Éditeur(s) : HAL CCSD
Résumé : International audience
Background: Comparative analysis, which aims at investigating ecological and evolutionary patterns among species, may help at targeting reservoirs of zoonotic diseases particularly in countries presenting high biodiversity. Here, we developed a simple method to target rodent reservoirs using published studies screening microparasite infections. Methods: We compiled surveys of microparasites investigated in rodents trapped in Thailand. The data comprise a total of 17,358 rodents from 18 species that have been investigated for a total of 10 microparasites (viruses, bacteria and protozoans). We used residual variation of microparasite richness controlled for both rodent sample size and pathogens' screening effort to identify major rodent reservoirs and potential risky habitats. Results: Microparasite species richness was positively related to rodent sample size and pathogens' screening effort. The investigation of the residual variations of microparasite species richness showed that several rodent species harboured more pathogens than expected by the regression model. Similarly, higher pathogen richness than expected was observed in rodents living in non-flooded lands, forests and paddy fields. Conclusion: Our results suggest to target some rodent species that are not commonly investigated for pathogen screening or surveillance such as R. andamanensis or B. savilei, and that non-flooded lands and forests should be more taken into caution, whereas much surveys focused on paddy rice fields and households.
Infection Ecology and Epidemiology

ird-00714369
http://hal.ird.fr/ird-00714369
http://hal.ird.fr/ird-00714369v2/document
DOI : 10.3402/iee.v2iO.18637
IRD : fdi:010055557

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) : 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 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 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) : 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 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

Éditeur(s) : HAL CCSD
Résumé : We present an experimental study of relations between hydraulic properties of clayey rocks and their deformation at bulk and micro scale. The experimentation is based on triaxial deformation of kaolinitic core samples, on permeability measurements, and on several methods of analysis of the microstructure. To produce the samples, remoulded kaolinite material is consolidated by axial loading up to 20 MPa in an oedometric cell. Then, in a triaxial cell, an undrained stress path is applied in order to induce shearing damage in the sample. The permeability of the sample is measured by fluid flow across the sample. Before and after these hydro-mechanical tests, the evolution and the homogeneity of the pore space and moreover the texture of the material are analysed by X-ray tomography, environmental scanning electron microscopy and thermic neutron diffraction. Contrary to expectations, the permeability at the sample scale does not vary significantly, although quite large deformation is reached. The final deformation is heterogeneous, with well-developed shear bands. It appears that the development of compacting and dilating zones generates a heterogeneous permeability field, which results in a negligible variation of the bulk permeability at the sample scale.
International Journal of Rock Mechanics and Mining Science

hal-00496407
https://hal.archives-ouvertes.fr/hal-00496407
DOI : 10.1016/j.ijrmms.2010.04.007

Éditeur(s) : HAL CCSD Springer
Résumé : The analysis of gamma ray measurements provides valuable information about the basement's lithospherical model and the radioactive elements contained in the subsurface. To be exploited, the raw data need pre-processing operations which consist of corrections of the Compton effect, altimetry and the aircraft background, and 2D interpolations. These transformations may modify the data's stochastic component which reflects heterogeneities of the investigated medium. In this study, a fractal analysis is carried out on airborne gamma ray data measured in the Hoggar's area (Algeria). First, it is shown that the analyzed data exhibit fractal properties. Due to the dependence of the latter on the spatial location of the measures, the data can be considered as paths of multifractional Brownian motions. Another result worth noting is that the fractal nature of the raw data is not modified by the pre-processing operations. The fractal analysis can be then performed on the raw spectrometric measurements without submitting them to any pre-processing; thus, the stochastic component of the measurements is kept intact.
ISSN: 1866-7411

hal-00817494
https://hal.archives-ouvertes.fr/hal-00817494
DOI : 10.1007/s12517-011-0407-3

