Éditeur(s) : HAL CCSD Elsevier
Résumé : In this study, we assessed past and present influence of ancient mining activity on metal(loid) enrichment in sediments of a former mining watershed (Gardon River, SE France), that is now industrialized and urbanized. A sedimentary archive and current sediments were characterized combining geochemical analyses, zinc isotopic analyses and sequential extractions. The archive was used to establish local geochemical background and recorded (i) increasing enrichment factors (EFs) for Pb, Zn, Cd, Tl, Hg, As and Sb throughout the industrial era, (ii) a contamination peak in 1976 attributed to a tailings dam failure, and (iii) current levels in 2002 and 2011 similar to those of 1969, except for Sb and Hg, reflecting a persisting contamination pattern. Inter-element relationships and spatial distribution of EF values of current sediments throughout the watershed suggested that both ancient and current contamination had a common origin for Pb, Zn, Cd, Tl and As related to the exploitation of Pb/Zn mineralization while old Sb mines and coal extraction area were the main sources for Sb and Hg respectively. This prevailing mining origin was reflected for Zn by a relatively uniform isotopic composition at δ66Zn = 0.23 ± 0.03‰, although slight decrease from 0.23‰ to 0.18‰ was recorded from upstream to downstream sites along the river course in relation with the contribution of the lighter δ66Zn signature (~ 0.08‰) of acid mine drainage impacted tributaries. Results from sequential extractions revealed that the potential mobility of the studied metal(loid)s varied in the order Sb < Tl ≈ As < Zn < Pb < Cd, with an increase of the mobile pool for Cd, Pb, Zn and to a lesser extent for As and Tl associated to increased enrichment. Altogether, these results tend to demonstrate that ancient mining activity still contributes to metal enrichment in the sediments of the Gardon River and that some of these metals may be mobilized toward the water compartment.
ISSN: 0048-9697

hal-01054163
https://hal.archives-ouvertes.fr/hal-01054163
DOI : 10.1016/j.scitotenv.2014.02.078

Éditeur(s) : HAL CCSD American Society for Microbiology
Résumé : International audience
This study aimed to evaluate the repeated sequence REP-529 compared to the B1 gene for the molecular diagnosis of toxoplasmosis by quantitative PCR (qPCR) in routine diagnosis.Over a ten-year period (2003-2013), all patients prospectively diagnosed with a positive REP-529 qPCR result for toxoplasmosis were included. All DNA samples (76 samples from 56 patients) were simultaneously tested using the two qPCR methods (REP-529 and B1).The mean Ct obtained with the B1 qPCR was significantly higher (+4.71 cycles) than that obtained with REP-529 qPCR (p<0.0001). Thirty-one out of 69 extracts (45.6%) positive with REP-529 qPCR were not amplified with the B1 qPCR (relative sensitivity 54.4%, compared to REP-529), yielding false negative results on 15/28 placentas, 5 cord blood, 2 amniotic fluids, 4 cerebrospinal fluids, 1 aqueous humor, 2 lymph node punctures and 1 abortion product. This defect in sensitivity would have left 20/56 patients undiagnosed, distributed as follows: 12/40 congenital toxoplasmosis, 4/5 cerebral toxoplasmosis, 2/8 patients with retinochoroiditis, and both patients with chronic lymphadenopathy. This poor performance of B1 qPCR could be related to low parasite loads, since the mean Toxoplasma quantification in extracts with B1 false negative results was 0.4 parasite/reaction.These results clearly show the superiority of the REP-529 sequence in the diagnosis of toxoplasmosis by PCR suggest that this target should be adopted as part of standardization of the PCR assay.
ISSN: 0095-1137

hal-01118293
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01118293
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01118293/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01118293/file/A%2010-Year%20Retrospective%20Comparison%20of%20Two%20Target%20Sequences-belaz2015.pdf
PUBMEDCENTRAL : PMC4365238

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
This work relates to the characterisation of the predominant gill protein of the white clam, Codakia orbicularis (Linné, 1758), which harbours endosymbiotic sulphur-oxidising chemoautotrophic bacteria. Total RNA was extracted from the clam to perform 3'rapid amplification of cDNA ends (3'RACE) using degenerate oligonucleotides prepared from a partial sequence of a predominant protein of about 14kDa, termed codakine. The partial peptide sequence was obtained by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and Edman degradation. Clones isolated from the cDNA library and containing the gene of interest were used in polymerase chain reaction (PCR). The PCR and RACE-PCR products were sequenced to determine the entire coding DNA sequence of codakine. BLAST analysis revealed about 23% to 29% sequence identity between codakine and various animal C-type lectins that are often involved in symbiosis and immune defences. Codakine also contains the motifs and domains of Ca(2+)-dependent C-type lectins, and in particular the tripeptide EPN motif frequently found in mannose-binding lectins (MBLs). Analysis of the protein by affinity chromatography on a mannose-agarose column is consistent with the findings that codakine is a dimeric Ca(2+)-dependent MBL of about 29kDa. Based on the present results, it is hypothesised that this novel C. orbicularis gill protein is involved in the recognition of symbiotic and pathogenic bacteria.
ISSN: 1050-4648

hal-00746015
https://hal.univ-antilles.fr/hal-00746015
DOI : 10.1016/j.fsi.2006.06.013
PUBMED : 17169576

