.
ISSN: 1932-6203

hal-01205641
https://hal.univ-antilles.fr/hal-01205641
https://hal.univ-antilles.fr/hal-01205641/document
https://hal.univ-antilles.fr/hal-01205641/file/Beggiatoa%20Plosone2015.pdf
DOI : 10.1371/journal.pone.0117832

Éditeur(s) : World Aquaculture Society, Aquaculture 2006
Résumé : Oysters are among the most familiar of all marine invertebrate taxa. However our knowledge of oyster phylogeny and systematics is fragmentary. This is principally due to the plastic growth patterns of these animals, which result in a wide range of overlapping, ecophenotypic variants that greatly reduce the value of analysis based on shell morphology. Besides that, many intentional or accidental anthropogenic transfers have emphasised this situation. In several cases of misclassification or misidentification of oysters, DNA molecular data, have provided valuable new insights on the tracing of introductions or more generally on the phylogeographic relationships between oyster species. We will illustrate this issue with recent case studies from our lab on several flat and cupped oysters: (1) the Crassostrea gigas – Crassostrea angulata couple of Asian species and their successive introductions in Europe, (2) the new species of cupped oysters, Crassostrea honkongensis, described in Hong-Kong and very divergent from the species Crassostrea gigas it was initially supposed to be, (3) the mangrove oyster Crassostrea gasar that was shown not only to be present along the coasts of Western Africa but also along the Atlantic coasts of South America, and (4) the geographic disjunction between Ostreola stentina, described in the Mediterranean Sea, and the genetically closely related species Ostrea aupouria (from New Zealand) and Ostreola equestris (from Mexico Gulf/Atlantic). At the intra specific level, we will focus on one of the main documented case in Europe, the flat oyster, Ostrea edulis. It is a marine bivalve whose natural geographical distribution ranges along the European Atlantic coast from Norway to Morocco, in addition to the Mediterranean and Black Sea. Studies of allozymes, microsatellites and mitochondrial differentiation over the whole range concluded that a significant divergence existed between Mediterranean and Atlantic populations, together with an isolation-by-distance pattern. However, the average mitochondrial haplotypic diversity displayed a high among populations variance, reflecting smaller effective population size in some locations. Additionally, a ten-fold quantitative difference was observed in the same study in Fst between the mitochondrial and the nuclear genomes, which could be due to sex biased differential reproductive success between males and females. In order to further document this hypothesis, two experiments at the population level were conducted. First, brooding females were sampled in a wild population and the number of males fertilizing a given female estimated. Then, parentage analyses were achieved under experimental conditions: successive mass spawnings were collected from a population of potential genitors kept in hatchery, whose genotypes were known, in order to infer a posteriori the relative contribution of each genitor. Moreover, we aimed to better understand the reproduction dynamics of this species. Several patterns of spawning could be distinguished: unique, successive or extended in time. The different parental contributions and reproductive behaviors observed in these experiments are discussed in the context of the hypothesis of a variance in the reproductive success of males and females and consequences in local and temporal reduced effective population sizes.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2006/acte-3475.pdf
http://archimer.ifremer.fr/doc/00000/3475/

Éditeur(s) : Taylor and Francis
Résumé : A new cumacean genus and species, Thalycrocuma sarradini gen. et sp. nov., belonging to the family Nannastacidae is described from several sites of the Lucky Strike hydrothermal vent field (Mid-Atlantic Ridge, 37N, 1700 m depth). The new genus differs from others in the family by males lacking exopods on the pereopods 3 and 4 and having an antenna with a five-articulate peduncle and a short flagellum. This is the first cumacean species that could be considered, at the moment, as endemic from hydrothermal vent areas. Data on the accompanying fauna including other cumacean species (Cyclaspis longicaudata, Bathycuma brevirostre, Procampylaspis sp. and Makrokylindrus sp.) and some ecological remarks are included. A key for the currently known genera of the family Nannastacidae is provided and the taxonomic position of some genera is discussed.
Marine Biology Research (1745-1000) (Taylor and Francis), 2008-06 , Vol. 4 , N. 3 , P. 180-192

