Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
Virus detection has often been difficult due to a low concentration in water. In this study, we developed a new procedure based on concentration of virus particles on an innovative support: poly-L-lysine dendrigrafts (DGL), coupled with directed nucleic acid extraction and real-time PCR quantification. Methods and Results: This method was evaluated using the bacteriophage MS2 as a model virus. This virus exhibited the size and structural properties of human pathogenic enteric viruses and has often been used to assess new supports of concentration. Moreover, this bacteriophage is also a faecal contamination indicator. In this study, many water filtration conditions were tested (volume of water, concentration, etc.), and more than 80% of bacteriophage were recovered after filtration on polymer, in most conditions. We demonstrated that the method was linear (slope = 0 99 0 04 and Y intercept when x = 0 02 0 28), valid (as manipulators, tested concentrations, volumes of sample and batch of polymer did not have any influence on concentration) and sensitive (allowing to concentrate up to 16 600-fold 1 l of sample and to detect and quantify down to 750 GC l 1 and 7500 GC l 1, respectively). Conclusions: To conclude, this support exhibits high interest to retain viruses and to allow to detect low concentration of virus in water. Significance and Impact of the Study: This study gives valuable advance in the methods of concentration and diagnosis of virus in water.
Journal of Applied Microbiology

hal-00932328
https://hal.archives-ouvertes.fr/hal-00932328
DOI : 10.1111/jam.12209

Éditeur(s) : HAL CCSD Society for Molecular Biology and Evolution
Résumé : International audience
Microsatellites (SSRs) are highly susceptible to expansions and contractions. When located in a coding sequence, the insertion or the deletion of a single unit for a mono-, di-, tetra-, or penta(nucleotide)-SSR creates a frameshift. As a consequence, one would expect to find only very few of these SSRs in coding sequences because of their strong deleterious potential. Unexpectedly, genomes contain many coding SSRs of all types. Here, we report on a study of their evolution in a phylogenetic context using the genomes of four primates: human, chimpanzee, orangutan, and macaque. In a set of 5,015 orthologous genes unambiguously aligned among the four species, we show that, except for tri- and hexa-SSRs, for which insertions and deletions are frequently observed, SSRs in coding regions evolve mainly by substitutions. We show that the rate of substitution in all types of coding SSRs is typically two times higher than in the rest of coding sequences. Additionally, we observe that although numerous coding SSRs are created and lost by substitutions in the lineages, their numbers remain constant. This last observation suggests that the coding SSRs have reached equilibrium. We hypothesize that this equilibrium involves a combination of mutation, drift, and selection. We thus estimated the fitness cost of mono-SSRs and show that it increases with the number of units. We finally show that the cost of coding mono-SSRs greatly varies from function to function, suggesting that the strength of the selection that acts against them can be correlated to gene functions.
ISSN: 1759-6653

hal-01544762
https://hal.archives-ouvertes.fr/hal-01544762
DOI : 10.1093/gbe/evt003

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
We analyze in this study a new set of marine data including 3D local tomography, 1992-2008 relocated earthquakes and two recent multichannel seismic lines to characterize the deformation style in the collision area offshore east Taiwan. We have mapped in detail the Mohos of the converging plates as well as the subduction interface with a resolution never reached before. We show that the sharp continental subduction of the Eurasia plate, beneath the middle part of the Central Range, indents the Philippine Sea plate (PSP) as attested by intra-oceanic slicing and incipient subduction of the PSP beneath the east coast of Taiwan. The westernmost part of the PSP slab is probably experiencing a beginning of break-off as attested by NW-trending en-échelon shear zones beneath the southern slope of the southern Ryukyu arc (SRA). These en-échelon shear zones have a sinistral component favored by the "collision-free" subduction of the PSP north of 24°30′N. The down-faulting of the subduction interface forms ramps along which earthquakes clusterize. Three M7 subduction earthquakes occurred offshore Suao city along these ramps with a recurrence interval of about 40 years: 1920 Mw7.7, 1963 Mw7.2 and 2002 Mw7.1 events. The 1966 Mw6.0-7.5 earthquakes sequence likely outlines a WNW-ESE left-lateral intra-slab shear zone. The SRA upper plate accommodates the complex geometry and deformation of the subducting PSP through seismic deformation. Shallow high velocities fringing the Luzon volcanic arc (LVA) beneath the Longitudinal Valley and north of the southernmost Ryukyu forearc basins are interpreted as relics of the LVA forearc basement squeezed in the collision zone. Based on the accommodation of a large part of the convergence through shortening within the PSP and the subsequent segmentation of the shallow subduction interface, we consider that the nucleation of a Mw ≥ 8 earthquake along the southernmost Ryukyu megathrust is unlikely.
ISSN: 0040-1951

