Thesis (Ph. D.)--University of Hong Kong, 1999. / Includes bibliographical references (leaves 154-168).

Thesis (M. Sc.)--University of Canterbury, 2009. / Typescript (photocopy). Includes bibliographical references (leaves 128-130) and index. Also available via the World Wide Web.

Thesis (M.Phil.) - University of Queensland, 2003. / Includes bibliography.

Thesis (MSc)--University of Stellenbosch, 2005. / Bibliography. Also available via the Internet.

Thesis (Ph. D.)--University of Washington, 2006. / Vita. Includes bibliographical references (p. 64-73).

Thesis (Ph.D.)--Baylor University, 2009. / Includes bibliographical references (p. 99-110).

Magister Scientiae - MSc / Viral genomes consist of either deoxyribonucleic acid (DNA) or ribonucleic acid (RNA). The viral RNA molecules are responsible for two functions, firstly, their sequences contain the genetic code, which encodes the viral proteins, and secondly, they may form structural elements important in the regulation of the viral life-cycle. Using a host of computational and bioinformatics techniques we investigated how predicted secondary structure may influence the evolutionary dynamics of a group of single-stranded RNA viruses from the Picornaviridae family. We detected significant and marginally significant correlations between regions predicted to be structured and synonymous substitution constraints in these regions, suggesting that selection may be acting on those sites to maintain the integrity of certain structures. Additionally, coevolution analysis showed that nucleotides predicted to be base paired, tended to co-evolve with one another in a complimentary fashion in four out of the eleven species examined. Our analyses were then focused on individual structural elements within the genome-wide predicted structures. We ranked the predicted secondary structural elements according to their degree of evolutionary conservation, their associated synonymous substitution rates and the degree to which nucleotides predicted to be base paired coevolved with one another. Top ranking structures coincided with well characterized secondary structures that have been previously described in the literature. We also assessed the impact that genomic secondary structures had on the recombinational dynamics of picornavirus genomes, observing a strong tendency for recombination breakpoints to occur in non-coding regions. However, convincing evidence for the association between the distribution of predicted RNA structural elements and breakpoint clustering was not detected.

Made available in DSpace on 2014-11-10T11:09:56Z (GMT). No. of bitstreams: 0 Previous issue date: 2014-04-25Bitstream added on 2014-11-10T11:57:42Z : No. of bitstreams: 1 000792126.pdf: 1460032 bytes, checksum: 893375b9efeacd9cd350165c560a9ac5 (MD5) / O trabalho objetiva avaliar o papel da comunidade bacteriana na dinâmica dos sedimentos. No presente trabalho, compararam-se as comunidades bacterianas presentes em sedimentos de dois viveiros de piscicultura, um reservatório de água (V1) e o outro com condições de elevada carga orgânica (V4), os quais estão inseridos em um sistema sequencial com fluxo contínuo de água. As coletas de sedimentos foram realizadas em dois períodos distintos, um sendo na seca (Julho e Agosto/2012) e outro na chuva (Janeiro e Fevereiro/2012). A comunidade bacteriana foi avaliada através do sequenciamento do gene 16S rRNA. Os filos bacterianos permaneceram praticamente inalterados nas amostras V1 comparadas nas duas épocas estudadas. Nas amostras do V4 observou-se variação na frequência dos organismos encontrados em relação às diferentes coletas. A predominância em V1 foi dos filos Firmicutes seguido do Proteobacteria, Acidobacteria e Actinobacteria. No V4, o maior número de sequências encontradas pertencia ao filo Proteobacteria, seguido de Acidobacteria, Firmicutes, Actinobacteria, Chloroflexi, Nitrospira, Gemmatimonadetes e TM7. A comparação da população bacteriana dos dois viveiros estudados em diferentes épocas mostrou que as bactérias variam de acordo com as condições climáticas e estão intimamente interligadas com a concentração de nutrientes do local. Estas diferenças são importantes na elucidação do papel desenvolvido pelos procariotos na dinâmica dos sedimentos / The aim of this study was identify the bacterial communities in dynamic of the sediment. In this study, we compared the bacterial communities present in sediment of two fish farm pond a used as water reservoir (V1) and the other with conditions of high nutrient load (V4), which are inserted in a sequential system with continous water flow (six ponds). The sediment sampling were conducted in two distinct periods one in dry season (July and August/2012) and another in the rain (January and February/2012). The bacterial community was assessed by sequencing the 16S rRNA. Through this data we observed in V1 regardless of time of year the bacterials phyla remained virtually unchanged.In V4 samples, was observed a variation in the frequency of organisms found in relation to different collections. In V1 was the predominance of the Phylum Firmicutes followed Proteobacteria, Acidobacteria and Actinobacteria. The largest number of sequences found at V4 belonged to the Proteobacteria phylum followed Acidobacteria, Firmicutes, Actinobacteria, Chloroflexi, Nitrospira, Gemmatimonadetes and TM7. A comparison of the bacterial population of the two ponds studied at different times showed that the bacteria at these sites varies according to the climatic conditions and are closely linked with nutrient concentration local. These differences are important in elucidating the role played by prokaryotes in the sediment dynamics

