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Data and Workflow Management for Exascale Global Adjoint Tomography
No full textInternational audienc
TAXREF-LD: A Reference Thesaurus for Biodiversity on the Web of Linked Data
No full textInternational audienc
Évaluation et indications des lasers pour les biopsies de la muqueuse buccale
No full textIl ne doit pas y avoir de doute concernant le diagnostic touchant une lésion persistante de la muqueuse buccale. Ainsi, le diagnostic clinique doit être confirmé par un diagnostic anatomo-pathologique, grâce à la réalisation d’une biopsie. Cet acte délicat engage la responsabilité du praticien. <br>L’objectif de ce travail est de savoir si les lasers peuvent être un outil chirurgical valable pour pratiquer des biopsies des tissus mous de la cavité buccale. En effet, ils présentent de nombreux avantages : précision de l’incision, effets hémostatique et antimicrobien, action antalgique et cicatrisante. Cependant, leurs effets photo-thermiques sont aussi responsables d’artefacts au niveau des marges d’exérèse. Pour évaluer, la fiabilité des lasers comme moyen de prélèvement, nous avons procédé à une revue de littérature comparant biopsie-laser et biopsie conventionnelle à lame froide. <br>Les études montrent que les lasers les plus utilisés pour pratiquer des biopsies, sont les lasers CO2, Er:YAG, Er,Cr:YSGG, Nd:YAG, KTP et Diode. Ceux engendrant le moins de dommages thermiques sont les lasers Er,Cr :YSGG, Er :YAG, et CO2. Dans tous les cas, les artéfacts thermiques n'ont jamais entravé l'établissement d'un diagnostic sûr par les pathologistes. Ainsi, l’emploi du laser en biopsie semble valide pour les lésions bénignes. En revanche, peu d’études sont disponibles concernant les lésions à potentiel de malignité, des essais cliniques contrôlés randomisés sont donc nécessaires pour compléter ces premiers résultats encourageants
Caractérisation des petits ARN régulateurs impliqués dans la formation des cellules géantes induites par les nématodes phytoparasites du genre Meloidogyne
No full textRoot-Knot-Nematodes are obligate plant parasites able to infect a large panel of cultivated plants. These parasites have the ability to induce redifferentiation of five to seven root cells into specialized giant cells, hypertrophied, multinucleated and metabolically overactive. These giant cells form the feeding site upon which nematodes feed continuously until reproduction. Giant cells development leads to a root deformation, named gall, which disturbs plant nutrients absorption causing its weakening. Transcriptomic studies showed that a huge transcriptional reprogramming occurs during gall development. This project aims to characterize the role of small RNAs, non-coding RNAs, during gall development induced by M. incognita. Small non-coding RNAs are key regulators of gene expression and include two major families: microRNAs (miRNAs) and small interfering RNAs (siRNAs). Thus, small RNAs from roots of the model plant Arabidopsis thaliana healthy or infected by M. incognita were characterized by Next Generation Sequencing at 7 and 14 days after infection, two important stages of gall development. This study led to the identification of 24 plant microRNAs differentially expressed in galls compared to uninfected roots. Functional analysis of these miRNAs validated the expression pattern in galls of five miRNAs and demonstrated the role of miR159 in the plant response to M. incognita. In addition, a genome-wide approach was used to identify genes that could be regulated by siRNAs during the interaction. In conclusion, this work contributed todemonstrate, on one hand, the involvement of microRNAs in the plant - RKN interaction and allowed the identification of genes potentially regulated by small interfering and involved in the formation of giant cells induced by root-knot nematodes.Les nématodes à galles du genre Meloidogyne sont des parasites obligatoires des plantes capables d’infecter un large panel de plantes d’intérêt agronomique. Ces parasites ont la capacité d’induire la différenciation de cinq à sept cellules racinaires en cellules géantes, hypertrophiées, métaboliquement actives et multinucléées. Ces cellules géantes constituent le site nourricier indispensable au nématode, et sur lequel il va s’alimenter jusqu’à sa reproduction. Le développement de ces cellules entraine une déformation racinaire appelée « galle » qui va perturber l’absorption de nutriments