Éditeur(s) : HAL CCSD
Résumé :  
Improvement of wood quality related traits is currently hampered by costly chemical and technological assays and the necessity to wait until the trees are nearly mature to evaluate wood properties. The availability of a vast quantity of genomic data opens now a new avenue to identify early selection criteria based on molecular information and therefore increase selection efficiency. Association mapping is becoming a method of choice to identify QTN (quantitative trait nucleotide) that contribute to complex trait variation. The implementation of this approach requires on the one hand knowledge of the molecular mechanisms underlying trait variation and polymorphism within candidate genes, and on the other hand the availability of phenotypically well characterized genetic material. We are developing this strategy in the frame of the French maritime pine breeding program, an economically important forest tree species in the South Western Europe. About 500 trees from the breeding population were evaluated for wood physical and chemical properties through the analysis of 2,800 half-sib progenies and 1,500 clones in 8 field tests. These same trees are being genotyped at 185 SNPs obtained from the sequencing of 41 candidate genes, and an additional set of 200 eSNPs detected in 147 EST-contigs (to be used as control). Statistical association between the breeding values of the 500 trees and their respective genotypes will be tested using mixed models accounting for relatedness among individuals of the breeding population.
IUFRO-CTIA joint conference, "Adaptation, Breeding and Conservation in the Era of Forest Tree Genomics and Environmental Change"
Québec City, Canada

hal-01032075
https://hal.archives-ouvertes.fr/hal-01032075

Éditeur(s) : HAL CCSD AGU and the Geochemical Society
Résumé : International audience
New magnetotelluric and receiver transfer function studies provide insights from the upper to the lower crust of the eastern Betic Cordillera, which is deformed by large folds, normal faults, and a major transcurrent left-lateral fault, the Carboneras Fault Zone (CFZ). Receiver function analysis determines a NNW dipping Moho reaching 20 degrees that increases in depth, from 20 km south of the CFZ up to 34 km in the Sierra de Los Filabres. In addition, seismic discontinuities determined in the upper crust are interpreted as major contacts between metamorphic complexes that are detached and folded. The MT inversion model reveals a conductive zone, also representing a crustal seismic discontinuity, associated with the Alpujarride/Nevado-Filabride contact and fitting the N vergent geometry of the Sierra Alhamilla antiform. A small flexure at Moho coincides with the CFZ, as revealed by the Bouguer anomaly trend, in agreement with the receiver function results. Moreover, the Bahr strike and tipper angle at the stations placed closest to the CFZ clearly reveal the continuity of the CFZ at least down to approximately 15 km in depth, crossing all the detected crustal discontinuities up to the Moho. The lack of a clear Moho offset associated with the Carboneras Fault supports the idea that some large strike-slip faults tend to accommodate the deformation by a broadening fault zone at lower crustal levels. Its nucleation could occur at the base of a thin crust, where melting processes critically reduced the lithospheric strength during the late Miocene, to then propagate upward, reaching the topographic surface. Northward, the lithosphere comprised moderately larger strength, and the crustal discontinuities favored the development of larger folds with kilometric amplitude instead of strike-slip faults since the late Miocene.
ISSN: 1525-2027

hal-00671024
https://hal.archives-ouvertes.fr/hal-00671024
DOI : 10.1029/2010GC003274

Éditeur(s) : HAL CCSD
Résumé : International audience
Background In life sciences, there is a growing need for new informatics tools designed to provide automated solutions in order to analyze big amounts of images obtained from high-throughput imaging systems. Among the most widely used assays in neurotoxicity, endocrinology and brain diseases, the neurite outgrowth assay is popular. New method Cell-to-cell quantification of the main morphological features of neurite outgrowth assays remains very challenging. Here, we provide a new pipeline developed on Fiji software for analysis of series of two-dimensional images. It allows the automated analysis of most of these features. Results We tested the accuracy and usefulness of the software by confirming the effects of estradiol and hypoxia on in vitro neuronal differentiation, previously published by different authors with manual analysis methods. With this new method, we highlighted original interesting data. Comparison with existing method(s) The innovation brought by this plugin lies in the fact that it can process multiple images at the same time, in order to obtain: the number of nuclei, the number of neurites, the length of neurites, the number of neurites junctions, the number of neurites branches, the length of each branch, the position of the branch in the image, the angle of each branch, but also the area of each cell and the number of neurites per cell. Conclusions This plugin is easy to use, highly sensitive, and allows the experimenter to acquire ready-to-use data coming from a vast amount of images. © 2016 Elsevier B.V.
Journal of Neuroscience Methods