hal-00853365
https://hal.archives-ouvertes.fr/hal-00853365
https://hal.archives-ouvertes.fr/hal-00853365/document
https://hal.archives-ouvertes.fr/hal-00853365/file/publallemandifremer.pdf
DOI : 10.1016/j.tecto.2013.03.020

Éditeur(s) : HAL CCSD Society for Molecular Biology and Evolution
Résumé : International audience
Vibrio metoecus is the closest relative of Vibrio cholerae, the causative agent of the potent diarrheal disease cholera. Although the pathogenic potential of this new species is yet to be studied in depth, it has been co-isolated with V. cholerae in coastal waters and found in clinical specimens in the USA. We used these two organisms to investigate the genetic interaction between closely related species in their natural environment. The genomes of twenty V. cholerae and four V. metoecus strains isolated from a brackish coastal pond on the US east coast, as well as four clinical V. metoecus strains were sequenced and compared to reference strains. Whole genome comparison shows 86-87% average nucleotide identity (ANI) in their core genes between the two species. On the other hand, the chromosomal integron, which occupies approximately 3% of their genomes, shows higher conservation in ANI between species than any other region of their genomes. The ANI of 93-94% observed in this region is not significantly greater within than between species, meaning that it does not follow species boundaries. V. metoecus does not encode toxigenic V. cholerae major virulence factors, the cholera toxin and toxin co-regulated pilus. However, some of the pathogenicity islands found in pandemic V. cholerae were either present in the common ancestor it shares with V. metoecus, or acquired by clinical and environmental V. metoecus in partial fragments. The virulence factors of V. cholerae are therefore both more ancient and more widespread than previously believed. There is high interspecies recombination in the core genome, which has been detected in 24% of the single-copy core genes, including genes involved in pathogenicity. V. metoecus was six times more often the recipient of DNA from V. cholerae as it was the donor, indicating a strong bias in the direction of gene transfer in the environment.
ISSN: 1759-6653

Droits : http://creativecommons.org/licenses/by/
hal-01264332
http://hal.upmc.fr/hal-01264332
http://hal.upmc.fr/hal-01264332/document
http://hal.upmc.fr/hal-01264332/file/Genome%20Biol%20Evol-2015-Orata-gbe_evv193.pdf
DOI : 10.1093/gbe/evv193

Éditeur(s) : HAL CCSD Wiley
Résumé : The evolutionary potential of long-lived species, such as forest trees, is fundamental for their local persistence under climate change (CC). Genome–environment association (GEA) analyses reveal if species in heterogeneous environments at the regional scale are under differential selection resulting in populations with potential preadaptation to CC within this area. In 79 natural [i]Fagus sylvatica[/i] populations, neutral genetic patterns were characterized using 12 simple sequence repeat (SSR) markers, and genomic variation (144 single nucleotide polymorphisms (SNPs) out of 52 candidate genes) was related to 87 environmental predictors in the latent factor mixed model, logistic regressions and isolation by distance/environmental (IBD/IBE) tests. SSR diversity revealed relatedness at up to 150m intertree distance but an absence of large-scale spatial genetic structure and IBE. In the GEA analyses, 16 SNPs in 10 genes responded to one or several environmental predictors and IBE, corrected for IBD, was confirmed. The GEA often reflected the proposed gene functions, including indications for adaptation to water availability and temperature. Genomic divergence and the lack of large-scale neutral genetic patterns suggest that gene flow allows the spread of advantageous alleles in adaptive genes. Thereby, adaptation processes are likely to take place in species occurring in heterogeneous environments, which might reduce their regional extinction risk under CC
ISSN: 0028-646X

hal-01309135
https://hal.archives-ouvertes.fr/hal-01309135
PRODINRA : 343710
DOI : 10.1111/nph.13809

