Éditeur(s) : HAL CCSD Wiley/Blackwell
Résumé : Whole genome sequencing is helping generate robust phylogenetic hypotheses for a range of taxonomic groups that were previously recalcitrant to classical molecular phylogenetic approaches. As a case study, we performed a shallow shotgun sequencing of eight species in the tropical tree family Chrysobalanaceae to retrieve large fragments of high-copy number DNA regions and test the potential of these regions for phylogeny reconstruction. We were able to assemble the nuclear ribosomal cluster (nrDNA), the complete plastid genome (ptDNA) and a large fraction of the mitochondrial genome (mtDNA) with approximately 1000x, 450x and 120x sequencing depth respectively. The phylogenetic tree obtained with ptDNA resolved five of the seven internal nodes. In contrast, the tree obtained with mtDNA and nrDNA data were largely unresolved. This study demonstrates that genome skimming is a cost-effective approach and shows potential in plant molecular systematics within Chrysobalanaceae and other under-studied groups.
ISSN: 1755-098X

hal-01204217
https://hal.archives-ouvertes.fr/hal-01204217
DOI : 10.1111/1755-0998.12246
PRODINRA : 283530

Éditeur(s) : HAL CCSD
Résumé : Transposable elements play a major role in the evolution of eukaryotic genomes. Knowing the distribution of transposable elements between different species within the same taxon is essential to study their dynamics and to better understand their role in the evolution of species. Given their abundance, species diversity and living environment, crustaceans are an excellent model for studying comparative genomics of retrotransposons. It is notably in the squat lobsters that the GalEa clade of Superfamily Copia was defined. We studied the distribution of two well-known LTR retrotransposons superfamilies: Gypsy and Copia, in crustaceans. By combining PCRs with degenerate primers and in silico analysis, we identified 35 families of Copia retrotransposons and 46 families of Gypsy retrotransposons in 15 and 18 species of crustaceans (mainly Malacostraca: crabs, shrimp, krill ...). These elements have different distribution and diversity in crustaceans. Gypsy elements appear relatively commonly and diverse in all species. Conversely, the Copia elements seem rare, and consequently more difficult to detect, and are largely dominated by the elements of the clade GalEa. These results suggest two different dynamic strategies for retrotransposons Gypsy (the Red Queen theory) and retrotransposons GalEa (‘domino days spreading’ branching process). In addition, GalEa elements present a great evolutionary success being widely distributed in many branches of metazoans. They are also present in certain red algae and we have also detected them in Fungi. Taking advantage of the large amount of available genomic data, we have studied the distribution of GalEa elements of Fungi, in order to compare it with the results obtained in crustaceans. In fact, they appear only in a large phylum of Ascomycetes, in Pezizomycotina, and they form a monophyletic group within the GalEa. Finally, in the Fungi, the GalEa elements are not majority among Copia retrotransposons. We have therefore initiated a new study in molluscs, to define if the results obtained in crustaceans are a feature of GalEa elements, Malacostraca or metazoans.
Les éléments transposables jouent un rôle majeur dans l’évolution des génomes eucaryotes. La connaissance de la distribution des éléments transposables entre différentes espèces au sein d’un même taxon est une condition essentielle pour étudier leur dynamique et mieux comprendre leur rôle dans l'évolution des espèces. Compte tenu de leur abondance, de leur diversité spécifique et de milieu de vie, les crustacés sont un excellent modèle pour étudier la génomique comparative des rétrotransposons. C’est notamment chez les Galathées qu’a été défini le clade GalEa des éléments de la superfamille des Copia. Nous avons étudié la distribution de deux superfamilles de rétrotransposons à LTR bien connus: les Gypsy et les Copia, au sein des crustacés. En combinant des PCRs avec amorces dégénérées et des analyses in silico, nous avons identifié 35 familles de rétrotransposons Copia et 46 familles de rétrotransposons Gypsy dans respectivement 15 et 18 espèces de crustacés (principalement des malacostracés : crabes, crevettes, krill...). Ces éléments présentent une distribution et une diversité différentes au sein des crustacés. Les éléments Gypsy apparaissent relativement fréquents et diversifiés dans toutes les espèces. A l’inverse, les éléments Copia semblent rares, donc difficilement détectables, et sont largement dominés par les éléments du clade GalEa. Ces résultats suggèrent deux stratégies différentes de dynamique pour les rétrotransposons Gypsy (théorie de la Reine Rouge) et les rétrotransposons GalEa (‘domino days spreading’ branching process). De plus, les éléments GalEa présentent un grand succès évolutif en étant largement distribués dans de nombreuses branches de métazoaires. Ils sont aussi présents chez quelques algues rouges et nous en avons également détecté chez des Fungi. Profitant des nombreuses données génomiques disponibles, nous avons donc étudié la distribution des éléments GalEa de Fungi, dans le but de comparer celle-ci aux résultats obtenus chez les crustacés. En fait, ils n’apparaissent qu’au sein d’un grand embranchement d’ascomycètes, les Pezizomycotina, et ils forment un groupe monophylétique au sein des GalEa. Enfin, chez les Fungi, les éléments GalEa ne sont pas majoritaire parmi les rétrotransposons Copia. Nous avons donc initié une nouvelle étude chez les mollusques, afin de définir si les résultats obtenus chez les crustacés sont une caractéristique des éléments GalEa, des malacostracés ou des métazoaires.
https://tel.archives-ouvertes.fr/tel-01132413

