Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
ISSN: 0003-4975

hal-01563338
http://hal.univ-brest.fr/hal-01563338
DOI : 10.1016/j.athoracsur.2016.03.093
PUBMED : 27262916

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
ISSN: 1752-0894

hal-01667978
https://hal.archives-ouvertes.fr/hal-01667978
DOI : 10.1038/s41561-017-0028-x

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
Marine protist diversity inventories have largely focused on planktonic environments, while benthic protists have received relatively little attention. We therefore hypothesize that current diversity surveys have only skimmed the surface of protist diversity in marine sediments, which may harbor greater diversity than planktonic environments. We tested this by analyzing sequences of the hypervariable V4 18S rRNA from benthic and planktonic protist communities sampled in European coastal regions. Despite a similar number of OTUs in both realms, richness estimations indicated that we recovered at least 70% of the diversity in planktonic protist communities, but only 33% in benthic communities. There was also little overlap of OTUs between planktonic and benthic communities, as well as between separate benthic communities. We argue that these patterns reflect the heterogeneity and diversity of benthic habitats. A comparison of all OTUs against the Protist Ribosomal Reference database showed that a higher proportion of benthic than planktonic protist diversity is missing from public databases; similar results were obtained by comparing all OTUs against environmental references from NCBI's Short Read Archive. We suggest that the benthic realm may therefore be the world's largest reservoir of marine protist diversity, with most taxa at present undescribed.
ISSN: 0168-6496

hal-01383722
http://hal.upmc.fr/hal-01383722
http://hal.upmc.fr/hal-01383722/document
http://hal.upmc.fr/hal-01383722/file/Forster_2016_Benthic_protists.pdf
DOI : 10.1093/femsec/fiw120

Éditeur(s) : HAL CCSD
Résumé : International audience
Conférence MISTRALS PAELOMEX
Montpellier, France

hal-01683548
https://hal-univ-tlse2.archives-ouvertes.fr/hal-01683548

Éditeur(s) : HAL CCSD The Company of Biologists
Résumé : International audience
The ability to produce sound has been known for decades inBalistidae. Sounds of many species have been recorded and a varietyof sound-producing mechanisms have been proposed, includingteeth stridulation, collision of the buccal teeth and movements of thefins. The best-supported hypothesis involves movements of thepectoral fin against the lateral part of the swimbladder, called adrumming membrane. In this study, we describe for the first time thesounds made by the blackbar triggerfish Rhinecanthus aculeatus,which are like short drum rolls with an average duration of 85 ms,193 Hz dominant frequency and 136 dB SPL level at 3 cm distance.The sounds are a series of pulses that result from alternate sweepingmovements of the right and left pectoral fins, which push a system ofthree scutes that are forced against the swimbladder wall. Pulses fromeach fin occur in consecutive pairs. High-speed videos indicate thateach pulse consists of two cycles. The first part of each cyclecorresponds to the inward buckling of the scutes, whereas the secondpart of the cycle corresponds to an apparent passive recoil of thescutes and swimbladder wall. This novel sound productionmechanism is probably found in many members of Balistidaebecause these peculiar scutes occur in other species in the family.Comparison of sound characteristics from fishes of different sizesshows that dominant frequency decreases with size in juveniles butnot in adults.KEY WORDS: Acoustic, Communication, Swimbladder
ISSN: 00220949

hal-01472506
https://hal-univ-perp.archives-ouvertes.fr/hal-01472506
DOI : 10.1242/jeb.146514

