Le cytomégalovirus humain (CMV) appartient à la sous-famille des Betaherpès virus. L’homme est son seul réservoir et il infecte 40 à 90% de la population mondiale. Ce virus, rarement dangereux pour le sujet immunocompétent, représente une réelle menace chez le patient immunodéprimé comme le transplanté d’organe. Après la primo-infection, le CMV diffuse dans tout l’organisme et alterne des phases de latence et de réactivation. Il consacre 20% de son génome à diverses stratégies d’échappement immunitaire.Les objectifs de notre travail sont de décrire dans une première partie 1- la variabilité de six gènes, codant quatre protéines immunomodulatrices (UL18, UL40, UL111a et US3) et deux protéines immunodominantes (IE1 et pp65), dans des souches de CMV directement séquencées à partir de sang total ou du LBA de patients infectés et immunodéprimés, 2- le mécanisme conduisant à cette variabilité 3- la répartition des souches virales dans le sang total et le LBA (compartimentation).La deuxième partie est consacrée à l’expression de la protéine immunomodulatrice pUL40.Nos travaux ont permis de confirmer l’existence d’un polymorphisme notable, supérieur à ce qui est déjà décrit. Des conséquences fonctionnelles pourraient en découler dans les protéines correspondantes. L’étude in silico de la variabilité du CMV met en lumière le rôle clé de la recombinaison comme mécanisme évolutif majeur. Nous n’avons pas mis en évidence de compartimentation des souches virales dans les échantillons analysés.Nos résultats préliminaires indiquent la faisabilité de la sur-expression de la protéine pUL40, permettant ultérieurement de mieux comprendre ses fonctions. / Human Cytomegalovirus (CMV) belongs to the Betaherpesviruses sub-family. Human beings are its sole reservoir and it infects 40 to 90% of the world population. This virus is rarely dangerous for the immunocompetent host, but represents a problematic opportunistic agent in immunocompromised patients, such as transplant recipients. After primary infection, CMV spreads widely in the organism and alternates latency and reactivation phases. CMV dedicates 20% of its genome to various immune escape strategies.Our aims were to describe, in a first part, 1- the variability of six CMV genes, which encode 4 immunomodulatory proteins (UL18, UL40, UL111a and US3) and two immunodominant proteins (IE1 and pp65), after direct amplification and sequencing from whole blood and bronchoalveolar lavages (BAL) taken from infected immune compromised patients, 2- the mechanism responsible for this variability 3- the distribution of CMV strains in whole blood and BAL (compartmentalization).In a second part, we attempted pUL40 expression.Our results confirmed the existence of a noticeable polymorphism, superior to what was previously described. Functional consequences could arise for the corresponding proteins. Our in silico study of CMV variation indicated a key role for recombination as a major evolutionary mechanism. We have observed little CMV compartmentalization among the investigated samples. Our preliminary results indicated pUL40 may be over-expressed, which could allow a better understanding of its functions in a near future.

