Genetics and Genomics Commons^™

Bioinformatic And Experimental Approaches For Deeper Metaproteomic Characterization Of Complex Environmental Samples, Ramsunder Mahadevan Iyer

Doctoral Dissertations

The coupling of high performance multi-dimensional liquid chromatography and tandem mass spectrometry for characterization of microbial proteins from complex environmental samples has paved the way for a new era in scientific discovery. The field of metaproteomics, which is the study of protein suite of all the organisms in a biological system, has taken a tremendous leap with the introduction of high-throughput proteomics. However, with corresponding increase in sample complexity, novel challenges have been raised with respect to efficient peptide separation via chromatography and bioinformatic analysis of the resulting high throughput data. In this dissertation, various aspects of metaproteomic characterization, including …

Investigating The Regulation Of Indole-3-Acetic Acid Production By The Plant Associated Microbe Pantoea Sp. Yr343, Kasey Noel Estenson

Doctoral Dissertations

The auxin indole-3-acetic acid (IAA) plays a central role in plant growth and development and many plant-associated microbes produce IAA. Several IAA biosynthetic pathways have been identified in microbes which use the precursor tryptophan. Pantoea sp. YR343, which was isolated from the Populus deltoides rhizosphere, is a robust plant root colonizer that produces IAA. Using genomic and metabolomics analyses, we predicted that the indole-3-pyruvate (IPA) pathway is the major pathway in Pantoea sp. YR343 for IAA production. To better understand IAA biosynthesis and the effects of IAA exposure on cell physiology, we performed proteomics on Pantoea sp. YR343 grown in …

Systematics And Biogeography Of The Cortinarius Violaceus Group And Sequestrate Evolution In Cortinarius (Agaricales), Emma Harrower

Doctoral Dissertations

Phylogenetics is a powerful tool used for illuminating the diversity of life on Earth, their evolution and their ecology. I created a multi-gene phylogenetic tree of Cortinarius section Cortinarius and uncovered five previously overlooked species, increasing the number of species in the section from seven to twelve. All members of the clade possess both cheilocystidia and pleurocystidia and possess a pigment known as (R)-39,49-dihydroxybphenylalanine. Ancestral state reconstruction estimated that the ancestral host was most likely an angiosperm, switching hosts when encountering novel host species in new lands, and only C. violaceus associating with the Pinaceae in North America. Biogeographic analysis …

Mediation And Moderation Of Intergenerational Epigenetic Effects Of Trauma, Stefanie Renee Pilkay

Doctoral Dissertations

Trauma and early-life stress have been linked to poor mental and physical health outcomes. In fact, research has identified trauma and stress can influence epigenetic marks on genes that can alter gene activity. It is suspected that epigenetically altered gene activity is involved in behavior and mental health. This may help explain why some individuals don’t experience great benefit from treatment for the effects of stress, and severe mental health symptoms can be chronic for decades or a lifetime. Moreover, some trauma-related mental health symptoms have shown generational patterns that appear linked to epigenetic marks. Therefore, this study sought to …

All Roads Lead To Weediness: Stories About Weedy Rice Origins, Weedy Genes And Weed Competitiveness, Zhongyun Huang

Doctoral Dissertations

Weedy rice (Oryza spp.), a weedy relative of cultivated rice (O.sativa), infests and persists in cultivated rice fields worldwide. Many weedy rice populations have evolved similar adaptive traits, considered part of the ‘agricultural weed syndrome’, making this an ideal model to study the genetic basis of parallel evolution. Using population genetics analyses of South Asian and US weedy rice, my research reveals multiple independent evolution events giving rise to weed groups in the two geographic areas. Weeds in South Asia have highly heterogenous genetic backgrounds, with contributions from both cultivated varieties (aus and indica) …

Assessment Of Genetic And Education Recovery Plan Objectives For The Bog Turtle (Glyptemys Muhlenbergii), Cassie Marie Dresser

Doctoral Dissertations

Unprecedented declines in biodiversity are threatening the natural world as we know it. Without human intervention, two thousand species listed under the US Endangered Species Act are likely to disappear. Fortunately, these species receive federal protection and increased research effort is needed to create and satisfy the objectives outlined in the mandated Species Recovery Plan. In this dissertation, I address three conservation objectives outlined in the Recovery Plan for North America’s smallest and rarest turtle, the Bog Turtle (Glyptemys muhlenbergii): (1) investigate the potential genetic differentiation in southern portions of the species’ range, (2) investigate the genetic impacts …

Detection, Diversity, And Evolution Of Fungal Nitric Oxide Reductases (P450nor), Steven Adam Higgins

Doctoral Dissertations

Nitrous oxide (N₂O) is a gas responsible for significant ozone layer depletion and contributes to greenhouse effects in Earth’s atmosphere. N₂O is primarily generated by denitrification, whereby nitrate (NO_3-) or nitrite (NO_2-) is converted to gaseous N₂O or N2. Teragram quantities of N₂O are emitted annually from agricultural soils treated with nitrogenous fertilizers due to the activity of soil microbiota. Although bacteria and fungi harbor genes permitting denitrification, fungi lack NosZ, an enzyme responsible for reducing N₂O into inert N2 gas. Historically, scientists have linked fungi …

On The Construction And Interpretation Of Fitness Landscapes For Hiv: A Computational Perspective, Elizabeth Grace Johnson

Doctoral Dissertations

To identify vulnerable viral targets to incorporate into an immunogen, fitness landscapes for the viral proteome have been constructed. These landscapes describe the sum or synergistic replicative cost exacted on the virus for any combination of non-synonymous mutations. Here we attempt to assess the robustness of current computational methods for measuring the fitness cost of HIV polymorphisms in these landscapes. We also address in the following chapters assumptions and shortcomings that may underlie current landscape's uneven ability to predict fitness effects.

