Éditeur(s) : Colloque IMBC - International Marine Biotechnology Conference
Résumé : Since 1997, a new pathology seasonally occurs in new caledonian shrimp farms during the warm season. Diseased Litopenaeus stylirostris shrimp suffer from a systemic vibriosis which was attributed to highly pathogenic Vibrio nigripulchritudo. At the present time, only two farms among 17 are affected by the so called "summer syndrome". In such a context it appears urgent to develop reliable diagnostic tools to detect V. nigripulchritudo strains and to differentiate highly virulent strains from non virulent ones in order to understand the mechanisms of infection and overcome disease spreading. Multilocus Sequencing Typing (MLST) analysis on 24 bacterial strains isolated in geographically distinct shrimp farms highlighted the existence of a cluster A containing only strains displaying moderate to high virulence. Since experimental infection procedure for virulence status determination is material intensive and time consuming, and MLST method not accurate enough to inform on the virulence status of strains, it appeared of great interest to develop other diagnostic tools. Two phylogenetically closed strains, one highly virulent SFn1 and the other non-virulent SFn118 were selected in order to characterize genes specific of the virulent strain by Substractive Suppression Hybridization (SSH). Firstly, a total of 622 DNA fragments specific of SFn1 were sequenced, characterized and further used as probes in a DNA macroarray. Testing 24 strains, hybridization profiles were found to be strongly correlated with both MLST genotypes and bacterial virulence status. A total of 96 representative probes were secondly selected to validate macroarray results on 34 more additionnal strains, allowing identification of genetic markers of virulence. Most of DNA fragments specific of highly virulent strains associated to summer syndrome were found to be bore by a plasmid successfully isolated in the laboratory. In next future, these results would permit the development of relevant diagnostic tools useful for accurate epidemiological survey of the summer syndrome.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2007/acte-3398.pdf
http://archimer.ifremer.fr/doc/00000/3398/

Éditeur(s) : London : Hamilton, Adams & Co
Siècle(s) traité(s) : 19
Droits : Domaine public
Provenance : Ville de Pointe-à-Pitre. Réseau des bibliothèques
Permalien : http://www.manioc.org/patrimon/HASH0103f0f83da4829c83c1b88d
HASH0103f0f83da4829c83c1b88d

Éditeur(s) : HAL CCSD Royal Society of Chemistry
Résumé : International audience
A full equilibrium treatment of molecular aggregation is presented for prototypes of 1D and 3D aggregates, with and without nucleation. By skipping complex kinetic parameters like aggregate size-dependent diffusion, the equilibrium treatment allows to predict directly time-independent quantities such as critical concentrations. The relationships between the macroscopic equilibrium constants for the different paths are first established by statistical corrections and so as to comply with the detailed balance constraints imposed by nucleation, and the composition of the mixture resulting from homogeneous aggregation is then analyzed using the polylogarithm function. Several critical concentrations are distinguished: the residual monomer concentation in equilibrium (RMC) and the critical nucleation concentration (CNC), that is the threshold concentration of total subunits necessary for initiating aggregation. When increasing the concentration of total subunits, the RMC converges more strongly to its asymptotic value, the equilibrium constant of depolymerization, for 3D aggregates and in case of nucleation. The CNC moderately depends on the number of subunits in the nucleus, but sharply increases with the difference between the equilibrium constants of polymerization and nucleation. As the RMC and CNC can be numerically but not analytically determined, ansatz equations connecting them to thermodynamic parameters are proposed
PCCP : Physical chemistry chemical physics

Droits : info:eu-repo/semantics/OpenAccess
hal-01565995
https://hal.archives-ouvertes.fr/hal-01565995
https://hal.archives-ouvertes.fr/hal-01565995/document
https://hal.archives-ouvertes.fr/hal-01565995/file/Aggregates_in_equilibrium.pdf
DOI : 10.1039/c6cp08369b

