No description available.

No description available.

[pt] A importância da rastreabilidade na evolução de sistemas é um fato amplamente reconhecido, mas apesar dos esforços despendidos até agora, ainda encontramos vários obstáculos a sua efetiva utilização. Esses obstáculos são relacionados a geração e validação das informações sobre os relacionamentos e interdependências entre o mundo real, os requisitos e o sistema de software. Estas informações freqüentemente não são confiáveis devido a inconsistência causada pela evolução distinta dos vários artefatos resultantes do processo de desenvolvimento de um sistema. Esta tese tem como objetivo estudar a utilização da tecnologia transformacional na implementação de um mecanismo de rastreamento de maneira a se obter a atualização automática das informações de rastreamento, através da identificação das mudanças ocorridas entre versões consecutivas dos artefatos produzidos e o seu subseqüente armazenamento na forma de transformações. Os benefícios obtidos pelo uso deste mecanismo permitirão: a eliminação dos problemas da falta de atualização das informações de rastreamento e o conseqüente aumento do valor destas informações para o desenvolvedor; a sistematização do processo de rastreamento; e a diminuição do custo para se obter, atualizar e validar as informações de rastreamento. Além destes benefícios, o armazenamento das informações de rastreamento na forma de transformações incorpora um maior conhecimento sobre a modelagem realizada, ao contrário de outros mecanismos que armazenam somente os artefatos e seus interrelacionamentos estáticos. / [en] The importance of traceability in software evolutions was quite established, but despite the effort spent, they are many issues that difficult they effective use. These issues are related to the generating and validating of trace information about the relationships and interdependencies between the real world, the requirements and the software system. This information is often mistrusted since they may have become obsolete due to separate evolution of models and systems. This thesis study the use of the transformational technology in the implementation of a traceability mechanism that automatically obtain trace information by identifying the changes made in consecutive artifact versions and store it as transformations. The main advantages gained with it uses are the elimination of the problems of the lack of trace information updating, the systematization of the trace process and the decrease of the cost to obtain, update and validate trace information. Besides these benefits, the storage of trace information in the form of transformations incorporates a larger knowledge on the accomplished modeling, unlike other mechanisms that only store the artifacts and their static inter- relationships.

Kuriant informacines sistemas, tenka kurti tuos pačius sistemos komponentus, o sistemą realizuojant komponentinio modeliavimo principu, galima panaudoti jau sukurtus komponentus juos papildant, susiaurinant bei pagal poreikius koreguojant. Pagrindinis darbo tikslas - integruoti veiklos modelį ir detalų IS projekto modelį, panaudojant komponentinį sistemos projektavimo metodą. Darbe išanalizuotos Magic Draw UML 12.5 galimybės, sukurtas profailas, skirtas nubraižyti komponentinį IS modelį. Realizuota komponentinio modelio transformacijos į klasių modelį programinė įranga, sukurta MS Visual Studio .NET 2005, kuri sugeba atlikti komponentinio IS modelio transformavimą į UML klasių modelį. Atliktas eksperimentas, palygintas sukurta programine įranga sugeneruotų komponentų programinis kodas su „Magic Draw UML 12.5“ programine įranga generuotais klasių aprašais. / Presented work covers an approach to applications development based on the principles of the model-driven architecture and using the component-based system model (CBSM). The CBSM helps to refine main components and interfaces of the application at the design stage. The information system’s architecture is structured considering a business system as a set of different domains (Business, Data, Information process) with definite types of components, and with interfaces between the components of different types. Presented work is topical, when creates the same information system’s components. These components can be used and they can be modified or changed. Component - based model transformation system is created and tested with special project.

Subject of this thesis is to design a web application for overhead calculation, whose purpose is to be a substitution for presently used solution, which is considered to be deprecated. This is being done as a part of strategy of SAP SE corporation for which the solution is designed. This ambition to develop and improve cloud portfolio of already existing applications of the company should lead to betterment of already existing applications of this type and in a long run an improvement of the company’s market position as well as it’s products. The thesis is divided into 3 parts. It begins with a description of theoretical concepts, tools and principles, which are then utilized in further chapters. The following chapter analyzes current state of the affairs, where it is illustrated, what the current solution looks like along with key parts of it. The final, 3rd chapter is dedicated to a description of implemented solution and it also closely describes key differences mentioned in chapter 2.

