Éditeur(s) : Elsevier
Résumé : Antimicrobial peptides play a major role in innate immunity. The penaeidins, initially characterized from the shrimp Litopenaeus vannamei, are a family of antimicrobial peptides that appear to be expressed in all penaeid shrimps. As of recent, a large number of penaeid nucleotide sequences have been identified from a variety of penaeid shrimp species and these sequences currently reside in several databases under unique identifiers with no nomenclatural continuity. To facilitate research in this field and avoid potential confusion due to a diverse number of nomenclatural designations, we have made a systematic effort to collect, analyse, and classify all the penaeidin sequences available in every database. We have identified a common penaeidin signature and subsequently established a classification based on amino acid sequences. In order to clarify the naming process, we have introduced a 'penaeidin nomenclature' that can be applied to all extant and future penaeidins. A specialized database, PenBase, which is freely available at http://www.penbase.immunaqua.com, has been developed for the penaeidin family of antimicrobial peptides, to provide comprehensive information about their properties, diversity and nomenclature. (c) 2005 Elsevier Ltd. All rights reserved.
Developmental & Comparative Immunology (0145-305X) (Elsevier), 2006 , Vol. 30 , N. 3 , P. 283-288

Droits : 2005 Elsevier Ltd All rights reserved
http://archimer.ifremer.fr/doc/2006/publication-2332.pdf
DOI:10.1016/j.dci.2005.04.003
http://archimer.ifremer.fr/doc/00000/2332/

Éditeur(s) : Oxford Univ Press
Résumé : The interrogation of genetic markers in environmental meta-barcoding studies is currently seriously hindered by the lack of taxonomically curated reference data sets for the targeted genes. The Protist Ribosomal Reference database (PR2, http://ssurrna. org/) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of hightroughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields. In total, 136 866 sequences are nuclear encoded, 45 708 (36 501 mitochondrial and 9657 chloroplastic) are from organelles, the remaining being putative chimeric sequences. The website allows the users to download sequences from the entire and partial databases (including representative sequences after clustering at a given level of similarity). Different web tools also allow searches by sequence similarity. The presence of both rRNA and rDNA sequences, taking into account introns (crucial for eukaryotic sequences), a normalized eight terms ranked-taxonomy and updates of new GenBank releases were made possible by a long-term collaboration between experts in taxonomy and computer scientists.
Nucleic Acids Research (0305-1048) (Oxford Univ Press), 2013-01 , Vol. 41 , N. D1 , P. D597-D604

Droits : The Author(s) 2012. Published by Oxford University Press.
http://archimer.ifremer.fr/doc/00114/22492/20174.pdf
DOI:10.1093/nar/gks1160
http://archimer.ifremer.fr/doc/00114/22492/