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
The susceptibility of Anopheles mosquitoes to Plasmodium infections relies on complex interactions between the insect vector and the malaria parasite. A number of studies have shown that the mosquito innate immune responses play an important role in controlling the malaria infection and that the strength of parasite clearance is under genetic control, but little is known about the influence of environmental factors on the transmission success. We present here evidence that the composition of the vector gut microbiota is one of the major components that determine the outcome of mosquito infections. A. gambiae mosquitoes collected in natural breeding sites from Cameroon were experimentally challenged with a wild P. falciparum isolate, and their gut bacterial content was submitted for pyrosequencing analysis. The meta-taxogenomic approach revealed a broader richness of the midgut bacterial flora than previously described. Unexpectedly, the majority of bacterial species were found in only a small proportion of mosquitoes, and only 20 genera were shared by 80% of individuals. We show that observed differences in gut bacterial flora of adult mosquitoes is a result of breeding in distinct sites, suggesting that the native aquatic source where larvae were grown determines the composition of the midgut microbiota. Importantly, the abundance of Enterobacteriaceae in the mosquito midgut correlates significantly with the Plasmodium infection status. This striking relationship highlights the role of natural gut environment in parasite transmission. Deciphering microbe-pathogen interactions offers new perspectives to control disease transmission.
ISSN: 1553-7366

hal-01546176
https://hal.archives-ouvertes.fr/hal-01546176
DOI : 10.1371/journal.ppat.1002742

Éditeur(s) : HAL CCSD
Résumé : This study is designed to improve the understanding of structural, mechanical and petrophysical characteristics of deformation bands in porous sandstone such as their potential influence on fluid storage or migration in reservoir setting. Structural and petrophysical analysis of band networks from Provence show that permeability of band is mainly controlled by the degree of cataclasis and diagenetic processes at depth. Map-scale analysis of band networks underlines the major influence of tectonic regime on band distribution, organization and permeability. Band associated to normal-fault regime (cataclasis and low-permeability) are located around map-sclae-fault whereas band associated to thurst-fault regime (moderate cataclasis and permeability) are pervasively distributed in all the area. Reverse-sense band are cataclastic and low-permeabiilty around the Roquemaure thrust, which show the potential role of large-scale fault on structural and petrophysical characteristics of bands. This analysis also shows the influence of fault propagation on formation of low permeability catacastic bands. This analysis suggests also granulometry as factor controlling organization of band networks.A mechanical analysis of deformation bands is realized based on results from Provence. Yield envelopes of these materials are calculated from analytical solution. Triaxial tests done on sandstone (L'Etang quarry, Orange) confirm the shape of yield envelope theoretically calculated. Triaxial tests done on the poorly-lithified sands (Boncavaï quarry, Uchaux) show grain size, sorting and packing influencing yield envelope and cataclastic band localization at shallow burial depth. Stress paths are calculated for burial and tectonic event (extension and contraction) using the relationship between main stress and secondary stresses (K0) calibrated from well data. These different results are integrated into a model which allows to estimate type and structural characteristics of bands susceptible to form for a known geological setting.A structural, mechanical and petrophysical model is established form these results. This model is calibrated by permeability data from deformation bands of Provence and results from the mechanical model of strain localization. This model is also confronted to a synthesis of permeability data from literature, which confirms the influence of the different controlling parameters integrated to the model. This model is applied for two sites of uranium exploration/exploitation in porous sandstone reservoirs and validated by field observations.
Cette étude est destinée à améliorer la compréhension des caractéristiques structurales, pétrophysiques et mécaniques des bandes de déformation dans les grès poreux ainsi que de leur rôle potentiel sur la migration ou le piégeage des fluides en milieu réservoir. L'analyse structurale et pétrophysique des réseaux de bandes de Provence montre que leur perméabilité découle principalement de l'intensité de la cataclase dans leur microstructure et des processus diagénétiques qui peuvent s'y localiser avec la profondeur. L'analyse régionale de ces réseaux de bandes souligne l'influence majeure du régime tectonique sur leur distribution, leur organisation et leur perméabilité. Les bandes associées au régime normal (cataclactiques et peu perméables) sont localisées autour des failles cartographiques, tandis que les bandes associées au régime inverse (modérement cataclastiques et perméables) sont distribuées dans toute la région. Les bandes inverses sont fortement cataclastiques et imperméables uniquement autour du chevauchement de Roquemaure ce qui montre le rôle potentiel de la présence de grande faille sur les caractéristiques structurales et pétrophysiques de ces bandes. D'autre part, cette analyse suggère que la granulométrie de l'encaissant peut influencer l'initiation et l'organisation des réseaux. L'analyse mécanique des bandes de déformation a ensuite été réalisée à partir des résultats obtenus en Provence. L'enveloppe de plasticité de ces matériaux est calculée à l'aide d'une solution analytique. Les essais triaxiaux menés sur le grès de la carrière de l'Etang (orange) confirment la forme de ces enveloppes estimées théoriquement. Les essais réalisés sur les sables de Boncavaï (Uchaux) montrent que la taille des grains, le tri et de la compaction dans ces matériaux peu lithifiés influent sur leurs enveloppes de plasticité et la localisation des bandes cataclastiques à faibles profondeurs. Les trajets de contraintes sont estimés pour les phases d'enfouissement et de chargement tectonique (extension et compression) à partir de la relation entre contrainte principale et contraintes secondaires (K0), calibrée à partir de données de forage. Ces résultats sont intégrés à un modèle permettant d'estimer la nature et les caractéristiques structurales des bandes susceptibles de se former dans un contexte géologique donné. Un modèle structural, mécanique et pétrophysique a été établir à partir de ces différents résultats. Ce modèle est calibré à partir des données de perméabilité mesurées sur les bandes de Provence et des résultats du modèle mécanique de localisation cité précédemment. Ce modèle a ensuite été confronté à une synthèse des données de perméabilité disponibles dans la littérature et confirme l'influence des différents paramètres de contrôle pris en compte dans le modèle. Ce modèle a enfin pu être appliqué sur deux sites d'explorations/exploitations d'uranium en réservoir gréseux poreux et validé par les résultats obtenus, en concordance avec les observations de terrain.
https://tel.archives-ouvertes.fr/tel-01001389

