GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts

Genomic projects heavily depend on genome annotations and are limited by the current deficiencies in the published predictions of gene structure and function. It follows that, improved annotation will allow better data mining of genomes, and more secure planning and design of experiments. The purpose of the GeneFarm project is to obtain homogeneous, reliable, documented and traceable annotations for Arabidopsis nuclear genes and gene products, and to enter them into an added-value database. This re-annotation project is being performed exhaustively on every member of each gene family. Performing a family-wide annotation makes the task easier and more efficient than a gene-by-gene approach since many features obtained for one gene can be extrapolated to some or all the other genes of a family. A complete annotation procedure based on the most efficient prediction tools available is being used by 16 partner laboratories, each contributing annotated families from its field of expertise. A database, named GeneFarm, and an associated user-friendly interface to query the annotations have been developed. More than 3000 genes distributed over 300 families have been annotated and are available at http://genoplante-info.infobiogen.fr/Genefarm/. Furthermore, collaboration with the Swiss Institute of Bioinformatics is underway to integrate the GeneFarm data into the protein knowledgebase Swiss-Prot

GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts

Genomic projects heavily depend on genome annotations and are limited by the current deficiencies in the published predictions of gene structure and function. It follows that, improved annotation will allow better data mining of genomes, and more secure planning and design of experiments. The purpose of the GeneFarm project is to obtain homogeneous, reliable, documented and traceable annotations for Arabidopsis nuclear genes and gene products, and to enter them into an added-value database. This re-annotation project is being performed exhaustively on every member of each gene family. Performing a family-wide annotation makes the task easier and more efficient than a gene-by-gene approach since many features obtained for one gene can be extrapolated to some or all the other genes of a family. A complete annotation procedure based on the most efficient prediction tools available is being used by 16 partner laboratories, each contributing annotated families from its field of expertise. A database, named GeneFarm, and an associated user-friendly interface to query the annotations have been developed. More than 3000 genes distributed over 300 families have been annotated and are available at http://genoplante-info.infobiogen.fr/Genefarm/. Furthermore, collaboration with the Swiss Institute of Bioinformatics is underway to integrate the GeneFarm data into the protein knowledgebase Swiss-Pro

Imagerie de l'endométriose : Rôle majeur de l'IRM pelvienne et défis diagnostics pour les radiologues inexpérimentés

L’endométriose est une maladie complexe, qui peut avoir un impact majeur sur la qualité de vie et sur la fertilité. Elle est définie par la présence de tissu endométrial en dehors de la cavité utérine. L’imagerie joue un rôle primordial, notamment l’IRM qui permet un bilan exhaustif de la maladie et de ces complications. Sa performance diagnostic est capitale pour une prise en charge adéquate, car elle peut avoir un impact sur la stratégie chirurgicale. Toutefois la détection de l’endométriose par IRM peut être subtile et complexe. Ainsi, nous avons évalué quel était l’impact de l’expérience du radiologue sur la performance diagnostic de l’IRM. Nos résultats montrent que les radiologues avec moins de deux ans d’expertise en imagerie de la femme avaient des performances diagnostics inférieurs à celles de l’expert, notamment pour le compartiment postérieur qui est une des localisations la plus fréquente

Formation of the Arabidopsis Pentatricopeptide Repeat Family

In Arabidopsis (Arabidopsis thaliana) the 466 pentatricopeptide repeat (PPR) proteins are putative RNA-binding proteins with essential roles in organelles. Roughly half of the PPR proteins form the plant combinatorial and modular protein (PCMP) subfamily, which is land-plant specific. PCMPs exhibit a large and variable tandem repeat of a standard pattern of three PPR variant motifs. The association or not of this repeat with three non-PPR motifs at their C terminus defines four distinct classes of PCMPs. The highly structured arrangement of these motifs and the similar repartition of these arrangements in the four classes suggest precise relationships between motif organization and substrate specificity. This study is an attempt to reconstruct an evolutionary scenario of the PCMP family. We developed an innovative approach based on comparisons of the proteins at two levels: namely the succession of motifs along the protein and the amino acid sequence of the motifs. It enabled us to infer evolutionary relationships between proteins as well as between the inter- and intraprotein repeats. First, we observed a polarized elongation of the repeat from the C terminus toward the N-terminal region, suggesting local recombinations of motifs. Second, the most N-terminal PPR triple motif proved to evolve under different constraints than the remaining repeat. Altogether, the evidence indicates different evolution for the PPR region and the C-terminal one in PCMPs, which points to distinct functions for these regions. Moreover, local sequence homogeneity observed across PCMP classes may be due to interclass shuffling of motifs, or to deletions/insertions of non-PPR motifs at the C terminus