Orientador: Reginaldo Palazzo Júnior / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia Elétrica e de Computação / Made available in DSpace on 2018-08-18T18:43:43Z (GMT). No. of bitstreams: 1 Faria_LuzineteCristinaBonanide_D.pdf: 17107444 bytes, checksum: 4faf2de7876247b3c74423dc7a3043d1 (MD5) Previous issue date: 2011 / Resumo: Um dos grandes desafios da comunidade científica em teorias da informação genética, comunicação genética e codificação genética é verificar a existência de uma estrutura matemática relacionada com a estrutura do DNA. Este trabalho propõe modelos para o sistema de comunicação de informação genética e genômica análogos ao modelo de um sistema de comunicação digital. Ambos os modelos são capazes de identificar, reproduzir e classificar matematicamente diferentes sequências de DNA. O primeiro identifica e reproduz a sequência de nucleotídeos de uma fita simples do DNA através da codificação genética e, o segundo identifica e reproduz a sequência das bases complementares da fita dupla do DNA através da codificação genômica. Os objetivos principais do presente trabalho são: a) caracterização matemática dos modelos de codificação genética e codificação genômica, b) proposta de um algoritmo para identificação de sequências de DNA; c) mostrar que sequências de DNA com características biológicas distintas, incluindo proteínas, gene e genoma em termos das fitas simples do DNA e da dupla hélice do DNA são identificadas como palavras-código dos códigos G-linearidade (BCH sobre corpos e BCH sobre anéis), reproduzidas e classificadas matematicamente, d) representação algébrica via polinômios primitivos/geradores e seus polinômios recíprocos das fitas simples do DNA (fita codante e fita não codante) e da dupla hélice do DNA, e) mostrar a existência de códigos concatenados (nested codes) entre algumas sequências de direcionamento e suas respectivas proteínas organelares, f) mostrar a arquitetura biológica (Biological frame) do genoma do plasmídeo Lactococcus lactis. Os resultados apresentados neste trabalho contribuem para o desenvolvimento de uma metodologia que poderá ser aplicada em análises mutacionais e de polimorfismos, produção de novos fármacos, melhoramento genético, entre outros, reduzindo tempo e custos laboratoriais / Abstract: One of the great challenges of the scientific community on theories of genetic information, genetic communication and genetic coding is to determine a mathematical structure related to the structure of DNA. This thesis proposes a model of a communication system for genetic and genomic information similar to the model of a digital communication system. Both models are able to identify, reproduce and classify mathematically different sequences of DNA. The first model identifies and reproduces the nucleotide sequence of a single DNA strand via the genetic encoding. The latter identifies and reproduces the sequence of the complementary bases of the double DNA strand through genomic encoding. The aims of this work are: a) a mathematical characterization of the models of genetic coding and genomic coding, b) the proposal of an algorithm for the identification of DNA sequences, c) to show that DNA sequences with distinct biological characteristics, including protein, gene and genome in terms of the single strands of DNA and of the double helix of DNA are identified as codewords of the G-linearity codes (BCH codes over fields and BCH codes over rings), mathematically reproduced and classified, d) algebraic representation via primitive/generator polynomials and their reciprocal polynomials of single DNA strands (coding strand and non-coding strand) and the double DNA strand, e) to show the existence of concatenated codes (nested codes) between some targeting sequences and their corresponding organelles proteins, f) to show the biological architecture (Biological frame) of the plasmid Lactococcus lactis genome. The results presented in this work contribute to the development of a methodology that can be applied to mutational analysis and polymorphisms, production of new drugs, genetic improvement, among others, reducing time and laboratory costs / Doutorado / Telecomunicações e Telemática / Doutor em Engenharia Elétrica

