Application de méthodes ab initio à l'étude de polymères semi-conducteurs

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal

Retropseudogenes derived from the human Ro/SS-A autoantigen-associated hY RNAs

We report the characterization in the human genome of 966 pseudogenes derived from the four human Y (hY) RNAs, components of the Ro/SS-A autoantigen. About 95% of the Y RNA pseudogenes are found in corresponding locations on the chimpanzee and human chromosomes. On the contrary, Y pseudogenes in mice are both infrequent and found in different genomic regions. In addition to this rodent/primate discrepancy, the conservation of hY pseudogenes relative to hY genes suggests that they occurred after rodent/primate divergence. Flanking regions of hY pseudogenes contain convincing evidence for involvement of the L1 retrotransposition machinery. Although Alu elements are found in close proximity to most hY pseudogenes, these are not chimeric retrogenes. Point mutations in hY RNA transcripts specifically affecting binding of Ro60 protein likely contributed to their selection for direct trans retrotransposition. This represents a novel requirement for the selection of specific RNAs for their genomic integration by the L1 retrotransposition machinery. Over 40% of the hY pseudogenes are found in intronic regions of protein-coding genes. Considering the functions of proteins known to bind subsets of hY RNAs, hY pseudogenes constitute a new class of L1-dependent non-autonomous retroelements, potentially involved in post-transcriptional regulation of gene expression

La pédagogie active en physique : les facteurs qui améliorent l'engagement et la collaboration des élèves

Affiche présentée dans le cadre du Colloque de l'ARC, «La relève scientifique et la recherche collégiale : pratiques inspirantes au regard des chercheuses et chercheurs, et enjeux spécifiques à la formation des étudiantes et étudiants», dans le cadre du 84e Congrès de l'Acfas, Université du Québec à Montréal, Montréal, le 10 mai 2016.La pédagogie active (PA) améliore nettement l’apprentissage des élèves. Le grand défi de la PA consiste à gérer un écosystème d’apprentissage et à mobiliser les ressources humaines, documents et outils d’apprentissage à sa disposition – un processus appelé l’« orchestration ». La présente étude compare deux enseignants travaillant en PA dans un cours de physique (38 et 32 élèves respectivement). Ces enseignants sont excellents, comme le montrent les résultats remarquables de leurs élèves à un test standardisé sur les concepts en physique. Cependant, leur démarche pédagogique n’est pas la même, en raison des différences entre leurs points de vue épistémologiques et leurs ressources respectives, chacun dans leur classe aménagée de façon unique. Pour la comparaison, les deux enseignants devaient réaliser les mêmes activités. À partir d’observations en classe et de productions des élèves, nous analysons : 1) l’orchestration différente des ressources; 2) l’effet sur les productions des élèves; 3) les conséquences de ces orchestrations sur l’apprentissage et la collaboration des élèves. Selon nos résultats : 1) l’accès à des tableaux interactifs réservés aux élèves augmente les possibilités d’orchestration de l’enseignant; 2) les ressources ont un effet sur l’ampleur du suivi et de la rétroaction (évaluation par les pairs, suivi des progrès du groupe, retour en groupe classe); et 3) l’ajout d’activités intéressantes préalables au cours favorise l’engagement des élèves en classe

RiboSubstrates: a web application addressing the cleavage specificities of ribozymes in designated genomes

BACKGROUND: RNA-dependent gene silencing is becoming a routine tool used in laboratories worldwide. One of the important remaining hurdles in the selection of the target sequence, if not the most important one, is the designing of tools that have minimal off-target effects (i.e. cleaves only the desired sequence). Increasingly, in the current dawn of the post-genomic era, there is a heavy reliance on tools that are suitable for high-throughput functional genomics, consequently more and more bioinformatic software is becoming available. However, to date none have been designed to satisfy the ever-increasing need for the accurate selection of targets for a specific silencing reagent. RESULTS: In order to overcome this hurdle we have developed RiboSubstrates . This integrated bioinformatic software permits the searching of a cDNA database for all potential substrates for a given ribozyme. This includes the mRNAs that perfectly match the specific requirements of a given ribozyme, as well those including Wobble base pairs and mismatches. The results generated allow rapid selection of sequences suitable as targets for RNA degradation. The current web-based RiboSubstrates version permits the identification of potential gene targets for both SOFA-HDV ribozymes and for hammerhead ribozymes. Moreover, a minimal template for the search of siRNAs is also available. This flexible and reliable tool is easily adaptable for use with any RNA tool (i.e. other ribozymes, deoxyribozymes and antisense), and may use the information present in any cDNA bank. CONCLUSION: RiboSubstrates should become an essential step for all, even including "non-RNA biologists", who endeavor to develop a gene-inactivation system

