Candidate virulence genes were sought through the genetic analyses of two strains of Mycobacterium tuberculosis, one virulent, H37Rv, one attenuated, H37Ra. Derived from the same parent, H37, genomic differences between strains were first examined via two-dimensional DNA technologies: two-dimensional bacterial genome display, and bacterial comparative genomic hybridisation. The two-dimensional technologies were optimised for mycobacterial use, but failed to yield reproducible genomic differences between the two strains. Expression differences between strains during their infection of murine bone-marrow-derived macrophages were then assessed using Bacterial Artificial Chromosome Fingerprint Arrays. This technique successfully identified expression differences between intracellular M. tuberculosis H37Ra and H37Rv, and six candidate genes were confirmed via quantitative real-time PCR for their differential expression at 168 hours post-infection. Genes identified to be upregulated in the attenuated H37Ra were frdB, frdC, and frdD. Genes upregulated in the virulent H37Rv were pks2, aceE, and Rv1571. Further qPCR analysis of these genes at 4 and 96h post-infection revealed that the frd operon (encoding for the fumarate reductase enzyme complex or FRD) was expressed at higher levels in the virulent H37Rv at earlier time points while the expression of aceE and pks2 was higher in the virulent strain throughout the course of infection. Assessment of frd transcripts in oxygen-limited cultures of M. tuberculosis H37Ra and H37Rv showed that the attenuated strain displayed a lag in frdA and frdB expression at the onset of culture when compared to microaerophilic cultures of H37Rv and aerated cultures of H37Ra. Furthermore, inhibition of the fumarate reductase complex in intracellular bacteria resulted in a significant reduction of intracellular growth. Microarray technology was also applied in the expression analysis of intracellular bacteria at 168h post-infection. Forty-eight genes were revealed to be differentially expressed between the H37Ra and H37Rv strains, and a subset were further analysed via qPCR to confirm and validate the microarray data. phoP was expressed at a lower level in the attenuated M. tuberculosis H37Ra, whereas members of the phoPR regulon were up-regulated in the virulent H37Rv. Additionally, a group of genes (Rv3616c-Rv3613c) that may associate with the region of difference 1 were also up-regulated in the virulent H37Rv.

This study analyzes the economic impact of a recent gene marker innovation for seedstock selection in beef cattle. Gene markers are being developed for many beef cattle attributes; this study focused on the tenderness quality of beef using two categories: tender and tough. The study begins by describing conventional procedures for seedstock selection, the science which underlies selection by gene markers and other non-genetic procedures currently being used to improve beef tenderness. After describing the commercialization of the gene marker innovation, a stylized model of a beef supply chain is constructed. The supply chain consists of a representative consumer, a producer/processor group and a monopolist supplier of the patented technology. Welfare changes resulting from the adoption of the innovation were simulated using four sets of demand elasticity data from literatures. An important focus of this research is determining how the economic surplus from the innovation will be shared by consumers, producers and the gene marker monopolist. The consumer and gene marker monopolist benefit from the technology unless the marginal and fixed cost variables (not estimated in this study) of the monopolist, are excessively high. Producer surplus was simulated as positive with three of the four elasticity data sets. The share of surplus capture by producers is generally low relative to the gains captured by consumers and the gene marker monopolist. Comparative static analysis reveal that the benefit from the innovation varies across breeds, being higher for breeds in which the favorable form of the marker gene is more likely to be present. Despite the apparent benefits of the innovation for beef supply chain participants, reported interviews with industry scientists reveal that markers should not be viewed as a replacement for conventional selection techniques. Indeed, selecting seedstock on the basis of a small number of available markers is not likely to produce the benefits that are currently being promised by life science companies. Consequently, this study recommends that the innovation be incorporated into existing seedstock selection practices. Much more analysis is needed to understand the full economic impact of gene markers for beef tenderness and for other beef quality attributes.

Thesis (Ph. D.)--University of Hong Kong, 2007. / Title proper from title frame. Also available in printed format.

Dissertation (Ph.D.).--University of Texas Graduate School of Biomedical Sciences at San Antonio, 2006. / Vita. Includes bibliographical references.

Thesis (M. Med. Sc.)--University of Hong Kong, 2006.