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Microalgae in the division Haptophyta play key roles in the marine ecosystem and in global biogeochemical processes. Despite their ecological importance, knowledge on seasonal dynamics, community composition and abundance at the species level is limited due to their small cell size and few morphological features visible under the light microscope. Here, we present unique data on haptophyte seasonal diversity and dynamics from two annual cycles, with the taxonomic resolution and sampling depth obtained with high-throughput sequencing. From outer Oslofjorden, S Norway, nano- and picoplanktonic samples were collected monthly for 2years, and the haptophytes targeted by amplification of RNA/cDNA with Haptophyta-specific 18S rDNA V4 primers. We obtained 156 operational taxonomic units (OTUs), from c. 400.000 454 pyrosequencing reads, after rigorous bioinformatic filtering and clustering at 99.5%. Most OTUs represented uncultured and/or not yet 18S rDNA-sequenced species. Haptophyte OTU richness and community composition exhibited high temporal variation and significant yearly periodicity. Richness was highest in September-October (autumn) and lowest in April-May (spring). Some taxa were detected all year, such as Chrysochromulina simplex, Emiliania huxleyi and Phaeocystis cordata, whereas most calcifying coccolithophores only appeared from summer to early winter. We also revealed the seasonal dynamics of OTUs representing putative novel classes (clades HAP-3-5) or orders (clades D, E, F). Season, light and temperature accounted for 29% of the variation in OTU composition. Residual variation may be related to biotic factors, such as competition and viral infection. This study provides new, in-depth knowledge on seasonal diversity and dynamics of haptophytes in North Atlantic coastal waters. See also the Perspective by Massana
ISSN: 0962-1083

hal-01545321
https://hal.archives-ouvertes.fr/hal-01545321
DOI : 10.1111/mec.13160

Éditeur(s) : HAL CCSD Oldendorf/Luhe
Résumé : International audience
Large filamentous sulfur-oxidizing bacteria belonging to the Beggiatoacae family can cover large portions of shallow marine sediments surrounding mangroves in Guadeloupe (French West Indies). In order to assess the importance of Beggiatoa mats as an infaunal food source, observations were conducted of the area within mats and at increasing distances from mats. We used natural isotopic compositions and a C-13 enrichment study. Both revealed an ingestion of bacterial mats by associated meiofauna, dominated by rotifers and to a smaller extent by small polychaetes and nematodes. Compared to adjacent sites, sediment covered by bacterial mats presented a higher abundance of diatoms, whereas the total biomass of bacteria did not vary. This constant bacterial abundance suggests that the proportion of organic matter represented by sulfur bacteria is limited compared to the fraction of total bacteria. There was no significant difference in infaunal abundance in mats, suggesting that the availability of this chemosynthetic food resource had a limited local effect. Grazers presented a delta C-13 value increasing with distance from the mat. However, isotopic composition of phospholipid-derived fatty acids specific for diatoms and bacteria revealed that this change is related to modifications of delta C-13 dietary components rather than to changes in diet composition. These complementary methods revealed that the occurrence of sulfur-oxidizing bacterial mats does not necessarily affect grazer abundance and importance of bacteria in their diet. Despite its wide occurrence, Beggiatoa mats would consequently have a minor influence on the structure of the mangrove food web.
ISSN: 0171-8630

hal-01545912
https://hal.archives-ouvertes.fr/hal-01545912
DOI : 10.3354/meps11035

Éditeur(s) : HAL CCSD
Résumé : International audience
EGU General Assembly 2015
Vienne, Austria

hal-01286324
https://hal.archives-ouvertes.fr/hal-01286324
BIBCODE : 2015EGUGA..1713337U

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Digestive tubules of Strombidae are composed by three cell types: digestive cells, vacuolated cells, and crypt cells. The last one is characterized by the presence of intracellular granules identified as spherocrystals. Such structures are known to occur in basophilic cells of gastropod digestive gland, where they are supposed to be involved in the regulation of some minerals and in detoxification. In this study, energy-dispersive X-ray analysis (EDX) and energy filtered transmission electron microscopy (EFTEM) were used to determine the elemental content of spherocrystals in two Strombidae, Strombus gigas and Strombus pugilis. In freshly collected individuals of both species, the following elements were detected: Ca, Fe, Mg, P, and Zn. Aluminum and Mn were also detected in S. gigas. Their presence in spherocrystals indicates that, in Strombidae, spherocrystals are involved in the regulation of minerals and essential trace metals. In order to answer the question ''are spherocrystals involved in nonessential trace metals scavenging?,'' artificial cadmium and lead exposure by both waterborne and dietary pathways was applied to S. pugilis. No evidence of cadmium (Cd(NO3)2) or lead (Pb(NO3)2) provided by food was found in spherocrystals. Cadmium provided in water (Cd(NO3)2 and CdCl2) causes structural modifications of the digestive gland; however, this element was not trapped in spherocrystals. These results suggest that spherocrystals are not involved in detoxification of such nonessential trace metals.
ISSN: 1059-910X