hal-01367152
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01367152
DOI : 10.1016/j.jneumeth.2016.07.011
PUBMED : 27450924

Éditeur(s) : HAL CCSD Wiley/Blackwell
Résumé : International audience
This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Alcippe morrisonia morrisonia, Bashania fangiana, Bashania fargesii, Chaetodon vagabundus, Colletes floralis, Coluber constrictor flaviventris, Coptotermes gestroi, Crotophaga major, Cyprinella lutrensis, Danaus plexippus, Fagus grandifolia, Falco tinnunculus, Fletcherimyia fletcheri, Hydrilla verticillata, Laterallus jamaicensis coturniculus, Leavenworthia alabamica, Marmosops incanus, Miichthys miiuy, Nasua nasua, Noturus exilis, Odontesthes bonariensis, Quadrula fragosa, Pinctada maxima, Pseudaletia separata, Pseudoperonospora cubensis, Podocarpus elatus, Portunus trituberculatus, Rhagoletis cerasi, Rhinella schneideri, Sarracenia alata, Skeletonema marinoi, Sminthurus viridis, Syngnathus abaster, Uroteuthis (Photololigo) chinensis, Verticillium dahliae, Wasmannia auropunctata, and Zygochlamys patagonica. These loci were cross-tested on the following species: Chaetodon baronessa, Falco columbarius, Falco eleonorae, Falco naumanni, Falco peregrinus, Falco subbuteo, Didelphis aurita, Gracilinanus microtarsus, Marmosops paulensis, Monodelphis Americana, Odontesthes hatcheri, Podocarpus grayi, Podocarpus lawrencei, Podocarpus smithii, Portunus pelagicus, Syngnathus acus, Syngnathus typhle,Uroteuthis (Photololigo) edulis, Uroteuthis (Photololigo) duvauceli and Verticillium albo-atrum. This article also documents the addition of nine sequencing primer pairs and sixteen allele specific primers or probes for Oncorhynchus mykiss and Oncorhynchus tshawytscha; these primers and assays were cross-tested in both species.
ISSN: 1755-098X

hal-01094222
https://hal-agroparistech.archives-ouvertes.fr/hal-01094222
DOI : 10.1111/j.1755-0998.2010.02916.x

Éditeur(s) : HAL CCSD Elsevier
Résumé : Spinel peridotite xenoliths from Persani Mountains, Southeastern Carpathians, Romania, were submitted to deformation by dislocation creep accompanied by dynamic recrystallization under variable stress and temperature conditions. Predominance of low-angle boundaries parallel to (100) with well-defined [Ovw] rotation axes in olivine indicates that subgrain rotation is the main recrystallization mechanism and that dislocation glide occurs mainly in [100]{0k1} systems. Analysis of olivine crystal preferred orientations highlights that recrystallization results in dispersion of the orientations of recrystallized grains relatively to the parent grains. This dispersion may be quantified by a dimension-less dispersion factor defined as the ratio of the random component of the [100] axis distributions between the recrystallized grains and porphyroclasts. This factor is largely independent from the overall fabric strength, the number of grains analyzed, and the recrystallized grain size. The olivine CPO strength and anisotropy at the rock scale, quantified by J-index, are largely controlled by the volume of recrystallized grains, which depends on finite strain. Comparison of olivine CPO in coarse- and fine-grained porphyroclastic peridotites shows that deviatoric stress and temperature conditions play nevertheless a role on the CPO evolution during recrystallization; selective grain growth, which is favored at high temperature and low stresses, does counteract the dispersion produced by the nucleation processes.
ISSN: 0191-8141

hal-00669963
https://hal.archives-ouvertes.fr/hal-00669963
DOI : 10.1016/j.jsg.2011.09.010