Made available in DSpace on 2015-03-03T11:52:26Z (GMT). No. of bitstreams: 0 Previous issue date: 2014-06-26Bitstream added on 2015-03-03T12:07:14Z : No. of bitstreams: 1 000811079.pdf: 653843 bytes, checksum: 1a6121bfd564e4f78371a2dd8f5accf0 (MD5) / Caracterizada por sua grande versatilidade em várias modalidades equestres, a raça Quarto de Milha se destaca mundialmente, representando 52% de toda população equina no mundo. Dentro da raça há subdivisão em diferentes segmentos de aptidão, provenientes de distintos objetivos de seleção, consideradas linhagens, entre elas corrida e trabalho. Objetivou-se com este estudo avaliar as diferenças morfológicas e genômicas que ocorrem entre as linhagens de corrida e trabalho como resultado da seleção para diferentes objetivos, a identificação de regiões genômicas que tenham sido alteradas pela seleção na formação da linhagem de corrida em relação à linhagem de trabalho e realizar dois estudos, independentes, de associação ampla do genoma (GWAS) para identificar regiões cromossômicas e genes candidatos posicionais associados com características de desempenho na linhagem de corrida e com características morfométricas na raça como um todo. Para as análises foram utilizados 120 animais de corrida e 64 animais de trabalho de ambos os sexos registrados na Associação Brasileira de Criadores de Cavalo Quarto de Milha. As características morfométricas avaliadas foram: peso, altura à cernelha, comprimentos corporal, da canela, da quartela, da garupa, da cabeça, e do pescoço, perímetros torácico, da canela e do casco e a característica de desempenho índice de velocidade. A análise das diferenças morfológicas foi realizada por meio do procedimento GLM do programa SAS utilizando-se modelo que incluiu os efeitos de sexo e linhagem e a covariável idade à mensuração. Para a análise das diferenças genômicas, 54.602 SNPs foram genotipados utilizando-se o painel de marcadores Illumina Equine SNP50 BeadChip. Os resultados obtidos revelaram mudanças significativas entre as linhagens para todas as características morfométricas avaliadas. Animais de corrida apresentaram maiores pesos, alturas, comprimentos ... / Characterized by its versatility in several sporting activities, the Quarter Horse breed excels globally, representing 52% of the entire equine population in the world. The Quarter Horse breed is subdivided into different lines according to skills resulting from distinct selection objectives, including cutting and racing horses. The aims of the present study were to investigate the morphological and genomic difference, between cutting and racing lines as a result of selection for different objectives; identification of the genomic regions divergently selected in racing line in relation to cutting line and to perform two genome-wide association studies, independently, to identify chromosomal regions and positional candidate genes associated with performance trait in the racing line and morphometric traits in the breed as a whole. To perform the analyses 120 racing animals and 64 cutting animals of both sexes and registered at the Brazilian Association of Quarter Horse Breeders were used. The evaluated morphometric traits were: weight; height at withers; length of the body, shank, pastern, rump, head, and neck; circumference of the chest, shank, and hoof and speed index performance trait. Morphological differences analysis was performed using a model that included the fixed effects of sex and line, and age at recording as covariate. The GLM procedure of the SAS program was used for statistical analysis. To perform genomic differences analysis, 54,602 SNPs were genotyped by the Illumina Equine SNP50 BeadChip array. The results showed significant changes in the morphometric traits of the animals. Racing animals were heavier and taller and presented greater body lengths and perimeters than cutting horses. The number of informative SNPs and the SNP density found in the genome of cutting and racing animals suggest that the Equine SNP50 BeadChip can be used for different purposes in the Quarter Horse breed. To identify genomic regions ...

