Exploration of plant genomes in the FLAGdb++ environment

Background : In the contexts of genomics, post-genomics and systems biology approaches, data integration presents a major concern. Databases provide crucial solutions: they store, organize and allow information to be queried, they enhance the visibility of newly produced data by comparing them with previously published results, and facilitate the exploration and development of both existing hypotheses and new ideas. Results : The FLAGdb++ information system was developed with the aim of using whole plant genomes as physical references in order to gather and merge available genomic data from in silico or experimental approaches. Available through a JAVA application, original interfaces and tools assist the functional study of plant genes by considering them in their specific context: chromosome, gene family, orthology group, co-expression cluster and functional network. FLAGdb++ is mainly dedicated to the exploration of large gene groups in order to decipher functional connections, to highlight shared or specific structural or functional features, and to facilitate translational tasks between plant species (Arabidopsis thaliana, Oryza sativa, Populus trichocarpa and Vitis vinifera). Conclusion : Combining original data with the output of experts and graphical displays that differ from classical plant genome browsers, FLAGdb++ presents a powerful complementary tool for exploring plant genomes and exploiting structural and functional resources, without the need for computer programming knowledge. First launched in 2002, a 15th version of FLAGdb++ is now available and comprises four model plant genomes and over eight million genomic features

Genetic determinism of sensitivity to Corynespora cassiicola exudates in rubber tree (Hevea brasiliensis)

An indirect phenotyping method was developed in order to estimate the susceptibility of rubber tree clonal varieties to Corynespora Leaf Fall (CLF) disease caused by the ascomycete Corynespora cassiicola. This method consists in quantifying the impact of fungal exudates on detached leaves by measuring the induced electrolyte leakage (EL%). The tested exudates were either crude culture filtrates from diverse C. cassiicola isolates or the purified cassiicolin (Cas1), a small secreted effector protein produced by the aggressive isolate CCP. The test was found to be quantitative, with the EL% response proportional to toxin concentration. For eight clones tested with two aggressive isolates, the EL% response to the filtrates positively correlated to the response induced by conidial inoculation. The toxicity test applied to 18 clones using 13 toxinic treatments evidenced an important variability among clones and treatments, with a significant additional clone x treatment interaction effect. A genetic linkage map was built using 306 microsatellite markers, from the F1 population of the PB260 x RRIM600 family. Phenotyping of the population for sensitivity to the purified Cas1 effector and to culture filtrates from seven C. cassiicola isolates revealed a polygenic determinism, with six QTL detected on five chromosomes and percentages of explained phenotypic variance varying from 11 to 17%. Two common QTL were identified for the CCP filtrate and the purified cassiicolin, suggesting that Cas1 may be the main effector of CCP filtrate toxicity. The CCP filtrate clearly contrasted with all other filtrates. The toxicity test based on Electrolyte Leakage Measurement offers the opportunity to assess the sensitivity of rubber genotypes to C. cassiicola exudates or purified effectors for genetic investigations and early selection, without risk of spreading the fungus in plantations. However, the power of this test for predicting field susceptibility of rubber clones to CLF will have to be further investigated. (Résumé d'auteur

Fungal X-Intrinsic Protein Aquaporin from Trichoderma atroviride: Structural and Functional Considerations

The major intrinsic protein (MIP) superfamily is a key part of the fungal transmembrane transport network. It facilitates the transport of water and low molecular weight solutes across biomembranes. The fungal uncharacterized X-Intrinsic Protein (XIP) subfamily includes the full protein diversity of MIP. Their biological functions still remain fully hypothetical. The aim of this study is still to deepen the diversity and the structure of the XIP subfamily in light of the MIP counterparts-the aquaporins (AQPs) and aquaglyceroporins (AQGPs)-and to describe for the first time their function in the development, biomass accumulation, and mycoparasitic aptitudes of the fungal bioagent Trichoderma atroviride. The fungus-XIP Glade, with one member (TriatXIP), is one of the three clades of MIPs that make up the diversity of T. atroviride MIPs, along with the AQPs (three members) and the AQGPs (three members). TriatXIP resembles those of strict aquaporins, predicting water diffusion and possibly other small polar solutes due to particularly wider ar/R constriction with a Lysine substitution at the LE2 position. The XIP loss of function in Delta TriatXIP mutants slightly delays biomass accumulation but does not impact mycoparasitic activities. Delta TriatMIP forms colonies similar to wild type; however, the hyphae are slightly thinner and colonies produce rare chlamydospores in PDA and specific media, most of which are relatively small and exhibit abnormal morphologies. To better understand the molecular causes of these deviant phenotypes, a wide-metabolic survey of the ATriatXIPs demonstrates that the delayed growth kinetic, correlated to a decrease in respiration rate, is caused by perturbations in the pentose phosphate pathway. Furthermore, the null expression of the XIP gene strongly impacts the expression of four expressed MIP-encoding genes of T. atroviride, a plausible compensating effect which safeguards the physiological integrity and life cycle of the fungus. This paper offers an overview of the fungal XIP family in the biocontrol agent T. atroviride which will be useful for further functional analysis of this particular MIP subfamily in vegetative growth and the environmental stress response in fungi. Ultimately, these findings have implications for the ecophysiology of Trichoderma spp. in natural, agronomic, and industrial systems

Heavy Ion Microbeam and Broadbeam Transients in SiGe HBTs

SiGe HBT heavy ion current transients are measured using microbeam and both high- and low-energy broadbeam sources. These new data provide detailed insight into the effects of ion range, LET, and strike location

Hormones endogenes et multiplication vegetative in vitro chez le Merisier (Prunus avium L)