Droits : 2008 Taylor & Francis Group
http://archimer.ifremer.fr/doc/2008/publication-4358.pdf
DOI:10.1080/17451000801898576
http://archimer.ifremer.fr/doc/00000/4358/

Éditeur(s) : HAL CCSD Mineralogical Society of America
Résumé : International audience
In situ mineralization of CO2 in ultramafic rock-hosted aquifers is one of the promising solutions for decreasing CO2 concentrations in the atmosphere. Naturally altered ultramafic rocks suggest that carbonation processes are controlled by local heterogeneities in the structure of the rock and fluid transport at the water-rock interfaces. We studied the role of rock crystallographic anisotropy relative to the global fluid flow direction on the mineralization of CO2 by means of electron microscope analyses from the macro- to the micrometer scale (EBSD-FIB). The sample used for the measurements was a hot pressed olivine core percolated by water enriched in CO2 (pCO2 = 10 MPa) at 180 °C. During the percolation experiment, olivine was dissolved and two types of carbonates, dolomite, and magnesite, were precipitated on olivine surfaces. The results showed that the dissolution of olivine is controlled by its crystallographic properties as shown by the development of etch-pits only on the (010)ol planes and with elongated shapes parallel to the [010]ol axes. In contrast, the precipitation of carbonates is governed by hydrodynamic properties. Carbonates are heterogeneously distributed in the percolated rock. They are mainly located along the moderate (for dolomite) and the minor (for magnesite) flow paths, both oriented parallel to the principal fluid flow direction, which allow carbonates to be supplied with divalent cations (e.g., Ca2+, Mg2+, and Fe2+). In these flow paths, carbonate growth is systematically oriented normal to the flow that facilitates the development of chemical gradients with cationic supersaturation conditions for carbonate precipitation near the walls.In natural systems, the (010)ol planes are parallel to the Moho and the (100)ol planes are vertical; our study suggests that flow of CO2-rich fluids will induce precipitation of carbonates localized along, and preferentially clogging, vertical flow paths while favoring olivine dissolution along horizontal fluid pathways. This dual control of structure and fluid flow on carbonation mechanisms could be an important parameter allowing sustainable CO2 storage in peridotites, while limiting the risks of leakage toward the surface.
ISSN: 0003-004X

hal-01143393
https://hal.archives-ouvertes.fr/hal-01143393
DOI : 10.2138/am-2015-4913

Éditeur(s) : Gauthier-Villars
Résumé : The Scopoletin-Peroxidase fluorescence decay method has been developed using standard additions and a flow injection manifold for hydrogen peroxide (H2O2) determination in marine waters. The limit of detection of the method was optimized using stored milli-Q water with a minimum of 5 nM (3 sigma). The method was found to be linear from 5 to 700 nM, with an approximate relative standard deviation of 10%. This accuracy was verified on both milli-Q and natural waters running systematically duplicate analysis. The validity and the sensitivity of the technique was studied through the influence of pH, salinity and the dissolved organic matter (DOM) concentration. Standard additions avoided all matrix and experimental interferences, making it possible to use this method under any field conditions and on ''humic-rich'' waters. Additionally, the flow injection manifold improved the accuracy and the runtime of the analytical procedure and simplified the field manipulation.
Oceanologica Acta (0399-1784) (Gauthier-Villars), 1995 , Vol. 18 , N. 3 , P. 353-361

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00097/20784/18409.pdf
http://archimer.ifremer.fr/doc/00097/20784/

