Apport des nouvelles générations de séquençage pour accéder à la diversité des communautés microbiennes du sol : nécessité d’un ‘pipeline’ bio-informatique pour les biologistes

Communication orale, résuméLa diversité microbienne d’un sol est difficile à caractériser. Ceci s’explique par une accessibilité plus ou moins importante des populations au sein d’une matrice hétérogène et structurée, mais aussi par l’incapacité à résoudre une information constituée de 100 000 à 1 000 000 d’espèces différentes par gramme de sol. Toutefois, récemment, d’importantes avancées en biologie moléculaire ont permis de mieux caractériser la diversité des communautés microbiennes du sol in situ et ce sans a priori. Ainsi, la puissance des nouvelles générations de séquençage comme le pyroséquençage permettent de travailler en haut-débit afin d’obtenir plusieurs dizaines, voire plusieurs centaines de milliers de séquences à partir d’un ADN méta-génomique. De premières études ont déjà été réalisées avec cette technique afin d’aborder la diversité bactérienne des sols. Ces études ont, pour la première fois, permis de quantifier de façon exhaustive la diversité microbienne de sols en termes de richesse spécifique et de démontrer la pertinence, la faisabilité et la robustesse de cette approche. Cette approche est maintenant unanimement reconnue pour sa pertinence et ses potentialités très importantes, et ce afin de déterminer la diversité des microorganismes telluriques. Notre approche consiste en la caractérisation de la diversité taxonomique (bactérienne et fongique) de sols sur des échantillonnages de grande ampleur dans le temps et dans l’espace, avec comme objectifs : (i) de faire un inventaire exhaustif de la diversité microbienne tellurique, (ii) d’évaluer sa distribution spatiale, (iii) de mieux comprendre sa régulation et, (iv) in fine, de pouvoir relier cette diversité en fonctionnement biologique du sol et en services écosystémiques [1-3]. Cependant, l’étude d’un aussi grand nombre d’échantillons va entraîner la production massive de séquences. Ce caractère massif, ainsi que les caractéristiques inhérentes aux séquences obtenues par cette technique requièrent le développement d’outils bioinformatiques adaptés, optimisés et évalués, afin d’analyser rapidement et efficacement ce type de données. Ce nouveau pipeline d’analyse doit tout d’abord être facile d’utilisation et répondre aux attentes des différents utilisateurs, qu’ils soient compétents en bio-informatique, ou novices dans l’analyse de tels jeux de données. Il doit également permettre de gérer un grand nombre de séquences et d’automatiser les grandes étapes d’analyse (prétraitement, filtration, clustérisation, assignation taxonomique, calculs d’indices d’abondance et de diversité, taux de couverture,…). L’ensemble du système devra enfin être transféré sur un serveur de calcul et accessible au travers d’un serveur Web pour être accessible à la collectivité des écologistes microbiens. L’objectif étant de coupler, sur un grand nombre d’échantillons, cette approche avec des mesures d’activités et de faire le lien entre la diversité microbienne et l’aptitude des sols à rendre des services

Down-Regulation of Vascular Endothelial Growth Factor by Tissue Inhibitor of Metalloproteinase-2: Effect on in Vivo Mammary Tumor Growth and Angiogenesis

The tissue inhibitor of metalloproteinases-2 (TIMP-2) has at least two independent functions, i.e., regulation of matrix metalloproteinases and growth promoting activity. We investigated the effects of TIMP-2 overexpression, induced by retroviral mediated gene transfer, on the in vivo development of mammary tumors in syngeneic mice inoculated with EF43.fgf-4 cells. The EF43.fgf-4 cells established by stably infecting the normal mouse mammary EF43 cells with a retroviral expression vector for the fgf-4 oncogene, are highly tumorigenic and overproduce vascular endothelial growth factor (VEGF). Despite a promotion of the in vitro growth rate of EF43.fgf-4 cells overexpressing timp-2, the in vivo tumor growth was delayed. At day 17 post-cell injection, the volume of tumor derived from TIMP-2-overexpressing cells was reduced by 80% as compared with that obtained with control cells. Overexpression of TIMP-2 was associated with a down-regulation of VEGF expression in vitro and in vivo, a reduction of vessel size, density, and blood supply in the induced tumors. In addition, TIMP-2 completely inhibited the angiogenic activity of EF43.fgf-4 cell-conditioned medium in vitro using a rat aortic ring model. Our findings suggest that overexpression of TIMP-2 delays growth and angiogenesis of mammary carcinoma in vivo and that down-regulation of VEGF expression may play an important role in this TIMP-2-mediated antitumoral and antiangiogenic effects. Finally the in vivo delivery of TIMP-2, as assessed by i.v. injection of recombinant adenoviruses vectors, significantly reduced the growth of the EF43.fgf-4-induced tumors. This effect of TIMP-2 was shown to be equally comparable with that of angiostatin, a known potent inhibitor of angiogenesis