hal-00743762
https://hal.univ-antilles.fr/hal-00743762
DOI : 10.1002/jemt.21073

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Aims: The aims of this study were to compare short-and long-term outcomes for clinical T2N0 oesophageal cancer with analysis of (i) primary surgery (S) versus neoadjuvant therapy plus surgery (NS), (ii) squamous cell carcinoma and adenocarcinoma subsets; and (iii) neoadjuvant chemoradiotherapy versus neoadjuvant chemotherapy.Methods: Data were collected from 30 European centres from 2000 to 2010. Among 2944 included patients, 355 patients (12.1%) had cT2N0 disease; 285 (S) and 70 (NS), were compared in terms of short-and long-term outcomes. Propensity score matching analyses were used to compensate for differences in baseline characteristics.Results: No significant differences between the groups were shown in terms of in hospital morbidity and mortality. Nodal disease was observed in 50% of S-group at the time of surgery, with 20% pN2/N3. Utilisation of neoadjuvant therapy was associated with significant tumour downstaging as reflected by increases in pT0, pN0 and pTNM stage 0 disease, this effect was further enhanced with neoadjuvant chemoradiotherapy. After adjustment on propensity score and confounding factors, for all patients and subset analysis of squamous cell and adenocarcinoma, neoadjuvant therapy had no significant effect upon survival or recurrence (overall, loco-regional, distant or mixed) compared to surgery alone. There were no significant differences between neoadjuvant chemotherapy and chemoradiotherapy in short-or long-term outcomes.Conclusion: The results of this study suggest that a surgery alone treatment approach should be recommended as the primary treatment approach for cT2N0 oesophageal cancer despite 50% of patients having nodal disease at the time of surgery.
ISSN: 0959-8049

hal-01666517
https://hal.univ-lorraine.fr/hal-01666517
DOI : 10.1016/j.ejca.2015.11.024

Éditeur(s) : HAL CCSD Springer
Résumé : International audience
We present here a synthesis of the evolution of rifted continental margin systems in the Gulf of Aden. These margins are volcanic to the west of the Gulf of Aden, where they are influenced by the Afar hotspot, and non-volcanic east of longitude 46° E. The combined use of magnetics, gravity, seismic reflection, field observations (tectonic, stratigraphic and sedimentological) and oil well data allowed us to obtain better constraints on the timing of continental rifting and seafloor spreading. From the Permo-Triassic to the Oligocene, the Arabian-African plate was subject to distributed extension, probably due, at least from the Cretaceous, to tensile stresses related to the subduction of the Tethysian slab in the north. In Late Eocene-Early Oligocene, 34-33 Ma ago, rifting started to localise along the future area of continental breakup. Initially guided by the inherited basins, continental rifting then occurred synchronously over the entire gulf before becoming localised on the northern and southern borders of the inherited grabens, in the direction of the Afar hotspot. In the areas with non-volcanic margins (in the east), the faults marking the end of rifting trend parallel to the inherited grabens. Only the transfer faults cross-cut the inherited grabens, and some of these faults later developed into transform faults. The most important of these transform faults follow a Precambrian trend. Volcanic margins were formed in the west of the Gulf, up to the Guban graben in the southeast and as far as the southern boundary of the Bahlaf graben in the northeast. Seaward dipping reflectors can be observed on many oil industry seismic profiles. The influence of the hotspot during rifting was concentrated on the western part of the gulf. Therefore, it seems that the western domain was uplifted and eroded at the onset of rifting, while the eastern domain was characterised by more continuous sedimentation. The phase of distributed deformation was followed by a phase of strain localisation during the final rifting stage, just before formation of the Ocean-Continent Transition (OCT), in the most distal graben (DIM graben). About 20 Ma ago, at the time of the continental break-up, the emplacement of the OCT started in the east with exhumation of the subcontinental mantle. Farther west, the system was heated up by the strong influence of the Afar hotspot, which led to breakup with much less extension. In the Gulf of Aden (s.str), up to the Shukra El Sheik fracture zone, oceanic spreading started 17.6 Ma ago. West of this fracture zone, oceanic accretion started 10 Ma ago, and 2 Ma ago in the Gulf of Tadjoura. Post-rift deformation of the eastern margins of the Gulf of Aden can be seen in the distal and proximal domains. Indeed, the substantial post-rift uplift of these margins could be associated with either the continental break-up, or activity of the Afar hotspot and related volcanic/magmatic activity. Uplift of the northern proximal margin was still active (e.g. stepped beach rocks exposed at 60 m of 2 Ma; 30 m of 35,200 years; 10 and 2 m) and active volcanoes can be inferred at depths of between 70 and 200 km beneath the margin (at 5-10 km distance from the coast). On the distal margin, heat flow measurements show a high value that is associated with post-rift volcanic activity and the development of a volcano (with flows and sills) shortly after the formation of the OCT. The Afar hotspot is therefore important for several reasons. It allows the localisation of deformation along the Red Sea/Aden system and the rapid opening of the Gulf after the continental break-up; its influence also seems to persist during the post-rift period.
ISSN: 1866-7411