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

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

Éditeur(s) : HAL CCSD
Résumé : The coastal intrusion of brine threatens populations. This is particularly prejudicial in carbonate environments. We have studied the Miocene coral reef of S-E Majorca for better understanding the relation between geological structure and intrusion. For that purpose, we have used multi-scalar and multi-disciplinary methods. The measurements in 25 boreholes over the whole coral platform have allowed defining the stratigraphic structure and some elements of the regional tectonic. The reef progrades in the NE-SW direction, starting from the Aquitanian to terminates at the Messinian. The Messinian Salinity Crisis involves a disappearance of the Mediterranean corals and results in a Terminal Carbonate Complex which overlays a great part of the previously living corals of Majorca. At the experimental site scale, the study of the mineral composition, the texture, and the diagenesis have allowed characterization of the carbonate sequence heterogeneity. Layers of mineralization accompanied by dolomitization and low porosity correspond to postdepositional eustatic levels. The causes for the existence and the orientation of fractures are studied. The permeability to porosity relation is approached. The porosity structure is studied by comparison between primary and secondary porosity. This study contributes to the knowledge of the world best documented site for the evolution of carbonate reef reservoirs, with applications for brine intrusion and for hydrocarbon extraction.
Les intrusions d'eau salée en zone côtière constituent une menace pour la population. Celles-ci sont particulièrement dommageables en contexte carbonaté. Nous avons étudié le récif corallien Miocène du sud-est de Majorque afin de comprendre la relation entre structure géologique et intrusion. Pour cela nous avons utilisé des méthodes multi-scalaires et multi-disciplinaires. Les mesures dans 25 forages sur l'ensemble de la plateforme corallienne ont permis de préciser la structure stratigraphique et certains éléments de la tectonique régionale. Le récif prograde dans la direction NE-SO, en partant de l'Aquitanien pour aboutir au Messinien. La Crise de Salinité Messinienne entraîne une disparition des coraux méditerranéens et se traduit par un Complexe Carbonaté Terminal qui s'étend sur une grande partie des coraux autrefois vivants de Majorque. A l'échelle du site expérimental, l'étude de la composition minérale, de la texture et de la diagenèse ont permis de caractériser l'hétérogénéité de la séquence carbonatée. Des couches de minéralisation accompagnées de dolomitisation et de faible porosité correspondent à différents niveaux eustatiques post-dépositionnels. Les causes de l'existence et de l'orientation des fractures sont étudiées. La relation de perméabilité à porosité est précisée. La structure de porosité est étudiée par comparaison entre la porosité primaire et la porosité secondaire. Cette étude contribue à la connaissance du site le mieux documenté au monde pour l'évolution des réservoirs carbonatés récifaux, avec applications pour les intrusions d'eau salée et l'extraction des hydrocarbures.
https://tel.archives-ouvertes.fr/tel-00440019

tel-00440019
https://tel.archives-ouvertes.fr/tel-00440019
https://tel.archives-ouvertes.fr/tel-00440019/document
https://tel.archives-ouvertes.fr/tel-00440019/file/thesemariasube.pdf