O Papel da 1,25(OH)2D3 (VD3) ou calcitriol, o metabolito ativo da Vitamina D, em câncer de mama tem sido extremamente explorado. Os efeitos antiproliferativos, prodiferenciativos e antiinflamatórios da VD3 são bem documentados na literatura. Análises de microarray vêm auxiliando a identificação de vários genes responsivos e modulados pela VD3 e seus análogos. A maioria desses genes apresentados na literatura é proveniente de estudos utilizando linhagens celulares de câncer de mama ou modelos animais. Pouco é sabido sobre a ação da VD3 em outros tipos celulares constituintes do microambiente tumoral. Fibroblasto associado ao câncer (FAC), o principal componente do microambiente tumoral, apresenta um papel central no complexo processo de interação entre tumor e estroma e consequentemente em todos os passos envolvidos na tumorigênese. O objetivo do nosso estudo foi identificar genes chaves regulados pela VD3 em fibroblastos associados ao câncer de mama. Para isso, culturas primárias de fibroblastos provenientes de cinco amostras de carcinoma mamário ductal invasivo foram estabelecidas e posteriormente caracterizadas fenotipicamente por um conjunto de marcadores. Após a confirmação da presença de receptor de vitamina D, os fibroblastos de cada amostra foram divididos em três grupos: um grupo controle e grupos de tratamento com 0,5 nM e 100 nM de VD3 durante 24 horas. A determinação do perfil de expressão gênica foi realizado utilizando tecnologia de oligo microarray com o GeneChip Human Genome U133 Plus 2.0 (Affymetrix). Foram obtidos 274 genes diferentemente expressos entre os grupos controle e tratamento com 0,5 nM de VD3, muitos deles envolvidos em processos como apoptose e migração celular. Os 161 genes diferentemente expressos obtidos a partir da comparação entre grupos controle e tratamento com 100 nM de VD3 apresentaram-se funcionalmente envolvidos em diversos processos biológicos, sendo que os mais significativos processos regulados pela VD3 em fibroblastos associados ao câncer de mama foram respostas inflamatória e imune, sugerindo que a ação antiinflamatória da VD3, anteriormente relatada em estudos utilizando células epiteliais de câncer de mama, pode também ser aplicada a fibroblastos associados ao câncer de mama / The role of 1,25(OH)2D3 (calcitriol), the active metabolite of Vitamin D, in breast cancer has been extremely explored. Antiproliferative, prodifferentiating and anti-inflammatory effects of calcitriol have been reported in breast cancer. Expression profile by microarray analysis has identified many responsive genes modulated by calcitriol and analogs. The majority of them defined to date are based on studies using breast cancer cell lines or mouse models. Little is known about the action of calcitriol in the others cell types present into the tumor microenvironment. Cancerassociated fibroblasts (CAFs), the principal cell component of the tumor microenvironment, play a central role in the complex process of tumour stroma interaction and consequently in all breast cancer tumorigenesis steps. The aim of our study was to identify key genes that are regulated by calcitriol in breast cancer associated fibroblasts. Primary fibroblasts cell cultures from five breast cancer samples were established and then phenotyping characterized by a set of markers. The occurrence of vitamin D receptor was confirmed in all samples and fibroblasts were divided in three groups: one control group and two treatment groups, 0.5 nM and 100 nM of calcitriol during 24 hours. The determination of gene expression profile was performed by oligo microarray technology using the GeneChip Human Genome U133 Plus 2.0 (Affymetrix). Control and 0.5 nM calcitriol analysis resulted in 274 differentially expressed genes, many of then involved in biological processes as apoptosis and cell migration. The 161 differentially expressed genes obtained from comparison between groups control and 100 nM calcitriol treatment were functionally involved in several biological processes. The most significantive processes regulated by VD3 in breast CAFs were the inflammatory and immune responses, suggesting that the anti-inflammatory action of calcitriol, yet reported in several studies using epithelial breast cancer cells, may also been applied to breast cancer associated fibroblasts

La sclérose en plaques (SEP) est une maladie neurologique chronique du jeune adulte affectant environ 100 000 personnes en France. Au cours des deux dernières décennies, les stratégies thérapeutiques ont fortement évolué avec l’apparition de nouvelles molécules dont les premières formes orales. Le parcours de soins dans la SEP implique plusieurs professionnels de santé médicaux (généralistes, neurologues) et paramédicaux (kinésithérapeutes, infirmiers). Actuellement, aucune recommandation sur ces parcours n’a été définie, et peu de données existent sur le recours aux soins des individus ayant une SEP et l’utilisation des traitements spécifiques à la SEP en France. L’utilisation des données du Système National des Données de Santé (SNDS), c’est-à-dire les bases de l'Assurance Maladie, couplée avec les méthodes d’analyse de séquences donne l’opportunité d’étudier ces parcours de soins. L’objectif principal de cette thèse était d’étudier les parcours de soins des personnes ayant une SEP en France, à partir du SNDS, afin de décrire