NNT : 2013MON20067
tel-01001389
https://tel.archives-ouvertes.fr/tel-01001389
https://tel.archives-ouvertes.fr/tel-01001389/document
https://tel.archives-ouvertes.fr/tel-01001389/file/36072_BALLAS_2013_archivage-1_cor.pdf

Éditeur(s) : Université des Antilles Études caribéennes
Résumé : With participation in ecotourism, eco-immigrant communities in the Three Rivers’ Source area attempt to use abundant cultural resources in Tibetan region to make their own development path. As an example, the villagers of Kunlun eco-immigrant has attempted to develop tourism by producing and selling Mani stone (a Tibetan stone engraved of sacred Buddhist formulae). However, this practice is queried by some Tibetan intellectuals, community members, and relevant scholars. Besides, the complexity of Tibetan culture also has some negative effects on the project. Therefore, the project does not run smoothly. In the terms of protecting traditional Tibetan culture, in this essay, phenomenon mentioned above will be analyzed in three aspects: acculturation theory, stereotype and influences of interest structures.
Avec la participation de l'écotourisme, les communautés éco-immigrants de la zone de la Source des Trois-Rivières tentent à utiliser les ressources culturelles abondantes de la région tibétaine pour faire leur propre voie de développement. A titre d'exemple, les villageois de Kunlun éco-immigrant a tenté de développer le tourisme en produisant et en vendant les pierres-Mani (une pierre tibétaine gravée de formules bouddhistes sacrées). Cependant, cette pratique est interrogée par certains intellectuels tibétains, membres de la communauté, et des universitaires concernés. En outre, la complexité de la culture tibétaine a aussi des effets négatifs sur le projet. Par conséquent, le projet ne fonctionne pas correctement. Dans les termes de protection de la culture traditionnelle tibétaine, dans cet essai, phénomène mentionné ci-dessus sera analysé sous trois aspects: la théorie de l'acculturation, les stéréotypes et les influences de structures d'intérêt.
Chine
Tibet

Droits : info:eu-repo/semantics/openAccess
urn:doi:10.4000/etudescaribeennes.7654
http://journals.openedition.org/etudescaribeennes/7654

Éditeur(s) : Port-au-Prince : Imprimerie Aug. A. Heraux
Siècle(s) traité(s) : 19
Droits : Domaine public
Provenance : Ville de Pointe-à-Pitre. Réseau des bibliothèques
Permalien : http://www.manioc.org/patrimon/PAP11111
PAP11111

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) : Paris : Bleuet, libraire
Résumé : Dédicace en latin et un tampon en cire de 1805