Thesis (Ph.D.)--York University, 2002. Graduate Programme in Psychology. / Typescript. Includes bibliographical references (leaves 63-76). Also available on the Internet. MODE OF ACCESS via web browser by entering the following URL: http://wwwlib.umi.com/cr/yorku/fullcit?pNQ99177

Resumo: Xanthomonas axonopodis pv. citri (Xac) constitui um dos principais patógenos da citricultura mundial. Essa litobactéria causa cancro em folhas. ramos e frutos de citros em geral. ocasionando grandes perda econômicas anuais. A fim de estudar a interação dessa bactéria com seu hospedeiro empregou-se a análise de mutantes e da expressão gênica global por meio de microarranjos de DNA (transcrissoma). Na primeira parte do estudo foi obtida uma biblioteca de cerca de 10.000 Illutantes do isolado 306 de Xac. Desses. 3.300 foram inoculados em folhas de limoeiro cravo e sua capacidade em causar cancro cítrico foi avaliada aos três dias da inoculação. Após quatro inoculaçàes. 56 mutantes foram selecionados por apresentarem virulência alterada e suas ORFs interrompidas foram identificadas por meio de seqüenciamento. Uma análise dessas ORFs mostrou que havia tanto ORFs quc codificavam para genes relacionados com a patogenicidade em fitobactérias como possihilitou identificar novos genes associados à infecção. além de ORFs hipotéticas. para as quais ainda não foi atrihuída nenhuma função. Dentre os genes previamente implicados na patogênese. pode-se citar o gene "rpB4. o qual participa do sistema de secreção do tipo três. Já o gene hrlA. que contribui na virulência de algumas bactérias patogênicas de animais. até o presente ainda não tinha sido relatado como tendo importância no processo de patogênese em fitobactérias. A ORF XACO~40 é um exemplo de uma proteína hipotética que interfere significativamente no processo infeccioso. uma vez que o mutante para esse locos não induziu sintomas da doença. assim como os demais mutantes citados acima. Na segunda parte deste trabalho. produziu-se um microarranjo de DNA contendo 6.9 I 2 sondas imobilizadas (2.673 ORFs. 87 ORFs repetidas. 312 controles negativos e X4 controles positivos...(Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Xanthomonas axonopodis pv. citri constitutes one of the main and most damaging pathogcn of lhe world-wide citriculture. This phytobacteria causes canker in leaves, branches and fruits of citrus. causing scvcre cconomic losses. In order to study the interaction of this bacterium with its citrus host. two approaches had been used to proceed a post-genomic functional analysis: wholc genol11c mutagcncsis and global expression analysis by cDNA microarrays technique. In the first part of this study a Xac 306 mutants library with '" 10,000 mutants was obtained. From thesc. 3.300 wcrc inoculatcd in mexicam lemon tree leaves and its capacity to cause citrus canker was cvalualcd. Aftcr four inoculation cicIes, 56 mutants had been selected as having modified palhogcnicily. The inlcrruplcd ORFs were identified by DNA sequencing and analysis of these ORFs identificd ORFs coding for genes previously known as related to pathogenicity proccss in phytobactcrilll11 as wcll gcnes not yet described as involved in pathogenicity, incIuding hypothetical gcncs. Al110ng the gencs previously known as implied in pathogens attack, the hrpB4 gene is one that was found, whic participates of the type three secretion system. To the hrtA gene, whose participation in the virulcnce process has been described to some animal pathogenic bacteria but never yet as having a role in to pathogenicity process in phytobacteria, was found to be involved in the pathogenicity of Xac. The ORF XAC0340 is an example of hypothetical protein which presents grcat intcrfcrcncc in thc infcctious process: the mutant for this gene does not induce any diseasc sYl11ploms in citric Icaves...(Complete abstract, click electronic access below) / Orientador: Jesus Aparecido Ferro / Coorientador: Julio Cezar Franco de Oliveira / Banca: Acelino Couto Alfenas / Banca: Shaker Chuck Parah / Banca: Eliana Gertrudes Macedo Lemos / Banca: Maria Helena de Souza Goldman / Doutor