les consommations de soins et de mettre en évidence une typologie de parcours. Les objectifs secondaires étaient d’étudier l’utilisation des traitements de fond de la SEP en France (fréquence et place dans la séquence thérapeutique), et d’étudier la faisabilité de mesurer le niveau de handicap moteur dans ces bases. Au total sur la période de suivi de 2010 à 2015, 112 745 patients ont été identifiés, dont 47,4% avaient reçu au moins une délivrance d’un traitement de fond spécifique à la SEP. Une typologie a été obtenue identifiant cinq groupes cliniquement distincts. En parallèle, un indicateur de quantification du niveau de handicap moteur, pouvant être répliqué dans d’autres études, a été proposé afin d’enrichir les données du SNDS. Au travers des différentes analyses réalisées et des questions méthodologiques soulevées, des éléments clés permettant l’utilisation des méthodes d’analyse de séquences en santé, notamment la multichannel sequence analysis, ont pu être mis en évidence. / Multiple sclerosis (MS) is a chronic neurological disease starting in young adulthood and affecting about 100,000 persons in France. During the last two decades, therapeutic practices have evolved with the release of new substances, especially oral disease-modifying therapies (DMTs). Care pathways in MS involve both medical (general practitioners, neurologists) and paramedical (physiotherapists and nurses) health care professionals. However, no recommendation on care pathways in MS exists so far in France. Moreover, few data are available on care-seeking of persons with MS (PwMS) and the utilization of DMTs in France. The use of state sequence analysis (SSA) on data issued from the French National Health Data System (SNDS, i.e. databases from the French Health Insurance System) offers the opportunity to study care pathways. The main objective of this PhD thesis was to study the care pathways of PwMS in France using data from SNDS, in order to describe care-seeking and to create a typology of pathways. The secondary objectives were to study MS DMTs utilization in France (frequency and therapeutic sequences), and the feasibility to measure the level of motor disability in SNDS. Over the 2010-2015 study period, 112,745 PwMS were identified. Amongst them, 47.4% had at least one delivery of a MS-specific DMT. A typology was obtained allowing the identification of five clinically distinct groups of patients. In parallel, a parameter quantifying the level of motor disability in SNDS, which could be replicated in other studies, was defined. Thanks to the different analyses and raised methodological questions, key-elements allowing the use of SSA in health field, especially multichannel sequence analysis, were highlighted.

Background: To allow an immediate treatment of an infection with suitable antibiotics and bactericides or fungicides, there is an urgent need for fast and precise identification of the causative human pathogens. Methods based on DNA sequence comparison like 16S rRNA analysis have become standard tools for pathogen verification. However, the distinction of closely related organisms remains a challenging task. To overcome such limitations, we identified a new genomic target sequence located in the single copy gene for tRNA nucleotidyltransferase fulfilling the requirements for a ubiquitous, yet highly specific DNA marker. In the present study, we demonstrate that this sequence marker has a higher discriminating potential than commonly used genotyping markers in pro- as well as eukaryotes, underscoring its applicability as an excellent diagnostic tool in infectology. Results: Based on phylogenetic analyses, a region within the gene for tRNA nucleotidyltransferase (CCA-adding enzyme) was identified as highly heterogeneous. As prominent examples for pro- and eukaryotic pathogens, several Vibrio and Aspergillus species were used for genotyping and identification in a multiplex PCR approach followed by gel electrophoresis and fluorescence-based product detection. Compared to rRNA analysis, the selected gene region of the tRNA nucleotidyltransferase revealed a seven to 30-fold higher distinction potential between closely related Vibrio or Aspergillus species, respectively. The obtained data exhibit a superb genome specificity in the diagnostic analysis. Even in the presence of a 1,000-fold excess of human genomic DNA, no unspecific amplicons were produced. Conclusions: These results indicate that a relatively short segment of the coding region for tRNA nucleotidyltransferase has a higher discriminatory potential than most established diagnostic DNA markers. Besides identifying microbial pathogens in infections, further possible applications of this new marker are food hygiene controls or metagenome analyses.

No description available.