Droits : Domaine public
Provenance : Fondation Clément
Permalien : http://www.manioc.org/patrimon/FCL18018
FCL18018

Éditeur(s) : HAL CCSD American Geophysical Union (AGU)
Résumé : International audience
The Ama Drime range located at the transition between the high Himalayan range and south Tibet is a N-S active horst that offsets the South Tibetan Detachment System (STDS). Within the horst, a paragneissic unit, possibly attributed to the upper Himalayan crystalline series, overly the lower Himalayan crystalline series Ama Drime orthogneissic unit containing large metabasite layers and pods that have experienced pressure >= 1.4 GPa. Combining structural analysis with new and published pressure-temperature (P-T) estimates as well as U-Th/Pb, Ar-39/Ar-40 and (U-Th)/He ages, the P-T-deformation-time (P-T-D-t) paths of the main units within and on both sides of the horst are reconstructed. They imply that N-S normal faults initiated prior to 11 Ma and have accounted for a total exhumation <= 0.6 GPa (22 km) that probably occurred in two phases: the first one until similar to 9 Ma and the second one since 6 to 4 Ma at a rate of similar to 1 mm/yr. In the Ama Drime unit, 1 to 1.3 GPa (37 to 48 km) of exhumation occurred after partial melting since similar to 30 Ma until similar to 13 Ma, above the Main Central Trust (MCT) and below the STDS when these two fault systems were active together. The switch from E-W (STDS) to N-S (Ama Drime horst) normal faulting between 13 and 12 Ma occurs at the time of propagation of thrusting from the MCT to the Main Boundary Thrust. These data are in favor of a wedge extrusion or thrust system rather than a crustal flow model for the building of the Himalaya. We propose that the kinematics of south Tibet Cenozoic extension phases is fundamentally driven by the direction and rate of India underthrusting.
ISSN: 0278-7407

hal-00486405
https://hal.archives-ouvertes.fr/hal-00486405
DOI : 10.1029/2009TC002551

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The late Carboniferous accretionary system of the South Tianshan orogen (North-Western China) underwent complex structural and polymetamorphic evolution. Combined petrological, geochronological and microstructural analysis of (ultra)high-pressure (UHP) metabasites (eclogites and blueschists) enclosed in metapelites show a relict coarse-grained eclogitic fabric S2 surrounded by a dominant fine-grained eclogite and blueschist facies retrograde fabric S2. The S2 fabric is reworked by upright folds F3 that are responsible for a major shortening of the whole accretionary system. For both the eclogite and blueschist, peak and retrograde P–T conditions have been thermodynamically constrained at 25–26 kbar and 425–500 °C and 10–13 kbar and 500−550 °C respectively, suggesting a shared exhumation history. The garnet-whole rock-amphibole isochron in the blueschist yielded Lu–Hf and Sm–Nd ages of 326.0 ± 2.9 Ma and 318.4 ± 3.9 Ma respectively, interpreted to date the prograde to peak metamorphic assemblage. The retrograde path of the eclogite is characterized by heterogeneous omphacite recrystallization into a mylonitic fine-grained matrix and crystallization of blue amphibole. Microstructures in both pristine porphyroclastic and recrystallized fine-grained domains in the eclogite indicate a gradual evolution from constriction-dominated (L>S-type) to flattening-dominated (S>L-type) type of deformation, increase of fabric intensity reflected by gradually growing M-indexes and the development of lattice preferred orientation (LPO) typical for dislocation creep under slightly hydrated conditions. Recrystallization of the matrix in the blueschist is homogeneous, which indicates a matrix dominated channel flow during exhumation. These LPOs evolutions suggest a significant mechanical coupling with the upper plate concomitant with oroclinal bending of the Kazakh orocline. Lock up of Kazakh orocline is responsible for further stress increase resulting in horizontal shortening of South Tianshan accretionary wedge and development of D3 upright folding and steepening of the whole sequence.
ISSN: 1342-937X

hal-01481263
https://hal.archives-ouvertes.fr/hal-01481263
DOI : 10.1016/j.gr.2016.07.007

