Genomic Exploration of the Hemiascomycetous Yeasts: 1. A set of yeast species for molecular evolution studies11Sequences and annotations are accessible at: Génoscope (http://www.genoscope.cns.fr), FEBS Letters Website (http://www.elsevier.nl/febs/show/), Bordeaux (http://cbi.genopole-bordeaux.fr/Genolevures) and were deposited into the EMBL database (accession number from AL392203 to AL441602).

AbstractThe identification of molecular evolutionary mechanisms in eukaryotes is approached by a comparative genomics study of a homogeneous group of species classified as Hemiascomycetes. This group includes Saccharomyces cerevisiae, the first eukaryotic genome entirely sequenced, back in 1996. A random sequencing analysis has been performed on 13 different species sharing a small genome size and a low frequency of introns. Detailed information is provided in the 20 following papers. Additional tables available on websites describe the ca. 20 000 newly identified genes. This wealth of data, so far unique among eukaryotes, allowed us to examine the conservation of chromosome maps, to identify the ‘yeast-specific’ genes, and to review the distribution of gene families into functional classes. This project conducted by a network of seven French laboratories has been designated ‘Génolevures’

Genomic Exploration of the Hemiascomycetous Yeasts: 19. Ascomycetes-specific genes

AbstractComparisons of the 6213 predicted Saccharomyces cerevisiae open reading frame (ORF) products with sequences from organisms of other biological phyla differentiate genes commonly conserved in evolution from ‘maverick’ genes which have no homologue in phyla other than the Ascomycetes. We show that a majority of the ‘maverick’ genes have homologues among other yeast species and thus define a set of 1892 genes that, from sequence comparisons, appear ‘Ascomycetes-specific’. We estimate, retrospectively, that the S. cerevisiae genome contains 5651 actual protein-coding genes, 50 of which were identified for the first time in this work, and that the present public databases contain 612 predicted ORFs that are not real genes. Interestingly, the sequences of the ‘Ascomycetes-specific’ genes tend to diverge more rapidly in evolution than that of other genes. Half of the ‘Ascomycetes-specific’ genes are functionally characterized in S. cerevisiae, and a few functional categories are over-represented in them

Évolution des génomes de levures (analyse de la redondance et génomique comparative)

PARIS7-Bibliothèque centrale (751132105) / SudocSudocFranceF

Socialisation et développement des compétences<br />de l'élève ingénieur: Contribution au colloque "Compétences et socialisation" organisé à Montpellier, les 7 et 8 septembre 2007, par le CERFEE (Université Montpellier 3), le LIRDEF (IUFM de Montpellier) avec le concours de Montpellier Sup'Agro

La notion de compétence fait l'objet de nombreux débats. Néanmoins, les écoles d'ingénieur sont obligées d'intégrer une « logique compétence » (CEFI, 2005 ; 2006), imposée indirectement par la loi de modernisation sociale du 17/01/2002 et son décret d'application (26/04/2002). Reprenant la directive EUROPASS, la loi a créé le Répertoire national de la certification professionnelle, le décret précise que chaque diplôme inscrit au répertoire doit être associé à un référentiel décrivant les compétences, aptitudes et connaissances liées aux activités professionnelles auxquelles il permet d'accéder.Plutôt que de remettre en cause cette « logique compétence », l'Ecole d'ingénieurs du CESI a formé le projet de se doter d'une approche développementale de la compétence, ayant comme référence l'organisation de l'activité de « l'ingénieur généraliste » CESI.Dans cette approche, nous considérons trois dimensions de la compétence, avec des indicateurs propres à chacune d'elle :- Une dimension « cognitive », construite par le sujet au cours de son activité, qui mobilise et enrichit ses représentations (au sens large : conceptuelles, sociales, organisationnelles, expérientielles...) et ses « organisateurs d'activités » (schèmes, procédures...) (Pastré, 2004 ; 2005).- Une dimension « identitaire », qui se développe sur la base des relations sociales au sein du collectif où se déroule l'activité, et se nourrit du sentiment de compétence résultant de la mesure par le sujet de l'efficacité de son activité ainsi que du jugement de compétence porté par le collectif (Pastré, 2005 ; Hillau, 2006).- Une dimension « institutionnelle », qui définit le territoire dans lequel l'activité du sujet est considérée comme légitime, ce qui est le sens historiquement premier du terme « compétence » (Hillau, 2006).Une série de travaux de recherche menés par les auteurs sont en cours, pour établir la référence, comprendre les étapes du développement et les effets des dispositifs de formation. Ces travaux portent sur 6 promotions d'élèves ingénieurs (formation continue et apprentissage). La communication proposée rend compte des premiers résultats et notamment de l'articulation entre le développement « cognitif » et la construction identitaire, à partir de l'étude des trajectoires d'une centaine d'élèves ingénieurs

Comment on: A novel dysferlin-mutant pseudoexon bypassed with antisense oligonucleotides

International audienc

Genomic Exploration of the Hemiascomycetous Yeasts: 12. Kluyveromyces marxianus var. marxianus

AbstractAs part of the comparative genomics project ‘GENOLEVURES’, we studied the Kluyveromyces marxianus var. marxianus strain CBS712 using a partial random sequencing strategy. With a 0.2×genome equivalent coverage, we identified ca. 1300 novel genes encoding proteins, some containing spliceosomal introns with consensus splice sites identical to those of Saccharomyces cerevisiae, 28 tRNA genes, the whole rDNA repeat, and retrotransposons of the Ty1/2 family of S. cerevisiae with diverged Long Terminal Repeats. Functional classification of the K. marxianus genes, as well as the analysis of the paralogous gene families revealed few differences with respect to S. cerevisiae. Only 42 K. marxianus identified genes are without detectable homolog in the baker’s yeast. However, we identified several genetic rearrangements between these two yeast species

