Modulation de l'épissage alternatif de Bcl-x par les protéines hnRNP F et H in vitro

L'épissage alternatif est un mécanisme permettant d'augmenter la diversité protéique dans une cellule. Dans certains cas, les isoformes ainsi créés peuvent avoir des activités complètement différentes. Une telle situation implique le gène apoptotique Bcl-x qui produit des isoformes ayant des activités antagonistes dans l'apoptose. Ces isoformes sont formés par l'utilisation de sites d'épissage 5' alternatifs. L'isoforme Bcl-xL possède une activité anti-apoptotique alors que Bcl-xS possède une activité pro-apoptotique. Mes recherches ont permis de trouver deux régions exoniques responsables de la régulation de l'épissage alternatif de ce gène. Une première région B2, située en aval du site d'épissage de Bcl-xS , active la formation de l'isoforme Bcl-xS alors qu'une deuxième région B3, située en amont du site d'épissage de Bcl-xL, active la formation de l'isoforme Bcl-xL. Plus précisément, une sous-région B2G est principalement responsable de l'activité de la région B2 et possède une séquence constituée de trois séries de G pouvant recruter les protéines hnRNP F et hnRNP H. De plus, les deux dernières séries de G sont importantes pour l'activité de l'élément B2G ainsi que pour la liaison des protéines à cette séquence. Nous avons aussi montré que l'ajout de hnRNP F ou H dans une réaction d'épissage in vitro permet de moduler l'épissage de Bcl-x en favorisant la formation de l'isoforme Bcl-xS. Cette modulation n'est cependant pas obtenue lorsque que l'élément B2G est muté. Mon étude montre aussi que, in vitro, l'ajout des protéines hnRNP Al et SRp30c stimule la production de l'isoforme Bcl-xL. Cet effet se ferait via un autre élément que B2G puisque ni hnRNP A1, ni SRp30c ne lient cette séquence

La reconnaissance juridique d'une déviation de la norme biomédicale : un concept interdisciplinaire dynamique et complexe

La reconnaissance qu'un travailleur est handicapé selon l'article 329 de la du travail et les maladies professionnelles Loi sur les accidents (LATMP) requiert l'application de critères développés par la jurisprudence. Cette qualification est primordiale puisqu'elle permet à l'employeur de réduire l'impact des coûts de la lésion professionnelle sur sa cotisation. L'existence d'un handicap préalable à une lésion professionnelle nécessite la présence d'une condition déviant par rapport à la norme biomédicale, un concept interdisciplinaire intégrant un aspect juridique et médical. La complexité de la norme biomédicale et la détermination de sa déviance occupent une part importante des débats juridiques dans le contexte d'une lésion professionnelle lorsqu'il est question d'imputation. Pour s'assurer de la valeur probante de son opinion médico-légale, l'expert médical doit s'appuyer sur des preuves scientifiques respectant les exigences juridiques. Dans ce mémoire, l'auteur analyse la démarche juridique permettant d'établir le degré de preuve requis et les paramètres essentiels à l'appréciation d'une déviation par rapport à une norme biomédicale du p oint de vue légal. L'objectif est de préciser la reconnaissance de la déviation les critères d'analyse juridiques de d'une norme biomédicale et de déterminer leurs influences. La méthodologie repose sur l'analyse des décisions rendues par le Tribunal administratif du travail en relation avec le concept de « déviation de la norme biomédicale » qui oriente la notion de travailleur déjà handicapé. Les jugements décortiqués ont contribué à l'identification des paramètres juridiques indispensables qui doivent être appuyés par des moyens de preuve essentiels à une démonstration prépondérante de la déviation d'une condition par rapport à une norme biomédicale. Les résultats de l'étude fournissent un outil permettant aux employeurs, à leurs représentants et à leurs experts, ainsi qu'aux décideurs, de mieux préparer ou analyser, au moyen d'une démarche systématique et rigoureuse, une demande de partage de coûts fondée sur l'article 329 LATMP

LeXFiles and LegalLAMA: Facilitating English Multinational Legal Language Model Development

In this work, we conduct a detailed analysis on the performance of legal-oriented pre-trained language models (PLMs). We examine the interplay between their original objective, acquired knowledge, and legal language understanding capacities which we define as the upstream, probing, and downstream performance, respectively. We consider not only the models' size but also the pre-training corpora used as important dimensions in our study. To this end, we release a multinational English legal corpus (LeXFiles) and a legal knowledge probing benchmark (LegalLAMA) to facilitate training and detailed analysis of legal-oriented PLMs. We release two new legal PLMs trained on LeXFiles and evaluate them alongside others on LegalLAMA and LexGLUE. We find that probing performance strongly correlates with upstream performance in related legal topics. On the other hand, downstream performance is mainly driven by the model's size and prior legal knowledge which can be estimated by upstream and probing performance. Based on these findings, we can conclude that both dimensions are important for those seeking the development of domain-specific PLMs.Comment: 9 pages, long paper at ACL 2023 proceeding

Modulation of 5' splice site selection using tailed oligonucleotides carrying splicing signals