Éditeur(s) : HAL CCSD
Résumé : Spermatogenesis in mammals is a complex biological function including cellular processes such as proliferation, meiosis and differentiation, aiming to the production of male gametes in the testis. If the seminiferous epithelium is well described in terms of organization and cellular morphology of cells that compose it, the processes by which undifferentiated diploid germ cells enter meiosis and give haploid cells that undergo many morphological transformations, are not fully decrypted. These processes rely on the coordinated and sequential expression of genes, including specific products for each stage of germ cell development These gene products are essential at each key stage of spermatogenesis. Transcriptomics since the 1990s, and proteomics since the 2000s have contributed to the improved. understanding of these mechanisms. A long term proteomic study aiming at characterizing the proteomes of Sertoli cells and germ cells, and a recent study that characterized and quantified the transcriptome of isolated rat testicular cells at high resolution using de novo sequencing of transcripts (RNA-Seq), have been the basis of my thesis work. The latter study showed the accumulation of long non-Coding RNAs (lncRNAs) and testicular unannotated transcripts (TUTs) at meiotic and post-Meiotic stages of spermatogenesis in the rat. In this context, my thesis work aimed at validating the coding potential of many genes expressed in germ cells using RNA-Seq combined with shotgun proteomics, a so-Called PIT (Proteomics Informed by transcriptomics) approach. In this approach, the protein sequences translated from the transcripts assembled by RNA-Seq in the different testicular cell types are integrated into a custom database of protein sequences used to query mass spectrometry data obtained from proteins of meiotic and post-Meiotic cells. The PIT approach showed that 69 TUTs or lncRNA (corresponding to 44 loci) code for proteins in meiotic cells and post meiotic cells, and we confirmed experimentally the meiotic and post-Meiotic expression for two new transcripts encoding for VAMP9, a protein of the SNARE family, and a new testicular enolase T-ENOL. The post-Meiotic expression of T-ENOL protein was confirmed by immunohistochemistry using a polyclonal antibody raised against the recombinant protein. This approach also allowed us to identify new isoforms of known proteins, specific to each stage of spermatogenesis. Germ cells and Sertoli cells maintain a dialogue which is necessary to the success of spermatogenesis and spermiogenesis. Another part of my work aimed at identifying membrane proteins, in germ cells and residual bodies, that may be involved in the dialogue between Sertoli cells and germ cells, using a ICPL relative quantification proteomic approach. The ICPL analysis enabled us to establish a list of 166 proteins whose expression is differential between pachytene spermatocytes, round spermatids and residual bodies. Their differential expression suggests that these proteins may play a role in spermiogenesis. Thanks to the Gene Ontology annotations, a list of 8 proteins with a putative role in signal transduction, cell recognition or differentiation, thus potentially involved in the dialogue between Sertoli and germ cells was drawn. In addition, I provided a first proteome of rat Sertoli cells, germ cells and residual bodies obtained by shotgun proteomics.
La spermatogenèse chez les mammifères est une fonction biologique complexe incluant des processus de prolifération cellulaire, de méiose et de différenciation uniques visant à la production des gamètes mâles au sein du testicule. Si l’épithélium séminifère est bien décrit sur le plan de son organisation et de la morphologie des cellules qui le composent, les processus par lesquels les cellules germinales diploïdes indifférenciées entrent en méiose pour donner ensuite des cellules haploïdes subissant par la suite de nombreuses transformations morphologiques, ne sont pas totalement décryptés. Ils reposent sur l’expression coordonnée et séquentielle de gènes dont les produits spécifiques de chaque stade de développement des cellules germinales sont essentiels aux étapes clés de la spermatogenèse. La transcriptomique depuis les années 1990 et la protéomique depuis les années 2000 ont contribué à l’amélioration de la connaissance de ces mécanismes. Une étude protéomique visant à caractériser par des approches systématiques et différentielles les protéomes des cellules de Sertoli et de la lignée germinale, et d’autre part une étude récente, réalisée dans notre unité, qui a permis de caractériser et de quantifier le transcriptome des cellules testiculaires isolées de rat en utilisant le séquençage de novo des transcrits (RNA-Seq), ont été à la base de mes travaux de thèse. Cette dernière étude a mis en évidence l’accumulation de longs ARNs non codants (lncRNAs) et de transcrits testiculaires non annotés (TUTs) aux stades méiotique et post- méiotique de la spermatogenèse chez le rat. Dans ce contexte, mon travail a consisté à valider le potentiel codant de nombreux gènes exprimés dans les cellules germinales par une approche dite PIT (Proteomics Informed by Transcriptomics) couplant protéomique Shotgun et RNA-Seq. Dans ce type d’approche, les séquences protéiques déduites des transcrits des différents types cellulaires, assemblés par RNA-Seq, sont intégrées dans une base personnalisée de séquences protéiques utilisée pour interroger les données de spectrométrie de masse obtenues à partir de protéines de cellules méiotiques et post-Méiotiques. L’approche PIT a permis de montrer que 69 TUTs ou lncRNA (correspondant à 44 loci) codent pour des protéines dans les cellules méiotiques et post méiotiques. L’expression post-Méiotique de deux nouveaux transcrits, l’un codant pour la protéine VAMP9, une protéine de la famille SNARE, et l’autre pour une nouvelle énolase T-ENOL a pu être confirmée. L’expression post-Méiotique de T-ENOL a été confirmée par immunohistochimie à l’aide d’un anticorps polyclonal produit contre la protéine recombinante. Cette approche nous a également permis d’identifier de nouvelles isoformes de protéines connues spécifiques de chaque stade de la spermatogenèse. Les cellules germinales et les cellules de Sertoli entretiennent le dialogue nécessaire au bon déroulement de la spermatogenèse. Une autre partie de mon travail a consisté à identifier des protéines membranaires des cellules germinales et des corps résiduels, susceptibles d’intervenir dans le dialogue entre les cellules de Sertoli et les cellules germinales, par une approche protéomique de quantification relative ICPL. Cette approche a permis d’établir une liste de 166 protéines différentiellement exprimées entre les spermatocytes pachytène, les spermatides rondes et les corps résiduels, qui sont susceptibles de jouer un rôle dans la spermiogénèse. Grâce aux annotations de le Gene Ontology, j’ai pu établir une liste de 8 protéines ayant un rôle supposé dans la transduction du signal, la reconnaissance cellulaire ou bien la différenciation. Par ailleurs, j’ai pu établir par protéomique Shotgun un premier protéome des cellules de Sertoli, des cellules germinales et des corps résiduels chez le rat.
https://tel.archives-ouvertes.fr/tel-01127389