Éditeur(s) : HAL CCSD
Résumé : The bacterial microbiota of ants (Hymenoptera: Formicidae) is known to have a defensive role in social insects, particularly for leaf-cutting ants (Formicidae: Attini) due to the use of antimicrobial molecules produced by cuticular actinobacteria. In this thesis, we studied the bacterial microbiota of ants in French Guyana using different approaches based on natural products chemistry and molecular ecology. The first chapter describes the isolation, identification, culture and biological evaluations of 43 cuticular actinobacteria. Antagonism bioassays of isolated strains and antibiotic activities of the culture extracts against human pathogens are presented as well as the identification of an antimicrobial cyclic dipeptide (Cyclo (LPro-LPhe)) isolated from a strain close to Streptomyces thioluteus. Moreover, the implementation of molecular networks applied to UPLC/MS/MS analysis of actinobacterial cocultures allowed us to explore the diversity of metabolites produced under these conditions. The second chapter presents a methodological study to evaluate the capacity of four DNA extraction methods, in terms of richness and composition of the cuticular bacterial microbiota, in high-throughput sequencing from Atta cephalotes and Pseudomyrmex penetrator. The results of metabarcoding highlight two methods of extraction and reveal inter- and intraspecific differences in the composition of cuticular bacterial communities. Finally, chapter three describes the composition of the cuticular bacterial microbiota of Camponotus femoratus and Crematogaster levior in ant garden and the results reveal the acquisition in the environment of a part of the microbiota. In parallel, metabolomic analyses of ant’s cuticle show, on the contrary, a greater specificity related to the ant species. Future researches focusing on statistical analysis strategies combining metabarcoding and metabolomics data are discussed.
Le microbiote bactérien cuticulaire des fourmis (Hymenoptera : Formicidae) est connu pour avoir un rôle défensif chez ces insectes sociaux, notamment chez les fourmis attines (Formicidae : Attini) grâce l’utilisation de molécules antimicrobiennes produites par des actinobactéries cuticulaires. Dans le cadre de cette thèse, nous avons étudié le microbiote bactérien des fourmis de Guyane en utilisant différentes approches en chimie des produits naturels et en écologie moléculaire. Le premier chapitre décrit l’isolement, l’identification, la culture et l’évaluation biologique de 43 actinobactéries cuticulaires de fourmis de Guyane. Les tests d’antagonismes des souches isolées et l’activité antibiotique des extraits de culture contre des micro-organismes pathogènes humains sont présentés ainsi que l’identification d’un dipeptide cyclique (Cyclo(LPro-LPhe)) antimicrobien qui a été isolé à partir d’une souche proche de Streptomyces thioluteus. Par ailleurs, la mise en œuvre de réseaux moléculaires appliqués à une analyse par UPLC/MS/MS de cocultures d’actinobactéries a permis d’explorer la diversité des métabolites produits dans ces conditions. Le deuxième chapitre présente une étude méthodologique pour comparer quatre méthodes d’extraction d’ADN, en termes de richesse et de composition du microbiote bactérien cuticulaire, par séquençage haut débit à partir des espèces Atta cephalotes et Pseudomyrmex penetrator. Les résultats du métabarcoding ADN mettent en lumière deux méthodes d’extraction et révèlent des différences inter- et intraspécifiques dans la composition des communautés bactériennes cuticulaires. Enfin, le chapitre trois décrit la composition du microbiote bactérien cuticulaire des espèces Camponotus femoratus et Crematogaster levior dans les jardins de fourmis. Les résultats soulignent l’acquisition d’une partie du microbiote dans l’environnement. En parallèle l’analyse métabolomique des cuticules montre à contrario une plus grande spécificité liée à l’espèce de fourmi. Les recherches futures axées sur les stratégies d’analyses statistiques combinant le métabarcoding et la métabolomique sont discutées.
https://tel.archives-ouvertes.fr/tel-01537793

NNT : 2017YANE0003
tel-01537793
https://tel.archives-ouvertes.fr/tel-01537793
https://tel.archives-ouvertes.fr/tel-01537793/document
https://tel.archives-ouvertes.fr/tel-01537793/file/thesecarolinebirer.pdf

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 Wiley
Résumé : International audience
Well studied in mammals, amelogenesis is less known at the molecular level in reptiles and amphibians. In the course of extensive studies of enamel matrix protein (EMP) evolution in tetrapods, we look for correlation between changes in protein sequences and temporospatial protein gene expression during amelogenesis, using an evo-devo approach. Our target is the major EMP, amelogenin (AMEL) that plays a crucial role in enamel structure. We focused here our attention to an amphibian, the salamander Pleurodeles waltl. RNAs were extracted from the lower jaws of a juvenile P. waltl and the complete AMEL sequence was obtained using PCR and RACE PCR. The alignment of P. waltl AMEL with other tetrapodan (frogs, reptiles and mammals) sequences revealed residue conservation in the N- and C-terminal regions, and a highly variable central region. Using sense and anti-sense probes synthetized from the P. waltl AMEL sequence, we performed in situ hybridization on sections during amelogenesis in larvae, juveniles, and adults. We demonstrated that (i) AMEL expression was always found to be restricted to ameloblasts, (ii) the expression pattern was conserved through ontogeny, even in larvae where enameloid is present in addition to enamel, and (iii) the processes are similar to those described in lizards and mammals. These findings indicate that high variations in the central region of AMEL have not modified its temporospatial expression during amelogenesis for 360 million years of tetrapod evolution. J. Exp. Zool. (Mol. Dev. Evol.) 320B:200209, 2013.
ISSN: 1552-5007

hal-01545483
https://hal.archives-ouvertes.fr/hal-01545483
DOI : 10.1002/jez.b.22494