Éditeur(s) : HAL CCSD Wiley
Résumé :  
The symbiotic interactions between Frankia strains and their associated plants from the Casuarinaceae under controlled conditions are well documented but little is known about these interactions under natural conditions. We explored the symbiotic interactions between eight genotypically characterized Frankia strains and five Casuarinaceae species in long-term field trials. Characterization of strains was performed using the polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) for the nifD-nifK intergenic transcribed spacer (ITS) and 16S-23S ITS. Assessments of the symbiotic interactions were based on nodulation patterns using nodule dry weight and viability, and on actual N-2 fixation using the delta N-15 method. The PCR-RFLP patterns showed that the analyzed strains belonged to the same genotypic group (CeD group), regardless of the host species and environment of origin. The nodule viability index is introduced as a new tool to measure the viability of perennial nodules and to predict their effectiveness. The host Casuarinaceae species was a key factor influencing both the actual N-2-fixing activity of the associated Frankia strain and the viability of nodules within a location. This is the first study providing information on the symbiotic interactions between genotypically characterized Frankia strains and actinorhizal plants under natural conditions. The results revealed a way to improve a long-term management of the Casuarinaceae symbiosis.
ISSN: 0031-9317

hal-01032134
https://hal.archives-ouvertes.fr/hal-01032134
DOI : 10.1111/j.1399-3054.2007.00856.x