Oxymonads are a group of poorly studied protists living as intestinal endosymbionts in the gut of insects and vertebrates. In this thesis I focused on the study of phylogeny, genomics and cell biology of oxymonads. Using culture-based approaches, we uncovered the hidden diversity of small oxymonads and described one new genus and six new species. In Monocercomonoides exilis, the only oxymonad with a published genome, we investigated the genome organization using fluorescence in situ hybdridization (FISH) against the telomeric regions and single-copy genes. Our results show that the genome is most probably haploid being organized in 6-7 chromosomes. Annotation of the genome revealed that the DNA replication and repair mechanisms in M. exilis are canonical and they seem more complete than those of other metamonads whose genomes are available. Although M. exilis lacks in any traces of mitochondria, its genome annotation revealed that other cellular systems do not markedly differ from other eukaryotes. Our taxon-rich phylogenetic analyses suggested that the genus Monocercomonoides is closely related to the oxymonad Streblomastix strix, which is found exclusively in the gut of the termites. Streblomastix strix, as opposed to M. exilis, is highly adapted to harbour bacterial ectosymbionts. Since S. strix...

Talaromyces versatilis est un champignon filamenteux d’intérêt industriel grâce à sa capacité deproduction d’enzymes hydrolytiques. La Société Adisseo commercialise un cocktail enzymatiqueproduit par fermentation à partir de T. versatilis, sous le nom de Rovabio™. Ce cocktail est utilisé entant qu'additif alimentaire en nutrition animale, car la grande variété d'enzymes hydrolytiques qu’ilcontient peut dégrader les polysaccharides présents dans l’enveloppe des céréales, améliorant ainsila digestibilité la valeur nutritionnelle des matières premières agricoles. Malgré les efforts consentispour mieux connaître la biologie de T. versatilis, très peu est connu sur ce champignon.L’étudeprésentée ici vise à décrire les réseaux de régulation qui contrôlent l’expression des gènes codantpour ces enzymes hydrolytiques, en utilisant des approches génomiques et transcriptomiques.Avoir accès à une annotation correcte de la séquence génomique et posséder les outilsnécessaires pour l'ingénierie génétique sont essentiels pour réaliser des études de génomiquefonctionnelle. Donc, le premier volet de cette thèse a été l’analyse de la séquence génomique et lacuration manuelle de l'annotation, ce qui nous a conduits à évaluer le vaste potentiel génétique de T.versatilis pour la production et la sécrétion d'enzymes hydrolytiques impliquées dans la dégradationde la lignocellulose. Deuxièmement, un système de délétion des gènes initialement conçu pourAspergillus niger a été adapté à T. versatilis. Cette méthode permet le recyclage du marqueur desélection et est efficace dans des souches dont le système NHEJ est actif (Delmas, et al., 2014, AEM).Au cours de ce travail, deux mutants de délétion de T. versatilis ont été obtenus: ΔxlnR et ΔclrA.La première approche mise en place pour avoir une meilleure compréhension des réseaux derégulation via une vue globale du transcriptome, fut l’utilisation de la technique de RNAseq sur troiséchantillons issus de la souche sauvage de T. versatilis exposée au glucose, à la paille de blé et auglucose et paille de blé simultanément comme sources de carbone, respectivement. Les données ontmontré une augmentation massive des niveaux d’expression de nombreux gènes, en particulier ceuxcodant pour des enzymes hydrolytiques, lorsque le mycélium est exposé à la lignocellulose. Enfin, la dernière partie du projet s’est appuyée sur la la RT-qPCR, technique appropriée pourétudier un nombre limité de gènes dans une grande variété de conditions. Toutefois la normalisationdes données est une étape essentielle du flux de travail qui peut conduire à une interprétationbiologique incorrecte de la régulation des gènes. Le travail effectué sur les données de RNAseq nousa amené à reconsidérer la nature des gènes de référence classiquement utilisés, puisque la plupartd'entre eux présentaient des changements d'expression considérables en présence de lignocellulose.En conséquence, un nouvel ensemble de gènes de référence