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Accumulating evidence suggests that developmental exposure to environmental chemicals may modify the course of brain development, ultimately leading to neuropsychiatric / neurodegenerative disorders later in life. In the present study, we assessed the impact of one of the most frequently used pesticides in both residential and agricultural applications - the synthetic pyrethroid cypermethrin (CYP) - on developmental neurotoxicity (DNT). Female mice were perinatally exposed to low doses of CYP (5 and 20 mg/kg body weight) from gestation to postnatal day 15. Behavioral analyses were performed during the offspring's early life and during adulthood. Postnatal analyses revealed that perinatal exposure to CYP disturbed motor development without modifying sensory and communicative skills. We found that later in life, CYP-exposed offspring expressed maladaptive behaviors in response to highly challenging tasks and abnormal sociability. Transcriptomic analyses performed in the offspring's brain at the end of the exposure, highlighted mitochondrial dysfunction as a relevant pathomechanism underlying CYP-induced DNT. Interestingly, several genes involved in proteostasis maintenance were also shown to be dysregulated suggesting that alterations in biogenesis, folding, trafficking and degradation of proteins may significantly contribute to CYP-related DNT. From a regulatory perspective, this study highlights that behavioral and transcriptomic analyses are complementary tools providing useful direction for better DNT characterization, and as such, should be used together more systematically.
ISSN: 1932-6203

hal-01616489
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01616489
DOI : 10.1371/journal.pone.0184475
PUBMED : 29020013

Éditeur(s) : HAL CCSD
Résumé : The Green and Blue infrastructure (Trame verte et bleue ?TVB) is a new conservation policy tool based on the notions of ecological network and corridor. The TVB's implementation process establishes the connection of multi and nested decisional and action levels and needs permanent adjustment to change that is analyzed as adaptive governance mechanisms. The implementation of an adaptive governance is described as an mean to overpass those failures. The literature on adaptive governance gives learning process a central place as it permits to systematically improve policies and practices for an effective preservation of the environment. The aim of this article is to provide a critical perspective on learning processes in adaptive governance. We aim at reintroducing two blind spots. First, knowledge theory frequently forget to consider the strategic issue of knowledge. Second, knowledge theory implicitly recognizes that an actor acts but, it is often true that an actor can «be acted».
ESEE 2013 - Ecological Economics and Institutional Dynamics - 10th International Conference of the European Society for Ecological Economics
Lille, France

hal-01195358
https://hal.archives-ouvertes.fr/hal-01195358
PRODINRA : 226906

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
We isolated and characterized 26 microsatellite loci for Macrorhynchia phoenicea (Busk, 1852), a rather common tropical hydrozoan from the Indo-Pacific. The number of alleles per locus ranged from 4 to 24. The observed heterozygosity ranged from 0.000 to 0.970 and the expected heterozygosity from 0.029 to 0.833. Ten loci were at HardyeWeinberg equilibrium. No pair of loci presented linkage disequilibrium. Transferability of up to 18 loci was positive across four other Aglaopheniidae species from different genera. These loci will be used in studying reef population connectivity for these particular species at the scale of the Indo-Pacific, a promising but little explored research field.
ISSN: 0305-1978

hal-01359419
https://hal.archives-ouvertes.fr/hal-01359419
DOI : 10.1016/j.bse.2015.08.011

Résumé : The consciousness of a necessary international co-operation about the fight against marine pollution is relatively recent. In a first time, the concerned states have contracted, at the universal and regional level, some agreements in a punctual way, to organize this fight. From the 1970th, the United States are going to systematize and rationalize this conventional movement aimed to preserve the marine environnement by the working of a standardizing planning liable to be used in some threatened zones, it is the Activities Programm for the regional seas proceeding from the United States Programm for the Environment. For each regional sea reserved by the Programm ; corresponds a whole appliance contained in an Action Plan. Amid each Action Plan, a juridical appliance is foreseen which enables the riverside states to juridically, institutionally and financially organize their co-operation in touch with the International Organizations of the United States system. [NOT CONTROLLED OCR]
La prise de conscience d'une nécessaire coopération internationale en matière de lutte contre la pollution marine est relativement récente. Dans un premier temps, les Etats concernés ont contracté de manière ponctuelle des accords au niveau universel et régional pour organiser cette lutte. A partir des années 1970, les Nations Unies vont systématiser et rationaliser ce mouvement conventionnel destiné à préserver l'environnement marin par la mise en oeuvre d'une planification normative susceptible d'être employée dans un certain nombre de zones menacées, il s'agit du Programme d'activités pour les mers régionales découlant du Programme des Nations Unies pour l'environnement. Pour chaque mer régionale retenue par le Programme correspond un dispositif d'ensemble contenu dans un Plan d'Action. Au sein de chaque Plan d'Action est prévu un dispositif juridique qui permet aux Etats riverains d'organiser juridiquement, institutionnellement et financièrement leur coopération en liaison avec les organisations Internationales du système des Nations Unies. [OCR NON CONTRÔLE]