NNT : 2015PA066017
tel-01132413
https://tel.archives-ouvertes.fr/tel-01132413
https://tel.archives-ouvertes.fr/tel-01132413/document
https://tel.archives-ouvertes.fr/tel-01132413/file/these_archivage_2600252o.pdf

Éditeur(s) : Université Montpellier 2 - Sciences et Techniques du Languedoc
Résumé : The work reported here was motivated by the economical importance of the pacific blue shrimp Litopenaeus stylirostris farming where high mortality rates are due to bacterial and viral diseases. It consists in the characterisation of two original peptides, the first members of a new multifunctional family of peptides from peneide shrimps, the stylicines. Those two peptides, named stylicines 1 and 2, are negatively charged (pI < 6.0), and characterised by a proline-rich N-terminal region and a C-terminal region containing 13 cysteine residues. Stylicines are synthesized by heamocytes where they are stored within small cytoplasmic granules. To understand the role of these peptides in the immune response of shrimps to a vibrio infection, their recombinant forms were produced in E. coli BL21 (DE3) plysS, purified and characterised. The two rstylicines display biological anti-proliferative and blood clotting activities. Only rstylicine 1 displays antimicrobial activities: antifungal against Fusarium oxysporum (MIC<2.5μM) and bacteriostatic against Gram (−) bacteria, Vibrio sp. (MIC<80μM). Moreover this peptide displays an LPS-binding activity (dissociation constant (Kd) of 9.6×10−8 M) and agglutinate Vibrio. penaeicida "in vitro". Finally, the presence of sequences coding for modified forms of stylicine 1 in some shrimp’s genome may be in relation with their lower ability to survive infections.
Les travaux présentés dans ce mémoire ont été motivés par l’importance économique de l’élevage de la crevette bleue du pacifique Litopenaeus stylirostris dont les fortes mortalités sont principalement dues au développement de maladies bactériennes et virales. Ils ont consisté en la caractérisation des deux premiers membres d’une famille originale de peptides multifonctionnels présents chez les crevettes pénéides, les stylicines. Ces peptides, nommés stylicines 1 et 2, sont des peptides anioniques (pI < 6.0), formés d’une région amino-terminale riche en résidus de type proline et d’une région carboxyterminale riche de treize résidus cystéines. Ces molécules sont synthétisées et stockées dans de petits granules présents dans le cytoplasme des hémocytes. Pour mieux appréhender leurs rôles dans la réponse immunitaire des crevettes à une infection par des Vibrio, leurs formes recombinantes ont été produites dans E. coli BL21 (DE3) plysS, purifiées et caractérisées. Les deux rstylicines présentent des activités antiproliférative et anticoagulante. Seule la rstylicine1 présente des activités antimicrobiennes : antifongique sur Fusarium oxysporum (CMI<2.5 μM), et antibactérienne (bactériostatique) sur Vibrio sp (CMI<80 μM). Ce peptide est également capable de se lier aux LPS des bactéries à Gram (-) (Kd= 9.6x10-8 M) et d’agglutiner V. penaeicida "in vitro". Enfin, l’existence de gènes codant des formes modifiées de la stylicine1, chez certaines crevettes, pourrait être en relation avec une diminution de la résistante des individus aux infections.

Droits : 2010 The Author, Univ Montpellier 2
http://archimer.ifremer.fr/doc/00024/13558/10612.pdf
http://archimer.ifremer.fr/doc/00024/13558/