Éditeur(s) : HAL CCSD
Résumé : International audience
Understanding subduction rheology in both space and time has been a challenge since the advent of plate tectonics. We herein focus on "subduction infancy", that is the first ~1-5 My immediately following subduction nucleation, when a newly born slab penetrates into the upper plate mantle and heats up. The only remnants of this critical yet elusive geodynamic step are thin metamorphic soles, commonly found beneath pristine, 100-1000 km long portions of oceanic lithosphere emplaced on continents (i.e., ophiolites).Through the (i) worldwide compilation of pressure-temperature conditions of metamorphic sole formation augmented by pseudosection thermodynamic modeling, (ii) calculations of the viscosity of materials along the plate interface and (iii) generic numerical thermal models, we provide a conceptual model of dynamic plate interface processes during subduction infancy (and initiation s.l.).We show in particular how major rheological switches across the subduction interface control slab penetration, and the formation of metamorphic soles. Due to the downward progression of hydration and weakening of the mantle wedge with cooling, the lower plate (basalt, sediment) and the upper plate (mantle wedge) rheologies equalize and switch over a restricted temperature-time-depth interval (e.g., at ~800°C and ~1 GPa, during 0.1-2 My, for high-temperature metamorphic sole formation). These switches result in episodes of maximum interplate mechanical coupling, thereby slicing the top of the slab and welding pieces (basalt, sediment) to the base of the mantle wedge. Similar mechanical processes likely apply for the later, deeper accretion and exhumation of high-temperature oceanic eclogites in serpentinite mélanges, or for the accretion of larger tectonic slices.This model provides constraints on the effective rheologies of the crust and mantle and general understanding, at both rock and plate scale, for accretion processes and early slab dynamics.
AGU Fall Meeting 2015
San Francisco, United States

insu-01242103
https://hal-insu.archives-ouvertes.fr/insu-01242103

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 Oxford University Press (OUP)
Résumé : International audience
To improve earthquake location, we create a 3-D a priori P-wave velocity model (3-DVM) that approximates the large velocity variations of the Ecuadorian subduction system. The 3-DVM is constructed from the integration of geophysical and geological data that depend on the structural geometry and velocity properties of the crust and the upper mantle. In addition, specific station selection is carried out to compensate for the high station density on the Andean Chain. 3-D synthetic experiments are then designed to evaluate the network capacity to recover the event position using only P arrivals and the MAXI technique. Three synthetic earthquake location experiments are proposed: (1) noise-free and (2) noisy arrivals used in the 3-DVM, and (3) noise-free arrivals used in a 1-DVM. Synthetic results indicate that, under the best conditions (exact arrival data set and 3-DVM), the spatiotemporal configuration of the Ecuadorian network can accurately locate 70 per cent of events in the frontal part of the subduction zone (average azimuthal gap is 289° ± 44°). Noisy P arrivals (up to ± 0.3 s) can accurately located 50 per cent of earthquakes. Processing earthquake location within a 1-DVM almost never allows accurate hypocentre position for offshore earthquakes (15 per cent), which highlights the role of using a 3-DVM in subduction zone. For the application to real data, the seismicity distribution from the 3-D-MAXI catalogue is also compared to the determinations obtained in a 1-D-layered VM. In addition to good-quality location uncertainties, the clustering and the depth distribution confirm the 3-D-MAXI catalogue reliability. The pattern of the seismicity distribution (a 13 yr record during the inter-seismic period of the seismic cycle) is compared to the pattern of rupture zone and asperity of the Mw = 7.9 1942 and the Mw = 7.7 1958 events (the Mw = 8.8 1906 asperity patch is not defined). We observe that the nucleation of 1942, 1958 and 1906 events coincides with areas of positive Simple Bouguer anomalies and areas where marine terraces are still preserved on the coastal morphology. From north to south: (1) the 1958 rupture zone is almost aseismic and is attributed to a zone of high coupling; (2) south of the Galera alignment (perpendicular to the trench), the 1942 rupture zone presents moderate seismicity, deeper on the seismogenic interplate zone, and abutting on the Jama cluster (to the south). This cluster is facing the Cabo Pasado cap and positive Bouguer anomalies on the overriding margin. We suspect that this cluster reflects a zone of local asperity (partial coupling). South of the Jama cluster, the spherical aseismic zone in the Bahia area is interpreted as having a low seismic coupling (steady creep motion or slow slip events). We suspect that the site that generated the three M > 7 events (1896, 1956 and 1998) correspond to a small patch of strong coupling. To the south, in the Manta-Puerto Lopez zone, the seismicity is mainly organized in earthquake swarms (1998, 2002, 2005). Although slow slip events have been observed in the area (Vallée et al. submitted), we infer from the coastline shape, the marine terraces and the high positive Bouguer anomalies that the seismicity here might reveal a significant amount of seismic coupling.
ISSN: 0956-540X