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/1981/rapport-4800.PDF
http://archimer.ifremer.fr/doc/00000/4800/

Éditeur(s) : HAL CCSD
Résumé : International audience
F.T. Kützing introduced Cocconeis molesta with only an uninformative description and a poor illustration: C. molesta has small, oblong valves and is an epiphyte. Another species, Cocconeis diaphana, described by William Smith, is said to have larger valves than C. molesta, with frustules that are relatively oblong. Smith described two forms: one with a distinct fascia on its raphe valve (var. β), the other without this feature. A third species, Cocconeis dirupta was described by Gregory, who expressed doubts that it differed from C. diaphana. Finally, Cocconeis molesta var. crucifera Grunow was first introduced in Van Heurck's Atlas but was subsequently treated by Van Heurck as a synonym of C. molesta. No previous account has examined the type material of these species. In this paper, we undertake that task and examine type slides and raw material in order to discriminate these different taxa. We conclude by recognizing three species: Cocconeis molesta Kütz., C. diaphana W.Sm. and C. dirupta W.Greg. Cocconeis diaphana var. β is considered to be a synonym of C. dirupta and C. molesta var. crucifera is considered to be a synonym of C. molesta. Lectotypes are designated for C. diaphana and C. dirupta.
ISSN: 2118-9773

Droits : http://creativecommons.org/licenses/by/
hal-01340453
https://hal-univ-perp.archives-ouvertes.fr/hal-01340453
https://hal-univ-perp.archives-ouvertes.fr/hal-01340453/document
https://hal-univ-perp.archives-ouvertes.fr/hal-01340453/file/329-1709-1-PB.pdf
DOI : 10.5852/ejt.2016.204

Éditeur(s) : Europe Aqauculture Symposium, October 14-17, San Sebastian, Spain
Résumé : Shrimp farming in New-Caledonia faces up to difficulties. A fluctuating quality of broodstock prevents sustainable production of larvae in quantity and quality. The traditional extensive rearing method of broodstock in outdoor earthen ponds used in New Caledonia raises several issues: poor water quality control and biosecurity. Therefore it is fundamental to modify the broodstock culture strategy in order to achieve an easier water quality management and maximal biosecurity. Biofloc technology (BFT) offers easier water quality management, higher natural productivity, higher level of biosecurity, and could be a good alternative. Since 2011 a R&D program started under the supervision of IFREMER in New Caledonia and French Polynesia in order to study and develop biofloc technology for rearing shrimp L. stylirostris broodstock. In a first step we showed that biofloc (BFT) improved significantly the reproductive performances of shrimps and the quality of their larvae compared to Clear Water (CW) or Earthen Pond (EP), with: • A better final survival rate of broodstock from BFT compare to CW. • Females from BFT produced more eggs per spawn and spawned more frequently compared to females from CW or EP. • The larvae from BFT females had a significantly higher survival rate compared to larvae from CW females, respectively 70% (n=4) and 45% (n=4). In a second step we studied the underlying biological mechanisms explaining the better reproductive performance and health status of the broodstock from BFT rearing system, and the better quality of their larvae. We showed that the juvenile shrimp fed actively on biofloc, which represented 60% of their whole food (40% coming from pelleted diet). Biofloc represents a significant source of essential nutrients (vitamins, antioxidants, highly unsaturated fatty acids, …) or dietary bacteria which could act as probiotic. These dietary complements could explain the improved health status (immunity and oxidative status status), the better resistance to oxidative stress and a systematically better survival rate of the shrimp reared in BFT compared to those reared in CW.