Éditeur(s) : Université de La Rochelle, Ecole doctorale Gay Lussac
Résumé : The thesis work is part of the very current issue on mass mortality outbreaks affecting Pacific oyster, C. gigas, spat and juveniles and questions about the involvement of pesticides in this phenomenon. The first part of this thesis was devoted to study the effects of pesticides on hemocyte parameters in the Pacific oyster (in vitro and in vivo). The immunomodulator effect of selected pesticides (alone or in mixture) has been explored principally through flow cytometry. The second part concerned the study of the effects of a pesticides mixture on OsHV-1 itself. No direct effects have been reported on the viral particles in presence of the pollutants. Moreover, pesticide effects on Pacific oysters were also explored through experimental pathology assays after treatment of animals with a polluant mixture. Results showed that pesticide treated oysters appeared more susceptible to the viral infection in experimental conditions. The third part concerned the study of autophagy in the Pacific oyster, C. gigas. The publication of the complete genome in 2012 has opened up new possibilities for the study of innate immunity in this species. The study of autophagy for the first time in oysters consisted in a first step in the in silico search for genes involved in this pathway and the corresponding proteins by Western blotting. Then, the role of this important process in innate immunity has been explored through reproduction infections tests with or without modulators of autophagy. Results showed that autophagy appeared as involved in defence mechanisms against viral and bacterial infection in Pacific oysters.
Le travail de thèse s’inscrit dans la problématique très actuelle des mortalités massives de naissain et de juvéniles d’huîtres creuses, C. gigas, et des questionnements autour de l’implication des pesticides dans ce phénomène. La première partie de la thèse a été consacrée à l’étude des effets de pesticides sur les capacités hémocytaires de l’huître creuse (in vitro et in vivo). L’effet immunomodulateur des xénobiotiques sélectionnés (seul ou en mélange) a été exploré principalement au travers de la cytométrie en flux. La deuxième partie de la thèse a concerné l’étude des effets d’un mélange de pesticides sélectionnés sur le virus OsHV-1 et l’infection qu’il induit chez l’huître creuse. Les effets des pesticides sur le virus lui-même ont été évalués. Les expériences réalisées non pas permis de mettre en évidence dans les conditions testées, de dégradation des particules virales en présence des polluants. D’autre part, leurs effets sur les huîtres elles-mêmes ont été explorés après traitement des animaux avec un mélange de pesticides lors d’essais de pathologie expérimentale. Il a ainsi pu être montré que des huîtres préalablement comtaminées par un mélange de pesticides à des concentrations retrouvées dans l’environnement semblaient être plus sensibles à l’infection virale. La troisième partie de la thèse a concerné l’étude de l’autophagie chez l’huître creuse, C. gigas. La publication du génome complet de cette espèce en 2012 a ouvert de nouvelles possibilités pour étudier l'immunité innée. L’étude de l’autophagie réalisée pour la première fois chez l’huître creuse a consisté lors d’une première étape en la recherche in silico de gènes impliqués dans cette voie et des protéines correspondantes par western blotting. Puis, le rôle de ce processus important dans l’immunité innée a été exploré au travers d’essais de reproduction d’infections en présence ou non de modulateurs de l’autophagie. Les résultats obtenus semblent montrer que l’autophagie soit un processus important pouvant être impliqué dans les capacités de défense de l’huître creuse vis-à-vis d’infections virales et bactériennes.

Droits : 2014 Université de La Rochelle
http://archimer.ifremer.fr/doc/00226/33740/32149.pdf
http://archimer.ifremer.fr/doc/00226/33740/

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Analysis of microbial biodiversity is hampered by a lack of reference genomes from most bacteria, viruses, and algae. This necessitates either the cultivation of a restricted number of species for standard sequencing projects or the analysis of highly complex environmental DNA metagenome data. Single-cell genomics (SCG) offers a solution to this problem by constraining the studied DNA sample to an individual cell and its associated symbionts, prey, and pathogens. We used SCG to study marine heterotrophic amoebae related to Paulinella ovalis (A. Wulff) P.W. Johnson, P.E. Hargraves & J.M. Sieburth (Rhizaria). The genus Paulinella is best known for its photosynthetic members such as P.chromatophora Lauterborn that is the only case of plastid primary endosymbiosis known outside of algae and plants. Here, we studied the phagotrophic sister taxa of P.chromatophora that are related to P.ovalis and found one SCG assembly to contain -cyanobacterial DNA. These cyanobacterial contigs are presumably derived from prey. We also uncovered an associated cyanophage lineage (provisionally named phage PoL_MC2). Phylogenomic analysis of the fragmented genome assembly suggested a minimum genome size of 200Kbp for phage PoL_MC2 that encodes 179 proteins and is most closely related to Synechococcus phage S-SM2. For this phage, gene network analysis demonstrates a highly modular genome structure typical of other cyanophages. Our work demonstrates that SCG is a powerful approach for discovering algal and protist biodiversity and for elucidating biotic interactions in natural samples.
ISSN: 0022-3646

hal-01544797
https://hal.archives-ouvertes.fr/hal-01544797
DOI : 10.1111/jpy.12028