Éditeur(s) : HAL CCSD Frontiers Media
Résumé : "Candidatus Liberibacter solanacearum" (Lso) has emerged as a serious threat world-wide. Five Lso haplotypes have been identified so far. Haplotypes A and B are present in the Americas and/or New Zealand, where they are vectored to solanaceous plants by the potato psyllid, Bactericera cockerelli (Sulc) (Hemiptera: Triozidae). The fastidious nature of these pathogens has hindered the study of the interactions with their eukaryotic hosts (vector and plant). To understand the strategies used by these pathogens to infect their vector, the effects of each Lso haplotype (A or B) on psyllid fitness was investigated, and genome-wide transcriptomic and RT-qPCR analyses were performed to evaluate Lso gene expression in association with its vector. Results showed that psyllids infected with haplotype B had significantly lower percentage of nymphal survival compared to psyllids infected with haplotype A. Although overall gene expression across Lso genome was similar between the two Lso haplotypes, differences in the expression of key candidate genes were found. Among the 16 putative type IV effector genes tested, four of them were differentially expressed between Lso haplotypes, while no differences in gene expression were measured by qPCR or transcriptomic analysis for the rest of the genes. This study provides new information regarding the pathogenesis of Lso haplotypes in their insect vector.
ISSN: 2235-2988

hal-01512244
https://hal.archives-ouvertes.fr/hal-01512244
https://hal.archives-ouvertes.fr/hal-01512244/document
https://hal.archives-ouvertes.fr/hal-01512244/file/Yao%202016%20Frontiers%20in%20Cellular%20and%20Infection%20Microbiology_%7BD6ACF6EB-9794-4F27-AB84-9EF4099B6D78%7D.pdf
DOI : 10.3389/fcimb.2016.00062

Éditeur(s) : HAL CCSD Wiley
Résumé : Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699
International audience
Potato can be severely affected by various pathogens, including Pectobacterium atrosepticum, the cause of bacterial soft rot on tubers and of blackleg on stems. To date, no complete resistance to P.similar to atrosepticum is available, so that only cultivars exhibiting partial resistance can be found. The mechanistic basis of this type of resistance is still poorly understood. A proteomic approach was thus developed to identify pathways specifically activated during the interaction between potato tubers and P.similar to atrosepticum. Protein profiles on silver-stained gels in the 58 similar to pH range were obtained from healthy and infected tubers from two cultivars differing for resistance level and analyzed by 2-DE and nano-LC-MS/MS. Thirteen proteins were differentially up-regulated in the partially resistant cv. Kerpondy; by contrast, no significant differences in protein profiles of inoculated and control tubers were observed in the susceptible cv. Bintje. Mass spectrometry and database searching showed that these proteins are involved in energetic metabolism (glyceraldehyde-3-phosphate dehydrogenase, 2-phosphoglycerate dehydratase or enolase, fructose biphosphate aldolase and ATPase a subunit), cytoskeleton structure (actin), protein catabolism (cysteine protease inhibitor) and patatins or patatin precursors. Their involvement in defence responses of cv. Kerpondy to P.similar to atrosepticum is discussed. Proteomic appears as an efficient approach to have insight into the mechanisms and pathways leading to potato resistance against P.similar to atrosepticum.
ISSN: 0931-1785

hal-01208654
https://hal.archives-ouvertes.fr/hal-01208654
PRODINRA : 213002
DOI : 10.1111/j.1439-0434.2012.01950.x

Éditeur(s) : HAL CCSD National Academy of Sciences
Résumé : International audience
The complexity and depth of the relationships between the three domains of life challenge the reliability of phylogenetic methods, encouraging the use of alternative analytical tools. We reconstructed a gene similarity network comprising the proteomes of 14 eukaryotes, 104 prokaryotes, 2,389 viruses and 1,044 plasmids. This network contains multiple signatures of the chimerical origin of Eukaryotes as a fusion of an archaebacterium and a eubacterium that could not have been observed using phylogenetic trees. A number of connected components (gene sets with stronger similarities than expected by chance) contain pairs of eukaryotic sequences exhibiting no direct detectable similarity. Instead, many eukaryotic sequences were indirectly connected through a ``eukaryote-archaebacterium-eubacterium-eukaryote'' similarity path. Furthermore, eukaryotic genes highly connected to prokaryotic genes from one domain tend not to be connected to genes from the other prokaryotic domain. Genes of archaebacterial and eubacterial ancestry tend to perform different functions and to act at different subcellular compartments, but in such an intertwined way that suggests an early rather than late integration of both gene repertoires. The archaebacterial repertoire has a similar size in all eukaryotic genomes whereas the number of eubacterium-derived genes is much more variable, suggesting a higher plasticity of this gene repertoire. Consequently, highly reduced eukaryotic genomes contain more genes of archaebacterial than eubacterial affinity. Connected componentswith prokaryotic and eukaryotic genes tend to include viral and plasmid genes, compatible with a role of gene mobility in the origin of Eukaryotes. Our analyses highlight the power of network approaches to study deep evolutionary events.
ISSN: 0027-8424