L'objectif de notre thèse est d'appliquer la génomique en temps réel pour déchiffrer les caractéristiques génomiques bactériennes et les événements de recombinaison du génome des bactéries atypiques ainsi que leur impact sur les maladies infectieuses. Au cours de ma thèse, nous avons effectué une revue sur les outils bioinformatiques les plus courants utilisés en microbiologie clinique et mis en évidence l’impact de la recombinaison sur le comportement des bacteries. Le deuxième projet de notre thèse est de déchiffrer une epidémis de Staphylococcus saprophyticus causant des infections urinaires en utilisant la technologie MALDI-TOF MS et une analyse comparative du génome de S. saprophyticus pour comprendre leur évolution génomique. Nous avons démontré qu'il existe un groupe de S. saprophyticus géographiquement restreint à Marseille comparé au souches de Nice. De plus, nous avons montré que S. saprophyticus qui était initialement considéré comme une bactérie saprophyte a evolué pour devenir une bactérie pathogène à travers des recombinaisons massives et des « single nucleotide polymorphism », résultant d'une perte significative de gènes. Le troisième projet de notre thèse est une analyse comparative des génomes d'Enterococcus faecalis et d'E.faecium isolé chez l'homme, les animaux et l'environnement pour déchiffrer la différence de propagation et l'acquisition de déterminants antimicrobiens. Nous avons démontré qu'il existe une association directe entre l'absence de système CRISPR, la présence du gène ardA et l'acquisition de gènes de résistance à la vancomycine, qui différencient E. faecalis de E. faecium. Enfin nous avons decrit un nouveau genre bacterien Nissabacter. / The objective of our thesis is to applied the Real-time genomic approaches to decipher bacterial genomic features and genome recombination events of atypical bacteria and their impact on infectious diseases. During my thesis, we have reviewed the most common bioinformatics tools applicable in clinical microbiology and highlight how bacterial genome recombination have impacted their behaviour. The second project of our PhD is to decipher a community outbreak of Staphylococcus saprophyticus involved in (UTI) using MALDI-TOF MS technology and a comparative genome analysis of clinical and non-clinical S. saprophyticus to understand their genomic evolution. We demonstrated that there is a geographically restricted cluster of S. saprophyticus circulating in Marseille community as compared to Nice. Moreover, we showed that S. saprophyticus which was initially considered as a saprophytic bacterium has drifted to becoming a pathogenic bacterium through massive genome recombination and single nucleotide polymorphism events, resulting from a significant loss of genes. The third project of our work is a comparative genome evolutionary analysis of Enterococcus faecalis and Enterococcus faecium isolated from human, animals, and environment to decipher the difference in spread and the acquisition of antimicrobial determinants. We demonstrated that there is a direct association between the absence of CRISPR system, the presence of gene ardA and the acquisition of vancomycin resistance genes, which differentiate E. faecalis from E. faecium. Our final project was focused on the discovering of a new genus Nissabacter and its description.