Éditeur(s) : HAL CCSD Frontiers Media
Résumé : International audience
To date 142 species have been described in the Vibrionaceae family of bacteria, classified into seven genera; Aliivibrio, Echinimonas, Enterovibrio, Grimontia, Photobacterium, Salinivibrio and Vibrio. As vibrios are widespread in marine environments and show versatile metabolisms and ecologies, these bacteria are recognized as one of the most diverse and important marine heterotrophic bacterial groups for elucidating the correlation between genome evolution and ecological adaptation. However, on the basis of 16S rRNA gene phylogeny, we could not find any robust monophyletic lineages in any of the known genera. We needed further attempts to reconstruct their evolutionary history based on multilocus sequence analysis (MLSA) and/or genome wide taxonomy of all the recognized species groups. In our previous report in 2007, we conducted the first broad multilocus sequence analysis (MLSA) to infer the evolutionary history of vibrios using nine housekeeping genes (the 16S rRNA gene, gapA, gyrB, ftsZ, mreB, pyrH, recA, rpoA, and topA), and we proposed 14 distinct clades in 58 species of Vibrionaceae. Due to the difficulty of designing universal primers that can amplify the genes for MLSA in every Vibrionaceae species, some clades had yet to be defined. In this study, we present a better picture of an updated molecular phylogeny for 86 described vibrio species and 10 genome sequenced Vibrionaceae strains, using 8 housekeeping gene sequences. This new study places special emphasis on (1) eight newly identified clades (Damselae, Mediterranei, Pectenicida, Phosphoreum, Profundum, Porteresiae, Rosenbergii, and Rumoiensis); (2) clades amended since the 2007 proposal with recently described new species; (3) orphan clades of genomospecies F6 and F10; (4) phylogenetic positions defined in 3 genome-sequenced strains (N418, EX25, and EJY3); and (5) description of V. tritonius sp. nov., which is a member of the “Porteresiae” clade.
ISSN: 1664-302X

hal-01546980
http://hal.upmc.fr/hal-01546980
DOI : 10.3389/fmicb.2013.00414

Éditeur(s) : HAL CCSD SpringerLink
Résumé : Trinucleotide microsatellites have proven to be the markers of choice in human genetic analysis because they are easier to genotype than dinucleotides. Their development can be more time-consuming due to their lower abundance in the genome. We isolated trinucleotide microsatellites in Norway spruce (Picea abies K.) using an enrichment procedure for the genomic-library construction. Here we report on the characterisation of 85 ATC microsatellite-containing clones, from which 39 markers were developed. Many of the clones showed the occurrence of tandem repeats of higher order than the trinucleotide ones, often resembling minisatellite repeats. The sequencing of a sample of the alleles at one of the loci revealed size homoplasy due to base substitutions within the microsatellite region. The presence of ATC motifs within repetitive sequence families was observed. We found a significant relationship between the level of polymorphism and the length of the microsatellite. The levels of variability for ATC trinucleotide markers were lower than those for dinucleotides, both when tested on all loci in a set of six individuals and on a subset of loci in four natural populations. This difference is most likely attributable to lower mutation rates for trinucleotide than for dinucleotide loci. The availability of markers with different mutation rates allows one to select the proper marker set to investigate population processes on different time scales.
Theoretical and Applied Genetics

hal-01032029
https://hal.archives-ouvertes.fr/hal-01032029
DOI : 10.1007/s00122-002-0986-1

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 Elsevier
Résumé : International audience
BACKGROUND: The insecticide chlordecone was extensively used in the French West Indies to control banana root borer. Its persistence in soils has led to the widespread pollution of the environment, and human beings are still exposed to this chemical. Chlordecone has been shown to impair neurological and behavioural functions in rodents when exposed gestationally or neonatally. OBJECTIVES: The aim of the study was to evaluate the impact of prenatal and postnatal exposure to chlordecone on the cognitive, visual, and motor development of 7-month-old infants from Guadeloupe. METHODS: Infants were tested at 7 months (n=153). Visual recognition memory and processing speed were assessed with the Fagan Tests of Infant Intelligence (FTII), visual acuity with the Teller Acuity Card, and fine motor development with the Brunet-Lezine. Samples of cord blood and breast milk at 3 months (n=88) were analyzed for chlordecone concentrations. Postnatal exposure was determined through breast feeding and frequency of contaminated food consumption by the infants. RESULTS: Cord chlordecone concentrations in tertiles were associated with reduced novelty preference on the FTII in the highly exposed group (β=-0.19, p=0.02). Postnatal exposure through contaminated food consumption was marginally related to reduced novelty preference (β=-0.14, p=0.07), and longer processing speed (β=0.16, p=0.07). Detectable levels of chlordecone in cord blood were associated with higher risk of obtaining low scores on the fine motor development scale (OR=1.25, p<0.01). CONCLUSION: These results suggest that pre- and postnatal low chronic exposure to chlordecone is associated with negative effects on cognitive and motor development during infancy.
ISSN: 0013-9351

hal-00875939
https://hal.archives-ouvertes.fr/hal-00875939
DOI : 10.1016/j.envres.2012.07.006
PUBMED : 22910562