Éditeur(s) : HAL CCSD
Résumé : The purpose of this work is to specify the deformation offshore East of Taiwan by characterizing major active faults in particular at the level of the Ryukyu forearc. The major problem associated with the study of this region is that earthquakes are located outside the permanent networks. Consequently, this led to some unprecise earthquake locations limiting tectonic and statistical analyses, and therefore the correct estimation of the seismic hazard. This work is included in the project ANR ACTS (Active Tectonics and Seismic Hazard in Taiwan). To achieve this goal, we worked on three different timescales for which a different localization method has been proposed to obtain a clear image of seismic deformation and highlight major faults offhore East of Taiwan. First, at the scale of the century (from the analysis of a seismicity catalogue with homogeneous magnitude), the instrumental historical earthquakes (1897-2007) show that the Ryukyu margin was affected by 6 earthquakes of magnitude greater than 7 with 4 of them for which the responsible fault is unknown. We propose a method of relative location to relocate the historic events from the time difference of P and S arrival times (Ts-Tp) at each station. The location is obtained by searching for "analogue" earthquakes in the recent instrumental catalogue (1991-2008) for which Ts-Tp at each station is close. This method has been applied to the largest (in terms of magnitude) earthquake ever recorded in Taiwan, the earthquake of June 5, 1920 (M7.7 +/- 0.2). A rupture along the interplate of the Ryukyu subduction with a possible nucleation at the downdip limit of a splay-fault is certainly responsible of this earthquake. Then, at the scale of the decade, the improvement of the method of absolute location based on MAXimum of Intersection of EDT (MAXI, EDT: Equal Differential Time) allows to better extract the erroneous arrival times and prevents the "trade-off" between depth and origin time, and between depth and epicentral position when the azimuthal coverage is low (gap Azimuthal > 180degre). Synthetic tests show the effectiveness of MAXI (using P-wave only) to determine the parameters x, y and z even when the azimuthal gap is important. In the latter case, the quality of the results is dependent on the velocity model to represent the 3D structure of the Earth. We propose an approach involving the use of a 3D a priori P-wave velocity model to locate earthquakes which are lateral and remote to the seismic network. An application to the case of Taiwan and Ecuador validates this approach. Finally, at the level of a few months, the marine geophysical campaign RATS (Ryukyu Arc: Tectonics and Seismology) was conducted in two stages. A passive seismology experiment from July to October, 2008 (RATS1) has been conducted over the forearc of the Ryukyus and then active seismic experiment (refraction and reflection) was conducted in May 2009 in a NNE - SSW line through the Ryukyu margin. These two combined experiments allow improving our knowledge about the crustal structure of the margin. At the level of the forearc, the basement of the forearc is characterized by vertical backstop and a very deformed basis certainly associated with a significant out of sequence deformation. In depth, the downgoing plate is certainly affected by a tear that controls the seismicity in the region of transition between the subduction and collision.
Le but de ce travail est de préciser la déformation en mer à l'est de Taïwan et de notamment caractériser les failles actives majeures en particulier au niveau de l'avant-arc des Ryukyus. Le problème majeur associé à l'étude de cette région est que les séismes sont localisés en dehors des réseaux permanents et que cela conduit à des localisations peu précises limitant les analyses statistiques, tectoniques et donc l'estimation correcte de l'aléa sismique. Ce travail est inclus dans le projet ANR ACTS (Active Tectonics and Seismic Hazard in Taiwan). Pour atteindre cet objectif, nous travaillons à trois échelles de temps différentes pour lesquelles une méthode de localisation différente a été proposée pour obtenir une image précise de la déformation sismique et mettre en évidence les failles majeures en mer à l'est de Taïwan. D'abord, à l'échelle du siècle (à partir de l'analyse d'un catalogue de sismicité homogène en magnitude), les séismes historiques instrumentaux (1897-2007) montrent que la marge des Ryukyus a été affectée par 6 séismes de magnitude supérieure à 7 dont 4 pour lesquels la faille responsable n'est pas connue. Nous proposons une méthode de localisation relative qui permet de relocaliser les évènements historiques à partir des différences de temps d'arrivées P et S (Ts-Tp) à chaque station. La localisation est obtenue en recherchant les séismes analogues dans le catalogue instrumental récent (1991-2008) pour lesquels Ts-Tp à chaque station est proche. Cette méthode a été appliquée au plus gros séisme (en terme de magnitude) jamais enregistré à Taïwan, le séisme du 5 juin 1920 (M7.7 $pm$ 0.2). Ce séisme a certainement pour origine une rupture sur l'interplaque sismogène de la subduction des Ryukyus avec une possible nucléation à la base d'une faille hors-séquence. Ensuite, à l'échelle de la dizaine d'années, l'amélioration de la méthode de localisation absolue du MAXimum d'Intersection EDT (MAXI, EDT: Equal Differential Time) permet de mieux extraire les temps d'arrivées erronés et empêche les "trade-off" entre profondeur et temps d'origine et, entre profondeur et position épicentrale lorsque la couverture azimutale est faible (gap azimutal > 180°). Des tests synthétiques montrent l'efficacité de MAXI (en utilisant les ondes P uniquement) à déterminer les paramètres x, y et z même lorsque le gap azimutal est important. Dans ce dernier cas, la qualité des résultats reste dépendant du modèle de vitesse à représenter la structure 3D de la Terre. Nous proposons une démarche associant l'utilisation d'un modèle de vitesse des ondes P 3D a priori avec la méthode MAXI pour localiser les séismes qui sont latéraux et éloignés du réseau. Une application au cas de Taïwan et en Équateur valide cette approche. Enfin, à l'échelle de quelques mois, la campagne de géophysique marine RATS (Ryukyu Arc: Tectonics and Seismology) a été menée en deux temps. Une expérience de sismologie passive de juillet à octobre 2008 (RATS1) a été menée au-dessus de l'avant-arc des Ryukyus puis une expérience de sismique active (réfraction et réflexion) a été menée en mai 2009 sur une ligne NNE-SSW à travers la marge des Ryukyus. Ces deux expériences combinées permettent d'améliorer notre connaissance de la structure crustale de la marge. Au niveau de l'avant-arc, le socle de l'avant-arc est caractérisé par une extrémité formant un butoir vertical et une base très déformée certainement associée à une importante déformation hors-séquence. En profondeur, la plaque plongeante est certainement affectée par une déchirure qui contrôle la sismicité dans cette région de transition entre la subduction et la collision.
https://tel.archives-ouvertes.fr/tel-00660737