Résumé : Cette thèse concerne la modélisation des dynamiques de maladies foliaires de cultures pérennes tropicales à différentes échelles spatiales. Cette approche de modélisation est appliquée à la cercosporiose noire du bananier. Il s’agit d’explorer et de déterminer les paramètres environnementaux et de résistance de l’hôte ayant une influence significative sur la dynamique spatiotemporelle de la maladie et d’apporter des éléments associés au contrôle de la cercosporiose noire.Deux modèles ont été développés dans le cadre de cette thèse. La dynamique épidémiologique au niveau de la plante est décrite par un modèle mécaniste décomposé en un modèle de croissance de la plante et un module épidémiologique décrivant le cycle épidémique du pathogène. L’architecture du bananier est prise en compte par le biais de compartiments foliaires positionnés dans l’espace. Le modèle a été validé par un jeu de données indépendant. Les expérimentations numériques et l’analyse de sensibilité du modèle réalisées par les méthodes de Morris et de e-FAST ont permis de mieux comprendre le fonctionnement épidémique de cette maladie et d’identifier les paramètres influant le plus la dynamique épidémique en particulier la vitesse d’extension des lésions, la durée d’incubation et l’efficacité d’infection .L’approche bayésienne a permis de prendre en compte l’information a priori disponible pour ces trois paramètres sur lesquels a porté l’inférence statistique. L’analyse de sensibilité du modèle a également permis d’identifier l’influence de deux paramètres liés à la croissance de la plante : le nombre de feuilles sur une plante et le rythme d’émission foliaire Un modèle de dynamique spatio-temporelle de la cercosporiose noire a été développé à l’échelle d’un territoire à partir d’enquêtes effectuées enMartinique pendant la période d’invasion de cette maladie de septembre 2010 à mai 2012. Les données récoltées étant censurées, l’inférence des paramètres du modèle a été réalisée dans un cadre bayésien en utilisant un algorithme d’augmentation de données. Le modèle et l’inférence développés permettent de reconstruire la dynamique spatio-temporelle de l’invasion et de prédire la fin d’invasion sur le territoire.Les deux modèles de dynamiques spatio-temporelles développés à deux échelles spatiales différentes ont permis d’acquérir des informations importantes pour construire des outils de conception de méthode de contrôle de la cercosporiose noire des bananiers.
This thesis concerns the modeling of the dynamics of foliar diseases of tropical tree crops at different spatial scales. This modeling approach is applied to black Sigatoka of banana. It is to explore and determine the environmental parameters and host resistance has a significant influence on the spatiotemporal dynamics of the disease and to provide elements associated with the control of Sigatoka noire.Deux models were developed as part of this thesis. The epidemiological dynamics at the plant is described by a mechanistic model decomposed into a growth model of the plant and an epidemiological unit describing the pathogen epidemic cycle. The architecture of the banana is taken into account through foliar compartments positioned in space. The model was validated by an independent data set. Numerical experiments and model sensitivity analysis performed by the methods of Morris and e-FAST enabled to better understand the functioning of this epidemic disease and identify the parameters affecting the most dynamic epidemic especially speed extension of the lesions, the incubation period and efficiency of Bayesian .L'approche infection allowed to take into account prior information available for these three parameters that were the statistical inference. The model sensitivity analysis also identified the influence of two parameters related to plant growth: the number of leaves on a plant and rate of leaf emission A dynamic model of space-time Black Sigatoka has been developed at the scale of a territory from surveys enMartinique during the period of invasion of the disease from September 2010 to May 2012. The data collected being censored, inference of model parameters has was performed in a Bayesian framework, using a data augmentation algorithm. The model developed and inference possible to reconstruct the spatiotemporal dynamics of the invasion and predict the end of the invasion territoire.Les two spatio-temporal dynamics models developed at two different spatial scales has been gained important information for build tools design method of control of black Sigatoka of banana.

http://www.theses.fr/2015AGUY0835/document

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
One of the main difficulties encountered when characterizing the hydrodynamic properties of a fractured aquifer is to identify the preferential flow paths within it. Different methods may be applied to determine the variability of the permeability at the borehole scale and to image the structure of the main flow zones between boreholes. In this paper, we compare the information obtained from different measurement techniques performed in a set of three 100 m depth wells (well-to-well spacing: 5­10 m) in a fractured crystalline rock setting. Geophysical logging and borehole-wall imaging are used to identify open and closed fractures intersecting the boreholes and their orientation. The comparison with flowmeter and single packer tests shows that few of the fractures interpreted as open from geophysical logs are significantly transmissive. Cross-borehole connectivity is first investigated from single packer tests with pressure monitoring in adjacent boreholes. To determine fracture zone connectivity, we propose a methodology simply based on the variation with packer depth of the ratio of the drawdown in the observation well and the drawdown in the pumping well. The results are compared to the analysis of cross-borehole flowmeter tests. We show that both methods provide consistent results with a similar level of information on connectivity.
ISSN: 0022-1694

insu-00221380
https://hal-insu.archives-ouvertes.fr/insu-00221380
DOI : 10.1016/j.jhydrol.2007.07.007