Droits : 2014 Ifremer
http://archimer.ifremer.fr/doc/00250/36084/34635.pdf
http://archimer.ifremer.fr/doc/00250/36084/

Éditeur(s) : HAL CCSD WILEY-BLACKWELL Wiley
Résumé : International audience
Connectivity among populations determines the dynamics and evolution of populations, and its assessment is essential in ecology in general and in conservation biology in particular. The robust basis of any ecological study is the accurate delimitation of evolutionary units, such as populations, metapopulations and species. Yet a disconnect still persists between the work of taxonomists describing species as working hypotheses and the use of species delimitation by molecular ecologists interested in describing patterns of gene flow. This problem is particularly acute in the marine environment where the inventory of biodiversity is relatively delayed, while for the past two decades, molecular studies have shown a high prevalence of cryptic species. In this study, we illustrate, based on marine case studies, how the failure to recognize boundaries of evolutionary-relevant unit leads to heavily biased estimates of connectivity. We review the conceptual framework within which species delimitation can be formalized as falsifiable hypotheses and show how connectivity studies can feed integrative taxonomic work and vice versa. Finally, we suggest strategies for spatial, temporal and phylogenetic sampling to reduce the probability of inadequately delimiting evolutionary units when engaging in connectivity studies.
ISSN: 0962-1083

hal-01218810
https://hal.archives-ouvertes.fr/hal-01218810
DOI : 10.1111/mec.13048

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
STUDY QUESTION: Do mild analgesics affect the endocrine system of the human adult testis? SUMMARY ANSWER: Mild analgesics induce multiple endocrine disturbances in the human adult testis in vitro. WHAT IS KNOWN ALREADY: Mild analgesics have recently been incriminated as potential endocrine disruptors. Studies of the effects of these widely used molecules on the androgenic status of men are limited and somewhat contradictory. This prompted us to investigate whether these compounds could alter the adult human testicular function. We therefore assessed in parallel the effects of paracetamol, aspirin and indomethacin on organo-cultured adult human testis and on the NCI-H295R steroid-producing human cell line. STUDY DESIGN, SIZE, DURATION: Adult human testis explants or NCI-H295R adrenocortical human cells were cultured with 10(-4) or 10(-5) M paracetamol, aspirin or indomethacin for 24-48 h. The effect of 10(-5) M ketoconazole, used as an anti-androgenic reference molecule, was also assessed. PARTICIPANTS/MATERIALS, SETTING, METHODS: Testes were obtained from prostate cancer patients, who had not received any hormone therapy. The protocol was approved by the local ethics committee of Rennes, France and informed consent was given by the donors. Only testes displaying spermatogenesis, as assessed by transillumination, were used in this study. Hormone levels in the culture media were determined by radioimmunoassay (testosterone, insulin-like factor 3), Enzyme-Linked Immunosorbent Assay (inhibin B) or Enzyme Immunosorbent Assay [prostaglandin (PG) D2, and PGE2]. Tissues were observed and cells counted using classical immunohistochemical methods. MAIN RESULTS AND THE ROLE OF CHANCE: The three mild analgesics caused multiple endocrine disturbances in the adult human testis. This was particularly apparent in the interstitial compartment. Effective doses were in the same range as those measured in blood plasma following standard analgesic treatment. The production of testosterone and insulin-like factor 3 by Leydig cells was altered by exposure to all these drugs. Inhibin B production by Sertoli cells was marginally affected by aspirin only. Our experiments also revealed that mild analgesics display direct anti-PG activity, which varied depending on the drug used, the dose and the duration of exposure. Nevertheless, associations between the alteration of the PG and testosterone profiles were not systematically observed, suggesting that a combination of mechanisms of endocrine disruption is at play. LIMITATIONS, REASONS FOR CAUTION: Our studies were performed in vitro. WIDER IMPLICATIONS OF THE FINDINGS: We provide the first evidence that direct exposure to mild analgesics can result in multiple endocrine disturbances in the human adult testis. Caution, concerning the consumption of mild analgesics by men, should be strengthened, particularly in high-risk population subgroups such as elite athletes.
ISSN: 0268-1161

inserm-00866016
http://www.hal.inserm.fr/inserm-00866016
PUBMED : 23670170
DOI : 10.1093/humrep/det112