tel-00660737
https://tel.archives-ouvertes.fr/tel-00660737
https://tel.archives-ouvertes.fr/tel-00660737/document
https://tel.archives-ouvertes.fr/tel-00660737/file/Thesis_small.pdf

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Deciphering the evolutionary processes driving nucleotide variation in multiallelic genes is limited by the number of genetic systems in which such genes occur. The complementary sex determiner (csd) gene in the honey bee Apis mellifera is an informative example for studying allelic diversity and the underlying evolutionary forces in a well-described model of balancing selection. Acting as the primary signal of sex determination, diploid individuals heterozygous for csd develop into females, whereas csd homozygotes are diploid males that have zero fitness. Examining 77 of the functional heterozygous csd allele pairs, we established a combinatorical criteria that provide insights into the minimum number of amino acid differences among those pairs. Given a data set of 244 csd sequences, we show that the total number of csd alleles found in A. mellifera ranges from 53 (locally) to 87 (worldwide), which is much higher than was previously reported (20). Using a coupon-collector model, we extrapolate the presence of in total 116-145 csd alleles worldwide. The hypervariable region (HVR) is of particular importance in determining csd allele specificity, and we provide for this region evidence of high evolutionary rate for length differences exceeding those of microsatellites. The proportion of amino acids driven by positive selection and the rate of nonsynonymous substitutions in the HVR-flanking regions reach values close to 1 but differ with respect to the HVR length. Using a model of csd coalescence, we identified the high originating rate of csd specificities as a major evolutionary force, leading to an origin of a novel csd allele every 400,000 years. The csd polymorphism frequencies in natural populations indicate an excess of new mutations, whereas signs of ancestral transspecies polymorphism can still be detected. This study provides a comprehensive view of the enormous diversity and the evolutionary forces shaping a multiallelic gene.
ISSN: 0737-4038

hal-01544758
https://hal.archives-ouvertes.fr/hal-01544758
DOI : 10.1093/molbev/mst207

Éditeur(s) : HAL CCSD Royal Society, The
Résumé : International audience
Endemic species are frequently assumed to have lower genetic diversity than species with large distributions, even if closely related. This assumption is based on research from the terrestrial environment and theoretical evolutionary modelling. We test this assumption in the marine environment by analysing the mitochondrial genetic diversity of 33 coral reef fish species from five families sampled from Pacific Ocean archipelagos. Surprisingly, haplotype and nucleotide diversity did not differ significantly between endemic and widespread species. The probable explanation is that the effective population size of some widespread fishes locally is similar to that of many of the endemics. Connectivity across parts of the distribution of the widespread species is probably low, so widespread species can operate like endemics at the extreme or isolated parts of their range. Mitochondrial genetic diversity of many endemic reef fish species may not either limit range size or be a source of vulnerability.
ISSN: 0962-8452

hal-01333327
https://hal-univ-perp.archives-ouvertes.fr/hal-01333327
DOI : 10.1098/rspb.2014.1068