Made available in DSpace on 2014-06-11T19:32:17Z (GMT). No. of bitstreams: 0 Previous issue date: 2007-02-26Bitstream added on 2014-06-13T19:21:47Z : No. of bitstreams: 1 laia_ml_dr_jabo_prot.pdf: 9478549 bytes, checksum: f92e822aa9f06920bc2065ca991c0323 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Xanthomonas axonopodis pv. citri (Xac) constitui um dos principais patógenos da citricultura mundial. Essa litobactéria causa cancro em folhas. ramos e frutos de citros em geral. ocasionando grandes perda econômicas anuais. A fim de estudar a interação dessa bactéria com seu hospedeiro empregou-se a análise de mutantes e da expressão gênica global por meio de microarranjos de DNA (transcrissoma). Na primeira parte do estudo foi obtida uma biblioteca de cerca de 10.000 Illutantes do isolado 306 de Xac. Desses. 3.300 foram inoculados em folhas de limoeiro cravo e sua capacidade em causar cancro cítrico foi avaliada aos três dias da inoculação. Após quatro inoculaçàes. 56 mutantes foram selecionados por apresentarem virulência alterada e suas ORFs interrompidas foram identificadas por meio de seqüenciamento. Uma análise dessas ORFs mostrou que havia tanto ORFs quc codificavam para genes relacionados com a patogenicidade em fitobactérias como possihilitou identificar novos genes associados à infecção. além de ORFs hipotéticas. para as quais ainda não foi atrihuída nenhuma função. Dentre os genes previamente implicados na patogênese. pode-se citar o gene rpB4. o qual participa do sistema de secreção do tipo três. Já o gene hrlA. que contribui na virulência de algumas bactérias patogênicas de animais. até o presente ainda não tinha sido relatado como tendo importância no processo de patogênese em fitobactérias. A ORF XACO~40 é um exemplo de uma proteína hipotética que interfere significativamente no processo infeccioso. uma vez que o mutante para esse locos não induziu sintomas da doença. assim como os demais mutantes citados acima. Na segunda parte deste trabalho. produziu-se um microarranjo de DNA contendo 6.9 I 2 sondas imobilizadas (2.673 ORFs. 87 ORFs repetidas. 312 controles negativos e X4 controles positivos... / Xanthomonas axonopodis pv. citri constitutes one of the main and most damaging pathogcn of lhe world-wide citriculture. This phytobacteria causes canker in leaves, branches and fruits of citrus. causing scvcre cconomic losses. In order to study the interaction of this bacterium with its citrus host. two approaches had been used to proceed a post-genomic functional analysis: wholc genol11c mutagcncsis and global expression analysis by cDNA microarrays technique. In the first part of this study a Xac 306 mutants library with ' 10,000 mutants was obtained. From thesc. 3.300 wcrc inoculatcd in mexicam lemon tree leaves and its capacity to cause citrus canker was cvalualcd. Aftcr four inoculation cicIes, 56 mutants had been selected as having modified palhogcnicily. The inlcrruplcd ORFs were identified by DNA sequencing and analysis of these ORFs identificd ORFs coding for genes previously known as related to pathogenicity proccss in phytobactcrilll11 as wcll gcnes not yet described as involved in pathogenicity, incIuding hypothetical gcncs. Al110ng the gencs previously known as implied in pathogens attack, the hrpB4 gene is one that was found, whic participates of the type three secretion system. To the hrtA gene, whose participation in the virulcnce process has been described to some animal pathogenic bacteria but never yet as having a role in to pathogenicity process in phytobacteria, was found to be involved in the pathogenicity of Xac. The ORF XAC0340 is an example of hypothetical protein which presents grcat intcrfcrcncc in thc infcctious process: the mutant for this gene does not induce any diseasc sYl11ploms in citric Icaves...(Complete abstract, click electronic access below)

abstract: Genomic structural variation (SV) is defined as gross alterations in the genome broadly classified as insertions/duplications, deletions inversions and translocations. DNA sequencing ushered structural variant discovery beyond laboratory detection techniques to high resolution informatics approaches. Bioinformatics tools for computational discovery of SVs however are still missing variants in the complex cancer genome. This study aimed to define genomic context leading to tool failure and design novel algorithm addressing this context. Methods: The study tested the widely held but unproven hypothesis that tools fail to detect variants which lie in repeat regions. Publicly available 1000-Genomes dataset with experimentally validated variants was tested with SVDetect-tool for presence of true positives (TP) SVs versus false negative (FN) SVs, expecting that FNs would be overrepresented in repeat regions. Further, the novel algorithm designed to informatically capture the biological etiology of translocations (non-allelic homologous recombination and 3&ndashD; placement of chromosomes in cells –context) was tested using simulated dataset. Translocations were created in known translocation hotspots and the novel&ndashalgorithm; tool compared with SVDetect and BreakDancer. Results: 53% of false negative (FN) deletions were within repeat structure compared to 81% true positive (TP) deletions. Similarly, 33% FN insertions versus 42% TP, 26% FN duplication versus 57% TP and 54% FN novel sequences versus 62% TP were within repeats. Repeat structure was not driving the tool's inability to detect variants and could not be used as context. The novel algorithm with a redefined context, when tested against SVDetect and BreakDancer was able to detect 10/10 simulated translocations with 30X coverage dataset and 100% allele frequency, while SVDetect captured 4/10 and BreakDancer detected 6/10. For 15X coverage dataset with 100% allele frequency, novel algorithm was able to detect all ten translocations albeit with fewer reads supporting the same. BreakDancer detected 4/10 and SVDetect detected 2/10 Conclusion: This study showed that presence of repetitive elements in general within a structural variant did not influence the tool's ability to capture it. This context-based algorithm proved better than current tools even with half the genome coverage than accepted protocol and provides an important first step for novel translocation discovery in cancer genome. / Dissertation/Thesis / Ph.D. Biomedical Informatics 2014