Droits : info:eu-repo/semantics/OpenAccess
NNT : 2014REN1S064
tel-01127389
https://tel.archives-ouvertes.fr/tel-01127389
https://tel.archives-ouvertes.fr/tel-01127389/document
https://tel.archives-ouvertes.fr/tel-01127389/file/2014REN1S064.pdf

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : We aimed to enhance understanding of the molecular diversity of arbuscular mycorrhizal fungi (AMF) by building a new global dataset targeting previously unstudied geographical areas. In total, we sampled 96 plant species from 25 sites that encompassed all continents except Antarctica. AMF in plant roots were detected by sequencing the nuclear SSU rRNA gene fragment using either cloning followed by Sanger sequencing or 454-sequencing. A total of 204 AMF phylogroups (virtual taxa, VT) were recorded, increasing the described number of Glomeromycota VT from 308 to 341 globally. Novel VT were detected from 21 sites; three novel but nevertheless widespread VT (Glomus spp. MO-G52, MO-G53, MO-G57) were recorded from six continents. The largest increases in regional VT number were recorded in previously little-studied Oceania and in the boreal and polar climatic zones - this study providing the first molecular data from the latter. Ordination revealed differences in AM fungal communities between different continents and climatic zones, suggesting that both biogeographic history and environmental conditions underlie the global variation of those communities. Our results show that a considerable proportion of Glomeromycota diversity has been recorded in many regions, though further large increases in richness can be expected in remaining unstudied areas.
ISSN: 0940-6360

hal-01190520
https://hal.archives-ouvertes.fr/hal-01190520
DOI : 10.1007/s00572-013-0482-2
PRODINRA : 206968

Éditeur(s) : HAL CCSD Wiley/Blackwell
Résumé : International audience
Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongoing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morphological characters and have complex life cycles. To interpret environmental sequences, metabarcoding necessarily relies on taxonomically curated databases containing reference sequences of the targeted gene (or barcode) from identified organisms. To date, no such reference framework exists for photosynthetic eukaryotes. In this study, we built the PhytoREF database that contains 6490 plastidial 16S rDNA reference sequences that originate from a large diversity of eukaryotes representing all known major photosynthetic lineages. We compiled 3333 amplicon sequences available from public databases and 879 sequences extracted from plastidial genomes, and generated 411 novel sequences from cultured marine microalgal strains belonging to different eukaryotic lineages. A total of 1867 environmental Sanger 16S rDNA sequences were also included in the database. Stringent quality filtering and a phylogeny-based taxonomic classification were applied for each 16S rDNA sequence. The database mainly focuses on marine microalgae, but sequences from land plants (representing half of the PhytoREF sequences) and freshwater taxa were also included to broaden the applicability of PhytoREF to different aquatic and terrestrial habitats. PhytoREF, accessible via a web interface (http://phytoref.fr), is a new resource in molecular ecology to foster the discovery, assessment and monitoring of the diversity of photosynthetic eukaryotes using high-throughput sequencing.
ISSN: 1755-098X

hal-01149047
http://hal.upmc.fr/hal-01149047
http://hal.upmc.fr/hal-01149047/document
http://hal.upmc.fr/hal-01149047/file/Decelle_2015_PhytoREF.pdf
DOI : 10.1111/1755-0998.12401

Éditeur(s) : HAL CCSD
Résumé : International audience
Mining sequential patterns in data streams is a new challenging problem for the datamining community since data arrives sequentially in the form of continuous rapid and infinite streams. In this paper, we propose a new on-line algorithm, SPAMS, to deal with the sequential patterns mining problem in data streams. This algorithm uses an automaton-based structure to maintain the set of frequent sequential patterns, i.e. SPA (Sequential Pat- tern Automaton). The sequential pattern automaton can be smaller than the set of frequent sequential patterns by two or more orders of magnitude, which allows us to overcome the problem of combinatorial explosion of se- quential patterns. Current results can be output constantly on any user 's specified thresholds. In addition, taking into account the characteristics of data streams, we propose a well-suited method said to be approximate since we can provide near optimal results with a high probability. Experimental studies show the relevance of the SPA data structure and the efficiency of the SPAMS algorithm on various datasets. Our contribution opens a promis- ing gateway, by using an automaton as a data structure for mining frequent sequential patterns in data streams.
Advances in Knowledge Discovery and Management

lirmm-00435841
https://hal-lirmm.ccsd.cnrs.fr/lirmm-00435841
https://hal-lirmm.ccsd.cnrs.fr/lirmm-00435841/document
https://hal-lirmm.ccsd.cnrs.fr/lirmm-00435841/file/akdmSPAMS.pdf