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

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

Éditeur(s) : HAL CCSD IOS Press
Résumé : International audience
Sickle cell anemia (SCA or SS homozygous sickle cell disease) is an inherited blood disorder caused by single 12 nucleotide substitution in the ␤-globin gene that renders their hemoglobin (HbS) much less soluble than normal hemoglobin 13 (HbA) when deoxygenated. The polymerization of HbS upon deoxygenation is the basic pathophysiologic event leading to 14 RBC sickling, hemolysis, vasoocclusion and ultimately to chronic organ damage. The metabolic changes imposed by exercise 15 may initiate sickling and vaso-occlusive episodes. Further, in patients with SCA, exercise limitation may be related to anemia 16 or chronic complications such as pulmonary vascular disease, congestive heart failure and chronic parenchymal lung disease. 17 Few studies have investigated the cardiorespiratory responses of patients with SCA during either symptom-limited maximal 18 exercise test on cyclo-ergometer or during a six minute walk test. Therefore, patients are advised to start exercise slowly and 19 progressively, to maintain adequate hydration during and after exercise, to avoid cold exposure or sudden change in temperature, 20 and to avoid sports associated with mechanical trauma. There are, however, lack of evidence to allow practitioners to prescribe 21 an exercise program for patients with SCA, and individuals are usually encouraged to exercise on a symptom-limited basis. 22 Finally, this review will also highlight the basic principles that are often used for exercise practice and could be used for exercise 23 prescription and rehabilitation in patients with sickle cell anemia.
ISSN: 1386-0291

hal-01163966
https://hal.univ-antilles.fr/hal-01163966
DOI : 10.3233/CH-2011-1465

Éditeur(s) : HAL CCSD Society for Molecular Biology and Evolution
Résumé : International audience
Complex nongradual evolutionary processes such as gene remodeling are difficult to model, to visualize, and to investigate systematically. Despite these challenges, the creation of composite (or mosaic) genes by combination of genetic segments from unrelated gene families was established as an important adaptive phenomena in eukaryotic genomes. In contrast, almost no general studies have been conducted to quantify composite genes in viruses. Although viral genome mosaicism has been well-described, the extent of gene mosaicism and its rules of emergence remain largely unexplored. Applying methods from graph theory to inclusive similarity networks, and using data from more than 3,000 complete viral genomes, we provide the first demonstration that composite genes in viruses are 1) functionally biased, 2) involved in key aspects of the arm race between cells and viruses, and 3) can be classified into two distinct types of composite genes in all viral classes. Beyond the quantification of the widespread recombination of genes among different viruses of the same class, we also report a striking sharing of genetic information between viruses of different classes and with different nucleic acid types. This latter discovery provides novel evidence for the existence of a large and complex mobilome network, which appears partly bound by the sharing of genetic information and by the formation of composite genes between mobile entities with different genetic material. Considering that there are around 10E31 viruses on the planet, gene remodeling appears as a hugely significant way of generating and moving novel sequences between different kinds of organisms on Earth.
ISSN: 1759-6653

Droits : http://creativecommons.org/licenses/by/
hal-01324848
http://hal.upmc.fr/hal-01324848
http://hal.upmc.fr/hal-01324848/document
http://hal.upmc.fr/hal-01324848/file/Genome%20Biol%20Evol-2014-Jachiet-2195-205.pdf
DOI : 10.1093/gbe/evu168

Éditeur(s) : HAL CCSD Frontiers Media
Résumé : International audience
We present high resolution observations of microstructure and texture evolution during dynamic recrystallization (DRX) of ice polycrystals deformed in the laboratory at high temperature (≈0.98Tm). Ice possesses a significant viscoplastic anisotropy that induces strong strain heterogeneities, which result in an early occurrence of DRX mechanisms. It is therefore a model material to explore these mechanisms. High resolution c-axis measurements at sample scale by optical techniques and full crystallographic orientation measurements by cryo-Electron Back Scattering Diffraction (EBSD) provide a solid database for analyzing the relative impact of the macroscopic imposed stress vs. the local and internal stress fields on DRX mechanisms. Analysis of misorientation gradients in the EBSD data highlights a heterogeneous dislocation distribution, which is quantified by the Nye tensor estimation. Joint analyses of the dislocation density maps and microstructural observations highlight spatial correlation between high dislocation density sites and the onset of nucleation taking place by grain-boundary bulging, subgrain rotation or by the formation of kink-bands.
ISSN: 2296-6463

hal-01515284
https://hal.univ-lorraine.fr/hal-01515284
DOI : 10.3389/feart.2015.00081