hal-00873478
https://hal.archives-ouvertes.fr/hal-00873478
DOI : 10.1093/gji/ggs083

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Geochemical studies of primitive basalts have documented the presence of crustal-derived garnet pyroxenite in their mantle sources. The processes whereby melts with the signature of garnet pyroxenite are produced in the mantle are, however, poorly understood and somewhat controversial. Here we investigate a natural example of the interaction between melts of garnet pyroxenite derived from recycled plagioclase-rich crust and surrounding mantle in the Ronda peridotite massif. Melting of garnet pyroxenite at ∼1.5 GPa generated spinel websterite residues with MREE/HREE fractionation and preserved the positive Eu anomaly of their garnet pyroxenite precursor in whole-rock and clinopyroxene. Reaction of melts from garnet pyroxenite with depleted surrounding peridotite generated secondary fertile spinel lherzolite. These secondary lherzolites differ from common spinel lherzolite from Ronda and elsewhere by their lower-Mg# in clinopyroxene, orthopyroxene and olivine, lower-Cr# in spinel and higher whole-rock Al2O3, CaO, Sm/Yb and FeO⁎ at a given SiO2. Remarkably, secondary spinel lherzolite shows the geochemical signature of ghost plagioclase in the form of positive Eu and Sr anomalies in whole-rock and clinopyroxene, reflecting the transfer of a low-pressure crustal imprint from recycled pyroxenite to hybridized peridotite. Garnet pyroxenite melting and melt-peridotite interaction, as shown in the Ronda massif, may explain how the signature of subducted or delaminated crust is transferred to the mantle and how a garnet pyroxenite component is introduced into the source region of basalts. The efficiency of these processes in conveying the geochemical imprint of crustal-derived garnet pyroxenite to extruded lavas depends on the reactivity of pyroxenite melt with peridotite and the mantle permeability, which may be controlled by prior refertilization reactions similar to those documented in the Ronda massif. Highly fertile heterogeneities produced by pyroxenite-peridotite interaction, such as secondary spinel lherzolite in Ronda, may nucleate magmatic channels that remain chemically isolated from the ambient mantle and act as preferential pathways for melts with the signature of recycled crust.
ISSN: 0012-821X

hal-00814010
https://hal.archives-ouvertes.fr/hal-00814010
DOI : 10.1016/j.epsl.2012.11.047