Orientador: Lucia Maria Carareto Alves / Banca: Rodrigo Matheus Pereira / Banca: Mariana Carina Frigieri / Resumo: O trabalho objetiva avaliar o papel da comunidade bacteriana na dinâmica dos sedimentos. No presente trabalho, compararam-se as comunidades bacterianas presentes em sedimentos de dois viveiros de piscicultura, um reservatório de água (V1) e o outro com condições de elevada carga orgânica (V4), os quais estão inseridos em um sistema sequencial com fluxo contínuo de água. As coletas de sedimentos foram realizadas em dois períodos distintos, um sendo na seca (Julho e Agosto/2012) e outro na chuva (Janeiro e Fevereiro/2012). A comunidade bacteriana foi avaliada através do sequenciamento do gene 16S rRNA. Os filos bacterianos permaneceram praticamente inalterados nas amostras V1 comparadas nas duas épocas estudadas. Nas amostras do V4 observou-se variação na frequência dos organismos encontrados em relação às diferentes coletas. A predominância em V1 foi dos filos Firmicutes seguido do Proteobacteria, Acidobacteria e Actinobacteria. No V4, o maior número de sequências encontradas pertencia ao filo Proteobacteria, seguido de Acidobacteria, Firmicutes, Actinobacteria, Chloroflexi, Nitrospira, Gemmatimonadetes e TM7. A comparação da população bacteriana dos dois viveiros estudados em diferentes épocas mostrou que as bactérias variam de acordo com as condições climáticas e estão intimamente interligadas com a concentração de nutrientes do local. Estas diferenças são importantes na elucidação do papel desenvolvido pelos procariotos na dinâmica dos sedimentos / Abstract: The aim of this study was identify the bacterial communities in dynamic of the sediment. In this study, we compared the bacterial communities present in sediment of two fish farm pond a used as water reservoir (V1) and the other with conditions of high nutrient load (V4), which are inserted in a sequential system with continous water flow (six ponds). The sediment sampling were conducted in two distinct periods one in dry season (July and August/2012) and another in the rain (January and February/2012). The bacterial community was assessed by sequencing the 16S rRNA. Through this data we observed in V1 regardless of time of year the bacterials phyla remained virtually unchanged.In V4 samples, was observed a variation in the frequency of organisms found in relation to different collections. In V1 was the predominance of the Phylum Firmicutes followed Proteobacteria, Acidobacteria and Actinobacteria. The largest number of sequences found at V4 belonged to the Proteobacteria phylum followed Acidobacteria, Firmicutes, Actinobacteria, Chloroflexi, Nitrospira, Gemmatimonadetes and TM7. A comparison of the bacterial population of the two ponds studied at different times showed that the bacteria at these sites varies according to the climatic conditions and are closely linked with nutrient concentration local. These differences are important in elucidating the role played by prokaryotes in the sediment dynamics / Mestre