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

Résumé : L’arc des Petites Antilles résulte de la lente subduction vers l'Ouest des plaques Nord et Sud-Américaines sous la plaque Caraïbes (2cm/an). A la latitude de l’archipel guadeloupéen et à ~150 km à l’Ouest du front de déformation, le bassin d'avant-arc de Marie-Galante forme un bassin perché, incliné vers la fosse et limité vers l’Est par un haut-fond, l’Eperon Karukéra. À cette latitude, le bassin de Marie-Galante domine le prisme d’accrétion de la Barbade et fait face à la ride de Tiburon qui balaye la zone du Nord au Sud depuis la fin du Miocène supérieur. Le remplissage sédimentaire du Bassin de Marie-Galante montre des déformations actives au moins depuis ~30 millions d’années. L’objectif du travail est de reconstituer l’évolution tectono-sédimentaire de ce bassin pour apporter de nouvelles contraintes sur la compréhension globale de la zone de subduction frontale des Petites Antilles. Ce travail s'appuie sur les données de bathymétrie multifaisceaux et de sismique réflexion multi-traces haute résolution acquises lors des campagnes du programme KaShallow. Cette base de données, complétée de profils sismiques plus basse résolution de campagnes antérieures, permet d’avoir une couverture pseudo 3D et à quatre échelles de résolution de l'ensemble du bassin. Un échantillonnage par ROV et carottage ciblé a fourni 40 prélèvements dans les principales unités sismiques. Les analyses pétrologiques et les datations biostratigraphiques autorisent des reconstitutions paléo-environnementales depuis le Paléogène supérieur jusqu’à Actuel. L’interprétation sismique multi-échelle montre un bassin sédimentaire atteignant ~4,5s temps double (~4500 à 5625 m) sur un substratum magmatique pré-structuré. Ce bassin est composé de 5 grands ensembles sédimentaires (E-1, E1, E2, E3 et E4) subdivisés en 13 unités limitées par 14 surfaces de discontinuités. L’organisation séquentielle des unités sismiques permet de mettre en évidence 10 séquences de dépôts de troisièmes ordres (S-1 à S9). Le calage biostratigraphique de l’ensemble des séquences permet de proposer une évolution tectono-sédimentaire du bassin de l’Éocène à l’Actuel. Ainsi, nous distinguons quatre systèmes de failles normales associées à trois phases d’extensions qui contrôlent l’évolution architecturale et sédimentaire du bassin. 1/ Un système N050±10°E hérité, actif dès le Paléogène supérieur, qui contrôle le basculement général du bassin vers le SSE. Il est responsable de la formation de l'escarpement de Désirade d’environ 4500 m de dénivelé. Cette première extension est interprétée comme résultant de la fragmentation de l'avant-arc en réponse à l'augmentation du rayon de courbure de la zone de subduction. 2/ Un système N130°-N150°E, structurant à l’échelle de l’Éperon Karukéra, qui contrôle la sédimentation dès le Miocène inférieur et marque une première phase d'extension transverse à l’arc. 3/ Un système N160°-N180°E qui segmente le Bassin de Marie-Galante en un sous-bassin à l'Ouest et l'Éperon Karukéra à l'Est. Cette seconde extension, globalement perpendiculaire à la marge, s'accompagne d’une subsidence et d'une inversion de la polarité du bassin en réponse à son basculement vers la fosse qui débute au cours du Miocène moyen et se poursuit actuellement à l'Est du bassin. Cette évolution à long terme de l'avant-arc, concomitante avec le recul de l'arc volcanique vers l’Ouest, est considérée comme résultant d’une érosion basale de la plaque supérieure. 4/ Un système N090±10°E plus tardif est localisé au centre du bassin et qui contrôle le développement de plates-formes carbonatées néritiques sur certaines têtes de blocs, comme par exemple à Marie-Galante. Cette dernière extension, parallèle à l’arc, se manifeste dans le bassin à partir du Pliocène inférieur. Elle se superpose au régime d'extension perpendiculaire à l'avant-arc et est interprétée comme l'accommodation du partitionnement de la déformation en réponse à l’obliquité croissante du front subduction vers le Nord.
The Lesser Antilles result of the slow westward subduction of the North and South American plate under the Caribbean plate (2 cm / year). At the latitude of the Guadeloupe archipelago and ~ 150 km to the west of the deformation front, the fore-arc basin of Marie-Galante forms a perched basin tilted to the pit and limited to the East by a shoal, the Spur Karukéra. At this latitude, Marie-Galante basin dominates the accretionary prism of Barbados and faces wrinkle Tiburon sweeping the area from North to South from the late Miocene. The sedimentary fill Basin Marie-Galante shows active deformation since at least ~ 30 million years. The aim of the work is to reconstruct the tectono-sedimentary evolution of the basin to provide new constraints on the overall understanding of the frontal subduction zone Lesser Antilles. This work relies on multibeam bathymetry data and high-resolution seismic reflection multi-traces acquired during campaigns KaShallow program. This database, supplemented by lower resolution of previous campaigns seismic profiles, provides a pseudo-3D coverage and four scales of resolution of the entire basin. ROV sampling and targeted core provided 40 samples in the main seismic units. Petrological analysis and biostratigraphic dating allow paleoenvironmental reconstructions from the upper Paleogene up Actuel. Seismic interpretation multiscale shows a sedimentary basin reaching ~ 4,5s double (~ 4500-5625 m) on a substrate pre-structured magma. This basin consists of 5 main sedimentary units (E-1, E1, E2, E3 and E4) divided into 13 units bounded by discontinuities 14 surfaces. The sequential organization of seismic units allows to highlight sequences 10 deposits of third order (S-1 to S9). The biostratigraphic calibration of all sequences able to offer a tectono-sedimentary evolution of the Eocene basin to Present. Thus, we distinguish four normal fault systems associated with three phases of extensions that control the architectural and sedimentary evolution of the basin. 1 / A system N050 ± 10 ° E inherited assets from the upper Paleogene, which controls the overall pelvic tilt towards the SSE. He is responsible for the formation of the escarpment Désirade about 4500 m elevation. The first extension is interpreted as resulting from the fragmentation of the fore-arc in response to the increase in the radius of curvature of subduction. 2 / A system N130 ° -N150 ° E, structuring across the Spur Karukéra, which controls sediment from the Miocene and marks the first phase of transverse extension arc. 3 / A system N160 ° E ° -N180 which segments Basin Marie-Galante in a sub-basin to the west and the Spur Karukéra in the East. This second extension, generally perpendicular to the margin, is accompanied by subsidence and reversing the polarity of the basin in response to his switch to the pit, beginning during the Middle Miocene and is ongoing in the East the basin. This long-term evolution of the forearc, concurrent with the decline in volcanic arc to the west, is considered as resulting from a basal erosion of the top plate. 4 / A system N090 ± 10 ° later E is located in the center of the basin and controlling the development of neritic carbonate platforms on certain blocks heads, such as Marie-Galante. This latest extension, parallel to the arc occurs in the basin from the lower Pliocene. It is superimposed on the expansion plan perpendicular to the fore-arc and is interpreted as the accommodation of the partitioning of deformation in response to the increasing obliquity front subduction north.