Seismotectonics of southeast France: from the Jura mountains to Corsica

The analysis of the seismicity catalog (1996 to 2019) covering the region from the Jura mountains to Corsica provides a first-order image of the distribution of earthquakes, highlighting large structures such as the Briançonnais and Piedmontais seismic arcs, the eastward deepening of the focal depths through the Western Alps, several large active faults (e.g. Belledonne, Middle Durance, Ligure). Over this period the magnitudes are moderate and the focal mechanisms of the main events display a diversity of seismic behaviors that can be explained by the complexity of the different geological domains with a more or less strong structural inheritage, by variable rheological characteristics at the scale of the crust and by the joint action of different mechanisms of deformation. The distribution of the historical events is in fairly good agreement with the instrumental seismicity, but several earthquakes of $M >6$ are highlighted since the 14th century until the beginning of the 20th

Seismotectonics of southeast France: from the Jura mountains to Corsica

The analysis of the seismicity catalog (1996 to 2019) covering the region from the Jura mountains to Corsica provides a first-order image of the distribution of earthquakes, highlighting large structures such as the Briançonnais and Piedmontais seismic arcs, the eastward deepening of the focal depths through the Western Alps, several large active faults (e.g. Belledonne, Middle Durance, Ligure). Over this period the magnitudes are moderate and the focal mechanisms of the main events display a diversity of seismic behaviors that can be explained by the complexity of the different geological domains with a more or less strong structural inheritage, by variable rheological characteristics at the scale of the crust and by the joint action of different mechanisms of deformation. The distribution of the historical events is in fairly good agreement with the instrumental seismicity, but several earthquakes of $M >6$ are highlighted since the 14th century until the beginning of the 20th

Oxo-Functionalization and Reduction of the Uranyl Ion through Lanthanide-Element Bond Homolysis:Synthetic, Structural, and Bonding Analysis of a Series of Singly Reduced Uranyl-Rare Earth 5f¹-4f^<em>n</em> Complexes

The heterobimetallic complexes [{UO2Ln-(py)2(L)}2], combining a singly reduced uranyl cation and a rare-earth trication in a binucleating polypyrrole Schiff-base macrocycle (Pacman) and bridged through a uranyl oxo-group, have been prepared for Ln = Sc, Y, Ce, Sm, Eu, Gd, Dy, Er, Yb, and Lu. These compounds are formed by the single-electron reduction of the Pacman uranyl complex [UO2(py)(H2L)] by the rare-earth complexes LnIII(A)3 (A = N(SiMe3)2, OC6H3But 2-2,6) via homolysis of a Ln−A bond. The complexes are dimeric through mutual uranyl exo-oxo coordination but can be cleaved to form the trimetallic, monouranyl “ate” complexes [(py)3LiOUO(μ-X)Ln(py)(L)] by the addition of lithium halides. X-ray crystallographic structural characterization of many examples reveals very similar features for monomeric and dimeric series, the dimers containing an asymmetric U2O2 diamond core with shorter uranyl U=O distances than in the monomeric complexes. The synthesis by LnIII−A homolysis allows [5f1-4fn]2 and Li[5f1-4fn] complexes with oxobridged metal cations to be made for all possible 4fn configurations. Variable-temperature SQUID magnetometry and IR, NIR, and EPR spectroscopies on the complexes are utilized to provide a basis for the better understanding of the electronic structure of f-block complexes and their f-electron exchange interactions. Furthermore, the structures, calculated by restricted-core or allelectron methods, are compared along with the proposed mechanism of formation of the complexes. A strong antiferromagnetic coupling between the metal centers, mediated by the oxo groups, exists in the UVSmIII monomer, whereas the dimeric UVDyIII complex was found to show magnetic bistability at 3 K, a property required for the development of single-molecule magnets.JRC.E.6-Actinide researc