hal-01544798
https://hal.archives-ouvertes.fr/hal-01544798
DOI : 10.1073/pnas.1211371110

Éditeur(s) : Academic Press Inc Elsevier Science
Résumé : Several Vibrio species are known to be pathogenic to the Pacific oyster Crassostrea gigas. Survival varies according to pathogen exposure and high mortality events usually occur in summer during gametogenesis. In order to study the effects of gametogenetic status and ploidy (a factor known to affect reproduction allocation in oysters) on vibriosis survival, we conducted two successive experiments. Our results demonstrate that a common bath challenge with pathogenic Vibrio splendidus and Vibrio aestuarianus on a mixture of mature, spawning and non-mature oysters can lead to significant mortality. Previous bath challenges, which were done using only non-mature oysters, had not produced mortality. Immunohisto-chemical analyses showed the affinity of Vibrio for gonadic tissues, highlighting the importance of sexual maturity for vibriosis infection processes in oysters. Mortality rate results showed poor repeatability between tanks, however, in this bath challenge. We then tested a standardized and repeatable injection protocol using two different doses of the same combination of two Vibrio species on related diploid and triploid oysters at four different times over a year. Statistical analyses of mortality kinetics over a 6-day period after injection revealed that active gametogenesis periods correspond to higher susceptibility to vibriosis and that there is a significant interaction of this seasonal effect with ploidy. However, no significant advantage of triploidy was observed. Triploid oysters even showed lower survival than diploid counterparts in winter. Results are discussed in relation to differing energy allocation patterns between diploid and triploid Pacific oysters. (C) 2010 Elsevier Inc. All rights reserved.
Journal Of Invertebrate Pathology (0022-2011) (Academic Press Inc Elsevier Science), 2011-02 , Vol. 106 , N. 2 , P. 179-191

Droits : 2010 Elsevier Inc. All rights reserved.
http://archimer.ifremer.fr/doc/00030/14108/11368.pdf
DOI:10.1016/j.jip.2010.09.003
http://archimer.ifremer.fr/doc/00030/14108/

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background: Increasingly, similarity networks are being used for evolutionary analyses of molecular datasets. These networks are very useful, in particular for the analysis of gene sharing, lateral gene transfer and for the detection of distant homologs. Currently, such analyses require some computer programming skills due to the limited availability of user-friendly freely distributed software. Consequently, although appealing, the construction and analyses of these networks remain less familiar to biologists than do phylogenetic approaches. Results: In order to ease the use of similarity networks in the community of evolutionary biologists, we introduce a software program, EGN, that runs under Linux or MacOSX. EGN automates the reconstruction of gene and genome networks from nucleic and proteic sequences. EGN also implements statistics describing genetic diversity in these samples, for various user-defined thresholds of similarities. In the interest of studying the complexity of evolutionary processes affecting microbial evolution, we applied EGN to a dataset of 571,044 proteic sequences from the three domains of life and from mobile elements. We observed that, in Borrelia, plasmids play a different role than in most other eubacteria. Rather than being genetic couriers involved in lateral gene transfer, Borrelia's plasmids and their genes act as private genetic goods, that contribute to the creation of genetic diversity within their parasitic hosts. Conclusion: EGN can be used for constructing, analyzing, and mining molecular datasets in evolutionary studies. The program can help increase our knowledge of the processes through which genes from distinct sources and/or from multiple genomes co-evolve in lineages of cellular organisms.
ISSN: 1471-2148

hal-01544799
https://hal.archives-ouvertes.fr/hal-01544799
DOI : 10.1186/1471-2148-13-146