http://www.theses.fr/2014AGUY0799/document

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

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

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Genetics and molecular biology have been instrumental for a better understanding of heritable defects causing human infertility over the past decades. More recently, the field of reproductive biology has harnessed genome biological approaches to gain insight into molecular processes underlying normal and pathological gametogenesis and gamete function. We are currently witnessing yet another quantum leap in our ability to monitor the flow of information from the genome via the transcriptome to the proteome: tiling arrays that cover both strands of a given target genome and RNA-Seq, a method based on ultra-high throughput DNA sequencing, enable us to study noncoding and protein-coding transcripts with unprecedented precision and depth at a reasonable cost. These technologies have spawned a thriving discipline within the bioinformatics field that employs information technology for managing and interpreting biological high-throughput data. This review outlines database projects and online analysis tools useful for life scientists in general and discusses in detail selected projects that have specifically been developed for researchers and clinicians in the field of reproductive biology. This article is part of a Special Issue entitled: Molecular Genetics of Human Reproductive Failure.
ISSN: 0006-3002

hal-00877444
https://hal.archives-ouvertes.fr/hal-00877444
DOI : 10.1016/j.bbadis.2012.05.018
PUBMED : 22687534

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background: Ameloblastin (AMBN) is a phosphorylated, proline/glutamine-rich protein secreted during enamel formation. Previous studies have revealed that this enamel matrix protein was present early in vertebrate evolution and certainly plays important roles during enamel formation although its precise functions remain unclear. We performed evolutionary analyses of AMBN in order to (i) identify residues and motifs important for the protein function, (ii) predict mutations responsible for genetic diseases, and (iii) understand its molecular evolution in mammals. Results: In silico searches retrieved 56 complete sequences in public databases that were aligned and analyzed computationally. We showed that AMBN is globally evolving under moderate purifying selection in mammals and contains a strong phylogenetic signal. In addition, our analyses revealed codons evolving under significant positive selection. Evidence for positive selection acting on AMBN was observed in catarrhine primates and the aye-aye. We also found that (i) an additional translation initiation site was recruited in the ancestral placental AMBN, (ii) a short exon was duplicated several times in various species including catarrhine primates, and (iii) several polyadenylation sites are present. Conclusions: AMBN possesses many positions, which have been subjected to strong selective pressure for 200 million years. These positions correspond to several cleavage sites and hydroxylated, O-glycosylated, and phosphorylated residues. We predict that these conserved positions would be potentially responsible for enamel disorder if substituted. Some motifs that were previously identified as potentially important functionally were confirmed, and we found two, highly conserved, new motifs, the function of which should be tested in the near future. This study illustrates the power of evolutionary analyses for characterizing the functional constraints acting on proteins with yet uncharacterized structure.
ISSN: 1471-2148

Droits : http://creativecommons.org/licenses/by/
hal-01212816
http://hal.upmc.fr/hal-01212816
http://hal.upmc.fr/hal-01212816/document
http://hal.upmc.fr/hal-01212816/file/s12862-015-0431-0.pdf
DOI : 10.1186/s12862-015-0431-0

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