SIGLECNRS T Bordereau / INIST-CNRS - Institut de l'Information Scientifique et TechniqueFRFranc

Etude de l'expression de gènes par type cellulaire dans le cambium de peuplier (Populus trichocarpa x P. deltoïdes var Boelare)

Le bois est produit par l'arbre grâce à un tissu méristématique, le cambium. Ce dernier est composé de deux types de cellules cambiales, les fusiformes et les radiales, déterminant pour partie la qualité et la quantité de bois produit. Nous proposons ici l'étude de ces deux types de cellules en mettant au point une méthode de microdissection cellulaire. La masse des cellules ainsi que la quantité de transcrits (ARNm) par type cellulaire sont mesurées. L'analyse de l'expression des gènes par la technique des puces à ADNc montre un patron d'expression avec des gènes plutôt impliqués dans la synthèse de la paroi primaire pour les cellules fusiformes et dans le métabolisme et le transport, notamment des lipides, pour les cellules radiales. De plus, de nombreux gènes de la photosynthèse caractérisent les cellules cambiales radiales. Ces résultats sont confirmés par la Reverse Transcription-PCR et le Reverse Northern Dot-Blot.ORLEANS-BU Sciences (452342104) / SudocSudocFranceF

ELISA quantitation and GC-MS identification of abscisic acid in stigma, ovary and pedicel of pollinated poplar flowers (Populus nigra L.)

29 ref.International audienc

<I>Discometra luberonensis</I> sp. nov. (Crinoidea, Himerometridae), a new feather star from the Late Burdigalian

Most fossil feather stars are known only from the centrodorsal often connected to the radial circlet. This is the case for Discometra rhodanica (Fontannes, 1877), the type species of the genus Discometra, collected from the Late Burdigalian of the Miocene Rhône-Provence basin (southeastern France). The quarries operating in this area have exposed layers from the Late Burdigalian on the northern flank of the Lubéron anticline near Ménerbes (basin of Apt, Vaucluse, southeastern France). These layers contain exceptionally well-preserved echinoderms, among which are three specimens of a feather star with cirri and arms still connected to the centrodorsal. They are attributed to a new species: Discometra luberonensis sp. nov. (Himerometridae). The number of arms can reach 60, as in extant species of the genus Himerometra, but the pattern of arm divisions is closer to that of the genus Heterometra, which has no more than 45 arms in extant species. Discometra luberonensis sp. nov. differs from D. rhodanica by the characters of its centrodorsal. Here we redescribe the centrodorsal and radial circlets of D. rhodanica based on previously and newly collected specimens. We designate a neotype for D. rhodanica, because the holotype is considered lost. Affinities between Discometra, Himerometra and Heterometra are discussed. </p

Les restes humains de la grotte ornée paléolithique des Deux-Ouvertures (Ardèche, France)

La grotte des Deux-Ouvertures s’ouvre en rive gauche peu avant la sortie des gorges de l’Ardèche, sur le territoire de la commune de Saint-Martin-d’Ardèche. Bien que connue depuis 1896, ce n’est qu’en 1985 qu’était découverte la partie profonde du réseau : une galerie qui présentait des ossements éparpillés sur le sol, dont plus de 90 % appartiennent à Ursus spelaeus. En 2007, deux fragments osseux humains – une partie distale d’un humérus adulte et une diaphyse de radius appartenant à un jeune sujet – ont été également mis au jour. Ils font l’objet de cet article. La datation de l’humérus (34 440–33 730 cal BP) s’inscrit au sein de la phase de fréquentation par les ours des cavernes, alors que la datation de la diaphyse du radius (4410–4570 cal BP) en plein cœur du « secteur orné paléolithique » laisse supposer qu’il a été déposé, peut-être, de façon délibérée. L’étude des deux os humains provenant de la grotte des Deux-Ouvertures montre que la diaphyse radiale, appartenant à un sujet jeune, d’âge Néolithique, ne présente pas de différence en regard de radius modernes. En revanche, la partie distale de l’humérus d’un sujet adulte, bien qu’incomplète et altérée, est le premier reste humain d’adulte, associé à une grotte ornée paléolithique en Ardèche, à avoir été daté. Ce dernier, exception faite peut-être pour la largeur du pilier médian, est plutôt gracile et ne présente pas de différence significative avec les autres restes du Paléolithique supérieur.The opening of the Deux-Ouvertures cave is on the left bank of the Ardèche River, just before the canyon exit on the land of the village of Saint-Martin d’Ardèche in the Southwest of France. Although it has been known since 1896, the deep part of one of the galleries was not discovered until 1985. The surface of this gallery was covered by animal bones, 90% of which belonged to Ursus spelaeus. In 2007, two osseous human fragments were discovered: the distal part of an adult humerus and the diaphysis of a radius belonging to a young individual. These two specimens are the topic of the present paper. Although the date of the humerus (34,440–33,730 cal BP) corresponds to the period when bears frequented the caves, the dates of the diaphysis of the radius (4410–4570 cal BP), found at the heart of the “decorated Paleolithic sector”, lead us to assume that it was transported there, perhaps deliberately. The study of the two human bones originating in the Deux-Ouvertures cave illustrates that the diaphysis of the radius, belonging to a young individual of the Neolithic period, does not exhibit any differences in comparison to modern radii. By contrast, the distal part of the adult humerus, although it is incomplete and altered, is the first example that has been dated in the Ardèche of adult human remains associated with a decorated Paleolithic cave. This specimen, aside perhaps from the width of its median column, is rather slender and does not present any significant difference in relation to other upper Paleolithic humeri.</p