Éditeur(s) : HAL CCSD BMJ Publishing Group
Résumé : International audience
OBJECTIVE:To identify local meteorological drivers of dengue fever in French Guiana, we applied an original data mining method to the available epidemiological and climatic data. Through this work, we also assessed the contribution of the data mining method to the understanding of factors associated with the dissemination of infectious diseases and their spatiotemporal spread.METHODS:We applied contextual sequential pattern extraction techniques to epidemiological and meteorological data to identify the most significant climatic factors for dengue fever, and we investigated the relevance of the extracted patterns for the early warning of dengue outbreaks in French Guiana.RESULTS:The maximum temperature, minimum relative humidity, global brilliance, and cumulative rainfall were identified as determinants of dengue outbreaks, and the precise intervals of their values and variations were quantified according to the epidemiologic context. The strongest significant correlations were observed between dengue incidence and meteorological drivers after a 4-6-week lag.DISCUSSION:We demonstrated the use of contextual sequential patterns to better understand the determinants of the spatiotemporal spread of dengue fever in French Guiana. Future work should integrate additional variables and explore the notion of neighborhood for extracting sequential patterns.CONCLUSIONS:Dengue fever remains a major public health issue in French Guiana. The development of new methods to identify such specific characteristics becomes crucial in order to better understand and control spatiotemporal transmission.Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.
ISSN: 1067-5027

lirmm-01379072
https://hal-lirmm.ccsd.cnrs.fr/lirmm-01379072
DOI : 10.1136/amiajnl-2013-002348
PUBMED : 24549761

Éditeur(s) : HAL CCSD
Résumé : International audience
In French Guiana, located on the northeastern coast of South America, bats of different species are very numerous. The infection of bats and their ticks with zoonotic bacteria, especially Rickettsia species, is so far unknown. In order to improve knowledge of these zoonotic pathogens in this French overseas department, the presence and diversity of tick-borne bacteria was investigated with molecular tools in bat ticks. In the beginning of 2013, 32 bats were caught in Saint-Jean-du-Maroni, an area close to the coast of French Guiana, and the ticks of these animals were collected. A total of 354 larvae of Argasidae soft ticks (Ornithodoros hasei) from 12 bats (Noctilio albiventris) were collected and 107 of them were analysed. DNA was extracted from the samples and quantitative real-time PCR was carried out to detect Rickettsia spp., Bartonella spp., Borrelia spp. and Coxiella burnetii. All tested samples were negative for Bartonella spp., Borrelia spp. and Coxiella burnetii. Rickettsia DNA was detected in 31 (28.9%) ticks. An almost entire (1118 base pairs long) sequence of the gltA gene was obtained after the amplification of some positive samples on conventional PCR and sequencing. A Bayesian tree was constructed using concatenated rrs, gltA, ompA, ompB, and gene D sequences. The study of characteristic sequences shows that this Rickettsia species is very close (98.3-99.8%) genetically to R. peacockii. Nevertheless, the comparative analysis of sequences obtained from gltA, ompA, ompB, rrs and gene D fragments demonstrated that this Rickettsia is different from the other members of the spotted fever group. The sequences of this new species were deposited in GenBank as Candidatus Rickettsia wissemanii. This is the first report showing the presence of nucleic acid of Rickettsia in Ornithodoros hasei ticks from South American bats. (C) 2016 Elsevier GmbH. All rights reserved.
TICKS AND TICK-BORNE DISEASES

hal-01459758
https://hal.archives-ouvertes.fr/hal-01459758
DOI : 10.1016/j.ttbdis.2016.09.004

Éditeur(s) : HAL CCSD Elsevier
Résumé : Iron content of the bulk marine sediment from the Chilean continental margin has been used to infer millenial-scale climate changes in southeast Pacific [Lamy, F., Klump, J., Hebbeln, D., Wefer, G., 2000. Rapid climate change in northern Chile over the last 80 ka recorded in a marine sediment core. Terra Nova 12: 8–13]. Changes of iron contents have been related to a varying contribution of Andean (Fe-rich) versus Coastal Range (Fe-poor) source rocks ultimately controlled by continental rainfall changes. However, variations observed could also be produced by changes in the proportions of two components in the sediment — a detrital component with low and constant Fe content and an authigenic phase (Fe oxide, pyrite, apatite, etc.) with high Fe content. A sequential extraction has been used to partition the total iron content in the sediment of core GeoB 7101 at the continental margin of Chile. The extraction steps included five fractions: exchangeable, bound to carbonates, bound to Fe–Mn oxides, bound to organic matter, and residual. Iron appeared to be mainly present in the residual fraction, i.e. in the detrital component. Our study indicates that total Fe or Fe/Al may be used to infer millenial-scales climate changes in the southeastern Pacific.
ISSN: 0025-3227

hal-00407253
https://hal.archives-ouvertes.fr/hal-00407253
DOI : 10.1016/j.margeo.2007.03.006