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
A comprehensive inventory of global biodiversity would be greatly improved by automating methods for species delimitation. The Automatic Barcode Gap Discovery method, the Poisson tree processes algorithm and the Generalized mixed Yule coalescent model have been proposed as means of increasing the rate of biodiversity description using single locus data. We applied these methods to explore the diversity within the Aglaopheniidae, a hydrozoan family with many species widely distributed across tropical and tem perate oceans. Our analyses revealed widespread cryptic diversity in this family, almost half of the morpho species presenting several independent evolutionary lineages, as well as support for cases of synonymy. For two common species of this family, Lytocarpia brevirostris and Macrorhynchia phoenicea, we compared the outputs to clustering analyses based on microsatellite data and to nuclear gene phylo genies. For L. brevirostris, microsatellite data were congruent with results of the species delimitation methods, revealing the existence of two cryptic species with Indo Pacific distribution. For M. phoenicea, all analyses confirmed the presence of two cryptic species within the South Western Indian Ocean. Our study suggests that the diversity of Aglaopheniidae might be much higher than assumed, likely related to low dispersal capacities. Sequence based species delimitation methods seem highly valuable to reveal cryptic diversity in hydrozoans; their application in an integrative framework will be very useful in describing the phyletic diversity of these organisms.
ISSN: 1055-7903

hal-01359407
https://hal.archives-ouvertes.fr/hal-01359407
https://hal.archives-ouvertes.fr/hal-01359407/document
https://hal.archives-ouvertes.fr/hal-01359407/file/Postaire-etal2016MolPhylEvol_sp_delim_hydraires_HAL.pdf
DOI : 10.1016/j.ympev.2016.08.013

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Background : Biological communities are normally composed of a few abundant and many rare species. This pattern is particularly prominent in microbial communities, in which most constituent taxa are usually extremely rare. Although abundant and rare subcommunities may present intrinsic characteristics that could be crucial for understanding community dynamics and ecosystem functioning, microbiologists normally do not differentiate between them. Here, we investigate abundant and rare subcommunities of marine microbial eukaryotes, a crucial group of organisms that remains among the least-explored biodiversity components of the biosphere. We surveyed surface waters of six separate coastal locations in Europe, independently considering the picoplankton, nanoplankton, and microplankton/mesoplankton organismal size fractions.Results : Deep Illumina sequencing of the 18S rRNA indicated that the abundant regional community was mostly structured by organismal size fraction, whereas the rare regional community was mainly structured by geographic origin. However, some abundant and rare taxa presented similar biogeography, pointing to spatiotemporal structure in the rare microeukaryote biosphere. Abundant and rare subcommunities presented regular proportions across samples, indicating similar species-abundance distributions despite taxonomic compositional variation. Several taxa were abundant in one location and rare in other locations, suggesting large oscillations in abundance. The substantial amount of metabolically active lineages found in the rare biosphere suggests that this subcommunity constitutes a diversity reservoir that can respond rapidly to environmental change.Conclusions : We propose that marine planktonic microeukaryote assemblages incorporate dynamic and metabolically active abundant and rare subcommunities, with contrasting structuring patterns but fairly regular proportions, across space and time.
ISSN: 0960-9822

hal-01149637
http://hal.upmc.fr/hal-01149637
http://hal.upmc.fr/hal-01149637/document
http://hal.upmc.fr/hal-01149637/file/Logares_et_al_CurrentBiol_accepted.pdf
DOI : 10.1016/j.cub.2014.02.050

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
We aimed to assess the impact of a postoperative drainage after RPN. A retrospective multicentric study included RPN performed at eight centers between 2010 and 2014. Three centers stopped using postoperative drainage early in their RPN experience, whereas other institutions systematically left a drain. Preoperative characteristics, complication rates, need for postoperative imaging or procedure (surgical or radiological) and length of hospital stay were compared between the two groups [drainage (D) and no drainage (ND)]. Among 636 RPNs, 140 were done without drainage (22 %). In the ND group, surgeons were more experienced (> 50 cases: 55.7 vs. 15.1 %; p < 0.0001), and tumors were more complex (RENAL score: 7.6 vs. 6.5; p < 0.0001). Complication rates were similar in both groups (21.9 vs. 20.2 %; p = 0.67). The omission of postoperative drainage did not increase requirement of CT scan (RR = 1.03; 95 % CI 0.64-1.67). Length of hospital stay was shorter in the ND group (4.5 vs. 5.5 days; p = 0.007). There were six urinary fistulas: four in the D group (0.8 %) and two in the ND group (1.4 %; p = 0.49). A CT scan was done to confirm the diagnosis of fistula in every case. In multivariate analysis, the omission of drainage was not associated with increased need of postoperative CT scan or major complications but was a predictor of decreased length of stay. The omission of postoperative drainage does not seem to increase the risk of postoperative complications and could safely be omitted after RPN.
ISSN: 0724-4983