hal-01053089
https://hal.archives-ouvertes.fr/hal-01053089
DOI : 10.1007/s12517-011-0475-4

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Cold seeps have recently been discovered in the Nile deep-sea fan (Eastern Mediterranean), and data regarding associated fauna are still scarce. In this study, two bivalve species associated with carbonate crusts and reduced sediment are identified based on sequence analysis of their 18S and 28S rRNAencoding genes, and associated bacterial symbioses are investigated using 16S rRNA gene sequencing and microscopy-based approaches. The specimens are closely related to Myrtea spinifera and Thyasira flexuosa, two species previously documented at various depths from other regions but not yet reported from the Eastern Mediterranean. Both species harbour abundant gammaproteobacterial endosymbionts in specialized gill epithelial cells. The Myrtea-associated bacterium is closely related to lucinid symbionts from both deep-sea and coastal species, whereas the Thyasira-associated bacterium is closely related to the symbiont of a T. flexuosa from coastal waters off the U.K. An epsilonproteobacterial sequence has also been identified in Thyasira which could correspond to a helicoid-shaped morphotype observed by electron microscopy, but this was not confirmed using fluorescent in situ hybridization. Virus-like particles were observed within some symbionts in Thyasira, mostly in bacteriocytes localized close to the ciliated zone of the gill filament. Overall, results indicate that very close relatives of shallow species M. spinifera and T. flexuosa occur at cold seeps in the Eastern Mediterranean and harbour chemoautotrophic symbioses similar to those found in their coastal relatives.
ISSN: 0173-9565

hal-00743765
https://hal.univ-antilles.fr/hal-00743765
DOI : 10.1111/j.1439-0485.2010.00413.x

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
A new genus and species of deep-sea eelpout (Zoarcidae), Barbapellis pterygalces, is herein described from a single adult female specimen carrying eggs and measuring 204 mm in total length. It was collected on the eastern Antarctic continental slope, off Terre Ad,lie, at ca. 1,200 m depth, on muddy bottom. Barbapellis is placed in the subfamily Gymnelinae and can be distinguished from all other genera by morphological characters unusual in zoarcids as well as by molecular barcoding. The genus is characterized by the presence of a complex system of cephalic skin crests and flaps, especially well developed around the mouth. A new terminology is proposed for the eleven crests and sevenfolds described. The skin folds may be used for foraging on muddy sea bottoms. The genus is also characterized by large, flexible, and highly palmate pectoral fins. The designation of the new genus is discussed.
ISSN: 0722-4060

hal-01544913
https://hal.archives-ouvertes.fr/hal-01544913
DOI : 10.1007/s00300-011-1057-3

