Fast matrix transposition computer implementation

Eklundh's (1972) algorithm to transpose a large matrix stored on an external device such as a disc has been programmed and tested. A simple description of computer implementation is given in this note.

The meleagrid herpesvirus 1 genome is partially resistant to transposition

The propagation of herpesvirus genomes as infectious bacterial artificial chromosomes (iBAC) has enabled the application of highly efficient strategies to investigate gene function across the genome. One of these strategies, transposition, has been used successfully on a number of herpesvirus iBACs to generate libraries of gene disruption mutants. Gene deletion studies aimed at determining the dispensable gene repertoire of the Meleagrid herpesvirus 1 (MeHV-1) genome to enhance the utility of this virus as a vaccine vector have been conducted in this report. A MeHV-1 iBAC was used in combination with the Tn5 and MuA transposition systems in an attempt to generate MeHV-1 gene interruption libraries. However, these studies demonstrated that Tn5 transposition events into the MeHV-1 genome occurred at unexpectedly low frequencies. Furthermore, characterization of genomic locations of the rare Tn5 transposon insertion events indicated a nonrandom distribution within the viral genome, with seven of the 24 insertions occurring within the gene encoding infected cell protein 4. Although insertion events with the MuA system occurred at higher frequency compared with the Tn5 system, fewer insertion events were generated than has previously been reported with this system. The characterization and distribution of these MeHV-1 iBAC transposed mutants is discussed at both the nucleotide and genomic level, and the properties of the MeHV-1 genome that could influence transposition frequency are discussed. © American Association of Avian Pathologists.

Characterization of the molecular components and function of BARE-1, Hin-Mu and Mu transposition machineries

Transposable elements, transposons, are discrete DNA segments that are able to move or copy themselves from one locus to another within or between their host genome(s) without a requirement for DNA homology. They are abundant residents in virtually all the genomes studied, for instance, the genomic portion of TEs is approximately 3% in Saccharomyces cerevisiae, 45% in humans, and apparently more than 70% in some plant genomes such as maize and barley. Transposons plays essential role in genome evolution, in lateral transfer of antibiotic resistance genes among bacteria and in life cycle of certain viruses such as HIV-1 and bacteriophage Mu. Despite the diversity of transposable elements they all use a fundamentally similar mechanism called transpositional DNA recombination (transposition) for the movement within and between the genomes of their host organisms. The DNA breakage and joining reactions that underlie their transposition are chemically similar in virtually all known transposition systems. The similarity of the reactions is also reflected in the structure and function of the catalyzing enzymes, transposases and integrases. The transposition reactions take place within the context of a transposition machinery, which can be particularly complex, as in the case of the VLP (virus like particle) machinery of retroelements, which in vivo contains RNA or cDNA and a number of element encoded structural and catalytic proteins. Yet, the minimal core machinery required for transposition comprises a multimer of transposase or integrase proteins and their binding sites at the element DNA ends only. Although the chemistry of DNA transposition is fairly well characterized, the components and function of the transposition machinery have been investigated in detail for only a small group of elements. This work focuses on the identification, characterization, and functional studies of the molecular components of the transposition machineries of BARE-1, Hin-Mu and Mu. For BARE-1 and Hin-Mu transpositional activity has not been shown previously, whereas bacteriophage Mu is a general model of transposition. For BARE-1, which is a retroelement of barley (Hordeum vulgare), the protein and DNA components of the functional VLP machinery were identified from cell extracts. In the case of Hin-Mu, which is a Mu-like prophage in Haemophilus influenzae Rd genome, the components of the core machinery (transposase and its binding sites) were characterized and their functionality was studied by using an in vitro methodology developed for Mu. The function of Mu core machinery was studied for its ability to use various DNA substrates: Hin-Mu end specific DNA substrates and Mu end specific hairpin substrates. The hairpin processing reaction by MuA was characterized in detail. New information was gained of all three machineries. The components or their activity required for functional BARE-1 VLP machinery and retrotransposon life cycle were present in vivo and VLP-like structures could be detected. The Hin-Mu core machinery components were identified and shown to be functional. The components of the Mu and Hin-Mu core machineries were partially interchangeable, reflecting both evolutionary conservation and flexibility within the core machineries. The Mu core machinery displayed surprising flexibility in substrate usage, as it was able to utilize Hin-Mu end specific DNA substrates and to process Mu end DNA hairpin substrates. This flexibility may be evolutionarily and mechanistically important.