Éditeur(s) : HAL CCSD
Résumé : International audience
The Corinth Rift is the most seismically active zone in Europe. The area is characterized by very localized NSextension at a rate of1.5cm/year, the occurrence of frequent and intensive microseismic crises and occasionalmoderate to large earthquakes like in 1995 (Mw=6.1).Since the year 2000, the Corinth Rift Laboratory (CRL, http://crlab.eu) consisting in a multidisciplinary naturalobservatory, aims at understanding the mechanics of faulting and earthquake nucleation in the Rift. Recent studieshave improved our view about fault geometry and mechanics within CRL, but there is still a critical need for a betterknowledge of the structure at depth both for the accuracy of earthquake locations and for mechanical interpretationof the seismicity.In this project, we aim to analyze the complete seismological database (13 years of recordings) of CRL by usingrecently developed methodologies of structural imaging, in order to determine at the same time and with highresolution, the local 3D structure and the earthquake locations.We perform an iterative joint determination of 3D velocity model and earthquake coordinates. In a first step, Pand S velocity models are determined using first arrival time tomography method proposed by Taillandier et al.(2009). It consists in the minimization of the cost function between observed and theoretical arrival times which isachieved by the steepest descent method (e.g. Tarantola 1987). This latter requires computing the gradient of thecost function by using the adjoint state method (Chavent 1974). In a second step, earthquakes are located in thenew velocity model with a non-linear inversion method based on a Bayesian formulation (Gesret et al. 2015). Step1 and 2 are repeated until the cost function no longer decreases.We present preliminary results consisting in: (1) the adjustement of a 1D velocity model that is used as initialmodel of the 3D tomography and (2) a first attempt of the joint determination of 3D velocity model and earthquakelocation.In addition to the tomographic imaging, we perform a preliminary receiver function analysis of teleseismic datarecorded by the broadband stations of the CRL network. The RF analysis should provide the interface depthsbeneath seismometers and increase the imaging resolution of the upper crustal structures provided by the 3Dtomography. In this first attempt, we adjust the 1D velocity model that produces a synthetic RF as similar aspossible to the observed RF for a subset of data. We compare the identified interfaces with structures imaged bythe tomography.
EGU general assembly 2016
Vienne, Austria

hal-01306224
https://hal-mines-paristech.archives-ouvertes.fr/hal-01306224

Éditeur(s) : HAL CCSD American Physical Society
Résumé : 1 tex, 16 figures
International audience
We make use of a subtraction procedure, introduced to overcome double--counting problems in beyond--mean--field theories, in the second random--phase--approximation (SRPA) for the first time. This procedure guarantees the stability of SRPA (so that all excitation energies are real). We show that the method fits perfectly into nuclear density--functional theory. We illustrate applications to the monopole and quadrupole response and to low--lying $0^+$ and $2^+$ states in the nucleus $^{16}$O. We show that the subtraction procedure leads to: (i) results that are weakly cutoff dependent; (ii) a considerable reduction of the SRPA downwards shift with respect to the random--phase approximation (RPA) spectra (systematically found in all previous applications). This implementation of the SRPA model will allow a reliable analysis of the effects of 2 particle--2 hole configurations ($2p2h$) on the excitation spectra of medium--mass and heavy nuclei.
ISSN: 0556-2813

in2p3-01193119
http://hal.in2p3.fr/in2p3-01193119
DOI : 10.1103/PhysRevC.92.034303
ARXIV : 1506.05975

Éditeur(s) : HAL CCSD AGU and the Geochemical Society
Résumé : International audience
The transition zone at the downdip end of seismic coupling along subduction interfaces is often the site of megathrust earthquake nucleation and concentrated postseismic afterslip, as well as the focus site of episodic tremor and slip features. Exhumed remnants of the former Alpine subduction zone found in the Swiss Alps allow analyzing fluid and deformation processes near the transition zone region (30–40 km paleodepth). The Dent Blanche Thrust (DBT) is a lower blueschist-facies shear zone interpreted as a fossilized subduction interface where granitic mylonites overlie a metamorphosed accretionary wedge. We report field observations from the DBT region where multiple, several tens of meters thick foliated cataclastic networks are interlayered within the basal DBT mylonites. Petrological results and microstructural observations indicate that the various cataclasis events took place at near-peak metamorphic conditions (400–500°C, 1.1–1.3 GPa) during subduction of the Tethyan seafloor in Eocene times (42–48 Ma). Some of these networks exhibit mutual crosscutting relationships between mylonites, foliated cataclasites, and vein systems indicating mutual overprinting between brittle deformation and ductile creep. Whole-rock chemical compositions, in situ 40Ar-39Ar age data of recrystallized phengite, and Sr isotopic signatures reveal that DBT rocks also underwent multiple hydrofracturing and metasomatic events via the infiltration of fluids mainly derived from the oceanic metasediments underneath the DBT. From the rock fabrics, we infer strain rate fluctuations of several orders of magnitude beyond subduction strain rates (∼10−12 s−1) accompanied by fluctuation of supralithostatic and quasi-lithostatic fluid pressures (1 ≥ λ > 0.95). DBT brittle-plastic deformation switches highlight the diversity of deformation processes and fluid-rock interactions in the transition zone region of the subduction interface.
ISSN: 1525-2027