Éditeur(s) : HAL CCSD Society for the Study of Reproduction
Résumé : International audience
Spermmotility notably depends on the structural integrity of the flagellum and the regulation ofmicrotubule dynamics. Although researchers have started to use " omics" techniques to characterize the human sperm's molecular landscape, the constituents responsible for the assembly, organization, and dynamics of the flagellum microtubule have yet to be fully defined. In this study, we defined a core set of 116 gene products associated with the human sperm microtubulome (including products potentially involved in abnormal ciliary phenotypes and male infertility disorders). To this end, we designed and applied an integrated genomics workflow and combined relevant proteomics, transcriptomics, and interactomics datasets to reconstruct a dynamic interactome map. By further integrating phenotypic information, we defined a disease-interaction network; this enabled us to highlight a number of novel factors potentially associated with altered sperm motility and male fertility. Lastly, we experimentally validated the expression pattern of two candidate genes (CUL3 and DCDC2C) that had never previously been associated with male germline differentiation. Our analysis suggested that CUL3 and DCDC2C's products have important roles in the sperm flagellum. Taken as a whole, our results demonstrate that an integrated genomics strategy can highlight relevant molecular factors in specific sperm components. This approach could be easily extended by including other " omics" data (from asthenozoospermic men, for example) and identifying other critical proteins from the human sperm microtubulome. Summary Sentence Although researchers have started to use "omics" techniques to characterize the human sperm's molecular landscape, the constituents responsible for the assembly, organization, and dynamics of the flagellum microtubule have yet to be fully defined.
ISSN: 0006-3363

hal-01515563
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01515563
DOI : 10.1095/biolreprod.116.143479
PUBMED : 28395323

Éditeur(s) : HAL CCSD Royal Society
Résumé : International audience
The 2 465 177 bp genome of Sulfolobus islandicus LAL14/1, host of the model rudivirus SIRV2, was sequenced. Exhaustive comparative genomic analysis of S. islandicus LAL14/1 and the nine other completely sequenced S. islandicus strains isolated from Iceland, Russia and USA revealed a highly syntenic common core genome of approximately 2 Mb and a long hyperplastic region containing most of the strain-specific genes. In LAL14/1, the latter region is enriched in insertion sequences, CRISPR (clustered regularly interspaced short palindromic repeats), glycosyl transferase genes, toxin-antitoxin genes and MITE (miniature inverted-repeat transposable elements). The tRNA genes of LAL14/1 are preferential targets for the integration of mobile elements but clusters of atypical genes (CAG) are also integrated elsewhere in the genome. LAL14/1 carries five CRISPR loci with 10 per cent of spacers matching perfectly or imperfectly the genomes of archaeal viruses and plasmids found in the Icelandic hot springs. Strikingly, the CRISPR_2 region of LAL14/1 carries an unusually long 1.9 kb spacer interspersed between two repeat regions and displays a high similarity to pING1-like conjugative plasmids. Finally, we have developed a genetic system for S. islandicus LAL14/1 and created ΔpyrEF and ΔCRISPR_1 mutants using double cross-over and pop-in/pop-out approaches, respectively. Thus, LAL14/1 is a promising model to study virus-host interactions and the CRISPR/Cas defence mechanism in Archaea.
ISSN: 2046-6390

hal-00818894
https://hal.archives-ouvertes.fr/hal-00818894
DOI : 10.1098/rsob.130010
PUBMED : 23594878

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 Elsevier
Résumé : International audience
Aryl hydrocarbon receptor-dependent genomic effects of environmental polycyclic aromatic hydrocarbons (PAHs) have been shown to be modulated by non-genomic protein kinase C (PKC)-related pathways. The present study was designed to determine whether PKC activation may also impair estrogenic genomic response triggered by PAHs. Treatment by the PKC activator phorbol 12-myristate 13-acetate (PMA) was found to markedly and differentially impair the up-regulation of estrogenic markers triggered by the estrogenic PAH benzanthracene (BZA) in cultured human mammary cells; BZA-mediated mRNA up-regulation of pS2 and amphiregulin was thus increased, whereas that of progesterone receptor and CXCL12 was repressed. BZA/PMA cotreatment however failed to alter BZA-mediated increase of activity of a luciferase gene reporter construct driven by an estrogen response element, thus discarding any global effect of PMA toward BZA-triggered estrogen receptor activation. Various chemicals inhibiting PKCs or extracellular signal-regulated kinase (ERK) as well as the knock-down of PKCδ expression counteracted the PMA-mediated increase of pS2 mRNA up-regulation triggered by BZA, demonstrating that it was dependent on PKCs, including PKCδ isoform, and ERKs. This non-genomic modulation of estrogenic effects of PAHs by PKC activation may have to be considered when considering the deleterious effects of these environmental contaminants towards the endocrine system.
ISSN: 0887-2333

inserm-00872862
http://www.hal.inserm.fr/inserm-00872862
DOI : 10.1016/j.tiv.2012.05.006
PUBMED : 22643241