Rapid response to the M_w 4.9 earthquake of November 11, 2019 in Le Teil, Lower Rhône Valley, France

On November 11, 2019, a Mw 4.9 earthquake hit the region close to Montelimar (lower Rhône Valley, France), on the eastern margin of the Massif Central close to the external part of the Alps. Occuring in a moderate seismicity area, this earthquake is remarkable for its very shallow focal depth (between 1 and 3 km), its magnitude, and the moderate to large damages it produced in several villages. InSAR interferograms indicated a shallow rupture about 4 km long reaching the surface and the reactivation of the ancient NE-SW La Rouviere normal fault in reverse faulting in agreement with the present-day E-W compressional tectonics. The peculiarity of this earthquake together with a poor coverage of the epicentral region by permanent seismological and geodetic stations triggered the mobilisation of the French post-seismic unit and the broad French scientific community from various institutions, with the deployment of geophysical instruments (seismological and geodesic stations), geological field surveys, and field evaluation of the intensity of the earthquake. Within 7 days after the mainshock, 47 seismological stations were deployed in the epicentral area to improve the Le Teil aftershocks locations relative to the French permanent seismological network (RESIF), monitor the temporal and spatial evolution of microearthquakes close to the fault plane and temporal evolution of the seismic response of 3 damaged historical buildings, and to study suspected site effects and their influence in the distribution of seismic damage. This seismological dataset, completed by data owned by different institutions, was integrated in a homogeneous archive and distributed through FDSN web services by the RESIF data center. This dataset, together with observations of surface rupture evidences, geologic, geodetic and satellite data, will help to unravel the causes and rupture mechanism of this earthquake, and contribute to account in seismic hazard assessment for earthquakes along the major regional Cévenne fault system in a context of present-day compressional tectonics

The Relationship between Population Structure and Aluminum Tolerance in Cultivated Sorghum

Background: Acid soils comprise up to 50% of the world's arable lands and in these areas aluminum (Al) toxicity impairs root growth, strongly limiting crop yield. Food security is thereby compromised in many developing countries located in tropical and subtropical regions worldwide. In sorghum, SbMATE, an Al-activated citrate transporter, underlies the Alt(SB) locus on chromosome 3 and confers Al tolerance via Al-activated root citrate release. Methodology: Population structure was studied in 254 sorghum accessions representative of the diversity present in cultivated sorghums. Al tolerance was assessed as the degree of root growth inhibition in nutrient solution containing Al. A genetic analysis based on markers flanking Alt(SB) and SbMATE expression was undertaken to assess a possible role for Alt(SB) in Al tolerant accessions. In addition, the mode of gene action was estimated concerning the Al tolerance trait. Comparisons between models that include population structure were applied to assess the importance of each subpopulation to Al tolerance. Conclusion/Significance: Six subpopulations were revealed featuring specific racial and geographic origins. Al tolerance was found to be rather rare and present primarily in guinea and to lesser extent in caudatum subpopulations. Alt(SB) was found to play a role in Al tolerance in most of the Al tolerant accessions. A striking variation was observed in the mode of gene action for the Al tolerance trait, which ranged from almost complete recessivity to near complete dominance, with a higher frequency of partially recessive sources of Al tolerance. A possible interpretation of our results concerning the origin and evolution of Al tolerance in cultivated sorghum is discussed. This study demonstrates the importance of deeply exploring the crop diversity reservoir both for a comprehensive view of the dynamics underlying the distribution and function of Al tolerance genes and to design efficient molecular breeding strategies aimed at enhancing Al tolerance.CGIAR[G3007.04]McKnight FoundationFundacao de Amparo a Pesquisa do Estado de Minas Gerais (FAPEMIG)National Council for Scientific and Technological Development (CNPq