hal-01243526
https://hal.archives-ouvertes.fr/hal-01243526
DOI : 10.1002/2015GC005776

Éditeur(s) : HAL CCSD SAGE Publications (UK and US)
Résumé : International audience
In the literature, the enamelin gene ENAM has been repeatedly designated as a possible candidate for caries susceptibility. Here, we checked whether ENAM variants could increase caries susceptibility. To this aim, we sequenced coding exons and exon-intron boundaries of ENAM in 250 children with a severe caries phenotype and in 149 caries-free patients from 9 French hospital groups. In total, 23 single-nucleotide polymorphisms (SNPs) were found, but none appeared to be responsible for a direct change of ENAM function. Six SNPs had a high minor allele frequency (MAF) and 6 others were identified for the first time. Statistical and evolutionary analyses showed that none of these SNPs was associated with caries susceptibility or caries protection when studied separately and challenged with environmental factors. However, haplotype interaction analysis showed that the presence, in a same variant, of 2 exonic SNPs (rs7671281 and rs3796704; MAF 0.12 and 0.10, respectively), both changing an amino acid in the protein region encoded by exon 10 (p.I648T and p.R763Q, respectively), increased caries susceptibility 2.66-fold independent of the environmental risk factors. These findings support ENAM as a gene candidate for caries susceptibility in the studied population.
ISSN: 0022-0345

hal-01545476
https://hal.archives-ouvertes.fr/hal-01545476
DOI : 10.1177/0022034514522060

Éditeur(s) : HAL CCSD American Society of Clinical Oncology
Résumé : International audience
PURPOSE: Determining whether environmental estrogens are associated with the risk of prostate cancer may have important implications for our general understanding of this disease. The estrogenic insecticide chlordecone was used extensively in the French West Indies, contaminating the population for more than 30 years. We analyzed the relationship between exposure to chlordecone and the risk of prostate cancer. PATIENTS AND METHODS: We investigated 623 men with prostate cancer and 671 controls. Exposure was analyzed according to case-control status, using either current plasma concentration or a cumulative exposure index based on years of exposure. We genotyped two single-nucleotide polymorphisms (rs3829125 and rs17134592) in the gene encoding chlordecone reductase. RESULTS: We found a significant increase in the risk of prostate cancer with increasing plasma chlordecone concentration (odds ratio [OR], 1.77; 95% CI, 1.21 to 2.58 for the highest tertile of values above the limit of detection [LD]; P trend = .002) and for cumulative exposure index (OR, 1.73; 95% CI, 1.04 to 2.88 for the highest quartile; P trend = .004). Stronger associations were observed among those with a positive family history of prostate cancer and among those who had lived in a Western country. The rs3829125 and rs17134592 allele variants were in complete linkage disequilibrium and were found at low frequency (0.04). Among subjects with plasma chlordecone concentrations above the LD, carriers of the allele variants had a higher risk of prostate cancer (OR, 5.23; 95% CI, 0.82 to 33.32). CONCLUSION: These findings support the hypothesis that exposure to environmental estrogens increases the risk of prostate cancer.
ISSN: 0732-183X

inserm-00518099
http://www.hal.inserm.fr/inserm-00518099
DOI : 10.1200/JCO.2009.27.2153
PUBMED : 20566993