Éditeur(s) : HAL CCSD E Schweizerbart Science Publishers
Résumé : The occurrence and preservation of aragonite in eclogite-facies rocks of north-eastern Corsica is linked to an uncommon microtexture. Aragonite exclusively occurs as oriented fibres in garnet crystals of a graphitic, more or less siliceous marble that immediately overlies a serpentinite body of the meta-ophiolitic unit. The arrangement of the fibres is grossly radial, but more clearly sectoral in subhedral garnet, the fibres growing perpendicular to the garnet/matrix interface. Raman mapping reveals that the carbonate is calcite in the matrix and in poikiloblastic garnet cores, and that the fibres in the garnet mantle are aragonite alone in the case of a carbonate matrix, and both aragonite and quartz (in distinct fibres) in a quartz–carbonate matrix. These features are interpreted as prograde intergrowths, the result of garnet nucleation and growth in a calcite and then aragonite matrix (±quartz). Upon further heating and/or decompression, the aragonite matrix transformed back to calcite while the carbonates included in garnet retained their original structure, in spite of the relatively high temperature attained (ca. 500 °C). These aragonite relics are one more example of the preservation of a high-pressure polymorph through mechanical shielding of inclusions in a rigid host. The aragonite–garnet intergrowths are similar to quartz–garnet intergrowths described in amphibolite-facies graphitic schists. They are evidence that oriented inclusions in garnet are not necessarily precipitates (‘exsolutions'). Unlike precipitates, their orientation is controlled more by the shape of the garnet growth front than by symmetry constraints.
ISSN: 0935-1221

hal-00411136
https://hal.archives-ouvertes.fr/hal-00411136
DOI : 10.1127/0935-1221/2008/0020-1892

Éditeur(s) : HAL CCSD SAGE Publications (UK and US)
Résumé : International audience
In this article, we focus on hypomaturation autosomal-recessive-type amelogenesis imperfecta (type IIA2) and describe 2 new causal Matrix metalloproteinase 20 (MMP20) mutations validated in two unrelated families: a missense mutation p.T130I at the expected homozygous state, and a compound heterozygous mutation having the same mutation combined with a nucleotide deletion, leading to a premature stop codon (p.N120fz*2). We characterized the enamel structure of the latter case using scanning electron microscopy analysis and microanalysis (Energy-dispersive X-ray Spectroscopy, EDX) and confirmed the hypomaturation-type amelogenesis imperfecta as identified in the clinical diagnosis. The mineralized content was slightly decreased, with magnesium substituting for calcium in the crystal structure. The anomalies affected enamel with minimal inter-rod enamel present and apatite crystals perpendicular to the enamel prisms, suggesting a possible new role for MMP20 in enamel formation.
ISSN: 0022-0345

hal-01545484
https://hal.archives-ouvertes.fr/hal-01545484
DOI : 10.1177/0022034513488393

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

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

Éditeur(s) : HAL CCSD Medknow Publications
Résumé : International audience
Multiple regions of the genome have been associated with the risk of prostate cancer in Caucasians, particularly including several polymorphisms located at 8q24. Region 2 of 8q24 has been repeatedly found to be associated with the risk of prostate cancer among men of African descent, although one study performed in the Caribbean island of Jamaica did not report this finding. In this study, the single nucleotide polymorphism rs16901979, located in region 2 of 8q24, was genotyped in 498 cases of histologically confirmed prostate cancer and 541 controls from the French Caribbean islands of Guadeloupe, where the population is largely of African descent. The AA genotype and the A allele at rs16901979 were associated with elevated risks of prostate cancer (odds ratios [ORs] = 1.84, 95% confidence interval [95% CI] = 1.26-2.69, P = 0.002 and OR = 1.36, 95% CI = 1.13-1.64, P = 0.001, respectively). Following stratification of the patients by disease aggressiveness, as defined by the Gleason score, the pooled genotypes AC + AA were associated with a higher risk of a Gleason score ≥7 at diagnosis (OR = 1.79, 95% CI = 1.17-2.73, P = 0.007). In summary, the A allele at rs16901979 was associated with the risk of prostate cancer in the Caribbean population of Guadeloupe, confirming its involvement in populations of African descent. Moreover, our study provides the first evidence of an association between this variant and the risk of aggressive prostate cancer.
ISSN: 1008-682X