Ambient-noise tomography of the wider Vienna Basin region

We present a new 3-D shear-velocity model for the top 30 km of the crust in the wider Vienna Basin region based on surface waves extracted from ambient-noise cross-correlations. We use continuous seismic records of 63 broad-band stations of the AlpArray project to retrieve interstation Green’s functions from ambient-noise cross-correlations in the period range from 5 to 25 s. From these Green’s functions, we measure Rayleigh group traveltimes, utilizing all four components of the cross-correlation tensor, which are associated with Rayleigh waves (ZZ, RR, RZ and ZR), to exploit multiple measurements per station pair. A set of selection criteria is applied to ensure that we use high-quality recordings of fundamental Rayleigh modes. We regionalize the interstation group velocities in a 5 km × 5 km grid with an average path density of ∼20 paths per cell. From the resulting group-velocity maps, we extract local 1-D dispersion curves for each cell and invert all cells independently to retrieve the crustal shear-velocity structure of the study area. The resulting model provides a previously unachieved lateral resolution of seismic velocities in the region of ∼15 km. As major features, we image the Vienna Basin and Little Hungarian Plain as low-velocity anomalies, and the Bohemian Massif with high velocities. The edges of these features are marked with prominent velocity contrasts correlated with faults, such as the Alpine Front and Vienna Basin transfer fault system. The observed structures correlate well with surface geology, gravitational anomalies and the few known crystalline basement depths from boreholes. For depths larger than those reached by boreholes, the new model allows new insight into the complex structure of the Vienna Basin and surrounding areas, including deep low-velocity zones, which we image with previously unachieved detail. This model may be used in the future to interpret the deeper structures and tectonic evolution of the wider Vienna Basin region, evaluate natural resources, model wave propagation and improve earthquake locations, among others

Crustal Thinning From Orogen to Back-Arc Basin: The Structure of the Pannonian Basin Region Revealed by P-to-S Converted Seismic Waves

We present the results of P-to-S receiver function analysis to improve the 3D image of the sedimentary layer, the upper crust, and lower crust in the Pannonian Basin area. The Pannonian Basin hosts deep sedimentary depocentres superimposed on a complex basement structure and it is surrounded by mountain belts. We processed waveforms from 221 three-component broadband seismological stations. As a result of the dense station coverage, we were able to achieve so far unprecedented spatial resolution in determining the velocity structure of the crust. We applied a three-fold quality control process; the first two being applied to the observed waveforms and the third to the calculated radial receiver functions. This work is the first comprehensive receiver function study of the entire region. To prepare the inversions, we performed station-wise H-Vp/Vs grid search, as well as Common Conversion Point migration. Our main focus was then the S-wave velocity structure of the area, which we determined by the Neighborhood Algorithm inversion method at each station, where data were sub-divided into back-azimuthal bundles based on similar Ps delay times. The 1D, nonlinear inversions provided the depth of the discontinuities, shear-wave velocities and Vp/Vs ratios of each layer per bundle, and we calculated uncertainty values for each of these parameters. We then developed a 3D interpolation method based on natural neighbor interpolation to obtain the 3D crustal structure from the local inversion results. We present the sedimentary thickness map, the first Conrad depth map and an improved, detailed Moho map, as well as the first upper and lower crustal thickness maps obtained from receiver function analysis. The velocity jump across the Conrad discontinuity is estimated at less than 0.2 km/s over most of the investigated area. We also compare the new Moho map from our approach to simple grid search results and prior knowledge from other techniques. Our Moho depth map presents local variations in the investigated area: the crust-mantle boundary is at 20–26 km beneath the sedimentary basins, while it is situated deeper below the Apuseni Mountains, Transdanubian and North Hungarian Ranges (28–33 km), and it is the deepest beneath the Eastern Alps and the Southern Carpathians (40–45 km). These values reflect well the Neogene evolution of the region, such as crustal thinning of the Pannonian Basin and orogenic thickening in the neighboring mountain belts