Éditeur(s) : HAL CCSD Elsevier
Résumé : Recent evolutionary studies clearly indicate that evolution is mainly driven by changes in the complex mechanisms of gene regulation and not solely by polymorphism in protein-encoding genes themselves. After a short description of the cis-regulatory mechanism, we intend in this review to argue that by applying newly available technologies and by merging research areas such as evolutionary and developmental biology, population genetics, ecology and molecular cell biology it is now possible to study evolution in an integrative way. We contend that, by analysing the effects of promoter sequence variation on phenotypic diversity in natural populations, we will soon be able to break the barrier between the study of extant genetic variability and the study of major developmental changes. This will lead to an integrative view of evolution at different scales. Because of their sessile nature and their continuous development, plants must permanently regulate their gene expression to react to their environment, and can, therefore, be considered as a remarkable model for these types of studies. (C) 2010 Elsevier Ireland Ltd. All rights reserved.
ISSN: 0168-9452

hal-01032399
https://hal.archives-ouvertes.fr/hal-01032399
DOI : 10.1016/j.plantsci.2010.09.009

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
The first studies of the 16S rRNA gene diversity of the bacterial symbionts found in lucinid clams did not clarify how symbiotic associations had evolved in this group. Indeed, although species-specific associations deriving from a putative ancestral symbiotic association have been described (coevolution scenario), associations between the same bacterial species and various host species (opportunistic scenario) have also been described. Here, we carried out a comparative molecular analysis of hosts, based on 18S and 28S rRNA gene sequences, and of symbionts, based on 16S rRNA gene sequences, to determine as to which evolutionary scenario led to modern lucinid/symbiont associations. For all sequences analyzed, we found only three bacterial symbiont species, two of which are harbored by lucinids colonizing mangrove swamps. The last symbiont is the most common and was found to be independent of biotope or depth. Another interesting feature is the similarity of ctenidial organization of lucinids from the Philippines to those described previously, with the exception that two bacterial morphotypes were observed in two different species (Gloverina rectangularis and Myrtea flabelliformis). Thus, there is apparently no specific association between Lucinidae and their symbionts, the association taking place according to which bacterial species is present in the environment.
ISSN: 0168-6496

hal-00743766
https://hal.univ-antilles.fr/hal-00743766
DOI : 10.1111/j.1574-6941.2010.00989.x

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Pathogenic agents can be very hard to detect, and usually they do not cause illness for several hours or days. To improve the speed and the accuracy of detection tests and satisfy the needs of early diagnosis, molecular biology methods such as PCR are now used. However, selecting a proper target gene and designing good primers is often not easy. We present a dedicated website, http://patho-genes.org, where we provide every sequence, functional annotation, published primer and relevant article for every annotated gene of major pathogenic bacterial species listed as key agents to be used for a bioterrorism attack. Each published primer was analysed to determine its melting temperature, its specificity and its coverage (i.e. its sensitivity against every allele of its target gene). Data generated have been organized in the form of data sheet for each gene, which are available through multiple browser panels and query systems.
ISSN: 1751-7915

hal-01546181
https://hal.archives-ouvertes.fr/hal-01546181
DOI : 10.1111/j.1751-7915.2012.00353.x

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/

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
BACKGROUND: This study examines gene-environment interaction between the MTHFR C667T polymorphism and folic acid in the etiology of orofacial clefts (OFC). We used a pooled-analytical approach on four studies that used similar methods. METHODS: We used logistic regression to analyze the pooled sample of 1149 isolated cases and 1161 controls. Fetal and maternal MTHFR C677T genotypes, and maternal periconceptional exposure to smoking, alcohol, vitamin containing folic acid and folic acid supplements were contrasted between the cleft types [non-syndromic clefts lip or without cleft palate (CL(P)) and non-syndromic cleft palate (CP)] and control groups. RESULTS: There was a reduced risk of CL(P) with maternal folic acid use (p = 0.008; OR = 0.70, 95% CI: 0.65-0.94) and with supplements containing folic acid (p = 0.028, OR = 0.80, 95% CI: 0.65-0.94). Maternal smoking increased the risk of both CL(P) (p < 10 e-3; OR = 1.62, 95% CI: 1.35-1.95) and CP (p = 0.028; OR = 1.38, 95% CI: 1.04-1.83). No significant risk was observed with either maternal or fetal MTHFR C677T genotypes. CONCLUSION: This individual participant data (IPD) meta-analysis affords greater statistical power and can help alleviate the problems associated with aggregate-level data-sharing. The result of this IPD meta-analysis is consistent with previous reports suggesting that folic acid and smoking influence OFC outcomes.
ISSN: 1542-0752

hal-00875899
https://hal.archives-ouvertes.fr/hal-00875899
DOI : 10.1002/bdra.23133
PUBMED : 23670871