We present a graphical user interface to facilitate the processing of teleseismic shear-wave splitting observations. In contrast to a fully automated technique, we present a manual, per-event approach that maintains user control during the sequence of processing. The SplitLab environment is intended to undertake the repetitive processing steps while enabling the user to focus on quality control and eventually the interpretation of the results. Pre-processing modules of SplitLab create a database of events and link the corresponding seismogram files. The seismogram viewer tool uses this database to perform the measurement interactively. Post-processing of the combined results of such a project includes a viewer and export option. Our emphasis lies in the application to teleseismic shear-wave splitting analysis, but our code can be extended easily for other purposes. SplitLab can be downloaded at http://www.gm.univ-montp2.fr/splitting/.
ISSN: 0098-3004

hal-00412372
https://hal.archives-ouvertes.fr/hal-00412372
https://hal.archives-ouvertes.fr/hal-00412372/document
https://hal.archives-ouvertes.fr/hal-00412372/file/Wuestefeld_Splitlab_CompGeosc2008_hal.pdf
DOI : 10.1016/j.cageo.2007.08.002

Éditeur(s) : HAL CCSD
Résumé : Enamel formation requires the involvement of secretory calcium-binding phosphoproteins. Three of them, amelogenin (AMEL), ameloblastin (AMBN) and enamelin (ENAM), have been extensively studied in mammals. More recently, a fourth protein belonging to the same family has been identified: amelotin (AMTN). AMTN has only been studied in rodents and its role during amelogenesis remains unclear.The aim of this thesis is to extend the knowledge on AMTN by studying its evolution in amniotes and its expression in the lizard Anolis carolinensis.AMTN sequences from many amniote species have been extracted from databases or obtained by PCR, and analyzed. Those analyses allowed us to reveal differences in the gene structure and to highlight residues that were conserved during mammalian or amniote evolution. These conserved amino acids are essential to the structure and/or function of the protein.The expression of AMTN and of AMEL, AMBN and ENAM has been studied by in situ hybridization on lizard jaw sections. Comparison of the expression pattern of these genes during amelogenesis in the lizard with that described in rodents points to similarities (AMEL, AMBN and ENAM) but also to important differences, especially in the spatio-temporal expression of AMTN. In order to better understand AMTN evolution in tetrapods, I studied its expression in an amphibian (Pleurodeles waltl) and a marsupial (Monodelphis domestica).Taken together, these results suggest a link between the evolution of AMTN gene structure (loss of exons and of functional domains in mammals) and its expression (early in non-mammals versus late in mammals) with the emergence of prismatic structure of enamel in early mammals.
La formation de l'émail dentaire met en jeu des phosphoprotéines sécrétées liant le calcium. Parmi celles-ci figurent amélogénine (AMEL), améloblastine (AMBN) et énaméline (ENAM), qui ont fait l'objet de nombreuses études chez les mammifères. Plus récemment, une quatrième protéine de la même famille a été découverte, l'amélotine (AMTN). Elle n'a été étudiée que chez les rongeurs et son rôle au cours de l'amélogenèse reste mal défini. L'objectif de cette thèse est d'élargir les connaissances sur AMTN en étudiant son évolution chez les amniotes et son expression au cours de l'amélogenèse chez le lézard Anolis carolinensis. Les séquences d'AMTN d'un grand nombre d'amniotes ont été extraites des bases de données ou obtenues par PCR, et analysées. Ces analyses ont mis en évidence différentes structures géniques et des acides aminés très conservés au cours de l'évolution. Cette conservation indique qu'ils sont essentiels à la structure ou à la fonction de la protéine. L'expression d'AMTN ainsi que celle d'AMEL, AMBN et ENAM ont été étudiées par hybridation in situ sur des coupes de mâchoires de lézard. La comparaison des patrons d'expression chez le lézard avec ceux décrits chez la souris a révélé des différences dans l'expression spatio-temporelle d'AMTN. De ce fait, afin de mieux comprendre l'évolution de ce gène, son expression a été étudiée chez un amphibien (Pleurodeles waltl) et un marsupial (Monodelphis domestica).Ces travaux suggère un lien entre l'évolution de la structure génique d'AMTN (perte d'exons et de domaines fonctionnels) et de son expression (précoce versus tardive) avec l'émergence de la structure prismatique de l'émail chez les mammifères.
https://tel.archives-ouvertes.fr/tel-01154518