hal-01361502
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01361502
DOI : 10.1007/s00345-015-1721-2
PUBMED : 26511751

Éditeur(s) : HAL CCSD Society for Molecular Biology and Evolution
Résumé : International audience
Complex nongradual evolutionary processes such as gene remodeling are difficult to model, to visualize, and to investigate systematically. Despite these challenges, the creation of composite (or mosaic) genes by combination of genetic segments from unrelated gene families was established as an important adaptive phenomena in eukaryotic genomes. In contrast, almost no general studies have been conducted to quantify composite genes in viruses. Although viral genome mosaicism has been well-described, the extent of gene mosaicism and its rules of emergence remain largely unexplored. Applying methods from graph theory to inclusive similarity networks, and using data from more than 3,000 complete viral genomes, we provide the first demonstration that composite genes in viruses are 1) functionally biased, 2) involved in key aspects of the arm race between cells and viruses, and 3) can be classified into two distinct types of composite genes in all viral classes. Beyond the quantification of the widespread recombination of genes among different viruses of the same class, we also report a striking sharing of genetic information between viruses of different classes and with different nucleic acid types. This latter discovery provides novel evidence for the existence of a large and complex mobilome network, which appears partly bound by the sharing of genetic information and by the formation of composite genes between mobile entities with different genetic material. Considering that there are around 10E31 viruses on the planet, gene remodeling appears as a hugely significant way of generating and moving novel sequences between different kinds of organisms on Earth.
ISSN: 1759-6653

Droits : http://creativecommons.org/licenses/by/
hal-01324848
http://hal.upmc.fr/hal-01324848
http://hal.upmc.fr/hal-01324848/document
http://hal.upmc.fr/hal-01324848/file/Genome%20Biol%20Evol-2014-Jachiet-2195-205.pdf
DOI : 10.1093/gbe/evu168

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Three soil DNA extraction procedures (homemade protocols and commercial kit) varying in their practicability were applied to contrasting soils to evaluate their efficiency in recovering: (i) soil DNA and (ii) bacterial diversity estimated by 16S rDNA pyrosequencing. Significant differences in DNA yield were systematically observed between tested procedures. For certain soils, 10 times more DNA was recovered with one protocol than with the others. About 15 000 sequences of 16S rDNA were obtained for each sample which were clustered to draw rarefaction curves. These curves, as well as the PCA ordination of community composition based on OTU clustering, did not reveal any significant difference between procedures. Nevertheless, significant differences between procedures were highlighted by the taxonomic identification of sequences obtained at the phylum to genus levels. Depending on the soil, differences in the number of genera detected ranged from 1% to 26% between the most and least efficient procedures, mainly due to a poorer capacity to recover populations belonging to Actinobacteria, Firmicutes or Crenarchaeota. This study enabled us to rank the relative efficiencies of protocols for their recovery of soil molecular microbial biomass and bacterial diversity and to help choosing an appropriate soil DNA extraction procedure adapted to novel sequencing technologies.
ISSN: 1751-7915

hal-01546177
https://hal.archives-ouvertes.fr/hal-01546177
DOI : 10.1111/j.1751-7915.2011.00307.x