Mu in vitro Transposition Technology in Functional Genetics and Genomics: Applications on Mouse and Bacteriophages

Transposons are mobile elements of genetic material that are able to move in the genomes of their host organisms using a special form of recombination called transposition. Bacteriophage Mu was the first transposon for which a cell-free in vitro transposition reaction was developed. Subsequently, the reaction has been refined and the minimal Mu in vitro reaction is useful in the generation of comprehensive libraries of mutant DNA molecules that can be used in a variety of applications. To date, the functional genetics applications of Mu in vitro technology have been subjected to either plasmids or genomic regions and entire genomes of viruses cloned on specific vectors. This study expands the use of Mu in vitro transposition in functional genetics and genomics by describing novel methods applicable to the targeted transgenesis of mouse and the whole-genome analysis of bacteriophages. The methods described here are rapid, efficient, and easily applicable to a wide variety of organisms, demonstrating the potential of the Mu transposition technology in the functional analysis of genes and genomes. First, an easy-to-use, rapid strategy to generate construct for the targeted mutagenesis of mouse genes was developed. To test the strategy, a gene encoding a neuronal K+/Cl- cotransporter was mutagenised. After a highly efficient transpositional mutagenesis, the gene fragments mutagenised were cloned into a vector backbone and transferred into bacterial cells. These constructs were screened with PCR using an effective 3D matrix system. In addition to traditional knock-out constructs, the method developed yields hypomorphic alleles that lead into reduced expression of the target gene in transgenic mice and have since been used in a follow-up study. Moreover, a scheme is devised to rapidly produce conditional alleles from the constructs produced. Next, an efficient strategy for the whole-genome analysis of bacteriophages was developed based on the transpositional mutagenesis of uncloned, infective virus genomes and their subsequent transfer into susceptible host cells. Mutant viruses able to produce viable progeny were collected and their transposon integration sites determined to map genomic regions nonessential to the viral life cycle. This method, applied here to three very different bacteriophages, PRD1, ΦYeO3 12, and PM2, does not require the target genome to be cloned and is directly applicable to all DNA and RNA viruses that have infective genomes. The method developed yielded valuable novel information on the three bacteriophages studied and whole-genome data can be complemented with concomitant studies on individual genes. Moreover, end-modified transposons constructed for this study can be used to manipulate genomes devoid of suitable restriction sites.

Mu in vitro transposition applications in protein engineering

Transposons, mobile genetic elements that are ubiquitous in all living organisms have been used as tools in molecular biology for decades. They have the ability to move into discrete DNA locations with no apparent homology to the target site. The utility of transposons as molecular tools is based on their ability to integrate into various DNA sequences efficiently, producing extensive mutant clone libraries that can be used in various molecular biology applications. Bacteriophage Mu is one of the most useful transposons due to its well-characterized and simple in vitro transposition reaction. This study establishes the properties of the Mu in vitro transposition system as a versatile multipurpose tool in molecular biology. In addition, this study describes Mu-based applications for engineering proteins by random insertional transposon mutagenesis in order to study structure-function relationships in proteins. We initially characterized the properties of the minimal Mu in vitro transposition system. We showed that the Mu transposition system works efficiently and accurately and produces insertions into a wide spectrum of target sites in different DNA molecules. Then, we developed a pentapeptide insertion mutagenesis strategy for inserting random five amino acid cassettes into proteins. These protein variants can be used especially for screening important sites for protein-protein interactions. Also, the system may produce temperature-sensitive variants of the protein of interest. Furthermore, we developed an efficient screening system for high-resolution mapping of protein-protein interfaces with the pentapeptide insertion mutagenesis. This was accomplished by combining the mutagenesis with subsequent yeast two-hybrid screening and PCR-based genetic footprinting. This combination allows the analysis of the whole mutant library en masse, without the need for producing or isolating separate mutant clones, and the protein-protein interfaces can be determined at amino acid accuracy. The system was validated by analysing the interacting region of JFC1 with Rab8A, and we show that the interaction is mediated via the JFC1 Slp homology domain. In addition, we developed a procedure for the production of nested sets of N- and C-terminal deletion variants of proteins with the Mu system. These variants are useful in many functional studies of proteins, especially in mapping regions involved in protein-protein interactions. This methodology was validated by analysing the region in yeast Mso1 involved in an interaction with Sec1. The results of this study show that the Mu in vitro transposition system is versatile for various applicational purposes and can efficiently be adapted to random protein engineering applications for functional studies of proteins.

Transposition didactique : des savoirs experts d'un programme technique vers les savoirs à enseigner en physique.