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

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

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
A laser ablation ICP-MS U-Pb age of 17.84 +/- 0.12 Ma (late Burdigalian) was obtained from monazites separated from a leucocratic diatexite collected in close proximity to a small peridotite massif incorporated into the lower crustal sequence of the Edough Massif (north-eastern Algeria), a southern segment of the peri-Mediterranean Alpine Belt. Monazites extracted from a neighbouring deformed leucogranite intruding early Paleozoic phyllites yield a consistent age of 17.4 +/- 1.3 Ma. Zircons occurring in the same leucogranite, with magmatic characteristics, have an age of 308 +/- 7 Ma interpreted as dating magmatic crystallisation of the leucogranite and reflecting partial melting during the Hercynian orogeny. Low Th/U domains (Th/U<0.10) from the same grains substantiate recrystallisation during a younger metamorphic event whose upper age limit is 286 +/- 11 Ma. These results emphasize the polycyclic evolution of basement rocks preserved in the crystalline units of the western Mediterranean and indicate that part of their metamorphic features were inherited from older, Hercynian, events. Taken together with published Ar-Ar dates, the late Burdigalian age of monazites indicates a rapid cooling rate of c. 370 degrees C/Ma and is regarded as closely approximating the emplacement of the peridotites into the Hercynian basement. The monazite ages are significantly younger than those recorded for orogenic peridotites from the Betic-Rif oroctine and for the timing of lithospheric extension forming the Alboran sea. It is also younger than rifting and back-arc extension opening the Liguro-Provencal basin. The late Burdigalian age is interpreted as dating the incipient rifting event that opened the Algerian basin, which is consequently not a continuation of the Liguro-Provencal basin. At the scale of the western Mediterranean, these observations concur with current models supporting slab roll-back and an eastwards migration of extension in the western Mediterranean, but suggest that the Algerian basin opened as a result of torsion and stretching of the Thethyan slab due to its steepening under the Alboran microplate.
ISSN: 0009-2541

hal-00424511
https://hal.archives-ouvertes.fr/hal-00424511
DOI : 10.1016/j.chemgeo.2008.11.016

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 American Geophysical Union (AGU)
Résumé : Present Address : ISTO - UMR7327
International audience
The pre-rift Mesozoic sequences of the Cretaceous passive margins fossilized in the North Pyrenean Zone (NPZ) are characterized by high temperature deformation in relation with thinning of the continental basement. Our compilation of chronological and geological data confirms a clear correlation between the distribution of the highest paleotemperatures in the pre-rift sedimentary cover and the loci of extreme crustal stretching. Geological evidences such as the occurrence of peridotite bodies directly underlying metamorphic pre-rift sediments indicate an early attenuation of the rifted continental crust. This leads us to propose a mechanism of rifting involving boudinage of the continental crust. The lateral extraction of the Paleozoic basement occurred under the pre-rift cover that is decoupled on the Triassic clays and evaporates. The thermal conditions allowing coeval ductile deformation of the crust and of the pre-rift sediments leaded to the widening of basins devoid of large faulted blocks. We discuss the implications on the origin and significance of the granulites and the relations between flysch deposition and high temperature metamorphism of the pre-rift sediments. In the NPZ, Albian-Cenomanian flysch sequences were deposited synchronously with the syn-metamorphic ductile deformation of the pre-rift sequences. Since the base of the flysch deposits also recorded locally the high-temperature tectonic event, we propose an original mechanism for the evolution of the basins involving continuous deformation of the pre-rift metamorphic sediments. At the scale of the Pyrenean domain, our results suggest a strong lateral variability in the tectonic style of passive margins, in direct link with their thermic pattern
ISSN: 0278-7407

insu-01017432
https://hal-insu.archives-ouvertes.fr/insu-01017432
https://hal-insu.archives-ouvertes.fr/insu-01017432/document
https://hal-insu.archives-ouvertes.fr/insu-01017432/file/tect20164.pdf
DOI : 10.1002/2013TC003471