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
The diffusion of titanium along with Ni, Co and Mn in pure synthetic forsterite has been studied as a function of temperature, oxygen fugacity, crystallographic orientation and chemical potentials in the four-component system MgO–SiO2–TiO2–TiO1·5. In over 100 different experimental conditions, no Ti diffusion profiles with the classical shape of the error function were observed. Instead, the profiles vary between ‘stepped’ at high fO2 (probably owing to diffusion on octahedral sites and trapping in tetrahedral sites), to hockey-stick shapes at low fO2 owing to concentration-dependent diffusion. The profile shapes vary systematically between these end-members according to oxygen fugacity. These profile shapes are also reproduced in experiments using natural San Carlos olivine. The change in profile shape is interpreted to be a function of valence-state change from Ti4+ to Ti3+, shown by a sigmoidal log fO2–diffusivity relationship. To distinguish between Ti4+ and Ti3+ in forsterite, a diffusion profile was also investigated using ‘hydroxylation spectroscopy’ whereby a crystal from a diffusion experiment was hydroxylated by annealing in an H2O-rich fluid at moderate pressure and temperature. The point defects associated with the added structural OH were then determined by infrared spectroscopy, providing evidence for the presence of Ti4+ and Ti3+ at intermediate oxygen fugacity. The transition from Ti4+ to Ti3+ occurs at considerably higher fO2 in these diffusion experiments than in equilibrium experiments in similar systems. Titanium diffusion, qualified using a mobility parameter (M), is fastest along the c-axis, at high activity of silica, low oxygen fugacity and high temperature. The rate of Ti diffusion is broadly similar to those of Mn, Ni and Co, and closer to published rates of Mg self-diffusion in olivine than Si self-diffusion. The observed Ti3+ and Ti4+ diffusion occurs on the M-sites. From statistical examination of the large Mn, Ni and Co diffusivity dataset, we determine that there is a 102/3 dependence of diffusion on aSiO2; the cations diffuse more rapidly at high aSiO2. In addition, diffusivity has a 10–1/8 dependence on fO2, suggested to be the result of increased concentration of loosely bound Ti3+–vacancy pairs, which enhance the mobility of other cations. This behaviour is likely to be present in natural systems where trivalent (e.g. Fe3+, Al3+, Cr3+) and divalent cations diffuse together. Consideration should be given to diffusive interference by highly charged, fast-moving cations when extracting time scales from frozen diffusion profiles.
ISSN: 0022-3530

hal-01531344
https://hal.archives-ouvertes.fr/hal-01531344
DOI : 10.1093/petrology/egw067

Éditeur(s) : HAL CCSD American Chemical Society
Résumé : International audience
The Chromosome-Centric Human Proteome Project (C-HPP) aims at cataloguing the proteins as gene products encoded by the human genome in a chromosome-centric manner. The existence of products of about 82% of the genes has been confirmed at the protein level. However, the number of so-called "missing proteins" remains significant. It was recently suggested that the expression of proteins that have been systematically missed might be restricted to particular organs or cell types, for example, the testis. Testicular function, and spermatogenesis in particular, is conditioned by the successive activation or repression of thousands of genes and proteins including numerous germ cell- and testis-specific products. Both the testis and postmeiotic germ cells are thus promising sites at which to search for missing proteins, and ejaculated spermatozoa are a potential source of proteins whose expression is restricted to the germ cell lineage. A trans-chromosome-based data analysis was performed to catalog missing proteins in total protein extracts from isolated human spermatozoa. We have identified and manually validated peptide matches to 89 missing proteins in human spermatozoa. In addition, we carefully validated three proteins that were scored as uncertain in the latest neXtProt release (09.19.2014). A focus was then given to the 12 missing proteins encoded on chromosomes 2 and 14, some of which may putatively play roles in ciliation and flagellum mechanistics. The expression pattern of C2orf57 and TEX37 was confirmed in the adult testis by immunohistochemistry. On the basis of transcript expression during human spermatogenesis, we further consider the potential for discovering additional missing proteins in the testicular postmeiotic germ cell lineage and in ejaculated spermatozoa. This project was conducted as part of the C-HPP initiatives on chromosomes 14 (France) and 2 (Switzerland). The mass spectrometry proteomics data have been deposited with the ProteomeXchange Consortium under the data set identifier PXD002367
ISSN: 1535-3893

hal-01187320
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01187320
DOI : 10.1021/acs.jproteome.5b00170
PUBMED : 26168773