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
We have inferred the deformation mechanisms of antigorite by high-resolution EBSD mapping of samples from Cerro del Almirez ultramafic massif (Betic Cordillera, SE Spain). Textural relations and phase diagram calculations constrain the foliation development conditions to the subduction prograde path at up to 600-630 °C and 1.6-1.9 GPa. Deformation was followed by static annealing of antigorite at ca. 680 °C. The Crystal Preferred Orientation (CPO) of antigorite is characterised by a strong alignment of (001) poles normal to the foliation plane and a weaker, but clear, parallelism between [100] axes and the macroscopic lineation defined by the elongation of magnetite aggregates. Analysis of misorientations across subgrains shows predominance of [010] rotation axis, consistent with activation of the [100](001) slip system. However, tilt subgrain boundaries subparallel to (100), probably formed by edge dislocations of this system, are subsidiary. Most subgrain boundaries are subparallel to (001) planes. They are interpreted as (001) twins wherein continuing viscoplastic deformation resulted in a slight increase of the misorientation between the twins. Modelling of the evolution of the antigorite CPO using a lower bound approach and considering different deformation regimes and sets of basal and non-basal slip systems has shown that intensities of [100] and [010] maxima reflect the relative strength of the antigorite [100](001) and [010](001) systems. Activation of other basal or non-basal slip systems does not change significantly the CPO patterns, but results in less concentrated CPO. 3D transpression models better reproduce the CPO of natural antigorite serpentinites. We propose that the widespread occurrence of strong CPO in high-pressure antigorite serpentinite is consistent with deformation by dislocation creep with dominant glide on [hk0](001), together with the activation of twinning, implying that a power law rheology would better account for the mechanical behaviour of antigorite serpentinite deep in the subduction channel and mantle wedge.
ISSN: 0012-821X

hal-00795511
https://hal.archives-ouvertes.fr/hal-00795511
DOI : 10.1016/j.epsl.2012.06.049

Éditeur(s) : Paris : Morizot
Résumé : Nouvelle édition
Description : Nouvelle édition continuée jusqu'à nos jours, d'après les documents scientifiques les plus récents, les derniers voyages et les dernières découvertes par V.-A. Malte-Brun fils,...

Droits : Domaine public
Provenance : Collectivité territoriale de Guyane. Bibliothèque Alexandre-Franconie
Permalien : http://www.manioc.org/patrimon/FRA11196
FRA11196

Éditeur(s) : Cluny : Imprimerie J.-M. Demoule
Siècle(s) traité(s) : 19
Droits : Domaine public
Provenance : Collectivité territoriale de Guyane. Bibliothèque Alexandre-Franconie
Permalien : http://www.manioc.org/patrimon/FRA11064
FRA11064

Éditeur(s) : HAL CCSD SPRINGER
Résumé : International audience
A key question in evolutionary biology is the reproducibility of adaptation. This question can now be quantitatively analyzed using experimental evolution coupled to whole genome sequencing (WGS). With complete sequence data, one can assess convergence among replicate populations. In turn, convergence reflects the action of natural selection and also the breadth of the field of possible adaptive solutions. That is, it provides insight into how many genetic solutions or adaptive paths may lead to adaptation in a given environment. Convergence is both a property of an adaptive landscape and, reciprocally, a tool to study that landscape. In this chapter we present the links between convergence and the properties of adaptive landscapes with respect to two types of microbial experimental evolution. The first tries to reconstruct a full adaptive landscape using a handful of carefully identified mutations (the reductionist approach), while the second uses WGS of replicate experiments to infer properties of the adaptive landscape. Reductionist approaches have highlighted the importance of epistasis in shaping the adaptive landscape, but have also uncovered a wide diversity of landscape architectures. The WGS approach has uncovered a very high diversity of beneficial mutations that affect a limited set of genes or functions and also suggests some shortcomings of the reductionist approach. We conclude that convergence may be better defined at an integrated level, such as the genic level or even at a phenotypic level, and that integrated mechanistic models derived from systems biology may offer an interesting perspective for the analysis of convergence at all levels.
ECOLOGICAL GENOMICS: ECOLOGY AND THE EVOLUTION OF GENES AND GENOMES

ISBN : 978-94-007-7347-9; 978-94-007-7346-2
hal-01544757
https://hal.archives-ouvertes.fr/hal-01544757
DOI : 10.1007/978-94-007-7347-9__11