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background: Ovarian failure (OF) is considered premature if it occurs before the age of 40. This study investigates the genetic aetiology underlying OF in women under the age of 40 years. Methods: We conducted an experimental prospective study performing all genome microarrays in 60 patients younger than 40 years presenting an OF revealed by a decrease of circulating Anti-Mullerian Hormone (AMH) and leading to an oocyte donation program. Results: We identified nine significant copy number variations (CNVs) including candidate genes potentially implicated in reproductive function. These genes are principally involved in cell division and chromosome segregation (SYCE1, CLASP1, CENP-A, CDC16), in ciliary development and/or function (RSPH1, KIF24), are linked with known gonadal genes or expressed in female genital tract (CSMD1, SEMA6D, KIAA1324). Conclusions: Our data strengthen the idea that microarrays should be used in combination with karyotype for aetiological assessment of patients with OF. This analysis may have a therapeutic impact as the identification of new molecular actors for gonadal development or ovarian physiology is useful for the prediction of an ovarian reserve decline and makes possible preventive fertility preservation.
ISSN: 1757-2215

hal-01390979
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01390979
DOI : 10.1186/s13048-016-0272-5
PUBMED : 27716277

Éditeur(s) : HAL CCSD Linnean Society of London
Résumé : International audience
Although migratory pelagic fishes generally exhibit little geographic differentiation across oceans, as expected from their life-history (broadcast spawning, pelagic larval life, swimming ability of adults) and the assumed homogeneity of the pelagic habitat, exceptions to the rule deserve scrutiny. One such exception is the narrow-barred Spanish mackerel (Scomberomorus commerson), where strong genetic heterogeneity at the regional scale has been previously reported. We investigated the genetic composition of S. commerson across the Indo-West Pacific range using control-region sequences (including previously published datasets), cytochrome-b gene partial sequences, and eight microsatellite loci, to further explore its phylogeographic structure. All haplotypes sampled from the Indo-Malay-Papua archipelago (IMPA) and the southwestern Pacific coalesced into a clade (Clade II) that was deeply separated (14.5% nucleotide divergence) from a clade grouping all haplotypes from the Persian Gulf and Oman Sea (Clade I). Such a high level of genetic divergence suggested the occurrence of two sister-species. Further phylogeographic partition was evident between the western IMPA and the regions sampled east and south of it, i.e. northern Australia, West Papua, and the Coral Sea. Strong allele-frequency differences were found between local populations in the southwestern Pacific, both at the mitochondrial locus (ΦST=0.282-0.609) and at microsatellite loci (^θ=0.202-0.313). Clade II consisted of four deeply divergent subclades (9.0-11.8% nucleotide divergence for the control region; 0.3-2.5% divergence at the cytochrome b locus). Mitochondrial sub-clades within Clade II generally had narrow geographic distribution, demonstrating further genetic isolation. However, one particular haplogroup within Clade II was present throughout the central Indo-West Pacific; that haplogroup was found to be sister-group to an haplogroup restricted to West Papua and the Coral Sea, yielding evidence of recent secondary westward colonization. Such a complex structure is in sharp contrast with the generally weak phylogeographic patterns uncovered to date in other widely distributed, large pelagic fishes with pelagic eggs and larvae. We hypothesize that in S. commerson and possibly other Scomberomorus species, philopatric migration may play a role in maintaining the geographic isolation of populations by annihilating the potential consequences of passive dispersal.
Biological Journal of the Linnean Society

ird-00759711
http://hal.ird.fr/ird-00759711
http://hal.ird.fr/ird-00759711/document