<p>Heterosis, or hybrid vigor, is a phenomenon observed in both plant and animal systems where hybrid offspring perform better when compared to their parents. For hybrid plants, this can result in increased biomass, crop yields, and vigor when compared to the inbred parents. Even though heterosis has been used in agriculture for over a century, the molecular mechanisms that result in hybrid vigor remain elusive even after years of investigation. A molecular understanding of heterosis is desirable because it will speed up the process of breeding compatible inbred lines for developing hybrid seeds, and it will provide us with the knowledge to potentially engineer inbred lines that can mimic the beneficial phenotypic effects of heterosis, eliminating the need for farmers to buy new hybrid seeds every year. The goal of this research project is to identify genes that are required for heterotic phenotypes in maize. Our working hypothesis is that a mutation in genes that are essential for heterosis will cause an altered heterotic phenotype in hybrid maize plants. To test this hypothesis, we applied combined approaches of EMS mutagenesis, trait phenotyping in field and controlled conditions, bulk segregant analysis, whole genome sequencing, and bioinformatics analysis. First, we applied a forward genetics approach to identify mutant hybrids with altered heterosis and detected potential causal genes <em>via</em> whole genome sequencing. We identified one mutation occurring in a protein coding gene (gene ID <em>Zm00001eb305590</em>) located in a region of interest on chromosome 7, whose genotypes across various samples assayed fit the observed segregation pattern of hybrid traits. This mutation leads to a moderate or high-level codon change, indicating that this gene may play a role in mediating heterosis in maize. By investigating this gene with further studies, the learned knowledge could speed up the process of hybrid maize breeding by selecting compatible inbred lines through sequencing or by engineering hybrids that have favorable alleles for this gene.</p>

No description available.

<p>  </p> <p>Microbiome studies are varied and involve the examination of microorganisms at different levels: individual cells to determine individual functions, populations of specific microorganisms to determine interactions between organisms, and/or communities of microorganisms for a broader investigation of interactions between organism and environment. These studies are typically done within the context of a particular niche or environment. There are two parts to this dissertation, separated by the types of research involved. First, the analysis of bacterial communities using 16S rRNA sequencing and analysis. In this first part the bacterial communities of the reproductive tract of bulls and the gastrointestinal tract of weanling pigs were studied. The reproductive organs of the male, domestic species had not been studied from an ecological perspective prior to the study. As such, the research was mainly focused on characterizing the bacterial communities found within the prepuce of bulls that were considered to be healthy, or that the breeding soundness exam was satisfactory and the bulls had no clinical disease in the urogenital tract. Through this study two distinct types of bacterial communities were found based on the diversity of the observed taxa; the groups were split into a low diversity group identified by the presence of <em>Bradyrhizobium</em> and a high diversity group distinguished by the abundance of mucosal-associated bacteria found in oral, respiratory, and vaginal communities of cattle. Second, the effects of supplementary, soluble fiber on the intestinal bacterial communities of piglets pre- and/or post-weaning were studied. The rationale behind this study was to determine if pre-weaning fiber could alter the microbiome prior to weaning and the change of diet from liquid to solid. Pre-weaning, supplementary, soluble fiber was found to increase short-chain fatty acid concentrations and bacterial taxa potentially involved in their production. Additionally, bacterial taxa implicated in an increased inflammatory response were reduced in groups fed supplementary fiber. Taken together, the two bacterial community studies highlight the gaps in knowledge for reproductive communities in male animals as well as the potential for reducing weaning stress in pigs. Part two of this dissertation focuses on whole genome sequence analysis as a way to study bacterial populations associated with bovine respiratory disease (BRD), a common and potentially fatal disease in cattle. Identification of BRD has low accuracy and the presence of antibiotic resistant