NNT : 2015PA066066
tel-01154518
https://tel.archives-ouvertes.fr/tel-01154518
https://tel.archives-ouvertes.fr/tel-01154518/document
https://tel.archives-ouvertes.fr/tel-01154518/file/2015PA066066.pdf

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background: Amelotin (AMTN) is an ameloblast-secreted protein that belongs to the secretory calcium-binding phosphoprotein (SCPP) family, which originated in early vertebrates. In rodents, AMTN is expressed during the maturation stage of amelogenesis only. This expression pattern strongly differs from the spatiotemporal expression of other ameloblast-secreted SCPPs, such as the enamel matrix proteins (EMPs). Furthermore, AMTN was characterized in rodents only. In this study, we applied various approaches, including in silico screening of databases, PCRs and transcriptome sequencing to characterize AMTN sequences in sauropsids and amphibians, and compared them to available mammalian and coelacanth sequences. Results: We showed that (i) AMTN is tooth (enamel) specific and underwent pseudogenization in toothless turtles and birds, and (ii) the AMTN structure changed during tetrapod evolution. To infer AMTN function, we studied spatiotemporal expression of AMTN during amelogenesis in a salamander and a lizard, and compared the results with available expression data from mouse. We found that AMTN is expressed throughout amelogenesis in non-mammalian tetrapods, in contrast to its expression limited to enamel maturation in rodents. Conclusions: Taken together our findings suggest that AMTN was primarily an EMP. Its functions were conserved in amphibians and sauropsids while a change occurred early in the mammalian lineage, modifying its expression pattern during amelogenesis and its gene structure. These changes likely led to a partial loss of AMTN function and could have a link with the emergence of prismatic enamel in mammals.
ISSN: 1471-2148

Droits : http://creativecommons.org/licenses/by/
hal-01212821
http://hal.upmc.fr/hal-01212821
http://hal.upmc.fr/hal-01212821/document
http://hal.upmc.fr/hal-01212821/file/s12862-015-0329-x.pdf
DOI : 10.1186/s12862-015-0329-x

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background - Pregnant women are a vulnerable population. Although regular follow-ups are recommended during pregnancy, not all pregnant women seek care. This pilot study wanted to assess whether the integration of data from administrative health information systems and socio-economic features allows identifying disparities in prenatal care trajectories.Methods - Prenatal care trajectories were extracted from the permanent sample of the French health insurance information system linked to the hospital discharge information system. The records of 2518 women who gave birth without complications in France in 2009 were analyzed. State sequence data analysis was performed to identify homogeneous groups of prenatal care trajectories. Socio-economic data were used to characterize their living environment.Results -We identified three groups of homogeneous prenatal care trajectories: (i) women with relatively high prenatal care consumption (~11 %), (ii) women with no prenatal care (~21 %), and (iii) women with an intermediate level of prenatal care (~66 %). Analysis of the socio-economic data demonstrated the association between disparities in prenatal care trajectories and the women’s living environment. Women with relatively high care consumption generally lived in socio-economically privileged areas (better education levels, employment status and housing conditions) compared with women with few or no prenatal care.Conclusions -Although ecological, our approach demonstrates that data from health administrative information systems could be used to describe prenatal care. However, more individual variables and an improvement of the data quality are needed to efficiently monitor the content and timing of prenatal care. Moreover, state sequence analysis, which was used in this context for the first time, proves to be an interesting approach to explore care trajectories. Finally, the integration of heterogeneous sources of data, including contextual information, might help identifying areas that require health promotion actions toward vulnerable populations, such as pregnant women.
ISSN: 1472-6963

hal-01169792
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01169792
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01169792/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01169792/file/Mining%20care%20trajectories%20using%20health%20administrative.pdf
DOI : 10.1186/s12913-015-0857-5