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Bruggemann, J.H. (2016). Phylogenetic relationships within Aglaopheniidae (Cnidaria, Hydrozoa) reveal unexpected generic diversity. — Zoologica Scripta, 45, 103–114. Morphology can be misleading in the representation of phylogenetic relationships, especially in simple organisms like cnidarians and particularly in hydrozoans. These suspension feeders are widely distributed in many marine ecosystems, and the family Aglaopheniidae Marktanner-Turneretscher, 1890 is among the most diverse and visible, especially on tropical coral reefs. The taxonomy of this family is based on morphological characters with emphasis on reproductive structures for the identification of genera. This study is the most comprehensive molecular phylogeny of the Aglaopheniidae to date, including six genera and 38 species, of which 13 were investigated for the first time and sampled on tropical coral reefs throughout the Indo-Pacific region. For newly sampled individuals, we sequenced the 16S rRNA, the nuclear locus comprising the complete ITS1-5.8S rRNA gene-ITS2 and the first intron of the calmodulin nuclear gene. Phylogenetic analyses of the data revealed and confirmed a general polyphyly, or doubtful monophyly, of all sampled genera in tropical regions based on both the mitochondrial and nuclear markers. Our results revealed that several morphological characters used today are unsuited to resolve phylogenetic relationships between species and genera, as well as the high phyletic diversity within this family. Future revision of the classification of this family will require extensive geographic sampling and the use of an integrative approach.
ISSN: 0300-3256

hal-01359414
https://hal.archives-ouvertes.fr/hal-01359414
DOI : 10.1111/zsc.12135

Résumé : The New-Caledonian shrimp industry is based on the controlled reproduction of the shrimp Litopenaeus stylirostris, a species which was introduced in the 80s. The major difficulty to which the industry has been faced for 10 years is the occurrence of the "syndrome 93", which corresponds to mortality phases when the temperature falls down in April-May-June. This mortality is associated to the pathogenic bacteria Vibrio penaecida and is expressed at different levels which are variable from year ta year and from pond to pond. No resistance to this pathology has been developed spontaneously. This is likely due to the protocole used to rear spawners, which does not allow to implement an efficient selective pressure at each generation An experimental selection on the criteria of survival after picks of syndrome 93 has been conducted at the Laboratoire Aquacole de Calédonie. The 3rd selected generation demonstrates survival rates improved by 20% during experimental infections with V. penaeicida in comparison with a non selected control population of same genetic origin. The comparison of the correlated responses on the level of expression of 5 genes which are potentially implicated in immunity phenomena (Peneidins, lysozyme, transglutaminase. profiline, annexine) shows that the selected population has a level of expression in lyzozyme twice higher than the control population. This result suggests that the lysozyme could be a genetic marker which could be used in a selective breeding program to he developed in relation with the private hatcheries.
La filière crevette de Nouvelle-Calédonie repose sur la maîtrise de la reproduction contrôlée de la crevette Litopenaeus stylirostris, espèce introduite dans les années 80. La difficulté majeure que rencontre la filière depuis une dizaine d'années est la récurrence du « syndrome 93 », qui correspond à des épisodes de mortalités lors des baisses de température en avril-mai-juin. Ces mortalités sont associées à la bactérie pathogène Vibrio penaeicida et s'expriment à des niveaux d'intensité variable d'une année à l'autre et d'un bassin à l'autre. Aucune résistance vis-à-vis de cette pathologie ne s'est développée spontanément. Ceci est vraisemblablement lié au protocole employé pour l'élevage des géniteurs qui ne permet pas d'exercer une pression de sélection efficace à chaque génération. Une expérience de sélection sur un critère de survie à des épisodes de syndrome 93 a été menée au Laboratoire Aquacole de Calédonie. La 3ème génération sélectionnée montre des survies améliorées de l'ordre de 20% lors d'infections expérimentales à V. penaeicida par rapport à une population témoin non sélectionnée de même origine génétique. La comparaison des réponses corrélées sur le niveau d'expression de 5 gènes potentiellement impliqués dans les phénomènes de défense immunitaire (penaeidine, lysozyme, transglutaminase, profiline, annexine) montre que la population sélectionnée a un niveau d'expression en lysozyme deux fois plus élevé que la population témoin. Ce résultat suggère que le lysozyme pourrait être un marqueur génétique utilisable dans un programme de sélection à développer en relation avec les écloseries de production.