Éditeur(s) : HAL CCSD SAGE Publications (UK and US)
Résumé : International audience
Genetic approaches have shown that several genes could modify caries susceptibility; AmelogeninX (AMELX) has been repeatedly designated. Here, we hypothesized that AMELX mutations resulting in discrete changes of enamel microstructure may be found in children with a severe caries phenotype. In parallel, possible AMELX mutations that could explain resistance to caries may be found in caries-free patients. In this study, coding exons of AMELX and exon-intron boundaries were sequenced in 399 individuals with extensive caries (250) or caries-free (149) individuals from nine French hospital groups. No mutation responsible for a direct change of amelogenin function was identified. Seven single-nucleotide polymorphisms (SNPs) were found, 3 presenting a high allele frequency, and 1 being detected for the first time. Three SNPs were located in coding regions, 2 of them being non-synonymous. Both evolutionary and statistical analyses showed that none of these SNPs was associated with caries susceptibility, suggesting that AMELX is not a gene candidate in our studied population.
ISSN: 0022-0345

hal-01545481
https://hal.archives-ouvertes.fr/hal-01545481
DOI : 10.1177/0022034513482941

Éditeur(s) : HAL CCSD Rockefeller University Press
Résumé : International audience
Accumulation of type I collagen fibrils in tumors is associated with an increased risk of metastasis. Invadosomes are F-actin structures able to degrade the extracellular matrix. We previously found that collagen I fibrils induced the formation of peculiar linear invadosomes in an unexpected integrin-independent manner. Here, we show that Discoidin Domain Receptor 1 (DDR1), a collagen receptor overexpressed in cancer, colocalizes with linear invadosomes in tumor cells and is required for their formation and matrix degradation ability. Unexpectedly, DDR1 kinase activity is not required for invadosome formation or activity, nor is Src tyrosine kinase. We show that the RhoGTPase Cdc42 is activated on collagen in a DDR1-dependent manner. Cdc42 and its specific guanine nucleotide-exchange factor (GEF), Tuba, localize to linear invadosomes, and both are required for linear invadosome formation. Finally, DDR1 depletion blocked cell invasion in a collagen gel. Altogether, our data uncover an important role for DDR1, acting through Tuba and Cdc42, in proteolysis-based cell invasion in a collagen-rich environment.
ISSN: 0021-9525

hal-01118481
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01118481
PUBMED : 25422375
DOI : 10.1083/jcb.201404079
PUBMEDCENTRAL : PMC4242841

Éditeur(s) : HAL CCSD PeerJ
Résumé : International audience
The tiger shark Galeocerdo cuvier (Carcharhinidae) is a large elasmobranch suspected to have, as other apex predators, a keystone function in marine ecosystems and is currently considered Near Threatened (Red list IUCN). Knowledge on its ecology, which is crucial to design proper conservation and management plans, is very scarce. Here we describe the isolation of eight polymorphic microsatellite loci using 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries. Their characteristics were tested on a population of tiger shark (n = 101) from Reunion Island (SouthWestern Indian Ocean). All loci were polymorphic with a number of alleles ranging from two to eight. No null alleles were detected and no linkage disequilibrium was detected after Bonferroni correction. Observed and expected heterozygosities ranged from 0.03 to 0.76 and from 0.03 to 0.77, respectively. No locus deviated from Hardy-Weinberg equilibrium and the global F IS of the population was of 0.04 NS. Some of the eight loci developed here successfully cross-amplified in the bull shark Carcharhinus leucas (one locus), the spinner shark Carcharhinus brevipinna (four loci), the sandbar shark Carcharhinus plumbeus (five loci) and the scalloped hammerhead shark Sphyrna lewini (two loci). We also designed primers to amplify and sequence a mitochondrial marker, the control region. We sequenced 862 bp and found a low genetic diversity, with four polymorphic sites, a haplotype diversity of 0.15 and a nucleotide diversity of 2 × 10 −4 .
ISSN: 2167-8359

hal-01317961
https://hal.archives-ouvertes.fr/hal-01317961
https://hal.archives-ouvertes.fr/hal-01317961/document
https://hal.archives-ouvertes.fr/hal-01317961/file/Pirog_2016PeerJ_microsat_tiger_shark.pdf
DOI : 10.7717/peerj.2041