Par expérience, les étudiantes et étudiants du collégial sont beaucoup plus motivés lorsque les activités d'apprentissage proposées dans le cours sont en lien direct avec leur programme, surtout lorsqu'il s'agit d'un cours d'une discipline contributive. Comme il y a seize cours de physique offerts dans neuf programmes techniques au cégep de Trois-Rivières, les applications pertinentes de chaque programme ne sont pas toujours connues du département de physique et il n'y a que peu de sources d'informations vulgarisées qui expliquent le fonctionnement de ces systèmes ou qui font des liens explicites avec la physique. Cet essai vise à élaborer une démarche permettant d'obtenir les informations pertinentes sur les systèmes utilisés dans les programmes de techniques physiques afin d'organiser les savoirs à enseigner de façon cohérente et pertinente dans les cours de physique. Cette démarche générale sera ensuite appliquée au cours de mécanique appliquée du programme de génie civil afin de la valider concrètement. Tout en s'appuyant sur les sources didactiques comme les savoirs disciplinaires, les savoirs à enseigner et le rapport des élèves aux savoirs, le cadre de référence propose un processus de transposition didactique pour déterminer et organiser les contenus du cours de physique en fonction des applications concrètes reliées au programme. Le cadre méthodologique de cette recherche-intervention propose une démarche cyclique permettant d'abord d'identifier les systèmes techniques pertinents et leurs liens avec la physique puis de modéliser le fonctionnement de ce système. Enfin, le processus de transposition didactique sera appliqué aux résultats et vérifié par des enseignantes et enseignants du département de physique.

Transposition of great arteries and single coronary artery: a new surgical technique for the arterial switch operation.

A single coronary artery can complicate the surgical technique of arterial switch operations, impairing early and late outcomes. We propose a new surgical approach, successfully applied in a 2.1 kg neonate, aimed at reducing the risk of early and late compression and/or distortion of the newly constructed coronary artery system.

Le design urbain au Québec : étude de la transposition des prescriptions empiriques dans la pratique urbanistique

Le design urbain, dimension de la pratique urbanistique, consiste principalement en la manipulation de la forme urbaine selon une démarche ciblée et encadrée. Les approches sont aussi nombreuses que diversifiées. On peut néanmoins les classer en deux catégories : les approches visant la forme urbaine en tant qu‟objet qui contient l‟organisation formelle de la ville et celles qui visent le travail sur la forme urbaine afin d‟organiser la dynamique urbaine humaine. Les deux types d‟approches soutiennent différentes démarches d‟aménagement qui contribuent à développer la forme urbaine et la dynamique des lieux. Parmi celles-ci se trouve la vision de type empirique, laquelle vise l‟expérience urbaine à l‟échelle du piéton. Les écrits et les théories à ce sujet sont variés et pertinents. La présente recherche porte sur la transposition des prescriptions empiriques dans la planification d‟un projet qui intègre une démarche de design urbain. Au moyen d‟une étude de cas, la Cité multimédia à Montréal, il s‟agit de comprendre plus spécifiquement comment le canevas maître du design urbain, soit l‟espace public, est étudié et reformulé et ce, en accordant une attention particulière pour la dimension empirique du futur aménagement. Quelles sont les balises ou les composantes qui permettent à la dimension empirique de se déployer dans la conception d‟un projet urbain qui vise une reformulation de la forme urbaine?

Synthèse totale de la pactamycine et d’une sélection d’analogues, progrès vers la synthèse totale de la daphniglaucine C et brève étude d’une transposition allylique réductrice

Il y a plus de cinquante ans, la pactamycine a été isolée en tant qu’agent antitumoral potentiel. Il a été réalisé plus tard qu’il s’agissait en fait d’un agent antibactérien capable d’inhiber la synthèse de protéines lors du procédé de traduction. Récemment, il a même été démontré que certains de ses analogues possèdent des propriétés antiprotozoaires prometteuses. La présente thèse détaille la première synthèse totale de la pactamycine, entreprise au sein du groupe Hanessian, ainsi que la préparation d’une sélection d’analogues testés pour leurs propriétés biologiques. En outre, la daphniglaucine C appartient à une vaste famille de composés naturels isolés des feuilles du daphniphyllum au cours des dix dernières années. Bien que relativement peu d’information soit connue par rapport à l’activité biologique de la daphniglaucine C, la synthèse de celle-ci représente certainement un défi intéressant pour un chimiste organicien. Au passage, nos efforts vers la synthèse totale du composé cible auront permis d’explorer l’emploi de plusieurs méthodes en vue de la formation de centres quaternaires. De plus, un réarrangement réductif atypique, catalysé au palladium à partir d’alcools allyliques non-activés, a été étudié et employé afin de générer une sélection de pyrrolidines polysubstituées.

The effect of nonlinear frequency compression and linear frequency transposition on speech perception in school-aged children

The primary objective of this study is to determine whether nonlinear frequency compression and linear transposition algorithms provide speech perception benefit in school-aged children.