Droits : 2003 Ifremer
http://archimer.ifremer.fr/doc/00109/22020/19643.pdf
http://archimer.ifremer.fr/doc/00109/22020/

Éditeur(s) : HAL CCSD
Résumé : Scope: TNF-Related Apoptosis-Inducing Ligand (TRAIL) induces apoptosis via the extrinsic death pathway in human colon cancer cells. Short Chain Fatty Acids (SCFA) by contrast induce apoptosis of cancer cells via the intrinsic death pathway. We have previously shown that food-grade dairy propionibacteria induce intrinsic apoptosis of colon cancer cells, via SCFA metabolites (propionate and acetate) acting on mitochondria. We investigate here the possible synergistic pro-apoptotic effect between Propionibacterium freudenreichii and TRAIL. Methods and results: Whole transcriptomic analysis demonstrated that propionibacterial supernatant or propionibacterial SCFA, in combination with TRAIL, increased pro-apoptotic gene expression (TRAIL-R2/DR5) and decreased anti-apoptotic gene expression (FLIPL, XIAP) in HT29 human colon cancer cells. The revealed synergistic pro-apoptotic effect, depending on both death receptors (TRAIL-R1/DR4, TRAIL-R2/DR5) and caspases (caspase-8, -9 and -3) activation, was lethal on cancer cells but not on normal human intestinal epithelial cells (HIEC), and was inhibited by Bcl-2 expression. Finally, milk fermented by P. freudenreichii induced HT29 cells apoptosis and enhanced TRAIL cytotoxic activity, as did P. freudenreichii culture supernatants or its SCFA metabolites.Conclusion: The revealed synergy opens new applications for food-grade P. freudenreichii-containing products as new adjuvants to potentiate TRAIL-based cancer therapy in colorectal cancer.
International Scientific Conference on Probiotics and Prebiotics - IPC2016
Budapest, Hungary

hal-01286497
https://hal.archives-ouvertes.fr/hal-01286497
PRODINRA : 349367

Éditeur(s) : HAL CCSD American Society for Microbiology
Résumé : International audience
: Estradiol signaling is ideally suited for analyzing molecular and functional linkages between the different layers of information directing transcriptional regulations: DNA sequence, chromatin modifications and the spatial organization of the genome. Hence, estrogen receptor (ER) can bind at a distance from its target genes and engages timely and spatially coordinated processes to regulate their expression. In the context of the coordinated regulations of co-linear genes, identifying which ER binding sites (ERBSs) regulate a given gene still remains a challenging question. Here, we investigated the coordination of such regulatory events at a 2 Mb genomic locus containing the estrogen-sensitive TFF cluster of genes in breast cancer cells. We demonstrated that this locus exhibits a hormone and cohesin-dependent reduction in the plasticity of its three-dimensional organization that allows multiple ERBSs to be dynamically brought to the vicinity of estrogen-sensitive genes. Additionally, by using triplex forming oligonucleotides, we could precisely document the functional links between ER engagement at given ERBSs and the regulation of particular genes. Hence, our data evidence a formerly suggested cooperation of enhancers towards gene regulations, and also show that redundancy between ERBSs can occur.
ISSN: 0270-7306

hal-00984591
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00984591
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00984591/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00984591/file/Mol._Cell._Biol.-2014-Quintin-MCB.00918-13.pdf
DOI : 10.1128/MCB.00918-13