Éditeur(s) : HAL CCSD
Résumé : The recent accumulation of genomic sequence data has shown that gene evolution is not strictly tree-Like. Many evolutionary processes, like exon shuffling, gene fusion or nonhomologous recombination remodel genes by creating composite structures that are made from parts with different evolutionary histories. The development of sequence similarity networks provides an analytical framework to study the impact of these processes on molecular evolution, by structuring the resemblance relationships between sequences and by formalizing, in terms of graph theory, the detection of composite genes (intransitive triplets) and gene families (clique minimal separators). The size of current data sets, typically several million sequences, has also required the development of new tools and methods: sequence comparison parallelization, large networks visualization with Louvain communities and large cycles identification. When applied to eukaryotic and viral genome data sets, these methods have shown that composite genes are found throughout cellular organisms and mobile genetic elements. Proportionally, composite genes are more numerous in eukaryotic genomes; in absolute number, they are more numerous in viruses. In the latter, composite genes functional distribution is biased (enrichment of genes families that are essential for the perpetuation of the viral cycle), and the various parts of composite genes sometimes even originate from the genetic material of different viral classes. More generally, the extent of combinatorial processes, by unravelling other evolutionary bonds than homology bonds in the strictest sense, legitimates a pluralistic study of similarity relationships between sequences.
L’accumulation récente de données de séquences génomiques a montré que l’évolution des gènes n’est pas strictement arborescente. De nombreux processus évolutifs, comme l’exon shuffling, la fusion de gènes ou la recombinaison illégitime remodèlent les gènes, créant des structures composites, formées de parties dont les histoires évolutives sont différentes. Le développement de réseaux de similarité de séquences fournit un cadre analytique permettant d’étudier l’impact de ces processus sur l’évolution moléculaire, en structurant les relations de ressemblance entre séquences et en formalisant en termes de graphes la détection de gènes (triplets intransitifs) et de familles de gènes (cliques minimales séparatrices) composites. La taille des jeux de données actuels, de l’ordre de plusieurs millions de séquences, a également requis le développement de nouveaux outils et méthodes : parallélisation des comparaisons de séquences, visualisation de très grands réseaux par simplification en communautés de Louvain et identification de grands cycles. Appliquées à des jeux de données de génomes eucaryotes et viraux, ces méthodes ont démontré la présence de gènes composites dans tout le vivant et les éléments génétiques mobiles. En proportion, les gènes composites sont plus nombreux dans les génomes eucaryotes ; en nombre absolu, ils sont plus nombreux à être portés par des virus. Chez ces derniers, la distribution fonctionnelle des gènes composites est biaisée (enrichissement dans les familles essentielles pour la perpétuation du cycle viral), et les éléments des gènes composites trouvent même parfois leurs origines dans le matériel génétique de classes virales différentes. Plus généralement, l’étendue des processus combinatoires, en révélant des liens évolutionnaires autres que les liens d’homologie au sens fort, justifie une étude pluraliste des relations de similarité entre séquences.
https://tel.archives-ouvertes.fr/tel-01127379

NNT : 2014PA066358
tel-01127379
https://tel.archives-ouvertes.fr/tel-01127379
https://tel.archives-ouvertes.fr/tel-01127379/document
https://tel.archives-ouvertes.fr/tel-01127379/file/2014PA066358.pdf

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background: The relative scarcity of Copia retrotransposons has been recently characterized in metazoans in comparison with the other superfamilies of LTR elements. Furthermore, Copia retrotransposons have often a particular dynamics that results in a highly predominant single clade of elements within a large host taxon, such as the GalEa-like retrotransposons in crustaceans. Taking advantage of the skyrocketing amount of genomic data available for fungi, we carried out the first large-scale comparative genomic analysis of the Copia clades in filamentous ascomycetes.Results: Screening 30 completely sequenced genomes allowed us to identify more than 2500 Copia copies with conserved LTR, which are distributed in 138 families. Their characterization revealed that fungal Copia diversity is much broader than previously thought with at least 27 clades, 23 of which likely correspond to new ones. While the Copia copy number is low in most species, the two clades GalEa and FunCo1 are widely distributed and highly dominate Copia content as they both account for 80% of the detected sequences.Conclusions: In Fungi, GalEa retrotransposons are restricted to Pezizomycotina in which they can make up an outstandingly high proportion of the genome (up to 10% in Cenococcum geophilum). At last, we revealed that fungal GalEa elements structurally differ from all other Copia elements with an absence of Primer Binding Site. These elements however harbor a Conserved Hairpin Site which is probably essential for their transposition.sequences.
ISSN: 1471-2164

Droits : http://creativecommons.org/licenses/by/
hal-01529914
http://hal.upmc.fr/hal-01529914
http://hal.upmc.fr/hal-01529914/document
http://hal.upmc.fr/hal-01529914/file/art_10.1186_s12864-017-3795-2.pdf
DOI : 10.1186/s12864-017-3795-2