Droits : http://creativecommons.org/licenses/by-nc-sa/
hal-01118552
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01118552
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01118552/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01118552/file/AsianJAndrol171117-1705456_044414.pdf
DOI : 10.4103/1008-682X.135127

Éditeur(s) : HAL CCSD Springer Verlag (Germany)
Résumé : International audience
A hybrid linear ion-trap Fourier-transform ion cyclotron resonance mass spectrometer was used for top-down characterization of the abundant human salivary Cystatins, including S, S1, S2, SA, SN, C, and D, using collisionally activated dissociation (CAD) after chromatographic purification of the native, disulfide intact proteins from saliva. Post-translational modifications and protein sequence polymorphisms arising from single nucleotide polymorphisms (SNPs) were assigned from precursor and product ion masses at a tolerance of 10 ppm allowing confident identification of individual intact mass tags. Cystatins S, S1, S2, SA and SN were cleaved of a N-terminal 20 amino-acid signal peptide, and Cystatin C a 26-residue peptide, to yield a generally conserved N-terminus. In contrast, Cystatin D isoforms with 24 and 28 amino-acid residue N-terminal truncations were found such that their N-termini were not conserved. Cystatin S1 was phosphorylated at Ser3, while S2 was phosphorylated at Ser1 and Ser3 of the mature protein, in agreement with previous work. Both Cystatin D isoforms carried the polymorphism C46R (SNP: rs1799841). The 14328 Da isoform of Cystatin SN previously assigned with polymorphism P31L due to a SNP (rs2070856) was found only in whole saliva. Parotid secretions contained no detectable Cystatins while whole saliva largely mirrored the contents of submandibular/sublingual (SMSL) secretions. Top-down high-resolution mass spectrometry is a powerful tool for the identification and characterization of potential protein biomarkers in saliva.
ISSN: 1044-0305

hal-00677483
https://hal.archives-ouvertes.fr/hal-00677483
DOI : 10.1016/j.jasms.2010.01.025

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 Taylor & Francis
Résumé : International audience
The functional organization of the circadian system and the location of the main circadian oscillators vary through phylogeny. Present study investigates by in situ hybridization the anatomical location of the clock gene gPer1b in forebrain and midbrain, pituitary, and in two peripheral locations, the anterior intestine and liver, in a teleost fish, the goldfish (Carassius auratus). Moreover, the daily expression profiles of this gene were also studied by quantitative Real Time-PCR. Goldfish were maintained under a 12L–12D photoperiod and fed daily at 2 h after lights were switched on. A wide distribution of gPer1b mRNA in goldfish brain and pituitary was found in telencephalon, some hypothalamic nuclei (including the homologous to mammalian SCN), habenular nucleus, optic tectum, cerebellum and torus longitudinalis. Moreover, gPer1b expression was observed, for the first time in teleosts, in the pituitary, liver and anterior intestine. Day/night differences in gper1b mRNA abundance were found by in situ hybridization, with higher signal at nighttime that correlates with the results obtained by RT-PCR, where a rhythmic gPer1b expression was found in all tissues with acrophases at the end of the night. Amplitudes of gper1b rhythms vary among tissues, being higher in liver and intestine than in the brain, maybe because different cues entrain clocks in these locations. These results support the existence of functional clocks in many central and peripheral locations in goldfish coordinated, ticking at the same time
ISSN: 0742-0528

hal-01197353
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01197353
DOI : 10.3109/07420528.2015.1049615
PUBMED : 26171989