de la plante et l’affaiblir. Des études transcriptomiques ont montré qu’une vaste reprogrammation transcriptionnelle a lieu lors de la formation de la galle. Cette thèse vise à caractériser le rôle des petits ARN, des ARN non codants, au cours de la formation des galles induites par M. incognita. Les petits ARN non codants sont des régulateurs clés de l’expression génique et comprennent deux grandes familles : les microARN (miARN) et les petits ARN interférents (siARN). Pour cela, les petits ARN de racines de la plante modèle Arabidopsis thaliana saines et infectées par le nématode à galle M. incognita ont été caractérisés par séquençage haut débit à 7 et 14 jours après infection, deux stades importants du développement des cellules géantes. Cette étude a permis d’identifier 24 miARN d’Arabidopsis différentiellement exprimés dans les galles en comparaison aux racines non infectées. L’analyse fonctionnelle de ces miARN a permis de valider le profil d’expression dans les galles de cinq miARN et de démontrer le rôle de miR159 dans la réponse de la plante à M. incognita. De plus, une approche pangénomique a été réalisée afin d’identifier les gènes susceptibles d’être régulés par les siARN lors de l’interaction. En conclusion, ce travail a contribué à démontrer d’une part l’implication des miARN dans l’interaction plante - nématode à galles et a permis l’identification des gènes potentiellement régulés par les siARN lors de l’interaction et impliqués dans la formation des cellules géantes induites par les nématodes à galles
myGenomeBrowser: building and sharing your own genome browser
No full textmyGenomeBrowser is a web-based environment that provides biologists with a way to build, query and share their genome browsers. This tool, that builds on JBrowse, is designed to give users more autonomy while simplifying and minimizing intervention from system administrators. We have extended genome browser basic features to allow users to query, analyze and share their data
DNA double-strand break repair is involved in desiccation resistance of Sinorhizobium meliloti, but is not essential for its symbiotic interaction with Medicago truncatula
No full textThe soil bacterium Sinorhizobium meliloti, a nitrogen-fixing symbiont of legume plants, is exposed to numerous stress conditions in nature, some of which cause the formation of harmful DNA double-strand breaks (DSBs). In particular, the reactive oxygen species (ROS) and the reactive nitrogen species (RNS) produced during symbiosis, and the desiccation occurring in dry soils, are conditions which induce DSBs. Two major systems of DSB repair are known in S. meliloti: homologous recombination (HR) and non-homologous end-joining (NHEJ). However, their role in the resistance to ROS, RNS and desiccation has never been examined in this bacterial species, and the importance of DSB repair in the symbiotic interaction has not been properly evaluated. Here, we constructed S. meliloti strains deficient in HR (by deleting the recA gene) or in NHEJ (by deleting the four ku genes) or both. Interestingly, we observed that ku and/ or recA genes are involved in S. meliloti resistance to ROS and RNS. Nevertheless, an S. meliloti strain deficient in both HR and NHEJ was not altered in its ability to establish and maintain an efficient nitrogen-fixing symbiosis with Medicago truncatula, showing that rhizobial DSB repair is not essential for this process. This result suggests either that DSB formation in S. meliloti is efficiently prevented during symbiosis or that DSBs are not detrimental for symbiosis efficiency. In contrast, we found for the first time that both recA and ku genes are involved in S. meliloti resistance to desiccation, suggesting that DSB repair could be important for rhizobium persistence in the soil
BRC4Env : un réseau de Centres de Ressources Biologiques et de collections dédié aux ressources environnementales
No full textBRC4Env : un réseau de Centres de Ressources Biologiques et de collections dédié aux ressources environnementales. Colloque Prospectives du CNRS-INEE 201
Detection of nucleic acid-protein interactions in plant leaves using fluorescence lifetime imaging microscopy