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
Interleukin-27 (IL-27) belongs to the IL-6/IL-12 family of cytokines, associated with different inflammatory diseases and orchestrates its biological activity via common heterodimeric receptor composed of WSX-1 (IL-27Rα) and gp130. The present study was aimed to investigate the regulation of CXCL9, CXCL10, and CXCL11 chemokines in hepatic cells (human LX-2 cell line derived from normal human stellate cells (HSC), primary human hepatocytes, HSC, and HepG2 cells) and concanavalin A (ConA)-induced liver inflammation. We demonstrated that IL-27, but not IL-6, induced/up-regulated CXCR3 ligand genes (CXCL9, CXCL10, and CXCL11; out of 26 selected genes) in a STAT1-dependent manner in hepatic cells in vitro both at transcript and protein levels. In ConA-induced T cell-mediated hepatic model, we showed that soluble IL-27/IFNγ was elevated following ConA hepatitis in association with increased CXCL9, CXCL10, and CXCL11 expression in the liver. The exogenous IL-27 administration induced CXCR3 ligands in mouse liver at 4 h with any significant effect on recruitment of CXCR3(+) immune cells in the liver. The neutralization of IL-27 during ConA hepatitis differentially modulated (transcript vs protein expression) CXCR3 ligands and IFNγ during ConA-induced hepatitis with down-regulated expression of CXCL9 and CXCL10 at transcript level. The IFNγ, complementary regulated the expression of CXCR3 ligands as their up-regulation during ConA hepatitis, was abolished in IFNγ KO mice. In summary, IL-27 up-regulated the CXCL9, CXCL10, and CXCL11 chemokine expression in hepatic cells. IL-27 regulated CXCR3 ligand expression in IFNγ-dependent manner during acute hepatitis suggesting a complementary role of IL-27 and IFNγ to moderate liver inflammation via regulation of CXCR3 ligands. KEY MESSAGE: IL-27 up-regulated CXCR3 ligand expression in human hepatic cells in vitro. IL-27 up-regulated CXCR3 ligand expression and secretion in ConA hepatitis in vivo. CXCR3 ligand expression was down-regulated by blocking IL-27 or IFNγ deficiency. IL-27 modulated liver injury by regulation of CXCR3 ligands in IFNγ-dependent manner.
ISSN: 0946-2716

hal-01214006
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01214006
DOI : 10.1007/s00109-015-1319-6
PUBMED : 26199110

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
The results from recent studies show that some benzophenones (BPs) and their hydroxylated metabolites can function as weak estrogens (E2) in the environment. However, little is known about the structure-activity relationship of these molecules. We have examined the effects of exposure to ten different BPs on the proliferation of estrogen receptor (ER)-positive breast cancer cells and on the transcriptional activity of E2-target genes. We analyzed two genes that are tightly linked with estrogen-mediated proliferation, the CXCL12 and amphiregulin genes and two classical estrogen-responsive genes, the pS2 and progesterone receptor. Significant differences in the BPs efficiency to induce cell proliferation and endogenous E2-target gene expressions were observed. Using ERE-, Sp1-, AP1- and C3-reporter genes that contain different ER-binding sites in their promoter, we also showed significant differences in the BPs efficiency in activation of the ER transactivation. Together, our analyzes showed that the most active molecule is 4-hydroxy-BP. Docking analysis of the interaction of BPs in the ligand-binding pocket of ERα suggests that the minimum structural requirement for the estrogenic activity of BPs is a hydroxyl (OH) group in the phenyl A-ring that allows interaction with Glu-353, Arg-394 or Phe-404, which enhances the stability between BPs and ERα. Our modeling also indicates a loss of interaction between the OH groups of the phenyl B-ring and His-524. In addition, the presence of some OH groups in the phenyl B-ring can create repulsion forces, which may constrain helix 12 in an unfavorable position, explaining the differential estrogenic effects of BPs. These results, together with our analysis of BPs for their potency in activation of cell proliferation and ER-mediated transcription, report an improved understanding of the mechanism and structure-activity relationship of BPs.
ISSN: 1932-6203

inserm-00838323
http://www.hal.inserm.fr/inserm-00838323
http://www.hal.inserm.fr/inserm-00838323/document
http://www.hal.inserm.fr/inserm-00838323/file/journal.pone.0060567.pdf
DOI : 10.1371/journal.pone.0060567

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
This study investigated the clinical epidemiology and resistance mechanisms of Acinetobacter baumannii and characterised the clonal diversity of carbapenem-resistant A. baumannii (CRAB) during an ICU-associated outbreak at Cayenne Hospital, French Guiana. All non-duplicate A. baumannii isolates from 2008 to 2014 were tested for antibiotic susceptibility by disk diffusion. Multilocus sequence typing, pulsed-field gel electrophoresis (PFGE) and characterisation of carbapenemase-encoding genes were performed on CRAB. Of the 441 A. baumannii isolates, most were from males (54.0%) and were detected mainly from the ICU (30.8%) and medicine wards (21.8%). In the ICU, strains were mainly isolated from the respiratory tract (44.1%) and bloodstream (14.0%), whereas in medicine wards they mainly were from wound/drainage (36.5%) and bloodstream (25.0%). A. baumannii showed the greatest susceptibility to piperacillin/tazobactam (92.7%), imipenem (92.5%), colistin (95.6%) and amikacin (97.2%), being lower in the ICU and medicine wards compared with other wards. An outbreak of OXA-23-producing CRAB occurred in the 13-bed ICU in 2010. CRAB strains were more co-resistant to other antimicrobials compared with non-CRAB. Molecular genetics analysis revealed five sequence types [ST78, ST107 and ST642 and two new STs (ST830 and ST831)]. Analysis of PFGE profiles indicated cross-transmissions of CRAB within the ICU, between the ICU and one medicine ward during transfer of patients, and within that medicine ward. This study provides the first clinical and molecular data of A. baumannii from French Guiana and the Amazon basin. The ICU was the highest risk unit of this nosocomial outbreak of OXA-23-producing CRAB, which could subsequently disseminate within the hospital.
ISSN: 0924-8579