Éditeur(s) : HAL CCSD Oldendorf/Luhe
Résumé : International audience
Non-calcifying photosynthetic anthozoans have emerged as a group that may thrive under high carbon dioxide partial pressure (pCO(2)) conditions via increased productivity. However, the physiological mechanisms underlying this potential success are unclear. Here we investigated the impact of high pCO(2) on the dissolved inorganic carbon (DIC) use in the temperate sea anemone Anemonia viridis. We assessed the impacts of long-term exposure to high pCO(2), i.e. sampling in situ natural CO2 vents (Vulcano, Italy), and short-term exposure, i.e. during a 3 wk controlled laboratory experiment. We focused on photo-physiological parameters (net photosynthesis rates, chlorophyll a content and Symbiodinium density) and on carbonic anhydrase (CA) activity, an enzyme involved in the energy-demanding process of DIC absorption. Long-term exposure to high pCO(2) had no impact on Symbiodinium density and chlorophyll a content. In contrst, short-term exposure to high pCO(2) induced a significant reduction in Symbiodinium density, which together with unchanged net photosynthesis resulted in the increase of Symbiodinium productivity per cell. Finally, in both in situ long-term and laboratory short-term exposure to high pCO(2), we observed a significant decrease in the CA activity of sea anemones, suggesting a change in DIC use (i.e. from an HCO3- to a CO2 user). This change could enable a shift in the energy budget that may increase the ability of non-calcifying photosynthetic anthozoans to cope with ocean acidification.
ISSN: 0171-8630

hal-01546163
https://hal.archives-ouvertes.fr/hal-01546163
DOI : 10.3354/meps11916

Éditeur(s) : HAL CCSD Institute of Electrical and Electronics Engineers
Résumé : International audience
This paper presents our response to the first interna- tional challenge on Facial Emotion Recognition and Analysis. We propose to combine different types of features to automatically detect Action Units in facial images. We use one multi-kernel SVM for each Action Unit we want to detect. The first kernel matrix is computed using Local Gabor Binary Pattern histograms and a histogram intersection kernel. The second kernel matrix is computed from AAM coefficients and an RBF kernel. During the training step, we combine these two types of features using the recently proposed SimpleMKL algorithm. SVM outputs are then averaged to exploit temporal information in the sequence. To eval- uate our system, we perform deep experimentations on several key issues: influence of features and kernel function in histogram- based SVM approaches, influence of spatially-independent in- formation versus geometric local appearance information and benefits of combining both, sensitivity to training data and interest of temporal context adaptation. We also compare our results to those of the other participants and try to explain why our method had the best performance during the FERA challenge.
ISSN: 1083-4419

hal-00731864
http://hal.upmc.fr/hal-00731864
http://hal.upmc.fr/hal-00731864/document
http://hal.upmc.fr/hal-00731864/file/senechal12tsmc_preprint.pdf
DOI : 10.1109/TSMCB.2012.2193567

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
Forest ecosystems have integral roles in climate stability, biodiversity and economic development. Soil stewardship is essential for sustainable forest management. Organic matter (OM) removal and soil compaction are key disturbances associated with forest harvesting, but their impacts on forest ecosystems are not well understood. Because microbiological processes regulate soil ecology and biogeochemistry, microbial community structure might serve as indicator of forest ecosystem status, revealing changes in nutrient and energy flow patterns before they have irreversible effects on long-term soil productivity. We applied massively parallel pyrosequencing of over 4.6 million ribosomal marker sequences to assess the impact of OM removal and soil compaction on bacterial and fungal communities in a field experiment replicated at six forest sites in British Columbia, Canada. More than a decade after harvesting, diversity and structure of soil bacterial and fungal communities remained significantly altered by harvesting disturbances, with individual taxonomic groups responding differentially to varied levels of the disturbances. Plant symbionts, like ectomycorrhizal fungi, and saprobic taxa, such as ascomycetes and actinomycetes, were among the most sensitive to harvesting disturbances. Given their significant ecological roles in forest development, the fate of these taxa might be critical for sustainability of forest ecosystems. Although abundant bacterial populations were ubiquitous, abundant fungal populations often revealed a patchy distribution, consistent with their higher sensitivity to the examined soil disturbances. These results establish a comprehensive inventory of bacterial and fungal community composition in northern coniferous forests and demonstrate the long-term response of their structure to key disturbances associated with forest harvesting. The ISME Journal (2012) 6, 2199-2218; doi:10.1038/ismej.2012.84; published online 2 August 2012
ISSN: 1751-7362

hal-01546179
https://hal.archives-ouvertes.fr/hal-01546179
DOI : 10.1038/ismej.2012.84