Éditeur(s) : HAL CCSD
Résumé : International audience
Spermatogenesis is a highly sophisticated process involved in the transmission of genetic heritage. It includes halving ploidy, repackaging of the chromatin for transport, and the equipment of developing spermatids and eventually spermatozoa with the advanced apparatus (e.g., tightly packed mitochondrial sheat in the mid piece, elongating of the tail, reduction of cytoplasmic volume) to elicit motility once they reach the epididymis. Mammalian spermatogenesis is divided into three phases. In the first the primitive germ cells or spermatogonia undergo a series of mitotic divisions. In the second the spermatocytes undergo two consecutive divisions in meiosis to produce haploid spermatids. In the third the spermatids differentiate into spermatozoa in a process called spermiogenesis. Paracrine, autocrine, juxtacrine, and endocrine pathways all contribute to the regulation of the process. The array of structural elements and chemical factors modulating somatic and germ cell activity is such that the network linking the various cellular activities during spermatogenesis is unimaginably complex. Over the past two decades, advances in genomics have greatly improved our knowledge of spermatogenesis, by identifying numerous genes essential for the development of functional male gametes. Large-scale analyses of testicular function have deepened our insight into normal and pathological spermatogenesis. Progress in genome sequencing and microarray technology have been exploited for genome-wide expression studies, leading to the identification of hundreds of genes differentially expressed within the testis. However, although proteomics has now come of age, the proteomics-based investigation of spermatogenesis remains in its infancy. Here, we review the state-of-the-art of large-scale proteomic analyses of spermatogenesis, from germ cell development during sex determination to spermatogenesis in the adult. Indeed, a few laboratories have undertaken differential protein profiling expression studies and/or systematic analyses of testicular proteomes in entire organs or isolated cells from various species. We consider the pros and cons of proteomics for studying the testicular germ cell gene expression program. Finally, we address the use of protein datasets, through integrative genomics (i.e., combining genomics, transcriptomics, and proteomics), bioinformatics, and modelling.
Systems Biology in Reproductive Medicine

hal-00877749
https://hal.archives-ouvertes.fr/hal-00877749
DOI : 10.3109/19396368.2012.691943
PUBMED : 22788530

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
Glioblastoma (GB) is the most frequent and aggressive type of primary brain tumor. Recurrences are mostly located at the margin of the resection cavity in the peritumoral brain zone (PBZ). Although it is widely believed that infiltrative tumor cells in this zone are responsible for GB recurrence, few studies have examined this zone. In this study, we analyzed PBZ left after surgery with a variety of techniques including radiology, histopathology, flow cytometry, genomic, transcriptomic, proteomic, and primary cell cultures. The resulting PBZ profiles were compared with those of the GB tumor zone and normal brain samples to identify characteristics specific to the PBZ. We found that tumor cell infiltration detected by standard histological analysis was present in almost one third of PBZ taken from an area that was considered normal both on standard MRI and by the neurosurgeon under an operating microscope. The panel of techniques used in this study show that the PBZ, similar to the tumor zone itself, is characterized by substantial inter-patient heterogeneity, which makes it difficult to identify representative markers. Nevertheless, we identified specific alterations in the PBZ such as the presence of selected tumor clones and stromal cells with tumorigenic and angiogenic properties. The study of GB-PBZ is a growing field of interest and this region needs to be characterized further. This will facilitate the development of new, targeted therapies for patients with GB and the development of approaches to refine the per-operative evaluation of the PBZ to optimize the surgical resection of the tumor.
ISSN: 0167-594X

hal-01117083
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01117083
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01117083/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01117083/file/Characterizing%20the%20Peritumoral%20Brain%20Zone_accepted.pdf
DOI : 10.1007/s11060-014-1695-8

Éditeur(s) : HAL CCSD Springer Verlag/EDP Sciences
Résumé : No efficient method is available to compare multi-locus estimates of diversity while taking into account inter-locus and inter-population stochastic variance. The advent of genome scan approaches makes the development of such tests absolutely necessary. We developed a method to compare genome-wide diversity estimates while taking into account-and factoring out-variation in census size and making use of inter-locus variance to assess significance of differences in diversity levels. An approach based on rarefaction with bootstrap re-sampling (RaBoT) was implemented into a test of multi-locus comparison of diversity coded in R. The properties of the test were studied by applying it to simulated populations with varying diversity levels and varying differences in diversity levels. The test was then applied to empirical data from disturbed and undisturbed populations of Virola michelii (Myristicaceae) genotyped at 693 amplified fragment length polymorphism (AFLP) markers. RaBoT was found to be rather conservative, with large numbers of false negatives when the diversity in the compared populations was similar, and false positives mostly associated to comparisons of populations with extremely high levels of diversity. When applied to empirical data, RaBoT detected higher genetic diversity in a post-disturbance than in an undisturbed population and lower genetic diversity in a seedling than in the corresponding adult population, but it also revealed differences in diversity between subgroups within the disturbed and undisturbed plots. RaBoT is a sensitive method to compare multi-locus levels of diversity that can be applied both at the genotype level for dominant markers (e.g. AFLP) and at the allele level for biallelic codominant markers (e.g. single-nucleotide polymorphisms).
ISSN: 1286-4560

hal-01032413
https://hal.archives-ouvertes.fr/hal-01032413
DOI : 10.1007/s13595-013-0302-z