hal-01506828
https://hal.archives-ouvertes.fr/hal-01506828
PUBMED : 27236843

Éditeur(s) : Copernicus Gesellschaft Mbh
Résumé : The Mediterranean Sea is one of the most oligotrophic marine areas on earth where nitrogen fixation has formally believed to play an important role in carbon and nitrogen fluxes. Although this view is under debate, the diazotrophs responsible for this activity have still not been investigated in the open sea. In this study, we characterised the surface distribution and species richness of unicellular and filamentous diazotrophs across the Mediterranean Sea by combining microscopic counts with size fractionated in situ hybridization (TSA-FISH), and 16S rDNA and nifH genes phylogenies. These genetic analyses were possible owing to the development of a new PCR protocol adapted to scarce microorganisms that can detect as few as 1 cell ml(-1) in cultures. Low concentrations of diazotrophic cyanobacteria were detected and this community was dominated at 99.9% by picoplankton hybridized to the Nitro821 probe, specific for unicellular diazotrophic cyanobacteria (UCYN). Among filamentous cyanobacteria only 0.02 filament ml(-1) of Richelia were detected in the eastern basin, while small (0.7-1.5 mu m) and large (2.5-3.2 mu m) Nitro821-targeted cells were recovered at all stations with a mean concentration of 3.5 cell ml(-1). The affiliation of the small Nitro821-targeted cells to UCYN-A was confirmed by 16S and nifH phylogenies in the western Mediterranean Sea. In the central and the eastern Mediterranean Sea no 16S rDNA and nifH sequence from UCYN was obtained as cells concentration were close to, or below PCR detection limit. Bradyrhizobium sequences dominated nifH clone libraries from picoplanktonic size fractions. A few sequences of gamma-proteobacteria were also detected in the central Mediterranean Sea. While low phosphate and iron concentrations could explain the absence of Trichodesmium sp., the factors that prevent the development of UCYN-B and C remain unknown. We also propose that the dominating picoplankters probably developed specific strategies, such as associations with protists or particles, and/or photosynthetic activity, to acquire carbon for sustaining diazotrophy.
Biogeosciences (1726-4170) (Copernicus Gesellschaft Mbh), 2011 , Vol. 8 , N. 3 , P. 827-840

Droits : Author(s) 2011. CC Attribution 3.0 License.
http://archimer.ifremer.fr/doc/00133/24392/22416.pdf
DOI:10.5194/bg-8-827-2011
http://archimer.ifremer.fr/doc/00133/24392/