Identification of Splicing Defects Caused by Mutations in the Dysferlin Gene

International audienceMissense, iso-semantic, and intronic mutations are challenging for interpretation, in particular for their impact in mRNA. Various tools such as the Human Splicing Finder (HSF) system could be used to predict the impact on splicing; however, no diagnosis result could rely on predictions alone, but requires functional testing. Here, we report an in vitro approach to study the impact of DYSF mutations on splicing. It was evaluated on a series of 45 DYSF mutations, both intronic and exonic. We confirmed splicing alterations for all intronic mutations localized in 5 or 3 splice sites. Then, we showed that DYSF missense mutations could also result in splicing defects: mutations c.463G>A and c.2641A>C abolished ESEs and led to exon skipping; mutations c.565C>G and c.1555G>A disrupted Exonic Splicing Enhancer (ESE), while concomitantly creating new 5 or 3 splice site leading to exonic out of frame deletions. We demonstrated that 20% of DYSF missense mutations have a strong impact on splicing. This minigene strategy is an efficient tool for the detection of splicing defects in dysferlinopathies, which could allow for a better comprehension of splicing defects due to mutations and could improve prediction tools evaluating splicing defects

The French National Registry of patients with Facioscapulohumeral muscular dystrophy

Abstract Background Facioscapulohumeral muscular dystrophy is a rare inherited neuromuscular disease with an estimated prevalence of 1/20,000 and France therefore harbors about 3000 FSHD patients. With research progress and the development of targeted therapies, patients’ identification through registries can facilitate and improve recruitment in clinical trials and studies. Results The French National Registry of FSHD patients was designed as a mixed model registry involving both patients and physicians, through self-report and clinical evaluation questionnaires respectively, to collect molecular and clinical data. Because of the limited number of patients, data quality is a major goal of the registry and various automatic data control features have been implemented in the bioinformatics system. In parallel, data are manually validated by molecular and clinical curators. Since its creation in 2013, data from 638 FSHD patients have been collected, representing about 21% of the French FSHD population. The mixed model strategy allowed to collect 59.1% of data from both patients and clinicians; 26 and 14.9% from respectively patients and clinicians only. With the identification of the FSHD1 and FSHD2 forms, specific questionnaires have been designed. Though FSHD2 patients are progressively included, FSHD1 patients still account for the majority (94.9%). The registry is compatible with the FAIR principles as data are Findable, Accessible and Interoperable. We thus used molecular standards and standardized clinical terms used by the FILNEMUS French network of reference centers for the diagnosis and follow-up of patients suffering from a rare neuromuscular disease. The implemented clinical terms mostly map to dictionaries and terminology systems such as SNOMED-CT (75% of terms), CTV3 (61.7%) and NCIt (53.3%). Because of the sensitive nature of data, they are not directly reusable and can only be accessed as aggregated data after evaluation and approval by the registry oversight committee. Conclusions The French National Registry of FSHD patients belongs to a national effort to develop databases, which should now interact with other initiatives to build a European and/or an international FSHD virtual registry for the benefits of patients. It is accessible at www.fshd.fr and various useful information, links, and documents, including a video, are available for patients and professionals

Evolution of non-LTR retrotransposons in the trypanosomatid genomes: Leishmania major has lost the active elements

The ingi and L1Tc non-LTR retrotransposons - which constitute the ingi clade - are abundant in the genome of the trypanosomatid species Trypanosoma brucei and Trypanosoma cruzi, respectively. The corresponding retroelements, however, are not present in the genome of a closely related trypanosomatid, Leishmania major. To study the evolution of non-LTR retrotransposons in trypanosomatids, we have analyzed all ingi/L1Tc elements and highly degenerate ingi/L1Tc-related sequences identified in the recently completed T. brucei, T. cruzi and L. major genomes. The coding sequences of 242 degenerate ingi/L1Tc-related elements (DIREs) in all three genomes were reconstituted by removing the numerous frame shifts. Three independent phylogenetic analyses conducted on the conserved domains encoded by these elements show that all DIREs, including the 52 L. major DIREs, form a monophyletic group belonging to the ingi clade. This indicates that the trypanosomatid ancestor contained active mobile elements that have been retained in the Trypanosoma species, but were lost from L. major genome, where only remnants (DIRE) are detectable. All 242 DIREs analyzed group together according to their species origin with the exception of 11 T. cruzi DIREs which are close to the T. brucei ingi/DIRE families. Considering the absence of known horizontal transfer between the African T. brucei and the South-American T. cruzi, this suggests that this group of elements evolved at a lower rate when compared to the other trypanosomatid elements. Interestingly, the only nucleotide sequence conserved between ingi and L1Tc (the first 79 residues) is also present at the 5′-extremity of all the full length DIREs and suggests a possible role for this conserved motif, as well as for DIREs.Fil: Bringaud, Frédéric. Universite Victor Segalen Bordeaux Ii; FranciaFil: Ghedin, Elodie. The Institute for Genomic Research; Estados Unidos. The George Washington University; Estados UnidosFil: Blandin, Gaëlle. The Institute for Genomic Research; Estados UnidosFil: Bartholomeu, Daniella C.. The Institute for Genomic Research; Estados UnidosFil: Caler, Elisabet. The Institute for Genomic Research; Estados UnidosFil: Levin, Mariano Jorge. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina. Universidad de Buenos Aires; ArgentinaFil: Baltz, Théo. Universite Victor Segalen Bordeaux Ii; FranciaFil: El Sayed, Najib M.. The George Washington University; Estados Unidos. The Institute for Genomic Research; Estados Unido