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

Résumé : En raison de la nature symbiotique des micro-organismes endophytes, cette étude visait à étudier l'activité antibactérienne, antifongique et cytotoxique chez les métabolites secondaires des extraits endophytes foliaires de plantes de l'Amazonie brésilienne et du Cerrado. Dans ce travail de thèse 147 micro-organismes cultivables ont été isolés (130 champignons, 3 bactéries e 14 champignons non-identifiés ou inconnus) à partir de 28 plantes (4 espèces collectées au Brésil et 24 en Guyane Française). Tous les micro-organismes furent identifiés par analyse moléculaire des régions spécifiques de l'ADNr en utilisant des techniques de séquençage génomique. Des champignons endophytes de l’ordre des Xylariales furent ceux de plus importante fréquence d’isolation dans cette étude, représentés par 25 isolats. Des extraits bruts à l’AcOEt furent produits à partir de cultures de chaque micro-organisme isolé. Une proportion relative signifiante (23,1%) des extraits démontra une activité sur Candida albicans ATCC 10213, pendant que 4% furent actifs sur Staphylococcus aureus ATCC 29213. Le potentiel cytotoxique des extraits fut évalué pour des lignées cellulaires humaines KB (carcinome cervical utérin), MDA-MB-435 (mélanome), et MRC-5 (fibroblastes de poumon normal), résultant en proportion signifiante avec activité d’inhibition de la prolifération cellulaire (24,4%, 23,1% e 16,3%, respectivement).Dix-huit métabolites secondaires furent isolés et identifiés à partir du fractionnement des extraits bruts de huit endophytes. Dix-sept de ces substances furent déjà décrites précédemment dans la littérature: l’acide piliformique (24) et la griséofulvine (25) isolés à partir de Xylaria cubensis SNB-GCI02; La phomopirone (26), la pyrenocine (27), l’alterpérilenol (28) et la novae-zelandine (29), isolés de Lewia infectoria SNB-GTC2402; 5-métilmelleina (31) et la dihidrosporothrioride (32) isolées à partir de Xylaria sp. SNB-GTC2501; La mycoleptodiscine (34) et la mycoleptodiscine B (35) isolées à partir de Mycoleptodiscus sp. SNB-GTC2304; le mycoepoxidiène (36) et la altiloxina A (37) isolés à partir de Diaporthe pseudomangiferae SNB-GSS10; L’acremonisol (40), le semicochliodinol (41) et le cochliodinol (42) isolés à partir de Chaetomium globosum SNB-GTC2114; la colletofragarone A2 (43) isolée à partir de Colletotrichum sp. SNB-GTC0201; la flavoglaucine (44) isolée à partir de Eurotium rubrum BBS01. Parmi ces substances, la flavoglaucine (44) isolée à partir de E. rubrum BBS01 démontra une activité comparable au contrôle fluconazol en C. albicans (CIM de 4 µg.mL-1). La substance (44) présenta IC50 >10 µM sur cellules normales MRC-5, ce qui en fait un candidat pour des études ultérieures. Dans ce travail, fut identifié pour la première fois l’activité de la colletofragarone A2 (43) isolée à partir de Colletotrichum sp. SNB-GTC0201. La substance inédite nommée pyrrocidine C (30) fut isolée à partir de L. infectoria SNB-GTC2402 et identifiée par des analyses spectroscopiques (Casella et al., 2013). La pyrrocidine C (30) fut active en S. aureus ATCC 10213 (CIM de 2 µg.mL-1) et ne fut pas considérées cytotoxique pour les cellules normales MRC-5 (IC50 >10 µM), démontrant une sélectivité dans l’action antimicrobienne. Ces résultats démontrent la grande diversité des endophytes fongiques chez les plantes de l'Amazonie brésilienne et du Cerrado et la grande chimiodiversité associée aux métabolites secondaires de ces micro-organismes. Des champignons endophytes tropicaux, comme ceux présentés dans cette étude, peuvent apparaître comme une nouvelle source de substances antimicrobiennes et cytotoxiques.
Because of the symbiotic nature of endophytes, this survey aims to investigate the probality of discovering antibacterial, antifungal and cytotoxic activities in secondary metabolites of leaf endophytes isolated from plants of Amazon and Cerrado biomes. In this study, 147 cultivable microorganisms were isolated (130 fungi, 3 bacteria and 14 unidentified or unknown microbes) from 28 plant species (4 species collected in Brazil and 24 in French Guyana). All endophytes were identified by molecular analyses of specific rDNA regions, with genomic sequencing techniques. Fungal endophytes belonging to Xylariales order were the most frequently isolated in this study, represented by 25 isolates. Crude AcOEt extracts were produced from cultures of each isolated endophyte. A significant relative proportion (23,1%) of extracts showed activity in Candida albicans ATCC 10213, while 4% were active in Staphylococcus aureus ATCC 29213. The cytotoxic potencial of the extracts was evaluated for human cell lines KB (uterin cervical carcinome), MDA-MB-435 (melanoma) and MRC-5 (normal lung fibroblasts), and a significant proportion of them showed cellular proliferation inhibition (24,4%, 23,1% e 16,3%, respectively).Eighteen secondary metabolites were isolated by the fractionation of eight endophytic extracts. Seventeen of these substances had already been previously described in the literature: piliformic acid (24) and griseofulvin (25) isolated from Xylaria