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background: The Ras/Raf/MEK/ERK signaling pathway is involved in essential cell processes and it is abnormally activated in similar to 30 % of cancers and cognitive disorders. Two ERK isoforms have been described, ERK1 and ERK2; ERK2 being regarded by many as essential due to the embryonic lethality of ERK2 knock-out mice, whereas mice lacking ERK1 are viable and fertile. The controversial question of why we have two ERKs and whether they have differential functions or display functional redundancy has not yet been resolved. Results: To investigate this question we used a novel approach based on comparing the evolution of ERK isoforms' sequences and protein expression across vertebrates. We gathered and cloned erk1 and erk2 coding sequences and we examined protein expression of isoforms in brain extracts in all major clades of vertebrate evolution. For the first time, we measured each isoforms' relative protein level in phylogenetically distant animals using anti-phospho antibodies targeting active ERKs. We demonstrate that squamates (lizards, snakes and geckos), despite having both genes, do not express ERK2 protein whereas other tetrapods either do not express ERK1 protein or have lost the erk1 gene. To demonstrate the unexpected squamates' lack of ERK2 expression, we targeted each ERK isoform in lizard primary fibroblasts by specific siRNA-mediated knockdown. We also found that undetectable expression of ERK2 in lizard is compensated by a greater strength of lizard's erk1 promoter. Finally, phylogenetic analysis revealed that ERK1 amino acids sequences evolve faster than ERK2' s likely due to genomic factors, including a large difference in gene size, rather than from functional differences since amino acids essential for function are kept invariant. Conclusions: ERK isoforms appeared by a single gene duplication at the onset of vertebrate evolution at least 400 Mya. Our results demonstrate that tetrapods can live by expressing either one or both ERK isoforms, supporting the notion that ERK1/2 act interchangeably. Substrate recognition sites and catalytic cleft are nearly invariant in all vertebrate ERKs further suggesting functional redundancy. We suggest that future ERK research should shift towards understanding the role and regulation of total ERK quantity, especially in light of newly described erk2 gene amplification identified in tumors.
ISSN: 1471-2148

hal-01546165
https://hal.archives-ouvertes.fr/hal-01546165
DOI : 10.1186/s12862-015-0450-x

Éditeur(s) : HAL CCSD
Résumé : International audience
BACKGROUND AND AIM: The impact of basal core promoter (BCP) and precore (PC) mutants of the hepatitis B virus (HBV) on liver disease severity remains controversial. The aim of the present study was to screen BCP and PC mutations in 252 HBV surface antigen (HBsAg) positive carriers in France and to assess relationships between these mutations and severe fibrosis. METHODS: Direct sequencing of the precore/core gene was used to detect A1762T/G1764A and G1757A mutations in the BCP and G1896A and G1899A mutations in the PC region. RESULTS: The prevalences of A1762T/G1764A, G1757A, G1896A, and G1899A mutations were 34.1%, 38.7%, 54.9%, and 29.3% (P < 0.001), respectively. The independent predictors of severe fibrosis (>/=F3 Metavir) were older age (P < 0.001), male gender (P = 0.012), elevated alanine aminotransferase (P < 0.001), and the double A1762T/G1764A mutant with no other mutations (P = 0.011). Interestingly, the association of the G1899A mutation with the double A1762T/G1764A mutant significantly counteracted the deleterious effect of the sole double A1762T/G1764A mutant (odds ratio [OR] = 0.28 vs. OR = 3.55, respectively, P = 0.028). CONCLUSIONS: Patients with the A1762T/G1764A mutation have a higher risk of severe fibrosis. The G1899A mutation is a protective factor against severe fibrosis that counteracted the deleterious effect of the A1762T/G1764A mutation. Finally, host phenotypic and HBV genotypic markers independently predict fibrosis severity.
Journal of gastroenterology and hepatology

hal-01477209
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01477209
DOI : 10.1111/jgh.13338
PUBMED : 26992056

Éditeur(s) : HAL CCSD Publisher : Baltimore : Williams & Wilkins, c1950-. Latest Publisher : Bethesda, MD : American Association of Immunologists
Résumé : International audience
Schistosome infection is a major public health concern affecting millions of people living in tropical regions of Africa, Asia, and South America. Schistosomes cause mild clinical symptoms in most subjects, whereas a small proportion of individuals presents severe clinical disease (as periportal fibrosis (PPF)) that may lead to death. Severe PPF results from an abnormal deposition of extracellular matrix proteins in the periportal spaces due to a chronic inflammation triggered by eggs and schistosome Ags. Extracellular matrix protein production is regulated by a number of cytokines, including IFN-gamma. We have now screened putative polymorphic sites within this gene in a population living in an endemic area for Schistosoma mansoni. Two polymorphisms located in the third intron of the IFN-gamma gene are associated with PPF. The IFN-gamma +2109 A/G polymorphism is associated with a higher risk for developing PPF, whereas the IFN-gamma +3810 G/A polymorphism is associated with less PPF. The polymorphisms result in changes in nuclear protein interactions with the intronic regions of the gene, suggesting that they may modify IFN-gamma mRNA expression. These results are consistent with the results of previous studies. Indeed, PPF is controlled by a major locus located on chromosome 6q22-q23, closely linked to the gene encoding the alpha-chain of the IFN-gamma receptor, and low IFN-gamma producers have been shown to have an increased risk of severe PPF. Together, these observations support the view that IFN-gamma expression and subsequent signal transduction play a critical role in the control of PPF in human hepatic schistosome infection (S. mansoni).
ISSN: 0022-1767