Éditeur(s) : HAL CCSD Wiley/Blackwell
Résumé : International audience
This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Alcippe morrisonia morrisonia, Bashania fangiana, Bashania fargesii, Chaetodon vagabundus, Colletes floralis, Coluber constrictor flaviventris, Coptotermes gestroi, Crotophaga major, Cyprinella lutrensis, Danaus plexippus, Fagus grandifolia, Falco tinnunculus, Fletcherimyia fletcheri, Hydrilla verticillata, Laterallus jamaicensis coturniculus, Leavenworthia alabamica, Marmosops incanus, Miichthys miiuy, Nasua nasua, Noturus exilis, Odontesthes bonariensis, Quadrula fragosa, Pinctada maxima, Pseudaletia separata, Pseudoperonospora cubensis, Podocarpus elatus, Portunus trituberculatus, Rhagoletis cerasi, Rhinella schneideri, Sarracenia alata, Skeletonema marinoi, Sminthurus viridis, Syngnathus abaster, Uroteuthis (Photololigo) chinensis, Verticillium dahliae, Wasmannia auropunctata, and Zygochlamys patagonica. These loci were cross-tested on the following species: Chaetodon baronessa, Falco columbarius, Falco eleonorae, Falco naumanni, Falco peregrinus, Falco subbuteo, Didelphis aurita, Gracilinanus microtarsus, Marmosops paulensis, Monodelphis Americana, Odontesthes hatcheri, Podocarpus grayi, Podocarpus lawrencei, Podocarpus smithii, Portunus pelagicus, Syngnathus acus, Syngnathus typhle,Uroteuthis (Photololigo) edulis, Uroteuthis (Photololigo) duvauceli and Verticillium albo-atrum. This article also documents the addition of nine sequencing primer pairs and sixteen allele specific primers or probes for Oncorhynchus mykiss and Oncorhynchus tshawytscha; these primers and assays were cross-tested in both species.
ISSN: 1755-098X

hal-01094222
https://hal-agroparistech.archives-ouvertes.fr/hal-01094222
DOI : 10.1111/j.1755-0998.2010.02916.x

Éditeur(s) : HAL CCSD
Résumé : This work aims at studying the sedimentary record of the Gulf of Lion margin during the post-rift evolution. Methodology is based on the exploitation of a disparate database (the BRGM Banque du Sous-Sol, industrial seismic reflection, exploration boreholes, onshore outcrops), which -through high-resolution onshore-ofshore correlations- leads to interpretations of the post-rift evolution of distinct segments of the margin. The part played by the Messinian salinity crisis in the margin evolution is underlined. The processes of the subsequent restoration of the margin during the Plio-Quaternary are analysed. The distinct evolutions observed on different segments o the margin are related to local forçings (structural heritage and /or variable sediment flux). The results are used to improve the knowledge of littoral aquifers reservoirs.
L'objectif de ce travail est l'étude de l'enregistrement sédimentaire de la marge du Golfe du Lion pendant son évolution post-rift. On met au point une méthodologie basée sur l'exploitation et de données disparates (Banque du Sous-Sol du BRGM, sismique réflexion industrielle, forages pétroliers profonds, affleurements de terrain), conduisant à des corrélations terre-mer haute-résolution et aboutissant à des interprétations de l'évolution post-rift de plusieurs segments de la marge. On met en évidence le rôle de la crise de salinité messinienne dans l'évolution de la marge et les modalités de la reconstruction de celle-ci, pendant le Plio-Quaternaire. Les évolutions variables selon les segments sont analysées, et mises en relation avec les contrôles locaux (héritages et /ou flux sédimentaires différents). Ces résultats sont appliqués à des problématiques de réservoirs aquifères littoraux.
https://tel.archives-ouvertes.fr/tel-00438146

tel-00438146
https://tel.archives-ouvertes.fr/tel-00438146
https://tel.archives-ouvertes.fr/tel-00438146/document
https://tel.archives-ouvertes.fr/tel-00438146/file/theseduvail.pdf