cubensis SNB-GCI02; phomopiron A (26), pyrenocin A (27), alterperilenol (28) and novae-zelandin A (29) isolated from Lewia infectoria SNB-GTC2402; 5-metilmellein (31) and dihidrosporothriorid (32) isolated from Xylaria sp. SNB-GTC2501; mycoleptodiscin A (34) and mycoleptodiscin B (35) isolated from Mycoleptodiscus sp. SNB-GTC2304; mycoepoxidien (36) and altiloxin A (37) isolated from Diaporthe pseudomangiferae SNB-GSS10; acremonisol A (40), semicochliodinol A (41) and cochliodinol (42) isolated from Chaetomium globosum SNB-GTC2114; colletofragaron A2 (43) isolated from Colletotrichum sp. SNB-GTC0201; flavoglaucin (44) isolated from Eurotium rubrum BBS01. Among these substances, flavoglaucin (44), isolated from E. rubrum BBS01, showed comparable antifungal activity with the positive control fluconazol in C. albicans (MIC of 4 µg.mL-1). Flavoglaucin (44) also showed IC50 >10 µM in normal MRC-5 cells, becoming a good candidate for further studies. In this work, the cytotoxic activity of colletofragaron A2 (43), isolated from Colletotrichum sp. SNB-GTC0201 was described for the first time. The unpublished substance named pyrrocidin C (30) isolated from L. infectoria SNB-GTC2402 was identified by spectroscopic analyses (Casella et al., 2013). The pyrrocidin C (30) was active in S. aureus ATCC 10213 (MIC of 2 µg.mL-1), and was not considered cytotoxic for normal MRC-5 cells (IC50 >10 µM), showing selectivity in antimicrobial activity. These results demonstrate the great endophytic fungal diversity in plants of Amazon and Cerrado biomes, along with the chemodiversity associated to the secondary metabolites of these endophytes. Tropical fungal endophytes, like those seen in this work, may emerge as a new source of antimicrobial and cytotoxic substances.
Devido à natureza simbiótica dos micro-organismos endofíticos, este estudo teve como objetivo investigar a atividade antibacteriana, antifúngica e citotóxica em metabólitos secundários de extratos de fungos endofíticos foliares de plantas do bioma Amazônia e Cerrado. Neste trabalho de tese foram isolados 147 micro-organismos cultiváveis (130 fungos, 3 bactérias e 14 fungos não-identificados ou desconhecidos) a partir de 28 plantas (4 espécies coletadas no Brasil e 24 na Guiana Francesa). Todos os micro-organismos foram identificados por análise molecular de regiões específicas de DNAr, com uso de técnicas de sequenciamento genômico. Fungos endofíticos da ordem Xylariales foram os de maior frequência de isolamento neste estudo, representados por 25 isolados. Extratos brutos em AcOEt foram produzidos a partir de culturas de cada micro-organismo isolado. Uma proporção relativa significante (23,1%) dos extratos demonstrou atividade em Candida albicans ATCC 10213, enquanto 4% foram ativos em Staphylococcus aureus ATCC 29213. O potencial citotóxico dos extratos foi avaliado para as linhagens celulares humanas KB (carcinoma cervical uterino), MDA-MB-435 (melanoma), e MRC-5 (fibroblastos de pulmão normal), resultando em proporção significante com atividade de inibição da proliferação celular (24,4%, 23,1% e 16,3%, respectivamente). Dezoito metabólitos secundários foram isolados a partir do fracionamento de oito extratos brutos endofíticos. Dezessete destas substâncias já tinham sido descritas anteriormente na literatura: ácido pilifórmico (24) e griseofulvina (25) isoladas de Xylaria cubensis SNB-GCI02; phomopirona A (26), pyrenocina A (27), alterperilenol (28) e novae-zelandina A (29) isoladas de Lewia infectoria SNB-GTC2402; 5-metilmelleina (31) e Dihidrosporothriolida (32) isoladas de Xylaria sp. SNB-GTC2501; mycoleptodiscina A (34) e mycoleptodiscina B (35) isoladas de Mycoleptodiscus sp. SNB-GTC2304; mycoepoxidieno (36) e altiloxina A (37) isoladas de Diaporthe pseudomangiferae SNB-GSS10; acremonisol A (40), semicochliodinol A (41) e cochliodinol (42) isoladas de Chaetomium globosum SNB-GTC2114; colletofragarona A2 (43) isolada de Colletotrichum sp. SNB-GTC0201; flavoglaucina (44) isolada de Eurotium rubrum BBS01. Dentre estas substâncias, a flavoglaucina (44) isolada de E. rubrum BBS01, demonstrou atividade comparável ao controle fluconazol em C. albicans (CIM de 4 µg.mL-1). Esta substância (44) apresentou IC50 >10 µM em células normais MRC-5, tornando-se candidata para estudos posteriores. Neste trabalho foi identificado pela primeira vez a atividade citotóxica da colletofragarona A2 (43), isolada de Colletotrichum sp. SNB-GTC0201. A substância inédita nomeada pyrrocidina C (30) foi isolada a partir de L. infectoria SNB-GTC2402 e identificada através de análises espectroscópicas (Casella et al., 2013). A pyrrocidina C (30) foi ativa em S. aureus ATCC 10213 (CIM de 2 µg.mL-1), e não foi considerada citotóxica para as células normais MRC-5 (IC50 >10 µM), demonstrando seletividade na ação antimicrobiana. Estes resultados demonstram a grande diversidade fúngica endofítica em plantas do bioma Amazônia e Cerrado, e a quimiodiversidade associada aos metabólitos secundários destes micro-organismos. Fungos endofíticos tropicais, como os vistos neste trabalho, podem emergir como uma nova fonte de substâncias antimicrobianas e citotóxicas.