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
Carbon is transported from Earth's surface into its interior at subduction zones. Carbonates in sediments overlying hydrothermally altered rocks (including serpentinites) within the subducted slab are the main carriers of this carbon1. Part of the carbon is recycled back to the surface by volcanism, but some is transferred to the deep Earth1, 2. Redox transformations during shallow subduction control the transfer and long-term fate of carbon, but are poorly explored1, 3. Here we use carbon stable isotopes and Raman spectroscopy to analyse the reduction of carbonate in an exhumed serpentinite-sediment contact in Alpine Corsica, France. We find that highly crystalline graphite was formed during subduction metamorphism and was concentrated in the sediment, within a reaction zone in direct contact with the serpentinite. The graphite in this reaction zone has a carbon isotopic signature (δ13C) of up to 0.8±0.1‰, similar to that of the original calcite that composed the sediments, and is texturally associated with the calcium-bearing mineral wollastonite that is also formed in the process. We use mass-balance calculations to show that about 9% of the total carbonaceous matter in the sedimentary unit results from complete calcite reduction in the reaction zone. We conclude that graphite formation, under reducing and low-temperature conditions, provides a mechanism to retain carbon in a subducting slab, aiding transport of carbon into the deeper Earth.
ISSN: 1752-0894

hal-00903464
https://hal.archives-ouvertes.fr/hal-00903464
DOI : 10.1038/NGEO1827

Éditeur(s) : HAL CCSD
Résumé : International audience
Symbiosis is a widespread phenomenon in the biosphere. In marine benthic environments breakdown of symbiosis is responsible for coral bleaching and dramatically affects coral reef ecosystems functioning [1]. In the water column, planktonic organisms are key component of pelagic ecosystems and a number of species form mutualistic association with microalgae forming a photosymbiosis [2]. Here we intended to investigate the genetic basis of photosymbiosis, through a transcriptomic approach on marine plankton organisms. We focused more specifically on associations occurring between radiolarian host (protist, zooplankton) and dinoflagellates symbiont (protist, phytoplankton) living inside the host cell. It has recently been highlighted that these holobionts are widespread in oligotrophic open oceans and there are also evidences of their fundamental implication in biogeochemical carbon, silica and strontium cycles [3, 4, 5, 6]. RNA-seq technologies allow obtaining an unprecedented amount of data for unicellular organisms isolated from the environment [7]. The study of such non-model holobionts datasets requires de novo assembly, which implies considerable computational resources and the potential production of chimeric sequences [8, 9].We therefore developed an original strategy aiming at accelerating and improving de novo assembly for holobiont datasets. We chose SIMKA [10] a fast kmer-based method initially developed to estimate the similarity between numerous metagenomic datasets, and which has been recently adapted to extract their common sequences. As our symbionts are identified, we used SIMKA to compare our holobionts transcriptomes to publicly available dinoflagellates transcriptomes [11] generating two datasets, one composed of reads from the symbionts and another with reads from the host (for which no reference data are currently available). Independent assemblies were then performed in parallel, accelerating the study process, and minimizing the proportion of resulting chimeric sequences. Our strategy produced a unique and comprehensive genomic dataset for Radiolaria [12, 13], and offers a pragmatic, large scale, comparison strategy to assemble and study holobionts [9]. Our new sequences obtained from holobionts study will be used for phylogenomics investigation, as reference for environmental metagenomic studies and ultimately to understand and characterize the molecular basis of symbiotic relationships in the plankton.Bibliografic references :[1] Simon K. Davy, Denis Allemand, and Virginia M. Weis. “Cell Biology of Cnidarian-Dinoflagellate Symbiosis”. In: Microbiology and Molecular Biology Reviews 76.2 (June 1, 2012), pp. 229–261. issn: 1092-2172, 1098- 5557. doi: 10.1128/MMBR.05014-11.[2] Janouškovec, J. et al. “Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics”. in: PNAS 201614842 (2016). doi:10.1073/pnas.1614842114[3] Tristan Biard et al. “In situ imaging reveals the biomass of giant protists in the global ocean”. In: Nature advance online publication (Apr. 20, 2016). issn: 0028-0836. doi: 10.1038/nature17652.[4] Lionel Guidi et al. “Plankton networks driving carbon export in the olig- otrophic ocean”. In: Nature 532.7600 (Apr. 28, 2016), pp. 465–470. issn: 0028-0836. doi: 10.1038/nature16942.[5] Diane K. Stoecker et al. “Acquired phototrophy in aquatic protists”. In: Aquatic Microbial Ecology 57.3 (Nov. 24, 2009), pp. 279–310. doi: 10.3354/ame01340.[6] Johan Decelle et al. “An original mode of symbiosis in open ocean plankton”. In: Proceedings of the National Academy of Sciences 109.44 (Oct. 30, 2012), pp. 18000–18005. issn: 0027-8424, 1091-6490. doi: 10. 1073/pnas.1212303109.[7] Sergio Balzano et al. “Transcriptome analyses to investigate symbiotic relationships between marine protists”. In: Frontiers in Microbiology 6 (Mar. 17, 2015). issn: 1664-302X. doi: 10.3389/fmicb.2015.00098.[8] Li, B. et al. “Evaluation of de novo transcriptome assemblies from RNA-Seq data”. In: Genome Biology 15, 553 (2014).[9] Sangwan, N., Xia, F. & Gilbert, J. A. “Recovering complete and draft population genomes from metagenome datasets”. In: Microbiome 4, 8 (2016).[10] Gaëtan Benoit et al. “Multiple comparative metagenomics using mul- tiset k -mer counting”. In: PeerJ Computer Science 2 (Nov. 14, 2016). doi: 10.7717/peerj-cs.94.[11] Patrick J. Keeling et al. “The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing”. In: PLOS Biol 12.6 (June 2014), e1001889. issn: 1545-7885. doi: 10.1371/journal.pbio.1001889.[12] Burki, F. et al. “Evolution of Rhizaria: new insights from phylogenomic analysis of uncultured protists”. In BMC Evolutionary Biology 10, 377 (2010).
International Conference on Holobionts
Paris, France

