Not available / text

Microorganisms are a goidmine for evolutionary genetics as their genomes can evolve at an extraordinary rate which results in some of the most extravagant adaptations in terms of genome structure and function as well as survival in the most unusual environments. One trend observed in several evolutionary scenarios is genome degeneration. It is most prominent in endosymbionts and obligate intracellular parasites and is a consequence of many constraints encountered in the intracellular environment. The process involves loss of many protein-coding genes, resulting in greater dependence on the host, and loss of non-coding DNA such as intergenic regions, which has a direct impact on regulation of genome function. I have chosen two evolutionarily distinct systems to analyze the stages and functional consequences of genome degeneration, namely the impact of genome compression on transcription in an obligate parasite Antonospora locustae (genus Microsporidia), and gene content in the mitochondrion of a diatom endosymbiont found in the dinoflagellate Durinskia baltica. I have successfully mapped transcriptional start and termination sites from 14 loci in Antonospora locustae, and cloned fragments of two genes that are part of the electron transport chain from the mitochondrion of the diatom endosymbiont in Durinskia baltica. My analysis reveals that transcription in A. locustae is always initiated immediately upstream of the open reading frame at a single point for every locus, whereas transcriptional termination can occur at several points for a single gene and, in some instances overlaps with a downstream reading frame. The identification ofNADH5 and ATPase9 from the mitochondrion of the endosymbiont in D. baltica is further evidence for the preservation of function in this enigmatic organelle.

Barley (Hordeum vulgare L.) is the preferred cereal for malting. Its suitability for malting depends on many criteria, including the size, shape and uniformity of the kernels. Malting quality is affected by many quantitative trait loci (QTL). Such loci have been mapped using phenotypic and genotypic information on all members of mapping populations. It may also be possible to detect marker-QTL associations using selective genotyping, in which only the progeny with high or low phenotypic values for a trait are genotyped with available markers. Information on marker-QTL associations may be used in marker-assisted selection. Marker-assisted selection could be particularly useful for barley malting quality traits, some of which are costly to assess. Here, three studies were conducted related to QTL for barley grain and malt quality characteristics. In the first study, QTL were mapped using kernel size and shape data obtained by image analysis on samples from a two-rowed by six-rowed barley cross. QTL were detected near vrs1 on chromosome 2(2H) and near int-c on chromosome 4(4H). Some QTL affected the within-sample variability without affecting the mean of kernel characteristics. QTL alleles that made kernels larger and/or rounder also tended to improve malt quality. Those that increased the variability of kernel size were associated with poor malt quality. In the second study, marker genotype data and grain and malt quality phenotype data from three mapping populations were used to investigate the feasibility of selective genotyping for QTL mapping. Almost all previously mapped QTL were detected often with only 10% of the population genotyped. Additional, possibly spurious, QTL were detected in regions of the genome where no significant QTL had been mapped. The results indicated that simultaneous investigation of two or more traits by selective genotyping could be worthwhile. In the third study, Morex alleles at a QTL on chromosome 7(5H) affecting alpha-amylase activ

No description available.

When Darwin introduced natural selection in 1859 as a key mechanism of evolution, little was known about the underlying cause of variation within a species. Today we know that this variation is caused by the acquired genomic differences between individuals. Polymorphism, defined as the existence of multiple alleles or forms at a genomic locus, is the technical term used for such genetic variations. Polymorphism, along with reproduction and inheritance of genetic traits, is a necessary condition for natural selection and is crucial in understanding how species evolve and adapt. Many questions regarding polymorphism, such as why certain species are more polymorphic than others or how different organisms tend to favor some types of polymorphism among others, when solved, have the potential to shed light on important problems in human medicine and disease research. Some of these studies require more diverse species and/or individuals to be sequenced. Of particular interest are species with the highest rates of polymorphisms. For instance, the sequencing of the sea squirt genome lead to exciting studies that would not be possible to conduct on species that possess lower levels of polymorphism. Such studies form the motivation of this thesis. Sequencing of genomes is, nonetheless, subject to its own research. Recent advances in DNA sequencing technology enabled researchers to lead an unprecedented amount of sequencing projects. These improvements in cost and abundance of sequencing revived a greater interest in advancing the algorithms and tools used for genome assembly. A majority of these tools, however, have no or little support for highly polymorphic genomes; which, we believe, require specialized methods. In this thesis, we look at challenges imposed by polymorphism on genome assembly and develop methods for polymorphic genome assembly via an overview of current and past methods. Though we borrow fundamental ideas from the literature, we introduce several novel concepts that can be useful not only for assembly of highly polymorphic genomes but also genome assembly and analysis in general.

Introduction The present study evaluated reported methodological characteristics of GWAS, investigating relationships between reported methodological characteristics and outcomes observed. Methods GWAS were identified from NHGRI’s catalogue of GWAS (2005 to 2009). Multivariate meta-regression models (random effects) were produced to identify the impact of reported study characteristics and the strength of relationships between the variables and outcomes. Results The summary odds ratios for replication components of GWAS in cancer was 1.34 (95% CI 1.25, 1.43) and neuropsychiatric disorders was 1.43 (95% CI 1.30, 1.57). Heterogeneity was accounted for by nature of the control group, relationship between case/control groups, whether cases/controls were drawn from the same population, if data was a primary collection or a build on pre-existing data, if quality assurance was reported, and if the study reported power/sample size. Conclusion Evidence supports the existence of variability in reporting, with index components demonstrating less variability than replication components in the GWAS.

Thesis (M.S.)--University of Hawaii at Manoa, 2006. / Includes bibliographical references (leaves 53-67). / x, 67 leaves, bound ill. 29 cm

Thesis (M.S.)--University of Hawaii at Manoa, 2006. / Includes bibliographical references (leaves 69-79). / ix, 79 leaves, bound ill. 29 cm

Thesis (M.S.)--University of Hawaii at Manoa, 2006. / Includes bibliographical references (leaves 53-62). / ix, 62 leaves, bound ill. (some col.) 29 cm

Thesis (Ph. D.)--University of Adelaide, Dept. of Paediatrics, Women's and Children's Hospital, 1995. / Includes publications and manuscripts by the author. Includes bibliographical references (leaves 196-215).