No full textDNA-binding proteins (DNA-BPs) and RNA-binding proteins (RNA-BPs) have critical roles in living cells in all kingdoms of life. Various experimental approaches exist for the study of nucleic acid-protein interactions in vitro and in vivo, but the detection of such interactions at the subcellular level remains challenging. Here we describe how to detect nucleic acid-protein interactions in plant leaves by using a fluorescence resonance energy transfer (FRET) approach coupled to fluorescence lifetime imaging microscopy (FLIM). Proteins of interest (POI) are tagged with a GFP and transiently expressed in plant cells to serve as donor fluorophore. After sample fixation and cell wall permeabilization, leaves are treated with Sytox Orange, a nucleic acid dye that can function as a FRET acceptor. Upon close association of the GFP-tagged POI with Sytox-Orange-stained nucleic acids, a substantial decrease of the GFP lifetime due to FRET between the donor and the acceptor can be monitored. Treatment with RNase before FRET-FLIM measurements allows determination of whether the POI associates with DNA and/or RNA. A step-by-step protocol is provided for sample preparation, data acquisition and analysis. We describe how to calibrate the equipment and include a tutorial explaining the use of the FLIM software. To illustrate our approach, we provide experimental procedures to detect the interaction between plant DNA and two proteins (the AeCRN13 effector from the oomycete Aphanomyces euteiches and the AtWRKY22 defensive transcription factor from Arabidopsis). This protocol allows the detection of protein-nucleic acid interactions in plant cells and can be completed in <2 d
Possible amphi-Atlantic dispersal of Scyllarus lobsters (Crustacea: Scyllaridae): molecular and larval evidence
No full textDNA methods may contribute to better understand larval dispersal of marine lobsters. The molecular analysis of phyllosoma specimens from the East Atlantic facilitated for the first time here the description of Scyllarus subarctus Crosnier, 1970 larvae. The identification of S. subarctus phyllosomae from Cabo Verde confirmed that this species has a much wider geographic distribution than previously thought. Moreover, the phylogenetic analyses placed S. depressus from the Western Atlantic together with the African species S. subarctus, instead of other American Scyllarus. In fact, S. depressus and S. subarctus formed a strongly supported clade with comparatively low genetic differentiation, suggesting the possibility that they might be recently-diverged sister taxa with an amphi-Atlantic distribution. Support for this is provided by the examination of S. subarctus larvae and the lack of any qualitative character that would allow for differentiation between the adults of S. subarctus and S. depressus. The results obtained highlight the challenges of current Scyllarus systematics and the need for further research on Atlantic slipper lobsters
Genome-wide analysis of expansin superfamily in wild Arachis discloses a stress-responsive expansin-like B gene.
No full textExpansins are plant cell wall-loosening proteins involved in adaptive responses to environmental stimuli and various developmental processes. The first genome-wide analysis of the expansin superfamily in the Arachis genus identified 40 members in A. duranensis and 44 in A. ipaënsis, the wild progenitors of cultivated peanut (A. hypogaea). These expansins were further characterized regarding their subfamily classification, distribution along the genomes, duplication events, molecular structure, and phylogeny. A RNA-seq expression analysis in different Arachis species showed that the majority of these expansins are modulated in response to diverse stresses such as water deficit, root-knot nematode (RKN) infection, and UV exposure, with an expansin-like B gene (AraEXLB8) displaying a highly distinct stress-responsive expression profile. Further analysis of the AraEXLB8 coding sequences showed high conservation across the Arachis genotypes, with eight haplotypes identified. The modulation of AraEXLB8 expression in response to the aforementioned stresses was confirmed by qRT-PCR analysis in distinct Arachis genotypes, whilst in situ hybridization revealed transcripts in different root tissues according to the stress imposed. The overexpression of AraEXLB8 in soybean (Glycine max) composite plants remarkably decreased the number of galls in transformed hairy roots inoculated with RKN. This study improves the current understanding of the molecular evolution, divergence, and gene expression of expansins in Arachis, and provides molecular and functional insights into the role of expansin-like B, the less-studied plant expansin subfamily