Errungenschaften und Herausforderungen bei der Entwicklung der Fachdidaktiken in der Schweiz – Die Perspektive des programmbegleitenden Expertinnen- und Expertengremiums P9

Im folgenden Beitrag wird der Entwicklungsstand der Fachdidaktiken in der Schweiz aus der Perspektive des begleitenden Expertinnen- und Expertengremiums zum Programm P9 «Aufbau der wissenschaftlichen Kompetenzen in den Fachdidaktiken» (swiss-universities 2017–2020) vorgestellt. Nach einer Einführung in den Kontext, in den Auftrag des Gremiums sowie in das Design des Monitorings werden die Umsetzung und die Erkenntnisse der Arbeit vorgestellt. Abschließend werden fünf zentrale Empfehlungen abgeleitet. Forschungsstarke Schweizer Fachdidaktiken können durch die institutionelle Anerkennung als eigenständige wissenschaftliche Disziplinen und durch ihre systematische Integration auf Augenhöhe in das schweizerische Hochschul- und Forschungsgefüge entwickelt werden. (DIPF/Orig.

Widespread anti-sense transcription in apple is correlated with siRNA production and indicates a large potential for transcriptional and/or post-transcriptional control

Characterizing the transcriptome of eukaryotic organisms is essential for studying gene regulation and its impact on phenotype. The realization that anti-sense (AS) and noncoding RNA transcription is pervasive in many genomes has emphasized our limited understanding of gene transcription and post-transcriptional regulation. Numerous mechanisms including convergent transcription, anti-correlated expression of sense and AS transcripts, and RNAi remain ill-defined.Here, we have combined microarray analysis and high-throughput sequencing of small RNAs (sRNAs) to unravel the complexity of transcriptional and potential post-transcriptional regulation in eight organs of apple (Malus × domestica). The percentage of AS transcript expression is higher than that identified in annual plants such as rice and Arabidopsis thaliana. Furthermore, we show that a majority of AS transcripts are transcribed beyond 3′UTR regions, and may cover a significant portion of the predicted sense transcripts. Finally we demonstrate at a genome-wide scale that anti-sense transcript expression is correlated with the presence of both short (21–23 nt) and long (> 30 nt) siRNAs, and that the sRNA coverage depth varies with the level of AS transcript expression. Our study provides a new insight on the functional role of anti-sense transcripts at the genome-wide level, and a new basis for the understanding of sRNA biogenesis in plants

The Warburg Effect Is Genetically Determined in Inherited Pheochromocytomas

The Warburg effect describes how cancer cells down-regulate their aerobic respiration and preferentially use glycolysis to generate energy. To evaluate the link between hypoxia and Warburg effect, we studied mitochondrial electron transport, angiogenesis and glycolysis in pheochromocytomas induced by germ-line mutations in VHL, RET, NF1 and SDH genes. SDH and VHL gene mutations have been shown to lead to the activation of hypoxic response, even in normoxic conditions, a process now referred to as pseudohypoxia. We observed a decrease in electron transport protein expression and activity, associated with increased angiogenesis in SDH- and VHL-related, pseudohypoxic tumors, while stimulation of glycolysis was solely observed in VHL tumors. Moreover, microarray analyses revealed that expression of genes involved in these metabolic pathways is an efficient tool for classification of pheochromocytomas in accordance with the predisposition gene mutated. Our data suggest an unexpected association between pseudohypoxia and loss of p53, which leads to a distinct Warburg effect in VHL-related pheochromocytomas