bacteria increases the chance of treatment failure. Using machine learning, the prediction of antibiotic resistance in bacterial isolates from animals with BRD was performed to find potential sequences for use in future molecular assays. While using known resistance genes was helpful for some antibiotics, several of the antibiotics used in treating BRD were better predicted using the machine learning models. Model output sequences should be further tested using molecular methods to determine function and importance before using as an assay target. Put together, the contents of this dissertation should serve as an introduction to bacterial ecology as well as how the concepts can be applied to food animal production systems.</p>

Angesichts von Rentenkürzungen hat Vermögen als Alternative zu gesetzlichen Renten zur Alterssicherung an Bedeutung zugenommen. Vermögen ist jedoch ungleicher zwischen Frauen und Männern verteilt als Einkommen, wobei Frauen ein durchschnittlich niedrigeres Vermögen haben. Diese Ungleichheit existiert auch innerhalb von Paarbeziehungen. Diese Dissertation untersucht, wie Erwerbs- und Ehebiografien mit dem persönlichen Vermögen von verheirateten Frauen und Männern ab 50 Jahren zusammenhängen. Basierend auf der Lebensverlaufsperspektive entwickelt Kapitel 1 ein Modell zum Vermögensaufbau innerhalb von Paaren. Kapitel 2 untersucht Geschlechterunterschiede im individuellen Vermögensaufbau durch Erwerbstätigkeit in Ost- und Westdeutschland. Die Studie zeigt geschlechtsspezifische Wege des Vermögensaufbaus auf, welche sich besonders im traditionellen Wohlfahrtsstaatskontext von Westdeutschland zeigen. Kapitel 3 untersucht, wie Erwerbs- und Ehebiografien von Frauen mit der Verteilung von individuellem und gemeinsamem Vermögen innerhalb von älteren Ehepaaren in Westdeutschland zusammenhängen. Die Ergebnisse zeigen, dass früh verheiratete Paare starke wirtschaftliche Einheiten bilden. Jedoch kann die Ehe Frauen mit geringer Arbeitsmarktbeteiligung nicht vor ökonomischer Abhängigkeit von ihrem Partner im Alter schützen. Kapitel 4 analysiert den Zusammenhang zwischen den Erwerbsbiografien beider Partner und der Vermögensungleichheit innerhalb von älteren Ehepaaren in Großbritannien und Westdeutschland. Die Studie zeigt, dass eine ähnliche Arbeitsteilung zu unterschiedlicher Vermögensungleichheit innerhalb der Paare in beiden Ländern führt, was insbesondere durch die Rolle des Immobilienmarktes erklärt wird. Diese Dissertation verdeutlicht, dass das Zusammenwirken von Geschlecht, Partnerschaft und institutionellem Kontext während des Lebensverlaufs wichtig ist, um die Determinanten von persönlichem Vermögen und der resultierenden Vermögensungleichheit im Alter zu verstehen. / In light of pension reductions, the importance to accumulate wealth as an alternative to pensions for old-age provision has increased. However, wealth is more unequally distributed between genders than income, with women having lower average wealth levels than men. This is also the case in married couples. This dissertation examines how gendered life course experiences of employment and marriage are associated with the personal wealth of married women and men aged 50 and older. Building on the life course framework, Chapter 1 develops a model of personal wealth accumulation within couples. Chapter 2 examines gender differences in individual wealth accumulation through employment in Eastern and Western Germany. The results reveal gendered ways of wealth accumulation, indicating that similar career paths result in different personal wealth outcomes for women and men in the gender-unequal welfare state context of Western Germany. Chapter 3 examines how the interplay of women’s employment and marriage biographies is associated with the ownership structure of sole and joint assets within married couples in later life in Western Germany. The results indicate that early and stably married couples build strong economic units that hold most wealth jointly. However, marriage does not protect women with a low labour market attachment from economic dependency on the partner in old age. Chapter 4 examines the association between married partners’ employment biographies and the within-couple gender wealth gap in later life in Britain and Western Germany. The results indicate that a similar division of labour throughout the life course can result in different levels of within-couple gender wealth inequality in later life across country contexts, particularly depending on the housing system. Overall, this dissertation concludes that the interplay of gender, partnership, and institutional context is important to understand the outcomes of personal wealth accumulation processes.