BACKGROUND: We previously described the use of tailed oligonucleotides as a means of reprogramming alternative pre-mRNA splicing in vitro and in vivo. The tailed oligonucleotides that were used interfere with splicing because they contain a portion complementary to sequences immediately upstream of the target 5' splice site combined with a non-hybridizing 5' tail carrying binding sites for the hnRNP A1/A2 proteins. In the present study, we have tested the inhibitory activity of RNA oligonucleotides carrying different tail structures. RESULTS: We show that an oligonucleotide with a 5' tail containing the human β-globin branch site sequence inhibits the use of the 5' splice site of Bcl-xL, albeit less efficiently than a tail containing binding sites for the hnRNP A1/A2 proteins. A branch site-containing tail positioned at the 3' end of the oligonucleotide also elicited splicing inhibition but not as efficiently as a 5' tail. The interfering activity of a 3' tail was improved by adding a 5' splice site sequence next to the branch site sequence. A 3' tail carrying a Y-shaped branch structure promoted similar splicing interference. The inclusion of branch site or 5' splice site sequences in the Y-shaped 3' tail further improved splicing inhibition. CONCLUSION: Our in vitro results indicate that a variety of tail architectures can be used to elicit splicing interference at low nanomolar concentrations, thereby broadening the scope and the potential impact of this antisense technology

Molecular and evolutionary basis of O-antigenic polysaccharide driven phage sensitivity in environmental pseudomonads

Pseudomonas protegens CHA0, a bacterial strain able to suppress plant pathogens as well as efficiently kill lepidopteran pest insects, has been studied as biocontrol agent to prevent ensuing agricultural damage. However, the success of this method is dependent on the efficient plant colonization by the bacterial inoculant while it faces competition from the resident microbiota as well as predators such as bacteriophages. One of these naturally occurring phages, ΦGP100, was found to drastically reduce the abundance of CHA0 once inoculated into plant microcosms, resulting in the loss of plant protection against a phytopathogen. Here, we investigated the molecular determinants implicated in the interaction between CHA0 and the phage ΦGP100 using a high-density transposon-sequencing approach. We show that lipopolysaccharide cell surface decorations, specifically the longer OBC3-type O-antigenic polysaccharide (O-PS, O-antigen) of the two dominant O-PS of CHA0 is essential for the attachment and infection of ΦGP100. Moreover, when exploring the distribution of the OBC3 cluster in bacterial genomes, we identified several parts of this gene cluster that are conserved in phylogenetically distant bacteria. Through heterologous complementation, we integrated an OBC3-type gene copy from a phylogenetically distant bacterium and were able to restore the phage sensitivity of a CHA0 mutant which lacked the ability to form long O-PS. Finally, we evidence that the OBC3 gene cluster of CHA0 displays a high genomic plasticity and likely underwent several horizontal acquisitions and genomic rearrangements. Collectively, this study underlines the complexity of phage-bacteria interaction and the multifunctional aspect of bacterial cell surface decorations

LeXFiles and LegalLAMA: Facilitating English Multinational Legal Language Model Development

In this work, we conduct a detailed analysis on the performance of legal-oriented pre-trained language models (PLMs). We examine the interplay between their original objective, acquired knowledge, and legal language understanding capacities which we define as the upstream, probing, and downstream performance, respectively. We consider not only the models' size but also the pre-training corpora used as important dimensions in our study. To this end, we release a multinational English legal corpus (LeXFiles) and a legal knowledge probing benchmark (LegalLAMA) to facilitate training and detailed analysis of legal-oriented PLMs. We release two new legal PLMs trained on LeXFiles and evaluate them alongside others on LegalLAMA and LexGLUE. We find that probing performance strongly correlates with upstream performance in related legal topics. On the other hand, downstream performance is mainly driven by the model's size and prior legal knowledge which can be estimated by upstream and probing performance. Based on these findings, we can conclude that both dimensions are important for those seeking the development of domain-specific PLMs

Bacillus subtilis Early Colonization of Arabidopsis thaliana Roots Involves Multiple Chemotaxis Receptors

ABSTRACT Colonization of plant roots by Bacillus subtilis is mutually beneficial to plants and bacteria. Plants can secrete up to 30% of their fixed carbon via root exudates, thereby feeding the bacteria, and in return the associated B. subtilis bacteria provide the plant with many growth-promoting traits. Formation of a biofilm on the root by matrix-producing B. subtilis is a well-established requirement for long-term colonization. However, we observed that cells start forming a biofilm only several hours after motile cells first settle on the plant. We also found that intact chemotaxis machinery is required for early root colonization by B. subtilis and for plant protection. Arabidopsis thaliana root exudates attract B. subtilis in vitro, an activity mediated by the two characterized chemoreceptors, McpB and McpC, as well as by the orphan receptor TlpC. Nonetheless, bacteria lacking these chemoreceptors are still able to colonize the root, suggesting that other chemoreceptors might also play a role in this process. These observations suggest that A. thaliana actively recruits B. subtilis through root-secreted molecules, and our results stress the important roles of B. subtilis chemoreceptors for efficient colonization of plants in natural environments. These results demonstrate a remarkable strategy adapted by beneficial rhizobacteria to utilize carbon-rich root exudates, which may facilitate rhizobacterial colonization and a mutualistic association with the host

The DExD/H box ATPase Dhh1 functions in translational repression, mRNA decay, and processing body dynamics

Dhh1 is a critical determinant in whether mRNAs are translated, stored, or decayed