Validation of the Perform-FES: a new fear of falling scale for hospitalized geriatric patients.

BACKGROUND: Fear of falling is highly prevalent in older adults and associated with numerous negative health events. The main objective of this study was to validate a scale to assess fear of falling, based on performance in real situation (Perform-FES), in a hospitalized geriatric population. METHODS: In this cross-sectional study, 55 patients (mean age: 85.3 years; 58% women) hospitalized in a geriatric hospital in Geneva (Switzerland) were enrolled. The Perform-FES scale was administered to all patients in conjunction with four other fear of falling scales. We determined the floor and ceiling effects, internal consistency, reliability, construct validity, and discriminative power of the Perform-FES scale. RESULTS: The Perform-FES scale did not demonstrate any significant floor or ceiling effect. It had a good internal consistency (Cronbach's alpha = 0.78) and an excellent reliability (intraclass correlation coefficient = 0.94). Regarding convergent validity, good correlations were shown between the score obtained on the Perform-FES scale and those obtained on other fear of falling scales. Also, the Perform-FES scale was able to discriminate patients with severe functional impairments (area under the ROC curve = 0.81) and had significantly better discriminating performance than other fear of falling scales. CONCLUSION: Findings suggest that the Perform-FES scale has good psychometric properties and may be a relevant tool to assess fear of falling in a geriatric hospitalized population. Future research should focus in particular on assessing the sensitivity to change and the predictive value of this scale in longitudinal studies, and its validity in other populations

Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis

72 ref. http://www.plantcell.org/cgi/doi/10.1105/tpc.104.022236International audienc

Genome-Wide Analysis of Arabidopsis Pentatricopeptide Repeat Proteins Reveals Their Essential Role in Organelle Biogenesis[W]

The complete sequence of the Arabidopsis thaliana genome revealed thousands of previously unsuspected genes, many of which cannot be ascribed even putative functions. One of the largest and most enigmatic gene families discovered in this way is characterized by tandem arrays of pentatricopeptide repeats (PPRs). We describe a detailed bioinformatic analysis of 441 members of the Arabidopsis PPR family plus genomic and genetic data on the expression (microarray data), localization (green fluorescent protein and red fluorescent protein fusions), and general function (insertion mutants and RNA binding assays) of many family members. The basic picture that arises from these studies is that PPR proteins play constitutive, often essential roles in mitochondria and chloroplasts, probably via binding to organellar transcripts. These results confirm, but massively extend, the very sparse observations previously obtained from detailed characterization of individual mutants in other organisms

The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.

International audienceThe analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on the basis of their genetics. These polyploidization events may have had important consequences in plant evolution, in particular for species radiation and adaptation and for the modulation of functional capacities. Here we report a high-quality draft of the genome sequence of grapevine (Vitis vinifera) obtained from a highly homozygous genotype. The draft sequence of the grapevine genome is the fourth one produced so far for flowering plants, the second for a woody species and the first for a fruit crop (cultivated for both fruit and beverage). Grapevine was selected because of its important place in the cultural heritage of humanity beginning during the Neolithic period. Several large expansions of gene families with roles in aromatic features are observed. The grapevine genome has not undergone recent genome duplication, thus enabling the discovery of ancestral traits and features of the genetic organization of flowering plants. This analysis reveals the contribution of three ancestral genomes to the grapevine haploid content. This ancestral arrangement is common to many dicotyledonous plants but is absent from the genome of rice, which is a monocotyledon. Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants