<p> Fungi are thought to be one of the most diverse groups of organisms in the Arctic. They drive mineral and energy cycles and influence the occurrence of other organisms as mutualists (mycorrhizae, endophytes, lichens), decomposers and pathogens. Nevertheless, information on fungal biodiversity and distribution patterns in relation to environments across the Arctic is still sparse. Molecular methods were used to examine the diversity and community structures of ectomycorrhizal fungi (EMF) associated with two principal arctic host plants, <i> Salix arctica</i> and <i>Dryas integrifolia,</i> as well as total soil fungal communities of adjacent disturbed and undisturbed areas of patterned-ground features across the five bioclimatic subzones (A-E) of the North American Arctic. Key findings include the following: (1) More diverse fungal communities had been observed than previously known. These communities encompass nearly all fungal phyla and included all fungal guilds. However, a few species-rich fungal families dominated these fungal communities. (2) Surprisingly, species richness did not decline with latitude. (3) The most abundant fungal taxa were widely distributed in and beyond the Arctic. Yet root (EMF) and soil fungal communities showed niche preferences in regard to bioclimatic subzones. Furthermore, disturbed and undisturbed patterned ground features harbored different soil fungal communities with the exception of the coldest subzone A. In contrast, EMF community composition was not affected by host plant identity. (4) Fungal communities in the warmest subzone E were distinct from the other arctic subzones and the majority of taxa matched fungi from the boreal forest. (5) Key drivers of fungal community and guild composition along the bioclimatic gradient included regional climate, pH as well as vegetation composition and productivity across the subzones. At the local scale of patterned-ground features, fungal communities were correlated with vegetation composition and microclimate. With a warming climate, I would expect an enhanced colonization of patterned-ground features by vascular plants that would then affect fungal community structure not only at the species level, but also at the level of fungal guilds. In particular I would expect increases in fungi that are symbiotic with plants and a northward shift of both plant and fungal taxa.</p>

<p> The RNA-binding proteins U2AF and PTB play important roles in gene expression in many eukaryotic species. Although U2AF and PTB have been well-studied, their functional requirements have not been investigated on a genome-wide scale. In this thesis, I analyze RNA expression data to determine the requirement of the general splicing factor U2AF in <i>S. pombe</i> and to identify genes misregulated in Drosophila PTB mutants. I find that many introns are insensitive to U2AF inactivation in a <i>Schizosaccharomyces pombe</i> U2AF59 mutant, <i>prp2.1.</i> Bioinformatics analysis indicates that U2AF-insensitive introns have stronger 5' splice sites and higher A/U composition. The importance of intronic nucleotide composition was further investigated using wild type RNA expression data sets. I show that nucleotide composition is a relatively important factor for regulated intron retention in a variety of species. I also analyzed the RNA-binding protein PTB using RNA Seq data to reveal genes misregulated in PTB mutants in <i>D. melanogaster.</i> I identify misregulation of alternative splicing in PTB mutants and putative PTB binding sites. In the PTB embryonic lethal mutant, which shows dorsoventral patterning defects, I show that dorsal fate genes are significantly up-regulated. I present a model to link PTB to dorsal closure defects. This thesis provides the first genome-wide analysis of U2AF in <i>S. pombe</i> and PTB in <i>Drosophila melanogaster. </i></p>

Nuclear substructures known as “nuclear bodies” associate with particular gene loci, and this may determine or reflect a mechanism of genetic control. The detection of these associations currently relies on the use of loci-specific probes, or immunoprecipitation of bulk cells with a particular protein. However, there is evidence that these associations respect the nuclear body, not necessarily any one constituent protein, and are statistically and/or functionally significant even when they occur over distances resolvable by light microscopy, or within single cells. A method is proposed that will allow for the identification of loci contained within the vicinity of an arbitrary nuclear structure in a single cell. It is demonstrated that the crucial aspects of this method are feasible; that DNA sequences originating from arbitrary subnuclear regions targeted by two-photon irradiation can be determined, and identified to a particular locus.

Nuclear substructures known as “nuclear bodies” associate with particular gene loci, and this may determine or reflect a mechanism of genetic control. The detection of these associations currently relies on the use of loci-specific probes, or immunoprecipitation of bulk cells with a particular protein. However, there is evidence that these associations respect the nuclear body, not necessarily any one constituent protein, and are statistically and/or functionally significant even when they occur over distances resolvable by light microscopy, or within single cells. A method is proposed that will allow for the identification of loci contained within the vicinity of an arbitrary nuclear structure in a single cell. It is demonstrated that the crucial aspects of this method are feasible; that DNA sequences originating from arbitrary subnuclear regions targeted by two-photon irradiation can be determined, and identified to a particular locus.

Thesis (Ph. D.)--University of California, San Francisco, 2008. / Source: Dissertation Abstracts International, Volume: 68-11, Section: B, page: 7314. Adviser: Kevan M. Shokat.

Thesis (Ph.D.)--University of California, San Francisco, 2008. / Source: Dissertation Abstracts International, Volume: 69-02, Section: B, page: 0761. Advisers: Alexander D. Johnson; Hao Li.

Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2008. / Source: Dissertation Abstracts International, Volume: 69-05, Section: B, page: 2984. Adviser: David F. Clayton. Includes bibliographical references. Available on microfilm from Pro Quest Information and Learning.

Thesis (Ph.D.)--University of California, San Francisco, 2008. / Source: Dissertation Abstracts International, Volume: 69-09, Section: B, page: 5304. Adviser: Susan J. Fisher.

Thesis (Ph.D.)--University of California, San Francisco, 2009. / Source: Dissertation Abstracts International, Volume: 71-02, Section: B, page: . Adviser: Geeta J. Narlikar.

Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2006. / Source: Dissertation Abstracts International, Volume: 67-07, Section: B, page: 3639. Adviser: Huimin Zhao. Includes bibliographical references. Available on microfilm from Pro Quest Information and Learning.