http://www.theses.fr/2014AGUY0836/document

Éditeur(s) : HAL CCSD American Society for Biochemistry and Molecular Biology
Résumé : International audience
The budding yeast Saccharomyces cerevisiae is a major model organism for important biological processes such as mitotic growth and meiotic development, it can be a human pathogen, and it is widely used in the food-, and biotechnology industries. Consequently, the genomes of numerous strains have been sequenced and a very large amount of RNA profiling data is available. Moreover, it has recently become possible to quantitatively analyze the entire yeast proteome; however, efficient and cost-effective high-throughput protein profiling remains a challenge. We report here a new approach to direct and label-free large-scale yeast protein identification using a tandem buffer system for protein extraction, two-step protein prefractionation and enzymatic digestion, and detection of peptides by iterative mass spectrometry. Our profiling study of diploid cells undergoing rapid mitotic growth identified 86% of the known proteins and its output was found to be widely concordant with genome-wide mRNA concentrations and DNA variations between yeast strains. This paves the way for comprehensive and straightforward yeast proteome profiling across a wide variety of experimental conditions.
ISSN: 1535-9476

hal-00682837
https://hal.archives-ouvertes.fr/hal-00682837
DOI : 10.1074/mcp.M111.012682
PUBMED : 21997732

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

Résumé : Face aux difficultés d’identification des arbres de la famille des Lauracées et dans un but d’établissement d’une production durable et certifiée d’huiles essentielles, l’entreprise KLR a voulu mettre en place un nouvel outil d’identification multi-critères qui consiste à croiser plusieurs types de caractères afin d’obtenir une détermination taxonomique fiable.Trois méthodes d’identification ont été utilisées : la chimie (analyse de l’odeur de l’écorce), le code barre génétique et l’anatomie du bois. Une analyse par positionnement multidimensionnel non-métrique a permis de faire un tri des critères anatomiques du bois pertinents dans l’identification des Lauracées étudiées, au final 14 critères ont été retenus. D’après les données anatomiques dont nous disposons, nous proposons une clé de détermination au genre. En génétique, la technique de code barres de la région chloroplastique intergénique trnH-psbA a été appliquée aux individus récoltés. En comparant les séquences de tous les individus, 40% des individus peuvent être identifiés au genre car ils présentent des haplotypes uniques. Des haplotypes au sein des genres ont été déterminés et permettent d’identifier l’espèce pour 40 à 100 % des individus selon le genre. L’analyse SPME de l’odeur des écorces a permis de définir pour chaque espèce une carte d’identité chimique à partir des molécules majoritaires. Des chémotypes ont été définis au sein des espèces Licaria cannella, Ocotea indirectinervia et Sextonia rubra. Ces trois domaines d’observation ont permis de constituer une base de type Xper2 pour l’identification.Un criblage des essences intéressantes de par leur rendement en huile essentielle a été effectué. En ce qui concerne la partie extraction de l’huile essentielle, trois espèces montrent un rendement en huile essentielle de l’écorce supérieur à 0,3% et 5 espèces montrent un rendement en huile essentielle du bois supérieur à 0,3%. Les évaluations olfactives menées par un expert ont permis de séparer les huiles distillées en 5 différentes notes. Nous avons jugé intéressant de savoir si l’outil d’identification multicritère pouvait prédire les compositions et rendements en huile essentielle de l’espèce identifiée avant l’abattage de l’arbre. Des études complémentaires ont donc été menées. Pour plus de la moitié des arbres, la signature de l’écorce, la composition de l’huile essentielle de l’écorce et la composition de l’huile essentielle du bois sont similaires. La tentative d’établir un lien entre les caractéristiques des cellules à huile et le rendement s’est avérée infructueuse.
In order to develop a sustainable production of certified essential oils extracts, the compangy KLR has struggled with the identification of the trees from the family of Lauraceae. This is the main reason that led to the project of creating an identification tool for this family.This tool would be based on three approaches: chemistry (chemical signature of the dark), wood anatomy and genetic barcoding. By means of a non-metric multidimensional scaling analysis, we selected a list of 14 relevant wood anatomical features that can identify the trees to the genera. For the genetics, the barcoding of trnH-psbA an intergenic region of the DNA has been used. When comparing all the sequences from all the individuals, 40% of the individuals can be identified to the genera because of their specific haplotype. Haplotypes within the genera have also been established. Chemical identity cards have been set with the SPME analysis technique and chemotypes have been defined inside the species Licaria cannella, Ocotea indirectinervia and Sextonia rubra. These three identification approaches allowed us to construct an identification tool on Xper².During the study, we aimed to screen what species would be interesting for its essential oil yield. Three species showed an essential oil bark yield above 0.3%. five species showed an essential oil wood yield above 0.3%. An expert held an olfactory evaluation on the oils and divided the essential oils in five olfactory groups. We found it relevant to improve the identification tool by trying to predict the compositions of the oils before the three was cut down. In the case of the half of trees studied by SPME analyses, the composition of the wood and the bark essential oils were similar. On the other hand, no link was found between the oil cells dimensions and the essential oil yield.

http://www.theses.fr/2012AGUY0516/document