In the first chapter, I appraise the robustness of current frame-works that derive fitness costs from patient sequence data. …

Statistical Methods For High Dimensional Data Arising From Large Epidemiological Studies, Hui Xu

Doctoral Dissertations

In this thesis, we propose statistical models for addressing commonly encountered data types and study designs in large epidemiologic investigations aimed at understanding the molecular basis of complex disorders. The motivating applications come from diverse disease areas in Women's Health, including the study of type II diabetes in the Women's Health Initiative (WHI), invasive breast cancer in the Nurses' Health Study and the study of the metabolomic underpinnings of cardiovascular disease in the WHI. We have also put significant effort into making the implementation of the proposed methods accessible through freely available, user-friendly software packages in R. The first chapter …

The Key Question In Symbiotic Nitrogen Fixation: How Does Host Maintain A Bacterial Symbiont?, Onur Oztas

Doctoral Dissertations

The fact that plants cannot use nitrogen in the gaseous form makes them dependent on the levels of usable nitrogen forms in the soil. Legumes overcome nitrogen limitation by entering a symbiotic association with rhizobia, soil bacteria that convert atmospheric nitrogen into usable ammonia. In root nodules, bacteria are internalized by host plant cells inside an intracellular compartment called the symbiosome where they morphologically differentiate into nitrogen-fixing forms by symbiosome-secreted host proteins. In this project, I explained the host proteins required to maintain bacterial symbionts and described their delivery to the symbiosome. I showed that the SYNTAXIN 132 (SYP132) gene …

Pathogenesis, Virulence And Population Genetics Of Puccinia Emaculata, The Causal Agent Of Switchgrass Rust, Qunkang Cheng

Doctoral Dissertations

The infection process of Puccinia emaculata on Panicum virgatum leaves was studied histologically. Appressoria were formed approximately 10 hr after inoculation and penetrations were observed over stomatal openings. Substomatal vesicles developed 3 days after inoculation (DAI) and at 5 DAI, both haustorial mother cells and haustoria were observed. At 11 DAI, uredinia were developing, but urediniospores were immature. Until 14 DAI, matured uredinia ruptured host epidermis and urediniospores were released for secondary infection. This clearly studied infection process will help understand resistance mechanisms of a resistant cultivar in future research.

Twelve agronomic and ornamental switchgrass cultivars were inoculated with 40 …

Systematics, Diversification, And Functional Diversity Of Russulaceae (Russulales), Brian Patrick Looney

Doctoral Dissertations

The family Russulaceae is an iconic family of mushroom-forming Basidiomycetes both because of their importance as edible mushrooms in many parts of the world and their species richness in both temperate and tropical forested biomes. While much mycological research has been focused on this group, recent systematic and ecological research has failed to develop a comprehensive or cohesive organization by which to understand the evolutionary relationships, patterns of diversification, or functional importance of the group. Recently, interest in ectomycorrhizal fungi (EmF), of which Russulaceae is a key lineage, has greatly increased due to the recognition of the importance of EmF …

Role Of Hormonal And Developmental Signaling In Plant-Cyst Nematode Interaction, Sarbottam Piya

Doctoral Dissertations

Plant-parasitic cyst nematodes are one of the most destructive root parasites that cause severe yield losses in many crop plants. These obligate parasites induce a specialized multi-nucleate feeding site called syncytium. This study was conducted to explore the roles of phytohormones particularly auxin and ethylene, and miRNA-mediated crosstalk between development and defense responses in establishing the compatible interaction between Arabidopsis and Heterodera schachtii. Using yeast two-hybrid assay, a complete protein-protein interaction map between Auxin/indole-3-acetic acid (Aux/IAA) proteins and auxin response factors (ARFs) was generated. In addition, gene co-expression profiles of ARFs and Aux/IAAs were incorporated with protein-protein interaction data. …

Ecological And Evolutionary Dynamics Of Plant-Soil Feedbacks: Influences On Evolution And Range Dynamics, Michael E. Van Nuland

Doctoral Dissertations

Plants interact with, modify, and are affected by their soil environments. Though plant-soil interactions are well known to be important and active regulators of ecosystem function and community structure, much less is known about how these interactions affect plant evolution. The primary goal of my dissertation was to examine plant-soil interactions under a range of ecological and evolutionary contexts to better understand patterns of biodiversity, ecosystem function, and whole system responses to environmental change. Taking such an eco-evolutionary perspective allows for a holistic understanding of the causes and consequences of complex abiotic and biotic interactions that link ecosystem ecology and …

Using Phylogenetic Comparative Methods To Understand Diversification And Geographic Range Evolution, Kathryn Aurora Massana

Doctoral Dissertations

Two key processes that have been modeled in a phylogenetic comparative framework are diversification and historical biogeography. Many questions arise on what process have shaped the abundance (or lack) of species we see today and what influences their survival and interconnectedness with other species. Many methods have been developed to answer these questions. Over the past several decades there has been a rise in parametric modeling and development of more adequate frameworks to answer biological questions of interest. However, many models still lack the incorporation of ecological, mainly biotic factors, which influence the evolution and ecology of species, while accounting …