The objective of this project was to investigate and determine the association between hospitalizations of respiratory diseases with one another and with isolations of viral infections in five age groups. Weekly data on all hospitalizations in Ontario, Canada, from week 14 of 2001 to week 13 of 2003 were obtained for 5 age groups (under 2 years, 2 to 4 years, 5 to 15 years, 16 to 49 years and over 50 years inclusive) for respiratory diseases including, asthma, respiratory tract infection (RTI) and chronic obstructive pulmonary disease (COPD)1. Furthermore, data for viral infections including influenza virus type A and type B (Flu AB) and respiratory syncytial virus (RSV) isolations were also obtained from Health Canada for the same weekly time periods. In order to test for independence and determine a relationship, if any, between hospitalizations of respiratory diseases with one another and with isolations of viral infections, structural time series models were developed for all age groups of the respiratory diseases and explanatory variables were modeled accordingly against the hospital admission counts for the respiratory diseases. These explanatory variables include, other respiratory diseases, viral infections, and lagged values of the dependent variable. Neither FLU AB nor RSV showed a significant relationship with asthma patients of all ages. Weekly RSV peaks coincided with RTI patients under 2 years and RTI peaks in patients 5 to 15 years preceded FLU AB peaks. A relationship between all three respiratory diseases, asthma RTI and COPD, was discovered for all age groups. Peaks of asthma coincided with various transformations of RTI peaks for the five age groups and peaks of COPD coincided with both the untransformed asthma and RTI peaks in patients over 50. For all other relationships, the null hypothesis of independence was accepted. These findings suggest that there is a strong association between respiratory diseases and that children and adults with respiratory diseases respond differently to viral infections. 1 Only data for patients over 50 years was obtained for COPD. / Thesis / Master of Science (MSc)

Philosophiae Doctor - PhD / The plasticity of single-stranded viral genomes permits the formation of secondary structures through complementary base-pairing of their component nucleotides. Such structures have been shown to regulate a number of biological processes during the viral life-cycle including, replication, translation, transcription, post-transcriptional editing and genome packaging. However, even randomly generated single-stranded nucleotide sequences have the capacity to form stable secondary structures and therefore, amongst the numerous secondary structures formed in large viral genomes only a few of these elements will likely be biologically relevant. While it is possible to identify functional elements through series of laboratory experiments, this is both excessively resource- and time-intensive, and therefore not always feasible. A more efficient approach involves the use of computational comparative analyses methods to study the signals of molecular evolution that are consistent with selection acting to preserve particular structural elements. In this study, I systematically deploy a collection of computationally-based molecular evolution detection methods to analyse the genomes of viruses belonging to a number of ssRNA viral families (Alphaflexiviridae, Arteriviridae, Caliciviridae, Closteroviridae, Coronavirinae, Flaviviridae, Luteoviridae, Picornaviridae, Potyviridae, Togaviridae and Virgaviridae), for evidence of selectively stabilised secondary structures. To identify potentially important structural elements the approach incorporates structure prediction data with signals of natural selection, sequence co-evolution and genetic recombination. In addition, auxiliary computational tools were used to; 1) quantitatively rank the identified structures in order of their likely biological importance, 2) plot co-ordinates of structures onto viral genome maps, and 3) visualise individual structures, overlaid with estimates from the molecular evolution analyses. I show that in many of these viruses purifying selection tends to be stronger at sites that are predicted to be base-paired within secondary structures, in addition to strong associations between base-paired sites and those that are complementarily co-evolving. Lastly, I show that in recombinant genomes breakpoint locations are weakly associated with co-ordinates of secondary structures. Collectively, these findings suggest that natural selection acting to maintain potentially functional secondary structures has been a major theme during the evolution of these ssRNA viruses.

Thesis--Ph. D., University of Hong Kong, 1978. / Typescript.

published_or_final_version / Microbiology / Master / Master of Philosophy

published_or_final_version / abstract / toc / Zoology / Master / Master of Philosophy

published_or_final_version / Microbiology / Doctoral / Doctor of Philosophy

Thesis (Ph. D. - Microbiology and Immunology)--University of Arizona, 1984. / Includes bibliographical references (leaves 201-208).

Thesis(M.S.)--Auburn University, 2006. / Abstract. Vita. Includes bibliographic references.

Thesis (M.S.)--University of Texas at El Paso, 2009. / Title from title screen. Vita. CD-ROM. Includes bibliographical references. Also available online.

Submitted by Chaylane Marques (chaylane.marques@ufpe.br) on 2015-03-12T18:59:12Z No. of bitstreams: 2 Dissertacao_Mestrado_Breno_Moacir_Farias_de_Albuquerque.pdf: 1983241 bytes, checksum: 2527dfa8747683b92433fbcc2a3e2bfc (MD5) license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) / Made available in DSpace on 2015-03-12T18:59:12Z (GMT). No. of bitstreams: 2 Dissertacao_Mestrado_Breno_Moacir_Farias_de_Albuquerque.pdf: 1983241 bytes, checksum: 2527dfa8747683b92433fbcc2a3e2bfc (MD5) license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Previous issue date: 2012 / O Papilomavírus bovino (BPV) é o agente etiológico da papilomatose bovina. Esta apresenta lesões que normalmente são benignas e tendem a regredir, porém podem progredir a uma neoplasia. Muitas metodologias utilizadas para detecção de BPV se mostram inespecíficas e apresentam reações cruzadas com outros organismos relacionados. No entanto, a reação quantitativa em tempo real em cadeia da polimerase (qPCR) é uma ferramenta de destaque na detecção, tipificação e quantificação de nucleotídeos e vem sendo utilizada na clínica para avaliar carga viral. O objetivo do trabalho foi desenvolver um novo protocolo de detecção, tipificação e quantificação de BPV através da qPCR. Foram desenhados cinco pares de primers, que possuem como alvo uma região conservada do genoma viral (gene L1) de diferentes BPVs. A seletividade dos primers foi testada in vitro e DNA extraído de células MDBK não infectadas foram utilizados como controle negativo. A técnica de qPCR permitiu detectar, tipificar e quantificar material viral dos BPVs 1, 2, 4, 5 e 6. O limiar relativo da detecção foi de 4fg de DNA, em torno de 30-40 cópias de DNA/μL. Dos cinco pares de primers produzidos, quatro apresentaram mesmo perfil térmico durante a qPCR (qPCRBPV2, 4, 5 e 6), permitindo em um único procedimento detectar e tipificar os quatro tipos virais. A distinção das amostras foi realizada através da análise de melting que permitiu tipificá-las. Através da metodologia desenvolvida foi observado que em lesões cutâneas de bovinos infectados com BPV a carga viral não se mostrou inferior a 1000 cópias/μL, enquanto que a técnica permite quantificar até um limiar de 40 copias de DNA/μl. Este trabalho possui relevância para validação de qPCR como diagnóstico da papilomatose bovina e particular importância quando aplicado em estudos da infecção pelo BPV e no monitoramento por veterinários da eficácia das futuras vacinas.