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
Genetic recombination occurs during meiosis, the key developmental programme of gametogenesis. Recombination in mammals has been recently linked to the activity of a histone H3 methyltransferase, PR domain containing 9 (PRDM9), the product of the only known speciation-associated gene in mammals. PRDM9 is thought to determine the preferred recombination sites--recombination hotspots--through sequence-specific binding of its highly polymorphic multi-Zn-finger domain. Nevertheless, Prdm9 knockout mice are proficient at initiating recombination. Here we map and analyse the genome-wide distribution of recombination initiation sites in Prdm9 knockout mice and in two mouse strains with different Prdm9 alleles and their F(1) hybrid. We show that PRDM9 determines the positions of practically all hotspots in the mouse genome, with the exception of the pseudo-autosomal region (PAR)--the only area of the genome that undergoes recombination in 100% of cells. Surprisingly, hotspots are still observed in Prdm9 knockout mice, and as in wild type, these hotspots are found at H3 lysine 4 (H3K4) trimethylation marks. However, in the absence of PRDM9, most recombination is initiated at promoters and at other sites of PRDM9-independent H3K4 trimethylation. Such sites are rarely targeted in wild-type mice, indicating an unexpected role of the PRDM9 protein in sequestering the recombination machinery away from gene-promoter regions and other functional genomic elements.
ISSN: 0028-0836

hal-00877666
https://hal.archives-ouvertes.fr/hal-00877666
DOI : 10.1038/nature11089
PUBMED : 22660327

Éditeur(s) : Université de Paris 6 – Pierre et Marie Curie
Résumé : Since 1997, a new pathology seasonally occurs in new caledonian shrimp farms during the warm season and was named Summer Syndrome. Diseased Litopenaeus stylirostris shrimp suffer from a septicemic vibriosis which was attributed to V. nigripulchritudo. Preliminary studies based on a collection of V. nigripulchritudo strains have brought to light different virulence levels according to experimental infections results; three virulence statuses were defined: highly (HP), moderately (MP) and non pathogenic (NP). The aim of this work was to genetically characterize virulent V. nigripulchritudo strains. In a first step the genetic diversity of 58 V. nigripulchritudo strains was analyzed by MLST and AP-PCR, revealing a cluster of HP and MP strains, characterized by a low genetic variability and that includes all Summer Syndrome-associated isolates. This confirms the emergence of one cluster of pathogenic V. nigripulchritudo simultaneously with the emergence of the Summer Syndrome ; in a second step, 368 genetic markers of virulence were identified by a Suppressive Subtractive Hybridization performed between the genomes of a HP strain and a genetically close, NP isolate; the distribution of the screened SSH fragments was studied in 58 V. nigripulchritudo isolates by macro-array: 78 DNA fragments were selected, allowing to characterize clusters identified and pathogenic statuses; 13 are specific of the HP strains involved in Summer Syndrome. Interestingly, 10 of these markers are carried by a plasmid pSFn1 that contains sequences highly similar to those of a plasmid pAK1, detected in Vibrio shilonii, a coral pathogen. The origin and consequences of this plasmid acquisition are discussed.
Depuis 1997, les élevages de crevettes en Nouvelle-Calédonie sont confrontés à une nouvelle maladie, le Syndrome d'été, une vibriose septicémique dont l'agent étiologique est Vibrio nigripulchritudo. Les résultats d'infection expérimentale sur une collection de souches, ont montré l'existence de trois pathotypes distincts : hautement (HP), moyennement (MP) et non pathogène (NP). L'étude du polymorphisme génétique de 58 souches par typage moléculaire en MLST et AP-PCR, a mis en évidence un groupe phylogénétique particulier caractérisé par un très faible degré de variabilité génétique (confirmant l'émergence de ce groupe en parallèle à l'émergence du Syndrome d'été) et constitué uniquement de souches HP (dont toutes celles associées au Syndromed'été) et de souches MP. Afin d'identifier des marqueurs génétiques de la virulence des souches responsables du Syndrome d'été, et parmi ces marqueurs des gènes codant potentiellement pour des effecteurs de la virulence, une approche soustractive par SSH a été développée entre une souche HP de type Syndrome d'été et une souche NP : 368 marqueurs génétiques ont ainsi été mis en évidence ; la distribution de ces marqueurs a été étudiée chez les 58 souches de la collection par une approche en macroarray : 78 marqueurs ont été sélectionnés, qui permettent de caractériser les différents groupes phylogénétiques et les différents pathotypes, dont 13 fragments spécifiques des souches HP type Syndrome d'été. Parmi ces 13 fragments, 10 ont été localisés sur le plasmide pSFn1 qui a été entièrement séquencé. Ce même plasmide a été purifié uniquement des souches HP de type Syndrome d'été. Par ailleurs, une très forte homologie a été mise en évidence entre pSFn1 et pAK1, un autre plasmide également séquencé et retrouvé chez la souche V. shilonii AK1, responsable du blanchiment du corail Oculina patagonica en Méditerranée. Ces résultats ont ouvert la discussion sur le rôle de pSFn1 dans la virulence de V. nigripulchritudo.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2008/these-3906.pdf
http://archimer.ifremer.fr/doc/00000/3906/