putatifs a été identifié et la stabilité deleur expression validée par RT-qPCR chez T. versatilis cultivé dans plus de 30 conditions différentes.Des jeux de données de RNAseq de 18 champignons filamenteux phylogénétiquement éloignés ontpar ailleurs été collectés, afin de démontrer que la sélection des gènes candidats pour lanormalisation des données de RT-qPCR chez T. versatilis peut être étendue à d'autres champignons(Llanos et al., 2014, BMC Genomics). Ces aspects méthodologiques validés, nous avons enfin réaliséune étude plus détaillée de la transcription d'un groupe de gènes d'intérêt par RT-qPCR, dans unegrande variété de conditions et 2 souches différentes, la souche sauvage et la mutante ΔxlnR.L'analyse de ces données a permis d'identifier des gènes aux profils d'expression similaires, quirépondent de la même façon aux substrats inducteurs et qui partagent probablement les mêmesmécanismes de régulation. / Talaromyces versatilis is an industrially important enzymes producing filamentous fungus.Adisseo Company commercializes the enzymatic cocktail, produced from T. versatilis fermentation,with the name of Rovabio™. This cocktail is applied as an animal feed additive as it contains a widevariety of hydrolytic enzymes that can degrade the polysaccharides present in the seed-coat and thusimproves the digestibility and increases the nutritional value of the agricultural raw materials.Although efforts have been done to study different aspects of the biology of T. versatilis, very little isknown about this fungus. This study aimed to describe the regulatory networks of genes encodingplant cell wall-degrading enzymes from this biotechnologically important fungus using genomic andtranscriptomic approaches.Having a correct annotation of the genomic sequence together with efficient tools for genomeengineering are essential for downstream functional genomics works and characterization of theregulatory networks. Therefore, the first task carried out an analysis of the genomic sequence and amanual curation of the annotation, which led us to assess the vast genetic potential of T. versatilis forthe production and secretion of hydrolytic enzymes involved in the degradation of lignocellulosicmaterials. Secondly, I adapted a gene deletion system initially designed for Aspergillus niger. Thismethod allows recycling of the selection marker and is efficient in a non-homologous end-joining(NHEJ)-proficient strain (Delmas, Llanos et al., 2014, AEM). During this work, two deletion mutants ofT. versatilis were obtained: ΔxlnR and ΔclrA.Towards better understanding of the regulatory network, I first contributed to an RNAseq-basedtranscriptomic study that was performed on the wild type strain of T. versatilis exposed to glucoseand wheat straw as carbon sources. The data showed a massive increase in transcript levels ofnumerous genes, in particular those encoding hydrolytic enzymes, when the mycelium wasincubated with lignocellulose.If RT-qPCR is indeed a suitable technique to study a limited number of genes in a large variety ofconditions, data normalisation is a critical step of the workflow that can lead to incorrect biologicalinterpretation of gene regulation. The work done on the RNA-seq data led me to reconsider the useof the classical reference genes, since most of them exhibited expression changes in the presence oflignocellulosic substrate. I therefore identified a new set of putative reference genes and validatedtheir expression stability by RT-qPCR in T. versatilis cultivated under more than 30 differentconditions. Then, I collected about a hundred RNA-seq datasets from 18 phylogenetically distantfilamentous fungi, to demonstrate that the use of the suitable candidates for RT-qPCR datanormalisation in T. versatilis can be extended to other fungi (Llanos et al., 2014 BMC genomics (minorrevisions)). Thereafter, I performed a more detailed RT-qPCR based transcriptional study of a groupof genes of interest, in a wide variety of conditions and in 2 strains, the wild-type and the ΔxlnRmutant. The analysis of expression data of the genes of interest allowed to identify genes with similarexpression patterns, which probably share the same regulatory mechanisms and also the substratesthat act as inducers for their expression