hal-01575069
https://hal.inria.fr/hal-01575069

Éditeur(s) : HAL CCSD
Résumé : International audience
La lagune de la Manche-à-Eau, écosystème d'eau saumâtre est soumis à la marée, aux alizés et aux ouragans. La carte IGN de 2004 est quadrillée selon une maille de 90 m pour placer 37 points dans un SIG et les borner sur le terrain avec un GPS. D'après les photographies aériennes, le dessin des contours rend possible le suivi morphologique depuis 1950. La profondeur est mesurée à 1437 points avec une perche et une sonde bathymétrique. L'orientation des courants est établie au flot et au jusant avec des penons fixés aux points, et une boussole. Les masses d'eau entrantes et sortantes permettent le calcul du volume d'eau renouvelé à chaque marée. Le suivi cartographique montre, une stabilisation des contours et de l'île due à " l'effet bouclier " et au sol (tourbe racinaire), et une agrégation/désagrégation des îlots selon le passage des ouragans. D'après la bathymétrie actuelle, le comblement de la lagune et le creusement des chenaux sont constatés. Les courants généraux sont gouvernés en surface par les alizés, vent de SSE-NNO et par le va-et-vient de la marée. Les descentes et remontées d'eau obligent ceux-ci à emprunter en profondeur les passages situés le long des berges et autour des dépressions et des hauts-fonds. Le volume d'eau renouvelé à chaque marée (14,8 %) combiné à l'hydrodynamisme actif et varié tend à vivifier cet écosystème.
Proceedings of the 61st Gulf and Caribbean Fisheries Institute
Gosier, Guadeloupe

hal-00755766
https://hal.univ-antilles.fr/hal-00755766
https://hal.univ-antilles.fr/hal-00755766/document
https://hal.univ-antilles.fr/hal-00755766/file/GCFI_61_2009_287-297.pdf

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