Droits : http://creativecommons.org/licenses/by-nc-nd/
hal-01211760
https://hal.archives-ouvertes.fr/hal-01211760
https://hal.archives-ouvertes.fr/hal-01211760/document
https://hal.archives-ouvertes.fr/hal-01211760/file/J%20Immunol-2003-Chevillard-5596-601.pdf
DOI : 10.4049/jimmunol.171.10.5596

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : Understanding the genetic mechanisms of speciation and basis of species differences is among the most important challenges in evolutionary biology. Two questions of particular interest are what roles divergent selection and chromosomal differentiation play in these processes. A number of recently proposed theories argue that chromosomal rearrangements can facilitate the development and maintenance of reproductive isolation and species differences by suppressing recombination within rearranged regions. Reduced recombination permits the accumulation of alleles contributing to isolation and adaptive differentiation and protects existing differences from the homogenizing effects of introgression between incipient species. Here, we examine patterns of genetic diversity and divergence in rearranged versus collinear regions in two widespread, extensively hybridizing sunflower species, Helianthus annuus and Helianthus petiolaris, using sequence data from 77 loci distributed throughout the genomes of the two species. We find weak evidence for increased genetic divergence near chromosomal break points but not within rearranged regions overall. We find no evidence for increased rates of adaptive divergence on rearranged chromosomes; in fact, collinear chromosomes show a far greater excess of fixed amino acid differences between the two species. A comparison with a third sunflower species indicates that much of the nonsynonymous divergence between H. annuus and H. petiolaris probably occurred during or soon after their formation. Our results suggest a limited role for chromosomal rearrangements in genetic divergence, but they do document substantial adaptive divergence and provide further evidence of how species integrity and genetic identity can be maintained at many loci in the face of extensive hybridization and gene flow.
ISSN: 0737-4038

hal-01032153
https://hal.archives-ouvertes.fr/hal-01032153
DOI : 10.1093/molbev/msp043

Éditeur(s) : Society for General Microbiology
Résumé : A novel piezotolerant, mesophilic, facultatively anaerobic, organotrophic, polarly flagellated bacterium (strain LT13a(T)) was isolated from a deep sediment layer in the Nankai Trough (Leg 190, Ocean Drilling Program) off the coast of Japan. This organism used a wide range of organic substrates as sole carbon and energy sources: pyruvate, glutamate, succinate, fumarate, lactate, citrate, peptone and tryptone. Oxygen, nitrate, fumarate, ferric iron and cystine were used as electron acceptors. Maximal growth rates were observed at a hydrostatic pressure of 10 MPa. Hydrostatic pressure for growth was in the range 0.1-50 MPa. Predominant cellular fatty acids were 16:1 omega7c, 15: 0 iso, 16: 0 and 13: 0 iso. The G + C content of the DNA was 44.9 mol%. On the basis of 16S rRNA gene sequences, strain LT13a(T) was shown to belong to the gamma-Proteobacteria, being closely related to Shewanella putrefaciens (98%), Shewanella oneidensis (97%) and Shewanella baltica (96 %). Levels of DNA homology between strain LT13a(T) and S. putrefaciens, S. oneidensis and S. baltica were < 20 %, indicating that strain LT13a(T) represents a novel species. Genetic evidence and phenotypic characteristics showed that isolate LT13a(T) constitutes a novel species of the genus Shewanella, Because of the deep origin of the strain, the name Shewanella profunda sp. nov. is proposed, with LT13a(T) (= DSM 15900(T)-JCM 12080(T)) as the type strain.
International journal of systematic and evolutionary microbiology (1466-5026) (Society for General Microbiology), 2004-11 , Vol. 54 , N. 6 , P. 1943-1949

Droits : 2004 International Union of Microbiological Societies
http://archimer.ifremer.fr/doc/2004/publication-590.pdf
DOI:10.1099/ijs.0.03007-0
http://archimer.ifremer.fr/doc/00000/590/