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Staphylococcus aureus is a highly versatile, opportunistic pathogen and the etiological agent of a wide range of infections in humans and warm-blooded animals. The epithelial surface is its principal site of colonization and infection. In this work, we investigated the cytopathic effect of S. aureus strains from human and animal origins and their ability to affect the host cell cycle in human HeLa and bovine MAC-T epithelial cell lines. S. aureus invasion slowed down cell proliferation and induced a cytopathic effect, resulting in the enlargement of host cells. A dramatic decrease in the number of mitotic cells was observed in the infected cultures. Flow cytometry analysis revealed an S. aureus-induced delay in the G2/M phase transition in synchronous HeLa cells. This delay required the presence of live S. aureus since the addition of the heat-killed bacteria did not alter the cell cycle. The results of Western blot experiments showed that the G2/M transition delay was associated with the accumulation of inactive cyclin-dependent kinase Cdk1, a key inducer of mitosis entry, and with the accumulation of unphosphorylated histone H3, which was correlated with a reduction of the mitotic cell number. Analysis of S. aureus proliferation in asynchronous, G1- and G2-phase-enriched HeLa cells showed that the G2 phase was preferential for bacterial infective efficiency, suggesting that the G2 phase delay may be used by S. aureus for propagation within the host. Taken together, our results divulge the potential of S. aureus in the subversion of key cellular processes such as cell cycle progression, and shed light on the biological significance of S. aureus-induced host cell cycle alteration.
ISSN: 1932-6203

hal-00873672
https://hal.archives-ouvertes.fr/hal-00873672
https://hal.archives-ouvertes.fr/hal-00873672/document
https://hal.archives-ouvertes.fr/hal-00873672/file/Staphylococcus_aureus-Induced.accepted.pdf
DOI : 10.1371/journal.pone.0063279

Éditeur(s) : HAL CCSD
Résumé : Water vapour is highly variable in the atmosphere with concentration reaching saturation in the tropics and with dry areas over elevated continental region. Good knowledge of the amount of integrated water vapour in the air is necessary to predict phase changes and in particular precipitation. Water vapour variability measurements are still insufficient with standard observing systems. Moreover accurate GPS antenna positioning is affected by the refractivity index variation in the troposphere. Consequently, vertical positioning component estimation is difficult. This variation is directly linked to distribution of variables such as pressure, temperature and humidity along the path between satellite and receiver. Here we study more specifically heavy rains et notably Cevenols events. This thesis work consists to check the GPS measurement validity to quantify water vapour in comparison with measurements from radiosoundings and meteorological model outputs. GPS observations and flux surface information have been analysed to see if water vapour quantification by GPS allowed characterising heavy rain events (cumulative rainfall amount greater than 150 mm). Then, we tested the GPS data assimilation impact on cumulative precipitation forecasts using the high resolution Meteo France AROME model (2.5 km). Finally the quality and the contribution of GPS measurement on sea is evaluated for water vapour measurement. This study has been realised in the framework of VAPIMED experiment.
La vapeur d'eau varie largement dans l'atmosphère avec des concentrations allant de la saturation dans les tropiques à des zones presque sèches au-dessus des zones continentales élevées. Une bonne connaissance du contenu en vapeur d'eau dans l'air est nécessaire pour la prévision des changements de phases, notamment les précipitations. La mesure de la variabilité de la vapeur d'eau est une lacune des systèmes d'observation. Par ailleurs, il est apparu que le positionnement précis des antennes GPS était affecté par la variation de l'indice de réfraction dans la troposphère, ce qui rend particulièrement difficile l'estimation de la composante verticale. Cette variation est directement liée à la distribution des variables pression, température et humidité sur les trajets satellite-récepteur. On s'intéresse ici à l'étude des précipitations intenses et notamment aux épisodes Cévenols. Ce travail de thèse consiste à vérifier la validité de la mesure GPS pour la quantification de la vapeur d'eau en la comparant avec des mesures issues de radiosondage et des sorties de modèle météorologique. On cherche à analyser si la quantification de vapeur d'eau par GPS permet de caractériser les forts événements précipitants (cumuls supérieurs à 150 mm) à l'aide d'observations conjointes sur les flux de surface. On étudie ensuite l'impact de l'assimilation de données GPS issues d'un réseau GPS dense sur la prévision des cumuls de pluies dans le modèle à hauterésolution (2.5 km) AROME de Météo France. Finalement on évalue la qualité et l'apport de la mesure de vapeur d'eau par GPS en mer dans le cadre d'une campagne de mesure VAPIMED).
https://tel.archives-ouvertes.fr/tel-00444081

Droits : info:eu-repo/semantics/OpenAccess
tel-00444081
https://tel.archives-ouvertes.fr/tel-00444081
https://tel.archives-ouvertes.fr/tel-00444081/document
https://tel.archives-ouvertes.fr/tel-00444081/file/These_KBoniface.pdf